Development of New Inhibitors of the Dihydroorotate Dehydrogenase Enzyme (DHODH) from Leishmania sp.
DOI:
https://doi.org/10.33448/rsd-v10i16.23087Keywords:
Leishmaniasis; DHODH; New inhibitors; Nitro derivatives.Abstract
Leishmaniasis is a neglected disease and is considered one of the greatest endemic diseases in the world. The disease-causing parasites developed resistance against the drugs used in the disease's pharmacotherapy. Because of this, new compounds need to be devised to effectively treat this parasitosis. Therefore, in this paper we use molecular modeling approaches to design new inhibitors of the enzyme Dihydroorotate dehydrogenase (DHODH), a molecular target against leishmaniasis. Initially we used molecular modeling by homology to build the DHODH enzyme, later Metronidazole and Benznidazole were used as molecular frameworks for the development of new compounds. Then, the molecular docking method was applied to evaluate the interaction mode of the compounds with the binding site of the enzyme. The enzymatic model obtained 96% of its residues in favorable regions during its validation process. In the docking simulations, the compounds were able to interact favorably with the binding site and exhibit interactions with protein residues.
References
Akhoundi, M., Kuhls, K., Cannet, A., Votýpka, J., Marty, P., Delaunay, P., & Sereno, D. (2016). A Historical Overview of the Classification, Evolution, and Dispersion of Leishmania Parasites and Sandflies. PLoS Neglected Tropical Diseases, 10(3), e0004349. https://doi.org/10.1371/journal.pntd.0004349
Almeida, V. M., Dias, Ê. R., Souza, B. C., Cruz, J. N., Santos, C. B. R., Leite, F. H. A., Queiroz, R. F., & Branco, A. (2021). Methoxylated flavonols from Vellozia dasypus Seub ethyl acetate active myeloperoxidase extract: in vitro and in silico assays . Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2021.1900916
Alves, F. S., Rodrigues Do Rego, J. de A., Da Costa, M. L., Lobato Da Silva, L. F., Da Costa, R. A., Cruz, J. N., & Brasil, D. D. S. B. (2020). Spectroscopic methods and in silico analyses using density functional theory to characterize and identify piperine alkaloid crystals isolated from pepper (Piper Nigrum L.). Journal of Biomolecular Structure and Dynamics, 38(9), 2792–2799. https://doi.org/10.1080/07391102.2019.1639547
Araújo, P. H. F., Ramos, R. S., da Cruz, J. N., Silva, S. G., Ferreira, E. F. B., de Lima, L. R., Macêdo, W. J. C., Espejo-Román, J. M., Campos, J. M., & Santos, C. B. R. (2020). Identification of potential COX-2 inhibitors for the treatment of inflammatory diseases using molecular modeling approaches. Molecules, 25(18), 4183. https://doi.org/10.3390/molecules25184183
Arenas, R., Torres-Guerrero, E., Quintanilla-Cedillo, M. R., & Ruiz-Esmenjaud, J. (2017). Leishmaniasis: A review. In F1000Research (Vol. 6). Faculty of 1000 Ltd. https://doi.org/10.12688/f1000research.11120.1
Castro, A. L. G., Cruz, J. N., Sodré, D. F., Correa-Barbosa, J., Azonsivo, R., de Oliveira, M. S., de Sousa Siqueira, J. E., da Rocha Galucio, N. C., de Oliveira Bahia, M., Burbano, R. M. R., do Rosário Marinho, A. M., Percário, S., Dolabela, M. F., & Vale, V. V. (2021). Evaluation of the genotoxicity and mutagenicity of isoeleutherin and eleutherin isolated from Eleutherine plicata herb. using bioassays and in silico approaches. Arabian Journal of Chemistry, 14(4), 103084. https://doi.org/10.1016/j.arabjc.2021.103084
CDC’s Division of Parasitic Diseases and Malaria. (2014). Guide for Specimen Collection and Reference Diagnosis of Leishmaniasis (p. 4).
