Frontiers in Computational Chemistry

Volume 4

by

Zaheer Ul-Haq , Angela K. Wilson

DOI: 10.2174/97816810844111180401
eISBN: 978-1-68108-441-1, 2018
ISBN: 978-1-68108-442-8
ISSN: 2352-944X (Print)
ISSN: 2352-9458 (Online)



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Table of Contents

Preface

- Pp. i-ii (2)
Zaheer Ul-Haq and Angela K. Wilson
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List of Contributors

- Pp. iii-iv (2)
Zaheer Ul-Haq and Angela K. Wilson
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Natural Lead Compounds and Strategies for Optimization

- Pp. 1-47 (47)
Dev Bukhsh Singh
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Computer-aided Drug Discovery Methodologies in the Modeling of Dual Target Ligands as Potential Parkinson’s Disease Therapeutics

- Pp. 48-90 (43)
Yunierkis Perez-Castillo, Stellamaris Sotomayor-Burneo, Aliuska Morales Helguera, M. Natália D. S. Cordeiro, Eduardo Tejera, Cesar Pazy- Mino, Aminael Sanchez-Rodriguez, María F. Moreno, Marta Teijeira- Bautista, Evys Ancede-Gallardo, Fernanda Borges and Maykel Cruz- Monteagudo
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Molecular Studies of the Inhibition of Aminoacyl tRNA Synthetases in Microbial Pathogens

- Pp. 91-143 (53)
Amrita Saha, Saheb Dutta, Soumya Kundu and Nilashis Nandi
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Advances in the Computational Modeling of Halogen Bonds in Biochemical Systems

- Pp. 144-183 (40)
Paulo J. Costa and Rafael Nunes
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Molecular Classification of Caffeine, Its Metabolites and Nicotine Metabolite

- Pp. 184-224 (41)
Francisco Torrens and Gloria Castellano
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Subject Index

- Pp. 225-232 (8)
Zaheer Ul-Haq and Angela K. Wilson
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Preface

Computational chemistry has grown to a large field that entails the use of computers to study a very broad range of chemical problems, and includes both the development (often referred to as “theoretical chemistry”) and applications. This broad range of computational approaches includes electronic structure calculations, molecules dynamics simulations, and free energy relationships (e.g., QSAR, QSPR). The focus of Frontiers in Computational Chemistry, is on the application of computational chemistry approaches to biological processes. While the overview of chapters included in this volume described below provides exciting specific studies, general topics covered in this series include computer aided molecular design, drug discovery and development, lead generation, lead optimization, database management, computer and molecular graphics, and the development of new computational methods or efficient algorithms for the simulation of chemical phenomena, including the analyses of biological activity.

In this fourth volume, five chapters that present a diverse spectrum of approaches towards biological processes are presented including:

Chapter 1 “Natural Lead Compounds and Strategies for Their Optimization as New Drugs” provides strategies to improve possible lead compounds for use in medicine. Dev Bukhsh Singh describes how a combination of approaches including high-throughput screening, structure activity relationships, absorption, distribution, metabolisms, excretion, and toxicity (ADMET) parameters can be used to optimize lead compounds.

Chapter 2 “Computer-aided Drug Discovery Methodologies in the Modeling of Dual Target Ligands as Potential Parkinson’s Disease Therapeutics” by Yunierkis Perez-Castillo and co-authors, presents advances in the application of drug discovery methodologies in modeling dual target ligands for the discovery of potential Parkinson’s Disease therapeutics. A virtual screening method was developed to aid in the prioritization of potential dual binder candidates.

Chapter 3 “Molecular Studies of the Inhibition of Aminoacyl tRNA Synthetases in Microbial Pathogens”. In this chapter, Nilashis Nandi describes progress made towards molecular-level insight into the inhibition of aminoacyl tRNA synthetases (aaRSs), which are promising targets for the development of new inhibitors. Insight is gained using a number of methods including structural analysis based on crystallographic and NMR measurements, as well as mutation studies, kinetic methods, and molecular dynamics simulations.

Chapter 4 “Advances in the Computational Modelling of Halogen Bonds in Biomolecular Systems: Implications for Drug Design”. P.J. Costa and Rafael Nunes provide an overview of computational methods to model halogen bond interactions in biomolecular systems such as protein-ligand complexes is provided. The practicality of the approaches in computer-aided drug design and discovery is discussed.

Chapter 5 “Molecular Classification of Caffeine, Its Metabolites, and Nicotine Metabolite” by Francisco Torrns and Gloria Catellano show the use of structure-property relationships to model retention times for caffeine and caffeine and nicotine metabolites.

We hope that the readers will find these reviews valuable and thought provoking so that they may trigger further research in the field. We are grateful for the timely efforts made by the editorial personnel, especially Ms. Mariam Mehdi (Assistant Manager Publications), Mr. Shehzad Naqvi (Editorial Manager Publications), and Mr. Mahmood Alam (Director Publications) at Bentham Science Publishers.

