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2013 Archived Content



MORNING SHORT COURSE: 9:00 am - 12:00 pm*  

Structure-Based Drug Design for Epigenetic Targets

Epigenetic processes are the focus of intense interest, and the families of proteins that mediate epigenetic signalling are a highly promising source of new drug targets.  Tackling this emerging field of novel drug targets is not without its challenges.  This workshop will review the contribution that structural biology has made to the discovery of small molecule modulators.  Structural information can be invaluable in determining the druggability of potential targets, and in enabling more efficient identification of hit molecules.  Structural information can also guide the design of compounds with improved affinity for the target, or selectivity versus other targets.  This introductory course on drug design for epigenetic targets will focus especially on emerging targets such as bromodomain (readers), methyltransferase (writers) and lysine demethylase (erasers).

Johnathan R. Whetstine, Ph.D., Assistant Professor of Medicine, Harvard Medical School
Philip Fallon, Ph.D., Senior Medicinal Chemist, Domainex Ltd. 


1:15 pm Chairperson’s Opening Remarks

Adam C. Palmer, Ph.D., Postdoctoral Fellow, Department of Systems Biology, Harvard Medical School(1) the special role that structure-based drug design can play in treating drug resistant infectious diseases
(2) how considering the evolution of resistance during drug development could produce drugs with more long-lasting clinical efficacy
(3) how drug resistance can be used as a tool to understand mechanism of drug action

1:20 Structure-Based Design of Potent and Selective Inhibitors of PI3-Kinase Delta

Jeremy M. Murray, Ph.D., Scientist, Structural Biology, Genentech

Inhibition of PI3Kδ is considered to be an attractive mechanism for the treatment of inflammatory diseases and leukocyte malignancies. Using a structure-based design approach, we have identified a series of potent and selective inhibitors of PI3Kδ. These inhibitors do not occupy the induced selectivity pocket between Trp760 and Met752 that is observed for other families of selective PI3Kδ inhibitors. Instead, the selectivity of the compounds for inhibition of PI3Kδ relative to other PI3K isoforms appears to be due primarily to the strong interactions these inhibitors are able to make with Trp760 in the PI3Kδ binding pocket. This talk will discuss the structural understanding of the selectivity of these inhibitors against other isoforms, pharmacokinetic properties and the ability of select compounds to inhibit the function of B-cells in vivo.

1:50 MD Simulations of Mutant and WT PI3Kα: Insights into the Mechanism of Overactivation and Implications for Drug Design

Zoe Cournia, Ph.D., Investigator, Biomedical Research Foundation, Academy of Athens

PI 3 kinase alpha (PI3Kα) is one of the most frequently mutated proteins in human cancers. Molecular dynamics simulations in aqueous solution performed for wild type (WT) and H1047R mutant PI3Kα proteins, revealed different dynamical and structural features for the two proteins, which may lead to kinase overactivation in the mutant variant. Binding site prediction and virtual screening further facilitated the development of novel mutant-specific PI3Kα inhibitors that exploit the altered conformation of the mutant with respect to the WT protein.



2:20 Drugging the Undruggable: Transforming Nature’s α-Helix into Breakthrough Medicines

Tomi SawyerTomi Sawyer, Ph.D., CSO, Aileron Therapeutics

A major challenge of drug discovery has been to successfully modulate the biological properties of those therapeutic targets deemed “undruggable” as defined relative to small-molecules. However, recent advancements leveraging peptides and macrocycles are expanding such drug space, especially for many intracellular protein–protein interaction targets deemed “hot” drug-wise. Structural biology and computational chemistry are key tools for such drug discovery. As a case study, advancements in stapled peptide technology to transform Nature’s α-helix into breakthrough medicines will be presented.

2:50 Refreshment Break in the Exhibit Hall with Poster Viewing



3:30 Towards a New Generation of Animicrobial Antifolates

Dennis WrightDennis L. Wright, Ph.D., Professor of Pharmaceutical Sciences and Chemistry, University of Connecticut

We are using a structure-based design approach to develop potent and selective inhibitors of the enzyme dihydrofolate reductase (DHFR) from a variety of pathogenic organisms. Analysis of crystal structures of trimethoprim-resistant and naturally-insensitive enzymes led to the design of a series of propargyl-linked antifolates characterized by high potency, good selectivity over the human form of the enzyme and good anti-microbial activity.

4:00 Understanding Drug Mechanism of Action by Target Gene Overexpression

Adam PalmerAdam C. Palmer, Ph.D., Postdoctoral Fellow, Department of Systems Biology, Harvard Medical School

The molecular targets of drugs can sometimes, but not always, be identified amongst genes that confer drug resistance when overexpressed. We quantitatively overexpressed genes encoding known antibiotic targets and observed that drug resistance does not only increase; it can remain unchanged, decrease, or even have a non-monotonic dependence on target expression. These diverse effects are explained by simple models considering gene toxicity and drug-induction of harmful target-catalyzed reactions. The relation between drug resistance and target expression may reveal unexpectedly complex mechanisms of drug action.

4:30 Close of the Day

DINNER SHORT COURSE (JUNE 19, 6:00-8:00 PM)*  

Chemical Computing Group-DO NOT USEA Uniform Framework for Computer-Aided Biologics Design

Chris Williams, Ph.D., Principal Scientist, Chemical Computing Group

Protein engineering plays a pivotal role in modulating the function, activity and physical properties of biologics. Representative strategies employed in protein engineering include rationale protein design and directed evolution. In general, disparate work has been done in applying computer-aided biologics design (CABD) to protein engineering for the development of novel biological therapeutics. Here, we describe a unified framework of in silico protein engineering tools and investigate its applicability to the modulation of protein properties such as affinity and stability. The course will cover current in silico technologies used in protein engineering and biologics design. More specifically, applications for visualizing, and analyzing mutations will be described. Tools for calculating surface properties such as electrostatic hot-spots or patches, as well as physicochemical properties will be presented. A number of case studies will be used to describe how residue scanning technology can be used to address challenges in species cross-reactivity, stability, and aggregation. 

*Separate registration required.

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