# Patent

## Title
Cytotoxic ribonuclease variants

## Abstract

This invention relates to altered forms of members of the RNase A superfamily. An RNase A can be modified to be cytotoxic by altering its amino acid sequence so that it is not bound easily by the ribonuclease inhibitor while still retaining catalytic properties. While earlier work had identified some modifications to RNase A that would result in cytotoxicity, the use of the FADE algorithm for molecular interaction analysis has led to several other locations that were candidates for modification. Some of those modifications did result in RNase A variants with increase cytotoxicity.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation of U.S. application Ser. No. 13/180,359, filed Jul. 11, 2011, now issued as U.S. Pat. No. 8,247,190 on Aug. 21, 2012, which is a divisional of U.S. application Ser. No. 12/177,229, filed Jul. 22, 2008, now issued as U.S. Pat. No. 7,977,079 on Jul. 12, 2011, which is a divisional of U.S. application Ser. No. 11/454,379, filed Jun. 16, 2006, and issued as U.S. Pat. No. 7,416,875 on Aug. 26, 2008, which claims priority from U.S. provisional patent application Ser. No. 60/690,970, filed Jun. 16, 2005. Each of these applications is incorporated herein by reference in its entirety.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with government support under CA073808 awarded by the National Institutes of Health. The government has certain rights in the invention.


BACKGROUND OF THE INVENTION
Ribonucleases are enzymes that catalyze the degradation of RNA. A well studied ribonuclease is bovine ribonuclease A (RNase A), the putative biological function of which it to break down the large amount of RNA that accumulates in the ruminant gut. The RNase A superfamily is a group of ribonuclease enzymes classified as homologous to RNase A. Some of the members of the superfamily possess a number of interesting biological properties including antiproliferative, cytotoxic, embryotoxic, aspermatogenic, and antitumoral activities. One member of this family is a homolog of RNase A originally isolated from oocytes and early embryos of the Northern leopard frog Rana pipiens, which is now known as Onconase® (ONC), a name used for the molecule which exhibits anti-tumor properties both in vitro and in vivo. The property of degrading RNA is essential to the cytotoxicity of ONC. ONC is currently being evaluated as a cancer therapeutic in clinical trials.
A significant limitation on the suitability of ONC as a chemotherapeutic is dose-limiting renal toxicity. ONC is retained in the kidney at concentrations much greater than mammalian members of the RNase superfamily. There may also be allergenic issues with ONC, since mice produce antibodies against ONC but not against RNase A, with which ONC shares about 30% of its amino acids. This suggests that other members of the RNase family may also be suitable candidates for evaluation as clinical therapeutics if they can be imbued with the cytotoxic properties similar to ONC.
In the body, levels of RNase activity are controlled by a ribonuclease inhibitor (RI), which is a 50-kDa protein found in the cytosol of all mammalian cells. RI is a member of a leucine rich family of proteins and is composed of 15 alternating repeats arranged symmetrically in a horseshoe-shaped molecule. RI has a large number of cysteine residues (32 in human RI) which means that it can only keep its shape and function in a reducing environment like the cytosol. RI acts to bind to members of the RNase superfamily, one RI to one molecule of RNase, and when so bound, RI completely inhibits the catalytic activity of the ribonuclease by steric blockage of the active site of the enzyme. The binding of RI to RNase is a very tight one, having a very high binding affinity.
Some RNase superfamily members, notably ONC and bovine seminal ribonuclease, possess the native ability to evade RI. The trait of evasion of RI is primarily responsible for the cytotoxicity of ONC and bovine seminal ribonuclease. It has also been found that RNase superfamily members which are not natively cytotoxic can be made cytotoxic by modifying their amino acid constituents so as to inhibit binding to RI, and in particular, by making substitutions of larger amino acids for smaller ones at one of the points of closest interaction between RI and the RNase. This method is described in U.S. Pat. No. 5,840,296, which describes a cytotoxic variant, G88R RNase A, which has lessened affinity for RI compared to native RNase A, but which is still ten fold less cytotoxic than ONC. The nomenclature G88R means that the RNase A molecule was altered by substituting an arginine (R) residue for the glycine (G) residue at amino acid position 88.
The methods and tools for modeling the three-dimensional structure of proteins continue to evolve. In analyzing the interaction between two molecules, such as that between RNase A and RI, the problem of defining the sites of interaction between the two molecules is only now becoming susceptible to solution. As molecular modeling tools develop, the sophistication of the analysis of that interaction can increase.
BRIEF SUMMARY OF THE INVENTION
The present invention is summarized by an engineered ribonuclease of the RNase A superfamily having at least two amino acid changes from its native sequence. The first change is an amino acid substitution in the region corresponding to amino acid residues 85 to 94 of bovine pancreatic RNase A (SEQ ID NO: 1). The second change is an alteration, substitution or amino acid swap at a location selected from the groups consisting of an amino acid corresponding to residues 38, 39, and 67 of bovine pancreatic RNase A.
It is an object of the present invention to define an engineered ribonuclease A that has improved cytotoxic properties compared to the prior engineered ribonucleases.
Other objects, advantages and features of the present invention will become apparent from the following specification taken in conjunction with the accompanying drawings.



BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
FIG. 1 is a representation of the three-dimensional structure of ribonuclease A and of ribonuclease inhibitor.
FIG. 2 is a representation of the interaction between the three-dimensional structure of ribonuclease A and ribonuclease inhibitor showing the sites targeted for modifications in the ribonuclease A.
FIG. 3 presents graphical data from the examples below showing the effect of ribonucleases on the proliferation of K-562 cells. The data points are the means of at least three experiments each carried out in triplicate. The curves are each labeled with the corresponding variant of RNase A.



