Structure-Based Drug Design
Royal Sonesta Hotel

Cambridge, Massachusetts


   Structure-Based Drug Design ( SBDD ) has been in use within the
   pharmaceutical industry for over twenty-five years. SBDD continues to
   play an important role in drug discovery, design, and optimization.
   Moreover, with the development of sophisticated biophysical and
   computational methodologies, SBDD is impacting hit identification and
   ‘hit to lead’ optimization approaches across the industry. In this
   program, we wish to highlight some recent breakthrough stories and
   successes using SBDD driven by medicinal chemistry, computational and
   biophysical approaches. We are especially interested in presentations
   of “unpublished work” that document recent breakthroughs in the
   following areas:

Schedule of Presentations:

Wednesday, June 23, 2010
07:45:00 Workshop Registration & Morning Coffee
08:25:00 Organizer’s Welcoming Remarks Micah Lieberman
08:30:00 MORNING WORKSHOP | Therapeutic Target Space: Methods for Druggability Assessment
08:35:00 Workshop Chairperson’s Remarks Tomi Sawyer
08:45:00 Assessing Druggability for Protein-Protein Complexes: The 2P2I Database Xavier Morelli
09:15:00 Combining Small Molecule and RNAi Screens for Target Prioritization Rajarshi Guha
09:45:00 Networking Coffee Break
10:00:00 Using Fragments to Assess Target Druggability Roderick Hubbard
10:00:00 Main Conference Registration
10:30:00 Identifying and Characterizing Binding Sites and Assessing Druggability Woody Sherman
10:55:00 Selectivity Optimization: Using Structure to Optimize Selectivity
11:00:00 Organizer’s Welcome & Chairperson’s Remarks Chris Williams, Micah Lieberman
11:15:00 Keynote Presentation | Structure-Based Design of AP24534, a pan-BCR-ABL Inhibitor Overriding the T315I Gatekeeper Mutation David Dalgarno
11:45:00 Special Co-Presentation | Achieving Remarkable Potency and Selectivity Against HCV Protease by Irreversible Covalent Inhibition Using Structure-Based Drug Design Juswinder Singh, Deqiang Niu
12:15:00 Embedding High-Throughput Structural Screening and Computational Bioactivity Prediction in Target Validation and Drug Discovery D. R. Artis
12:45:00 Luncheon Presentation (Sponsorship Opportunity) or Lunch on your Own
14:05:00 Protein-Protein Interaction Targeted Drug Discovery
14:10:00 Chairperson’s Remarks Chris Williams
14:15:00 Using Semi-Rational Design and Protein Folding to Engineer Highly Specific Protein-Protein Interactions for Therapeutic Intervention Jody Mason
14:45:00 Stapled α-Helical Peptides: The Twists and Turns of Drug Discovery Tomi Sawyer
15:15:00 Sponsored Presentation (Opportunity Available)
15:30:00 Networking Refreshment Break, Poster and Exhibit Viewing
16:00:00 Interactive Break-Out Discussion Groups
16:05:00 TABLE 1: Integration of 3-D and 2-D structural information, for instance the ones from the PDB with those from PubChem Talapady Bhat
16:10:00 TABLE 2: Use of Structure-Based Drug Design to Address Drug Resistance Juswinder Singh
16:20:00 TABLE 3: Computational Directions for Structure-Based Lead Optimization W. Patrick Walters
16:30:00 TABLE 4: Do We Get the Most Out of the Structural information in the PDB? Tips and Lessons Learned José Duca
16:35:00 TABLE 5: Why Aren’t We Designing the Perfect Drug as Soon as We Have a Crystal Structure? Rama K. Kondru
16:40:00 TABLE 6: The Role of Structural Waters in Drug Design Woody Sherman
16:45:00 TABLE 7: Matching SBDD Approaches with Targets: Do We Know How to Optimize Our Protocols? Sidney Topiol
