Targeting SARS-CoV-2 Nonstructural Protein 15 Endoribonuclease: an
            <i>in silico</i>
            Perspective

Mahmud, Shafi; Elfiky, Abdo A.; Amin, Al; Mohanto, Sumon Chandro; Rahman, Ekhtiar; Acharjee, Uzzal Kumar; Saleh, Abu

doi:10.2217/fvl-2020-0233

Cited by 8 publications

(10 citation statements)

References 63 publications

(64 reference statements)

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“…Computational predictions proved their crucial role in COVID-19 fighting (Mahmud et al 2021 ; Sonousi et al 2021 ; Gyebi et al 2021 ; Wang 2020 ). In the current study, molecular dynamics simulation for the spike RBD of the delta variant was performed, followed by protein–protein docking to test the efficacy of the binding of the spike to both human cell-surface receptors GRP78 and ACE2.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 Delta Variant is Recognized Through GRP78 Host-Cell Surface Receptor, In Silico Perspective

Elfiky

Ibrahim

Elgohary

2022

Int J Pept Res Ther

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Different SARS-CoV-2 new variants emerged and spread during the past few months, sparking infections and death counts. The new variant B.1.617 (delta variant) sparked in India in the past few months, causing the highest records. The B.1.617 variant of SARS-CoV-2 has the double mutations E484Q and L452R on its spike Receptor Binding Domain (RBD). The first mutation is like the reported South African and the Brazilian variants (501.V2 and B.1.1.248). This mutation lies in the region C480-C488, which we predicted before to be recognized by the host-cell receptor; Glucose Regulated Protein 78 (GRP78). In the current study, we test the binding affinity of the host-cell receptor GRP78 to the delta variant spike RBD using molecular docking and molecular dynamics simulations of up to 100 ns. Additionally, the ACE2-RBD is tested by protein–protein docking. The results reveal equal average binding affinities of the GRP78 against wildtype and delta variant spikes. This supports our previous predictions of the contribution of GRP78 in SARS-CoV-2 spike recognition as an auxiliary route for entry.

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Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 Delta Variant is Recognized Through GRP78 Host-Cell Surface Receptor, In Silico Perspective

Elfiky

Ibrahim

Elgohary

2022

Int J Pept Res Ther

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“…Borgio et al 305 screened 23 FDA-approved drugs to target the helicase of SARS-CoV-2 and reported vapreotide having a binding affinity of −11.58 kcal/mol as the most potent candidate. Mahmud et al 306 showed that drugs such as valrubicin, aprepitant, and saquinair have excellent docking scores to SARS-CoV-2 nsp15. Khan et al 307 used docking to study the interaction between N protein and nsp3.…”

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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“…Results of in silico studies show that curcumin/curcuminoids can form strong bonds with the active site of SARS-CoV-2 M pro ( Ibrahim et al, 2020 ; Bahun et al, 2022 ). Due to high binding affinity and its binding with the interface region of M pro may cause the protein conformational changes, indicating that curcumin/curcuminoids could be the potential ligands for COVID-19 therapy ( Ibrahim et al, 2020 ; Li and Kang 2020 ; Kumar M. et al, 2021 ; Mahmud et al, 2021a ; Babaeekhou et al, 2021 ; Teli et al, 2021 ; Halder et al, 2022 ). One more study demonstrated that demethoxycurcumin and bisdemethoxycurcumin had an optimum binding affinity with COVID-19 M pro by molecular modeling and showed the stable state by molecular dynamic (MD) simulation assay, suggesting these could be one of the potential ligands for COVID-19 therapy ( Mulu et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Pharmaceutical Prospects of Curcuminoids for the Remedy of COVID-19: Truth or Myth

Fu¹,

Kang³

et al. 2022

Front. Pharmacol.

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Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is a positive-strand RNA virus, and has rapidly spread worldwide as a pandemic. The vaccines, repurposed drugs, and specific treatments have led to a surge of novel therapies and guidelines nowadays; however, the epidemic of COVID-19 is not yet fully combated and is still in a vital crisis. In repositioning drugs, natural products are gaining attention because of the large therapeutic window and potent antiviral, immunomodulatory, anti-inflammatory, and antioxidant properties. Of note, the predominant curcumoid extracted from turmeric (Curcuma longa L.) including phenolic curcumin influences multiple signaling pathways and has demonstrated to possess anti-inflammatory, antioxidant, antimicrobial, hypoglycemic, wound healing, chemopreventive, chemosensitizing, and radiosensitizing spectrums. In this review, all pieces of current information related to curcumin-used for the treatment and prevention of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection through in vitro, in vivo, and in silico studies, clinical trials, and new formulation designs are retrieved to re-evaluate the applications based on the pharmaceutical efficacy of clinical therapy and to provide deep insights into knowledge and strategy about the curcumin’s role as an immune booster, inflammatory modulator, and therapeutic agent against COVID-19. Moreover, this study will also afford a favorable application or approach with evidence based on the drug discovery and development, pharmacology, functional foods, and nutraceuticals for effectively fighting the COVID-19 pandemic.

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Targeting SARS-CoV-2 Nonstructural Protein 15 Endoribonuclease: an in silico Perspective

Cited by 8 publications

References 63 publications

SARS-CoV-2 Delta Variant is Recognized Through GRP78 Host-Cell Surface Receptor, In Silico Perspective

SARS-CoV-2 Delta Variant is Recognized Through GRP78 Host-Cell Surface Receptor, In Silico Perspective

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

Pharmaceutical Prospects of Curcuminoids for the Remedy of COVID-19: Truth or Myth

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