DETAILED DESCRIPTION OF THE INVENTION
The present invention is directed to altered ribonucleases of the superfamily of RNase A which have been engineered to have a new level of cytotoxicity. This was achieved through the use of a new molecular interaction modeling tool, the Fast Atomic Density Evaluation (FADE) algorithm. This algorithm was used to model the locations of molecular contact between RNase A and the ribonuclease inhibitor. Based on this model, variants in the amino acid sequence of RNase A were designed in order to create novel RNase A variants that through steric hindrance are able to evade the RI. These variants were also tested for ribnucleolytic activity and for cytotoxicity. Variants are identified here that are more cytotoxic than any previously know RNase A variants.
The analysis began with a study of the interaction between RNase A and the RI molecule. There are many properties of a protein-protein interface that can endow the complex with stability, including total surface area, nonpolar surface area, packing density, and polar interactions. The 2,550 Å2 of solvent-accessible surface area buried upon formation of the pRI•RNase A complex is relatively large for an enzyme inhibitor complex, and is considerably larger than the 1600 Å2 that is typical for protease inhibitor complexes. In general, protein interfaces resemble the chemical character of solvent-exposed protein surfaces, which are comprised of approximately 57% nonpolar, 24% neutral polar, and 19% charged amino acid residues. Typical protein-protein interfaces do, however, contain fewer charged residues and more neutral polar residues than do solvent-exposed protein surfaces. Deviating from this trend, the pRI-RNase A interface is significantly more charged, with 49% nonpolar, 27% neutral polar, and 24% charged residues. Indeed, electrostatics seem to play an important role in the complex formed between the basic Rnase A (p/9.3) and the acidic RI protein (p/4.7) at cytosolic pH.
In contrast to the larger role of charge-charge interactions within the pRI•RNase A complex, the degree of shape complementarity between the two surfaces is lower than average. The shape correlation statistic, Sc, describes how well two surfaces mesh, with a value of 1.0 describing a perfect match and 0.0 describing two unrelated surfaces. The pRI•RNase A interface has a relatively low Sc value of 0.58, as compared to values of 0.70-0.76 for typical protease inhibitor complexes and 0.64-0.68 for typical antibody•antigen complexes. The packing of atoms at the pRI-RNase A interface is also less dense than a typical protein interior or protein-protein interface. The large amount of buried surface area could compensate for the relatively low degree of shape complementarity, to yield a highly stable interaction between RI and RNase A.
Prior to the work described here, K7A/K41R/G88R RNase A was the most RI-evasive of previously produced variants. Again, under the nomenclature used here, G88R means that the RNase A molecule was altered by substituting an arginine (R) residue for the glycine (G) residue at amino acid position 88, and the accumulation of K47A/K41R/G88R means that all three substitutions were made to the same RNAse A variant. This variant formed a complex with pRI that had a Kd value of 47 nM, nearly 102-fold greater than that of G88R RNase A. Still, K7A/K41R/G88R RNase A is not a potent cytotoxin, owing largely to the 102-fold decrease in ribonucleolytic activity caused by the replacement of its active-site lysine residue with arginine. Thus to be effective as a cytotoxic agent, the variant must combine reduced affinity to the RI with the maintenance of effective catalytic activity as an RNAse.
The FADE algorithm revealed new “knobs” and “holes” in the pRI•RNase A complex for disruption by site-directed mutagenesis as illustrated in FIGS. 1 and 2, and listed in Table 1. In the RNase A variants created in this work, the D38R/R39D swap and N67R substitution produced the largest decrease in affinity for RI. Alone, each of these substitutions effected a destabilization of the pRI•RNase A complex nearly equal to that of the G88R substitution. Combining the most disruptive FADE-inspired substitutions resulted in ribonucleases that were not only 30-fold more RI-evasive than K7A/K41R/G88R RNase A, but also retained nearly wild-type catalytic activity (see Table 2 below). Moreover, the D38R/R39D/G88R, D38R/R39D/N67R/G88R, and K31A/D38R/R39D/N67R/G88R variants were all more cytotoxic to K-562 cells than was ONC (see FIG. 3).
The application of the FADE algorithm to the interaction of RNase A and RI thus lead to models of the interaction between the structures of the two molecules as illustrated in FIGS. 1 and 2. This analysis was performed with bovine RNase A and porcine ribonuclease inhibitor (pRI). In these figures, FADE geometric complementarity markers are displayed as solid spheres. These spheres do not represent atoms. Instead, the spheres represent points in the molecular interface near which local complementarity is most significant. Complementarity markers within 2 Å of any atom within a particular residue were summed to determine the cluster sizes listed in Table 1. The residues in RNase A that were proximal to the largest number of complementarity markers and distal from the enzymic active site of RNase A were targeted for disruption.
One interesting finding is the difference in affinity of the porcine and human homologs of RI observed for some of the RNase A variants. In general, the RNase A variants were bound more tightly by pRI than hRI (data presented in Table 2 below). This higher affinity of pRI for RNase A was not observed when the equilibrium dissociation constants were measured originally for complexes of wild-type RNase A with pRI (Kd=6.7×10−14 M) and hRI (Kd=4.4×10−14 M). Of the 28 pRI residues that contact RNase A, 25 are identical in hRI. The three differences among the RNase A binding residues are the replacements of His6 in pRI with a glutamine residue in pRI, Asp228 with alanine, and Val405 with leucine. All three of these pRI residues make atom-atom contacts exclusively with FADE-identified RNase A residues. His6 makes three contacts with Lys31 of RNase A, Asp228 makes two contacts with Ser89, and Val405 makes three contacts with Asn67. These three changes are likely to contribute to the differential affinity of pRI and hRI for the RNase A variants.







TABLE 1







Residues of highest shape complementarity in the pRI•RNase


A complex as identified with the FADE algorithm











Chain
Residue
Cluster sizea















RNase A
Lys7
2




Asn24
5




Gln28
3




Lys31
2




Arg39
31




Asn67
6




Gly88
5




Ser89
14




Lys91
9



RI
Tyr430
22




Asp431
10




Tyr433
38







aNumber of FADE complementarity markers within 2 Å of an atom in the indicated residue.






