Frontiers in Computational Chemistry

Volume 2

by

Zaheer Ul-Haq, Jeffry D. Madura

DOI: 10.2174/97816080597821150201
eISBN: 978-1-60805-978-2, 2015
ISBN: 978-1-60805-979-9
ISSN: 2352-944X (Print)
ISSN: 2352-9458 (Online)



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Frontiers in Computational Chemistry presents contemporary research on molecular modeling techniques used in drug discovery and the drug devel...[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-v (3)

Zaheer Ul-Haq and Jeffry D. Madura

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The Use of Dedicated Processors to Accelerate the Identification of Novel Antibacterial Peptides

- Pp. 3-26 (24)

Gabriel del Rio, Miguel Arias-Estrada and Carlos Polanco González

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Computational Chemistry for Photosensitizer Design and Investigation of DNA Damage

- Pp. 27-70 (44)

Kazutaka Hirakawa

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How to Judge Predictive Quality of Classification and Regression Based QSAR Models?

- Pp. 71-120 (50)

Kunal Roy and Supratik Kar

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Density Functional Studies of Bis-alkylating Nitrogen Mustards

- Pp. 121-186 (66)

Pradip Kr. Bhattacharyya, Sourab Sinha, Nabajit Sarmah and Bhabesh Chandra Deka

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From Conventional Prodrugs to Prodrugs Designed by Molecular Orbital Methods

- Pp. 187-249 (63)

Rafik Karaman

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Structural and Vibrational Investigation on a Benzoxazin Derivative with Potential Antibacterial Activity

- Pp. 250-280 (31)

María V. Castillo, Elida Romano, Ana B. Raschi and Silvia A. Brandán

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First Principles Computational Biochemistry with deMon2k

- Pp. 281-325 (45)

A. Alvarez-Ibarra, P. Calaminici, A. Goursot, C. Z. Gómez-Castro, R. Grande-Aztatzi, T. Mineva, D. R. Salahub, J. M. Vásquez-Pérez, A. Vela, B. Zuniga-Gutierrez and A. M. Köster

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Recent Advances in Computational Simulations of Lipid Bilayer Based Molecular Systems

- Pp. 326-388 (63)

R. Galeazzi, E. Laudadio and L. Massaccesi

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Data Quality Assurance and Statistical Analysis of High Throughput Screenings for Drug Discovery

- Pp. 389-425 (37)

Yang Zhong, Zuojun Guo and Jianwei Che

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Subject Index

- Pp. 426-431 (6)

Zaheer Ul-Haq and Jeffry D. Madura

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Preface

Computational chemistry 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 on molecular modeling techniques used in drug discovery and the drug development process. 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 analyses of biological activity. In this volume, we have collected nine different perspectives in the application of computational methods towards drug design.

Chapter 1 “The Use of Dedicated Processors to Accelerate the Identification of Novel Antibacterial Peptides” reviews the use of modern hardware advances to accelerate the identification of new antibacterial peptides. Identification of new antibiotics is of paramount importance as bacterial develop resistances to the current compounds used. The authors highlight the advantages as well as the difficulties in developing algorithms for Field Programmable Gate Arrays and Graphic Processing Units.

DNA damage by singlet oxygen is a well-known method to mitigate the presence of singlet oxygen that remains elusive. In Chapter 2 “Computational Chemistry for Photosensitizer Design and Investigation of DNA Damage” the authors review electronic structure methods to aid understanding how singlet oxygen damages DNA as well as using what they have learned to aid in the design of novel photosensitizers. They review the development of several porphyrin photosensitziers based on molecular orbital calculations.

One challenge in the QSAR field is how to judge the predictive quality of the models. The authors of Chapter 3 “How to Judge Predictive Quality of Classification and Regression Based QSAR Models?” present a review of validating QSAR models using both traditional and new validation metrics.

In Chapter 4 “Density Functional Studies of Bis-alkylating Nitrogen Mustards”, the authors present a review of the application of DFT and DFRT methods on understanding the action of nitrogen mustards. Nitrogen mustards are extensively used as a chemotherapeutic agent. Identification of new nitrogen mustards is important in order to reduce their cytotoxicity and increase their effectiveness.

The authors of Chapter 5 “From Conventional Prodrugs to Prodrugs Designed By Molecular Orbital Methods” review a novel approach in the design of novel prodrugs using molecular mechanics and molecular orbital methods. In this approach, the authors review methods in which the prodrug is converted into the active drug without the enzyme.

Chapter 6 “Structural and Vibrational Investigation on a Benzoxazin Derivative with Potential Antibacterial Activity” highlights the use of DFT methods along with experimental data to understand the properties and behavior of benzoxazin derivative. The authors present the use of scaled quantum mechanical force field methodology and Atomis in Molecules theory to explain the vibrational and bonding characteristics in benzoxazin.

In Chapter 7 “First Principles Computational Biochemistry with deMon2k” the authors present a first principles approach to investigating biochemical principles using density functional methods with the program deMon2k. Having an all-electron method to explore biochemical and pharmacological processes; is an important tool in the computational chemist’s toolbox.

In Chapter 8 “Recent Advances in Computational Simulations of Lipid Bilayer based molecular systems” the authors review computational simulations of lipid bilayers. Cell membranes are a complex mixture of lipids and play a vital role in cellular function such as the control of processes that cross the cell membranes. A review of several computational methods and complex lipid mixtures is presented.

