Molecular Docking and Computational Exploration of Isolated Drugs from Daphne Species Against COVID-19

Document Type : Research Article

Authors

1 Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, SAUDI ARABIA

2 Department of Chemistry, University of Gujrat, Gujrat-50700, PAKISTAN

3 Center for Clinical and Nutritional Chemistry, School of Chemistry, University of Punjab, New Campus, Lahore, PAKISTAN

Abstract

The SARS-CoV-2 has initiated in Wuhan city of China and then extend all around the world as a health emergency. It begins a new research area to produce potential drugs using data-driven approaches to identify potential therapies for the treatment of the virus. This is the time to develop specific antiviral drugs using molecular docking, quantum chemical approaches, and natural products. The protease inhibitors that constitute plant derivatives may become highly efficient to cure virus-prompted illnesses. A systematic study of isolated phytochemicals was executed then frontier molecular orbitals, docking score, molecular descriptors, and active sites were compared with favipiravir, dexamethasone, redeliver, and hydroxychloroquine which are being used against COVID19 nowadays. This is the first study on the phytochemicals of Daphne species to explore their anti-SARS-CoV-2 behavior by molecular docking and quantum chemical methods.  

Keywords

Main Subjects

References

[1] Chen J., Pathogenicity and Transmissibility of 2019-Ncov—A Quick Overview and Comparison with Other Emerging Viruses, Microbes and Infection, 22(2): 69-71 (2020).
[2] Tipnis S.R., Hooper N.M., Hyde R., Karran E., Christie G., Turner A.J., A Human Homolog of Angiotensin-Converting Enzyme. Cloning and Functional Expression as a Captopril-Insensitive Carboxypeptidase, J Biol Chem, 275(43): 33238-33243 (2000).
[3] Wu C., Liu Y., Yang Y., Zhang P., Zhong W., Wang Y., Wang Q., Xu Y., Li M., Li X., Analysis of Therapeutic Targets for Sars-Cov-2 and Discovery of Potential Drugs by Computational Methods, Acta Pharmaceutica Sinica B:  10(5): 766-788 (2020).
[4] Gurung A.B., Ali M.A., Lee J., Farah M.A., Al-Anazi K.M., Unravelling Lead Antiviral Phytochemicals for the Inhibition of Sars-Cov-2 Mpro Enzyme through in Silico Approach, Life Sciences, 255: 117831 (2020).
[5] Mani J.S., Johnson J.B., Steel J.C., Broszczak D.A., Neilsen P.M., Walsh K.B., Naiker M., Natural Product-Derived Phytochemicals as Potential Agents against Coronaviruses: A Review, Virus Research, 284: 197989 (2020).
[6] Joshi T., Joshi T., Sharma P., Mathpal S., Pundir H., Bhatt V., Chandra S., In Silico Screening of Natural Compounds against Covid-19 by Targeting Mpro and Ace2 Using Molecular Docking, Eur. Rev. Med. Pharmacol. Sci, 24: 4529-4536 (2020).
[7] Wan S., Xiang Y., Fang W., Zheng Y., Li B., Hu Y., Lang C., Huang D., Sun Q., Xiong Y., Clinical Features and Treatment of Covid‐19 Patients in Northeast Chongqing, Journal of medical virology, 92(7): (2020).
[8]    Penta S., Advances in Structure and Activity Relationship of Coumarin Derivatives: Academic Press; (2015).
[9] Moshiashvili G., Tabatadze N., Mshvildadze V., The Genus Daphne: A Review of Its Traditional Uses, Phytochemistry and Pharmacology, Fitoterapia, 143: 104540 (2020).
[10] Elsharkawy E.R., Almalki F., Ben Hadda T., Rastija V., Lafridi H., Zgou H., DFT Calculations and Pom Analyses of Cytotoxicity of Some Flavonoids from Aerial Parts of Cupressus Sempervirens: Docking and Identification of Pharmacophore Sites, Bioorg. Chem., 100: 103850 (2020).
[11] Jin R.-Y., Tang T., Zhou S., Long X., Guo H., Zhou J., Yan H., Li Z., Zuo Z.-Y., Xie H.-L., Tang Y.-P., Design, Synthesis, Antitumor Activity and Theoretical Calculation of Novel PI3Ka Inhibitors, Bioorg. Chem., 98: 103737 (2020).
[12] Najafi M., Naqvi S.A.R., Theoretical Study of the Substituent Effect on the Hydrogen Atom Transfer Mechanism of the Irigenin Derivatives Antioxidant Action, J. Theor. Comput. Chem., 13(02): 1450010 (2014).
