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<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ali="http://www.niso.org/schemas/ali/1.0/" article-type="research-article" dtd-version="1.2" xml:lang="en"><front><journal-meta><journal-id journal-id-type="publisher-id">Combinatorial Chemistry &amp; High Throughput Screening</journal-id><journal-title-group><journal-title xml:lang="en">Combinatorial Chemistry &amp; High Throughput Screening</journal-title><trans-title-group xml:lang="ru"><trans-title>Combinatorial Chemistry &amp; High Throughput Screening</trans-title></trans-title-group></journal-title-group><issn publication-format="print">1386-2073</issn><issn publication-format="electronic">1875-5402</issn><publisher><publisher-name xml:lang="en">Bentham Science</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">644560</article-id><article-id pub-id-type="doi">10.2174/0113862073268297231025110913</article-id><article-categories><subj-group subj-group-type="toc-heading"><subject>Chemistry</subject></subj-group><subj-group subj-group-type="article-type"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title xml:lang="en">Molecular Dynamics of a N-Cyclohexyl-1,2,4-Oxadiazole Derivative as a Reversible Cruzain Inhibitor in Trypanosoma cruzi</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Rocha</surname><given-names>Yasmim</given-names></name><email>info@benthamscience.net</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><name><surname>de Moura</surname><given-names>Gabriel</given-names></name><email>info@benthamscience.net</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><name><surname>Rodrigues</surname><given-names>João</given-names></name><email>info@benthamscience.net</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><name><surname>Pinheiro</surname><given-names>Cristian</given-names></name><email>info@benthamscience.net</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><name><surname>de Oliveira</surname><given-names>Ronaldo</given-names></name><email>info@benthamscience.net</email><xref ref-type="aff" rid="aff2"/></contrib><contrib contrib-type="author"><name><surname>Marinho</surname><given-names>Marcia</given-names></name><email>info@benthamscience.net</email><xref ref-type="aff" rid="aff3"/></contrib><contrib contrib-type="author"><name><surname>Nicolete</surname><given-names>Roberto</given-names></name><email>info@benthamscience.net</email><xref ref-type="aff" rid="aff1"/></contrib></contrib-group><aff id="aff1"><institution>Graduate Program in Pharmaceutical Sciences, Federal University of Ceará</institution></aff><aff id="aff2"><institution>Department of Organic Chemistry, Rural Federal University of Pernambuco</institution></aff><aff id="aff3"><institution>Department of Chemistry, Ceara State University</institution></aff><pub-date date-type="pub" iso-8601-date="2024-10-01" publication-format="electronic"><day>01</day><month>10</month><year>2024</year></pub-date><volume>27</volume><issue>19</issue><issue-title xml:lang="ru"/><fpage>2935</fpage><lpage>2939</lpage><history><date date-type="received" iso-8601-date="2025-01-07"><day>07</day><month>01</month><year>2025</year></date></history><permissions><copyright-statement xml:lang="en">Copyright ©; 2024, Bentham Science Publishers</copyright-statement><copyright-year>2024</copyright-year><copyright-holder xml:lang="en">Bentham Science Publishers</copyright-holder><ali:free_to_read xmlns:ali="http://www.niso.org/schemas/ali/1.0/"/></permissions><self-uri xlink:href="https://rjpbr.com/1386-2073/article/view/644560">https://rjpbr.com/1386-2073/article/view/644560</self-uri><abstract xml:lang="en"><p id="idm46041443804192">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.</p><p id="idm46041443808192">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.</p><p id="idm46041443812160">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.</p><p id="idm46041443817216">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.</p></abstract><kwd-group xml:lang="en"><kwd>Trypanosoma cruzi</kwd><kwd>chagas disease</kwd><kwd>oxadiazole derivative</kwd><kwd>molecular dynamics</kwd><kwd>molecular docking simulation</kwd><kwd>computational biology.</kwd></kwd-group></article-meta></front><body></body><back><ref-list><ref id="B1"><label>1.</label><mixed-citation>Stanaway, J.D.; Roth, G. The burden of Chagas disease: Estimates and challenges. Glob. Heart, 2015, 10(3), 139-144. doi: 10.1016/j.gheart.2015.06.001 PMID: 26407508</mixed-citation></ref><ref id="B2"><label>2.</label><mixed-citation>Trachtenberg, B.H.; Hare, J.M. Inflammatory cardiomyopathic syndromes. Circ. Res., 2017, 121(7), 803-818. doi: 10.1161/CIRCRESAHA.117.310221 PMID: 28912184</mixed-citation></ref><ref id="B3"><label>3.</label><mixed-citation>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. doi: 10.1111/j.1537-2995.2012.03581.x PMID: 22404755</mixed-citation></ref><ref id="B4"><label>4.