So these residues were the targets for potential modification. Note the variants at the position Gly88 had previously been explored, as described in U.S. Pat. No. 5,840,296, so we looked at other alterations, alone or in combination with G88R. We reasoned that disruption of the RI-RNase A complex could, in general, be achieved best by replacing small neutral or anionic residues in RNase A with arginine. We suspected that arginine, as the most polar and second largest amino acid, could generate electrostatic repulsion and steric strain while increasing the net positive charge, which is known to enhance cell internalization. In addition, we replaced lysine residues in RNase A with alanine to create truncated neutral side chains and thereby eliminate favorable interactions within the complex.
The following substitutions were thus identified as having promise for study:
D38R/R39D Swap (FIG. 2C). Arg39 was identified by the FADE algorithm as being proximal to the greatest number of complementarity markers of any residue in RNase A (Table 1). With 14 atom-atom contacts to pRI, Arg39 also makes more contacts with RI than any residue in RNase A with the exception of Glu111, which also makes 14 contacts. Together, Asp38 and Arg39 of RNase A form three hydrogen bonds with Arg453 and Glu397 of pRI, respectively, with Arg39 interacting with Glu397 in a bidentate manner. Additionally, these two RNase A residues make van der Waals contacts with Gln426, Val428, Tyr430, and Ile455 of RI. Although Asp38 was not identified explicitly by the FADE analysis, we reasoned that by interchanging this residue with Arg39, we could disrupt three favorable interactions at the pRI•RNase A interface simultaneously. Moreover, the D38R/R39D swap was conservative in that it preserved the local amino acid content.
B4-β5 loop (FIG. 2D). Four surface loops of RNase A contribute 16 of the 24 residues that contact RI. The β4-β5 loop of RNase A, containing residues 87-96, packs against an especially hydrophobic region of pRI defined by three tryptophan residues: Trp257, Trp259, and Trp314. Three RNase A residues within this loop, Gly88, Ser89, and Lys91, were identified by FADE as being important for mediating shape complementarity with RI. Earlier attempts to create an RI-evasive RNase A showed the replacement of Gly88 (FADE cluster size 5) with an arginine residue to be extremely effective at introducing steric and electrostatic strain, increasing the Kd value of the pRI•RNase A complex by nearly four orders of magnitude. Therefore, although residues Ser89 and Lys91 were identified by the FADE algorithm as being near large complementarity clusters, we assumed this region of the complex to be disrupted maximally by the G88R substitution and hence did not pursue further alteration of this loop.
N67R substitution (FIG. 2A). Asn67 was proximal to the third largest cluster of complementarity markers, following Arg39 and residues of the β4-β5 loop of RNase A. Asn67 makes six contacts with pRI residues Cys404, Val405, Gly406, and Tyr433, including a hydrogen bond with the main-chain oxygen of Val405. It is noteworthy that Tyr433 of pRI, which makes contacts with Asn67 of RNase A, was identified as being proximal to the largest number of complementarity markers of any residue in either protein. In accordance, Tyr433 of RI and Asn67 of RNase A have been identified by others as the “anchor residues” in the pRI•RNase A complex.
Other FADE-identified residues. Lys7 (FIG. 2B) was the lowest scoring of the RNase A residues with a complementarity cluster size of 2. Nonetheless, Lys7 makes seven atom-atom contacts with Ser456 of pRI, including several hydrogen bonds. Previous studies had shown this residue to contribute significantly to complex stability. We also examined Asn24 and Lys31, which make seven and four atom-atom contacts and are located near cluster sizes of 5 and 2, respectively. Asn24 makes seven van der Waals contacts and two hydrogen bonds with Asp89 and Asp117 of RI; Lys31 makes three atom-atom contacts with His6 of pRI and one contact with Asp31.
While these particular amino acid locations are identified with reference to the specific sequence of bovine pancreatic ribonuclease A, it is to be understood that there are many members of the RNase A superfamily of enzymes to which this information can be applied. Those of skill in the art today understand how to perform sequence alignment and determine for members of this superfamily how to identify the corresponding amino acid location in other members of this closely linked family of enzymes.
To be successful for the purposes we envisioned, the RNase A variants had to have reduced affinity for RI and still retain significant catalytic activity. Hopefully, the combination of reduced affinity for RI and catalytic activity would make the variants cytotoxic and perhaps more cytotoxic than the previous G88R RNase A variants. So modifications of the enzyme at each of the locations identified above were tried and the results presented in the Examples below. This work established that several of these variants exhibited increased cytotoxicity. In particular, the variants D38R/R39D/G88R and D38R/R39D/N67R/G88R both exhibited lowered affinity for RI, a high level of catalytic activity and both were found to have increased cytotoxicity, as exemplified by the data presented in Tables 2 and 3 below.
We used the FADE algorithm to identify quickly and objectively RNase A residues within the pRI•RNase A complex that exhibit a high degree of shape complementarity. Several of the residues identified by the FADE algorithm were previously shown experimentally to contribute a significant amount of binding energy to the pRI•RNase A complex or to be excellent targets for disruption by mutagenesis. The success of the FADE algorithm in predicting the importance of these regions gave credence to its utility and justified our subsequent analysis of additional RNase A residues identified by FADE. Although, a similar list of residues could have been identified by careful examination of the three-dimensional structure, the evident advantage of FADE is the extreme speed at which it identifies regions of high complementarity. Additionally, the computational algorithm is objective, eliminating possible human error or bias.
An important characteristic of any drug is its therapeutic index, which is the ratio of its toxic dose to its effective dose. In humans, ONC exhibits a highly favorable therapeutic index as a cancer chemotherapeutic, enabling its progress to Phase III clinical trials. Mammalian ribonucleases could exhibit an even greater therapeutic index than does ONC. For example, the Hep-3B liver carcinoma cell line is the most vulnerable to all of the ribonucleases tested herein (Table 3). ONC has a therapeutic index (TI), here defined as IC50NmuMG/IC50Hep-3B, of 31. In contrast, the D38R/R39D/N67R/G88R, D38R/R39D/G88R, and G88R variants of RNase A have TI values of >323, >500, and >118, respectively. A biochemical explanation for the therapeutic index of ribonucleases (amphibian or mammalian) awaits further experimentation.
EXAMPLES
Experimental Protocol and Results
To explore which of the potential RNase A variants would be successful, we make expression vectors and produced each RNase A variants for each of the propose alterations suggested above. Those variants were than tested for their catalytic properties, their affinity for RI, their stability and their cytotoxicity.
Catalytic Activity
A ribonuclease must retain its catalytic activity to be cytotoxic. Accordingly, the catalytic activity of each ribonuclease was assayed to determine which, if any, of the amino acid substitutions compromised cytotoxicity by reducing the ability of the enzyme to degrade RNA. Values of kcat/KM for wild-type RNase A, its variants, and ONC are listed in Table 2, which summarizes the results of this analysis. The kcat/KM values of wild-type RNase A, G88R RNase A, K7A/G88R RNase A, and ONC were 5.2×107, 7.4×107, 5.3×106, and 2.2×105 M−1s−1, respectively, which are in good agreement with values reported previously. Swapping residues 38 and 39 of RNase A had a minor effect on catalysis by the enzyme. The value of kcat/KM for D38R/R39D RNase A was 1.8×107 M−1s1, which represents only a 3-fold loss in ribonucleolytic activity. A similarly small effect was seen in the D38R/R39D/G88R variant; its kcat/KM value of 3.1×107 M−1s−1 was 2.5-fold less than that of G88R RNase A. Interestingly, when the single R39D substitution was made in the context of the G88R substitution, the effect on ribonucleolytic activity was more pronounced, reducing the kcat/KM value of G88R RNase A by 17-fold to 4.3×106 M−1s−1. This decrease could result from enhanced negative charge in this region, possibly reducing the number of productive collisions between the enzyme and its anionic substrate.
The P2 substrate binding site of RNase A, which contains Lys7, plays an important role in catalysis by RNase A. Consistent with previous results, K7A/G88R RNase A displayed an almost 10-fold decrease in ribonucleolytic activity, having a kcat/KM value of 5.3×106 M−1s−1. This deleterious contribution to catalysis was additive when combined with other amino acid substitutions that diminished activity; the D38R/R39D swap (3-fold decrease in kcat/KM) when combined with the K7A substitution (10-fold decrease in kcat/KM) resulted in a K7A/D38R/R39D variant with an activity of 1.6×106 M−1s−1, which is 30-fold less than that of wild-type RNase A. Additionally, the K7A substitution was responsible for a 15-fold reduction in the activity of D38R/R39D/G88R RNase A, reducing the activity of the quadruple variant K7A/D38R/R39D/G88R RNase A to 1.6×106 M−1s−1.
The majority of the FADE-inspired substitutions had no significant effect on ribonucleolytic activity. The N67R, K31A, and N24R substitutions, when combined individually with the G88R substitution, produced enzymes with catalytic activity roughly comparable to that of G88R RNase A itself. Values of kcat/KM for these three variants were 9.2×107, 5.2×107, and 7.8×107 M−1s−1, respectively. Therefore, RNase A variants combining many of these substitutions (such as K31A/D38R/R39D/N67R/G88R RNase A and D38R/R39D/N67R/G88R RNase A) possessed nearly the kcat/KM value of the wild-type enzyme (4.8×107 and 3.8×107 M−1s−1, respectively). In short, enzymatic activity did not seem to be a limiting parameter for these variants.







