Published on Web 03/03/2007
Protein Flexibility and Species Specificity in Structure-Based Drug Discovery: Dihydrofolate Reductase as a Test System Anna L. Bowman,† Michael G. Lerner,‡ and Heather A. Carlson*,†,‡ Contribution from the Department of Medicinal Chemistry and Biophysics Research DiVision, UniVersity of Michigan, Ann Arbor, Michigan 48109-1065 Received November 17, 2006; E-mail:
[email protected] Abstract: In structure-based drug discovery, researchers would like to identify all possible scaffolds for a given target. However, techniques that push the boundaries of chemical space could lead to many false positives or inhibitors that lack specificity for the target. Is it possible to broadly identify the appropriate chemical space for the inhibitors and yet maintain target specificity? To address this question, we have turned to dihydrofolate reductase (DHFR), a well-studied metabolic enzyme of pharmacological relevance. We have extended our multiple protein structure (MPS) method for receptor-based pharmacophore models to use multiple X-ray crystallographic structures. Models were created for DHFR from human and Pneumocystis carinii. These models incorporate a fair degree of protein flexibility and are highly selective for known DHFR inhibitors over drug-like non-inhibitors. Despite sharing a highly conserved active site, the pharmacophore models reflect subtle differences between the human and P. carinii forms, which identify species-specific, high-affinity inhibitors. We also use structures of DHFR from Candida albicans as a counter example. The available crystal structures show little flexibility, and the resulting models give poorer performance in identifying species-specific inhibitors. Therapeutic success for this system may depend on achieving species specificity between the related human host and these key fungal targets. The MPS technique is a promising advance for structure-based drug discovery for DHFR and other proteins of biomedical interest.
Introduction
Candida albicans and Pneumocystis carinii are opportunistic fungal pathogens that present a major health problem. The individuals at highest risk for pathogenic infections include those with hematological malignancies, AIDS patients with low CD4+ counts, and transplant recipients. Fungal infections of the blood are an increasingly important cause of morbidity and mortality in immunocompromised patients.1 C. albicans is among the most significant fungal pathogens,2 and hospital-acquired infections due to C. albicans are almost as prevalent as those due to bacteria such as E. coli.3 P. carinii is important in the study of Pneumocystis pneumonia, one of the major AIDS-defining infections.4 Dihydrofolate reductase (DHFR; EC. 1.5.1.3) is a common target for drug action. DHFR is a small enzyme that plays an essential role in various cellular processes including the biosynthesis of DNA. It catalyzes the reduction of dihydrofolate to tetrahydrofolate (and, more slowly, folate to dihydrofolate). These reductions take place via the transfer of a hydride ion † ‡
Department of Medicinal Chemistry. Biophysics Research Division.
(1) Viudes, A.; Peman, J.; Canton, E.; Ubeda, P.; Lopez-Ribot, J. L.; Gobernado, M. Eur. J. Clin. Microbiol. Infect. Dis. 2002, 21, 767-774. (2) Sullivan, D. J.; Moran, G. P.; Pinjon, E.; Al-Mosaid, A.; Stokes, C.; Vaughan, C.; Coleman, D. C. FEMS Yeast Res. 2004, 4, 369-376. (3) Edwards, J. E. N. Engl. J. Med. 1991, 324, 1060-1062. (4) Morris, A.; Lundgren, J. D.; Masur, H.; Walzer, P. D.; Hanson, D. L.; Frederick, T.; Huang, L.; Beard, C. B.; Kaplan, J. E. Emerg. Infect. Dis. 2004, 10, 1713-1720. 3634
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from the nicotinamide adenine dinucleotide phosphate (NADPH) cofactor bound to the enzyme.5 However, problems arise from the use of DHFR as a therapeutic target because the enzyme is found in both microorganisms and humans. To decrease toxic effects in the human host, drugs should selectively target the fungal binding site versus the human.6 The active site residues of human DHFR (hDHFR), P. carinii DHFR (pcDHFR), and C. albicans DHFR (caDHFR) are highly conserved with only three differences, Figure 1: (1) D21 in hDHFR corresponds to S24 in pcDHFR and K24 in caDHFR, (2) F31 in hDHFR corresponds to I33 in the two fungal species, and (3) N64 in hDHFR corresponds to F69 in pcDHFR and F66 in caDHFR. These residues line the edges of the pocket and provide contacts to the “tails” of bound folate molecules. There are differences in the cleft geometry that are apparent in Figure 1. The protein conformation of caDHFR creates a slightly larger active site than that of hDHFR.7 However, the active site volume of pcDHFR is smaller than that found in hDHFR.8 Furthermore, studies have shown that distant residues affect catalysis through altered dynamics of the whole protein.9,10 It (5) Schweitzer, B. I.; Dicker, A. P.; Bertino, J. R. FASEB J. 1990, 4, 24412452. (6) Chan, J. H.; Hong, J. S.; Kuyper, L. F.; Baccanari, D. P.; Joyner, S. S.; Tansik, R. L.; Boytos, C. M.; Rudolph, S. K. J. Med. Chem. 1995, 38, 3608-3616. (7) Whitlow, M.; Howard, A. J.; Stewart, D.; Hardman, K. D.; Kuyper, L. F.; Baccanari, D. P.; Fling, M. E.; Tansik, R. L. J. Biol. Chem. 1997, 272, 30289-30298. (8) Gschwend, D. A.; Good, A. C.; Kuntz, I. D. J. Mol. Recognit. 1996, 9, 175-186. 10.1021/ja068256d CCC: $37.00 © 2007 American Chemical Society
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Figure 1. The average surface of the substrate binding pocket is shown in gray. The three residues that are not conserved in the binding site are labeled and shown in stick formation; their contribution to the protein surface is colored accordingly: (a) hDHFR, (b) pcDHFR, and (c) caDHFR. The black line denotes where each protein surface is cut away to reveal the penetration of the binding pocket into the interior of the protein. Methotrexate (MTX, colored by atom with carbons in green) has been manually added to the average structure to aid the viewer in interpreting the potential interactions with substrates.
