Key Points
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Serine hydrolases are one of the largest and most diverse classes of enzymes found in eukaryotes and prokaryotes, including ∼240 members in humans.
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Several clinically approved drugs target serine hydrolases. Prominent among these therapeutics are inhibitors of thrombin, acetylcholinesterase and dipeptidyl peptidase 4 that are used to treat clotting disorders, Alzheimer's disease-associated dementia and diabetes, respectively.
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Many serine hydrolases have recently emerged as enzymes with therapeutic potential and are the focus of intense inhibitor discovery efforts.
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Compounds that act through covalent mechanisms have proved to be especially effective at selectively inhibiting serine hydrolases. Here, we highlight the mechanism-based electrophiles that have successfully formed the basis of selective, in vivo-active inhibitors (including several approved drugs) and also review promising new chemotypes that have recently been discovered.
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Activity-based protein profiling has facilitated the discovery of dysregulated serine hydrolases in disease and has enabled the rapid development of selective inhibitors for the functional characterization of these enzymes.
Abstract
Serine hydrolases perform crucial roles in many biological processes, and several of these enzymes are targets of approved drugs for indications such as type 2 diabetes, Alzheimer's disease and infectious diseases. Despite this, most of the human serine hydrolases (of which there are more than 200) remain poorly characterized with respect to their physiological substrates and functions, and the vast majority lack selective, in vivo-active inhibitors. Here, we review the current state of pharmacology for mammalian serine hydrolases, including marketed drugs, compounds that are under clinical investigation and selective inhibitors emerging from academic probe development efforts. We also highlight recent methodological advances that have accelerated the rate of inhibitor discovery and optimization for serine hydrolases, which we anticipate will aid in their biological characterization and, in some cases, therapeutic validation.
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References
Long, J. Z. & Cravatt, B. F. The metabolic serine hydrolases and their functions in mammalian physiology and disease. Chem. Rev. 111, 6022–6063 (2011). This is a comprehensive review of the mammalian metabolic serine hydrolases.
Davie, E. W. & Ratnoff, O. D. Waterfall sequence for intrinsic blood clotting. Science 145, 1310–1312 (1964).
Whitcomb, D. C. & Lowe, M. E. Human pancreatic digestive enzymes. Dig. Dis. Sci. 52, 1–17 (2007).
Lane, R. M., Potkin, S. G. & Enz, A. Targeting acetylcholinesterase and butyrylcholinesterase in dementia. Int. J. Neuropsychopharmacol. 9, 101–124 (2006).
Bonventre, J. V. et al. Reduced fertility and postischaemic brain injury in mice deficient in cytosolic phospholipase A2. Nature 390, 622–625 (1997).
Menendez, J. A. & Lupu, R. Fatty acid synthase and the lipogenic phenotype in cancer pathogenesis. Nature Rev. Cancer 7, 763–777 (2007).
Simon, G. M. & Cravatt, B. F. Activity-based proteomics of enzyme superfamilies: serine hydrolases as a case study. J. Biol. Chem. 285, 11051–11055 (2010).
Nomura, D. K. et al. Monoacylglycerol lipase regulates a fatty acid network that promotes cancer pathogenesis. Cell 140, 49–61 (2010).
Steuber, H. & Hilgenfeld, R. Recent advances in targeting viral proteases for the discovery of novel antivirals. Curr. Top. Med. Chem. 10, 323–345 (2010).
White, M. J. et al. The HtrA-like serine protease PepD interacts with and modulates the Mycobacterium tuberculosis 35-kDa antigen outer envelope protein. PLoS ONE 6, e18175 (2011).
Damblon, C. et al. The catalytic mechanism of β-lactamases: NMR titration of an active-site lysine residue of the TEM-1 enzyme. Proc. Natl Acad. Sci. USA 93, 1747–1752 (1996).
Bachovchin, D. A. et al. Superfamily-wide portrait of serine hydrolase inhibition achieved by library-versus-library screening. Proc. Natl Acad. Sci. USA 107, 20941–20946 (2010). This paper reports the findings of a global survey of carbamate-containing compounds for inhibition against a large panel of serine hydrolases.
Li, W., Blankman, J. L. & Cravatt, B. F. A functional proteomic strategy to discover inhibitors for uncharacterized hydrolases. J. Am. Chem. Soc. 129, 9594–9595 (2007).
Johnson, D. S. et al. Discovery of PF-04457845: a highly potent, orally bioavailable, and selective urea FAAH inhibitor. ACS Med. Chem. Lett. 2, 91–96 (2011).
Adibekian, A. et al. Click-generated triazole ureas as ultrapotent in vivo-active serine hydrolase inhibitors. Nature Chem. Biol. 7, 469–478 (2011).
Leung, D., Hardouin, C., Boger, D. L. & Cravatt, B. F. Discovering potent and selective reversible inhibitors of enzymes in complex proteomes. Nature Biotech. 21, 687–691 (2003).
Hoover, H. S., Blankman, J. L., Niessen, S. & Cravatt, B. F. Selectivity of inhibitors of endocannabinoid biosynthesis evaluated by activity-based protein profiling. Bioorg. Med. Chem. Lett. 18, 5838–5841 (2008).
Tew, D. G., Boyd, H. F., Ashman, S., Theobald, C. & Leach, C. A. Mechanism of inhibition of LDL phospholipase A2 by monocyclic-β-lactams. Burst kinetics and the effect of stereochemistry. Biochemistry 37, 10087–10093 (1998).
Stedman, E. & Barger, G. J. Physostigmine (eserine). Part III. J. Chem. Soc. 127, 247–258 (1925).
Weibel, E. K., Hadvary, P., Hochuli, E., Kupfer, E. & Lengsfeld, H. Lipstatin, an inhibitor of pancreatic lipase, produced by Streptomyces toxytricini. I. Producing organism, fermentation, isolation and biological activity. J. Antibiot. 40, 1081–1085 (1987).
Li, J., Wilk, E. & Wilk, S. Aminoacylpyrrolidine-2-nitriles: potent and stable inhibitors of dipeptidyl-peptidase IV (CD 26). Arch. Biochem. Biophys. 323, 148–154 (1995).
