Pteridine reductase (PTR1): initial structure-activity relationships studies of potential leishmanicidal arylindole derivatives compounds

References

• R.W. Ashford, P. Desjeux, and P. Deraadt, Estimation of population at risk of infection and number of cases of leishmaniasis, Parasitol. Today 8 (2022), pp. 104–105. doi:10.1016/0169-4758(92)90249-2.
   Google Scholar
• S. Burza, S.L. Croft, and M. Boelaert, Leishmaniasis, The Lancet 392 (2018), pp. 951–970. doi:10.1016/S0140-6736(18)31204-2.
   PubMed Web of Science ®Google Scholar
• J. Ruiz-Esmenjaud, E. Torres-Guerrero, M.R. Quintanilla-Cedillo, and J. Ruiz-Esmenjaud, Leishmaniasis: A review, F1000Res. 6 (2017), pp. 750. doi:10.12688/f1000research.11120.1.
   PubMedGoogle Scholar
• Interregional meeting on leishmaniasis among neighbouring endemic countries in the Eastern Mediterranean, African and European regions. Available athttps://www.who.int/publications/i/item/WHO-EM-CTD-081-E.
   Google Scholar
• Manual de vigilância e controle da leishmaniose visceral. Available at https://bvsms.saude.gov.br/bvs/publicacoes/manual_vigilancia_controle_leishmaniose_visceral_1edicao.pdf.
   Google Scholar
• Manual de vigilância da leishmaniose tegumentar. Available at https://bvsms.saude.gov.br/bvs/publicacoes/manual_vigilancia_leishmaniose_tegumentar.pdf.
   Google Scholar
• L. Anversa, M.G.S. Tiburcio, V.B. Richini-Pereira, and L.E. Ramirez, Human leishmaniasis in Brazil: A general review, Rev. Assoc. Med. Bras. 64 (2018), pp. 281–289. doi:10.1590/1806-9282.64.03.281.
   PubMed Web of Science ®Google Scholar
• N.K. Copeland and N.E. Aronson, Leishmaniasis: Treatment updates and clinical practice guidelines review, Curr. Opin. Infect. Dis. 28 (2015), pp. 426–437. doi:10.1097/QCO.0000000000000194.
   PubMed Web of Science ®Google Scholar
• B.S. Mcgwire and A.R. Satoskar, Leishmaniasis: Clinical syndromes and treatment, QMJ 107 (2014), pp. 7–14. doi:10.1093/qjmed/hct116.
   Web of Science ®Google Scholar
• T.L. Blundell, Structure-based drug design, Nature 384 (1996), pp. 23–26.
   PubMed Web of Science ®Google Scholar
• L.G. Ferreira, R.N. dos Santos, G. Oliva, and A.D. Andricopulo, Molecular docking and structure-based drug design strategies, Molecules 20 (2015), pp. 13384–13421. doi:10.3390/molecules200713384.
   PubMed Web of Science ®Google Scholar
• B. Zulfiqar, T.B. Shelper, and V.M. Avery, Leishmaniasis drug discovery: Recent progress and challenges in assay development, Drug. Discov. Today 22 (2017), pp. 1516–1531. doi:10.1016/j.drudis.2017.06.004.
   PubMed Web of Science ®Google Scholar
• D. Gourley, A. Schüttelkopf, G. Leonard, J. Luba, L. Hardy, S. Beverley, and W.N. Hunter, Pteridine reductase mechanism correlates pterin metabolism with drug resistance in trypanosomatid parasites, Nat. Struct. Biol. 8 (2001), pp. 521–525. doi:10.1038/88584.
   PubMedGoogle Scholar
• A. Gaulton, A. Hersey, M. Nowotka, A. Bento, J. Chambers, D. Mendez, P. Mutowo, F. Atkinson, L.J. Bellis, E. Cibrián-Uhalte, M. Davies, N. Dedman, A. Karlsson, M.P. Magariños, J.P. Overington, G. Papadatos, I. Smit, and A.R. Leach, The ChEMBL database in 2017, Nucleic. Acids. Res. 45 (2017), pp. D945–D954. doi:10.1093/nar/gkw1074.
