Biochemical assay; Coumarin; Factor XIIa; Fragment-based drug discovery; Medical device-induced thrombosis; Serine proteinase inhibitors; factor XIIa inhibitor; Coumarins; Humans; Blood Coagulation; Coumarins/pharmacology; Coumarins/metabolism; Thrombosis; Pharmacology; Drug Discovery; Organic Chemistry; General Medicine
Abstract :
[en] Previously, we described weak coumarin inhibitors of factor XIIa, a promising target for artificial surface-induced thrombosis and various inflammatory diseases. In this work, we used fragment-based drug discovery approach to improve our coumarin series. First, we screened about 200 fragments for the S1 pocket. The S1 pocket of trypsin-like serine proteases, such as factor XIIa, is highly conserved and is known to drive a major part of the association energy. From the screening, we selected fragments displaying a micromolar activity and studied their selectivity on other serine proteases. Then, these fragments were merged to our coumarin templates, leading to the generation of nanomolar inhibitors. The mechanism of inhibition was further studied by mass spectrometry demonstrating the covalent binding through the formation of an acyl enzyme complex. The most potent compound was tested in plasma to evaluate its stability and efficacy on coagulation assays. It exhibited a plasmatic half-life of 1.9 h and a good selectivity for the intrinsic coagulation pathway over the extrinsic one.
Research Center/Unit :
CIRM - Centre Interdisciplinaire de Recherche sur le Médicament - ULiège NARILIS - NAmur Research Institute for LIfe Sciences - UNamur
Disciplines :
Pharmacy, pharmacology & toxicology
Author, co-author :
Davoine, Clara ; Université de Liège - ULiège > Unités de recherche interfacultaires > Centre Interdisciplinaire de Recherche sur le Médicament (CIRM)
Traina, Amandine; Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
Evrard, Jonathan; Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
Lanners, Steve; Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
Fillet, Marianne ; Université de Liège - ULiège > Département de pharmacie > Analyse des médicaments
Pochet, Lionel ; Université de Liège - ULiège > Département de pharmacie > Chimie pharmaceutique ; Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium. Electronic address: lionel.pochet@unamur.be
Language :
English
Title :
Coumarins as factor XIIa inhibitors: Potency and selectivity improvements using a fragment-based strategy.
F.R.S.-FNRS - Fonds de la Recherche Scientifique Fondation Léon Fredericq
Funding text :
C.D. received funding from the National Fund for Scientific Research (FNRS) grant 40000455 and Fondation Léon Frédéricq grant 2020-2021-30-C.F.F. L.P. received funding from the University of Namur FSR Grant L. POCHET-12/2021 . M.F. received funding from the University of Liège Fonds Spéciaux—Crédits facultaires ID 14758 . We gratefully acknowledge the contribution of Oliver Garot for his technical assistance.
Roth, G.A., et al. Global, regional, and national age-sex-specific mortality for 282 causes of death in 195 countries and territories, 1980–2017: a systematic analysis for the global burden of disease study 2017. Lancet 392:10159 (2018), 1736–1788, 10.1016/S0140-6736(18)32203-7.
Jaffer, I.H., Fredenburgh, J.C., Hirsh, J., Weitz, J.I., Medical device-induced thrombosis: what causes it and how can we prevent it?. J. Thromb. Haemostasis 13:S1 (2015), S72–S81, 10.1111/jth.12961.
Jaffer, I.H., Weitz, J.I., The blood compatibility challenge. Part 1: blood-contacting medical devices: the scope of the problem. Acta Biomater. 94 (2019), 2–10, 10.1016/j.actbio.2019.06.021.
Hong, J.K., Gao, L., Singh, J., Goh, T., Ruhoff, A.M., Neto, C., Waterhouse, A., Evaluating medical device and material thrombosis under flow: current and emerging Technologies. Biomater. Sci. 8:21 (2020), 5824–5845, 10.1039/D0BM01284J.
Tillman, B., Gailani, D., Inhibition of factors XI and XII for prevention of thrombosis induced by artificial surfaces. Semin. Thromb. Hemost. 44:1 (2018), 60–69, 10.1055/s-0037-1603937.
Kalinin, D.V., Factor XII(a) inhibitors: a review of the patent literature. Expert Opin. Ther. Pat. 31:12 (2021), 1155–1176, 10.1080/13543776.2021.1945580.
