Tetracycline Derivatives Inhibit Plasmodial Cysteine Protease Falcipain-2 through Binding to a Distal Allosteric Site

Author(s)

Gonzalez, Jorge Enrique Hernandez ^[1] ; Alberca, Lucas N. ^[2] ; Gonzalez, Yordanka Masforrol ^[3] ; Acosta, Osvaldo Reyes ^[3] ; Talevi, Alan ^[2] ; Salas-Sarduy, Emir ^[4]

Affiliation

^[1] Univ Estadual Paulista, Inst Biociencias Letras & Ciencias Exatas, Dept Fis, BR-15054000 Sao Jose Do Rio Preto, SP - Brazil

^[2] Univ Nacl La Plata, Dept Biol Sci, Lab Bioact Cpds Res & Dev LIDeB, Exact Sci Coll, B1900ADU, La Plata - Argentina

^[3] Ctr Genet Engn & Biotechnol, Chem & Phys Dept, Havana 10600 - Cuba

^[4] Univ Nacl San Martin, Inst Invest Biotecnol Dr Rodolfo Ugalde, CONICET, San Martin B1650HMP, Buenos Aires, DF - Argentina

• Document type: Journal article
• Source: JOURNAL OF CHEMICAL INFORMATION AND MODELING; DEC 2021.
• Web of Science Citations: 0

Abstract

Allosteric inhibitors regulate enzyme activity from remote and usually specific pockets. As they promise an avenue for less toxic and safer drugs, the identification and characterization of allosteric inhibitors has gained great academic and biomedical interest in recent years. Research on falcipain-2 (FP-2), the major papain-like cysteine hemoglobinase of Plasmodium falciparum, might benefit from this strategy to overcome the low selectivity against human cathepsins shown by active site-directed inhibitors. Encouraged by our previous finding that methacycline inhibits FP2 noncompetitively, here we assessed other five tetracycline derivatives against this target and characterized their inhibition mechanism. As previously shown for methacycline, tetracycline derivatives inhibited FP-2 in a noncompetitive fashion, with Ki values ranging from 121 to 190 mu M. A possible binding to the S ` side of the FP-2 active site, similar to that described by X-ray crystallography (PDB: 6SSZ) for the noncompetitive inhibitor E-chalcone 48 (EC48), was experimentally discarded by kinetic analysis using a large peptidyl substrate spanning the whole active site. By combining lengthy molecular dynamics (MD) simulations that allowed methacycline to diffuse from solution to different FP-2 surface regions and free energy calculations, we predicted the most likely binding mode of the ligand. Of note, the proposed binding pose explains the low differences in Ki values observed for the tested tetracycline derivatives and the calculated binding free energies match the experimental values. Overall, this study has implications for the design of novel allosteric inhibitors against FP-2 and sets the basis for further optimization of the tetracycline scaffold to produce more potent and selective inhibitors. (AU)

• FAPESP's process: 20/10214-1 - Integrated computational and experimental strategies for the inhibition of exfoliative toxins from Staphylococcus aureus
• Grantee: Jorge Enrique Hernández González
• Support Opportunities: Scholarships in Brazil - Post-Doctoral