scholarly journals A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments

2019 ◽  
Vol 20 (18) ◽  
pp. 4648 ◽  
Author(s):  
Nathalie Lagarde ◽  
Elodie Goldwaser ◽  
Tania Pencheva ◽  
Dessislava Jereva ◽  
Ilza Pajeva ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Virtual Screening ◽  
Web Service ◽  
Molecular Mechanics ◽  
In Silico ◽  
Chemical Biology ◽  
In Silico Screening ◽  
Web Based ◽  
Screening Experiments ◽  
The Web

Chemical biology and drug discovery are complex and costly processes. In silico screening approaches play a key role in the identification and optimization of original bioactive molecules and increase the performance of modern chemical biology and drug discovery endeavors. Here, we describe a free web-based protocol dedicated to small-molecule virtual screening that includes three major steps: ADME-Tox filtering (via the web service FAF-Drugs4), docking-based virtual screening (via the web service MTiOpenScreen), and molecular mechanics optimization (via the web service AMMOS2 [Automatic Molecular Mechanics Optimization for in silico Screening]). The online tools FAF-Drugs4, MTiOpenScreen, and AMMOS2 are implemented in the freely accessible RPBS (Ressource Parisienne en Bioinformatique Structurale) platform. The proposed protocol allows users to screen thousands of small molecules and to download the top 1500 docked molecules that can be further processed online. Users can then decide to purchase a small list of compounds for in vitro validation. To demonstrate the potential of this online-based protocol, we performed virtual screening experiments of 4574 approved drugs against three cancer targets. The results were analyzed in the light of published drugs that have already been repositioned on these targets. We show that our protocol is able to identify active drugs within the top-ranked compounds. The web-based protocol is user-friendly and can successfully guide the identification of new promising molecules for chemical biology and drug discovery purposes.

Screening of phytochemicals from Curcuma longa for their inhibitory activity on SARS-CoV-2: An in-silico study

2021 ◽  
Vol 19 ◽  
Author(s):  
Preeya Negi ◽  
Lalita Das ◽  
Surya Prakash ◽  
Vaishali M. Patil
Keyword(s):  
Drug Discovery ◽  
In Silico ◽  
Curcuma Longa ◽  
Docking Studies ◽  
Primary Objective ◽  
In Silico Screening ◽  
Rational Drug ◽  
In Silico Study ◽  
Speed Up ◽  
Novel Coronavirus

Introduction: Natural products or phytochemicals have always been useful as effective therapeutics and for providing the lead for rational drug discovery approaches specific to anti-viral therapeutics. Methods: The ongoing pandemic caused by novel coronavirus has created a demand for effective therapeutics. Thus, to achieve the primary objective to search for effective anti-viral therapeutics, in silico screening of phytochemicals present in Curcuma longa extract (ex. Curcumin) has been planned. Results: The present work involves the evaluation of ADME properties and molecular docking studies. Conclusion: The application of rationalized drug discovery approaches to screen the diverse natural resources will speed up the anti-COVID drug discovery efforts and benefit the global community.

scholarly journals Systemic In Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server

2020 ◽  
Vol 60 (12) ◽  
pp. 5735-5745 ◽  
Author(s):  
Chi Xu ◽  
Zunhui Ke ◽  
Chuandong Liu ◽  
Zhihao Wang ◽  
Denghui Liu ◽  
...  
Keyword(s):  
Drug Discovery ◽  
In Silico ◽  
Web Server ◽  
In Silico Screening

scholarly journals IN-SILICO SCREENING AGAINST ANTIMALARIAL TARGET PLASMODIUM FALCIPARUM ENOYL-ACYL CARRIER PROTEIN REDUCTASE