Flentke, G. R. et al. Inhibition of dipeptidyl aminopeptidase IV (DP-IV) by Xaa-boroPro dipeptides and use of these inhibitors to examine the role of DP-IV in T-cell function. Proc. Natl Acad. Sci. USA 88, 1556–1559 (1991).
Perona, J. J. & Craik, C. S. Structural basis of substrate specificity in the serine proteases. Protein Sci. 4, 337–360 (1995).
Yousef, G. M., Kopolovic, A. D., Elliott, M. B. & Diamandis, E. P. Genomic overview of serine proteases. Biochem. Biophys. Res. Commun. 305, 28–36 (2003).
Holmes, R. S. et al. Recommended nomenclature for five mammalian carboxylesterase gene families: human, mouse, and rat genes and proteins. Mamm. Genome 21, 427–441 (2010).
Kienesberger, P. C., Oberer, M., Lass, A. & Zechner, R. Mammalian patatin domain containing proteins: a family with diverse lipolytic activities involved in multiple biological functions. J. Lipid Res. 50, S63–S68 (2009).
Shin, S. et al. Structure of malonamidase E2 reveals a novel Ser-cisSer-Lys catalytic triad in a new serine hydrolase fold that is prevalent in nature. EMBO J. 21, 2509–2516 (2002).
Bracey, M. H., Hanson, M. A., Masuda, K. R., Stevens, R. C. & Cravatt, B. F. Structural adaptations in a membrane enzyme that terminates endocannabinoid signaling. Science 298, 1793–1796 (2002).
Shi, Y. & Burn, P. Lipid metabolic enzymes: emerging drug targets for the treatment of obesity. Nature Rev. Drug Discov. 3, 695–710 (2004).
Singh, J., Petter, R. C., Baillie, T. A. & Whitty, A. The resurgence of covalent drugs. Nature Rev. Drug Discov. 10, 307–317 (2011). This is a comprehensive review of the advantages and challenges of covalent drugs.
Bar-On, P. et al. Kinetic and structural studies on the interaction of cholinesterases with the anti-Alzheimer drug rivastigmine. Biochemistry 41, 3555–3564 (2002).
Metzler, W. J. et al. Involvement of DPP-IV catalytic residues in enzyme–saxagliptin complex formation. Protein Sci. 17, 240–250 (2008).
Villhauer, E. B. et al. 1-[[(3-hydroxy-1-adamantyl)amino]acetyl]-2-cyano-(S)-pyrrolidine: a potent, selective, and orally bioavailable dipeptidyl peptidase IV inhibitor with antihyperglycemic properties. J. Med. Chem. 46, 2774–2789 (2003).
Hadvary, P., Sidler, W., Meister, W., Vetter, W. & Wolfer, H. The lipase inhibitor tetrahydrolipstatin binds covalently to the putative active site serine of pancreatic lipase. J. Biol. Chem. 266, 2021–2027 (1991).
Kawabata, K. et al. ONO-5046, a novel inhibitor of human neutrophil elastase. Biochem. Biophys. Res. Commun. 177, 814–820 (1991).
Nakayama, Y. et al. Clarification of mechanism of human sputum elastase inhibition by a new inhibitor, ONO-5046, using electrospray ionization mass spectrometry. Bioorg. Med. Chem. Lett. 12, 2349–2353 (2002).
Silver, L. L. Multi-targeting by monotherapeutic antibacterials. Nature Rev. Drug Discov. 6, 41–55 (2007).
Flores, M. V., Strawbridge, J., Ciaramella, G. & Corbau, R. HCV-NS3 inhibitors: determination of their kinetic parameters and mechanism. Biochim. Biophys. Acta 1794, 1441–1448 (2009).
Papp-Wallace, K. M., Endimiani, A., Taracila, M. A. & Bonomo, R. A. Carbapenems: past, present, and future. Antimicrob. Agents Chemother. 55, 4943–4960 (2011).
Llarrull, L. I., Testero, S. A., Fisher, J. F. & Mobashery, S. The future of the β-lactams. Curr. Opin. Microbiol. 13, 551–557 (2010).
Schlutter, J. Therapeutics: new drugs hit the target. Nature 474, S5–S7 (2011).
Mackman, N. Triggers, targets and treatments for thrombosis. Nature 451, 914–918 (2008).
Macfarlane, R. G. An enzyme cascade in the blood clotting mechanism, and its function as a biochemical amplifier. Nature 202, 498–499 (1964).
Gustafsson, D. et al. A new oral anticoagulant: the 50-year challenge. Nature Rev. Drug Discov. 3, 649–659 (2004).
Markwardt, F. The development of hirudin as an antithrombotic drug. Thromb. Res. 74, 1–23 (1994).
White, H. D. & Chew, D. P. Bivalirudin: an anticoagulant for acute coronary syndromes and coronary interventions. Expert Opin. Pharmacother. 3, 777–788 (2002).
Okamoto, S. A synthetic thrombin inhibitor taking extremely active stereostructure. Thromb. Haemost. 42, A205 (1979).
Walenga, J. M. An overview of the direct thrombin inhibitor argatroban. Pathophysiol. Haemost. Thromb. 32 (Suppl. 3), 9–14 (2002).
Boudes, P. F. The challenges of new drugs benefits and risks analysis: lessons from the ximelagatran FDA Cardiovascular Advisory Committee. Contemp. Clin. Trials 27, 432–440 (2006).
Brandstetter, H. et al. Refined 2.3 Å X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics. J. Mol. Biol. 226, 1085–1099 (1992).
Hauel, N. H. et al. Structure-based design of novel potent nonpeptide thrombin inhibitors. J. Med. Chem. 45, 1757–1766 (2002).
Eisert, W. G. et al. Dabigatran: an oral novel potent reversible nonpeptide inhibitor of thrombin. Arterioscler. Thromb. Vasc. Biol. 30, 1885–1889 (2010).
Schulman, S. et al. Dabigatran versus warfarin in the treatment of acute venous thromboembolism. N. Engl. J. Med. 361, 2342–2352 (2009).