   PubMed Web of Science ®Google Scholar
• S. Lal and T.J. Snape, Send orders of reprints at [email protected] 2-arylindoles: A privileged molecular scaffold with potent, broad-ranging pharma-cological activity, Curr. Med. Chem. 19 (2012), pp. 4828–4837. doi:10.2174/092986712803341449.
   PubMed Web of Science ®Google Scholar
• G. Landi, P. Linciano, G. Tassone, M. Costi, S. Mangani, and C. Pozzi, High-resolution crystal structure of Trypanosoma brucei pteridine reductase 1 in complex with an innovative tricyclic-based inhibitor, Acta Crystallogr. D Struct. Biol. 76 (2020), pp. 558–564. doi:10.1107/S2059798320004891.
   PubMedGoogle Scholar
• B. Nare, L. Hardy, and S. Beverley, The roles of pteridine reductase 1 and dihydrofolate reductase-thymidylate synthase in pteridine metabolism in the protozoan parasite Leishmania major, J. Biol. Chem. 272 (1997), pp. 13883–13891. doi:10.1074/jbc.272.21.13883.
   PubMed Web of Science ®Google Scholar
• A. Schüttelkopf, L. Hardy, S. Beverley, and W. Hunter, Structures of Leishmania major pteridine reductase complexes reveal the active site features important for ligand binding and to guide inhibitor design, J. Mol. Biol. 352 (2005), pp. 105–116. doi:10.1016/j.jmb.2005.06.076.
   PubMed Web of Science ®Google Scholar
• M. Taha, I. Uddin, M. Gollapalli, N. Almandil, F. Rahim, R.K. Farooq, M. Nawaz, M. Ibrahim, M.A. Alqahtani, Y.A. Bamarouf, and M. Selvaraj, Synthesis, anti-leishmanial and molecular docking study of bis-indole derivatives, BMC Chem.13 (2019), pp. 102. doi:10.1186/s13065-019-0617-4.
   PubMed Web of Science ®Google Scholar
• Protein Data Bank, PDB, Available at https://www.rcsb.org.
   Google Scholar
• EMBL’s European bioinformatics institute (EMBL-EBI), PROCHECK; software available at https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/.
   Google Scholar
• H. Ong, N. Sienkiewicz, S. Wyllie, and A. Fairlamb, Dissecting the metabolic roles of pteridine reductase 1 in Trypanosoma brucei and Leishmania major, J. Biol. Chem. 286 (2011), pp. 10429–10438. doi:10.1074/jbc.M110.209593.
   PubMed Web of Science ®Google Scholar
• L. Tulloch, V. Martini, J. Iulek, J. Huggan, J. Lee, C. Gibson, C.L. Gibson, T.K. Smith, C.J. Suckling, and W.N. Hunter, Structure-based design of pteridine reductase inhibitors targeting African sleeping sickness and the leishmaniases, J. Med. Chem. 53 (2010), pp. 221–229. doi:10.1021/jm901059x.
   PubMed Web of Science ®Google Scholar
• Accelrys Software Inc, Discovery studio 2019; software available at https://discover.3ds.com/discovery-studio-visualizer-download.
   Google Scholar
• PerkinElmer, ChemDraw 17.0; software available at https://revvitysignals.com/products/research/chemdraw.
   Google Scholar
• E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin, UCSF 1.15 chimera; software available at https://www.cgl.ucsf.edu/chimera/download.html.
   Google Scholar
• WaveFunction, Inc, Spartan; software available at https://www.wavefun.com/spartan.
