Molecular docking of rutenum complex with epiisopyloturin and nitric oxide against nucleoside diphosphate kinase protein Leishmania
DOI:
https://doi.org/10.33448/rsd-v9i2.2121Keywords:
Computational Biology; Anti-Infective Agents; Trypanosomatina.Abstract
Leishmaniasis is an infectious disease that affects both animals and humans, caused by flagellated parasites belonging to the genus Leishmania may present in different clinical forms depending on the infecting strain and the immune reaction of the host. The disease is estimated to reach about 700,000 to 1 million people, causing the deaths of 20 to 30,000 individuals annually. Thus, the present study aims to perform a molecular coupling simulation of the ruthenium complex with epiisopiloturin and nitric oxide against the protein Nucleoside diphosphate kinase from Leishmania amazonensis. The NDK 3D molecule was extracted from the PDB nucleic proteins and acids database. The 3D molecular structure of the Epiruno2 complex was designed using gaussview 5.0 software. The NDK target and Epiruno2 complex were prepared for docking simulations, where NDK was considered rigid and Epiruno2 was considered flexible. The Epiruno2 complex presented a good molecular affinity rate with the target protein, making it attractive for experimental trials in laboratories for Leishmania's NDK protein and NDKs of other pathogens, however, the drug miltefosin presented low molecular affinity for the same target, corroborating studies presented in the literature on the reduced efficacy of current drugs against leishmaniosis.
References
Berman, H. M. et al. (2000). The Protein Data Bank. Nucleic Acids Res, 28:235-242.
Boucher, H. W. et al. (2009). Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America. Clinical infectious diseases, 48(1):1-12.
Cosconati, S. et al. (2010). Virtual screening with AutoDock: theory and practice. Expert opinion on drug discovery, 5(6):597-607.
Dennington, R.; Keith, T.; Millam, J. (2009). GaussView, Version 5.0. 8, R.
Frisch, M. J. et al. (2009). Gaussian 09, Revision D. 01, Gaussian. Inc.: Wallingford, CT.
Garbin, S. et al. (2015). Complexos de rutênio (II) contendo 2- mercaptoimidazol e derivados: síntese, caracterização e avaliação da atividade biológica.
Goodsell, D. S.; Morris, G. M.; Olson, A. J. (1996). Automated docking of flexible ligands: applications of AutoDock. Journal of Molecular Recognition, 9(1):1-5.
Kantor, J. D. et al. (1993). Inhibition of cell motility after nm23 transfection of human and murine tumor cells. Cancer research, 53(9):1971-1973.
Kasbekar, N. (2006). Tigecycline: a new glycylcycline antimicrobial agent. American journal of health-system pharmacy, 63(13):1235-1243.
Khamesipour, A. (2014). Therapeutic vaccines for leishmaniasis. Expert opinion on biological therapy, 14(11):1641-1649.
Kohn, W.; Sham, L. J. (1965). Self-consistent equations including exchange and correlation effects. Physical review, 140(4A):A1133.
Lacombe, M. L. et al. (2000). The human Nm23/nucleoside diphosphate kinases. Journal of bioenergetics and biomembranes, 32(3):247-258.
Macdonald, N. J. et al. (1993). A serine phosphorylation of Nm23, and not its nucleoside diphosphate kinase activity, correlates with suppression of tumor metastatic potential. Journal of Biological Chemistry, 268(34):25780-25789.
Macedo, T. S. et al. (2017). Platinum (ii)–chloroquine complexes are antimalarial agents against blood and liver stages by impairing mitochondrial function. Metallomics, 9(11):1548-1561.
Meng, Xuan-Yu. et al. (2011). Molecular docking: a powerful approach for structure-based drug discovery. Current computer-aided drug design, 7(2):146-157.
Mishra, A. K. et al. (2017). Discovery of novel inhibitors for Leishmania nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization. Journal of computer-aided molecular design, 31(6):547-562.
Morris, G. M. et al. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of computational chemistry, 19(14):1639-1662.
Parks, R. E. et al. (1973). Purine metabolism in primitive erythrocytes. Comparative Biochemistry and Physiology--Part B: Biochemistry and, 45(2):355-364.
Perryman, A. L. et al. (2015). A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA. Journal of chemical information and modeling, 55(3):645-659.
Ramos, R. M. et al. (2012). Interaction of wild type, G68R and L125M isoforms of the arylamine-N-acetyltransferase from Mycobacterium tuberculosis with isoniazid: a computational study on a new possible mechanism of resistance. Journal of molecular modeling, 18(9):4013-4024.
Rocha, J. A. et al. (2018). Computational quantum chemistry, molecular docking, and ADMET predictions of imidazole alkaloids of Pilocarpus microphyllus with schistosomicidal properties. PloS one, 13(6):e0198476.
Rojas, R. et al. (2006). Resistance to antimony and treatment failure in human Leishmania (Viannia) infection. The Journal of infectious diseases, 193(10):1375-1383.
Sánchez-delgado, R. A. et al. (1998). Toward a novel metal based chemotherapy against tropical diseases 4. Synthesis and characterization of new metal-clotrimazole complexes and evaluation of their activity against Trypanosoma cruzi. Inorganica chimica acta, 275:528-540.
Solis, F. J.; Wets, R. J.-B. (1981). Minimization by random search techniques. Mathematics of operations research, 6(1):19-30.
Srivastava, S. K.; Rajasree, K.; Gopal, B. (2011). Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1814(10):1349-1357.
Theuretzbacher, U. (2009). Future antibiotics scenarios: is the tide starting to turn?. International journal of antimicrobial agents, 34(1):15-20.
WHO. Control of Leishmaniasis Report of a meeting of the WHO Committee of Experts on the Control of Leishmaniasis. 2019. Available from: http://www.who.int/mediacentre/factsheets/fs375/en/
Downloads
Published
How to Cite
Issue
Section
License
Authors who publish with this journal agree to the following terms:
1) Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
2) Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
3) Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work.