Fujikawa, K., Legaz, M. E., Kato, H. & Davie, E. W. The mechanism of activation of bovine factor IX (Christmas factor) by bovine factor XIa (activated plasma thromboplastin antecedent). Biochemistry 13, 4508–4516 (1974).
Nutt, E. et al. The amino acid sequence of antistasin. A potent inhibitor of factor Xa reveals a repeated internal structure. J. Biol. Chem. 263, 10162–10167 (1988).
Tuszynski, G. P., Gasic, T. B. & Gasic, G. J. Isolation and characterization of antistasin. An inhibitor of metastasis and coagulation. J. Biol. Chem. 262, 9718–9723 (1987).
Waxman, L., Smith, D. E., Arcuri, K. E. & Vlasuk, G. P. Tick anticoagulant peptide (TAP) is a novel inhibitor of blood coagulation factor Xa. Science 248, 593–596 (1990).
Bauer, K. A. et al. Fondaparinux, a synthetic pentasaccharide: the first in a new class of antithrombotic agents — the selective factor Xa inhibitors. Cardiovasc. Drug Rev. 20, 37–52 (2002).
Perzborn, E., Roehrig, S., Straub, A., Kubitza, D. & Misselwitz, F. The discovery and development of rivaroxaban, an oral, direct factor Xa inhibitor. Nature Rev. Drug Discov. 10, 61–75 (2011).
Becker, R. C., Alexander, J., Dyke, C. K. & Harrington, R. A. Development of DX-9065a, a novel direct factor Xa antagonist, in cardiovascular disease. Thromb. Haemost. 92, 1182–1193 (2004).
Sato, K. et al. YM-60828, a novel factor Xa inhibitor: separation of its antithrombotic effects from its prolongation of bleeding time. Eur. J. Pharmacol. 339, 141–146 (1997).
Lam, P. Y. et al. Structure-based design of novel guanidine/benzamidine mimics: potent and orally bioavailable factor Xa inhibitors as novel anticoagulants. J. Med. Chem. 46, 4405–4418 (2003).
Pinto, D. J. et al. Discovery of 1-[3-(aminomethyl)phenyl]-N-3-fluoro-2′-(methylsulfonyl)-[1,1′-biphenyl]-4 -yl]-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide (DPC423), a highly potent, selective, and orally bioavailable inhibitor of blood coagulation factor Xa. J. Med. Chem. 44, 566–578 (2001).
Roehrig, S. et al. Discovery of the novel antithrombotic agent 5-chloro-N-({(5S)-2-oxo-3- [4-(3-oxomorpholin-4-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)thiophene- 2-carboxamide (BAY 59–7939): an oral, direct factor Xa inhibitor. J. Med. Chem. 48, 5900–5908 (2005).
Eriksson, B. I., Quinlan, D. J. & Eikelboom, J. W. Novel oral factor Xa and thrombin inhibitors in the management of thromboembolism. Annu. Rev. Med. 62, 41–57 (2011).
Giacobini, E. Cholinesterases: new roles in brain function and in Alzheimer's disease. Neurochem. Res. 28, 515–522 (2003).
Bowen, D. M., Smith, C. B., White, P. & Davison, A. N. Neurotransmitter-related enzymes and indices of hypoxia in senile dementia and other abiotrophies. Brain 99, 459–496 (1976).
Davies, P. & Maloney, A. J. Selective loss of central cholinergic neurons in Alzheimer's disease. Lancet 2, 1403 (1976).
Perry, E. K., Gibson, P. H., Blessed, G., Perry, R. H. & Tomlinson, B. E. Neurotransmitter enzyme abnormalities in senile dementia. Choline acetyltransferase and glutamic acid decarboxylase activities in necropsy brain tissue. J. Neurol. Sci. 34, 247–265 (1977).
Bartus, R. T., Dean, R. L., Beer, B. & Lippa, A. S. The cholinergic hypothesis of geriatric memory dysfunction. Science 217, 408–414 (1982).
Hansen, R. A., Gartlehner, G., Kaufer, D. J., Lohr, K. N. & Carey, T. Drug class review on Alzheimer's drugs: final report. Drug Class Reviews (2006).
Ellis, J. M. Cholinesterase inhibitors in the treatment of dementia. J. Am. Osteopath. Assoc. 105, 145–158 (2005).
Casida, J. E. & Quistad, G. B. Serine hydrolase targets of organophosphorus toxicants. Chem. Biol. Interact. 157–158, 277–283 (2005).
Kawakami, Y. et al. The rationale for E2020 as a potent acetylcholinesterase inhibitor. Bioorg. Med. Chem. 4, 1429–1446 (1996).
Nochi, S., Asakawa, N. & Sato, T. Kinetic-study on the inhibition of acetylcholinesterase by 1-benzyl-4-[(5,6-dimethoxy-L-indanon)-2-Yl]methylpiperidine hydrochloride (E2020). Biol. Pharm. Bull. 18, 1145–1147 (1995).
Sugimoto, H., Iimura, Y., Yamanishi, Y. & Yamatsu, K. Synthesis and structure-activity relationships of acetylcholinesterase inhibitors: 1-benzyl-4-[(5, 6-dimethoxy-1-oxoindan-2-yl)methyl]piperidine hydrochloride and related compounds. J. Med. Chem. 38, 4821–4829 (1995).
Harvey, A. L. The pharmacology of galanthamine and its analogues. Pharmacol. Ther. 68, 113–128 (1995).
Thomsen, T. & Kewitz, H. Selective inhibition of human acetylcholinesterase by galanthamine in vitro and in vivo. Life Sci. 46, 1553–1558 (1990).
Thomsen, T., Bickel, U., Fischer, J. P. & Kewitz, H. Stereoselectivity of cholinesterase inhibition by galanthamine and tolerance in humans. Eur. J. Clin. Pharmacol. 39, 603–605 (1990).
Hemsworth, B. A. & West, G. B. The anticholinesterase activity of physostigmine. J. Pharm. Pharmacol. 20, 406–407 (1968).
