Main description:

This volume covers several aspects of rational drug design, such as synthesis of novel bioactive drugs; development and application of new methodologies; computational methods valuable for the establishment of new approaches in drug discovery; and the effects of physical-chemical and ADMET properties of the designed potential drugs. Chapters guide readers through amyloid deposits, Saturation Transfer Difference (STD) NMR, methods on bioguided design, the importance of lipophilicity in drug design, ADMET, FRET, structural biology, and homology modeling. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Rational Drug Design: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Contents:

1. Conformational Properties of hIAPP22-29 (NFGAILSS) and Rational Drug Design

Panagiotis Lagarias, Youness Elkhou, Jason Vedad, Adam Profit, Tahsin F. Kellici, Antonios Kolocouris, Ruel Desamero, and Thomas Mavromoustakos

2. Electronic and Electrostatic Approaches to the Development of Peptide-based Inhibitors of Amylin Aggregation

Adam A. Profit and Ruel Z. B. Desamero

3. In Silico Drug Design: Applications of non-peptide mimetics towards the Immunotherapy of Multiple Sclerosis

Haralambos Tzoupis and Theodore Tselios

4. Binding Moiety Mapping by Saturation Transfer Difference NMR

Jeffrey R. Brender, Janarthanan Krishnamoorthy, Anirban Ghosh, and Anirban Bhunia

5. Protein Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection

Flavio Ballante

6. Rational Drug Design using Integrative Structural Biology

Magda S. Chegkazi, Michael Mamais, Anastasia I. Sotiropoulou, and Evangelia D. Chrysina

7. Enalos+Knime Nodes: New Cheminformatics Tools for Drug Discovery

Dimitra-Danai Varsou, Spyridon Nikolakopoulos, Andreas Tsoumanis, Georgia Melagraki, and Antreas Afantitis

8. Bioguided Design of Trypanosomicidal Compounds: A Successful Strategy in Drug Discovery

Guzman Ignacio Alvarez Touron

9. A Hybrid Virtual Screening Protocol Based on Binding Mode Similarity

Andrew Anighoro and Jurgen Bajorath

10. Single Step Determination of Unlabelled Compound Kinetics Using a Competition Association Binding Method Employing Time-resolved FRET

David A. Sykes and Steven J. Charlton

11. Dynamic Undocking: A Novel Method for Structure-based Drug Discovery

Maciej Majewski, Sergio Ruiz-Carmona, and Xavier Barril

12. The impact of Lipophilicity in Drug Discovery - Rapid Measurements by Means of Reversed Phase HPLC

Constantinos Giaginis, Fotios Tsopelas, and Anna Tsantili-Kakoulidou

13. Exploring Polypharmacology in Drug Design

Patricia Saenz-Mendez and Leif A. Eriksson

14. Development of Nuclear Receptor Modulators

Simone Schierle and Daniel Merk

15. In silico Screening of Compound Libraries using a Consensus of Orthogonal Methodologies

Vassilios Myrianthopoulos, Georgios Lamprinidis and Emmanuel Mikros

16. Insights in Organometallic Synthesis of Various Adamantane Derivatives with Sigma Receptor ( R) Binding Affinity and Antiproliferative / Anticancer Activity

Ioannis Papanastasiou

17. Supervised Molecular Dynamics (SuMD) Approaches in Drug Design

Davide Sabbadin, Veronica Salmaso, Mattia Sturlese, and Stefano Moro

18. Lead Identification through the Synergistic Action of Biomolecular NMR and in Silico Methodologies

Konstantinos D. Marousis, Aikaterini C. Tsika, Maria Birkou, Minos-Timotheos Matsoukas, and Georgios A. Spyroulias

19. The use of Dynamic Pharmacophore in Computer Aided Hit Discovery: A Case Study

Ugo Perricone, Marcus Wieder, Thomas Seidel, Thierry Langer, and Alessandro Padova

20. Rational Design of MAGL inhibitors

Carlotta Granchi, Flavio Rizzolio, Isabella Caligiuri, Marco Macchia, Adriano Martinelli, Filippo Minutolo, and Tiziano Tuccinardi

21. Application of Virtual Screening Approaches for the Identification of Small Molecule Inhibitors of the Methyllysine Reader Protein Spindlin1

Chiara Luise and Dina Robaa

22. Designing Natural Product Hybrids Bearing Triple Antiplatelet Profile and Enhanced Human Plasma Stability

Antonis Tsiailanis, Maria Tsoumani, Evgenios Stylos, Maria V. Chatziathanasiadou, Tahsin Kellici, Thomas Mavromoustakos, Alexandros D. Tselepis, and Andreas G. Tzakos

23. Pharmacophore Generation and 3D-QSAR Model Development using PHASE

Eleni Vrontaki and Antonios Kolokouris

24. Design of Drugs by Filtering through ADMET, Physicochemical, and Ligand-Target Flexibility Properties

Marlet Martinez-Archundia, Martiniano Bello, and Jose Correa-Basurto

25. Reactions in NMR tubes as Key Weapon in Rational Drug Design

Dimitrios Ntountaniotis

26. Application of Multiscale Simulations Tools on GPCRs. An Example with Angiotensin-II type 1 Receptor

Ismail Erol, Busecan Aksoydan, Isik Kantarcioglu, and Serdar Durdagi

27. Angiotensin II Type 1 Receptor Homology Models: A Comparison between In Silico and the Crystal Structures

Tahsin F. Kellici