scholarly journals An Overview of Computational Approaches in Structure Based Drug Design

1970 ◽  
Vol 2 (1) ◽  
pp. 53-61 ◽  
Author(s):  
Dipali Singh ◽  
Anushree Tripathi ◽  
Gautam Kumar
Keyword(s):  
Drug Design ◽  
Computer Aided Drug Design ◽  
Structure Based Drug Design ◽  
Computational Approaches ◽  
Ras Protein ◽  
Design Structure ◽  
Drug Lead ◽  
Computer Aided ◽  
Drug Designing

Drug design is a costly and difficult process. Drug must fulfill several criteria of being active, nontoxic and bioavailable. The conventional way of synthesizing drugs is a monotonous process. But computer aided drug design is a proficient way to overcome the tedious process of conventional method. Drugs can be designed computationally by structure or target based drug designing (SBDD). This review summarizes the methods of structure based drug design, usage of related softwares and a case study that explores to find a suitable drug (lead) molecule for the mutated state of H-Ras protein in order to prevent complex formation with Raf protein.Keywords: computer aided drug design; structure based drug design; Ras-proteinDOI: http://dx.doi.org/10.3126/njb.v2i1.5680Nepal Journal of Biotechnology Jan.2012, Vol.2(1): 53-61

Experimental and Computational Approaches to Improve Binding Affinity in Chemical Biology and Drug Discovery

2020 ◽  
Vol 20 (19) ◽  
pp. 1651-1660
Author(s):  
Anuraj Nayarisseri
Keyword(s):  
Drug Discovery ◽  
Drug Design ◽  
Binding Affinity ◽  
Chemical Biology ◽  
De Novo ◽  
Structure Based Drug Design ◽  
Computational Approaches ◽  
Drug Designing ◽  
Traditional Drug ◽  
Computer Based

Drug discovery is one of the most complicated processes and establishment of a single drug may require multidisciplinary attempts to design efficient and commercially viable drugs. The main purpose of drug design is to identify a chemical compound or inhibitor that can bind to an active site of a specific cavity on a target protein. The traditional drug design methods involved various experimental based approaches including random screening of chemicals found in nature or can be synthesized directly in chemical laboratories. Except for the long cycle design and time, high cost is also the major issue of concern. Modernized computer-based algorithm including structure-based drug design has accelerated the drug design and discovery process adequately. Surprisingly from the past decade remarkable progress has been made concerned with all area of drug design and discovery. CADD (Computer Aided Drug Designing) based tools shorten the conventional cycle size and also generate chemically more stable and worthy compounds and hence reduce the drug discovery cost. This special edition of editorial comprises the combination of seven research and review articles set emphasis especially on the computational approaches along with the experimental approaches using a chemical synthesizing for the binding affinity in chemical biology and discovery as a salient used in de-novo drug designing. This set of articles exfoliates the role that systems biology and the evaluation of ligand affinity in drug design and discovery for the future.

scholarly journals COMPUTER AIDED DRUG DESIGN: AN OVERVIEW

2018 ◽  
Vol 8 (5) ◽  
pp. 504-509 ◽  
Author(s):  
Surabhi Surabhi ◽  
BK Singh
Keyword(s):  
Molecular Docking ◽  
Drug Discovery ◽  
Virtual Screening ◽  
Drug Design ◽  
Computer Aided Drug Design ◽  
Structure Based Drug Design ◽  
Drug Discovery And Development ◽  
Research Areas ◽  
Computer Aided ◽  
Pharmaceutical Industries