</label><mixed-citation>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. doi: 10.3389/fimmu.2019.01073 PMID: 31139194</mixed-citation></ref><ref id="B5"><label>5.</label><mixed-citation>Santos, M. Oral trypanosoma cruzi acute infection in mice targets primary lymphoid organs and triggers extramedullary hematopoiesis. Front. Cell. Infect. Microbiol., 2022, 12, 800395.</mixed-citation></ref><ref id="B6"><label>6.</label><mixed-citation>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. doi: 10.3389/fcimb.2022.1017040 PMID: 36530434</mixed-citation></ref><ref id="B7"><label>7.</label><mixed-citation>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. doi: 10.1007/s40264-018-0696-5 PMID: 30006773</mixed-citation></ref><ref id="B8"><label>8.</label><mixed-citation>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. doi: 10.3390/ijms22052367 PMID: 33673430</mixed-citation></ref><ref id="B9"><label>9.</label><mixed-citation>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. doi: 10.1007/s00706-020-02553-1</mixed-citation></ref><ref id="B10"><label>10.</label><mixed-citation>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. doi: 10.2174/1389557516666160211120835 PMID: 26864552</mixed-citation></ref><ref id="B11"><label>11.</label><mixed-citation>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. doi: 10.1007/s00436-022-07554-z PMID: 35610523</mixed-citation></ref><ref id="B12"><label>12.</label><mixed-citation>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. doi: 10.1186/1758-2946-4-17 PMID: 22889332</mixed-citation></ref><ref id="B13"><label>13.</label><mixed-citation>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. doi: 10.1021/jm901633v PMID: 20088534</mixed-citation></ref><ref id="B14"><label>14.</label><mixed-citation>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. doi: 10.1016/j.ijbiomac.2013.12.007 PMID: 24333230</mixed-citation></ref><ref id="B15"><label>15.</label><mixed-citation>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. doi: 10.1002/jcc.21256 PMID: 19399780</mixed-citation></ref><ref id="B16"><label>16.</label><mixed-citation>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. doi: 10.1002/jcc.21334 PMID: 19499576</mixed-citation></ref><ref id="B17"><label>17.</label><mixed-citation>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. doi: 10.2147/AABC.S63749</mixed-citation></ref><ref id="B18"><label>18.</label><mixed-citation>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. doi: 10.1021/ci800084x PMID: 18598022</mixed-citation></ref><ref id="B19"><label>19.</label><mixed-citation>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. doi: 10.1093/glycob/1.6.631 PMID: 1822243</mixed-citation></ref><ref id="B20"><label>20.</label><mixed-citation>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. doi: 10.1016/0010-4655(95)00042-E</mixed-citation></ref><ref id="B21"><label>21.</label><mixed-citation>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. doi: 10.1002/1097-0282(2000)56:43.0.CO;2-W PMID: 11754339</mixed-citation></ref><ref id="B22"><label>22.</label><mixed-citation>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. doi: 10.1002/jcc.21816 PMID: 21541964</mixed-citation></ref><ref id="B23"><label>23.</label><mixed-citation>Bussi, G.; Donadio, D.; Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys., 2007, 126(1), 014101. doi: 10.1063/1.2408420 PMID: 17212484</mixed-citation></ref><ref id="B24"><label>24.</label><mixed-citation>Parrinello, M.; Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method. J. Appl. Phys., 1981, 52(12), 7182-7190. doi: 10.1063/1.328693</mixed-citation></ref><ref id="B25"><label>25.</label><mixed-citation>Van Gunsteren, W.F.; Berendsen, H.J.C. A leap-frog algorithm for stochastic dynamics. Mol. Simul., 1988, 1(3), 173-185. doi: 10.1080/08927028808080941</mixed-citation></ref><ref id="B26"><label>26.</label><mixed-citation>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. doi: 10.3390/molecules22122041 PMID: 29186046</mixed-citation></ref><ref id="B27"><label>27.</label><mixed-citation>Scharfstein, J. Subverting bradykinin-evoked inflammation by co-opting the contact system. Curr. Opin. Hematol., 2018, 25(5), 347-357. doi: 10.1097/MOH.0000000000000444 PMID: 30028741</mixed-citation></ref><ref id="B28"><label>28.</label><mixed-citation>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.</mixed-citation></ref><ref id="B29"><label>29.</label><mixed-citation>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. doi: 10.1016/j.bmc.2011.09.037 PMID: 22000947</mixed-citation></ref><ref id="B30"><label>30.</label><mixed-citation>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. doi: 10.1080/14756366.2021.1900162 PMID: 34060396</mixed-citation></ref></ref-list></back></article>
