scholarly journals Identification of SARS-CoV-2 Papain-like protease (PLpro) inhibitors using combined computational approach

Author(s):  
Milan Sencanski ◽  
Vladimir Perovic ◽  
Jelena Milicevic ◽  
Tamara Todorovic ◽  
Radivoje Prodanovic ◽  
...  

In the current pandemic finding an effective drug to prevent or treat the infection is the highest priority. A rapid and safe approach to counteract COVID-19 is in silico drug repurposing. The SARS-CoV-2 PLpro promotes viral replication and modulates the host immune system, resulting in inhibition of the host antiviral innate immune response, and therefore is an attractive drug target. In this study, we used a combined in silico virtual screening for candidates for SARS-CoV-2 PLpro protease inhibitors. We used the Informational spectrum method applied for Small Molecules for searching the Drugbank database followed by molecular docking. After in silico screening of drug space, we identified 44 drugs as potential SARS-CoV-2 PLpro inhibitors that we propose for further experimental testing.

2021 ◽  
Author(s):  
Milan Sencanski ◽  
Vladimir Perovic ◽  
Jelena Milicevic ◽  
Tamara Todorovic ◽  
Radivoje Prodanovic ◽  
...  

The need for an effective drug against COVID-19, is, after almost 18 months since the global pandemics outburst, still very high. A very quick and safe approach to counteract COVID-19 is in silico drug repurposing. The SARS-CoV-2 PLpro promotes vi-ral replication and modulates the host immune system, resulting in inhibition of the host antiviral innate immune response, and there-fore is an attractive drug target. In this study, we used a combined in silico virtual screening candidates for SARS-CoV-2 PLpro protease inhibitors. We used the Informational spectrum method applied for Small Molecules for searching the Drugbank database and further followed by molecular docking. After in silico screening of drug space, we identified 44 drugs as potential SARS-CoV-2 PLpro inhibitors that we propose for further experimental testing.


Author(s):  
Milan Sencanski ◽  
Vladimir Perovic ◽  
Snezana Pajovic ◽  
Miroslav Adzic ◽  
Slobodan Paessler ◽  
...  

<p>The SARS-CoV-2 outbreak caused an unprecedented global public health threat, having a high transmission rate with currently no drugs or vaccines approved. An alternative powerful additional approach to counteract COVID-19 is <em>in silico</em> drug repurposing. The SARS-CoV-2 main protease is essential for viral replication and an attractive drug target. In this study, we used the virtual screening (VS) protocol with both long-range and short-range interactions to select candidate SARS-CoV-2 main protease inhibitors. First, the ISM applied for Small Molecules was used for searching the Drugbank database and further followed by molecular docking. After <em>in silico</em> screening of drug space, we identified 57 drugs as potential SARS-CoV-2 main protease inhibitors that we propose for further experimental testing.</p>


2020 ◽  
Author(s):  
Milan Sencanski ◽  
Vladimir Perovic ◽  
Snezana Pajovic ◽  
Miroslav Adzic ◽  
Slobodan Paessler ◽  
...  

<p>The SARS-CoV-2 outbreak caused an unprecedented global public health threat, having a high transmission rate with currently no drugs or vaccines approved. An alternative powerful additional approach to counteract COVID-19 is <em>in silico</em> drug repurposing. The SARS-CoV-2 main protease is essential for viral replication and an attractive drug target. In this study, we used the virtual screening (VS) protocol with both long-range and short-range interactions to select candidate SARS-CoV-2 main protease inhibitors. First, the ISM applied for Small Molecules was used for searching the Drugbank database and further followed by molecular docking. After <em>in silico</em> screening of drug space, we identified 57 drugs as potential SARS-CoV-2 main protease inhibitors that we propose for further experimental testing.</p>


2020 ◽  
Author(s):  
Milan Sencanski ◽  
Vladimir Perovic ◽  
Snezana Pajovic ◽  
Miroslav Adzic ◽  
Slobodan Paessler ◽  
...  

<p>The SARS-CoV-2 outbreak caused an unprecedented global public health threat, having a high transmission rate with currently no drugs or vaccines approved. An alternative powerful additional approach to counteract COVID-19 is <em>in silico</em> drug repurposing. The SARS-CoV-2 main protease is essential for viral replication and an attractive drug target. In this study, we used the virtual screening (VS) protocol with both long-range and short-range interactions to select candidate SARS-CoV-2 main protease inhibitors. First, the ISM applied for Small Molecules was used for searching the Drugbank database and further followed by molecular docking. After <em>in silico</em> screening of drug space, we identified 57 drugs as potential SARS-CoV-2 main protease inhibitors that we propose for further experimental testing.</p>


Molecules ◽  
2020 ◽  
Vol 25 (17) ◽  
pp. 3830 ◽  
Author(s):  
Milan Sencanski ◽  
Vladimir Perovic ◽  
Snezana B. Pajovic ◽  
Miroslav Adzic ◽  
Slobodan Paessler ◽  
...  

The SARS-CoV-2 outbreak caused an unprecedented global public health threat, having a high transmission rate with currently no drugs or vaccines approved. An alternative powerful additional approach to counteract COVID-19 is in silico drug repurposing. The SARS-CoV-2 main protease is essential for viral replication and an attractive drug target. In this study, we used the virtual screening protocol with both long-range and short-range interactions to select candidate SARS-CoV-2 main protease inhibitors. First, the Informational spectrum method applied for small molecules was used for searching the Drugbank database and further followed by molecular docking. After in silico screening of drug space, we identified 57 drugs as potential SARS-CoV-2 main protease inhibitors that we propose for further experimental testing.


