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Frontiers in Computational Chemistry: Volume 2
Computer Applications for Drug Design and Biomolecular Systems
1st Edition - November 24, 2015
Authors: Zaheer Ul-Haq, Jeffry D. Madura
Language: English
Paperback ISBN:9781608059799
9 7 8 - 1 - 6 0 8 0 5 - 9 7 9 - 9
eBook ISBN:9781608059782
9 7 8 - 1 - 6 0 8 0 5 - 9 7 8 - 2
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…Read more
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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.
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
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
No. of pages: 444
Language: English
Edition: 1
Published: November 24, 2015
Imprint: Bentham Science Publishers
Paperback ISBN: 9781608059799
eBook ISBN: 9781608059782
ZU
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
JM
Jeffry D. 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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