Three Decades of Targeting Falcipains to Develop Antiplasmodial Agents: What have we Learned and What can be Done Next?


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Abstract

Malaria is a devastating infectious disease that affects large swathes of human populations across the planet’s tropical regions. It is caused by parasites of the genus Plasmodium, with Plasmodium falciparum being responsible for the most lethal form of the disease. During the intraerythrocytic stage in the human hosts, malaria parasites multiply and degrade hemoglobin (Hb) using a battery of proteases, which include two cysteine proteases, falcipains 2 and 3 (FP-2 and FP-3). Due to their role as major hemoglobinases, FP-2 and FP-3 have been targeted in studies aiming to discover new antimalarials and numerous inhibitors with activity against these enzymes, and parasites in culture have been identified. Nonetheless, cross-inhibition of human cysteine cathepsins remains a serious hurdle to overcome for these compounds to be used clinically. In this article, we have reviewed key functional and structural properties of FP-2/3 and described different compound series reported as inhibitors of these proteases during decades of active research in the field. Special attention is also paid to the wide range of computer-aided drug design (CADD) techniques successfully applied to discover new active compounds. Finally, we provide guidelines that, in our understanding, will help advance the rational discovery of new FP-2/3 inhibitors.

About the authors

Jorge González

Multiuser Center for Biomolecular Innovation, IBILCE/UNESP,

Author for correspondence.
Email: info@benthamscience.net

Emir Salas-Sarduy

Instituto de Investigaciones Biotecnológicas Dr. Rodolfo Ugalde, Universidad Nacional de San Martín

