# Patent

## Title
Recognition of cellular target binding by a bioactive agent using intracellular bioluminescence resonance energy transfer

## Abstract

Provided herein are compositions and methods for detection and analysis of intracellular binding of a bioactive agent to a cellular target. In particular, bioactive agents tethered to fluorophores, cellular targets fused to bioluminescent reporters, and methods of detecting and analyzing the interaction of bioactive agents with cellular targets therewith.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
The present application is a continuation of U.S. patent application Ser. No. 14/104,845, filed Dec. 12, 2013, now U.S. Pat. No. 10,067,149, which claims priority to U.S. Provisional Patent Application Ser. No. 61/736,429 filed Dec. 12, 2012; and U.S. Provisional Patent Application Ser. No. 61/794,461 filed Mar. 15, 2013; each of which are hereby incorporated by reference in their entireties.


FIELD
The present invention provides compositions and methods for detection and analysis of intracellular binding of a bioactive agent to a cellular target. In particular, provided herein are bioactive agents tethered to fluorophores, cellular targets fused to bioluminescent reporters, and methods of detecting and analyzing the interaction of bioactive agents with cellular targets therewith.
BACKGROUND
The interaction of molecular species with cellular targets is critically important in understanding cellular physiology and developing therapeutic interventions, such as new synthetic drugs and biopharmaceuticals. Methods are needed for accurately and efficiently determining target engagement, particularly within living cells where these interactions mediate their phenotypic responses. The ability to affectively interrogate target engagement has broad implications to the discovery process, ranging from high-throughput screening, optimization of screening hit into drug leads, and the discovery and characterization of therapeutically relevant cellular targets.
Phenotypic-based screening with a small molecule library plays an important role in the drug discovery field. Using such screening approaches, compound libraries, without prior knowledge of their underlying cellular targets, are screened for their ability to mitigate disease symptoms. While this approach can be used to identify small molecules that are able to modulate cellular physiology, determining the biological relevant targets of these small molecule hits is a major technical challenge. In addition, small molecules promoting some desirable phenotypic responses may pose in vivo liabilities due to off-target interactions. In order to predict drug selectivity and minimize potential side effects, it is important to also profile lower affinity, off-target interactions. Most methods today rely on the enrichment of these targets from complex cellular lysate using “bi-functionalized” lead compounds that contain a selective moiety (the lead compound) and a sorting moiety (affinity). As the enrichment is based on the binding properties of the lead compounds, where the inherent affinity of these leads for their target is insufficient, compound analogs are designed to photo-crosslink to the target. By either approach, the specificity of target isolation is essential, and the failure rate of these methods is high. Failure of these approaches can be due to: hit compounds binding multiple targets with low to moderate affinity with these relative weak interactions difficult to detect; lack of robust, straightforward, unbiased technologies to characterize the detected interactions; inability to perform target isolation within the native cellular environment upon which interactions may depend; limited information provided about the binding potency of targets in the cell; and high background of false positive interactions due to non-specific binding to the solid support or functionalized small molecule.
SUMMARY
In some embodiments, the present invention provides BRET assay systems comprising: (a) a bioactive agent tethered to a fluorophore; (b) a cellular target fused to a bioluminescent reporter; and (c) a substrate for the bioluminescent reporter. In some embodiments, the bioactive agent is a small molecule. In some embodiments, the fluorophore is a carboxy rhodamine analog. In some embodiments, the bioluminescent reporter comprises a polypeptide with at least 70% sequence identity (e.g., 75% identity, 80% identity, 85% identity, 90% identity, 95% identity, 98% identity, 99% identity) with SEQ ID NO: 1. In some embodiments, (a) and (b) are within a cell. In some embodiments, (b) is expressed intracellularly as a fusion protein with a protein of interest, e.g., cellular target. In some embodiments, (a) is added extracellularly and enters the cell. In some embodiments, the cellular target is a binding partner of the bioactive agent. In some embodiments, the emission spectrum of the bioluminescent reporter overlaps with the absorption spectrum of the fluorophore. In some embodiments, upon binding of the bioactive agent to the cellular target, conversion of the substrate to a reaction product by the bioluminescent reporter results in excitation of the fluorophore by BRET and fluorescence emission from the fluorophore. In some embodiments, (a) is one of a library of bioactive agents tethered to fluorophores. In some embodiments, (b) is one of a plurality of cellular targets fused to a bioluminescent reporter. In some embodiments, (b) is a library of cells expressing one of a plurality of cellular targets fused to a bioluminescent reporter.
In some embodiments, the present invention provides methods of detecting, analyzing, characterizing, etc. the binding of a bioactive agent to a cellular target. In some embodiments, the cellular target may be the primary drug target. In some embodiments, the cellular target is an off-target liability that may cause undesirable side effects in vivo. In some embodiments, the present invention provides cells comprising one or more of (e.g., each of) (a) a bioactive agents tethered to a fluorophore; (b) a cellular target fused to a bioluminescent reporter; and (c) a substrate for the bioluminescent reporter.
In some embodiments, the present invention provides methods for detection of an interaction between a bioactive agent and a cellular target comprising: (a) expressing in a cell a fusion of said cellular target and a bioluminescent reporter that emits energy at a first wavelength; (b) contacting said cell with said bioactive agent tethered to a fluorophore, wherein said fluorophore accepts energy at said first wavelength and emits energy at a second wavelength; (c) contacting said cell with a substrate for said bioluminescent reporter; (d) detecting energy at said second wavelength, wherein the presence of said energy at said second wavelength indicates the interaction of said bioactive agent with said cellular target.



DRAWINGS
FIG. 1 shows a schematic representation of an embodiment of the present invention: (Panel A) fluorophore-tethered bioactive agent and bioluminescent-reporter-tethered cellular target; (Panel B) binding of bioactive agent to cellular target; (Panel C) addition of reporter substrate results in BRET; and (Panel D) displacement by excess untethered bioactive agent results in loss of BRET and fluorescence.
FIGS. 2A-B show graphs comparing the BRET profiles of two different fluorophore-SAHA derivatives as BRET acceptors for NANOLUC-HDAC6 fusions in live cells.
FIGS. 3A-B show graphs depicting the effect of dilution of expression on assay performance. FIG. 3A demonstrates the effect of lowered expression on the BRET assay window using competitive displacement of fluorophore-tethered SAHA from NANOLUC-fused HDAC6. FIG. 3B shows the effect of lowered expression on both BRET assay window, as well as observed compound potency (EC50) for a drug tracer binding to NANOLUC-Histamine H1 receptor.
FIG. 4, Panels A and B show graphs demonstrating the requirement of the cellular milieu for pro-drug processing.
FIGS. 5A-C show graphs demonstrating the ability to use permeabilization agents to potentiate the entry of impermeable drug tracers.
FIG. 6 shows a graph depicting competitive displacement of fluorophore-tethered BIRB-796 from NANOLUC-fused p38.
FIG. 7, Panels A and B show graphs depicting measurement of the kinetics of fluorophore-tethered BIRB-796 from NANOLUC-fused p38.
FIGS. 8A-B show exemplary fluorophore-tethered bioactive agents and other compounds that find use in embodiments described herein.
FIGS. 9A-B show a comparison of p38 fusions with Renilla luciferase and NANOLUC luciferase within an embodiment described herein.
FIGS. 10A-B show dose-response curves for NANOLUC-p38alpha binding to a BIRB-TOM conjugate compared to a BIRB-TMR conjugate.
FIG. 11 shows dose-response curves for PKCalpha-NANOLUC binding to a BIM-TOM conjugate compared to a BIM-TMR conjugate.
FIG. 12 shows selectivity of PBI-4838 to Jnk2, p38beta and p38alpha.
FIG. 13 shows a graph depicting detection of specific BRET response in live cells.
FIGS. 14A-C show affinity of PBI-4838 to Jnk2, p38beta, and p38alpha.
FIGS. 15A-C shows relative affinities of PBI-4966 to wild-type BRD4 versus the mutant BRD4.
FIGS. 16A-D show structurally-distinct compounds can be identified by competitive displacement of drug tracers using the method of the present invention.
FIGS. 17A-C show graphs depicting competitive displacement of drug tracers with unlabeled drug.
FIG. 18 shows a graph depicting measurement of specific binding between a drug tracer and the NANOLUC-target fusion in a cell-free system.
FIG. 19, Panels A and B show graphs depicting a specific BRET response in TNT.
FIGS. 20A-B show graphs depicting measurement of binding of fluorescently-labeled cytokines to NANOLUC-EGFR.



