Quantum Mechanics in Drug Discovery

ISBN-13: 9781071602812 / Angielski / Twarda / 2020 / 360 str.

Alexander Heifetz

Spis treści

1. Current and Future Challenges in Modern Drug Discovery

            Christofer S. Tautermann

 

2. QM Implementation in Drug Design: Does It Really Help?

            Jinfeng Liu and Xiao He

 

3. Guiding Medicinal Chemistry with Fragment Molecular Orbital (FMO) Method  

            Alexander Heifetz, Tim James, Michelle Southey, Mike Bodkin, and Steven Bromidge

 

4. Analyzing Interactions with the Fragment Molecular Orbital Method

            Dmitri G. Fedorov

 

5. Underappreciated Chemical Interactions in Protein-Ligand Complexes

            Andrew Anighoro

 

6. Geometry Optimization, Transition State Search, and Reaction Path Mapping Accomplished with the Fragment Molecular Orbital Method

            Hiroya Nakata and Dmitri G. Fedorov

 

7. Taking Water into Account with the Fragment Molecular Orbital Method

            Yoshio Okiyama, Kaori Fukuzawa, Yuto Komeiji, and Shigenori Tanaka

 

8. Computational Methods for Biochemical Simulations Implemented in GAMESS

            Dmitri G. Fedorov, Hui Li, Vladimir Mironov, and Yuri Alexeev

 

9. QM in Seconds with the Fragment Molecular Orbital and Density-Functional Tight-Binding Methods

            Inaki Morao, Alexander Heifetz, and Dmitri G. Fedorov

 

10. Protein Molecular Dynamics Simulations with Approximate QM: What Can We Learn?

            Stephan Irle, Van Q. Vuong, Mouhmad H. Elayyan, Marat R. Talipov, and Steven M. Abel

 

11. Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method

            Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Dmitri G. Fedorov, Mike J. Bodkin, and Andrea Townsend-Nicholson

 

12. Characterizing Rhodopsin-Arrestin Interactions with the Fragment Molecular Orbital (FMO) Method

            Alexander Heifetz and Andrea Townsend-Nicholson

 

13. Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method

            Alexander Heifetz, Vladimir Sladek, Andrea Townsend-Nicholson, and Dmitri G. Fedorov

 

14. Conformational Searching with Quantum Mechanics

            Matthew Habgood, Tim James, and Alexander Heifetz

 

15. User-Friendly Quantum Mechanics: Applications for Drug Discovery

            Martin Kotev, Laurie Sarrat, and Constantino Diaz Gonzalez

 

16. Binding Free Energy Calculation Using Quantum Mechanics Aimed for Drug Lead Optimization

            Claudio N. Cavasotto

 

17. Molecular Docking Using Quantum Mechanical-Based Methods

            M. Gabriela Aucar and Claudio N. Cavasotto

 

18. QM Calculations in ADMET Prediction

            Alfonso Pozzan

 

19. Design and SAR Analysis of Covalent Inhibitors Driven by Hybrid QM/MM Simulations

            Alessio Lodola, Donatella Callegari, Laura Scalvini, Silvia Rivara, and Marco Mor

 

20. What’s Next for Quantum Mechanics in Structure-Based Drug Discovery?

            Richard A. Bryce

Blurb

This volume looks at applications of quantum mechanical (QM) methods in drug discovery. The chapters in this book describe how QM approaches can be applied to address key drug discovery issues, such as characterizing protein-water-ligand and protein-protein interactions, providing estimates of binding affinities, determining ligand energies and bioactive conformations, refinement of molecular geometries, scoring docked protein–ligand poses, describing molecular similarity, structure–activity-relationship (SAR) analysis, and ADMET prediction. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary software and tools, step-by-step, readily reproducible modeling protocols, and tips on troubleshooting and avoiding known pitfalls. 

Cutting-edge and unique, Quantum Mechanics in Drug Discovery is a valuable resource for structural and molecular biologists, computational and medicinal chemists, pharmacologists, and drug designers.