# Patent

## Title
Polypeptides to inhibit epstein barr viral protein BHRF1 and B cell lymphoma family proteins

## Abstract

The present invention provides designed polypeptides that selectively bind to and inhibit Epstein Barr protein BHFR1, and B cell lymphoma family proteins, and are thus useful for treating Epstein Barr-related diseases and cancer.

## Background
CROSS REFERENCE
This application claims priority to U.S. Provisional Patent Application Ser. No. 62/232,936 filed Sep. 25, 2015, and is a continuation in part of PCT application PCT/US2015/020155 filed Mar. 12, 2015, which claims priority to U.S. Provisional Patent Application Ser. No. 61/951,988 filed Mar. 12, 2014, each incorporated by reference herein in its entirety.


FEDERAL FUNDING STATEMENT
This invention was made with U.S. government support under P41 GM103533 awarded by the National Institutes of Health, under HDTRA1-10-1-0040 awarded by the Defense Threat Reduction Agency, and under DGE-1256082 awarded by the National Science Foundation. The U.S. Government has certain rights in the invention.


BACKGROUND
Following virus infection, cells may undergo apoptosis to prevent further virus spread in the host. This has spurred viruses to evolve counteracting mechanisms to prevent host cell death, and during latent infection these factors may contribute to the development of cancer. This includes multiple cancers associated with Epstein-Barr virus (EBV), in particular Burkitt's lymphoma (BL).
Apoptosis and cell survival are regulated by the homeostatic balance of B cell lymphoma-2 (Bcl-2) family proteins (reviewed in (Martinou and Youle, 2011)), which fall in to three classes. The ‘executioners’, Bak and Bax, initiate apoptosis by increasing mitochondrial outer membrane permeability and facilitating the release of mitochondrial cytochrome c to the cytosol, which activates downstream signaling. Six human pro-survival Bcl-2 proteins (Bcl-2, Bcl-XL, Bcl-B, Mcl-1, Bcl-w and Bfl-1) inhibit this process. Counterbalancing these are numerous pro-apoptotic BH3-only proteins (BOPs), including Bim. These factors share an approximately 26 residue Bcl-2 homology 3 (BH3) motif, an amphipathic α-helical element which binds a hydrophobic groove on the surface of the canonical Bcl-2 fold. Cellular stresses activate pro-apoptotic BOPs, which bind and inhibit pro-survival Bcl-2 members, and directly interact with Bak and Bax to favor mitochondrial permeabilization. Conversely, pro-survival Bcl-2 proteins dampen apoptotic triggers and enhance chemoresistance by sequestering BOPs or directly inhibiting Bak and Bax. Increased expression of pro-survival Bcl-2 proteins is a common feature of many cancers.
Epstein-Barr virus encodes a pro-survival Bcl-2 homologue, BHRF1, which prevents lymphocyte apoptosis during initial infection by sequestering pro-apoptotic BOPs (especially Bim), and interacting directly with the executioner Bak (Desbien et al., 2009; Kvansakul et al., 2010) (Altmann and Hammerschmidt, 2005) (Henderson et al., 1993). Even though BHRF1 is under the control of an early lytic cycle promoter, low levels of constitutive expression have been observed in some cases of EBV-positive BL when the virus is latent, and it has been speculated that BHRF1 may be a necessary viral factor for lymphomagenesis (Kelly et al., 2009; Leao et al., 2007; Watanabe et al., 2010).
SUMMARY OF THE INVENTION
In a first aspect, the invention provides polypeptides comprising an amino acid sequence having at least 50% amino acid sequence identity over its length relative to the amino acid sequence of SEQ ID NO.:1, wherein the polypeptide selectively binds to a protein selected from the group consisting of Epstein Barr protein BHFR1, and B cell lymphoma family proteins selected from the group consisting of myeloid cell leukemia 1 (Mcl-1), B-cell lymphoma 2 (Bcl-2), Bcl-2-like protein 1 (BCL2L1/Bcl-XL), Bcl-2-like protein 10 (BCL2L10/Bcl-B), Bcl-2-like protein A1 (A1/Bfl-1), and Bcl-2-like protein 2 (BCL2L2/Bcl-w). In one embodiment, the polypeptide comprises an amino acid sequence having at least 50% amino acid sequence identity over its length relative to the amino acid sequence selected from the group consisting of SEQ ID NOS:2-6 and 265. In various further embodiments, the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOS: 7-13 and 276, wherein the polypeptide binds to a specific target. In a further embodiment, the polypeptides further comprise a cell-penetrating peptide and/or an antibody or antibody fragment.
In another aspect, the invention provides pharmaceutical composition, comprising a polypeptide of the invention and a pharmaceutically acceptable carrier. In one embodiment, the pharmaceutical composition further comprises an antibody. In another embodiment, the carrier comprises a polymer, such as a polymer comprising a hydrophilic block and an endosomolytic block, or a stimuli-responsive polymer.
In various further embodiments, the invention provides recombinant nucleic acids encoding a polypeptide of the invention, recombinant expression vectors comprising the nucleic acid of the invention operatively linked to a promoter, and recombinant host cells comprising the recombinant expression vectors of the invention.
In another aspect, the invention provides methods for treating an Epstein-Barr virus-related diseases comprising administering to a subject in need thereof a therapeutically effective amount of one or more of the polypeptides of the invention, or salts thereof, pharmaceutical compositions thereof, a recombinant nucleic acid encoding the one or more polypeptides, a recombinant expression vector comprising the recombinant nucleic acids, and/or a recombinant host cells comprising the recombinant expression vector, to treat Epstein-Barr virus related diseases wherein the polypeptide or encoded polypeptide selectively inhibits BHRF1.
In further aspect, the invention provides methods for treating cancer, comprising administering to a subject in need thereof a therapeutically effective amount of one or more of the polypeptides of the invention, salts thereof, a pharmaceutical composition thereof, a recombinant nucleic acid encoding the one or more polypeptides, a recombinant expression vector comprising the recombinant nucleic acid, and/or a recombinant host cell comprising the recombinant expression vector, to treat cancer, wherein the polypeptide or encoded polypeptide selectively inhibits one or more of Mcl-1, Bcl-2, BCL2L1/Bcl-XL, BCL2L10/Bcl-B, A1/Bfl-1, and BCL2L2/Bcl-w.
In another aspect, the invention provides methods for determining the Bcl-2 phenotype of a tumor, comprising contacting tumor cells, tumor cell lysates or tumor cellular components with one or more polypeptides selected from the group consisting of SEQ ID NOS: 1-6, 8-12, 262-273, or 276, under conditions suitable to promote apoptosis signaling in cells of the tumor that express a BCL2 homolog targeted by the one or more polypeptides; and determining Bcl-2 dependency of the tumor based on the polypeptide that causes apoptosis or apoptotic signaling in the cells of the tumor.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1. De novo protein assembly protocol. (A) A scaffold (grey ribbon) is aligned to the Bim-BH3 motif (black) bound to BHRF1 (white) (i). The Bim-BH3 peptide is extended on both ends and a new protein structure (black tube) is built using fragment-based assembly (ii), followed by rounds of minimization and sequence design. The newly assembled protein is docked to BHRF1 and the surrounding interface is designed (iii). Many designs are generated that are filtered by multiple criteria (iv). (B) Computational models of designed proteins BbpD04 and BbpD07 (black) that bind BHRF1 (white). Apparent affinities (mean±SE, n=3-6) are from yeast display titrations. (C) Seventy-four computationally designed proteins without human modifications (Indexes-01 to 74) were sorted by FACS for surface expression and BHRF1 binding. BbpD04 (Index-00) was included as a positive control. The gene frequencies in the sorted population were divided by their frequencies in the naive library to calculate a log2 enrichment ratio, plotted from −4 (i.e. depleted, black) to +4 (i.e. enriched, white). See Table 3. (D) Histogram of the mean RMSD between the ten lowest energy structures found in ab initio structure prediction calculations and the intended designed structure for each of the sets of designs included in (C). Designs with computed energy minima near the designed target conformation have a higher probability of binding BHRF1.
FIG. 2. Diversity of designed proteins. (A) Index-21 (black) bound to BHRF1 (white). Human-made modifications of computationally-designed Index-21 to form derivative BbpD04 are indicated with labels and side chain spheres. (B) Structures of designs that bound BHRF1 (Indexes-00 to 04) are aligned via the Bim-BH3 incorporation motif (boxed with broken line). Side view showing structural diversity. (C) As in (B), viewed from N-termini. (D) Sequence alignment of BHRF1-binding designs (Indexes-00 to 04) and the guiding scaffold (3LHP chain S). Amino acid identity (black shading) or chemical similarity (grey) to design Index-00/BbpD04 is shown. The Bim-BH3 incorporation site is marked with a bar above.
FIG. 3. Predictions of folding probability correlate with designed protein functionality. (A) Putative binders (Indexes-01 to 04) were expressed on yeast and validated by titrating BHRF1 to determine apparent binding affinities. Three randomly chosen ‘failed’ designs did not show interactions with BHRF1. (B) Examples of forward folding landscapes. Proteins index-00, 01 and 04 bind BHRF1. Protein index-15, 47 and 67 do not. 1. 30,000-100,000 decoys were predicted for each query (black points). Cα-Cα RMSD is measured between each decoy and the intended computational model. (C-E) Properties of the designed interfaces plotted against the experimental enrichment ratios after selection for binding to 100 nM BHRF1. Each data point represents a designed protein (Indexes-01 to 74). Plotted are the (C) interface buried solvent-accessible surface area, (D) the calculated interface binding energy, and (E) the number of unsatisfied buried polar atoms at the interface. (F-H) As for (C-E), except showing computed metrics for the unbound designed proteins. Plotted are enrichment ratios versus (F) the holes (packing) score of the apo-protein, (G) calculated energy, and (H) unsatisfied buried polar atoms.
FIG. 4. Affinity maturation of designed protein BbpD04. (A) Computational model of BHRF1 (white ribbon) bound to design BbpD04 (surface). The electric field from BHRF1 is mapped to the BbpD04 surface; regions experiencing a positive field are shaded dark grey. (B) Based on a computational model of the Mcl-1•BbpD04 complex, the electric field from Mcl-1 (ribbon) is mapped to the surface of BbpD04. A positive field is shown as dark grey. (C) Model of BbpD04. Residues rationally mutated to specifically enhance electrostatic complementarity to BHRF1 are shown as spheres and labeled. These mutated sites are located in regions where the electric fields from BHRF1 and Mcl-1 differ. (D) The effect of BbpD04 mutations on specificity. (E) Sorting a randomly mutated library of BbpD04.1 yielded evolved variant BbpD04.2. The four mutations in BbpD04.2 (white sticks) are shown on the computational model of BHRF1-bound BbpD04.1 (black). (B) Purified proteins were analyzed by SEC. In the left panel, BbpD04.2 (black trace) forms a left-shifted higher MW complex (pale grey) when mixed with BHRF1 (dark grey). In the right panel, BbpD04.2 L54E (black) with a mutation in the binding site does not shift (pale grey) when mixed with BHRF1 (dark grey).
FIG. 5. Mutagenesis of an internal cysteine allows site-specific conjugation at the termini. (A) Short peptide linkers were genetically fused to the BbpD04.2 termini. Linker-3 termini were used in all later experiments where conjugation to a single cysteine was required. (B) Cysteine-linkers reacted with 5 kD polyethylene glycol (PEG)-maleimide (Creative PEGWorks), producing higher MW products on Coomassie-stained sodium dodecylsulphate (SDS)-polyacrylamide gels. BbpD04.2 has a buried cysteine, which becomes exposed for PEG-maleimide conjugation in the presence of the harsh detergent SDS. (C) Cysteine-linker BbpD04.2 proteins were conjugated to HPDP-biotin for 4 h at room temperature. Biotinylated protein was incubated with streptavidin and aggregation measured by absorbance at 350 nm. Mutation of the internal cysteine (C103A) markedly diminishes aggregation. (D) DMSO, the solvent used for dissolving HPDP-biotin, did not increase exposure of the internal cysteine for PEG-maleimide modification. (E) PEG-maleimide reacted with a fraction of the BbpD04.2 protein when incubated together overnight at room temperature (RT). (F) Both BbpD04.2 C103A and C103V mutations were predicted by the ROSETTA energy function to be tolerated following minimization. BbpD04.2 C103V had reduced specificity by yeast surface display for BHRF1 over other prosurvival Bcl-2 proteins, whereas BbpD04.2 C103A (called BbpD04.3) had only a minor loss of affinity and specificity.
FIG. 6. BINDI has improved bacterial expression and stability. (A) All single amino acid substitutions of BbpD04.3 were expressed in a yeast display library and sorted by FACS for high affinity binding to BHRF1. Plotted for each substitution is the log 2 enrichment ratio from −3.5 (depleted, black) to +3.5 (enriched, white). Stop codons, *. The region of the incorporated Bim-BH3 motif is boxed with a broken line. Secondary structure and core residues are indicated above. Substitutions to aspartate (depleted for core residues) and to proline (depleted for helical residues) are boxed. (B) As in (A), except the library was sorted for high affinity and specificity. (C) The modeled structure of BbpD04.3 is shaded by sequence Shannon entropy from 2.8 (highly conserved, dark) to 4.3 (variable, white), based on the sequence-fitness landscapes. (D) BbpD04.3 and its derivative BINDI were expressed as C-terminal 6his-tagged proteins in E. coli, precipitated from cleared lysate with NiNTA-agarose and analyzed on a Coomassie-stained SDS-polyacrylamide electrophoretic gel. An arrow indicates the expected MW of the designed proteins at 15 kD. (E) CD spectra of BbpD04 and its variants (10 μM in PBS) were collected at 25° C. in the presence of guanidinium hydrochloride. The fraction of protein folded was monitored by the change in CD signal at 222 nm. (F-H) BbpD04 and its variants were digested with proteases of different substrate specificities: trypsin (F), chymotrypsin (G) and elastase (H). Shown is mean±range for 3 repeats. Also see FIG. 7H. (I) Summary of all mutations made to BbpD04 during affinity maturation.
FIG. 7. BINDI has increased bacterial expression and protein stability. (A) BbpD04.3 point mutants were expressed overnight at 22° C. in E. coli Rosetta 2 cells. Cells were harvested, the C-terminally 6his-tagged proteins precipitated with NiNTA-agarose to partially remove background bands, and analyzed on Coomassie-stained SDS-polyacrylamide electrophoretic gels. White arrows indicate mutations with elevated expression. (B) As in (A), with mutations now combined to provide a large increase in expression. (C) Computational model of BHRF1-bound BbpD04.3. Combined mutations in variant BINDI are highlighted with dark sticks. (D) Molar ellipticity at 222 nm as the protein is heated and cooled. Substantial helical structure remains at 95° C. Evolved variants BbpD04.3 and BINDI fully renature. (E) Molar ellipticity of original design BbpD04 as a function of wavelength, recorded at 25° C., 95° C., and after cooling back to 25° C. (F) As in (E), measured for variant BbpD04.3. (G) As in (E), measured for variant BINDI. (H) Protease-susceptibility of BbpD04 and affinity-matured variants BbpD04.3 and BINDI. Protein substrates were incubated for 0, 5, 15, 30, 60, and 120 minutes with protease at 37° C., reactions were terminated with inhibitors, and proteolysis followed on Coomassie-stained SDS-polyacrylamide gels.
FIG. 8. BINDI binds BHRF1 with high affinity and specificity. (A) BINDI or knockout mutant BINDI L54E were mixed with BHRF1 and separated by SEC. A shift in elution volume upon mixing BINDI and BHRF1 is abrogated by the knockout mutation. (B) Biotinylated BHRF1 was immobilized to a BLI sensor and the interaction with BINDI was measured at the indicated concentrations. (C) BLI kinetic analysis of BINDI interactions with BHRF1 (as in panel B) and human Bcl-2 proteins. (D) BLI kinetic analysis of interactions between the Bim-BH3 motif fused to the C-terminus of maltose-binding protein (MBP) and Bcl-2 proteins immobilized to the sensor surface.
FIG. 9. Structural basis for exceptional affinity and specificity of BINDI. (A) Slice through the crystal structure of BINDI (black ribbon) bound to BHRF1 (white ribbon with surface). The guiding scaffold 3LHP_S (grey) is aligned to BINDI at the Bim-BH3 incorporation site. A direct graft of the BH3 motif into 3LHP_S at this position causes clashes elsewhere with the BHRF1 surface. (B) Crystal structure of BINDI (black) bound to BHRF1 (white). (C) The surface of BHRF1, with the buried contact surface in BHRF1•BINDI shaded black. (D) The surface of BINDI, with the buried contact surface in BHRF1•BINDI shaded. Buried residues from the incorporated Bim-BH3 motif are dark grey. Buried residues in the surrounding designed surface are black. (E) The crystal structure (PDB 2WH6) of Bim-BH3 (black) bound to BHRF1 (white). (F) The surface of BHRF1, with the buried contact surface in BHRF1 •Bim-BH3 shaded black. (G) The surface of Bim-BH3, with the buried contact surface in BHRF1•Bim-BH3 black.
FIG. 10. Mutations within the incorporated Bim-BH3 motif are not the major source of the exceptional specificity of BINDI. (A) Crystal structure of BINDI (surface) bound to BHRF1 (black ribbon). The buried contact surface areas are indicated below. (B) The surface of BINDI, with the buried contact surface shaded. Buried residues from the incorporated Bim-BH3 motif are dark grey. Buried residues in the surrounding designed surface are black. (C) Residues of BINDI that changed during affinity maturation are black. Only two residues at the edge of the incorporated Bim-BH3 motif were substituted (W49Y and F61Y). (D) Sequences of the Bim-BH3 motif and equivalent regions in BbpD04 and BINDI. Residues of Bim-BH3 that were fixed in the design of BbpD04 are shaded. Based on these sequences, two 26-residue peptides were fused to maltose-binding protein (MBP): BimBH3-W57Y-F69Y and BimBH3-5*. These have mutations to the Bim-BH3 motif based on changes during affinity maturation of BINDI. (E) MBP-peptide fusions were tested by BLI for binding to Bcl-2 proteins. Neither peptide had the affinity or specificity for BHRF1 of BINDI.
FIG. 11. BINDI triggers apoptosis in an EBV-positive cell line. (A) Cytochrome c release from mitochondria harvested from Ramos (EBV-negative) or Ramos-AW cells (EBV-positive) treated with Bim-BH3 peptide. Bim-BH3 L62E has a knockout mutation in the binding interface. Mean±SD, n=4, for all panels. (B) As in (A), with mitochondria treated with BINDI protein. BINDI L54E has the equivalent interface mutation as Bim-BH3 L62E. (C) At left, the crystal structure of BINDI bound to BHRF1 showing the interaction of Asn62 with the N-terminus of helix α6. At right, BINDI mutation N62S is predicted to maintain interface interactions. (D) BLI kinetic analysis of BINDI N62S interactions with Bcl-2 proteins. (E) Cytochrome c release from Ramos and Ramos-AW mitochondria treated with BINDI N62S or inactive guide scaffold 3LHP(S). (F-H) Mitochondria were harvested from four EBV-negative and six EBV-positive lines. Cytochrome c release was measured after treatment with 10 μM Bim-BH3 peptide (F), guide scaffold 3LHP(S) (G), or BINDI N62S (H).
FIG. 12. Intracellular delivery of BINDI induces cell death in an EBV-positive cancer line in vitro. (A) Cells were incubated with 4 μM antennapedia peptide-fusions of BINDI, BINDI-L54E or 3LHP chain S. Cell viability after 24 h was assessed by quantifying metabolic activity. (B) Cells were incubated with sub-lethal doses (2 μM) of antennapedia peptide-fused proteins. Diblock copolymer Pol300 was conjugated to the proteins via a terminal cysteine for enhanced endosomal escape. Cell viability (mean±SD, n=3) was measured after 24 hours.
FIG. 13. Treatment of EBV-positive B lymphoma xenograft tumors by intracellular delivery of BINDI in vivo. (A) Schematic representation of the copolymer-based treatment. Pol950 has stabilizing and endosomolytic blocks and forms a micelle at physiological pH. The stabilizing block couples to αCD19 and BINDI. Nude mice with subcutaneous Ramos-AW xenografts were treated on days 0, 3 and 6 with Pol950 (300 mg/kg): αCD19 (15 mg/kg): BINDI or 3LHP(S) (105 mg/kg). Mice were injected 30 minutes prior to each treatment with CTX (35 mg/ml) and BTZ (0.5 mg/ml). (B-E) Tumor growth is plotted for each individual mouse until day 11 when the first mice are euthanized. (B) PBS control treatment, black, n=8; (C) chemo-only, grey, n=9; (D) 3LHP(S)-copolymer treatment, n=9; (E) BINDI-copolymer treatment, n=10. (F) Kaplan-Meier survival plot. There is a significant increase in survival with treatment (log-rank test χ2=46, P<0.0001).
FIG. 14. (A) Based on the experimental enrichment ratios for all single amino acid substitutions of BbpD04.3, a conservation score was calculated for all residue positions. SEQ ID NO: 73 (B) Beginning with a hypothetical population of BbpD04.3 variants that evenly spans all single amino acid substitutions, we applied the experimental enrichment ratios to evolve our population in silico. The probability of finding a particular amino acid at any given position was then calculated. This analysis gives an indication of the tolerated sequence diversity in BbpD04.3/BINDI SEQ ID NO: 74.
FIG. 15. (A) BINDI (black) was docked to the hydrophobic binding groove of Mcl-1 (white) by alignment to a bound BH3 peptide (not shown). The docked configuration is computationally designed. (B) Designed ionic interactions in MINDI. (C) Chemical denaturation measured by following loss of CD signal (222 nm). (D) BLI titration experiment for accurate KD determination. Biotinylated Mcl-1 was immobilized to a streptavidin-coated sensor and incubated with the indicated concentrations of soluble MINDI. Raw data is grey, fitted curves are black. (E) Isoaffinity plot from BLI titrations of MINDI interactions with BCL2 family members (only Mcl-1 is labeled).
FIG. 16. Qualitative measurements of binding by BLI analysis at a single analyte concentration. The BCL2 proteins are biotinylated and immobilized on streptavidin-sensors. The sensors are dipped for 600 s in 50 nM of the indicated designed Mcl-1 binding proteins, followed by incubation in buffer to monitor dissociation. Mcl-1-specific peptide MB1 was purified as a MBP fusion and used as a positive control.
FIG. 17. Quantitative BLI analysis of optimized designs binding each BCL2 protein. For a given binding pair, the biotinylated BCL2 protein was immobilized on the surface of streptavidin-coated sensors, incubated with a range of concentrations of soluble designed protein (association), and then placed back in buffer (dissociation). Data were fitted with analysis software. (A) The determined on- and off-rates are plotted, where dashed lines indicate where binding was too weak to be accurately measured. Weak interactions that fall below the dashed lines are not plotted. (B) KDs of pre-optimized computational designs compared to optimized variants are plotted. KDs can also be found in Table 10 (mean+/−SD; n=3).
FIG. 18. Computationally designed proteins 2-CDP06(A), X-CDP07 (B), 10-CDP01 (C), F-CDP01 (D) and W-CDP03 (E) and their experimentally optimized derivatives 2-INDI (A), XINDI (B), 10-ECM01 and 10-INDI (C), F-ECM04 and FINDI (D) and WINDI (E) were denatured with guanidinium hydrochloride. Loss of CD signal at 222 nm was used to calculate the fraction folded.
FIG. 19. Beginning with a hypothetical population of diverse protein variants, we applied experimental enrichment ratios for all single amino acid substitutions to evolve our population in silico. The probability of finding a particular amino acid at any given position was then calculated. This analysis gives an indication of the tolerated sequence diversity in the protein. (A) 2-CDP06 (optimized to 2-INDI) (SEQ ID NO: 39), (B) 10-CDP01 (optimized to 10-INDI) (SEQ ID NO: 52), (C) F-CDP01 (optimized to FINDI) (SEQ ID NO: 53), (D) X-CDP07 (optimized to XINDI) (SEQ ID NO: 47), and (E) W-CDP03 (optimized to WINDI) (SEQ ID NO: 264).
FIG. 20. (A) Sequence alignment of specific BCL2 protein binders. Differences from BINDI, the original designed binder targeting viral BHRF1 that was repurposed for binding other BCL2 family members, are highlighted (from top to bottom SEQ ID NOs: 1, 5, 2, 6, 3, and 4). The Bcl-w binder, WINDI, has been excluded as it binds its target via a shifted interaction surface. Residues that differ from BINDI in one or two sequences are shaded grey, while residues that differ in three or more of the derived binders are shaded black. (B) Sequence variation amongst the INDI family is mapped to the structure of BINDI (surface representation) bound to BHRF1 (ribbon).
FIG. 21. Designed inhibitors induce apoptosis in vitro by engaging the BH3-binding grooves of specific pro-survival homologs. (A) Western blot for cytochrome c in pelleted (P) and soluble (S) fractions of engineered MEFs after permeabilization and treatment with 10 BCL2 inhibitors. Bim-BH3, which binds all pro-survival homologs, is a positive control. Bim-BH3 peptide with four mutations to glutamate at interface residues (Bim4E) is a negative control. BOPs Bad and Noxa, and small molecule drugs tested have the indicated binding specificities in parentheses. (B) HeLa cells were transduced with constructs for designed inhibitor expression, and viability was assayed after 72 hours (mean±SD; n=3).
FIG. 22. Long-term MEF survival and HeLa co-immunoprecipitation studies. (A) Long-term survival of engineered MEFs (pro-survival protein dependence as indicated) was assayed by counting colonies after seven to ten days of doxycycline-induced expression of αMCL1 or αBFL1 (mean±SD, n=3). (B) Expression of FLAG-tagged designed inhibitors in transduced HeLa cells validated with Western blotting. (C) Bim coIP experiments in wild-type and engineered HeLa cells, with and without expression of αMCL1. Expression of αMCL1 caused a dramatic increase in the quantities of Mcl-1 protein present in all cell lines, consistent with previous studies showing increased Mcl-1 half-life in the presence of BH3-peptides (Lee et al., 2008). Bound αMCL1 may stabilize Mcl-1 or occlude Mule (Mcl-1 ubiquitin ligase E3), which binds and ubiquitinates Mcl-1 via a BH3 motif. Despite elevating Mcl-1 protein levels, αMCL1 expression potently induces apoptosis in the expected cell contexts (see FIG. 21A).
FIG. 23. Determination of functional BCL2 profiles in melanoma and glioblastoma cell lines. (A) Melanoma and (B) glioblastoma cell lines were transduced with constructs for designed inhibitor expression and viability was assayed after 72 hours (mean±SD; n=3).
FIG. 24. Determination of functional BCL2 profiles in colon cancer cell lines. (A) Colon cancers were treated with small molecule drugs and/or doxycycline to induce expression of designed inhibitors, as indicated, and viability was assayed after 24 hours (mean±SD; n=3). (B) Long-term survival was assessed after expression of αMCL1 (mean±SD; n=3) or αBFL1 (mean±SD; n=3 for Bfl-1-dependent cell line, n=2 for all others).
FIG. 25. Drug titration assays in colon cancers. (A) Drug titrations for EC50 determination of ABT-263 and A-1331852 in colon cancer lines, with (dotted lines) and without (solid lines) expression of αMCL1 (mean±SD, n=3). (B) EC50 values were determined from titration data using linear regression. (C) Western blotting confirms expression of HA-tagged αMCL1 and αBFL1 in transformed cell lines (actin loading control). (D) Western blotting assays expression of pro-survival proteins in glioblastoma and melanoma cell lines.



DETAILED DESCRIPTION OF THE INVENTION
Within this application, unless otherwise stated, the techniques utilized may be found in any of several well-known references such as: Molecular Cloning: A Laboratory Manual (Sambrook, et al, 1989, Cold Spring Harbor Laboratory Press), Gene Expression Technology (Methods in Enzymology, Vol. 185, edited by D. Goeddel, 1991. Academic Press, San Diego, Calif.), “Guide to Protein Purification” in Methods in Enzymology (M. P. Deutshcer, ed., (1990) Academic Press, Inc.); PCR Protocols: A Guide to Methods and Applications (Innis, et al. 1990. Academic Press, San Diego, Calif.), Culture of Animal Cells: A Manual of Basic Technique, 2nd Ed. (R. I. Freshney. 1987. Liss, Inc. New York, N.Y.), Gene Transfer and Expression Protocols, pp. 109-128, ed. E. J. Murray, The Humana Press Inc., Clifton, N.J.), and the Ambion 1998 Catalog (Ambion, Austin, Tex.)
As used herein and unless otherwise indicated, the terms “a” and “an” are taken to mean “one”, “at least one” or “one or more”. Unless otherwise required by context, singular terms used herein shall include pluralities and plural terms shall include the singular.
All scientific and technical terms used in this application have meanings commonly used in the art unless otherwise specified.
All embodiments of any aspect of the invention can be used in combination, unless the context clearly dictates otherwise.
In a first aspect, the present invention provides polypeptides comprising or consisting of an amino acid sequence having at least 50% amino acid sequence identity over their length relative to the amino acid sequence of SEQ ID NO.: 1, wherein the polypeptide selectively binds to a protein selected from the group consisting of Epstein Barr protein BHFR1, and B cell lymphoma family proteins selected from the group consisting of myeloid cell leukemia 1 (Mcl-1), B-cell lymphoma 2 (Bcl-2), Bcl-2-like protein 1 (BCL2L1/Bcl-XL), Bcl-2-like protein 10 (BCL2L10/Bcl-B), Bcl-2-like protein A1 (A1/Bfl-1), and Bcl-w.







SEQ ID NO: 1







ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRRKLELR


 


YIAAMLMAIGDIYNAIRQAKQEADKLKKAGLVNSQQLDELKRRLEELK


 


EEASRKARDYGREFQLKLEY (BINDI; Target: BHRF1)






The polypeptides of the invention are high-affinity (as low as picomolar affinity), specific protein inhibitors of BHRF1 and B cell lymphoma (BCL) family proteins. And can be used, for example, in methods of treating cancer and Epstein-Barr virus-related diseases. Rather than repurposing an existing natural protein of known structure, the polypeptides of the invention were designed de novo for optimum BHRF1 or and BCL family protein interactions, and are shown herein to trigger apoptosis in relevant cancer lines and slow BL progression in an animal model in the examples herein. This work therefore represents a major bioengineering accomplishment; the creation of an entirely new class of designer polypeptides and their demonstrated therapeutic potential from the ground up.
The polypeptides of the invention have at least 50% amino acid sequence identity over their length relative to the amino acid sequence of SEQ ID NO.: 1, which was designed as shown in the examples that follow to selectively and at very high affinity bind to Epstein Barr protein BHFR1. The inventors have carried out saturation mutagenesis on the polypeptide of SEQ ID NO:1 to identify modifiable residues. Furthermore, the inventors have demonstrated that polypeptides of the invention can be modified for selective binding against BCL family proteins. In various embodiments, the polypeptides of the invention have at least 55%, 60%, 66%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% identity over their length relative to the amino acid sequence of SEQ ID NO:1. As will be understood by those of skill in the art, the polypeptides may include additional residues at the N-terminus, C-terminus, or both that are not present in SEQ ID NO:1; these additional residues are not included in determining the percent identity of the polypeptides of the invention relative to the reference polypeptide (i.e.: SEQ ID NO:1 in this case).
The polypeptides selectively bind to a protein selected from the group consisting of Epstein Barr protein BHFR1, and B cell lymphoma family proteins selected from the group consisting of myeloid cell leukemia 1 (Mcl-1), B-cell lymphoma 2 (Bcl-2), Bcl-2-like protein 1 (BCL2L1/Bcl-XL), Bcl-2-like protein 10 (BCL2L10/Bcl-B), Bcl-2-like protein A1 (A1/Bfl-1), and Bcl-w. As used herein, “selectively binds” or “specifically binds” refers to the ability of a polypeptide of the invention to bind to its target, such as a BHRF1 molecule or BCL family member, with a KD 10−5 M (10000 nM) or less, e.g., 10−6 M, 10−7 M, 10−8M, 10−9M, 10−10 M, 10−11 M, 10−12 M, or less. Selective binding can be influenced by, for example, the affinity and avidity of the polypeptide agent and the concentration of polypeptide agent. The person of ordinary skill in the art can determine appropriate conditions under which the polypeptides described herein selectively bind the targets using any suitable methods, such as titration of a polypeptide agent in a suitable cell binding assay, or as described in the examples that follow. A polypeptide specifically bound to a target is not displaced by a non-similar competitor. In certain embodiments, a polypeptide is said to selectively bind an antigen when it preferentially recognizes its target antigen in a complex mixture of proteins and/or macromolecules.
In one embodiment, the polypeptide comprises or consists of an amino acid sequence having at least 50% amino acid sequence identity over its length relative to the amino acid sequence selected from the group consisting of SEQ ID NOS:2-6 and 265.







SEQ ID NO: 2







ADPKKVLDKAKDQAENRVRELKQVLEELYKEARKLDLTQEMRKKLIERY


 


AAAIIRAIGDINNAIYQAKQEAEKLKKAGLVNSQQLDELLRRLDELQKE


 


ASRKANEYGREFELKLEY


(MINDI, also referred to as αMCL1; Target: Mcl-1)


 







SEQ ID NO: 3







ADPKKVLDKAKDEAENRVRELKQRLEELYKEARKLDLTQEMRQELVDKA


 


RAASLQANGDIFYAILRALAEAEKLKKAGLVNSQQLDELKRRLEELAEE


 


ARRKAEKLRDEFRLKLEY


(2-INDI,, also referred to as αBCL2; Target:


Bcl-2)


 







SEQ ID NO: 4







ADPKKVLDKAKDRAENVVRKLKKELEELYKEARKLDLTQEMRDRIRRT


 


AIAARFQAHGDIFHAIKHAKEEARKLKKAGLVNSQQLDELKRRLRELDE


 


EAEQRAEKLGKEFRLKLEY


(XINDI, also referred to as αBCLXL; Target:


BCL2L1/Bcl-XL)


 







SEQ ID NO: 5







ADPKKILDKAKDQVENRVRELKQELERLYKEARKLDLTQEMRRKLHVR


 


YIEAMLKAIAAIMNAIAQAENEADKLKKAGLVNSQQLDELRRRLEELTE


 


EAAQKAHDYGRELQLKLEY


(10-INDI, also referred to as αBCLB; Target:


BCL2L10/Bcl-B)


 







SEQ ID NO: 6







ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEKRKKLEVA


 


TLGAVLAAHGDILNAIMQAKEEADKLKKAGLVNSQQLDELKRRLEELKE


 


EALRKASDYGNEFHLKRRY


(FINDI, also referred to as αBFL1;


Target: A1/Bfl-1)


 







SEQ ID NO: 265







DPKKVFDELKDRAENNVRRLKQKLEELYKEARKKDLTQEEREKLKTKYK


 


TAMQLAALAAEGDIMNALLKARKLHKNGQVNEQQLEELARRLMELAKEA


 


FQKAKDYANEFKYKLEY


(WINDI, also referred to as αBCLW, previously


W-ECM01)






The polypeptide of each of SEQ ID NOS:2-6 and 262-273 shares very high levels of sequence identity with BIND1 (SEQ ID NO:1), but were designed by the inventors as selective inhibitors of different BCL-family members, as described in detail in the examples that follow. These differing specificities allow use of the polypeptides in methods to treat cancer with different Bcl phenotypes, as well as to determine the Bcl-2 phenotype of a tumor. The BCL-family member target for each of SEQ ID NOS: 2-6 and 262-273 are provided above. The amino acid sequence of the respective targets for each of SEQ ID NOS:1-6 and 262-273 are shown below:







BHRF1 (Target for SEQ ID NO: 1)







(SEQ ID NO: 67)







AYSTREILLALCIRDSRVHGNGTLHPVLELAARETPLRLSPEDTVVLRY


 


HVLLEEIIERNSETFTETWNRFITHTEHVDLDFNSVFLEIFHRGDPSLG


 


RALAWMAWCMHACRTLCCNQSTPYYVVDLSVRGMLEASEGLDGWIHQQG


 


GWSTLIEDNIPGS


 


Mcl-1 (Target for SEQ ID NO: 1)







(SEQ ID NO: 68)







GSDELYRQSLEIISRYLREQATGAKDTKPMGRSGATSRKALETLRRVGD


 


GVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTL


 


ISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFV


 


EFFHVEDLEGG


 


Bcl-2 (Target for SEQ ID NO: 3)







(SEQ ID NO: 69)







AHAGRTGYDNREIVMKYIHYKLSQRGYEWDAGDVGAAPPGAAPAPGIFS


 


SQPGHTPHPAASRDPVARTSPLQTPAAPGAAAGPALSPVPPVVHLTLRQ


 


AGDDFSRRYRRDFAEMSSQLHLTPFTARGRFATVVEELFRDGVNWGRIV


 


AFFEFGGVMCVESVNREMSPLVDNIALWMTEYLNRHLHTWIQDNGGWDA


 


FVELYGPSMR


 


Bcl-XL (Target for SEQ ID NO: 4)







(SEQ ID NO: 70)







SQSNRELVVDFLSYKLSQKGYSWSQFSDVEENRTEAPEGTESEMETPSA


 


INGNPSWHLADSPAVNGATGHSSSLDAREVIPMAAVKQALREAGDEFEL


 


RYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGG


 


ALCVESVDKEMQVLVSRIAAWMATYLNDHLEPWIQENGGWDTFVELYGN


 


NAAAESRK


 


Bcl-B (Target for SEQ ID NO: 5)







(SEQ ID NO: 71)







ADPLRERTELLLADYLGYCAREPGTPEPAPSTPEAAVLRSAAARLRQIH


 


RSFFSAYLGYPGNRFELVALMADSVLSDSPGPTWGRVVTLVTFAGTLLE


 


RGPLVTARWKKWGFQPRLKEQEGDVARDCQRLVALLSSRLMGQHRAWLQ


 


AQGGWDGFCHFFRTPFP


 


Bfl-1 (Target for SEQ ID NO: 6)







(SEQ ID NO: 72)







TDSEFGYIYRLAQDYLQCVLQIPQPGSGPSKTSRVLQNVAFSVQKEVEK


 


NLKSCLDNVNVVSVDTARTLFNQVMEKEFEDGIINWGRIVTIFAFEGIL


 


IKKLLRQQIAPDVDTYKEISYFVAEFIMNNTGEWIRQNGGWENGFVKKF


 


EPKSG






Bcl-w (Target for SEQ ID NOS: 262-273):

Various isoforms of Bcl-w exist. Exemplary embodiments are:







(SEQ ID NO: 274)







MATPASAPDTRALVADFVGYKLRQKGYVCGAGPGEGPAADPLHQAMRAA


 


GDEFETRFRRTFSDLAAQLHVTPGSAQQRFTQVSDELFQGGPNWGRLVA


 


FFVFGAALCAESVNKEMEPLVGQVQEWMVAYLETQLADWIHSSGGWAEF


 


TALYGDGALEEARRLREGNWASVRTVLTGAVALGALVTVGAFFASK


 







(SEQ ID NO: 275)







MATPASAPDTRALVADFVGYKLRQKGYVCGAGPGEGPAADPLHQAMRAA


 


GDEFETRFRRTFSDLAAQLHVTPGSAQQRFTQVSDELFQGGPNWGRLVA


 


FFVFGAALCAESVNKEMEPLVGQVQEWMVAYLETQLADWIHSSGGWELE


 


AIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSIEEKMEA


 


DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYI


 


EFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYR


 


ARTTNYNSSRSRFYSGFNSRPRGRVYRGRARATSWYSPY






The inventors have carried out saturation mutagenesis on the polypeptides according to each of SEQ ID NOS:3-6 and 264, while the polypeptide of SEQ ID NO:2 shares 84% identity and 93% similarity to the polypeptide of SEQ ID NO:1, and therefore likely has a similar tolerance for sequence variations, especially at the majority of positions not making interfacial contacts with its target. In various embodiments, the polypeptides of the invention have at least 55%, 60%, 66%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% identity over their length relative to the amino acid sequence of SEQ ID NO:1-6 and 262-273. As will be understood by those of skill in the art, the polypeptides may include additional residues at the N-terminus, C-terminus, or both that are not present in SEQ ID NOS:1-6 and 262-273; these additional residues are not included in determining the percent identity of the polypeptides of the invention relative to the reference polypeptide (i.e.: SEQ ID NOS:1-6 and 262-273 in this case).
In one embodiment, the polypeptide comprises or consists of an amino acid sequence according to SEQ ID NO: 7, wherein the polypeptide binds to BHFR1.







(SEQ ID NO: 7)







(A/E/G/H/I/K/M/P/R/S/T/V/W/Y)(A/C/D/E/F/G/H/I/K/L/


 


M/N/P/Q/R/S/T/V/W/Y)(A/C/D/E/F/G/H/K/L/M/N/P/Q/R/


 


S/T/V/W/Y)(A/E/G/H/I/K/M/N/P/Q/R/T/V/W)(F/G/I/K/L/


 


Q/R/T/V/W)(A/F/G/I/L/P/S/V/W)(A/D/E/G/I/L/M/Q/R/S/


 


T/V/W/Y)(A/C/D/F/G/I/K/L/N/P/Q/R/S/V/W/Y)(H/K/L/N/


 


Q/R/W)(A/H/S/T)(A/D/E/G/H/K/N/Q/R/S/T/Y)(A/D/E/F/


 


G/H/K/L/M/N/Q/R/S/T/V/W/Y)(D/E/G/I/K/L/M/N/Q/R/S/


 


T/V/W/Y)(A/C/I/L/M/N/Q/S/T/V)(A/D/E/M/N/R/V/W/Y)


 


(A/D/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y)(A/C/E/G/H/I/


 


K/L/M/P/R/S/T/V)(A/I/K/M/T/V)(A/C/D/E/F/G/K/L/M/N/


 


Q/R/T/V/W/Y)(A/D/E/F/G/I/K/L/M/N/Q/R/S/T/V/W/Y)


 


(F/H/I/L/M/Q/T/Y)(A/C/H/I/K/Q/R)(A/C/E/F/G/H/I/M/


 


N/Q/R/S/T/W/Y)(A/D/G/H/I/K/N/Q/R/T/Y)(I/L/M/Q)(A/


 


C/D/E/G/I/K/N/Q/R/S/T/V/W)(A/C/D/E/F/G/H/I/K/L/M/


 


N/Q/R/S/T/V/W/Y)(C/F/H/I/K/L/M/N/P/R/T/V/Y)(A/D/E/


 


H/I/L/P/Q/R/W/Y)(A/E/F/G/H/K/L/M/N/Q/R/S/T/W/Y)(A/


 


D/E/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y)(A/F/G/H/K/L/N/


 


P/R/S/T/Y)(F/H/I/K/L/M/P/Q/R/T/V/Y)(C/H/I/K/L/M/Q/


 


R/S/T/V/Y)(A/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W)(A/


 


C/D/E/G/H/K/L/M/N/Q/R/S/T/V/W/Y)(A/D/E/F/H/I/K/L/


 


M/N/P/Q/R/S/T/V/W/Y)(A/D/E/G/K/N/P/Q/R/S/T)(A/D/E/


 


G/K/N/P/Q/R/S/T/V)(A/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T


 


/V)(F/G/H/K/L/M/N/Q/R/T/V/W/Y)(K/R)(R)(K/R)(F/G/I/


 


L/Q/V/W/Y)(D/E/M/N/Q/T)(F/L/M/W)(R)(E/F/W/Y)(I)


 


(A/G)(A/F/I/Q)(D/H/L/M/N/W)(I/L)(G/I/M/S/V)(A/C/F/


 


G/I/L/M/P/S/T/V)(A/I/M/S/T/V)(G)(D)(I/L/M)(F/M/W/


 


Y)(A/D/F/G/I/L/M/N/Q/S/T/V/W)(A/F/I/L/M/T/V/Y)(A/


 


H/I/M/Y)(R/Y)(A/F/I/K/L/M/Q/R/V/W/Y)(A/G)(K/Q/R)


 


(A/F/G/I/K/L/N/Q/R/S/T/V/W/Y)(A/D/E/F/G/H/I/K/L/M/


 


N/Q/R/S/T/V/W/Y)(A/G/I/M/S)(A/D/E/F/G/H/I/L/M/Q/S/


 


T/V/W/Y)(F/K/R/Y)(A/F/L/M/R/W/Y)(A/F/H/K/N/R/S/T/


 


Y)(I/K/N/R/W)(A/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y)(A/


 


D/G/H/Q/R/S/T)(A/K/L/R/T/V/W/Y)(I/L/M/V)(A/D/E/K/


 


N/Q/R/S/T)(D/E/G/K/M/P/Q/R/S/T/V)(A/D/E/F/H/I/L/N/


 


Q/R/S/T/V)(D/E/H/M/N/Q/T/Y)(A/F/G/H/L/M/R/T/V/W/Y)


 


(D/E/F/G/I/K/L/N/Q/S/T/V/W/Y)(A/E/F/I/K/L/M/Q/T/W)


 


(A/F/I/L/M/T/V)(A/I/K/Q/R/V)(A/G/I/K/L/M/N/Q/R/S/


 


T/V/W/Y)(A/C/D/E/G/H/K/L/N/Q/R/S/T/V/Y)(I/L)(A/D/


 


E/H/I/M/N/Q/T)(A/C/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/V/


 


Y)(A/L/T/V)(K/Q/R)(A/D/E/G/H/Q/S/T/V)(A/D/E/F/H/K/


 


M/N/P/Q/R/S/W/Y)(A/S/V)(A/G/N/Q/S/T)(K/R)(K/R)(A/


 


I/M/N/S/T/V)(D/K/N/R)(A/D/E/F/G/H/K/L/M/N/R/T/V/W/


 


Y)(A/E/G/H/I/T/Y)(D/G/S)(K/Q/R)(A/D/E/F/G/H/K/L/R/


 


S/V/W)(F)(D/E/H/M/Q)(A/D/F/I/L/P/Q/R)(K/Q)(A/H/K/


 


L/M/P/R/S/T/V/Y)(D/E/P/R/T)(D/E/G/H/K/Q/R/T/Y)


 


(Target: BHRF1)






This embodiment is based on saturation mutagenesis studies described in the examples that follow, in which all residues of SEQ ID NO:1 were tested to identify allowed sequence variability for the designed proteins that retained function (i.e.: BHFR1 binding).
In another embodiment, the polypeptide comprises or consists of an amino acid sequence according to SEQ ID NO: 8, wherein the polypeptide binds to Bcl-2.