   Google Scholar
• G. Jones, P. Willett, R.C. Glen, A.R. Leach, and R. Taylor, GOLD 5.7.0; software available at https://www.ccdc.cam.ac.uk/solutions/software/gold/.
   Google Scholar
• P. Bauer, B. Hess, and E. Lindahl, GROMACS (version 2022.4); software available at https://www.gromacs.org/Downloads.
   Google Scholar
• D.A. Case, T.E. Cheatham, T. Darden, H. Gohlke, R. Luo, K.M. Merz, A. Onufriev, C. Simmerling, B. Wang, and R.J. Woods, AmberTools22; software available at https://ambermd.org/GetAmber.php.
   Google Scholar
• M.S. Valdés-Tresanco, M.E. Valdés-Tresanco, P.A. Valiente, and E. Moreno, Gmx_MMPBSA: A new tool to perform end-state free energy calculations with GROMACS, J. Chem. Theory. Comput. 17 (2021), pp. 6281–6291. doi:10.1021/acs.jctc.1c00645.
   PubMed Web of Science ®Google Scholar
• M. Valdés-Tresanco, M. Valdés-Tresanco, E. Moreno, and P. Valiente, Assessment of different parameters on the accuracy of computational alanine scanning of protein-protein complexes with the molecular mechanics/generalized born surface area method, J. Phys. Chem. B 127 (2023), pp. 944–954. doi:10.1021/acs.jpcb.2c07079.
   PubMed Web of Science ®Google Scholar
• I.A. Guedes, C.S. de Magalhães, and L.E. Dardenne, Receptor-ligand molecular docking, Biophys. Rev. 6 (2014), pp. 75–87. doi:10.1007/s12551-013-0130-2.
   PubMedGoogle Scholar
• G.L. Warren, C.W. Andrews, A.M. Capelli, B. Clarke, J. LaLonde, M.H. Lambert, M. Lindvall, N. Nevins, S.F. Semus, S. Senger, G. Tedesco, I.D. Wall, J.M. Woolven, C.E. Peishoff, and M.S. Head, A critical assessment of docking programs and scoring functions, J. Med. Chem. 49 (2006), pp. 5912–5931. doi:10.1021/jm050362n.
   PubMed Web of Science ®Google Scholar
• E.J. Barreiro, A.E. Kümmerle, and C.A.M. Fraga, The methylation effect in medicinal chemistry, Chem. Rev. 111 (2011), pp. 5215–5246. doi:10.1021/cr200060g.
   PubMed Web of Science ®Google Scholar
• H. Schönherr and T. Cernak, Profound methyl effects in drug discovery and a call for new C-H methylation reactions, Angew. Chem. Int. Ed. Engl. 52 (2013), pp. 12256–12267. doi:10.1002/anie.201303207.
   PubMed Web of Science ®Google Scholar
• Q. Zhao, J. Qu, and F. He, Chlorination: An effective strategy for high-performance organic solar cells, Adv. Sci. (Weinh) 7 (2020), pp. 2000509. doi:10.1002/advs.202000509.
   PubMedGoogle Scholar
• J.C. Biffinger, H.W. Kim, and S.G. DiMagno, The polar hydrophobicity of fluorinated compounds, Chembiochem 5 (2004), pp. 622–627. doi:10.1002/cbic.200300910.
   PubMed Web of Science ®Google Scholar
• V.H. Dalvi and P.J. Rossky, Molecular origins of fluorocarbon hydrophobicity, Proc. Natl. Acad. Sci. U.S.A 107 (2010), pp. 13603–13607. doi:10.1073/pnas.0915169107.
   PubMed Web of Science ®Google Scholar
• M. Pouzet, M. Dubois, K. Charlet, and A. Béakou, From hydrophilic to hydrophobic wood using direct fluorination: A localized treatment, C. R. Chim. 21 (2018), pp. 800–807. doi:10.1016/j.crci.2018.03.009.