16:50:00 TABLE 8:The Issue of Protein Flexibility in the Structure-Based Drug Design Jie Zheng
16:55:00 TABLE 9: Getting Around Scoring Matthias Rarey, Chris Williams
17:00:00 Networking Reception in the Exhibit Hall
Thursday, June 24, 2010
07:45:00 Breakfast Presentation (Sponsorship Opportunity) or Morning Coffee
08:40:00 New Computational Methods in SBDD
08:45:00 Chairperson’s Remarks José Duca
09:00:00 Chem-BLAST — A Rule-Based Method to Develop Advanced Structural Ontologies for Structure-Based Drug Design Talapady Bhat
09:30:00 LowModeMD: Conformational Search of Small Molecules, Macrocycles and Protein Loops Chris Williams
10:00:00 Sponsored Presentation (Opportunity Available)
10:15:00 Networking Coffee Break, Poster and Exhibit Viewing
11:00:00 An Enriched Structural Kinase Database to Enable Structure-Based Drug Discovery Natasja Brooijmans
11:30:00 Thermodynamic Characterization of Interfacial Water Molecules Involved in Binding Affinity and Specificity Woody Sherman
12:00:00 Luncheon Presentation (Sponsorship Opportunity) or Lunch on your Own
13:20:00 In Silico Discovery of Small Molecule Binders
13:25:00 Chairperson’s Remarks Alan C Rigby
13:30:00 In Silico Discovery of Small Molecule Transcription Factor Inhibitors Alan C Rigby
14:00:00 Structure-Based Investigation of Wnt Signaling Inhibitors Jie Zheng
14:30:00 Sponsored Presentation (Opportunity Available)
14:45:00 Networking Refreshment Break, Poster and Exhibit Viewing
15:30:00 Docking-Based Virtual Screenings for GPCR Ligands: Area of Applicability and Strategies for Optimization Stefano Costanzi
16:00:00 Mutation Data Driven Binding Modes for CCR5 Antagonists: Applications in Structure Based Design Rama K. Kondru
16:30:00 An Analysis of the Binding Efficiencies of Drugs and Their Leads in Successful Drug Discovery Programs Emanuele Perola
17:00:00 End of Day
Friday, June 25, 2010
07:45:00 Breakfast Presentation(Sponsorship Opportunity)or Morning Coffee
08:40:00 New Advances in Docking
08:45:00 Chairperson’s Remarks Gergely Toth
09:00:00 Docking and Scoring: From Fragments to Drug-Sized Molecules Paul Mortenson
09:30:00 Dock - Score - Analyze: Novel Approaches to Structure-Based Virtual Screening Matthias Rarey
10:00:00 Fast Docking-Based Free Energy Calculation Applied to Understanding Ligand Efficiency Jeffrey S. Wiseman
10:15:00 Networking Coffee Break, Poster and Exhibit Viewing
11:00:00 Implementation of Protein Flexibility and Water Molecules in Docking and Scoring Methods Nicolas Moitessier
11:25:00 Special Case Study
11:30:00 Combating Drug Resistance: Lessons from HIV Protease and Beyond Celia Schiffer
12:00:00 Luncheon Presentation (Sponsorship Opportunity) or Lunch on your Own
13:20:00 Impact of SBDD on Small Molecule Drug Discovery
13:25:00 Chairperson’s Remarks Roderick Hubbard
13:30:00 Beyond Growing and Linking: Impact of Fragments on the Discovery of Kinas e Inhibitors Andreas Kuglstatter
14:00:00 Sponsored Presentation (Opportunity Available)
14:15:00 Networking Refreshment Break, Poster and Exhibit Viewing
15:00:00 The Impact of Recent X-Ray Structure Determinations on Structure-Based Drug Design for GPCRs and other CNS Targets Sidney Topiol
15:30:00 From Enzymes to GPCRs: Experiences with Structure-Based Design Including Fragment Screening, Biophysical Mapping and In Silico Approaches Jonathan Mason
16:00:00 Coupling the GPCR Structural Determination Process with Discovery and Optimization of Small Molecule Ligands Michael Hanson
16:30:00 Closing Remarks
16:45:00 Close of Conference
3D Tissue Models
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