Email: info@benthamscience.net

Lilian Alvarez

Multiuser Center for Biomolecular Innovation,, IBILCE/UNESP

Email: info@benthamscience.net

Pedro Valiente

Donnelly Centre for Cellular & Biomolecular Research, University of Toronto

Email: info@benthamscience.net

Raghuvir Arni

Multiuser Center for Biomolecular Innovation, I, IBILCE/UNESP

Email: info@benthamscience.net

Pedro Pascutti

Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro

Email: info@benthamscience.net

References

  1. Bekono, B.D.; Ntie-Kang, F.; Owono Owono, L.C.; Megnassan, E. Targeting cysteine proteases from Plasmodium falciparum: A general overview, rational drug design and computational approaches for drug discovery. Curr. Drug Targets, 2018, 19(5), 501-526. doi: 10.2174/1389450117666161221122432 PMID: 28003005
  2. Teixeira, C.; Gomes, J.R.; Gomes, P. Falcipains, Plasmodium falciparum cysteine proteases as key drug targets against malaria. Curr. Med. Chem., 2011, 18(10), 1555-1572. doi: 10.2174/092986711795328328 PMID: 21428877
  3. Rosenthal, P.J. Falcipain cysteine proteases of malaria parasites: An update. Biochim. Biophys. Acta. Proteins Proteomics, 2020, 1868(3), 140362. doi: 10.1016/j.bbapap.2020.140362 PMID: 31927030
  4. World malaria report. 2022. Available From: https://www.who.int/teams/global-malaria-programme/reports/world-malaria-report-2022 (Accessed on March 27th 2023).
  5. Zhu, L.; van der Pluijm, R.W.; Kucharski, M.; Nayak, S.; Tripathi, J.; White, N.J.; Day, N.P.J.; Faiz, A.; Phyo, A.P.; Amaratunga, C.; Lek, D.; Ashley, E.A.; Nosten, F.; Smithuis, F.; Ginsburg, H.; von Seidlein, L.; Lin, K.; Imwong, M.; Chotivanich, K.; Mayxay, M.; Dhorda, M.; Nguyen, H.C.; Nguyen, T.N.T.; Miotto, O.; Newton, P.N.; Jittamala, P.; Tripura, R.; Pukrittayakamee, S.; Peto, T.J.; Hien, T.T.; Dondorp, A.M.; Bozdech, Z. Artemisinin resistance in the malaria parasite, Plasmodium falciparum, originates from its initial transcriptional response. Commun. Biol., 2022, 5(1), 274. doi: 10.1038/s42003-022-03215-0 PMID: 35347215
  6. Ashley, E.A.; Dhorda, M.; Fairhurst, R.M.; Amaratunga, C.; Lim, P.; Suon, S.; Sreng, S.; Anderson, J.M.; Mao, S.; Sam, B.; Sopha, C.; Chuor, C.M.; Nguon, C.; Sovannaroth, S.; Pukrittayakamee, S.; Jittamala, P.; Chotivanich, K.; Chutasmit, K.; Suchatsoonthorn, C.; Runcharoen, R.; Hien, T.T.; Thuy-Nhien, N.T.; Thanh, N.V.; Phu, N.H.; Htut, Y.; Han, K.T.; Aye, K.H.; Mokuolu, O.A.; Olaosebikan, R.R.; Folaranmi, O.O.; Mayxay, M.; Khanthavong, M.; Hongvanthong, B.; Newton, P.N.; Onyamboko, M.A.; Fanello, C.I.; Tshefu, A.K.; Mishra, N.; Valecha, N.; Phyo, A.P.; Nosten, F.; Yi, P.; Tripura, R.; Borrmann, S.; Bashraheil, M.; Peshu, J.; Faiz, M.A.; Ghose, A.; Hossain, M.A.; Samad, R.; Rahman, M.R.; Hasan, M.M.; Islam, A.; Miotto, O.; Amato, R.; MacInnis, B.; Stalker, J.; Kwiatkowski, D.P.; Bozdech, Z.; Jeeyapant, A.; Cheah, P.Y.; Sakulthaew, T.; Chalk, J.; Intharabut, B.; Silamut, K.; Lee, S.J.; Vihokhern, B.; Kunasol, C.; Imwong, M.; Tarning, J.; Taylor, W.J.; Yeung, S.; Woodrow, C.J.; Flegg, J.A.; Das, D.; Smith, J.; Venkatesan, M.; Plowe, C.V.; Stepniewska, K.; Guerin, P.J.; Dondorp, A.M.; Day, N.P.; White, N.J. Spread of artemisinin resistance in Plasmodium falciparum malaria. N. Engl. J. Med., 2014, 371(5), 411-423. doi: 10.1056/NEJMoa1314981 PMID: 25075834
  7. van der Pluijm, R.W.; Imwong, M.; Chau, N.H.; Hoa, N.T.; Thuy-Nhien, N.T.; Thanh, N.V.; Jittamala, P.; Hanboonkunupakarn, B.; Chutasmit, K.; Saelow, C.; Runjarern, R.; Kaewmok, W.; Tripura, R.; Peto, T.J.; Yok, S.; Suon, S.; Sreng, S.; Mao, S.; Oun, S.; Yen, S.; Amaratunga, C.; Lek, D.; Huy, R.; Dhorda, M.; Chotivanich, K.; Ashley, E.A.; Mukaka, M.; Waithira, N.; Cheah, P.Y.; Maude, R.J.; Amato, R.; Pearson, R.D.; Gonçalves, S.; Jacob, C.G.; Hamilton, W.L.; Fairhurst, R.M.; Tarning, J.; Winterberg, M.; Kwiatkowski, D.P.; Pukrittayakamee, S.; Hien, T.T.; Day, N.P.J.; Miotto, O.; White, N.J.; Dondorp, A.M. Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: A prospective clinical, pharmacological, and genetic study. Lancet Infect. Dis., 2019, 19(9), 952-961. doi: 10.1016/S1473-3099(19)30391-3 PMID: 31345710
  8. Laurens, M.B. RTS,S/AS01 vaccine (Mosquirix™): An overview. Hum. Vaccin. Immunother., 2020, 16(3), 480-489. doi: 10.1080/21645515.2019.1669415 PMID: 31545128
  9. World malaria report. 2021. Available From: https://www.who.int/teams/global-malaria-programme/reports/world-malaria-report-2021 (Accessed on March 27th 2023).
  10. Silal, S.P. Seasonal targeting of the RTS,S/AS01 malaria vaccine: A complementary tool but sustained funding is required. Lancet Glob. Health, 2022, 10(12), e1693-e1694. doi: 10.1016/S2214-109X(22)00477-6 PMID: 36400073
  11. Rosenthal, P.J. Falcipains and other cysteine proteases of malaria parasites. Adv. Exp. Med. Biol., 2011, 712, 30-48. doi: 10.1007/978-1-4419-8414-2_3 PMID: 21660657
  12. Roy, K.K. Targeting the active sites of malarial proteases for antimalarial drug discovery: Approaches, progress and challenges. Int. J. Antimicrob. Agents, 2017, 50(3), 287-302. doi: 10.1016/j.ijantimicag.2017.04.006 PMID: 28668681
  13. Ettari, R.; Bova, F.; Zappalà, M.; Grasso, S.; Micale, N. Falcipain-2 inhibitors. Med. Res. Rev., 2010, 30(1), 136-167. doi: 10.1002/med.20163 PMID: 19526594
  14. Ettari, R.; Previti, S.; Di Chio, C.; Zappalà, M. Falcipain-2 and falcipain-3 inhibitors as promising antimalarial agents. Curr. Med. Chem., 2021, 28(15), 3010-3031. doi: 10.2174/1875533XMTA4nNzUc3 PMID: 32744954
  15. Marco, M.; Miguel Coteron, J. Falcipain inhibition as a promising antimalarial target. Curr. Top. Med. Chem., 2012, 12(5), 408-444. doi: 10.2174/156802612799362913 PMID: 22242849
  16. Khan, S.M.; Waters, A.P. Malaria parasite transmission stages: An update. Trends Parasitol., 2004, 20(12), 575-580. doi: 10.1016/j.pt.2004.10.001 PMID: 15522667
  17. Dimopoulos, G.; Kafatos, F.C.; Waters, A.P.; Sinden, R.E. Malaria parasites and the anopheles mosquito. Chem. Immunol., 2002, 80, 27-49. doi: 10.1159/000058838 PMID: 12058645
  18. Kappe, S.H.I.; Kaiser, K.; Matuschewski, K. The Plasmodium sporozoite journey: A rite of passage. Trends Parasitol., 2003, 19(3), 135-143. doi: 10.1016/S1471-4922(03)00007-2 PMID: 12643997
  19. Wells, T.N.C.; van Huijsduijnen, R.H.; Van Voorhis, W.C. Malaria medicines: A glass half full? Nat. Rev. Drug Discov., 2015, 14(6), 424-442. doi: 10.1038/nrd4573 PMID: 26000721
  20. Rosenthal, P.J.; McKerrow, J.H.; Aikawa, M.; Nagasawa, H.; Leech, J.H. A malarial cysteine proteinase is necessary for hemoglobin degradation by Plasmodium falciparum. J. Clin. Invest., 1988, 82(5), 1560-1566. doi: 10.1172/JCI113766 PMID: 3053784
  21. Rosenthal, P.J.; Nelson, R.G. Isolation and characterization of a cysteine proteinase gene of Plasmodium falciparum. Mol. Biochem. Parasitol., 1992, 51(1), 143-152. doi: 10.1016/0166-6851(92)90209-3 PMID: 1565129
  22. Shenai, B.R.; Sijwali, P.S.; Singh, A.; Rosenthal, P.J. Characterization of native and recombinant falcipain-2, a principal trophozoite cysteine protease and essential hemoglobinase of Plasmodium falciparum. J. Biol. Chem., 2000, 275(37), 29000-29010. doi: 10.1074/jbc.M004459200 PMID: 10887194
