Some Selected Phytoconstituents from Rhus succedanea as SARS CoV-2 Main Protease and Spike protein (COVID-19) Inhibitors Selective Phytoconstituents from Rhus succedanea against SARS CoV-2: In silico approach
Iranian Journal of Pharmaceutical Sciences,
Vol. 17 No. 4 (2021),
1 October 2021
,
Page 107-122
https://doi.org/10.22037/ijps.v17.40249
Abstract
Rhus succedanea (Anacardiaceae) was used to treat multiple human afflictions. Literary works demonstrate that it has many biological activities. Today's research aims to recognize Rhus succedanea Phyto-derived anti-viral compounds against the main protease and spike protein of the viral agent of COVID-19 (SARS-CoV-2) gain insight into the molecular interactions. In the current study, ten molecules taken from R. succedanea are analyzed through docking, derived from the PubChem database. Docking experiments with Autodock vina and PyRx tools were conducted. AdmetSAR and DruLito servers were eventually used for drug-like prediction. Our research shows that the phytoconstituents from R. succedanea, namely, Amentoflavone, Rhoifolin, and Agathisflavone acts against SARS CoV-2 main protease with the binding affinity of -9.3, -8.6 and -8.4 Kcal/mol; Hinokiflavone Robustaflavone and Amentoflavone acts against the SARS-CoV-2 receptor-binding domain of spike protein with a binding affinity of -10.5, -10.4 and -10.1 Kcal/mol respectively. These phyto-compounds can use contemporary strategies to develop effective medicines from natural origins. The substances identified potential anti-viral as likely. However, In-vitro studies are even more necessary to assess their effectiveness versus SARS CoV-2.
Keywords:
- ADMET, In-silico
- Lipinski's Rule
- PyRx
- Rhus succedanea
How to Cite
D. S. N. B. K., P., Achanta, S., Prasad Panda, S., Rao Atmakuri, L., Guntupalli, C., Rao Alla, N., Jamullamudi, R. N., Mohammed, J., Lanka, H., Nayudu, T., Tera, S., Koti, B., Chigurupati, M., Kolla, L., Tata, P., & Chittiprolu, P. (2021). Some Selected Phytoconstituents from Rhus succedanea as SARS CoV-2 Main Protease and Spike protein (COVID-19) Inhibitors: Selective Phytoconstituents from Rhus succedanea against SARS CoV-2: In silico approach. Iranian Journal of Pharmaceutical Sciences, 17(4), 107–122. https://doi.org/10.22037/ijps.v17.40249
References
[1] Organization WH. Coronavirus disease 2019 (COVID-19): situation report, 70. (2020).
[2] Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y, Qiu Y, Wang J, Liu Y, Wei Y, Xia J, Yu T, Zhang X, and Zhang L. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. (2020) 395: 507-13.
[3] Li Q, Guan X, Wu P, Wang X, Zhou L, Tong Y, Ren R, Leung KS, Lau EH, and Wong JY. Early transmission dynamics in Wuhan, China, of novel coronavirus–infected pneumonia. N. Engl. J. Med. (2020)
[4] Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, Bi Y, Ma X, Zhan F, Wang L, Hu T, Zhou H, Hu Z, Zhou W, Zhao L, Chen J, Meng Y, Wang J, Lin Y, Yuan J, Xie Z, Ma J, Liu WJ, Wang D, Xu W, Holmes EC, Gao GF, Wu G, Chen W, Shi W, and Tan W. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. (2020) 395: 565-74.
[5] Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y, Zhang B, Li X, Zhang L, and Peng C. Structure of Mpro from COVID-19 virus and discovery of its inhibitors. bioRxiv. Preprint. (2020)
[6] Hui DS, Azhar EI, Madani TA, Ntoumi F, Kock R, Dar O, Ippolito G, Mchugh TD, Memish ZA, and Drosten C. The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health—The latest 2019 novel coronavirus outbreak in Wuhan, China. Int. J. Infect. Dis. (2020) 91: 264-6.
[7] Veeramachaneni GK, Thunuguntla V, Bobbillapati J, and Bondili JS. Structural and simulation analysis of hotspot residues interactions of SARS-CoV 2 with human ACE2 receptor. J. Biomol. Struct. Dyn. (2020) 1-11.
