1. Final Agenda June 19-21, 2013 The Revere Hotel Boston, MACambridge Healthtech Institute and Bio-IT Worlds Thirteenth AnnualStructure-BasedDrug DesignGenome to Drug Leadwith Big Data ApproachKeynote Presentation:Drugging the Undruggable: TransformingNatures -Helix into Breakthrough MedicinesTomi Sawyer, Ph.D., CSO, Aileron Therapeutics Corporate Sponsors: Register by March 22 & save up to $350!Organized by:Cambridge Healthtech Institutehealthtech.com/SBD

2. Structure-BasedDrug DesignDear Colleague,Thank you for your continued interest and supportWho You Will Meetregarding our Structure-Based Drug Design conference.Titles: Lab Head/HeadThe growing protein structure information has given structure-based methods a place of Team Leaderprominence in drug discovery. The current state of in silico technology for effectively using Chief Scientific Officerbiological big data for structure-based drug design is significantly limited by the lack of Directora realistic environment for simulations and an absence of fully integrated infrastructure. Research Scientist/Principal Scientist/Moreover, the emerging deluge of biological data of all kinds available to the field ofScientistbiomedicine and the pharmaceutical industry represents a significant opportunity to Senior Researcher/Researcherfundamentally change the process of disease target discovery and drug design. Graduate Student ProfessorLeveraging ever-increasing computing power and large-scale informatics framework that PostDocintegrate functional, structural and expression information, we face ample opportunities tofine-tune our protein-ligand modeling algorithm and modify the molecule to get the desiredproperties.Departments: BiochemistryIn silico approaches to rational structure-based drug discovery are leveraging big data Bioinformaticstechnology in the identification and optimization of lead compounds and the identification Chemical Biologyand validation of drug targets, followed by the prediction of ligands for the target protein Chemistryfrom molecular modeling computation. Computational Biology Computational ChemistryAt CHIs thirteenth annual Structure-Based Drug Design conference, you will hear about Discovery Chemistrydevelopments in in silico technology, as well as experimental approaches useful for accurately Drug Discoverypredicting and modeling the structures of proteins in structure-based drug design efforts. InformaticsIn addition, examples of successful applications of such technology approaches to Lead Discoverygenome-to-drug lead investigations will be addressed. Medicinal Chemistry Molecular Modeling Scientific ComputingRegister by March 22 at the early rate and save up to $350 off Stuctural Biologyyour conference registration. Structural Chemistry Structural SciencesWarmest regards, Co-Located Event: Eleventh AnnualMing Guo Next-GenConference Director Kinase Inhibitors:Cambridge Healthtech Institute Given both the overwhelming amount of available data Moving Towards a Successful Pipeline and the fact that traditional pharma approaches to innovation seem to have largely run out of steam, a bet June 17-19 on big data analytics might make a lot of sense now. healthtech.com/KIN - David Shaywitz, M.D., Ph.D., Physician, Scientist andBest Value! Register for the Management ConsultantStructure-Based Drug Designand Kinase conferences at aspecial rate.2 healthtech.com/SBD 3. WEDNESDAY, JUNE 19 THURSDAY, JUNE 20 STRUCTURE-BASED DRUG DESIGN FOR KINASE7:30 am Morning Coffee1:15 pm Chairpersons Opening Remarks8:30 Chairpersons Remarks1:20 Structure-Based Design of Potent and Selective inhibitors of PI3-Kinase Delta KEYNOTE PRESENTATION:Jeremy M. Murray, Ph.D., Scientist, Structural Biology, Genentech8:40 Drugging the Undruggable: Transforming Natures -Helix intoInhibition of PI3K is considered to be an attractive mechanism for the treatment ofinflammatory diseases and leukocyte malignancies. Using a structure-based designBreakthrough Medicinesapproach, we have identified a series of potent and selective inhibitors of PI3K.Tomi Sawyer, Ph.D., CSO, Aileron TherapeuticsThese inhibitors do not occupy the induced selectivity pocket between Trp760 and A major challenge of drug discovery has been to successfullyMet752 that is observed for other families of selective PI3K inhibitors. Instead, modulate the biological