Discovery and development of a new drug is generally known as a very complex process which takes a lot of time and resources. So now a day’s computer aided drug design approaches are used very widely to increase the efficiency of the drug discovery and development course. Various approaches of CADD are evaluated as promising techniques according to their need, in between all these structure-based drug design and ligand-based drug design approaches are known as very efficient and powerful techniques in drug discovery and development. These both methods can be applied with molecular docking to virtual screening for lead identification and optimization. In the recent times computational tools are widely used in pharmaceutical industries and research areas to improve effectiveness and efficacy of drug discovery and development pipeline. In this article we give an overview of computational approaches, which is inventive process of finding novel leads and aid in the process of drug discovery and development research. Keywords: computer aided drug discovery, structure-based drug design, ligand-based drug design, virtual screening and molecular docking

scholarly journals COMPUTER AIDED DRUG DESIGN: A PARADIGM SHIFT TO RATIONAL DRUG DESIGN (A CASE STUDY OF ALZHEIMER’S DRUG INTERPIRDINE FAILURE)

2020 ◽  
Vol 4 (12) ◽  
pp. 13-18
Author(s):  
Dr. Kalpana Virendra Singh ◽  
Dr. Shobha Shouche ◽  
Dr. Ramchander Merugu ◽  
Dr. Jeeven Singh Solanki
Keyword(s):  
Clinical Trials ◽  
Drug Discovery ◽  
Drug Design ◽  
Final Stage ◽  
Financial Burden ◽  
Rational Drug Design ◽  
Financial Loss ◽  
Computer Aided Drug Design ◽  
Computer Aided

Drug discovery and design is a tedious and lengthy process which takes enormous time, andwhen this process reaches it’s final stage that is the final stage of clinical trials 90% of thepromising drug candidates fail levying a huge financial burden of around $2-3bn on thedeveloper company. The drug failure not only incurs a financial loss to the company, but alsosmashes the hopes of the patients and families waiting for the successful approval of the drug.The scenario is even complicated when it comes to the drug approval for diseases likeAlzheimer’s. Computer aided drug design may help in the drug discovery process by slashingthe time required for searching the potential drug target through computer aided software andprograms. However the key to the success of the drug still lies in the understanding of themechanism of the cause of disease and prognosis. Computer aided drug design help in theselection and modification of leads out of number of hits available. The present study dealswith a case study of Intepridine an ambitious Axovant drug molecule which failed in the finalphase of clinical trials and was withdrawn from the market by Axovant the developer pharmacompany.

Combined approach of homology modeling, molecular dynamics, and docking: computer-aided drug discovery

2019 ◽  
Vol 4 (10) ◽  
Author(s):  
Varun Chahal ◽  
Sonam Nirwan ◽  
Rita Kakkar
Keyword(s):  
Drug Design ◽  
Homology Modeling ◽  
3D Structure ◽  
Structure Based Drug Design ◽  
Combined Application ◽  
Cytoplasmic Proteins ◽  
Software Algorithms ◽  
Computer Aided ◽  
Drug Designing ◽  
Process Structure

Abstract With the continuous development in software, algorithms, and increase in computer speed, the field of computer-aided drug design has been witnessing reduction in the time and cost of the drug designing process. Structure based drug design (SBDD), which is based on the 3D structure of the enzyme, is helping in proposing novel inhibitors. Although a number of crystal structures are available in various repositories, there are various proteins whose experimental crystallization is difficult. In such cases, homology modeling, along with the combined application of MD and docking, helps in establishing a reliable 3D structure that can be used for SBDD. In this review, we have reported recent works, which have employed these three techniques for generating structures and further proposing novel inhibitors, for cytoplasmic proteins, membrane proteins, and metal containing proteins. Also, we have discussed these techniques in brief in terms of the theory involved and the various software employed. Hence, this review can give a brief idea about using these tools specifically for a particular problem.

scholarly journals Computer Aided Drug Designing

2017 ◽  
Vol 6 (1) ◽  
pp. 1433
Author(s):  
Vijay Kumar Sehgal ◽  
Supratik Das ◽  
Anand Vardhan
Keyword(s):  
Drug Design ◽  
Medical Science ◽  
Quantitative Structure ◽  
Structure Property ◽  
Structure Based Drug Design ◽  
Safety Issues ◽  
Computer Aided ◽  
Drug Designing ◽  
Quantitative Structure Property Relationships

