In silico investigation of phytoconstituents of medicinal herb ‘Piper Longum’ against SARS-CoV-2 by molecular docking and molecular dynamics analysis

Lakhera, Shradha; Devlal, Kamal; Ghosh, Arabinda; Rana, Meenakshi

doi:10.1016/j.rechem.2021.100199

Cited by 43 publications

(25 citation statements)

References 52 publications

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“…These proteases are responsible for the replication of the virus in the human body and enclosing ubiquitin and ISG15 into the host cell preventing regulation of protein circulation in human cells, respectively (Mengist 2020 ; Barretto 2005 ). It causes swift death of the healthy cells and rapid fall in the immunity of the patient (Shree 2022 ; Lakhera 2021 , Altay 2020 ). In this study, we have taken 3D coordinates of M pro (PDB ID: 6LU7) and PL pro (PDB ID: 4OVZ) in their native states derived by X-ray crystallography from protein data bank with resolution 2.16 Å and 2.50 Å, respectively, as drug target macromolecule.…”

Section: Methodsmentioning

confidence: 99%

Modelling the DFT structural and reactivity study of feverfew and evaluation of its potential antiviral activity against COVID-19 using molecular docking and MD simulations

et al. 2022

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The unavailability of a proper drug against SARS-CoV-2 infections and the emergence of various variants created a global crisis. In the present work, we have studied the antiviral behavior of feverfew plant in treating COVID-19. We have reported a systematic in silico study with the antiviral effects of various phytoconstituents Borneol (C 10 H 18 O), Camphene (C 10 H 16 ), Camphor (C 10 H 16 O), Alpha-thujene (C 10 H 16 ), Eugenol (C 10 H 14 O), Carvacrol (C 10 H 14 O) and Parthenolide (C 15 H 20 O 3 ) of feverfew on the viral protein of SARS-CoV-2. Parthenolide shows the best binding affinity with both main protease (M pro ) and papain-like protease (PL pro ). The molecular electrostatic potential and Mulliken atomic charges of the Parthenolide molecule shows the high chemical reactivity of the molecule. The docking of Parthenolide with PL pro give score of −8.0 kcal/mol that validates the good binding of Parthenolide molecule with PL pro . This complex was further considered for molecular dynamics simulations. The binding energy of the complex seems to range in between −3.85 to −11.07 kcal/mol that is high enough to validate the stability of the complex. Free energy decomposition analysis have been also performed to understand the contribution of residues that reside into the binding site. Good binding affinity and reactivity response suggested that Parthenolide can be used as a promising drug against the COVID-19. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s11696-022-02067-6.

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Section: Methodsmentioning

confidence: 99%

Modelling the DFT structural and reactivity study of feverfew and evaluation of its potential antiviral activity against COVID-19 using molecular docking and MD simulations

et al. 2022

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“…The in-silico modeling is generally used computer-aided drug designing (CADD) technique that is preferred by the chemists and researchers for the evaluation of the drug-like character of the selected systems. Thousands of research works had been reported based on CADD like Feverfew and Piper longum which were used against the M pro and PL pro of COVID-19 [17,18], Tridax procumbens was used against MCM7 breast cancer [19], Blumea mollis was used as an anti-fungal candidate [20], Bjerkandera adusta was used against Proteostasis Network Modules [21], and Curcuma Fig. 1 Morphology of Clitoria ternatea plant longa (Turmeric) and Cymbopogon citratus (lemongrass) as lipoxygenase inhibitor [22].…”

Section: Highlightsmentioning

confidence: 99%

Study of nonlinear optical responses of phytochemicals of Clitoria ternatea by quantum mechanical approach and investigation of their anti-Alzheimer activity with in silico approach

et al. 2022

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Clitoria ternatea is a flowering plant with promising medicinal plants with a wide variety of active phytochemicals. The present study aimed at the computational investigation of the nonlinear optical (NLO) responses of the active phytochemicals of the Clitoria ternatea. The computational investigation of the NLO features was done by using the density functional theory (DFT) by B3LYP/6-311G + + (d, p) basis set. The structural parameters, mulliken charge distribution, and molecular electrostatic potential (MEP) surface clearly show the intramolecular charge transfer within Clitorin. The NLO properties were identified by computing the polarizability parameters. As the plant has high medicinal characteristics, the inhibiting properties of its phytochemicals were also investigated to combat Alzheimer disease (AD). The systematic in silico study identifies Clitorin as the most active and inhibiting phytochemicals of the plant. The results obtained from molecular dynamics (MD) simulation tell the stability of the complex and make it a fair selection as a drug-like molecule against AD. The cardio-toxicity analysis done for the Clitorin molecule verifies that it is harmless for the heart.

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“…Optimized geometry helps in nding the net polarity of the molecule by the means of dipole moment. More the dipole moment, more the compound will be polarizable (Lakhera et al 2021;Visscher and Geerke 2019;Rana et al 2017). In the present case, the selected EAA Histidine (5.58 Debye) have the maximum dipole moment as compared to Isoleucine (1.65 Debye), Leucine (1.85 Debye), Lysine (0.88 Debye), Methionine (0.96 Debye), Phenylalanine (1.62 Debye), Threonine (2.50 Debye), Tryptophan (2.95 Debye), and Valine (1.31 Debye) (SD 1).…”

Section: Structurementioning

confidence: 99%

Theoretical Study on Optoelectronic and Various Quantum Chemical Properties of Essential Amino Acids: A Comparative Study

Lakhera

Rana

Devlal

2022

Preprint

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In the present work, a theoretical study has been performed targeting essential amino acids (EAA) Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, and predicted their different physical and chemical properties by using computational techniques. Amino acids (AA), a fundamental structural unit of protein are amino and carboxyl-rich compounds having electrophilic and nucleophilic regions in it. The reactivity of AA were determined by computing molecular electrostatic potential (MEP) surfaces, counter plots, dipole moment, band gap, global reactivity parameters, and polarizability parameters. Spectral analysis (UV-Vis, Raman) helps in studying their electronic and vibrational properties. The polarizability and first order hyperpolarizability parameters were also computed to detect the nonlinear optical (NLO) behavior of AA. The comparison done with reference NLO materials Urea, Phenyl urea, and 3-nitroaniline showed that Phenylalanine have higher hyperpolarizability and can better to be used as a potent NLO material.

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In silico investigation of phytoconstituents of medicinal herb ‘Piper Longum’ against SARS-CoV-2 by molecular docking and molecular dynamics analysis

Abstract: Graphical abstract

Cited by 43 publications

References 52 publications

Modelling the DFT structural and reactivity study of feverfew and evaluation of its potential antiviral activity against COVID-19 using molecular docking and MD simulations

Modelling the DFT structural and reactivity study of feverfew and evaluation of its potential antiviral activity against COVID-19 using molecular docking and MD simulations

Study of nonlinear optical responses of phytochemicals of Clitoria ternatea by quantum mechanical approach and investigation of their anti-Alzheimer activity with in silico approach

Theoretical Study on Optoelectronic and Various Quantum Chemical Properties of Essential Amino Acids: A Comparative Study

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