Generic placeholder image

Combinatorial Chemistry & High Throughput Screening

Editor-in-Chief

ISSN (Print): 1386-2073
ISSN (Online): 1875-5402

Research Article

Molecular Dynamics of a N-Cyclohexyl-1,2,4-Oxadiazole Derivative as a Reversible Cruzain Inhibitor in Trypanosoma cruzi

Author(s): Yasmim Mendes Rocha, Gabriel Acácio de Moura, João Pedro Viana Rodrigues, Cristian Vicson Gomes Pinheiro, Ronaldo Nascimento de Oliveira, Marcia Machado Marinho and Roberto Nicolete*

Volume 27, Issue 19, 2024

Published on: 10 November, 2023

Page: [2935 - 2939] Pages: 5

DOI: 10.2174/0113862073268297231025110913

open access plus

Abstract

Background: Chagas disease kills around 10,000 people yearly, primarily in Latin America, where it is prevalent. Current treatment has limited chronic effectiveness, is unsafe, and has substantial side effects. As a result, the use of oxadiazole derivatives and similar heterocyclic compounds as bioisosteres are well known, and they are prospective candidates in the hunt for novel anti-Trypanosoma cruzi chemicals. Recent research has revealed that the cysteine protease cruzain from T. cruzi is a validated target for disease treatment.

Objective: Thus, using a molecular dynamics simulation, the current study attempted to determine if a significant interaction occurred between the enzyme cruzain and its ligand.

Results: Interactions with the catalytic site and other critical locations were observed. Also, the RMSD values suggested that the molecule under research had stable interactions with its target.

Conclusion: Finally, the findings indicate that the investigated molecule 2b can interfere enzymatic activity of cruzain, indicating that it might be a promising antichagasic drug.