  23. Sijwali, P.S.; Shenai, B.R.; Gut, J.; Singh, A.; Rosenthal, P.J. Expression and characterization of the Plasmodium falciparum haemoglobinase falcipain-3. Biochem. J., 2001, 360(2), 481-489. doi: 10.1042/bj3600481 PMID: 11716777
  24. Singh, N.; Sijwali, P.S.; Pandey, K.C.; Rosenthal, P.J. Plasmodium falciparum: Biochemical characterization of the cysteine protease falcipain-2′. Exp. Parasitol., 2006, 112(3), 187-192. doi: 10.1016/j.exppara.2005.10.007 PMID: 16337629
  25. Sijwali, P.S.; Kato, K.; Seydel, K.B.; Gut, J.; Lehman, J.; Klemba, M.; Goldberg, D.E.; Miller, L.H.; Rosenthal, P.J. Plasmodium falciparum cysteine protease falcipain-1 is not essential in erythrocytic stage malaria parasites. Proc. Natl. Acad. Sci. USA, 2004, 101(23), 8721-8726. doi: 10.1073/pnas.0402738101 PMID: 15166288
  26. Eksi, S.; Czesny, B.; Greenbaum, D.C.; Bogyo, M.; Williamson, K.C. Targeted disruption of Plasmodium falciparum cysteine protease, falcipain 1, reduces oocyst production, not erythrocytic stage growth. Mol. Microbiol., 2004, 53(1), 243-250. doi: 10.1111/j.1365-2958.2004.04108.x PMID: 15225318
  27. Sijwali, P.S.; Koo, J.; Singh, N.; Rosenthal, P.J. Gene disruptions demonstrate independent roles for the four falcipain cysteine proteases of Plasmodium falciparum. Mol. Biochem. Parasitol., 2006, 150(1), 96-106. doi: 10.1016/j.molbiopara.2006.06.013 PMID: 16890302
  28. Gluzman, I.Y.; Francis, S.E.; Oksman, A.; Smith, C.E.; Duffin, K.L.; Goldberg, D.E. Order and specificity of the Plasmodium falciparum hemoglobin degradation pathway. J. Clin. Invest., 1994, 93(4), 1602-1608. doi: 10.1172/JCI117140 PMID: 8163662
  29. Banerjee, R.; Liu, J.; Beatty, W.; Pelosof, L.; Klemba, M.; Goldberg, D.E. Four plasmepsins are active in the Plasmodium falciparum food vacuole, including a protease with an active-site histidine. Proc. Natl. Acad. Sci. USA, 2002, 99(2), 990-995. doi: 10.1073/pnas.022630099 PMID: 11782538
  30. Eggleson, K.K.; Duffin, K.L.; Goldberg, D.E. Identification and characterization of falcilysin, a metallopeptidase involved in hemoglobin catabolism within the malaria parasite Plasmodium falciparum. J. Biol. Chem., 1999, 274(45), 32411-32417. doi: 10.1074/jbc.274.45.32411 PMID: 10542284
  31. Klemba, M.; Gluzman, I.; Goldberg, D.E. A Plasmodium falciparum dipeptidyl aminopeptidase I participates in vacuolar hemoglobin degradation. J. Biol. Chem., 2004, 279(41), 43000-43007. doi: 10.1074/jbc.M408123200 PMID: 15304495
  32. Rosenthal, P.J. Plasmodium falciparum: Effects of proteinase inhibitors on globin hydrolysis by cultured malaria parasites. Exp. Parasitol., 1995, 80(2), 272-281. doi: 10.1006/expr.1995.1033 PMID: 7895837
  33. Omara-Opyene, A.L.; Moura, P.A.; Sulsona, C.R.; Bonilla, J.A.; Yowell, C.A.; Fujioka, H.; Fidock, D.A.; Dame, J.B. Genetic disruption of the Plasmodium falciparum digestive vacuole plasmepsins demonstrates their functional redundancy. J. Biol. Chem., 2004, 279(52), 54088-54096. doi: 10.1074/jbc.M409605200 PMID: 15491999
  34. Subramanian, S.; Hardt, M.; Choe, Y.; Niles, R.K.; Johansen, E.B.; Legac, J.; Gut, J.; Kerr, I.D.; Craik, C.S.; Rosenthal, P.J. Hemoglobin cleavage site-specificity of the Plasmodium falciparum cysteine proteases falcipain-2 and falcipain-3. PLoS One, 2009, 4(4), e5156. doi: 10.1371/journal.pone.0005156 PMID: 19357776
  35. Rosenthal, P.J.; Wollish, W.S.; Palmer, J.T.; Rasnick, D. Antimalarial effects of peptide inhibitors of a Plasmodium falciparum cysteine proteinase. J. Clin. Invest., 1991, 88(5), 1467-1472. doi: 10.1172/JCI115456 PMID: 1939639
  36. Sijwali, P.S.; Rosenthal, P.J. Gene disruption confirms a critical role for the cysteine protease falcipain-2 in hemoglobin hydrolysis by Plasmodium falciparum. Proc. Natl. Acad. Sci. USA, 2004, 101(13), 4384-4389. doi: 10.1073/pnas.0307720101 PMID: 15070727
  37. Hanspal, M.; Dua, M.; Takakuwa, Y.; Chishti, A.H.; Mizuno, A. Plasmodium falciparum cysteine protease falcipain-2 cleaves erythrocyte membrane skeletal proteins at late stages of parasite development. Blood, 2002, 100(3), 1048-1054. doi: 10.1182/blood-2002-01-0101 PMID: 12130521
  38. Drew, M.E.; Banerjee, R.; Uffman, E.W.; Gilbertson, S.; Rosenthal, P.J.; Goldberg, D.E. Plasmodium food vacuole plasmepsins are activated by falcipains. J. Biol. Chem., 2008, 283(19), 12870-12876. doi: 10.1074/jbc.M708949200 PMID: 18308731
  39. Wang, S.X.; Pandey, K.C.; Somoza, J.R.; Sijwali, P.S.; Kortemme, T.; Brinen, L.S.; Fletterick, R.J.; Rosenthal, P.J.; McKerrow, J.H. Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease. Proc. Natl. Acad. Sci., 2006, 103(31), 11503-11508. doi: 10.1073/pnas.0600489103 PMID: 16864794
  40. Hogg, T.; Nagarajan, K.; Herzberg, S.; Chen, L.; Shen, X.; Jiang, H.; Wecke, M.; Blohmke, C.; Hilgenfeld, R.; Schmidt, C.L. Structural and functional characterization of Falcipain-2, a hemoglobinase from the malarial parasite Plasmodium falciparum. J. Biol. Chem., 2006, 281(35), 25425-25437. doi: 10.1074/jbc.M603776200 PMID: 16777845
  41. Kerr, I.D.; Lee, J.H.; Pandey, K.C.; Harrison, A.; Sajid, M.; Rosenthal, P.J.; Brinen, L.S. Structures of falcipain-2 and falcipain-3 bound to small molecule inhibitors: Implications for substrate specificity. J. Med. Chem., 2009, 52(3), 852-857. doi: 10.1021/jm8013663 PMID: 19128015
  42. Chakraborty, S.; Alam, B.; Biswas, S. New insights of falcipain 2 structure from Plasmodium falciparum 3D7 strain. Biochem. Biophys. Res. Commun., 2022, 590, 145-151. doi: 10.1016/j.bbrc.2021.12.080 PMID: 34974303
  43. Kerr, I.D.; Lee, J.H.; Farady, C.J.; Marion, R.; Rickert, M.; Sajid, M.; Pandey, K.C.; Caffrey, C.R.; Legac, J.; Hansell, E.; McKerrow, J.H.; Craik, C.S.; Rosenthal, P.J.; Brinen, L.S. Vinyl sulfones as antiparasitic agents and a structural basis for drug design. J. Biol. Chem., 2009, 284(38), 25697-25703. doi: 10.1074/jbc.M109.014340 PMID: 19620707
  44. Machin, J.M.; Kantsadi, A.L.; Vakonakis, I. The complex of Plasmodium falciparum falcipain-2 protease with an (E)-chalcone-based inhibitor highlights a novel, small, molecule-binding site. Malar. J., 2019, 18(1), 388. doi: 10.1186/s12936-019-3043-0 PMID: 31791339
  45. Wang, S.X.; Pandey, K.C.; Scharfstein, J.; Whisstock, J.; Huang, R.K.; Jacobelli, J.; Fletterick, R.J.; Rosenthal, P.J.; Abrahamson, M.; Brinen, L.S.; Rossi, A.; Sali, A.; McKerrow, J.H. The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family. Structure, 2007, 15(5), 535-543. doi: 10.1016/j.str.2007.03.012 PMID: 17502099
  46. Hansen, G.; Heitmann, A.; Witt, T.; Li, H.; Jiang, H.; Shen, X.; Heussler, V.T.; Rennenberg, A.; Hilgenfeld, R. Structural basis for the regulation of cysteine-protease activity by a new class of protease inhibitors in Plasmodium. Structure, 2011, 19(7), 919-929. doi: 10.1016/j.str.2011.03.025 PMID: 21742259
  47. Pandey, K.C.; Sijwali, P.S.; Singh, A.; Na, B.K.; Rosenthal, P.J. Independent intramolecular mediators of folding, activity, and inhibition for the Plasmodium falciparum cysteine protease falcipain-2. J. Biol. Chem., 2004, 279(5), 3484-3491. doi: 10.1074/jbc.M310536200 PMID: 14625277
  48. Pandey, K.C.; Wang, S.X.; Sijwali, P.S.; Lau, A.L.; McKerrow, J.H.; Rosenthal, P.J. The Plasmodium falciparum cysteine protease falcipain-2 captures its substrate, hemoglobin, via a unique motif. Proc. Natl. Acad. Sci. USA, 2005, 102(26), 9138-9143. doi: 10.1073/pnas.0502368102 PMID: 15964982