DETAILED DESCRIPTION
The present invention provides compositions and methods for detection and analysis of intracellular binding of a bioactive agent to a cellular target. In particular, provided herein are bioactive agents tethered to fluorophores, potential cellular targets fused to bioluminescent reporter proteins and methods of detecting and analyzing the interaction of bioactive agents with cellular targets therewith (See FIG. 1).
The interaction of a first entity (e.g., bioactive agent) and a second entity (e.g., cellular target) is detected, characterized, quantified, analyzed, etc. through the detection/measurement of a signal produced by signal transfer (e.g., transfer of energy (e.g., fluorescence, light energy, resonance, by BRET, etc.)) between a third entity (e.g., fluorophore) connected, fused, tethered, linked, etc. to the first entity and a fourth entity (e.g., bioluminescent reporter protein) connected, fused, tethered, linked, etc. to the second entity. The interaction and/or binding of the first and second entities bring the third and fourth entities into close enough proximity to allow signal transfer (e.g., energy transfer) from one to another. In some embodiments, the fourth entity (e.g., bioluminescent reporter protein) emits energy (e.g., upon interaction with its substrate), and that emitted energy is absorbed by the third entity (e.g., fluorophore), causing the third entity to emit measurable different energy form the fourth entity (e.g., light at a different wavelength). In such embodiments, detection of the energy emitted from the third entity (e.g., light at the emission maximum of the third entity) upon addition to the system of the substrate for the fourth entity (e.g., bioluminescent reporter) indicates interaction of the first and second entities. In some embodiments, the duration, kinetics, affinity, strength, and/or specificity, of the binding of the first and second entities is detected, measured, quantified, determined, interrogated, etc. based on measurement of the signal output of the fourth entity (e.g., bioluminescent reporter protein) under various conditions.
In various embodiments, a cellular target fused to a bioluminescent reporter protein and a bioactive agent tethered to a fluorophore are provided (e.g., intracellularly, extracellularly, in lysate, in vitro, etc.). Substrate for the bioluminescent reporter protein is added to the system. If an interaction has occurred (e.g., binding) between the bioactive agent and the cellular target, the bioluminescent reporter protein and fluorophore are brought into close enough proximity for BRET to occur, and a detectable signal to be emitted from the fluorophore.
In some embodiments, the cellular target and bioluminescent reporter fusion is expressed in cells in which an assay is to be performed. In some embodiments, the fusion is expressed at or near the native abundance for the cellular target. In some embodiments, the fluorophore-tethered bioactive agent is added extracellularly (e.g., added to the culture medium) and enters the cell via diffusion, active transport, passive transport, endocytosis, or any suitable mechanism. In some embodiments, varying amount of fluorophore-tethered bioactive agent is added to the cells to assay binding kinetics, assay binding affinity, provide sufficient signal, etc.
In certain embodiments, the present invention provides compositions, methods, and systems for detection of intracellular interactions between a bioactive agent and cellular target (e.g., known or unknown). In some embodiments, a fusion of a bioluminescent reporter and a cellular target are expressed within a cell. The bioactive agent, tethered to a fluorophore, is introduced to the cell (e.g., conjugate of fluorophore and bioactive agent is cell permeable, cell is permeablized, etc.). A substrate for the bioluminescent reporter protein is added to the cell prior, concurrently or subsequent to the addition of the bioactive agent. Detection of a fluorescent signal from the fluorophore (as the result of BRET) indicates an intracellular interaction (e.g., binding) between the bioactive agent and cellular target. In some embodiments, a cellular target fused to a bioluminescent reporter is expressed at a natural cellular abundance (e.g., relative to the native cellular target, or at a level appropriate for proper biological function of the fused target). In some embodiments, interaction of a bioactive agent with a cellular target is detected intracellularly.
In some embodiments, characteristics of the interaction between the bioactive agent and cellular target are interrogated by altering the cellular conditions or the conditions of the system. For example, in some embodiments, a competitive binder of the cellular target (e.g., untethered bioactive agent) is added to the cell to compete with the fluorophore-tethered bioactive agent.
In some embodiments, a library of bioluminescent reporter protein-tagged cellular targets is provided (e.g., in solution, in a lysate, immobilized on a surface, expressed within a cell, etc.). In some embodiments, a bioactive agent is provided which lacks a known cellular target or where knowledge of the cellular target is uncertain or incomplete. The cellular target of a bioactive agent is determined by adding the bioactive agent to the library and determining which cellular-target fusion produces BRET induced fluorescence of the bioactive agent-tethered fluorophore. In some embodiments, the library of bioluminescent reporter-tagged cellular targets is provided as a collection of nucleic acids or vectors comprising nucleic acids (e.g., plasmids, BacMam viruses, Lentiviruses, etc.) encoding the protein fusions. In some embodiments, the library of bioluminescent reporter protein-tagged cellular targets is expressed within cells. In some embodiments, the library of bioluminescent reporter-tagged cellular targets is provided by translating nucleic acids in cell-free translation reactions. In some embodiments, a library of cellular targets fusions, or cells expressing cellular target fusions, are provided in a microplate format. In such embodiments, the interaction of a bioactive agent (e.g., one identified through a phenotypic assay or screen) with the entire library of cellular targets can be interrogated (e.g., in solution, in lysates, intracellularly, etc.) in a high-throughput manner. In some embodiments, bioluminescent reporter-tagged cellular targets are immobilized on a solid surface to create a protein array. For example, in some embodiments, in addition to the bioluminescent reporter, cellular targets are also expressed as fusions with a tag or coupled to a protein (e.g., HALOTAG, Promega) that allows for the proteins to be covalently immobilized on a solid surface (e.g., a surface displaying appropriate ligands (e.g., HALOTAG Ligand)). In certain embodiments, a library of bioactive agents (e.g., lead compounds or drug-like small molecules) is added to the system (e.g., array) and any pairs capable of producing BRET are identified. In some embodiments, cellular targets for all or a portion of a library of bioactive agents are unknown.
In certain embodiments, compositions, methods, and systems herein provide a conjugate of a bioactive agent and an energy acceptor (e.g., fluorophore, chromophore). In some embodiments, a bioactive agent is any small molecule (e.g., >2000 daltons, >1000 daltons, >500 daltons, etc.), macromolecule, or molecular complex capable of interacting with the biology of a cell. In some embodiments, an energy acceptor is an entity capable of generating, exhibiting, and/or emitting a signal (e.g., light, heat, chemical reaction, fluorescence, resonance energy, etc.) when triggered by energy absorption (e.g., resonance energy transfer). In some embodiments, a bioactive agent and energy acceptor (e.g., fluorophore, chromophore) are fused, tethered, connected, etc., by any suitable structure or mechanism (e.g., expressed as a fusion construct (e.g., with or without peptide linker), chemically linked (e.g., directly or indirectly), enzymatically linked, linked by a linker (e.g., peptide, nucleic acid, polymer, ester linkage, PEG linker, carbon chain, etc.)). In some embodiments, the conjugate of a bioactive agent and an energy acceptor (e.g., bioactive agent tethered to a fluorophore) is produced by non-natural chemical synthesis (e.g., a purposeful execution of chemical reactions not present in natural cells). The type of linkage should not be viewed as limiting.
As used herein, the term “bioactive agent” refers generally to any physiologically or pharmacologically active substance or a substance suitable for detection. In some embodiments, a bioactive agent is a potential therapeutic compound (e.g., small molecule, peptide, nucleic acid, etc.), or drug-like molecule. In some embodiments, the bioactive agent is produced by non-natural chemical synthesis (e.g., a purposeful execution of chemical reactions not present in natural cells). Bioactive agents for use in embodiments described herein are not limited by size or structure.
In certain embodiments, libraries of bioactive agents (e.g., >50 agents, >100 agents, >500 agents, >1000 agents, >5000 agents, >10,000 agents, >50,000 agents, etc.) are provided. In some embodiments, systems, methods, and compositions are provided for screening libraries of bioactive agents for a phenotypic effect and/or activity. In some embodiments, the present invention provides means of identifying the bioactive agent in a library responsible for producing, eliciting, inducing, etc. phenotypic effect and/or activity. In some embodiments, the present invention provides means of identifying the cellular target of a bioactive agent (e.g., a bioactive agent responsible for the phenotypic effect and/or activity).
As used herein, the term “energy acceptor” refers to any small molecule (e.g., dye), macromolecule (e.g., autofluorescent protein, phycobiliproteins, nanoparticle, surface, etc.), or molecular complex that produces a readily detectable signal in response to energy absorption (e.g., resonance energy transfer). In certain embodiments, an energy acceptor is a fluorophore or other detectable chromophore. Suitable fluorophores include, but are not limited to: xanthene derivatives (e.g., fluorescein, rhodamine, Oregon green, eosin, Texas red, etc.), cyanine derivatives (e.g., cyanine, indocarbocyanine, oxacarbocyanine, thiacarbocyanine, merocyanine, etc.), naphthalene derivatives (e.g., dansyl and prodan derivatives), oxadiazole derivatives (e.g., pyridyloxazole, nitrobenzoxadiazole, benzoxadiazole, etc.), pyrene derivatives (e.g., cascade blue), oxazine derivatives (e.g., Nile red, Nile blue, cresyl violet, oxazine 170, etc.), acridine derivatives (e.g., proflavin, acridine orange, acridine yellow, etc.), arylmethine derivatives (e.g., auramine, crystal violet, malachite green, etc.), tetrapyrrole derivatives (e.g., porphin, phtalocyanine, bilirubin, etc.), CF dye (Biotium), BODIPY (Invitrogen), ALEXA FLOUR (Invitrogen), DYLIGHT FLUOR (Thermo Scientific, Pierce), ATTO and TRACY (Sigma Aldrich), FluoProbes (Interchim), DY and MEGASTOKES (Dyomics), SULFO CY dyes (CYANDYE, LLC), SETAU and SQUARE DYES (SETA BioMedicals), QUASAR and CAL FLUOR dyes (Biosearch Technologies), SURELIGHT DYES (APC, RPE, PerCP, Phycobilisomes)(Columbia Biosciences), APC, APCXL, RPE, BPE (Phyco-Biotech), autofluorescent proteins (e.g., YFP, RFP, mCherry, mKate), quantum dot nanocrystals, etc. In some embodiments, a fluorophore is a rhodamine analog (e.g., carboxy rhodamine analog), such as those described in U.S. patent application Ser. No. 13/682,589, herein incorporated by reference in its entirety. Some such fluorophores are described herein in Example 8. In some embodiments, BRET efficiency is significantly enhanced by the technical features of rhodamine analog (e.g., carboxy rhodamine analog) as an energy acceptor compared to other fluorophores. For example, the left shifted EC50 and reduced nonspecific background of these dyes is advantageous for use in some embodiments.
In certain embodiments, compositions, methods, and systems herein provide a fusion of a cellular target and a bioluminescent reporter protein (e.g., luciferase). In some embodiments, a cellular target and bioluminescent reporter protein are fused, tethered, connected, etc. by any suitable structure or mechanism (e.g., expressed as a fusion construct (e.g., with or without peptide linker), chemically linked (e.g., directly or indirectly), enzymatically linked, linked by a linker (e.g., peptide, nucleic acid, other polymer (e.g., ester linkage, PEG linker, carbon chain, etc.)). In some embodiments, an amino acid chain (e.g., 3-100 amino acids) is used to connect the cellular target and a bioluminescent reporter protein. In some embodiments, the structure and/or function of neither the cellular target nor the bioluminescent reporter are impacted (e.g., significantly impacted) by fusion or the presence of the linker. In certain embodiments, a linker allows fusion without loss of activity or one or both of the elements. In other embodiments, an amino acid linker properly spaces and/or orients the bioluminescent reported for energy transfer with the fluorophore.
In some embodiments, a cellular target comprises any suitable binding/interaction partner (e.g., receptor, enzyme) for a bioactive agent (e.g., small molecule, protein, nucleic acid, lipid, etc.). However, in some embodiments, knowledge of the interaction between a cellular target and bioactive agent is not required to practice the invention. In particular embodiments, a cellular target is a protein that binds to or otherwise interacts with (e.g., has a binding affinity to) a bioactive agent. In more particular embodiments, a cellular target is a receptor protein or an enzyme that binds to or otherwise interacts with (e.g., has a binding affinity to) a small molecule bioactive agent. The present invention is not limited by the identity, type, or class of cellular targets. In certain embodiments, libraries of hundreds, thousands, tens of thousands, more different cellular targets find use in the present invention. In some embodiments, a cellular target is a G-protein coupled receptor or a protein kinase.
In certain embodiments, the bioluminescent reporter is a luciferase. In some embodiments, a luciferase is selected from those found in Gaussia, Coleoptera, (e.g., fireflies), Renilla, Vargula, Oplophorus, mutants thereof, portions thereof, variants thereof, and any other luciferase enzymes suitable for the systems and methods described herein. In some embodiments, the bioluminescent reporter protein is a modified, enhanced luciferase enzyme from Oplophorus (e.g., NANOLUC enzyme from Promega Corporation, SEQ ID NO: 1, or a sequence with at least 70% identity (e.g., >70%, >80%, >90%, >95%) thereto). In some embodiments, the bioluminescent reporter protein is a thermostable Photuris pennsylvanica luciferase or a sequence with at least 70% identity (e.g., >70%, >80%, >90%, >95%) thereto). Exemplary bioluminescent reporters are described, for example, in U.S. Pat. App. No. 2010/0281552 and U.S. Pat. App. No. 2012/0174242, both of which are herein incorporated by reference in their entireties.
In some embodiments, the bioluminescent reporter protein comprises NANOLUC (See U.S. Pat. App. Nos. 2010/0281552 and 2012/0174242, herein incorporated by reference in their entireties). In some embodiments, the bioluminescent reporter protein comprises a polypeptide with at least 70% identity (e.g., >70%, >80%, >90%, >95%) to SEQ ID NO: 1 that retains bioluminescent characteristics. In certain embodiments, the use of the NANOLUC enzyme, or a variant thereof, provides features (e.g., signal intensity, brightness, high light output, etc.) that enable the use of the BRET assays described herein. In some embodiments, the high light output of NANOLUC enables the low concentration (e.g., <1 μM, <100 nM, <10 nm, <1 nm, etc.) of assay components, e.g., DNA encoding NANOLUC, useful to carry out assays under physiologically relevant conditions. In some embodiments, NANOLUC enables the use of BRET in characterizing cellular targets identified in a phenotypic screen.
In some embodiments, a substrate for the bioluminescent reporter protein is provided. In some embodiments, the bioluminescent reporter protein converts the substrate into a reaction product and releases light energy as a by-product. In some embodiments, the substrate is a substrate for a luciferase enzyme. In some embodiments, the substrate is a substrate for a modified, enhanced luciferase enzyme from Oplophorus, e.g., NANOLUC enzyme from Promega Corporation (e.g., SEQ ID NO: 1). In some embodiments, a pro-substrate for the bioluminescent reporter protein is provided, which produces a substrate through a chemical or physical process (e.g., hydrolysis, enzymatic reaction, photo-cleavage, etc). In some embodiments, the pro-substrate comprises coelenterazine, a coelenterazine derivative, a structural or functional equivalent of coelenterazine, a molecule substantially equivalent to coelenterazine (e.g., structurally and/or functionally), or molecule functionally or structurally similar to coelenterazine. In some embodiments, the bioluminescent reporter protein converts the coelenterazine, coelenterazine derivative, structural or functional equivalent of coelenterazine, or substantial equivalent to coelenterazine into coelenteramide, a coelenteramide derivative, a structural or functional equivalent of coelenteramide, or a substantial equivalent to coelenteramide and releases light energy as a by-product.
In some embodiments, fluorophore and bioluminescent reporter are selected that exhibit sufficient overlap of emission (e.g., of bioluminescent reporter) and excitation (e.g., of fluorphore) spectra to provide efficient energy transfer between the two. In some embodiments, the peak emission of the bioluminescent reporter is substantially separated from the peak emission of the fluorophore, for example by at least 80 nm, 100 nm, 120 nm, 140 nm, etc., in wavelength. In particular embodiments, the Forster distance of the fluorophore and bioluminescent reporter pair is small (e.g., <20 nm, <10 nm, <5 nm, <3 nm, etc.). In such embodiments, the short Forster distance results in the requirement that the fluorophore and bioluminescent reporter must be brought into very close proximity for energy transfer to occur. Therefore, the short Forster distance reduces aberrant and/or background signal (e.g., created by diffusing fluorophore and/or reporter).
In certain embodiments, a fluorophore and bioluminescent reporter pair are selected that are sufficiently bright to allow detection of the transferred signal at a native abundance (or near native abundance) of the cellular target fused to the bioluminescent reporter. In some embodiments, should either the selected fluorophore or bioluminescent reporter produce insufficient energy (light) emission, either the fusion of the cellular target and bioluminescent reporter will need to be overexpressed (e.g., beyond native abundance, beyond a biologically relevant level, etc.), and/or the amount of fluorophore-tethered bioactive agent will have to be increased (e.g., to a potentially toxic level, beyond a physiologically relevant level, above the amount when kinetic experiments can be performed, etc.). In some embodiments, sufficient brightness of the bioluminescent reporter and fluorophore allows detection of bioactive agent and cellular target interaction at a range of concentrations and ratios.