TABLE 2







Biochemical parameters and cytotoxic activities of RNase A, its variants, and ONC













Tm a
kcat/KM b
Kd (pRI) c
ΔΔG d (pRI)
Kd e (hRI)


Ribonuclease
(° C.)
(106 M−1s−1)
(nM)
(kcal/mol)
(nM)





wild-type Rnase A
64
52 ± 4
67 × 10−6 h
—
ND


D38R/R39D RNase A
60
18 ± 3
0.30 ± 0.01
5.0
—


N67R RNase A
57
 73 ± 19
0.36 ± 0.01
5.1
ND


K7A/D38R/R39D Rnase A
62
 1.6 ± 0.1
3.5
6.4
ND


N24R/G88R RNase A
60
78 ± 5
 0.27
4.9
ND


G88R RNase A
  60 i
74 ± 4
  0.57 ± 0.05 j
5.3
7.8 k


K31A/G88R RNase A
ND
52 ± 2
ND
ND
58 ± 6


K7A/G88R Rnase A
  62 l
 5.3 ± 0.4
17 ± 1 
7.4
510 ± 20


R39D/G88R RNase A
61
4.3 ± 1 
ND
ND
(6.4 ± 0.3) × 103


N67R/G88R RNase A
58
92 ± 4
45 ± 2 
8.0
44 ± 7


K7A/D38R/R39D/G88R RNase A
60
 1.6 ± 0.2
120 ± 10 
8.5
 (27 ± 3) × 103


ONC
   90 m
 0.22 ± 0.01
≧103    
—
≧103   


D38R/R39D/G88R RNase A
60
31 ± 3
8.0 ± 0.4
6.9
670 ± 40


K31 A/D38R/R39D/N67R/G88R
54
48 ± 7
ND
—
 (19 ± 1) × 103


RNase A


D38R/R39D/N67R/G88R RNase A
56
38 ± 6
(1.4 ± 0.1) × 103
10.0 
(3.4 ± 0.1) × 103





ND, not determined.


a Values of Tm (±2° C.) for RNase A and its variants were determined in PBS by UV spectroscopy.


b Values of kcat/KM (±SE) for RNase A and its variants are for catalysis of 6-FAM-dArU(dA)2-6-TAMRA cleavage at (23 ± 2) ° C. in 0.10M MES-NaOH buffer (OVS-free) at pH 6.0, containing NaCl (0.10M). The value of kcat/KM (±SE) for ONC is for catalysis of 6-FAM-dArUdGdA-6-TAMRA cleavage at (23 ± 2) ° C. in 0.020M MES-NaOH buffer (OVS-free) at pH 6.0, containing NaCl (0.010M).


c Values of Kd (±SE) are for the complex with pRI at (23 ± 2) ° C. The Kd value for ONC is an estimate from Wu et al., (1993) J. Biol. Chem. 268, 10686-10693.


d Values of ΔΔG were calculated with the equation: ΔΔG = −RTIn(Kdwild-type/Kdvariant).


e Values of Kd (±SE) are for the complex with hRI at (23 ± 2) ° C.


f Values of (kcat/KM)cyto were calculated with eq 1 and values of Kd for the complex with hRI.


g Values of IC50 (±SE) are for incorporation of [methyl-3H]thymidine into the DNA of K-562 cells exposed to a ribonuclease, and were calculated with eq 3.


h From Vicentini et al., (1990) Biochemistry 29, 8827-8834.


i From Leland et al., (1998) Proc. Natl. Acad. Sci. USA 95, 10407-10412.


j From Abel et al., (2002) Anal. Biochem. 306, 100-107.


k For fluorescein-labeled G88R RNase A.


l From Haigis et al., (2002) J Biol Chem 277, 11576-11581.


m From Leland et al., (1998) Proc. Natl. Acad. Sci. USA 95, 10407-10412 and determined by circular dichroism spectroscopy.