[1]
Stanaway, J.D.; Roth, G. The burden of Chagas disease: Estimates and challenges. Glob. Heart, 2015, 10(3), 139-144.
[http://dx.doi.org/10.1016/j.gheart.2015.06.001] [PMID: 26407508]
[2]
Trachtenberg, B.H.; Hare, J.M. Inflammatory cardiomyopathic syndromes. Circ. Res., 2017, 121(7), 803-818.
[http://dx.doi.org/10.1161/CIRCRESAHA.117.310221] [PMID: 28912184]
[3]
Cantey, P.T.; Stramer, S.L.; Townsend, R.L.; Kamel, H.; Ofafa, K.; Todd, C.W.; Currier, M.; Hand, S.; Varnado, W.; Dotson, E.; Hall, C.; Jett, P.L.; Montgomery, S.P. The United States trypanosoma cruzi infection study: Evidence for vector-borne transmission of the parasite that causes Chagas disease among United States blood donors. Transfusion, 2012, 52(9), 1922-1930.
[http://dx.doi.org/10.1111/j.1537-2995.2012.03581.x] [PMID: 22404755]
[4]
Antunes, D.; Marins-Dos-Santos, A.; Ramos, M.T.; Mascarenhas, B.A.S.; Moreira, C.J.C.; Farias-de-Oliveira, D.A.; Savino, W.; Monteiro, R.Q.; de Meis, J. Oral route driven acute Trypanosoma cruzi infection unravels an IL-6 dependent hemostatic derangement. Front. Immunol., 2019, 10, 1073.
[http://dx.doi.org/10.3389/fimmu.2019.01073] [PMID: 31139194]
[5]
Santos, M. Oral trypanosoma cruzi acute infection in mice targets primary lymphoid organs and triggers extramedullary hematopoiesis. Front. Cell. Infect. Microbiol., 2022, 12, 800395.
[6]
Ferreira, R.R.; de Souza, E.M.; Vilar-Pereira, G.; Degrave, W.M.S.; Abreu, R.S.; Meuser-Batista, M.; Ferreira, N.V.C.; Ledbeter, S.; Barker, R.H.; Bailly, S.; Feige, J.J.; Lannes-Vieira, J.; de Araújo-Jorge, T.C.; Waghabi, M.C. In Chagas disease, transforming growth factor beta neutralization reduces Trypanosoma cruzi infection and improves cardiac performance. Front. Cell. Infect. Microbiol., 2022, 12, 1017040.
[http://dx.doi.org/10.3389/fcimb.2022.1017040] [PMID: 36530434]
[7]
Crespillo-Andújar, C.; Venanzi-Rullo, E.; López-Vélez, R.; Monge-Maillo, B.; Norman, F.; López-Polín, A.; Pérez-Molina, J.A. Safety profile of benznidazole in the treatment of chronic Chagas disease: Experience of a referral center and systematic literature review with meta-analysis. Drug Saf., 2018, 41(11), 1035-1048.
[http://dx.doi.org/10.1007/s40264-018-0696-5] [PMID: 30006773]
[8]
Yang, S.; Ren, C.L.; Ma, T.Y.; Zou, W.Q.; Dai, L.; Tian, X.Y.; Liu, X.H.; Tan, C.X. 1, 2, 4-Oxadiazole-based bio-isosteres of benzamides: Synthesis, biological activity, and toxicity to zebrafish embryo. Int. J. Mol. Sci., 2021, 22(5), 2367.
[http://dx.doi.org/10.3390/ijms22052367] [PMID: 33673430]
[9]
Vaidya, A.; Jain, S.; Prashantha Kumar, B.; Singh, S.K.; Kashaw, S.K.; Agrawal, R.K. Synthesis of 1,2,4-oxadiazole derivatives: Anticancer and 3D QSAR studies. Monatsh. Chem., 2020, 151(3), 385-395.
[http://dx.doi.org/10.1007/s00706-020-02553-1]
[10]
Vaidya, A.; Jain, S.; Jain, P.; Jain, P.; Tiwari, N.; Jain, R.; Jain, R.; Jain, A.K.; Agrawal, R.K. Synthesis, and biological activities of oxadiazole derivatives: A review. Mini Rev. Med. Chem., 2016, 16(10), 825-845.
[http://dx.doi.org/10.2174/1389557516666160211120835] [PMID: 26864552]
[11]
Rocha, Y.M.; Magalhães, E.P.; de Medeiros, C.M.; Machado, M.M. Nascimento e Melo de Oliveira, V.; de Oliveira, N.R.; Lima Sampaio, T.; de Menezes, R.R.P.P.B.; Martins, A.M.C.; Nicolete, R. Antiparasitary and antiproliferative activities in vitro of a 1,2,4-oxadiazole derivative on Trypanosoma cruzi. Parasitol. Res., 2022, 121(7), 2141-2156.
[http://dx.doi.org/10.1007/s00436-022-07554-z] [PMID: 35610523]
[12]
Hanwell, M.D.; Curtis, D.E.; Lonie, D.C.; Vandermeersch, T.; Zurek, E.; Hutchison, G.R. Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. J. Cheminform., 2012, 4(1), 17.
[http://dx.doi.org/10.1186/1758-2946-4-17] [PMID: 22889332]
[13]
Brak, K.; Kerr, I.D.; Barrett, K.T.; Fuchi, N.; Debnath, M.; Ang, K.; Engel, J.C.; McKerrow, J.H.; Doyle, P.S.; Brinen, L.S.; Ellman, J.A.; Ellman, J. Nonpeptidic tetrafluorophenoxymethyl ketone cruzain inhibitors as promising new leads for Chagas disease chemotherapy. J. Med. Chem., 2010, 53(4), 1763-1773.
