Frontiers in Computational Chemistry: Volume 2 - 1st Edition - ISBN: 9781608059799, 9781608059782

Frontiers in Computational Chemistry: Volume 2

1st Edition

Computer Applications for Drug Design and Biomolecular Systems

Authors: Zaheer Ul-Haq Jeffry Madura
eBook ISBN: 9781608059782
Paperback ISBN: 9781608059799
Imprint: Bentham Science Publishers
Published Date: 11th November 2015
Page Count: 444
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Frontiers in Computational Chemistry, originally published by Bentham and now distributed by Elsevier, presents the latest research findings and methods in the diverse field of computational chemistry, focusing on molecular modeling techniques used in drug discovery and the drug development process. This includes 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 Volume 2, the authors continue the compendium with nine additional perspectives in the application of computational methods towards drug design. This volume covers an array of subjects from modern hardware advances that accelerate new antibacterial peptide identification, electronic structure methods that explain how singlet oxygen damages DNA, to QSAR model validation, the application of DFT and DFRT methods on understanding the action of nitrogen mustards, the design of novel prodrugs using molecular mechanics and molecular orbital methods, computational simulations of lipid bilayers, high throughput screening methods, and more.

Key Features

  • Brings together a wide range of research into a single collection to help researchers keep up with new methods
  • Uniquely focuses on computational chemistry approaches that can accelerate drug design
  • Makes a solid connection between experiment and computation, and the novel application of computational methods in the fields of biology, chemistry, biochemistry, physics, and biophysics


Professionals and students in experimental and computational chemistry, biochemistry, biophysics, and computer science studying drug design methods

Table of Contents

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  • Preface
  • List of Contributors
  • Chapter 1: The Use of Dedicated Processors to Accelerate the Identification of Novel Antibacterial Peptides
    • Abstract:
    • Introduction
    • Antibacterial Peptides
    • Algorithms used to Predict Antibacterial Peptides
    • Dedicated Processors used to Predict Antibacterial Peptides
    • Prospective Analysis
    • Acknowledgements
    • Conflict of Interest
  • Chapter 2: Computational Chemistry for Photosensitizer Design and Investigation of DNA Damage
    • Abstract:
    • Introduction
    • Relationship Between the DNA-Damaging Abilities of Photosensitizers and their HOMO Energies
    • Computational Evaluation of Chemopreventive Action on Photosensitized DNA Damage
    • Computational Invesitigation of Fluorescence Probe for Reactive Oxygen Detection
    • Computational Study of the Photochemical Property of Berberine and Palmatine
    • Molecular Design of Porphyrin Photosensitizers for Control of Singlet Oxygen Generation through Interaction with DNA
    • Structure Calculation of Phosphorus(V) Porphyrin Derivatives
    • Concluding Remarks
    • Acknowledgements
    • Conflict of Interest
    • Disclosure
  • Chapter 3: How to Judge Predictive Quality of Classification and Regression Based QSAR Models?
    • Abstract:
    • Introduction
    • Importance of Validation of a QSAR Model
    • Validation Metrics for Regression based QSAR Models
    • Measurements of Quality of QSAR Models
    • Internal Validation
    • External Validation
    • Additional Functions for Model Predictive Ability RMSEP
    • Assessment of Chance Correlation: Y-Randomization
    • Validation Metrics for Classification based QSAR Models
    • Applicability Domain (AD)
    • Conclusion
    • Acknowledgements
    • Conflict of Interest
    • Disclosure
    • Abbreviations
  • Chapter 4: Density Functional Studies of Bis-alkylating Nitrogen Mustards
    • Abstract:
    • Introduction to Nitrogen Mustards
    • Introduction to DFT and DFRT
    • Computational Studies on Nitrogen Mustards
    • Some Applications of DFT and DFRT on Nitrogen Mustards
    • Concluding Remark
    • Acknowledgements
    • Conflict of Interest
  • Chapter 5: From Conventional Prodrugs to Prodrugs Designed by Molecular Orbital Methods
    • Abstract:
    • Introduction
    • Prodrug Overview
    • Intramolecular Processes used for the Design of Potential Prodrugs
    • Enzyme Models used in the Prodrug Design
    • Computational Methods Background
    • Calculation Methods used for Exploring the Enzyme Models Mechanisms and for Prodrugs Design
    • Bruice’s Enzyme Model Based on Ring-Closing of Di-Carboxylic Semi-Esters [95]
    • Computationalyy Designed Prodrugs Based on Bruice’s Enzyme Model - The Antimalarial Agent Atovaquone (ATQ)
    • Bitterless Paracetamol Prodrugs Based on Bruice’s Enzyme Model
    • In Vitro Intra-Conversion of Paracetamol ProD 1-ProD 2 to their Active Drug, Paracetamol
    • Kirby’s Enzyme Model Based on the Acid-Catalyzed Hydrolysis of N-Alkylmaleamic Acids [58, 93, 140-145].
    • Computationally Designed Prodrugs Based on Intramolecular Acid-Catalyzed Hydrolysis of Kirby’s N-Alkylmaleamic Acids - Tranexamic Acid Prodrugs
    • Bitterless Atenolol Prodrugs
    • Atenolol ProD 1 Kinetic Study
    • Bitterless Amoxicillin and Cephalexin Prodrugs
    • Amoxicillin
    • Cephalexin
    • In Vitro Intraconversion of Amoxicillin and Cephalexin Prodrugs to their Parent Drugs
    • Concluding Remarks
    • Acknowledgements
    • Conflict of Interest
  • Chapter 6: Structural and Vibrational Investigation on a Benzoxazin Derivative with Potential Antibacterial Activity
    • Abstract:
    • Introduction
    • Computational Details
    • Results and Discussion
    • Vibrational Analysis
    • Bands Assignments
    • Force Field
    • HOMO-LUMO Study
    • Conclusion
    • Acknowledgements
    • Conflict of Interest
  • Chapter 7: First Principles Computational Biochemistry with deMon2k
    • Abstract:
    • 1 Introduction
    • 2 The Electron Repulsion Integrals Bottleneck
    • 3 Copper Coordination Modes in the Human Prion Protein: The Second and Third Sites
    • Conclusion
    • 4 DFT-BOMD Study of High Energy Conformations of Glycerol and Their Contribution to NMR Chemical Shifts
    • Conclusion
    • Acknowledgements
    • Conflict of Interest
  • Chapter 8: Recent Advances in Computational Simulations of Lipid Bilayer Based Molecular Systems
    • Abstract:
    • Introduction
    • Force Fields for Lipid Bilayers Simulations
    • Running Molecular Dynamics Simulation for Lipid Bilayers Systems
    • Full Atoms Molecular Dynamics of Lipid Bilayers: State of ART and CASE Studies
    • Simulation of Proteins and Peptides in Membrane Bilayers
    • Coarse-Grained Models: Usefulness and Application
    • Aknowledgements
    • Conflict of Interest
  • Chapter 9: Data Quality Assurance and Statistical Analysis of High Throughput Screenings for Drug Discovery
    • Abstract:
    • 1 Introduction
    • 2 High Throughput Screening Process
    • 3 Hit Identification Strategies
    • 4 HTS Hits Analysis
    • Summary
    • Acknowledgements
    • Conflict of Interest
  • Subject Index


