Review on Discovery Studio: An important Tool for Molecular Docking

 

Shravani S. Pawar*, Sachin H. Rohane

Department of Pharmacy, Yashoda Technical Campus, Wadhe, Satara 415003.

*Corresponding Author E-mail: shravanipawar118@gmail.com

 

ABSTRACT:

In this paper, an overview on discovery studio docking program for analyze and modeling molecular structure, sequence of relevance to life science researcher. This software covers the areas such as ligand design, structure-based design, macromolecule design and engineering, simulations, pharmacophore modeling, quantitative structure activity relationship (QSAR), ADME, predictive toxicity. Discovery Studio help to analyze activities such as anti-convulsant, anti-viral, antidepressant, antibacterial, anti-tubercular, anti-Alzheimer, anti-malarial, anti-cancer. This software gives better result correlation with in-view pharmacological activity. So, this is a helping tool for a researcher to minimize the time as well as cost of research activity and also gives better understanding to study ligand and receptor complex.

 

KEYWORDS: Drug Discovery, Molecular Docking, Discovery Studio software.

 

 


INTRODUCTION:

Computer-Aided drug design represents computational resources that used to facilitate the design and discovery of new therapeutic solutions. Molecular docking is widely used in CADD due to its reliable prediction properties and is one of the essential backbones of CADD. Molecular docking is a rapid and inexpensive technique in academics as well as in industrial settings. Molecular Docking is a technique to find best matching molecular structure by interaction between enzyme and ligand. It also analyses the orientation of one molecule with other into the binding site of a macromolecular target. Docking has a major role in virtual screening, drug discovery, bioremediation.

 

Discovery studio software is an agglomeration to transcript small molecules and macromolecule system. It is developed by Dassault Systemes BIOVIA (Accelrys). Discovery Studio is a single unified, graphical interface for advanced drug design and protein modeling research. This software provides bunch of viewers for display plots and graphical representation of data.

 

Review of literature:

Ana-Maria Udrea and et al use Discovery Studio software to check the potential of phenothiazine in Covid-19 infection. They found that data given by docking software is correlated with in vivo activity. The data found to be suitable and correct with in vivo activity.

 

Shiben Wang and et al synthesized the different series of 1,3,4-oxadiazole derivatives using discovery studio and the compound were studied gives best anticonvulsant activity. In silico studies were carried out to explore the binding interaction of the most active compound. They found the target compounds were related with in vivo and vitro activity.

 

Fatma Gur and et al studied the adverse effect of Atomoxetine which issubstitute for methylphenidate in the long-term treatment of ADHD. They conduct molecular docking study using Discovery Studio programs. The data found to be match with in vivo activity.

 

K. Sangeetha and et al use the discovery studio to check the antiviral activities of plant derived compounds against zika virus. By In silico studies, the software used for screening of various phytochemicals against Zika virus to identify new promising drug candidates. In this study, around 5550 phytochemicals retrieved from various databases were subjected for molecular docking in Discovery studio program.

 

Shi-Ben Wang and et al designed and synthesized the derivatives of coumarin and 3, 4-dihydroquinolinone. They found that compound check in the discovery studio software have best antidepressant activityand also exhibits good affinity for the 5-HT1A receptor. These findings can be useful in the design and synthesis of novel antidepressants.

 

Fathima Rizwana B and et al studied the molecular docking and binding structures on famciclovir and entecavir compound simulated from Discovery studio program. The geometric structures were optimizedand the band gap energies were calculated using software. Electrostatic Potential (ESP) maps identifies Negative and positive potential regions with help of software. Molecular docking studies confirmed the antiviral activity of the selected compounds.

 

Geethalakshmi Rajarathinam and et al uses discovery studio for docking of T. decandra with FabZ. They found that isolated flavonoid compound possess excellent anti- P. aeruginosa activity. The in-silico analysis of isolated compound shows possible action in a hypothetical way. The molecular docking of flavonoid was carried out using Discovery Studio.

 

Sugunadevi Sakkiah and et al developed 3D pharmacophore model based on the known inhibitors. This Pharmacophore model was generated using HYPOGEN algorithm in discovery studio program. From the molecular docking studies around 36 compounds were obtained based on consensus scoring function and selected as HSP90 inhibitors.

 

The aim of Ran Joo Choi and et al was to evaluate the anti-Alzheimer's disease activities of selected ginsenosides. They use the docking software to check thepotential of ginsenosides in the development of therapeutic agents for Alzheimer's disease. They predict binding energies of the ginsenosides with β-site amyloid and obtained result were corelated with in vitro activity.

 

Nafees Ahmed and et al use discovery studio for synthesis of tricyclic guanidine derivatives and biological evaluation against P. falciparum. The docking studies show that there is very strong correlation between in silico and in vitro results. Based on the data obtained by software, more potent inhibitor against P. falciparum can be designed. Docking was performed using DS program to understand the mechanism of inhibition and to identify pharmacophore required for anti-malarial activity.

 

Prashant Bhardwaj and et al uses DS program for identification of novel proteintargets for triclosan. They conduct the inverse virtual screening study for protein targets. A text mining study of triclosan was initially performed to find outinteraction in various biochemical processes.

 

Amer Hosny and et al use the software for development of a predictive model to identify potential HIV-1 attachment inhibitors. They performed the study in two phased computational process to identify useful compounds capable of binding to the protein for therapeutic purposes using the Discovery Studio docking and screening software.

 

Mohammad Heiat and et al conduct the study in docking program to analyze isolated ssDNA aptamers against angiotensin II. They found that the structural and sequential homology between aptamers can be considered as a sign of similar characteristics and Output PDB files were modified from RNA to DNA in the discovery studio visualizer software. The in-silico study was performed and uses to find aptameric fragments binding potency.

 

Sagir Yusuf Ismail and et al performed in-silico QSAR study of sulfur containing shikonin oxime derivatives. The docking study also carried out between this derivatives and target protein. This study provides an approach for the design of more potent anti-colon drug. The data found to be match and correct with anti-cancer agent for colon cancer.

 

Shola Elijah Adeniji and et al use discovery studio software to molecular docking evaluation of selected quinoline derivatives. Discovery Studio software was used to visualized and analyzed the docked results. They found that activity of quinoline derivatives checked in software exhibits as best anti-tubercular agents.

 

CONCLUSION:

This study paved better understanding of Discovery Studio software for viewing, sharing, analysing protein and small molecule data. The DS program provides applications covering areas including molecular mechanism, molecular dynamics, quantum mechanics. Software also have ability to perform hybrid QM/MM calculations. It employed for small molecule and macromolecule applications. The molecular properties can found by editing structures and performing calculations.

 

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Received on 06.11.2020                    Modified on 26.11.2020

Accepted on 08.12.2020                   ©AJRC All right reserved

Asian J. Research Chem. 2021; 14(1):86-88.

DOI: 10.5958/0974-4150.2021.00014.6