  49. Cotrin, S.S.; Gouvêa, I.E.; Melo, P.M.S.; Bagnaresi, P.; Assis, D.M.; Araújo, M.S.; Juliano, M.A.; Gazarini, M.L.; Rosenthal, P.J.; Juliano, L.; Carmona, A.K. Substrate specificity studies of the cysteine peptidases falcipain-2 and falcipain-3 from Plasmodium falciparum and demonstration of their kininogenase activity. Mol. Biochem. Parasitol., 2013, 187(2), 111-116. doi: 10.1016/j.molbiopara.2013.01.002 PMID: 23354130
  50. Rzychon, M.; Chmiel, D.; Stec-Niemczyk, J. Modes of inhibition of cysteine proteases. Acta Biochim. Pol., 2004, 51(4), 861-873. PMID: 15625558
  51. Powers, J.C.; Asgian, J.L.; Ekici, Ö.D.; James, K.E. Irreversible inhibitors of serine, cysteine, and threonine proteases. Chem. Rev., 2002, 102(12), 4639-4750. doi: 10.1021/cr010182v PMID: 12475205
  52. Ring, C.S.; Sun, E.; McKerrow, J.H.; Lee, G.K.; Rosenthal, P.J.; Kuntz, I.D.; Cohen, F.E. Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc. Natl. Acad. Sci. USA, 1993, 90(8), 3583-3587. doi: 10.1073/pnas.90.8.3583 PMID: 8475107
  53. Li, R.; Chen, X.; Gong, B.; Selzer, P.M.; Li, Z.; Davidson, E.; Kurzban, G.; Miller, R.E.; Nuzum, E.O.; McKerrow, J.H.; Fletterick, R.J.; Gillmor, S.A.; Craik, C.S.; Kuntz, I.D.; Cohen, F.E.; Kenyon, G.L. Structure-based design of parasitic protease inhibitors. Bioorg. Med. Chem., 1996, 4(9), 1421-1427. doi: 10.1016/0968-0896(96)00136-8 PMID: 8894100
  54. Rosenthal, P.J.; Olson, J.E.; Lee, G.K.; Palmer, J.T.; Klaus, J.L.; Rasnick, D. Antimalarial effects of vinyl sulfone cysteine proteinase inhibitors. Antimicrob. Agents Chemother., 1996, 40(7), 1600-1603. doi: 10.1128/AAC.40.7.1600 PMID: 8807047
  55. Rosenthal, P.J.; Lee, G.K.; Smith, R.E. Inhibition of a Plasmodium vinckei cysteine proteinase cures murine malaria. J. Clin. Invest., 1993, 91(3), 1052-1056. doi: 10.1172/JCI116262 PMID: 8450035
  56. Gamboa de Domínguez, N.D.; Rosenthal, P.J. Cysteine proteinase inhibitors block early steps in hemoglobin degradation by cultured malaria parasites. Blood, 1996, 87(10), 4448-4454. doi: 10.1182/blood.V87.10.4448.bloodjournal87104448 PMID: 8639807
  57. Mane, U.R.; Gupta, R.C.; Nadkarni, S.S.; Giridhar, R.R.; Naik, P.P.; Yadav, M.R. Falcipain inhibitors as potential therapeutics for resistant strains of malaria: A patent review. Expert Opin. Ther. Pat., 2013, 23(2), 165-187. doi: 10.1517/13543776.2013.743992 PMID: 23228154
  58. Cianni, L.; Feldmann, C.W.; Gilberg, E.; Gütschow, M.; Juliano, L.; Leitão, A.; Bajorath, J.; Montanari, C.A. Can cysteine protease cross-class inhibitors achieve selectivity? J. Med. Chem., 2019, 62(23), 10497-10525. doi: 10.1021/acs.jmedchem.9b00683 PMID: 31361135
  59. Citarella, A.; Micale, N. Peptidyl fluoromethyl ketones and their applications in medicinal chemistry. Molecules, 2020, 25(17), 4031. doi: 10.3390/molecules25174031 PMID: 32899354
  60. Kato, D.; Boatright, K.M.; Berger, A.B.; Nazif, T.; Blum, G.; Ryan, C.; Chehade, K.A.H.; Salvesen, G.S.; Bogyo, M. Activity-based probes that target diverse cysteine protease families. Nat. Chem. Biol., 2005, 1(1), 33-38. doi: 10.1038/nchembio707 PMID: 16407991
  61. Sajid, M.; Robertson, S.A.; Brinen, L.S.; McKerrow, J.H. Cruzain. Adv. Exp. Med. Biol., 2011, 712, 100-115. doi: 10.1007/978-1-4419-8414-2_7 PMID: 21660661
  62. Dunny, E.; Evans, P. Vinyl sulfone containing parasitic cysteinyl protease inhibitors. Curr. Bioact. Compd., 2011, 7(4), 218-236. doi: 10.2174/157340711798375859
  63. Shenai, B.R.; Lee, B.J.; Alvarez-Hernandez, A.; Chong, P.Y.; Emal, C.D.; Neitz, R.J.; Roush, W.R.; Rosenthal, P.J. Structure-activity relationships for inhibition of cysteine protease activity and development of Plasmodium falciparum by peptidyl vinyl sulfones. Antimicrob. Agents Chemother., 2003, 47(1), 154-160. doi: 10.1128/AAC.47.1.154-160.2003 PMID: 12499184
  64. Aratikatla, E.K.; Kalamuddin, M.; Malhotra, P.; Mohmmed, A.; Bhattacharya, A.K. Enantioselective synthesis of γ-phenyl-γ-amino vinyl phosphonates and sulfones and their application to the synthesis of novel highly potent antimalarials. ACS Omega, 2020, 5(45), 29025-29037. doi: 10.1021/acsomega.0c03470 PMID: 33225134
  65. Shokhen, M.; Khazanov, N.; Albeck, A. The mechanism of papain inhibition by peptidyl aldehydes. Proteins, 2011, 79(3), 975-985. doi: 10.1002/prot.22939 PMID: 21181719
  66. Smith, R.A.; Copp, L.J.; Donnelly, S.L.; Spencer, R.W.; Krantz, A. Inhibition of cathepsin B by peptidyl aldehydes and ketones: Slow-binding behavior of a trifluoromethyl ketone. Biochemistry, 1988, 27(17), 6568-6573. doi: 10.1021/bi00417a056 PMID: 3219354
  67. Ma, Y.; Yang, K.S.; Geng, Z.Z.; Alugubelli, Y.R.; Shaabani, N.; Vatansever, E.C.; Ma, X.R.; Cho, C.C.; Khatua, K.; Xiao, J.; Blankenship, L.R.; Yu, G.; Sankaran, B.; Li, P.; Allen, R.; Ji, H.; Xu, S.; Liu, W.R. A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals. Eur. J. Med. Chem., 2022, 240, 114570. doi: 10.1016/j.ejmech.2022.114570 PMID: 35779291
  68. Lee, B.J.; Singh, A.; Chiang, P.; Kemp, S.J.; Goldman, E.A.; Weinhouse, M.I.; Vlasuk, G.P.; Rosenthal, P.J. Antimalarial activities of novel synthetic cysteine protease inhibitors. Antimicrob. Agents Chemother., 2003, 47(12), 3810-3814. doi: 10.1128/AAC.47.12.3810-3814.2003 PMID: 14638488
  69. Ehmke, V.; Kilchmann, F.; Heindl, C.; Cui, K.; Huang, J.; Schirmeister, T.; Diederich, F. Peptidomimetic nitriles as selective inhibitors for the malarial cysteine protease falcipain-2. MedChemComm, 2011, 2(8), 800-804. doi: 10.1039/c1md00115a
  70. Gauthier, J.Y.; Chauret, N.; Cromlish, W.; Desmarais, S.; Duong, L.T.; Falgueyret, J.P.; Kimmel, D.B.; Lamontagne, S.; Léger, S.; LeRiche, T.; Li, C.S.; Massé, F.; McKay, D.J.; Nicoll-Griffith, D.A.; Oballa, R.M.; Palmer, J.T.; Percival, M.D.; Riendeau, D.; Robichaud, J.; Rodan, G.A.; Rodan, S.B.; Seto, C.; Thérien, M.; Truong, V.L.; Venuti, M.C.; Wesolowski, G.; Young, R.N.; Zamboni, R.; Black, W.C. The discovery of odanacatib (MK-0822), a selective inhibitor of cathepsin K. Bioorg. Med. Chem. Lett., 2008, 18(3), 923-928. doi: 10.1016/j.bmcl.2007.12.047 PMID: 18226527
  71. Oballa, R.M.; Truchon, J.F.; Bayly, C.I.; Chauret, N.; Day, S.; Crane, S.; Berthelette, C. A generally applicable method for assessing the electrophilicity and reactivity of diverse nitrile-containing compounds. Bioorg. Med. Chem. Lett., 2007, 17(4), 998-1002. doi: 10.1016/j.bmcl.2006.11.044 PMID: 17157022
  72. Ang, K.K.H.; Ratnam, J.; Gut, J.; Legac, J.; Hansell, E.; Mackey, Z.B.; Skrzypczynska, K.M.; Debnath, A.; Engel, J.C.; Rosenthal, P.J.; McKerrow, J.H.; Arkin, M.R.; Renslo, A.R. Mining a cathepsin inhibitor library for new antiparasitic drug leads. PLoS Negl. Trop. Dis., 2011, 5(5), e1023. doi: 10.1371/journal.pntd.0001023 PMID: 21572521
  73. Coterón, J.M.; Catterick, D.; Castro, J.; Chaparro, M.J.; Díaz, B.; Fernández, E.; Ferrer, S.; Gamo, F.J.; Gordo, M.; Gut, J.; de las Heras, L.; Legac, J.; Marco, M.; Miguel, J.; Muñoz, V.; Porras, E.; de la Rosa, J.C.; Ruiz, J.R.; Sandoval, E.; Ventosa, P.; Rosenthal, P.J.; Fiandor, J.M. Falcipain inhibitors: Optimization studies of the 2-pyrimidinecarbonitrile lead series. J. Med. Chem., 2010, 53(16), 6129-6152. doi: 10.1021/jm100556b PMID: 20672841
