Frontiers in Computational Chemistry

Volume 3

by

Zaheer Ul-Haq, Jeffry D. Madura

DOI: 10.2174/97816810816701170301
eISBN: 978-1-68108-167-0, 2017
ISBN: 978-1-68108-168-7
ISSN: 2352-944X (Print)
ISSN: 2352-9458 (Online)



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Frontiers in Computational Chemistry presents contemporary research on molecula...[view complete introduction]

Table of Contents

Preface

- Pp. i-ii (2)

Zaheer Ul Haq and Jeffry D. Madura

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List of Contributors

- Pp. iii-iv (2)

Zaheer Ul Haq and Jeffry D. Madura

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In Silico Approaches for Drug Discovery and Development

- Pp. 3-74 (72)

Thomas Leonard Joseph, Vigneshwaran Namasivayam, Vasanthanathan Poongavanam and Srinivasaraghavan Kannan

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Computational Chemistry Assisted Design and Screening of Ligand-Solvent Systems for Metal Ion Separation

- Pp. 75-184 (110)

Sk. Musharaf Ali, Anil Boda, Ashish Kumar Singha Deb, Pooja Sahu and Kalsanka Trivikram Shenoy

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Molecular Mechanisms of Cellular Transport, Resistance and Cytotoxic Side Effects of Platinum and Adjuvant Anti-cancer Drugs – A Molecular Orbital Study

- Pp. 185-259 (75)

Clifford W. Fong

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Elucidating Allosteric Communications in Proteins via Computational Methods

- Pp. 260-309 (50)

Burak Alakent and Z. Nevin Gerek Ince

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Information-Theoretic Representation of the Chemical Space of Many Electron Systems

- Pp. 310-353 (44)

R.O. Esquivel, S. López-Rosa, M. Molina-Espíritu, C. Soriano-Correa, J.C. Angulo and J.S. Dehesa

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Subject Index

- Pp. 354-360 (7)

Zaheer Ul Haq and Jeffry D. Madura

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Preface

The branch of chemistry that uses computers to study chemical questions is known as Computational Chemistry which is a very diverse field spanning from the development and application of linear free energy relationships (e.g. QSAR, QSPR), to electronic structure calculations, molecular dynamics simulations, and to solving coupled differential equations (e.g. drug metabolism). The focus of Frontiers in Computational Chemistry is to present material for the application of computational techniques used in biological processes. Topics falling under this umbrella 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 analysis of biological activity. In this third volume, we have collected five different perspectives on the application of computational methods towards drug design.

Chapter 1 “In Silico Approaches for Drug Discovery and Development” reviews the main computational tools used in the drug discovery process. Joseph, et al. also presented the application of physics-based methods that are currently being developed and applied to the drug discovery process.

The removal of toxic metal ions from nuclear and chemical waste streams is an imperative and demanding problem. In Chapter 2 “Computational Chemistry Assisted Design and Screening of Ligand-Solvent Systems for Metal Ion Separation” Ali et al. review electronic structure methods to aid the design and development of new ligands that can be used to extract metal ions from the environment. The goal is to use electronic structure methods to identify a suitable ligand anchored on a solid matrix that can be used in a complex separation process.

One challenge in the biochemical field is understanding the side effects of anti-cancer drugs containing platinum. The authors of Chapter 3 “Molecular Mechanisms of Cellular Transport, Resistance and Cytotoxic Side Effects of Platinum and Adjuvant Anti-cancer Drugs ― A Molecular Orbital Study” present a review of the application of electronic structure methods to understand the side effects, acquired resistance, and combination of platinum drugs with adjuvant drugs in treating cancer.

In Chapter 4 “Elucidating Allosteric Communications in Proteins Via Computational Methods”, the authors present a review of the application of different normal mode analyses based on molecular dynamics methods to understanding allosteric communication in proteins. Alakent and Ince also present the application of graph theory, perturbation methods, and statistical methods to investigate allosteric mechanisms.

The authors of Chapter 5 “Information-theoretic chemical space for many electron systems: from atoms to biological and pharmacological molecules” review the utility of an information-theoretic three-dimensional (IT-3D) space to unveil the unique physical, chemical and biological aspects of a great diversity of many electron systems. These multiple electrons systems range from simple atomic systems to more complex systems such as amino acids. Esquivel et al. claim that “All chemical families recognized by the existing energy-based classifications are embraced by this entropic scheme”.

Zaheer Ul Haq
Panjwani Center for Molecular Medicine & Drug Research
International Center for Chemical & Biological Sciences
University of Karachi
Pakistan

&

Jeffry D. Madura
Department of Chemistry & Biochemistry
Center for Computational Sciences Duquesne University
Pittsburgh
USA

List of Contributors

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


Jeffry D. Madura
Department of Chemistry & Biochemistry
Center for Computational Sciences Duquesne University
Pittsburgh
USA




Contributor(s):
Anil Boda
Chemical Engineering Division
Bhabha Atomic Research Centre
Mumbai
India


Ashish Kumar Singha Deb
Chemical Engineering Division
Bhabha Atomic Research Centre
Mumbai
India


Burak Alakent
Department of Chemical Engineering
Bogazici University
Istanbul
Turkey


Clifford W. Fong
Eigenenergy, Adelaide
South Australia
Australia


C. Soriano-Correa
Qu´ımica Computacional, FES-Zaragoza
Universidad Nacional Aut´onoma de M´exico
09230-Iztapalapa, M´exico, D.F
Mexico


J.C. Angulo
Instituto Carlos I de F´ısica Te´orica y Computacional
Universidad de Granada
18071-Granada
Spain
/
Departamento de F´ısica At´omica, Molecular y Nuclear
Universidad de Granada
18071-Granada
Spain


J.S. Dehesa
Instituto Carlos I de F´ısica Te´orica y Computacional
Universidad de Granada
18071-Granada
Spain
/
Departamento de F´ısica At´omica, Molecular y Nuclear
Universidad de Granada
18071-Granada
Spain


KalsankaTrivikram Shenoy
Chemical Engineering Division
Bhabha Atomic Research Centre
Mumbai
India


M. Molina-Esp´ıritu
Departamento de Qu´ımica
Universidad Aut´onoma Metropolitana
09340-M´exico, D.F.
M´exico


Pooja Sahu
Chemical Engineering Division
Bhabha Atomic Research Centre
Mumbai
India


R.O. Esquivel
Departamento de Qu´ımica
Universidad Aut´onoma Metropolitana
09340-M´exico, D.F.
M´exico
/
Instituto Carlos I de F´ısica Te´orica y Computacional
Universidad de Granada
18071-Granada
Spain


S. L´opez-Rosa
Instituto Carlos I de F´ısica Te´orica y Computacional
Universidad de Granada
18071-Granada
Spain
/
Departamento de F´ısica Aplicada II
Universidad de Sevilla
41012-Sevilla
Spain


Srinivasaraghavan Kannan
Bioinformatics Institute
A STAR, Singapore 138671



Sk. Musharaf Ali
Chemical Engineering Division
Bhabha Atomic Research Centre
Mumbai
India


Thomas Leonard Joseph
Bioinformatics Institute
A STAR, Singapore 138671



Vasanthanathan Poongavanam
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, DK-5230, Odense M
Denmark


Vigneshwaran Namasivayam
Department of Life Science Informatics, B-IT
Rheinische Friedrich-Wilhelms-Universitaet, Dahlmannstr
2, 53113 Bonn
Germany


Z. Nevin Gerek Ince
Institute for Genomics and Evolutionary Medicine
Temple University
Philadelphia
USA




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