Kennedy, J. S. et al. Preferential cerebrospinal fluid acetylcholinesterase inhibition by rivastigmine in humans. J. Clin. Psychopharmacol. 19, 513–521 (1999).
Kathuria, S. et al. Modulation of anxiety through blockade of anandamide hydrolysis. Nature Med. 9, 76–81 (2003).
Long, J. Z. et al. Selective blockade of 2-arachidonoylglycerol hydrolysis produces cannabinoid behavioral effects. Nature Chem. Biol. 5, 37–44 (2009).
Bongers, J., Lambros, T., Ahmad, M. & Heimer, E. P. Kinetics of dipeptidyl peptidase IV proteolysis of growth hormone-releasing factor and analogs. Biochim. Biophys. Acta 1122, 147–153 (1992).
Rosenblum, J. S. & Kozarich, J. W. Prolyl peptidases: a serine protease subfamily with high potential for drug discovery. Curr. Opin. Chem. Biol. 7, 496–504 (2003).
Murphy, K. G., Dhillo, W. S. & Bloom, S. R. Gut peptides in the regulation of food intake and energy homeostasis. Endocr. Rev. 27, 719–727 (2006).
Thorens, B. Glucagon-like peptide-1 and control of insulin secretion. Diabetes Metab. 21, 311–318 (1995).
Meier, J. J., Nauck, M. A., Schmidt, W. E. & Gallwitz, B. Gastric inhibitory polypeptide: the neglected incretin revisited. Regul. Pept. 107, 1–13 (2002).
Drucker, D. J. Biological actions and therapeutic potential of the glucagon-like peptides. Gastroenterology 122, 531–544 (2002).
Holst, J. J. & Deacon, C. F. Inhibition of the activity of dipeptidyl-peptidase IV as a treatment for type 2 diabetes. Diabetes 47, 1663–1670 (1998).
Feng, J. et al. Discovery of alogliptin: a potent, selective, bioavailable, and efficacious inhibitor of dipeptidyl peptidase IV. J. Med. Chem. 50, 2297–2300 (2007).
Lambeir, A. M. et al. Dipeptide-derived diphenyl phosphonate esters: mechanism-based inhibitors of dipeptidyl peptidase IV. Biochim. Biophys. Acta 1290, 76–82 (1996).
Hughes, T. E., Mone, M. D., Russell, M. E., Weldon, S. C. & Villhauer, E. B. NVP-DPP728 (1-[[[2-[(5-cyanopyridin-2-yl)amino]ethyl]amino]acetyl]-2-cyano-(S)-pyrrolidine), a slow-binding inhibitor of dipeptidyl peptidase IV. Biochemistry 38, 11597–11603 (1999).
Oefner, C. et al. High-resolution structure of human apo dipeptidyl peptidase IV/CD26 and its complex with 1-[([2-[(5-iodopyridin-2-yl)amino]-ethyl]amino)-acetyl]-2-cyano-(S)-pyrrol idine. Acta Crystallogr. D Biol. Crystallogr. 59, 1206–1212 (2003).
Villhauer, E. B. et al. 1-[2-[(5-cyanopyridin-2-yl)amino]ethylamino]acetyl-2-(S)-pyrrolidinecarbon itrile: a potent, selective, and orally bioavailable dipeptidyl peptidase IV inhibitor with antihyperglycemic properties. J. Med. Chem. 45, 2362–2365 (2002).
Magnin, D. R. et al. Synthesis of novel potent dipeptidyl peptidase IV inhibitors with enhanced chemical stability: interplay between the N-terminal amino acid alkyl side chain and the cyclopropyl group of α-aminoacyl-l-cis-4,5-methanoprolinenitrile-based inhibitors. J. Med. Chem. 47, 2587–2598 (2004).
Augeri, D. J. et al. Discovery and preclinical profile of saxagliptin (BMS-477118): a highly potent, long-acting, orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes. J. Med. Chem. 48, 5025–5037 (2005).
Kim, D. et al. (2R)-4-oxo-4-[3-(trifluoromethyl)-5,6-dihydro[1,2,4]triazolo[4,3-a]pyrazin-7(8H)-yl]-1-(2,4,5-trifluorophenyl)butan-2-amine: a potent, orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes. J. Med. Chem. 48, 141–151 (2005).
Eckhardt, M. et al. 8-(3-(R)-aminopiperidin-1-yl)-7-but-2-ynyl-3-methyl-1-(4-methyl-quinazolin -2-ylmethyl)-3,7-dihydropurine-2,6-dione (BI 1356), a highly potent, selective, long-acting, and orally bioavailable DPP-4 inhibitor for the treatment of type 2 diabetes. J. Med. Chem. 50, 6450–6453 (2007).
Xu, J. et al. Discovery of potent and selective β-homophenylalanine based dipeptidyl peptidase IV inhibitors. Bioorg. Med. Chem. Lett. 14, 4759–4762 (2004).
Cravatt, B. F. et al. Molecular characterization of an enzyme that degrades neuromodulatory fatty-acid amides. Nature 384, 83–87 (1996).
Naidu, P. S. et al. Evaluation of fatty acid amide hydrolase inhibition in murine models of emotionality. Psychopharmacology 192, 61–70 (2007).
Cravatt, B. F. et al. Supersensitivity to anandamide and enhanced endogenous cannabinoid signaling in mice lacking fatty acid amide hydrolase. Proc. Natl Acad. Sci. USA 98, 9371–9376 (2001).
Lichtman, A. H. et al. Reversible inhibitors of fatty acid amide hydrolase that promote analgesia: evidence for an unprecedented combination of potency and selectivity. J. Pharmacol. Exp. Ther. 311, 441–448 (2004).
Russo, R. et al. The fatty acid amide hydrolase inhibitor URB597 (cyclohexylcarbamic acid 3′-carbamoylbiphenyl-3-yl ester) reduces neuropathic pain after oral administration in mice. J. Pharmacol. Exp. Ther. 322, 236–242 (2007).
Justinova, Z. et al. Fatty acid amide hydrolase inhibition heightens anandamide signaling without producing reinforcing effects in primates. Biol. Psychiatry 64, 930–937 (2008).
