Identification of potential novel inhibitors against glutamine synthetase enzyme of Leishmania major by using computational tools

References

• Akilov, O. E., Khachemoune, A., & Hasan, T. (2007). Clinical manifestations and classification of Old World cutaneous leishmaniasis. International Journal of Dermatology, 46(2), 132–142. https://doi.org/10.1111/j.1365-4632.2007.03154.x
   PubMed Web of Science ®Google Scholar
• Allarakhia, M. (2013). Open-source approaches for the repurposing of existing or failed candidate drugs: Learning from and applying the lessons across diseases. Drug Design, Development and Therapy, 7, 753–766. https://doi.org/10.2147/DDDT.S46289
   PubMed Web of Science ®Google Scholar
• Anversa, L., Tiburcio, M. G. S., Richini-Pereira, V. B., & Ramirez, L. E. (2018). Human leishmaniasis in Brazil: A general review. Revista da Associação Médica Brasileira, 64(3), 281–289. https://doi.org/10.1590/1806-9282.64.03.281
   PubMed Web of Science ®Google Scholar
• Ashburn, T. T., & Thor, K. B. (2004). Drug repositioning: Identifying and developing new uses for existing drugs. Nature Reviews. Drug Discovery, 3(8), 673–683. https://doi.org/10.1038/nrd1468
   PubMed Web of Science ®Google Scholar
• Bellera, C. L., Balcazar, D. E., Vanrell, M. C., Casassa, A. F., Palestro, P. H., Gavernet, L., Labriola, C. A., Gálvez, J., Bruno-Blanch, L. E., Romano, P. S., Carrillo, C., & Talevi, A. (2015). Computer-guided drug repurposing: Identification of trypanocidal activity of clofazimine, benidipine and saquinavir. European Journal of Medicinal Chemistry, 93, 338–348. https://doi.org/10.1016/j.ejmech.2015.01.065
   PubMed Web of Science ®Google Scholar
• Burbaeva, G. S., Boksha, I. S., Tereshkina, E. B., Savushkina, O. K., Starodubtseva, L. I., & Turishcheva, M. S. (2005). Glutamate metabolizing enzymes in prefrontal cortex of Alzheimer’s disease patients. Neurochemical Research, 30(11), 1443–1451. https://doi.org/10.1007/s11064-005-8654-x
   PubMed Web of Science ®Google Scholar
• Chen, J., Yin, B., Pang, L., Wang, W., Zhang, J. Z. H., & Zhu, T. (2020). Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: Insight into molecular mechanisms based on multiple simulation technologies. Journal of Biomolecular Structure & Dynamics, 38(7), 2141–2155. https://doi.org/10.1080/07391102.2019.1624616
   PubMed Web of Science ®Google Scholar
• Chen, J., Zeng, Q., Wang, W., Sun, H., & Hu, G. (2022). Decoding the identification mechanism of an SAM-III Riboswitch on ligands through multiple independent Gaussian-accelerated molecular dynamics simulations. Journal of Chemical Information and Modeling, 62(23), 6118–6132. https://doi.org/10.1021/acs.jcim.2c00961
   PubMedGoogle Scholar
• Crispim, M., Damasceno, F. S., Hernández, A., Barisón, M. J., Pretto Sauter, I., Souza Pavani, R., Santos Moura, A., Pral, E. M. F., Cortez, M., Elias, M. C., & Silber, A. M. (2018). The glutamine synthetase of Trypanosoma cruzi is required for its resistance to ammonium accumulation and evasion of the parasitophorous vacuole during host-cell infection. PLoS Neglected Tropical Diseases, 12(1), e0006170. https://doi.org/10.1371/journal.pntd.0006170
   PubMed Web of Science ®Google Scholar
• Crowther, G. J., Shanmugam, D., Carmona, S. J., Doyle, M. A., Hertz-Fowler, C., Berriman, M., Nwaka, S., Ralph, S. A., Roos, D. S., Van Voorhis, W. C., & Agüero, F. (2010). Identification of attractive drug targets in neglected-disease pathogens using an in silico approach. PLoS Neglected Tropical Diseases, 4(8), e804. https://doi.org/10.1371/journal.pntd.0000804
   PubMed Web of Science ®Google Scholar
• Cruzat, V., Macedo Rogero, M., Noel Keane, K., Curi, R., & Newsholme, P. (2018). Glutamine: Metabolism and immune function, supplementation and clinical translation. Nutrients, 10(11), E1564. https://doi.org/10.3390/nu10111564
   PubMed Web of Science ®Google Scholar