[8] Murgueitio MS, Bermudez M, Mortier J, and Wolber G. In silico virtual screening approaches for anti-viral drug discovery. Drug Discov. Today Technol. (2012) 9: e219-25.
[9] Castro T, Barbosa K, Albarello N, and Figueiredo S. Caracterização de pseudofrutos, frutos, sementes e plântulas obtidas a partir de germinação in vivo e in vitro da espécie medicinal Hovenia dulcis (Rhamnaceae). Rev. Cuba. de Plantas Medicinales. (2005) 10: 1-16.
[10] Shen B. A New Golden Age of Natural Products Drug Discovery. Cell. (2015) 163: 1297-300.
[11] Thomford NE, Senthebane DA, Rowe A, Munro D, Seele P, Maroyi A, and Dzobo K. Natural Products for Drug Discovery in the 21st Century: Innovations for Novel Drug Discovery. Int. J. Mol. Sci. (2018) 19: 1578.
[12] Rastogi S, Pandey DN, and Singh RH. COVID-19 pandemic: A pragmatic plan for ayurveda intervention. J. Ayurveda Integr. Med. (2020)
[13] Panyod S, Ho CT, and Sheen LY. Dietary therapy and herbal medicine for COVID-19 prevention: A review and perspective. J. Tradit. Complement. Med. (2020) 10: 420-7.
[14] Cao P, Wu S, Wu T, Deng Y, Zhang Q, Wang K, and Zhang Y. The important role of polysaccharides from a traditional Chinese medicine-Lung Cleansing and Detoxifying Decoction against the COVID-19 pandemic. Carbohydr. Polym. (2020) 240: 116346.
[15] Lin YM, Anderson H, Flavin MT, Pai YH, Mata-Greenwood E, Pengsuparp T, Pezzuto JM, Schinazi RF, Hughes SH, and Chen FC. In vitro anti-HIV activity of biflavonoids isolated from Rhus succedanea and Garcinia multiflora. J. Nat. Prod. (1997) 60: 884-8.
[16] Shrestha S, Subaramaihha SR, Subbaiah SG, Eshwarappa RS, and Lakkappa DB. Evaluating the antimicrobial activity of methanolic extract of Rhus succedanea leaf gall. Bioimpacts. (2013) 3: 195-8.
[17] Pourahmad J, Eskandari MR, Shakibaei R, and Kamalinejad M. A search for hepatoprotective activity of aqueous extract of Rhus coriaria L. against oxidative stress cytotoxicity. Food Chem. Toxicol. (2010) 48: 854-8.
[18] Lin Y-M, Chen F-C, and Lee K-H. Hinokiflavone, a Cytotoxic Principle from Rhus succedanea and the Cytotoxicity of the Related Biflavonoids1. Planta Med. (1989) 55: 166-8.
[19] Wu P-L, Lin S-B, Huang C-P, and Chiou RY-Y. Antioxidative and Cytotoxic Compounds Extracted from the Sap of Rhus succedanea. J. Nat. Prod. (2002) 65: 1719-21.
[20] Baheti J, Kumar V, Shah G, and Goyal R. Free radical scavenging activity of aqueous extract of Rhus succedanea galls. J. Nat. Remedies (2005) 5: 15-8.
[21] Kang JS, Lee CW, Lee KH, Han MH, Lee H, Han S-B, Kim H-C, Lee K, Park S-K, and Kim HM. Anti-inflammatory Activity of Methanolic Extract Isolated from Immature Fruit of Rhus succedanea. Lab. Anim. Res. (2008) 24: 297-302.
[22] Kumar V, Shah T, Shah G, and Parmar N. Anti-bacterial activity of Rhus succedanea galls. J. Nat. Remedies (2003) 3: 95-6.
[23] Mohanraj K, Karthikeyan BS, Vivek-Ananth R, Chand RB, Aparna S, Mangalapandi P, and Samal A. IMPPAT: A curated database of I Indian Medicinal Plants, Phytochemistry And therapeutics. Sci. Rep. (2018) 8: 1-17.
[24] Chaudhuri S, Symons JA, and Deval J. Innovation and trends in the development and approval of anti-viral medicines: 1987–2017 and beyond. Anti-viral research. (2018) 155: 76-88.