  74. Nizi, E.; Sferrazza, A.; Fabbrini, D.; Nardi, V.; Andreini, M.; Graziani, R.; Gennari, N.; Bresciani, A.; Paonessa, G.; Harper, S. Peptidomimetic nitrile inhibitors of malarial protease falcipain-2 with high selectivity against human cathepsins. Bioorg. Med. Chem. Lett., 2018, 28(9), 1540-1544. doi: 10.1016/j.bmcl.2018.03.069 PMID: 29615344
  75. Chakka, S.K.; Kalamuddin, M.; Sundararaman, S.; Wei, L.; Mundra, S.; Mahesh, R.; Malhotra, P.; Mohmmed, A.; Kotra, L.P. Identification of novel class of falcipain-2 inhibitors as potential antimalarial agents. Bioorg. Med. Chem., 2015, 23(9), 2221-2240. doi: 10.1016/j.bmc.2015.02.062 PMID: 25840796
  76. Hernández González, J.E.; Hernández Alvarez, L.; Pascutti, P.G.; Valiente, P.A. Predicting binding modes of reversible peptide-based inhibitors of falcipain-2 consistent with structure-activity relationships. Proteins, 2017, 85(9), 1666-1683. doi: 10.1002/prot.25322 PMID: 28543724
  77. Royo, S.; Schirmeister, T.; Kaiser, M.; Jung, S.; Rodríguez, S.; Bautista, J.M.; González, F.V. Antiprotozoal and cysteine proteases inhibitory activity of dipeptidyl enoates. Bioorg. Med. Chem., 2018, 26(16), 4624-4634. doi: 10.1016/j.bmc.2018.07.015 PMID: 30037754
  78. Linington, R.G.; Clark, B.R.; Trimble, E.E.; Almanza, A.; Ureña, L.D.; Kyle, D.E.; Gerwick, W.H. Antimalarial peptides from marine cyanobacteria: Isolation and structural elucidation of gallinamide A. J. Nat. Prod., 2009, 72(1), 14-17. doi: 10.1021/np8003529 PMID: 19161344
  79. Stolze, S.C.; Deu, E.; Kaschani, F.; Li, N.; Florea, B.I.; Richau, K.H.; Colby, T.; van der Hoorn, R.A.L.; Overkleeft, H.S.; Bogyo, M.; Kaiser, M. The antimalarial natural product symplostatin 4 is a nanomolar inhibitor of the food vacuole falcipains. Chem. Biol., 2012, 19(12), 1546-1555. doi: 10.1016/j.chembiol.2012.09.020 PMID: 23261598
  80. Conroy, T.; Guo, J.T.; Elias, N.; Cergol, K.M.; Gut, J.; Legac, J.; Khatoon, L.; Liu, Y.; McGowan, S.; Rosenthal, P.J.; Hunt, N.H.; Payne, R.J. Synthesis of gallinamide A analogues as potent falcipain inhibitors and antimalarials. J. Med. Chem., 2014, 57(24), 10557-10563. doi: 10.1021/jm501439w PMID: 25412465
  81. Stoye, A.; Juillard, A.; Tang, A.H.; Legac, J.; Gut, J.; White, K.L.; Charman, S.A.; Rosenthal, P.J.; Grau, G.E.R.; Hunt, N.H.; Payne, R.J. Falcipain inhibitors based on the natural product gallinamide a are potent in vitro and in vivo antimalarials. J. Med. Chem., 2019, 62(11), 5562-5578. doi: 10.1021/acs.jmedchem.9b00504 PMID: 31062592
  82. Aratikatla, E.K.; Kalamuddin, M.; Rana, K.C.; Datta, G.; Asad, M.; Sundararaman, S.; Malhotra, P.; Mohmmed, A.; Bhattacharya, A.K. Combating multi-drug resistant malaria parasite by inhibiting falcipain-2 and heme-polymerization: Artemisinin-peptidyl vinyl phosphonate hybrid molecules as new antimalarials. Eur. J. Med. Chem., 2021, 220, 113454. doi: 10.1016/j.ejmech.2021.113454 PMID: 33901900
  83. Schulz, F.; Gelhaus, C.; Degel, B.; Vicik, R.; Heppner, S.; Breuning, A.; Leippe, M.; Gut, J.; Rosenthal, P.J.; Schirmeister, T. Screening of protease inhibitors as antiplasmodial agents. Part I: Aziridines and epoxides. ChemMedChem, 2007, 2(8), 1214-1224. doi: 10.1002/cmdc.200700070 PMID: 17562535
  84. Li Petri, G.; Di Martino, S.; De Rosa, M. Peptidomimetics: An overview of recent medicinal chemistry efforts toward the discovery of novel small molecule inhibitors. J. Med. Chem., 2022, 65(11), 7438-7475. doi: 10.1021/acs.jmedchem.2c00123 PMID: 35604326
  85. Micale, N.; Kozikowski, A.P.; Ettari, R.; Grasso, S.; Zappalà, M.; Jeong, J.J.; Kumar, A.; Hanspal, M.; Chishti, A.H. Novel peptidomimetic cysteine protease inhibitors as potential antimalarial agents. J. Med. Chem., 2006, 49(11), 3064-3067. doi: 10.1021/jm060405f PMID: 16722625
  86. Ettari, R.; Nizi, E.; Di Francesco, M.E.; Dude, M.A.; Pradel, G.; Vičík, R.; Schirmeister, T.; Micale, N.; Grasso, S.; Zappalà, M. Development of peptidomimetics with a vinyl sulfone warhead as irreversible falcipain-2 inhibitors. J. Med. Chem., 2008, 51(4), 988-996. doi: 10.1021/jm701141u PMID: 18232656
  87. Ettari, R.; Nizi, E.; Di Francesco, M.E.; Micale, N.; Grasso, S.; Zappalà, M.; Vičík, R.; Schirmeister, T. Nonpeptidic vinyl and allyl phosphonates as falcipain-2 inhibitors. ChemMedChem, 2008, 3(7), 1030-1033. doi: 10.1002/cmdc.200800050 PMID: 18428116
  88. Ettari, R.; Micale, N.; Schirmeister, T.; Gelhaus, C.; Leippe, M.; Nizi, E.; Di Francesco, M.E.; Grasso, S.; Zappalà, M. Novel peptidomimetics containing a vinyl ester moiety as highly potent and selective falcipain-2 inhibitors. J. Med. Chem., 2009, 52(7), 2157-2160. doi: 10.1021/jm900047j PMID: 19296600
  89. Ettari, R.; Pinto, A.; Tamborini, L.; Angelo, I.C.; Grasso, S.; Zappalà, M.; Capodicasa, N.; Yzeiraj, L.; Gruber, E.; Aminake, M.N.; Pradel, G.; Schirmeister, T.; De Micheli, C.; Conti, P. Synthesis and biological evaluation of papain-family cathepsin L-like cysteine protease inhibitors containing a 1,4-benzodiazepine scaffold as antiprotozoal agents. ChemMedChem, 2014, 9(8) doi: 10.1002/cmdc.201402079 PMID: 24919925
  90. Verissimo, E.; Berry, N.; Gibbons, P.; Cristiano, M.L.S.; Rosenthal, P.J.; Gut, J.; Ward, S.A.; O’Neill, P.M. Design and synthesis of novel 2-pyridone peptidomimetic falcipain 2/3 inhibitors. Bioorg. Med. Chem. Lett., 2008, 18(14), 4210-4214. doi: 10.1016/j.bmcl.2008.05.068 PMID: 18554905
  91. Oliveira, R.; Guedes, R.C.; Meireles, P.; Albuquerque, I.S.; Gonçalves, L.M.; Pires, E.; Bronze, M.R.; Gut, J.; Rosenthal, P.J.; Prudêncio, M.; Moreira, R.; O’Neill, P.M.; Lopes, F. Tetraoxane-pyrimidine nitrile hybrids as dual stage antimalarials. J. Med. Chem., 2014, 57(11), 4916-4923. doi: 10.1021/jm5004528 PMID: 24824551
  92. Weldon, D.J.; Shah, F.; Chittiboyina, A.G.; Sheri, A.; Chada, R.R.; Gut, J.; Rosenthal, P.J.; Shivakumar, D.; Sherman, W.; Desai, P.; Jung, J.C.; Avery, M.A. Synthesis, biological evaluation, hydration site thermodynamics, and chemical reactivity analysis of α-keto substituted peptidomimetics for the inhibition of Plasmodium falciparum. Bioorg. Med. Chem. Lett., 2014, 24(5), 1274-1279. doi: 10.1016/j.bmcl.2014.01.062 PMID: 24507921
  93. Musyoka, T.M.; Kanzi, A.M.; Lobb, K.A.; Tastan Bishop, Ö. Analysis of non-peptidic compounds as potential malarial inhibitors against Plasmodial cysteine proteases via integrated virtual screening workflow. J. Biomol. Struct. Dyn., 2016, 34(10), 2084-2101. doi: 10.1080/07391102.2015.1108231 PMID: 26471975
  94. Bertoldo, J.B.; Chiaradia-Delatorre, L.D.; Mascarello, A.; Leal, P.C.; Cordeiro, M.N.S.; Nunes, R.J.; Sarduy, E.S.; Rosenthal, P.J.; Terenzi, H. Synthetic compounds from an in house library as inhibitors of falcipain-2 from Plasmodium falciparum. J. Enzyme Inhib. Med. Chem., 2015, 30(2), 299-307. doi: 10.3109/14756366.2014.920839 PMID: 24964346
  95. Musyoka, T.M.; Kanzi, A.M.; Lobb, K.A.; Tastan Bishop, Ö. Structure based docking and molecular dynamic studies of plasmodial cysteine proteases against a South African natural compound and its analogs. Sci. Rep., 2016, 6(1), 23690. doi: 10.1038/srep23690 PMID: 27030511