Ahn, K. et al. Novel mechanistic class of fatty acid amide hydrolase inhibitors with remarkable selectivity. Biochemistry 46, 13019–13030 (2007).
Ahn, K. et al. Discovery and characterization of a highly selective FAAH inhibitor that reduces inflammatory pain. Chem. Biol. 16, 411–420 (2009).
Khanna, I. K. & Alexander, C. W. Fatty acid amide hydrolase inhibitors — progress and potential. CNS Neurol. Disord. Drug Targets 10, 545–558 (2011). This is a detailed review of the current panel of FAAH inhibitors, which includes an array of hydrolase-directed chemotypes.
Zalewski, A., Macphee, C. & Nelson, J. J. Lipoprotein-associated phospholipase A2: a potential therapeutic target for atherosclerosis. Curr. Drug Targets Cardiovasc. Haematol. Disord. 5, 527–532 (2005).
Packard, C. J. et al. Lipoprotein-associated phospholipase A2 as an independent predictor of coronary heart disease. West of Scotland Coronary Prevention Study Group. N. Engl. J. Med. 343, 1148–1155 (2000).
MacPhee, C. H. et al. Lipoprotein-associated phospholipase A2, platelet-activating factor acetylhydrolase, generates two bioactive products during the oxidation of low-density lipoprotein: use of a novel inhibitor. Biochem. J. 338, 479–487 (1999).
Davis, B. et al. Electrospray ionization mass spectrometry identifies substrates and products of lipoprotein-associated phospholipase A2 in oxidized human low density lipoprotein. J. Biol. Chem. 283, 6428–6437 (2008).
Blackie, J. A. et al. The identification of clinical candidate SB-480848: a potent inhibitor of lipoprotein-associated phospholipase A2. Bioorg. Med. Chem. Lett. 13, 1067–1070 (2003).
Boyd, H. F. et al. 2-(alkylthio)pyrimidin-4-ones as novel, reversible inhibitors of lipoprotein-associated phospholipase A2. Bioorg. Med. Chem. Lett. 10, 395–398 (2000).
Wilensky, R. L. et al. Inhibition of lipoprotein-associated phospholipase A2 reduces complex coronary atherosclerotic plaque development. Nature Med. 14, 1059–1066 (2008).
Mallela, J., Yang, J. & Shariat-Madar, Z. Prolylcarboxypeptidase: a cardioprotective enzyme. Int. J. Biochem. Cell Biol. 41, 477–481 (2009).
Wallingford, N. et al. Prolylcarboxypeptidase regulates food intake by inactivating α-MSH in rodents. J. Clin. Invest. 119, 2291–2303 (2009).
Zhou, C. et al. Design and synthesis of prolylcarboxypeptidase (PrCP) inhibitors to validate PrCP as a potential target for obesity. J. Med. Chem. 53, 7251–7263 (2010).
Shen, H. C. et al. Discovery of benzimidazole pyrrolidinyl amides as prolylcarboxypeptidase inhibitors. Bioorg. Med. Chem. Lett. 21, 1299–1305 (2011).
Lehner, R. & Verger, R. Purification and characterization of a porcine liver microsomal triacylglycerol hydrolase. Biochemistry 36, 1861–1868 (1997).
Lehner, R. & Vance, D. E. Cloning and expression of a cDNA encoding a hepatic microsomal lipase that mobilizes stored triacylglycerol. Biochem. J. 343, 1–10 (1999).
Dolinsky, V. W., Gilham, D., Alam, M., Vance, D. E. & Lehner, R. Triacylglycerol hydrolase: role in intracellular lipid metabolism. Cell. Mol. Life Sci. 61, 1633–1651 (2004).
Wei, E. et al. Loss of TGH/Ces3 in mice decreases blood lipids, improves glucose tolerance, and increases energy expenditure. Cell Metab. 11, 183–193 (2010).
Gilham, D. et al. Inhibitors of hepatic microsomal triacylglycerol hydrolase decrease very low density lipoprotein secretion. FASEB J. 17, 1685–1687 (2003).
Zechner, R., Kienesberger, P. C., Haemmerle, G., Zimmermann, R. & Lass, A. Adipose triglyceride lipase and the lipolytic catabolism of cellular fat stores. J. Lipid Res. 50, 3–21 (2009).
Das, S. K. et al. Adipose triglyceride lipase contributes to cancer-associated cachexia. Science 333, 233–238 (2011).
McCoy, M. G. et al. Characterization of the lipolytic activity of endothelial lipase. J. Lipid Res. 43, 921–929 (2002).
Ma, K. et al. Endothelial lipase is a major genetic determinant for high-density lipoprotein concentration, structure, and metabolism. Proc. Natl Acad. Sci. USA 100, 2748–2753 (2003).
Ishida, T. et al. Endothelial lipase is a major determinant of HDL level. J. Clin. Invest. 111, 347–355 (2003).
Goodman, K. B. et al. Discovery of potent, selective sulfonylfuran urea endothelial lipase inhibitors. Bioorg. Med. Chem. Lett. 19, 27–30 (2009).
Kato, T., Okada, M. & Nagatsu, T. Distribution of post-proline cleaving enzyme in human brain and the peripheral tissues. Mol. Cell. Biochem. 32, 117–121 (1980).
Wilk, S. Prolyl endopeptidase. Life Sci. 33, 2149–2157 (1983).
Lopez, A., Tarrago, T. & Giralt, E. Low molecular weight inhibitors of prolyl oligopeptidase: a review of compounds patented from 2003 to 2010. Expert Opin. Ther. Pat. 21, 1023–1044 (2011).
Bakker, A. V., Jung, S., Spencer, R. W., Vinick, F. J. & Faraci, W. S. Slow tight-binding inhibition of prolyl endopeptidase by benzyloxycarbonyl-prolyl-prolinal. Biochem. J. 271, 559–562 (1990).
Toide, K., Iwamoto, Y., Fujiwara, T. & Abe, H. JTP-4819: a novel prolyl endopeptidase inhibitor with potential as a cognitive enhancer. J. Pharmacol. Exp. Ther. 274, 1370–1378 (1995).