In some embodiments, compositions, methods, and systems are provided for identification of the cellular targets of lead compounds emerging from a phenotypic assay or phenotypic screen. In some embodiments, binding of a bioactive agent (e.g., small molecule) to a cellular target is characterized using a competitive binding assay (SEE FIG. 1, Panel C and 1, Panel D). In some embodiments, following identification of bioactive agents capable of eliciting a phenotype, “lead compounds” tethered to fluorophores are used to identify cellular targets, through their linkage to a bioluminescence reporter protein (e.g., binding of bioactive agent to cellular target results in BRET between bioluminescence reporter protein and fluorophore). In such embodiments, although a phenotype has been associated with a particular bioactive agent, the interaction partner (e.g., cellular target) for that bioactive agent in unknown. In some embodiments, the bioactive agent tethered to a fluorophore is able to regenerate a phenotype, thereby validating that tethering the bioactive agent to the fluorophore (or the cellular target to the bioluminescent reporter) does not affect the cellular binding patterns. In some embodiments, the use of a library of cellular targets, each fused to bioluminescent reporter protein (e.g., NANOLUC), provides less interference due to relative solubility or native abundance of the cellular target compared to other detection methods (e.g., mass spectrometry analysis). In some embodiments, such a detection method provides a greater degree of sensitivity or specificity. In some embodiments, target identification through linkage to a bioluminescence reporter protein enables detection through energy transfer, even when binding of the target is inefficient or incomplete. In some embodiments, BRET allows for analysis of the lead compound's binding affinity in live cells using competitive displacement of a fluorescent tracer that binds to the same site on the cellular target. In some embodiments, systems and methods described herein provide the ability to use two distinct methods with the same library for target identification, thus providing higher stringency for identifying cellular targets, complementary methods addressing all the major limitations with other approaches, detection of low affinity targets (e.g., BRET provides the advantage of maintaining the bioactive agent in equilibrium with the target throughout the experiment).
Some embodiments described herein find use in drug discovery, drug validation, drug target discovery, or drug target validation. In certain embodiments, the binding interaction between a bioactive agent (e.g., drug-like small molecule) and a cellular target can be detected, validated, and/or characterized. In some embodiments, the relative binding affinity of bioactive agents for a cellular target (e.g., in solution, in a lysate, on a surface, in a cell, etc.), can be determined by their ability to displace a bioactive agent that has been tethered to a fluorophore. Specifically, higher binding affinity of a first bioactive agent relative to a second bioactive agent is indicated by requiring a lower concentration of the first bioactive agent to displace a tethered bioactive agent relative to the second bioactive agent. Displacement of the tethered bioactive agent is determined by the loss or reduction of energy transfer from the bioluminescent reporter protein fused to a cellular target. In some embodiments, the concentration of bioactive agent needed to displace a tethered bioactive agent is used to estimate the binding EC50 or the inhibition constant (Ki) for bioactive agent. In some embodiments, the development of new or modified bioactive agents is guided by their ability to displace one or more bioactive agents, each tethered to a fluorophore, from one or more cellular targets, each fused to a bioluminescent reporter protein.
In some embodiments, a collection of compounds which may have unknown binding affinity to a cellular target may be screened for their ability to bind the target fused to a bioluminescent protein by determining their ability to displace a bioactive agent tethered to a fluorophore. In some embodiments, compounds may be screened for their ability to bind a first cellular target preferentially relative to a second cellular target by their ability to displace a first tethered bioactive agent from the first cellular target relative to a second tethered bioactive agent from the second bioactive target. In some embodiments, the first and second tethered bioactive agents are the same.
In some embodiments, systems and methods described herein provide the ability to determine the affinity of a bioactive agent (e.g., lead compound) for wild-type and mutant version(s) of a cellular target, e.g., target protein. In some embodiments, characterization of the affinity and selectivity of the fluorescently-labeled bioactive agent (e.g., drug) to a disease-relevant mutant protein may be performed in cells. Such systems and methods may be useful to identify bioactive agent(s) (e.g., drug) that selectively bind a wild-type or mutant protein differentially.
In addition to primary targets, intended targets, and/or known targets, bioactive agents (e.g., lead compounds) may also bind to unexpected and/or unintended cellular targets (off targets). In some cases, off target of a bioactive agent is responsible for a portion of the therapeutic and/or adverse effects associated with administration of the bioactive agent. In some embodiments, systems and methods described herein provide the ability to identify off targets of a bioactive agent. Understanding the identity and extent of off-target bioactive agent binding provides valuable information regarding the pharmacology of the agent.
In some embodiments, systems and methods described herein provide the ability to estimate the binding characteristics of a bioactive agent tethered with a fluorophore to a cellular target fused to a bioluminescent reporter (e.g., EC50, Kd, binding rate, environmental influences, etc.) In some embodiments, the binding characteristics are correlated to biochemical, physical, or phenotypic characteristics related to the cellular target. In some embodiments, displacement of the tethered bioactive agent by a separate agent may occur through separate sites on the cellular target. In some embodiments, the binding characteristics of the tethered bioactive agent may be used to determine the influence of post-translational modification (e.g., cleavage, phosphorylation, methylation, acetylation, lipidation, etc.), intracellular translocation (e.g., movement to a nucleus, mitochondria, membrane, etc.), or protein interaction (e.g., interactions with other proteins, nucleic acids, lipids, etc.) on the cellular target. An example is determining the binding characteristics of an antibody to a cellular target by its influence on the binding characteristics of the tethered bioactive agent. In some embodiments, the binding characteristics of the tethered bioactive agent may be used to determine the influence of chemical modifications or transformation of the bioactive agent or the tethered fluorophore (e.g., intracellular metabolism, change in ionic state, etc.)
In some embodiments, the cellular target may comprise more than one molecular component. For example, the target may comprise more than one polypeptide, and may further comprise other natural or synthetic molecules (e.g., prosthetic groups, cofactors, metabolites, nucleic acids, lipids, carbohydrates, etc.). In some embodiments, a bioactive agent tethered to a fluorophore binds to a first molecular component, and a bioluminescent reporter is fused to a second molecular component, so that a signal from the tethered bioactive agent is produced when bound to the first molecular component and the first molecular component is in close proximity to the second molecular component.
A priori knowledge of the existence of an interaction between a bioactive agent and cellular target is not need to practice the invention. In some embodiments, detection and/or characterization of an unknown or previously unidentified interaction by energy transfer is provided. Advantages of the systems, compositions, and methods described herein, over other methods of target discovery may include: a broad range of possible bioactive agent concentrations because (in some embodiments) it need not be expressed within cells (e.g., allows for addition of enough acceptor fluorophore to generate detectable signal), natural protein concentration of cellular target (e.g., no need for overexpression to gain enough signal for detection), signal detectable on a plate reader (e.g., high throughput detection, no imaging necessary), detection of interactions within a cell, etc.
In some embodiments, bioactive agents (e.g., lead compounds) are conjugated to a fluorescent energy acceptor dye, and therefore the binding of the modified agent to its luciferase-fused (e.g., NANOLUC-fused) cellular target results in energy transfer from NANOLUC to the acceptor dye. Such a system provides a homogenous assay that can be performed in living cells. In some embodiments, the labeled bioactive agent remains in equilibrium with the cellular target throughout the experiment allowing detection of targets that interact with the lead compounds with low affinity. In some embodiments, BRET enables measurements of binding affinity in living cells by the competitive displacement of a fluorescent tracer designed for the same binding site.
In some embodiments, BRET efficiency is significantly enhanced by the technical features of NANOLUC as an energy donor compared to other luciferases. For example, NANOLUC is significantly brighter than other luciferases commonly used for BRET, thereby allowing energy transfer to be quantitated at lower expression levels which are more suitable for maintaining relevant biology within a cell. In some embodiments, the narrow emission spectrum of NANOLUC increases the dynamic range by reducing spectral cross-over in the acceptor channel. In some embodiments, the dynamic range can be further increased by using long-wavelength acceptors that emit in the near-red region of the spectrum (600 to 650 nm). In some embodiments, evaluation of multiple dye ligands during development of embodiments of the present invention revealed that rhodamine analogs (e.g., carboxy rhodamine analog), such as those described in U.S. patent application Ser. No. 13/682,589, herein incorporated by reference in its entirety, delivers an optimal dynamic range for use with NANOLUC and/or in the BRET applications described herein.
EXPERIMENTAL
Example 1
Experiments were conducted during development of embodiments of the present invention to demonstrate the improved performance of PBI tracer conjugates and compared to conjugates with standard dyes for drug tracer applications. In this example, conjugates of suberoylanilide hydroxamic acid (SAHA), an inhibitor of histone deacetylase 6 (HDAC6), and a PBI dye (SAHA-TOM (PBI-4968); See FIGS. 8A-B) or standard dye (SAHA-TAMRA (PBI-4967); See FIGS. 8A-B) were utilized in an intracellular BRET assay using a NANOLUC-HDAC fusion protein (SEQ ID NO: 3).
HEK293 cells were transfected using FuGene HD (Promega Corp.) with plasmid DNA encoding a NANOLUC-HDAC6 fusion protein. NANOLUC-HDAC6 DNA was diluted 1:1000 with a promoterless carrier DNA (pGEM3Z) to yield a final concentration of 50 ng/well total DNA in 96-well plate format (at a seeding density of 20,000 cells/well). Twenty-four hours post-transfection, cells were then incubated with serially-diluted tracer in the presence or absence of a molar excess of unlabeled SAHA (as a specificity control). Following equilibration with the drug tracers, furimazine (a coelenterazine derivative substrate for NANOLUC; Promega Corp.) was added at a concentration of 20 uM, and BRET was quantified on a Varioskan luminometer. The specific BRET signal was calculated by subtracting the non-specific signal (in the presence of unlabeled SAHA) from the signal generated from the SAHA tracer alone.
Results in FIGS. 2A-B demonstrate that the SAHA-TOM (PBI-4968) conjugate/tracer generated a superior, specific BRET signal compared to SAHA-TMR (PBI-4967) and also generated a left-shifted EC50 value for binding within living cells. As a drug conjugate for BRET applications, the benefit of the PBI-4968 TOM dye over other commonly used fluorophores can be applied to competitive binding assays or target identification (chemical proteomics) screening using NANOLUC fusion protein libraries.
While this example demonstrates the binding of a drug tracer to a known high-affinity target, in other embodiments such a tracer is combined with a library of NANOLUC fusion proteins to profile relative drug affinities and specificities across target families. In such embodiments, profiling efforts aide in identification of drugs with promiscuous binding profiles, which may correlate with undesirable drug side effects in vivo.
Example 2
Experiments were conducted during development of embodiments of the present invention to demonstrate the unexpected benefit of low expression levels of NANOLUC for BRET applications.
A) HEK293 cells were transfected using Fugene HD with varying amounts of NANOLUC-HDAC6 DNA and seeded in a 96-well plate format. For the transfection, NANOLUC-HDAC6 DNA was diluted with promoterless carrier DNA (pGEM3Z). The final DNA concentration/well remained 50 ng/well; however the NANOLUC-HDAC6 DNA was diluted 1:10, 1:100, and 1:1000 (at a seeding density of 20,000 cells/well in 96-well format). Twenty-four hours post-transfection, cells were treated with serially-diluted SAHA in the presence of a fixed concentration (1 uM) of SAHA-TOM (PBI-4968; See FIGS. 8A-B) conjugate. After two hours of incubation, furimazine was added to 20 uM, and BRET detected on a Varioskan luminometer. The results in FIGS. 3A-B demonstrate that an unexpectedly high dilution of DNA encoding the NANOLUC fusion was required to achieve proper signal to background for BRET applications.
B) DNA encoding a NANOLUC-Histamine H1 (GPCR) fusion protein was transfected into HEK293 cells using varying amounts of DNA ranging from undiluted to 1:10,000 (diluted with promoterless carrier DNA (pGEM3Z as described above) to maintain a constant amount of DNA/transfection as described above). Twenty-four hours post-transfection, cells were treated with serially-diluted with mepyramine-bodipy-633 (CellAura) and equilibrated for 2 hours. Cells were then treated with furimazine to a concentration of 20 uM, and BRET detected on a Varioskan luminometer.
The results in FIG. 3B indicate that a large dilution of DNA encoding the NANOLUC fusion was required to generate a high affinity interaction with optimal signal-to-background. The ability to dilute NANOLUC fusion proteins to exceedingly low levels is beneficial in various BRET applications, including competitive binding assays or target identification (chemical proteomics) screening of NANOLUC fusion proteins.
Example 3
Experiments were conducted during development of embodiments of the present invention to demonstrate the predictive value of intracellular BRET measurement for quantifying the binding of pro-drugs compared to traditional biochemical (activity-based) formats. The example includes the natural pro-drug, FK228, which requires the reducing environment of the cell cytoplasm to become activated and capable of binding to HDAC6.
HEK293 cells were transfected with DNA encoding NANOLUC-HDAC6 at a 1:1000 dilution with carrier DNA as previously described. Twenty-four hours post-transfection, cells were incubated with serially-diluted natural pro-drug, FK-228; in the presence of a fixed concentration (1 uM) of SAHA-TOM (PBI-4968) conjugate. For comparison, a biochemical, activity-based HDAC6 assay was run in parallel. Briefly, a 3-fold serial dilution of FK-228 (Selleckchem catalog #S3020) was performed at 100× in 100% DMSO in wells of a 96-well plate. A 5 μL aliquot of this 100×/100% DMSO titration series was added to 245 μL of HDAC-GloTM I/II assay buffer alone (Promega Corp.) or 245 μL of HDAC-GloTM I/II assay buffer supplemented with 2× (0.5 mM) DTT to make a 2×/2% DMSO master intermediate titration series of FK-228 in wells of a 96-well plate. From this master intermediate titration series, 5 replicates were transferred to wells of a white 384-well assay plate (Corning 3673). A 5 addition of 2×(2 nM) HDAC 6 (BPS Bioscience catalog #50006) was added to all wells for a final concentration of 1 nM HDAC6/well. The 104, enzyme/inhibitor mixes was allowed to pre-incubate for 45 minutes at room temperature. An equal volume (10 μL) of HDAC-GloTM I/II Final Detection Reagent (Promega Corp.) was added to all wells (20 μL final assay volume), and luminescence was measured after a 10 minute incubation at room temperature. For all test conditions, the final concentration of HDAC-GloTM I/II substrate was 50 μM. The data was plotted (sigmoidal dose response—variable slope) using PrismTM software from GraphPad (no DTT: closed circles; 0.25 mM DTT: open squares).
The results in FIGS. 4A and 4B indicate the requirement of the cellular milieu for measuring binding of pro-drugs that must be processed by the cell to become activated.
Example 4
Experiments were conducted during development of embodiments of the present invention to demonstrate the use of permeabilization agents to introduce impermeable drug tracers to cells.
HEK293 cells were transfected with DNA encoding PKCalpha (PKCa)-NANOLUC or NANOLUC-PKCalpha at a 1:1000 dilution of DNA with promoterless carrier DNA as described previously. Twenty-four hours post-transfection, cells were treated with or without digitonin to a final concentration of 50 ug/mL. Cells were then treated with serially-diluted a staurosporine-PBI-dye conjugate (PBI-5129; See FIGS. 8A-B). Cells were co-incubated in the presence or absence of 5 uM unconjugated staurosporine as a specificity control for binding. Following two hours of equilibration with a tracer, furimazine was added to a final concentration of 20 uM, and BRET ratios were measured on a Varioskan luminometer (FIGS. 5A and 5B).
In a second experiment, identically-transfected PKCa-NANOLUC cells were treated with serially diluted digitonin prior to treatment with a fixed concentration of staurosporine-TOM (PBI-5129; See FIGS. 8A-B) tracer (5 uM final concentration) in the presence or absence of 5 uM unlabeled staurosporine (specificity control) (FIG. 5C).
FIG. 5A-C demonstrate the ability to use permeabilization agent to potentiate the entry of impermeable drug tracers and applied to BRET-based chemical proteomics screens of NANOLUCTM fusion protein libraries.
Example 5
Experiments were conducted during development of embodiments of the present invention to demonstrate the use of NANOLUC/BRET to measure relative drug affinities in living cells. In some embodiments, similar experiments are configured to optimize leads from high-throughput chemical screens.
HEK293 cells were transfected with DNA encoding a NANOLUC-p38 fusion protein (to a final concentration of 50 ng/well DNA in 96-well format). Twenty-four hours post-transfection, cells were treated with serially diluted BIRB-796 or PBI-4835 in the presence of 0.5 uM PBI-4838 (BIRB796 dye conjugate derivative; see, e.g., U.S. Ser. No. 13/682,589; herein incorporated by reference in its entirety).