(SEQ ID NO: 8)







(A/E/G/P/S/T/V)(A/D/E/G/H/K/N/S/T/V/Y)(A/E/F/I/K/


 


L/P/Q/R/S/T/V)(E/H/K/N)(D/E/K/M/Q)(D/V)(C/D/L/Y)


 


(D/L/N/W/Y)(E/K/Q/T/V)(A/C/F/I/L/M/P/S/T/V/W)(F/G/


 


K/M/N/Q/S)(D/E/H/N/P)(E/F/H/K/R/V)(A/C/D/F/H/I/L/


 


M/P/W)(E/F/S)(K/N/R/W/Y)(C/K/N/R)(M/P/V)(P/R)(A/C/


 


E/F/G/H/I/K/L/M/N/R/S/T/V/Y)(F/K/L/M/R/V/Y)(K/N)


 


(K/P/Q/R/W)(K/R)(F/I/K/L/R/W/Y)(E/M/T)(E/H/I/R/


 


W)(I/L/N)(C/G/H/Y)(E/K/N)(E/M/R/T/W)(A/F/I/L/M/R/)


 


T/V/W/Y)(R(K)(E/H/I/L/P/T/Y)(D/E/N/V/Y)(A/E/L/M/V)


 


(A/I/N/R/T)(H/P/Q)(D/E/V)(M/R)(D/H/P/Q/R/Y)(H/K/Q/


 


V)(E/L/W)(K/L/M/V)(A/C/D/E/F/G/H/K/L/M/N/R/T/V/W)


 


(C/D/F/H/I/L/M/V/W/Y)(K)(A/G/H/K/N/Q/R/T/W/Y)(A/D/


 


E/G/L/M/R/V/W)(A/G)(A/N/R)(D/H/I/K/M/N/R/S/W)(L/N)


 


(A/K/Q)(A/C/F/H/K/L/M/N/Q/S/V/W/Y)(A/G/H/N/S/Y)(G)


 


(D/N)(C/E/F/G/I/L/M/N/Q/T)(F)(Y)(A/F/T)(D/I/R)(L/


 


M)(C/I/K/L/R/V)(A)(G/I/L/M/N/R/W/Y)(A/F/M/W/Y)(E/


 


S)(A/C/F/L/M/W)(E/F/S/T/W)(K/M)(L)(K/V/W)(I/K)(A/


 


K)(G)(L/M/S)(A/M/V)(A/K/N/R)(Q/S)(L/Q/R)(C/F/Q/W)


 


(I/L/T)(A/D/I/L/M/Q/R/V/W/Y)(E)(F/L/Q/V)(K/L)(L/R)


 


(H/K/L/Q/R)(D/I/K/L/N/R/T/V)(D/E/Q)(E/W)(D/L/N/P/


 


S)(A/H/I/Q/V)(E)(D/E/F)(A/P/V)(A/C/F/G/K/R/V/Y)(L/


 


Q/R/V)(K)(A/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y)(A/


 


D/E/G/P/S)(K/P/Q/S)(A/F/I/L/V/W)(D/G/I/K/M/Q/R/T/


 


W)(A/D/E/H/K/N/R/V/Y)(C/E/H/K/P/R/W)(C/F/H/Q/R/W)


 


(H/R)(G/L/N/P/Q/R/S)(H/K/N/P)(A/C/F/I/L/M/P/Q/R/S/


 


W)(A/C/E/G/H/K/N/Q/R/S/V/Y)(D/F/H/N/S/Y)


 


(Target: Bcl-2)






This embodiment is based on saturation mutagenesis studies described in the examples that follow, in which all residues of SEQ ID NO:39 were tested to identify allowed sequence variability for the designed proteins that retained function (i.e.: Bcl-2 binding).
In another embodiment, the polypeptide comprises or consists of an amino acid sequence according to SEQ ID NO:9, and wherein the polypeptide binds to binds to Bcl-2-like protein 1.







(SEQ ID NO: 9)







(A/E/G/P/R/S/T/V)(A/D/E/G/H/N/S/V/Y)(A/L/P/Q/R/S/


 


T)(A/E/I/K/N/Q/R/T)(C/K/N/Q/R)(G/I/M/S/V/W/Y)(C/G/


 


I/L)(D/F/H/M/N/S/T/V/Y)(K)(A/E/H/Q/V/W/Y)(C/G/K/Q/


 


R)(D/E/L/M/P/R/S/W/Y)(R/S)(A/D/F/G/H/L/M/N/R/V/Y)


 


(E/R)(C/H/K/N)(A/G/T/V)(K/P/R/V)(H/P/R/Y)(E/K/N/Q/


 


T/W)(F/H/L/R/Y)(K)(G/H/K/M/N/Q/V)(A/C/E/F/G/H/I/K/


 


L/M/N/P/Q/R/S/V/W/Y)(L/P)(A/D/E/G/K/N/P/V/Y)(E/G/


 


I/K/L/M/R/S/V/W)(E/F/G/I/K/L/M/Q/R/S/T/V/Y)(F/H/N/


 


Y)(C/K/N/R)(A/C/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W/


 


Y)(A/G/S/T/V)(R)(F/K/N)(L/R/W/Y)(A/C/D/E/H/I/K/L/


 


M/P/Q/R/T/V/W)(A/L/M/N)(K/N/T)(H/I/K/Q/R/S)(E/F/G/


 


H/I/K/M/N/P/R/T/V/W/Y)(F/I/M)(E/R)(A/D/F/G/N/P/R/


 


W)(Q/R/Y)(F/I/K/L/M/N/R/V/W/Y)(R)(L/M/P/R/T)(A/I/


 


K/L/Q/R/S/T/V/Y)(A)(F/I/L/W/Y)(A/E/G/I/L/M/T/V)(A/


 


H/I/K/L/M/N/Q/R/W)(R)(F/I/W/Y)(A/G/K/P/Q/R/W)(A/F/


 


H/I/K/L/M/P/S/T/V/W)(F/H)(A/G)(D)(D/E/F/I/L/Y)(F)


 


(A/C/D/F/G/H/L/R/S/V/W/Y)(A/F/L/S/T/V/W)(A/D/E/G/


 


I/K/L/R/S/W/Y)(H/I/K/L/M/R/T)(A/D/E/G/H/I/K/L/P/Q/


 


R/S/T/V/W/Y)(A/F/N/R/W)(A/D/G/H/I/K/L/M/N/P/R/S/T)


 


(A/D/E/F/G/K/L/M/R/S/T/W/Y)(A/C/E/F/G/I/P/Q/R/S/T/


 


V/W)(A/G/P/R/T)(R)(K)(K/L/M/P/Q/R/V)(K/R)(K)(A/K/


 


T/W)(G/I/K/L/R/S)(E/G/I/K/L/M/R/S)(K/N/V/W)(G/N/W)


 


(K/Q/R/S/Y)(K/Q)(F/K/L/Q/R/W/Y)(C/L/S/Y)(D/E/G/K/


 


R/T)(E/K/R/W/Y)(I/L/M/R)(K/L/N)(R)(L/R)(G/H/L/R/T/


 


V/Y)(A/E/F/G/H/I/K/L/M/Q/R/S/T/V/W/Y)(E)(E/K/L/M/


 


S/Y)(D/F/I/P/S/T/V/Y)(E/L/S)(C/E/H/M/Q/R)(A/G/K/M/


 


Q/T)(A/E/F/H/I/K/L/Q/T/V/Y)(A/D/L/Q/T/W)(R)(A/C/I/


 


K/L/V)(A/E/G/K/Q/V)(A/C/K/L/M/S)(L/Y)(G/W)(K/R/W)


 


(E/N/R/W)(C/F/I/V)(A/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/


 


V/W/Y)(F/L/M/R/T)(K)(K/L/M/P)(A/D/E/G/K/Q/V)(C/D/


 


F/H/L/N/S/Y)(Target:BCL2L1/Bcl-XL)






This embodiment is based on saturation mutagenesis studies described in the examples that follow, in which all residues of SEQ ID NO:44 were tested to identify allowed sequence variability for the designed proteins that retained function (i.e.: BCL2L1/Bcl-XL binding).
In another embodiment, the polypeptide comprises an amino acid sequence according to SEQ ID NO: 10, wherein the polypeptide binds to Bcl-2-like protein 10.







(SEQ ID NO: 10)







(A/D/E/F/M/S/T/V)(A/D/E/G/H/L/M/N/R/S/Y)(C/F/G/L/


 


P/Q/R/S/T/V)(E/G/I/K/N/Q/R/S/T/W)(A/E/F/K/L/N/P/Q/


 


T/W)(A/D/F/I/S/V)(G/L/M/P/Q/T/V)(A/D/E/G/H/N/R/S/


 


T/W/Y)(A/E/F/I/K/L/N/Q/R/T/Y)(A/E)(E/G/K/L/M/N/Q/


 


R/S/T)(A/C/D/E/F/G/H/N/V/Y)(F/G/H/K/P/Q/R/V)(A/C/


 


E/G/L/S/T/V)(A/C/D/E/K/S/W/Y)(D/I/K/N/T)(A/C/F/H/


 


L/M/N/R/S/T/V/Y)(V)(A/C/G/H/K/R/S/T)(A/D/E/G/K/Q/


 


V/W/Y)(L/M/P/T)(A/E/F/I/K/N/Q/T/Y)(A/H/K/N/P/Q/R/


 


V)(A/C/D/E/F/G/H/I/K/L/M/Q/R/T/V/Y)(L/M/P/R)(D/E/


 


F/G/I/K/M/N/R)(C/H/L/R/S)(L/M/N/R)(C/D/H/N/S/Y)(K/


 


M/N/Q/T/W)(A/D/E/F/G/K/L/M/P/Q/T/W)(A/E/G/M/P/S/T)


 


(C/H/I/L/N/R)(D/G/H/K/N/Q/T)(L/M/Q/R)(A/D/H/K/N/Q/


 


R/T/V/Y)(L/M/P/Q/R)(A/G/N/P/T)(F/G/H/K/L/M/P/Q/R/


 


T/W/Y)(A/D/E/G/K/Q)(C/F/I/K/L/M/R/S/V/W)(C/G/H/L/


 


P/R/S)(A/C/D/F/G/H/I/L/N/P/Q/R/V/W/Y)(K)(L)(A/C/D/


 


E/F/G/H/I/L/M/N/P/Q/S/T/V/W/Y)(F/H/I/K/L/M/P/R/T/


 


V/W)(D/E/G/Q/R)(F/Y)(I/L)(A/D/E/G/H/I/K/L/M/N/P/Q/


 


R/S/T/V/Y)(A/G/I/T)(M/N)(I/L)(F/G/K/M/P/S)(A)(I)


 


(A/C/F/G/P/R/S/W)(A/C/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/


 


T/V/W/Y)(I/W)(A/L/M/P/S/T/V/W)(A/G/M/N/P/Q/S)(A/F/


 


I/L/P)(I/R)(A/E/F/L/W/Y)(F/N/Q/Y)(A)(C/E/G/H/N/R/


 


S/T/V/W/Y)(I/N)(E)(A/K/R/V)(D/F/G/H/K/M/N/Q/R/S/T/


 


V/W/Y)(E/K)(K/L)(K)(E/H/K)(A)(D/G)(C/F/G/L/M/P/Q/


 


R/S/V/W)(A/C/D/F/G/I/V/Y)(D/H/I/K/N/S/T/Y)(A/C/F/


 


I/L/N/P/S/T/Y)(E/F/H/K/L/P/Q/R)(A/E/H/K/P/Q/R)(A/


 


K/L/M/P/Q/R/V)(A/D/E/G/L/N/R/V/Y)(E/G/K/Q)(L/M/P/


 


R/T)(A/C/G/H/P/Q/R)(C/G/I/L/P/R/V)(C/F/H/P/R/S/V/


 


Y)(F/L/M/P/Q/R)(A/D/E/G/H/I/K/L/M/N/P/Q/R/S/T/V/Y)


 


(D/E/G/I/K/L/P/R/V)(A/E/G/K/L/M/P/R/T/V)(A/C/E/G/


 


M/P/Q/S/T/V)(A/D/E/G/H/K/N/Q/R/S/T/Y)(C/D/E/F/G/M/


 


Q/S/V/W)(A/D/F/H/M/P/Q/S/T/V)(A/D/G/S/T/V)(A/C/D/


 


E/G/H/I/L/M/N/Q/R/S/T/V/Y)(A/E/G/I/K/M/R/S/T)(A/E/


 


F/G/S/T)(D/H/K/M/N/P/Q/R)(A/C/D/E/G/L/N/Q/S/V/Y)


 


(C/D/F/H/T/Y)(C/D/G/L)(C/E/H/L/R/S/T/Y)(D/E/K/P/T)


 


(C/F/I/L/S/V/Y)(E/F/H/K/Q/R/S/Y)(H/I/L/N/P/Q/R/S/


 


T)(A/E/H/I/K/N/Q/Y)(E/L/M/P/Q/V)(D/E/G/H/K/L/N/S/


 


V/W)(C/D/G/H/L/R/Y)(Target: BCL2L10/Bcl-B)






This embodiment is based on saturation mutagenesis studies described in the examples that follow, in which all residues of SEQ ID NO:52 were tested to identify allowed sequence variability for the designed proteins that retained function (i.e.: BCL2L10/Bcl-B binding).
In another embodiment the polypeptide comprises or consists of an amino acid sequence according to SEQ ID NO: 11, wherein the polypeptide binds to Bcl-2-like protein A1 (A1/Bfl-1).







(SEQ ID NO: 11)







(A/D/F/G/H/K/L/M/P/R/S/T/V/W/Y)(A/C/D/E/F/G/H/I/


 


L/M/N/P/Q/S/T/V/W/Y)(A/C/D/F/G/I/K/L/P/Q/R/S/T/V/


 


W/Y)(C/D/E/F/I/K/L/M/N/Q/R/T/V/W/Y)(E/H/I/K/M/N/P/


 


Q/R/T)(A/D/E/F/G/I/V)(A/E/F/H/L/M/P/Q/R/T/V/W/Y)


 


(A/C/D/E/G/H/I/K/L/M/N/P/R/S/V/W/Y)(A/C/D/E/F/G/H/


 


I/K/L/M/N/P/Q/R/S/T/V/W/Y)(A/E/F/G/H/I/L/M/N/P/S/


 


T/V/W/Y)(E/F/I/K/L/M/N/Q/T/V/W/Y)(A/D/E/G/H/I/K/L/


 


M/N/R/V/W/Y)(C/D/E/H/I/K/L/M/P/Q/W/Y)(A/C/E/F/G/I/


 


L/M/N/Q/S/T/V/W/Y)(A/C/D/E/F/G/K/L/M/N/S/V/Y)(A/D/


 


E/G/H/I/K/N/Q/S/T/V/W)(A/H/I/L/P/R/S/T/V)(A/D/G/H/


 


M/S/T/V)(A/C/E/G/H/L/M/R/T/W)(A/D/E/F/G/H/I/K/L/M/


 


N/P/Q/R/S/T/V/W/Y)(A/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/


 


W/Y)(E/G/H/I/K/L/M/N/Q/R/T/W/Y)(A/D/E/H/K/M/N/Q/R/


 


S/T/W)(K)(A/C/E/F/G/H/I/K/L/M/P/Q/R/S/T/V/W/Y)(A/


 


C/D/E/F/G/H/K/L/M/Q/R/S/V/W/Y)(A/D/E/F/G/H/I/K/L/


 


M/N/Q/R/S/T/V/W/Y)(I/L/S/T/V)(A/C/D/F/G/H/I/L/M/P/


 


R/S/T/V/W/Y)(H/I/K/N/Q/T/Y)(A/C/D/E/F/G/H/I/K/L/M/


 


N/P/Q/R/S/T/V/W/Y)(A/C/D/F/G/H/I/L/M/P/R/S/V/W/Y)


 


(C/H/K/M/N/R/S/T/Y)(K/L/N/R)(F/H/I/L/P/R)(A/D/E/F/


 


G/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y)(A/D/E/F/H/I/K/L/M/


 


N/P/Q/R/S/T/V/W)(A/D/E/G/H/I/K/M/N/P/Q/R/S/T/V/Y)


 


(A/E/G/H/I/K/L/M/N/P/Q/S/T/V)(A/D/E/F/G/K/N/Y)(A/


 


F/G/H/I/K/L/M/P/S/T/W/Y)(A/C/D/E/F/G/H/I/L/M/N/P/


 


Q/R/S/V/W/Y)(A/E/G/H/I/K/L/M/N/P/Q/R/S/T/V)(K/N/Q/


 


R/T)(I/L/P/V)(A/D/E/F/G/H/K/L/N/P/Q/R/S/W)(A/D/E/


 


F/H/I/L/M/N/P/T/V/Y)(A/E/G)(A/C/D/E/F/G/H/I/K/L/M/


 


N/P/Q/S/T/V/W/Y)(F/I/L/M/N/S/T)(G)(A/E/F/G/I/L/S/


 


T/V/W/Y)(C/F/G/I/L/M/N/P/V/W/Y)(L/M)(A/G)(A/C/F/G/


 


L/M/N/T/V/W/Y)(H/I/N/T/V)(G)(A/D/E/N/V/Y)(F/I/L/W)


 


(I/L/V)(D/H/K/N/S/T)(A/C/D/E/F/G/I/L/M/N/Q/S/T/V)


 


(C/E/I/M/T/V/W)(M/W)(C/D/E/G/H/K/L/M/N/P/Q/R/S/T)


 


(A/D/E/G/H/N/R/S/W/Y)(K/M/N/P/R/T/W/Y)(A/C/D/E/F/


 


G/H/I/K/L/N/P/Q/R/S/T/V/W/Y)(A/D/E/I/K/M/N/W)(A/P/


 


T)(A/D/E/F/G/H/I/N/P/V/W/Y)(A/D/E/F/G/H/I/K/L/M/N/


 


P/Q/R/S/T/V/W/Y)(A/C/D/E/F/H/I/L/M/P/Q/R/T/V)(A/E/


 


H/I/K/N/P/R/S/W)(A/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/


 


V/W/Y)(A/D/E/F/G/H/K/L/N/P/Q/R/S/T/V/W/Y)(G/K/N/P/


 


Q/R)(F/G/I/L/M/P/Q/R/S/T/V/W/Y)(A/D/G/I/P/R/V)(I/


 


K/N/R/S)(A/C/E/F/G/H/I/K/L/M/N/P/R/S/T/V/W/Y)(A/F/


 


H/I/K/L/N/P/Q/R/T/V/Y)(G/H/I/K/L/M/Q/R/S/T)(A/C/E/


 


H/K/L/M/P/Q/R/V)(A/C/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/


 


V/W/Y)(A/D/E/F/G/H/I/K/M/N/P/Q/R/S/T/V)(A/C/E/L/M/


 


N/R/S/T/Y)(A/C/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W/


 


Y)(D/H/K/R/T)(K/R/W/Y)(A/C/I/L/M/N/P/Q/S/T)(A/E/I/


 


K/L/P/Q/R/T/V)(D/E/F/G/I/K/L/M/N/Q/R/S/T/V/W/Y)(A/


 


E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y)(K/Y)(A/D/E/N/S)


 


(A/E/F/G/M/Q/R/T/V/W/Y)(A/E/F/I/T)(F/L/N/Y)(H/Q/R/


 


S)(A/E/G/H/I/K/N/Q/R/S/V/W)(A/C/E/F/G/H/I/K/L/M/N/


 


P/Q/S/T/V/Y)(A/C/D/E/G/H/K/N/P/Q/R/S/T/Y)(A/D/E/F/


 


G/I/L/P/Q/V)(A/C/D/E/F/G/H/I/K/L/N/P/Q/R/S/T/V/W/


 


Y)(A/C/D/F/G/I/L/M/N/P/Q/R/S/T/V/W)(A/D/E/G/H/K/N/


 


P/Q/R/S)(D/E/F/M/P/V/Y)(A/C/D/E/F/G/H/I/K/L/M/N/P/


 


Q/R/S/T/V/W/Y)(A/C/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/


 


V/W/Y)(A/C/D/E/G/H/K/L/M/N/P/Q/R/S/T/V/W/Y)(A/E/I/


 


K/P/Q/R)(A/C/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/V/W/Y)(A/


 


D/E/G/H/K/L/M/N/P/Q/R/S/T/V/W)(A/C/D/E/F/G/H/K/L/


 


M/N/P/Q/R/S/T/W/Y)(Target: A1/Bfl-1)






This embodiment is based on saturation mutagenesis studies described in the examples that follow, in which all residues of SEQ ID NO:53 were tested to identify allowed sequence variability for the designed proteins that retained function (i.e.: Bcl-2-like protein A1 (A1/Bfl-1)binding).
In another embodiment, the polypeptide comprises or consists of an amino acid sequence according to SEQ ID NO: 12, and wherein the polypeptide binds to Bcl-2-like protein Mcl-1.










SEQ ID NO: 12








Residue
Allowable Residues





A1
A/E/G/H/I/K/M/P/R/S/T/V/W/Y


 


D2
A/C/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y


 


W3
A/C/D/E/F/G/H/K/L/M/N/P/Q/R/S/T/V/W/Y


 


K4
A/E/G/H/I/K/M/N/P/Q/R/T/V/W


 


K5
F/G/I/K/L/Q/R/T/V/W


 


V6
A/F/G/I/L/P/S/V/W


 


L7
A/D/E/G/I/L/M/Q/R/S/T/V/W/Y


 


D8
A/C/D/F/G/I/K/L/N/P/Q/R/S/V/W/Y


 


K9
H/K/L/N/Q/R/W


 


A10
A/H/S/T


 


K11
A/D/E/G/H/K/N/Q/R/S/T/Y


 


D12
A/D/E/F/G/H/K/L/M/N/Q/R/S/T/V/W/Y


 


I13
D/E/G/I/K/L/M/N/Q/R/S/T/V/W/Y


 


A14
A/C/I/L/M/N/Q/S/T/V


 


E15
A/D/E/M/N/R/V/W/Y


 


N16
A/D/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y


 


R17
A/C/E/G/H/I/K/L/M/P/R/S/T/V


 


V18
A/I/K/M/T/V


 


R19
A/C/D/E/F/G/K/L/M/N/Q/R/T/V/W/Y


 


E20
A/D/E/F/G/I/K/L/M/N/Q/R/S/T/V/W/Y


 


L21
F/H/I/L/M/Q/T/Y


 


K22
A/C/H/I/K/Q/R


 


Q23
A/C/E/F/G/H/I/M/N/Q/R/S/T/W/Y


 


K24
A/D/G/H/I/K/N/Q/R/T/Y/V


 


L25
I/L/M/Q


 


E26
A/C/D/E/G/I/K/N/Q/R/S/T/V/W


 


E27
A/C/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y


 


F28
C/F/H/I/K/L/M/N/P/R/T/V/Y


 


Y29
A/D/E/H/I/L/P/Q/R/W/Y


 


K30
A/E/F/G/H/K/L/M/N/Q/R/S/T/W/Y


 


E31
A/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y


 


A32
A/F/G/H/K/L/N/P/R/S/T/Y


 


M33
F/H/I/K/L/M/P/Q/R/T/V/Y


 


K34
C/H/I/K/L/M/Q/R/S/T/V/Y


 


L35
A/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W


 


D36
A/C/D/E/G/H/K/L/M/N/Q/R/S/T/V/W/Y


 


L37
A/D/E/F/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y


 


T38
A/D/E/G/K/N/P/Q/R/S/T


 


Q39
A/D/E/G/K/N/P/Q/R/S/T/V


 


E40
A/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V


 


M41
F/G/H/K/L/M/N/Q/R/T/V/W/Y


 


R42
K/R


 


R43
K


 


K44
K/R


 


L45
F/G/I/L/Q/V/W/Y


 


M46
D/E/M/N/Q/T/I


 


L47
F/L/M/W/E


 


R48
R


 


W49
E/F/W/Y


 


I50
A


 


A51
A/G


 


A52
A/F/I/Q


 


M53
D/H/L/M/N/W/I


 


L54
I/L


 


M55
G/I/M/S/V/R


 


A56
A/C/F/G/I/L/M/P/S/T/V


 


I57
A/I/M/S/T/V


 


G58
G


 


D59
D


 


I60
I/L/M


 


F61
F/M/W/Y/N


 


N62
A/D/F/G/I/L/M/N/Q/S/T/V/W


 


A63
A/F/I/L/M/T/V/Y


 


I64
A/H/I/M/Y


 


R65
R/Y


 


Q66
A/F/I/K/L/M/Q/R/V/W/Y


 


A67
A/G


 


K68
K/Q/R


 


Q69
A/F/G/I/K/L/N/Q/R/S/T/V/W/Y


 


E70
A/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y


 


A71
A/G/I/M/S


 


D72
A/D/E/F/G/H/I/L/M/Q/S/T/V/W/Y


 


K73
F/K/R/Y


 


L74
A/F/L/M/R/W/Y


 


K75
A/F/H/K/N/R/S/T/Y


 


K76
I/K/N/R/W


 


A77
A/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y


 


G78
A/D/G/H/Q/R/S/T


 


L79
A/K/L/R/T/V/W/Y


 


V80
I/L/M/V


 


N81
A/D/E/K/N/Q/R/S/T


 


S82
D/E/G/K/M/P/Q/R/S/T/V


 


Q83
A/D/E/F/H/I/L/N/Q/R/S/T/V


 


Q84
D/E/H/M/N/Q/T/Y


 


L85
A/F/G/H/L/M/R/T/V/W/Y


 


D86
D/E/F/G/I/K/L/N/Q/S/T/V/W/Y


 


E87
A/E/F/I/K/L/M/Q/T/W


 


L88
A/F/I/L/M/T/V


 


K89
A/I/K/Q/R/V/L


 


R90
A/G/I/K/L/M/N/Q/R/S/T/V/W/Y


 


R91
A/C/D/E/G/H/K/L/N/Q/R/S/T/V/Y


 


L92
I/L


 


E93
A/D/E/H/I/M/N/Q/T


 


E94
A/C/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/V/Y


 


L95
A/L/T/V


 


K96
K/Q/R


 


E97
A/D/E/G/H/Q/S/T/V


 


E98
A/D/E/F/H/K/M/N/P/Q/R/S/W/Y


 


A99
A/S/V


 


S100
A/G/N/Q/S/T


 


R101
K/R


 


K102
K/R


 


A103
A/I/M/N/S/T/V


 


R104
D/K/N/R


 


D105
A/D/E/F/G/H/K/L/M/N/R/T/V/W/Y


 


Y106
A/E/G/H/I/T/Y


 


G107
D/G/S


 


R108
K/Q/R


 


E109
A/D/E/F/G/H/K/L/R/S/V/W


 


F110
F


 


Q111
D/E/H/M/Q


 


L112
A/D/F/I/L/P/Q/R


 


K113
K/Q


 


L114
A/H/K/L/M/P/R/S/T/V/Y


 


E115
D/E/P/R/T


 


Y116
D/E/G/H/K/Q/R/T/Y









In another embodiment, the polypeptide comprises or consists of the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-6.
In another embodiment the polypeptide comprises or consist of an amino acid sequence having at least 50% identity to the amino acid sequence of SEQ ID NO:13.







SEQ ID NO.: 13







ADWKKVLDKAKDIAENRVREIKQKLEEFYKKAMKLDLTQEMRRKLMLE


 


WIAAMLMAIGDIFNAIEQAKQEADKLKKAGQVNSQLLDELKRRLEELKE


 


EASRKCHDYGREFQLKLEY (BbpD04)






As shown in the examples that follow, the polypeptide of SEQ ID NO:13 is a selective high affinity binder of Epstein Barr protein BHFR1. The inventors have carried out saturation mutagenesis on the polypeptide of SEQ ID NO:13 to identify modifiable residues. In various embodiments, the polypeptides of this embodiment have at least 55%, 60%, 66%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 100% identity over their length relative to the amino acid sequence of SEQ ID NO:13. As will be understood by those of skill in the art, the polypeptides may include additional residues at the N-terminus, C-terminus, or both that are not present in SEQ ID NO:1; these additional residues are not included in determining the percent identity of the polypeptides of the invention relative to the reference polypeptide (i.e.: SEQ ID NO:13 in this case).
In one embodiment, the polypeptide comprises at least one conservative amino acid substitution corresponding to residues 3, 13, 21, 28, 31, 33, 46, 48, 49, 61, 62, 65, 79, 84, 103, and 104 of the amino acid sequence of SEQ ID NO: 13.
As used herein, “conservative amino acid substitution” means amino acid or nucleic acid substitutions that do not alter or substantially alter polypeptide or polynucleotide function or other characteristics. A given amino acid can be replaced by a residue having similar physiochemical characteristics, e.g., substituting one aliphatic residue for another (such as Ile, Val, Leu, or Ala for one another), or substitution of one polar residue for another (such as between Lys and Arg; Glu and Asp; or Gln and Asn). Other such conservative substitutions, e.g., substitutions of entire regions having similar hydrophobicity characteristics, are well known. Polypeptides comprising conservative amino acid substitutions can be tested in any one of the assays described herein to confirm that a desired activity, e.g. antigen-binding activity and specificity of a native or reference polypeptide is retained.
Amino acids can be grouped according to similarities in the properties of their side chains (in A. L. Lehninger, in Biochemistry, second ed., pp. 73-75, Worth Publishers, New York (1975)): (1) non-polar: Ala (A), Val (V), Leu (L), Ile (I), Pro (P), Phe (F), Trp (W), Met (M); (2) uncharged polar: Gly (G), Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N), Gln (Q); (3) acidic: Asp (D), Glu (E); (4) basic: Lys (K), Arg (R), His (H). Alternatively, naturally occurring residues can be divided into groups based on common side-chain properties: (1) hydrophobic: Norleucine, Met, Ala, Val, Leu, Ile; (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gln; (3) acidic: Asp, Glu; (4) basic: His, Lys, Arg; (5) residues that influence chain orientation: Gly, Pro; (6) aromatic: Trp, Tyr, Phe. Non-conservative substitutions will entail exchanging a member of one of these classes for another class. Particular conservative substitutions include, for example; Ala into Gly or into Ser; Arg into Lys; Asn into Gln or into H is; Asp into Glu; Cys into Ser; Gln into Asn; Glu into Asp; Gly into Ala or into Pro; His into Asn or into Gln; Ile into Leu or into Val; Leu into Ile or into Val; Lys into Arg, into Gln or into Glu; Met into Leu, into Tyr or into Ile; Phe into Met, into Leu or into Tyr; Ser into Thr; Thr into Ser; Trp into Tyr; Tyr into Trp; and/or Phe into Val, into Ile or into Leu.
In a further embodiment, the polypeptide includes the substitutions K31E, E48R, and E65R relative to SEQ ID NO:13. In another embodiment, the polypeptide includes the substitutions I21L, Q79L, L84Q, and H104R relative to SEQ ID NO:13. In a further embodiment, the polypeptide includes the substitution C103A relative to SEQ ID NO:13. In a still further embodiment, the polypeptide includes substitutions W3P, I13Q, F28L, M33R, M46E, W49Y, and F61Y relative to SEQ ID NO:13. In another embodiment, the polypeptide includes the substitution N62S relative to SEQ ID NO:13. These embodiments may be combined in any suitable combination.
In another embodiment, the polypeptide comprises or consists of a polypeptide having at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or 100% amino acid sequence identity over their length relative to the amino acid sequence of SEQ ID NO: 276, wherein the polypeptide selectively binds to Bcl-w.










SEQ ID NO: 276 WINDI Allowable Residues








Residue
Allowable Residues











1
C/D/E/K/L/M/N/R/S/V/W/Y


 


2
A/D/E/G/H/L/N/P/Q/R/T/W


 


3
A/C/F/G/H/I/K/M/Q/R/T/V/Y


 


4
D/F/G/I/K/M/N/R/S/T/V/W


 


5
I/L/M/N/T/V/W/Y


 


6
E/F/I/L/Q/T/V/W/Y


 


7
A/C/D/F/L/W/Y


 


8
D/E/H/I/V


 


9
A/E/H/L/Y


 


10
A/H/I/K/M/N/Q/R/S/T/Y


 


11
C/D/E/G/H/K/M/Q/R/S/T/W


 


12
A/D/E/G/L/N/Q/R/S/V/W


 


13
A/C/F/H/K/L/M/N/S/T/V


 


14
A/D/E/F/G/H/I/L/M/Q/S/V/W/Y


 


15
A/E/G/H/M/N/Q/R/W/Y


 


16
A/F/L/M/N/S/V/W/Y


 


17
F/G/H/I/K/M/Q/R/T/V


 


18
A/C/E/H/K/L/N/Q/R/S/V/W


 


19
I/M/N/Q/R


 


20
A/F/G/I/K/L/M/P/T/V/W/Y


 


21
I/K/N/S/T/W


 


22
A/F/G/H/I/K/L/M/N/P/Q/R/S/V/W/Y


 


23
I/K/L/R/V


 


24
A/D/F/H/K/L/M/R/S/V


 


25
A/C/D/E/G/H/L/M/S/V/W


 


26
A/D/E/F/G/H/I/L/M/Q/R/S/V/W/Y


 


27
A/F/G/I/K/L/M/Y


 


28
F/H/I/K/L/Q/S/V/W/Y


 


29
A/F/G/H/I/K/M/N/P/Q/R/S/T/V/W/Y


 


30
D/E/G/H/L/M/N/Q/S/V/W/Y


 


31
A/F/G/M/P/S/V/Y


 


32
A/E/G/H/I/M/N/P/Q/R/T


 


33
A/H/I/K/M/P/R/T/V/W/Y


 


34
A/E/G/H/I/K/N/P/R/S/T/W


 


35
A/C/D/E/G/H/K/L/M/N/P/R/S/T/V/W/Y


 


36
A/D/E/F/K/L/R/S


 


37
G/R/S/T


 


38
A/E/G/H/K/L/P/Q/S/V/W


 


39
A/D/E/G/I/K/M/N/P/Q/R/S/T/V/W/Y


 


40
A/D/E/G/I/R/W/Y


 


41
H/K/L/Q/R/Y


 


42
A/D/E/G/K/Q/R/T/V


 


43
E/G/H/I/K/L/N/R/S/T/V/W/Y


 


44
F/H/K/L/T/V/W/Y


 


45
I/K/L/M/R/S/T/V/W


 


46
A/D/E/G/I/K/L/M/N/Q/S/T/V/W


 


47
D/F/H/I/K/M/R/S/T/V/Y


 


48
A/C/E/F/G/H/I/K/L/M/R/S/T/V/W/Y


 


49
I/K/M/N/P/Q/R/W


 


50
D/I/N/P/S/T


 


51
A/F/G/H/I/K/L/M/Q/R/S/T/W


 


52
A/F/L/M/R/V/W/Y


 


53
A/E/F/G/H/I/M/N/Q/T/V/W/Y


 


54
A/G/H/I/L/M/N/P/S/T/V


 


55
A/C/F/G/M/P/T/W/Y


 


56
A/F/I/K/L/M/V


 


57
K/L/W/Y


 


58
A/G/K/M/Q/R/S/V/W


 


59
A/D/I/L/M/T/V/W


 


60
A/D/E/F/G/H/I/L/M/P/S/T/V/W/Y


 


61
F/G/N/Q


 


62
C/D/Y


 


63
A/C/F/H/I/K/L/M/P/T/V/W/Y


 


64
E/F/L/M


 


65
D/F/H/M/N/W


 


66
A/G/S/W


 


67
F/K/L/V/W/Y


 


68
K/L/M/W


 


69
F/H/I/K/Q/R/T/Y


 


70
A/F/G/I/L/M


 


71
Q/R


 


72
I/K/R/T


 


73
A/K/L/M


 


74
F/G/H/K/L/R/V/W/Y


 


75
I/K/M/N/R


 


76
A/D/F/G/H/I/K/L/M/N/Q/R/V/W/Y


 


77
F/G/Q/R/S


 


78
E/G/H/L/M/N/P/Q/T/V/Y


 


79
A/I/L/M/S/T/V/W/Y


 


80
E/G/M/N/S/T


 


81
A/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y


 


82
D/E/F/G/I/K/L/N/P/Q/R/S/W/Y


 


83
A/D/E/G/P/Q/W


 


84
A/F/G/H/I/K/L/V/Y


 


85
A/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y


 


86
A/D/E/F/G/H/R/S/T/V/W/Y


 


87
F/H/I/K/L/M/Q/V


 


88
A/H/N/P/R/S/W


 


89
H/L/Q/R/V/Y


 


90
A/D/G/L/P/Q/R/Y


 


91
C/F/H/I/K/L/P/R/T/V/Y


 


92
C/F/G/I/K/L/M/N/P/Q/S/T/V/W/Y


 


93
A/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y


 


94
A/C/D/E/G/I/K/L/M/N/Q/R/S/T/V/Y


 


95
A/C/D/F/H/I/L/M/P/T/V/W/Y


 


96
H/I/K/N/P/Q/R/T/V


 


97
C/D/E/G/L/M/P/R/S/V


 


98
A/C/F/G/I/K/L/Q/T/V/W


 


99
E/F/G/I/L/M/W


 


100
A/E/G/H/K/P/Q/R/V


 


101
A/D/E/G/H/I/K/P/R/S/V


 


102
A/C/F/I/L/M/T/V/Y


 


103
I/K/R


 


104
A/C/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/V/W/Y


 


105
C/F/H/I/M/R/S/W/Y


 


106
A/E/H/K/L/M/R/V


 


107
A/E/F/G/I/K/L/M/N/Q/R/S/V/Y


 


108
A/D/E/G/I/K/L/Q/R/T


 


109
C/E/F/H/L/N/R/V/Y


 


110
A/D/E/F/G/H/I/K/L/M/N/P/R/S/T/V/W/Y


 


111
D/I/L/R/S/V/W/Y


 


112
A/C/D/G/H/I/K/L/V


 


113
C/E/F/K/L/Q/R/T/V


 


114
A/D/E/G/I/K/L/M/N/P/Q/R/S/T/V/W/Y


 


115
A/D/G/I/L/M/P/R/T/W/Y









This embodiment is based on saturation mutagenesis studies described in the examples that follow, in which all possible single amino acid substitutions of SEQ ID NO: 264 were tested to identify allowed sequence variability for the designed proteins that retained function (i.e.: Bcl-w binding).
In preferred embodiments, the polypeptide of SEQ ID NO: 276 include polypeptides with one or more (i.e.: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16 of the following specific amino acid residues: 10L, 20N, 20Q, 47D, 47T, 54E, 54H, 54Q, 55I, 55L, 55M, 55S, 55T, 55V, 60I, 60M, 60T, 60V, 61E, 64F, 64I, 64L, 64M, 65I, 65L, 65M, 77R, 86R, 93M, 93T, 94V, 98D, 100E, and 111K. In further preferred embodiments, the polypeptides of SEQ ID NO: 276 have 1, 2, 3, 4, 5, 6, 7, 8, or all 9 of the following specific amino acid residues: 10L, 47T, 54Q, 55L, 61E, 64I, 65M, 93M, and 111K.
As noted above, the polypeptides of the invention may include additional residues at the N-terminus, C-terminus, or both. Such residues may be any residues suitable for an intended use, including but not limited to detection tags (i.e.: fluorescent proteins, antibody epitope tags, etc.), linkers, ligands suitable for purposes of purification (His tags, etc.), and peptide domains that add functionality to the polypeptides. In one embodiment, the polypeptide of the invention further comprises a cell penetrating peptide. Cell penetrating peptides are useful, for example, to facilitate uptake of the polypeptides by cells, and are known to those of skill in the art. Non-limiting examples of such cell penetrating peptides that can be used with the polypeptides of the invention include:









TAT:







(SEQ ID NO: 14)









GRKKRRQRRRPPQ;



 



penetratin:







(SEQ ID NO: 15)









RQIKIWFQNRRMKWKK;



 



MAP:







(SEQ ID NO: 16)









KLALKLALKALKAALKLA;



 



transportan/TP10:







(SEQ ID NO: 17)









GWTLNS/AGYLLGKINLKALAALAKKIL;



 



VP22







(SEQ ID NO: 18)









NAKTRRHERRRKLAIER;



 



polyarginine:







(SEQ ID NO: 19)









Rn, n >7;



 



MPG:







(SEQ ID NO: 20)









GALFLGFLGAAGSTMGA;



 



Pep-1:







(SEQ ID NO: 21)









KETWWETWWTEWSQPKKKRKV;



 



pVEC:







(SEQ ID NO: 22)









LLIILRRRIRKQAHAHSK;



 



YTA2:







(SEQ ID NO: 23)









YTAIAWVKAFIRKLRK;



 



YTA4:







(SEQ ID NO: 24)









IAWVKAFIRKLRKGPLG;



 



M918:







(SEQ ID NO: 25)









MVTVLFRRLRIRRACGPPRVRV;



and



 



CADY:







(SEQ ID NO: 26)









GLWRALWRLLRSLWRLLWRA.