Davoine, C., Bouckaert, C., Fillet, M., Pochet, L., Factor XII/XIIa inhibitors: their discovery, development, and potential indications. Eur. J. Med. Chem., 2020, 112753, 10.1016/j.ejmech.2020.112753 Elsevier Masson SAS December 15.
U.S. National Library of Medecine. Safety and efficacy study of AB023 (xisomab 3G3) in end stage renal disease patients on chronic hemodialysis. https://clinicaltrials.gov/ct2/show/NCT03612856?term=xisomab&draw=2&rank=2. (Accessed 22 December 2022)
U.S. National Library of Medecine. Xisomab 3G3 for the prevention of catheter-associated thrombosis in patients with cancer receiving chemotherapy. https://clinicaltrials.gov/ct2/show/NCT04465760?term=xisomab&draw=2&rank=1. (Accessed 22 December 2022)
Oehmcke-Hecht, S., Berlin, P., Müller-Hilke, B., Kreikemeyer, B., Vasudevan, P., Henze, L., Khaimov, V., Vollmar, B., David, R., Maletzki, C., The versatile role of the contact system in cardiovascular disease, inflammation, sepsis and cancer. Biomed. Pharmacother., 145, 2022, 112429, 10.1016/j.biopha.2021.112429.
Singh, P.K., Badimon, A., Chen, Z., Strickland, S., Norris, E.H., The contact activation system and vascular factors as alternative targets for Alzheimer's disease therapy. Res. Pract. Thromb. Haemost., 5(4), 2021, 10.1002/rth2.12504.
U.S. National Library of Medecine. Long-term safety and efficacy of CSL312 (Garadacimab) in the prophylactic treatment of hereditary angioedema attacks. https://clinicaltrials.gov/ct2/show/NCT04739059?term=garadacimab&draw=2&rank=2. (Accessed 22 December 2022)
Korff, M., Imberg, L., Will, J.M., Bückreiß, N., Kalinina, S.A., Wenzel, B.M., Kastner, G.A., Daniliuc, C.G., Barth, M., Ovsepyan, R.A., Butov, K.R., Humpf, H.-U., Lehr, M., Panteleev, M.A., Poso, A., Karst, U., Steinmetzer, T., Bendas, G., Kalinin, D.V., Acylated 1 H -1,2,4-Triazol-5-Amines targeting human coagulation factor XIIa and thrombin: conventional and microscale synthesis, anticoagulant properties, and mechanism of action. J. Med. Chem. 63:21 (2020), 13159–13186, 10.1021/acs.jmedchem.0c01635.
Platte, S., Korff, M., Imberg, L., Balicioglu, I., Erbacher, C., Will, J.M., Daniliuc, C.G., Karst, U., Kalinin, D.V., Microscale parallel synthesis of acylated aminotriazoles enabling the development of factor XIIa and thrombin inhibitors. ChemMedChem 16:24 (2021), 3672–3690, 10.1002/cmdc.202100431.
Imberg, L., Platte, S., Erbacher, C., Daniliuc, C.G., Kalinina, S.A., Dörner, W., Poso, A., Karst, U., Kalinin, D.V., Amide-functionalized 1,2,4-triazol-5-amines as covalent inhibitors of blood coagulation factor XIIa and thrombin. ACS Pharmacol. Transl. Sci. 5:12 (2022), 1318–1347, 10.1021/acsptsci.2c00204.
Chen, J.J.F., Visco, D.P., Identifying novel factor XIIa inhibitors with PCA-GA-SVM developed VHTS models. Eur. J. Med. Chem. 140 (2017), 31–41, 10.1016/j.ejmech.2017.08.056.
Robert, S., Bertolla, C., Masereel, B., Dogné, J.-M., Pochet, L., Novel 3-carboxamide-coumarins as potent and selective FXIIa inhibitors. J. Med. Chem. 51:11 (2008), 3077–3080, 10.1021/jm8002697.
Bouckaert, C., Serra, S., Rondelet, G., Dolušić, E., Wouters, J., Dogné, J.-M., Frédérick, R., Pochet, L., Synthesis, evaluation and structure-activity relationship of new 3-carboxamide coumarins as FXIIa inhibitors. Eur. J. Med. Chem. 110 (2016), 181–194, 10.1016/j.ejmech.2016.01.023.
