title: Identification of novel class of falcipain-2 inhibitors as potential antimalarial agents.
abstract: Falcipain-2 is a papain family cysteine protease and an emerging antimalarial drug target. A pseudo-tripeptide scaffold I was designed using in silico screening tools and the three dimensional structures of falcipain-2, falcipain-3, and papain. This scaffold was investigated at four positions, T1, T2, T3, and T3', with various targeted substitutions to understand the structure-activity relationships. Inhibitor synthesis was accomplished by first obtaining the appropriate dipeptide precursors with common structural components. The pyrrolidine moiety introduced interesting rotamers in a number of synthesized molecules, which was confirmed using high-temperature (1)H NMR spectroscopy. Among the synthesized compounds, 61, 62, and 66 inhibited falcipain-2 activity with inhibition constants (Ki) of 1.8 ± 1.1, 0.2 ± 0.1 and 7.0 ± 2.3 μM, respectively. A group of molecules with a pyrrolidine moiety at the T2 position (68, 70, 71, 72, and 73) also potently inhibited falcipain-2 activity (Ki=0.4 ± 0.1, 2.5 ± 0.5, 3.3 ± 1.1, 7.5 ± 1.9, and 4.6 ± 0.7 μM, respectively). Overall, compound 74 exhibited potent anti-parasitic activity (IC₅₀=0.9 ± 0.1 μM), corresponding with its inhibitory activity against falcipain-2, with a Ki of 1.1 ± 0.1 μM. Compounds 62 and 67 inhibited the growth of the drug resistant parasite Dd2 with better efficacy, and compound 74 exhibited a 7- to 12-fold higher potency against Dd2 and MCamp isolates, than the laboratory strain (3D7). These data suggest that this novel series of compounds should be further investigated as potential antimalarial agents.
authors.affiliation: Center for Molecular Design and Preformulations, and Toronto General Research Institute, University Health Network, #5-356, Toronto Medical Discoveries Tower/MaRS Center, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
authors.forename: Sai Kumar
authors.initials: SK
authors.lastname: Chakka
authors.affiliation: International Centre for Genetic Engineering & Biotechnology, Aruna Asif Ali Marg, New Delhi 100 067, India.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Kalamuddin
authors.affiliation: International Centre for Genetic Engineering & Biotechnology, Aruna Asif Ali Marg, New Delhi 100 067, India.
authors.forename: Srividhya
authors.initials: S
authors.lastname: Sundararaman
authors.affiliation: Center for Molecular Design and Preformulations, and Toronto General Research Institute, University Health Network, #5-356, Toronto Medical Discoveries Tower/MaRS Center, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada.
authors.forename: Lianhu
authors.initials: L
authors.lastname: Wei
authors.affiliation: Center for Molecular Design and Preformulations, and Toronto General Research Institute, University Health Network, #5-356, Toronto Medical Discoveries Tower/MaRS Center, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Pharmacy, Birla Institute of Technology & Science, Pilani, Rajasthan 333031, India.
authors.forename: Sourabh
authors.initials: S
authors.lastname: Mundra
authors.affiliation: Department of Pharmacy, Birla Institute of Technology & Science, Pilani, Rajasthan 333031, India.
authors.forename: Radhakrishnan
authors.initials: R
authors.lastname: Mahesh
authors.affiliation: International Centre for Genetic Engineering & Biotechnology, Aruna Asif Ali Marg, New Delhi 100 067, India. Electronic address: pawanm@icgeb.res.in.
authors.forename: Pawan
authors.initials: P
authors.lastname: Malhotra
authors.affiliation: International Centre for Genetic Engineering & Biotechnology, Aruna Asif Ali Marg, New Delhi 100 067, India. Electronic address: amohd@icgeb.res.in.
authors.forename: Asif
authors.initials: A
authors.lastname: Mohmmed
authors.affiliation: Center for Molecular Design and Preformulations, and Toronto General Research Institute, University Health Network, #5-356, Toronto Medical Discoveries Tower/MaRS Center, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada. Electronic address: lkotra@uhnres.utoronto.ca.
authors.forename: Lakshmi P
authors.initials: LP
authors.lastname: Kotra
mesh_terms: D000818:Animals; D000962:Antimalarials / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D016466:CHO Cells; D049109:Cell Proliferation / Q000187:drug effects; D003412:Cricetulus; D003546:Cysteine Endopeptidases / Q000378:metabolism*; D015853:Cysteine Proteinase Inhibitors / Q000138:chemical synthesis / Q000737:chemistry / Q000145:classification* / Q000494:pharmacology*; D004305:Dose-Response Relationship, Drug; D015195:Drug Design; D004351:Drug Resistance / Q000187:drug effects; D008958:Models, Molecular; D015394:Molecular Structure; D021261:Parasitic Sensitivity Tests; D010963:Plasmodium falciparum / Q000187:drug effects* / Q000201:enzymology* / Q000254:growth & development; D013329:Structure-Activity Relationship
chemical_list: D000962:Antimalarials; D015853:Cysteine Proteinase Inhibitors; D003546:Cysteine Endopeptidases; C416224:falcipain 2
keywords: Anti-parasitic agents; Antimalarial agents; Cysteine proteases; Docking; Falcipain-2 inhibitors; Malaria; Structure–activity relationship