In Silico Chemistry and Biology

Current and Future Prospects

Girish Kumar Gupta, Mohammad Hassan Baig, Girish Kumar Gupta, Mohammad Hassan Baig

• Publisher: De Gruyter
• Year: 2022
• Print ISBN: 9783110495171
• eBook ISBN: 9783110492453
• Edition: 1
• Topic: Physical Sciences
• Subtopic: Bioinformatics

In Silico Chemistry and Biology: Current and Future Prospects provides a compact overview on recent advances in this highly dynamic branch of chemistry. Various methods of protein modelling and computer-assisted drug design are presented, including fragment- and ligand-based approaches. Many successful practical applications of these techniques are demonstrated. The authors also look to the future and describe the main challenges of the field.

1 Pharmaceutical interest of in-silico approaches

Dinesh Kumar

Sri Sai College of Pharmacy, Amritsar

ORCID:https://orcid.org/0000-0002-4342-4124

Pooja Sharma

Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India

Khalsa College of Pharmacy, Amritsar, India

Ayush Mahajan

Sri Sai College of Pharmacy, Amritsar

Ravi Dhawan

Khalsa College of Pharmacy, Amritsar, India

Kamal Dua

Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, Australia

Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia

Abstract

The virtual environment within the computer using software performed on the computer is known as in-silico studies. These drugs designing software play a vital task in discovering new drugs in the field of pharmaceuticals. These designing programs and software are employed in gene sequencing, molecular modeling, and in assessing the three-dimensional structure of the molecule, which can further be used in drug designing and development. Drug development and discovery is not only a powerful, extensive, and an interdisciplinary system but also a very complex and time-consuming method. This book chapter mainly focused on different types of in-silico approaches along with their pharmaceutical applications in numerous diseases.

Keywords: in-silico approaches , lead optimization, molecular docking, pharmaceutical application,

1.1 Introduction

The in-silico means “performed on the computer” by creating a virtual environment within the computer using the software. These drugs designing software play a significant job in designing new drugs in the field of pharmaceuticals. These programs and software have been engaged in gene sequencing, molecular modeling, and in assessing the three-dimensional (3D) structure of drug candidates, which can further be used in drug designing, formulation, and development. Drug development and discovery is an extensive, authoritative, potential, and an interdisciplinary system but is of complex and time-consuming process. The substantial impetus toward the practice of in-silico studies and molecular docking has been increased for computer-aided drug design [1]. There are many aspects that are responsible for its failure may be due to some side effects, less efficacy, or poor pharmacokinetics. The in-silico drug design requires skills from different fields like structural and molecular biology, nanotechnology, biochemistry, biophysics, and computational scientist. The major objective is to implement research projects for discovering new compounds with desired therapeutic effect [2, 3]. The process of drug discovery involves different steps which are given as below:

1.1.1 Target recognition

Target Identification includes detection and isolation of the specific targets to examine their association with disease.

1.1.2 Target confirmation

Target Validation is the characterization of the pharmacological response resulted from the alterations done in the activity of a target protein.

1.1.3 Lead discovery

Lead discovery involves a chemical compound that has some specificity and effectiveness in contrast to the biological target and is expected that the drug formed can cure the specific disease.

1.1.4 Lead optimization

Lead Optimization is the modification in the chemical structure to improve targets selectivity and specificity. This also helps to improve potency, pharmacodynamic, and pharmacokinetic properties of the drug. Both in-vitro and in-vivo experiments are performed in the screening of the lead compound and for developing an efficient and safe drug.

1.1.5 Preclinical studies

A preclinical study is a stage that starts before the clinical trials and during which important tests are conducted on animals for checking the potency as well as the toxicity of the drug. During the preclinical trials, the drug safety data are collected. The major aim is to provide the safe dose for the clinical trials done on humans.

1.1.6 Clinical trials

Clinical trials include human volunteers on which testing of the new drug which passed the preclinical trial is done, to check if there is any harmful side effect is present or not also to determine its effectiveness a...

Table of contents

• Title Page
• Copyright
• Contents
• 1 Pharmaceutical interest of in-silico approaches
• 2 Novel drug design and bioinformatics: an introduction
• 3 In silico drug design: application and success
• 4 Protein modeling
• 5 Fragment based drug design
• 6 An overview of in silico methods used in the design of VEGFR-2 inhibitors as anticancer agents
• 7 Molecular docking and MD: mimicking the real biological process
• 8 Molecular docking studies of tea (Thea sinensis Linn.) polyphenols inhibition pattern with Rat P-glycoprotein
• 9 Statistical methods for in silico tools used for risk assessment and toxicology
• 10 Systems biology–the transformative approach to integrate sciences across disciplines Systems Biology: Integrating Biological Sciences
• Index