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Integration of methods in cheminformatics and biocalorimetry for the design of trypanosomatid enzyme inhibitors

    Igor M Prokopczyk

    Grupo de Química Medicinal do Instituto de Química de São Carlos da Universidade de São Paulo Av. Trabalhador Sancarlense, 400, 13566–590, São Carlos/SP, Brazil

    ,
    Jean FR Ribeiro

    Grupo de Química Medicinal do Instituto de Química de São Carlos da Universidade de São Paulo Av. Trabalhador Sancarlense, 400, 13566–590, São Carlos/SP, Brazil

    ,
    Geraldo R Sartori

    Grupo de Química Medicinal do Instituto de Química de São Carlos da Universidade de São Paulo Av. Trabalhador Sancarlense, 400, 13566–590, São Carlos/SP, Brazil

    ,
    Renata Sesti-Costa

    Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049–900, Ribeirão Preto/SP, Brazil

    ,
    João S Silva

    Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049–900, Ribeirão Preto/SP, Brazil

    ,
    Renato F Freitas

    Grupo de Química Medicinal do Instituto de Química de São Carlos da Universidade de São Paulo Av. Trabalhador Sancarlense, 400, 13566–590, São Carlos/SP, Brazil

    ,
    Andrei Leitão

    Grupo de Química Medicinal do Instituto de Química de São Carlos da Universidade de São Paulo Av. Trabalhador Sancarlense, 400, 13566–590, São Carlos/SP, Brazil

    &
    Carlos A Montanari

    * Author for correspondence

    Grupo de Química Medicinal do Instituto de Química de São Carlos da Universidade de São Paulo Av. Trabalhador Sancarlense, 400, 13566–590, São Carlos/SP, Brazil.

    Published Online:https://doi.org/10.4155/fmc.13.185

    Background: The enzyme GAPDH, which acts in the glycolytic pathway, is seen as a potential target for pharmaceutical intervention of Chagas disease. Results: Herein, we report the discovery of new Trypanosoma cruzi GAPDH (TcGAPDH) inhibitors from target- and ligand-based virtual screening protocols using isothermal titration calorimetry (ITC) and molecular dynamics. Molecular dynamics simulations were used to gain insight on the binding poses of newly identified inhibitors acting at the TcGAPDH substrate (G3P) site. Conclusion: Nequimed125, the most potent inhibitor to act upon TcGAPDH so far, which sits on the G3P site without any contact with the co-factor (NAD+) site, underpins the result obtained by ITC that it is a G3P-competitive inhibitor. Molecular dynamics simulation provides biding poses of TcGAPDH inhibitors that correlate with mechanisms of inhibition observed by ITC. Overall, a new class of dihydroindole compounds that act upon TcGAPDH through a competitive mechanism of inhibition as proven by ITC measurements also kills T. cruzi.