Bouckaert, C., Zhu, S., Govers-Riemslag, J.W.P., Depoorter, M., Diamond, S.L., Pochet, L., Discovery and assessment of water soluble coumarins as inhibitors of the coagulation contact pathway. Thromb. Res. 157 (2017), 126–133, 10.1016/j.thromres.2017.07.015.
de Esch, I.J.P., Erlanson, D.A., Jahnke, W., Johnson, C.N., Walsh, L., Fragment-to-Lead medicinal chemistry publications in 2020. J. Med. Chem. 65:1 (2022), 84–99, 10.1021/acs.jmedchem.1c01803.
Coyle, J., Walser, R., Applied biophysical methods in fragment-based drug discovery. SLAS Discov. Adv. Sci. Drug Discov. 25:5 (2020), 471–490, 10.1177/2472555220916168.
Lamoree, B., Hubbard, R.E., Current perspectives in fragment-based lead discovery (FBLD). Essays Biochem. 61:5 (2017), 453–464, 10.1042/EBC20170028.
Katz, B.A., Luong, C., Ho, J.D., Somoza, J.R., Gjerstad, E., Tang, J., Williams, S.R., Verner, E., Mackman, R.L., Young, W.B., Sprengeler, P.A., Chan, H., Mortara, K., Janc, J.W., McGrath, M.E., Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial Ala190 protease (Ala190 UPA). J. Mol. Biol. 344:2 (2004), 527–547, 10.1016/j.jmb.2004.09.032.
Walsh, L., Erlanson, D.A., de Esch, I.J.P., Jahnke, W., Woodhead, A., Wren, E., Fragment-to-Lead medicinal chemistry publications in 2021. J. Med. Chem., 2023, 10.1021/acs.jmedchem.2c01827.
Davoine, C., Fillet, M., Pochet, L., Capillary electrophoresis as a fragment screening tool to cross-validate hits from chromogenic assay: application to FXIIa. Talanta, 226, 2021, 122163, 10.1016/j.talanta.2021.122163.
MolPort. MolPort database. https://www.molport.com/shop/access-databases. (Accessed 18 April 2023)
St Denis, J.D., Hall, R.J., Murray, C.W., Heightman, T.D., Rees, D.C., Fragment-based drug discovery: opportunities for organic synthesis. RSC Med. Chem. 12:3 (2021), 321–329, 10.1039/D0MD00375A.
Rewinkel, J.B.M., Lucas, H., van Galen, P.J.M., Noach, A.B.J., van Dinther, T.G., Rood, A.M.M., Jenneboer, A.J.S.M., van Boeckel, C.A.A., 1-Aminoisoquinoline as benzamidine isoster in the design and synthesis of orally active thrombin inhibitors. Bioorg. Med. Chem. Lett. 9:5 (1999), 685–690, 10.1016/S0960-894X(99)00069-4.
Choi-Sledeski, Y.M., Becker, M.R., Green, D.M., Davis, R., Ewing, W.R., Mason, H.J., Ly, C., Spada, A., Liang, G., Cheney, D., Barton, J., Chu, V., Brown, K., Colussi, D., Bentley, R., Leadley, R., Dunwiddie, C., Pauls, H.W., Aminoisoquinolines: design and synthesis of an orally active benzamidine isostere for the inhibition of factor XA. Bioorg. Med. Chem. Lett. 9:17 (1999), 2539–2544, 10.1016/S0960-894X(99)00421-7.
Frédérick, R., Robert, S., Charlier, C., de Ruyck, J., Wouters, J., Pirotte, B., Masereel, B., Pochet, L., 3,6-Disubstituted coumarins as mechanism-based inhibitors of thrombin and factor Xa. J. Med. Chem. 48:24 (2005), 7592–7603, 10.1021/jm050448g.
Pochet, L., Doucet, C., Schynts, M., Thierry, N., Boggetto, N., Pirotte, B., Jiang, K.Y., Masereel, B., de Tullio, P., Delarge, J., Reboud-Ravaux, M., Esters and amides of 6-(chloromethyl)-2-oxo-2 H -1-Benzopyran-3-Carboxylic acid as inhibitors of α-chymotrypsin: significance of the “aromatic” nature of the novel ester-type coumarin for strong inhibitory activity. J. Med. Chem. 39:13 (1996), 2579–2585, 10.1021/jm960090b.