As used throughout the present application, the term “polypeptide” is used in its broadest sense to refer to a sequence of subunit amino acids. The polypeptides of the invention may comprise L-amino acids, D-amino acids (which are resistant to L-amino acid-specific proteases in vivo), or a combination of D- and L-amino acids. The polypeptides described herein may be chemically synthesized or recombinantly expressed. The polypeptides may be linked to other compounds to promote an increased half-life in vivo, such as by PEGylation, HESylation, PASylation, glycosylation, or may be produced as an Fc-fusion or in deimmunized variants. Such linkage can be covalent or non-covalent as is understood by those of skill in the art.
In another aspect, the invention provides pharmaceutical composition, comprising a polypeptide of any embodiment or combination of embodiments of the invention, and a pharmaceutically acceptable carrier. The pharmaceutical compositions of the invention can be used, for example, in the methods of the invention described below. The pharmaceutical composition may comprise in addition to the polypeptide of the invention (a) a lyoprotectant; (b) a surfactant; (c) a bulking agent; (d) a tonicity adjusting agent; (e) a stabilizer; (f) a preservative and/or (g) a buffer. In some embodiments, the buffer in the pharmaceutical composition is a Tris buffer, a histidine buffer, a phosphate buffer, a citrate buffer or an acetate buffer. The pharmaceutical composition may also include a lyoprotectant, e.g. sucrose, sorbitol or trehalose. In certain embodiments, the pharmaceutical composition includes a preservative e.g. benzalkonium chloride, benzethonium, chlorohexidine, phenol, m-cresol, benzyl alcohol, methylparaben, propylparaben, chlorobutanol, o-cresol, p-cresol, chlorocresol, phenylmercuric nitrate, thimerosal, benzoic acid, and various mixtures thereof. In other embodiments, the pharmaceutical composition includes a bulking agent, like glycine. In yet other embodiments, the pharmaceutical composition includes a surfactant e.g., polysorbate-20, polysorbate-40, polysorbate-60, polysorbate-65, polysorbate-80 polysorbate-85, poloxamer-188, sorbitan monolaurate, sorbitan monopalmitate, sorbitan monostearate, sorbitan monooleate, sorbitan trilaurate, sorbitan tristearate, sorbitan trioleaste, or a combination thereof. The pharmaceutical composition may also include a tonicity adjusting agent, e.g., a compound that renders the formulation substantially isotonic or isoosmotic with human blood. Exemplary tonicity adjusting agents include sucrose, sorbitol, glycine, methionine, mannitol, dextrose, inositol, sodium chloride, arginine and arginine hydrochloride. In other embodiments, the pharmaceutical composition additionally includes a stabilizer, e.g., a molecule which, when combined with a protein of interest substantially prevents or reduces chemical and/or physical instability of the protein of interest in lyophilized or liquid form. Exemplary stabilizers include sucrose, sorbitol, glycine, inositol, sodium chloride, methionine, arginine, and arginine hydrochloride.
The polypeptides of the invention may be the sole active agent in the pharmaceutical composition, or the composition may further comprise one or more other active agents suitable for an intended use, including but not limited to anti-HA and anti-NA antibodies. As used herein, the term “pharmaceutically acceptable” is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
In one embodiment, the pharmaceutical compositions further comprise an antibody, or antibody fragment. In this embodiment, the antibody or antibody fragment adds functionality to the composition by, for example, helping target the composition to a cell type that has a cell surface receptor to which the antibody selectively binds. As a result, compositions of this embodiment are particularly useful for therapeutic applications. As will be understood by those of skill in the art, any suitable antibody or fragment thereof can be employed that targets a cell or tissue of interest. The antibody or fragment may be recombinantly expressed as part of the polypeptide, may be linked to the polypeptide directly (such as by a covalent linkage or non-covalent interaction), or may not be directly linked to the polypeptide at all (i.e.: present in the same composition, but unlinked).
In another embodiment, the pharmaceutical carrier may comprise a polymer. Any suitable polymer may be used that is pharmaceutically acceptable and which does not interfere with function of the polypeptide. In one embodiment, the polymer is a block polymer and comprises a hydrophilic block and an endosomolytic block. Any suitable hydrophilic block and endosomlytic blocks may be used. In one embodiment, the hydrophilic block comprises polyethylene glycol methacrylate. In another embodiment, the endosomolytic block comprises a diethylaminoethyl methacrylate-butyl methacrylate copolymer. In a further embodiment, the polymer is a stimuli-responsive polymer that responds to one or more stimuli selected from the group consisting of pH, temperature, UV-visible light, photo-irradiation, exposure to an electric field, ionic strength, and the concentration of certain chemicals by exhibiting a property change. As used herein, a “stimuli-responsive polymer” is a polymer that changes its associative properties in response to a stimulus. The stimuli-responsive polymer responds to changes in external stimuli such as the pH, temperature, UV-visible light, photo-irradiation, exposure to an electric field, ionic strength, and the concentration of certain chemicals by exhibiting property change. The chemicals could be polyvalent ions such as calcium ion, polyions of either charge, or enzyme substrates such as glucose. For example, a temperature-responsive polymer may be responsive to changes in temperature by exhibiting a LCST in aqueous solution. A stimuli-responsive polymer may be a multi-responsive polymer, where the polymer exhibits property change in response to combined simultaneous or sequential changes in two or more external stimuli. The stimuli-responsive polymers may be synthetic or natural polymers that exhibit reversible conformational or physico-chemical changes such as folding/unfolding transitions, reversible precipitation behavior, or other conformational changes to in response to stimuli, such as to changes in temperature, light, pH, ions, or pressure. Representative stimuli-responsive polymers include temperature-sensitive polymers, pH-sensitive polymers, and light-sensitive polymers.
In a further aspect, the present invention provides isolated nucleic acids encoding a polypeptide of the present invention. The isolated nucleic acid sequence may comprise RNA or DNA. As used herein, “isolated nucleic acids” are those that have been removed from their normal surrounding nucleic acid sequences in the genome or in cDNA sequences. Such isolated nucleic acid sequences may comprise additional sequences useful for promoting expression and/or purification of the encoded protein, including but not limited to polyA sequences, modified Kozak sequences, and sequences encoding epitope tags, export signals, and secretory signals, nuclear localization signals, and plasma membrane localization signals. It will be apparent to those of skill in the art, based on the teachings herein, what nucleic acid sequences will encode the polypeptides of the invention.
In another aspect, the present invention provides recombinant expression vectors comprising the isolated nucleic acid of any aspect of the invention operatively linked to a suitable control sequence. “Recombinant expression vector” includes vectors that operatively link a nucleic acid coding region or gene to any control sequences capable of effecting expression of the gene product. “Control sequences” operably linked to the nucleic acid sequences of the invention are nucleic acid sequences capable of effecting the expression of the nucleic acid molecules. The control sequences need not be contiguous with the nucleic acid sequences, so long as they function to direct the expression thereof. Thus, for example, intervening untranslated yet transcribed sequences can be present between a promoter sequence and the nucleic acid sequences and the promoter sequence can still be considered “operably linked” to the coding sequence. Other such control sequences include, but are not limited to, polyadenylation signals, termination signals, and ribosome binding sites. Such expression vectors can be of any type known in the art, including but not limited plasmid and viral-based expression vectors. The control sequence used to drive expression of the disclosed nucleic acid sequences in a mammalian system may be constitutive (driven by any of a variety of promoters, including but not limited to, CMV, SV40, RSV, actin, EF) or inducible (driven by any of a number of inducible promoters including, but not limited to, tetracycline, ecdysone, steroid-responsive). The construction of expression vectors for use in transfecting host cells is well known in the art, and thus can be accomplished via standard techniques. (See, for example, Sambrook, Fritsch, and Maniatis, in: Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1989; Gene Transfer and Expression Protocols, pp. 109-128, ed. E. J. Murray, The Humana Press Inc., Clifton, N.J.), and the Ambion 1998 Catalog (Ambion, Austin, Tex.). The expression vector must be replicable in the host organisms either as an episome or by integration into host chromosomal DNA. In various embodiments, the expression vector may comprise a plasmid, viral-based vector, or any other suitable expression vector.
In a further aspect, the present invention provides host cells that comprise the recombinant expression vectors disclosed herein, wherein the host cells can be either prokaryotic or eukaryotic. The cells can be transiently or stably engineered to incorporate the expression vector of the invention, using standard techniques in the art, including but not limited to standard bacterial transformations, calcium phosphate co-precipitation, electroporation, or liposome mediated-, DEAE dextran mediated-, polycationic mediated-, or viral mediated transfection. (See, for example, Molecular Cloning: A Laboratory Manual (Sambrook, et al., 1989, Cold Spring Harbor Laboratory Press; Culture of Animal Cells: A Manual of Basic Technique, 2nd Ed. (R. I. Freshney. 1987. Liss, Inc. New York, N.Y.). A method of producing a polypeptide according to the invention is an additional part of the invention. The method comprises the steps of (a) culturing a host according to this aspect of the invention under conditions conducive to the expression of the polypeptide, and (b) optionally, recovering the expressed polypeptide. The expressed polypeptide can be recovered from the cell free extract, but preferably they are recovered from the culture medium. Methods to recover polypeptide from cell free extracts or culture medium are well known to the person skilled in the art.
In another aspect, the invention provides methods of treating an Epstein-Barr virus-related disease comprising administering to a subject in need thereof a therapeutically effective amount of one or more of the polypeptides of the invention that selectively inhibits BHRF1, or salts thereof, pharmaceutical compositions thereof, a recombinant nucleic acid encoding the one or more polypeptides, a recombinant expression vector comprising the recombinant nucleic acids, and/or a recombinant host cells comprising the expression vector, to treat and/or limit the Epstein-Barr virus related disease.
Epstein-Barr virus encodes a pro-survival Bcl-2 homologue, BHRF1, which prevents lymphocyte apoptosis during initial infection by sequestering pro-apoptotic BOPs (especially Bim), and interacting directly with the executioner Bak (Desbien et al., 2009; Kvansakul et al., 2010) (Altmann and Hammerschmidt, 2005) (Henderson et al., 1993). Even though BHRF1 is under the control of an early lytic cycle promoter, low levels of constitutive expression have been observed in some cases of EBV-positive BL when the virus is latent, and it has been speculated that BHRF1 may be a necessary viral factor for lymphomagenesis (Kelly et al., 2009; Leao et al., 2007; Watanabe et al., 2010). Thus, inhibitors of BHRF1 can be used to treat and/or limit development of Epstein-Barr virus related disease, as is evidenced by the examples that follow.
In various embodiments, the Epstein-Barr virus-related disease is selected from the group comprising of infectious mononucleosis, Burkitt's lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, mantle cell lymphoma, nasopharyngeal carcinoma, multiple sclerosis, Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. In other embodiments, the Epstein-Barr virus-related disease is a cancer selected from the group consisting of Burkitt's lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, mantle cell lymphoma, or nasopharyngeal carcinoma.
In various embodiments, polypeptides for use in this aspect of the invention are selected from polypeptides comprising or consisting of the amino acid sequence of SEQ ID NOS: 1 and 7, including any embodiments thereof such as, but not limited to, further including cell penetrating peptides or antibodies.
In another aspect, the invention provides methods for treating cancer, comprising administering to a subject in need thereof a therapeutically effective amount of one or more of the polypeptides that selectively inhibits one or more of Mcl-1, Bcl-2, BCL2L1/Bcl-XL, BCL2L10/Bcl-B, A1/Bfl-1, and Bcl-w, or salts thereof, a pharmaceutical composition thereof, a recombinant nucleic acid encoding the one or more polypeptides, a recombinant expression vector comprising the recombinant nucleic acid, and/or a recombinant host cell comprising the recombinant expression vector, to treat cancer in the subject.
Apoptosis and cell survival are regulated by the homeostatic balance of B cell lymphoma-2 (Bcl-2) family proteins. The ‘executioners’, Bak and Bax, initiate apoptosis by increasing mitochondrial outer membrane permeability and facilitating the release of mitochondrial cytochrome c to the cytosol, which activates downstream signaling. Six human pro-survival Bcl-2 proteins (Bcl-2, Bcl-XL, Bcl-B, Mcl-1, Bcl-w and Bfl-1) inhibit this process. Cellular stresses activate pro-apoptotic BOPs, which bind and inhibit pro-survival Bcl-2 members, and directly interact with Bak and Bax to favor mitochondrial permeabilization. Conversely, pro-survival Bcl-2 proteins dampen apoptotic triggers and enhance chemoresistance by sequestering BOPs or directly inhibiting Bak and Bax. Increased expression of pro-survival Bcl-2 proteins is a common feature of many cancers. Thus, the polypeptides of the present invention, which bind to and inhibit the pro-survival Bcl-2 proteins, can be used to treat cancer.
In various embodiments, polypeptides for use in this aspect of the invention are selected from polypeptides comprising or consisting of the amino acid sequence of SEQ ID NOS: 1-6, 8-12, 262-273 and 276, including any embodiments thereof such as, but not limited to, further including cell penetrating peptides or antibodies.
The methods may be used alone or in conjunction with other therapies for treating cancer, such as chemotherapy, radiation therapy, and/or surgical removal of the tumor. In one embodiment, the polypeptides permit reduced (sub-therapeutic) dosages of current therapies; in another embodiment, such a combination therapy permits the use of otherwise sub-therapeutic dosages of the polypeptide of the invention; these embodiments can be combined. In these various embodiments, the methods may be used to overcome tumor resistance to the treatment.
As used herein, the phrase “therapeutically effective amount”, “effective amount” or “effective dose” refers to an amount that provides a therapeutic benefit in the treatment, prevention, or management of Epstein-Barr virus and Epstein-Barr related diseases, or cancer. Determination of a therapeutically effective amount is well within the capability of those skilled in the art. Generally, a therapeutically effective amount can vary with the subject's history, age, condition, sex, as well as the severity and type of the medical condition in the subject, and administration of other pharmaceutically active agents.
As used herein, the term “treat,” “treatment,” or “treating,” means to reverse, alleviate, ameliorate, inhibit, slow down or stop the progression or severity of a symptom or condition of the disorder being treated. The term “treating” includes reducing or alleviating at least one adverse effect or symptom of a condition. Treatment is generally “effective” if one or more symptoms are reduced. Alternatively, treatment is “effective” if the progression of a condition is reduced or halted. That is, “treatment” may include not just the improvement of symptoms, but also a cessation or slowing of progress or worsening of symptoms that would be expected in the absence of treatment. Beneficial or desired clinical results include, but are not limited to, alleviation of one or more symptom(s), diminishment of extent of the deficit, stabilized (i.e., not worsening) state of a tumor or malignancy, delay or slowing of tumor growth and/or metastasis, and an increased lifespan as compared to that expected in the absence of treatment.
As used herein, the term “administering,” refers to the placement of a therapeutic into a subject by a method or route deemed appropriate. The therapeutic can be administered by any appropriate route which results in an effective treatment in the subject including orally, parentally, by inhalation spray, rectally, or topically in dosage unit formulations containing conventional pharmaceutically acceptable carriers, adjuvants, and vehicles. The term parenteral as used herein includes, subcutaneous, intravenous, intra-arterial, intramuscular, intrasternal, intratendinous, intraspinal, intracranial, intrathoracic, infusion techniques or intraperitoneally. Dosage regimens can be adjusted to provide the optimum desired response (e.g., a therapeutic response). A suitable dosage range may, for instance, be 0.1 ug/kg-100 mg/kg body weight; alternatively, it may be 0.5 ug/kg to 50 mg/kg; 1 ug/kg to 25 mg/kg, or 5 ug/kg to 10 mg/kg body weight. The polypeptides can be delivered in a single bolus, or may be administered more than once (e.g., 2, 3, 4, 5, or more times) as determined by an attending physician.
In another aspect, the invention provides methods for determining the Bcl-2 phenotype of a tumor, comprising contacting tumor cells, tumor cell lysates or tumor cellular components with one or more polypeptides selected from the group consisting of SEQ ID NOS: 1-6, 8-12, 262-273 and 276 under conditions suitable to promote apoptosis signaling in cells of the tumor that express a bcl-2 homologue targeted by the one or more polypeptides; and determining bcl-2 dependency of the tumor based on the polypeptide that causes apoptosis or apoptotic signaling in the cells of the tumor.
The methods of this aspect of the invention can be used, for example, to determine an appropriate polypeptide inhibitor of the invention to treat a tumor, by identifying the bcl-2 dependency of the tumor. In one embodiment, the method comprises contacting tumor cells, tumor cell lysates or tumor cellular components with each of the polypeptides of SEQ ID NOS:1-6 and 262-273, or each of the polypeptides of SEQ ID NOS:8-12 and 276, which permits simultaneously determining the bcl-2 dependency of the tumor for each of the Bcl-2 family proteins.
The particulars shown herein are by way of example and for purposes of illustrative discussion of the preferred embodiments of the present invention only and are presented in the cause of providing what is believed to be the most useful and readily understood description of the principles and conceptual aspects of various embodiments of the invention. In this regard, no attempt is made to show structural details of the invention in more detail than is necessary for the fundamental understanding of the invention, the description taken with the drawings and/or examples making apparent to those skilled in the art how the several forms of the invention may be embodied in practice.
EXAMPLES
The Epstein-Barr virus (EBV), also called human herpesvirus 4 (HHV-4), is a virus of the herpes family. Epstein-Barr virus has been implicated in several diseases that include infectious mononucleosis, Burkitt's lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, mantle cell lymphoma, nasopharyngeal carcinoma and multiple sclerosis. The Epstein-Barr virus has been implicated also in disorders related to alpha-synuclein aggregation, such as Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. As used herein, “Epstein-Barr related diseases” are any diseases related to or caused by Epstein-Barr virus, including those listed immediately above.
Pro-survival Bcl-2 proteins share a common domain that resembles a cupped hand, with a characteristic hydrophobic surface groove that clasps one side of an amphipathic BH3 domain helix (Czabotar et al., 2007; Kvansakul et al., 2010; Liu et al., 2003). Rigidifying BH3 peptides by use of hydrocarbon staples, disulfides or lactam bridges on the non-interactive back side of the helix can reduce the entropic penalty of a partially-folded peptide acquiring a rigid helical conformation upon binding, and improves BH3 peptide affinity (Azzarito et al., 2013). We reasoned that building a folded structure around a BH3 peptide would similarly pre-stabilize the bound helical conformation. In previous work, interacting residues of the BH3 domain were grafted to the surface of a minimal structured peptide, but after directed evolution these folded peptides displayed only moderate affinity and specificity, and did not always bind to the correct interaction site on the target Bcl-2 protein (Chin and Schepartz, 2001; Gemperli et al., 2005). We instead sought to incorporate the interacting residues of the BH3 domain on the exposed surface of a larger 3-helix bundle, which makes additional contacts extending beyond the BH3 motif. This much larger interaction footprint provides opportunity for making many new contacts to increase affinity and specificity.
Creating New Proteins for Optimized Interactions with the BHRF1 Ligand-Binding Groove.
Current protein design methods nearly always involve the repurposing of an existing protein of known structure from the PDB. This protein of known structure acts as a scaffold on which new side chains can be grafted to an assumed rigid backbone by site-directed mutagenesis. The grafted residues form a new functional site for binding to a target protein of interest. However, designed proteins from side chain grafting are limited by the rigid backbone of the scaffold, and may have suboptimal steric complementarity for binding to the target surface. To escape this constraint, we used a computational method (Correia et al., 2014) that builds a new de novo protein with an amino acid sequence unseen in nature that incorporates the Bim-BH3 motif. A helical bundle scaffold protein of known structure is used only as a topology guide. From the crystal structure of Bim-BH3 bound by BHRF1, the Bim-BH3 helix acts as a folding nucleus, around which protein fragments from the PDB are assembled to build a new protein of matching topology to the guiding scaffold (3LHP chain S (Correia et al., 2010)). Cα-Cα atom-pair distances from the scaffold constrain the assembling protein to within a defined deviation threshold (3.0 Å root mean square deviation, RMSD). Thousands of designed proteins were computationally generated to form a family of structural homologues, all with unique sequences and slightly different backbone structures (FIG. 1).
The designed proteins were docked to the BHRF1 surface via alignment of the incorporated Bim-BH3 motif, and surrounding interface residues (within 8 Å) were then further designed, as the incorporated Bim-BH3 motif provides only a fraction of the interaction surface, and many additional contacts across an expansive interface should be designed. Scaffold residues surrounding the graft site were designed to minimize the energy of the modeled bound complex in the ROSETTA energy function (Kuhlman et al., 2003) (Leaver-Fay et al., 2011). BHRF1 interface residues, which normally reach over the backside of the Bim-BH3 helix, were simultaneously repacked to alternative low energy rotamers compatible with the new designed interface.
The proteins were filtered both for stability of the monomer (by computed monomer energy, packing based on RosettaHoles (Sheffler and Baker, 2009) and for the lowest number of buried unsatisfied hydrogen bonding atoms) and for interface quality (high shape complementarity, computed binding energy and a low number of buried unsatisfied hydrogen bonding atoms). From thousands of computer-assembled proteins, a small number of designs were selected for further manual modifications, synthetic E. coli codon-optimized genes were constructed, and those proteins that were expressed and soluble in E. coli were tested by yeast surface display for binding to BHRF1 (Table 1). Two structural homologues of PDB 3LHP chain S were designed with apparent KDs 58-60 nM (BbpD04 and BbpD07; FIG. 1B and Tables 1 and 2). These designs were ‘seeded’ by a fifteen-residue fragment of the Bim-BH3 motif of which nine side chains contacting the BHRF1 surface were kept fixed. Other residues, primarily on the backside of the motif and buried in the protein core, were designed to minimize the calculated potential energy. The equivalent 3LHP_S fixed backbone graft (i.e. side chain grafting) described in the methods failed (Table 1). Thus backbone modification by in silico refolding can be critical for shaping scaffolds to precisely fit against a desired target.







TABLE 1







Summary of designs based on a seeded ab initio fragment


assembly strategy.














Expressed



Design 
Topology

and soluble
Binds 400 nM 


Name
Guide
Site † 
in E. coli ¶
BHRF1 *





BbpD01
3LHP(S)
Bim: 56-70
−



(S103A)

Scaffold: 54-68
(−)



BbpD02


−



BbpD03


−



(A60V)


(−)



BbpD04


+
Yes: 58 ± 3 nM 


BbpD05


−



BbpD06


+
No


BbpD07


+
Yes: 60 ± 10 nM










Summary of designs based on a side chain-grafting strategy.













Grafted




Design

Bim-BH3 
Designed 
KD


Name
Scaffold
Residues §
Residues §
BHRF1





BbpG1
3LHP(S)
V55W,
None
−


BbpG1.D

R56I,
E45D, E46Q,
−




G57A,
I48K, K49H,





E60L, R63I,
D50Q, L52V,





V64G,
K53H, I54Y,





A65D,
E58L, Q61E,





R67F
R71E,






T102R,






D103W,






I106F,






K107Q,






E110T,






L113A,






A114K,






E117A,






L120A,






T121Q





† Indicates the region of Bim-BH3 from crystal structure 2WH6 that was used to nucleate ab initio folding, and the site within the topology guide where the Bim-BH3 folding nucleus was located.


¶ E. coli BL21(DE3) cells cultured in terrific broth to an OD(600 nm) ~0.5 were induced with 0.1 mM IPTG overnight at 20° C. and protein expression investigated by SDS-PAGE.


* Designs were expressed on the yeast surface and incubated with 400 nM monomeric BHRF1-biotin, washed, and stained with anti-myc-FITC (expression) and streptavidin-PE (binding).


§ The native scaffold residue (identity and number) is given first, followed by the amino acid type it was mutated to.






In Silico Folding Probability Correlates with Binding Activity

The success rate for designing functional proteins is low, and computational design still requires substantial human intervention to choose and modify the designs prior to experimental validation. For example, working design BbpD04 contained 15 human-introduced mutations out of 116 total residues from its inactive computational ‘precursor’ (FIG. 2A). These mutations increased packing within the hydrophobic core and hydrophilicity of the exposed surface. This motivated us to test a library of designs ‘direct from the computer’, without any human modifications. Using the Bim-BH3 motif as a seed for ab initio protein assembly, 5,000 proteins were designed as described for BbpD04 and BbpD07 above (i.e. the guiding scaffold was 3LHP chain S and the Bim-BH3 incorporation site spanned residues 54-67). This was reduced to 74 designs (Indexes-01 to 74) after filtering for strong interface binding energy, low monomer folding energy and a low number of buried unsatisfied hydrogen bonding atoms. Barcoded genes were synthesized (Table 3) and the library transformed in to yeast for surface display (6×105 transformants). BbpD04 (Index-00) was included as a positive control, and the computational precursor for BbpD04 (Index-21; prior to human modification) was also present. The library was sorted by a single round of FACS for cells expressing surface protein (FIG. 1C; lane 1), for the 2% of cells with highest expression (lane 2), and for cells showing binding signal after incubation with 100 nM (lane 3) or 400 nM BHRF1 (lane 4). DNA from the naive and post-sorted populations was harvested and sequenced by Illumina deep sequencing, and the recovery of each designed sequence determined. A minority of designs (Indexes-00 to 27) were enriched following sorting for expression, and just five designs (Indexes-00 to 04) were highly expressed and enriched after sorting for BHRF1 interaction (FIG. 1C). While the four new functional designs share the same 3-helix topology, the structural details and sequences differ considerably (FIG. 2A-D). BHRF1 binding was validated on clonal yeast populations (FIG. 3A).







TABLE 3





Sequences of seeded ab initio designs tested by high throughput library sorting.


Enrichment ratios following yeast display and sorting are indicated.















Index 00 (Design BbpD04) DNA Barcode: AGTCATTGCAGTCATTGC (SEQ ID NO: 167)


GADWKKVLDKAKDIAENRVREIKQKLEEFYKKAMKLDLTQEMRRKLMLEWIAAMLMAIG


DIFNAIEQAKQEADKLKKAGQVNSQLLDELKRRLEELKEEASRKCHDYGREFQLKLEYG


(SEQ ID NO: 92)


Log2 Enrichment Ratios: Expression 1.13, High Expression 2.54, 100 nM BHRF1 3.92, 400 nM


BHRF1 3.19


 


Index 01 DNA Barcode: TCAACTGGTTCAACTGGT (SEQ ID NO: 168)


GKRLEETVEETERRLREALREVYLLILLLAEEAKKKDLKEQNRHEYVFKWIAFMLMAIGDIF


NIAEESKRRLDLFAKWGLHDRNKIDEAKKKIDKLALEAIERAKKYGDWFLNELDKG (SEQ ID


NO: 93)


Log2 Enrichment Ratios: Expression 1.16, High Expression 1.23, 100 nM BHRF1 4.02, 400 nM


BHRF1 3.54


 


Index 02 DNA Barcode: TTAAGCCTGTTAAGCCTG (SEQ ID NO: 169)


GKSLLGIALEALEEAKRDLEKAKKQMEEMLKKKWKFDTTRDLKARASAEWIAAALKAIGD


RFNAKLLIELGLDELFNKGLITQDIKEDIKRRAEEIFEKIERLIKQAIKDKDRFEKLG (SEQ ID


NO: 94)


Log2 Enrichment Ratios: Expression 1.13, High Expression 1.08, 100 nM BHRF1 3.92, 400 nM


BHRF1 3.43


 


Index 03 DNA Barcode: TTAGACCACTTAGACCAC (SEQ ID NO: 170)


GLDHDKIVDEARKKMEKKIREAKDKAKEFVLKALDNNHDLKQFRELAHKWIALMLMAIGD


AFNIMMEAKRKAEWLREQGQQDEDKAEEAKEKLDKAFKEAAERFEEIAKIYGKQAKNG


(SEQ ID NO: 95)


Log2 Enrichment Ratios: Expression 1.10, High Expression −0.16, 100 nM BHRF1 2.52, 400 nM


BHRF1 3.17


 


Index 04 DNA Barcode: GCTATCATCGCTATCATC (SEQ ID NO: 171)


GLLAEEGREQAEERLREARKKAEKAGDKIKDLAKYGQDSDDEKKKFMLKWIAAQLMVIGD


MFNHAMEALWELLRRLKNNKISWDAFLKAKEEIEREEKEAARDSREKGREAAKMIDQG


(SEQ ID NO: 96)


Log2 Enrichment Ratios: Expression 0.40, High Expression 0.07, 100 nM BHRF1 2.11, 400 nM


BHRF1 1.96


 


Index 05 DNA Barcode: ACAGCTTCAACAGCTTCA (SEQ ID NO: 172)


GKDADKKKDEAKKKAEWKEREVFERLEKMEWKKRKDSVSKDDARKFTLKWIADDLELIG


DLFNLKEEAREVAEDAARNNQITEEQREEDEKDLEKLAKEHSWRAAYRGKLKAKEFWEG


(SEQ ID NO: 97)


Log2 Enrichment Ratios: Expression 1.07, High Expression 0.31, 100 nM BHRF1 −2.50, 400 nM


BHRF1 −0.83


 


Index 06 DNA Barcode: TCCAACATGTCCAACATG (SEQ ID NO: 173)


GRSANDILKQFLEMLQEALRKFDEKKNKIEDEWKQFDLSTQRREEATHKWIAAALMAIGDM


FNALRWALEEALKAKLKNLQSSDDLKEAIERMMKLMLEKAQEIQEKGRELADKIEQG (SEQ


ID NO: 98)


Log2 Enrichment Ratios: Expression 0.86, High Expression 2.77, 100 nM BHRF1 −2.35, 400 nM


BHRF1 −1.45


 


Index 07 DNA Barcode: CTGAACTGACTGAACTGA (SEQ ID NO: 174)


GEEFKKKLKKWEEWLLKATNEAENQARNMWQKAEQTDLEDQQRIRAVDFWIAIALMAIGD


KFNADQEGDEEFEKYKKKGRASEDKIKEAKDERDRAKKRWEQFVKEAGERAFRGEQLG


(SEQ ID NO: 99)


Log2 Enrichment Ratios: Expression 1.33, High Expression 0.72, 100 nM BHRF1 −2.79, 400 nM


BHRF1 −1.16


 


Index 08 DNA Barcode: TGACGCATTTGACGCATT (SEQ ID NO: 175)


GWDARRALKYVYERMREDLEYARNQIDNMEDRADQYDARTEERKEFTKRWIALALMLIGD


GFNAFERAKEWIDDGKNNNQRSSDEADYAKDEALKFIFYAAFEARRKGDELDKKAEGG


(SEQ ID NO: 100)


Log2 Enrichment Ratios: Expression 1.53, High Expression 2.32, 100 nM BHRF1 −3.06, 400 nM


BHRF1 −0.80


 


Index 09 DNA Barcode: GGAATCGATGGAATCGAT (SEQ ID NO: 176)


GKEAKKRIQEALEEAKRKAEKLLREHEKKKKEHLLGDKRDREKTEETDKWIAEALMLIGDIF


NLYMKFEWEKEREKKLGLLREEEEKEVEDEAKDAYLKALKLAYLVSKKGHEVAELG (SEQ


ID NO: 101)


Log2 Enrichment Ratios: Expression 0.18, High Expression 0.86, 100 nM BHRF1 −2.55, 400 nM


BHRF1 −2.05


 


Index 10 DNA Barcode: GAAGGCTATGAAGGCTAT (SEQ ID NO: 177)


GDSDDDDLKDALLRMLWAAAQAIYHSLENMERKEKFDMHFEEERRDTLQWIADALRAIGD


AFNEMMRRRRELEKKRENNIISEQRARLYEEFLKRFAEWASRELAKAGKKEANKLNEG (SEQ


ID NO: 102)


Log2 Enrichment Ratios: Expression 1.30, High Expression 1.47, 100 nM BHRF1 −0.72, 400 nM


BHRF1 0.62


 


Index 11 DNA Barcode: GACGTTACAGACGTTACA (SEQ ID NO: 178)


GNILDEAKDEMREEMEKLWKKFKDEVEEERKEAEREEKHFQERAELTKRWIARALMAIGD


MFNRFREAKEKLEKRRELGLISEEDARKALLLLEEFMRRMAEFAKKLGDDLMRDAEKG


(SEQ ID NO: 103)


Log2 Enrichment Ratios: Expression 0.34, High Expression 2.13, 100 nM BHRF1 −2.62, 400 nM


BHRF1 −1.55


 


Index 12 DNA Barcode: AGTGGCATAAGTGGCATA (SEQ ID NO: 179)


GEDDDKVLKWALEALRKVLDEAKEKLEKLKKYTDGDGFGEDYRREFFRKWIAIALEAIGDIF


NIMMEALQKADKHKKLNTHDSQKADEAKEKIKKFADEAEERAKELAKKGEAWLLKG (SEQ


ID NO: 104)


Log2 Enrichment Ratios: Expression 1.13, High Expression 1.08, 100 nM BHRF1 −2.56, 400 nM


BHRF1 −1.37


 


Index 13 DNA Barcode: TAGATCGAGTAGATCGAG (SEQ ID NO: 180)


GSKWEEDREKAKREAEKKLDEAKDKLDLYKDFALRFDASDELKTKWTLEWIALALEMIGD


VFNYALEAKEFAEKKARNNLLLDDLKDLYKLYLALLAKEESKKAIEEGDKLREAIEKG (SEQ


ID NO: 105)


Log2 Enrichment Ratios: Expression 1.19, High Expression 1.58, 100 nM BHRF1 −3.07, 400 nM


BHRF1 −1.60


 


Index 14 DNA Barcode: CCTTGAGAACCTTGAGAA (SEQ ID NO: 181)


GLSADDLFDYAEDRMREGWKDFEELAGEAEKKAKEHTLSDQERREATEKWIAAALELIGDA


FNAIRWAEELGKLYVKLNLDDKQKVEELKKKLEERAKEEAQKARKRGDKLEDLADSG (SEQ


ID NO: 106)


Log2 Enrichment Ratios: Expression 1.32, High Expression 1.78, 100 nM BHRF1 −2.91, 400 nM


BHRF1 −0.65


 


Index 15 DNA Barcode: CATGTCTCACATGTCTCA (SEQ ID NO: 182)


GNDRDQIEEYHRERMDEELDRAKKRLEELKKLWEKLDGDDLMKFFWTFKWIAESLKIIGDL


FNRLLRTWEFAEALKKGIGFDEKKAEEAKERAYERAAEAAWKAAKLSREMREFLLKG (SEQ


ID NO: 107)


Log2 Enrichment Ratios: Expression 1.60, High Expression 2.73, 100 nM BHRF1 −2.77, 400 nM


BHRF1 −0.71


 


Index 16 DNA Barcode: CATCTGCTACATCTGCTA (SEQ ID NO: 183)


GNSADDILDEARDRHERTALWAKDQEDNLKDEAEKGDIGTEQLIRLTMKWIAIQLMAIGDAF


NFAMEAKKKLDLLKKLNLVQAQKLEEAKERADKFEKKADQLSSKFGREMARDLAQG (SEQ


ID NO: 108)


Log2 Enrichment Ratios: Expression 0.13, High Expression −2.21, 100 nM BHRF1 1.40, 400 nM


BHRF1 1.61


 


Index 17 DNA Barcode: CCATCTTAGCCATCTTAG (SEQ ID NO: 184)


GRSAEIMREILEKQAEDDAKKIRDIAQKWKERRKRYDPRDEEREEEVEKWIAFALMAIGDIFN


LARWALLQARWERRWNLSHEDEGKNHEENVKDAEDRAHWKAREAAREGAKMSWEG


(SEQ ID NO: 109)


Log2 Enrichment Ratios: Expression 0.20, High Expression −3.24, 100 nM BHRF1 −3.41, 400 nM


BHRF1 −2.54


 


Index 18 DNA Barcode: TTGCCGATTTTGCCGATT (SEQ ID NO: 185)


GGTEDDIKDLAEKWRDDMKKEFLREFLRIKEWTKYWGWREEGRKLATLRWIALSLMHIGD


LFNLKELAKKLVDDIKKKGLEHEERAERAREEAEKIMEKAAKLDSILSKLAAKLIEEG (SEQ


ID NO: 110)


Log2 Enrichment Ratios: Expression 0.69, High Expression −1.70, 100 nM BHRF1 −1.36, 400 nM


BHRF1 0.98


 


Index 19 DNA Barcode: CACGATTCTCACGATTCT (SEQ ID NO: 186)


GERVEEILRKMLDDALLHFLEHRDDARERKERGERHQPRDEEREELSHDWIAAALMAIGDIF


NAKLRAEERAEEFLKWGLRSQDDKKELEERAKEAAKIALKWAEEAGKEADEAEKAG (SEQ


ID NO: 111)


Log2 Enrichment Ratios: Expression 0.40, High Expression −2.28, 100 nM BHRF1 −2.97, 400 nM


BHRF1 −1.98


 


Index 20 DNA Barcode: AGAATTGCCAGAATTGCC (SEQ ID NO: 187)


GLRFEEIERYAREEADKIADEAKERFEKLKKLFLWLTDKDEERLKMTHLWIAGALEAIGDLF


NAAELAKELAEKAARLTSQDANRRDEARKKIDEAEKEAADKVSKAAKEAAKFFEQG (SEQ


ID NO: 112)


Log2 Enrichment Ratios: Expression 0.54, High Expression −1.99, 100 nM BHRF1 −3.87, 400 nM


BHRF1 −3.65


 


Index 21 DNA Barcode: ATTAGTCGGATTAGTCGG (SEQ ID NO: 188)


GFDWKKVLDKAKDLAENDVREAKQKLEEFYKKAMKLDLTQEMRRKLMLEWIAAMLMAIG


DIFNAIEQGKQEADKLKKLGKVLSQLLDELKRRLEELKEEAALKAHDFGREFELKLLFG (SEQ


ID NO: 113)


Log2 Enrichment Ratios: Expression 0.49, High Expression −1.20, 100 nM BHRF1 −3.38, 400 nM


BHRF1 −2.81


 


Index 22 DNA Barcode: GATGACTTCGATGACTTC (SEQ ID NO: 189)


GSSAEDLRDWARDQHEKDVDKMEKRLRLLYFELARKDFNEEELKKATEKWIAAALDAIGD


HFNAALKARLLARDAAKKGLIDRNKLDEVEKMAELFEELGERKAALKGREFLRWVLLG


(SEQ ID NO: 114)


Log2 Enrichment Ratios: Expression 0.59, High Expression −3.19, 100 nM BHRF1 −3.03, 400 nM


BHRF1 −2.40


 


Index 23 DNA Barcode: ATCGATCTCATCGATCTC (SEQ ID NO: 190)


GEDEEKDHKDTEEKARRLHERARDMLDKVKDLEEKTDAQDNERRRATHDWIAAALMMIG


DAFNSFEDTKRRAEKKRELNLISEDEAKEKIKRAEELRKRIYELLKKAAEFAREAEKGG (SEQ


ID NO: 115)


Log2 Enrichment Ratios: Expression 0.78, High Expression −1.37, 100 nM BHRF1 −1.72, 400 nM


BHRF1 −0.17


 


Index 24 DNA Barcode: TGTCTAGTGTGTCTAGTG (SEQ ID NO: 191)


GELAREAAEEAHRRVEEDARDAKNRLDEFKKRYKITQLSKSDISRATALWIAAALDAIGDIFN


AKQKAEKILGLWYKLGLVQLQEFLEKEDKARYHWQAALERAFEAGRDMLEVAAYG (SEQ


ID NO: 116)


Log2 Enrichment Ratios: Expression 0.48, High Expression −1.95, 100 nM BHRF1 −3.02, 400 nM


BHRF1 −2.95


 


Index 25 DNA Barcode: GGATGTTCTGGATGTTCT (SEQ ID NO: 192)


GANHEDAIWEALYKAEDAFKDHLKEIEIYREFSEKFWPLDDYKDNLRAHWIAAALAAIGDW


FNVFFEAELKFREAKRKNLRSEDDIKKYRWRLFKALDIAIDLADRVGDEAEKAERLG (SEQ


ID NO: 117)


Log2 Enrichment Ratios: Expression 0.95, High Expression −1.01, 100 nM BHRF1 −2.90, 400 nM


BHRF1 −1.53


 


Index 26 DNA Barcode: ATGGTGTCTATGGTGTCT (SEQ ID NO: 193)


GRFAERLFKKMLIKQLLNTQYFRDQLKQLKDRSKKYDASDDDKDEATHRWIAFALMAIGDV


FNDKLEIELLIELFAKYGLVHEEERKEFRKRLDEFEKIFRKWLDELKKLALEALNQG (SEQ ID


NO: 118)


Log2 Enrichment Ratios: Expression 0.50, High Expression −1.87, 100 nM BHRF1 −2.74, 400 nM


BHRF1 −2.00


 


Index 27 DNA Barcode: CTCAGATCACTCAGATCA (SEQ ID NO: 194)


GLDGDYLMDEAFKFIERERERAEEEAKKMYELAEKGKYYEERKTKATKFWIALALEMIGDF


FNFEMWFRKYAEKNRENNQRREDLLRRWELLLRFQAWDAAERARELGKRLELWFKKG


(SEQ ID NO: 119)


Log2 Enrichment Ratios: Expression 0.71, High Expression −2.21, 100 nM BHRF1 −0.72, 400 nM


BHRF1 0.86


 


Index 28 DNA Barcode: CTACGACATCTACGACAT (SEQ ID NO: 195)


GKEGSRLREEAERRGLRKLLEVILRWLEDALRMIYGQDKDEDRKEATHRWIADALELIGDIF


NALLEAFIKMELARRFGLLEEQRARDEKKKALERAEEFSKRARELGEKLTQILEGG (SEQ ID


NO: 120)


Log2 Enrichment Ratios: Expression −2.87, High Expression −4.25, 100 nM BHRF1 −4.52, 400 nM


BHRF1 −2.85


 


Index 29 DNA Barcode: CTAGGTGTACTAGGTGTA (SEQ ID NO: 196)


GEVAKDLAKLAIDLAKKLMLLFWWFFELFKLFAKFTDEWQEWKARGTAFWIALSLAAIGDF


FNARRRAELQAREGKQKGLTTEEKEKRWREHLKEAWEKLEKISRLAFLFAQEAENQG (SEQ


ID NO: 121)


Log2 Enrichment Ratios: Expression −1.14, High Expression −2.44, 100 nM BHRF1 −1.66, 400 nM


BHRF1 −2.43


 


Index 30 DNA Barcode: AAGTTGACCAAGTTGACC (SEQ ID NO: 197)


GSRWFDAEDKMRERKDRAILQLLFMLWIIFYILWYGDDTEEAKRKAMAAWIALALIGIGDIF


NAEAEFLEELERAIKQGQVSDQLKEELLKRMEDDKRDLEKRLYEFLLKALLQWMQG (SEQ


ID NO: 122)


Log2 Enrichment Ratios: Expression −1.26, High Expression −1.69, 100 nM BHRF1 −2.58, 400 nM


BHRF1 −4.10


 


Index 31 DNA Barcode: AAGGCCATTAAGGCCATT (SEQ ID NO: 198)


GDQADKIKDKIKDEAKKKADEFKKRLEQFREYLEKVYSDDLKEIYLTIFWIALALMLIGDAF


NEKMLLEWEFKERKKRNLRHEEELKEEKKKREEAEKALEWASKYASQVGKEAAEEG (SEQ


ID NO: 123)


Log2 Enrichment Ratios: Expression −2.65, High Expression −3.58, 100 nM BHRF1 −3.55, 400 nM


BHRF1 −4.21


 


Index 32 DNA Barcode: TGGCTTCTATGGCTTCTA (SEQ ID NO: 199)


GGDENKLKDYVKDEIERGLNEIEDLARKIEQLARRFFPKDEERMKFTMWWIAAALMAIGDIF


NAKEYARERAEEIRRKGLRREEEARRIEKFIEEEAEKAAKKAAKLGDHLAEELFRG (SEQ ID


NO: 124)


Log2 Enrichment Ratios: Expression −0.75, High Expression −0.86, 100 nM BHRF1 −2.00, 400 nM


BHRF1 −2.56


 


Index 33 DNA Barcode: GTCTTCTGAGTCTTCTGA (SEQ ID NO: 200)


GKQWQEAFEEARRRIEEKAREFEDRAKKEALLHLFFIPHDKEIADNSKKWIAWALMLIGDIFN


LEEEAAERARRHVKRGEISEDDAKQIRKRLQEQAKRAAWWMRYWGEESAKFAFIG (SEQ ID


NO: 125)


Log2 Enrichment Ratios: Expression −2.15, High Expression −3.65, 100 nM BHRF1 −4.18, 400 nM


BHRF1 −3.85


 


Index 34 DNA Barcode: TGCTCACAATGCTCACAA (SEQ ID NO: 201)


GKFKKLFENYAELFARWVADKGKKLAEELREKAEKGLKLQKLWLIFTMIWIAIMLMSIGDA


FNLALLAELWVQAAKNYGWLRDNEADEAEDRVRKFADEASRRALEKGLEALRKILEG (SEQ


ID NO: 126)


Log2 Enrichment Ratios: Expression −3.29, High Expression −4.31, 100 nM BHRF1 −3.41, 400 nM


BHRF1 −2.21


 


Index 35 DNA Barcode: ATAGCTGAGATAGCTGAG (SEQ ID NO: 202)


GGDGVKELEELEKRKDEKKNKAEDRIKKFKDEAKYADDRTEDKEKLAHRWIALALDIIGDA


FNLKEEARRRFLRHKFRGELDDSKKEYAEKEMKRFEDDVEKDAEELAQKAKEAFKEG (SEQ


ID NO: 127)


Log2 Enrichment Ratios: Expression −2.24, High Expression −3.49, 100 nM BHRF1 −3.51, 400 nM


