scholarly journals Screening nucleotide and nucleoside analogues as potential inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase by the molecular docking method for the treatment of COVID-19

2021 ◽  
Vol 63 (9) ◽  
pp. 14-21
Author(s):  
Thi Thu Hang Ta ◽  
◽  
Bao Kim Nguyen ◽  
Dang Huy Le ◽  
Thanh Tung Bui ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Health Concern ◽  
Pharmacokinetic Parameters ◽  
Rna Dependent Rna Polymerase ◽  
Lipinski’S Rule ◽  
Docking Method ◽  
Lipinski’S Rule Of Five

The COVID-19 pandemic triggering acute respiratory syndrome is a major global health concern. The SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) enzyme regulating viral replication has been evaluated as a potential therapeutic target for inhibition of the infection of SARS-CoV-2. In this study, we evaluated the ability of RNA-dependent RNA polymerase drug inhibitors by using molecular docking in silico model. Lipinski’s rule of Five was used to evaluate drug - like properties of potential compound. Pharmacokinetic parameters of potential compounds were assessed using the pkCSM tool. Based on previous publications, we have collected 100 compounds. The results exhibited that 18 compounds have RdRp inhibitory activity stronger than the remdesivir as reference compounds. The Lipinski’s rule of Five showed that 17 among 18 compounds had proprietary drug-likenesss. Compounds including novuridine, didanosine, sofosbuvir, puromycin, defibrotite, gemcitabine, and nikkomycins are the most negative energies and have pharmacokinetic good absorption, not metabolised in the liver, excreted by the kidney and may have hepatotoxicity properties. Therefore, it is necessary to conduct the in vitro and in vivo assays to developthese compounds into drugs for COVID-19 treatment

scholarly journals In silico screening of drug inhibitors of SARS-CoV-2RNA-dependent RNA polymerase target

2021 ◽  
Vol 63 (4) ◽  
pp. 47-54
Author(s):  
Thanh Tung Bui ◽  
◽  
Bao Kim Nguyen ◽  
Minh Ngoc Le ◽  
The Toan Nguyen ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
In Silico ◽  
Profile Analysis ◽  
3D Structure ◽  
Data Bank ◽  
Health Concern ◽  
Pharmacokinetic Parameters ◽  
Rna Dependent Rna Polymerase ◽  
Lipinski’S Rule

Objectives: the COVID-19 pandemic triggering acute respiratory syndrome has become a major global health concern. After one year into this pandemic, special therapies for COVID-19 remain an unprecedented challenge to mankind and finding drugs to treat this disease is extremely urgent. The SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) enzyme that regulates viral replication has been examined as a potential therapeutic target for the inhibition of SARS-CoV-2 infection. In this study, the authors evaluated the ability of RNA-dependent RNA polymerase drug inhibitors by using an in silico molecular docking model. Methods: the 3D structure of RdRp enzyme (PDB ID:6M71, resolution of 2.90 Å) was derived from the Protein Data Bank RCSB. The ligand structures were collected from DrugBank for the RdRp target. Molecular docking was done by AutoDock Vina software. Lipinski’s rule of five is used to compare compounds with drug-like and non-drug-like properties. Pharmacokinetic parameters of potential compounds were evaluated using the pkCSM tool. Results: based on the DrugBank database, we collected 192 antiviral molecules and compared them to remdesivir, which has inhibitory activity with this protein target. Results showed that 26 out of 192 compounds have a higher ability to inhibit the SARS-CoV-2 RdRp enzyme than remdesivir. Next, 6 drugs were selected by visually inspecting the docking results with focus on the main interaction between crucial residues at the binding site of the SARS-CoV-2 RdRp enzyme. For the visual inspection, the existence of polar interactions with ASP760 and ASP761 were utilised as the preference criterion. Finally, Lipinski’s rule of 5 criteria and absorption, distribution, metabolism, excretion and toxicity (ADMET) profile analysis suggested five drugs that have good pharmacokinetic properties. Conclusions: these drugs were dihydroergotamine, sofosbuvir, nilotinib, tipranavir, and darunavir and may be used as anti-SARS-CoV-2 agents.