Doucet, C., Pochet, L., Thierry, N., Pirotte, B., Delarge, J., Reboud-Ravaux, M., 6-Substituted 2-oxo-2 H -1-Benzopyran-3-Carboxylic acid as a core structure for specific inhibitors of human leukocyte elastase. J. Med. Chem. 42:20 (1999), 4161–4171, 10.1021/jm990070k.
Pochet, L., Doucet, C., Dive, G., Wouters, J., Masereel, B., Reboud-Ravaux, M., Pirotte, B., Coumarinic derivatives as mechanism-based inhibitors of α-chymotrypsin and human leukocyte elastase. Bioorg. Med. Chem. 8:6 (2000), 1489–1501, 10.1016/S0968-0896(00)00071-7.
Meth-Cohn, O., Tarnowski, B., A useful synthon for sulphur heterocycles; I. The synthesis of thiocoumarins. Synthesis(1), 1978, 56–58, 10.1055/s-1978-24675 1978.
Yin, J., Xiang, B., Huffman, M.A., Raab, C.E., Davies, I.W., A general and efficient 2-amination of pyridines and quinolines. J. Org. Chem. 72:12 (2007), 4554–4557, 10.1021/jo070189y.
Górski, B., Basiak, D., Talko, A., Basak, T., Mazurek, T., Barbasiewicz, M., Olefination with sulfonyl halides and esters: E -selective synthesis of alkenes from semistabilized carbanion precursors. Eur. J. Org Chem.(15), 2018, 1774–1784, 10.1002/ejoc.201701766 2018.
Dar'in, D., Kantin, G., Kalinin, S., Sharonova, T., Bunev, A., Ostapenko, G.I., Nocentini, A., Sharoyko, V., Supuran, C.T., Krasavin, M., Investigation of 3-sulfamoyl coumarins against cancer-related IX and XII isoforms of human carbonic anhydrase as well as cancer cells leads to the discovery of 2-oxo-2H-Benzo[h]Chromene-3-Sulfonamide – a new caspase-activating proapoptotic agent. Eur. J. Med. Chem., 222, 2021, 113589, 10.1016/j.ejmech.2021.113589.
Hickey, S.M., Nitschke, S.O., Sweetman, M.J., Sumby, C.J., Brooks, D.A., Plush, S.E., Ashton, T.D., Cross-coupling of amide and amide derivatives to umbelliferone nonaflates: synthesis of coumarin derivatives and fluorescent materials. J. Org. Chem. 85:12 (2020), 7986–7999, 10.1021/acs.joc.0c00813.
Copeland, R.A., Evaluation of Enzyme Inhibitors in Drug Discovery : A Guide for Medicinal Chemists and Pharmacologists. second ed., 2013, John Wiley & Sons, Hoboken, New Jersey.
Pochet, L., Dieu, M., Frédérick, R., Murray, A.-M., Kempen, I., Pirotte, B., Masereel, B., Investigation of the inhibition mechanism of coumarins on chymotrypsin by mass spectrometry. Tetrahedron 59:25 (2003), 4557–4561, 10.1016/S0040-4020(03)00660-4.
Pochet, L., Frederick, R., Masereel, B., Coumarin and isocoumarin as serine protease inhibitors. Curr. Pharmaceut. Des. 10:30 (2004), 3781–3796, 10.2174/1381612043382684.
Douxfils, J., Mullier, F., Loosen, C., Chatelain, C., Chatelain, B., Dogné, J.-M., Assessment of the impact of rivaroxaban on coagulation assays: laboratory recommendations for the monitoring of rivaroxaban and review of the literature. Thromb. Res. 130:6 (2012), 956–966, 10.1016/j.thromres.2012.09.004.
Koitka, M., Höchel, J., Gieschen, H., Borchert, H.-H., Improving the ex vivo stability of drug ester compounds in rat and dog serum: inhibition of the specific esterases and implications on their identity. J. Pharm. Biomed. Anal. 51:3 (2010), 664–678, 10.1016/j.jpba.2009.09.023.
