Molecular docking studies of different phytochemicals obtained from medicinal Plants of Uttarakhand region for identification of potential inhibitors against mucormycosis causing fungal species
Article Main
Pallavi Singh
https://orcid.org/0000-0003-4537-4607
P.K Sudhanshu
K.G. Revathi
M. Maheswari
Shailejkumar D Bonde
Bharanidharan R
https://orcid.org/0000-0003-4537-4607
P.K Sudhanshu
K.G. Revathi
M. Maheswari
Shailejkumar D Bonde
Bharanidharan R
Abstract
Mucormycosis is an insidious fungal infection caused by members of Mucorales and zygomycotic species. During the last few years, mucormycosis has become the third most common invasive fungal infection in patients with haematological malignancies and organ transplantations. The incidence of mucormycosis is particularly high in patients with immunocompromised health. It has been reported that CotH receptor proteins have a potential role in binding Rhizopus species with the host cells. Further, CotH1, CotH2, and CotH3 are the spore-coating protein of mucormycosis, which are mostly responsible for the invasion of host cells and causing diseases. The present study aimed to predict the structure of CotH1, CotH2, and CotH3 receptors in Rhizpous delemar using homology modelling on SWISS Server and validated the model based on GMQE and QMEAN scores followed by analysis of the predicted model on Ramachandran plot. Further, molecular docking studies of the predominant 46 phytochemicals found in the medicinal plants of Uttarakhand region, India were done against these three receptors. Autodock vina results have shown that the binding energy value of Curcumin was -8.5 Kcal/mol against CotH1, and the binding energy value of Allosecurinin was -7.6 Kcal/mol against CotH2 and binding energy value of Isoquercetin was -7.7 Kcal/mol against CotH3. Evaluation of the ADMET parameters has shown the high efficacy of these compounds. The present Insilico study suggests that Curcumin, Allosecurinine, and Isoquercetin are effective lead molecules against the receptors CotH1, CotH2, and CotH3 in the mucormycosis caused by fungal species R. delemar.
Article Details
Article Details
Keywords
Allosecurinine, CotH, Curcumin, Docking, Homology Modelling, Isoquercetin, Mucormycosis, Pharmacokinetics, Rhizopus delemar
References
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Bienert, S., Waterhouse, A., de Beer, T.A.P., Tauriello, G., Studer, G., Bordoli, L. & Schwede, T.(2017). The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Res. 45, D313-D319. https://doi.org/10.1093/nar/gkw1132
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Dallakyan, Sargis & Olson, Arthur mall (2015)Molecule Library Screening by Docking with PyRx. Methods in molecular biology (Clifton, N.J.), 1263. 243-250. https://doi.org/10.1007/978-1-4939-2269-7_19.
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Deutsch, Peter George, Joshua Whittaker & Shashi Prasad (2019). Invasive and non-invasive fungal rhinosinusitis—a review and update of the evidence. Medicina 55.7: 319.
de Lira Mota, K. S., de Oliveira Pereira F, de Oliveira, W. A., Lima, I. O. & de Oliveira Lima E. (2012)Antifungal activity of Thymus vulgaris L. essential oil and its constituent phytochemicals against Rhizopus oryzae: interaction with ergosterol. Molecules.17(12):14418-33. doi: 10.3390/molecules171214418
García-Carnero L.C. & Mora-Montes H. M.(2022). Mucormycosis and COVID-19-Associated Mucormycosis: Insights of a Deadly but Neglected Mycosis. J Fungi (Basel). ;8(5):445. doi: 10.3390/jof8050445.
Gebremariam, T., Liu, M, Luo, G., Bruno, V., Phan, Q. T. & Waring, A. J. Edwards J. E. Jr, Filler, S.G., Yeaman, M.R. & Ibrahim, A. S. (2014). CotH3 mediates fungal invasion of host cells during mucormycosis. J Clin Invest.Jan;124(1):237-50. doi: 10.1172/JCI71349
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Ibrahim, A. S., Spellberg, B., Avanessian, V., Fu, Y. & Edwards, J. E., Jr (2005). Rhizopus oryzae adheres to, is phagocytosed by, and damages endothelial cells in vitro. Infection and immunity, 73(2), 778–783. https://doi.org/10.1128/IAI.73.2.778-783.2005
Ibrahim, A. S., Spellberg, B., Walsh, T. J., & Kontoyiannis, D. P. (2012). Pathogenesis of mucormycosis. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 54 Suppl 1(Suppl 1), S16–S22. https://doi.org/10.1093/cid/cir865
Kauffman, C. A. (2004). Zygomycosis: reemergence of an old pathogen. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 39(4), 588–590. https://doi.org/10.1086/422729
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J. & Bolton, E. E.(2019). PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res., ,49(D1), D1388–D1395. https://doi.org/10.1093/nar/gkaa971
Lipinski, Christopher A. (2004).Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov. Today Technol. 1, 337-341. Drug Discovery Today: Technologies.,1. 337-341. https://doi.org/10.1016/j.ddtec.2004.11.007.
