Molecular Docking Analysis of Selected Natural Products from Plants for Inhibition of SARS-CoV-2 Main Protease

Sampangi-Ramaiah, Megha Hastantram

doi:10.18520/cs/v118/i7/1087-1092

Cited by 91 publications

(16 citation statements)

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“…As the binding affinity of Saquinavir (Sampangi-Ramaiah et al, 2020), the synthetic control drug, with 6LU7 protease showed 12 van der Waals, one alkyl, one Pi-alkyl, on Pi-cation, one Pistacked, four conventional hydrogen bonds, which indicates that it has less affinity when compared with Rosmarinic acid.…”

Section: Discussionmentioning

confidence: 99%

“…com/tools/smiles2pdb the output was saved as PDB file for the molecules. The target proteins are 6LU7 and 6Y2E of SARS-CoV-2 (2019) were obtained from https://www.rcsb.org/website in PDB format (Sampangi-Ramaiah et al, 2020).…”

Section: Ligand Preparationmentioning

confidence: 99%

“…The COVID-19, an infectious dreadful virus disease, has been pandemic since December 2019, and the unimaginable volume of human casualties witnessed so far has propelled the scientific community to explore the possibilities of developing safe herbal drugs (Chojnacka et al, 2020), either as preventive or curative (Kiran et al, 2020), against the COVID-19 (Sampangi-Ramaiah et al, 2020). The present investigation on 16 therapeutic ligands of Ocimum tenuiflorum L., (Vernacular name, "Tulasi" in Tamil) (Singh & Chaudhuri, 2018) the latter being the key ingredient in Kandankathiri Legiyam-a Siddha polyherbal formulation used in respiratory diseases, comprise the binding affinities of them to the two main proteases of COVID-19, viz., 6LU7 (Peele et al, 2020) and 6Y2E, and their ability to arrest the virus replication (Sampangi-Ramaiah et al, 2020). The PyRx software and Discovery studio were used in the study to discover lead molecules for the drug design and explore the possibility of repurposing the popular herbal drug in the treatment of COVID-19 (Trott & Olson, 2010).…”

Section: Introductionmentioning

confidence: 99%

“…The PyRx software and Discovery studio were used in the study to discover lead molecules for the drug design and explore the possibility of repurposing the popular herbal drug in the treatment of COVID-19 (Trott & Olson, 2010). The COVID-19 proteases, 6LU7 (Sisakht et al, 2021) and 6Y2E, are critical for viral replication and the effective binding of the viral proteases will arrest viral replication and the disease (Sampangi-Ramaiah et al, 2020). Hence, the present investigation was taken up towards achieving this purpose.…”

Section: Introductionmentioning

confidence: 99%

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Molecular docking analysis on 16 therapeutic ligands of Ocimum tenuiflorum L. (Tulasi) and their prospects in drug design for COVID-19

Anantharam

Geetha²,

Pandi³

et al. 2022

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The PyRx software and Discovery studio were used in the present molecular docking studies of the 16 ligands of Ocimum tenuiflorum L., selected based on their high therapeutic potentials, viz., (E)-6-hydroxy-4,6-dimethylhept-3-en-2-one, Apigenin, Bieugenol, Cirsilineol, Cirsimaritin, β-Caryophyllene epoxide, Dehydrodieugenol B, Eugenol, Ferulaldehyde, Isothymonin, Isothymusin, Linalool, Luteolin, Ocimarin, Rosmarinic acid, and Thymol. Saquinavir was used as a positive control. The binding affinities of the 16 ligands to the main proteases of COVID-19 6LU7 and 6Y2E (critical for viral replication) and their ability to arrest the virus replication were recorded. The binding affinities of the ligands to 6LU7 and 6Y2E ranged from -4.3 and -4.7 kcal/mol (for (E)-6-hydroxy-4,6-dimethylhept-3-en-2-one) to -7.6 (for Rosmarinic acid to both target proteins). While the corresponding values for the control drug Saquinavir were -7.8 and -7.6 respectively. The Rosmarinic acid, in binding with both the proteases (-7.6 and -7.6 kcal/mol) showed six conventional hydrogen bonds, one carbon hydrogen bond (ASP 153 had one conventional hydrogen bond and one carbon hydrogen bond), one Pi-alkyl bond, one Pi-Pi stacked bond, eight van der waals bonds for 6LU7 protease; it formed three conventional hydrogen bonds, two Pi-alkyl bonds, one unfavourable donor – donor bond and 14 van der waals bonds with 6Y2E protease. The control drug – Saquinavir in binding with 6LU7 protease showed 12 van der waals, one alkyl, one Pi-alkyl, one Pi-cation, one Pi-stacked and four conventional hydrogen bonds, which indicates that it has less affinity when compared with Rosmarinic acid. Similarly, the control drug on binding with 6Y2E protease exhibited ten van der waals, four Pi-alkyl, one cation and three hydrogen bonds. The results are in conformity to similar other studies, and herald a promising scope for Rosmarinic acid as lead molecule in the drug discovery for COVID-19.