After two hours of equilibration, furimazine was added to a concentration of 20 uM, and BRET was measured on a Varioskan luminometer.
FIG. 6 demonstrates that the dose-response BRET curves support the higher known affinity of BIRB-796 over PBI-4835. The ability to measure the relative affinities of unlabeled drugs can be applied to HTS screens, lead optimization or chemical proteomics applications. In some embodiments, similar experiments are configured to characterize optimized lead compounds from high-throughput chemical screens (e.g., compounds with lower IC50 values for tracer displacement would indicate higher binding efficiency to the target of interest).
Example 6
Experiments were conducted during development of embodiments of the present invention to demonstrate the use of NANOLUC/BRET to monitor the kinetics of drug binding in living cells. In some embodiments, similar experiments are configured to optimize leads from high-thoughput chemical screens.
HEK293 cells were transfected with DNA encoding a NANOLUC-p38 fusion (to a final concentration of 50 ng/well DNA in 96-well format). Twenty-four hours post-transfection, cells were pretreated for 2 hours with protected furimazine (PBI-4378; See FIGS. 8A-B) to a final concentration of 20 uM. BRET was measured over time on a Varioskan luminometer set to 37° C. After a short pre-read, cells were stimulated with varying concentrations of PBI-4838 (in the presence or absence of 1 uM BIRB796 as a specificity control). Dose and time-dependent increases in BRET were then monitored kinetically over 4 hours.
In a separate experiment, transfected cells were pretreated with both 20 uM PBI-4377 and 1 uM PBI-4838 to generate a steady BRET signal.