Liu M, et al. (2010) The endothelial cell receptor GRP78 is required for mucormycosis pathogenesis in diabetic mice. J Clin Invest., 120(6):1914–1924. doi: 10.1172/JCI42164
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. J. Computational Chemistry 2009, 16: 2785-91. doi: 10.1002/jcc.21256
Neblett Fanfair, R., Benedict, K., Bos, J., Bennett, S. D., Lo, Y. C., Adebanjo, T., Etienne, K., Deak, E., Derado, G., Shieh, W. J., Drew, C., Zaki, S., Sugerman, D., Gade, L., Thompson, E. H., Sutton, D. A., Engelthaler, D. M., Schupp, J. M., Brandt, M. E., Harris, J. R., …& Park, B. J. (2012). Necrotizing cutaneous mucormycosis after a tornado in Joplin, Missouri, in 2011. The New England Journal of Medicine, 367(23), 2214–2225. https://doi.org/10.1056/NEJMoa1204781
Prakash H, Chakrabarti A (2019).Global Epidemiology of Mucormycosis. Journal of Fungi. 5(1):26. https://doi.org/10.3390/jof5010026
Petrikkos, G., Skiada, A., Lortholary, O., Roilides, E., Walsh, T. J. & Kontoyiannis, D. P. (2012). Epidemiology and clinical manifestations of mucormycosis. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 54 Suppl 1, S23–S34. https://doi.org/10.1093/cid/cir866
Ribes, J. A., Vanover-Sams, C. L. & Baker, D. J. (2000). Zygomycetes in human disease. Clinical Microbiology Reviews, 13(2), 236–301. https://doi.org/10.1128/CMR.13.2.236.
Renu Jangid, Tahira Begum (2022). Antimycotic activity of some medicinal plants against Mucor circinelloides. Biomed Research International, 22, 1-5, https://doi.org/1 0.1155/2022/3523920.
Roden, M. M., Zaoutis, T. E., Buchanan, W. L., Knudsen, T. A., Sarkisova, T. A., Schaufele, R. L., Sein, M., Sein, T., Chiou, C. C., Chu, J. H., Kontoyiannis, D. P. & Walsh, T. J. (2005). Epidemiology and outcome of zygomycosis: a review of 929 reported cases. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 41(5), 634–653. https://doi.org/10.10 86/432579
Sander, T. (2001). OSIRIS Property Explorer. Organic Chemistry Portal.
Sharma, S., Sharma, A., Gupta, U. (2021). Molecular Docking studies on the Antifungal activity of Allium sativum (Garlic) against Mucormycosis (black fungus) by BIOVIA discovery studio visualizer 21.1.0.0. Ann Antivir Antiretrovir 5(1): 028-032. DOI: https://dx.doi.org/10.1 7352/aaa.000013
Spellberg, B., Edwards Jr, J. & Ibrahim, A. (2005). Novel perspectives on mucormycosis: pathophysiology, presentation, and management. Clinical microbiology reviews, 18(3), 556-569. https://doi.org/10.1128/CMR.18.3.556-569.2 005
Skiada A, Pavleas I, Drogari-Apiranthitou M.(2020). Epidemiology and Diagnosis of Mucormycosis: An update. Journal of Fungi, 6(4),265. https://doi.org/10.3390/jof6040265
Skiada, A, L. Pagano, A. Groll, S. Zimmerli, B. Dupont, K. Lagrou, C. Lass-Florl, E. Bouza, N. Klimko, P. Gaustad, M. Richardson, P. Hamal, M. Akova, J.F. Meis, J.-L. Rodriguez-Tudela, E. Roilides, A. & Mitrousia-Ziouva, G. Petrikkos (2011).Zygomycosis in Europe: analysis of 230 cases accrued by the registry of the European Confederation of Medical Mycology (ECMM) Working Group on Zygomycosis between 2005 and 2007,Clinical Microbiology and Infection, Volume 17 (12)Pages 1859-1867,https://doi.org/10.1111/j.1469-0691.2010.03456.x.