[25] Veeramachaneni GK, Thunuguntla V, Bhaswant M, Mathai ML, and Bondili JS. Pharmacophore Directed Screening of Agonistic Natural Molecules Showing Affinity to 5HT2C Receptor. Biomolecules (2019) 9: 556.
[26] Bokka CS, Veeramachaneni GK, Thunuguntla V, Bobbillapati J, and Bondili JS. Peptide Mapping, In Silico and In Vivo Analysis of Allergenic Sorghum Profilin Peptides. Medicine (Kaunas). (2019) 55: 178.
[27] Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, and Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. (2009) 30: 2785-91.
[28] Satyanarayana SDV, Krishna MSR, Pavan Kumar P, and Jeereddy S. In silico structural homology modeling of nif A protein of rhizobial strains in selective legume plants. J. Genet. Eng. Biotechnol. (2018) 16: 731-7.
[29] O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, and Hutchison GR. Open Babel: An open chemical toolbox. J. Cheminform. (2011) 3: 33.
[30] Pangastuti A, Amin IF, Amin AZ, and Amin M. Natural bioactive compound from Moringa oleiferaagainst cancer based on in silico screening. Jurnal Teknologi. (2016) 78:
[31] Eda SR, Veeramachaneni GK, Bondili JS, and Jinka R. Screening of caspase-3 inhibitors from natural molecule database using e-pharmacophore and docking studies. Bioinformation (2019) 15: 240-5.
[32] Bokka CS, Veeramachaneni GK, Thunuguntla VBSC, Manda NK, and Bondili JS. Specific panallergen peptide of Sorghum Polcalcin showing IgE response identified based on in silico and in vivo peptide mapping. Biosci. Rep. (2019) 39:
[33] Dallakyan S and Olson AJ, Small-molecule library screening by docking with PyRx, in Chemical biolog;y 2015, Springer. p. 243-50.
[34] Seeliger D and de Groot BL. Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J. Comput. Aided Mol. Des. (2010) 24: 417-22.
[35] Eda SR and Jinka R. Combined e-pharmacophore based screening and docking of PI3 kinase with potential inhibitors from a database of natural compounds. Bioinformation (2019) 15: 709-15.
[36] Yang H, Lou C, Sun L, Li J, Cai Y, Wang Z, Li W, Liu G, and Tang Y. admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties. Bioinformatics (2019) 35: 1067-9.
[37] Cheng F, Li W, Zhou Y, Shen J, Wu Z, Liu G, Lee PW, and Tang Y, admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. 2012, ACS Publications.
[38] Ertl P, Rohde B, and Selzer P. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. J. Med. Chem. (2000) 43: 3714-7.
[39] To KK, Hung IF, Chan JF, and Yuen KY. From SARS coronavirus to novel animal and human coronaviruses. J. Thorac. Dis. (2013) 5 Suppl 2: S103-8.
[40] Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF, Tan W, China Novel Coronavirus I, and Research T. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N. Engl. J. Med. (2020) 382: 727-33.
[41] Zhou Y, Hou Y, Shen J, Huang Y, Martin W, and Cheng F. Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discov. (2020) 6: 14.
[42] Lin LT, Hsu WC, and Lin CC. Anti-viral natural products and herbal medicines. J. Tradit. Complement. Med. (2014) 4: 24-35.
[43] Martinez JP, Sasse F, Bronstrup M, Diez J, and Meyerhans A. Anti-viral drug discovery: broad-spectrum drugs from nature. Nat. Prod. Rep. (2015) 32: 29-48.
[2] Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y, Qiu Y, Wang J, Liu Y, Wei Y, Xia J, Yu T, Zhang X, and Zhang L. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. (2020) 395: 507-13.
[3] Li Q, Guan X, Wu P, Wang X, Zhou L, Tong Y, Ren R, Leung KS, Lau EH, and Wong JY. Early transmission dynamics in Wuhan, China, of novel coronavirus–infected pneumonia. N. Engl. J. Med. (2020)
[4] Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, Bi Y, Ma X, Zhan F, Wang L, Hu T, Zhou H, Hu Z, Zhou W, Zhao L, Chen J, Meng Y, Wang J, Lin Y, Yuan J, Xie Z, Ma J, Liu WJ, Wang D, Xu W, Holmes EC, Gao GF, Wu G, Chen W, Shi W, and Tan W. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. (2020) 395: 565-74.