• Ekins, S., Williams, A. J., Krasowski, M. D., & Freundlich, J. S. (2011). In silico repositioning of approved drugs for rare and neglected diseases. Drug Discovery Today, 16(7–8), 298–310. https://doi.org/10.1016/j.drudis.2011.02.016
   PubMed Web of Science ®Google Scholar
• Fatumo, S., Plaimas, K., Mallm, J.-P., Schramm, G., Adebiyi, E., Oswald, M., Eils, R., & König, R. (2009). Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 9(3), 351–358. https://doi.org/10.1016/j.meegid.2008.01.007
   PubMed Web of Science ®Google Scholar
• Ferrari, A. M., Degliesposti, G., Sgobba, M., & Rastelli, G. (2007). Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors. Bioorganic & Medicinal Chemistry, 15(24), 7865–7877. https://doi.org/10.1016/j.bmc.2007.08.019
   PubMed Web of Science ®Google Scholar
• Fisher, S. H. (1999). Regulation of nitrogen metabolism in Bacillus subtilis: Vive la différence! Molecular Microbiology, 32(2), 223–232. https://doi.org/10.1046/j.1365-2958.1999.01333.x
   PubMed Web of Science ®Google Scholar
• Forde, B. G., & Lea, P. J. (2007). Glutamate in plants: Metabolism, regulation, and signalling. Journal of Experimental Botany, 58(9), 2339–2358. https://doi.org/10.1093/jxb/erm121
   PubMed Web of Science ®Google Scholar
• Gaillard, T. (2018). Evaluation of AutoDock and AutoDock Vina on the CASF-2013 benchmark. Journal of Chemical Information and Modeling, 58(8), 1697–1706. https://doi.org/10.1021/acs.jcim.8b00312
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Gervazoni, L., F. O., Barcellos, G. B., Ferreira-Paes, T., & Almeida-Amaral, E. E. (2020). Use of natural products in leishmaniasis chemotherapy: An overview. Frontiers in Chemistry, 8, 579891. https://doi.org/10.3389/fchem.2020.579891
   PubMed Web of Science ®Google Scholar
• Ghatee, M. A., Taylor, W. R., & Karamian, M. (2020). The geographical distribution of cutaneous leishmaniasis causative agents in iran and its neighboring countries. Frontiers in Public Health, 8, 11. https://doi.org/10.3389/fpubh.2020.00011
   PubMed Web of Science ®Google Scholar
• Haber, A., Friedman, S., Lobel, L., Burg-Golani, T., Sigal, N., Rose, J., Livnat-Levanon, N., Lewinson, O., & Herskovits, A. A. (2017). L-glutamine induces expression of Listeria monocytogenes virulence genes. PLoS Pathogens, 13(1), e1006161. https://doi.org/10.1371/journal.ppat.1006161
   PubMed Web of Science ®Google Scholar
• Herrera Acevedo, C., Scotti, L., Feitosa Alves, M., Formiga Melo Diniz, M. D. F., & Scotti, M. T. (2017). Computer-aided drug design using sesquiterpene lactones as sources of new structures with potential activity against infectious neglected diseases. Molecules (Basel, Switzerland), 22(1), 79. https://doi.org/10.3390/molecules22010079
   PubMed Web of Science ®Google Scholar
• Irwin, J. J., & Shoichet, B. K. (2005). ZINC–a free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling, 45(1), 177–182. https://doi.org/10.1021/ci049714+
   PubMed Web of Science ®Google Scholar
• Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997). Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology, 267(3), 727–748. https://doi.org/10.1006/jmbi.1996.0897
   PubMed Web of Science ®Google Scholar
• Kashif, M., Hira, S. K., & Manna, P. P. (2021). Immunoinformatics based design and prediction of proteome-wide killer cell epitopes of Leishmania donovani: Potential application in vaccine development. Journal of Biomolecular Structure & Dynamics, 40(21), 1–14. https://doi.org/10.1080/07391102.2021.1945495
   Web of Science ®Google Scholar
• Kashif, M., Hira, S. K., Upadhyaya, A., Gupta, U., Singh, R., Paladhi, A., Khan, F. I., Rub, A., & Manna, P. P. (2019). In silico studies and evaluation of antiparasitic role of a novel pyruvate phosphate dikinase inhibitor in Leishmania donovani infected macrophages. International Journal of Antimicrobial Agents, 53(4), 508–514. https://doi.org/10.1016/j.ijantimicag.2018.12.011
   PubMed Web of Science ®Google Scholar