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Section: Discussionmentioning

confidence: 99%

Section: Ligand Preparationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Molecular docking analysis on 16 therapeutic ligands of Ocimum tenuiflorum L. (Tulasi) and their prospects in drug design for COVID-19

Anantharam

Geetha²,

Pandi³

et al. 2022

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“…During the COVID-19 pandemic, the O. aristatus is a potential plant to be developed. Based on silico studies, several compounds have potential as COVID-19 inhibitors, including rosmarinic acid [23][24][25], sinensetin [26], cirsimaritin [27], caffeic acid derivatives [28], sagerinic acids [29], β-caryophyllene [30], and 1,8-cineole [31]. In addition to this inhibitive character, the O. aristatus plant's active compound has potential as an antiherpetic [32] (caffeic acid [33], Ntransferulolyl tyramine [34], β-caryophyllene [35], limonene [36], eugenol [37,38], p-cymene) [39], as anti-influenza virus (sinensetin [40], caffeic acid [41], limonene [42], 1,8-cineol [43], linalool [44], eugenol [45], aurantiamide) [46], as anti-viral hepatitis (rosmarinic acid [47], ladanein [48], oleanolic acid [49], ursolic acid [50], danshensu) [51], as anti-Japanese viral encephalitis (rosmarinic acid) [52], as anti-enterovirus 71 (rosmarinic acid) [53], and as antihuman immunodeficiency virus (HIV) (lithospermic acid [54], chicoric acid [55], 2,3-dicaffeoyltartaric acid [56], thansione Ⅱ A [57], oleanolic acid [58,59], maslinic acid) [60].…”

Section: Introductionmentioning

confidence: 99%

Standardization of Orthosiphon Aristatus, Blume Miq

et al. 2022

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Objective: The main compounds in O. aristatus are rosmarinic acid, sinensetin, and eupatorin. Sinensetin and rosmarinic acid compounds have the potential as antiviral agents. The focus of this research is O. aristatus purple and white-purple varieties. This study aimed to determine the levels of three main secondary metabolites of O. aristatus, one of the specific standardizations. Methods: The standardization parameters to be tested were to determine the main compound levels by using thin-layer chromatography densitometry on two varieties of O. aristatus. Results: The highest value levels of sinensetin and rosmarinic acid in purple variety O. aristatus were 0.53 and 1.32% w/w, respectively. The highest level of eupatorin was 0.88% w/w in the ethanol extract of white-purple varieties of O. aristatus. The main secondary metabolites in the two varieties of O. aristatus were more significant in the leaves than in the stems. Meanwhile, the sinensetin and rosmarinic acid levels in the ethanol extract of leaves and stems of the purple variety O. aristatus were higher and significantly different than in the white-purple ones. However, the levels of eupatorin were higher and significantly (p<0.05) different in the white-purple variety compared to the purple variety. Conclusion: The purple variety is due to greater sinensetin and rosmarinic acid levels in the purple variety than in the white-purple ones.

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A Computational Insight on the Inhibitory Potential of 8‐Hydroxydihydrosanguinarine (8‐HDS), a Pyridone Containing Analog of Sanguinarine, against SARS CoV2**

Jena

Kanungo

Chainy

et al. 2022

Chemistry & Biodiversity

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The unprecedented global pandemic of COVID‐19 has created a daunting scenario urging an immediate generation of therapeutic strategy. Interventions to curb the spread of viral infection primarily include setting targets against the virus. Here in this study we target S protein to obstruct the viral attachment and entry and also the M pro to prevent the viral replication. For this purpose, the interaction of S protein and M pro with phytocompounds, sanguinarine and eugenol, and their derivatives were studied using computational tools. Docking studies gave evidence that 8‐Hydroxydihydrosanguinarine, a derivative of sanguinarine, showed maximum binding affinity with both the targets. The binding energies of the ligand with S protein and M pro scored to be ΔGb ‐9.4 Kcal/mol and ΔGb ‐10.3 Kcal/mol respectively. MD simulation studies depict that the phytocompound could effectively cause structural perturbations in the targets which would affect their functions.8‐Hydroxydihydrosanguinarine distorts the α‐helix in the secondary structure of M pro and RBD site of S protein. Protein‐protein interaction study in presence of 8‐hydroxydihydrosanguinarine (8‐HDS) also corroborate the above findings which indicate that this polyphenol interfere in the coupling of S Protein and ACE2. The alterations in protonation of M pro suggest that the protein structure undergoes significant structural changes at neutral pH. ADME (Physicochemical, Lipophilicity, Water Solubility, Pharmacokinetics, Drug‐likeness) property of 8‐ hydroxydihydrosanguinarine indicates this could be a potential drug. This makes the phyto‐alkaloid a possible therapeutic molecule for antiCOVID‐19 drug design.

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Molecular Docking Analysis of Selected Natural Products from Plants for Inhibition of SARS-CoV-2 Main Protease

Cited by 91 publications

References 0 publications

Molecular docking analysis on 16 therapeutic ligands of Ocimum tenuiflorum L. (Tulasi) and their prospects in drug design for COVID-19

Molecular docking analysis on 16 therapeutic ligands of Ocimum tenuiflorum L. (Tulasi) and their prospects in drug design for COVID-19

Standardization of Orthosiphon Aristatus, Blume Miq

A Computational Insight on the Inhibitory Potential of 8‐Hydroxydihydrosanguinarine (8‐HDS), a Pyridone Containing Analog of Sanguinarine, against SARS CoV2**

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