Cheleski, J., Rocha, J. R., Pinheiro, M. P., Wiggers, H. J., Da Silva, A. B. F., Nonato, M. C., & Montanari, C. A. (2010). Novel insights for dihydroorotate dehydrogenase class 1A inhibitors discovery. European Journal of Medicinal Chemistry, 45(12), 5899–5909. https://doi.org/10.1016/j.ejmech.2010.09.055
Chibli, L. A., Schmidt, T. J., Nonato, M. C., Calil, F. A., & Da Costa, F. B. (2018). Natural products as inhibitors of Leishmania major dihydroorotate dehydrogenase. European Journal of Medicinal Chemistry, 157, 852–866. https://doi.org/10.1016/j.ejmech.2018.08.033
Costa, E. B. B., Silva, R. C. C., Espejo-Román, J. M. M., Neto, M. F. de A. F. d. A., Cruz, J. N. N., Leite, F. H. A. H. A., Silva, C. H. T. P. H. T. P., Pinheiro, J. C. C., Macêdo, W. J. C. J. C., & Santos, C. B. R. B. R. (2020). Chemometric methods in antimalarial drug design from 1,2,4,5-tetraoxanes analogues. SAR and QSAR in Environmental Research, 31(9), 1–19. https://doi.org/10.1080/1062936X.2020.1803961
da Silva Júnior, O. S., Franco, C. de J. P., de Moraes, A. A. B., Cruz, J. N., da Costa, K. S., do Nascimento, L. D., & Andrade, E. H. de A. (2021). In silico analyses of toxicity of the major constituents of essential oils from two Ipomoea L. species. Toxicon, 195, 111–118. https://doi.org/10.1016/j.toxicon.2021.02.015
Grant, J. A., & Pickup, B. T. (1997). Gaussian shape methods. Computer Simulation of Biomolecular Systems, 150–176. https://doi.org/10.1007/978-94-017-1120-3_5
Hof, H. (1989). Antibacterial activities of the antiparasitic drugs nifurtimox and benznidazole. Antimicrobial Agents and Chemotherapy, 33(3), 404–405. https://doi.org/10.1128/AAC.33.3.404
Leão, R. P., Cruz, J. V. J. N., da Costa, G. V., Cruz, J. V. J. N., Ferreira, E. F. B., Silva, R. C., de Lima, L. R., Borges, R. S., Dos Santos, G. B., & Santos, C. B. R. (2020). Identification of new rofecoxib-based cyclooxygenase-2 inhibitors: A bioinformatics approach. Pharmaceuticals, 13(9), 1–26. https://doi.org/10.3390/ph13090209
Lima, A. R. J. A. de M., Siqueira, A. S., Möller, M. L. S., Souza, R. C. de, Cruz, J. N., Lima, A. R. J. A. de M., Silva, R. C. da, Aguiar, D. C. F., Junior, J. L. da S. G. V., & Gonçalves, E. C. (2020). In silico improvement of the cyanobacterial lectin microvirin and mannose interaction. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1821782
Lima, M. V. N. de, Oliveira, R. Z. de, Lima, A. P. de, Cerino, D. A., & Silveira, T. G. V. (2007). Leishmaniose cutânea com desfecho fatal durante tratamento com antimonial pentavalente. Anais Brasileiros de Dermatologia, 82, 269–271. http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0365-05962007000300010&nrm=iso
Limeira, C. H., Alves, C. J., De Azevedo, S. S., Santos, C. D. S. A. B., De Melo, M. A., Soares, R. R., Barnabé, N. N. D. C., & Rodrigues, G. D. Q. (2019). Clinical aspects and diagnosis of leishmaniasis in equids: A systematic review and meta-analysis. Revista Brasileira de Parasitologia Veterinaria, 28(4), 574–581. https://doi.org/10.1590/s1984-29612019074
Liu, L., Dong, Z., Lei, Q., Yang, J., Hu, H., Li, Q., Ji, Y., Guo, L., Zhang, Y., Liu, Y., & Cui, H. (2017). Inactivation/deficiency of DHODH induces cell cycle arrest and programed cell death in melanoma. Oncotarget, 8(68), 112354–112370. https://doi.org/10.18632/oncotarget.19379
Lovell, S. C., Davis, I. W., Arendall, W. B., De Bakker, P. I. W., Word, J. M., Prisant, M. G., Richardson, J. S., & Richardson, D. C. (2003). Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins, 50(3), 437–450. https://doi.org/10.1002/PROT.10286
Mandlik, V., & Singh, S. (2016). Integrative approaches for identification of novel ISCL inhibitors in Leishmaniasis: A computational insight into the structure. Gene Reports, 4, 162–168. https://doi.org/10.1016/j.genrep.2016.05.002
Marchler-Bauer, A., Bo, Y., Han, L., He, J., Lanczycki, C. J., Lu, S., Chitsaz, F., Derbyshire, M. K., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Lu, F., Marchler, G. H., Song, J. S., Thanki, N., Wang, Z., Yamashita, R. A., Zhang, D., … Bryant, S. H. (2017). CDD/SPARCLE: Functional classification of proteins via subfamily domain architectures. Nucleic Acids Research, 45(D1), D200–D203. https://doi.org/10.1093/nar/gkw1129
Melo, F., & Feytmans, E. (1998). Assessing protein structures with a non-local atomic interaction energy. Journal of Molecular Biology, 277(5), 1141–1152. https://doi.org/10.1006/jmbi.1998.1665
Ministério da Saúde. (2017). Manual de Vigilância da Leishmaniose Tegumentar Americana. In Ministério da Saúde.Secretaria de Vigilância em Saúde.
