Fragment-based Lead Discovery Conference 2008
San Diego, CA February 18-20

FBLD Methods & Implementation Workshop

Sunday, February 17^th 9:00 a.m.-5:00 p.m.

Join us for an interdisciplinary and interactive workshop covering the methods and processes for implementing Fragment-based Lead Discovery. Learn about biophysical techniques such as surface plasmon resonance and calorimetry, as well as the structural biology techniques such as nuclear magnetic resonance and X-ray crystallography. We'll also give you guidelines on how to build and maintain a fragment library, as well as how to move from fragment hits to lead compounds. For each topic, we have provided enough time for a group discussion and questions, and morning coffee and lunch will be provided so that you can talk with the speakers and others implementing FBLD. Learn FBLD from the experts, and get a primer on the technologies so that you will get the most out of attending FBLD 2008.

Workshop Schedule

9:00 Coffee, Pastries, Introductions

9:20 Introduction: Case Studies of FBLD Implementation

Roderick Hubbard, Professor, University of York and Senior Fellow, Vernalis

This introduction will emphasise how fragment based methods have been implemented within various organisations and integrated with medicinal chemistry for drug discovery. I will begin with a brief overview of the development of the methods over the past ten years, including the central concepts of what fragments are and why they provide a new paradigm for drug discovery against some targets. I will then summarise the main methods for detecting fragment binding and the different approaches used for design of fragment libraries. I will conclude with an overview and examples of the different approaches to fragment evolution. The talk will provide a general introduction to the more detailed treatment of the methods by the rest of the speakers at the workshop.

9:50 Fragment-Based Discovery Using Optical Biosensors

Tony Giannetti, Ph.D., Research Scientist II, Roche, Palo Alto

Advances in surface plasmon resonance (SPR) biosensor technique have allowed applications of the technology, such as that implemented with Biacores, to extend beyond the protein-protein applications into studying small molecule/protein interactions. By combining the latest methods in biosensor operation with the standard methodologies of high throughput screening, we have developed a high throughput procedure for hit identification from fragment libraries for entry into lead generation chemistry. Key features are the ability to screen and verify thousands of compounds in a short time, large dynamic range of the assay (100 pM to 5 mM) and the low amounts of protein required to complete a fragment screening campaign (< 0.5 mg protein from assay development through hit validation). Details from assay to design, to how to convince a chemist to work with fragments, will be discussed.

10:50 Break

11:00 Lets Stick Together - Thermodynamic Measures of Fragment Binding

Glyn Williams, Ph.D., Director of Biophysics, Astex Therapeutics

The interaction of a fragment with a protein has a number of thermodynamic consequences. One is a change in the total free energy of the system, which may also be accompanied by a measurable change in enthalpy (heat). Another is a change in the free energy difference between the native conformation(s) of the protein and its unfolded form(s) which is reflected in a change in the temperature at which the protein unfolds. Both can be used to determine or rank the strength of a protein-fragment interaction. The basis of the methods will be outlined and the relative advantages of both, in the context of fragment-based lead discovery and lead optimisation, will be discussed.

11:30 The Heat Is On - Accuracy vs. Speed in ITC and DSC

Ronan O'Brien, Ph.D., Applications Research and Development Manager, MicroCal, LLC

With the latest developments in ITC, the iTC₂₀₀, it is now possible to measure the affinities of even weakly interacting fragments with as little as 5 µg of protein. Binding data for a range of ligands and affinities will be presented to demonstrate the wide applicability of this technology. These instruments will be supported by automation that will allow up to 50 measurements a day making high quality affinity data readily available for FBLD platforms.

ITC is a universally applicable method for the determination of accurate affinities. It also provides complementary information to the structural data which is central to most FBLD campaigns. The technique directly measures the heat of interaction, which is common to all binding processes. This removes the need for immobilization, labelling or specific assay design.

Thermal stability by DSC is also becoming increasingly employed in rapid affinity screening. The advantages and limitations of stability shifting will also be discussed.

12:00 Lunch (Provided)

1:00 The Use of NMR for Hit Detection and Evolution in FBLD

Gregg Siegal, Ph.D., Chief Scientific Officer, ZoBio

Screening fragment libraries requires tools capable of reliably detecting very weak binding of the compounds to the target. NMR has proven itself a powerful analytical tool for this purpose. In this workshop we will review the use of NMR for finding ligands in fragment libraries, including both target and compound based approaches. We will also discuss the advantages and disadvantages of each and assess the requirements that the various methods place on the library. Finally, we will look at the impact of NMR on the hit evolution stage of FBLD evaluating the potential of low resolution structural methods such as chemical shift perturbation guided docking and paramagnetic NMR constraints.

1:50 Fragment Screening Using High-throughput X-ray Crystallography

Robin Rosenfeld, Principal Scientist, ActiveSight

Implementing a Fragment-based lead discovery (FBLD) program using X-ray crystallography as an initial screen has many benefits, including the ability to immediately optimize fragment hits based on structural information. Facile fragment screening using X-ray crystallography has been made possible through advancements in instrumentation and software which allow data to be collected, processed and analyzed quickly, often generating up to 20 structures per day. Methods must also developed to grow, soak, and mount 100+ crystals. At ActiveSight, we have successfully screened several human drug targets and have developed techniques that will be of general use to crystallographers at any level who are interested in starting an X-ray crystallography-based FBLD project.

2:40 Practical design of a fragment library for crystallographic screening

John Badger, Ph.D., Director, Structural Biology, ActiveSight

Both theoretical considerations and practical experience have demonstrated that the chemical space for ligand binding can be covered with ~1000 fragment compounds provided that these molecules are sufficiently small, simple and selected for diversity. Regardless of whether screening library compounds are chosen from an internal collection or obtained from commercial suppliers, the developer of the library must find a practical system for selecting a relatively small number of compounds from a large collection. Beyond the issue of library composition, a practical screening library must also be formatted for use in crystallographic analysis and be supported by convenient access to chemical information. This talk will describe the approaches used to establish fragment screening libraries at ActiveSight and their implementation for practical protein crystallography. Our successful use of these libraries in crystallographic fragment screening projects has been demonstrated by the identification of chemically diverse hits against multiple classes of protein molecule.

3:10 Break

3:20 Fragment Library Creation and Materials Management

Rick Hammar Director, Compound Management Services, ASDI Group of Companies, Michael J. Kates, Ph.D. Director of Custom & High Throughput Chemistry, ASDI Group of Companies,Brian Maduskuie, Director, Customer Service, ASDI Group of Companies

A fragment-based discovery program requires a robust infrastructure to enable successful implementation, productive investigation, and viable results. ASDI will discuss options around fragment library identification, creation, analysis, distribution, and screening. Reference will be made to case studies and proven successful practices supporting increased productivity, lead identification, and cost-saving initiatives.

4:10 "Chemistry on Demand" Approach to Support Fragment Based Lead Discovery

Olga Issakova, Ph.D., Executive Vice President, Nanosyn