2017 ◽  
Vol 10 (17) ◽  
pp. 127
Author(s):  
Berwi Fazri Pamudi ◽  
Azizahwati Azizahwati ◽  
Arry Yanuar
Keyword(s):  
Plasmodium Falciparum ◽  
Virtual Screening ◽  
In Silico ◽  
Acyl Carrier Protein ◽  
Parasitic Infection ◽  
Antimalarial Drugs ◽  
Chemotherapeutic Agents ◽  
Effective Vaccine ◽  
Carrier Protein ◽  
In Silico Screening

  Objective: Malaria is a parasitic infection that causes worldwide health problems. The absence of an effective vaccine and Plasmodium strains that are resistant to antimalarial drugs emphasize the importance of developing new chemotherapeutic agents. The use of computers for in-silico screening, or virtual screening, is currently being developed as a method for discovering antimalarial drugs. One of the enzymes that can support the development of the malaria parasite is the Plasmodium falciparum enoyl-acyl carrier protein reductase (PfENR). Inhibition of these enzymes leads to Type II lipid biosynthesis inhibition on the parasite.Methods: This research investigates the use of virtual screening to find PfENR inhibitor candidates. A molecular docking method using GOLD software and the medicinal plants in Indonesia database will be used. This target has been optimized by the removal of residues and the addition of charge. Ligand is expected to be an inhibitor of PfENR.Results: In-silico screening, or virtual screening, found that the top five compounds with the highest GOLD score at trial are kaempferol 3-rhamnosyl- (1-3)-rhamnosyl-(1-6)-glucoside; cyanidin 3,5-di-(6-malonylglucoside); 8-hydroxyapigenin 8-(2’’, 4’’-disulfato glucuronide); epigallocatechin 3,5,-di- O-gallat; quercetin 3,4’-dimethyl ether 7-alpha-L-arabinofuranosyl-(1-6)-glucoside. They had GOLD scores of 94.73, 95.90, 86.46, 85.39, and 84.40, respectively.Conclusions: There are two candidate inhibitor compounds from tea (Camellia sinensis), which have potential for development as an antimalarial drug, which are kaempferol 3-rhamnosyl-(1-3)-rhamnosyl-(1-6)-glucoside and epigallocatechin 3,5,-di-O-gallate, with a GOLD score of 94.73 and 85.39, respectively.

scholarly journals Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace

2020 ◽  
Author(s):  
Natesh Singh ◽  
Ludovic Chaput ◽  
Bruno O Villoutreix
Keyword(s):  
Virtual Screening ◽  
Drug Repositioning ◽  
Pharmaceutical Research ◽  
Bioactive Molecules ◽  
Screening Methods ◽  
Web Servers ◽  
Web Based ◽  
Drug Candidates ◽  
Screening Experiments ◽  
Molecule Docking

Abstract The interplay between life sciences and advancing technology drives a continuous cycle of chemical data growth; these data are most often stored in open or partially open databases. In parallel, many different types of algorithms are being developed to manipulate these chemical objects and associated bioactivity data. Virtual screening methods are among the most popular computational approaches in pharmaceutical research. Today, user-friendly web-based tools are available to help scientists perform virtual screening experiments. This article provides an overview of internet resources enabling and supporting chemical biology and early drug discovery with a main emphasis on web servers dedicated to virtual ligand screening and small-molecule docking. This survey first introduces some key concepts and then presents recent and easily accessible virtual screening and related target-fishing tools as well as briefly discusses case studies enabled by some of these web services. Notwithstanding further improvements, already available web-based tools not only contribute to the design of bioactive molecules and assist drug repositioning but also help to generate new ideas and explore different hypotheses in a timely fashion while contributing to teaching in the field of drug development.

scholarly journals Novel Compounds Identified by Structure-Based Prion Disease Drug Discovery Using In Silico Screening Delay the Progression of an Illness in Prion-Infected Mice

2020 ◽  
Author(s):  
Daisuke Ishibashi ◽  
Takeshi Ishikawa ◽  
Satoshi Mizuta ◽  
Hiroya Tange ◽  
Takehiro Nakagaki ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Prion Disease ◽  
In Silico ◽  
In Silico Screening

scholarly journals Analysis Docking Of Plasmodium Falciparum Enoyl Acyl Carrier Protein Reductase (Pfenr) With Organic Compunds From Virtual Screening Of Herbal Database