Moreira, D. de S., Xavier, M. V., & Murta, S. M. F. (2018). Ascorbate peroxidase overexpression protects leishmania Braziliensis against trivalent antimony effects. Memorias Do Instituto Oswaldo Cruz, 113(12), 1–5. https://doi.org/10.1590/0074-02760180377
Moreno-Herrera, A., Cortez-Maya, S., Bocanegra-Garcia, V., Banik, B. K., & Rivera, G. (2020). Recent Advances in the Development of Broad-Spectrum Antiprotozoal Agents. Current Medicinal Chemistry, 28(3), 583–606. https://doi.org/10.2174/0929867327666200303170000
Neto, R. de A. M. M., Santos, C. B. R. R., Henriques, S. V. C. C., Machado, L. de O., Cruz, J. N., da Silva, C. H. T. d. P. T. de P., Federico, L. B., Oliveira, E. H. C. d. C. de, de Souza, M. P. C. C., da Silva, P. N. B. B., Taft, C. A., Ferreira, I. M., & Gomes, M. R. F. F. (2020). Novel chalcones derivatives with potential antineoplastic activity investigated by docking and molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1839562
Neves Cruz, J., da Costa, K. S., de Carvalho, T. A. A., & de Alencar, N. A. N. (2020). Measuring the structural impact of mutations on cytochrome P450 21A2, the major steroid 21-hydroxylase related to congenital adrenal hyperplasia. Journal of Biomolecular Structure and Dynamics, 38(5), 1425–1434. https://doi.org/10.1080/07391102.2019.1607560
No, J. H. (2016). Visceral leishmaniasis: Revisiting current treatments and approaches for future discoveries. Acta Tropica, 155, 113–123. https://doi.org/10.1016/j.actatropica.2015.12.016
Oliveira, A. A., Oliveira, A. P. A., Franco, L. L., Ferencs, M. O., Ferreira, J. F. G., Bachi, S. M. P. S., Speziali, N. L., Farias, L. M., Magalhães, P. P., & Beraldo, H. (2018). 5-Nitroimidazole-derived Schiff bases and their copper(II) complexes exhibit potent antimicrobial activity against pathogenic anaerobic bacteria. BioMetals 2018 31:4, 31(4), 571–584. https://doi.org/10.1007/S10534-018-0106-6
Oliveira, M. S. de, Cruz, J. N. da, Costa, W. A. da, Silva, S. G., Brito, M. da P., Menezes, S. A. F. de, Neto, A. M. de J. C., Andrade, E. H. de A., & Junior, R. N. de C. (2020). Chemical Composition, Antimicrobial Properties of Siparuna guianensis Essential Oil and a Molecular Docking and Dynamics Molecular Study of its Major Chemical Constituent. Molecules, 25(17), 3852. https://doi.org/10.3390/molecules25173852
Oliveira, L. F. G., Souza-Silva, F., Cysne-Finkelstein, L., Rabelo, K., Amorim, J. F., Azevedo, A. de S., Bourguignon, S. C., Ferreira, V. F., Paes, M. V., & Alves, C. R. (2017). Evidence for Tissue Toxicity in BALB/c Exposed to a Long-Term Treatment with Oxiranes Compared to Meglumine Antimoniate. BioMed Research International, 2017, 9840210. https://doi.org/10.1155/2017/9840210
Patel, O. P. S., Jesumoroti, O. J., Legoabe, L. J., & Beteck, R. M. (2021). Metronidazole-conjugates: A comprehensive review of recent developments towards synthesis and medicinal perspective. European Journal of Medicinal Chemistry, 210, 112994. https://doi.org/10.1016/J.EJMECH.2020.112994
Pelozo, M. F., Lima, G. F. S., Cordeiro, C. F., Silva, L. S., Caldas, I. S., Carvalho, D. T., Lavorato, S. N., Hawkes, J. A., & Franco, L. L. (2021). Synthesis of New Hybrid Derivatives from Metronidazole and Eugenol Analogues as Trypanocidal Agents. Journal of Pharmacy & Pharmaceutical Sciences, 24, 421–434. https://doi.org/10.18433/JPPS31839
Pfaendner, R. (2006). Nitroxyl radicals and nitroxylethers beyond stabilization: radical generators for efficient polymer modification. Comptes Rendus Chimie, 9(11–12), 1338–1344. https://doi.org/10.1016/J.CRCI.2006.08.001
Ponte-Sucre, A., Gamarro, F., Dujardin, J. C., Barrett, M. P., López-Vélez, R., García-Hernández, R., Pountain, A. W., Mwenechanya, R., & Papadopoulou, B. (2017). Drug resistance and treatment failure in leishmaniasis: A 21st century challenge. In PLoS Neglected Tropical Diseases (Vol. 11, Issue 12, p. e0006052). Public Library of Science. https://doi.org/10.1371/journal.pntd.0006052
Raether, W., & Hänel, H. (2003). Nitroheterocyclic drugs with broad spectrum activity. Parasitology Research 2003 90:1, 90(1), S19–S39. https://doi.org/10.1007/S00436-002-0754-9
Ramos, R. S., Macêdo, W. J. C., Costa, J. S., da Silva, C. H. T. d. P., Rosa, J. M. C., da Cruz, J. N., de Oliveira, M. S., de Aguiar Andrade, E. H., e Silva, R. B. L., Souto, R. N. P., & Santos, C. B. R. (2020). Potential inhibitors of the enzyme acetylcholinesterase and juvenile hormone with insecticidal activity: study of the binding mode via docking and molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 38(16), 4687–4709. https://doi.org/10.1080/07391102.2019.1688192
Ramya, N. (2016). Design, Synthesis, Characterization and Biological Evaluation of Some Novel Anti Tubercular Agents Targeting: Decaprenylphosphoryl-Beta-D-Ribose 2’Epimerase-1.