[5] Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y, Zhang B, Li X, Zhang L, and Peng C. Structure of Mpro from COVID-19 virus and discovery of its inhibitors. bioRxiv. Preprint. (2020)
[6] Hui DS, Azhar EI, Madani TA, Ntoumi F, Kock R, Dar O, Ippolito G, Mchugh TD, Memish ZA, and Drosten C. The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health—The latest 2019 novel coronavirus outbreak in Wuhan, China. Int. J. Infect. Dis. (2020) 91: 264-6.
[7] Veeramachaneni GK, Thunuguntla V, Bobbillapati J, and Bondili JS. Structural and simulation analysis of hotspot residues interactions of SARS-CoV 2 with human ACE2 receptor. J. Biomol. Struct. Dyn. (2020) 1-11.
[8] Murgueitio MS, Bermudez M, Mortier J, and Wolber G. In silico virtual screening approaches for anti-viral drug discovery. Drug Discov. Today Technol. (2012) 9: e219-25.
[9] Castro T, Barbosa K, Albarello N, and Figueiredo S. Caracterização de pseudofrutos, frutos, sementes e plântulas obtidas a partir de germinação in vivo e in vitro da espécie medicinal Hovenia dulcis (Rhamnaceae). Rev. Cuba. de Plantas Medicinales. (2005) 10: 1-16.
[10] Shen B. A New Golden Age of Natural Products Drug Discovery. Cell. (2015) 163: 1297-300.
[11] Thomford NE, Senthebane DA, Rowe A, Munro D, Seele P, Maroyi A, and Dzobo K. Natural Products for Drug Discovery in the 21st Century: Innovations for Novel Drug Discovery. Int. J. Mol. Sci. (2018) 19: 1578.
[12] Rastogi S, Pandey DN, and Singh RH. COVID-19 pandemic: A pragmatic plan for ayurveda intervention. J. Ayurveda Integr. Med. (2020)
[13] Panyod S, Ho CT, and Sheen LY. Dietary therapy and herbal medicine for COVID-19 prevention: A review and perspective. J. Tradit. Complement. Med. (2020) 10: 420-7.
[14] Cao P, Wu S, Wu T, Deng Y, Zhang Q, Wang K, and Zhang Y. The important role of polysaccharides from a traditional Chinese medicine-Lung Cleansing and Detoxifying Decoction against the COVID-19 pandemic. Carbohydr. Polym. (2020) 240: 116346.
[15] Lin YM, Anderson H, Flavin MT, Pai YH, Mata-Greenwood E, Pengsuparp T, Pezzuto JM, Schinazi RF, Hughes SH, and Chen FC. In vitro anti-HIV activity of biflavonoids isolated from Rhus succedanea and Garcinia multiflora. J. Nat. Prod. (1997) 60: 884-8.
[16] Shrestha S, Subaramaihha SR, Subbaiah SG, Eshwarappa RS, and Lakkappa DB. Evaluating the antimicrobial activity of methanolic extract of Rhus succedanea leaf gall. Bioimpacts. (2013) 3: 195-8.
[17] Pourahmad J, Eskandari MR, Shakibaei R, and Kamalinejad M. A search for hepatoprotective activity of aqueous extract of Rhus coriaria L. against oxidative stress cytotoxicity. Food Chem. Toxicol. (2010) 48: 854-8.
[18] Lin Y-M, Chen F-C, and Lee K-H. Hinokiflavone, a Cytotoxic Principle from Rhus succedanea and the Cytotoxicity of the Related Biflavonoids1. Planta Med. (1989) 55: 166-8.
[19] Wu P-L, Lin S-B, Huang C-P, and Chiou RY-Y. Antioxidative and Cytotoxic Compounds Extracted from the Sap of Rhus succedanea. J. Nat. Prod. (2002) 65: 1719-21.
[20] Baheti J, Kumar V, Shah G, and Goyal R. Free radical scavenging activity of aqueous extract of Rhus succedanea galls. J. Nat. Remedies (2005) 5: 15-8.
[21] Kang JS, Lee CW, Lee KH, Han MH, Lee H, Han S-B, Kim H-C, Lee K, Park S-K, and Kim HM. Anti-inflammatory Activity of Methanolic Extract Isolated from Immature Fruit of Rhus succedanea. Lab. Anim. Res. (2008) 24: 297-302.