Affinity for Ribonuclease Inhibitor

The amino acid sequences of pRI and hRI are quite similar (77% identity). Moreover, of the 28 residues in pRI that contact RNase A, only two are replaced by dissimilar residues in hRI. Despite the assumption that the two inhibitor proteins would possess similar affinities for the RNase A variants, we determined the Kd values of complexes with both pRI and hRI. These Kd values are listed in Table 2 above.
As a rigorous test of the utility of the FADE algorithm for identifying residues important for protein-protein interactions, we determined the Kd values of the FADE-inspired variants in complexes with pRI. The Kd values of 0.57 and 17 nM obtained for G88R RNase A and K7A/G88R RNase A in complexes with pRI, were in good agreement with those determined previously. The N24R substitution was the only change that did not diminish the affinity of pRI for RNase A. Indeed, with a Kd value of 0.27 nM, N24R/G88R RNase A actually appeared to form a slightly tighter complex with pRI than did G88R RNase A. The most significant increases in values of Kd were observed for the D38R/R39D swap and the N67R substitution, whose complexes exhibited Kd values of 0.30 and 0.36 nM, respectively. These amino acid changes were responsible for 4,500- and 5,400-fold increases in Kd value, respectively. The K7A/D38R/R39D, N67R/G88R, and D38R/R39D/G88R variants formed complexes with pRI that have Kd values of 3.5, 45, and 8.0 nM, respectively.
The combination of multiple substitutions produced the most RI-evasive variants of RNase A. Of note are the K7A/D38R/R39D/G88R and D38R/R39D/N67R/G88R variants, which formed complexes with pRI having Kd values of 0.12 and 1.4 μM, respectively. Notably, D38R/R39D/N67R/G88R RNase A is the first RNase A variant observed to form a complex with pRI that has a micromolar Kd value. By changing only four out of 124 residues in RNase A, the Kd value of the pRI•RNase A complex was increased by 20-million fold with the D38R/R39D/N67R/G88R variant.
Values of Kd for the complexes of pRI with RNase A variants are ideal for assessing the ability of the FADE algorithm to identify shape-complementarity markers. As a chemotherapeutic, however, cytotoxic ribonucleases must be capable of eluding human RI. For this reason, values of Kd were also determined for the hRI complexes with RNase A variants. With the exception of N67R/G88R RNase A (Kd=44 nM), Kd values for the hRI complexes were greater than those obtained for pRI, with the magnitude of the differences ranged from 2- to 230-fold. The highest Kd value observed for a complex with hRI was that of K7A/D38R/R39D/G88R RNase A at 27 μM, which represents a 400 million-fold decrease in affinity for hRI.
Importantly, the destabilizing effects of these substitutions on the complex were not entirely additive, indicating that the pRI•RNase A interface is plastic. The accommodating nature of the binding interface can be seen upon comparison of LAG values (Table 2). For example, the G88R and N67R substitutions destabilized the complex by approximately 5 kcal/mol each. Yet, the N67R/G88R double variant exhibited an 8 kcal/mol loss in binding free energy, despite the spatial separation of these two substitutions.
Stability
The conformational stability of a ribonuclease is necessary for biological function, including cytotoxicity. Hence, the Tm value of each RNase A variant was determined and is listed in Table 2. The N67R substitution was the most destabilizing, decreasing the Tm value of wild-type RNase A by 7° C. to a value of 57° C. This loss in conformational stability was not recovered by additional substitutions, being observed in all variants containing the N67R substitution. The N67R/G88R and D38R/R39D/N67R/G88R variants had Tm values of 58 and 56 C, respectively. K31A/D38R/R39D/N67R/G88R RNase A had the lowest Tm value of 54° C., which is nearly 10 C lower than that of the wild-type enzyme. Still, this Tm value is significantly greater than physiological temperature. None of the other amino acid substitutions reduced the Tm value by more than a few degrees C.
Cytotoxicity
The toxicity of each ribonuclease was measured with the K-562 human leukemia cell line. Ribonucleases are listed in order of increasing cytotoxicity in Table 2, using IC50 values derived by applying equation 3 (set forth below) to the data in FIG. 3 (h=1.43±0.02 for the 12 cytotoxic ribonucleases). ONC, G88R RNase A, and K7A/G88R RNase A displayed IC50 values similar to those reported previously. D38R/R39D RNase A (FIG. 3A) and N67R RNase A (FIG. 3C) exhibited no cytotoxic activity, even at concentrations of 25 μM. The lack of cytotoxicity for the latter two variants is interesting, considering the large increase in cytotoxicity they exhibited in the context of the G88R substitution.
Upon incorporation of the K7A substitution into the D38R/R39D/G88R variant, its affinity for hRI decreased 40-fold, consistent with the loss of favorable interactions between the lysine side chain and C-terminal serine residue of hRI. This larger Kd value was accompanied by a loss in catalytic activity, leading to an IC50 value nearly twice that of D38R/R39D/G88R RNase A. Although Asp38 was not identified explicitly by the FADE analysis, its importance in the conservative D38R/R39D swap is apparent when the IC50 value of R39D/G88R RNase A (IC50=0.69 μM) is compared with that of D38R/R39D/G88R RNase A (IC50=0.22 μM).
Two of the most cytotoxic variants of RNase A discovered in this work, D38R/R39D/G88R and D38R/R39D/N67R/G88R, as well as ONC, wild-type RNase A, and G88R RNase A, were screened for cytotoxic activity against ten different cell lines. The resulting IC50 values of these ribonucleases are listed in Table 3. All of the cell lines are of human origin except for NmuMG, which is a mouse mammary normal epithelial cell line. With the exception of the Hep3B cell line, all of the human cancer cell lines, like the human leukemia K-562 line, are among the 60 cell lines screened by the National Cancer Institute in search of novel cancer chemotherapeutics.
The cell lines are listed in Table 3 according to increasing doubling times. There did not appear to be any direct correlation between doubling time and sensitivity to the ribonucleases as had been reported previously. In general, the trend of cytotoxicity among the RNase A variants reflected that seen in the K-562 cell line, namely D38R/R39D/N67R/G88R>D38R/R39D/G88R>G88R>wild-type RNase A, with the D38R/R39D/N67R/G88R variant consistently having the lowest IC50 value. The HCT-116, A549, and SF268 cell lines were exceptions to this general trend, as all were more sensitive to wild-type RNase A than was G88R RNase A. Others have reported that wild-type human pancreatic ribonuclease (RNase 1) is toxic to some cell lines, just as we found several cell lines susceptible to wild-type RNase A. These three cell lines derive from three different tissue types: colon, lung, and CNS, respectively.
A goal of this work was to identify RNase A variants possessing cytotoxicity equal to or greater than that of ONC. This goal was achieved with the D38R/R39D/N67R/G88R variant in the K-562, Du145, Hep-3B, and SF268 cell lines. In the remaining six cell lines, ONC exhibited 3- to 30-fold greater cytotoxicity than did the RNase A variants. Interestingly, none of the RNase A-derived variants tested in this screen was toxic to the normal cell line NmuMG at the maximum concentrations tested. This discrimination was not observed with ONC, which had an IC50 of 1.62 μM for the normal mouse cell line.