BHRF1 −3.29


 


Index 36 DNA Barcode: AAGTCAGAGAAGTCAGAG (SEQ ID NO: 203)


GYTKEWIRDRAKEELDRFADEAKDKADKIRDDFEKRDDKNQIAAELTKKWIAAELEAIGDA


FNRAEEAKERLKKLLKLGLTRKEEAEEAAEKLEKLEKEASEKLSKIAHEVSKHDDQG (SEQ


ID NO: 128)


Log2 Enrichment Ratios: Expression −2.73, High Expression −3.32, 100 nM BHRF1 −3.60, 400 nM


BHRF1 −3.65


 


Index 37 DNA Barcode: TATTGCCTCTATTGCCTC (SEQ ID NO: 204)


GDFWLKAIEIAGGRMLERARESWYRALYFILMVKLFYPSDDLRRIFTLRWIAESLKLIGDAFN


LFELARELLELYYKYGWITLEKALKALWILLKLEEIFSKASKDLGERLAEEIERG (SEQ ID NO:


129)


Log2 Enrichment Ratios: Expression −1.72, High Expression −3.52, 100 nM BHRF1 −3.13, 400 nM


BHRF1 −2.14


 


Index 38 DNA Barcode: GCTTATGGTGCTTATGGT (SEQ ID NO: 205)


GEKLKKLAEELEKKFRKLFFILKDELDRAYLIALKTQVQRQELARDTKLWIAVALMIIGDLFN


AEIQGKELRDKLIKKNQVEEQKAKEFWKKWEEVKQRAEELIKKGGEMVERLADYG (SEQ ID


NO: 130)


Log2 Enrichment Ratios: Expression −0.73, High Expression 0.48, 100 nM BHRF1 −1.71, 400 nM


BHRF1 −1.46


 


Index 39 DNA Barcode: GCTGTATACGCTGTATAC (SEQ ID NO: 206)


GKKYLKAARLALYLLWEAYLRGYLNLLLDELEAEFFDPHDERKIRYTINWIADALMLIGDLF


NARLKMEKALWELKKEGKLREEDYEKMERLFRKWMELAFKWLEHFREMAEKAKKKG


(SEQ ID NO: 131)


Log2 Enrichment Ratios: Expression −1.76, High Expression −2.01, 100 nM BHRF1 −2.08, 400 nM


BHRF1 −2.01


 


Index 40 DNA Barcode: GAATCCTCAGAATCCTCA (SEQ ID NO: 207)


GNEAEQRREEFKEIMEKKKDEAEKKSEKIKRLALAFDLSDDDKTKATDEWIAISLEIIGDAFN


FGEGLKDEAKRRKKRGLKRDEEVDKFEKIAEQAIEELRKLAEEADERGAKHLRDG (SEQ ID


NO: 132)


Log2 Enrichment Ratios: Expression −2.67, High Expression −3.15, 100 nM BHRF1 −3.70, 400 nM


BHRF1 −4.69


 


Index 41 DNA Barcode: CATCAGTGTCATCAGTGT (SEQ ID NO: 208)


GEQEDKVKERAKRGALERAREMFEKMRKAIYLAELYINNDEGKTKLTDRWIAFALMMIGDI


FNIALEARLEALKLVLKGLRSQEDAEKVKKLAEEAEREAAKRAAKLGDKMDEKEHEG (SEQ


ID NO: 133)


Log2 Enrichment Ratios: Expression −0.27, High Expression −1.86, 100 nM BHRF1 −2.17, 400 nM


BHRF1 −2.39


 


Index 42 DNA Barcode: ACCTGTAACACCTGTAAC (SEQ ID NO: 209)


GQQEEQFIEDFKKEVLRAADDAKDDMEKRAEEFLKKDGDDNEKKRKILKWIADALEAIGDL


FNAAQEAKRRAELYFKLGLLKKERKEEAEEEAEKAKEEASKKLHKAAREARIKMEKG (SEQ


ID NO: 134)


Log2 Enrichment Ratios: Expression −3.04, High Expression −3.00, 100 nM BHRF1 −3.63, 400 nM


BHRF1 −3.15


 


Index 43 DNA Barcode: CCGTAATTGCCGTAATTG (SEQ ID NO: 210)


GKKAEEVLKEARKLHEAQLRYAYLMMKDWREKKQQEEKQTQREEKWTAWWIALMLMAI


GDIFNFAEWAKEELDKLREKGLVEKKKAEEAKEKAEKLAEEASRRASEFAQLFAKWDKEG


(SEQ ID NO: 135)


Log2 Enrichment Ratios: Expression −2.29, High Expression −1.97, 100 nM BHRF1 −2.44, 400 nM


BHRF1 −3.04


 


Index 44 DNA Barcode: CCAAGCAATCCAAGCAAT (SEQ ID NO: 211)


GESGEWILEKTREKIERAIRDAEKKLRLIILLIRLFHPGDDLRALFAAIWIAAELELIGDIFNEKQ


DAEEKFKELLKKNQFRWEELWRKWLILEWIFQKARRKSKELAERAKKAFDFG (SEQ ID NO:


136)


Log2 Enrichment Ratios: Expression −0.78, High Expression −3.17, 100 nM BHRF1 −3.29, 400 nM


BHRF1 −3.16


 


Index 45 DNA Barcode: TAGCGTACTTAGCGTACT (SEQ ID NO: 212)


GYSLDDFLKLAKLLAELLKRFIRKEAERLRELKEWLLDTTLGRLILTLEWIAIELMIIGDIFNAK


MLLDKFAKYAEWLGLMKEEEAKQAKKLAKLLLDEVKDEARKKADDGEKFAEEG (SEQ ID


NO: 137)


Log2 Enrichment Ratios: Expression −2.31, High Expression −2.28, 100 nM BHRF1 −2.44, 400 nM


BHRF1 −3.17


 


Index 46 DNA Barcode: GCAACTATGGCAACTATG (SEQ ID NO: 213)


GRDGERVVKWAKNQHENTVDEAKDKMDNQEDEMRKKNADDEKLRKETHKWIAFALEAIG


DVFNDAMQAFELLERFKKFGQQEQKKLDEFKEKVERLAREASRKLTYLGKRFALDIESG


(SEQ ID NO: 138)


Log2 Enrichment Ratios: Expression −0.31, High Expression −3.37, 100 nM BHRF1 −3.41, 400 nM


BHRF1 −3.60


 


Index 47 DNA Barcode: CTGTCGTAACTGTCGTAA (SEQ ID NO: 214)


GWSADWIKDQAKELMLRAAEEMKKRADEEEKKFKYKQFTTEFLTKATMRWIALALMAIGD


VFNVLMWALEWAKRMAKLNQYRKEELEKAKEEAKKLAEKAARRITEIGREAEQKALKG


(SEQ ID NO: 139)


Log2 Enrichment Ratios: Expression −2.07, High Expression −2.42, 100 nM BHRF1 −3.13, 400 nM


BHRF1 −2.79


 


Index 48 DNA Barcode: TTACTGACGTTACTGACG (SEQ ID NO: 215)


GEKGKEKAQKFRDIIKDILEEAIRLAKDLAEDAKKFDLKLEKLLEATLKWIAAALMAIGDLFN


FKDLAEKEVRERHDRGEISSDRRDKYEKEAREGADEAAKELSKLAKIAEKKILEG (SEQ ID


NO: 140)


Log2 Enrichment Ratios: Expression −2.24, High Expression −3.39, 100 nM BHRF1 −2.80, 400 nM


BHRF1 −2.33


 


Index 49 DNA Barcode: CGTATGATGCGTATGATG (SEQ ID NO: 216)


GWSKDWVLEWLREKLEEIDREALWKFILIWIEKMLGVDDDEQRRKDAAKWIAGSLEAIGDIF


NAMMWAKRLLEWLEKANLVRREELEKAKQKAEELAKKAALRAAIYSKIAEEWLWKG


(SEQ ID NO: 141)


Log2 Enrichment Ratios: Expression −2.07, High Expression −3.05, 100 nM BHRF1 −2.70, 400 nM


BHRF1 −1.22


 


Index 50 DNA Barcode: ATCGGTAGTATCGGTAGT (SEQ ID NO: 217)


GKRAEELREEAEERAKEAFKETEQKLREVEERSRQTLARDEELRKAALLWIAAALMGIGDLF


NKKEKGKEALEKEEKNGKRRTERAEREKERLEKEVSREAQRFKKKGEEEEKKHKYG (SEQ


ID NO: 142)


Log2 Enrichment Ratios: Expression −2.93, High Expression −2.75, 100 nM BHRF1 −3.79, 400 nM


BHRF1 −3.47


 


Index 51 DNA Barcode: GATCAACTGGATCAACTG (SEQ ID NO: 218)


GWTALWLKDFTEQEARKKFREALYYGWMMAMRALEHQLQADELAMWTALWIAAMLEAI


GDMFNDKLRAEKYALLLIWLNLYHKDIAEKWREEHEEKLKEALQEMFEAAEKFDKFAKFG


(SEQ ID NO: 143)


Log2 Enrichment Ratios: Expression −1.53, High Expression −2.24, 100 nM BHRF1 −2.53, 400 nM


BHRF1 −2.43


 


Index 52 DNA Barcode: AGTCTACCTAGTCTACCT (SEQ ID NO: 219)


GNDKEKFREDVKKKAKYALWKLKKLADEAKERALKFDPSEEMKREFTLEWIAWALEAIGDI


FNAWLDGKKYADEAKKQGKARKEEAEETKKEATRIAKEAHEKASELARKILYHMLLG (SEQ


ID NO: 144)


Log2 Enrichment Ratios: Expression −0.35, High Expression −3.17, 100 nM BHRF1 −0.83, 400 nM


BHRF1 −0.20


 


Index 53 DNA Barcode: ATGATCGGTATGATCGGT (SEQ ID NO: 220)


GHVAEEEIRRFLRKAEKVLQEARRKMEKRRREAEEHDTTTWLLARGTIEWIADALMLIGDAF


NFRREAYIRGELYKKFGLIREDDLKDRLKEADQRLDEFAKKMALFGLELHLRLREG (SEQ ID


NO: 145)


Log2 Enrichment Ratios: Expression −0.27, High Expression −2.43, 100 nM BHRF1 −0.29, 400 nM


BHRF1 0.40


 


Index 54 DNA Barcode: GTGCAATGTGTGCAATGT (SEQ ID NO: 221)


GDKHEEAKEEAEKKFEKLRIEARLKAEWLKKAGKYGLQLQELWAKLSDYWIAFALEIIGDLF


NFLEEHKEKIEKDLKKGEALDDRADDILKDLEKKAKEVSKHAMKLGREAQQFIELG (SEQ ID


NO: 146)


Log2 Enrichment Ratios: Expression −1.26, High Expression −1.71, 100 nM BHRF1 −3.22, 400 nM


BHRF1 −2.24


 


Index 55 DNA Barcode: TGAATGCCATGAATGCCA (SEQ ID NO: 222)


GEEAEKLIKEAKDKFEDLREKAEELLYKMWLIRYLSSKDTKRGEIYTKKWIAIMLMMIGDAF


NMALRARLYLEERRKRGEKHEEEAEEKERRARWEQEDAYKKAKKGAKRARLYDKLG (SEQ


ID NO: 147)


Log2 Enrichment Ratios: Expression −1.78, High Expression −1.88, 100 nM BHRF1 −2.69, 400 nM


BHRF1 −3.29


 


Index 56 DNA Barcode: AACAGTCCAAACAGTCCA (SEQ ID NO: 223)


GESAEKWRERLREKAGYWAEYAFWLADEAEKRAKIYSASSERRAEWTMRWIAIALAAIGD


VFNEGQKADEKFDELKKQNKRSDDDLDDYKDKFKEEVEKALRKLLKAGDKIADLAEQG


(SEQ ID NO: 148)


Log2 Enrichment Ratios: Expression −2.62, High Expression −3.45, 100 nM BHRF1 −3.49, 400 nM


BHRF1 −3.81


 


Index 57 DNA Barcode: TCCTAACGTTCCTAACGT (SEQ ID NO: 224)


GDLKEELKERAKKIIRRALDEAKDAEDLIKKEAEKRYVTTEMATKFVAWWIAGALMIIGDIF


NAAREVKERAEKALKWGVLSQDDIKELLLELENLEQEAKERAKEFGEKAEKFKKMG (SEQ


ID NO: 149)


Log2 Enrichment Ratios: Expression −0.83, High Expression −3.04, 100 nM BHRF1 −1.97, 400 nM


BHRF1 −2.85


 


Index 58 DNA Barcode: AGCAGATGTAGCAGATGT (SEQ ID NO: 225)


GEKAKKLEEYAREEIERALREGGDLMEEEREFGEKTELTTEWKHRAMAYWIAAALMIIGDG


FNALQFIEEEGRKFIRKGEFARQKIEEHKERAKERLEKALKQAKKRGDELDRFARLG (SEQ ID


NO: 150)


Log2 Enrichment Ratios: Expression −0.99, High Expression −2.52, 100 nM BHRF1 −2.36, 400 nM


BHRF1 −2.11


 


Index 59 DNA Barcode: GTATCAGTCGTATCAGTC (SEQ ID NO: 226)


GITLEKLWKEAKEKIRKREDEALLKAEWFKKKANNVLDLNDMKAKMTAKWIALALMAIGD


IFNYLLETEIKARLLVRLGLFRQEEAEKKKEEAKEEAIKSSRNIAKRGEEAAKQMEQG (SEQ


ID NO: 151)


Log2 Enrichment Ratios: Expression −1.98, High Expression −2.63, 100 nM BHRF1 −2.86, 400 nM


BHRF1 −2.36


 


Index 60 DNA Barcode: AATCGTGGAAATCGTGGA (SEQ ID NO: 227)


GRQEDEIKDEATKRALEILQKLEQKVRKAKKFAKYGLLLQRWWAWITKVWIAAALDAIGD


AFNLGEELKRILEELRRRGLSSEEKAQEIKNWIEWLEKWVAIMAKLFGEELEKQFKQG (SEQ


ID NO: 152)


Log2 Enrichment Ratios: Expression −0.86, High Expression −3.77, 100 nM BHRF1 −2.91, 400 nM


BHRF1 −2.63


 


Index 61 DNA Barcode: CTCGTAATGCTCGTAATG (SEQ ID NO: 228)


GEHLDELLLKLLWLAIQFAERAKLTIELWKLWGKITQSYNEWAEKAARDWIAAALMIIGDM


FNHKQKAEEEAKKFAKKGLKRKEELEELLKKLEEFIKRAKKLIKETAQKHEEASKMG (SEQ


ID NO: 153)


Log2 Enrichment Ratios: Expression −1.82, High Expression −2.20, 100 nM BHRF1 −2.79, 400 nM


BHRF1 −3.54


 


Index 62 DNA Barcode: TTCAGTGAGTTCAGTGAG (SEQ ID NO: 229)


GKLGEELREDAEKKGEEDMRRFERRIREIKRKLKFGYDFEQRKREATHKWIAFALEMIGDAF


NFAQKLERALELFKKWNIYSEDDLRELKKRFEEAKEKLKKFADRIRDEGLKAVLLG (SEQ ID


NO: 154)


Log2 Enrichment Ratios: Expression −1.89, High Expression −2.70, 100 nM BHRF1 −3.21, 400 nM


BHRF1 −2.65


 


Index 63 DNA Barcode: GTAAGTCACGTAAGTCAC (SEQ ID NO: 230)


GDDKEKVKDYAKKRALEDVLRAKELAEKFIDEAKKSDHSKQNERQYIIAWIAFMLMAIGDV


FNAMMEAKRLAELLKRLGLRRWEEAEEVKQKAEELAEEASRLLADLGKDFAKKIEQG (SEQ


ID NO: 155)


Log2 Enrichment Ratios: Expression −0.98, High Expression −2.63, 100 nM BHRF1 −2.52, 400 nM


BHRF1 −2.41


 


Index 64 DNA Barcode: CTTATCCAGCTTATCCAG (SEQ ID NO: 231)


GLSGDDAEDFARQEIEKRAREAEEKARKLIWLASKYDAKREEALKFHLRWIAFALMMIGDA


FNAEEIAREMLEIARELGLTREEEAKEKLEKIRKKETEASKKMAERGRRLDNQANNG (SEQ


ID NO: 156)


Log2 Enrichment Ratios: Expression −1.81, High Expression −2.68, 100 nM BHRF1 −3.51, 400 nM


BHRF1 −1.68


 


Index 65 DNA Barcode: AGGACAGTTAGGACAGTT (SEQ ID NO: 232)


GNDLKDIARQIEEQAKKALDDMAKLIRELAEKAEKFYPSKDDIRRLTHYWIAAALMAIGDAF


NRLQEARRRAEWLRKWGLRREEEAEKAKKEAEERHERAKELAHKMGDEMEEKLKRG (SEQ


ID NO: 157)


Log2 Enrichment Ratios: Expression −3.11, High Expression −2.45, 100 nM BHRF1 −3.20, 400 nM


BHRF1 −2.31


 


Index 66 DNA Barcode: GTCATGCATGTCATGCAT (SEQ ID NO: 233)


GRSKDDATKEAWERLERLLKEFKEKAEKLRDKAQAHYVYKQFALKVTILWIAWALKLIGD


AFNFIEEAEKKMRENRERNLISEDDAREEKRKLEEFARRASKKANKIGDDLDRQLELG (SEQ


ID NO: 158)


Log2 Enrichment Ratios: Expression −0.97, High Expression −2.30, 100 nM BHRF1 −2.03, 400 nM


BHRF1 −2.49


 


Index 67 DNA Barcode: TTCACCGTATTCACCGTA (SEQ ID NO: 234)


GNRSEEVKELMRELAERVLLKFRWRADEMNKEKDKKYDKEELKRELTEKWIAFALDAIGDL


FNAAELAKKLADLFKKGTGFLEERLERRKEEIEKLEEKGSRKVSYEGRREAEKIESG (SEQ ID


NO: 159)


Log2 Enrichment Ratios: Expression −1.41, High Expression −3.44, 100 nM BHRF1 −3.48, 400 nM


BHRF1 −3.44


 


Index 68 DNA Barcode: TAGTACGCTTAGTACGCT (SEQ ID NO: 235)


GVSIEWAFDFLENKAEEDAREARRLAQKLAEEFFKHSAREEDRAKLTKKWIAVALMIIGDIF


NVEQFTKQQGEEFVKRGLRSEDDFKEYLRKMEEKKEEAERIAKRAKDDMLKARDLG (SEQ


ID NO: 160)


Log2 Enrichment Ratios: Expression −2.49, High Expression −2.65, 100 nM BHRF1 −2.57, 400 nM


BHRF1 −3.63


 


Index 69 DNA Barcode: TCGTTGAAGTCGTTGAAG (SEQ ID NO: 236)


GEQAEKALRRAKRRAKWGLDDAKDILDDIEAEIRWYYPRDEERFKFVDRWIAAMLMVIGDL


FNAKREALERALRLMRKGLISQDQFKKFMEKLEKIILWGKFQARKLGREKESEITQG (SEQ ID


NO: 161)


Log2 Enrichment Ratios: Expression −2.56, High Expression −2.78, 100 nM BHRF1 −3.25, 400 nM


BHRF1 −3.99


 


Index 70 DNA Barcode: CATTAACGCCATTAACGC (SEQ ID NO: 237)


GLLWLAIILKAEELARKKDDEAEERIRRLEDEKRKGDPGTLGEAERTDRWIAIMLMAIGDAF


NVMLEAKEEAEKLEKLGLVHKELLEKVKEEAERLFERSSDNFEEAAKRADDMEKEG (SEQ


ID NO: 162)


Log2 Enrichment Ratios: Expression −1.16, High Expression −2.58, 100 nM BHRF1 −3.02, 400 nM


BHRF1 −3.13


 


Index 71 DNA Barcode: TAGTGGCAATAGTGGCAA (SEQ ID NO: 238)


GERAERARDWAKDQMDDELEKAREKLWKLAFIAFKFYLKLELLFKLMFRWIAIMLEAIGDF


FNVWAIAKRWLERYKLQNNIRKEEIEKAKERAKKLYEEAADKAAKLGRFYMKLLTSG (SEQ


ID NO: 163)


Log2 Enrichment Ratios: Expression −2.79, High Expression −3.00, 100 nM BHRF1 −2.58, 400 nM


BHRF1 −3.07


 


Index 72 DNA Barcode: ACCGTAAGAACCGTAAGA (SEQ ID NO: 239)


GGSYDDIADLAKKLHKKIAEEAKKKIDELLKEAFEDKPYEEEFAKKMFKWIAIALMAIGDLF


NAAELAKRLAEDLKKDNNRDENKAEEAKQRAEQFEKEGAEELAKKGEEAAKKLAGG (SEQ


ID NO: 164)


Log2 Enrichment Ratios: Expression −2.19, High Expression −3.48, 100 nM BHRF1 −3.34, 400 nM


BHRF1 −3.47


 


Index 73 DNA Barcode: GACGAGATTGACGAGATT (SEQ ID NO: 240)


GKDLDEIIDEARKEMDDDADDGKKKAEKLLKLHAGTNHSQDDFNEAHRRWIAVALEEIGDL


FNAALRAWRKIEEEIRKNQRRKEEAEKAKEKVSKEYERASRKAAELGKEFEERVEQG (SEQ


ID NO: 165)


Log2 Enrichment Ratios: Expression −0.07, High Expression −2.31, 100 nM BHRF1 −3.14, 400 nM


BHRF1 −2.27


 


Index 74 DNA Barcode: TACGAAGTCTACGAAGTC (SEQ ID NO: 241)


GTDHQAFDEWARRELERIVEEARERAERLREWIEQKDASREELTKFFAIWIAISLMAIGDLFN


VKEQAKRLAELLEFLGLQRKEEIEKSKKNAEKLADEAMKKASKLDAKVEKELMQG (SEQ ID


NO: 166)


Log2 Enrichment Ratios: Expression −1.92, High Expression −2.09, 100 nM BHRF1 −3.38, 400 nM


BHRF1 −2.62









Standard metrics for assessing interface quality (FIG. 3C-E) or monomer stability (FIG. 3F-H) did not distinguish the working designs. We hypothesized that many of the failed designs (Indexes-05 to 74) may simply not fold to the designed conformation. The design calculations find the lowest energy sequence for a given structure, but there is no guarantee that the lowest energy state of that designed sequence is the intended target structure. The likelihood of a protein folding depends on many factors, including the probability of an amino acid stretch adopting the correct secondary structure, the formation of a well-packed hydrophobic core, and a single native conformation of lowest energy amongst a vast assortment of alternative states. We used ROSETTA ab initio structure prediction to assess the likelihood that the designed sequence folds to the designed target conformation. Many folding simulations were carried out to give tens of thousands of possible structures (called decoys) that map out a protein energy landscape. An ideal protein would have an energy funnel from distant high-energy conformers towards a low energy folded state, and therefore a small mean RMSD between the lowest energy decoys and the intended designed conformation (plotted in FIG. 1D). Representative energy landscapes are plotted in FIG. 3B. A high calculated probability of correct folding is a common attribute of designs that bind BHRF1 (FIG. 1D). Notably, the human-modified BbpD04/Index-00 control sequence was predicted to fold, but its nonfunctional computational precursor Index-21 was not. This “forward folding” method should be broadly useful in future design efforts.
Enhanced Affinity and Specificity of a BHRF1-Binding Protein Through Improved Electrostatic Complementarity
To illuminate BHRF1 biology, the designed protein should not only bind with high affinity, but do so specifically. Design BbpD04, a de novo designed protein without sequence homologues identified by BLAST (Altschul et al., 1997), bound BHRF1 with moderate affinity (apparent KD=58±3 nM) and reasonable specificity, and was therefore chosen for further optimization.
Design BbpD04 binds BHRF1 tighter than all human prosurvival Bcl-2 proteins with the exception of Mcl-1 (Table 2). Based on a Poisson-Boltzmann electrostatics model (Whitehead et al.), the computed electric field experienced by BbpD04 when bound to BHRF1 is markedly more negative than when bound to Mcl-1 (FIG. 4A-B). We therefore introduced nine point substitutions to eight residues of BbpD04 to specifically increase electrostatic complementarity for BHRF1 (FIG. 4C). Six decreased the KD(BHRF1)/KD(Mcl-1) ratio as predicted (FIG. 4D). However, putting many of these beneficial mutations together in combination generally caused a loss in yeast surface expression, possibly indicating poor protein stability. The variant BbpD04.1 containing the best two point mutations (E48R and E65R), together with a third compensatory mutation (K31E) to preserve a putatively stabilizing salt-bridge, bound BHRF1 slightly tighter (apparent KD=8±4 nM) than any of the other human prosurvival Bcl-2 proteins (Table 2).














TABLE 2





Protein
BHRF1
Bcl-2
Bcl-w
Mcl-1
Bfl-1
Bcl-XL
Bcl-B















Apparent dissociation constants (nM; mean ± SE, n = 3-6) from yeast surface


display titrations














Bim-BH3
12 ± 4 
 2.02 ± 0.08
2.1 ± 0.1
0.6 ± 0.2
2.1 ± 0.3
 3 ± 1
12.2 ± 0.1 


BbpD07
60 ± 10
76 ± 7
—
3.1 ± 0.3
>100
—
  >100


BbpD04
58 ± 3 
—
—
17 ± 7 
>100
—
—


BbpD04.1
8 ± 4
110 ± 20
14 ± 5 
30 ± 10
>100
25 ± 1
—


BbpD04.2
0.6 ± 0.2
33 ± 4
40 ± 10
26 ± 4 
70 ± 20
31 ± 2
—


BbpD04.3
0.54 ± 0.01
20 ± 2
34 ± 3 
19 ± 1 
32 ± 6 
34 ± 7
—


BINDI
0.9 ± 0.2
45 ± 7
60 ± 10
21.6 ± 0.8 
>100
>100
—







Accurate dissociation constants (nM; mean ± SD, n = 4-6) measured by BLI














Bim-
7 ± 3
 0.75 ± 0.09
20 ± 10
0.17 ± 0.02
0.61 ± 0.04
 1.56 ± 0.09
7 ± 2


BH3


BINDI
0.22 ± 0.05
2,100 ± 100 
870 ± 40 
40 ± 10
2,600 ± 800  
810 ± 80
>10,000


BINDI
0.16 ± 0.08
 30,000 ± 10,000
4,600 ± 400  
230 ± 40 
4,000 ± 2,000
 8,000 ± 2,000
50,000 ± 10,000


N62S









Enhanced Affinity and Specificity of the Designed Protein Via Mutations Distant from the Interface

To optimize the design, the BbpD04.1 gene was diversified by error prone-PCR (average error rate 1.3 amino acid substitutions per clone) and a subsequent yeast display library of 2×106 transformants was sorted by three rounds of fluorescence-activated cell sorting (FACS). During each sort, the library was incubated with 5 nM biotinylated BHRF1 and 15 nM of each unlabeled human Bcl-2 protein as competitors to favor selectivity. Five mutated sites were identified that increased binding signal in the final sorted population: two mutations at the designed interface (H104R, predicted to enhance electrostatic complementarity, and N62S, predicted to improve specificity based on sequence-fitness landscape mapping described below), while three mutations were distal from the interface and might alter protein stability (shown later). I21V/L slightly alters packing in the hydrophobic core, Q79L increases hydrophobic interactions buttressing the second connecting loop, and L84Q forms a stabilizing hydrogen bond to the loop backbone. The mutations were mixed combinatorially (72 protein variants) in a yeast display library with 1×106 transformants that was further sorted for affinity and specificity. Over two rounds of sorting, the library was incubated with 1 nM biotinylated BHRF1 and 8 nM of each unlabeled human Bcl-2 protein, and the top one percent of cells based on binding signal intensity relative to surface expression were selected. Of 20 clones sequenced from the final sorted library, there were 12 unique sequences. The poor convergence in such a low complexity library suggests many sequences had similar binding signals under the yeast display conditions.
Screening a number of clones, we identified one (BbpD04.2 with four mutations: I21L, Q79L, I84Q and H104R, see FIG. 4E) that was monodisperse and monomeric by size exclusion chromatography (SEC) after protein purification from E. coli. BbpD04.2 eluted as a higher molecular weight (MW) complex by SEC when mixed with BHRF1, indicating their interaction in solution (FIG. 4F). A single point mutation of a conserved Bim leucine buried within the hydrophobic interface, L62E, severely diminishes binding of Bim-BH3 to all Bcl-2 family members (data not shown). The equivalent mutation of BbpD04.2, L54E, similarly abolishes the interaction of BbpD04.2 with BHRF1 observed by SEC (FIG. 4F).
Conjugation of various chemical agents to exposed cysteine residues can allow intracellular delivery, fluorescence detection or surface immobilization for affinity measurements, as described below. BbpD04.2 was incompatible with single labeling of an added terminal cysteine residue, due to the presence of a second internal cysteine (FIG. 5). Short peptide linkers containing single cysteines were genetically fused to the BbpD04.2 termini (FIG. 5A) and found to react in seconds with polyethylene glycol (PEG)-maleimide, producing a higher MW product with reduced electrophoretic mobility (FIG. 5B). BbpD04.2 has an internal buried cysteine, which becomes exposed for PEG-maleimide conjugation in the presence of the harsh detergent SDS, indicating the protein is folded and the hydrophobic core is generally shielded from solvent unless chemically denatured. However, when cysteine-linker BbpD04.2 proteins were conjugated to HPDP-biotin for longer incubations (4 h) at room temperature, the proteins would subsequently aggregate when mixed with tetrameric streptavidin. We hypothesized that, in addition to the exposed terminal cysteine, the internal cysteine was weakly conjugated under these conditions to form aggregated streptavidin-complexes. Mutation of the internal cysteine (C103A) markedly diminished aggregation (FIG. 5C). BbpD04.2 C103A (called BbpD04.3) had only a small loss of affinity and specificity (FIG. 5F), and was therefore chosen for further experiments.
Interface Interactions and Folded Structure are Both Critical
To probe the sequence-fitness landscape of the designed protein, site-specific saturation mutagenesis according to the protocol of (Procko et al., 2013) was used to independently diversify every codon of the BbpD04.3 gene to NNK (N is any base, K is G or T), producing a library of (116 positions)×(20 amino acids+stop codon)=2,436 protein variants. The variants were expressed by yeast surface display (2.5×106 transformants) and the library was sorted by a single round of FACS for the 1% of cells with highest binding signal for 400 pM biotinylated BHRF1 (FIG. 6A). Alternatively, the library was sorted for affinity and specificity (yeast were incubated with 400 pM biotinylated BHRF1 and 8 nM of an equimolar mixture of unlabeled human Bcl-2 proteins as competitors; FIG. 6B). DNA was extracted from the naive and post-sorted yeast populations, the BbpD04.3 gene amplified as two fragments to provide full sequencing coverage, and the samples were deep sequenced using Illumina MiSeq sequencing. The frequency of each protein variant is compared between the naive/pre-sorted and enriched/post-sorted populations to calculate an enrichment ratio, which acts as a proxy for the affinity/specificity fitness of each substitution (Fowler et al., 2010; McLaughlin et al., 2012; Procko et al., 2013; Whitehead et al., 2012).
The BbpD04.3 affinity sequence-fitness landscape reveals the critical nature of the incorporated Bim-BH3 motif, with most substitutions of interface residues being depleted (FIG. 6A). In addition, substitutions to proline, which can break regular helical secondary structure, are depleted across the first, second and third helical spans of the designed helical bundle fold (FIG. 6A). Substitutions to aspartate, a short and charged amino acid, are depleted within the hydrophobic core as anticipated (FIG. 6A). The BbpD04.3 affinity-specificity sequence-fitness landscape, in which unlabeled Bcl-2 proteins were included as competitors for BHRF1 binding, is similar (FIG. 6B).
Using the sequence-fitness landscape for BHRF1 affinity, we are able to determine the allowed sequence variation of BbpD04.3. The most conserved residues for BHRF1 interaction are found within the second helix of BbpD04.3 and span the incorporated Bim-BH3 motif (FIG. 14A). Residues near the BbpD04.3 C-terminus that also contact BHRF1 are similarly conserved. We applied our experimental enrichment ratios to a hypothetical population that evenly covered all single amino acid substitutions at a given residue, and from the evolved population calculated the probability of finding each amino acid. This analysis reveals that significant diversity is tolerated for any single amino acid substitution, except at critically conserved residues (FIG. 14B and Table 4). Presumably the tolerance for any two amino acid substitutions would be less, less again for three substitutions and so forth, but it is clear that some positions have little preference for amino acid type. A large number of BbpD04.3 sequence variants can therefore maintain the folded structure and favorable binding to a target BCL2 protein.