scholarly journals Point mutations in the West Nile virus (Flaviviridae; Flavivirus) RNA-dependent RNA polymerase alter viral fitness in a host-dependent manner in vitro and in vivo

Virology ◽  
2012 ◽  
Vol 427 (1) ◽  
pp. 18-24 ◽  
Author(s):  
Greta A. Van Slyke ◽  
Alexander T. Ciota ◽  
Graham G. Willsey ◽  
Joachim Jaeger ◽  
Pei-Yong Shi ◽  
...  
Keyword(s):  
West Nile Virus ◽  
Rna Polymerase ◽  
Point Mutations ◽  
Viral Fitness ◽  
Dependent Manner ◽  
The West ◽  
Rna Dependent Rna Polymerase ◽  
West Nile

scholarly journals Comprehensive physicochemical, pharmacokinetic and activity profiling of anti-TB agents

2014 ◽  
Vol 70 (3) ◽  
pp. 857-867 ◽  
Author(s):  
Suresh B. Lakshminarayana ◽  
Tan Bee Huat ◽  
Paul C. Ho ◽  
Ujjini H. Manjunatha ◽  
Véronique Dartois ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Volume Of Distribution ◽  
Metabolic Stability ◽  
New Drugs ◽  
Pharmacokinetic Parameters ◽  
Lipinski’S Rule ◽  
Drug Classes ◽  
Human Pharmacokinetic

Abstract Objectives The discovery and development of TB drugs has met limited success, with two new drugs approved over the last 40 years. Part of the difficulty resides in the lack of well-established in vitro or in vivo targets of potency and physicochemical and pharmacokinetic parameters. In an attempt to benchmark and compare such properties for anti-TB agents, we have experimentally determined and compiled these parameters for 36 anti-TB compounds, using standardized and centralized assays, thus ensuring direct comparability across drugs and drug classes. Methods Potency parameters included growth inhibition, cidal activity against growing and non-growing bacteria and activity against intracellular mycobacteria. Pharmacokinetic parameters included basic physicochemical properties, solubility, permeability and metabolic stability. We then attempted to establish correlations between physicochemical, in vitro and in vivo pharmacokinetic and pharmacodynamic indices to tentatively inform future drug discovery efforts. Results Two-thirds of the compounds tested showed bactericidal and intramacrophage activity. Most compounds exhibited favourable solubility, permeability and metabolic stability in standard in vitro pharmacokinetic assays. An analysis of human pharmacokinetic parameters revealed associations between lipophilicity and volume of distribution, clearance, plasma protein binding and oral bioavailability. Not surprisingly, most compounds with favourable pharmacokinetic properties complied with Lipinski's rule of five. Conclusions However, most attempts to detect in vitro–in vivo correlations were unsuccessful, emphasizing the challenges of anti-TB drug discovery. The objective of this work is to provide a reference dataset for the TB drug discovery community with a focus on comparative in vitro potency and pharmacokinetics.

scholarly journals Docking against Lung cancer protein and Drug-likeliness of Bioactive Compounds from Phymatosorus scolopendria (Burm.F.) Pic. Serm.

2020 ◽  
pp. 437-441
Author(s):  
Sujatha Srinivasan ◽  
Catharin S. Sivaraman ◽  
Ramya R. Issac ◽  
Gayathiri Mahalingam ◽  
Gnana D. R. Roke
Keyword(s):  
Lung Cancer ◽  
Bioactive Compounds ◽  
Vinyl Ester ◽  
In Vivo Studies ◽  
Lipinski’S Rule ◽  
Lipinski’S Rule Of Five ◽  
Gas Chromatography Mass Spectroscopy ◽  
Nitrophenyl Ester