After a short pre-read, cells were stimulated with 1 uM unlabeled BIRB-796, and competitive displacement was monitored by BRET in real-time.
The results in FIG. 7A-B support use of BRET for monitoring binding and displacement of drug tracers in living cells. Such formats can be exploited for HTS or chemical proteomics screening of NANOLUC fusion proteins in live cells. In some embodiments, similar experiments are configured to characterize optimized lead compounds from high-throughput chemical screens (e.g., compounds with altered kinetics of displacement by a fluorescent drug tracer indicate altered binding kinetics to the target of interest).
Example 7
The following example relates to the use of specific NANOLUCTM substrates (SEE FIG. 8) or enzyme components to discriminate the subcellular localization of a drug binding event using BRET.
The physical separation of complementary NANOLUCTM enzyme polypeptides or peptide allows the isolation of NANOLUC (donor) signal to the extracellular space. For example, the small signal peptide is genetically tethered to a cell surface receptor. Upon exogenous addition of the large signal polypeptide to the cell medium, the donor signal is isolated to the extracellular space. This signal isolation increases the signal/background generated in various BRET applications including drug tracer binding/displacement.
In some embodiments, full length NANOLUCTM protein fusions are utilized if impermeable NANOLUCTM substrate is applied.
Example 8
The following provides synthesis schemes for exemplary compounds that find use in embodiments of the present invention.
Boc-Protected SAHA Amine
7-Trityloxycarbamoyl heptanoic acid (200 mg, 463 umol) was combined with 4-[(N-Boc)aminomethyl]aniline (113 mg, 510 umol), HBTU (352 mg, 927 umol) and triethylamine (194 uL, 1.4 mmol) in 3 mL of DMF. The reaction was stirred overnight, then adsorbed onto Celite, and the product was obtained by column chromatography eluting with a gradient of 0->100% EtOAc in heptanes. Calcd for M+H: 635.3; found 635.9.
SAHA Amine
Suberoyl(4-[(N-Boc)aminomethyl]anilide) hydroxamic acid (286 mg, 450 mmol) was dissolved in 2 mL of DCM to which was added 0.25 mL of TIS. Trifluoroacetic acid (0.9 mL) was then added, and the reaction was stirred for 30 min. Solvents were removed under reduced pressure, and the crude reaction product could be purified by preparative HPLC or used without further purification.
PBI-4967 SAHA-TAMRA




