Description
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. 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, Adrin G. Turjanski, Marcelo A. Mart, and Stefano Forli 4. Binding Mode Prediction and Virtual Screening Applications by Covalent Docking Andrea Scarpino, Gyrgy G. Ferenczy, and Gyrgy M. Keseru 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 Hozzov, Ondrej Vvra, David Bednr, and Jir Filipovic 7. Negative Image-Based Screening: Rigid Docking Using Cavity Information Pekka A. Postila, Sami T. Kurkinen, and Olli T. Pentikinen 8. Negative Image-Based Rescoring: Using Cavity Information to Improve Docking Screening Olli T. Pentikinen 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 qvist, and Hugo Gutirrez-de-Tern 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 Giosu 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