  96. Wang, L.; Zhang, S.; Zhu, J.; Zhu, L.; Liu, X.; Shan, L.; Huang, J.; Zhang, W.; Li, H. Identification of diverse natural products as falcipain-2 inhibitors through structure-based virtual screening. Bioorg. Med. Chem. Lett., 2014, 24(5), 1261-1264. doi: 10.1016/j.bmcl.2014.01.074 PMID: 24530004
  97. Shah, F.; Mukherjee, P.; Gut, J.; Legac, J.; Rosenthal, P.J.; Tekwani, B.L.; Avery, M.A. Identification of novel malarial cysteine protease inhibitors using structure-based virtual screening of a focused cysteine protease inhibitor library. J. Chem. Inf. Model., 2011, 51(4), 852-864. doi: 10.1021/ci200029y PMID: 21428453
  98. Hernández-González, J.E.; Salas-Sarduy, E.; Hernández Ramírez, L.F.; Pascual, M.J.; Álvarez, D.E.; Pabón, A.; Leite, V.B.P.; Pascutti, P.G.; Valiente, P.A. Identification of (4-(9H-fluoren-9-yl) piperazin-1-yl) methanone derivatives as falcipain 2 inhibitors active against Plasmodium falciparum cultures. Biochim. Biophys. Acta, Gen. Subj., 2018, 1862(12), 2911-2923. doi: 10.1016/j.bbagen.2018.09.015 PMID: 30253205
  99. Zhu, J.; Chen, T.; Liu, J.; Ma, R.; Lu, W.; Huang, J.; Li, H.; Li, J.; Jiang, H. 2-(3,4-dihydro-4-oxothieno2,3-d pyrimidin-2-ylthio) acetamides as a new class of falcipain-2 inhibitors. 3. design, synthesis and biological evaluation. Molecules, 2009, 14(2), 785-797. doi: 10.3390/molecules14020785 PMID: 19223827
  100. Liu, Y.; Cui, K.; Lu, W.; Luo, W.; Wang, J.; Huang, J.; Guo, C. Synthesis and antimalarial activity of novel dihydro-artemisinin derivatives. Molecules, 2011, 16(6), 4527-4538. doi: 10.3390/molecules16064527 PMID: 21629181
  101. Liu, Y.; Lu, W.Q.; Cui, K.Q.; Luo, W.; Wang, J.; Guo, C. Synthesis and biological activities of novel artemisinin derivatives as cysteine protease falcipain-2 inhibitors. Arch. Pharm. Res., 2012, 35(9), 1525-1531. doi: 10.1007/s12272-012-0902-4 PMID: 23054708
  102. Rana, D.; Kalamuddin, M.; Sundriyal, S.; Jaiswal, V.; Sharma, G.; Das Sarma, K.; Sijwali, P.S.; Mohmmed, A.; Malhotra, P.; Mahindroo, N. Identification of antimalarial leads with dual falcipain-2 and falcipain-3 inhibitory activity. Bioorg. Med. Chem., 2020, 28(1), 115155. doi: 10.1016/j.bmc.2019.115155 PMID: 31744777
  103. Batra, S.; Sabnis, Y.A.; Rosenthal, P.J.; Avery, M.A. Structure-based approach to falcipain-2 inhibitors: Synthesis and biological evaluation of 1,6,7-trisubstituted dihydroisoquinolines and isoquinolines. Bioorg. Med. Chem., 2003, 11(10), 2293-2299. doi: 10.1016/S0968-0896(03)00117-2 PMID: 12713840
  104. Sharma, K.; Shrivastava, A.; Mehra, R.N.; Deora, G.S.; Alam, M.M.; Zaman, M.S.; Akhter, M. Synthesis of novel benzimidazole acrylonitriles for inhibition of Plasmodium falciparum growth by dual target inhibition. Arch. Pharm., 2018, 351(1), 1700251. doi: 10.1002/ardp.201700251 PMID: 29227011
  105. Singh, A.K.; Rajendran, V.; Pant, A.; Ghosh, P.C.; Singh, N.; Latha, N.; Garg, S.; Pandey, K.C.; Singh, B.K.; Rathi, B. Design, synthesis and biological evaluation of functionalized phthalimides: A new class of antimalarials and inhibitors of falcipain-2, a major hemoglobinase of malaria parasite. Bioorg. Med. Chem., 2015, 23(8), 1817-1827. doi: 10.1016/j.bmc.2015.02.029 PMID: 25766631
  106. Klayman, D.L.; Bartosevich, J.F.; Griffin, T.S.; Mason, C.J.; Scovill, J.P. 2-Acetylpyridine thiosemicarbazones. 1. A new class of potential antimalarial agents. J. Med. Chem., 1979, 22(7), 855-862. doi: 10.1021/jm00193a020 PMID: 376848
  107. Greenbaum, D.C.; Mackey, Z.; Hansell, E.; Doyle, P.; Gut, J.; Caffrey, C.R.; Lehrman, J.; Rosenthal, P.J.; McKerrow, J.H.; Chibale, K. Synthesis and structure-activity relationships of parasiticidal thiosemicarbazone cysteine protease inhibitors against Plasmodium falciparum, Trypanosoma brucei, and Trypanosoma cruzi. J. Med. Chem., 2004, 47(12), 3212-3219. doi: 10.1021/jm030549j PMID: 15163200
  108. Chipeleme, A.; Gut, J.; Rosenthal, P.J.; Chibale, K. Synthesis and biological evaluation of phenolic Mannich bases of benzaldehyde and (thio)semicarbazone derivatives against the cysteine protease falcipain-2 and a chloroquine resistant strain of Plasmodium falciparum. Bioorg. Med. Chem., 2007, 15(1), 273-282. doi: 10.1016/j.bmc.2006.09.055 PMID: 17052908
  109. Chiyanzu, I.; Hansell, E.; Gut, J.; Rosenthal, P.J.; McKerrow, J.H.; Chibale, K. Synthesis and evaluation of isatins and thiosemicarbazone derivatives against cruzain, falcipain-2 and rhodesain. Bioorg. Med. Chem. Lett., 2003, 13(20), 3527-3530. doi: 10.1016/S0960-894X(03)00756-X PMID: 14505663
  110. Ehmke, V.; Heindl, C.; Rottmann, M.; Freymond, C.; Schweizer, W.B.; Brun, R.; Stich, A.; Schirmeister, T.; Diederich, F. Potent and selective inhibition of cysteine proteases from Plasmodium falciparum and Trypanosoma brucei. ChemMedChem, 2011, 6(2), 273-278. doi: 10.1002/cmdc.201000449 PMID: 21275051
  111. Schirmeister, T.; Kaeppler, U. Non-peptidic inhibitors of cysteine proteases. Mini Rev. Med. Chem., 2003, 3(4), 361-373. doi: 10.2174/1389557033488079 PMID: 12678829
  112. Liu, M.; Wilairat, P.; Go, M.L. Antimalarial alkoxylated and hydroxylated chalcones (corrected): Structure-activity relationship analysis. J. Med. Chem., 2001, 44(25), 4443-4452. doi: 10.1021/jm0101747 PMID: 11728189
  113. Li, R.; Kenyon, G.L.; Cohen, F.E.; Chen, X.; Gong, B.; Dominguez, J.N.; Davidson, E.; Kurzban, G.; Miller, R.E.; Nuzum, E.O.; Rosenthal, P.J.; McKerrow, J.H. In vitro antimalarial activity of chalcones and their derivatives. J. Med. Chem., 1995, 38(26), 5031-5037. doi: 10.1021/jm00026a010 PMID: 8544179
  114. Domínguez, J.N.; León, C.; Rodrigues, J.; Gamboa de Domínguez, N.; Gut, J.; Rosenthal, P.J. Synthesis and evaluation of new antimalarial phenylurenyl chalcone derivatives. J. Med. Chem., 2005, 48(10), 3654-3658. doi: 10.1021/jm058208o PMID: 15887974
  115. Chen, M.; Theander, T.G.; Christensen, S.B.; Hviid, L.; Zhai, L.; Kharazmi, A.; Licochalcone, A. Licochalcone A, a new antimalarial agent, inhibits in vitro growth of the human malaria parasite Plasmodium falciparum and protects mice from P. yoelii infection. Antimicrob. Agents Chemother., 1994, 38(7), 1470-1475. doi: 10.1128/AAC.38.7.1470 PMID: 7979274
  116. Chen, M.; Christensen, S.B.Ø.; Zhai, L.; Rasmussen, M.H.; Theander, T.G.; FrØkjaer, S.; Steffansen, B.; Davidsen, J.; Kharazmi, A. The novel oxygenated chalcone, 2,4-dimethoxy-4′-butoxychalcone, exhibits potent activity against human malaria parasite Plasmodium falciparumin vitro and rodent parasites Plasmodium berghei and Plasmodium yoeliiin vivo. J. Infect. Dis., 1997, 176(5), 1327-1333. doi: 10.1086/514129 PMID: 9359735
  117. Shah, F.; Wu, Y.; Gut, J.; Pedduri, Y.; Legac, J.; Rosenthal, P.J.; Avery, M.A. Design, synthesis and biological evaluation of novel benzothiazole and triazole analogs as falcipain inhibitors. MedChemComm, 2011, 2(12), 1201-1207. doi: 10.1039/c1md00129a
  118. Singh, A.; Kalamuddin, M.; Mohmmed, A.; Malhotra, P.; Hoda, N. Quinoline-triazole hybrids inhibit falcipain-2 and arrest the development of Plasmodium falciparum at the trophozoite stage. RSC Advances, 2019, 9(67), 39410-39421. doi: 10.1039/C9RA06571G PMID: 35540629
