Protein-Ligand Interactions and Drug Design

ISBN-13: 9781071612118 / Angielski / Miękka / 2022

Opis

This detailed book collects modern and established computer-based methods aimed at addressing the drug discovery challenge from disparate perspectives by exploiting information on ligand-protein recognition. Beginning with methods that allow for the exploration of specific areas of chemical space and the designing of virtual libraries, the volume continues with sections on methods based on docking, quantitative models, and molecular dynamics simulations, which are employed for ligand discovery or development, as well as methods exploiting an ensemble of protein structures for the identification of potential protein targets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and cutting-edge, Protein-Ligand Interactions and Drug Design provides detailed practical procedures of solid computer-aided drug design methodologies employed to rationalize and optimize protein-ligand interactions, for experienced researchers and novices alike.

Spis treści

Part I: Chemical Space

 

1. Investigation of the Click-Chemical Space for Drug Design Using ZINClick

            Alberto Massarotti

 

2. Molecular Scaffold Hopping via Holistic Molecular Representation

            Francesca Grisoni and Gisbert Schneider

 

Part II: Hit Identification and Hit-to-Lead Optimization

 

3. Biased Docking for Protein-Ligand Pose Prediction

            Juan Pablo Arcon, Adrián G. Turjanski, Marcelo A. Martí, and Stefano Forli

 

4. Binding Mode Prediction and Virtual Screening Applications by Covalent Docking

            Andrea Scarpino, György G. Ferenczy, and György M. Keserű

 

5. Ligand-Receptor, Ligand-DNA Interactions and Drug Design

            Aggeliki Syriopoulou, Ioannis Markopoulos, Andreas G. Tzakos, and Thomas Mavromoustakos

 

6. Simulation of Ligand Transport in Receptors Using CaverDock

            Jana Hozzová, Ondřej Vávra, David Bednář, and Jiří Filipovič

 

7. Negative Image-Based Screening: Rigid Docking Using Cavity Information

            Pekka A. Postila, Sami T. Kurkinen, and Olli T. Pentikäinen

 

8. Negative Image-Based Rescoring: Using Cavity Information to Improve Docking Screening

            Olli T. Pentikäinen and Pekka A. Postila

 

9. Fragment-Based Drug Design of Selective HDAC6 Inhibitors

            Dusan Ruzic, Nemanja Djokovic, and Katarina Nikolic

 

10. A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time

            Gaurav K. Ganotra, Ariane Nunes-Alves, and Rebecca C. Wade

 

11. Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level

            Gert-Jan Bekker and Narutoshi Kamiya

 

12. Free Energy Calculations for Protein-Ligand Binding Prediction

            Willem Jespers, Johan Åqvist, and Hugo Gutiérrez-de-Terán

 

13. Exploiting Water Dynamics for Pharmacophore Screening

            David Schaller, Szymon Pach, Marcel Bermudez, and Gerhard Wolber

 

14. Markov State Models to Elucidate Ligand Binding Mechanism

            Yunhui Ge and Vincent A. Voelz

 

Part III: Target Identification

 

15. From Homology Modeling to the Hit Identification and Drug Repurposing: A Structure-Based Approach in the Discovery of Novel Potential Anti-Obesity Compounds

            Giosuè Costa, Anna Artese, Francesco Ortuso, and Stefano Alcaro

 

16. Multiple Target Drug Design Using LigBuilder 3

            Xiaoyu Qing, Shiwei Wang, Yaxia Yuan, Jianfeng Pei, and Luhua Lai

 

17. Bionoi: A Voronoi Diagram-Based Representation of Ligand-Binding Sites in Proteins for Machine Learning Applications

            Joseph Feinstein, Wentao Shi, J. Ramanujam, and Michal Brylinski

 

18. MDock: A Suite for Molecular Inverse Docking and Target Prediction

            Zhiwei Ma and Xiaoqin Zou

O autorze

Flavio Ballante is a researcher in the Department of Cell and Molecular Biology at Uppsala University (Sweden). He graduated in Medicinal Chemistry from Sapienza University in Rome (Italy) where he also obtained a Ph.D. in Pharmaceutical Sciences. During his academic career, he conducted research in France (University of Lorraine, Metz), the USA (Washington University School of Medicine in St. Louis, MO), and Sweden (Uppsala University, Uppsala), working on computer-aided drug design, chemistry, and biology experiments. His primary research goals are directed toward understanding the basis for molecular recognition at the atomic level, and his scientific activity is mainly focused on the design, development, and application of computational methods for ligand discovery.