[13] Mikulski D., Eder K., Molski M., Quantum-Chemical Study on Relationship between Structure and Antioxidant Properties of Hepatoprotective Compounds Occurring in Cynara Scolymus and Silybum Marianum, J. Theor. Comput. Chem., 13(01): 1450004 (2014).
[14] Sadasivam K., Jayaprakasam R., Kumaresan R., A DFT Study on the Role of Different Oh Groups in the Radical Scavenging Process, J. Theor. Comput. Chem., 11(04): 871-893 (2012).
[15] Khalil Warad I., Al-Nuri M., Ali O., Abu-Reidah I.M., Barakat A., Ben Hadda T., Zarrouk A., Radi S., Touzani R., Hicham E., Synthesis, Physico-Chemical, Hirschfield Surface and Dft/B3lyp Calculation of Two New Hexahydropyrimidine Heterocyclic Compounds, Iranian Journal of Chemistry and Chemical Engineering (IJCCE), 38(4): 59-68 (2019).
[16] Demirtaş G., Dege N., Ağar E., Şahin S., The Crystallographic, Spectroscopic and Theoretical Studies on (E)-2-[((4-Fluorophenyl)Imino)Methyl]-4-Nitrophenol and (E)-2-[((3-Fluorophenyl)Imino)Methyl]-4-Nitrophenol Compounds, Iranian Journal of Chemistry and Chemical Engineering (IJCCE), 37(5): 55-65 (2018).
[17] Mahmood A., Irfan A., Effect of Fluorination on Exciton Binding Energy and Electronic Coupling in Small Molecule Acceptors for Organic Solar Cells, Comp. Theor. Chem., 1179: 112797 (2020).
[18] Irfan A., Comparison of Mono- and Di-Substituted Triphenylamine and Carbazole Based Sensitizers @(Tio2)38 Cluster for Dye-Sensitized Solar Cells Applications, Comp. Theor. Chem., 1159: 1-6 (2019).
[19] Frisch MJ, Trucks GW, Schlegel HB, et al.,. Gaussian-16, Revision A.1, Gaussian, Inc., Wallingford, Ct. (2016).
[20] Morris G.M., Huey R., Lindstrom W., Sanner M.F., Belew R.K., Goodsell D.S., Olson A.J., Autodock4 and Autodocktools4: Automated Docking with Selective Receptor Flexibility, J. Comput. Chem., 16: 2785-2791 (2009).
[21] Ali M.Y., Seong S.H., Jung H.A., Choi J.S., Angiotensin-I-Converting Enzyme Inhibitory Activity of Coumarins from Angelica Decursiva, Molecules, 24(21): 3937 (2019).
[22] Su W., Zhao J., Yang M., Yan H.-W., Pang T., Chen S.-H., Huang H.-Y., Zhang S.-H., Ma X.-C., Guo D.-A., A Coumarin Lignanoid from the Stems of Kadsura Heteroclita, Bioorganic & Medicinal Chemistry Letters, 25(7): 1506-1508 (2015).
[23] Liu H., Li F., Li C.-J., Yang J.-Z., Li L., Chen N.-H., Zhang D.-M., Bioactive Furanocoumarins from Stems of Clausena Lansium, Phytochemistry, 107: 141-147 (2014).
[24] Marumoto S., Miyazawa M., Structure-Activity Relationships for Naturally Occurring Coumarins as Β-Secretase Inhibitor, Bioorganic & Medicinal chemistry, 20(2): 784-788 (2012).
[25] Liu C.-B., Shen Q.-P., Wang Y., Zhang F.-M., He P., Si X.-X., Wang K.-M., Zhu R.-Z., Xiang N.-J., Liu Z.-H., Coumarins from the Leaves of Nicotiana Tabacum and Their Anti-Tobacco Mosaic Virus Activities, Chemistry of Natural Compounds, 52(6): 992-995 (2016).
[26] Vektariene A., Vektaris G., Svoboda J., A Theoretical Approach to the Nucleophilic Behavior of Benzofused Thieno [3, 2-B] Furans Using Dft and Hf Based Reactivity Descriptors, Arkivoc, 7: 311-329 (2009).
[27] Geerlings P., De Proft F., Langenaeker W., Conceptual Density Functional Theory, Chemical Reviews, 103(5): 1793-1874 (2003).
[28] Akaike T., Role of Free Radicals in Viral Pathogenesis and Mutation, Reviews in Medical Virology, 11(2): 87-101 (2001).
[29] Irfan A., Imran M., Khalid M., Sami Ullah M., Khalid N., Assiri M.A., Thomas R., Muthu S., Raza Basra M.A., Hussein M., Al-Sehemi A.G., Shahzad M., Phenolic and Flavonoid Contents in Malva Sylvestris and Exploration of Active Drugs as Antioxidant and Anti-Covid19 by Quantum Chemical and Molecular Docking Studies, Journal of Saudi Chemical Society, 25(8): 101277 (2021).
[30] https://www.rcsb.org/structure/6LU7 
Iranian Journal of Chemistry and Chemical Engineering
Volume 40, Issue 6 - Serial Number 110
November and December 2021
Pages 2019-2027

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