Barelli, H. et al. S 17092–1, a highly potent, specific and cell permeant inhibitor of human proline endopeptidase. Biochem. Biophys. Res. Commun. 257, 657–661 (1999).
Bellemere, G., Morain, P., Vaudry, H. & Jegou, S. Effect of S 17092, a novel prolyl endopeptidase inhibitor, on substance P and α-melanocyte-stimulating hormone breakdown in the rat brain. J. Neurochem. 84, 919–929 (2003).
Nolte, W. M., Tagore, D. M., Lane, W. S. & Saghatelian, A. Peptidomics of prolyl endopeptidase in the central nervous system. Biochemistry 48, 11971–11981 (2009).
Toide, K. et al. Effect of a novel prolyl endopeptidase inhibitor, JTP-4819, on neuropeptide metabolism in the rat brain. Naunyn Schmiedebergs Arch. Pharmacol. 353, 355–362 (1996).
Shinoda, M., Okamiya, K. & Toide, K. Effect of a novel prolyl endopeptidase inhibitor, JTP-4819, on thyrotropin-releasing hormone-like immunoreactivity in the cerebral cortex and hippocampus of aged rats. Jpn J. Pharmacol. 69, 273–276 (1995).
Schneider, J. S., Giardiniere, M. & Morain, P. Effects of the prolyl endopeptidase inhibitor S 17092 on cognitive deficits in chronic low dose MPTP-treated monkeys. Neuropsychopharmacology 26, 176–182 (2002).
Morain, P. et al. S 17092: a prolyl endopeptidase inhibitor as a potential therapeutic drug for memory impairment. Preclinical and clinical studies. CNS Drug Rev. 8, 31–52 (2002).
Morain, P., Boeijinga, P. H., Demazieres, A., De Nanteuil, G. & Luthringer, R. Psychotropic profile of S 17092, a prolyl endopeptidase inhibitor, using quantitative EEG in young healthy volunteers. Neuropsychobiology 55, 176–183 (2007).
Lambeir, A. M. Translational research on prolyl oligopeptidase inhibitors: the long road ahead. Expert Opin. Ther. Pat. 21, 977–981 (2011).
Puustinen, P. et al. PME-1 protects extracellular signal-regulated kinase pathway activity from protein phosphatase 2A-mediated inactivation in human malignant glioma. Cancer Res. 69, 2870–2877 (2009).
Andreasen, P. A., Egelund, R. & Petersen, H. H. The plasminogen activation system in tumor growth, invasion, and metastasis. Cell. Mol. Life Sci. 57, 25–40 (2000).
Nomura, D. K., Dix, M. M. & Cravatt, B. F. Activity-based protein profiling for biochemical pathway discovery in cancer. Nature Rev. Cancer 10, 630–638 (2010). This review summarizes the use of ABPP to provide information on the metabolic and signalling enzymes in cancer and to enable the development of selective chemical probes to characterize their functions.
Scanlan, M. J. et al. Molecular cloning of fibroblast activation protein α, a member of the serine protease family selectively expressed in stromal fibroblasts of epithelial cancers. Proc. Natl Acad. Sci. USA 91, 5657–5661 (1994).
Rettig, W. J. et al. Regulation and heteromeric structure of the fibroblast activation protein in normal and transformed cells of mesenchymal and neuroectodermal origin. Cancer Res. 53, 3327–3335 (1993).
Garin-Chesa, P., Old, L. J. & Rettig, W. J. Cell surface glycoprotein of reactive stromal fibroblasts as a potential antibody target in human epithelial cancers. Proc. Natl Acad. Sci. USA 87, 7235–7239 (1990).
Cheng, J. D. et al. Promotion of tumor growth by murine fibroblast activation protein, a serine protease, in an animal model. Cancer Res. 62, 4767–4772 (2002).
Cheng, J. D. et al. Abrogation of fibroblast activation protein enzymatic activity attenuates tumor growth. Mol. Cancer Ther. 4, 351–360 (2005).
Adams, S. et al. PT-100, a small molecule dipeptidyl peptidase inhibitor, has potent antitumor effects and augments antibody-mediated cytotoxicity via a novel immune mechanism. Cancer Res. 64, 5471–5480 (2004).
Kraman, M. et al. Suppression of antitumor immunity by stromal cells expressing fibroblast activation protein-α. Science 330, 827–830 (2010).
Edosada, C. Y. et al. Selective inhibition of fibroblast activation protein protease based on dipeptide substrate specificity. J. Biol. Chem. 281, 7437–7444 (2006).
Wolf, B. B., Quan, C., Tran, T., Wiesmann, C. & Sutherlin, D. On the edge of validation — cancer protease fibroblast activation protein. Mini Rev. Med. Chem. 8, 719–727 (2008).
Patterson, S. D. & Aebersold, R. H. Proteomics: the first decade and beyond. Nature Genet. 33, S311–S323 (2003).
Yates, J. R. Mass spectral analysis in proteomics. Annu. Rev. Biophys. Biomol. Struct. 33, 297–316 (2004).
Domon, B. & Aebersold, R. Mass spectrometry and protein analysis. Science 312, 212–217 (2006).
Cravatt, B. F., Simon, G. M. & Yates, J. R. The biological impact of mass-spectrometry-based proteomics. Nature 450, 991–1000 (2007).
Golub, T. R. et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531–537 (1999).
Brown, P. O. & Botstein, D. Exploring the new world of the genome with DNA microarrays. Nature Genet. 21, 33–37 (1999).
Evans, M. J. & Cravatt, B. F. Mechanism-based profiling of enzyme families. Chem. Rev. 106, 3279–3301 (2006).
Cravatt, B. F., Wright, A. T. & Kozarich, J. W. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu. Rev. Biochem. 77, 383–414 (2008). This is a review of the principles and applications of ABPP.
Liu, Y., Patricelli, M. P. & Cravatt, B. F. Activity-based protein profiling: the serine hydrolases. Proc. Natl Acad. Sci. USA 96, 14694–14699 (1999).
Weerapana, E., Simon, G. M. & Cravatt, B. F. Disparate proteome reactivity profiles of carbon electrophiles. Nature Chem. Biol. 4, 405–407 (2008).