[22] Kumar V, Shah T, Shah G, and Parmar N. Anti-bacterial activity of Rhus succedanea galls. J. Nat. Remedies (2003) 3: 95-6.
[23] Mohanraj K, Karthikeyan BS, Vivek-Ananth R, Chand RB, Aparna S, Mangalapandi P, and Samal A. IMPPAT: A curated database of I Indian Medicinal Plants, Phytochemistry And therapeutics. Sci. Rep. (2018) 8: 1-17.
[24] Chaudhuri S, Symons JA, and Deval J. Innovation and trends in the development and approval of anti-viral medicines: 1987–2017 and beyond. Anti-viral research. (2018) 155: 76-88.
[25] Veeramachaneni GK, Thunuguntla V, Bhaswant M, Mathai ML, and Bondili JS. Pharmacophore Directed Screening of Agonistic Natural Molecules Showing Affinity to 5HT2C Receptor. Biomolecules (2019) 9: 556.
[26] Bokka CS, Veeramachaneni GK, Thunuguntla V, Bobbillapati J, and Bondili JS. Peptide Mapping, In Silico and In Vivo Analysis of Allergenic Sorghum Profilin Peptides. Medicine (Kaunas). (2019) 55: 178.
[27] Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, and Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. (2009) 30: 2785-91.
[28] Satyanarayana SDV, Krishna MSR, Pavan Kumar P, and Jeereddy S. In silico structural homology modeling of nif A protein of rhizobial strains in selective legume plants. J. Genet. Eng. Biotechnol. (2018) 16: 731-7.
[29] O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, and Hutchison GR. Open Babel: An open chemical toolbox. J. Cheminform. (2011) 3: 33.
[30] Pangastuti A, Amin IF, Amin AZ, and Amin M. Natural bioactive compound from Moringa oleiferaagainst cancer based on in silico screening. Jurnal Teknologi. (2016) 78:
[31] Eda SR, Veeramachaneni GK, Bondili JS, and Jinka R. Screening of caspase-3 inhibitors from natural molecule database using e-pharmacophore and docking studies. Bioinformation (2019) 15: 240-5.
[32] Bokka CS, Veeramachaneni GK, Thunuguntla VBSC, Manda NK, and Bondili JS. Specific panallergen peptide of Sorghum Polcalcin showing IgE response identified based on in silico and in vivo peptide mapping. Biosci. Rep. (2019) 39:
[33] Dallakyan S and Olson AJ, Small-molecule library screening by docking with PyRx, in Chemical biolog;y 2015, Springer. p. 243-50.
[34] Seeliger D and de Groot BL. Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J. Comput. Aided Mol. Des. (2010) 24: 417-22.
[35] Eda SR and Jinka R. Combined e-pharmacophore based screening and docking of PI3 kinase with potential inhibitors from a database of natural compounds. Bioinformation (2019) 15: 709-15.
[36] Yang H, Lou C, Sun L, Li J, Cai Y, Wang Z, Li W, Liu G, and Tang Y. admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties. Bioinformatics (2019) 35: 1067-9.
[37] Cheng F, Li W, Zhou Y, Shen J, Wu Z, Liu G, Lee PW, and Tang Y, admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. 2012, ACS Publications.
[38] Ertl P, Rohde B, and Selzer P. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. J. Med. Chem. (2000) 43: 3714-7.
[39] To KK, Hung IF, Chan JF, and Yuen KY. From SARS coronavirus to novel animal and human coronaviruses. J. Thorac. Dis. (2013) 5 Suppl 2: S103-8.
[40] Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF, Tan W, China Novel Coronavirus I, and Research T. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N. Engl. J. Med. (2020) 382: 727-33.
[41] Zhou Y, Hou Y, Shen J, Huang Y, Martin W, and Cheng F. Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discov. (2020) 6: 14.
[42] Lin LT, Hsu WC, and Lin CC. Anti-viral natural products and herbal medicines. J. Tradit. Complement. Med. (2014) 4: 24-35.
[43] Martinez JP, Sasse F, Bronstrup M, Diez J, and Meyerhans A. Anti-viral drug discovery: broad-spectrum drugs from nature. Nat. Prod. Rep. (2015) 32: 29-48.
- Abstract Viewed: 175 times
- IJPS_Volume 17_Issue 4_Pages 107-122 Downloaded: 78 times