Chemoinformatics and Bioinformatics in the Pharmaceutical Sciences

1st Edition - May 21, 2021
Imprint: Academic Press
Editors: Navneet Sharma, Himanshu Ojha, Pawan Raghav, Ramesh K. Goyal
Language: English
Paperback ISBN:
9 7 8 - 0 - 1 2 - 8 2 1 7 4 8 - 1
eBook ISBN:
9 7 8 - 0 - 1 2 - 8 2 1 7 4 7 - 4

Chemoinformatics and Bioinformatics in the Pharmaceutical Sciences brings together two very important fields in pharmaceutical sciences that have been mostly seen as diverging… Read more

Purchase options

BLOOM INTO SPRING SAVINGS

Save up to 25% on books and eBooks!

Shop now

Institutional subscription on ScienceDirect

Request a sales quote

Chemoinformatics and Bioinformatics in the Pharmaceutical Sciences brings together two very important fields in pharmaceutical sciences that have been mostly seen as diverging from each other: chemoinformatics and bioinformatics. As developing drugs is an expensive and lengthy process, technology can improve the cost, efficiency and speed at which new drugs can be discovered and tested. This book presents some of the growing advancements of technology in the field of drug development and how the computational approaches explained here can reduce the financial and experimental burden of the drug discovery process.

This book will be useful to pharmaceutical science researchers and students who need basic knowledge of computational techniques relevant to their projects. Bioscientists, bioinformaticians, computational scientists, and other stakeholders from industry and academia will also find this book helpful.

Cover image
Title page
Table of Contents
Copyright
Contributors
Chapter 1. Impact of chemoinformatics approaches and tools on current chemical research
1.1. Background
1.2. Ligand and target resources in chemoinformatics
1.3. Pharmacophore modeling
1.4. QSAR models
1.5. Docking methods
1.6. Conclusion
Chapter 2. Structure- and ligand-based drug design: concepts, approaches, and challenges
2.1. Introduction
2.2. Ligand-based drug design
2.3. Structure-based drug design
Chapter 3. Advances in structure-based drug design
3.1. Introduction
3.2. Molecular docking
3.3. High-throughput screening
3.4. De novo ligand design
3.5. Biomolecular simulations
3.6. ADMET profiling
3.7. Conclusion
Chapter 4. Computational tools in cheminformatics
4.1. Introduction
4.2. Molecules and their reactions: representation
4.3. Preparation before building libraries for databases in cheminformatics
4.4. High-throughput screening and virtual screening
4.5. Combinatorial libraries
4.6. Additional computational tools in cheminformatics: molecular modeling
4.7. Conclusions
Chapter 5. Structure-based drug designing strategy to inhibit protein-protein-interactions using in silico tools
5.1. Introduction
5.2. Methods to identify inhibitors of PPIs
5.3. Nature of the PPI interface
5.4. Computational drug designing
5.5. Databases that play a significant role in the process of predicting PPI inhibitors: databases of PPIs, PPI modulators, and decoys
5.6. Transcription factors as one of the PPI drug targets: importance, case study, and specific databases
5.7. Pharmacokinetic properties of small-molecule inhibitors of PPI
5.8. Strategies and tools to identify small-molecule inhibitors of PPIs
5.9. Conclusion
Chapter 6. Advanced approaches and in silico tools of chemoinformatics in drug designing
6.1. Introduction
6.2. Current chemoinformatics approaches and tools
6.3. Machine learning approaches and tools for chemoinformatics
6.4. Conclusion
Chapter 7. Chem-bioinformatic approach for drug discovery: in silico screening of potential antimalarial compounds
7.1. Importance of technology in medical science
7.2. Origin of cheminformatics
7.3. Role of bioinformatics in drug discovery
7.4. Applications of cheminformatics and bioinformatics in the development of antimalarial drugs
7.5. Conclusions
Electronic Supplementary information
Chapter 8. Mapping genomes by using bioinformatics data and tools
8.1. Background
8.2. Genome
8.3. Sequence analysis
8.4. Sequence database
8.5. Structure prediction
8.6. Bioinformatics and drug discovery
8.7. Pharmacogenomics
8.8. Future aspects
Chapter 9. Python, a reliable programming language for chemoinformatics and bioinformatics
9.1. Introduction
9.2. Desired skill sets
9.3. Python
9.4. Python in bioinformatics and chemoinformatics
9.5. Use Python interactively
9.6. Prerequisites to working with Python
9.7. Quick overview of Python components
9.8. Bioinformatics and cheminformatics examples
9.9. Conclusion
Chapter 10. Unveiling the molecular basis of DNA–protein structure and function: an in silico view
10.1. Background
10.2. Structural aspects of DNA
10.3. Structural aspects of proteins
10.4. In silico tools for unveiling the mystery of DNA–protein interactions
10.5. Future perspectives
10.6. Abbreviations
Chapter 11. Computational cancer genomics
11.1. Introduction
11.2. Cancer genomics technologies
11.3. Computational cancer genomics analysis
11.4. Pathway analysis
11.5. Network analysis
11.6. Conclusion
Chapter 12. Computational and functional annotation at genomic scale: gene expression and analysis
12.1. Introduction: background (history)
12.2. Genome sequencing
12.3. Genome assembly
12.4. Genome annotation
12.5. Techniques for gene expression analysis
12.6. Gene expression data analysis
12.7. Software for gene expression analysis
12.8. Computational methods for clinical genomics
12.9. Conclusion
Abbreviations
Chapter 13. Computational methods (in silico) and stem cells as alternatives to animals in research
13.1. Introduction
13.2. Need for alternatives
13.3. What are the alternative methods to animal research
13.4. Potential of in silico and stem cell methods to sustain 3Rs
13.5. Challenges with alternatives
13.6. Conclusion
Chapter 14. An introduction to BLAST: applications for computer-aided drug design and development
14.1. Basic local alignment search tool
14.2. Building blocks
14.3. Basic local alignment search tool
14.4. How BLAST works
14.5. Codons, reading frames, and open reading frames
14.6. Bioinformatics and drug design
14.7. Applications of BLAST
14.8. Understanding coronavirus: the menace of 2020
14.9. Conclusions
Chapter 15. Pseudoternary phase diagrams used in emulsion preparation
15.1. Introduction
15.2. Classification of emulsions
15.3. Emulsifying agents (surfactants)
15.4. Pseudoternary phase diagrams
15.5. Software used for the preparation of pseudoternary phase diagrams
15.6. Conclusion
Index