TABLE 4







Allowed sequence variability in BbpD04.3 from single site


saturation mutagenesis









% Probability














Conserv.
Charged
Polar
Apolar
Aromatic
Other


Residue
score
DEHRK
STNQ
ILVAM
FYW
GCP
















A1
0.02
25
18
24
18
15


D2
0.04
21
28
22
14
16


W3
0.02
25
28
20
11
16


K4
0.03
32
19
28
10
11


K5
0.04
22
18
28
23
10


V6
0.05
14
15
32
22
17


L7
0.04
19
24
30
18
10


D8
0.02
19
21
25
20
15


K9
0.06
31
23
23
15
8


A10
0.07
16
22
34
15
13


K11
0.04
30
30
17
11
12


D12
0.04
21
18
27
27
7


I13
0.05
30
29
18
15
8


A14
0.11
7
31
45
3
14


E15
0.15
20
13
29
31
6


N16
0.06
18
13
35
27
8


R17
0.06
20
20
37
7
17


V18
0.09
17
22
45
5
11


R19
0.05
24
23
30
13
10


E20
0.04
18
20
29
24
8


L21
0.18
20
19
32
24
4


K22
0.08
33
23
28
2
15


O23
0.01
20
23
28
17
12


K24
0.09
42
22
20
8
8


L25
0.19
3
20
49
12
15


E26
0.12
20
29
35
6
11


E27
0.04
24
25
24
18
8


F28
0.06
23
17
34
14
12


Y29
0.02
29
20
25
13
14


K30
0.01
28
22
20
19
10


E31
0.01
17
26
31
14
12


A32
0.02
20
27
17
19
17


M33
0.05
30
23
21
13
13


K34
0.01
28
19
29
13
11


L35
0.02
28
23
25
9
14


D36
0.01
24
22
23
13
18


L37
0.03
28
26
23
14
8


T38
0.03
31
25
20
8
16


O39
0.07
30
33
21
3
13


E40
0.02
23
19
35
10
12


M41
0.05
21
22
26
23
8


R42
0.08
35
24
25
3
12


R43
0.18
52
21
12
4
11


K44
0.00
28
23
23
14
13


L45
0.09
7
20
29
32
13


M46
0.11
32
35
24
3
5


L47
0.32
3
1
35
58
3


R48
0.15
41
24
20
6
9


W49
0.26
43
9
4
41
4


I50
0.30
4
16
64
13
3


A51
0.43
15
8
24
1
51


A52
0.14
8
23
42
17
10


M53
0.13
31
25
20
22
1


L54
0.39
4
3
84
2
6


M55
0.13
11
21
45
8
16


A56
0.09
5
22
44
9
20


I57
0.24
1
28
59
9
3


G58
0.25
12
12
19
8
49


D59
0.14
44
15
15
17
9


I60
0.18
3
23
58
10
5


F61
0.20
5
8
31
51
5


N62
0.04
14
21
35
19
11


A63
0.08
10
12
49
20
8


I64
0.05
17
21
33
20
8


R65
0.17
34
17
8
37
3


O66
0.05
22
14
37
20
7


A67
0.09
26
20
25
6
22


K68
0.10
34
37
13
8
8


O69
0.04
23
25
25
18
9


E70
0.03
26
17
32
19
6


A71
0.13
9
18
50
8
16


D72
0.04
17
22
32
18
11


K73
0.11
35
11
19
31
4


L74
0.06
23
11
26
31
9


K75
0.03
29
21
23
21
7


K76
0.06
25
20
34
15
7


A77
0.03
24
19
23
27
8


G78
0.10
42
31
12
7
8


L79
0.03
27
19
27
20
7


V80
0.07
13
14
49
14
11


N81
0.06
36
31
15
7
11


S82
0.01
30
19
27
10
14


O83
0.01
25
23
26
17
9


O84
0.02
32
26
21
9
13


L85
0.01
23
17
30
20
10


D86
0.01
23
23
28
18
7


E87
0.02
25
20
30
17
7


L88
0.07
10
19
44
17
10


K89
0.03
30
23
29
10
8


R90
0.03
22
27
29
14
8


R91
0.02
25
26
21
13
15


L92
0.06
31
13
39
9
8


E93
0.03
24
27
31
11
7


E94
0.00
27
22
27
11
13


L95
0.08
24
20
44
7
6


K96
0.11
44
30
11
11
4


E97
0.06
31
30
25
4
11


E98
0.00
29
20
19
20
11


A99
0.04
20
30
29
11
10


S100
0.15
6
53
14
11
16


R101
0.09
34
21
33
3
9


K102
0.04
38
27
22
6
8


A103
0.14
5
40
43
1
11


R104
0.24
66
21
6
1
6


D105
0.03
27
22
28
14
9


Y106
0.04
30
18
29
12
11


G107
0.21
25
35
13
11
16


R108
0.26
60
26
6
1
7


E109
0.11
36
9
20
28
6


F110
0.07
13
19
22
33
12


O111
0.11
43
28
19
4
6


L112
0.02
25
18
30
10
17


K113
0.08
32
35
16
4
12


L114
0.05
37
15
28
11
9


E115
0.11
45
26
14
2
13


Y116
0.04
38
24
15
10
12









Bacterial expression of BbpD04.3 was very low, limiting the quantity and purity that could be purified for biochemical applications. Simply combining mutations enriched in the sequence-fitness landscapes within libraries, while achieving enhanced BHRF1 affinity and specificity by yeast surface display, gave clones with undetectable protein expression in E. coli. Therefore, we sought instead to only combine mutations that improved bacterial expression. Twenty-nine BbpD04.3 point mutants with positive enrichment ratios in either the affinity or affinity-specificity sequence-fitness landscapes were expressed in E. coli and analyzed for increased soluble protein levels by small scale NiNTA-agarose precipitation (FIG. 7A). Nine mutations were identified: W3A and W3P increase helical propensity of the initiating residue in the starting helix; I13Q, M33R, F61Y, W49E/Y and M46E decrease surface hydrophobicity; and F28L slightly increases packing in the hydrophobic core while again reducing surface hydrophobicity (the lowest energy Phe rotamer at this position is predicted to point towards solvent, while Leu is directed inwards to the core in the crystal structure described below). Because the mutations are generally surface-exposed at distinct sites on a long helical bundle, we reasoned they could likely be combined without negative interference (FIG. 7B). A BbpD04.3 variant with seven mutations—W3P, I13Q, F28L, M33R, M46E, W49Y and F61Y (FIG. 7C)—had significantly increased bacterial expression and improved specificity with no significant change in BHRF1 affinity by yeast surface display (FIG. 6D and Table 2). This variant is named BHRF1-INhibiting Design acting Intracellularly (BINDI).
The increased expression of BINDI compared to BbpD04.3 is not due to enhanced protein stability; both BbpD04.3 and BINDI undergo cooperative unfolding at high concentrations (>3 M) of the chemical denaturant guanidinium hydrochloride measured by circular dichroism (CD) spectroscopy (FIG. 6E). However, the original design, BbpD04, has nearly linear loss of CD signal over a 0 to 6 M range of guanidinium hydrochloride (FIG. 6E). The absence of a cooperative melting transition is associated with molten globules that lack a rigid core or single native conformation. While BbpD04, BbpD04.3 and BINDI have high thermostability and retain partly α-helical CD spectra at 95° C., only the evolved BbpD04.3 and BINDI fully renature when the heated protein solutions are cooled (FIG. 7D-G). Further, the original BbpD04 design is sensitive to rapid hydrolysis by proteases, which require unfolded substrate backbone to access the enzyme active site (FIGS. 6F-H and 7H). BbpD04.3 and BINDI are similarly resistant to protease digestion with differences attributable to sequence variation (i.e. trypsin cuts after lys or arg residues that are more abundant in BINDI, and chymotrypsin cuts after aromatic residues that are more abundant in BbpD04.3). Increased affinity for BHRF1 following in vitro evolution correlates with enhanced protein stability. A summary of all mutations introduced in the original design is provided in FIG. 61.
The Designed BINDI Protein has High Affinity and Specificity
Apparent dissociation constants by yeast surface display are useful approximations, but may be artificially tight due to avidity effects or ligand rebinding to a dense receptor surface, or may be artificially weak if binding equilibrium is not reached during the incubation time. The BINDI•BHRF1 interaction was therefore further characterized by alternative methods. BINDI eluted as a higher molecular weight complex by SEC when mixed with BHRF1 in solution, whereas BINDI L54E with a knockout mutation in the designed interface did not (FIG. 8A). Using bio-layer interferometry (BLI) to measure the kinetic rate constants, BINDI•BHRF1 was found to form an extraordinarily tight complex (KD 220±50 pM) with a slow dissociation rate (koff=[2.8±0.9]×10−5 s−1) (FIG. 8B-C). BINDI bound human Mcl-1 with KD 40±10 nM (180-fold increase compared to BHRF1), Bcl-2 with KD 2.1±0.1 μM (10,000-fold increase), Bcl-w with KD 870±40 nM (4,000-fold increase), Bfl-1 with KD 2.6±0.8 μM (12,000-fold increase), Bcl-B with KD>10 μM (>45,000-fold increase) and Bcl-XL with KD 810±80 nM (4,000-fold increase). Compared to the measured affinities of Bcl-2 proteins for Bim-BH3 (FIG. 8D) and to other published values (Dutta et al., 2013; Dutta et al., 2010; Gemperli et al., 2005; Lessene et al., 2013) (Tse et al., 2008) (Caria et al., 2012; Flanagan and Letai, 2008; Kvansakul et al., 2010), the affinity and specificity of BINDI for BHRF1 is considerably greater than any previously described BHRF1 ligand, and is similar to or exceeds that of any other protein, peptide or drug designed to specifically bind a Bcl-2 family protein.
BINDI incorporates the Bim-BH3 motif within a de novo designed fold guided by the topology of PDB 3LHP chain S. The direct graft of Bim-BH3 interaction residues to the equivalent site within the 3LHP_S scaffold (design BbpG1) failed to bind BHRF1. Even after extensive design of the surrounding interaction surface (design BbpG1.D), the grafted protein did not bind BHRF1. While 3LHP_S is structurally similar to BINDI, it is nonetheless a poor steric fit for the BHRF1 binding groove in this design protocol. Aligning the graft site within 3LHP_S to the Bim-BH3 motif of BINDI in the BINDI•BHRF1 structure demonstrates how the C-terminal helix of the grafted design comes too close to the BHRF1 surface, such that side chains would clash (FIG. 9A). This simple structural alignment demonstrates why building new proteins with unique backbone atom positions can be essential for designing productive interactions. BINDI has an ideal structure and amino acid sequence found after computationally filtering thousands of potential designs for optimum interactions with BHRF1.
Compared to the native Bim-BH3 interaction, BINDI contacts an additional 404 Å2 on the surface of BHRF1 (FIG. 9B-G). Residues from the incorporated Bim-BH3 motif account for just 587 Å2 of the BINDI surface buried in the complex, whereas surrounding designed residues account for 839 Å2. Only two residues at the periphery of the incorporated Bim-BH3 motif changed during the final round of affinity maturation (the conservative W49Y and F61Y substitutions), while all residues in the core of the motif remained unchanged (FIG. 10A-C). Introducing these two mutations into a Bim-BH3 peptide, or mutating the Bim-BH3 peptide at all five positions within the BH3 region that distinguish nonspecific BbpD04 from specific BINDI, failed to achieve the high affinity and specificity of BINDI (FIG. 10D-E). The extraordinary specificity of BINDI is therefore accomplished through interactions across an expansive interface, extending well beyond the central Bim-BH3 residues.
BINDI Triggers Apoptosis Preferentially in an EBV-Infected Cell Line
We tested whether inhibition of BHRF1 via steric occlusion of the BH3-binding groove with BINDI could induce mitochondrial cytochrome c release in the EBV-positive BL cell line Ramos-AW. Ramos-AW expresses BHRF1 at very low levels (Leao et al., 2007), and therefore presents a challenging biological target that likely expresses much higher levels of off-target endogenous Bcl-2 family proteins. BINDI was applied to mitochondria isolated from both Ramos-AW and the EBV-negative parental line Ramos (Andersson and Lindahl, 1976). BINDI elicited greater cytochrome c release from Ramos-AW mitochondria (FIG. 11B), indicating an EBV-associated factor is likely a BINDI target. Strikingly, the non-specific Bim-BH3 peptide had opposite behavior; mitochondria from EBV-negative Ramos cells were more sensitive to Bim-BH3 treatment than those from EBV-positive Ramos-AW cells (FIG. 11A). Indeed, EBV-positive cell lines are widely reported as more resistant to nonselective apoptotic stimuli (Ishii et al., 1995; Kvansakul et al., 2010; Leao et al., 2007), making the enhanced activity of BINDI against Ramos-AW cells all the more significant.
While significantly weaker than the picomolar affinity of BINDI for BHRF1, the moderate affinity for Mcl-1 is likely the reason BINDI still triggers apoptosis in the EBV-negative Ramos cell line. It is possible that the enhanced toxicity of BINDI towards Ramos-AW reflects increased Mcl-1-dependency in this line, rather than expression of EBV BHRF1. To rule out this possibility, we tested a variant, BINDI N62S, with even greater specificity. During affinity maturation, the N62S mutation was found to enhance specificity both in the error-prone PCR-based library and in the comprehensive site-specific saturation mutagenesis library (FIG. 6). However, the N62S mutation simply wasn't present in clone BbpD04.2 isolated from the combinatorial library, and neither did this mutation improve expression of soluble protein in bacteria, the criterion used for combining mutations to generate BINDI. Asn62 of BINDI (Asn70 in Bim-BH3) hydrogen bonds to the N-terminus of BHRF1 helix α6, and serine at this position is predicted to similarly interact at the interface (FIG. 11C). BINDI N62S still binds BHRF1 with extraordinarily tight affinity (KD 160±80 pM), but now with even better specificity (Table 2 and FIG. 11D). Most notably, the affinity for Mcl-1 is diminished six-fold (KD 230±40 nM). Like parental BINDI, the N62S variant has enhanced apoptotic activity against EBV-positive Ramos-AW (FIG. 11E). Indeed, BINDI N62S, with greater specificity amongst the Bcl-2 family for BHRF1, has even greater discrimination between Ramos and Ramos-AW cells (FIGS. 11B and 11E). The enhanced activity of BINDI to initiate cytochrome c release preferentially in EBV-positive cells is therefore due to BHRF1 inhibition.
Expression profiling of EBV-positive BLs has revealed distinct subgroups (Kelly et al., 2013; Watanabe et al., 2010), and BHRF1 may not be important for cell survival in all cases. Mitochondria were isolated from six EBV-positive and four EBV-negative cancer lines. Bim-BH3 peptide triggered cytochrome c release (FIG. 11F), whereas the inactive guide scaffold 3LHP(S) had no effect (FIG. 11G; we switched from the L54E knockout mutation to using the scaffold 3LHP(S) as a generic negative control suitable for comparison to any BINDI variant). Incubation with BINDI N62S induced high cytochrome c release in four EBV-positive lines (FIG. 11H): BL lines Ramos-AW and Daudi, mantle cell lymphoma line Granta 519, and B-prolymphocytic leukemia JVM-13. Two of the EBV-positive lines had low levels of cytochrome c release similar to EBV-negative cells: BL line Raji and mantle cell lymphoma line JVM-2. Hence only a subset of EBV-positive cancer lines are dependent on BHRF1 for survival.
Treatment of EBV-Positive B Lymphoma in a Xenograft Mouse Model by Intracellular Delivery of BINDI
BINDI was genetically fused with a C-terminal antennapedia peptide for non-specific cellular uptake and intracellular delivery in vitro. BINDI-antennapedia applied to the growth medium at 4 μM selectively killed 40% of EBV-positive Ramos-AW cells, with no measurable death of EBV-negative Ramos cells (FIG. 12A). Antennapedia-fused proteins concentrate in endocytic organelles and escape to the cytosol with low efficiency (Duvall et al., 2010). To enhance endosomal escape, BINDI-antennapedia was conjugated via a terminal cysteine to a diblock copolymer carrier, Pol300, containing a hydrophilic first block for stability and a pH-responsive endosomolytic second block (Duvall et al, 2010; Mamganiello et al., 2012; Convertine et al., 2010). A lower 2 μM dose of BINDI-antennapedia induced 60% cell death preferentially in Ramos-AW cells when conjugated to the Pol300 polymeric carrier for enhanced cytosolic delivery (FIG. 12B). Our data suggest inhibition of BHRF1 can effectively kill EBV-positive BL.
Intracellular delivery of proteins in vivo is exceptionally challenging, with no efficient artificial methods currently available. Taking inspiration from the entry mechanisms of natural viruses, we developed an antibody-copolymer-based formulation to deliver BINDI to the cytosolic compartment of B cells within an animal. BINDI is coupled via a C-terminal cysteine to diblock copolymer Pol950 synthesized by reversible addition-fragmentation chain transfer. The copolymer's hydrophilic first block is composed of polyethylene glycol methacrylate (MA) for stability in the host, pyridyldisulfide MA for cysteine conjugation to BINDI, and biotin-hydroxylethyl MA for coupling to streptavidin-antiCD19 (αCD19; human monoclonal CAT-13.1E10-SA). The endosomolytic second block is composed of diethylaminoethyl MA and butyl MA. The entire complex of copolymer:αCD19:BINDI forms large micelles that disassociate at low pH to expose membrane-destabilizing groups (FIG. 13A). CD19 is a rapidly internalizing surface antigen, and bound αCD19-complex is endocytosed. Copolymer allows escape from the acidic endosome, and presumably BINDI is then released in the reducing cytosolic environment.
Subcutaneous Ramos-AW xenograft tumors were established in nude BALB/c mice. The mice were treated intravenously on days 0, 3 and 6 with antibody-copolymer coupled to the inactive scaffold 3LHP(S) or to BINDI. Thirty minutes prior to each treatment, cyclophosphamide (CTX) and bortezomib (BTZ) were injected intraperitoneally at subtherapeutic doses to prime cells for apoptosis (O'Connor et al., 2006). The treatments were nontoxic, with no substantial change in mouse body weight.
The intracellular delivery of BINDI to the B lymphoma xenograft slowed tumor progression and prolonged survival. Tumors grew rapidly in the untreated/PBS and chemo-only control groups (FIG. 13B-C), with mean tumor sizes of 1080±500 mm3 and 680±410 mm3, respectively, at day 11 when the first mice were euthanized due to excessive tumor burden. Due to the therapeutic effects of αCD19 coupled to an endosomolytic polymer, both scaffold 3LHP(S) and BINDI treatment groups had reduced tumor sizes, though volumes were significantly smaller (unpaired t test, P=0.003) in the BINDI (140±60 mm3) than 3LHP(S) (330±140 mm3) treatment group (FIG. 13D-E). Lifespan was extended in the BINDI-treated mice compared to the scaffold treatment (log-rank test, P=0.006), with median survival of 15 days for PBS treatment, 16 days for chemo-only, and 21 days for 3LHP(S) treatment, extending to 24 days following BINDI treatment (FIG. 13F). In addition to validating BHRF1 as a therapeutic target in EBV-positive B lymphoma, our data represent the first demonstration that a de novo computationally-designed protein can treat cancer in a preclinical model.
BCL2 family proteins share similar sequences (>50% similarity between any two family members) and similar structures ( ̃3 Å RMSD). It therefore seemed likely that the BINDI protein, having high complementarity with the binding pocket of BHRF1, could serve as an excellent scaffold for engineering new specificities to other BCL2 proteins. Since earlier variants of BINDI prior to exhaustive optimization bound Mcl-1 with high affinity, we began by repurposing the BINDI protein as a Mcl-1 binder. First, BINDI (PDB 4OYD chain D) was ‘docked’ into the hydrophobic binding cavity of existing crystallographic models of Mcl-1. In these models, Mcl-1 is bound to nonspecific BH3 peptides from Bim (PDBID 2PQK), Bax (PDBID 3PK1), or the Mcl-1 specific peptide MB7 (PDBID 3KZ0). The bound peptide was used to align the BH3-equivalent residues of BINDI. The docked complex was then designed (FIG. 15A-B). Residues of BINDI within 8 Å of the interface were computationally mutated to minimize the bound proteins' energy, keeping critical residues shared with Bim-BH3 fixed. Since design calculations use repeated random sampling, the process is done numerous times to give different possible sequences. Genes encoding six Mcl1-targeted computationally designed proteins, M-CDP01 to M-CDP06, were synthesized (Tables 5 and 6) and five expressed in E. coli. The affinities of the five proteins for BCL2 family members were tested by biolayer interferometry (BLI), with the specific Mcl-1-binding peptide MB1 tested as a positive control. All five proteins had tight affinity for Mcl-1 due to slow off rates, and two appeared to be highly specific (FIG. 16). This is despite only interactions with Mcl-1 being designed; specificity was achieved without explicitly designing against interactions with other BCL2 proteins.
When exposed to chemical denaturants and measuring the loss of helical structure by CD, two partially-specific binders (M-CDP02 and M-CDP05) unfolded over broad denaturant concentration ranges, suggestive of poorly packed or ‘molten’ cores (FIG. 15C). Binders specific for just Mcl-1 have narrow, cooperative unfolding transitions. A well-packed structure therefore appears to be necessary for specificity. We chose highly specific M-CDP04 (subsequently called MINDI for Mcl-1-inhibiting design acting intracellularly) for accurate determination of binding affinities in BLI experiments (FIG. 15D-E). MINDI bound Mcl1 with 150±60 pM affinity, with over ten thousand-fold weaker affinity for other BCL2 family members.
We sought to evolve a partially-specific Mcl-1 binder (M-CDP02) to specifically associate with single BCL2 proteins. However, this approach enriched for mutations that damaged regions of structure (data not shown). Since our aim is to engineer specific binders that are compact and well-folded, we abandoned directed evolution at this point and instead explicitly designed proteins to bind each BCL2 family member.
The structure of BINDI (PDB 4OYD chain D) was docked into the BH3 binding cavity in the structures of Bax-BH3-bound Bcl-2 (PDB 2XA0), small molecule inhibitors bound to Bcl-2 (PDBs 4AQ3, 4IEH and 4LVT), Bim-BH3-bound Bcl-XL (PDB 1PQ1; structure of mouse Bcl-XL, which is 97% identical to the human sequence), modified Bim peptides bound to Bcl-XL (PDBs 2YQ6 and 2YQ7), Bax-bound Bcl-XL (PDB 3PL7), a Puma-derived αβ peptide bound to Bcl-XL (PDB 4BPK), Bim-bound Bcl-B (PDB 4B4S), and Bak-bound Bfl-1 (PDB 3I1H). Critical interaction residues from the peptide ligand were grafted to the BINDI scaffold, or alternatively, residues of the BINDI BH3-like motif were kept fixed (Tables 5 and 6). Then, surrounding residues at the edges of the interface were computationally designed. The designed proteins were filtered for favorable binding energies, shape complementarity with the Bcl-2 homolog's BH3 binding cavity, and minimal buried unsatisfied polar atoms. Codon-optimized genes were synthesized and the proteins were expressed and purified from E. coli.







TABLE 5







Computationally designed derivatives of BINDI









Computational metrics























Buried





Residues kept fixed
Residues


Shape
unsatisfied



Target

(numbered as on
borrowed
Binds
Binding
complementarity
polar atoms


Design
PDB
PDB description
BINDI scaffold)
from
target?
energy (ddg)
(Sc)
(unsat)


















2-
2XA0
Bcl-2·Bax-
L54, I57, G58,
Bad-BH3
+
−35.2669
0.509289
10


CDP01

BH3
D59, F61


2-
2XA0
Bcl-2·Bax-
L54, I57, G58,
Bad-BH3
+
−41.0808
0.529427
9


CDP02

BH3
D59, F61


2-
4AQ3
Bcl-
A51, L54, G58,
BINDI
+
−29.2064
0.580547
2


CDP03

2·phenylacyl
D59




sulfonamide


2-
4IEH
Bcl-2/Bcl-
Y49, A51, L54,
BINDI
−
−24.6658
0.528941
7


CDP04

XL·N-
G58, D59, N62




heteroaryl




sulfonamide


2-
4IEH
Bcl-2/Bcl-
A51, L54, G58,
BINDI
−
−17.011
0.554712
5


CDP05

XL·N-
D59




heteroaryl




sulfonamide


2-
4LVT
Bcl-
L54, G58, D59
BINDI
+
−25.7035
0.467105
5


CDP06

2·navitoclax


2-
4LVT
Bcl-
L54, G58, D59,
BINDI
+
−25.7202
0.466163
11


CDP07

2·navitoclax
N62


X-
1PQ1
Bcl-XL·Bim-
I50, A51, L54,
Bim-BH3
+
−40.5426
0.613795
9


CDP01

BH3
G58, D59


X-
1PQ1
Bcl-XL·Bim-
Y49, I50, A51,
Bim-BH3,
+
−37.9138
0.575281
7


CDP02

BH3
L54, G58, D59
BINDI


X-
2YQ6
Bcl-
I50, A51, L54,
Bim-BH3
+
−32.0914
0.622902
8


CDP03

XL·BimSAHB
I57, G58, D59,





N62


X-
2YQ6
Bcl-
Y49, I50, A51,
Bim-BH3,
+
−34.2881
0.554852
4


CDP04

XL·BimSAHB
L54, I57, G58,
BINDI





D59, N62


X-
2YQ6
Bcl-
Y49, I50, A51,
BINDI
+
−32.6508
0.603245
11


CDP05

XL·BimSAHB
L54, I57, G58,





D59, N62


X-
2YQ7
Bcl-
A52, I54, F57,
XG10
+
−44.9274
0.643131
6


CDP06

XL·BimLOCK
G58, D59, F61
peptide1


X-
2YQ7
Bcl-
A52, I54, F57,
XG10
+
−47.9744
0.61353
4


CDP07

XL·BimLOCK
G58, D59, F61
peptide1


X-
2YQ7
Bcl-
A52, I54, F57,
XG10
+
−31.7966
0.631045
7


CDP08

XL·BimLOCK
G58, D59, F61
peptide1


X-
3PL7
Bcl-XL·Bax-
L50, S51, L54,
Bax-BH3
−
−24.8947
0.637508
7


CDP09

BH3
K55, I57, G58,





D59, D62


X-
4BPK
Bcl-
I50, A51, L54,
BINDI
+
−40.6185
0.587325
3


CDP10

XL·Puma-
G58, D59




α/β-foldamer


X-
4BPK
Bcl-
Y49, I50, A51,
BINDI
+
−31.2246
0.549465
4


CDP11

XL·Puma-
L54, I57, G58,




α/β-foldamer
D59, N62


M-
2PQK
Mcl-1·Bim-
E47, I50, A51,
Bim-BH3
+
−38.3045
0.665342
8


CDP01

BH3
L54, R55, I57,





G58, D59, F61,





N62


M-
2PQK
Mcl-1·Bim-
E47, I50, A51,
Bim-BH3,
+
−37.4996
0.678787
8


CDP02

BH3
L54, R55, I57,
BINDI





G58, D59, F61,





N62


M-
3KZ0
Mcl-1·MB7
E47, A50, A51,
MB7
+
−31.2833
0.660599
11


CDP03


I54, R55, I57,
peptide





G58, D59, N61,





N62, Y65


M-
3KZ0
Mcl-1·MB7
E47, A50, A51,
MB7
+
−31.1976
0.656449
5


CDP04


I54, R55, I57,
peptide;





G58, D59, N61,
BINDI





N62, Y65; Y49


M-
3PK1
Mcl-1·Bax-
T47, L50, S51,
Bax-BH3
+
−30.7442
0.694437
5


CDP05

BH3
L54, I57, G58,





D59, L61, D62,





M65


F-
3I1H
Bfl-1·Bak-
I50, A51, L54,
Bak-BH3
+
−28.74
0.671393
5


CDP01

BH3
I57, G58, D59,





N62


B-
4B4S
Bcl-B·Bim-
I50, A51, L54,
Bim-BH3
+
−29.0724
0.700157
5


CDP01

BH3
I57, G58, D59,





N62


W-
1PQ1*
Bcl-XL·Bim-
L54, I57, G58,
Bim-BH3
+
−29.6374
0.563108
7


CDP01

BH3
D59, F61, N62


W-
2YJ1*
Bcl-
L54, I57, G58,
Bim-BH3
+
−28.4893
0.557322
10


CDP02

XL·Puma-
D59, F61, N62




α/β-foldamer


W-
3FDL*
Bcl-XL·Bim-
L54, I57, G58,
Bim-BH3
+
−29.7158
0.532155
4


CDP03

BH3
D59, F61, N62





*Bcl-w models were generated by threading the aligned Bcl-w sequence onto the crystal structure of the Bcl-2 pro-survival homolog with indicated PDBID


1XG10 is a synthetic peptide designed for specificity to Bcl-xL, as described in Dutta et al., 2010.













TABLE 6





Sequences of computationally designed proteins (CDPs) prior to experimental


optimization and evolved combinatorial mutants (ECM) selected for BLI


screening.















> M-CDP01 (Target: Mcl-1)


ADPKKVLDKAKDQAENRVRELKQELEELYKKARKLDLTQEERRKLEEEAIAALLRAIGDIYN


AIQQALNEADKLKKAGLVNSQQLDELKRRLEELKKEASKKARDYGLEFFEKLDY (SEQ ID NO: 28)


 


> M-CDP02 (Target: Mcl-1)


ADPKKVLDKAKDQAENRVRELKQELEELYKEARKLDLTQEERRKLEESYIAAMLRAIGDIFN


AIMQAKNEADKLKKAGLVNSQQLDELRRRLEELRKEASLKAEDYGREFQEKLEY (SEQ ID NO: 29)


 


> M-CDP03 (Target: Mcl-1)


ADPKKVLDKAKDQAENRVRELKQDLERLYKEARKLDLTQEMRRKLQEKAAAAMIRAIGDI


NNAIYQALQEADKLKKAGLVNSQQLDELKRRLEELQKEASRKAQAYGEEFMLKLEY (SEQ ID NO: 30)


 


> M-CDP04 (Target: Mcl-1)


ADPKKVLDKAKDQAENRVRELKQVLEELYKEARKLDLTQEMRKKLIERYAAAIIRAIGDINN


AIYQAKQEAEKLKKAGLVNSQQLDELLRRLDELQKEASRKANEYGREFELKLEY (SEQ ID NO: 2)


 


> M-CDP05 (Target: Mcl-1)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEERHRLETKALSALLAAIGDIL


DAIMQALQEAAKLKKAGLVNSQQLDELKRRLEELRKEASRKARDYGREFWLKLDY (SEQ ID NO: 32)


 


> M-CDP06 (Target: Mcl-1)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEEREKLKTKYLSAMLAAIGDIL


DAIMQALNEAQKLKKAGLVNSQQLDELKRRLEELRKEASRKARDYGREFELKLDY (SEQ ID NO: 33)


 


> 2-CDP01 (Target: Bcl-2)


ADPKKVLDKAKDQAENVVRKLKQELEELYKEARKLDLTQDMREKIKLRAEAAELQAIGDIF


QAILQAKMEAKKLYDAGLVNSQQLDELKRRLEELAKEAEDRAAKLGKEFLQKLEYG (SEQ ID NO: 34)


 


> 2-CDP02 (Target: Bcl-2)


ADPKKVLDKAKDRAENAVRELKQKLEELYKEARKLDLTQDMRNKLIMKAIAAELRAIGDIF


QAILEAKAEAKKLLDAGLVNSQQFDELKRRLEELEEEAAERARKLGDEFRQKLEYG (SEQ ID NO: 35)


 


> 2-CDP03 (Target: Bcl-2)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRRELKERALAARLQAVGDI


FYAILQAKSEADKLKKAGLVNSQQLDELKRRLEELAEEAQRKARDYGIEFALKLEY (SEQ ID NO: 36)


 


> 2-CDP04 (Target: Bcl-2)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMREKLQEQALAAWLNAAGDI


IEAISRALQEADKLKKAGLVNSQQLDELKRRLEELAEEAARKAEKYGEEFKKKLEY (SEQ ID NO: 37)


 


> 2-CDP05 (Target: Bcl-2)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRAELNARFAAATLAAAGDII


NAISEALAEADKLKKAGLVNSQQLDELKRRLEELAQEAERKAEEYGQEFLLKLEY (SEQ ID NO: 38)


 


> 2-CDP06 (Target: Bcl-2)


ADPKKVLDKAKDEAENRVRELKQKLEELYKEARKLDLTQEMRQELVDKARAASLQASGDIF


YAILRALAEAEKLKKAGLVNSQQLDELKRRLEELAEEARRKAEKLGDEFRLKLEY (SEQ ID NO: 39)


 


> 2-CDP07 (Target: Bcl-2)


ADPKKVLDKAKDDAENRVRELKQKLEELYKEARKLDLTQEERDELKLKAIAASLQASGDIY


NAILRALEEARKLKKAGLVNSQQLDELKRRLEELAEEAQRKANKLGDEFRLKLEY (SEQ ID NO: 40)


 


> X-CDP01 (Target: Bcl-xL)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRRELQARYIAAMLAAAGDI


MEAIQQAKNEADKLKKAGLVNSQQLDELKRRLEELAKEAARKAEDYGREFQLKLEY (SEQ ID NO: 41)


 


> X-CDP02 (Target: Bcl-xL)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRKELVARYIAAMLAAAGDI


VQAIQDAKNEADKLKKAGLVNSQQLDELKRRLEELAKEAARKATDYGREFQLKLEY (SEQ ID NO: 42)


 


> X-CDP03 (Target: Bcl-xL)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRRELRNRAIAAILQAIGDLL


NAIQQAKDEADKLKKAGLVNSQQLDELKRRLEELQNEAAEKAADYGEEFWLKLEY (SEQ ID NO: 43)


 


> X-CDP04 (Target: Bcl-xL)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEDRKRLLLQYIAAMLAAIGDLE


NAIRWAKREADKLKKAGLVNSQQLDELKRRLEELAKEAAEKAADYGEEFNLKLEY (SEQ ID NO: 44)


 


> X-CDP05 (Target: Bcl-xL)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRRQLRDQYIAAMLAAIGDL


LNAIMQAKREADKLKKAGLVNSQQLDELKRRLEELEEEAAQKAADYGQEFLLKLEY (SEQ ID NO: 45)


 


> X-CDP06 (Target: Bcl-xL)


ADPKKVLDKAKDRAENRVRELKKKLEKLYKEARKLDLTQEQRNKIINAAMAAMIAAFGDIF


HAIQEAKEEAKKLKKAGLVNSQQLDELKRRLDELDEEAAQRAEKLGKEFNLKFEY (SEQ ID NO: 46)


 


> X-CDP07 (Target: Bcl-xL)


ADPKKVLDKAKDRAENVVRKLKKELEELYKEARKLDLTQEMRDRIRLAAIAARIAAFGDIFH


AIMEALEEARKLKKAGLVNSQQLDELKRRLEELDEEAAQRAEKLGKEFELKLEY (SEQ ID NO: 47)


 


> X-CDP08 (Target: Bcl-xL)


ADPKKVLDKAKDRAENRVRKLKKELEKLYKEARKLDLTQEQRDRIINAAIAAMIAAFGDIFH


AIMEAKEEARKLKKAGLVNSQQLDELKRRLDELDEEAAQRAEKLGKEFRLKFEY (SEQ ID NO: 48)


 


> X-CDP09 (Target: Bcl-xL)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRKKLIQKALSALLKAIGDIL


DAIARAKAEADKLKKAGLVNSQQLDELKRRLEELLKEAARKALDYGREFWLKLEY (SEQ ID NO: 49)


 


> X-CDP10 (Target: Bcl-xL)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRRELRERYIAAMLAAAGDL


WYAITQAKREADKLKKAGLVNSQQLDELKRRLEELLEEAARKAEDYGEEFRLKLEY (SEQ ID NO: 50)


 


> X-CDP11 (Target: Bcl-xL)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRRELRDRYIAAMLAAIGDLF


NAIQWAKQEADKLKKAGLVNSQQLDELKRRLEELAEEAARKAEDYGEEFKLKLEY (SEQ ID NO: 51)


 


> 10-CDP01 (Target: Bcl-B)


ADPKKVLDKAKDQAENRVRELKQELERLYKEARKLDLTQEMRRKLEWRYIAAMLKAIGDIL


NAIAQAENEADKLKKAGLVNSQQLDELRRRLEELAKEAARKAHDYGREFQLKLEY (SEQ ID NO: 52)


 


> F-CDP01 (Target: Bfl-1)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRKKLQYAAIGAMLAAIGDI


LNAIMQAKQEADKLKKAGLVNSQQLDELKRRLEELKEEALRKAHDYGSEFYLKLEY (SEQ ID NO: 53)


 


> X-ECM01 (Target: Bcl-xL)


ADPKKVLDKAKDRAENVVRKLKKELEELYKEARKLDLTQEMRDRIRRAAIAARIQAHGDIF


HAIKHALREARKLKKAGLVNSQQLDELKRRLEELDEEAEQRAEKLGKEFELKLEYG (SEQ ID NO: 54)


 


> X-ECM02 (Target: Bcl-xL)


ADPKKVLDKAKDRAENVVRKLKKELEELYKEARKLDLTQEMRDRIRRTAIAARFQAHGDIF


HAIKEAKREARKLKKAGLVNSQQLDELKRRLEELDEEAEQRAEKLGKEFELKLEYG (SEQ ID NO: 55)


 


> X-ECM03 (Target: Bcl-xL)


ADPKKVLDKAKDRAENVVRKLKKELEELYKEARKLDLTQEMRDRIRRAAIAARFAAHGDIF


HAIKEAKEEARKLKKAGLVNSQQLDELKRRLRELDEEAEQRAEKLGKEFRLKLEYG (SEQ ID NO: 56)


 


> X-ECM04(XINDI) (Target: Bcl-xL)


ADPKKVLDKAKDRAENVVRKLKKELEELYKEARKLDLTQEMRDRIRRTAIAARFQAHGDIF


HAIKHAKEEARKLKKAGLVNSQQLDELKRRLRELDEEAEQRAEKLGKEFRLKLEYG (SEQ ID NO: 4)


 


> 10-ECM01 (Target: Bcl-B)


ADPKKILDKAKDQVENRVRELKQELERLYKEARKLDLTQEMRRKLHVRYIAAMLKAIAAIL


NAIAQAENEADKLKKAGLVNSQQLDELRRRLEELTEEAAQKAHDYGREFQLKLEYG (SEQ ID NO: 58)


 


> 10-ECM02 (Target: Bcl-B)


ADPKKILDKAKDQVENRVRELKQELERLYKEARKLDLTQEMRRKLHVRYIAAMLKAIASIL


NAIAQAENEADKLKKAGLVNSQQLDELRRRLEELTEEAAQKAHDYGREFQLKLEYG (SEQ ID NO: 59)


 


> 10-ECM03 (Target: Bcl-B)


ADPKKILDKAKDQVENRVRELKQELERLYKEARKLDLTQEMRRKLHVRYIAAMLKAIADIL


NAIAQAENEADKLKKAGLVNSQQLDELRRRLEELTEEAARKAHDYGREFQLKLEYG (SEQ ID NO: 60)


 


> 10-ECM04 (Target: Bcl-B)


ADPKKILDKAKDQVENRVRELKQELERLYKEARKLDLTQEMRRKLHWRYIAAMLKAIADIL


NAIAQAENEADKLKKAGLVNSQQLDELRRRLEELTEEAARKAHDYGREFQLKLEYG (SEQ ID NO: 61)


 


> F-ECM01 (Target: Bfl-1)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRKKLEIAALGAVLAAHGDI


LNAIMQAKEEADKLKKAGLVNSQQLDELKRRLEELKEEALRKASDYGKEFHLKRQYG (SEQ ID NO: 62)


 


> F-ECM02 (Target: Bfl-1)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRKKLEIAALGAVLAAHGDI


LNAIMQAKEEADKLKKAGLVNSQQLDELKRRLEELKEEALRKASDYGKEFHLKRRYG (SEQ ID NO: 63)


 


> F-ECM03 (Target: Bfl-1)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRKKLEVAALGAVLAAHGDI


LNAIMQAKEEADKLKKAGLVNSQQLDELKRRLEELKEEALRKASDYGKEFHLKRQYG (SEQ ID NO: 64)


 


> F-ECM04 (Target: Bfl-1)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRKKLEVAALGAVLAAHGDI


LNAIMQAKEEADKLKKAGLVNSQQLDELKRRLEELKEEALRKASDYGKEFHLKRRYG (SEQ ID NO: 65)


 


> F-ECM05 (Target: Bfl-1)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRKKLQIAALGAMLAAIGDIL


NAIMQAKEEADKLKKAGLVNSQQLDELKRRLEELKEEALRKASDYGKEFHLKRQYG (SEQ ID NO: 66)


 


> F-ECM06 (Target: Bfl-1)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRKKLQIAALGAMLAAIGDIL


NAIMQAKEEADKLKKAGLVNSQQLDELKRRLEELKEEALRKASDYGSEFHLKREYG (SEQ ID NO: 31)


 


> F-ECM07 (Target: Bfl-1)


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRKKLQIAALGAMLAAIGDIL


NAIMQAKEEADKLKKAGLVNSQQLDELKRRLEELKEEALRKASDYGSEFHLKLEYG (SEQ ID NO: 57)


 


> W-CDP01 (Target: Bcl-w)


DPKKVFDKAKDKAENQVRYLKQRLEELYKEARKKDLTQEQRRKLKEKYLAAKLAAILAAIG


DAFNALAEARELHKQGKVNKQQLDELAKRLDRLAEEAIQKAEDYAREFAYKLEY (SEQ ID NO: 262)


 


> W-CDP02 (Target: Bcl-w)


DPKKVLDKARDQALKRLEEMRKKLEESYKEARKKDLTQEERRKLEEKYAEAMKRAAEDIY


NMIQQALKEAEKEKKAGQVNSQQLDKLREDLNNKLIAAALAAIGDAFNMAANLRT (SEQ ID NO: 263)


 


> W-CDP03 (Target: Bcl-w)


DPKKVFDEAKDRAENNVRRLKQKLEELYKEARKKDLTQEEREKLKEKYKTAMAAAALAAI


GDAFNALLKARKLHKNGQVNEQQLEELARRLQELAKEAFQKAKDYANEFEYKLEY (SEQ ID NO: 264)


 


> W-ECM01 (Target: Bcl-w; also referred to as WINDI, or αBCLW)


DPKKVFDELKDRAENNVRRLKQKLEELYKEARKKDLTQEEREKLKTKYKTAMQLAALAAE


GDIMNALLKARKLHKNGQVNEQQLEELARRLMELAKEAFQKAKDYANEFKYKLEY (SEQ ID NO: 265)


 


> W-ECM02 (Target: Bcl-w)


DPKKVFDELKDRAENNVRQLKQKLEELYKEARKKDLTQEEREKLKDKYKTAMHIAALAAE


GDIMNALLKARKLHKRGQVNEQQLRELARRLMELAKEAFQKAKDYANEFKYKLEY (SEQ ID NO: 266)


 


> W-ECM03 (Target: Bcl-w)


DPKKVFDELKDRAENNVRRLKQKLEELYKEARKKDLTQEEREKLKTKYKTAMHIAALAAE


GDIINALLKARKLHKRGQVNEQQLRELARRLMELAKEAFQKAKDYANEFEYKLEY (SEQ ID NO: 267)


 


> W-ECM04 (Target: Bcl-w)


DPKKVFDELKDRAENNVRNLKQKLEELYKEARKKDLTQEEREKLKDKYKTAMQIAALAAE


GDIMNALLKARKLHKNGQVNEQQLRELARRLMELAKEAFQKAKDYANEFKYKLEY (SEQ ID NO: 268)


 


> W-ECM05 (Target: Bcl-w)


DPKKVFDELKDRAENNVRNLKQKLEELYKEARKKDLTQEEREKLKTKYKTAMAIAALAAE


GDLLNALLKARKLHKRGQVNEQQLRELARRLMELAKEAFQKAKDYANEFKYKLEY (SEQ ID NO: 269)


 


> W-ECM50 (Target: Bcl-w)


DPKKVFDELKDRAENNVRRLKQKLEELYKEARKKDLTQEEREKLKTKYKTAMAIAALAAE


GDIMNALLKARKLHKRGQVNEQQLRELARRLMELAKEAFQKAKDYANEFKYKLEY (SEQ ID NO: 270)


 


> W-ECM60 (Target: Bcl-w)


DPKKVFDELKDRAENNVRRLKQKLEELYKEARKKDLTQEEREKLKTKYKTAMAAAALAAE


GDAFNALLKARKLHKRGQVNEQQLRELARRLMELAKEAFQKAKDYANEFKYKLEY (SEQ ID NO: 271)


 


> W-ECM70 (Target: Bcl-w)


DPKKVFDELKDRAENNVRRLKQKLEELYKEARKKDLTQEEREKLKEKYKTAMAAAALAAE


GDAFNALLKARKLHKNGQVNEQQLRELARRLMELAKEAFQKAKDYANEFKYKLEY (SEQ ID NO: 272)


 


> W-ECM80 (Target: Bcl-w)


DPKKVFDELKDRAENNVRRLKQKLEELYKEARKKDLTQEEREKLKEKYKTAMAAAALAAE


GDAFNALLKARKLHKNGQVNEQQLRELARRLMELAKEAFQKAKDYANEFEYKLEY (SEQ ID NO: 273)









Initial screening by BLI indicated designed proteins generally bound their intended targets with nanomolar affinity and moderate specificity, but lacked the exceptional specificity of MINDI for Mcl-1 or BINDI for BHRF1. The designed proteins were therefore now improved by directed evolution. Selecting individual designs with promising partial specificity for each target BCL2 protein, the genes were diversified at every codon position to encode all possible single amino acid substitutions, and the libraries were transformed into yeast as Aga2p fusions for surface display. Each library was selected by one round of FACS for high affinity binding to the intended target (biotinylated for detection with streptavidin-phycoerythrin), with the other five human BCL2 proteins (unlabeled) added to the binding reaction as competitors to favor specific interactions. The pre- and post-sort populations were deep sequenced and enrichment ratios for all single amino acid substitutions calculated. From these sequence-fitness landscapes, mutations were chosen that were highly enriched during selection (Table 7). In the cases of the designed Bcl-XL, Bcl-B, and Bfl-1 binders, these enriching mutations were then combined in a combinatorial library that was selected by five (Bcl-XL binder) or three (Bfl-1 and Bcl-B binders) rounds of FACS to find variants with significantly improved affinity and/or specificity, each round under more stringent conditions including lower concentrations of target Bcl-2 paralogue and/or higher concentrations of competitors (Tables 7 and 8). Another round of directed evolution was required to further improve specificity of the Bfl-1 and Bcl-B binders. In these cases, the most specific evolved combinatorial mutants (10-ECM01 and F-ECM04) were diversified by error prone PCR, expressed on the yeast cell surface and selected as previously (Tables 7 and 8). In the case of the designed Bcl-2 binder, the computationally designed protein 2-CDP06 bound Bcl-2 with high affinity prior to in vitro evolution. Therefore, 20 point mutants indicating improved affinity and specificity in the sequence-fitness landscape were screened by BLI in lieu of further evolution. Point mutants that improved affinity for Bcl-2 while diminishing affinity for other paralogues were combined. Ultimately protein variants were found that bind each BCL2 paralogue with high affinity and specificity (FIG. 17 and Table 9).







TABLE 7







Design and directed evolution of BCL2-protein specific binders











Combinatorial
No combinatorial




library created
library

















SSM
Mutations in

Point
Additional


Name

Name of
mutations
isolated

mutants
mutations


of

Original
included in
clone from
SSM-guided
combined
from error


Final

Computational
combinatorial
combinatorial
point mutants
for final
prone-PCR


Variant
Target
Design
library
library
screened
design
library





MINDI
Mcl-1
M-CDP04
NA
NA
NA
NA
NA


2-
Bcl-2
2-CDP06
NA
NA
E20N, K24R,
K24R,
NA


INDI




V46E, V46R,
S57N,







D47F, D47W,
G107R







R50D, R50L,







R50M, S53D,







S53K, S53R,







S57H, S57N,







L68R, R100F,







R100K,







R100N,







G107M,







G107R


XINDI
Bcl-XL
X-CDP07
E24R, L28K,
L47R,
NA
NA
NA





D43R, L47R,
A48T, I54F,





A48E, A48K
A55Q,





A48Q, A48T,
F57H,





I54F, A55Q,
M65K,





F57H
E66H,





M65H,
L68K,





M65K,
E93R,





M65R,
A100E,





E66H, E66K,
E111R





E66R, L68K,





L68N, L68R,





E69R, E70R,





E93K, E93R,





D96T,





A100E,





A100K,





A100Q,





E111R


10-
Bcl-B/
10-CDP01
I6V, A14V,
V6I, A14V,
NA
NA
A51E,


INDI
BCL2L

N16K, E20F,
E46H,


L61M,



10

L21V, E46H,
W47V,


F110L





E46Q, E46Y,
G58A,





W47F, W47I,
D58A,





W47L,
A96T,





W47V,
K97E,





Y49F, I50L,
R101Q





A51E, A51I,





A51K, A51R,





L54I, G58A,





G58S, D59A,





D59K,





D59N, D59S,





D59T, A63L,





A63V, E93K,





A96T, K97E,





R101Q


FINDI
Bfl-1
F-CDP01
Q46S, Q46E,
Q46E,
NA
NA
M41K,





Y47I, Y47V,
Y47V, I50L,


A49T,





I50K, I50L,
M53V,


N108K





I50M, M53C,
I57H, Q69E,





M53I, M53V,
H104S,





L54N, I57F,
S108K,





I57H, I57L,
L114R,





I57N, I57S,
E115R





I57T, Q69E,





H104E,





H104R,





H104S,





H104T,





S108K,





S108N,





Y111H,





Y111K,





Y111W,





L114R,





E115G,





E115Q,





E115R


WINDI
Bcl-w
W-CDP03
A9L, R19N,
A9L, E46T,
NA
NA
NA





R19Q, E46D,
A53Q,





E46T, A53E,
A54L, I60E,





A53H,
A63I,





A53Q, A54I,
F64M,





A54L,
Q92M,





A54M
E110K





A54S, A54T,





A54V, A59I,





A59M,





A59T, A59V,





I60E, A63F,





A63I, A63L,





A63M, F64I,





F64L, F64M,





N76R, E85R,





Q92M,





Q92T, E93V,





E97D, F99E,





E110K
















TABLE 8







Sort conditions for SSM, combinatorial and error-prone PCR libraries











Incubation conditions












Target
Competitor




concentration
concentration


Library 
Sort
(nM)
(nM)













2-CDP06 SSM
1
0.5
40


2-CDP06 SSM
2
0.25
40


X-CDP07 SSM
1
2
4


X-CDP07 SSM
2
2
4


X-CDP07 combinatorial
1
1
8


X-CDP07 combinatorial
2
0.5
32


X-CDP07 combinatorial
3
0.35
64


X-CDP07 combinatorial
4
0.2
100


X-CDP07 combinatorial
5
0.1
200


10-CDP01 SSM
1
4
8


10-CDP01 SSM
2
4
8


10-CDP combinatorial
1
4
8


10-CDP combinatorial
2
2
8


10-CDP combinatorial
3
2
16


10-CDP combinatorial
4
2
16


10-ECM01 error-prone
1
0.5
40


PCR





10-ECM01 error-prone
2
0.2
40


PCR





10-ECM01 error-prone
3
0.2
40


PCR





10-ECM01 error-prone
4
0.1
40


PCR





10-ECM01 error-prone
5
0.1
40


PCR





F-CDP01 SSM
1
4
4


F-CDP01 SSM
2
4
4


F-CDP01 combinatorial
1
4
8


F-CDP01 combinatorial
2
2
8


F-CDP01 combinatorial
3
2
16


F-CDP01 combinatorial
4
2
16


F-ECM04 error-prone PCR
1
0.75
40


F-ECM04 error-prone PCR
2
0.5
40


F-ECM04 error-prone PCR
3
0.5
40


F-ECM04 error-prone PCR
4
0.5
40


F-ECM04 error-prone PCR
5
0.5
40


W-CDP03 SSM 
1
2
8


W-CDP03 SSM 
2
0.5
2


W-CDP03 combinatorial
1
0.5
2


W-CDP03 combinatorial
2
0.15
3


W-CDP03 combinatorial
3
0.05
20


W-CDP03 combinatorial
4
0.05
40


W-CDP03 combinatorial
5
0.05
80
















TABLE 9





Sequences of BINDI derivatives that specifically


bind BCL2 family members















Name: MINDI Target: Mcl-1


ADPKKVLDKAKDQAENRVRELKQVLEELYKEARKLDLTQEMRKKLIERY


AAAIIRAIGDINNAIYQAKQEAEKLKKAGLVNSQQLDELLRRLDELQKE


ASRKANEYGREFELKLEY (SEQ ID NO: 2)


 


Name: 2-INDI Target: Bcl-2


ADPKKVLDKAKDEAENRVRELKQRLEELYKEARKLDLTQEMRQELVDKA


RAASLQANGDIFYAILRALAEAEKLKKAGLVNSQQLDELKRRLEELAEE


ARRKAEKLRDEFRLKLEY (SEQ ID NO: 3)


 


Name: XINDI Target: Bcl-XL


ADPKKVLDKAKDRAENVVRKLKKELEELYKEARKLDLTQEMRDRIRRTA


IAARFQAHGDIFHAIKHAKEEARKLKKAGLVNSQQLDELKRRLRELDEE


AEQRAEKLGKEFRLKLEY (SEQ ID NO: 4)


 


Name: 10-INDI Target: Bcl-B/BCL2L10


ADPKKILDKAKDQVENRVRELKQELERLYKEARKLDLTQEMRRKLHVRY


IEAMLKAIAAIMNAIAQAENEADKLKKAGLVNSQQLDELRRRLEELTEE


AAQKAHDYGRELQLKLEY (SEQ ID NO: 5)


 


Name: FINDI Target: Bfl-1


ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEKRKKLEVAT


LGAVLAAHGDILNAIMQAKEEADKLKKAGLVNSQQLDELKRRLEELKEE


ALRKASDYGNEFHLKRRY (SEQ ID NO: 6)


 


Name: WINDI Target: Bcl-w


ADPKKVFDELKDRAENNVRRLKQKLEELYKEARKKDLTQEEREKLKTKY


KTAMQLAALAAEGDIMNALLKARKLHKNGQVNEQQLEELARRLMELAKE


AFQKAKDYANEFKYKLEY (SEQ ID NO: 265)









The final variants that specifically bind Bcl-2, Bcl-XL, Bcl-B/BCL2L10, and Bfl-1 with high affinity are named 2-INDI, XINDI, 10-INDI and FINDI, respectively. Based on BLI measurements at multiple analyte concentrations (FIG. 17), 2-INDI binds Bcl-2 with KD 0.839±0.005 nM and >2,000-fold weaker affinity for the next tightest binding BCL2 family protein; XINDI binds Bcl-XL with KD 5.59±0.03 nM and >660-fold weaker affinity for other BCL2 proteins; 10-INDI binds Bcl-B with 24.7±0.1 nM affinity, and 1000-fold specificity; and FINDI binds Bfl-1 with KD 0.91±0.01 nM and >350-fold specificity (Table 10). These affinities and specificities are similar or better than other engineered peptides or small molecule ligands of BCL2 family proteins. When exposed to the chemical denaturant guanidinium hydrochloride, all the optimized inhibitors had sharp unfolding transitions as measured by loss of CD absorbance for helical structure (FIG. 18). For 2-INDI, XINDI and FINDI, the protein stabilities were slightly to moderately decreased from the original computational designs. However, unfolding was still a cooperative reaction over narrow guanidinium concentrations, suggestive of a well-packed protein core.