TABLE 3







IC50 values of RNase A, its variants, and ONC for ten cell lines










Doubling
IC50 (μM)a














Cell line
Description
time (h)
wild-type
DRNGb
DRGb
G88R
ONC

















HCT-116
colon carcinoma
17.4
4.7
0.49
1.4
10.4
0.14


NCI-H460
lung carcinoma
17.8
39
0.71
0.60
11.0
0.13


A549
lung
22.9
15.5
4.8
13.7
27.0
0.15



adenocarcinoma


MCF-7
breast
25.4
21.7
0.27
0.42
4.4
0.086



adenocarcinoma


Du145
prostate carcinoma
32.3
5.5
0.085
0.45
2.0
0.11


SF-268
CNS glioblastoma
33.1
3.8
0.18
0.64
4.6
0.088


NCI/ADR-RES
breast
34.0
19
1.00
2.3
5.8
0.06



adenocarcinoma


SK-OV-3
ovary
48.7
3.2
0.76
1.5
2.8
0.13



adenocarcinoma


Hep-3B
liver carcinoma
ND
2.8
0.031
0.040
0.34
0.051


NmuMG
mammary normal
ND
>40
>10
>20
>40
1.6



epithelial (mouse)





aValues of IC50 are for the conversion of calcein AM to calcein in cells exposed to a ribonuclease, and were calculated with eq 4.


bDRNG and DRG refer to the D38R/R39D/N67R/G88R and D38R/R39D/G88R variants of RNase A, respectively.






Methods and Materials
Materials
Escherichia coli BL21(DE3) cells and pET22b(+) and pET27b(+) plasmids were from Novagen (Madison, Wis.). K-562 cells were derived from a continuous human chronic myelogenous leukemia line obtained from the American Type Culture Collection (Manassas, Va.). Cell culture medium and supplements were from Invitrogen (Carlsbad, Calif.). [methyl-3H]Thymidine (6.7 Ci/mmol) was from Perkin Elmer (Boston, Mass.). Enzymes were obtained from Promega (Madison, Wis.) or New England Biolabs (Beverly, Mass.). Ribonuclease substrates 6-FAM-dArUdAdA-6-TAMRA and 6-FAM ̃dArUdGdA ̃6-TAMRA were from Integrated DNA Technologies (Coralville, Iowa). All other chemicals used were of commercial reagent grade or better, and were used without further purification.
Terrific Broth (TB) contained (in 1.00 L) tryptone (12 g), yeast extract (24 g), glycerol (4 mL), KH2PO4 (2.31 g), and K2HPO4 (12.54 g). Phosphate-buffered saline (PBS) contained (in 1.00 L) NaCl (8.0 g), KCl (2.0 g), Na2HPO4.7H2O (1.15 g), KH2PO4 (2.0 g), and NaN3 (0.10 g), and had pH 7.4.
Instruments
[methyl-3H]Thymidine incorporation into K-562 genomic DNA was quantitated by scintillation counting using a Microbeta TriLux liquid scintillation and luminescence counter (Perkin Elmer, Wellesley, Mass.). The mass of each protein variants was confirmed by MALDI-TOF mass spectrometry using a Voyager-DE-PRO Biospectrometry Workstation (Applied Biosystems, Foster City, Calif.). Fluorescence measurements were made with a QuantaMaster1 photon-counting fluorometer equipped with sample stirring (Photon Technology International, South Brunswick, N.J.). Thermal denaturation data were acquired using a Cary 3 double-beam spectrophotometer equipped with a Cary temperature controller (Varian, Palo Alto, Calif.).
Design of Ribonuclease A Variants
The Fast Atomic Density Evaluator (FADE) program calculates shape-complementarity markers of proteins at complex interfaces. Atomic density is measured using fast Fourier transform algorithms based on methods described previously. Using the structure of the crystalline pRI•RNase A complex (PDB entry 1 DFJ), critical RNase A residues in close proximity to large clusters of shape-complementarity markers were identified and are listed in Table 1 above. Amino acid substitutions were chosen to create maximal electrostatic or steric conflict as well as eliminate any favorable Coulombic or short-range interactions.
At the onset of this research, the most cytotoxic variant of RNase'A known was K7A/G88R RNase A. Subsequent amino acid substitutions inspired by FADE analysis were initially made in the background of these established changes, with the expectation that any additional contributions to evasivity would be additive. As discussed here, we found that the loss of enzymatic activity accompanying the K7A substitution compromised cytotoxicity, and hence, later substitutions were made in the background of the G88R substitution alone. The G88R background provided a well-characterized benchmark of cytotoxicity and RI-evasion from which we could identify improvements using our established assays. Substitutions that were successful in the G88R background were also made alone to assess their individual contribution to evasion of RI and cytotoxicity.
Production of Ribonucleases
cDNA molecules encoding RNase A variants were created by oligonucleotide-mediated site-directed mutagenesis using a pET22b(+) or pET27b(+) plasmid that contained cDNA encoding wild-type RNase A or its G88R variant, respectively. ONC, wild-type RNase A, and RNase A variants were produced as described previously in Haigis et al., (2002) J Biol Chem 277, 11576-11581, with the following exceptions. Inclusion bodies from E. coli were stirred in 20 mM Tris-HCl buffer at pH 8.0, containing guanidine-HCl (7 M), DTT (0.1 M), and EDTA (10 mM) until dissolved thoroughly. Ribonucleases were refolded overnight at room temperature following slow dilution into 0.10 M Tris-HCl buffer at pH 8.0, containing NaCl (0.1 M), reduced glutathione (1.0 mM), and oxidized glutathione (0.2 mM). Following purification, proteins were dialyzed against PBS and filtered with a 0.2 μm syringe prior to use in biochemical assays. Protein concentration was determined by UV spectroscopy using an extinction coefficient of ε278=0.72 mg·ml−1cm−1 for RNase A and its variants and ε280=0.87 mg·ml−1cm−1 for ONC.
Production of Ribonuclease Inhibitor
Porcine ribonuclease inhibitor (pRI) was prepared as described in Klink et al., (2001) Protein Expr. Purif. 22, 174-179. Freshly prepared pRI was confirmed to be 100% active by its ability to titrate the ribonucleolytic activity of wild-type RNase A.
Human ribonuclease inhibitor (hRI) was produced in E. coli BL21(DE3) cells transformed with a pET22b(+) plasmid that contained cDNA encoding hRI between its NdeI and SalI sites. Cultures (1.0 L) of TB were inoculated to an OD of 0.005 at 600 nm from an overnight culture. The culture was grown at 37 C to an OD of 1.8-2.0 at 600 nm. IPTG was added to a final concentration of 0.5 mM, and induction was carried out overnight at 18 C. Subsequent purification of soluble protein and activity determination of hRI was carried out in the same manner as for pRI. The purity and size of both RIs were confirmed by electrophoresis and mass spectrometry.
Assays of Ribonuclease Inhibitor Binding
The affinity of RNase A variants for both pRI and hRI was determined by using a slight modification of a competition assay reported previously in Abel et al., (2002) Anal. Biochem. 306, 100-107. Briefly, both fluorescein-labeled G88R RNase A (final concentration: 50 nM) and varying concentrations of an unlabeled ribonuclease were added to 2.0 ml of PBS containing DTT (5 mM). Following a 15 min incubation at (23±2)° C., protected from light, the initial fluorescence intensity of the unbound fluorescein-labeled G88R RNase A was monitored for 3 min (excitation: 493 nm, emission: 515 nm). pRI was then added (final concentration: 50 nM, which is sufficient to bind 90% of the fluorescein-labeled G88R RNase A in the absence of unlabeled competitor), and the final fluorescence intensity was measured. The competition assay was carried out identically for hRI, except that more hRI was necessary (final concentration of 115 nM) to achieve 90% binding of fluorescein-labeled G88R RNase A because of the lower affinity of hRI. The affinity of hRI for fluorescein-labeled G88R RNase A was determined by titrating 50 nM fluorescein-labeled G88R RNase A with varying amounts of hRI (0.5-1000 nM) and recording the decrease in fluorescence upon binding. The value of Kd was found to be 7.8 nM.
Assays of Catalytic Activity
The ribonucleolytic activities of RNase A and its variants were determined by assaying their ability to cleave the hypersensitive fluorogenic substrate 6-FAM ̃dArUdAdA ̃6-TAMRA (50 nM), which exhibits a 180-fold increase in fluorescence (excitation: 493 nm, emission: 515 nm) upon cleavage. Assays were carried out at (23±2)° C. in 2.0 ml of 0.10 M MES-NaOH buffer at pH 6.0, containing NaCl (0.10 M). The MES used to prepare the assay buffer was purified by anion-exchange chromatography to remove trace amounts of oligomeric vinylsulfonic acid, which is a byproduct of commercial buffer synthesis and has been shown to be a potent inhibitor of RNase A. Values of kcat/KM were obtained with the equation:




  
    
      
        
          
            k
            cat
          
          /
          
            K
            M
          
        
        =
        
          
            (
            
              
                Δ
                ⁢
                
                  
                
                ⁢
                
                  I
                  /
                  Δ
                
                ⁢
                
                  
                
                ⁢
                t
              
              
                
                  I
                  max
                
                -
                
                  I
                  0
                
              
            
            )
          
          ⁢
          
            1
            
              [
              ribonuclease
              ]
            
          
        
      
    
    
      
        (
        1
        )
      
    
  




where ΔI/Δt represents the initial reaction velocity generated by cleavage of the 6-FAM-dArUdAdA-6-TAMRA substrate upon addition of ribonuclease to the cuvette. I0 and Imax are, respectively, the fluorescence intensities prior to enzyme addition and following the complete cleavage of substrate by excess wild-type RNase A. Activity values for ONC were determined at (23±2) C in 2.0 ml of OVS-free 20 mM MES-NaOH buffer at pH 6.0, containing NaCl (0.010 M) using the substrate 6-FAM ̃dArUdGdA ̃6-TAMRA (50 nM).
Assays of Cytotoxicity
IC50 values for RNase A, its variants, and ONC were determined by measuring the incorporation of [methyl-3H]thymidine into the cellular DNA of K-562 cells in the presence of ribonucleases. All cytotoxicity assays were repeated at least three times in triplicate. Each data point represents the mean of three or more experimental values (±SE). IC50 values were calculated by fitting the curves using nonlinear regression to a sigmoidal dose-response curve with the equation:




  
    
      
        y
        =
        
          
            100
            ⁢
            %
          
          
            1
            +
            
              10
              
                
                  (
                  
                    
                      log
                      ⁡
                      
                        (
                        
                          IC
                          50
                        
                        )
                      
                    
                    -
                    
                      log
                      ⁡
                      
                        [
                        ribonuclease
                        ]
                      
                    
                  
                  )
                
                h
              
            
          
        
      
    
    
      
        (
        2
        )
      
    
  




In eq 3, y is the total DNA synthesis following a 4-h [methyl-3H]thymidine pulse, and h is the slope of the curve.
Cytotoxicity assays other than those carried out using K-562 cells were performed at the Keck-UWCCC Small Molecule Screening Facility. These assays used ten cell lines from a broad spectrum of tissues. Following a 72-h incubation with ribonucleases, IC50 values were determined by measuring the enzymatic conversion of the profluorophore calcein AM (Molecular Probes, Eugene, Oreg.) to calcein in live cells. Coefficient of variation and Z-scores were determined for each cell line using doxorubicin as an internal control. All cytotoxicity assays were performed in triplicate three times. IC50 values were calculated with the equation:




  
    
      
        
          IC
          50
        
        =
        
          
            
              (
              
                
                  
                    50
                    ⁢
                    %
                  
                  -
                  
                    low
                    ⁢
                    
                      
                    
                    ⁢
                    %
                  
                
                
                  
                    high
                    ⁢
                    
                      
                    
                    ⁢
                    %
                  
                  -
                  
                    low
                    ⁢
                    
                      
                    
                    ⁢
                    %
                  
                
              
              )
            
            ⁢
            
              (
              
                
                  
                    [
                    ribonuclease
                    ]
                  
                  high
                
                -
                
                  
                    [
                    ribonuclease
                    ]
                  
                  low
                
              
              )
            
          
          +
          
            
              [
              ribonuclease
              ]
            
            low
          
        
      
    
    
      
        (
        3
        )
      
    
  




where low % and high % refer to inhibition by the two concentrations, [ribonuclease]low and [ribonuclease]high, that bracket 50% inhibition.
Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it is understood that certain adaptations of the invention are a matter of routine optimization for those skilled in the art, and can be implemented without departing from the spirit of the invention, or the scope of the appended claims.