Suberoyl[4-(aminomethyl)anilide] hydroxamic acid crude reaction product (27 mg) was combined with 4 mg (7.6 umol) of tetramethylrhodamine6-succinimidyl ester in 1 mL of DMF with 5 drops of TEA. After 30 min, the reaction was diluted with H2O and MeCN, and the product was isolated by preparative HPLC (5->60% MeCN in 0.1% aqueous TFA). Lyophilization of the appropriate fractions yielded the desired product as a magenta solid. Calcd for M+H: 706.3; found 706.6.
PBI-4968 SAHA-TOM




Suberoyl[4-(aminomethyl)anilide] hydroxamic acid crude reaction product (8 mg) was combined with 5 mg (7.6 umol) of TOM 6-succinimidyl ester in 0.8 mL of DMF with 3 drops of TEA. After 30 min, the reaction was diluted with H2O and MeCN, and the product was isolated by preparative HPLC (5->60% MeCN in 0.1% aqueous TFA). Lyophilization of the appropriate fractions yielded the desired product. Calcd for M+H: 838.4; found 838.7.
Staurosporine-Amine
Staurosporine p-nitrophenylcarbamate (3 mg, 4.8 umol) was dissolved in 0.5 mL of DMF and treated with excess cadaverine. The reaction was warmed in a 70° C. oil bath for 2 h, then diluted with H2O, acidified with formic acid, and subjected to preparative HPLC eluting with 25%->75% MeCN in 10 mM aqueous NH4OAc. The appropriate fractions were lyophilized to afford a slightly yellow solid. Calcd for M+H: 595.3; found 595.5.
PBI-5129 Staurosporine-TOM




Staurosporine 5-aminopentylcarboxamide (5 mg, 8.4 umol) was dissolved in 1 mL DMF and treated with triethylamine and TOM 6-SE (4 mg, 6 umol). The reaction was monitored by analytical HPLC. Upon completion of the reaction, MeCN and H2O were added, and the TEA was neutralized by addition of a small amount of AcOH. Preparative HPLC (25%->100% MeOH in 10 mM NH4OAc) and subsequent concentration yielded 1.8 mg of a dark blue solid. Calcd for M+H: 1139.5; found 1139.8.
Dasatinib-TOM
TOM-pentylamine




TOM 6-carboxylic acid (26 mg, 46 umol) was stirred in 1 mL of DMF with 2 equiv of triethylamine and treated with TSTU (17 mg, 56.5 umol, 1.2 equiv), and the reaction was monitored by HPLC. After 40 min, the reaction was added to a solution of cadaverine (94 mg, 0.92 mmol, 20 equiv) in 0.5 mL DMF and stirred for 20 min. The reaction was then neutralized by addition of TFA and diluted with MeCN and water. Preparative HPLC (25->100% MeCN in 0.1% aqueous TFA) and subsequent lyophilization afforded the desired product as a purple solid. LCMS: Calcd for ((M+2H)/2) 324.4; found 324.3.