• Kashif, M., Manna, P. P., Akhter, Y., Alaidarous, M., & Rub, A. (2017). Screening of novel inhibitors against leishmania donovani calcium ion channel to fight leishmaniasis. Infectious Disorders Drug Targets, 17(2), 120–129. https://doi.org/10.2174/1871526516666161230124513
   PubMedGoogle Scholar
• Kashif, M., Paladhi, A., Singh, R., Bhattacharyya, S., Hira, S. K., & Manna, P. P. (2020). Leishmanicidal activity of an in silico-screened novel inhibitor against ascorbate peroxidase of Leishmania donovani. Antimicrobial Agents and Chemotherapy, 64(7), e01766-19. https://doi.org/10.1128/AAC.01766-19
   PubMed Web of Science ®Google Scholar
• Kashif, M., Tabrez, S., Husein, A., Arish, M., Kalaiarasan, P., Manna, P. P., Subbarao, N., Akhter, Y., & Rub, A. (2018). Identification of novel inhibitors against UDP-galactopyranose mutase to combat leishmaniasis. Journal of Cellular Biochemistry, 119(3), 2653–2665. https://doi.org/10.1002/jcb.26433
   PubMed Web of Science ®Google Scholar
• Kumar, V., Ghosh, S., Roy, K., Pal, C., & Singh, S. (2021). Deletion of glutamine synthetase gene disrupts the survivability and infectivity of Leishmania donovani. Frontiers in Cellular and Infection Microbiology, 11, 622266. https://doi.org/10.3389/fcimb.2021.622266
   PubMed Web of Science ®Google Scholar
• Kumari, M., & Subbarao, N. (2020). Virtual screening to identify novel potential inhibitors for Glutamine synthetase of Mycobacterium tuberculosis. Journal of Biomolecular Structure & Dynamics, 38(17), 5062–5080. https://doi.org/10.1080/07391102.2019.1695670
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R, & Lynn, A. (2014). g_mmpbsa—A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., Rullmannn, J. A., MacArthur, M. W., Kaptein, R., & Thornton, J. M. (1996). AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular NMR, 8(4), 477–486. https://doi.org/10.1007/BF00228148
   PubMed Web of Science ®Google Scholar
• Liu, Z., Fang, H., Reagan, K., Xu, X., Mendrick, D. L., Slikker, W., & Tong, W. (2013). In silico drug repositioning: What we need to know. Drug Discovery Today, 18(3–4), 110–115. https://doi.org/10.1016/j.drudis.2012.08.005
   PubMed Web of Science ®Google Scholar
• Mann, S., Frasca, K., Scherrer, S., Henao-Martínez, A. F., Newman, S., Ramanan, P., & Suarez, J. A. (2021). A review of leishmaniasis: Current knowledge and future directions. Current Tropical Medicine Reports, 8(2), 121–132. https://doi.org/10.1007/s40475-021-00232-7
   PubMedGoogle Scholar
• Martins, D. R. A., Jeronimo, S. M. B., Donelson, J. E., & Wilson, M. E. (2006). Leishmania chagasi T-cell antigens identified through a double library screen. Infection and Immunity, 74(12), 6940–6948. https://doi.org/10.1128/IAI.02032-05
   PubMed Web of Science ®Google Scholar
• Morris, A. L., MacArthur, M. W., Hutchinson, E. G., & Thornton, J. M. (1992). Stereochemical quality of protein structure coordinates. Proteins, 12(4), 345–364. https://doi.org/10.1002/prot.340120407
   PubMed Web of Science ®Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Newsholme, P., Lima, M. M. R., Procopio, J., Pithon-Curi, T. C., Doi, S. Q., Bazotte, R. B., & Curi, R. (2003). Glutamine and glutamate as vital metabolites. Brazilian Journal of Medical and Biological Research = Revista Brasileira de Pesquisas Medicas e Biologicas, 36(2), 153–163. https://doi.org/10.1590/s0100-879x2003000200002
   PubMed Web of Science ®Google Scholar
• Paz, C., Samake, S., Anderson, J. M., Faye, O., Traore, P., Tall, K., Cisse, M., Keita, S., Valenzuela, J. G., & Doumbia, S. (2013). Leishmania major, the predominant Leishmania species responsible for cutaneous leishmaniasis in Mali. The American Journal of Tropical Medicine and Hygiene, 88(3), 583–585. https://doi.org/10.4269/ajtmh.12-0434
   PubMed Web of Science ®Google Scholar
• Pham, T. N. H., Nguyen, T. H., Tam, N. M., Y., Vu, T., Pham, N. T., Huy, N. T., Mai, B. K., Tung, N. T., Pham, M. Q., V., Vu, V., & Ngo, S. T. (2022). Improving ligand-ranking of AutoDock Vina by changing the empirical parameters. Journal of Computational Chemistry, 43(3), 160–169. https://doi.org/10.1002/jcc.26779