Spellberg, B., Walsh, T. J., Kontoyiannis, D. P., Edwards, J., Jr. & Ibrahim, A. S. (2009). Recent advances in the management of mucormycosis: from bench to bedside. Clinical Infectious Diseases, 48(12), 1743–1751. https://doi.org/10.1086/599105
Spellberg, B., Edwards, J., Jr., & Ibrahim, A. (2005). Novel perspectives on mucormycosis: pathophysiology, presentation, and management. Clinical Microbiology Reviews, 18(3), 556–569. https://doi.org/10.1128/CMR.1 8.3.556-569.2005
Studer, G., Rempfer, C., Waterhouse, A.M., Gumienny, G., Haas, J. & Schwede, T. (2020). Q MEAND is Co - distance constraints applied on model quality estimation. Bioinformatics 36, 1765-1771 https://doi.org/10.1093/bioinformatics/btz828
Vikas Jha, Bhakti Madaye, Esha Gupta, Shreya Thube, Sankalp Kasbe, Darpan Kaur Matharoo, Piya Shah, Mafiz Shaikh & Arpita Marick. (2022). Molecular Docking Studies of Phytochemicals Against RNA-dependent RNA Polymerase of Mucormycosis, Journal of Diseases and Medicinal Plants. 8 (2), 34-40. doi: 10.11648/j.jdmp.20 220802.13
Wächtler, B., Citiulo, F., Jablonowski, N., Förster, S., Dalle, F., Schaller, M., Wilson, D. & Hube, B. (2012). Candida albicans-epithelial interactions: dissecting the roles of active penetration, induced endocytosis and host factors on the infection process. PloS one, 7(5), e36952. https://doi.org/10.1371/journal.pone.0036952
41) Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R. & Schwede, T. (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1), W296-W303 https://doi.org/10.1093/nar/gky427
Ashraf S. Ibrahim, Brad Spellberg, Thomas J. Walsh & Dimitrios P. Kontoyiannis. (2012) Pathogenesis of Mucormycosis, Clinical Infectious Diseases, Volume 54, Pages S16–S22, https://doi.org/10.1093/cid/cir865
Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L. & Schwede, T.(2017). Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports 7 . https://doi.org/10.1038/s41598-017-09654-8
Bhadauria S & P. Kumar. (2011).In vitro antimycotic activity of some medicinal plants against human pathogenic dermatophytes Indian journal of fundamental and Applied Life Sciences, vol. 1, pp. 2231–6345.
Bienert, S., Waterhouse, A., de Beer, T.A.P., Tauriello, G., Studer, G., Bordoli, L. & Schwede, T.(2017). The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Res. 45, D313-D319. https://doi.org/10.1093/nar/gkw1132
Biswas, S. & Hasija, Y. (2022).Mucormycosis Vaccine Design using Bioinformatic Tools. Lecture Notes in Electrical Engineering .[DOI: 10.1007/978-981-16-9885-9_21]
BIOVIA, Dassault Systèmes, BIOVIA Workbook, Release (2020). BIOVIA Pipeline Pilot, Release 2020, San Diego
Chander, J., Kaur, M., Singla, N., Punia, R. P.S., Singhal, S. K., Attri, A.K., Alastruey-Izquierdo, A., Stchigel, A. M., Cano-Lira, J. F. & Guarro, J. (2018). Mucormycosis: Battle with the Deadly Enemy over a Five-Year Period in India. J. Fungi (Basel). 6;4(2):46. doi: 10.3390/jof4020046
Clara Baldin, Ashraf S. Ibrahim (2017). Molecular mechanisms of mucormycosis-The bitter and the sweet. PLOS. 13(8).
Dallakyan, Sargis & Olson, Arthur mall (2015)Molecule Library Screening by Docking with PyRx. Methods in molecular biology (Clifton, N.J.), 1263. 243-250. https://doi.org/10.1007/978-1-4939-2269-7_19.