TABLE 10







KD values for designed binder-BCL2 protein interactions















Mcl-1
Bcl-2
Bcl-XL
Bcl-B
Bfl-1
Bcl-w
Specificity


















MINDI
 0.15 ± 0.06
14,200 ± 700  
400,000 ± 100,000
 40,000 ± 10,000
30,000 ± 10,000
200,000 ± 200,000
93,000


2-INDI
>75 μM
 0.839 ± 0.005
3,500 ± 200  
>75 μM
>75 μM
1,850 ± 80  
2210


2-CDP06
>50 μM
 8.9 ± 0.9
12,000 ± 2,000 
>50 μM
>50 μM
1,670 ± 40  
190


XINDI
>50 μM
3,700 ± 100 
5.59 ± 0.03
>50 μM
>50 μM
40,000 ± 6,000 
660


X-CDP07
174.2 ± 0.2 
 3.81 ± 0.04
0.590 ± 0.003
107 ± 3 
>50 μM
14.89 ± 0.06 
6.46


10-INDI
>25 μM
>25 μM
>25 μM
24.7 ± 0.1
>25 μM
>25 μM
1010


10-ECM01
3,650 ± 60  
12,500 ± 700  
7,800 ± 300  
77 ± 7
2,380 ± 80  
19,000 ± 1,000 
31


10-CDP01
 0.47 ± 0.07
14 ± 4
16 ± 2 
 9 ± 1
250 ± 100
900 ± 700
0.05


FINDI
1,700 ± 100 
321 ± 20
900 ± 100
31,000 ± 6,000
0.91 ± 0.01
7,400 ± 600  
350


F-ECM04
255 ± 8 
100 ± 1 
540 ± 20 
 4,000 ± 1,000
1.1 ± 0.3
3,800 ± 100  
91


F-CDP01
 4.6 ± 0.7
 20 ± 11
9 ± 1
210,000 ± 74,000
2.6 ± 0.4
590 ± 40 
1.8


W-CDP03
55.3 ± 0.8
18.8 ± 2  
7.43 ± 0.08
400 ± 8 
400 ± 20 
8.00 ± 0.08
0.9


WINDI
>25 μM
5700 ± 900
1,610 ± 61  
>25 μM
>25 μM
1.013 ± 0.005
1590









Using the experimental sequence-fitness landscapes described above, we could determine the allowed sequence variability for the designed proteins (FIG. 19, Tables 11-20). While our saturation mutagenesis data are for the original computational designs, they nonetheless likely capture the capacity of the final optimized variants to tolerate mutations. As described for BINDI earlier, sequence conservation varies across the protein sequence, and while some positions are reasonably conserved for high affinity and specific interaction with a BCL2 family member, other positions are not. The BINDI scaffold is able to tolerate many mutations while preserving function. The different BCL2 inhibitors differ from each other by as many as 39 mutations, yet when any of the sequences is queried against GenBank for homologues by BLAST (E-value threshold 0.1), the proteins are found to be related only to each other, without homologous natural proteins. We have therefore designed an unnatural protein scaffold that can be easily repurposed for binding any BCL2 family member. Any modified version of BINDI or its derivatives will similarly belong to our designed protein family but lack homology to any natural protein, and should therefore be covered by the claims in this patent.
An alignment of the optimized binders demonstrates that some amino acids differ in just one or a couple of the proteins, while other residues diverge among most of the binders and are likely strong determinants of specificity (FIG. 20A). When mapped to the structure of BHRF1-bound BINDI, residues that differ in just a couple of the binders tend to be localized to the extreme edges of the interface where there is minimal direct contact, with a few positions in the very center of the interface that are conserved for binding across the BCL2 family (FIG. 20B). By comparison, the primary specificity-determining residues are localized around the interface core at sites of direct contact (FIG. 20B). Our interface can therefore be divided into three regions from the center outwards: (i) a conserved core for binding all BCL2 family members, (ii) a region that principally determines specific interactions, and (iii) an extreme periphery that can offer an occasional specificity contact.







TABLE 11







Allowed sequence variability in 2-CDP06 from single site


saturation mutagenesis










Conser-
% Probability














vation
Charged
Polar
Hydrophobic
Aromatic
Other


Residue
score
DEHRK
STNQ
ILVAM
FYW
GCP
















A1
0.35
16
30
27
0
26


D2
0.2
35
25
20
13
8


P3
0.13
25
32
27
4
12


K4
0.27
68
20
8
2
2


K5
0.24
40
22
37
1
1


V6
0,3
22
7
55
5
10


L7
0.24
22
7
23
15
33


D8
0.2
26
14
19
33
7


K9
0.16
45
23
15
11
5


A10
0.58
0
1
27
69
2


K11
0.18
21
30
23
17
9


D12
0.34
36
9
7
7
41


E13
0.21
62
8
17
10
3


A14
0.37
4
2
40
47
6


E15
0.23
27
24
10
27
13


N16
0.18
32
19
11
29
9


R17
0.19
30
32
17
8
13


V18
0.57
2
5
18
2
72


R19
0.35
28
8
11
2
51


E20
0.18
23
36
19
10
12


L21
0.64
69
1
4
27
0


K22
0.39
47
36
7
1
8


Q23
0.31
22
14
9
17
38


K24
0.81
94
4
1
0
0


L25
0.48
41
1
2
55
1


E26
0.36
26
30
38
1
5


E27
0.45
76
4
10
8
3


L28
0.29
21
21
45
8
5


Y29
0.24
16
5
11
26
43


K30
0.36
40
37
15
1
8


E31
0.22
33
21
23
19
4


A32
0.3
3
4
44
47
1


R33
0.33
48
8
12
1
31


K34
0.32
52
30
14
1
3


L35
0.2
42
13
19
15
10


D36
0.22
36
20
26
11
8


L37
0.32
46
6
37
3
8


T38
0.31
20
44
30
2
3


Q39
0.25
30
27
11
1
30


E40
0.23
50
11
19
3
13


M41
0.18
21
13
43
8
15


R42
0.31
61
15
4
10
11


Q43
0.37
33
18
42
1
5


E44
0.21
37
9
21
29
5


L45
0.25
26
17
51
1
6


V46
0.15
52
19
16
5
8


D47
0.59
2
0
27
70
1


K48
0.28
49
28
9
11
3


A49
0.47
84
3
1
11
1


R50
0.21
26
3
39
25
6


A51
0.95
0
0
1
0
98


A52
0.3
20
46
18
11
5


S53
0.37
70
9
8
11
2


L54
0.36
3
29
47
13
8


Q55
0.48
21
15
60
0
4


A56
0.33
12
27
24
35
3


S57
0.56
61
27
4
4
4


G58
0.4
16
8
23
2
51


D59
0.31
48
19
11
16
6


I60
0.31
10
37
30
17
6


F61
0.37
5
10
29
53
4


Y62
0.38
17
15
3
57
9


A63
0.34
12
17
28
40
2


I64
0.39
61
8
26
5
0


L65
0.61
1
3
89
2
5


R66
0.35
16
5
67
0
12


A67
0.43
8
13
65
7
6


L68
0.29
15
8
46
24
8


A69
0.61
2
1
6
90
1


E70
0.26
40
27
26
2
5


A71
0.4
4
2
19
69
5


E72
0.33
10
30
5
52
3


K73
0.28
37
16
30
16
2


L74
0.23
18
7
40
8
27


K75
0.3
30
9
39
22
0


K76
0.33
40
31
26
1
1


A77
0.31
41
17
33
4
5


G78
0.27
14
11
30
6
39


L79
0.27
14
24
45
11
6


V80
0.18
13
12
57
15
4


N81
0.29
52
19
17
10
3


S82
0.21
7
37
23
11
21


Q83
0.25
38
33
19
0
8


Q84
0.33
9
25
1
56
9


L85
0.39
11
23
60
0
6


D86
0.24
12
7
41
37
2


E87
0.25
56
19
6
1
18


L88
0.43
2
22
25
48
4


K89
0.26
45
27
23
4
2


R90
0.29
40
3
40
4
14


R91
0.26
45
17
20
6
12


L92
0.35
54
15
29
0
1


E93
0.44
42
47
4
1
6


E94
0.36
55
3
8
22
12


L95
0.29
21
29
12
1
36


A96
0.34
31
25
39
3
1


E97
0.36
64
24
3
3
5


E98
0.32
60
3
4
30
4


A99
0.41
4
12
48
0
35


R100
0.28
16
4
20
43
17


R101
0.34
26
11
51
0
11


K102
0.22
46
28
8
2
16


A103
0.3
49
23
6
20
2


E104
0.29
24
29
17
1
30


K105
0.57
12
11
5
0
73


L106
0.2
8
3
52
33
3


G107
0.26
41
14
31
9
5


D108
0.26
68
6
15
8
3


E109
0.22
49
6
6
10
30


F110
0.3
53
15
8
20
5


R111
0.31
52
10
6
9
23


L112
0.27
10
58
12
1
19


K113
0.38
29
45
6
2
18


L114
0.13
24
21
28
9
17


E115
0.11
42
25
13
8
12


Y116
0.37
41
23
0
31
6
















TABLE 12







Allowed sequence variability in X-CDP07 from single site


saturation mutagenesis










Conser-
% Probability














vation
Charged
Polar
Hydrophobic
Aromatic
Other


Residue
score
DEHRK
STNQ
ILVAM
FYW
GCP
















A1
0.31
27
25
22
0
25


D2
0.4
20
52
13
7
8


P3
0.42
26
27
40
0
7


K4
0.21
42
31
22
2
3


K5
0.26
31
27
5
6
31


V6
0.15
10
14
42
15
19


L7
0.27
10
7
33
4
47


D8
0.16
23
21
34
18
4


K9
0.27
48
33
14
0
5


A10
0.33
17
45
18
19
2


K11
0.22
44
25
8
1
22


D12
0.19
22
17
26
28
8


R13
0.36
48
31
7
5
10


A14
0.44
12
4
11
71
3


E15
0.24
64
8
13
5
10


N16
0.16
37
32
9
7
15


V17
0.55
2
5
50
1
41


V18
0.53
10
7
11
2
70


R19
0.31
39
4
5
18
34


K20
0.25
29
27
8
34
2


L21
0.47
45
0
11
42
2


K22
0.21
42
26
6
7
19


K23
0.34
30
15
46
0
9


E24
0.23
10
4
19
62
3


L25
0.29
12
5
50
16
16


E26
0.26
15
9
34
9
33


E27
0.27
23
6
60
5
6


L28
0.34
60
15
15
6
4


Y29
0.25
29
16
9
36
9


K30
0.55
20
9
5
1
65


E31
0.19
6
44
35
11
3


A32
0.25
9
40
28
6
17


R33
0.26
45
17
18
2
18


K34
0.77
8
5
1
85
0


L35
0.37
14
8
19
55
4


D36
0.13
29
18
43
6
5


L37
0.4
2
17
75
0
7


T38
0.17
33
31
12
10
14


Q39
0.27
24
39
24
5
8


E40
0.1
34
10
20
26
10


M41
0.34
10
7
49
30
3


R42
0.33
65
5
15
8
7


D43
0.17
30
13
10
19
28


R44
0.26
29
35
9
18
8


I45
0.64
76
1
4
19
0


R46
0.4
60
4
16
1
19


L47
0.8
89
4
5
0
2


A48
0.24
24
40
29
5
1


A49
0.41
10
23
59
4
4


I50
0.64
0
1
2
97
0


A51
0.57
0
1
98
0
1


A52
0.26
20
28
46
3
3


R53
0.38
61
8
10
1
19


I54
0.65
0
2
3
94
1


A55
0.43
19
52
5
4
21


A56
0.39
36
3
42
10
8


F57
0.44
39
3
16
40
1


G58
0.83
2
2
91
0
6


D59
0.37
58
16
6
17
3


I60
0.56
6
2
11
81
0


F61
0.33
2
12
31
44
10


H62
0.32
5
3
45
29
17


A63
0.64
2
7
10
80
1


I64
0.21
61
7
11
12
8


M65
0.64
96
1
2
0
0


E66
0.23
47
18
14
7
14


A67
0.3
23
41
12
22
2


L68
0.3
55
26
7
1
11


E69
0.18
25
7
22
43
4


E70
0.17
29
22
17
12
19


A71
0.4
39
13
10
1
37


R72
0.24
48
13
12
2
25


K73
0.33
61
17
15
4
4


L74
0.24
18
15
49
4
14


K75
0.28
58
9
14
13
6


K76
0.28
52
25
14
7
3


A77
0.45
62
10
14
11
4


G78
0.21
41
8
29
5
18


L79
0.26
53
9
23
1
14


V80
0.22
34
11
35
17
2


N81
0.25
17
20
6
32
26


S82
0.31
18
55
11
9
6


Q83
0.24
45
25
16
7
7


Q84
0.33
24
9
5
59
3


L85
0.45
6
9
9
17
59


D86
0.13
48
17
12
10
13


E87
0.2
47
5
9
34
6


L88
0.52
12
0
81
2
5


K89
0.54
20
12
67
0
0


R90
0.31
65
5
21
1
7


R91
0.36
41
10
32
1
16


L92
0.18
37
16
19
12
16


E93
0.29
61
14
16
6
2


E94
0.25
46
6
32
10
6


L95
0.11
25
26
24
19
7


D96
0.51
3
21
66
6
4


E97
0.3
25
36
35
0
3


E98
0.18
45
16
15
9
14


A99
0.26
21
33
30
0
16


A100
0.4
60
20
15
4
0


Q101
0.19
24
29
34
8
6


R102
0.19
43
10
19
16
13


A103
0.53
6
4
82
2
6


E104
0.36
49
12
26
0
13


K105
0.36
7
14
65
4
11


L106
0.31
13
4
42
22
18


G107
0.31
29
3
3
26
38


K108
0.38
61
9
10
20
0


E109
0.25
35
24
19
20
1


F110
0.3
3
10
31
35
21


E111
0.13
23
28
33
15
1


L112
0.24
19
14
32
19
15


K113
0.24
36
31
23
6
3


L114
0.25
29
9
41
3
17


E115
0.36
44
22
19
0
14


Y116
0.31
25
20
13
24
18
















TABLE 13







Allowed sequence variability in 10-CDP01 from single site


saturation mutagenesis










Conser-
% Probability














vation
Charged
Polar
Hydrophobic
Aromatic
Other


Residue
score
DEHRK
STNQ
ILVAM
FYW
GCP
















A1
0.25
14
19
45
16
5


D2
0.2
36
30
18
11
5


P3
0.21
4
27
14
26
29


K4
0.23
28
47
12
5
9


K5
0.16
25
34
14
11
16


V6
0.35
7
9
66
16
1


L7
0.31
2
27
57
3
11


D8
0.24
29
29
3
34
3


K9
0.18
38
28
21
12
0


A10
0.4
38
12
42
1
7


K11
0.18
33
40
16
3
7


D12
0.21
40
12
16
22
10


Q13
0.23
40
28
10
8
14


A14
0.27
9
25
51
1
14


E15
0.25
55
9
8
16
12


N16
0.22
33
42
15
8
3


R17
0.13
30
25
27
7
11


V18
0.47
6
2
79
6
7


R19
0.21
48
22
14
4
11


E20
0.26
46
6
27
16
5


L21
0.46
1
39
46
3
11


K22
0.22
32
40
16
12
0


Q23
0.28
41
34
18
0
6


E24
0.1
45
8
22
19
6


L25
0.43
24
5
54
2
14


E26
0.21
49
13
26
9
4


R27
0.31
50
13
19
5
13


L28
0.17
16
24
46
2
12


Y29
0.22
26
41
5
17
11


K30
0.17
19
44
17
13
7


E31
0.06
21
19
28
14
18


A32
0.17
27
22
25
7
19


R33
0.2
24
27
18
13
17


K34
0.19
40
41
8
0
11


L35
0.2
23
18
33
10
17


D36
0.19
26
48
14
7
5


L37
0.18
21
20
30
11
18


T38
0.26
8
29
20
1
42


Q39
0.21
24
8
10
45
13


E40
0.15
34
16
32
8
10


M41
0.14
22
12
36
20
10


R42
0.21
19
13
26
3
39


R43
0.08
17
16
24
27
17


K44
0.25
61
24
9
4
2


L45
0.22
9
16
27
21
27


E46
0.34
4
2
33
60
1


W47
0.35
10
2
55
29
4


R48
0.19
28
24
18
5
25


Y49
0.21
14
10
20
34
21


I50
0.14
17
27
46
4
6


A51
0.46
78
9
11
0
1


A52
0.16
12
22
40
12
14


M53
0.14
32
26
31
2
8


L54
0.21
14
17
50
1
17


K55
0.15
11
19
27
9
35


A56
0.11
14
18
26
15
26


I57
0.16
21
33
38
6
1


G58
0.85
2
92
3
1
2


D59
0.24
10
40
23
21
7


I60
0.2
5
24
36
25
11


L61
0.18
5
39
31
17
9


N62
0.21
12
16
32
1
40


A63
0.28
8
5
57
10
19


I64
0.13
29
23
25
21
2


A65
0.13
27
12
22
33
6


Q66
0.14
22
24
10
39
5


A67
0.18
26
19
31
3
20


E68
0.41
16
11
7
62
5


N69
0.18
27
31
37
2
3


E70
0.2
37
37
9
13
4


A71
0.47
71
6
20
1
2


D72
0.08
36
27
13
19
5


K73
0.3
72
13
7
4
5


L74
0.25
32
7
38
10
12


K75
0.31
68
24
3
2
3


K76
0.36
76
11
5
5
3


A77
0.25
23
18
47
3
8


G78
0.33
56
9
5
1
29


L79
0.12
13
15
33
16
22


V80
0.2
19
5
29
19
28


N81
0.17
43
32
8
15
2


S82
0.11
10
31
32
10
17


Q83
0.18
46
21
12
6
15


Q84
0.22
41
26
11
2
20


L85
0.12
20
15
44
5
17


D86
0.15
37
9
29
8
16


E87
0.15
44
22
14
7
12


L88
0.24
17
14
45
3
21


R89
0.16
33
16
14
3
34


R90
0.13
31
9
28
6
26


R91
0.18
32
16
13
18
22


L92
0.29
17
20
42
5
16


E93
0.11
49
16
21
5
9


E94
0.2
55
5
28
2
11


L95
0.2
39
12
37
1
11


A96
0.17
15
34
33
4
13


K97
0.35
67
17
9
1
6


E98
0.25
26
8
39
15
12


A99
0.24
25
22
29
19
5


A100
0.33
20
21
40
1
18


R101
0.1
33
31
20
6
11


K102
0.27
35
11
47
0
7


A103
0.34
11
19
46
10
13


H104
0.2
42
28
13
7
10


D105
0.15
29
22
23
10
15


Y106
0.29
37
12
2
34
15


G107
0.36
14
7
18
1
59


R108
0.22
45
24
13
11
8


E109
0.27
43
34
8
4
11


F110
0.31
4
5
45
27
19


Q111
0.24
39
37
4
16
4


L112
0.19
16
39
30
6
9


K113
0.29
45
27
20
7
1


L114
0.3
28
13
49
1
8


E115
0.22
57
14
16
8
5


Y116
0.31
23
4
8
24
41
















TABLE 14







Allowed sequence variability in F-CDP01 from single site


saturation mutagenesis










Conser-
% Probability














vation
Charged
Polar
Hydrophobic
Aromatic
Other


Residue
score
DEHRK
STNQ
ILVAM
FYW
GCP
















A1
0.04
33
13
28
17
10


D2
0.02
20
19
29
18
15


P3
0.03
21
24
20
21
14


K4
0.02
26
19
24
19
11


K5
ND
ND
ND
ND
ND
ND


V6
ND
ND
ND
ND
ND
ND


L7
0.07
19
16
33
24
8


D8
0.04
36
14
28
9
13


K9
0.02
27
19
23
20
10


A10
0.11
11
17
27
37
8


K11
0.05
24
20
26
23
7


D12
0.04
32
15
27
18
8


Q13
0.04
31
15
20
18
16


A14
0.09
9
21
37
23
10


E15
0.06
22
18
30
19
11


N16
0.05
31
32
20
8
8


R17
0.12
18
15
45
9
13


V18
0.13
14
23
45
7
11


R19
0.04
32
15
23
15
15


E20
0.04
24
23
34
11
8


L21
0.3
34
8
16
41
1


K22
0.08
30
20
16
25
9


Q23
0.06
37
28
18
12
5


K24
0.25
50
23
17
2
8


L25
0.22
20
8
14
50
9


E26
0.07
26
11
30
25
8


E27
0.04
23
24
29
17
8


L28
0.18
9
24
51
7
9


Y29
0.09
11
11
48
14
16


K30
0.07
32
26
22
16
4


E31
0.19
17
17
12
6
48


A32
0.08
16
8
32
33
10


R33
0.1
29
24
23
13
10


K34
0.08
35
23
20
11
11


L35
0.08
24
10
37
14
15


D36
0.03
22
26
23
11
19


L37
0.05
34
16
23
19
7


T38
0.03
28
26
21
10
14


Q39
0.07
31
28
26
2
13


E40
0.08
28
19
19
27
7


M41
0.1
16
10
34
29
11


R42
0.12
21
9
18
42
11


K43
0.06
25
35
27
3
10


K44
0.18
32
44
12
3
10


L45
0.22
8
11
65
5
12


Q46
0.11
26
26
12
7
28


Y47
0.47
3
3
82
3
9


A48
0.39
13
8
27
5
47


A49
0.29
42
6
5
44
3


I50
0.49
2
7
84
6
1


G51
0.33
17
7
22
3
51


A52
0.48
2
4
14
77
4


M53
0.23
3
10
30
23
34


L54
0.49
10
10
74
1
6


A55
0.37
9
8
36
1
46


A56
0.31
2
5
33
51
9


I57
0.38
19
51
26
3
0


G58
0.39
13
10
12
2
62


D59
0.2
33
15
30
12
10


I60
0.18
11
15
43
29
1


L61
0.39
8
3
81
3
5


N62
0.26
34
52
7
4
3


A63
0.22
6
13
67
3
11


I64
0.1
24
16
38
12
10


M65
0.2
11
13
58
17
2


Q66
0.25
44
32
4
1
18


A67
0.14
45
19
12
17
6


K68
0.07
29
21
17
19
13


Q69
0.12
42
15
18
10
15


E70
0.08
34
19
26
10
10


A71
0.2
15
26
26
1
32


D72
0.13
19
10
16
43
13


K73
0.04
26
18
20
11
24


L74
0.07
25
19
30
10
15


K75
0.05
32
18
26
9
15


K76
0.03
35
18
22
16
9


A77
0.07
36
23
16
15
9


G78
0.13
42
14
12
8
24


L79
0.03
17
20
31
19
13


V80
0.08
22
12
33
10
22


N81
0.07
30
27
19
15
9


S82
0.03
23
15
28
23
11


Q83
0.05
30
19
25
20
7


Q84
0.06
28
29
26
8
9


L85
0.03
31
18
29
6
16


D86
0.05
29
14
26
24
7


E87
0.04
31
24
29
6
10


L88
0.06
19
24
32
16
10


K89
0.07
27
8
23
32
9


R90
0.08
48
20
17
5
9


R91
0.07
35
8
21
26
10


L92
0.09
9
26
37
7
21


E93
0.09
21
16
41
8
14


E94
0.03
28
22
25
16
10


L95
0.02
23
26
23
16
12


K96
0.25
36
20
13
30
1


E97
0.29
23
57
15
1
5


E98
0.06
22
20
23
27
8


A99
0.14
18
17
36
22
7


L100
0.31
10
14
19
48
9


R101
0.12
32
35
18
7
8


K102
0.08
24
20
21
20
15


A103
0.21
6
14
60
14
5


H104
0.35
9
46
9
1
34


D105
0.31
12
10
17
8
53


Y106
0.07
20
27
29
9
15


G107
0.18
3
35
45
8
10


S108
0.21
54
29
3
3
12


E109
0.06
22
13
22
29
14


F110
0.08
9
16
27
5
13


Y111
0.13
10
24
43
4
20


L112
0.07
32
24
12
12
20


K113
0.21
26
17
20
3
34


L114
0.11
34
12
15
28
10


E115
0.13
22
37
22
2
16


Y116
0.13
39
34
12
4
11
















TABLE 15







Allowed sequence variability in W-CDP03 from single site


saturation mutagenesis










Conser-
% Probability














vation
Charged
Polar
Hydrophobic
Aromatic
Other


Residue
score
DEHRK
STNQ
ILVAM
FYW
GCP
















D1
0.14
20.5
18.0
19.3
27.5
14.7


P2
0.22
44.4
18.1
25.7
3.8
8.0


K3
0.13
17.9
32.4
32.2
10.4
7.0


K4
0.13
28.1
29.6
23.0
12.4
6.9


V5
0.22
4.4
26.8
54.8
13.3
0.6


F6
0.28
13.8
12.2
58.2
14.1
1.6


D7
0.16
18.3
3.7
36.0
23.8
18.3


E8
0.24
61.1
8.6
22.3
3.3
4.8


A9
0.56
8.7
2.0
48.1
40.7
0.4


K10
0.10
25.3
30.1
30.8
12.0
1.8


D11
0.09
43.9
17.9
10.3
11.4
16.4


R12
0.13
19.4
43.3
20.3
6.8
10.3


A13
0.28
21.4
31.8
42.8
1.8
2.2


E14
0.08
25.3
13.5
31.6
23.6
6.0


N15
0.20
13.5
25.4
23.1
33.8
4.3


N16
0.39
2.5
6.4
15.8
73.9
1.4


V17
0.11
30.0
17.6
32.3
12.2
7.8


R18
0.12
37.1
25.6
19.9
10.0
7.4


R19
0.27
19.7
47.9
28.1
1.6
2.7


L20
0.17
9.7
19.2
36.1
12.2
22.8


K21
0.22
16.3
42.5
25.9
10.5
4.7


Q22
0.06
13.0
17.9
24.6
26.6
17.9


K23
0.21
31.0
9.5
49.1
6.0
4.4


L24
0.20
34.5
29.2
23.4
9.7
3.1


E25
0.25
13.7
31.2
36.1
11.7
7.3


E26
0.09
28.9
21.0
29.5
14.4
6.2


L27
0.19
18.9
3.0
33.8
34.4
9.9


Y28
0.12
22.1
14.3
29.4
28.6
5.6


K29
0.05
20.4
24.3
28.2
17.0
10.1


E30
0.12
34.6
33.4
14.7
11.1
6.2


A31
0.22
7.9
5.3
44.3
28.5
14.1


R32
0.07
28.8
26.5
23.8
8.7
12.2


K33
0.08
24.8
10.3
41.1
11.4
12.4


K34
0.07
27.5
24.0
25.5
6.4
16.5


D35
0.06
28.4
23.7
15.3
10.4
22.1


L36
0.10
39.8
13.3
22.8
20.3
3.9


T37
0.15
25.8
48.3
12.0
2.4
11.5


Q38
0.18
43.9
13.9
17.2
6.5
18.5


E39
0.05
32.3
21.1
21.9
13.1
11.6


E40
0.15
30.0
5.9
25.4
29.9
8.8


R41
0.11
33.8
26.4
17.5
12.6
9.7


E42
0.08
40.7
22.1
19.8
6.0
11.3


K43
0.15
29.0
33.3
16.8
16.1
4.8


L44
0.12
32.3
10.9
20.1
30.8
5.8


K45
0.12
22.5
15.5
43.8
11.7
6.5


E46
0.10
19.4
29.5
34.3
5.0
11.4


K47
0.07
25.6
18.9
28.4
21.5
5.6


Y48
0.24
27.8
6.6
51.9
7.1
6.5


K49
0.22
22.8
16.0
44.8
5.5
10.8


T50
0.21
10.6
40.6
21.5
6.9
20.4


A51
0.13
26.2
31.7
24.2
13.1
4.9


M52
0.23
11.0
3.5
42.3
39.3
3.9


A53
0.29
44.3
20.2
11.5
22.7
1.3


A54
0.36
10.7
4.7
76.4
0.2
8.0


A55
0.21
4.6
12.9
33.3
37.5
11.7


A56
0.24
8.0
2.6
71.7
12.5
5.3


L57
0.66
3.9
0.4
2.1
93.0
0.6


A58
0.18
26.4
25.0
28.6
6.1
13.9


A59
0.68
0.4
3.7
94.7
0.8
0.5


I60
0.57
36.8
1.3
6.5
54.6
0.8


G61
0.25
15.1
33.1
12.8
24.0
15.1


D62
0.27
25.4
4.7
12.8
24.0
33.1


A63
0.46
1.3
0.3
40.0
54.2
4.2


F64
0.70
8.4
1.5
83.5
4.6
2.0


N65
0.20
23.1
19.4
35.2
18.8
3.6


A66
0.24
7.1
16.4
28.1
13.9
34.5


L67
0.23
25.6
10.2
28.6
33.8
1.8


L68
0.34
39.8
2.9
36.4
15.7
3.3


K69
0.17
26.6
15.0
25.9
29.3
3.2


A70
0.21
2.5
9.4
50.0
21.9
16.1


R71
0.40
31.2
46.5
13.9
3.8
4.6


K72
0.27
47.9
15.0
25.3
9.0
23


L73
0.23
32.3
6.0
46.0
10.7
5.1


H74
0.20
23.8
3.7
16.4
42.7
13.4


K75
0.26
46.0
9.2
33.4
9.2
2.2


N76
0.09
27.5
14.4
37.5
16.3
4.2


G77
0.20
14.8
30.9
12.0
27.0
15.2


Q78
0.09
18.1
27.4
26.2
9.9
18.3


V79
0.24
5.0
17.0
62.6
12.8
2.6


N80
0.26
14.0
51.1
23.8
1.4
9.7


E81
0.08
19.5
21.9
38.7
12.2
7.7


Q82
0.08
22.1
19.4
27.5
16.9
14.1


Q83
0.14
34.2
15.5
9.5
16.2
24.5


L84
0.12
25.0
8.2
34.9
23.6
8.3


E85
0.07
23.4
10.7
31.2
29.5
5.1


E86
0.09
32.6
19.1
22.0
20.4
5.9


L87
0.30
18.6
5.1
49.3
24.8
2.2


A88
0.31
10.1
44.2
9.4
23.3
13.0


R89
0.23
28.8
20.0
21.1
24.7
5.5


R90
0.10
25.0
21.7
21.4
15.4
16.5


L91
0.21
20.0
7.9
39.6
8.8
23.7


Q92
0.40
1.4
12.7
76.7
6.0
3.2


E93
0.05
25.2
21.8
28.3
19.4
5.3


L94
0.08
18.3
39.9
24.3
6.6
11.0


A95
0.62
2.4
1.7
7.5
84.5
3.8


K96
0.10
27.2
23.0
30.5
5.6
13.7


E97
0.10
28.8
14.3
32.0
7.5
17.4


A98
0.24
10.1
19.9
46.9
16.7
6.5


F99
0.25
16.4
4.0
45.9
27.3
6.4


Q100
0.19
43.7
13.7
13.5
1.3
27.8


K101
0.12
31.5
9.0
38.9
4.6
16.0


A102
0.32
0.6
2.8
70.7
15.7
10.1


K103
0.28
37.3
4.2
52.0
1.6
4.9


D104
0.04
28.1
16.1
29.3
9.7
16.9


Y105
0.12
18.2
7.8
27.9
37.0
9.2


A106
0.19
48.9
8.0
38.6
0.9
3.5


N107
0.11
25.8
22.3
38.3
10.5
3.0


E108
0.19
41.2
17.2
32.7
3.6
5.3


F109
0.16
46.4
13.9
14.9
13.9
11.0


E110
0.12
36.5
10.9
29.3
18.3
5.0


Y111
0.24
16.1
6.8
47.4
25.5
4.3


K112
0.11
27.3
8.5
45.1
5.4
13.8


L113
0.14
36.2
18.2
19.7
16.8
9.1


E114
0.08
31.0
14.2
31.9
16.1
6.8


Y115
0.10
17.3
8.8
34.7
23.3
15.9
















TABLE 16







Allowable residues for BINDI based on


experimental saturation mutagenesis data


(enrichment ratios of 0 or greater after one


round of sorting). (SEQ ID NO: 7)










Residue
Allowable Residues







A1
A/E/G/H/I/K/M/P/R/S/T/V/W/Y



 



D2
A/C/D/E/F/G/H/I/K/L/M/N/P/Q/R/




S/T/V/W/Y



 



W3
A/C/D/E/F/G/H/K/L/M/N/P/Q/R/S/




T/V/W/Y



 



K4
A/E/G/H/I/K/M/N/P/Q/R/T/V/W



 



K5
F/G/I/K/L/Q/R/T/V/W



 



V6
A/F/G/I/L/P/S/V/W



 



L7
A/D/E/G/I/L/M/Q/R/S/T/V/W/Y



 



D8
A/C/D/F/G/I/K/L/N/P/Q/R/S/V/W/Y



 



K9
H/K/L/N/Q/R/W



 



A10
A/H/S/T



 



K11
A/D/E/G/H/K/N/Q/R/S/T/Y



 



D12
A/D/E/F/G/H/K/L/M/N/Q/R/S/T/




V/W/Y



 



I13
D/E/G/I/K/L/M/N/Q/R/S/T/V/W/Y



 



A14
A/C/I/L/M/N/Q/S/T/V



 



E15
A/D/E/M/N/R/V/W/Y



 



N16
A/D/F/G/H/I/K/L/M/N/P/Q/R/S/T/




V/W/Y



 



R17
A/C/E/G/H/I/K/L/M/P/R/S/T/V



 



V18
A/I/K/M/T/V



 



R19
A/C/D/E/F/G/K/L/M/N/Q/R/T/V/




W/Y



 



E20
A/D/E/F/G/I/K/L/M/N/Q/R/S/T/V/




W/Y



 



L21
F/H/I/L/M/Q/T/Y



 



K22
A/C/H/I/K/Q/R



 



Q23
A/C/E/F/G/H/I/M/N/Q/R/S/T/W/Y



 



K24
A/D/G/H/I/K/N/Q/R/T/Y



 



L25
I/L/M/Q



 



E26
A/C/D/E/G/I/K/N/Q/R/S/T/V/W



 



E27
A/C/D/E/F/G/H/I/K/L/M/N/Q/R/S/




T/V/W/Y



 



F28
C/F/H/I/K/L/M/N/P/R/T/V/Y



 



Y29
A/D/E/H/I/L/P/Q/R/W/Y



 



K30
A/E/F/G/H/K/L/M/N/Q/R/S/T/W/Y



 



E31
A/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/




V/W/Y



 



A32
A/F/G/H/K/L/N/P/R/S/T/Y



 



M33
F/H/I/K/L/M/P/Q/R/T/V/Y



 



K34
C/H/I/K/L/M/Q/R/S/T/V/Y



 



L35
A/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/




T/V/W



 



D36
A/C/D/E/G/H/K/L/M/N/Q/R/S/T/




V/W/Y



 



L37
A/D/E/F/H/I/K/L/M/N/P/Q/R/S/T/




V/W/Y



 



T38
A/D/E/G/K/N/P/Q/R/S/T



 



Q39
A/D/E/G/K/N/P/Q/R/S/T/V



 



E40
A/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/




T/V



 



M41
F/G/H/K/L/M/N/Q/R/T/V/W/Y



 



R42
K/R



 



R43
R



 



K44
K/R



 



L45
F/G/I/L/Q/V/W/Y



 



M46
D/E/M/N/Q/T



 



L47
F/L/M/W



 



R48
R



 



W49
E/F/W/Y



 



I50
I



 



A51
A/G



 



A52
A/F/I/Q



 



M53
D/H/L/M/N/W



 



L54
I/L



 



M55
G/I/M/S/V



 



A56
A/C/F/G/I/L/M/P/S/T/V



 



I57
A/I/M/S/T/V



 



G58
G



 



D59
D



 



I60
I/L/M



 



F61
F/M/W/Y



 



N62
A/D/F/G/I/L/M/N/Q/S/T/V/W



 



A63
A/F/I/L/M/T/V/Y



 



I64
A/H/I/M/Y



 



R65
R/Y



 



Q66
A/F/I/K/L/M/Q/R/V/W/Y



 



A67
A/G



 



K68
K/Q/R



 



Q69
A/F/G/I/K/L/N/Q/R/S/T/V/W/Y



 



E70
A/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/




V/W/Y



 



A71
A/G/I/M/S



 



D72
A/D/E/F/G/H/I/L/M/Q/S/T/V/W/Y



 



K73
F/K/R/Y



 



L74
A/F/L/M/R/W/Y



 



K75
A/F/H/K/N/R/S/T/Y



 



K76
I/K/N/R/W



 



A77
A/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y



 



G78
A/D/G/H/Q/R/S/T



 



L79
A/K/L/R/T/V/W/Y



 



V80
I/L/M/V



 



N81
A/D/E/K/N/Q/R/S/T



 



S82
D/E/G/K/M/P/Q/R/S/T/V



 



Q83
A/D/E/F/H/I/L/N/Q/R/S/T/V



 



Q84
D/E/H/M/N/Q/T/Y



 



L85
A/F/G/H/L/M/R/T/V/W/Y



 



D86
D/E/F/G/I/K/L/N/Q/S/T/V/W/Y



 



E87
A/E/F/I/K/L/M/Q/T/W



 



L88
A/F/I/L/M/T/V



 



K89
A/I/K/Q/R/V



 



R90
A/G/I/K/L/M/N/Q/R/S/T/V/W/Y



 



R91
A/C/D/E/G/H/K/L/N/Q/R/S/T/V/Y



 



L92
I/L



 



E93
A/D/E/H/I/M/N/Q/T



 



E94
A/C/D/E/F/G/H/I/K/L/M/N/Q/R/S/




T/V/Y



 



L95
A/L/T/V



 



K96
K/Q/R



 



E97
A/D/E/G/H/Q/S/T/V



 



E98
A/D/E/F/H/K/M/N/P/Q/R/S/W/Y



 



A99
A/S/V



 



S100
A/G/N/Q/S/T



 



R101
K/R



 



K102
K/R



 



A103
A/I/M/N/S/T/V



 



R104
D/K/N/R



 



D105
A/D/E/F/G/H/K/L/M/N/R/T/V/W/Y



 



Y106
A/E/G/H/I/T/Y



 



G107
D/G/S



 



R108
K/Q/R



 



E109
A/D/E/F/G/H/K/L/R/S/V/W



 



F110
F



 



Q111
D/E/H/M/Q



 



L112
A/D/F/I/L/P/Q/R



 



K113
K/Q



 



L114
A/H/K/L/M/P/R/S/T/V/Y



 



E115
D/E/P/R/T



 



Y116
D/E/G/H/K/Q/R/T/Y

















TABLE 17







Allowable residues for 2-INDI based on


experimental saturation mutagenesis data


(enrichment ratios of −1 or greater after two


rounds of sorting). (SEQ ID NO: 8)










Residue
Allowable Residues







A1
A/E/G/P/S/T/V



 



D2
A/D/E/G/H/K/N/S/T/V/Y



 



P3
A/E/F/I/K/L/P/Q/R/S/T/V



 



K4
E/H/K/N



 



K5
D/E/K/M/Q



 



V6
D/V



 



L7
C/D/L/Y



 



D8
D/L/N/W/Y



 



K9
E/K/Q/T/V



 



A10
A/C/F/I/L/M/P/S/T/V/W



 



K11
F/G/K/M/N/Q/S



 



D12
D/E/H/N/P



 



E13
E/F/H/K/R/V



 



A14
A/C/D/F/H/I/L/M/P/W



 



E15
E/F/S



 



N16
K/N/R/W/Y



 



R17
C/K/N/R



 



V18
M/P/V



 



R19
P/R



 



E20
A/C/E/F/G/H/I/K/L/M/N/R/S/T/V/Y



 



L21
F/K/L/M/R/V/Y



 



K22
K/N



 



Q23
K/P/Q/R/W



 



K24
K/R



 



L25
F/I/K/L/R/W/Y



 



E26
E/M/T



 



E27
E/H/I/R/W



 



L28
I/L/N



 



Y29
C/G/H/Y



 



K30
E/K/N



 



E31
E/M/R/T/W



 



A32
A/F/I/L/M/R/T/V/W/Y



 



R33
R



 



K34
K



 



L35
E/H/I/L/P/T/Y



 



D36
D/E/N/V/Y



 



L37
A/E/L/M/V



 



T38
A/I/N/R/T



 



Q39
H/P/Q



 



E40
D/E/V



 



M41
M/R



 



R42
D/H/P/Q/R/Y



 



Q43
H/K/Q/V



 



E44
E/L/W



 



L45
K/L/M/V



 



V46
A/C/D/E/F/G/H/K/L/M/N/R/T/V/W



 



D47
C/D/F/H/I/L/M/V/W/Y



 



K48
K



 



A49
A/G/H/K/N/Q/R/T/W/Y



 



R50
A/D/E/G/L/M/R/V/W



 



A51
A/G



 



A52
A/N/R



 



S53
D/H/I/K/M/N/R/S/W



 



L54
L/N



 



Q55
A/K/Q



 



A56
A/C/F/H/K/L/M/N/Q/S/V/W/Y



 



S57
A/G/H/N/S/Y



 



G58
G



 



D59
D/N



 



I60
C/E/F/G/I/L/M/N/Q/T



 



F61
F



 



Y62
Y



 



A63
A/F/T



 



I64
D/I/R



 



L65
L/M



 



R66
C/I/K/L/R/V



 



A67
A



 



L68
G/I/L/M/N/R/W/Y



 



A69
A/F/M/W/Y



 



E70
E/S



 



A71
A/C/F/L/M/W



 



E72
E/F/S/T/W



 



K73
K/M



 



L74
L



 



K75
K/V/W



 



K76
I/K



 



A77
A/K



 



G78
G



 



L79
L/M/S



 



V80
A/M/V



 



N81
A/K/N/R



 



S82
Q/S



 



Q83
L/Q/R



 



Q84
C/F/Q/W



 



L85
I/L/T



 



D86
A/D/I/L/M/Q/R/V/W/Y



 



E87
E



 



L88
F/L/Q/V



 



K89
K/L



 



R90
L/R



 



R91
H/K/L/Q/R



 



L92
D/I/K/L/N/R/T/V



 



E93
D/E/Q



 



E94
E/W



 



L95
D/L/N/P/S



 



A96
A/H/I/Q/V



 



E97
E



 



E98
D/E/F



 



A99
A/P/V



 



R100
A/C/F/G/K/R/V/Y



 



R101
L/Q/R/V



 



K102
K



 



A103
A/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/




V/W/Y



 



E104
A/D/E/G/P/S



 



K105
K/P/Q/S



 



L106
A/F/I/L/V/W



 



G107
D/G/I/K/M/Q/R/T/W



 



D108
A/D/E/H/K/N/R/V/Y



 



E109
C/E/H/K/P/R/W



 



F110
C/F/H/Q/R/W



 



R111
H/R



 



L112
G/L/N/P/Q/R/S



 



K113
H/K/N/P



 



L114
A/C/F/I/L/M/P/Q/R/S/W



 



E115
A/C/E/G/H/K/N/Q/R/S/V/Y



 



Y116
D/F/H/N/S/Y

















TABLE 18







Allowable residues for XINDI based on


experimental saturation mutagenesis data


(enrichment ratios of −1 or greater after two


rounds of sorting). (SEQ ID NO: 9)










Residue
Allowable Residues







A1
A/E/G/P/R/S/T/V



 



D2
A/D/E/G/H/N/S/V/Y



 



P3
A/L/P/Q/R/S/T



 



K4
A/E/I/K/N/Q/R/T



 



K5
C/K/N/Q/R



 



V6
G/I/M/S/V/W/Y



 



L7
C/G/I/L



 



D8
D/F/H/M/N/S/T/V/Y



 



K9
K



 



A10
A/E/H/Q/V/W/Y



 



K11
C/G/K/Q/R



 



D12
D/E/L/M/P/R/S/W/Y



 



R13
R/S



 



A14
A/D/F/G/H/L/M/N/R/V/Y



 



E15
E/R



 



N16
C/H/K/N



 



V17
A/G/T/V



 



V18
K/P/R/V



 



R19
H/P/R/Y



 



K20
E/K/N/Q/T/W



 



L21
F/H/L/R/Y



 



K22
K



 



K23
G/H/K/M/N/Q/V



 



E24
A/C/E/F/G/H/I/K/L/M/N/P/Q/R/S/




V/W/Y



 



L25
L/P



 



E26
A/D/E/G/K/N/P/V/Y



 