properties of those therapeutic targetsthe selectivity of the compounds for inhibition of PI3K relative to other PI3Kdeemed undruggable as defined relative to small-molecules.isoforms appears to be due primarily to the strong interactions these inhibitors However, recent advancements leveraging peptides and macrocycles areare able to make with Trp760 in the PI3K binding pocket. This talk will discuss expanding such drug space, especially for many intracellular proteinproteinthe structural understanding of the selectivity of these inhibitors against otherinteraction targets deemed hot drug-wise. Structural biology and computationalisoforms, pharmacokinetic properties and the ability of select compounds to inhibitchemistry are key tools for such drug discovery. As a case study, advancementsthe function of B-cells in vivo. in stapled peptide technology to transform Natures -helix into breakthrough medicines will be presented.1:50 MD Simulations of Mutant and WT PI3K: Insights into the Mechanismof Overactivation and Implications for Drug Design 9:10 A Beacon in the Dark: Structural Information in the Absence of StructureZoe Cournia, Ph.D., Investigator, Biomedical Research Foundation, Academy of Athens Edward R. Zartler, President and CSO, Quantum Tessera Consulting, LLC The current (and next) generation of drug targets are very difficultPI 3 kinase alpha (PI3K) is one of the most frequently mutated proteins in human to ligand: membrane proteins, multimeric protein complexes,cancers. Molecular dynamics simulations in aqueous solution performed for wild post-translationally modified proteins, protein-protein interactions.type (WT) and H1047R mutant PI3K proteins, revealed different dynamical and Advances in structural biology have been made where we can obtainstructural features for the two proteins, which may lead to kinase overactivation in high resolution structural information for many of these targets. However, for athe mutant variant. Binding site prediction and virtual screening further facilitated large swath of the current, and next-gen targets, we are simply working in thethe development of novel mutant-specific PI3K inhibitors that exploit the altered structural dark. Recent advances in NMR-based methods, coupled with novel ideasconformation of the mutant with respect to the WT protein. in fragment-based hit generation, can now shine a light into this darkness, yielding crucial structural details to allow ligands to be rationally designed. We will discuss2:20 Sponsored Presentation (Opportunity Available)these advances and their application to drug discovery.2:50 Refreshment Break in the Exhibit Hall with Poster Viewing FORCE FIELD CALCULATION DRUG RESISTANCE 9:40 Docking: Is It Possible to Know When It Works? Greg Warren, Ph.D., Senior Applications Scientist,3:30 Sponsored Presentation (Opportunity Available) OpenEye Scientific Software, Inc. It is commonly held that the same, protein-centric approach, can be used4:00 Towards a New Generation of Animicrobial Antifolatessuccessfully both to predict the bound conformation of a ligand in complex with a Dennis L. Wright, Ph.D., Professor of Pharmaceutical Sciences and given protein (pose prediction) and to rank molecules based on their probability of Chemistry, University of Connecticutbeing a binder to that protein (structure-based virtual screening). We will present We are using a structure-based design approach to develop potenttools in the OEDocking Suite that approach these two problems as issues of a and selective inhibitors of the enzyme dihydrofolate reductase (DHFR) rather different nature. Successful results in virtual screening using the rigid protein from a variety of pathogenic organisms. Analysis of crystal structuresapproximation in docking will be presented along with a flexible, ligand-centricof trimethoprim-resistant and naturally-insensitive enzymes led to the design of a approach to pose prediction that is much more reliable than traditional protein-series of propargyl-linked antifolates characterized by high potency, good selectivity centric posing tools. We also show that whether the problem is pose prediction orover the human form of the enzyme and good anti-microbial activity.virtual screening, combining ligand and protein information in the same calculation produces better results.4:30 