An in-silico pharmacophore-based molecular docking study to evaluate the inhibitory potentials of novel fungal triterpenoid Astrakurkurone analogues against a hypothetical mutated main protease of SARS-CoV-2 virus

Nag, Anish; Dasgupta, Asish; Sengupta, Sutirtha; Lai, Tapan Kumar; Acharya, Krishnendu

doi:10.1016/j.compbiomed.2022.106433

Cited by 7 publications

(5 citation statements)

References 100 publications

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“…The uniqueness of PCA lies in the conversion of measured variables into principal components. The use of the PCA tool for categorization of ligands and thereby establishing a correlation between the ligands was successfully implemented in our previous works (Nag et al 2021a , 2022b , 2023 ). Considering the robustness of the PCA tool and based on our results, the compounds in cluster 4 were selected for pharmacophore study.…”

Section: Resultsmentioning

confidence: 99%

“…Further, we successfully deployed molecular alignment elsewhere to evaluate the interaction of the phytochemicals with the residues of the target protein (Nag et al 2021b , 2023 ; Nag and Banerjee 2021 ). All these studies combined PCA and molecular alignment.…”

Section: Resultsmentioning

confidence: 99%

“…This step was followed as a prerequisite for conducting molecular docking studies. For optimization of the ligands, a universal force field (UFF) algorithm was applied for the energy minimization of the ligands, followed by adding polar hydrogens to the ligands at pH, 7.4 (Hanwell et al 2012 ; Nag et al 2021b , 2023 ; Cho et al 2022 ). Two-dimensional structures of the ligands are represented in Fig.…”

Section: Materials and Methodologymentioning

confidence: 99%

“…The measured distance between protein residues and ligands is determined by RMSD. The significance of the radius of gyration lies in the analysis of the compactness of the protein structure in the free and bound forms (Nag et al 2023 ). RMSF represents the differences in flexibility among residues with respect to the average molecular dynamic simulation conformation (Rao et al 2020 ).…”

Section: Active Site Prediction and Molecular Dockingmentioning

confidence: 99%

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Evaluation of therapeutic potentials of selected phytochemicals against Nipah virus, a multi-dimensional in silico study

Rababi,

Nag

2023

3 Biotech

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The current study attempted to evaluate the potential of fifty-three (53) natural compounds as Nipah virus attachment glycoprotein (NiV G) inhibitors through in silico molecular docking study. Pharmacophore alignment of the four (4) selected compounds (Naringin, Mulberrofuran B, Rutin and Quercetin 3-galactoside) through Principal Component Analysis (PCA) revealed that common pharmacophores, namely four H bond acceptors, one H bond donor and two aromatic groups were responsible for the residual interaction with the target protein. Out of these four compounds, Naringin was found to have the highest inhibitory potential ( – 9.19 kcal mol −1 ) against the target protein NiV G, when compared to the control drug, Ribavirin ( – 6.95 kcal mol −1 ). The molecular dynamic simulation revealed that Naringin could make a stable complex with the target protein in the near-native physiological condition. Finally, MM-PBSA (Molecular Mechanics-Poisson–Boltzmann Solvent-Accessible Surface Area) analysis in agreement with our molecular docking result, showed that Naringin ( – 218.664 kJ mol −1 ) could strongly bind with the target protein NiV G than the control drug Ribavirin ( – 83.812 kJ mol −1 ). Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03595-y.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Materials and Methodologymentioning

confidence: 99%

Section: Active Site Prediction and Molecular Dockingmentioning

confidence: 99%

See 2 more Smart Citations

Evaluation of therapeutic potentials of selected phytochemicals against Nipah virus, a multi-dimensional in silico study

Rababi,

Nag

2023

3 Biotech

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“…The ligand-protein complexes of garciniaxanthon B_HIV-1 protease, garcinone B_HIV-1 protease, and beta-mangostin_HIV-1 protease ( Figure 4) was identified as having RMSF values > 3 (Å). Ligand-protein complexes with RMSF values > 3 at interaction hotspots show stable properties and may trigger the inhibitory activity on the target [45][46][47]. RMSF shows the fluctuation of atoms that form amino acid residues in an active protein.…”

Section: Interaction Stabilitymentioning

confidence: 99%

Bioinformatics study of selective inhibitor from <i>Garcinia mangostana</i> L. tackle HIV‑1 infection

Kharisma,

Ansori,

Jakhmola

et al. 2024

Food systems

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HIV has a host cell, T‑cell lymphocytes with CD4+ receptors. HIV drugs have the inhibitory activity on HIV‑1 protease by producing chemical bonding interactions such as hydrogen and hydrophobic. However, some cases show long-term side effects that may be harmful from the use of synthetic antiretrovirals. This requires new innovations to make drugs based on natural resources or alternative medicine for handling these cases. Natural-based drugs are claimed to reduce the side effects produced. Garcinia mangostana L. or queen of fruit is widely found in Southeast Asia. Many parts of this plant, such as fruits, are used for traditional medicine. Research with in vitro and in vivo approaches reveals that mangostin compounds from Garcinia mangostana L. can be an antiviral candidate. Garcinia mangostana L. has the main chemical compounds of garciniaxanthone, garcinone A, and mangostin. This study uses garciniaxanthone, garcinone A, and mangostin compounds to reveal the molecular mechanism of the antiviral activity in Garcinia mangostana L. through inhibition of HIV‑1 protease with a bioinformatics approach. In silico methods used in this study are druglikeness, molecular docking, interactions, visualization, and dynamic simulation. Garciniaxanthon B, garcinone B, and beta-mangostin from Garcinia mangostana L. have potential as antiretroviral agents for the treatment of HIV‑1 infection. The three compounds are predicted to inhibit the protease activity in HIV‑1 with a more negative binding affinity score, form ligand-protein molecular complexes with van der Waals, hydrogen, pi/alkyl/anion/ sigma bonds, form stable bonds and drug-like molecules.

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In silico investigation of potential phytoconstituents against ligand- and voltage-gated ion channels as antiepileptic agents

Salaria,

Subrahmanyeswara Rao,

Dhameliya

et al. 2024

3 Biotech

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An in-silico pharmacophore-based molecular docking study to evaluate the inhibitory potentials of novel fungal triterpenoid Astrakurkurone analogues against a hypothetical mutated main protease of SARS-CoV-2 virus

Cited by 7 publications

References 100 publications

Evaluation of therapeutic potentials of selected phytochemicals against Nipah virus, a multi-dimensional in silico study

Evaluation of therapeutic potentials of selected phytochemicals against Nipah virus, a multi-dimensional in silico study

Bioinformatics study of selective inhibitor from <i>Garcinia mangostana</i> L. tackle HIV‑1 infection

In silico investigation of potential phytoconstituents against ligand- and voltage-gated ion channels as antiepileptic agents

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