In-silico studies on potential inhibitors of SARS-CoV2 (original) (raw)
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Health Science Monitor
The severe acute respiratory syndrome coronavirus 2 (known as COVID-19), initially appeared in the Wuhan city of China in December 2019, has become a current medical issue around the world. Due to its highly contagious nature, COVID-19 has spread widely to all countries. As no effective treatment or vaccine is developed for this infectious disease, preventive measures are the only mandatory strategy to stop its human-to-human transmission. In the present spread of COVID-19, the discovery of antiviral drugs is crucially important as the development of these drugs often takes time. However, no specific drug has yet been approved for COVID-19. In this review, we focus on the available drug candidates used for the treatment of infections caused by COVID-19 to identify potential inhibitors through molecular docking.
European Journal of Pharmacology, 2021
Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre-including this research content-immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
WJPR, 2020
COVID-19(corona virus disease-19) is a viral flu which is caused by SARS-CoV-2(severe acute respiratory syndrome corona virus 2) has affected more than 1.5 million people around the world. Currently there are 19 different ways to tackle this pandemic approved by USFDA, one of it is drug repurposing or positioning of current existing drugs. In this study more than 1800 molecules approved by the USFDA were chosen for the molecular docking studies. These molecules were docked on PDB code; 6LU7 (The crystal structure of COVID-19 main protease in complex with an inhibitor N3) using Molegro virtual docker version 6.0.1. The study helped in identifying HITS and further in vitro and in-vivo studies of the selected HITS can be studied for their therapeutic potential in treating COVID-19.
Journal of biomolecular structure & dynamics, 2021
Severe acute respiratory syndrome coronavirus (SARS-CoV-2), a novel member of the betacoronavirus family is a single-stranded RNA virus that has spread worldwide prompting the World Health Organization to declare a global pandemic. This creates an alarming situation and generates an urgent need to develop innovative therapeutic agents. In this context, an in silico molecular docking and molecular dynamics (MD) simulation study on the existing 58 antiviral and antimalarial compounds was performed on 3CLpro, PLpro and RdRp SARS-CoV-2 proteins. The antiviral compounds are best fitted in the binding pockets and interact more profoundly with the amino acid residues compared to antimalarial compounds. An HIV protease inhibitor, saquinavir showed a good dock score and binding free energy with varied binding interactions against 3CLpro and PLpro. While, adefovir, a nucleotide HBV DNA polymerase inhibitor exhibited good dock score and binding interactions against RdRp. Although, the antimala...
DOCKING STUDIES AGAINST SARS-COV-2 M PRO INHIBITORS
Cellolose Chemical Technology, 2021
Several carbohydrate-based drugs are currently being used to treat a number of diseases in humans worldwide. Thus, our research group has focused on the synthesis of new methyl α-D-mannopyranoside (MDM) derivatives and their antimicrobial evaluation through computational studies. A series of MDM derivatives (2-6) were synthesized through facile regioselective acylation, using the direct method affording 6-O-(3-chlorobenzoyl) derivatives. This isolated 6-Oderivative was further transformed to 2,3,4-triO -acyl derivatives, bearing a wide variety of functionalities in a single molecular framework. The structures of the newly designed molecules were elucidated with the aid of IR, 1 H NMR, mass spectroscopy, and elemental analysis. The prediction of the activity spectra for the compounds (PASS) and their in vitro antimicrobial evaluation were performed, demonstrating them to be potential antimicrobial agents. The antimicrobial tests demonstrated that the compounds 3 and 5 were the most potent with the minimum inhibitory concentration (MIC) values, ranging from 0.312±0.01 to 1.25±0.03 mg/mL, and minimum bactericidal concentration (MBC) values, ranging from 0.625±0.02 to 2.50±0.05 mg/mL. A quantum chemical study was performed to calculate the thermodynamic, molecular orbital and electrostatic potential properties of the designed compounds. Molecular docking simulation was carried out against SARS-CoV-2 M pro protein 7BQY and 6Y84 to investigate their binding energy and binding tactics with the viral protein, and better binding affinity than that of the parent drug was observed. Also, pharmacokinetic prediction revealed an improved drug-likeness profile for all MDM derivatives.
2022
Background: Amidst the second wave of COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) led the world devastated, and resulted in the death of millions of people with its deadly virulence potential. In comparison to similar virus outbreaks, such as severe acute respiratory syndrome coronavirus (SARS CoV) and middle east respiratory syndrome coronavirus (MERS CoV), COVID-19 led to severe morbidity and mortality. Various therapeutic interventions to combat the SARS-CoV-2 infection are actively investigated, but still, there is no specific drug with high anti-viral efficacy against the SARS-CoV-2 virus has been reported yet. The present work is an effort to represent the promising therapeutic efficacy of 52 broad-spectrum anti-viral drugs as a potential lead molecule to suppress SARS-CoV-2 infection. These are the drugs that have shown potential efficacy against several viral infections earlier. The present article discusses the comparative analys...
Applied Microbiology: Theory ＆ Technology, 2021
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2) is a causative agent of the potentially fatal coronavirus disease (COVID-19). Coronavirus targets the human respiratory system primarily. It can also infect the gastrointestinal, hepatic, and central nervous systems of humans, avians, bats, livestock, mice, and many other wild animals, as these are primary targets of the pathogen. This study aims to screen out the most potent inhibitor for SARS-CoV-2 (COVID-19) spike glycoproteins among the selected drugs, and computational tools have been utilized for this purpose. The selected drugs have been designed to explore their structural properties in this study by molecular orbital calculation. To inhibit the spike glycoproteins, the performance of these drugs was also examined by molecular docking calculation. In improving the performance of drugs, non-bond interactions play a significant role. To determine the chemical reactivity of all the medicines, HOMO and LUMO energy values were also calculated. The combined calculations exhibited that Ledipasvir among the selected drugs can be the most potent drug to treat SARS-CoV-2 compared to other medications.
2020
This computational study comprises screening and prediction of interaction of selected antimalarial drug hydroxychloroquine with targeted two proteins of coronavirus. One is SARS enveloped E pantameric ion channel protein and another is SARS-CoV-2 main apoprotein protease. Both are vital for viral attachment and entry to the host cell for infection. After molecular protein docking with different confirmations, stable interacting complex of ligand and macromolecules were obtained. Interacting Lysine, Threonine and Tyrosine of E protein were found for participation of stable interaction with selected drug having docking affinity energy of -6.3kcal/mol. For apoprotein protease stable confirmation was screened out having bonding Threonine residue with same drug of energy -6.0 kcal/mol. Irreversible covalent bond formation and van der Waals interaction favours the selectivity and stability of both targeted proteins towards selected drug. Conventional as well as hydrophobic interactions a...
F1000Research
Background: The severe acute respiratory syndrome coronavirus (SARS-CoV)-2 virus causes an infectious illness named coronavirus disease 2019 (COVID-19). SARS-CoV is a positive-sense single-stranded RNA virus from the Betacoronavirus genus. The SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) has an important role in the viral life cycle and its active site is a very accessible region, thus a potential therapeutic approach may be to target this region to study the inhibition of viral replication. Various preexisting drugs have been proposed for the treatment of COVID-19 and the use of existing antiviral agents may reduce the time and cost of new drug discoveries, but the efficacy of these drugs is limited. Therefore, the aim of the present study was to evaluate a number of ligands used as SARS-CoV-2 virus inhibitors to determine the suitability of them for potential COVID-19 treatment. Methods: In this study, we selected a series of ligands used as SARS-CoV-2 virus inhibitors such as: ...