2020 ◽  
Author(s):  
Bharath B R ◽  
Hrishikesh Damle ◽  
Shiban Ganju ◽  
LathaDamle

Abstract Human coronavirus (SARS-CoV-2) is causing a pandemic with significant morbidity and mortality. Although, no effective novel drugs are available, drug repurposing is emerging as an effective strategy. In this study, we present an in silico drug repurposing study implementing successful concepts of computer aided drug design (CADD) technology with an objective to repurpose known drugs to interfere the viral cellular entry via the spike glycoprotein (SARS-CoV-2-S), which mediates the virus–cell receptor interaction. SARS-CoV-2-S uses ACE2 to enter cells. Totally, 4015 known and approved small molecules were screened for interaction with SARS-CoV-2 S through docking studies and 15 lead molecules were shortlisted. Further, three molecules streptomycin, ciprofloxacin and Glycyrrhizic acid (GA) were selected based on their reported anti-viral activity, safety, availability, affordability and subjected for Molecular Dynamics (MD) simulation. The MD simulation results indicate that GA from plant origin may be repurposed against SARS-CoV-2 and further studies are needed for validation.


2016 ◽  
Vol 35 (8) ◽  
pp. 1833-1848 ◽  
Author(s):  
Vivek Kumar Singh ◽  
Hsin-Huei Chang ◽  
Ching-Chuan Kuo ◽  
Hui-Yi Shiao ◽  
Hsing-Pang Hsieh ◽  
...  

2020 ◽  
Author(s):  
F Pieropan ◽  
AD Rivera ◽  
G Williams ◽  
F Calzolari ◽  
AM Butt ◽  
...  

AbstractOligodendrocytes are the myelin forming cells of the central nervous system (CNS) and are generated from oligodendrocyte progenitor cells (OPCs). Disruption or loss of oligodendrocytes and myelin has devastating effects on CNS function and integrity, which occurs in diverse neurological disorders, including Multiple Sclerosis (MS), Alzheimer’s disease (AD) and neuropsychiatric disorders. Hence, there is a need to develop new therapies that promote oligodendrocyte regeneration and myelin repair. A promising approach is drug repurposing, but most agents have potentially contrasting biological actions depending on the cellular context and their dose-dependent effects on intracellular regulatory pathways. Here, we have used a combined drug connectivity systems biology and neurobiological approach to identify compounds that exert positive and negative effects on oligodendroglia, depending on concentration. Notably, LY294002, a potent inhibitor of PI3K/Akt signalling, was the most highly ranked small molecule for both pro- and anti-oligodendroglial effects. We validated these in silico findings in multiple in vivo and ex vivo neurobiological models and demonstrate that low and high doses of LY294002 have a profoundly bipartite effect on the generation of OPCs and their differentiation into myelinating oligodendrocytes. Finally, we employed transcriptional profiling and signalling pathway activity assays to determine cell-specific mechanisms of action of LY294002 on oligodendrocytes and resolve optimal in vivo conditions required to promote myelin repair. These results demonstrate the power of multifactorial neurobiological and in silico strategies in determining the therapeutic potential of small molecules in neurodegenerative disorders.One-sentence summaryDrug discovery and CNS myelination


2020 ◽  
Author(s):  
Rameez Jabeer Khan ◽  
Rajat Kumar Jha ◽  
Ekampreet Singh ◽  
Monika Jain ◽  
Gizachew Muluneh Amera ◽  
...  

<div>The recent COVID-19 pandemic caused by SARS-CoV-2 has recorded a high number of infected people across the globe. The notorious nature of the virus makes it necessary for us to identify promising therapeutic agents in a time-sensitive manner. The current study utilises an <i>in silico</i> based drug repurposing approach to identify potential drug candidates targeting non-structural protein 15 (NSP15), i.e. a uridylate specific endoribonuclease of SARS-CoV-2</div><div>which plays an indispensable role in RNA processing and viral immune evasion from the host immune system. NSP15 was screened against an in-house library of 123 antiviral drugs obtained from the DrugBank database from which three promising drug candidates were identified based on their estimated free energy of binding (<i>ΔG</i>), estimated inhibition constant (<i>Ki</i>), the orientation of drug molecules in the active site and the key interacting residues of</div><div>NSP15. The MD simulations were performed for the selected NSP15-drug complexes along with free protein to mimic on their physiological state. The binding free energies of the selected NSP15-drug complexes were also calculated using the trajectories of MD simulations of NSP15-drug complexes through MM/PBSA (Molecular Mechanics with Poisson-Boltzmann and surface area solvation) approach where NSP15-Simeprevir (-242.559 kJ/mol) and NSP15-Paritaprevir (-149.557 kJ/mol) exhibited the strongest binding affinities. Together with the results of molecular docking, global dynamics, essential dynamics and binding free energy analysis, we propose that Simeprevir and Paritaprevir are promising drug candidates for the inhibition of NSP15 and could act as potential therapeutic agents against SARS-CoV-2.</div>


2021 ◽  
Author(s):  
Gherman Novakovsky ◽  
Shugo Sasaki ◽  
Oriol Fornes ◽  
Meltem E. Omur ◽  
Helen Huang ◽  
...  

Improving methods for human embryonic stem cell differentiation represents a challenge in modern regenerative medicine research. Using drug repurposing approaches, we discover small molecules that regulate the formation of definitive endoderm. Among them are inhibitors of known processes involved in endoderm differentiation (mTOR, PI3K, and JNK pathways) and a new compound, with an unknown mechanism of action, capable of inducing endoderm formation in the absence of growth factors in the media. Optimization of the classical protocol by including this compound achieves the same differentiation efficiency with a 90% cost reduction. The gene expression profile induced by the compound suggests that it is an inhibitor of the MYC pathway. The proposed in silico procedure for candidate molecule selection has broad potential for improving stem cell differentiation protocols.


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