Dasatinib-TOM





Dasatinib (25 mg, 51 umol) was combined with p-nitrophenyl chloroformate (14 mg, 69 umol, 1.36 equiv) and 30 uL TEA in 0.9 mL of 2:1 DMF:THF. The reaction was stirred overnight and then 35 mg additional p-nitrophenyl chloroformate added. After stirring for an additional 24 h, 1⁄2 the volume of the reaction was added to a solution of 7 mg (10 umol) of TOM-pentylamine in 0.5 mL of DMF and 30 uL TEA. The reaction was then stirred for 1 h, followed by dilution with MeCN and water and purification by preparative HPLC. Lyophilization afforded the desired product as a purple solid. MS: Calcd for ((M+2H)/2) 580.8; found 581.0.

Purvalanol-TOM PBI 5077





Purvalanol (10 mg, 23 umol) was stirred in 1 mL of DMF with 20 mg of TEA (198 umol) and treated with 7.7 mg (25.4 umol, 1.1 equiv) of TSTU. After 30 min, the reaction was diluted with Et2O and 1⁄2 of the total reaction volume was added to a vial containing 6 mg (9 umol) of TOM (5-aminopentyl)-6-carboxamide. The reaction was stirred for 3 h, and the volatile organics were removed under reduced pressure. The resulting DMF solution was diluted with water and MeCN and acidified with TFA, then the product was isolated by preparative HPLC (25->100% MeCN in 0.1% aqueous TFA) and subsequent lyophilization to yield 3.5 mg of a purple solid. MS: Calcd for M+H: 1061.5, found 1061.6.
Example 9
Use of Renilla Luciferase or NANOLUC Luciferase in the Compound Identification Method of the Present Invention
HEK293 cells were transfected with plasmid DNA encoding NANOLUC-p38alpha or Renilla Luc-p38alpha using Fugene HD(Promega Corporation) at a 3:1 lipid:DNA ratio and seeded into 96-well plates at a density of 20,000 cells per well (to yield 50 ng/well of DNA). 24 h post-transfection, cell medium was replaced with serum-free medium (Opti-MEM) and incubated with serially-diluted PBI-4838 (BIRB796 derivative conjugated to TOM dye) in the presence/absence of BIRB796 at 1 uM. Cells were incubated at 37° C. for two hours. To the NANOLUC-expressing samples, furimazine was added to a final concentration of 20 uM. To the Renilla Luc-expressing samples, native coelenterazine was added to a final concentration of 20 uM. BRET was then measured on a Varioskan luminometer equipped with 450 nm bandpass and 630 nm longpass filters. The BRET ratio was determined by dividing the signal in the 630 channel by the signal in the 450 channel.
FIGS. 9A-B demonstrates that both Renilla luciferase and NANOLUC luciferase can be used in the method of the present invention. Upon treatment of cells expressing NANOLUC-p38alpha or Renilla Luc-p38alpha with serially-diluted PBI4838, a dose-dependent increase in BRET is observed. Saturating concentrations of unlabeled BIRB-796 are able to block this BRET signal, indicating specificity of binding using either luciferase fusion to p38alpha.
Example 10
Comparison of TOM-BIRB Vs. TMR-BIRB Against NANOLUC-p38 Alpha
As described above, HEK293 cells were transfected with plasmid DNA encoding NANOLUC-p38alpha using Fugene HD and seeded into 96-well plates (to yield 50 ng/well of DNA). 24 h post-transfection, cell medium was replaced with serum-free medium (Opti-MEM) and incubated with serially-diluted PBI4838 (BIRB796 derivative conjugated to TOM dye) or PBI-4836 (BIRB derivative conjugated to TMR dye) in the presence/absence of BIRB796 at 1 uM. Cells were incubated at 37° C. for two hours. To the NANOLUC-expressing samples, furimazine was added to a final concentration of 20 uM. BRET was then measured on a Varioskan luminometer equipped with 450 nm bandpass and 630 nm longpass filters. The BRET ratio was determined by dividing the signal in the 630 channel by the signal in the 450 channel.
FIGS. 10A-B demonstrates another example of the increased potency of the TOM adduct over the TMR adduct for binding to a target protein in a cell-based format. Dose-response curves for NANOLUC-p38alpha binding indicate an EC50 of 38 nM for the BIRB-TOM conjugate, compared to an EC50 of 450 nM for the BIRB-TMR conjugate. The reported affinity of BIRB-TOM is more consistent with literature reports compared to the BIRB-TMR (Chem Biol Drug Des 2009; 74: 547-559).
Example 11
Comparison of BIM-TOM Vs. BIM-TMR Against PKCalpha-NANOLUC
As described above, HEK293 cells were transfected with plasmid DNA encoding PKCalpha-NANOLUC (diluted 1:1000 into pGEM3Z carrier DNA) using Fugene HD and seeded into 96-well plates (to yield 50 ng/well of total DNA). 24 h post-transfection, cell medium was replaced with serum-free medium (Opti-MEM) and incubated with serially-diluted PBI-5075 (BIM conjugated to TOM dye) or PBI-5051 (BIM conjugated to TMR dye) in the presence/absence of staurosporine at 5 uM. Cells were incubated at 37° C. for two hours. To the NANOLUC-expressing samples, furimazine was added to a final concentration of 20 uM. BRET was then measured on a Varioskan luminometer equipped with 450 nm bandpass and 630 nm longpass filters. The BRET ratio was determined by dividing the signal in the 630 channel by the signal in the 450 channel. To determine specific BRET signals, the BRET ratio at each concentration of tracer+unlabeled staurosporine was subtracted from the BRET ratio at each concentration of tracer without unlabeled staurosporine.
FIG. 11 demonstrates another example of the increased potency of the TOM adduct over the TMR adduct for binding to a target protein in a permeabilized cell format. Dose-response curves for PKCalpha-NANOLUC binding indicate an EC50 of 483 nM for the BIM-TOM conjugate, compared to dramatically right-shifted potency for the BIM-TMR conjugate. The reported affinity of BIM-TOM is more consistent with literature reports compared to the BIM-TMR (J Biol Chem. 1991 Aug. 25; 266(24):15771-81.).
Example 12
Target Identification Across p38/MAPK Pathway-Determination of Selectivity
The following example serves to demonstrate the ability to profile the selectivity of a drug tracer against a panel of putative targets within a given phylogenetic target family. Similar experimental configurations may be used to identify the target of fluorescently labeled drugs using BRET in cells. This configuration may lead to the identification of the primary drug target, as well as off-target interactors. Engagement of multiple targets may be indicative of drug promiscuity and potential drug side effects. This example serves to demonstrate the ability to measure both primary, as well s secondary target interactions via BRET.
HEK293 cells were transfected with plasmid DNA encoding N or C-terminal NANOLUC fusions to various members of the MAPK pathway (Jnk1, Jnk2, Jnk3, p38alpha, p38beta, p38gamma, p38 delta, or PKCalpha or MAPK 8, 9, 10, 14, 11, 12, or 13, PKCalpha respectively) using Fugene HD (Promega Corporation) at a 3:1 lipid:DNA ratio and seeded into 96-well plates at a density of 20,000 cells per well (yield 50 ng/well of DNA). Twenty-four hours post-transfection, cell medium was replaced with serum-free medium (Opti-MEM) and incubated with 2 uM PBI-4838 in the presence or absence of BIRB796 at 4 uM. Cells were incubated at 37° C. for two hours. To the NANOLUC-expressing samples, furimazine was added to a final concentration of 20 uM. BRET was then measured on a Varioskan luminometer equipped with 450 nm bandpass and 630 nm longpass filters. The BRET ratio was determined by dividing the signal in the 630 channel by the signal in the 450 channel. To determine response ratios, the BRET values with tracer alone were divided by the BRET values with tracer+unmodified BIRB796.
FIG. 12 indicates selectivity of PBI-4838 to Jnk2, p38beta and p38alpha, consistent with literature reports. P38alpha is recognized as the primary target of BIRB796. However, interactions with targets such as Jnk2 and p38beta could indicate potential off-target liabilities. As expected, PKCalpha showed relatively little specific BRET signal owing to poor affinity of BIRB796 toward this target.
Example 13
Target Identification Across p38/MAPK Pathway-Determination of Affinity
The following example serves to demonstrate the ability to profile the affinity of a drug tracer against a panel of putative targets within a given phylogenetic target family. Similar experimental configurations may be used to characterize the affinity of the fluorescently labeled drug to a given target using BRET in cells.
HEK293 cells were transfected with plasmid DNA encoding NANOLUC-p38alpha, NANOLUC-p38beta, Jnk2-NANOLUC, PKCalpha-NANOLUC, or NANOLUC-HDAC6 using Fugene HD (Promega Corporation) at a 3:1 lipid:DNA ratio and seeded into 96-well plates at a density of 20,000 cells per well (yield 50 ng/well of DNA). Twenty-four hours post-transfection, cell medium was replaced with serum-free medium (Opti-MEM) and incubated with serially-diluted PBI-4838 in the presence or absence of BIRB796 at 4 uM. Cells were incubated at 37° C. for two hours. To a separate set of samples, transfected cells were treated with serially-diluted BIRB796 in the presence of 1 uM PBI-4838. To the NANOLUC-expressing samples, furimazine was added to a final concentration of 20 uM. BRET was then measured on a Varioskan luminometer equipped with 450 nm bandpass and 630 nm longpass filters. The BRET ratio was determined by dividing the signal in the 630 channel by the signal in the 450 channel.
FIGS. 13 and 14 demonstrate the apparent affinity of PBI-4838 to Jnk2, p38beta, and p38alpha. As expected, PKCalpha and HDAC6 showed relatively little specific BRET signal owing to poor affinity of PBI-4838 to these targets. Furthermore, the high affinity of BIRB796 toward Jnk2, p38alpha, and p38beta is demonstrated by competitive displacement in cells. Similar experiments could be configured to rank-order the affinity of drug tracers to a given set of targets (by an increase in BRET) or unmodified drugs (by competitive displacement). As indicated above, high-affinity interactions with targets such as Jnk2 and p38beta could indicate potential off-target liabilities.
Example 14
Affinity Determination of a Drug Tracer for Wild-Type Versus Mutant Version of Target Protein
The following example serves to demonstrate the ability to measure the relative affinity of a drug tracer to a wild-type versus mutant target protein. In this example, the affinity of a fluorescently-labeled iBET compound (small-molecule inhibitor that binds BRD4 preventing its interaction with acetylated histones) was determined for wild-type and mutant version (N140 A/N433A; lacks full binding capacity to iBET) of BRD4 (Bromodomain-containing protein 4). Similar experimental configurations may be used to characterize the affinity and selectivity of the fluorescently-labeled drug to a disease-relevant mutant protein in cells. Such experiments may be useful to identify drugs that selectively bind to wild-type or mutant proteins differentially.
HEK293 cells were transfected with plasmid DNA encoding NANOLUC-BRD4 or NANOLUC-BRD4 (N140A/N433A) using Fugene HD (Promega Corporation) at a 3:1 lipid:DNA ratio and seeded into 96-well plates at a density of 20,000 cells per well (yield 50 ng/well of DNA). Twenty-four hours post-transfection, cell medium was replaced with serum-free medium (Opti-MEM) and incubated with serially-diluted PBI-4966 (iBET conjugated to TOM dye) in the presence/absence of iBET at 10 uM. Cells were incubated at 37° C. for two hours. To the NANOLUC-expressing samples, furimazine was added to a final concentration of 20 uM. BRET was then measured on a Varioskan luminometer equipped with 450 nm bandpass and 630 nm longpass filters. The BRET ratio was determined by dividing the signal in the 630 channel by the signal in the 450 channel.
FIG. 15 indicates relative affinities of PBI-4966 to wild-type BRD4 versus the mutant BRD4. As expected, a right-shifted potency is observed with the mutant BRD4 indicating a lowered affinity for PBI-X. Similar experiments could be configured to rank the order of the affinity of drug tracers to disease-relevant mutants of a target. This principle could be expanded to measuring relative affinities of drugs toward wild-type or mutant proteins by competitive tracer displacement. Since increased BRET signal is only indicative of binding to the NANOLUC fusion, this method enables measurements of target engagement amidst a complex mixture of similar antigens present in the assay sample. These antigens could include targets of similar properties, but non-identical to the target of interest (for instance, to discriminate heterologous vs. endogenous analyte or mutant vs. wt. analyte, etc.).
Example 15
Screening Compound Panel to Determine Target Engagement
The following example demonstrates that the method of the present invention can be used to screen compound panels to determine target engagement. This screening method could be expanded to larger compound libraries (e.g. LOPAC) as well.
HEK293 cells were transfected with NANOLUC-HDAC6 DNA using Fugene HD and seeded into wells of a 96-well plate. For the transfection, NANOLUC-HDAC6 DNA was diluted with promoterless carrier DNA (pGEM3Z). The final DNA concentration/well remained 50 ng/well; however the NANOLUC-HDAC6 DNA was diluted 1:1000 (at a seeding density of 20,000 cells/well in 96-well format). Twenty-four hours post-transfection, cells were treated with serially-diluted inhibitors (SEE FIG. 17) in the presence of a fixed concentration (1 uM) of SAHA-TOM conjugate (PBI-4968). After two hours of incubation, furimazine was added to 20 uM, and BRET detected on a Varioskan luminometer.
The results in FIGS. 16A-D demonstrate that structurally-distinct compounds can be identified by competitive displacement of drug tracers using the method of the present invention. Furthermore, relative potency of various compound classes can be confirmed. The results indicate little/no binding efficiency of apicidin to HDAC6 compared to high binding efficiency of panabinostat or SAHA to HDAC6. This is consistent with literature reports using orthogonal assay formats. This screening method could be expanded to include high-throughput screening of large chemical libraries to identify/characterize new chemical matter with inhibitory potential against a given target.
Example 16
Monitoring Drug-Target Interactions
It is commonly accepted that a high degree of non-specific BRET occurs in medium containing a luciferase in the presence of a fluorophore of significant spectral overlap (Couturier 2012). This has been described as a liability to using BRET for high-throughput chemical screens. The following example serves to demonstrate the ability to monitor drug/target interactions using fluorophore-drug conjugates in the presence of a luciferase, NANOLUC, in medium at concentration ranges commonly recognized as problematic for BRET.
HEK293 cells were transfected with plasmid DNA encoding CDK2-NANOLUC (diluted 1:100 into pGEM3Z carrier DNA) using Fugene HD (Promega Corporation) at a 3:1 lipid:DNA ratio and seeded into wells of 96-well plates at a density of 20,000 cells per well (yield 50 ng/well of total DNA). Twenty-four hours post-transfection, cell medium was replaced with serum-free medium (Opti-MEM) and incubated with serially-diluted PBI-5077 (purvalanol B conjugated to TOM dye) in the presence/absence of Purvalanol B at 10 uM. Cells were incubated at 37° C. for two hours.
To the NANOLUC-expressing samples, furimazine was added to a final concentration of 20 uM. BRET was then measured on a Varioskan luminometer equipped with 450 nm bandpass and 630 nm longpass filters. The BRET ratio was determined by dividing the signal in the 630 channel by the signal in the 450 channel (FIGS. 17A-C).
This example supports use of fluorophore tracers in medium for monitoring drug/target interactions via BRET. By co-incubating the sample (+drug tracer) with purvalonol B (unmodified drug), the non-specific BRET signal between the NANOLUC and the tracer can be measured. Over the tracer concentration range tested, this background BRET signal was low. These results demonstrate that specific binding between the drug tracer and the NANOLUC-target fusion can be monitored in cell medium despite significant spectral overlap between the NANOLUC (donor) and fluorophore (acceptor).
Example 17
Target ID Screening Using Protein Arrays
The following example demonstrates the ability to generate NANOLUC fusion arrays using cell-free expression and measure drug binding and relative affinity by BRET.
A panel of 11 kinases (N- and C-terminal NANOLUC fusions) including putative targets of BIRB796 (such as members of the MAPK and Jnk families), putative targets of Dasatinib (such as Src and LCK) as well as an irrelevant HDAC6 negative control was expressed in TnT® T7 Quick Coupled Reticulocyte Transcription/Translation System (Promega Corporation) as recommended by the manufacturer to create an array with 23 different NANOLUC fusions. Each TNT® reaction was diluted 1:100 in PBS and plated in replicates into wells of 96-well plates. The NANOLUC fusion array was screened with 2 different TOM-drug tracer (BIRB-TOM; PBI-4838 and Dasatinib-TOM; PBI-5170) in the presence and absence of excess relevant free drug. For each TNT® reaction, 4 replicates with 2 uM BIRB TOM/4 replicates with 2 uM BIRB-TOM+4 uM BIRB796 (total of 2×96-well plates) and 4 replicas with 1 uM Dasatinib-TOM/4 replicates with 1 uM Dasatinib-TOM+5 uM Dasatinib (total of 2×96-well plates) were performed. The reactions were incubated with constant mixing for 2 h at room temperature. Following the incubation, furimazine was added to a final concentration of 20 uM. BRET was then measured on a Varioskan luminometer equipped with 450 nm bandpass and 610 nm longpass filters. The BRET ratio was determined by dividing the signal in the 610 channel by the signal in the 450 channel. To determine response ratios, the BRET values with tracer alone were divided by the BRET values with tracer+unmodified.
The results (FIG. 18) demonstrate selectivity of the BIRB-TOM tracer to JNk2, JNk3, MAPK14, MAPK11 and MAPK13 as well as selectivity of the Dasatinib-TOM tracer to ABL1, Src, LCK, MEK5, MAPK11 and MAPK14 consistent with literature reports. These results demonstrate the ability to profile the drug tracer's against a panel of putative targets expressed in cell free expression system and to identify hits. This no wash protein NANOLUC fusion array configuration may lead to the identification of the primary drug target, as well as off-target interactors.
Following the above screen, the BIRB-TOM hits were further analyzed for binding affinity to the BIRB-TOM tracer and competitive displacement of the BIRB TOM Tracer with the BIRB796. Binding affinity experiments to the BIRB-TOM tracer were preformed by incubating 3 replicates of the diluted TNT reactions with serially-diluted BIRB-TOM tracer in the presence/absence of BIRB796 at 10 uM. Reactions were incubated at room temperature with constant mixing for two hours and after adding furimazine to a final concentration of 20 uM analyzed as described above. Competitive displacement experiments were preformed by incubating 3 replicates of the diluted TNT reactions with serially-diluted BIRB796 in the presence of BIRB-TOM tracer at 2 uM. Reactions were incubated at room temperature with constant mixing for two hours and after adding furimazine to a final concentration of 20 uM analyzed as described above. The competitive displacement experiments results in FIG. 19 indicates that BIRB796 had highest affinity to MAPK14 and Jnk2 with lower affinity to MAPK11, MAPK13, and Jnk3. Consistent with literature reports, BIRB796 binds efficiently to MAPK14, but also engages other MAPK and Jnk family members indicating off-target liabilities for BIRB-796. These results demonstrate that hits expressed in cell free expression systems and identified in the protein array screen can be further analyzed by BRET for binding affinity to the drug. Furthermore thee results supports the use of cell-free expression systems to generate NANOLUC protein fusions as suitable analytes for target engagement applications.
Example 18
Expression Level of NANOLUC Fusions
The following example demonstrates that high affinity interaction with the drug tracer with optimal signal to background is achieved when the expression of the NANOLUC fusion is close to endogenous level. As previously described, it was demonstrated that a 1:1000 dilution of the NANOLUC HDAC6 DNA with a carrier DNA was required to achieve a high affinity interaction. In this example, the expression of serial dilutions of the NANOLUC HDAC6 DNA was compared to the expression of the endogenous HDAC6 using western blot analysis.
HEK293 cells were seeded into wells of 6-well plates at 2.5×105 cells/well and transfected with PEI with varying amounts of NANOLUC HDAC6 DNA. The NANOLUC HDAC6 DNA was diluted with a non-expressing carrier DNA (pCI neo). The final concentration of DNA remained 2 ug/well while the NANOLUC HDAC6 DNA was diluted 1:0, 1:10, 1:100, 1:1000 and 1:10000. The control was un-transfected cells. 24 hours post transfection, the media was removed, and cells washed with PBS and lysed for 10 min with 400 ul of mammalian lysis buffer (Promega)+1:50 RQ1 DNase (Promega)+1× RQ1 buffer. Following lysis, 133 ul of 4λ SDS-loading buffer was added to each well, and the cell lysates were collected, analyzed on a SDS-PAGE gel and electro-transferred onto a PVDF membrane (Invitrogen). The membrane was blocked for 1 hour with 5% BSA (Promega) in TBS buffer and probed overnight at 4° C. with 1:500 dilution of HDAC6 antibody (Millipore) in TBS supplemented with 0.1% tween (TBST).
After 3× washes in TBST, the membrane was incubated with Anti-Rabbit HRP antibody (Jackson) in TBST for 1 hour, then washed 5× with TBST and 1× with TBS. The membrane was then incubated for 1 min with the ECL substrate from Promega and scanned on the Image Quant LAS4000 (GE). The results indicate that dilution of 1:1000 of the NANOLUC HDAC6 DNA results with expression level that is similar to the expression level of endogenous HDAC6. This is the same dilution that provided the high affinity interaction with the drug tracer with optimal signal to background.
Example 19
Quantification of Binding of Fluorescent Cytokines to a Fusion of a Cell Surface Receptor and NANOLUC
Experiments were conducted during development of embodiments of the present invention to demonstrate the ability to measure the relative affinities of therapeutic antibodies against a cell surface receptor by competitive displacement of a fluorescently-labeled cytokine. In this example, commercially-available TAMRA-epidermal growth factor (TMR-EGF; Life Technologies) was applied in a cellular BRET assay using a stable cell line expressing a NANOLUC-EGFR (Her1) fusion protein. The BRET signal generated between TMR-EGF and NANOLUC-EGFR can be inhibited upon treatment with therapeutic antibodies known to interfere with binding of EGF.
A HEK293 stable cell line was generated by transfection of pF5 NANOLUC-EGFR plasmid DNA (Promega Corp.) and FuGene HD (Promega Corp.). After transfection, the stable cell line was generated by G418 selection, followed by limited dilution cloning. Clonally-derived cells expressing NANOLUC-EGFR were seeded into 96-well plates at a density of 20,000 cells per well. 20 hours after seeding, medium was replaced with serum-free OptiMEM and cells were serum starved. After starvation, cells were treated with serially-diluted TMR-EGF (Life Technologies). Following equilibration with the TMR-EGF, furimazine (a coelenterazine derivative substrate for NANOLUC; Promega Corp.) was added at a concentration of 20 uM, and BRET was quantified on a Varioskan luminometer. In subsequent experiments, antibody-mediated displacement of TMR-EGF was measured by pretreating cells with Vectibix, Erbitux, or Herceptin (negative control) prior to stimulation with TMR-EGF (long/mL final concentration).
Results in FIG. 20 demonstrate that the BRET can be used to quantify binding of fluorescent cytokines to cell surface receptors, tethered to NANOLUC. Furthermore, the affinities of therapeutic antibodies capable of inhibiting cytokine binding can be measured by competitive displacement of the fluorescent cytokine. Vectibix and Erbitux were capable of inhibiting the binding of TMR-EGF to NANOLUC-EGFR, whereas Herceptin (a Her2 binder with negligible affinity to Her1) were incapable of inhibiting TMR-EGF binding. This example demonstrates that the binding of a fluorescent cytokine to a known high-affinity target can be quantified by BRET, in a format that can be readily reconfigured to monitor binding of therapeutic antibodies (e.g. Vectibix, Erbitux, etc.) or other binders (e.g. cytokine biologics) by competitive displacement of the fluorescent cytokine. This demonstrates the ability to use BRET as a technique to measure the relative potencies of biologic drugs in a cellular format.
All publications and patents mentioned in the present application and/or listed below are herein incorporated by reference. Various modification and variation of the described methods and compositions of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention that are obvious to those skilled in the relevant fields are intended to be within the scope of the following claims.

