vi
Preface
The present book is aimed at a relatively broad readership that includes advanced
undergraduate and graduate students of chemistry, physics and engineering, postdoctoral associates and specialists from both academia and industry who carry out
research in the fields that require molecular and QSA(P)R modeling. This book
could also be useful to students in biochemistry, structural biology, bioengineering,
bioinformatics, pharmaceutical chemistry, as well as other related areas, who have
an interest in molecular-level computational techniques.
The book starts from the reviews that describe the studies of biological systems
which are performed by the methods of quantum chemistry and classical molecular dynamics. The two initial chapters describe the theory and application of such
methods as hybrid quantum-mechanical/molecular mechanical approximation,
Monte-Carlo, molecular docking and molecular dynamics, in conjunction with the
application of experimental techniques as Infra-Red, Raman, UV-VIS spectroscopies, and microcalorimetry. Next four chapters continue to describe the current
status of the investigations in such vital area as functioning of DNA. It covers formation of DNA lesions, computational rational design of DNA polymerase inhibitors, modeling the structure of DNA quadruplexes, and the study on the structure,
relative stability, and proton affinities of such building blocks as nucleotides. The
seventh, eighth, ninth and tenth chapters are devoted to the application of computational and experimental techniques in such areas of medical and pharmaceutical
chemistry as enzyme-inhibitor interactions, interaction of enzymes with biological
membranes and a probe of polyphenol glycosides as potential remedies in kidney
stones therapy and transformations of epoxided in vivo and in vitro. The following
six reviews describe the advantages in the area of chemoinformatics. Most of them
are devoted to developing and applications of the QSAR methodology to predict
an activity and design of novel biologically active compounds. In particular, the
criteria for correct QSAR models, their opprtunities and limitations are studied in
the eleventh chapter. Very original QSAR methodoly named MICROCOSM is presented in chapter twelfth. The chapters 11
th
, 13
th
and 14
th
devoted to analysis such
important properties of biologivally active compounds (possible drugs) as toxicity
and farmokinetics. Very interesting methodology which combines molecular dynamics and docking approaches is described in the 15
th
chapter. The book is closing up by the 16
th
chapter which describes modern state of chemoinformatics, new
problems and perspectives of treatment of avalanche-like amount of experimental
chemical and biological information.
The editors of this book gratefully thank all the authors for their time and contribution. We hope that this volume may give the reader (both in academia and in
an industrial pharmaceutical community) a useful overview of the computational
and experimental techniques that are currently in use in the areas of computational
pharmacy and medicine.
May, 2014
Leonid Gorb
Victor Kuz’min
Eugene Muratov
Preface
The present book is aimed at a relatively broad readership that includes advanced
undergraduate and graduate students of chemistry, physics and engineering, postdoctoral associates and specialists from both academia and industry who carry out
research in the fields that require molecular and QSA(P)R modeling. This book
could also be useful to students in biochemistry, structural biology, bioengineering,
bioinformatics, pharmaceutical chemistry, as well as other related areas, who have
an interest in molecular-level computational techniques.
The book starts from the reviews that describe the studies of biological systems
which are performed by the methods of quantum chemistry and classical molecular dynamics. The two initial chapters describe the theory and application of such
methods as hybrid quantum-mechanical/molecular mechanical approximation,
Monte-Carlo, molecular docking and molecular dynamics, in conjunction with the
application of experimental techniques as Infra-Red, Raman, UV-VIS spectroscopies, and microcalorimetry. Next four chapters continue to describe the current
status of the investigations in such vital area as functioning of DNA. It covers formation of DNA lesions, computational rational design of DNA polymerase inhibitors, modeling the structure of DNA quadruplexes, and the study on the structure,
relative stability, and proton affinities of such building blocks as nucleotides. The
seventh, eighth, ninth and tenth chapters are devoted to the application of computational and experimental techniques in such areas of medical and pharmaceutical
chemistry as enzyme-inhibitor interactions, interaction of enzymes with biological
membranes and a probe of polyphenol glycosides as potential remedies in kidney
stones therapy and transformations of epoxided in vivo and in vitro. The following
six reviews describe the advantages in the area of chemoinformatics. Most of them
are devoted to developing and applications of the QSAR methodology to predict
an activity and design of novel biologically active compounds. In particular, the
criteria for correct QSAR models, their opprtunities and limitations are studied in
the eleventh chapter. Very original QSAR methodoly named MICROCOSM is presented in chapter twelfth. The chapters 11
th
, 13
th
and 14
th
devoted to analysis such
important properties of biologivally active compounds (possible drugs) as toxicity
and farmokinetics. Very interesting methodology which combines molecular dynamics and docking approaches is described in the 15
th
chapter. The book is closing up by the 16
th
chapter which describes modern state of chemoinformatics, new
problems and perspectives of treatment of avalanche-like amount of experimental
chemical and biological information.
The editors of this book gratefully thank all the authors for their time and contribution. We hope that this volume may give the reader (both in academia and in
an industrial pharmaceutical community) a useful overview of the computational
and experimental techniques that are currently in use in the areas of computational
pharmacy and medicine.
May, 2014
Leonid Gorb
Victor Kuz’min
Eugene Muratov