Designing of drugs and their development are a time and resource consuming process. There is an increasing effort to introduce the role of computational approach to chemical and biological space in order to organise the design and development of drugs and their optimisation. The role of Computer Aided Drug Designing (CADD) are nowadays expressed in Nanotechnology, Molecular biology, Biochemistry etc. It is a diverse discipline where various forms of applied and basic researches are interlinked with each other. Computer aided or in Silico drug designing is required to detect hits and leads. Optimise/ alter the absorption, distribution, metabolism, excretion and toxicity profile and prevent safety issues. Some commonly used computational approaches include ligand-based drug design, structure-based drug design, and quantitative structure-activity and quantitative structure-property relationships. In today's world, due to an avid interest of regulatory agencies and, even pharmaceutical companies in advancing drug discovery and development process by computational means, it is expected that its power will grow as technology continues to evolve. The main purpose of this review article is to give a brief glimpse about the role Computer Aided Drug Design has played in modern medical science and the scope it carries in the near future, in the service of designing newer drugs along with lesser expenditure of time and money.

scholarly journals An Updated Review of Computer-Aided Drug Design and Its Application to COVID-19

2021 ◽  
Vol 2021 ◽  
pp. 1-18
Author(s):  
Arun Bahadur Gurung ◽  
Mohammad Ajmal Ali ◽  
Joongku Lee ◽  
Mohammad Abul Farah ◽  
Khalid Mashay Al-Anazi
Keyword(s):  
Drug Discovery ◽  
Drug Design ◽  
Drug Targets ◽  
Pharmacophore Modeling ◽  
Review Article ◽  
Drug Candidate ◽  
Computational Techniques ◽  
Computer Aided Drug Design ◽  
Structure Based Drug Design ◽  
Computer Aided

The recent outbreak of the deadly coronavirus disease 19 (COVID-19) pandemic poses serious health concerns around the world. The lack of approved drugs or vaccines continues to be a challenge and further necessitates the discovery of new therapeutic molecules. Computer-aided drug design has helped to expedite the drug discovery and development process by minimizing the cost and time. In this review article, we highlight two important categories of computer-aided drug design (CADD), viz., the ligand-based as well as structured-based drug discovery. Various molecular modeling techniques involved in structure-based drug design are molecular docking and molecular dynamic simulation, whereas ligand-based drug design includes pharmacophore modeling, quantitative structure-activity relationship (QSARs), and artificial intelligence (AI). We have briefly discussed the significance of computer-aided drug design in the context of COVID-19 and how the researchers continue to rely on these computational techniques in the rapid identification of promising drug candidate molecules against various drug targets implicated in the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The structural elucidation of pharmacological drug targets and the discovery of preclinical drug candidate molecules have accelerated both structure-based as well as ligand-based drug design. This review article will help the clinicians and researchers to exploit the immense potential of computer-aided drug design in designing and identification of drug molecules and thereby helping in the management of fatal disease.

scholarly journals VIRTUAL SCREENING STATEGIES IN DRUG DISCOVERY – A BRIEF OVERVIEW

2021 ◽  
Vol 59 (4) ◽  
pp. 415
Author(s):  
Quan Minh PHAM ◽  
Long Quoc PHAM
Keyword(s):  
Drug Discovery ◽  
Virtual Screening ◽  
Development Process ◽  
Biological Activities ◽  
Computer Aided Drug Design ◽  
Computational Approaches ◽  
Drug Discovery And Development ◽  
Drug Lead ◽  
Lead Identification ◽  
Computer Aided

Computer-aided drug design has now become a compulsory tool in the drug discovery and development process which uses computational approaches to discover potential compounds with expected biological activities. Firstly, this review provides a comprehensive introduction of the virtual screening technique, knowledge and advances in both SBVS and LBVS strategies also presented. Secondly, recent database of compounds provided worldwide and drug-like parameters which are helpful in supporting the VS process will be discussed. These information will provides a good platform to estimate the advance of applying these techniques in the new drug-lead identification and optimization.

