Drug repositioning to target <scp>NSP15</scp> protein on <scp>SARS‐CoV</scp>‐2 as possible <scp>COVID</scp>‐19 treatment

Sixto-López, Yudibeth; Martínez‐Archundia, Marlet

doi:10.1002/jcc.26512

Cited by 16 publications

(7 citation statements)

References 26 publications

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“…A flavonoid glycoside compound was isolated and identified from E. polyantha as myricitrin with 2D Spectral Analysis ( 1 H-and 13 C-NMR) using NMR JEOL 500 MHz. It was elucidated by spectroscopic data and by comparison with the myricitrin NMR data from the reference.…”

Section: Methodsmentioning

confidence: 99%

“…The TIP3P water model was selected for solvating complexes, followed by adding ions to neutralize. MD simulation was done using NVT and NPT ensemble for 30000 ps or 30 ns [13]. The trajectories were set to be generated save every 250 ps.…”

Section: Molecular Dynamic Simulationmentioning

confidence: 99%

“…The protein-ligand complexes results were then analyzed. The stability of the myricitrin-EndoRNAse complex interaction was seen based on the RMSD and RMSF [13].…”

Section: Molecular Dynamic Simulationmentioning

confidence: 99%

“…The purification and isolation results of the methanol extract of E. polyantha, followed by identification using NMR, showed a myricitrin compound A. Based on the spectroscopic data in Table 1, there were three aromatic signals in the 1 H-NMR spectrum, namely two doublets at δ 6.20 (1H, J = 2.1 Hz, H-6) and δ 6.30 (1H, J = 2.1 Hz, H-8), and one broad singlet (2H, H-2 'and -6') in addition to 13 C-NMR peaks at δ 99.8, 94.7, and 109.6. In addition, 1 The NMR was identical to the reference data from previous studies [14].…”

Section: Isolation and Identification Of Compoundsmentioning

confidence: 99%

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The potential of Myricitrin, a Flavonoid Compound in Eugenia polyantha from Indonesia, as an Antiviral Drug for SARS-Cov-2 through the Molecular Docking Analysis

Falah,

Ambarsari,

Andrianto

et al. 2023

J. Kim. Sains Apl.

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A Flavonoid glycoside compound, isolated and identified from E. polyantha as myricitrin, was analyzed as a ligand for its molecular binding activity against SARS-CoV-2 protein (receptor binding domain on Spike/RBD, main protease/nsp5, EndoRNAse, RNA-dependent-RNA-polymerase/RdRp), and its receptor, ACE2, and computationally assessed via molecular docking method. This study aims to determine the potential of myricitrin in E. polyantha from Indonesia as an antiviral drug for SARS-CoV-2 through molecular docking and molecular dynamic simulation analysis. The results showed that the myricitrin had the strongest binding affinity energy towards the three important SARS-CoV-2 proteins, namely endoRNAse, main protease (3CLpro), and RdRp with ∆G values of −9.60 kcal/mol, −8.40 kcal/mol, and −8.30 kcal/mol, respectively. These values are stronger than the comparator ligands of favipiravir (−5.60 kcal/mol), atazanavir (−7.20 kcal/mol), and remdesivir (−7.70 kcal/mol). This indicated that the compound has the potential as an inhibitor against 3CLpro, endoRNAse, and RdRp of SARS-CoV-2 proteins. This result was supported by the prediction made according to the Molprobity and PASS Online web servers, which showed that myricitrin has high bioactivity potential as an enzyme inhibitor (with a score of 0.38) and antiviral (with a score of 0.704).

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Section: Methodsmentioning

confidence: 99%

Section: Molecular Dynamic Simulationmentioning

confidence: 99%

“…The protein-ligand complexes results were then analyzed. The stability of the myricitrin-EndoRNAse complex interaction was seen based on the RMSD and RMSF [13].…”

Section: Molecular Dynamic Simulationmentioning

confidence: 99%

Section: Isolation and Identification Of Compoundsmentioning

confidence: 99%

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The potential of Myricitrin, a Flavonoid Compound in Eugenia polyantha from Indonesia, as an Antiviral Drug for SARS-Cov-2 through the Molecular Docking Analysis

Falah,

Ambarsari,

Andrianto

et al. 2023

J. Kim. Sains Apl.

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“…Liang et al predicted the affinities of 300 potential molecule inhibitors to the nsp10–nsp16 methyltransferase complex via docking and MD simulations. Sixto-López et al and Kumar et al predicted the potency of more than 2000 ligands to nsp15. Tatar et al aimed to repurpose 34 antiviral compounds to inhibit N protein .…”

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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Drug repositioning to target NSP15 protein on SARS‐CoV‐2 as possible COVID‐19 treatment

Sixto-López

Martínez‐Archundia

2021

J Comput Chem

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SARS‐CoV and SARS‐CoV‐2 belong to the subfamily Coronaviridae and infect humans, they are constituted by four structural proteins: Spike glycoprotein (S), membrane (M), envelope (E) and nucleocapsid (N), and nonstructural proteins, such as Nsp15 protein which is exclusively present on nidoviruses and is absent in other RNA viruses, making it an ideal target in the field of drug design. A virtual screening strategy to search for potential drugs was proposed, using molecular docking to explore a library of approved drugs available in the DrugBank database in order to identify possible NSP15 inhibitors to treat Covid19 disease. We found from the docking analysis that the antiviral drugs: Paritaprevir and Elbasvir, currently both approved for hepatitis C treatment which showed some of the lowest free binding energy values were considered as repositioning drugs to combat SARS‐CoV‐2. Furthermore, molecular dynamics simulations of the Apo and Holo‐Nsp15 systems were performed in order to get insights about the stability of these protein‐ligand complexes.

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Drug repositioning to target NSP15 protein on SARS‐CoV‐2 as possible COVID‐19 treatment

Cited by 16 publications

References 26 publications

The potential of Myricitrin, a Flavonoid Compound in Eugenia polyantha from Indonesia, as an Antiviral Drug for SARS-Cov-2 through the Molecular Docking Analysis

The potential of Myricitrin, a Flavonoid Compound in Eugenia polyantha from Indonesia, as an Antiviral Drug for SARS-Cov-2 through the Molecular Docking Analysis

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

Drug repositioning to target NSP15 protein on SARS‐CoV‐2 as possible COVID‐19 treatment

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