Navneet Sharma

Dr. Navneet Sharma is an Assistant Professor at the Amity Institute of Pharmacy, Amity University, India. He has an M.Pharm, Ph.D and PGDRA, and his expertise lies in the realm of biomaterials and applied R & D, especially needs-based product development. He has taken pivotal roles as an investigator in three projects supported by DST-India. He has won several awards, including eight national and international awards. The most prestigious among them are SCO and Ministry of External Affairs, Government of India Covid-19 best innovation award 2020, and Department of Science and Technology, Young Scientist Award for the year 2018 and 2022. He has more than 40 publications including four books, five book chapters, 10 patents and 4 technologies successfully transferred to the industry.

Affiliations and expertise

Scientist, Institute of Information Technology (IIT), Delhi, India

Himanshu Ojha

Dr. Himanshu Ojha has a BSc, MSc, and Ph.D. in Chemistry Honors from University of Delhi. His Ph.D. work involved the design, synthesis and biological evaluation of s-triazine derivatives for antimalarial activity against Plasmodium falciparum. He is now a senior scientist in Division of CBRN Defence of Institute of Nuclear Medicine and Allied Sciences.He had extensively worked on DFT studies of bimolecular interactions and reaction pathways. He has designed quite large number of new drug like compounds for various applications using virtual computational algorithms, QSAR and molecular docking. He has worked extensively in the field of 2D and 3D Quantitative structure activity relation (QSAR) studies to identify lead compounds for various particular applications. He has 29 research articles in various peer reviewed international journals, one book chapter and edited one book and 03 intellectual property rights.

Affiliations and expertise

Division of CBRN Defense, Institute of Nuclear Medicine and Allied Sciences, New Delhi, India

Pawan Raghav

Dr. Pawan Kumar Raghav completed his MSc in Bioinformatics (2008) from Punjabi University Patiala, India; PG Diploma in Chemoinformatics (2009) from Jamia Hamdard; MPhil in Bioinformatics (2010) from The Global Open University, Nagaland; and PhD at the Institute of Nuclear Medicine and Allied Sciences (INMAS), DRDO, Delhi in Life Sciences from Bharathiar University, Coimbatore. During his Ph.D., he had designed molecules and evaluated their applications through response modification that regulates stem cells proliferation, differentiation, and apoptosis. His recent research activities are in the field of machine learning, deep learning, and molecular biology, as well as in the development of new scoring function parameterizations for use in docking, simulations, and complex network analysis. Currently, he is working as Scientist ‘D’ in Stem Cell Facility, AIIMS on stem cell informatics to establish a bridge between the experimental science and computational biology.

Affiliations and expertise

BioExIn, Delhi, India

Ramesh K. Goyal

Prof. Ramesh K. Goyal, the Vice Chancellor, Delhi Pharmaceutical Sciences and Research University (DPSRU) has been the Vice-Chancellor of Maharaja Sayajirao University of Baroda, Executive Director (Research & strategies) at V ClinBio Labs., Chennai, Director (Pharmacology) at NMIMS University, Mumbai; Director ISF College of Pharmacy, Moga, Punjab and Professor at L. M. College of Pharmacy, Ahmedabad. He has over 41 years of experience in Teaching and Research. Dr Goyal has three patents, 18 books, over 325 full papers articles and book chapters, over 500 abstracts published in National and International journals. He is the recipient of 72 awards, including Best Pharmacy Teacher and Best Pharmaceutical Research Scientist from APTI and Life Time Achievement & Distinguished Service Awards from International Academy of Cardiovascular Sciences, Canada (IACS). He is the Fellow of eight professional bodies and is currently Council member of the IACS, Canada and the Vice President of IACS, (India Chapter).

Affiliations and expertise

Professor, Vice Chancellor, Delhi Pharmaceutical Sciences and Research University (DPSRU), India

Life Sciences

Physical Sciences & Engineering

Social Sciences & Humanities

Health

Chemoinformatics and Bioinformatics in the Pharmaceutical Sciences

Purchase options

BLOOM INTO SPRING SAVINGS

Institutional subscription on ScienceDirect

Navneet Sharma

Himanshu Ojha

Pawan Raghav

Ramesh K. Goyal

Related books