Identification of Papain-Like Protease inhibitors of SARS CoV-2 through HTVS, Molecular docking, MMGBSA and Molecular dynamics approach

Jupudi, Srikanth; Rajagopal, Kalirajan; Murugesan, Sankaranarayanan; Kumar, Banoth Karan; Raman, Kannan; Byran, Gowramma; Chennaiah, Jayakuamar; Muthiah, Velayutham pillai; P, Bharathi Dasan; Sankaran, Sathianarayanan

doi:10.1016/j.sajb.2021.11.033

Cited by 13 publications

(12 citation statements)

References 33 publications

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“…Molecular mechanics with generalized Born and surface area solvation (MMGB-SA) calculations have also been performed. The MM/GBSA method − was used to calculate the binding free energies between the amyloids and the RBD. The free energy was obtained from separate MMGB-SA calculations into three parts (amyloids, RBD, and the whole complex) by extracting them from the explicit solvent MD simulation.…”

Section: Methodsmentioning

confidence: 99%

Coupling of SARS-CoV-2 to Aβ Amyloid Fibrils

Coppola,

Pavlíček,

Král

2024

ACS Omega

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The COVID-19 infection has been more problematic for individuals with certain health predispositions. Coronaviruses could also interfere with neural diseases if the viruses succeed in entering the brain. Therefore, it might be of principal interest to examine a possible coupling of coronaviruses and amyloid fibrils. Here, molecular dynamics simulations were used to investigate direct coupling of SARS-CoV-2 and Aβ fibrils, which play a central role in neural diseases. The simulations revealed several stable binding configurations and their dynamics of Aβ42 fibrils attached to spike proteins of the Omicron and Alpha variants of SARS-CoV-2.

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Section: Methodsmentioning

confidence: 99%

Coupling of SARS-CoV-2 to Aβ Amyloid Fibrils

Coppola,

Pavlíček,

Král

2024

ACS Omega

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“… 38 The total free energy binding was calculated using eqn (2) Δ G bind = Δ G complex − (Δ G protein + Δ G ligand ) where, Δ G bind = binding free energy, Δ G complex = free energy of the complex, Δ G protein = free energy of the protein, and Δ G ligand = free energy of the ligand. 39 …”

Section: Methodsmentioning

confidence: 99%

“…where, DG bind = binding free energy, DG complex = free energy of the complex, DG protein = free energy of the protein, and DG ligand = free energy of the ligand. 39 The free energy of each component complex, protein, and ligand was calculated by using eqn (3)…”

Section: Molecular Dynamics Simulation (Mds)mentioning

confidence: 99%

Exploring the therapeutic mechanisms of Gleditsiae Spina acting on pancreatic cancervianetwork pharmacology, molecular docking and molecular dynamics simulation

Duan,

Zhang,

Yuan

et al. 2023

RSC Adv.

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“…Papain-Like Proteases is a cysteine protease, essential for viral replication and proliferation, as a highly conserved enzyme it cleaves peptide linkage between Nsp1, Nsp2, Nsp3, and Nsp4. As valid therapeutic targets, it stops viral reproduction and boosts host [36]. Surprisingly, free Hb at 1mM inhibited viral replication (99%), and its interaction with SARS-CoV-2 was localized into the RBD region of the S protein.…”

Section: Introductionmentioning

confidence: 99%

Endogenous piRNAs Can Interact with Omicron Variant of the SARS-CoV-2 Genome

Rakhmetullina¹,

Akimniyazova²,

Niyazova³

et al. 2023

Preprint

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that caused the COVID-19 pandemic still able to infect the population in many countries. The Omicron strain is the most mutated variant of SARS-CoV-2. The high transmissibility of the strain and the ability to evade immunity require a priority study of its properties in order to quickly create effective means of preventing it. The present work is devoted to the study of in silico interaction of piRNAs with the genome of the SARS-CoV-2 (gRNA) in order to identify endogenous piRNAs and propose synthetic piRNAs with high antiviral activity for drug development. The studies were carried out using proven bioinformatic methods of interaction of the entire SARS-CoV-2 genome with more than eight million piRNAs. Binding sites (BSs) of piRNAs in the 5'UTR were located with overlapping nucleotide sequences called clusters of BSs. Several clusters of BSs were found in the nsp3, nsp7, RNA-dependent RNA polymerase, endoRNAse, S surface glycoprotein, ORF7a and nucleocapsid. 16 synthetic piRNAs have been proposed that interact with gRNA with free binding energy from -170 kJ/mol to -175 kJ/mol, which can be used to create drugs that suppress the reproduction of SARS-CoV-2.

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Identification of Papain-Like Protease inhibitors of SARS CoV-2 through HTVS, Molecular docking, MMGBSA and Molecular dynamics approach

Cited by 13 publications

References 33 publications

Coupling of SARS-CoV-2 to Aβ Amyloid Fibrils

Coupling of SARS-CoV-2 to Aβ Amyloid Fibrils

Exploring the therapeutic mechanisms of Gleditsiae Spina acting on pancreatic cancervianetwork pharmacology, molecular docking and molecular dynamics simulation

Endogenous piRNAs Can Interact with Omicron Variant of the SARS-CoV-2 Genome

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