Phymatosorus scolopendria (Burm.F.) Pic. Serm. is a medicinally important fern which is used traditionally by various people all over the World. The aim of this research focuses on the docking against lung cancer protein (2ITO) with bioactive compounds of Phymatosorus scolopendria (Burm.F.) Pic. Serm. which is obtained by using Gas Chromatography Mass Spectroscopy.  The same compounds were analysed using Lipinski’s rule of five for its pharmacological prediction. The bioactive compounds were further referred for ADMET property to find its pharmacokinetic potency and prediction towards its potential as drug in future.   Among the four compounds docked with the Lung cancer protein (2ITO) 4-Nitrophenyl laurate shows high docking score followed by Hexadecanoic acid, 4 Nitrophenyl ester and Myristic acid Vinyl ester. Out of four compounds studied three compounds satisfied the  drug-likeliness based on Lipinski’s rule of five. The present work suggests the bioactive compounds of Phymatosorus scolopendria (Burm.F.) Pic. Serm.  for further in vitro and in vivo studies for its anticancer benefits especially related to lung cancer.

scholarly journals In silico identification of novel chemical compounds with anti-TB potential for the inhibition of InhA and EthR from Mycobacterium tuberculosis

2020 ◽  
Author(s):  
Sajal Kumar Halder ◽  
Fatiha Elma
Keyword(s):  
Molecular Dynamics ◽  
Mycobacterium Tuberculosis ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Chemical Compounds ◽  
Dynamics Simulation ◽  
Health Concern ◽  
Radius Of Gyration

ABSTRACTTuberculosis (TB) continuously pose a major public health concern around the globe, with a mounting death toll of approximately 1.4 million in 2019. The reduced bioavailability, increased toxicity and resistance of several first-line and second-line anti-TB drugs such as isoniazid, ethionamide have necessitated the search for new medications. In this research, we have identified several novel chemical compounds with anti-TB properties using various computational tools like molecular docking analysis, drug-likeness evaluation, ADMET profiling, P450 site of metabolism prediction and molecular dynamics simulation study. This study involves fifty drug-like compounds with antibacterial activity that inhibit InhA and EthR involved in the synthesis of one of the major lipid components, mycolic acid, which is crucial for the viability of Mycobacterium tuberculosis. Among these fifty compounds, 3-[3-(4-Fluorophenyl)-1,2,4-oxadiazol-5-yl]-N-(2-methylphenyl) piperidine-1-carboxamide (C22) and 5-(4-Ethyl-phenyl)-2-(1H-tetrazol-5-ylmethyl)-2H-tetrazole (C29) were found to pass the two-step molecular docking, P450 site of metabolism prediction and pharmacokinetics filtering analysis successfully. Their binding stability for target proteins have been evaluated through RMSD, RMSF, Radius of gyration analysis from 10 ns Molecular Dynamics Simulation (MDS) run. Our identified drugs could be a capable therapeutic for Tuberculosis drug discovery, having said that more in vitro and in vivo testing is required to justify their potential as novel drug and mode of action.

scholarly journals Preliminary Study on the Effect of Quinolone against Rec A Protein for the Possible Role in the Treatment of Tuberculosis through Molecular Docking

2021 ◽  
Vol 9 (VII) ◽  
pp. 227-232
Author(s):  
Priyanka Gautam
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Molecular Docking ◽  
Chronic Disease ◽  
In Vivo Studies ◽  
Online Database ◽  
Docking Method ◽  
Preliminary Study ◽  
Molecular Docking Method

Tuberculosis is a type of ancient, chronic disease which affects humans and caused by Mycobacterium tuberculosis. They affect the lungs and other organs. The treatment is curable but in some cases it is fatal if not treated properly. The molecular docking method was used to see the interaction of the protein with the ligand. Thus, molecular docking was used to analyse the Rec A (PDB ID 1U94) target protein with their known type of ligand by using molecular docking tools. The Rec A (PDB ID 1U94) structure of protein was downloaded through online database. The best ligand after molecular docking was Quinolone, which may act as a drug after in vitro and in vivo studies.