  119. Schmidt, I.; Pradel, G.; Sologub, L.; Golzmann, A.; Ngwa, C.J.; Kucharski, A.; Schirmeister, T.; Holzgrabe, U. Bistacrine derivatives as new potent antimalarials. Bioorg. Med. Chem., 2016, 24(16), 3636-3642. doi: 10.1016/j.bmc.2016.06.003 PMID: 27316542
  120. Schmidt, I.; Göllner, S.; Fuß, A.; Stich, A.; Kucharski, A.; Schirmeister, T.; Katzowitsch, E.; Bruhn, H.; Miliu, A.; Krauth-Siegel, R.L.; Holzgrabe, U. Bistacrines as potential antitrypanosomal agents. Bioorg. Med. Chem., 2017, 25(16), 4526-4531. doi: 10.1016/j.bmc.2017.06.051 PMID: 28698054
  121. Huang, H.; Lu, W.; Li, X.; Cong, X.; Ma, H.; Liu, X.; Zhang, Y.; Che, P.; Ma, R.; Li, H.; Shen, X.; Jiang, H.; Huang, J.; Zhu, J. Design and synthesis of small molecular dual inhibitor of falcipain-2 and dihydrofolate reductase as antimalarial agent. Bioorg. Med. Chem. Lett., 2012, 22(2), 958-962. doi: 10.1016/j.bmcl.2011.12.011 PMID: 22192590
  122. Chen, W.; Huang, Z.; Wang, W.; Mao, F.; Guan, L.; Tang, Y.; Jiang, H.; Li, J.; Huang, J.; Jiang, L.; Zhu, J. Discovery of new antimalarial agents: Second-generation dual inhibitors against FP-2 and PfDHFR via fragments assembely. Bioorg. Med. Chem., 2017, 25(24), 6467-6478. doi: 10.1016/j.bmc.2017.10.017 PMID: 29111368
  123. Bhat, A.S.; Dustin Schaeffer, R.; Kinch, L.; Medvedev, K.E.; Grishin, N.V. Recent advances suggest increased influence of selective pressure in allostery. Curr. Opin. Struct. Biol., 2020, 62, 183-188. doi: 10.1016/j.sbi.2020.02.004 PMID: 32302874
  124. Wagner, J.R.; Lee, C.T.; Durrant, J.D.; Malmstrom, R.D.; Feher, V.A.; Amaro, R.E. Emerging computational methods for the rational discovery of allosteric drugs. Chem. Rev., 2016, 116(11), 6370-6390. doi: 10.1021/acs.chemrev.5b00631 PMID: 27074285
  125. Novinec, M.; Korenč, M.; Caflisch, A.; Ranganathan, R.; Lenarčič, B.; Baici, A. A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods. Nat. Commun., 2014, 5(1), 3287. doi: 10.1038/ncomms4287 PMID: 24518821
  126. Novinec, M.; Lenarčič, B.; Baici, A. Probing the activity modification space of the cysteine peptidase cathepsin K with novel allosteric modifiers. PLoS One, 2014, 9(9), e106642. doi: 10.1371/journal.pone.0106642 PMID: 25184245
  127. Novinec, M.; Rebernik, M.; Lenarčič, B. An allosteric site enables fine-tuning of cathepsin K by diverse effectors. FEBS Lett., 2016, 590(24), 4507-4518. doi: 10.1002/1873-3468.12495 PMID: 27859061
  128. Marques, A.F.; Esser, D.; Rosenthal, P.J.; Kassack, M.U.; Lima, L.M.T.R. Falcipain-2 inhibition by suramin and suramin analogues. Bioorg. Med. Chem., 2013, 21(13), 3667-3673. doi: 10.1016/j.bmc.2013.04.047 PMID: 23680445
  129. Marques, A.F.; Gomes, P.S.F.C.; Oliveira, P.L.; Rosenthal, P.J.; Pascutti, P.G.; Lima, L.M.T.R. Allosteric regulation of the Plasmodium falciparum cysteine protease falcipain-2 by heme. Arch. Biochem. Biophys., 2015, 573, 92-99. doi: 10.1016/j.abb.2015.03.007 PMID: 25791019
  130. Okeke, C.J.; Musyoka, T.M.; Sheik Amamuddy, O.; Barozi, V.; Tastan Bishop, Ö. Allosteric pockets and dynamic residue network hubs of falcipain 2 in mutations including those linked to artemisinin resistance. Comput. Struct. Biotechnol. J., 2021, 19, 5647-5666. doi: 10.1016/j.csbj.2021.10.011 PMID: 34745456
  131. Hernández González, J.E.; Hernández Alvarez, L.; Pascutti, P.G.; Leite, V.B.P. Prediction of noncompetitive inhibitor binding mode reveals promising site for allosteric modulation of falcipain-2. J. Phys. Chem. B, 2019, 123(34), 7327-7342. doi: 10.1021/acs.jpcb.9b05021 PMID: 31366200
  132. Hernández González, J.E.; Salas-Sarduy, E.; Hernández Alvarez, L.; Barreto Gomes, D.E.; Pascutti, P.G.; Oostenbrink, C.; Leite, V.B.P. In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2. J. Comput. Aided Mol. Des., 2021, 35(10), 1067-1079. doi: 10.1007/s10822-021-00420-7 PMID: 34617191
  133. Alberca, L.N.; Chuguransky, S.R.; Álvarez, C.L.; Talevi, A.; Salas-Sarduy, E. In silico guided drug repurposing: Discovery of new competitive and non-competitive inhibitors of falcipain-2. Front Chem., 2019, 7, 534. doi: 10.3389/fchem.2019.00534 PMID: 31448257
  134. Hernández González, J.E.; Alberca, L.N.; Masforrol González, Y.; Reyes Acosta, O.; Talevi, A.; Salas-Sarduy, E. Tetracycline derivatives inhibit plasmodial cysteine protease falcipain-2 through binding to a distal allosteric site. J. Chem. Inf. Model., 2022, 62(1), 159-175. doi: 10.1021/acs.jcim.1c01189 PMID: 34962803
  135. Pant, A.; Kumar, R.; Wani, N.A.; Verma, S.; Sharma, R.; Pande, V.; Saxena, A.K.; Dixit, R.; Rai, R.; Pandey, K.C. Allosteric site inhibitor disrupting auto-processing of malarial cysteine proteases. Sci. Rep., 2018, 8(1), 16193. doi: 10.1038/s41598-018-34564-8 PMID: 30385827
  136. Stjernschantz, E.; Oostenbrink, C. Improved ligand-protein binding affinity predictions using multiple binding modes. Biophys. J., 2010, 98(11), 2682-2691. doi: 10.1016/j.bpj.2010.02.034 PMID: 20513413
  137. Lindström, A.; Edvinsson, L.; Johansson, A.; Andersson, C.D.; Andersson, I.E.; Raubacher, F.; Linusson, A. Postprocessing of docked protein-ligand complexes using implicit solvation models. J. Chem. Inf. Model., 2011, 51(2), 267-282. doi: 10.1021/ci100354x PMID: 21309544
  138. Clark, A.J.; Tiwary, P.; Borrelli, K.; Feng, S.; Miller, E.B.; Abel, R.; Friesner, R.A.; Berne, B.J. Prediction of protein–ligand binding poses via a combination of induced fit docking and metadynamics simulations. J. Chem. Theory Comput., 2016, 12(6), 2990-2998. doi: 10.1021/acs.jctc.6b00201 PMID: 27145262
  139. Desai, P.V.; Patny, A.; Sabnis, Y.; Tekwani, B.; Gut, J.; Rosenthal, P.; Srivastava, A.; Avery, M. Identification of novel parasitic cysteine protease inhibitors using virtual screening. 1. The ChemBridge database. J. Med. Chem., 2004, 47(26), 6609-6615. doi: 10.1021/jm0493717 PMID: 15588096
  140. Sharma, R.K.; Younis, Y.; Mugumbate, G.; Njoroge, M.; Gut, J.; Rosenthal, P.J.; Chibale, K. Synthesis and structure–activity-relationship studies of thiazolidinediones as antiplasmodial inhibitors of the Plasmodium falciparum cysteine protease falcipain-2. Eur. J. Med. Chem., 2015, 90, 507-518. doi: 10.1016/j.ejmech.2014.11.061 PMID: 25486422
  141. Desai, P.V.; Patny, A.; Gut, J.; Rosenthal, P.J.; Tekwani, B.; Srivastava, A.; Avery, M. Identification of novel parasitic cysteine protease inhibitors by use of virtual screening. 2. The available chemical directory. J. Med. Chem., 2006, 49(5), 1576-1584. doi: 10.1021/jm0505765 PMID: 16509575
  142. Uddin, A.; Gupta, S.; Mohammad, T.; Shahi, D.; Hussain, A.; Alajmi, M.F.; El-Seedi, H.R.; Hassan, I.; Singh, S.; Abid, M. Target-based virtual screening of natural compounds identifies a potent antimalarial with selective falcipain-2 inhibitory activity. Front. Pharmacol., 2022, 13, 850176. doi: 10.3389/fphar.2022.850176 PMID: 35462917
  143. Friesner, R.A.; Banks, J.L.; Murphy, R.B.; Halgren, T.A.; Klicic, J.J.; Mainz, D.T.; Repasky, M.P.; Knoll, E.H.; Shelley, M.; Perry, J.K.; Shaw, D.E.; Francis, P.; Shenkin, P.S. Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem., 2004, 47(7), 1739-1749. doi: 10.1021/jm0306430 PMID: 15027865
  144. Li, H.; Li, C.; Gui, C.; Luo, X.; Chen, K.; Shen, J.; Wang, X.; Jiang, H. GAsDock: A new approach for rapid flexible docking based on an improved multi-population genetic algorithm. Bioorganic Med. Chem., 2004, 14(18), 4671-4676. doi: 10.1016/j.bmcl.2004.06.091
