Identification of SARS‐CoV‐2 Main Protease Inhibitors Using Structure Based Virtual Screening and Molecular Dynamics Simulation of DrugBank Database

Debnath, Pradip; Bhaumik, Samhita; Sen, Debanjan; Muttineni, Ravi Kumar; Debnath, Sudhan

doi:10.1002/slct.202100854

Cited by 18 publications

(8 citation statements)

References 48 publications

(90 reference statements)

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“…The three-dimensional structure of SARS-CoV-2's main protease has been determined, offering valuable insights for drug design. This information helps researchers identify compounds specifically targeting and inhibiting the main protease, disrupting the viral life cycle [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

6-Octadecenoic and Oleic Acid in Liquid Smoke Rice Husk Showed COVID-19 Inhibitor Properties

Arundina,

Frimayanti,

Surboyo

et al. 2024

Advances in Pharmacological and Pharmaceutical Sciences

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In recent years, liquid smoke rice husk (LSRH) has shown its therapeutic potency to diabetes, wound healing, stomatitis, and periodontitis. The phenol, 6-octadecenoic acid, oleic acid, and 9-octadecanoic acid were responsible for their therapeutic effect. The LSRH also demonstrated their potential for infectious diseases such as coronavirus disease (COVID-19). Therefore, the molecular dynamics (MDs) simulation and pharmacophore analysis was performed to analyse the binding stability of 6-octadecenoic and oleic acid. Based on MD simulation, 6-octadecenoic and oleic acids seemed to retain their interactions with Ser144 and Thr24, respectively, with hydrogen bond distance less than 2.9 Å. This interaction was stable during the simulation and has hydrophobic and hydrogen bonds/acceptors. The 6-octadecenoic acid and oleic acid were confirmed to have great potency as inhibitors for COVID-19. These compounds also showed that the existence of hydrophobic and hydrogen bonds/acceptors could increase biological activity.

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Section: Discussionmentioning

confidence: 99%

6-Octadecenoic and Oleic Acid in Liquid Smoke Rice Husk Showed COVID-19 Inhibitor Properties

Arundina,

Frimayanti,

Surboyo

et al. 2024

Advances in Pharmacological and Pharmaceutical Sciences

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“…Studying protein–drug interactions is essential to comprehending the structural requirements for ligand affinity. 45,46 The DrugBank 47 dataset is also used to construct protein-drug interactions. We used this (version 1.0) 48 database to find potential medications that significantly interact with genes.…”

Section: Methodsmentioning

confidence: 99%

Molecular Biomarker Identification Using a Network-Based Bioinformatics Approach That Links COVID-19 With Smoking

Rahman

Amin

Yeasmin

et al. 2023

Bioinform Biol Insights

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The COVID-19 coronavirus, which primarily affects the lungs, is the source of the disease known as SARS-CoV-2. According to “Smoking and COVID-19: a scoping review,” about 32% of smokers had a severe case of COVID-19 pneumonia at their admission time and 15% of non-smokers had this case of COVID-19 pneumonia. We were able to determine which genes were expressed differently in each group by comparing the expression of gene transcriptomic datasets of COVID-19 patients, smokers, and healthy controls. In all, 37 dysregulated genes are common in COVID-19 patients and smokers, according to our analysis. We have applied all important methods namely protein-protein interaction, hub-protein interaction, drug-protein interaction, tf-gene interaction, and gene-MiRNA interaction of bioinformatics to analyze to understand deeply the connection between both smoking and COVID-19 severity. We have also analyzed Pathways and Gene Ontology where 5 significant signaling pathways were validated with previous literature. Also, we verified 7 hub-proteins, and finally, we validated a total of 7 drugs with the previous study.

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“…Cobicistat, flavin adenine dinucleotide, and simeprevir were suggested through drug ranking according to binding energy by MM/PB(GB)SA calculations. Other assessments based on docking and MM/PB(GB)SA calculations focused on specific drugs or compounds such as ravidasvir, lopinavir, ritonavir, saquinavir, teicoplanin, GC-376, calpain XII, calpain II, anti-HIV drugs, doxorubicin, chloroquine, quinoline, hydroxychloroquine, noscapine, echinocandins, coumarins, and their derivatives. − …”

Section: Methods and Approachesmentioning

confidence: 99%

Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2

Gao¹,

Wang²,

Chen³

et al. 2022

Chem. Rev.

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Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus–host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein–protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.

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Identification of SARS‐CoV‐2 Main Protease Inhibitors Using Structure Based Virtual Screening and Molecular Dynamics Simulation of DrugBank Database

Cited by 18 publications

References 48 publications

6-Octadecenoic and Oleic Acid in Liquid Smoke Rice Husk Showed COVID-19 Inhibitor Properties

6-Octadecenoic and Oleic Acid in Liquid Smoke Rice Husk Showed COVID-19 Inhibitor Properties

Molecular Biomarker Identification Using a Network-Based Bioinformatics Approach That Links COVID-19 With Smoking

Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2

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