In this last chapter, “Data Quality Assurance and Statistical Analysis of High Throughput Screenings for Drug Discovery”, the authors review high throughput screening (HTS) methods bringing to light the challenges to identifying novel molecules from vast and diverse databases. The authors also note the use of data from sophisticated biological assays in HTS.

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

&

J. 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):
A. Alvarez-Ibarra
Departamento de Química
Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
Av. Instituto Politécnico Nacional 2508
A. P. 14-740 México, D.F. 07000
México


A. Goursot
Institut Charles Gerhardt Montpellier
UMR5253 CNRS
ENSCM/UM2/UM1, 8 rue de l'Ecole Normale
34296 Montpellier Cedex 5
France


A. M. Köster
Departamento de Química
Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
Av. Instituto Politécnico Nacional 2508
A. P. 14-740 México, D.F. 07000
México


A. Vela
Departamento de Química
Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
Av. Instituto Politécnico Nacional 2508
A. P. 14-740 México, D.F. 07000
México


Raschi Ana B.
General Chemistry Inorganic Chemistry Institute
Faculty of Biochemistry, Chemistry and Pharmacy, National of Tucuman University
Ayacucho 471, (4000).
San Miguel de Tucumán
Tucumán
Argentina


B. Zuniga-Gutierrez
Departamento de Química
Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
Av. Instituto Politécnico Nacional 2508
A. P. 14-740 México, D.F. 07000
México


Bhabesh Chandra Deka
Department of Chemistry
Arya Vidyapeeth College
Assam-781016
India


C.Z. Gómez-Castro
Departamento de Química
Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
Av. Instituto Politécnico Nacional 2508
A. P. 14-740 México, D.F. 07000
México


Carlos Polanco González
Departamento de Matemáticas, Facultad de Ciencias
Universidad Nacional Autónoma de México. Cd. Universitaria
04510 México
D.F. México
/
Subdirección de Epidemiología Hospitalaria y Control de Calidad de la Atención Médica
Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán
Vasco de Quiroga 15
Col. Sección XVI
D.F. México


D. R. Salahub
Department of Chemistry
Centre for Molecular Simulation and Institute for Quantum Science and Technology
University of Calgary 2500 University Drive NW
Calgary
Alberta
Canada T2N1N4


E. Laudadio
Dipartimento di Scienze della Vita e dell’Ambiente (DISVA)
Università Politecnica delle Marche
via Brecce bianche
60128 Ancona
Italy


Elida Romano
General Chemistry, Inorganic Chemistry Institute
Faculty of Biochemistry, Chemistry and Pharmacy, National of Tucuman University
Ayacucho 471, (4000).
San Miguel de Tucumán. Tucumán
Argentina


Gabriel del Rio
Computer Science Department
Instituto Nacional de Astrofísica
Óptica y Electrónica
Puebla
Puebla
México


J.M. Vásquez-Pérez
Departamento de Química
Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
Av. Instituto Politécnico Nacional 2508
A. P. 14-740 México, D.F. 07000
México


Jianwei Che
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego
California 92121
USA


Kazutaka Hirakawa
Department of Applied Chemistry and Biochemical Engineering
Graduate School of Engineering Shizuoka University
Japan


Kunal Roy
Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology
Jadavpur University
Kolkata 700032
India
/
Manchester Institute of Biotechnology
University of Manchester
Manchester M1 7DN
Great Britain


L. Massaccesi
Dipartimento di Scienze della Vita e dell’Ambiente (DISVA)
Università Politecnica delle Marche
via Brecce bianche
60128 Ancona
Italy


María V. Castillo
General Chemistry, Inorganic Chemistry Institute
Faculty of Biochemistry, Chemistry and Pharmacy, National of Tucuman University
Ayacucho 471, (4000).
San Miguel de Tucumán. Tucumán
Argentina


Miguel Arias-Estrada
Computer Science Department
Instituto Nacional de Astrofísica
Óptica y Electrónica
Puebla
Puebla
México


Nabajit Sarmah
Department of Chemistry
Arya Vidyapeeth College
Assam-781016
India


P. Calaminici
Departamento de Química
Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
Av. Instituto Politécnico Nacional 2508
A. P. 14-740 México, D.F. 07000
México


Pradip Kr. Bhattacharyya
Department of Chemistry
Arya Vidyapeeth College
Assam-781016
India


R. Galeazzi
Dipartimento di Scienze della Vita e dell’Ambiente (DISVA)
Università Politecnica delle Marche
via Brecce bianche
60128 Ancona
Italy


R. Grande-Aztatzi
Departamento de Física Aplicada
Centro de Investigación y de Estudios Avanzados
Unidad Mérida, Km. 6 Antigua Carretera a Progreso, A.P. 73 Cordemex
Mérida 97310
Yucatán
México


Rafik Karaman
Bioorganic Chemistry Department
Faculty of Pharmacy Al-Quds University
P.O. Box 20002
Jerusalem
Palestine


Silvia A. Brandán
General Chemistry, Inorganic Chemistry Institute
Faculty of Biochemistry, Chemistry and Pharmacy, National of Tucuman University
Ayacucho 471, (4000).
San Miguel de Tucumán
Tucumán
Argentina


Sourab Sinha
Department of Chemistry
Arya Vidyapeeth College
Assam- 781016
India


Supratik Kar
Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology
Jadavpur University
Kolkata 700032
India


T. Mineva
Institut Charles Gerhardt Montpellier
UMR5253 CNRS, ENSCM/UM2/UM1
8 rue de l'Ecole Normale
34296 Montpellier Cedex 5
France


Yang Zhong
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego
California 92121
USA


Zuojun Guo
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego
California 92121
USA




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