may be possible for inhibitors to take advantage of these differences in size and conformational sampling. A disparity in activities indicates subtle binding specificities in the active site of the enzymes.6,11 This implies that there are exploitable differences within the active site that could be probed to develop potent and selective inhibitors. Currently, the drug of choice for Pneumocystis pneumonia is trimethoprim, which is selective for pcDHFR12 but has only moderate affinity (IC50 value ∼20 µM).13 Because of this low potency, trimethoprim must be given in combination with sulfa drugs like sulfamethoxazole or dapsone.14 However, sulfa drugs cause allergic and toxic side effects in up to 54% of patients, and treatment must be altered or discontinued.15 A more potent inhibitor, selective for pcDHFR over hDHFR, would be a valuable lead for a drug that is effective without the coadministration of a sulfa drug.16 The main drug for treating C. albicans infections is Amphotericin B; however, it can cause severe side effects.17 DHFR is not the target of Amphotericin B, but recent research has discovered inhibitors with significant selectivity for caDHFR over hDHFR.6 This is a promising avenue for new pharmacological treatment. Here, we present a computational study of species specificity for inhibitors of DHFR that focuses on incorporating protein flexibility into structure-based drug discovery. Ignoring protein flexibility by using a “static” structure (a single, rigid conformation of a protein) can considerably reduce the computational expense of virtual screening or de novo design, but it can limit the resulting inhibitors to a minute fraction of the appropriate chemical space that could complement that receptor.18 Our (9) Wong, K. F.; Selzer, T.; Benkovic, S. J.; Hammes-Schiffer, S. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6807-6812. (10) Rajagopalan, P. T. R.; Lutz, S.; Benkovic, S. J. Biochemistry 2002, 41, 12618-12628. (11) Gschwend, D. A.; Sirawaraporn, W.; Santi, D. V.; Kuntz, I. D. Proteins: Struct., Funct., Genet. 1997, 29, 59-67. (12) Baccanari, D. P.; Daluge, S.; King, R. W. Biochemistry 1982, 21, 50685075. (13) Delves, C. J.; Ballantine, S. P.; Tansik, R. L.; Baccanari, D. P.; Stammers, D. K. Protein Expression Purif. 1993, 4, 16-23. (14) Medina, I.; Mills, J.; Leoung, G.; Hopewell, P. C.; Lee, B.; Modin, G.; Benowitz, N.; Wofsy, C. B. N. Engl. J. Med. 1990, 323, 776-782. (15) Lee, S. A. J. Pharm. Pract. 2006, 19, 5-9. (16) Rosowsky, A.; Forsch, R. A.; Queener, S. F. J. Med. Chem. 2002, 45, 233-241. (17) Sternberg, S. Science 1994, 266, 1632-1634.
technique uses multiple protein structures (MPS) to represent an ensemble of conformational states of the receptor.19-21 Our MPS method maps out complementary interactions with the binding sites of each protein conformation. Regions of rigidity and flexibility are identified by the conserved regions where the same complementary interactions are consistently made with most of the MPS. The method, initially applied to HIV integrase,20 has seen considerable success with HIV-1 protease.21,22 However, our previous studies have focused on using molecular dynamics (MD) simulations to generate the ensemble of protein conformations for MPS studies. MD simulations are appropriate for this use, but they are time-consuming. Because of this, they are not typically used during drug discovery in the pharmaceutical industry. Here, we further extend our method to use a collection of crystal structures. By using structures from the PDB (Protein Data Bank),23 the method will be faster to apply and more accessible to scientists. Incorporating protein flexibility allows structure-based drug design to expand the conformational and chemical space of the hit list. Of course, a more broad description of the chemical space could identify weaker, more promiscuous inhibitors. For the case of DHFR, a loss of species specificity is detrimental. In this study, we show that the inclusion of flexibility does not lose specificity between hDHFR versus pcDHFR inhibitors. The MPS models are highly selective for known DHFR inhibitors over drug-like non-inhibitors, and, furthermore, they display species specificity in these highly conserved systems. Conversely, we show that the limited conformational flexibility in caDHFR structures leads to moderate performance and a loss of species specificity. (18) Carlson, H. A.; McCammon, J. A. Mol. Pharmacol. 2000, 57, 213218. (19) Carlson, H. A.; Masukawa, K. M.; McCammon, J. A. J. Phys. Chem. A 1999, 103, 10213-10219. (20) Carlson, H. A.; Masukawa, K. M.; Rubins, K.; Bushman, F. D.; Jorgensen, W. L.; Lins, R. D.; Briggs, J. M.; McCammon, J. A. J. Med. Chem. 2000, 43, 2100-2114. (21) Meagher, K. L.; Carlson, H. A. J. Am. Chem. Soc. 2004, 126, 1327613281. (22) Meagher, K. L.; Lerner, M. G.; Carlson, H. A. J. Med. Chem. 2006, 49, 3478-3484. (23) Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235242; http://www.rcsb.org/pdb/. J. AM. CHEM. SOC.
