Drug Design Strategies

Computational Techniques and Applications

By: Lee Banting (Editor), Tim Clark (Editor)

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Hardcover | 18 January 2012

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239 Pages

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23.9 x 16.5 x 2

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This book documents the latest research into the theory and application of force-fields, semi-empirical molecular orbital, density functional and ab initio calculations, Quantum Mechanical (QM) based modelling, Atoms in Molecules (AIM) approach, and biomolecular dynamics. It also covers theory and application of 2D cheminformatics, QSAR/QSPR, ADME properties of drugs, drug docking/scoring protocols and approaches, topological methodology, and modelling accurate inhibition constants of enzymes. Finally, the book gives the theory and applications of multiscale modelling of proteins and biomolecular systems. The information need for a book in this area is due to the continuing rapid advance of firstly theoretical approaches, secondly software/hardware and lastly the successful application of the technology and this book fills a gap in the literature. The co-editors have extensive experience of teaching and researching in the field and the book includes contributions from cutting-edge academic and industrial researchers in their respective fields. It is essential reading for medicinal chemists, computational chemists and those in the pharmaceutical industry.

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Non-Fiction Medicine Other Branches of Medicine Pharmacology Science Chemistry Physical Chemistry Quantum & Theoretical Chemistry Engineering & Technology Industrial Chemistry & Manufacturing Technologies Industrial Chemistry Pharmaceutical Technology

Quantum Mechanical/Molecular Mechanical Approaches in Drug Design	p. 1
Introduction	p. 1
QM/MM Methods	p. 4
Additive QM/MM Methods	p. 5
Subtractive QM/MM Methods	p. 7
Applications of QM/MM Methods to Structure-based Drug Design	p. 8
QM/MM Methods to Aid the Understanding of Ligand-Receptor Interactions	p. 9
QM/MM Methods in Scoring Refinement	p. 16
Summary	p. 18
Acknowledgements	p. 19
References	p. 19
Transition Metal Systems	p. 27
Introduction	p. 27
Methods for Modelling Transition Metal Centres	p. 29
Density Functional Theory	p. 30
Molecular Mechanics	p. 33
Ligand Field Effects in Molecular Mechanics	p. 35
Scenarios	p. 39
Predicting log P for Pt Complexes	p. 40
Predicting log P for CuII Complexes	p. 42
Interactions Involving Explicit Receptors	p. 44
Scenario 1: Metallodrug-DNA Intercalation	p. 45
Platinum-DNA Binding	p. 47
Drug Binding in the Cytochrome P450 Active Site Cavity	p. 48
Drug-Zinc Binding and Substrate Oxidation by P450	p. 50
Conclusions	p. 53
References	p. 53
Modeling Protein-Protein Interactions by Rigid-body Docking	p. 56
Protein-Protein Interactions	p. 56
Predicting Protein Interaction Surfaces	p. 57
Protein-Protein Interaction Databases	p. 58
The Protein Docking Problem	p. 59
Rigid Body Docking	p. 60
Docking By Geometric Hashing	p. 61
Cartesian Grid-based FFT Docking	p. 61
Spherical Polar Fourier Basis Functions	p. 64
Spherical Polar Fourier Correlations	p. 67
Multi-dimensional Spherical Polar FFTs	p. 70
Exploiting Graphics Processor Units	p. 70
The 'Hex' Docking Program	p. 75
Conclusions and Future Prospects	p. 79
Acknowledgements	p. 80
References	p. 80
QM Based Modelling	p. 87
Introduction	p. 87
Computational Demands	p. 88
The Molecular Electrostatic Potential	p. 89
Local Properties and Intermolecular Interactions	p. 91
Local Properties and Molecular Surfaces	p. 93
Spherical Harmonic Expansions	p. 93
Surface Autocorrelations	p. 98
Surface Integral Models	p. 99
Local Properties on Grids	p. 100
Summary and Conclusions	p. 102
Acknowledgments	p. 102
References	p. 103
Semi-empirical Methods: Current Status and Future Directions	p. 107
Introduction	p. 107
MNDO and MNDO/d Based Methods	p. 108
MNDO/d	p. 109
An Overview of Other Semi-empirical Approaches	p. 111
OMx Schemes	p. 111
DFTB	p. 111
MSINDO	p. 111
Hydrogen Bonds, Non-covalent Interaction and Effects of Environment	p. 112
Excited States	p. 113
Electron and Excitation Energy Transfer	p. 114
Linear Scaling	p. 114
Concluding Remarks and Perspectives	p. 115
References	p. 116
Quantum Chemical Topology: on Descriptors, Potentials and Fragments	p. 120
Introduction	p. 120
Quantum Chemical Topology (QCT)	p. 121
Quantum Topological Molecular Similarity (QTMS)	p. 126
Force Field Development: QCTFF	p. 143
Bioisosterism	p. 154
Conclusions	p. 156
Acknowledgement	p. 157
References	p. 157
Cheminformatics in Diverse Dimensions	p. 164
Introduction	p. 164
Zero-dimensional Code Representations	p. 165
CAS Registry Numbers	p. 165
Hash Structural Codes	p. 166
Molecular Descriptors	p. 167
One Dimensional Code Representations	p. 169
Nomenclature of Chemical and Biochemical Compounds	p. 169
Notation of Chemical Compounds	p. 170
Bit String Representations	p. 173
Two-dimensional Code Representations	p. 174
Matrices	p. 175
Connection Table	p. 175
Standard Structure Exchange Formats	p. 176
Conclusion	p. 179
References	p. 179
Analysing Molecular Surface Properties	p. 184
Introduction	p. 184
Molecular Surface Models	p. 185
Molecular Surface Properties	p. 192
Molecular Surface Similarity	p. 194
Molecular Surface Property Graphs	p. 198
Concluding Remarks	p. 204
References	p. 204
Atomistic Modelling of Drug Delivery Systems	p. 210
Introduction	p. 210
Molecular Mechanics - Energy Minimisation	p. 211
Encapsulation of Multinuclear Platinum Complexes	p. 211
Carbon Nanotubes	p. 213
Fullerenes	p. 215
Molecular Dynamics	p. 220
Zeolites as Drug Delivery Agents	p. 220
Other Examples of MD Simulations	p. 225
Quantum Mechanical Methods	p. 226
Delivery of Vancomycin using Mesoporous Materials	p. 226
Design of Conducting Polymers for Drug Delivery	p. 227
Summary	p. 230
References	p. 230
Subject Index	p. 232
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Drug Design Strategies

Computational Techniques and Applications

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Hardcover

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