Understanding Drug Mechanism of Action by Target Gene Overexpression Adam C. Palmer, Ph.D., Postdoctoral Fellow, Department of Systems 10:10 Coffee Break in the Exhibit Hall with Poster Viewing Biology, Harvard Medical School The molecular targets of drugs can sometimes, but not always, 10:40 Incorporating Ligand Polarisation in Binding Free Energy Calculations be identified amongst genes that confer drug resistance whenJonathan W. Essex, Ph.D., Professor, Head, Computational Systems overexpressed. We quantitatively overexpressed genes encoding Chemistry, Chairman, Institute for Complex Systems Simulation (ICSS),known antibiotic targets and observed that drug resistance does not only increase; School of Chemistry, University of Southamptonit can remain unchanged, decrease, or even have a non-monotonic dependence on While the methods underpinning the calculation of protein-ligandtarget expression. These diverse effects are explained by simple models considering binding free energies are well understood, accurate calculations aregene toxicity and drug-induction of harmful target-catalyzed reactions. The relation still fundamentally limited by inadequate sampling of the protein-ligand complex,between drug resistance and target expression may reveal unexpectedly complexand inaccurate modeling of the associated intermolecular interactions. To addressmechanisms of drug action. the second issue, we have developed a simple and computationally inexpensive correction to the calculated free energies based on a hybrid quantum mechanics/5:00 Close of the Daymolecular mechanics approach. In this presentation, the method will be described and its performance assessed in the calculation of small and drug-like molecules free energies of hydration, and on the calculation of protein-ligand binding affinities Dinner Short Course (June 19, 6:00-8:00 pm)*in neuraminidase, CDK2 and COX2. Structure-Based Drug Design for Epigenetic Targets Johnathan R. Whetstine, Ph.D., Assistant Professor of Medicine, Harvard Medical School Philip Fallon, Ph.D., Senior Medicinal Chemist, Domainex Ltd.*Separate registration required.healthtech.com/SBD 3 4. 11:10 Site Identification by Ligand Competitive Saturation (SILCS): Structure- a significant portion of the total binding energy, and thus represent opportunities Based Free Energy Computational Approach for Ligand Discovery for ligand design. Computing desolvation energetics typically requires lengthy simulations, but this talk presents a fast and easy-to-use method (3D-RISM) which and Optimizationcomputes desolvation energies in minutes, without using explicit simulations. Alexander D. MacKerell, Jr., Ph.D., Grollman-Glick Professor of Application to ligand optimization is demonstrated using case studies. Pharmaceutical Sciences, Director, Computer-Aided Drug Design Center,School of Pharmacy, University of Maryland 3:10 Refreshment Break in the Exhibit Hall with Poster ViewingThe Site Identification by Ligand Competitive Saturation (SILCS) method usesexplicit solvent all-atom molecular dynamics simulations to identify binding sites 3:40 Characterizing and Exploiting the Solvation of Protein Surfaces foron proteins for functional group classes based on rigorous free energy criteria thatincludes protein flexibility and fragment desolvation. Information from the SILCSApplications in Drug Design and Discoveryapproach, termed FragMaps, may be used for the identification of novel ligands Tom Kurtzman Young, Ph.D., Assistant Professor, Department of Chemistry, Lehmantargeting protein, including de novo ligand design. In addition, the SILCS methodCollege, CUNYmay be combined with structural information on a ligand-protein complex to The displacement of water from a binding site by a ligand is a principal, and oftenfacilitate modification of the ligand to improve its binding affinity. dominant, source of binding free energy. In recent years, a number of techniques based on Inhomogeneous Solvation Theory have been developed that map out the11:40 Blurring to Bring Binding Free Energies into Focus solvation thermodynamics of protein binding sites (STOW, WaterMap, GIST). We outline the physical basis of these mapping techniques and present some possibleKenneth M. Merz, Jr., University of Florida Research Foundation Professor, applications in drug discovery