The New Era of Structure-Based Drug Design for GPCRs

Authored by: Jonathan S. Mason, Ph.D., Drug Design & Computational Chemistry, Heptares Therapeutics Ltd.

• GPCRs & the Heptares Approach to Drug Discovery
• GPCR SBDD: Case study – A(2A) Antagonists
• A fragment perspective
• A water perspective: druggability, SAR & kinetics
• A structural biology update

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Rationalization and Visualization of Non-bonded Interactions

Authored by: Drs. Paul Labute, Alain Ajamian, and Chris Williams, Chemical Computing Group

• Extended Huckel theory for non-bonded interaction energies
• Updated models of non-bonded interactions in MOE 2011.10

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Making Docking/Scoring Calculations More Accurate via Error Analysis

Authored by: Kenneth M. Merz, Jr., Ph.D., Department of Chemistry, Quantum Theory Project, University of Florida

• Challenges facing computational biology
• Water models and water dimer
• 2010 GPCR docking and modeling competition
• What about the docking funnel?

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Rational Approaches to Improving Selectivity in Drug Design

Authored by: Woody Sherman, Ph.D., Vice President, Applications Science, Shrodinger

• Factors contributing to selectivity 
• Shape complementarity: Clash with decoy  
  • Remove decoy interactions
   
• Induced fit of target
• Experimental validation

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Structure based Ligand Discovery for GPCRs

Authored by: Ruben Abagyan, Ph.D., Professor, Skaggs School of Pharmacy & Pharmaceutical Sciences, San Diego Supercomputer Center, University of California, San Diego

• Growing understanding of GPCR structure and function
• Docking to flexible sites: methods and benchmarks
• 2010 GPCR docking and modeling competition
• Ligand guided modeling of unsolved GPCRs and alternative states

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Making Decisions in Fragment-Based Drug Discovery

Authored by: Rod Hubbard, Ph.D., Director, Structural Sciences, Vernalis Ltd.

• Overview of fragment-based methods
  • Some (old) examples of successes
   
• Some fragmentology
  • Hit rates and target druggability
  • Predicting fragment poses
  • Selectivity
   
• How to make decisions on which fragments to progress?
• What are the opportunities for computational methods?

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Kinase-Targeted Therapeutics: Development Pipelines, Challenges, and Opportunities
Part of the Insight Update Series 

This report analyzes:

• The considerable array of therapeutic development efforts directed at kinases
• Current and emerging technologies being applied to development of these compounds
• The major companies and projects involved with kinase modulation
• How unique characteristics of different kinase classes impact therapeutic development
• Current trends and major challenges faced by the industry
• How to make decisions on which fragments to progress?
• What are the opportunities for computational methods?

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23rd American Peptide Symposium
June 22 – 27, 2013
Hilton Waikoloa Village
Hawai‘i
http://aps2013.org/

10th Australian Peptide Conference 2013
September 13th – 18th 2013
Malaysia, Penang
www.peptideoz.org

Anton: Molecular Dynamics Simulation for Drug Design

Previously recorded

David E. Shaw, Chief Scientist of D. E. Shaw Research, talks with Bio-IT World editor Kevin Davies about a specialized supercomputer, called Anton, that has simulated the behavior of proteins for periods as long as two milliseconds. Excerpts from some of these simulations, showing events such as drugs finding their own binding sites.

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