Daina, A., Michielin, O. & Zoete, V. (2017).SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 7, 42717. https://doi.org/10.1038/srep42717
Deutsch, Peter George, Joshua Whittaker & Shashi Prasad (2019). Invasive and non-invasive fungal rhinosinusitis—a review and update of the evidence. Medicina 55.7: 319.
de Lira Mota, K. S., de Oliveira Pereira F, de Oliveira, W. A., Lima, I. O. & de Oliveira Lima E. (2012)Antifungal activity of Thymus vulgaris L. essential oil and its constituent phytochemicals against Rhizopus oryzae: interaction with ergosterol. Molecules.17(12):14418-33. doi: 10.3390/molecules171214418
García-Carnero L.C. & Mora-Montes H. M.(2022). Mucormycosis and COVID-19-Associated Mucormycosis: Insights of a Deadly but Neglected Mycosis. J Fungi (Basel). ;8(5):445. doi: 10.3390/jof8050445.
Gebremariam, T., Liu, M, Luo, G., Bruno, V., Phan, Q. T. & Waring, A. J. Edwards J. E. Jr, Filler, S.G., Yeaman, M.R. & Ibrahim, A. S. (2014). CotH3 mediates fungal invasion of host cells during mucormycosis. J Clin Invest.Jan;124(1):237-50. doi: 10.1172/JCI71349
Guex, N., Peitsch, M.C. & Schwede, T.(2009). Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis 30, S162-S173 . https://doi.org/10.1002/elps.200900140
Hamaamin Hussen N, Hameed Hasan A, Jamalis J, Shakya S, Chander S, Kharkwal H, Murugesan S, Ajit Bastikar V, Pyarelal Gupta P.(2022). Potential inhibitory activity of phytoconstituents against black fungus: In silico ADMET, molecular docking and MD simulation studies. Comput Toxicol. ,24:100247. doi: 10.1016/j.comtox.2022.100247.
Ibrahim, A. S., Spellberg, B., Avanessian, V., Fu, Y. & Edwards, J. E., Jr (2005). Rhizopus oryzae adheres to, is phagocytosed by, and damages endothelial cells in vitro. Infection and immunity, 73(2), 778–783. https://doi.org/10.1128/IAI.73.2.778-783.2005
Ibrahim, A. S., Spellberg, B., Walsh, T. J., & Kontoyiannis, D. P. (2012). Pathogenesis of mucormycosis. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 54 Suppl 1(Suppl 1), S16–S22. https://doi.org/10.1093/cid/cir865
Kauffman, C. A. (2004). Zygomycosis: reemergence of an old pathogen. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 39(4), 588–590. https://doi.org/10.1086/422729
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J. & Bolton, E. E.(2019). PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res., ,49(D1), D1388–D1395. https://doi.org/10.1093/nar/gkaa971
Lipinski, Christopher A. (2004).Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov. Today Technol. 1, 337-341. Drug Discovery Today: Technologies.,1. 337-341. https://doi.org/10.1016/j.ddtec.2004.11.007.
Liu M, et al. (2010) The endothelial cell receptor GRP78 is required for mucormycosis pathogenesis in diabetic mice. J Clin Invest., 120(6):1914–1924. doi: 10.1172/JCI42164
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. J. Computational Chemistry 2009, 16: 2785-91. doi: 10.1002/jcc.21256
Neblett Fanfair, R., Benedict, K., Bos, J., Bennett, S. D., Lo, Y. C., Adebanjo, T., Etienne, K., Deak, E., Derado, G., Shieh, W. J., Drew, C., Zaki, S., Sugerman, D., Gade, L., Thompson, E. H., Sutton, D. A., Engelthaler, D. M., Schupp, J. M., Brandt, M. E., Harris, J. R., …& Park, B. J. (2012). Necrotizing cutaneous mucormycosis after a tornado in Joplin, Missouri, in 2011. The New England Journal of Medicine, 367(23), 2214–2225. https://doi.org/10.1056/NEJMoa1204781
Prakash H, Chakrabarti A (2019).Global Epidemiology of Mucormycosis. Journal of Fungi. 5(1):26. https://doi.org/10.3390/jof5010026
Petrikkos, G., Skiada, A., Lortholary, O., Roilides, E., Walsh, T. J. & Kontoyiannis, D. P. (2012). Epidemiology and clinical manifestations of mucormycosis. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 54 Suppl 1, S23–S34. https://doi.org/10.1093/cid/cir866
Ribes, J. A., Vanover-Sams, C. L. & Baker, D. J. (2000). Zygomycetes in human disease. Clinical Microbiology Reviews, 13(2), 236–301. https://doi.org/10.1128/CMR.13.2.236.