2020 ◽  
Vol 3 (1) ◽  
pp. 127
Author(s):  
Nya Daniaty Malau ◽  
St Fatimah Azzahra
Keyword(s):  
Plasmodium Falciparum ◽  
Virtual Screening ◽  
In Silico ◽  
Fatty Acid Biosynthesis ◽  
Acyl Carrier Protein ◽  
Chemotherapeutic Agents ◽  
Effective Vaccine ◽  
Carrier Protein ◽  
Autodock Vina ◽  
In Silico Screening

Malaria is one of problematic infectious diseases worldwide. The absence of an effective vaccine and the spread of drug resistant strains of Plasmodium clearly indicate the necessity for the deveploment of new chemotherapeutic agents. Recent method being developed is searching a new drug of antimalarial using in silico screening, or also known as virtual screening. One of enzyme target that important for growth of the malaria parasite is Plasmodium falciparum Enoyl Acyl Carrier Protein Reductase (PfENR). Inhibition of this enzyme cause the fatty acid biosynthesis type II will be terminated. In this research, in silico screening was performed using AUTODOCK VINA software to find inhibitor candidates of PfENR by using ligands from the database of Medicinal Plants in Indonesia. On the AUTODOCK VINA software moleculer docking experiments were performed between ligands and macromolecule target PfENR. This target that has been optimized with residue removal and charges addition. Ligand is expected to be the PfENR inhibitors.

scholarly journals Sanitize It Yourself: Web-based molecular sanitization for machine-generated chemical structures

2021 ◽  
Author(s):  
Naruki Yoshikawa ◽  
Kentaro Rikimaru ◽  
Kazuki Yamamoto
Keyword(s):  
Deep Learning ◽  
Web Service ◽  
Chemical Space ◽  
Computer Aided Drug Design ◽  
Web Based ◽  
Chemical Structures ◽  
Structural Formulas ◽  
Computer Aided ◽  
Novel Structures ◽  
The Web

Many computer-aided drug design (CADD) methods using deep learning have recently been proposed to explore the chemical space toward novel scaffolds efficiently. However, there is a tradeoff between the ease of generating novel structures and the chemical feasibility of structural formulas. To overcome the limitations of computational filtering, we have implemented a web-based software in which users can share and evaluate computer-generated compounds. The web service is available at https://sanitizer.chemical.space/.

scholarly journals The CombineArchiveWeb application – A web based tool to handle files associated with modelling results

2014 ◽  
Author(s):  
Martin Scharm ◽  
Florian Wendland ◽  
Martin Peters ◽  
Markus Wolfien ◽  
Tom Theile ◽  
...  
Keyword(s):  
Computational Biology ◽  
In Silico ◽  
Simulation Studies ◽  
Meta Data ◽  
Web Based ◽  
Manual Handling ◽  
The Web

Sharing in silico experiments is essential for the advance of research in computational biology. Consequently, the COMBINE archive was designed as a digital container format. It eases the management of files related to a modelling result, fosters collaboration, and ultimately enables the exchange of reproducible simulation studies. However, manual handling of COMBINE archives is tedious and error prone. We therefore developed the CombineArchiveWeb application to support scientists in promoting and publishing their research by means of creating, exploring, modifying, and sharing archives. All files are equipped with meta data and can be distributed over the Web through shareable workspaces.

High-Throughput and In Silico Screening in Drug Discovery

2017 ◽  
pp. 247-273 ◽  
Author(s):  
Nandu Thrithamarassery Gangadharan ◽  
Ananda Baskaran Venkatachalam ◽  
Shiburaj Sugathan
Keyword(s):  
Drug Discovery ◽  
High Throughput ◽  
In Silico ◽  
In Silico Screening
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