  145. Wang, L.; Li, X.; Zhang, S.; Lu, W.; Liao, S.; Liu, X.; Shan, L.; Shen, X.; Jiang, H.; Zhang, W.; Huang, J.; Li, H. Natural products as a gold mine for selective matrix metalloproteinases inhibitors. Bioorg. Med. Chem., 2012, 20(13), 4164-4171. doi: 10.1016/j.bmc.2012.04.063 PMID: 22658537
  146. Kubinyi, H. QSAR and 3D QSAR in drug design Part 1: methodology. Drug Discov. Today, 1997, 2(11), 457-467. doi: 10.1016/S1359-6446(97)01079-9
  147. Gálvez, J.; Gálvez-Llompart, M.; García-Domenech, R. Advances in Mathematical Chemistry and Applications; Basak, S.C.; Restrepo, G.; Villaveces, J.L., Eds.; Elsevier and Bentham Science Publisher, 2015, 1, pp. 161-195.
  148. Chintakrindi, A.S.; Shaikh, M.S.; Coutinho, E.C. De novo design of 7-aminocoumarin derivatives as novel falcipain-3 inhibitors. J. Mol. Model., 2012, 18(4), 1481-1493. doi: 10.1007/s00894-011-1177-2 PMID: 21785935
  149. Potshangbam, A.M.; Tanneeru, K.; Reddy, B.M.; Guruprasad, L. 3D-QSAR and molecular docking studies of 2-pyrimidinecarbonitrile derivatives as inhibitors against falcipain-3. Bioorg. Med. Chem. Lett., 2011, 21(23), 7219-7223. doi: 10.1016/j.bmcl.2011.09.107 PMID: 22018459
  150. Teixeira, C.; Gomes, J.R.B.; Couesnon, T.; Gomes, P. Molecular docking and 3D-quantitative structure activity relationship analyses of peptidyl vinyl sulfones: Plasmodium falciparum cysteine proteases inhibitors. J. Comput. Aided Mol. Des., 2011, 25(8), 763-775. doi: 10.1007/s10822-011-9459-4 PMID: 21786172
  151. Wang, J.; Li, Y.; Yang, Y.; Zhang, S.; Yang, L. Profiling the structural determinants of heteroarylnitrile scaffold-based derivatives as falcipain-2 inhibitors by in silico methods. Curr. Med. Chem., 2013, 20(15), 2032-2042. doi: 10.2174/0929867311320150008 PMID: 23410155
  152. Wang, J.; Li, F.; Li, Y.; Yang, Y.; Zhang, S.; Yang, L. Structural features of falcipain-3 inhibitors: An in silico study. Mol. Biosyst., 2013, 9(9), 2296-2310. doi: 10.1039/c3mb70105k PMID: 23765034
  153. Thillainayagam, M.; Anbarasu, A.; Ramaiah, S. Comparative molecular field analysis and molecular docking studies on novel aryl chalcone derivatives against an important drug target cysteine protease in Plasmodium falciparum. J. Theor. Biol., 2016, 403, 110-128. doi: 10.1016/j.jtbi.2016.05.019 PMID: 27185536
  154. Wolber, G.; Langer, T. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J. Chem. Inf. Model., 2005, 45(1), 160-169. doi: 10.1021/ci049885e PMID: 15667141
  155. Seidel, T.; Bryant, S.D.; Ibis, G.; Poli, G.; Langer, T. 3D pharmacophore modeling techniques in computer-aided molecular design using LigandScout. J. Tutorials Chemoinform, 2017, 281, 279-309. doi: 10.1002/9781119161110.ch20
  156. Allangba, K.N.G.P.G.; Keita, M.; Kre N’Guessan, R.; Megnassan, E.; Frecer, V.; Miertus, S. Virtual design of novel Plasmodium falciparum cysteine protease falcipain-2 hybrid lactone–chalcone and isatin–chalcone inhibitors probing the S2 active site pocket. J. Enzyme Inhib. Med. Chem., 2019, 34(1), 547-561. doi: 10.1080/14756366.2018.1564288 PMID: 30696325
  157. Southall, N.T.; Dill, K.A.; Haymet, A.D.J. A view of the hydrophobic effect. J. Phys. Chem. B, 2002, 106(3), 521-533. doi: 10.1021/jp015514e
  158. Snyder, P.W.; Mecinović, J.; Moustakas, D.T.; Thomas, S.W., III; Harder, M.; Mack, E.T.; Lockett, M.R.; Héroux, A.; Sherman, W.; Whitesides, G.M. Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase. Proc. Natl. Acad. Sci. USA, 2011, 108(44), 17889-17894. doi: 10.1073/pnas.1114107108 PMID: 22011572
  159. García-Sosa, A.T. Hydration properties of ligands and drugs in protein binding sites: Tightly-bound, bridging water molecules and their effects and consequences on molecular design strategies. J. Chem. Inf. Model., 2013, 53(6), 1388-1405. doi: 10.1021/ci3005786 PMID: 23662606
  160. Young, T.; Abel, R.; Kim, B.; Berne, B.J.; Friesner, R.A. Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding. Proc. Natl. Acad. Sci. USA, 2007, 104(3), 808-813. doi: 10.1073/pnas.0610202104 PMID: 17204562
  161. Abel, R.; Young, T.; Farid, R.; Berne, B.J.; Friesner, R.A. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. J. Am. Chem. Soc., 2008, 130(9), 2817-2831. doi: 10.1021/ja0771033 PMID: 18266362
  162. Shah, F.; Gut, J.; Legac, J.; Shivakumar, D.; Sherman, W.; Rosenthal, P.J.; Avery, M.A. Computer-aided drug design of falcipain inhibitors: Virtual screening, structure-activity relationships, hydration site thermodynamics, and reactivity analysis. J. Chem. Inf. Model., 2012, 52(3), 696-710. doi: 10.1021/ci2005516 PMID: 22332946
  163. Homeyer, N.; Gohlke, H. Free energy calculations by the molecular mechanics poisson−boltzmann surface area method. Mol. Inform., 2012, 31(2), 114-122. doi: 10.1002/minf.201100135 PMID: 27476956
  164. Hernández González, J.E.; Hernández Alvarez, L.; Leite, V.B.P.; Pascutti, P.G. Water bridges play a key role in affinity and selectivity for malarial protease falcipain-2. J. Chem. Inf. Model., 2020, 60(11), 5499-5512. doi: 10.1021/acs.jcim.0c00294 PMID: 32634311
  165. Pérez, B.C.; Teixeira, C.; Figueiras, M.; Gut, J.; Rosenthal, P.J.; Gomes, J.R.B.; Gomes, P. Novel cinnamic acid/4-aminoquinoline conjugates bearing non-proteinogenic amino acids: Towards the development of potential dual action antimalarials. Eur. J. Med. Chem., 2012, 54, 887-899. doi: 10.1016/j.ejmech.2012.05.022 PMID: 22683112
  166. Jumper, J.; Evans, R.; Pritzel, A.; Green, T.; Figurnov, M.; Ronneberger, O.; Tunyasuvunakool, K.; Bates, R.; Žídek, A.; Potapenko, A.; Bridgland, A.; Meyer, C.; Kohl, S.A.A.; Ballard, A.J.; Cowie, A.; Romera-Paredes, B.; Nikolov, S.; Jain, R.; Adler, J.; Back, T.; Petersen, S.; Reiman, D.; Clancy, E.; Zielinski, M.; Steinegger, M.; Pacholska, M.; Berghammer, T.; Bodenstein, S.; Silver, D.; Vinyals, O.; Senior, A.W.; Kavukcuoglu, K.; Kohli, P.; Hassabis, D. Highly accurate protein structure prediction with AlphaFold. Nature, 2021, 596(7873), 583-589. doi: 10.1038/s41586-021-03819-2 PMID: 34265844
  167. Gentile, F.; Yaacoub, J.C.; Gleave, J.; Fernandez, M.; Ton, A.T.; Ban, F.; Stern, A.; Cherkasov, A. Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking. Nat. Protoc., 2022, 17(3), 672-697. doi: 10.1038/s41596-021-00659-2 PMID: 35121854
  168. Mugumbate, G.; Newton, A.S.; Rosenthal, P.J.; Gut, J.; Moreira, R.; Chibale, K.; Guedes, R.C. Novel anti-Plasmodial hits identified by virtual screening of the ZINC database. J. Comput. Aided Mol. Des., 2013, 27(10), 859-871. doi: 10.1007/s10822-013-9685-z PMID: 24158745
  169. Bajorath, J. Deep machine learning for computer-aided drug design. Front. Drug Discov., 2022, 2, 829043. doi: 10.3389/fddsv.2022.829043
  170. Kumar, A.; Zhang, K.Y.J. Advances in the development of shape similarity methods and their application in drug discovery. Front Chem., 2018, 6, 315. doi: 10.3389/fchem.2018.00315 PMID: 30090808
  171. Bhhatarai, B.; Walters, W.P.; Hop, C.E.C.A.; Lanza, G.; Ekins, S. Opportunities and challenges using artificial intelligence in ADME/Tox. Nat. Mater., 2019, 18(5), 418-422. doi: 10.1038/s41563-019-0332-5 PMID: 31000801

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