and design.Edmund H. Prominski Professor of Chemistry, Department of Chemistry,Quantum Theory Project, University of Florida4:10 Mapping Protein Surfaces with MixMD to Identify New Binding SitesDocking calculations coupled with binding free energy estimates(scoring) are a mainstay of structure-based drug design. This talkHeather Carlson, Professor, Medicinal Chemistry, University of Michiganaddresses how to use ensemble principles to estimate and reduce uncertainty of Mixed-solvent molecular dynamics (MixMD) is an emerging technique incomputed binding free energies. We have developed methods to evaluate potentialstructure-based drug design (SBDD). The most significant benefits are thefunction error and in this talk we will demonstrate how to use this knowledge to ability of a protein to adapt in the presence of a probe and the identificationimprove the outcome of a docking and scoring exercise. This was accomplished via of binding sites where organic molecules specifically out-compete water.the development of novel scoring approaches that employ statistical mechanical Rather than ignoring the complicated role of water as most SBDD methods do, it is trulyprinciples and are coupled with error propagation. Importantly, our approach yieldsembraced in MixMD. Blinded, experimental validation of the method will be presented.free energies as well as estimates of the random and systematic errors in thesequantities, providing insight into the reliability of the computed free energies.4:40 The Potency-Insolubility Conundrum in Drug Discovery: Mechanism andSolution for Hepatitis C Inhibitors12:10 pm Luncheon Presentation (Opportunity Available)Patrick R. Connelly, Ph.D., Principal Scientific Fellow, Vertexor Lunch on Your OwnPharmaceuticals, Inc. As compounds are optimized for greater potency duringGPCR pharmaceutical discovery, their aqueous solubility often decreases, making them less viable as orally-administered drugs. The potency-insolubility1:30 Chairpersons Remarks conundrum has prompted speculation, concern, and attempts to taxonomize the problem or overcome it technologically. However, a fundamental molecular connection between binding potency and aqueous insolubility has yet to be1:40 An Automated Pipeline for the Modeling and Simulation of GPCRs: elucidated. By examination of the structural and thermodynamic properties Applications to Structure-Based Drug Design of telaprevir, a sparingly soluble inhibitor of the NS3 protease of the Hepatitis Hugo Gutierrez-de-Teran, Ph.D., Parga Pondal Research Fellow, C virus, it is revealed that potency and insolubility share a common origin. A Bioinformatics, Public Galician Foundation of Genomic Medicinedesign strategy based on supramolecular graph set considerations provides a The recent advances in membrane protein crystallography havegeneralizable solution to the conundrum. provided extremely valuable structural information of the superfamilyof G-protein-coupled receptors (GPCRs). Recently, we have developed GPCR-5:10 Welcome Reception in the Exhibit Hall with Poster ViewingModSim (http://gpcr.usc.es), a web-based, automated pipeline to generate high-quality 3D models of the remaining GPCRs and to perform molecular dynamics(MD) simulations with an explicit representation of the cellular membrane, 6:30 End of Daystructural water, cholesterol or lipid molecules. With this computational tool,research groups without prior experience in computational chemistry can set up FRIDAY, JUNE 21ambitious projects on SBDD in GPCRs in a systematic and comprehensive way. 7:30 am Breakfast Roundtable Discussions2:10 How Drugs Bind and Control Their Targets: Characterizing GPCR Signaling through Long-Timescale Simulation FRAGMENT-BASED DRUG DESIGN Ron O. Dror, Senior Research Scientist, D. E. Shaw ResearchOne-third of drugs act by binding to G proteincoupled receptors 8:30 Chairpersons Remarks(GPCRs) and either triggering or preventing receptor activation, but theprocess by which they do so has proven difficult to characterize either8:40 Case Histories of Recent Fragment-Based Drug Discovery Projectsexperimentally or computationally. Anton, a special-purpose machine that wedesigned to accelerate molecular dynamics simulations by orders of magnitude, Christopher W. Murray, Ph.D., Vice President, Discovery Technology, Astexhas enabled simulations