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About the Author

Zaheer Ul-Haq

Dr. Zaheer Ul-Haq is heading a computational chemistry group at the Dr. Panjwani Center for Molecular Medicine and Drug research (PCMD), University of Karachi. He obtained his PhD under the supervision of Prof. Atta-ur-Rahman and completed his post-doctoral studies in computational chemistry with Prof. Bernd M. Rode in Innsbruck, Austria. He is a recipient of the Fulbright and Humboldt Fellowship from USA and Germany, respectively. Dr. Zaheer also received a Gold medal in Chemistry from the Pakistan Science Foundation. He has published 80+ research articles in international journals. His research interests include designing new bio-active compounds using in silico tools, generation and screening of large commercially available compounds, and Molecular Dynamics (MD) simulation of bio-molecules. He is currently serving as an editorial board member of Journal of Molecular Graphics and Modelling.

Affiliations and Expertise

University of Karachi, Pakistan

Jeffry Madura

Jeffry is the Lambert F. Minucci Endowed Chair in Engineering and Computational Sciences and Professor in the Department of Chemistry and Biochemistry at Duquesne University. He earned a B.A. from Thiel College, a PhD in Physical Chemistry from Purdue University, and was a postdoctoral fellow at the University of Houston. His research interests include the development and application of biomolecular simulation software, the study of neurotransmitter transporters, the electronic structure of solid-state materials, and the thermoresponsive behavior of smart polymers. He has published 100+ peer-reviewed papers in physical chemistry and received over $6M in external research funding. He was a recipient of a Dreyfus Teacher-Scholar Award, was the chair of the ACS COMP Division, and is an ACS Fellow. Dr. Madura received the 2014 ACS Pittsburgh Local Section Award. He is a co-author to the textbook titled General Chemistry: Principles and Modern Applications as well as a co-author to a physical chemistry solutions manual. He received the Bayer School of Natural and Environmental Sciences and the Duquesne University Presidential Award for Excellence in Scholarship in 2007, and the Bayer School of Natural and Environmental Sciences Award for Excellence in Service in 2004. He is currently a co-editor of the Journal of Molecular Graphics and Modelling.

Affiliations and Expertise

Duquesne University, Pittsburgh, PA, USA

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