Potential Candidates against COVID-19 Targeting RNA-Dependent RNA Polymerase: A Comprehensive Review

2021 ◽  
Vol 22 ◽  
Author(s):  
Neetu Agrawal ◽  
Ahsas Goyal
Keyword(s):  
Rna Polymerase ◽  
In Silico ◽  
Host Cells ◽  
Rna Dependent Rna Polymerase ◽  
In Vivo Experiments ◽  
Contagious Nature ◽  
In Silico Studies ◽  
Viral Enzyme

: Due to the extremely contagious nature of SARS-COV-2, it presents a significant threat to humans worldwide. A plethora of studies are going on all over the world to discover the drug to fight SARS-COV-2. One of the most promising targets is RNA-dependent RNA polymerase (RdRp), responsible for viral RNA replication in host cells. Since RdRp is a viral enzyme with no host cell homologs, it allows the development of selective SARS-COV-2 RdRp inhibitors. A variety of studies used in silico approaches for virtual screening, molecular docking, and repurposing of already existing drugs and phytochemicals against SARS-COV-2 RdRp. This review focuses on collating compounds possessing the potential to inhibit SARS-COV-2 RdRp based on in silico studies to give medicinal chemists food for thought so that the existing drugs can be repurposed for the control and treatment of ongoing COVID-19 pandemic after performing in vitro and in vivo experiments.

scholarly journals Virtual Screening of Acetylcholinesterase Inhibitors Using the Lipinski’s Rule of Five and ZINC Databank

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Pablo Andrei Nogara ◽  
Rogério de Aquino Saraiva ◽  
Diones Caeran Bueno ◽  
Lílian Juliana Lissner ◽  
Cristiane Lenz Dalla Corte ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
Ache Activity ◽  
Acetylcholinesterase Inhibitors ◽  
Behavioral Changes ◽  
Lipinski’S Rule ◽  
Memory Impairments ◽  
Compound C ◽  
Lipinski’S Rule Of Five

Alzheimer’s disease (AD) is a progressive and neurodegenerative pathology that can affect people over 65 years of age. It causes several complications, such as behavioral changes, language deficits, depression, and memory impairments. One of the methods used to treat AD is the increase of acetylcholine (ACh) in the brain by using acetylcholinesterase inhibitors (AChEIs). In this study, we used the ZINC databank and the Lipinski’s rule of five to perform a virtual screening and a molecular docking (using Auto Dock Vina 1.1.1) aiming to select possible compounds that have quaternary ammonium atom able to inhibit acetylcholinesterase (AChE) activity. The molecules were obtained by screening and furtherin vitroassays were performed to analyze the most potent inhibitors through the IC50value and also to describe the interaction models between inhibitors and enzyme by molecular docking. The results showed that compound D inhibited AChE activity from different vertebrate sources and butyrylcholinesterase (BChE) fromEquus ferus(EfBChE), with IC50ranging from 1.69 ± 0.46 to 5.64 ± 2.47 µM. Compound D interacted with the peripheral anionic subsite in both enzymes, blocking substrate entrance to the active site. In contrast, compound C had higher specificity as inhibitor ofEfBChE. In conclusion, the screening was effective in finding inhibitors of AChE and BuChE from different organisms.

scholarly journals In silico Screening of Food Bioactive Compounds to Predict Potential Inhibitors of COVID-19 Main protease (Mpro) and RNA-dependent RNA polymerase (RdRp)

2020 ◽  
Author(s):  
Brahmaiah Pendyala ◽  
Ankit Patras
Keyword(s):  
Rna Polymerase ◽  
Bioactive Compounds ◽  
In Silico ◽  
World Health ◽  
Rna Dependent Rna Polymerase ◽  
In Silico Screening ◽  
Main Protease ◽  
Health Organization

<p>As novel corona virus (COVID-19) infections has spread throughout the world, world health organization (WHO) has announced COVID-19 as a pandemic infection. Henceforth investigators are conducting extensive research to find possible therapeutic agents against COVID-19. Main protease (Mpro) that plays an essential role in processing the polyproteins that are translated from the 2019-nCOV RNA and RNA-dependent RNA polymerase (RdRp) that catalyzes the replication of RNA from RNA template becomes as a potential targets for in silico screening of effective therapeutic compounds to COVID-19. In this study we used COVID-19 Docking Server to predict potential food bioactive compounds to inhibit Mpro and RdRp. The results showed that Phycocyanobilin, Riboflavin, Cyanidin, Daidzein, Genistein are potent inhibitor bioactive compounds to Mpro and RdRp in comparison to antiviral drugs. Though, further in vitro and/or in vivo research is required to validate the docking results. <br></p>

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