in which drugs spontaneously associate with GPCRs Pharmaceuticalsto achieve bound conformations that match crystal structures almost perfectly. Here we describe some case histories of applying fragment-basedAnton simulations have also captured transitions of a GPCR between its active anddrug discovery to challenging drug targets. This will include the designinactive states, allowing us to characterize the mechanism of receptor activation. of protein-protein interaction inhibitors of IAP family proteins and theOur results suggest opportunities for the design of drugs that achieve greater design of allosteric inhibitors of full-length NS3 proteins from the Hepatitis C Virus.specificity and control receptor signaling more precisely. The presentation will discuss the difficulties associated with applying fragment- based drug discovery to challenging target classes and will discuss ways in which these can be mitigated.WATER & SOLVATION IN DRUG DESIGN2:40 Exploiting Solvent Effects in Drug Design and OptimizationSponsored by 9:10 Computational Protein Mapping to Drive the Development of FragmentChris Williams, Ph.D., Principal Scientist, Chemical Computing Group Hits into LeadsUpon ligand binding, solvent molecules around the binding pocket Sandor Vajda, Ph.D., Professor of Biomedical Engineering and Chemistry, Director,and the ligand become displaced or rearranged. These desolvation energies can be Biomolecular Engineering Research Center, Boston University healthtech.com/SBD 4 5. Fragment-based drug design (FBDD) starts with finding fragment-sized compoundsA promising way to interfere with biological processes is through the control ofthat are highly ligand efficient and can serve as a core moiety for developingprotein-protein interactions by means of small molecules. Recent advances in thehigh-affinity leads. Although the core-bound structure of a protein facilitates the understanding of the energetics and dynamics of protein-binding interfaces openconstruction of leads, effective design is far from straightforward. We show that up a way to apply rational design approaches for finding protein-protein interactionprotein mapping, a computational method developed to find binding hot spots,modulators (PPIM). Here, we successfully identify small-molecule inhibitors of theprovides information that complements the fragment screening results and candimer to tetramer transition of the NHR2 domain within the RUNX1/ETO fusiondrive the evolution of core fragments into larger leads with a minimal loss or, inprotein, a novel target for the treatment of acute myeloid leukemia.some cases, even a gain in ligand efficiency.2:30 Structure-Based Guided Development of Focused Chemical Library9:40 Determination of Binding Poses, Kinetics and Energetics in Fragment- Dedicated to Orthosteric Modulation of Protein-Protein Interactions Based Design Xavier Morelli, Ph.D., Group Leader, Cancer Research Center of Marseille, Gianni De Fabritiis, Ph.D., Computational Biophysics Laboratory (GRIB- CNRS IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park This talk will address some challenging issues: biological and (PRBB)chemical spaces of PPI with known orthosteric inhibitors, ligandability assessment of protein-protein interactions, design and validation ofchemical libraries dedicated to PPIs.10:10 Coffee Break in the Exhibit Hall with Poster Viewing3:00 Refreshment Break10:40 The Tip of the Iceberg and the Chemical Universe: Fuzzy Hit FindingUnder Synthetic Feasibility ConditionsEPIGENETIC TARGETINGCarsten Detering, Ph.D., CEO, BioSolveIT, Inc.We have come up with a method that addresses the problem of3:15 Design and Develop Bromodomain Inhibitor for Cancer Therapycrowded patent space. It captures existing available chemistry in aJun Qi, Ph.D., Senior Research Scientist, Medical Oncology, Dana-Farbercompany and thus allows the researcher to fuzzily search in a larger Cancer Instituteportion of the chemical universe available to him/her. Results are returned withIn cancer, epigenetic proteins are promising and intensely studiedtheir underlying chemical synthesis, which renders retro-synthesis unnecessary. targets for therapeutic drug discovery. Among the chromatin-Time saved can be invested in other Medicinal Chemistry efforts. The talk willmodifying enzymes, so-called epigenetic writers