Kato, D. et al. Activity-based probes that target diverse cysteine protease families. Nature Chem. Biol. 1, 33–38 (2005).
Weerapana, E. et al. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature 468, 790–795 (2010).
Patricelli, M. P. et al. Functional interrogation of the kinome using nucleotide acyl phosphates. Biochemistry 46, 350–358 (2007).
Salisbury, C. M. & Cravatt, B. F. Activity-based probes for proteomic profiling of histone deacetylase complexes. Proc. Natl Acad. Sci. USA 104, 1171–1176 (2007).
Salisbury, C. M. & Cravatt, B. F. Optimization of activity-based probes for proteomic profiling of histone deacetylase complexes. J. Am. Chem. Soc. 130, 2184–2194 (2008).
Madsen, M. A., Deryugina, E. I., Niessen, S., Cravatt, B. F. & Quigley, J. P. Activity-based protein profiling implicates urokinase activation as a key step in human fibrosarcoma intravasation. J. Biol. Chem. 281, 15997–16005 (2006).
Pan, Z. et al. Development of activity-based probes for trypsin-family serine proteases. Bioorg. Med. Chem. Lett. 16, 2882–2885 (2006).
Jessani, N. et al. Carcinoma and stromal enzyme activity profiles associated with breast tumor growth in vivo. Proc. Natl Acad. Sci. USA 101, 13756–13761 (2004).
Jessani, N. et al. A streamlined platform for high-content functional proteomics of primary human specimens. Nature Methods 2, 691–697 (2005).
Blankman, J. L., Simon, G. M. & Cravatt, B. F. A comprehensive profile of brain enzymes that hydrolyze the endocannabinoid 2-arachidonoylglycerol. Chem. Biol. 14, 1347–1356 (2007).
Mahrus, S. & Craik, C. S. Selective chemical functional probes of granzymes A and B reveal granzyme B is a major effector of natural killer cell-mediated lysis of target cells. Chem. Biol. 12, 567–577 (2005).
Barglow, K. T. & Cravatt, B. F. Discovering disease-associated enzymes by proteome reactivity profiling. Chem. Biol. 11, 1523–1531 (2004).
Morak, M. et al. Differential activity-based gel electrophoresis for comparative analysis of lipolytic and esterolytic activities. J. Lipid Res. 50, 1281–1292 (2009).
Kaschani, F. et al. Diversity of serine hydrolase activities of unchallenged and botrytis-infected Arabidopsis thaliana. Mol. Cell. Proteomics 8, 1082–1093 (2009).
Jessani, N., Liu, Y., Humphrey, M. & Cravatt, B. F. Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness. Proc. Natl Acad. Sci. USA 99, 10335–10340 (2002).
Chiang, K. P., Niessen, S., Saghatelian, A. & Cravatt, B. F. An enzyme that regulates ether lipid signaling pathways in cancer annotated by multidimensional profiling. Chem. Biol. 13, 1041–1050 (2006).
Chang, J. W., Nomura, D. K. & Cravatt, B. F. A potent and selective inhibitor of KIAA1363/AADACL1 that impairs prostate cancer pathogenesis. Chem. Biol. 18, 476–484 (2011).
Nomura, D. K. et al. Monoacylglycerol lipase exerts dual control over endocannabinoid and fatty acid pathways to support prostate cancer. Chem. Biol. 18, 846–856 (2011).
Long, J. Z., Nomura, D. K. & Cravatt, B. F. Characterization of monoacylglycerol lipase inhibition reveals differences in central and peripheral endocannabinoid metabolism. Chem. Biol. 16, 744–753 (2009).
Kinsey, S. G. et al. Blockade of endocannabinoid-degrading enzymes attenuates neuropathic pain. J. Pharmacol. Exp. Ther. 330, 902–910 (2009).
Nomura, D. K. et al. Endocannabinoid hydrolysis generates brain prostaglandins that promote neuroinflammation. Science 334, 809–813 (2011).
Woitach, J. T., Zhang, M., Niu, C. H. & Thorgeirsson, S. S. A retinoblastoma-binding protein that affects cell-cycle control and confers transforming ability. Nature Genet. 19, 371–374 (1998).
Shields, D. J. et al. RBBP9: a tumor-associated serine hydrolase activity required for pancreatic neoplasia. Proc. Natl Acad. Sci. USA 107, 2189–2194 (2010).
Bachovchin, D. A., Brown, S. J., Rosen, H. & Cravatt, B. F. Identification of selective inhibitors of uncharacterized enzymes by high-throughput screening with fluorescent activity-based probes. Nature Biotech. 27, 387–394 (2009). This paper describes the introduction of competitive ABPP for high-throughput screening.
Bachovchin, D. A. et al. Oxime esters as selective, covalent inhibitors of the serine hydrolase retinoblastoma-binding protein 9 (RBBP9). Bioorg. Med. Chem. Lett. 20, 2254–2258 (2010).
Kidd, D., Liu, Y. & Cravatt, B. F. Profiling serine hydrolase activities in complex proteomes. Biochemistry 40, 4005–4015 (2001).
Greenbaum, D. et al. Chemical approaches for functionally probing the proteome. Mol. Cell. Proteomics 1, 60–68 (2002).
Johnson, D. S., Weerapana, E. & Cravatt, B. F. Strategies for discovering and derisking covalent, irreversible enzyme inhibitors. Future Med. Chem. 2, 949–964 (2010).
Potashman, M. H. & Duggan, M. E. Covalent modifiers: an orthogonal approach to drug design. J. Med. Chem. 52, 1231–1246 (2009).
Knuckley, B. et al. A fluopol-ABPP HTS assay to identify PAD inhibitors. Chem. Commun. (Camb.) 46, 7175–7177 (2010).
Bachovchin, D. A. et al. Organic synthesis toward small-molecule probes and drugs special feature: academic cross-fertilization by public screening yields a remarkable class of protein phosphatase methylesterase-1 inhibitors. Proc. Natl Acad. Sci. USA 108, 6811–6816 (2011).