E27
E/G/I/K/L/M/R/S/V/W



 



L28
E/F/G/I/K/L/M/Q/R/S/T/V/Y



 



Y29
F/H/N/Y



 



K30
C/K/N/R



 



E31
A/C/D/E/F/G/H/I/K/L/M/N/P/Q/R/




S/T/V/W/Y



 



A32
A/G/S/T/V



 



R33
R



 



K34
F/K/N



 



L35
L/R/W/Y



 



D36
A/C/D/E/H/I/K/L/M/P/Q/R/T/V/W



 



L37
A/L/M/N



 



T38
K/N/T



 



Q39
H/I/K/Q/R/S



 



E40
E/F/G/H/I/K/M/N/P/R/T/V/W/Y



 



M41
F/I/M



 



R42
E/R



 



D43
A/D/F/G/N/P/R/W



 



R44
Q/R/Y



 



I45
F/I/K/L/M/N/R/V/W/Y



 



R46
R



 



L47
L/M/P/R/T



 



A48
A/I/K/L/Q/R/S/T/V/Y



 



A49
A



 



I50
F/I/L/W/Y



 



A51
A/E/G/I/L/M/T/V



 



A52
A/H/I/K/L/M/N/Q/R/W



 



R53
R



 



I54
F/I/W/Y



 



A55
A/G/K/P/Q/R/W



 



A56
A/F/H/I/K/L/M/P/S/T/V/W



 



F57
F/H



 



G58
A/G



 



D59
D



 



I60
D/E/F/I/L/Y



 



F61
F



 



H62
A/C/D/F/G/H/L/R/S/V/W/Y



 



A63
A/F/L/S/T/V/W



 



I64
A/D/E/G/I/K/L/R/S/W/Y



 



M65
H/I/K/L/M/R/T



 



E66
A/D/E/G/H/I/K/L/P/Q/R/S/T/V/W/Y



 



A67
A/F/N/R/W



 



L68
A/D/G/H/I/K/L/M/N/P/R/S/T



 



E69
A/D/E/F/G/K/L/M/R/S/T/W/Y



 



E70
A/C/E/F/G/I/P/Q/R/S/T/V/W



 



A71
A/G/P/R/T



 



R72
R



 



K73
K



 



L74
K/L/M/P/Q/R/V



 



K75
K/R



 



K76
K



 



A77
A/K/T/W



 



G78
G/I/K/L/R/S



 



L79
E/G/I/K/L/M/R/S



 



V80
K/N/V/W



 



N81
G/N/W



 



S82
K/Q/R/S/Y



 



Q83
K/Q



 



Q84
F/K/L/Q/R/W/Y



 



L85
C/L/S/Y



 



D86
D/E/G/K/R/T



 



E87
E/K/R/W/Y



 



L88
I/L/M/R



 



K89
K/L/N



 



R90
R



 



R91
L/R



 



L92
G/H/L/R/T/V/Y



 



E93
A/E/F/G/H/I/K/L/M/Q/R/S/T/V/W/Y



 



E94
E



 



L95
E/K/L/M/S/Y



 



D96
D/F/I/P/S/T/V/Y



 



E97
E/L/S



 



E98
C/E/H/M/Q/R



 



A99
A/G/K/M/Q/T



 



A100
A/E/F/H/I/K/L/Q/T/V/Y



 



Q101
A/D/L/Q/T/W



 



R102
R



 



A103
A/C/I/K/L/V



 



E104
A/E/G/K/Q/V



 



K105
A/C/K/L/M/S



 



L106
L/Y



 



G107
G/W



 



K108
K/R/W



 



E109
E/N/R/W



 



F110
C/F/I/Y



 



E111
A/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/




V/W/Y



 



L112
F/L/M/R/T



 



K113
K



 



L114
K/L/M/P



 



E115
A/D/E/G/K/Q/V



 



Y116
C/D/F/H/L/N/S/Y

















TABLE 19







Allowable residues for 10-INDI based on


experimental saturation mutagenesis data


(enrichment ratios of −1 or greater after two


rounds of sorting). (SEQ ID NO: 10)










Residue
Allowable Residues







A1
A/D/E/F/M/S/T/V



 



D2
A/D/E/G/H/L/M/N/R/S/Y



 



P3
C/F/G/L/P/Q/R/S/T/V



 



K4
E/G/I/K/N/Q/R/S/T/W



 



K5
A/E/F/K/L/N/P/Q/T/W



 



V6
A/D/F/I/S/V



 



L7
G/L/M/P/Q/T/V



 



D8
A/D/E/G/H/N/R/S/T/W/Y



 



K9
A/E/F/I/K/L/N/Q/R/T/Y



 



A10
A/E



 



K11
E/G/K/L/M/N/Q/R/S/T



 



D12
A/C/D/E/F/G/H/N/V/Y



 



Q13
F/G/H/K/P/Q/R/V



 



A14
A/C/E/G/L/S/T/V



 



E15
A/C/D/E/K/S/W/Y



 



N16
D/I/K/N/T



 



R17
A/C/F/H/L/M/N/R/S/T/V/Y



 



V18
V



 



R19
A/C/G/H/K/R/S/T



 



E20
A/D/E/G/K/Q/V/W/Y



 



L21
L/M/P/T



 



K22
A/E/F/I/K/N/Q/T/Y



 



Q23
A/H/K/N/P/Q/R/V



 



E24
A/C/D/E/F/G/H/I/K/L/M/Q/R/T/V/Y



 



L25
L/M/P/R



 



E26
D/E/F/G/I/K/M/N/R



 



R27
C/H/L/R/S



 



L28
L/M/N/R



 



Y29
C/D/H/N/S/Y



 



K30
K/M/N/Q/T/W



 



E31
A/D/E/F/G/K/L/M/P/Q/T/W



 



A32
A/E/G/M/P/S/T



 



R33
C/H/I/L/N/R



 



K34
D/G/H/K/N/Q/T



 



L35
L/M/Q/R



 



D36
A/D/H/K/N/Q/R/T/V/Y



 



L37
L/M/P/Q/R



 



T38
A/G/N/P/T



 



Q39
F/G/H/K/L/M/P/Q/R/T/W/Y



 



E40
A/D/E/G/K/Q



 



M41
C/F/I/K/L/M/R/S/V/W



 



R42
C/G/H/L/P/R/S



 



R43
A/C/D/F/G/H/I/L/N/P/Q/R/V/W/Y



 



K44
K



 



L45
L



 



E46
A/C/D/E/F/G/H/I/L/M/N/P/Q/S/T/




V/W/Y



 



W47
F/H/I/K/L/M/P/R/T/V/W



 



R48
D/E/G/Q/R



 



Y49
F/Y



 



I50
I/L



 



A51
A/D/E/G/H/I/K/L/M/N/P/Q/R/S/T/




V/Y



 



A52
A/G/I/T



 



M53
M/N



 



L54
I/L



 



K55
F/G/K/M/P/S



 



A56
A



 



I57
I



 



G58
A/C/F/G/P/R/S/W



 



D59
A/C/D/E/F/G/H/I/K/L/M/N/P/Q/R/




S/T/V/W/Y



 



I60
I/W



 



L61
A/L/M/P/S/T/V/W



 



N62
A/G/M/N/P/Q/S



 



A63
A/F/I/L/P



 



I64
I/R



 



A65
A/E/F/L/W/Y



 



Q66
F/N/Q/Y



 



A67
A



 



E68
C/E/G/H/N/R/S/T/V/W/Y



 



N69
I/N



 



E70
E



 



A71
A/K/R/V



 



D72
D/F/G/H/K/M/N/Q/R/S/T/V/W/Y



 



K73
E/K



 



L74
K/L



 



K75
K



 



K76
E/H/K



 



A77
A



 



G78
D/G



 



L79
C/F/G/L/M/P/Q/R/S/V/W



 



V80
A/C/D/F/G/I/V/Y



 



N81
D/H/I/K/N/S/T/Y



 



S82
A/C/F/I/L/N/P/S/T/Y



 



Q83
E/F/H/K/L/P/Q/R



 



Q84
A/E/H/K/P/Q/R



 



L85
A/K/L/M/P/Q/R/V



 



D86
A/D/E/G/L/N/R/V/Y



 



E87
E/G/K/Q



 



L88
L/M/P/R/T



 



R89
A/C/G/H/P/Q/R



 



R90
C/G/I/L/P/R/V



 



R91
C/F/H/P/R/S/V/Y



 



L92
F/L/M/P/Q/R



 



E93
A/D/E/G/H/I/K/L/M/N/P/Q/R/S/T/




V/Y



 



E94
D/E/G/I/K/L/P/R/V



 



L95
A/E/G/K/L/M/P/R/T/V



 



A96
A/C/E/G/M/P/Q/S/T/V



 



K97
A/D/E/G/H/K/N/Q/R/S/T/Y



 



E98
C/D/E/F/G/M/Q/S/V/W



 



A99
A/D/F/H/M/P/Q/S/T/V



 



A100
A/D/G/S/T/V



 



R101
A/C/D/E/G/H/I/L/M/N/Q/R/S/T/V/Y



 



K102
A/E/G/I/K/M/R/S/T



 



A103
A/E/F/G/S/T



 



H104
D/H/K/M/N/P/Q/R



 



D105
A/C/D/E/G/L/N/Q/S/V/Y



 



Y106
C/D/F/H/T/Y



 



G107
C/D/G/L



 



R108
C/E/H/L/R/S/T/Y



 



E109
D/E/K/P/T



 



F110
C/F/I/L/S/V/Y



 



Q111
E/F/H/K/Q/R/S/Y



 



L112
H/I/L/N/P/Q/R/S/T



 



K113
A/E/H/I/K/N/Q/Y



 



L114
E/L/M/P/Q/V



 



E115
D/E/G/H/K/L/N/S/V/W



 



Y116
C/D/G/H/L/R/Y

















TABLE 20







Allowable residues for FINDI based on


experimental saturation mutagenesis data


(enrichment ratios of −1 or greater after two


rounds of sorting). (SEQ ID NO: 11)










Residue
Allowable Residues







A1
A/D/E/F/M/S/T/V



 



D2
A/D/E/G/H/L/M/N/R/S/Y



 



P3
C/F/G/L/P/Q/R/S/T/V



 



K4
E/G/I/K/N/Q/R/S/T/W



 



K5
A/E/F/K/L/N/P/Q/T/W



 



V6
A/D/F/I/S/V



 



L7
G/L/M/P/Q/T/V



 



D8
A/D/E/G/H/N/R/S/T/W/Y



 



K9
A/E/F/I/K/L/N/Q/R/T/Y



 



A10
A/E



 



K11
E/G/K/L/M/N/Q/R/S/T



 



D12
A/C/D/E/F/G/H/N/V/Y



 



Q13
F/G/H/K/P/Q/R/V



 



A14
A/C/E/G/L/S/T/V



 



E15
A/C/D/E/K/S/W/Y



 



N16
D/I/K/N/T



 



R17
A/C/F/H/L/M/N/R/S/T/V/Y



 



V18
V



 



R19
A/C/G/H/K/R/S/T



 



E20
A/D/E/G/K/Q/V/W/Y



 



L21
L/M/P/T



 



K22
A/E/F/I/K/N/Q/T/Y



 



Q23
A/H/K/N/P/Q/R/V



 



K24
A/C/D/E/F/G/H/I/K/L/M/Q/R/T/V/Y



 



L25
L/M/P/R



 



E26
D/E/F/G/I/K/M/N/R



 



E27
C/H/L/R/S



 



L28
L/M/N/R



 



Y29
C/D/H/N/S/Y



 



K30
K/M/N/Q/T/W



 



E31
A/D/E/F/G/K/L/M/P/Q/T/W



 



A32
A/E/G/M/P/S/T



 



R33
C/H/I/L/N/R



 



K34
D/G/H/K/N/Q/T



 



L35
L/M/Q/R



 



D36
A/D/H/K/N/Q/R/T/V/Y



 



L37
L/M/P/Q/R



 



T38
A/G/N/P/T



 



Q39
F/G/H/K/L/M/P/Q/R/T/W/Y



 



E40
A/D/E/G/K/Q



 



M41
C/F/I/K/L/M/R/S/V/W



 



R42
C/G/H/L/P/R/S



 



K43
A/C/D/F/G/H/I/L/N/P/Q/R/V/W/Y



 



K44
K



 



L45
L



 



Q46
A/C/D/E/F/G/H/I/L/M/N/P/Q/S/T/




V/W/Y



 



Y47
F/H/I/K/L/M/P/R/T/V/W



 



A48
D/E/G/Q/R



 



A49
F/Y



 



I50
I/L



 



G51
A/D/E/G/H/I/K/L/M/N/P/Q/R/S/T/




V/Y



 



A52
A/G/I/T



 



M53
M/N



 



L54
I/L



 



A55
F/G/K/M/P/S



 



A56
A



 



I57
I



 



G58
A/C/F/G/P/R/S/W



 



D59
A/C/D/E/F/G/H/I/K/L/M/N/P/Q/R/




S/T/V/W/Y



 



I60
I/W



 



L61
A/L/M/P/S/T/V/W



 



N62
A/G/M/N/P/Q/S



 



A63
A/F/I/L/P



 



I64
I/R



 



M65
A/E/F/L/W/Y



 



Q66
F/N/Q/Y



 



A67
A



 



K68
C/E/G/H/N/R/S/T/V/W/Y



 



Q69
I/N



 



E70
E



 



A71
A/K/R/V



 



D72
D/F/G/H/K/M/N/Q/R/S/T/V/W/Y



 



K73
E/K



 



L74
K/L



 



K75
K



 



K76
E/H/K



 



A77
A



 



G78
D/G



 



L79
C/F/G/L/M/P/Q/R/S/V/W



 



V80
A/C/D/F/G/I/V/Y



 



N81
D/H/I/K/N/S/T/Y



 



S82
A/C/F/I/L/N/P/S/T/Y



 



Q83
E/F/H/K/L/P/Q/R



 



Q84
A/E/H/K/P/Q/R



 



L85
A/K/L/M/P/Q/R/V



 



D86
A/D/E/G/L/N/R/V/Y



 



E87
E/G/K/Q



 



L88
L/M/P/R/T



 



K89
A/C/G/H/P/Q/R



 



R90
C/G/I/L/P/R/V



 



R91
C/F/H/P/R/S/V/Y



 



L92
F/L/M/P/Q/R



 



E93
A/D/E/G/H/I/K/L/M/N/P/Q/R/S/T/




V/Y



 



E94
D/E/G/I/K/L/P/R/V



 



L95
A/E/G/K/L/M/P/R/T/V



 



K96
A/C/E/G/M/P/Q/S/T/V



 



E97
A/D/E/G/H/K/N/Q/R/S/T/Y



 



E98
C/D/E/F/G/M/Q/S/V/W



 



A99
A/D/F/H/M/P/Q/S/T/V



 



L100
A/D/G/S/T/V



 



R101
A/C/D/E/G/H/I/L/M/N/Q/R/S/T/V/Y



 



K102
A/E/G/I/K/M/R/S/T



 



A103
A/E/F/G/S/T



 



H104
D/H/K/M/N/P/Q/R



 



D105
A/C/D/E/G/L/N/Q/S/V/Y



 



Y106
C/D/F/H/T/Y



 



G107
C/D/G/L



 



S108
C/E/H/L/R/S/T/Y



 



E109
D/E/K/P/T



 



F110
C/F/I/L/S/V/Y



 



Y111
E/F/H/K/Q/R/S/Y



 



L112
H/I/L/N/P/Q/R/S/T



 



K113
A/E/H/I/K/N/Q/Y



 



L114
E/L/M/P/Q/V



 



E115
D/E/G/H/K/L/N/S/V/W



 



Y116
C/D/G/H/L/R/Y

















TABLE 21







Allowable residues for MIND1 (SEQ ID NO: 12)








Residue
Allowable Residues





A1
A/E/G/H/I/K/M/P/R/S/T/V/W/Y


 


D2
A/C/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y


 


W3
A/C/D/E/F/G/H/K/L/M/N/P/Q/R/S/T/V/W/Y


 


K4
A/E/G/H/I/K/M/N/P/Q/R/T/V/W


 


K5
F/G/I/K/L/Q/R/T/V/W


 


V6
A/F/G/I/L/P/S/V/W


 


L7
A/D/E/G/I/L/M/Q/R/S/T/V/W/Y


 


D8
A/C/D/F/G/I/K/L/N/P/Q/R/S/V/W/Y


 


K9
H/K/L/N/Q/R/W


 


A10
A/H/S/T


 


K11
A/D/E/G/H/K/N/Q/R/S/T/Y


 


D12
A/D/E/F/G/H/K/L/M/N/Q/R/S/T/V/W/Y


 


I13
D/E/G/I/K/L/M/N/Q/R/S/T/V/W/Y


 


A14
A/C/I/L/M/N/Q/S/T/V


 


E15
A/D/E/M/N/R/V/W/Y


 


N16
A/D/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y


 


R17
A/C/E/G/H/I/K/L/M/P/R/S/T/V


 


V18
A/I/K/M/T/V


 


R19
A/C/D/E/F/G/K/L/M/N/Q/R/T/V/W/Y


 


E20
A/D/E/F/G/I/K/L/M/N/Q/R/S/T/V/W/Y


 


L21
F/H/I/L/M/Q/T/Y


 


K22
A/C/H/I/K/Q/R


 


Q23
A/C/E/F/G/H/I/M/N/Q/R/S/T/W/Y


 


K24
A/D/G/H/I/K/N/Q/R/T/Y/V


 


L25
I/L/M/Q


 


E26
A/C/D/E/G/I/K/N/Q/R/S/T/V/W


 


E27
A/C/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y


 


F28
C/F/H/I/K/L/M/N/P/R/T/V/Y


 


Y29
A/D/E/H/I/L/P/Q/R/W/Y


 


K30
A/E/F/G/H/K/L/M/N/Q/R/S/T/W/Y


 


E31
A/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y


 


A32
A/F/G/H/K/L/N/P/R/S/T/Y


 


M33
F/H/I/K/L/M/P/Q/R/T/V/Y


 


K34
C/H/I/K/L/M/Q/R/S/T/V/Y


 


L35
A/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W


 


D36
A/C/D/E/G/H/K/L/M/N/Q/R/S/T/V/W/Y


 


L37
A/D/E/F/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y


 


T38
A/D/E/G/K/N/P/Q/R/S/T


 


Q39
A/D/E/G/K/N/P/Q/R/S/T/V


 


E40
A/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V


 


M41
F/G/H/K/L/M/N/Q/R/T/V/W/Y


 


R42
K/R


 


R43
K


 


K44
K/R


 


L45
F/G/I/L/Q/V/W/Y


 


M46
D/E/M/N/Q/T/I


 


L47
F/L/M/W/E


 


R48
R


 


W49
E/F/W/Y


 


I50
A


 


A51
A/G


 


A52
A/F/I/Q


 


M53
D/H/L/M/N/W/I


 


L54
I/L


 


M55
G/I/M/S/V/R


 


A56
A/C/F/G/I/L/M/P/S/T/V


 


I57
A/I/M/S/T/V


 


G58
G


 


D59
D


 


I60
I/L/M


 


F61
F/M/W/Y/N


 


N62
A/D/F/G/I/L/M/N/Q/S/T/V/W


 


A63
A/F/I/L/M/T/V/Y


 


I64
A/H/I/M/Y


 


R65
R/Y


 


Q66
A/F/I/K/L/M/Q/R/V/W/Y


 


A67
A/G


 


K68
K/Q/R


 


Q69
A/F/G/I/K/L/N/Q/R/S/T/V/W/Y


 


E70
A/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y


 


A71
A/G/I/M/S


 


D72
A/D/E/F/G/H/I/L/M/Q/S/T/V/W/Y


 


K73
F/K/R/Y


 


L74
A/F/L/M/R/W/Y


 


K75
A/F/H/K/N/R/S/T/Y


 


K76
I/K/N/R/W


 


A77
A/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y


 


G78
A/D/G/H/Q/R/S/T


 


L79
A/K/L/R/T/V/W/Y


 


V80
I/L/M/V


 


N81
A/D/E/K/N/Q/R/S/T


 


S82
D/E/G/K/M/P/Q/R/S/T/V


 


Q83
A/D/E/F/H/I/L/N/Q/R/S/T/V


 


Q84
D/E/H/M/N/Q/T/Y


 


L85
A/F/G/H/L/M/R/T/V/W/Y


 


D86
D/E/F/G/I/K/L/N/Q/S/T/V/W/Y


 


E87
A/E/F/I/K/L/M/Q/T/W


 


L88
A/F/I/L/M/T/V


 


K89
A/I/K/Q/R/V/L


 


R90
A/G/I/K/L/M/N/Q/R/S/T/V/W/Y


 


R91
A/C/D/E/G/H/K/L/N/Q/R/S/T/V/Y


 


L92
I/L


 


E93
A/D/E/H/I/M/N/Q/T


 


E94
A/C/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/V/Y


 


L95
A/L/T/V


 


K96
K/Q/R


 


E97
A/D/E/G/H/Q/S/T/V


 


E98
A/D/E/F/H/K/M/N/P/Q/R/S/W/Y


 


A99
A/S/V


 


S100
A/G/N/Q/S/T


 


R101
K/R


 


K102
K/R


 


A103
A/I/M/N/S/T/V


 


R104
D/K/N/R


 


D105
A/D/E/F/G/H/K/L/M/N/R/T/V/W/Y


 


Y106
A/E/G/H/I/T/Y


 


G107
D/G/S


 


R108
K/Q/R


 


E109
A/D/E/F/G/H/K/L/R/S/V/W


 


F110
F


 


Q111
D/E/H/M/Q


 


L112
A/D/F/I/L/P/Q/R


 


K113
K/Q


 


L114
A/H/K/L/M/P/R/S/T/V/Y


 


E115
D/E/P/R/T


 


Y116
D/E/G/H/K/Q/R/T/Y
















TABLE 22







Allowable residues for WINDI


(SEQ ID NO: 265)










Residue
Allowable Residues







D1
C/D/E/K/L/M/N/R/S/V/W/Y



 



P2
A/D/E/G/H/L/N/P/Q/R/T/W



 



K3
A/C/F/G/H/I/K/M/Q/R/T/V/Y



 



K4
D/F/G/I/K/M/N/R/S/T/V/W



 



V5
I/L/M/N/T/V/W/Y



 



F6
E/F/I/L/Q/T/V/W/Y



 



D7
A/C/D/F/L/W/Y



 



E8
D/E/H/I/V



 



A9
A/E/H/L/Y



 



K10
A/H/I/K/M/N/Q/R/S/T/Y



 



D11
C/D/E/G/H/K/M/Q/R/S/T/W



 



R12
A/D/E/G/L/N/Q/R/S/V/W



 



A13
A/C/F/H/K/L/M/N/S/T/V



 



E14
A/D/E/F/G/H/I/L/M/Q/S/V/W/Y



 



N15
A/E/G/H/M/N/Q/R/W/Y



 



N16
A/F/L/M/N/S/V/W/Y



 



V17
F/G/H/I/K/M/Q/R/T/V



 



R18
A/C/E/H/K/L/N/Q/R/S/V/W



 



R19
I/M/N/Q/R



 



L20
A/F/G/I/K/L/M/P/T/V/W/Y



 



K21
I/K/N/S/T/W



 



Q22
A/F/G/H/I/K/L/M/N/P/Q/R/S/V/W/Y



 



K23
I/K/L/R/V



 



L24
A/D/F/H/K/L/M/R/S/V



 



E25
A/C/D/E/G/H/L/M/S/V/W



 



E26
A/D/E/F/G/H/I/L/M/Q/R/S/V/W/Y



 



L27
A/F/G/I/K/L/M/Y



 



Y28
F/H/I/K/L/Q/S/V/W/Y



 



K29
A/F/G/H/I/K/M/N/P/Q/R/S/T/V/W/Y



 



E30
D/E/G/H/L/M/N/Q/S/V/W/Y



 



A31
A/F/G/M/P/S/V/Y



 



R32
A/E/G/H/I/M/N/P/Q/R/T



 



K33
A/H/I/K/M/P/R/T/V/W/Y



 



K34
A/E/G/H/I/K/N/P/R/S/T/W



 



D35
A/C/D/E/G/H/K/L/M/N/P/R/S/T/V/W/Y



 



L36
A/D/E/F/K/L/R/S



 



T37
G/R/S/T



 



Q38
A/E/G/H/K/L/P/Q/S/V/W



 



E39
A/D/E/G/I/K/M/N/P/Q/R/S/T/V/W/Y



 



E40
A/D/E/G/I/R/W/Y



 



R41
H/K/L/Q/R/Y



 



E42
A/D/E/G/K/Q/R/T/V



 



K43
E/G/H/I/K/L/N/R/S/T/V/W/Y



 



L44
F/H/K/L/T/V/W/Y



 



K45
I/K/L/M/R/S/T/V/W



 



E46
A/D/E/G/I/K/L/M/N/Q/S/T/V/W



 



K47
D/F/H/I/K/M/R/S/T/V/Y



 



Y48
A/C/E/F/G/H/I/K/L/M/R/S/T/V/W/Y



 



K49
I/K/M/N/P/Q/R/W



 



T50
D/I/N/P/S/T



 



A51
A/F/G/H/I/K/L/M/Q/R/S/T/W



 



M52
A/F/L/M/R/V/W/Y



 



A53
A/E/F/G/H/I/M/N/Q/T/V/W/Y



 



A54
A/G/H/I/L/M/N/P/S/T/V



 



A55
A/C/F/G/M/P/T/W/Y



 



A56
A/F/I/K/L/M/V



 



L57
K/L/W/Y



 



A58
A/G/K/M/Q/R/S/V/W



 



A59
A/D/I/L/M/T/V/W



 



I60
A/D/E/F/G/H/I/L/M/P/S/T/V/W/Y



 



G61
F/G/N/Q



 



D62
C/D/Y



 



A63
A/C/F/H/I/K/L/M/P/T/V/W/Y



 



F64
E/F/L/M



 



N65
D/F/H/M/N/W



 



A66
A/G/S/W



 



L67
F/K/L/V/W/Y



 



L68
K/L/M/W



 



K69
F/H/I/K/Q/R/T/Y



 



A70
A/F/G/I/L/M



 



R71
Q/R



 



K72
I/K/R/T



 



L73
A/K/L/M



 



H74
F/G/H/K/L/R/V/W/Y



 



K75
I/K/M/N/R



 



N76
A/D/F/G/H/I/K/L/M/N/Q/R/V/W/Y



 



G77
F/G/Q/R/S



 



Q78
E/G/H/L/M/N/P/Q/T/V/Y



 



V79
A/I/L/M/S/T/V/W/Y



 



N80
E/G/M/N/S/T



 



E81
A/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y



 



Q82
D/E/F/G/I/K/L/N/P/Q/R/S/W/Y



 



Q83
A/D/E/G/P/Q/W



 



L84
A/F/G/H/I/K/L/V/Y



 



E85
A/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/T/V/W/Y



 



E86
A/D/E/F/G/H/R/S/T/V/W/Y



 



L87
F/H/I/K/L/M/Q/V



 



A88
A/H/N/P/R/S/W



 



R89
H/L/Q/R/V/Y



 



R90
A/D/G/L/P/Q/R/Y



 



L91
C/F/H/I/K/L/P/R/T/V/Y



 



Q92
C/F/G/I/K/L/M/N/P/Q/S/T/V/W/Y



 



E93
A/D/E/F/G/H/I/K/L/M/N/Q/R/S/T/V/W/Y



 



L94
A/C/D/E/G/I/K/L/M/N/Q/R/S/T/V/Y



 



A95
A/C/D/F/H/I/L/M/P/T/V/W/Y



 



K96
H/I/K/N/P/Q/R/T/V



 



E97
C/D/E/G/L/M/P/R/S/V



 



A98
A/C/F/G/I/K/L/Q/T/V/W



 



F99
E/F/G/I/L/M/W



 



Q100
A/E/G/H/K/P/Q/R/V



 



K101
A/D/E/G/H/I/K/P/R/S/V



 



A102
A/C/F/I/L/M/T/V/Y



 



K103
I/K/R



 



D104
A/C/D/E/F/G/H/I/K/L/M/N/P/Q/R/S/V/W/Y



 



Y105
C/F/H/I/M/R/S/W/Y



 



A106
A/E/H/K/L/M/R/V



 



N107
A/E/F/G/I/K/L/M/N/Q/R/S/V/Y



 



E108
A/D/E/G/I/K/L/Q/R/T



 



F109
C/E/F/H/L/N/R/V/Y



 



E110
A/D/E/F/G/H/I/K/L/M/N/P/R/S/T/V/W/Y



 



Y111
D/I/L/R/S/V/W/Y



 



K112
A/C/D/G/H/I/K/L/V



 



L113
C/E/F/K/L/Q/R/T/V



 



E114
A/D/E/G/I/K/L/M/N/P/Q/R/S/T/V/W/Y



 



Y115
A/D/G/I/L/M/P/R/T/W/Y










Experimental Procedures

Computational Methods: General Information

ROSETTA® software can be downloaded from the Rosetta Commons web site, wherein online documentation and ROSETTASCRIPTS® syntax can be found.
Computational Methods: Side Chain Grafting on a Fixed Backbone Toward BHRF1 Binding
A suitable helical region of the scaffold protein was aligned to the Bim-BH3 motif of PDB 2WH6 (Bim-BH3•BHRF1) using PyMOLTM (Schrödinger, LLC). The structural alignment was visually inspected for minimal backbone clashes between the scaffold protein and BHRF1 (side chain clashes may be fixed later by sequence design of the scaffold and by rotamer repacking on the target). Based on the structural alignment, scaffold residues were mutated in PyMolTM to the corresponding Bim-BH3 residue within the interface core; this ‘grafted’ important Bim interaction residues to the scaffold surface by mutation. A new PDB file containing the partially mutated scaffold bound to BHRF1 was saved and used as the input for ROSETTA-based design.
Design with ROSETTATM. An example command line to launch ROSETTATM (Leaver-Fay et al., 2011) and example recipe/protocol file (Fleishman et al., 2011a) was developed. The design run was launched ten times. The consensus sequence was chosen for experimental validation after minor manual modification (e.g. a less-represented amino acid amongst the set of ten designs may be substituted for the consensus residue based on user preference).
Filtering. Proteins that passed the interface design filters (buried SASA>800 Å2, calculated ΔΔG<−15 REU, unsatisfied buried polar atoms <20) were further filtered based on properties of the unbound designed protein. The lowest scoring 10-20 designs for monomer energy, unsatisfied buried polar atoms, and ROSETTAHOLESTM score were selected for manual inspection. Designs were human modified to increase packing within the hydrophobic core and increase surface hydrophilicity, using the ROSETTATM graphical user interface FoldItTM (Cooper et al., 2010). Those designs considered most promising by the human eye were then selected for experimental validation.
For the ‘direct-from-computer’ designs tested in a high-throughput yeast display library (FIG. 1C), 5,000 structures were initially assembled using the FFL procedure. The lowest scoring 1,000 were designed at the interface, with 423 designs passing the minimum threshold for interface binding energy. From these 423, the 74 designs with the lowest number of buried unsatisfied hydrogen bonding atoms in the unbound monomer were chosen for experimental testing.
Other Computational Methods Toward BHRF1 Binding
Predicted binding probabilities for BbpD04 point mutants were calculated using the method of (Whitehead et al., 2012), with mutations ranked according to specificity improvements based on the electrostatics term in the score function.
Computational Methods: Design Based on the BINDI Scaffold
Input Models
The following crystallographic models of ligand-bound human BCL2 pro-survival homologs, found in the Protein Data Bank, were used to manually graft side chains onto a fixed backbone, as described below: 2PQK (Mcl-1•Bim-BH3), 3PK1 (Mcl-1•Bax-BH3), 3KZ0 (Mcl-1•MB7 peptide), 2XA0 (Bcl-2•Bax-BH3), 4AQ3 (Bcl-2-phenylacylsulfonamide), 4IEH (Bcl-2•sulfonamide), 4LVT (Bcl-2•Navitoclax), 1PQ1 (Bcl-xL•Bim-BH3), 2YQ6 (Bcl-xL•BimSAHB), 2YQ7 (Bcl-xL•BimLOCK), 3PL7 (Bcl-xL•Bax-BH3), 4BPK (Bcl-xL•α/β-Puma-BH3), 4K5A (Bcl-w•DARPin) 3I1H (Bfl-1•Bak-BH3), and 4B4S (Bcl-B•Bim-BH3).
Additional models of Bcl-w were generated for input into an automated motif grafting protocol described below. The Bcl-w sequence was threaded onto structurally analogous positions in existing crystallographic models of other BCL2 homologs. Only models bound to helical motifs were used: 1PQ1, 2BZW (Bcl-xL•Bad-BH3), 2YJ1 (Bcl-xL•α/β-Puma-BH3), 2YQ6, 2YQ7, 3FDL (Bcl-xL•Bim-BH3), 4A1U (Bcl-xL•designed α/β-foldamer), 4A1W (Bcl-xL•designed α/β-foldamer), 4BPK, 4HNJ (Bcl-xL•Puma-BH3), and 4OYD (BHRF1•BINDI). The TM-align software (Zhang, 2005) was used to generate structural alignments. Each new Bcl-w model then underwent constrained backbone and side chain minimization in the presence of the bound helical motif borrowed from the initial crystallographic model. The Bcl-w•helix complex was then aligned to a common 20-amino-acid truncated BH3-motif using PyMOLTM (Schrödinger). New PDB files of each Bcl-w model positioned to bind the common BH3-motif were saved and input as “context” in the automated motif grafting protocol described below.
Additional conformations of the partially-nonspecific Mcl-1-targeting binder, M-CDP02, were sampled by submitting the M-CDP02 sequence to the ROSETTATM ab initio structure prediction protocol (Rohl et al., 2004). Of 30,200 generated models, any having greater than 2.5 Å RMSD relative to the starting model of M-CDP02 were discarded. 250 models with the most favorable (lowest) total score in ROSETTATM energy units were input as “scaffolds” for the automated motif grafting protocol described below.
Manual Side-Chain Grafting on a Fixed Backbone
A suitable helical region of the BINDI protein (PDB 4OYD chain B) was aligned to the BH3-motif ligand in crystallographic models of each BCL2 pro-survival homolog, using PyMOLTM. If the target structure was bound to an unnatural ligand, such as a small molecule or α/β-foldamer, the model of the pro-survival homolog was first aligned to an alternative structure bound to a helical BH3 motif, which then served as a guide for structural alignment of BINDI. The structural alignment was visually inspected, and any docked configurations with backbone clashes between the scaffold protein and BCL2 homolog were discarded. Side chain clashes were tolerated, as they may be resolved later by sequence design of the scaffold and by rotamer repacking on the target. Important interfacial residues from each BH3-motif were transferred, or grafted, to the aligned BINDI scaffold and kept fixed during the subsequent design protocol. A new PDB file containing the partially mutated scaffold bound to the target homolog was saved and used as the input for ROSETTATM-based design.
Computational Motif Grafting on a Fixed Backbone
Grafting is a ‘seeded interface’ protein design approach (Correia et al., 2010), in which a small motif of known structure that binds to a target site of interest is used to initiate the protein design process. The motif is then grafted (i.e. embedded) into a larger protein scaffold, which both stabilizes the structure of the small motif and contributes additional favorable interactions with the target protein. We have implemented a new computational grafting protocol as the MOTIFGRAFTTM mover in ROSETTASCRIPTSTM, described in detail by Silva et al (2016). The input of MOTIFGRAFTTM is composed of three structures: 1) the motif, which is a protein fragment that is intended for grafting in a new protein scaffold; 2) the context, which is the macromolecule interacting with the motif; and 3) the target scaffolds, which are protein scaffolds that the protocol will use to search insertion points for the motif. The goal of MOTIFGRAFTTM is to find fragments in the target scaffolds that are geometrically compatible with the specified motif(s), and then replace those fragments with the motif(s) itself. In this case, the parameters of grafting were settled to perform full backbone alignment of the input motif, with a maximum RMSD of the backbone of 3.0 Å and RMSD for the endpoints of 2.0 Å. For the input motif “truncatedBH3.pdb” the hotspot residues were defined as: LEU-9, GLY-13, ASP-14, PHE-16 and ASN-17. The protocol was instructed to revert all other residues to their native identities in the target scaffold. No clashes between the grafted design and the context protein were allowed. The following mover was added to the XML script to implement this protocol within the ROSETTASCRIPTSTM framework:















<MotifGraft name=“motif_grafting”



  context_structure=“%%context%%”



  motif_structure=“truncatedBH3.pdb”



  RMSD_tolerance=“3.0”



  NC_points_RMSD_tolerance=“2.0”



  clash_score_cutoff=“0”



  clash_test_residue=“ALA”



  hotspots=“9:12:13:14:16:17”



  combinatory_fragment_size_delta=“0:0”



  max_fragment_replacement_size_delta=“0:0”



  full_motif_bb_alignment=“1”



  allow_independent_alignment_per_fragment=“0”



  graft_only_hotspots_by_replacement=“0”



  only_allow_if_N_point_match_aa_identity=“0”



  only_allow_if_C_point_match_aa_identity=“0”



  revert_graft_to_native_sequence=“1”