readers and ,highlight the method as well as several application examples. erasers chromatin-binding modules or epigenetic readers have received ,comparatively little attention perhaps owing to perceptions regarding the difficultyof targeting protein-protein interactions. Motivated by this challenge, we have11:10 Advances in Predicting Protein-Protein BindingSponsored bydeveloped first-in-class, drug-like inhibitors of bromodomain and extraterminal Affinity and Protein Stability domain epigenetic readers (BETs) for mechanistic study and therapeutic Woody Sherman, Ph.D., Vice President, Applications application in cancer. We are continuously integrating the transcriptional Science, Schrodinger, Inc. consequences of BETi with changes in the epigenomic landscapes of cancer cellsto elucidate the mechanisms underlying response to BETi using chemical andgenetic perturbations.11:40 Sponsored Presentation (Opportunity Available)3:45 The Impact of Structural Data on Epigenetic Probe Discovery for the12:10 pm Luncheon Presentation (Opportunity Available)Public Domainor Lunch on Your Own Dafydd Owen, Ph.D., Associate Research Fellow, Biotherapeutics Worldwide R&D, Pfizer Worldwide Medicinal Chemistry PROTEIN-PROTEIN INTERACTIONResearch into the role of epigenetics in disease could be significantlyaccelerated if cell-active chemical probes for such targets were1:25 Chairpersons Remarksavailable to the research community, through a collaborative, open-innovation model. Pfizer is a member of a public-private partnership led by the1:30 How Does a Small-Molecule Inhibitor Bind at the Protein-ProteinStructural Genomics Consortium (SGC) to help identify a suite of high-qualitychemical probes for epigenetic targets. This partnership is unique in that it bringsInterface of Interleukin 2? the medicinal chemistry expertise within industry together with biological expertiseYibing Shan, Senior Scientist, DE Shaw Research in academia to drive basic research in an emerging area of important biology ofpotential relevance to many diseases. The impact of structural biology on probediscovery will be presented.2:00 From Determinants of RUNX1/ETO Tetramerization to Small-Molecule 4:15Closing Remarks Protein-Protein Interaction Inhibitors Targeting Acute Myeloid Leukemia 4:30End of Conference Holger Gohlke, Ph. D., Professor, Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, DsseldorfSponsoring Society: Media Partners:Media Sponsor:5 healthtech.com/SBD 6. Sponsorship & ExhibitCHI offers comprehensive sponsorship packages which include presentationopportunities, exhibit space and branding, as well as the use of the pre- andpost-show delegate list. Sponsorship allows you to achieve your objectives Informationbefore, during, and long after the event. Any sponsorship can be customizedto meet your companys needs and budget. 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Cambridge Healthtech Institute and Bio-IT Worlds Thirteenth AnnualJune 19-21, 2013Structure-BasedThe Revere HotelBoston, MADrug DesignPricing and Registration InformationReceive a FREE eNewsletter by signing upDINNER SHORT COURSE at chimediagroup.com Academic, Government,June 19 6:00pm-8:00pm Commercial Hospital-affiliatedThe latest industry news, commentaryand highlights from Bio-IT WorldStructure-Based Drug Design for Epigenetic Targets$495 $295 Innovative management in clinical trialsConference Pricing(Excludes short course)A series of diverse reports designed toEarly Registration until March 22, 2013 $1745$845 keep life science professionals informedof the salient trends in pharmaceuticalAdvance Registration until May 10, 2013 $1895$925 technology, business, clinical development,and therapeutic disease markets.Registrations after May 10, 2013, and on-site $2095 $995 For a detailed list of reports, visitInsightPharmaReports.com, or contactRose LaRaia, rlaraia@healthtech.com,+1-781-972-5444.Special Package Pricing(Includes access to Structure-Based Drug Design & Next-Gen Kinase Inhibitors, excludes short course) Barnett is a recognized leader in clinicalEarly Registration until March 22, 2013 $2995$1495 education, training, and reference guides for life science professionals involved inAdvance Registration until May 10, 2013 $3145$1565 the drug development process. 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