    Papers of special note have been highlighted as: ▪ of interest

    References

    • Lozano R, Naghavi M, Foreman K et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet380(9859),2095–2128 (2012).
    • Bern C, Kjos S, Yabsley MJ, Montgomery SP. Trypanosoma cruzi and Chagas‘ disease in the United States. Clin. Microbiol. Rev.24(4),655–681 (2011)
    • Gascon J, Bern C, Pinazo M-J. Chagas disease in Spain, the United States and other non-endemic countries. Acta Trop.115(1–2),22–27 (2010).
    • Hotez PJ, Dumonteil E, Woc-Colburn L et al. Chagas disease: ‘The New HIV/AIDS of the Americas‘. PLoS Negl. Trop. Dis.6(5),e1498 (2012).▪ Describes how endemic Chagas disease has emerged as an important health disparity in the Americas. As a result, a situation in both Latin America and the USA bears a resemblance to the early years of the HIV/AIDS pandemic.
    • Teixeira DE, Benchimol M, Crepaldi PH, De Souza W. Interactive multimedia to teach the life cycle of Trypanosoma cruzi, the causative agent of Chagas disease. PLoS Negl. Trop. Dis.6(8),e1749 (2012).
    • Pink R, Hudson A, Mouries M-A, Bendig M. Opportunities and challenges in antiparasitic drug discovery. Nat. Rev. Drug Discov.4(9),727–740 (2005).▪ Describes a disease of poverty with few support market-driven drug-discovery endeavors. Discusses advances mostly from scientific research with some public–private partnerships.
    • Coura JR. Present situation and new strategies for chagas disease chemotherapy – a proposal. Mem. Inst. Oswaldo Cruz104(4),549–554 (2009).▪ Discusses the way Chagas disease should be considered to help development.
    • Jackson Y, Alirol E, Getaz L, Wolff H, Combescure C, Chappuis F. Tolerance and safety of nifurtimox in patients with chronic Chagas disease. Clin. Infect. Dis.51(10),e69–e75 (2010).
    • Van Minnebruggen G, François IEJA, Cammue BPA et al. A general overview on past, present and future antimycotics. Open Mycol. J.4,22–32 (2010).
    • 10  Buckner F, Yokoyama K, Lockman J et al. A class of sterol 14-demethylase inhibitors as anti-Trypanosoma cruzi agents. Proc. Natl Acad. Sci. USA100(25),15149–15153 (2003).▪ Tests disubstituted imidazoles that represent a structural class of compounds with potent anti-Trypanosoma cruzi activity both in vitro and in an animal model of Chagas disease.
    • 11  Clayton J. Chagas disease: pushing through the pipeline. Nature465,S12–S15 (2010).▪ Overview of Chagas disease aiming to ascertain the way forward in development.
    • 12  Bakker BM, Michels PaM, Opperdoes FR, Westerhoff HV. What controls glycolysis in bloodstream form Trypanosoma brucei? J. Biol. Chem.274(21),14551–14559 (1999).
    • 13  Ismail SA, Park HW. Structural analysis of human liver glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallogr. Sect. D61(11),1508–1513 (2005).
    • 14  Schuster R, Holzhütter H-G. Use of mathematical models for predicting the metabolic effect of large-scale enzyme activity alterations. Eur. J. Biochem.229(2),403–418 (1995).
    • 15  Freitas RF, Prokopczyk IM, Zottis A et al. Discovery of novel Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase inhibitors. Bioorg. Med. Chem.17(6),2476–2482 (2009).
    • 16  de Macedo EMS, Wiggers HJ, Silva MGV, Braz-Filho R, Andricopulo AD, Montanari CA. A new bianthron glycoside as inhibitor of Trypanosoma cruzi glyceraldehyde 3-phosphate dehydrogenase activity. J. Brazil. Chem. Soc.20(5),947–953 (2009).
    • 17  Ladame S, Fauré R, Denier C, Lakhdar-Ghazal F, Willson M. Selective inhibition of Trypanosoma cruzi GAPDH by ‘bi-substrate‘ analogues. Org. Biomol. Chem.3(11),2070–2072 (2005).
    • 18  Bressi JC, Verlinde CLMJ, Aronov AM et al. Adenosine analogues as selective inhibitors of glyceraldehyde-3-phosphate dehydrogenase of trypanosomatidae via structure-based drug design. J. Med. Chem.44(13),2080–2093 (2001).
    • 19  Soares FA, Sesti-Costa R, Da Silva JS et al. Molecular design, synthesis and biological evaluation of 1,4-dihydro-4-oxoquinoline ribonucleosides as TcGAPDH inhibitors with trypanocidal activity. Bioorg. Med. Chem. Lett.23(16),4597–4601 (2013).▪ New nucleoside analogs that inhibit T. cruzi GAPDH and kill T. cruzi through a different and new putative mechanism of action.
    • 20  Heikamp K, Bajorath J. The future of virtual compound screening. Chem. Biol. Drug Design81(1),33–40 (2013).
    • 21  Wiggers HJ, Rocha JR, Cheleski J, Montanari CA. Integration of ligand- and target-based virtual screening for the discovery of cruzain inhibitors. Mol. Inform.30(6–7),565–578 (2011).▪ Successful integration of ligand-based virtual screening and target-based virtual screening in consensus scoring to search for new enzyme inhibitors.
    • 22  Drwal MN, Griffith R. Combination of ligand- and structure-based methods in virtual screening. Drug Discov. Today Technol.10(3),e395–e401 (2013).