## Claims

1. A system comprising:
(a) a bioactive agent conjugated to a fluorophore;
(b) a cell that expresses a protein fusion of: (i) a protein of interest and (ii) a luciferase, wherein the bioactive agent is capable of binding non-covalently to the protein of interest upon interaction therewith, wherein the emission spectrum of the luciferase overlaps with the excitation spectrum of the fluorophore; and
(c) a substrate for the luciferase.

2. The system of claim 1, wherein the bioactive agent is a peptide or nucleic acid.

3. The system of claim 2, wherein the nucleic acid is RNA.

4. The system of claim 2, wherein the nucleic acid is DNA.

5. The system of claim 1, wherein the fluorophore is a small molecule fluorophore.

6. The system of claim 5, wherein the small molecule fluorophore is a carboxy rhodamine analog.

7. The system of claim 1, wherein the luciferase comprises a polypeptide with at least 70% sequence identity with SEQ ID NO.: 1.

8. The system of claim 1, wherein the substrate for the luciferase is coelenterazine or a coelenterazine derivative.

9. The system of claim 8, wherein the substrate is 2-furanylmethyl-deoxy-coelenterazine.

10. The system of claim 1, wherein the bioactive agent conjugated to the fluorophore is within the cell.

11. The system of claim 1, wherein the conjugate of the bioactive agent and fluorophore is added extracellularly and enters the cell.

12. The system of claim 1, wherein the bioactive agent conjugated to the fluorophore is cell permeable.

13. The system of claim 12, further comprising a permeabilization agent to potentiate entry of the bioactive agent conjugated to the fluorophore into the cell.

14. The system of claim 1, wherein the bioactive agent conjugated to the fluorophore is part of a library of different non-small molecule bioactive agents tethered to fluorophores.

15. The system of claim 1, wherein the protein fusion is one of a plurality of different proteins of interest fused to luciferase.

16. The system of claim 1, wherein the non small molecule bioactive agent is produced by non-natural chemical synthesis.

17. The system of claim 1, wherein:
(i) said luciferase has a first emission spectrum with a first peak emission;
(ii) said fluorophore has an excitation spectrum that overlaps said first emission spectrum; and
(iii) said fluorophore has a second emission spectrum with a second peak emission, said second peak emission being separated from said first peak emission.

18. The system of claim 17, wherein said second peak emission is separated from said first peak emission by at least 80 nm.

19. The system of claim 17, wherein the Forster distance of the fluorophore and luciferase pair is less than 20 nm.

20. The system of claim 19, wherein the Forster distance of the fluorophore and luciferase pair is less than 5 nm.

21. The system of claim 17, wherein upon binding of the bioactive agent to the protein of interest, conversion of the substrate to a reaction product by the luciferase results in excitation of the fluorophore by bioluminescence resonance energy transfer (BRET) and fluorescence emission from the fluorophore.

22. The system of claim 1, wherein upon binding of the bioactive agent to the protein of interest, conversion of the substrate to a reaction product by the luciferase results in excitation of the fluorophore by bioluminescence resonance energy transfer (BRET) and fluorescence emission from the fluorophore.

23. The system of claim 1, wherein the protein of interest of the fusion protein is displayed on the cell surface or the protein of interest of the fusion protein is intracellular and the bioactive agent conjugated to a fluorophore is cell permeable.