   Web of Science ®Google Scholar
• D.K. Blumenthal, X. Cheng, M. Fajer, K.Y. Ho, J. Rohrer, O. Gerlits, P. Taylor, P. Juneja, A. Kovalevsky, and Z. Radic, Covalent inhibition of hAChE by organophosphates causes homodimer dissociation through long-range allosteric effects, J. Biol. Chem. 297 (2021), pp. 101007. doi:10.1016/j.jbc.2021.101007.
   PubMed Web of Science ®Google Scholar
• S. Brogi, R. Ibba, S. Rossi, S. Butini, V. Calderone, S. Gemma, and G. Campiani, Covalent reversible inhibitors of cysteine proteases containing the nitrile warhead: Recent advancement in the field of viral and parasitic diseases, Molecules 27 (2022), pp. 2561. doi:10.3390/molecules27082561.
   PubMed Web of Science ®Google Scholar
• L. Cole, N. Chu, J. Kilpatrick, J. Volanakis, S. Narayana, and Y. Babu, Structure of diisopropyl fluorophosphate-inhibited factor D, Acta Crystallogr. D Biol. Crystallogr. 53 (1997), pp. 143–150. doi:10.1107/S0907444996012991.
   PubMedGoogle Scholar
• A. Lodola, D. Callegari, L. Scalvini, S. Rivara, and M. Mor, Design and SAR analysis of covalent inhibitors driven by hybrid QM/MM simulations, Meth. Mol. Biol. 2114 (2020), pp. 307–337.
   PubMedGoogle Scholar
• S. Ngo, T. Nguyen, N. Tung, and B. Mai, Insights into the binding and covalent inhibition mechanism of PF-07321332 to SARS-CoV-2 M pro, RSC Adv. 12 (2022), pp. 3729–3737. doi:10.1039/D1RA08752E.
   PubMed Web of Science ®Google Scholar
• J. Dutta, D. Sahoo, S. Jena, K. Tulsiyan, and H. Biswal, Non-covalent interactions with inverted carbon: A carbo-hydrogen bond or a new type of hydrogen bond?, Phys. Chem. Chem. Phys. 22 (2020), pp. 8988–8997. doi:10.1039/D0CP00330A.
   PubMed Web of Science ®Google Scholar
• L. Lima and E. Barreiro, Bioisosterism: A useful strategy for molecular modification and drug design, Curr. Med. Chem. 12 (2005), pp. 23–49. doi:10.2174/0929867053363540.
   PubMed Web of Science ®Google Scholar
• G.L. Patrick, An Introduction to Medicinal Chemistry, 5th ed., Oxford University Press, USA, 2015.
   Google Scholar
• G. Xiong, Z. Wu, J. Yi, L. Fu, Z. Yang, C. Hsieh, M. Yin, X. Zeng, C. Wu, A. Lu, X. Chen, T. Hou, and D. Cao, Admetlab 2.0: An integrated online platform for accurate and comprehensive predictions of ADMET properties, Nucleic. Acids Res. 49 (2021), pp. W5–W14. doi:10.1093/nar/gkab255.
   PubMed Web of Science ®Google Scholar
• S. Kim, J. Chen, T. Cheng, A. Gindulyte, J. He, S. He, Q. Li, B.A. Shoemaker, P.A. Thiessen, B. Yu, L. Zaslavsky, J. Zhang, and E.E. Bolton, Pubchem 2023 update, Nucleic. Acids. Res. 51 (2023), pp. D1373–D1380. doi:10.1093/nar/gkac956.
   PubMed Web of Science ®Google Scholar
• M. Davies, M. Nowotka, G. Papadatos, N. Dedman, A. Gaulton, F. Atkinson, L. Bellis, and J.P. Overington, Chembl web services: Streamlining access to drug discovery data and utilities, Nucleic. Acids Res. 43 (2015), pp. W612–620. doi:10.1093/nar/gkv352.
   PubMed Web of Science ®Google Scholar