scholarly journals Use of computer in drug design and drug discovery: A review

2012 ◽  
Vol 1 (2) ◽  
Author(s):  
Md Mofizur Rahman ◽  
Md Rezaul Karim ◽  
Md Qamrul Ahsan ◽  
Abul Bashar Ripon Khalipha ◽  
Mohammed Raihan Chowdhury ◽  
...  
Keyword(s):  
Drug Design ◽  
Dna Cleavage ◽  
Cost Effective ◽  
Cancer Disease ◽  
Computer Aided Drug Design ◽  
Structure Based Drug Design ◽  
Software Libraries ◽  
Computer Aided ◽  
Modeling Software ◽  
Data Collections

Drug design through computer, a recent, very effective technique in modern arena. Now a days Computer Aided Drug Design (CADD) technologies are used in nanotechnology, molecular biology, biochemistry etc. The main benefit of the CADD is cost effective in research and development of drugs. There are wide ranges of software are used in CADD, Grid computing, window based general PBPK/PD modeling software, PKUDDS for structure based drug design,APIS, JAVA, Perl and Python, CADD as well as software including software libraries. There are different techniques used in CADD visualization, homology, molecular dynamic, energy minimization molecular docking, QSAR etc. Computer aided drug design is applicable in Cancer disease, transportation of drug to specific site in body, data collections and storages of organics and biologicals. Conformational properties and energetics of small molecules and DNA cleavage, molecular diagnostics based on fluorescences are focusing using this technique. DOI: http://dx.doi.org/10.3329/ijpls.v1i2.12955 International Journal of Pharmaceutical and Life Sciences Vol.1(2) 2012

Computer-Aided Drug Design Applied to Secondary Metabolites as Anticancer Agents

2020 ◽  
Vol 20 (19) ◽  
pp. 1677-1703
Author(s):  
Rodrigo Santos Aquino de Araújo ◽  
Edeildo Ferreira da Silva-Junior ◽  
Thiago Mendonça de Aquino ◽  
Marcus Tullius Scotti ◽  
Hamilton M. Ishiki ◽  
...  
Keyword(s):  
Drug Design ◽  
Anticancer Agents ◽  
Cost Reduction ◽  
Computer Aided Drug Design ◽  
Structure Based Drug Design ◽  
Chemical Structures ◽  
Computer Aided ◽  
Low Costs ◽  
New Compounds

: Computer-Aided Drug Design (CADD) techniques have garnered a great deal of attention in academia and industry because of their great versatility, low costs, possibilities of cost reduction in in vitro screening and in the development of synthetic steps; these techniques are compared with highthroughput screening, in particular for candidate drugs. The secondary metabolism of plants and other organisms provide substantial amounts of new chemical structures, many of which have numerous biological and pharmacological properties for virtually every existing disease, including cancer. In oncology, compounds such as vimblastine, vincristine, taxol, podophyllotoxin, captothecin and cytarabine are examples of how important natural products enhance the cancer-fighting therapeutic arsenal. : In this context, this review presents an update of Ligand-Based Drug Design and Structure-Based Drug Design techniques applied to flavonoids, alkaloids and coumarins in the search of new compounds or fragments that can be used in oncology. : A systematical search using various databases was performed. The search was limited to articles published in the last 10 years. : The great diversity of chemical structures (coumarin, flavonoids and alkaloids) with cancer properties, associated with infinite synthetic possibilities for obtaining analogous compounds, creates a huge chemical environment with potential to be explored, and creates a major difficulty, for screening studies to select compounds with more promising activity for a selected target. CADD techniques appear to be the least expensive and most efficient alternatives to perform virtual screening studies, aiming to selected compounds with better activity profiles and better “drugability”.

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