Breidenbach, J., Bartz, U., Gütschow, M., Coumarin as a structural component of substrates and probes for serine and cysteine proteases. Biochim. Biophys. Acta, Proteins Proteomics, 1868(9), 2020, 140445, 10.1016/j.bbapap.2020.140445.
Wouters, J., Huygens, M., Pochet, L., Pirotte, B., Durant, F., Masereel, B., Structural approach of the mechanism of inhibition of α-chymotrypsin by coumarins. Bioorg. Med. Chem. Lett. 12:7 (2002), 1109–1112, 10.1016/S0960-894X(02)00073-2.
Sandhu, H.S., Sapra, S., Gupta, M., Nepali, K., Gautam, R., Yadav, S., Kumar, R., Jachak, S.M., Chugh, M., Gupta, M.K., Suri, O.P., Dhar, K.L., Synthesis and biological evaluation of arylidene analogues of Meldrum's acid as a new class of antimalarial and antioxidant agents. Bioorg. Med. Chem. 18:15 (2010), 5626–5633, 10.1016/j.bmc.2010.06.033.
Jiang, X., Guo, J., Lv, Y., Yao, C., Zhang, C., Mi, Z., Shi, Y., Gu, J., Zhou, T., Bai, R., Xie, Y., Rational design, synthesis and biological evaluation of novel multitargeting anti-AD iron chelators with potent MAO-B inhibitory and antioxidant activity. Bioorg. Med. Chem., 28(12), 2020, 115550, 10.1016/j.bmc.2020.115550.
Woods, K.W., Fischer, J.P., Claiborne, A., Li, T., Thomas, S.A., Zhu, G.-D., Diebold, R.B., Liu, X., Shi, Y., Klinghofer, V., Han, E.K., Guan, R., Magnone, S.R., Johnson, E.F., Bouska, J.J., Olson, A.M., Jong, R. de, Oltersdorf, T., Luo, Y., Rosenberg, S.H., Giranda, V.L., Li, Q., Synthesis and SAR of indazole-pyridine based protein kinase B/akt inhibitors. Bioorg. Med. Chem. 14:20 (2006), 6832–6846, 10.1016/j.bmc.2006.06.047.
Armstrong, V., Soto, O., Valderrama, J.A., Tapia, R., Synthesis of 3-carboxycoumarins from O-methoxybenzylidene Meldrum's acid derivatives. Synth. Commun. 18:7 (1988), 717–725, 10.1080/00397918808077361.
Li, M., Petersen, J.L., Hoover, J.M., Silver-mediated oxidative decarboxylative trifluoromethylthiolation of coumarin-3-carboxylic acids. Org. Lett. 19:3 (2017), 638–641, 10.1021/acs.orglett.6b03806.
Davoine, C., Pardo, A., Pochet, L., Fillet, M., Fragment hit discovery and binding site characterization by indirect affinity capillary electrophoresis: application to factor XIIa. Anal. Chem. 93:44 (2021), 14802–14809, 10.1021/acs.analchem.1c03611.
Kuzmič, P., Elrod, K.C., Cregar, L.M., Sideris, S., Rai, R., Janc, J.W., High-throughput screening of enzyme inhibitors: simultaneous determination of tight-binding inhibition constants and enzyme concentration. Anal. Biochem. 286:1 (2000), 45–50, 10.1006/abio.2000.4685.
Schwartz, P.A., Kuzmic, P., Solowiej, J., Bergqvist, S., Bolanos, B., Almaden, C., Nagata, A., Ryan, K., Feng, J., Dalvie, D., Kath, J.C., Xu, M., Wani, R., Murray, B.W., Covalent EGFR inhibitor analysis reveals importance of reversible interactions to potency and mechanisms of drug resistance. Proc. Natl. Acad. Sci. USA 111:1 (2014), 173–178, 10.1073/pnas.1313733111.
Evrard, J., Siriez, R., Bouvy, C., Favresse, J., Yildiz, H., Hainaut, P., Mullier, F., Dogné, J., Douxfils, J., Comparison of analytical performances between clot waveform analysis and FibWave in edoxaban-treated patients and healthy controls. Res. Pract. Thromb. Haemost., 6(7), 2022, e12804, 10.1002/rth2.12804.