Reis, R. A. G., Lorenzato, E., Silva, V. C., & Nonato, M. C. (2015). Recombinant production, crystallization and crystal structure determination of dihydroorotate dehydrogenase from Leishmania (Viannia) braziliensis. Acta Crystallographica Section F:Structural Biology Communications, 71(Pt 5), 547–552. https://doi.org/10.1107/S2053230X15000886
Santana de Oliveira, M., Pereira da Silva, V. M., Cantão Freitas, L., Gomes Silva, S., Nevez Cruz, J., & de Aguiar Andrade, E. H. (2021). Extraction Yield, Chemical Composition, Preliminary Toxicity of Bignonia nocturna (Bignoniaceae) Essential Oil and in Silico Evaluation of the Interaction. Chemistry and Biodiversity, 18(4), cbdv.202000982. https://doi.org/10.1002/cbdv.202000982
Santos, C. B. R., Santos, K. L. B., Cruz, J. N., Leite, F. H. A., Borges, R. S., Taft, C. A., Campos, J. M., & Silva, C. H. T. P. (2020). Molecular modeling approaches of selective adenosine receptor type 2A agonists as potential anti-inflammatory drugs. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1761878
Santos Filho, O. A., & Alencastro, R. B. de. (2003). Modelagem de proteínas por homologia. Química Nova, 26(2), 253–259. https://doi.org/10.1590/s0100-40422003000200019
Thakur, S., Joshi, J., & Kaur, S. (2020). Leishmaniasis diagnosis: an update on the use of parasitological, immunological and molecular methods. In Journal of Parasitic Diseases 44(2), 253–272. Springer. https://doi.org/10.1007/s12639-020-01212-w
Thomsen, R., & Christensen, M. H. (2006). MolDock: A new technique for high-accuracy molecular docking. Journal of Medicinal Chemistry, 49(11), 3315–3321. https://doi.org/10.1021/jm051197e
Weetall, M., Kojima, K., Piya, S., Trotta, C., Baird, J., O’Keefe, K., Furia, B., Borthakur, G. M., & Spiegel, R. (2019). Inhibition of De Novo Pyrimidine Nucleotide Synthesis By the Novel DHODH Inhibitor PTC299 Induces Differentiation and/or Death of AML Cells. Blood, 134(Supplement_1), 5152–5152. https://doi.org/10.1182/blood-2019-124569
WHO. (2020). Leishmaniasis. https://www.who.int/news-room/fact-sheets/detail/leishmaniasis
Wu, D., Wang, W., Chen, W., Lian, F., Lang, L., Huang, Y., Xu, Y., Zhang, N., Chen, Y., Liu, M., Nussinov, R., Cheng, F., Lu, W., & Huang, J. (2018). Pharmacological inhibition of dihydroorotate dehydrogenase induces apoptosis and differentiation in acute myeloid leukemia cells. Haematologica, 103(9), 1472–1483. https://doi.org/10.3324/haematol.2018.188185
Xu, Y., Colletier, J. P., Weik, M., Jiang, H., Moult, J., Silman, I., & Sussman, J. L. (2008). Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray versus molecular dynamics. Biophysical Journal, 95(5), 2500–2511. https://doi.org/10.1529/biophysj.108.129601
Yerragunta, V., Gayathri, R., Srujana, S., patil, P., Srujana, S., Devi, R., & Divya, A. (2014). Benzimidazole Derivatives and its Biological Importance: A Review. PharmaTutor, 2(3), 109–113. http://www.pharmatutorjournal.com/index.php/pt/article/view/66
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