  allow_repeat_same_graft_output=“1”/>










Plasmids, Gene Synthesis and Mutagenesis

Genes encoding Bcl-2 proteins were synthesized (Genscript) and cloned with C-terminal avi-6his tags (GLNDIFEAQKIEWHEGSHHHHHH (SEQ ID NO: 75)) into plasmid pET29b (NdeI-XhoI sites; Novagen): human Bcl-2 a.a. 1-207 (Accession No. NP_000624.2), Bcl-w a.a. 1-182 (AAB09055.1), Bfl-1 a.a. 1-153 (C4S mutation; NP_004040), Bcl-B a.a. 11-175 (NP_065129.1), Mcl-1 a.a. 172-327 (Q07820.3), Bcl-XL a.a. 1-205 (CAA80661), and EBV BHRF1 a.a. 1-161 (YP_401646). For later BLI analysis, Bcl-B and Bfl-1 were genetically fused to C-terminal maltose-binding-protein with an avi-6his tag for improved solution properties. Codon usage was optimized for E. coli expression. Human Bim-BH3 (a.a. 141-166, Accession No. O43521) was cloned into pETCON (NdeI-XhoI sites). The genes for individually-tested designed proteins were assembled from oligos (Hoover and Lubkowski, 2002) and cloned into pET29b (NdeI-XhoI sites) with C-terminal 6his tags for purification from E. coli, or cloned into PETCON (NdeI-XhoI sites; (Fleishman et al., 2011)) for yeast surface expression. Alternative tags were added using PCR methods. Point mutations were made by overlapping PCR (Procko et al., 2013). Error-prone PCR with an average error rate of 1.3 amino acid substitutions per clone used GeneMorph II Random Mutagenesis (Agilent Technologies).
Protein Purification
E. coli BL21* (DE3) (Invitrogen) transformed with the relevant plasmid were grown at 37° C. in terrific broth with 50 μg/ml kanamycin to OD600 0.5-0.8, transferred to 21° C. and expression induced overnight with 0.1 mM IPTG. Centrifuged cells were resuspended in lysis buffer (20 mM Tris-Cl pH 8.0, 20 mM imidazole, 300 mM NaCl, 0.5 mM PMSF) supplemented with 0.2 mg/ml lysozyme and 0.06 mg/ml DNase I, and sonicated. Cleared lysate was incubated with NiNTA-agarose at 4° C. for 1 h and collected in a chromatography column. The resin was washed with 100 CV lysis buffer and protein was eluted with 6 CV elution buffer (20 mM Tris-Cl pH 8.0, 250 mM imidazole, 300 mM NaCl, 0.5 mM PMSF, 0.05% β-mercaptoethanol). Proteins were concentrated using a centrifugal ultrafiltration device (Sartorius) and separated from remaining contaminants by SEC using a Sephacryl-100 16/600 column (GE Healthcare) with running buffer (20 mM Tris-Cl pH 7.5, 150 mM NaCl, 1 mM DTT). Fractions containing pure protein were pooled, concentrated to 5-20 mg/ml based on calculated extinction coefficients for absorbance at 280 nm, and aliquots snap frozen in liquid N2 for storage at −80° C. For animal studies, endotoxin was removed with a high-capacity endotoxin removal spin column (Pierce) and reducing agent was removed with a PD-10 desalting column (GE Healthcare).
Enzymatic Ligand Biotinylation
Purified avi-6his-tagged ligands (20 μM) in reaction buffer (250 mM potassium glutamate, 20 mM Tris-Cl [pH 7.5], 50 mM bicine [pH 8.3], 10 mM ATP, 10 mM MgOAc, 100 μM d-biotin) were enzymatically biotinylated with 150 U/μl BirA (Avidity) at room temperature overnight, followed by purification with NiNTA-agarose and SEC. Biotinylated ligands were stored at 4° C. in 150 mM NaCl, 20 mM Tris-Cl (pH 7.5), 1 mM DTT, 0.02% sodium azide.
Yeast Surface Display
Transformed yeast were cultured, induced and binding of surface displayed protein to biotinylated ligands was assessed by flow cytometry as reported (Chao et al., 2006; Procko et al., 2013). All yeast displayed proteins had C-terminal myc epitope tags for detection with FITC-conjugated anti-myc (Immunology Consultants Laboratory). Binding of biotinylated protein to the yeast surface is detected with phycoerythrin-conjugated streptavidin (Invitrogen).
Deep Sequencing Analysis
Yeast cells were sorted on a BD Influx cytometer operated by Spigot (BD Biosciences) and recovered in SDCAA media at 30° C. overnight. Yeast were lysed with 125 U/ml Zymolase at 37° C. for 5 h, and DNA was harvested (Zymoprep kit from Zymo Research). Genomic DNA was digested with 2 U/μl Exonuclease I and 0.25 U/μl Lambda exonuclease (New England Biolabs) for 90 min at 30° C., and plasmid DNA purified with a QIAquickTM kit (Qiagen). DNA was deep sequenced with a MiSeqTM sequencer (Illumina) and sequences were analyzed with adapted scripts from Enrich (Fowler et al., 2011).
For the library of designs in FIG. 1C, genes were synthesized (Gen9) with barcodes downstream of the stop codon for easy identification during deep sequencing (Table 3). After yeast cell transformation, expression, sorting and plasmid DNA purification, the genes were PCR amplified using primers that annealed to external regions within the plasmid, followed by a second round of PCR to add flanking sequences for annealing to the Illumina flow cell oligonucleotides and a 6-bp sample identification sequence. PCR rounds were 12 cycles each with high-fidelity Phusion polymerase (New England Biolabs). Barcodes were read on a MiSeqTM sequencer using a 50-cycle reagent kit (Illumina). 257,812 sequences passing the chastity filter were read in the naive population (ranging from 260 to 17,192 reads per gene, with a median of 2,492). The sorted populations had 117,720 to 232,195 reads.
For the single-site saturation mutagenesis library (FIG. 6), the BbpD04.3 gene was amplified as two overlapping fragments to provide complete sequencing coverage, and additional flanking DNA for annealing to the Illumina flow cell was added by PCR as described above. Gel-purified DNA was sequenced on a MiSeqTM sequencer using a 300-cycle paired-end reads reagent kit (Illumina). 3,058,244 sequences passing the chastity filter were read for the naive population. Each single amino acid substitution had 10 to 10,856 reads, with a median of 451 reads per mutant, and only mutation E109F was not represented. Parental protein sequences accounted for  ̃25% of reads. 2,930,499 and 2,548,997 sequences passing the chastity filter were read for the affinity and affinity-specificity sorted populations, respectively.
Analytical Size Exclusion Chromatography
Proteins (20 nmol each) were injected in a 200 μl loop in line with a Superdex-75 10/300 column (GE Healthcare) and separated with running buffer (20 mM Tris-Cl pH 7.5, 150 mM NaCl, 1 mM DTT) at room temperature.
Proteolysis Susceptibility Assay
Substrates (0.5 mg/ml) were incubated at 37° C. with protease (0.01 mg/ml) in 50 mM Tris-HCl (pH 8.0), 10 mM CaCl2. Reactions were terminated with benzamidine (12.5 mM final), PMSF (1.25 mM final) and 4× load dye. Samples were run on 18% SDS-polyacrylamide gels, stained with Coomassie dye, and the decrease in full-length protein quantified using ImageJ software (National Institute of Mental Health).
Circular Dichroism
CD spectra were recorded with a Model 420 spectrometer (AVIV Biomedical) or a J-1500 Circular Dichroism Spectrometer (JASCO). Unless stated otherwise, proteins were at 20 μM in PBS and data were collected at 25° C.
Bio-Layer Interferometry
Data were collected on an Octet RED96 (Forte Bio) and processed using the instrument's integrated software. Enzymatically-biotinylated Bcl-2 proteins (25 nM) in binding buffer (10 mM HEPES [pH 7.4], 150 mM NaCl, 3 mM EDTA, 0.05% surfactant P20, 0.5% non-fat dry milk) were immobilized for 360 s at 30° C. to streptavidin biosensors. Biosensors were dipped in solutions containing the analyte of interest to measure association, and transferred back to empty binding buffer for monitoring dissociation. Kinetic constants were determined from the mathematical fit of a 1:1 binding model.
Cytochrome c Release
Cells ( ̃109) were equilibrated in 5 ml of homogenization buffer (0.25 M sucrose, 1 mM EGTA, 10 mM HEPES/NaOH, 0.5% BSA, pH 7.4, Roche Complete protease inhibitors) for 5 min. Samples were kept on ice or at 4° C. until assayed. Cells were homogenized under N2 pressure (400 psi) in a steel disruption vessel (Parr Instrument Company) for 10 min, then centrifuged (750 g) for 10 min to remove intact cells. Supernatant was centrifuged again (12,000 g) for 12 min to collect mitochondria. The pellet was resuspended in 300 μl wash buffer (0.25 M sucrose, 1 mM EDTA, 10 mM Tris/HCl pH 7.4). Proteins at the indicated concentrations were incubated with mitochondria (25 μg mitochondrial protein based on BCA assay, Sigma) in 50 μl final volume of experimental buffer (125 mM KCl, 10 mM Tris-MOPS pH 7.4, 5 mM glutamate, 2.5 mM malate, 1 mM K-PO4, 10 μM EGTA-Tris pH 7.4) for 30 min at room temperature. Reaction solutions were centrifuged (18,000 g) for 10 min at 4° C. and cytochrome c release was quantified using a Cytochrome c ELISA kit (Life Technologies). Complete cytochrome c release was quantified by treatment with 0.5% Triton-X100.
Cell Viability Assays, BINDI-Polymer Conjugates
A 25,000 Da diblock copolymer (Pol300) composed of 95% polyethylene glycol methacrylate (300 Da) for stability and 5% pyridyl disulfide methacryate for conjugation in the first block, and 60% diethylaminoethyl methacrylate and 40% butyl methacrylate in the second block, was synthesized by reversible addition-fragmentation chain transfer. Development and characterization of the diblock copolymer will be published in a separate article. After purification, Pol300 was dissolved in ethanol at 100 mg/ml then diluted into PBS at 1 mg/ml and spin filtered to remove ethanol. Proteins with exposed terminal cysteines were incubated with Pol300 at a molar ratio of 2:1 (protein:polymer) overnight. Protein-polymer conjugation was quantified by measuring pyridyl disulfide release and the absorbance of 2-mercaptopyridine at 343 nm with 8,080 M−1 cm−1 as the extinction coefficient. For cell viability studies, protein and protein-polymer conjugates were incubated with Ramos or Ramos-AW cells in a 96 well round bottom plate with 50,000 cells per well in 100 μl media. Cells were cultured in RPMI 1640 containing L-glutamine and 25 mM HEPES supplemented with 1% penicillin-streptomycin (GIBCO) and 10% fetal bovine serum (Invitrogen) at 37° C. and 5% CO2. After 24 h, cell viability was measured using a CellTiter 96 Aqueous One Solution Cell Proliferation Assay, MTS (Promega).
Tissue Culture, BINDI-Polymer Conjugates
Ramos, Ramos-AW, Daudi, Raji, DOHH2, JVM-2, and JVM-13 were grown in RPMI 1640 containing L-glutamine and 25 mM HEPES supplemented with 1% penicillin-streptomycin (GIBCO) and 10% fetal bovine serum (FBS, Invitrogen). Jeko-1 were grown in similar RPMI 1640 media supplemented with 20% FBS. Granta-519 and K562 were grown in Iscove's DMEM supplemented with 10% FBS. All cell lines were maintained in log growth phase at 37° C. and 5% CO2.
Xenograft Mouse Model, BINDI-Polymer Conjugates
To prepare mAb-polymer-protein conjugates, a 44,000 Da diblock copolymer (Pol950) composed of 80% polyethylene glycol methacrylate (950 Da), 10% pyridyl disulfide methacrylate, and 10% biotin-hydroxyethyl methacrylate for mAb-streptavidin conjugation in the first block, and 60% diethylaminoethyl methacrylate and 40% butyl methacrylate in the second block, was synthesized by reversible addition-fragmentation chain transfer. Development and characterization of the Pol950 diblock copolymer will be published in a separate article. Pol950 was dissolved in ethanol at 100 mg/mL, then diluted in PBS at 10 mg/ml and spin filtered to remove ethanol. Proteins were incubated with Pol950 at an equimolar ratio overnight and conjugation was quantified by A343 absorbance. αCD19 was conjugated to protein-polymer through the streptavidin linkage at a molar ratio of 90:1 (polymer:mAb).
BALB/c nu/nu mice (6 to 8 weeks old) were used from Harian Sprague-Dawley and housed under protocols approved by the FHCRC Institutional Animal Care and Use Committee. Mice were placed on biotin-free diet (Purina Feed) for the duration of study. To form tumor-xenografts, Ramos-AW cells were resuspended in PBS (5×107 cells/mL) and injected in the right flank with 107 cells/mouse. Tumors were allowed to grow for 6 days to a volume of 50 mm3. Mice with similar sized tumors were sorted randomly into treatment groups (n=8 to 10). On days 6, 9, and 12, mice were injected intraperitoneally with cyclophosphamide (35 mg/kg) and bortezomib (0.5 mg/kg). After 30 min, mice were injected via tail vein with conjugates at a dose of 15 mg/kg (αCD19), 300 mg/kg (Pol950) and 105 mg/kg (BINDI or 3LHP). Body weight was monitored for toxicity and tumor sizes were measured while blinded to treatment groups. Measurements were performed in the x, y, and z plane using calipers three times a week. Mice were euthanized when tumors reached a volume of 1250 mm3. Tumor volumes and deaths were recorded into Prism (GraphPad Software, Inc.) for statistical analysis and a log-rank (Mantel-Cox) test was performed to determine if survival curves and trends were statistically different (P<0.0001). Significance in tumor volumes was verified by an unpaired t test with Welch's correction.
MEF-Derivative Cell Line Generation
Mouse embryonic fibroblasts were generated from E13-E14.5 embryos derived from CreERT2/Bcl-xfl/fl/Mcl-Ifl/fl C57BL/6 mice (Kelly et al., 2014) and immortalized (at passage 2-4) with SV40 large T antigen. Retroviral expression constructs in the pMIG vector (Murine Stem Cell Virus-IRES-GFP) expressing each FLAG-tagged pro-survival protein were transiently transfected using LIPOFECTAMINETM (Invitrogen), into Phoenix ecotropic packaging cells. Filtered virus-containing supernatants were used to infect the MEFs by spin inoculation as previously described (Lee et al., 2008). Cells stably expressing each pro-survival protein were selected by sorting GFP+ve cells 24 hours after spin inoculation and protein expression verified by Western blotting using an anti-FLAG antibody. Following verification of exogenous pro-survival protein expression, each cell line was treated with 1 μM Tamoxifen (Sigma-Aldrich) to enable deletion of endogenous Mcl-1 and Bcl-xL. Deletion of endogenous Mcl-1 and Bcl-xL was shown by Western blotting using anti-Mcl-1 (Rockland Clone, 600-401-394) and anti-Bcl-xL (BD Transduction Laboratories Clone 44/Bcl-x) antibodies. Cells were maintained in DME Kelso medium supplemented with 10% (v/v) fetal bovine serum, 250 mM L-asparagine and 50 mM 2-mercaptoethanol.
HeLa-Derivative Cell Line Generation
HeLa cells were transfected with pSFFV vectors encoding human Mcl-1, Bcl-2, Bcl-xL, or empty vector (Neo) and selected with 1 mg/ml geneticin for 48 hours. Cells were maintained afterwards in DMEM with 10% (v/v) fetal bovine serum (FBS) supplemented with 500 μg/ml geneticin. Increased expression of pro-survival BCL2 proteins was confirmed by Western blotting using anti-Bcl-2, anti-Bcl-xL (Santa Cruz Biotechnology), and anti-Mcl-1 (Cell Signaling) antibodies.
Lentiviral Infection
Inducible αMCL1 and αBFL1 constructs were generated in a lentiviral vector described in Aubrey et al. (2015). Ligand expression is linked via the T2A peptide to mCherryTM fluorescent reporter protein. Lentiviral particles were produced by transient transfection of 293T cells with plasmid DNA along with the packaging constructs pMDL, pRSV-rev and pVSV-G using calcium chloride precipitation. Viral supernatants were then filtered prior to target cell transduction. SW620, HCT-116, DLD1, RKO, HT-29, Caco-2, and SW48 colon cancer cell lines were generously provided by John Mariadason at the Olivia Newton-John Cancer Research Institute. For infection of MEFs and colon cancer cell lines, equal volume of virus-containing supernatant was added to target cells pre-incubated with 10 ng/μL polybrene, and centrifuged at 2500 rpm for 2 hours at 32° C. Following spin inoculation, cells were then incubated overnight at 37° C. Cells expressing the doxycycline-inducible constructs were then selected by sorting mCherry+ve cells. MEFs were maintained in DME Kelso medium supplemented with 10% (v/v) FBS, 250 mM L-asparagine and 50 mM 2-mercaptoethanol. Colon cancer cell lines were maintained in DMEM/F-12 supplemented with 10% (v/v) FBS.
For constitutive expression of αBCL2, αBCLXL, αBCLW, αMCL1 and αBFL1, genes were first codon optimized for human expression including a 5′ Kozak sequence (GCCACC) and 3′ FLAG tag, then cloned into the SparQTM lentivector containing GFP reporter gene downstream of an internal ribosome entry site (QM530A-1; System Biosciences). Lentiviral particles were produced by transient transfection of 293T cells with plasmid DNA along with packaging constructs pMD2.G and psPAX using calcium chloride precipitation. Viral supernatants were harvested 48 or 72 hours after transfection, filtered and used immediately or stored in aliquots at −80° C.
MEF Cytochrome c Release Assay
Small molecule inhibitors used for cytochrome c release and survival assays were purchased from ChemiTek (ABT-263 and ABT-199) or prepared according to published methods (A-1331852; Leverson et al., 2015a; Wang et al., 2013). Mouse embryonic fibroblasts (1×106) were pelleted and lysed in 0.05% (w/v) digitonin containing lysis buffer (20 mM Hepes-pH 7.2, 100 mM KCl, 5 mM MgCl2, 1 mM EDTA, 1 mM EGTA, 250 mM Sucrose), supplemented with protease inhibitors (Roche) for 3 min on ice. Crude lysates containing the mitochondria were incubated with 10 μM ligand at 30° C. for 1 hour before pelleting. The supernatant was retained as the soluble fraction (S), while the pellet, containing the mitochondria (P), was solubilized in lysis buffer (20 mM Tris-pH 7.4, 135 mM NaCl, 1.5 mM MgCl2, 1 mM EGTA, 10% (v/v) glycerol and 1% (v/v) Triton X-100. Both soluble and pellet fractions were subsequently analyzed by Western blotting using an anti-cytochrome c antibody (clone 7H8.2C12; BD Biosciences).
Short-Term Survival Assays
MEF and colon cancer cells were aliquoted in 96-well tissue culture plates in 50 culture media at 20,000 cells per mL. Cells were treated with doxycycline at a final concentration of 1 mg/mL to induce protein expression, and/or small molecule drugs at the indicated final concentrations and a final total volume of 100 μL per well. Viability was assayed after 24 hours with Cell Titer Glo (Promega). For drug titrations, ABT-263 and A-1331852 were serially diluted 2-fold from 250 nM to 2 nM (eight concentrations in total) and combined with doxycycline (to induce expression of αMCL1) or media (drug only). EC50 values were determined with nonlinear regression.
HeLa, melanoma, and glioblastoma cell lines (maintained in DMEM with 10% [v/v] FBS) were seeded at 3,000-5,000 cells per well in 96 well plates in 100 μl culture medium. Cells were transduced the next day with 100 μl lentiviral supernatant to induce expression of each designed inhibitor. For experiments using combinations of three inhibitors, 75 μl media was removed before virus addition to accommodate the appropriate volume of virus. Viability was assayed at 72 hours post-infection with Cell Titer Glo (Promega). Expression of constructs was confirmed by flow cytometry (GFP) and western blotting (anti-FLAG).
Long-Term Survival Assays
MEF and colon cancers were seeded in 6-well tissue culture plates in 2 mL culture media at 150 cells per mL. The next day and every 48 hours following, doxycycline was added at a final concentration of 1 μg/mL to each well, while nothing was added to control wells. After seven to ten days, media was aspirated and colonies were stained (5:4:1 MeOH:H2O:AcOH, 0.25% Coomassie Blue R-250) and counted.
Immunoprecipitation
Cells were harvested, washed with PBS, and extracted with ice-cold Chaps buffer (40 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 2% CHAPS, and Complete Protease Inhibitors [Roche]) for 20 minutes, on ice. Extracts were spun down at 10,000 g for 10 min and supernatants were removed and used for SDS-PAGE analysis. Expression of proteins of interest was analyzed using antibodies against Bcl-2, Bcl-xL, Mcl-1 (as above), Bfl-1 (ProsSci, Inc.), Bim (BD Biosciences), and tubulin (SigmaAldrich). For immunoprecipitation experiments, 1,000 μg protein lysates were pre-cleared and then incubated with 3 μg Bim antibody for 2 hours at 4° C., followed by addition of Protein A/G Plus agarose beads (Santa Cruz Biotechnology) and overnight incubation with rotation at 4° C. Negative control reactions used normal IgG. Immunoprecipitates were washed four times with lysis buffer and eluted with loading buffer at 95° C., 2 times for 10 min, followed by SDS-PAGE analysis.
Discussion
By breaking free of the conformational constraints imposed by repurposing pre-existing scaffolds and instead building a new protein with structure tailored for the target surface, a remarkably tight and specific binder of the EBV apoptosis regulator BHRF1 was designed. The elevated toxicity of the engineered BINDI protein towards EBV-positive cancer lines supports the hypothesis that BHRF1 is necessary for survival in at least some EBV-associated cancers. BINDI should provide a useful tool for characterizing primary isolates of EBV-associated cancers in which the molecular mechanisms of cell transformation remain poorly understood, including EBV-positive BL, Hodgkin's lymphoma, and nasopharyngeal and gastric carcinomas (Young and Murray, 2003).
BINDI has a structure and amino acid sequence found after computationally filtering thousands of potential designed conformations for optimum interactions with BHRF1. The ability to custom-tailor the backbone conformation to the challenge at hand helped achieve very high affinity and specificity.
BINDI is an artificial polypeptide sequence that folds to a designed structure, with no identifiable homologues in nature. We demonstrate how sequence variants of BINDI (see FIGS. 2, 4, 6 and 14) can also bind BHRF1 with high affinity and specificity. Redesigning BINDI to bind other BCL2 family proteins yielded a set of related sequences (MINDI, 2-INDI, XINDI, 10-INDI, FINDI and WINDI), with any two differing by as many as 51 mutations (44% of the protein). Each of these redesigned BINDI variants were related to each other but not to any naturally occurring proteins. Saturation mutagenesis of all these designed proteins consistently revealed that significant sequence diversity is tolerated (FIG. 19 and Table 11-22). We have therefore designed a new family of proteins that share a common structure and architecture. We have shown that many sequence homologues can maintain our artificially designed structure and functional inhibition of BCL2 family proteins.
We demonstrate that BINDI can slow progression of EBV-positive B lymphoma and prolong survival in a human xenograft mouse model. More doses, higher dosage, alternative targeting antibodies, and copolymer optimization may all increase therapeutic efficacy. Intracellular delivery of BINDI, either of encoding nucleic acid or of the polypeptide, is expected to have therapeutic effects in Epstein-Barr related diseases generally. Quantitative analysis of mRNA expression has shown that different cancer lines overexpress different BCL2 family members. The designed proteins described herein can specifically inhibit BCL2 family members at the protein level, thereby demonstrating which BCL2 proteins are functionally important for preventing apoptosis in different cancers. This will lead to better tumor characterization and future diagnostics, in addition targeted therapies as described for BINDI delivery to EBV-positive cancer.
We demonstrate that the designed peptides targeting human pro-survival BCL2 proteins engage the BH3-binding grooves of only their specific target family members. The designs were used to determine the BCL2-dependence of different cancers, providing a more direct guide for therapy than knockdown/knockout strategies or mRNA analysis by mimicking the mechanism of action of BCL2-targeting small molecule drugs. While mRNA profiling suggests that Bfl-1 confers apoptotic resistance in SK-MEL-5 and LOX-IMVI melanomas (Hind et al., 2015), our combinatorial antagonism of pro-survival homologs indicates that Mcl-1 plays a more critical role and further discriminates between sensitive LOX-IMVI and resistant SK-MEL-5 We also provide further evidence that many colon cancers are generally dependent on Mcl-1 and Bcl-xL for survival; mRNA profiling indicates Mcl-1 and Bcl-xL are indeed more prevalent than other BCL2 homologs in many colon cancers, but resistant HCT-116 is indistinguishable from sensitive lines like Caco-2 and HT-29 (Placzek et al., 2010). Further, the detection of RKO sensitivity to Bfl-1 inhibition highlights the capacity of the designed inhibitors to determine unique BCL2-dependence profiles, even among cancers with similar general characteristics.
More generally, computationally designed inhibitors enable the investigation of the biological roles of specific protein interactions with the high spatio-temporal control that can be achieved with tissue-specific and inducible promoters. Competing approaches offer less control. The distribution of small molecules is difficult to spatially or temporally control in vivo, and broadly eliminating the protein of interest with CRISPR or RNAi cannot probe interactions with a specific interface or capture mechanistic intricacies. The designed peptide inhibitors presented here will thus provide a useful toolset for studying apoptotic regulation and dysfunction and treating associated pathologies.
Unless the context clearly requires otherwise, throughout the description and the claims, the words ‘comprise’, ‘comprising’, and the like are to be construed in an inclusive sense as opposed to an exclusive or exhaustive sense; that is to say, in the sense of “including, but not limited to”. Words using the singular or plural number also include the plural and singular number, respectively. Additionally, the words “herein,” “above,” and “below” and words of similar import, when used in this application, shall refer to this application as a whole and not to any particular portions of the application.
REFERENCES


    Altmann, M., and Hammerschmidt, W. (2005). Epstein-Barr virus provides a new paradigm: a requirement for the immediate inhibition of apoptosis. PLoS Biol 3, e404.
    Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
    Andersson, M., and Lindahl, T. (1976). Epstein-Barr virus DNA in human lymphoid cell lines: in vitro conversion. Virology 73, 96-105.
    Azzarito, V., Long, K., Murphy, N. S., and Wilson, A. J. (2013). Inhibition of alpha-helix-mediated protein-protein interactions using designed molecules. Nat Chem 5, 161-173.
    Carta, S., Chugh, S., Nhu, D., Lessene, G., and Kvansakul, M. (2012). Crystallization and preliminary X-ray characterization of Epstein-Barr virus BHRF1 in complex with benzoylurea peptidomimetic. Acta Crystallogr F Struct Biol Cryst Commun 1, 1521-1524.
    Chao, G., Lau, W. L., Hackel, B. J., Sazinsky, S. L., Lippow, S. M., and Wittrup, K. D. (2006). Isolating and engineering human antibodies using yeast surface display. Nat Protoc 1, 755-768.
    Chin, J. W., and Schepartz, A. (2001). Design and Evolution of a Miniature Bcl-2 Binding Protein. Angew Chem Int Ed Engl 40, 3806-3809.
    Convertine, A. J., Diab, C., Prieve, M., Paschal, A., Hoffman, A. S., Johnson, P. H., and Stayton, P. S. (2010). pH-Responsive Polymeric Micelle Carriers for siRNA Drugs. Biomacromolecules.
    Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popovic, Z., and Players, F. (2010). Predicting protein structures with a multiplayer online game. Nature 466, 756-760.
    Correia, B. E., Ban, Y. E., Holmes, M. A., Xu, H., Ellingson, K., Kraft, Z., Carrico, C., Boni, E., Sather, D. N., Zenobia, C., et al. (2010). Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope. Structure 18, 1116-1126.
    Correia, B. E., Bates, J. T., Loomis, R. J., Baneyx, G., Carrico, C., Jardine, J. G., Rupert, P., Correnti, C., Kalyuzhniy, O., Vittal, V., et al. (2014). Proof of principle for epitope-focused vaccine design. Nature.
    Czabotar, P. E., Lee, E. F., van Delft, M. F., Day, C. L., Smith, B. J., Huang, D. C., Fairlie, W. D., Hinds, M. G., and Colman, P. M. (2007). Structural insights into the degradation of Mcl-1 induced by BH3 domains. Proc Natl Acad Sci USA 104, 6217-6222.
    Desbien, A. L., Kappler, J. W., and Marrack, P. (2009). The Epstein-Barr virus Bcl-2 homolog, BHRF1, blocks apoptosis by binding to a limited amount of Bim. Proc Natl Acad Sci USA 106, 5663-5668.
    Dutta, S., Chen, T. S., and Keating, A. E. (2013). Peptide ligands for pro-survival protein Bfl-1 from computationally guided library screening. ACS Chem Biol 8, 778-788.
    Dutta, S., Gulla, S., Chen, T. S., Fire, E., Grant, R. A., and Keating, A. E. (2010). Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL. J Mol Biol 398, 747-762.
    Duvall, C. L., Convertine, A. J., Benoit, D. S., Hoffman, A. S., and Stayton, P. S. (2010). Intracellular delivery of a proapoptotic peptide via conjugation to a RAFT synthesized endosomolytic polymer. Mol Pharm 7, 468-476.
    Flanagan, A. M., and Letai, A. (2008). BH3 domains define selective inhibitory interactions with BHRF-1 and KSHV BCL-2. Cell Death Differ 15, 580-588.
    Fleishman, S. J., Leaver-Fay, A., Corn, J. E., Strauch, E. M., Khare, S. D., Koga, N., Ashworth, J., Murphy, P., Richter, F., Lemmon, G., et al. (2011a). RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS One 6, e20161.
    Fleishman, S. J., Whitehead, T. A., Ekiert, D. C., Dreyfus, C., Corn, J. E., Strauch, E. M., Wilson, I. A., and Baker, D. (2011). Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332, 816-821.
    Fowler, D. M., Araya, C. L., Fleishman, S. J., Kellogg, E. H., Stephany, J. J., Baker, D., and Fields, S. (2010). High-resolution mapping of protein sequence-function relationships. Nat Methods 7, 741-746.
    Fowler, D. M., Araya, C. L., Gerard, W., and Fields, S. (2011). Enrich: software for analysis of protein function by enrichment and depletion of variants. Bioinformatics 27, 3430-3431.
    Gemperli, A. C., Rutledge, S. E., Maranda, A., and Schepartz, A. (2005). Paralog-selective ligands for bcl-2 proteins. J Am Chem Soc 127, 1596-1597.
    Gront, D., Kulp, D. W., Vernon, R. M., Strauss, C. E., and Baker, D. (2011). Generalized fragment picking in Rosetta: design, protocols and applications. PLoS One 6, e23294.
    Henderson, S., Huen, D., Rowe, M., Dawson, C., Johnson, G., and Rickinson, A. (1993). Epstein-Barr virus-coded BHRF1 protein, a viral homologue of Bcl-2, protects human B cells from programmed cell death. Proc Natl Acad Sci USA 90, 8479-8483.
    Hind, C. K., Carter, M. J., Harris, C. L., Chan, H. T. C., James, S., and Cragg, M. S. (2015). Role of pro-survival molecule Bfl-1 in melanoma. Int J Biochem Cell B 59, 94-102.
    Hoover, D. M., and Lubkowski, J. (2002). DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis. Nucleic Acids Res 30, e43.
    Ishii, H. H., Etheridge, M. R., and Gobe, G. C. (1995). Cycloheximide-induced apoptosis in Burkitt lymphoma (BJA-B) cells with and without Epstein-Barr virus infection. Immunol Cell Biol 73, 463-468.
    Jones, D. T. (1999). Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292, 195-202.
    Leaver-Fay, A., Tyka, M., Lewis, S. M., Lange, O. F., Thompson, J., Jacak, R., Kaufman, K., Renfrew, P. D., Smith, C. A., Sheffler, W., et al. (2011). ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 487, 545-574.
    Kelly, G. L., Long, H. M., Stylianou, J., Thomas, W. A., Leese, A., Bell, A. I., Bornkamm, G. W., Mautner, J., Rickinson, A. B., and Rowe, M. (2009). An Epstein-Barr virus anti-apoptotic protein constitutively expressed in transformed cells and implicated in burkitt lymphomagenesis: the Wp/BHRF1 link. PLoS Pathog 5, e1000341.
    Kelly, G. L., Stylianou, J., Rasaiyaah, J., Wei, W., Thomas, W., Croom-Carter, D., Kohler, C., Spang, R., Woodman, C., Kellam, P., et al. (2013). Different patterns of Epstein-Barr virus latency in endemic Burkitt lymphoma (BL) lead to distinct variants within the BL-associated gene expression signature. J Virol 87, 2882-2894.
    Koga, N., Tatsumi-Koga, R., Liu, G., Xiao, R., Acton, T. B., Montelione, G. T., and Baker, D. (2012). Principles for designing ideal protein structures. Nature 491, 222-227.
    Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L., and Baker, D. (2003). Design of a novel globular protein fold with atomic-level accuracy. Science 302, 1364-1368.
    Kvansakul, M., Wei, A. H., Fletcher, J. I., Willis, S. N., Chen, L., Roberts, A. W., Huang, D. C., and Colman, P. M. (2010). Structural basis for apoptosis inhibition by Epstein-Barr virus BHRF1. PLoS Pathog 6, e1001236.
    Lanci, C. J., MacDermaid, C. M., Kang, S. G., Acharya, R., North, B., Yang, X., Qiu, X. J., DeGrado, W. F., and Saven, J. G. (2012). Computational design of a protein crystal. Proc Natl Acad Sci USA 109, 7304-7309.
    Leao, M., Anderton, E., Wade, M., Meekings, K., and Allday, M. J. (2007). Epstein-barr virus-induced resistance to drugs that activate the mitotic spindle assembly checkpoint in Burkitt's lymphoma cells. J Virol 81, 248-260.
    Leaver-Fay, A., Tyka, M., Lewis, S. M., Lange, O. F., Thompson, J., Jacak, R., Kaufman, K., Renfrew, P. D., Smith, C. A., Sheffler, W., et al. (2011). ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 487, 545-574.
    Lessene, G., Czabotar, P. E., Sleebs, B. E., Zobel, K., Lowes, K. N., Adams, J. M., Baell, J. B., Colman, P. M., Deshayes, K., Fairbrother, W. J., et al. (2013). Structure-guided design of a selective BCL-X(L) inhibitor. Nat Chem Biol 9, 390-397.
    Liu, X., Dai, S., Zhu, Y., Marrack, P., and Kappler, J. W. (2003). The structure of a Bcl-xL/Bim fragment complex: implications for Bim function. Immunity 19, 341-352.
    Manganiello, M. J., Cheng, C., Convertine, A. J., Bryers, J. D., and Stayton, P. S. (2012). Diblock copolymers with tunable pH transitions for gene delivery. Biomaterials 33, 2301-2309.
    Martinou, J. C., and Youle, R. J. (2011). Mitochondria in apoptosis: Bcl-2 family members and mitochondrial dynamics. Dev Cell 21, 92-101.
    McLaughlin, R. N., Jr., Poelwijk, F. J., Raman, A., Gosal, W. S., and Ranganathan, R. (2012). The spatial architecture of protein function and adaptation. Nature 491, 138-142.
    O'Connor, O. A., Smith, E. A., Toner, L. E., Teruya-Feldstein, J., Frankel, S., Rolfe, M., Wei, X., Liu, S., Marcucci, G., Chan, K. K., and Chanan-Khan, A. (2006). The combination of the proteasome inhibitor bortezomib and the bcl-2 antisense molecule oblimersen sensitizes human B-cell lymphomas to cyclophosphamide. Clin Cancer Res 12, 2902-2911.
    Placzek, W. J., Wei, J., Kitada, S., Zhai, D., Reed, J. C., and Pellecchia, M. (2010). A survey of the anti-apoptotic Bcl-2 subfamily expression in cancer types provides a platform to predict the efficacy of Bcl-2 antagonists in cancer therapy. Cell Death and Disease 1, e40•e49.
    Procko, E., Hedman, R., Hamilton, K., Seetharaman, J., Fleishman, S. J., Su, M., Aramini, J., Kornhaber, G., Hunt, J. F., Tong, L., et al. (2013). Computational Design of a Protein-Based Enzyme Inhibitor. J Mol Biol.
    Sheffler, W., and Baker, D. (2009). RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation. Protein Sci 18, 229-239.
    Tse, C., Shoemaker, A. R., Adickes, J., Anderson, M. G., Chen, J., Jin, S., Johnson, E. F., Marsh, K. C., Mitten, M. J., Nimmer, P., et al. (2008). ABT-263: a potent and orally bioavailable Bcl-2 family inhibitor. Cancer Res 68, 3421-3428.
    Watanabe, A., Maruo, S., Ito, T., Ito, M., Katsumura, K. R., and Takada, K. (2010). Epstein-Barr virus-encoded Bcl-2 homologue functions as a survival factor in Wp-restricted Burkitt lymphoma cell line P3HR-1. J Virol 84, 2893-2901.
    Whitehead, T. A., Chevalier, A., Song, Y., Dreyfus, C., Fleishman, S. J., De Mattos, C., Myers, C. A., Kamisetty, H., Blair, P., Wilson, I. A., and Baker, D. (2012). Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat Biotechnol 30, 543-548.
    Young, L. S., and Murray, P. G. (2003). Epstein-Barr virus and oncogenesis: from latent genes to tumours. Oncogene 22, 5108-5121.


Example 2. Validation of Binding Specificity and Mechanism in Engineered Cell Lines
We investigated the BCL2 binding profiles and mechanism of action of the optimized inhibitors in mammalian cells, employing a suite of engineered mouse embryonic fibroblasts (MEFs). We first tested whether our inhibitors could selectively induce a hallmark of apoptosis by monitoring cytochrome c release from mitochondria into the cytosol of MEFs with engineered dependence on a single pro-survival BCL2 homolog. Strikingly, permeabilized MEFs treated with each designed inhibitor induced cytochrome c release only in the cell line dependent on the corresponding target BCL2 protein. No cytochrome c release was observed in Bak−/−Bax−/− cells, confirming that mitochondrial outer membrane permeability following inhibitor treatment occurs specifically via the BCL2-regulated intrinsic pathway, as expected (FIG. 21A).
To further validate binding specificity we examined the effect of a subset of inhibitors (αMCL1 and αBFL1) on long-term (i.e. seven day) colony survival in MEFs engineered to inducibly express each inhibitor. Consistent with binding profiles and cytochrome c release data, large effects were only seen with αMCL1 in the Mcl-1-dependent line, causing a 90±11% decrease in survival, and with αBFL1 in the Bfl-1-dependent line, causing a 85±6% decrease in survival (FIG. 22A). Minimal effects on cell survival were observed in lines expressing non-cognate pro-survival proteins. These data validate the specificity of the designed proteins and their capacity to functionally engage BCL2 family members in a cellular milieu.
While engineered MEFs provided an excellent model system to study our designed proteins, we sought further mechanistic validation in a context relevant to their primary application: probing BCL2 family interactions and generating functional BCL2 dependency profiles in cancer. A representative cancer cell line (HeLa) was engineered to overexpress Mcl-1, Bcl-2 or Bcl-xL, and we assayed the activity of the designed inhibitors in each setting (FIG. 21B). Previous studies revealed that HeLa cells are resistant to expression of Noxa (which targets Mcl-1 and Bfl-1) and ABT-737 (Bcl-2 and Bcl-xL) independently, but are potently killed with the combination of Noxa with ABT-737 (van Delft et al., 2006). Likewise, single designed inhibitors had little effect on survival. However, the combination of αMCL1 with αBCL2 caused more substantial cell death (28±5% survival) than αMCL1 with αBCLXL (53±6%) and even more so than αBCL2 with αBCLXL (70±5%). These data, and similar results in Mcl-1-overexpressing (Mcl-1+) HeLa cells, suggest that Mcl-1 plays a more crucial role in wild-type HeLa survival than Bcl-2 or Bcl-xL, and Bcl-2 is a more important secondary target than Bcl-xL. Thus the designed inhibitors not only recapitulate the previous study's results, further validating their specificity and activity in vitro, but also offer improved sensitivity in delineating BCL2 dependencies.
Compared to wild-type and Mcl-1+HeLa cells, Bcl-xL-overexpressing (Bcl-xL+) cells are more resistant to the combination of αMCL1 with αBCL2, and likewise, Bcl-2-overexpressing (Bcl-2+) cells are more resistant to the combination of αMCL1 with αBCLXL. Thus, increased expression of a given BCL2 protein can compensate for the inhibition of others. The triple combination of αMCL1, αBCL2, and αBCLXL had greater efficacy than double combinations, indicating a contribution of each pro-survival protein to basal survival. Bcl-xL+ cells were generally more resistant than all other cell lines; the inability to completely inhibit Bcl-xL's survival function in Bcl-xL+ cells suggests that in this context, Bcl-xL may interact with proteins that are not displaced efficiently by αBCLXL.
To investigate potential mechanisms underlying these results, we assessed the binding profile of a representative BOP, Bim, to pro-survival homologs with co-immunoprecipitation (co-IP) experiments in wild-type and over-expressing cell lines, with and without added αMCL1 (FIG. 22C). In wild-type HeLa cells, Bim associated primarily with Mcl-1. Introduction of αMCL1 resulted in displacement of Bim from Mcl-1, with modest compensatory sequestration of Bim by Bcl-2. In Bcl-2+ cells, Bim is redistributed and preferentially binds Bcl-2 rather than Mcl-1, likely due to the stoichiometric excess of Bcl-2, and αMCL1 has no effect. The cell-killing activity of αMCL1 with αBCL2 in wild-type, Mcl-1+ and Bcl-2+ cells is consistent with these data; inhibition of both Mcl-1 and Bcl-2 in these settings likely overwhelms BOP sequestration, and a higher proportion of Bim and other activator BOPs may be free to interact with Bak and Bax, inducing apoptosis.
Designed Inhibitors Elucidate the Dependence of Human Cancer Cell Lines on Pro-Survival BCL2 Homologs
Next, we set out to define functional BCL2 dependency profiles of other cancer cell lines using a larger set of our designed inhibitors. Apoptotic resistance in melanoma is thought to act via Bfl-1 (Hind et al., 2015), and likewise in glioblastoma via Bcl-2 (Weller et al., 1995) and Bcl-xL (Nagane et al., 2000). Further, oncogenic EGFR mutations in glioblastoma are associated with apoptotic resistance via increased Bcl-xL expression (Latha et al., 2012). Therefore, the selected melanoma and EGFR-modified series of glioblastoma cell lines provide diverse contexts to test the BCL2-profiling capacity of the designed proteins.
In all cell lines, single inhibitors again were unable to induce apoptosis. While SK-MEL-5 were overall more resistant to apoptosis, LOX-IMVI melanoma cells were sensitive to double combinations that included αMCL1 and triple combinations (FIG. 23A). αBFL1 with αBCL2 or αBCLXL had less effect; thus, our results indicate that Mcl-1 plays a more critical role in survival than Bfl-1 in LOX-IMVI, in contrast to mRNA profiling suggesting the opposite (Hind et al., 2015). All glioblastoma cell lines showed similar trends in response to all combinations, while EGFR variants were in some instances more resistant than parental (FIG. 23B). Sensitivity to many different double combinations suggests that in these contexts, pro-survival homologs may resist apoptosis via “mode 1” interactions with the pan- or partially-specific BOPs (Llambi et al., 2011).
To more fully assess the capacity of the designed inhibitors to determine BCL2 profiles, we tested them alongside existing, selective BH3-mimetics in a larger number of cell lines from one type of cancer. Previously, colon cancers showed variable response to small-molecule-mediated Bcl-xL inhibition, and RNAi experiments identified Mcl-1 as a resistance factor (Zhang et al., 2015). To determine whether Mcl-1 antagonism could render colon cancers sensitive to Bcl-xL neutralization and assess the influence of other pro-survival homologs on survival, we modified a panel of seven colon cancer lines to inducibly express either αMCL1 or αBFL1, and treated them with small molecules to selectively inhibit Bcl-2 (ABT-199), Bcl-xL (A-1331852), or Bcl-2 and Bcl-xL simultaneously (ABT-263).
Inhibiting a single pro-survival homolog had little effect on short-term survival; only SW48 cells showed greater than a 50% decrease in viability after treatment with A-1331852, consistent with the previous study showing SW48 is sensitive to Bcl-xL inhibition (Zhang et al., 2015; FIG. 24A). Combined inhibition of both Mcl-1 and Bcl-xL caused nearly complete cell death after 24 hours in all colon cancers except HCT-116; further analyses showed that αMCL1-mediated Mcl-1 inhibition strongly sensitizes most colon cancers to A-1331852 (and to a lesser extent ABT-263), with a 4.6-fold or greater decrease in EC50 values observed in all cell lines except HCT-116 (FIG. 25A-B). All other combinations had much smaller effects. Thus, inhibition of two pro-survival proteins was required and sufficient for cell killing, contrasting glioblastoma in which pro-survival proteins appeared largely redundant. These results suggest that in context of colon cancer, pro-survival proteins may resist apoptosis primarily via “mode 2” inhibition of the direct effector Bak, which interacts preferentially with Mcl-1 and Bcl-xL (Llambi et al., 2011). As αMCL1 targets Mcl-1 in a manner more akin to a drug (i.e. antagonism) compared to RNAi, our data provide further evidence that treatment strategies involving Mcl-1 and Bcl-xL inhibition could be effective in these malignancies.
In long-term survival assays, αMCL1 had negligible effect, but remarkably, αBFL1 caused a significant (63±4%) decrease in RKO cell survival (FIG. 24B). Thus, long-term assays detect sensitivities that short-term assays miss, on a timescale that may provide a more informative preview of therapy. Overall, these data show the utility and sensitivity of the inhibitors in establishing the critical survival factors in colon cancer.

## Claims

1. A polypeptide comprising an amino acid sequence having at least 50% amino acid sequence identity over its length relative to the amino acid sequence of SEQ ID NO. 1, wherein the polypeptide selectively binds to a protein selected from the group consisting of Epstein Barr protein BHFR1, and B cell lymphoma family proteins selected from the group consisting of myeloid cell leukemia 1 (Mcl-1), B-cell lymphoma 2 (Bcl-2), Bcl-2-like protein 1 (BCL2L1/Bcl-XL), Bcl-2-like protein 10 (BCL2L10/Bcl-B), Bcl-2-like protein A1 (A1/Bfl-1), and Bcl-w.

2. The polypeptide of claim 1, comprising an amino acid sequence having at least 66% identity over its length relative to the amino acid sequence of SEQ ID NO. 1.

3. The polypeptide of claim 1, wherein the polypeptide comprises an amino acid sequence having at least 50% amino acid sequence identity over its length relative to the amino acid sequence selected from the group consisting of SEQ ID NOS:2-6 and 265.

4. The polypeptide of claim 3, wherein the polypeptide comprises an amino acid sequence having at least 66% amino acid sequence identity over its length relative to the amino acid sequence selected from the group.

5. The polypeptide of claim 1, wherein the polypeptide is selected from the group consisting of:
(a) a polypeptide that comprises an amino acid sequence according to SEQ ID NO: 7, wherein the polypeptide binds to BHFR1;
(b) a polypeptide that comprises an amino acid sequence according to SEQ ID NO: 8, wherein the polypeptide binds to Bcl-2;
(c) a polypeptide that comprises an amino acid sequence according to SEQ ID NO:9, wherein the polypeptide binds to binds to Bcl-2-like protein 1 (BCL2L1/Bcl-xL);
(d) a polypeptide that comprises an amino acid sequence according to SEQ ID NO: 10, wherein the polypeptide binds to Bcl-2-like protein 10 (BCL2L10/Bcl-B);
(e) a polypeptide that comprises an amino acid sequence according to SEQ ID NO: 11, wherein the polypeptide binds to Bcl-2-like protein A1 (A1/Bfl-1);
(f) a polypeptide that comprises an amino acid sequence according to SEQ ID NO: 12, wherein the polypeptide binds to Bcl-2-like protein Mcl-1;
(g) a polypeptide that comprises an amino acid sequence according to SEQ ID NO: 276, wherein the polypeptide binds to Bcl-2-like protein 2 (BCL2L2/Bcl-w).

6. The polypeptide of claim 1, wherein the polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NOS: 1-6 and 262-273.

7. The polypeptide of claim 1, wherein the polypeptide comprises an amino acid sequence having at least 50% identity over its length relative to the amino acid sequence of SEQ ID NO:13.

8. The polypeptide of claim 7, comprising at least one conservative substitution corresponding to residues 3, 13, 21, 28, 31, 33, 46, 48, 49, 61, 62, 65, 79, 84, 103, and 104 of the amino acid sequence of SEQ ID NO: 13.

9. The polypeptide of claim 8, comprising the substitutions K31E, E48R, and E65R.

10. The polypeptide of claim 9, further comprising the substitutions I21L, Q79L, L84Q, and H104R.

11. The polypeptide of claim 1, further comprising a cell-penetrating peptide.

12. A pharmaceutical composition, comprising the polypeptide of claim 1 and a pharmaceutically acceptable carrier.

13. The pharmaceutical composition of claim 12 further comprising an antibody.

14. The pharmaceutical composition of claim 12, wherein the carrier comprises a polymer.

15. The pharmaceutical composition of claim 14, wherein the polymer comprises a hydrophilic block and an endosomolytic block.

16. The pharmaceutical composition of claim 15, wherein the hydrophilic block comprises polyethylene glycol methacrylate, and wherein the endosomolytic block comprises a diethylaminoethyl methacrylate-butyl methacrylate copolymer.

17. The pharmaceutical composition of claim 14, wherein the polymer is a stimuli-responsive polymer that responds to one or more stimuli selected from the group consisting of pH, temperature, UV-visible light, photo-irradiation, exposure to an electric field, ionic strength, and the concentration of certain chemicals by exhibiting a property change.

18. A recombinant nucleic acid encoding the polypeptide of claim 1.

19. A recombinant expression vector comprising the nucleic acid of claim 18 operatively linked to a promoter.

20. A recombinant host cell comprising the recombinant expression vector of claim 19.

21. A method of treating an Epstein-Barr virus-related disease comprising administering to a subject in need thereof a therapeutically effective amount of one or more of the polypeptide of claim 1, or salts thereof, pharmaceutical compositions thereof, a recombinant nucleic acid encoding the one or more polypeptide, a recombinant expression vector comprising the recombinant nucleic acids, and/or a recombinant host cells comprising the recombinant expression vector, to treat and/or limit Epstein-Barr virus related diseases wherein the polypeptide or encoded polypeptide selectively inhibits BHRF 1.

22. A method for treating cancer, comprising administering to a subject in need thereof a therapeutically effective amount of one or more of the polypeptide of claim 1, or salts thereof, to treat cancer, wherein the or encoded polypeptide selectively inhibits one or more of Mcl-1, Bcl-2, BCL2L1/Bcl-XL, BCL2L10/Bci-B, A1/Bfl-1, and Bci-w.

23. A method for determining the Bcl-2 phenotype of a tumor, comprising contacting tumor cells, tumor cell lysates or tumor cellular components with one or more polypeptides selected from the group consisting of SEQ ID NOS: 1-6, 8-12, 262-273 and 276, under conditions suitable to promote apoptosis signaling in cells of the tumor that express a bcl-2 homologue targeted by the one or more polypeptides; and determining BCL2 dependency of the tumor based on the polypeptide.