   PubMed Web of Science ®Google Scholar
• Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van der Spoel, D., Hess, B., & Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England), 29(7), 845–854. https://doi.org/10.1093/bioinformatics/btt055
   PubMed Web of Science ®Google Scholar
• Richmond, T. J. (1984). Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. Journal of Molecular Biology, 178(1), 63–89. https://doi.org/10.1016/0022-2836(84)90231-6
   PubMed Web of Science ®Google Scholar
• Rodrigues, B. C., Ferreira, M. F., Barroso, D. H., Motta, J. O. C., da, P., de, C. D. R., Porto, C., Martins, S. S., Gomes, C. M., & Sampaio, R. N. R. (2020). A retrospective cohort study of the effectiveness and adverse events of intralesional pentavalent antimonials in the treatment of cutaneous leishmaniasis. International Journal for Parasitology. Drugs and Drug Resistance, 14, 257–263. https://doi.org/10.1016/j.ijpddr.2020.11.002
   PubMed Web of Science ®Google Scholar
• Sánchez-Suárez, J., Bernal, F. A., & Coy-Barrera, E. (2020). Colombian contributions fighting leishmaniasis: A systematic review on antileishmanials combined with chemoinformatics analysis. Molecules (Basel, Switzerland), 25(23), 5704. https://doi.org/10.3390/molecules25235704
   PubMed Web of Science ®Google Scholar
• Saunders, E. C., Ng, W. W., Kloehn, J., Chambers, J. M., Ng, M., & McConville, M. J. (2014). Induction of a stringent metabolic response in intracellular stages of Leishmania mexicana leads to increased dependence on mitochondrial metabolism. PLoS Pathogens, 10(1), e1003888. https://doi.org/10.1371/journal.ppat.1003888
   PubMed Web of Science ®Google Scholar
• Sbaraglini, M. L., Vanrell, M. C., Bellera, C. L., Benaim, G., Carrillo, C., Talevi, A., & Romano, P. S. (2016). Neglected tropical protozoan diseases: Drug repositioning as a rational option. Current Topics in Medicinal Chemistry, 16(19), 2201–2222. https://doi.org/10.2174/1568026616666160216154309
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Uliana, S. R. B., Trinconi, C. T., & Coelho, A. C. (2018). Chemotherapy of leishmaniasis: Present challenges. Parasitology, 145(4), 464–480. https://doi.org/10.1017/S0031182016002523
   PubMed Web of Science ®Google Scholar
• van Aalten, D. M., Bywater, R., Findlay, J. B., Hendlich, M., Hooft, R. W., & Vriend, G. (1996). PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. Journal of Computer-Aided Molecular Design, 10(3), 255–262. https://doi.org/10.1007/BF00355047
   PubMed Web of Science ®Google Scholar
• Vojtkova, B., Spitzova, T., Votypka, J., Lestinova, T., Kominkova, I., Hajkova, M., Santos-Mateus, D., Miles, M. A., Volf, P., & Sadlova, J. (2020). Central Asian rodents as model animals for Leishmania major and Leishmania donovani research. Microorganisms, 8(9), 1440. https://doi.org/10.3390/microorganisms8091440
   PubMedGoogle Scholar
• Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8(2), 127–134. https://doi.org/10.1093/protein/8.2.127
   PubMedGoogle Scholar
• Waseem, M., Thakur, J. K., & Subbarao, N. (2022). Prediction of novel and potent inhibitors of lanosterol 14-α demethylase. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2022.2096116
   Web of Science ®Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue), W407–410. https://doi.org/10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12(1), 7–8. https://doi.org/10.1038/nmeth.3213
   PubMed Web of Science ®Google Scholar
• Zhang, C., Freddolino, P. L., & Zhang, Y. (2017). COFACTOR: Improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Research, 45(W1), W291–W299. https://doi.org/10.1093/nar/gkx366
   PubMed Web of Science ®Google Scholar
• Zheng, W., Zhang, C., Li, Y., Pearce, R., Bell, E. W., & Zhang, Y. (2021). Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Reports Methods, 1(3), 100014. https://doi.org/10.1016/j.crmeth.2021.100014
   PubMedGoogle Scholar