[http://dx.doi.org/10.1021/jm901633v] [PMID: 20088534]
[14]
Yan, J.; Zhang, G.; Pan, J.; Wang, Y. α-Glucosidase inhibition by luteolin: Kinetics, interaction and molecular docking. Int. J. Biol. Macromol., 2014, 64, 213-223.
[http://dx.doi.org/10.1016/j.ijbiomac.2013.12.007] [PMID: 24333230]
[15]
Morris, G.M.; Huey, R.; Lindstrom, W.; Sanner, M.F.; Belew, R.K.; Goodsell, D.S.; Olson, A.J. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem., 2009, 30(16), 2785-2791.
[http://dx.doi.org/10.1002/jcc.21256] [PMID: 19399780]
[16]
Trott, O.; Olson, A.J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem., 2009, 31(2), NA.
[http://dx.doi.org/10.1002/jcc.21334] [PMID: 19499576]
[17]
Shityakov, S.; Förster, C. In silico predictive model to determine vector-mediated transport properties for the blood-brain barrier choline transporter. Adv. Appl. Bioinforma. Chem., 2014, 7, 23-36.
[http://dx.doi.org/10.2147/AABC.S63749]
[18]
Yusuf, D.; Davis, A.M.; Kleywegt, G.J.; Schmitt, S. An alternative method for the evaluation of docking performance: RSR vs RMSD. J. Chem. Inf. Model., 2008, 48(7), 1411-1422.
[http://dx.doi.org/10.1021/ci800084x] [PMID: 18598022]
[19]
Imberty, A.; Hardman, K.D.; Carver, J.P.; Pérez, S. Molecular modelling of protein-carbohydrate interactions. Docking of monosaccharides in the binding site of concanavalin A. Glycobiology, 1991, 1(6), 631-642.
[http://dx.doi.org/10.1093/glycob/1.6.631] [PMID: 1822243]
[20]
Berendsen, H.J.C.; van der Spoel, D.; van Drunen, R. GROMACS: A message-passing parallel molecular dynamics implementation. Comput. Phys. Commun., 1995, 91(1-3), 43-56.
[http://dx.doi.org/10.1016/0010-4655(95)00042-E]
[21]
MacKerell, A.D., Jr; Banavali, N.; Foloppe, N. Development and current status of the CHARMM force field for nucleic acids. Biopolymers, 2000, 56(4), 257-265.
[http://dx.doi.org/10.1002/1097-0282(2000)56:4<257:AID-BIP10029>3.0.CO;2-W] [PMID: 11754339]
[22]
Zoete, V.; Cuendet, M.A.; Grosdidier, A.; Michielin, O. SwissParam: A fast force field generation tool for small organic molecules. J. Comput. Chem., 2011, 32(11), 2359-2368.
[http://dx.doi.org/10.1002/jcc.21816] [PMID: 21541964]
[23]
Bussi, G.; Donadio, D.; Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys., 2007, 126(1), 014101.
[http://dx.doi.org/10.1063/1.2408420] [PMID: 17212484]
[24]
Parrinello, M.; Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method. J. Appl. Phys., 1981, 52(12), 7182-7190.
[http://dx.doi.org/10.1063/1.328693]
[25]
Van Gunsteren, W.F.; Berendsen, H.J.C. A leap-frog algorithm for stochastic dynamics. Mol. Simul., 1988, 1(3), 173-185.
[http://dx.doi.org/10.1080/08927028808080941]
[26]
Vargas, E.; Echeverri, F.; Vélez, I.; Robledo, S.; Quiñones, W. Synthesis and evaluation of thiochroman-4-one derivatives as potential leishmanicidal agents. Molecules, 2017, 22(12), 2041.
[http://dx.doi.org/10.3390/molecules22122041] [PMID: 29186046]
[27]
Scharfstein, J. Subverting bradykinin-evoked inflammation by co-opting the contact system. Curr. Opin. Hematol., 2018, 25(5), 347-357.
[http://dx.doi.org/10.1097/MOH.0000000000000444] [PMID: 30028741]
[28]
Tomas, A.M. Overexpression of cruzipain, the major cysteine proteinase of Trypanosoma cruzi, is associated with enhanced metacyclogenesis. Eur. J. Biochem., 1997, 244(2), 596-603.
[29]
Caputto, M.E.; Fabian, L.E.; Benítez, D.; Merlino, A.; Ríos, N.; Cerecetto, H.; Moltrasio, G.Y.; Moglioni, A.G.; González, M.; Finkielsztein, L.M. Thiosemicarbazones derived from 1-indanones as new anti-Trypanosoma cruzi agents. Bioorg. Med. Chem., 2011, 19(22), 6818-6826.
[http://dx.doi.org/10.1016/j.bmc.2011.09.037] [PMID: 22000947]
[30]
Deb, P.K.; Al-Shar’i, N.A.; Venugopala, K.N.; Pillay, M.; Borah, P. In vitro anti-TB properties, in silico target validation, molecular docking and dynamics studies of substituted 1,2,4-oxadiazole analogues against Mycobacterium tuberculosis. J. Enzyme Inhib. Med. Chem., 2021, 36(1), 869-884.
[http://dx.doi.org/10.1080/14756366.2021.1900162] [PMID: 34060396]

© 2024 Bentham Science Publishers | Privacy Policy