Penambatan Molekuler dan Simulasi Dinamika Molekuler Senyawa Dari Genus Nigella Terhadap Penghambatan Aktivitas Enzim Protease HIV-1

Zubair, Muhammad Sulaiman; Maulana, Saipul; Mukaddas, Alwiyah

doi:10.22487/j24428744.2020.v6.i1.14982

Cited by 12 publications

(8 citation statements)

References 7 publications

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“…Hydrophobic interactions avoid a liquid environment and tend to cluster in proteins' inner globular structure [ 88 ]. Hydrophobic interactions can be in the form of Pi-Sigma and Alkyl/Pi-Alkyl bonds [ 89 ]. This study shows that each ligand has hydrophobic interactions that can support receptor inhibition.…”

Section: Discussionmentioning

confidence: 99%

Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

et al. 2020

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Since the outbreak of the COVID-19 (coronavirus disease 19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The present study aimed to evaluate bioactive compounds found in plants using a molecular docking approach to inhibit the main protease (Mpro) and spike (S) glycoprotein of SARS-CoV-2. The evaluation was performed on the docking scores calculated using AutoDock Vina (AV) as a docking engine. A rule of five (Ro5) was calculated to determine whether a compound meets the criteria as an active drug orally in humans. The determination of the docking score was performed by selecting the best conformation of the protein-ligand complex that had the highest affinity (most negative Gibbs’ free energy of binding/ Δ G ). As a comparison, nelfinavir (an antiretroviral drug), chloroquine, and hydroxychloroquine sulfate (antimalarial drugs recommended by the FDA as emergency drugs) were used. The results showed that hesperidin, nabiximols, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine, and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and nabiximols had about the same pose as nelfinavir but were better than chloroquine and hydroxychloroquine sulfate as Mpro inhibitors. This finding implied that several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine, and hydroxychloroquine sulfate, which so far are recommended in the treatment of COVID-19. From quantum chemical DFT calculations, the ascending order of chemical reactivity of selected compounds was pectolinarin > hesperidin > rhoifolin > morin > epigallocatechin gallate. All isolated compounds’ C=O regions are preferable for an electrophilic attack, and O-H regions are suitable for a nucleophilic attack. Furthermore, Homo-Lumo and global descriptor values indicated a satisfactory remarkable profile for the selected compounds. As judged by the RO5 and previous study by others, the compounds kaempferol, herbacetin, eugenol, and 6-shogaol have good oral bioavailability, so they are also seen as promising candidates for the development of drugs to treat infections caused by SARS-CoV-2. The present study identified plant-based compounds that can be further investigated in vitro and in vivo as lead compounds against SARS-CoV-2.

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Section: Discussionmentioning

confidence: 99%

Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

et al. 2020

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“…The parameter used for this docking validation is the Root Mean Square Deviation (RMSD) value. The docking method uses natural ligands with the AutodockTools 1.5.6 program and it is said to be valid if the RMSD value obtained is ≤ 2 Å (Zubair et al, 2020).…”

Section: Docking Validationmentioning

confidence: 99%

Antibacterial Activity of Streptococcus mutans from Saga Herbaceous Plant (Abrus precatorius): In Silico Study

Mardianingrum,

Suganda,

Endah

et al. 2023

ALCHEMY J. Pen. Kim

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Antibacterial is a substance that can inhibit growth or can even kill bacteria that cause infection. One of them is infection with Streptococcus mutans bacteria that cause damage to teeth, such as dental caries. Dental caries is a disease that affects many adults and children, permanently damaging the tooth layer and forming small holes in the teeth. The purpose of this study was to find active compounds from the herb Saga plant (Abrus precatorius), which has the potential to be antibacterial of S. mutans in silico. The methods used are pharmacokinetics and toxicity screening, Lipinski's Rule of Five, as well as simulations of molecular docking and molecular dynamics. The Abruquinone D (-6.43) and Abruquinone F (-7.08) were predicted to have stable interactions and be similar to amoxicillin (-7.69) and native ligand (-8.56 kcal/mol) based on the results of screening and molecular docking simulations of active compounds from Saga herbaceous (Abrus precatorius) against deoxycytidylate deaminase receptors. Molecular dynamics findings confirmed by MMGBSA methods that Abruquinone D (-41.3876 kcal/mol) had a lower energy value than Abruquinone F (-24.8521 kcal/mol). It can be inferred that Abruquinone D has a higher potential as an antibiotic (S. mutans) than Abruquinone F.

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“…We had extended the time, but we could not find interesting features The stability of the ligand-protein interaction can be examined too through the RMSF values. In contrast to RMSD, RMSF is calculated for each residue of to see how much fluctuation of each residue during the simulation [31]. In general, RMSF provides fluctuations of individual atoms throughout the simulation [29].…”

Section: Molecular Dynamics (Md)mentioning

confidence: 99%

In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease

et al. 2021

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In this work, Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone inhibition activity to SARS CoV-2 main protease were examined through in silico molecular docking and molecular dynamics simulation, with Remdesivir as control ligand. Docking score and MMGBSA were examined as well as molecular dynamics parameters: RMSD, RMSF and Protein ligand contact fraction. Our study found that Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone have comparable inhibition activity to SARS CoV-2 main protease in comparison to Remdesivir. 5-hydroxy7,8,2’,3’-tetramethoxyflavone has the lowest docking score, which was further validated by protein ligand contact fraction examination, although MMGBSA score is lowest for Remdesivir.

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Penambatan Molekuler dan Simulasi Dinamika Molekuler Senyawa Dari Genus Nigella Terhadap Penghambatan Aktivitas Enzim Protease HIV-1

Cited by 12 publications

References 7 publications

Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

Antibacterial Activity of Streptococcus mutans from Saga Herbaceous Plant (Abrus precatorius): In Silico Study

In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease

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