    • 23  Engel JC, Franke De Cazzulo BM, Stoppani AOM, Cannata JJB, Cazzulo JJ. Aerobic glucose fermentation by Trypanosoma cruzi axenic culture amastigote-like forms during growth and differentiation to epimastigotes. Mol. Biochem. Parasitol.26(1–2),1–10 (1987).
    • 24  Pavão F, Castilho MS, Pupo MT et al. Structure of Trypanosoma cruzi glycosomal glyceraldehyde-3-phosphate dehydrogenase complexed with chalepin, a natural product inhibitor, at 1.95 Å resolution. FEBS Lett.520(1–3),13–17 (2002).
    • 25  Ladame S, Castilho MS, Silva CHTP et al. Crystal structure of Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase complexed with an analogue of 1,3-bisphospho-d-glyceric acid. Eur. J. Biochem.270(22),4574–4586 (2003).▪ Mode of binding for a T. cruzi GAPDH inhibitor that resembles the 1,3-bisphosphoglyceric acid with implications for target-based virtual screening.
    • 26  Jenkins JL, Tanner JJ. High-resolution structure of human d-glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallogr. Sect. D62(3),290–301 (2006).▪ x-ray crystallographic data for structural biology and molecular docking using target-based virtual screening.
    • 27  Pettersen EF, Goddard TD, Huang CC et al. UCSF Chimera – a visualization system for exploratory research and analysis. J. Comp. Chem.25(13),1605–1612 (2004).
    • 28  Wiggers HJ, Cheleski J, Zottis A, Oliva G, Andricopulo AD, Montanari CA. Effects of organic solvents on the enzyme activity of Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase in calorimetric assays. Anal. Biochem.370(1),107–114 (2007).
    • 29  Todd MJ, Gomez J. Enzyme kinetics determined using calorimetry: a general assay for enzyme activity? Anal. Biochem.296(2),179–187 (2001).
    • 30  Ghai R, Falconer RJ, Collins BM. Applications of isothermal titration calorimetry in pure and applied research – survey of the literature from 2010. J. Mol. Recognit.25(1),32–52 (2012).
    • 31  Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev.46(1–3),3–26 (2001).▪ Describes the very important rule of five, which is a guide for drug discovery.
    • 32  Veber DF, Johnson SR, Cheng H-Y, Smith BR, Ward KW, Kopple KD. Molecular properties that influence the oral bioavailability of drug candidates. J. Med. Chem.45(12),2615–2623 (2002).▪ Molecular properties that need to be addressed when searching for drugs to be orally administered.
    • 33  Sastry GM, Adzhigirey M, Day T, Annabhimoju R, Sherman W. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J. Comput. Aided Mol. Des.27(3),221–234 (2013).▪ Describes very important tools to be used when carrying out molecular docking studies.
    • 34  Edelstein SJ, le Novère N. Cooperativity of allosteric receptors. J. Mol. Biol.425(9),1424–1432 (2013).
    • 35  Edelstein SJ. Allosteric interactions after 50 years. J. Mol. Biol.425(9),1391–1395 (2013).
    • 36  Proctor EA, Yin S, Tropsha A, Dokholyan NV. Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets. Biophys. J.102(1),144–151 (2012).▪ Describes a very important combination of molecular docking studies with molecular dynamics to improve pose assessment of ligand-bound compounds to target molecules.
    • 37  Wiggers HJ, Rocha JR, Fernandes WB et al. Non-peptidic cruzain inhibitors with trypanocidal activity discovered by virtual screening and in vitro assay. PLoS Negl. Trop. Dis.7(8),e2370 (2013).▪ Interesting example of a new noncovalently bound inhibitor to cruzain that kills T. cruzi.
    • 38  Salomon-Ferrer R, Case DA, Walker RC. An overview of the Amber biomolecular simulation package. WIREs Comput. Mol. Sci.3(2),198–210 (2013).
    • 39  Case DA, Darden TA, Cheatham III TE et al.AMBER 12. University of California, CA, USA (2012).
    • 40  Cheleski J, Freitas RF, Wiggers HJ, Rocha JR, De Araújo APU, Montanari CA. Expression, purification and kinetic characterization of His-tagged glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi.Protein Express. Purif.76(2),190–196 (2011).▪ New procedure for preparing T. cruzi GAPDH either for biochemical and biophysical studies.
    • 41  Brener Z. Therapeutic activity and criterion of cure on mice experimentally infected with Trypanosoma cruzi.Rev. Inst. Med. Trop. Sao Paulo4,389–396 (1962).
    • 42  Nogueira Silva JJ, Pavanelli WRR, Salazar Gutierrez FR et al. Complexation of the anti-Trypanosoma cruzi drug benznidazole improves solubility and efficacy. J. Med. Chem.51(14),4104–4114 (2008).
    • 43  Akaike H. A new look at statistical-model identification IEEE transactions on automatic control AC19. IEEE Trans. Automat. Contr.19(6),716–723 (1974).
    • 10  WHO: Chagas disease (American trypanosomiasis). www.who.int/mediacentre/factsheets/fs340/en/index.html