Editors: Zaheer Ul-Haq, Jeffry D. Madura

Frontiers in Computational Chemistry

Volume 2

eBook: US $165 Special Offer (PDF + Printed Copy): US $247
Printed Copy: US $165
Library License: US $660
ISSN: 2352-944X (Print)
ISSN: 2352-9458 (Online)
ISBN: 978-1-60805-979-9 (Print)
ISBN: 978-1-60805-978-2 (Online)
Year of Publication: 2015
DOI: 10.2174/97816080597821150201

Introduction

Frontiers in Computational Chemistry presents contemporary research on molecular modeling techniques used in drug discovery and the drug development process: 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.

The Second volume of this series features nine different articles covering topics such as antibacterial drug discovery, high throughput screening, computational biochemistry with deMon2k, lipid bilayer analysis and much more.

Indexed in: Book Citation Index, Science Edition, BIOSIS Previews, EBSCO.

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

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