This volume is dedicated to Jeffry D. Madura who was a professor at Duquesne University (USA) and an editor of the first three volumes of this series. We thank Jeff not only for his role as an editor of the prior volumes in this series, but, also acknowledge his scientific contributions. He passed away too early and the chemistry community will miss him.


Zaheer Ul-Haq
Dr. Panjwani Center for Molecular Medicine and Drug Research
International Center for Chemical and Biological Sciences
University of Karachi
Karachi
Pakistan

&

Angela K. Wilson
Department of Chemistry
Michigan State University
East Lansing, MI
USA

List of Contributors

Editor(s):
Zaheer Ul-Haq
Dr. Panjwani Center for Molecular Medicine & Drug Research
International Center for Chemical & Biological Sciences
University of Karachi
Karachi
UK


Angela K. Wilson
Department of Chemistry
Michigan State University
East Lansing
MI
USA




Contributor(s):
Aliuska Morales Helguera
Molecular Simulation and Drug Design Group, Centro de Bioactivos Químicos (CBQ)
Universidad Central “Marta Abreu” de Las Villas
Santa Clara
Cuba


Aminael Sánchez-Rodríguez
Departamento de Ciencias Naturales
Universidad Técnica Particular de Loja
Calle París S/N, EC1101608 Loja
Ecuador


Amrita Saha
Department of Chemistry
University of Kalyani
Kalyani, Nadia, West Bengal
India


Cesar Paz-y-Miño
Instituto de Investigaciones Biomédicas (IIB)
Universidad de Las Américas
Quito
Ecuador


Dev Bukhsh Singh
Department of Biotechnology, Institute of Biosciences and Biotechnology
Chhatrapati Shahu Ji Maharaj University
Kanpur
India


Eduardo Tejera
Instituto de Investigaciones Biomédicas (IIB)
Universidad de Las Américas
Quito
Ecuador


Evys Ancede-Gallardo
Molecular Simulation and Drug Design Group, Centro de Bioactivos Químicos (CBQ)
Universidad Central “Marta Abreu” de Las Villas
Santa Clara
Cuba


Fernanda Borges
CIQUP/Departamento de Química e Bioquímica, Faculdade de Ciências
Universidade do Porto
Porto
Portugal


Francisco Torrens
Institut Universitari de Ciència Molecular
Universitat de València, Edifici d’Instituts de Paterna
València
Spain


Gloria Castellano
Departamento de Ciencias Experimentales y Matemáticas, Facultad de Veterinaria y Ciencias Experimentales
Universidad Católica de Valencia San Vicente Mártir
València
Spain


Marta Teijeira-Bautista
Departamento de Química Orgánica, Facultade de Química
Universidade de Vigo
Vigo
Spain
/
Instituto de Investigación Biomédica (IVIB)
Universidade de Vigo
Vigo
Spain


María F. Moreno
Departamento de Ciencias Naturales
Universidad Técnica Particular de Loja
Calle París S/N, EC1101608 Loja
Ecuador


M. Natália D. S. Cordeiro
REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences
University of Porto
Porto
Portugal


Maykel Cruz-Monteagudo
Instituto de Investigaciones Biomédicas (IIB)
Universidad de Las Américas
Quito
Ecuador
/
CIQUP/Departamento de Química e Bioquímica, Faculdade de Ciências
Universidade do Porto
Porto
Portugal


Nilashis Nandi
Department of Chemistry
University of Kalyani
Kalyani, Nadia, West Bengal
India


Paulo J. Costa
Centro de Química e Bioquímica, DQB, Faculdade de Ciências
Universidade de Lisboa
Lisboa
Portugal


Rafael Nunes
Centro de Química e Bioquímica, DQB, Faculdade de Ciências
Universidade de Lisboa
Lisboa
Portugal


Saheb Dutta
Department of Chemistry
University of Kalyani
Kalyani, Nadia, West Bengal
India


Soumya Kundu
Department of Chemistry
University of Kalyani
Kalyani, Nadia, West Bengal
India


Stellamaris Sotomayor-Burneo
Sección Físico Química y Matemáticas, Departamento de Química
Universidad Técnica Particular de Loja
San Cayetano Alto S/N, EC1101608 Loja
Ecuador


Yunierkis Perez-Castillo
Sección Físico Química y Matemáticas, Departamento de Química
Universidad Técnica Particular de Loja
San Cayetano Alto S/N, EC1101608 Loja
Ecuador
/
Molecular Simulation and Drug Design Group, Centro de Bioactivos Químicos (CBQ)
Universidad Central “Marta Abreu” de Las Villas
Santa Clara
Cuba




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