Quantum Mechanics in Drug Discovery

1. Front Matter

   Pages i-x

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2. Current and Future Challenges in Modern Drug Discovery

   • Christofer S. Tautermann

   Pages 1-17

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

   • Jinfeng Liu, Xiao He

   Pages 19-35

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

   • Alexander Heifetz, Tim James, Michelle Southey, Mike J. Bodkin, Steven Bromidge

   Pages 37-48

5. Analyzing Interactions with the Fragment Molecular Orbital Method

   • Dmitri G. Fedorov

   Pages 49-73

6. Underappreciated Chemical Interactions in Protein–Ligand Complexes

   • Andrew Anighoro

   Pages 75-86

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

   • Hiroya Nakata, Dmitri G. Fedorov

   Pages 87-103

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

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

   Pages 105-122

9. Computational Methods for Biochemical Simulations Implemented in GAMESS

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

   Pages 123-142

10. Accurate Scoring in Seconds with the Fragment Molecular Orbital and Density-Functional Tight-Binding Methods

    • Inaki Morao, Alexander Heifetz, Dmitri G. Fedorov

    Pages 143-148

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

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

    Pages 149-161

12. 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 et al.

    Pages 163-175

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

    • Alexander Heifetz, Andrea Townsend-Nicholson

    Pages 177-186

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

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

    Pages 187-205

15. Conformational Searching with Quantum Mechanics

    • Matthew Habgood, Tim James, Alexander Heifetz

    Pages 207-229

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

    • Martin Kotev, Laurie Sarrat, Constantino Diaz Gonzalez

    Pages 231-255

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

    • Claudio N. Cavasotto

    Pages 257-268

18. Molecular Docking Using Quantum Mechanical-Based Methods

    • M. Gabriela Aucar, Claudio N. Cavasotto

    Pages 269-284

19. QM Calculations in ADMET Prediction

    • Alfonso Pozzan

    Pages 285-305

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

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

    Pages 307-337

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 resourcefor structural and molecular biologists, computational and medicinal chemists, pharmacologists, and drug designers.

• QM applications
• Computer-aided drug discovery
• Fragment Molecular Orbital Method
• Computational techniques
• Pharmacology
• Drug design
• Medicinal chemistry
• Structure-based drug discovery

• Evotec (UK) Ltd., Abingdon, UK

  Alexander Heifetz

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