## Claims

1. An engineered pancreatic ribonuclease A variant comprising an amino acid sequence which differs from the amino acid sequence of SEQ ID NO:1 solely by four to seven amino acid substitutions, wherein the four to seven amino acid substitutions are located at positions of SEQ ID NO:1 selected from the group consisting of 7, 31, 38, 39, 41, 67 and 85-94, wherein at least one of the four to seven amino acid substitutions is at a position corresponding to any one of positions 85-94 of SEQ ID NO:1, wherein at least three of the four to seven amino acid substitutions are at positions corresponding to positions 7, 31, 38, 39, 41, or 67 of SEQ ID NO:1, wherein if the engineered pancreatic ribonuclease A variant has an amino acid substitution at a position corresponding to position 41 of SEQ ID NO:1, said amino acid substitution corresponds to the amino acid substitution K41A of SEQ ID NO:1, and wherein the engineered pancreatic ribonuclease A variant retains ribonuclease activity.

2. The engineered pancreatic ribonuclease A variant of claim 1, wherein the four to seven amino acid substitutions are located at positions of SEQ ID NO:1 selected from the group consisting of 7, 31, 38, 39, 41, 67 and 88, wherein if the engineered pancreatic ribonuclease A variant has an amino acid substitution at position 41 of SEQ ID NO:1, said amino acid substitution corresponds to the amino acid substitution K41A of SEQ ID NO:1, and wherein the at least one of the four to seven amino acid substitutions is at a position corresponding to position 88 of SEQ ID NO: 1.

3. The engineered pancreatic ribonuclease A variant of claim 1, wherein the four to seven amino acid substitutions are located at positions of SEQ ID NO:1 selected from the group consisting of 7, 31, 38, 39, 67 and 85-94, and wherein the at least three of the four to seven amino acid substitutions are at positions corresponding to positions 7, 31, 38, 39, or 67 of SEQ ID NO: 1.

4. The engineered pancreatic ribonuclease A variant of claim 3, wherein the four to seven amino acid substitutions are located at positions corresponding to positions of SEQ ID NO:1 selected from the group consisting of 7, 31, 38, 39, 67 and 88.

5. The engineered pancreatic ribonuclease A variant of claim 4, wherein said variant comprises an amino acid sequence which differs from the amino acid sequence of SEQ ID NO:1 solely by four substitutions at positions 38, 39, 67 and 88 of SEQ ID NO:1.

6. The engineered pancreatic ribonuclease A variant of claim 4, wherein said variant comprises an amino acid sequence which differs from the amino acid sequence of SEQ ID NO:1 solely by four substitutions at positions 7, 38, 39 and 88 of SEQ ID NO:1.

7. The engineered pancreatic ribonuclease A variant of claim 4, wherein said variant comprises an amino acid sequence which differs from the amino acid sequence of SEQ ID NO:1 solely by five substitutions at positions 31, 38, 39, 67 and 88 of SEQ ID NO:1.

8. The engineered pancreatic ribonuclease A variant of claim 1, wherein the engineered pancreatic ribonuclease A variant exhibits enhanced cytotoxic activity relative to the native ribonuclease A of SEQ ID NO:1.

9. An engineered pancreatic ribonuclease A variant comprising an amino acid sequence which differs from the amino acid sequence of SEQ ID NO: 1 solely by three or more amino acid substitutions at positions corresponding to positions of SEQ ID NO:1 selected from the group consisting of 38, 39, 67 and 85-94, wherein at least one of the three or more amino acid substitutions is at a position corresponding to any one of positions 85-94 of SEQ ID NO:1, wherein at least two of the three or more amino acid substitutions are at positions corresponding to positions 38, 39 or 67 of SEQ ID NO:1; and wherein the variant has ribonuclease activity.

10. An engineered pancreatic ribonuclease A variant comprising an amino acid sequence which differs from the amino acid sequence of SEQ ID NO:1 solely by two or more modifications at positions corresponding to positions of SEQ ID NO:1 selected from the group consisting of 38, 39, 67 and 85-94, wherein at least one of the two or more modifications is an amino acid substitution at a position corresponding to any one of positions 85-94 of SEQ ID NO:1, and wherein at least one of the two or more modifications is selected from the group consisting of: (i) a substitution at a position corresponding to position 39 of SEQ ID NO:1, (ii) a substitution at a position corresponding to position 67 of SEQ ID NO:1, (iii) substitutions at positions corresponding to positions 38 and 39 of SEQ ID NO:1, and (iv) substitutions at positions corresponding to positions 38, 39 and 67 of SEQ ID NO:1; and wherein the variant has ribonuclease activity.

11. The engineered pancreatic ribonuclease A variant of claim 10, wherein the two or more modifications consist of amino acid substitutions at amino acid residue positions 39 and 88 of SEQ ID NO:1.

12. The engineered pancreatic ribonuclease A variant of claim 10, wherein the two or more modifications consist of amino acid substitutions at amino acid residue positions 67 and 88 of SEQ ID NO:1.

13. The engineered pancreatic ribonuclease A variant of claim 10, wherein the two or more modifications consist of amino acid substitutions at (i) amino acid residue positions 38 and 39 of SEQ ID NO:1, and (ii) amino acid residue position 88 of SEQ ID NO:1.

14. An engineered pancreatic ribonuclease A variant comprising an amino acid sequence differing from SEQ ID NO:1 at amino acid residue positions 31 and 88 of SEQ ID NO:1, wherein the difference consists of an amino acid substitution at these two positions; and wherein the variant has ribonuclease activity.