Renu Jangid, Tahira Begum (2022). Antimycotic activity of some medicinal plants against Mucor circinelloides. Biomed Research International, 22, 1-5, https://doi.org/1 0.1155/2022/3523920.
Roden, M. M., Zaoutis, T. E., Buchanan, W. L., Knudsen, T. A., Sarkisova, T. A., Schaufele, R. L., Sein, M., Sein, T., Chiou, C. C., Chu, J. H., Kontoyiannis, D. P. & Walsh, T. J. (2005). Epidemiology and outcome of zygomycosis: a review of 929 reported cases. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 41(5), 634–653. https://doi.org/10.10 86/432579
Sander, T. (2001). OSIRIS Property Explorer. Organic Chemistry Portal.
Sharma, S., Sharma, A., Gupta, U. (2021). Molecular Docking studies on the Antifungal activity of Allium sativum (Garlic) against Mucormycosis (black fungus) by BIOVIA discovery studio visualizer 21.1.0.0. Ann Antivir Antiretrovir 5(1): 028-032. DOI: https://dx.doi.org/10.1 7352/aaa.000013
Spellberg, B., Edwards Jr, J. & Ibrahim, A. (2005). Novel perspectives on mucormycosis: pathophysiology, presentation, and management. Clinical microbiology reviews, 18(3), 556-569. https://doi.org/10.1128/CMR.18.3.556-569.2 005
Skiada A, Pavleas I, Drogari-Apiranthitou M.(2020). Epidemiology and Diagnosis of Mucormycosis: An update. Journal of Fungi, 6(4),265. https://doi.org/10.3390/jof6040265
Skiada, A, L. Pagano, A. Groll, S. Zimmerli, B. Dupont, K. Lagrou, C. Lass-Florl, E. Bouza, N. Klimko, P. Gaustad, M. Richardson, P. Hamal, M. Akova, J.F. Meis, J.-L. Rodriguez-Tudela, E. Roilides, A. & Mitrousia-Ziouva, G. Petrikkos (2011).Zygomycosis in Europe: analysis of 230 cases accrued by the registry of the European Confederation of Medical Mycology (ECMM) Working Group on Zygomycosis between 2005 and 2007,Clinical Microbiology and Infection, Volume 17 (12)Pages 1859-1867,https://doi.org/10.1111/j.1469-0691.2010.03456.x.
Spellberg, B., Walsh, T. J., Kontoyiannis, D. P., Edwards, J., Jr. & Ibrahim, A. S. (2009). Recent advances in the management of mucormycosis: from bench to bedside. Clinical Infectious Diseases, 48(12), 1743–1751. https://doi.org/10.1086/599105
Spellberg, B., Edwards, J., Jr., & Ibrahim, A. (2005). Novel perspectives on mucormycosis: pathophysiology, presentation, and management. Clinical Microbiology Reviews, 18(3), 556–569. https://doi.org/10.1128/CMR.1 8.3.556-569.2005
Studer, G., Rempfer, C., Waterhouse, A.M., Gumienny, G., Haas, J. & Schwede, T. (2020). Q MEAND is Co - distance constraints applied on model quality estimation. Bioinformatics 36, 1765-1771 https://doi.org/10.1093/bioinformatics/btz828
Vikas Jha, Bhakti Madaye, Esha Gupta, Shreya Thube, Sankalp Kasbe, Darpan Kaur Matharoo, Piya Shah, Mafiz Shaikh & Arpita Marick. (2022). Molecular Docking Studies of Phytochemicals Against RNA-dependent RNA Polymerase of Mucormycosis, Journal of Diseases and Medicinal Plants. 8 (2), 34-40. doi: 10.11648/j.jdmp.20 220802.13
Wächtler, B., Citiulo, F., Jablonowski, N., Förster, S., Dalle, F., Schaller, M., Wilson, D. & Hube, B. (2012). Candida albicans-epithelial interactions: dissecting the roles of active penetration, induced endocytosis and host factors on the infection process. PloS one, 7(5), e36952. https://doi.org/10.1371/journal.pone.0036952
41) Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R. & Schwede, T. (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1), W296-W303 https://doi.org/10.1093/nar/gky427
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Molecular docking studies of different phytochemicals obtained from medicinal Plants of Uttarakhand region for identification of potential inhibitors against mucormycosis causing fungal species. (2023). Journal of Applied and Natural Science, 15(1), 162-177. https://doi.org/10.31018/jans.v15i1.4123
