Contents


Preface

The rise of chemical information and development of structure databases, as well as the need for new therapeutic agents or improved specific materials with controlled properties, has led to the development of chemoinformatic tools. These tools can be used to design new molecules and to model their chemical and/or biochemical environment and interactions. Molecular docking and dynamic simulations are such approaches whose methodologies have evolved in terms of accuracy. Thus, today researchers benefit from important *in silico* studies and new opportunities to identify and propose new hit molecules further to chemical synthesis or isolation from vegetal materials, as first step in the introduction in therapeutic practice of

This book clearly explains the principles of molecular docking and molecular dynamics. It includes examples of algorithms and procedures proposed by different software programs for visualizing and identifying potential interactions in com-

The book is organized into six chapters, each one discussing different molecular simulation methodologies and providing concrete examples of complex interactions. In each chapter, the authors provide an overview of the treated subject, a

Chapter 1 is an introductory chapter, familiarizing the reader with basic principles

Chapter 2 addresses one of the most common cancer diagnoses in women, breast cancer. The authors use homology modeling, ligand docking, and molecular dynamic simulations to explore aryl hydrocarbon receptor (AhR) structure and to identify its suitable binding site for some aromatic acrylonitrile ligands, potential drug candidates in therapeutics of breast malignancies. The work highlights the usefulness of homology modeling in cases when the protein domain of interest is not yet described and characterized by X-ray crystallography. The employed methodologies could serve to assess other compounds' potency as anticancer agents, in virtual screening, before chemical synthesis, evaluation, and pre-clinical trials.

In Chapter 3, the authors report results of docking simulations using quinolone derivatives to evaluate their potential antitumoral and antimycobacterial activity, compared to the standard therapeutic compounds of topotecan and levofloxacin.

Chapter 4 gives a detailed overview of molecular recognition occurring in proteinligand complexes, based on various type of interactions and other factors (surrounding solvent, ionization effects, conformational changes, entropy, desolvation, etc.) important for the understanding of biological functions and therapeutic action. The authors underline the importance of proper selection of modeling protocols to obtain desired accuracy. A virtual screening of sesquiterpenoid alcohols against cyclooxygenase isoenzymes is realized in an attempt to design and develop

description of the methodologies used, and a discussion of the results.

and terminology of docking and dynamic simulations.

new nonsteroidal anti-inflammatory drugs.

new agents.

plexes of biochemical interest.