Lee, J., Chen, Y., Tolstykh, T. & Stock, J. A specific protein carboxyl methylesterase that demethylates phosphoprotein phosphatase 2A in bovine brain. Proc. Natl Acad. Sci. USA 93, 6043–6047 (1996).
Sontag, J. M., Nunbhakdi-Craig, V., Mitterhuber, M., Ogris, E. & Sontag, E. Regulation of protein phosphatase 2A methylation by LCMT1 and PME-1 plays a critical role in differentiation of neuroblastoma cells. J. Neurochem. 115, 1455–1465 (2010).
Bachovchin, D. A. et al. Discovery and optimization of sulfonyl acrylonitriles as selective, covalent inhibitors of protein phosphatase methylesterase-1. J. Med. Chem. 54, 5229–5236 (2011).
Berlin, J. M. & Fu, G. C. Enantioselective nucleophilic catalysis: the synthesis of aza-β-lactams through [2 + 2] cycloadditions of ketenes with azo compounds. Angew. Chem. Int. Ed. Engl. 47, 7048–7050 (2008).
Wood, W. J., Patterson, A. W., Tsuruoka, H., Jain, R. K. & Ellman, J. A. Substrate activity screening: a fragment-based method for the rapid identification of nonpeptidic protease inhibitors. J. Am. Chem. Soc. 127, 15521–15527 (2005).
Patterson, A. W. et al. Identification of selective, nonpeptidic nitrile inhibitors of cathepsin S using the substrate activity screening method. J. Med. Chem. 49, 6298–6307 (2006).
Salisbury, C. M. & Ellman, J. A. Rapid identification of potent nonpeptidic serine protease inhibitors. Chembiochem. 7, 1034–1037 (2006).
Edwards, P. D., Zottola, M. A., Davis, M., Williams, J. & Tuthill, P. A. Peptidyl α-ketoheterocyclic inhibitors of human neutrophil elastase. 3. In vitro and in vivo potency of a series of peptidyl α-ketobenzoxazoles. J. Med. Chem. 38, 3972–3982 (1995).
Erlanson, D. A. et al. Site-directed ligand discovery. Proc. Natl Acad. Sci. USA 97, 9367–9372 (2000).
Erlanson, D. A., Wells, J. A. & Braisted, A. C. Tethering: fragment-based drug discovery. Annu. Rev. Biophys. Biomol. Struct. 33, 199–223 (2004).
Hagel, M. et al. Selective irreversible inhibition of a protease by targeting a noncatalytic cysteine. Nature Chem. Biol. 7, 22–24 (2011).
Levy, J. H. & O'Donnell, P. S. The therapeutic potential of a kallikrein inhibitor for treating hereditary angioedema. Expert Opin. Investig. Drugs 15, 1077–1090 (2006).
Stoop, A. A. & Craik, C. S. Engineering of a macromolecular scaffold to develop specific protease inhibitors. Nature Biotech. 21, 1063–1068 (2003).
Dennis, M. S. & Lazarus, R. A. Kunitz domain inhibitors of tissue factor–factor VIIa. II. Potent and specific inhibitors by competitive phage selection. J. Biol. Chem. 269, 22137–22144 (1994).
Xuan, J. A. et al. Antibodies neutralizing hepsin protease activity do not impact cell growth but inhibit invasion of prostate and ovarian tumor cells in culture. Cancer Res. 66, 3611–3619 (2006).
Sun, J., Pons, J. & Craik, C. S. Potent and selective inhibition of membrane-type serine protease 1 by human single-chain antibodies. Biochemistry 42, 892–900 (2003).
Lazarus, R. A., Olivero, A. G., Eigenbrot, C. & Kirchhofer, D. Inhibitors of tissue factor. Factor VIIa for anticoagulant therapy. Curr. Med. Chem. 11, 2275–2290 (2004).
Edwards, A. M. et al. Too many roads not taken. Nature 470, 163–165 (2011).
Subramanian, A. R., Kaufmann, M. & Morgenstern, B. DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Algorithms Mol. Biol. 3, 6 (2008).
Acknowledgements
We thank the Cravatt laboratory for helpful discussions. This work was supported by grants from the US National Institutes of Health (DA025285, GM090294, CA132630, DA017259, DA009789 and CA087660), the National Science Foundation (predoctoral fellowship to D.A.B.), the California Breast Cancer Research Program (predoctoral fellowship to D.A.B.), and The Skaggs Institute for Chemical Biology.
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Benjamin F. Cravatt is a co-founder and advisor for a biotechnology company interested in developing inhibitors for serine hydrolase as therapeutic targets.
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Supplementary information S1 (table)
Drugs that target viral and bacterial serine hydrolases. (PDF 283 kb)
Supplementary information S2 (table)
The human serine hydrolases. (PDF 188 kb)
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Glossary
- Warheads
-
Reactive chemical groups that covalently bind to specific amino acid residues of the target enzyme.
- Zymogens
-
Inactive enzyme precursors, or pro-enzymes, that require a biochemical event (for example, a hydrolysis reaction) to convert them into active enzymes.
- Thrombi
-
Aggregations of platelets, fibrin and cells.
- Coagulation cascade
-
A stepwise process involving the sequential activation of several serine protease zymogens by limited proteolysis that results in the formation of fibrin blood clots.
- Prodrug
-
A pharmacological entity administered in a largely inactive form that is metabolized in vivo into an active drug.
- Cachexia
-
A wasting syndrome characterized by the uncontrolled loss of muscle and adipose tissue.
- Fluorescence polarization
-
A measure of the apparent size of a fluorophore; it is widely used to study molecular interactions. Briefly, a fluorophore excited with plane-polarized light will emit polarized light parallel to the plane of excitation unless it rotates in the excited state. As the speed of rotational diffusion is inversely proportional to molecular volume, the resulting extent of depolarization gives a relative estimate of the size of the fluorophore.
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Bachovchin, D., Cravatt, B. The pharmacological landscape and therapeutic potential of serine hydrolases. Nat Rev Drug Discov 11, 52–68 (2012). https://doi.org/10.1038/nrd3620
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DOI: https://doi.org/10.1038/nrd3620
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