scholarly journals Switching Promotor Recognition of Phage RNA Polymerase in Silico along Lab Directed Evolution Path

2022 ◽  
Author(s):  
Chao E ◽  
Liqiang Dai ◽  
Jin Yu
Keyword(s):  
Rna Polymerase ◽  
Directed Evolution ◽  
In Silico ◽  
Evolution Path

In Silico Identification of a Potent Arsenic Based Approved Drug Darinaparsin against SARS-CoV-2: Inhibitor of RNA Dependent RNA polymerase (RdRp) and Essential Proteases

2020 ◽  
Vol 20 ◽  
Author(s):  
Trinath Chowdhury ◽  
Gourisankar Roymahapatra ◽  
Santi M. Mandal
Keyword(s):  
Rna Polymerase ◽  
Viral Entry ◽  
In Silico ◽  
Rna Dependent Rna Polymerase ◽  
Replication Complex ◽  
In Silico Study ◽  
Life Threatening ◽  
In Vivo Analysis ◽  
3Cl Protease

Background: COVID-19 is a life threatening novel corona viral infection to our civilization and spreading rapidly. Terrific efforts are generous by the researchers to search for a drug to control SARS-CoV-2. Methods: Here, a series of arsenical derivatives were optimized and analyzed with in silico study to search the inhibitor of RNA dependent RNA polymerase (RdRp), the major replication factor of SARS-CoV-2. All the optimized derivatives were blindly docked with RdRp of SARS-CoV-2 using iGEMDOCK v2.1. Results: Based on the lower idock score in the catalytic pocket of RdRp, darinaparsin (-82.52 kcal/mol) revealed most effective among them. Darinaparsin strongly binds with both Nsp9 replicase protein (-8.77 kcal/mol) and Nsp15 endoribonuclease (-8.3 kcal/mol) of SARS-CoV-2 as confirmed from the AutoDock analysis. During infection, the ssRNA of SARS-CoV2 is translated into large polyproteins forming viral replication complex by specific proteases like 3CL protease and papain protease. This is also another target to control the virus infection where darinaparsin also perform the inhibitory role to proteases of 3CL protease (-7.69 kcal/mol) and papain protease (-8.43 kcal/mol). Conclusion: In host cell, the furin protease serves as a gateway to the viral entry and darinaparsin docked with furin protease which revealed a strong binding affinity. Thus, screening of potential arsenic drugs would help in providing the fast invitro to in-vivo analysis towards development of therapeutics against SARS-CoV-2.

scholarly journals In silico study indicates antimalarials as direct inhibitors of SARS-CoV-2-RNA dependent RNA polymerase

2021 ◽  
pp. 1-18
Author(s):  
Pawan Kumar Doharey ◽  
Vishal Singh ◽  
Mallikarjuna Rao Gedda ◽  
Amaresh Kumar Sahoo ◽  
Pritish Kumar Varadwaj ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
In Silico ◽  
Rna Dependent Rna Polymerase ◽  
In Silico Study ◽  
Direct Inhibitors

Biophysical and in silico investigations of the molecular association between a potent RNA polymerase inhibitor, thiolutin and human serum albumin

2020 ◽  
Vol 303 ◽  
pp. 112648 ◽  
Author(s):  
Md. Zahirul Kabir ◽  
Zineddine Benbekhti ◽  
Nor Farrah Wahidah Ridzwan ◽  
Rabiâa Merrouche ◽  
Noureddine Bouras ◽  
...  
Keyword(s):  
Human Serum Albumin ◽  
Serum Albumin ◽  
Rna Polymerase ◽  
Human Serum ◽  
In Silico ◽  
Molecular Association ◽  
Polymerase Inhibitor

scholarly journals In Silico Analysis of Some Phytochemicals as Potent Anti-tubercular Agents Targeting Mycobacterium tuberculosis RNA Polymerase and InhA Protein

2020 ◽  
Author(s):  
Md Emran ◽  
Md. Mofijur Rahman ◽  
Afroza Khanam Anika ◽  
Sultana Hossain Nasrin ◽  
Abu Tayab Moin
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Rna Polymerase ◽  
In Silico ◽  
Acyl Carrier Protein ◽  
Low Cost ◽  
In Silico Analysis ◽  
The Past ◽  
Two Agents ◽  
In Silico Biology ◽  
Silico Analysis

Tuberculosis (TB) is a contagious disease, caused by Mycobacterium tuberculosis (MTB) that has infected and killed a lot of people in the past. At present treatments against TB are available at a very low cost. Since these chemical drugs have many adverse effects on health, more attention is now given on the plant-derived phytochemicals as potential agents to fight against TB. In this study, 5 phytochemicals, 4-hydroxybenzaldehyde, benzoic acid, bergapten, psoralen, and p-hydroxybenzoic acid, are selected to test their potentiality, safety, and efficacy against two potential targets, the MTB RNA polymerase and enoyl-acyl carrier protein (ACP) reductase, the InhA protein, using various tools of in silico biology. The molecular docking experiment, drug-likeness property test, ADME/T-test, P450 SOM prediction, pharmacophore mapping, and modeling, solubility testing, DFT calculations, and PASS prediction study had confirmed that all the molecules had the good potentiality to inhibit the two targets. However, two agents, 4-hydroxybenzaldehyde and bergapten were considered as the best agents among the five selected agents and they also showed far better results than the two currently used drugs, that function in these pathways, rifampicin (MTB RNA polymerase) and isoniazid (InhA protein). These two agents can be used effectively to treat tuberculosis.

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