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Figure 2. Average backbone structure for (a) hDHFR, (b) pcDHFR, and (c) caDHFR. A red, thicker tube indicates greater rmsd across the ensemble, whereas a blue, narrow tube shows limited flexibility. Residues with the greatest backbone flexibility are labeled in each model. The circle indicates the substrate-binding site region, and a close-up of the region is shown below. Active-site residues that are not conserved between species are labeled.
Methods Protein Preparation. For each species, X-ray crystallographic structures of the wild-type protein with unique ligands bound were downloaded from the PDB.23 If, within a species class, a structure with an identical ligand existed, the structure with the better resolution was used. This resulted in seven structures for hDHFR (1HFR,24 1OHJ,25 1PD8,26 1S3W,27 1U72,28 1KMS,29 and 1KMV29), eight structures for caDHFR (1AOE,7 1M78,7 1M79,7 1M7A,7 1IA1,30 1IA2,30 1IA3,30 and 1IA430), and nine structures for pcDHFR (1DAJ,31 1E26,32 2CD2,32 3CD2,32 1LY3,33 1LY4,33 1S3Y,34 1VJ3,35 and 1DYR36). (24) Cody, V.; Galitsky, N.; Luft, J. R.; Pangborn, W.; Blakley, R. L.; Gangjee, A. Anti-Cancer Drug Des. 1998, 13, 307-315. (25) Cody, V.; Galitsky, N.; Luft, J. R.; Pangborn, W.; Rosowsky, A.; Blakley, R. L. Biochemistry 1997, 36, 13897-13903. (26) Cody, V.; Luft, J. R.; Pangborn, W.; Gangjee, A. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2003, 59, 1603-1609. (27) Cody, V.; Luft, J. R.; Pangborn, W.; Gangjee, A.; Queener, S. F. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 646-655. (28) Cody, V.; Luft, J. R.; Pangborn, W. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2005, 61, 147-155. (29) Klon, A. E.; Heroux, A.; Ross, L. J.; Pathak, V.; Johnson, C. A.; Piper, J. R.; Borhani, D. W. J. Mol. Biol. 2002, 320, 677-693. (30) Whitlow, M.; Howard, A. J.; Stewart, D.; Hardman, K. D.; Chan, J. H.; Baccanari, D. P.; Tansik, R. L.; Hong, J. S.; Kuyper, L. F. J. Med. Chem. 2001, 44, 2928-2932. (31) Cody, V.; Galitsky, N.; Luft, J. R.; Pangborn, W.; Gangjee, A.; Devraj, R.; Queener, S. F.; Blakley, R. L. Acta Crystallogr., Sect. D: Biol. Crystallogr. 1997, 53, 638-649. (32) Cody, V.; Galitsky, N.; Rak, D.; Luft, J. R.; Pangborn, W.; Queener, S. F. Biochemistry 1999, 38, 4303-4312. (33) Cody, V.; Galitsky, N.; Luft, J. R.; Pangborn, W.; Queener, S. F.; Gangjee, A. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2002, 58, 1393-1399. (34) Cody, V.; Luft, J. R.; Pangborn, W.; Gangjee, A.; Queener, S. F. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 646-655. (35) Cody, V.; Chan, D.; Galitsky, N.; Rak, D.; Luft, J. R.; Pangborn, W.; Queener, S. F.; Laughton, C. A.; Stevens, M. F. Biochemistry 2000, 39, 3556-3564. (36) Champness, J. N.; Achari, A.; Ballantine, S. P.; Bryant, P. K.; Delves, C. J.; Stammers, D. K. Structure 1994, 2, 915-924. 3636 J. AM. CHEM. SOC.
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All ligands and solvent were removed from each structure; however, the cofactor was retained. Histidine residues were visually inspected to assign the appropriate protonation state. Hydrogen atoms were placed using the LEaP routine37 in AMBER38 and optimized to convergence with conjugate gradient energy minimization (convergence criterion: rms gradient
