8th Annual

Protein-Protein Interactions

Targeting PPIs for Therapeutic Interventions

April 21-22, 2015

Many biologically important processes are regulated by protein complexes. Such protein-protein interactions (PPIs) or protein-DNA interactions were considered ‘undruggable’ until recently. The main driver of recent PPI successes has been biophysical techniques such as surface plasma resonance (SPR) and nuclear magnetic resonance (NMR), sometimes using fragment-based approaches, that have resulted in inhibitors against even difficult PPIs. Computational approaches based on crystal structures of the PPIs being targeted have also accelerated drug design against PPIs. This conference will cover ‘success stories’ highlighting application of biophysical approaches, as well as the challenges that still exist in PPI-targeted drug design: should we inhibit the PPI directly or allosterically? Which interface should be targeted and how much of it? How strongly does the inhibitor need to bind? Join fellow drug discovery scientists for this day-and-a-half meeting that is in the first half of CHI's larger Drug Discovery Chemistry event

The Drug Discovery Chemistry conference offers a compact, dynamic event over
three days that allows the scientific community an excellent opportunity to stay aware of current trends.

Kenneth D., Director, FLAMMA

Tuesday, April 21

7:00 am Registration and Morning Coffee


8:00 Chairperson’s Opening Remarks

Edward R. Zartler, Ph.D., President & CSO, Quantum Tessera Consulting

8:10 Structural and Biophysical Studies of Novel, Potent HDM2-p53 Antagonists

Mark McCoyMark McCoy, Ph.D., Research Fellow, Medicinal Chemistry, Merck

The p53 tumor suppressor is normally ubiquitinated and targeted for degradation. HDM2 is a protein responsible for the ubiquitination of p53. Thus antagonists to the complex are thought to stabilize the presence of p53. This presentation will describe work spanning more than 12 years for finding antagonists of the p53/HDM2 complex. The talk will cover fragment screening, HTS hit validation, assay development, X-ray and NMR structure determination.

8:40 Macrocycles that Modulate the C-Terminus of HSP90: A New Mechanism for Inhibiting Protein Folding

 Shelli McAlpineJeanette McConnell, graduate student (replacement) for Shelli McAlpine, Ph.D., Associate Professor, Chemistry, University of New South Wales

Classic oncogenic heat shock protein 90 (Hsp90) inhibitors target the N-terminus of the protein, triggering a survival mechanism in cancer cells referred to as the heat shock response (HSR). Inhibiting Hsp90 by modulating the C-terminus does not trigger a HSR, making it a highly attractive chemotherapeutic approach. Our compounds are the first to effectively inhibit hsp90’s function, without triggering a cell protection mechanism.

9:10 Assessing Flexibility and Druggability of PPIs Using Molecular Dynamics

Soumya_RaySoumya Ray, Ph.D., Senior Scientist, Applications Science, Schrödinger

Protein-protein interactions (PPIs) are promising drug targets for modulating biological pathways. We present computational approaches for studying and targeting PPI interfaces with small-molecule inhibitors. We first explore PPIs with molecular dynamics and assess druggability of different conformational states; then, we study the thermodynamics of water molecules at PPI interfaces to detect binding hotspots. Finally, we use mixed solvent molecular dynamics to induce druggable pockets in PPIs. These studies show that computational approaches can offer insights into and facilitate inhibitor design for PPIs.

9:40 Coffee Break

10:05 Hit-to-Lead Optimization of Palm Site Binders as Selective Inhibitors of USP7

Chudi Ndubaku, Ph.D., Senior Scientist, Discovery Chemistry, Genentech

Dysregulation of the ubiquitin proteasome system (UPS) has been associated with disease pathogenesis, including several types of cancer. In particular, ubiquitin-specific protease 7 (USP7) has been shown to be a critical regulator of p53. Using fragment-based screening by SPR and NMR, we derived leads that were shown, by X-ray crystallography, to bind to the catalytic domain of USP7 within the Palm region. We will present our lead identification efforts including structural biology information that were crucial for compound optimization.By using computational tools, NMR site-mapping and medicinal chemistry optimization we were able to evolve compounds that bound to an adjacent site, known as the Palm site. These novel Palm site inhibitors have been shown to be quite selective for USP7 over other DUBs, are active in cells and demonstrate expected p53/Mdm2 biology. By using computational tools, NMR site-mapping and medicinal chemistry optimization we were able to evolve compounds that bound to an adjacent site, known as the Palm site. These novel Palm site inhibitors have been shown to be quite selective for USP7 over other DUBs, are active in cells and demonstrate expected p53/Mdm2 biology.  

10:35 Design and Synthesis of a New Generation of Protein-Protein Interaction Inhibitors

RomanKombarovRoman Kombarov, Ph.D., Head, Business Development, Asinex Corporation

Protein-Protein interactions (PPI) have great potential as therapeutic targets but are currently one of the most challenging areas in drug discovery partly due to specific structural features of PPI modulating ligands. This talk will focus on the lessons Asinex has learned and its unique approach to address the problem using a “compound-to-target” strategy, our design of lead like PPI ligands, and lead optimization strategy. We will also briefly introduce a case study in PPI drug discovery.

11:05 The Challenges of Targeting Protein-Protein Interactions in Ras-SOS Using Fragments

Joe PatelJoe Patel, Ph.D., FBLG Specialist, Discovery Sciences, AstraZeneca

Constitutively active mutant KRas displays a reduced rate of GTP hydrolysis via both intrinsic and GTPase activating protein-catalysed mechanisms, and perpetual activation of Ras pathways. A fragment screening campaign using X-ray crystallography led to the discovery of three fragment binding sites on the Ras:SOS complex. Identification of tool compounds binding at each of these sites allowed exploration of new approaches to Ras pathway inhibition by stabilising or covalently modifying the Ras:SOS complex.

11:35 A Systematic Approach for Developing Orthosteric Inhibitors of PPIs: Application to Ras/Sos Inhibitor Design

Paramjit AroraParamjit Arora, Ph.D., Professor, Department of Chemistry, New York University

Proteins often utilize small folded domains for interactions with other proteins.  The basic hypothesis guiding our research is that by mimicking these domains we can modulate the function of a particular protein-protein interaction with metabolically stable synthetic molecules. This presentation will discuss synthetic approaches to develop protein domain mimics as modulators of intracellular protein-protein interactions, with the Ras-Sos interaction as a case study.

12:05 pm Luncheon Presentation: Designing Inhibitors for Protein-Protein Interactions– Challenges and Approaches

Black_PhillipPhillip Black, Ph.D., Senior Scientist, Discovery Services, Charles River

Designing and synthesizing molecules tailored to the biological target or family of interest is key to enhancing hit rates and optimizing early discovery. For over 15 years, BioFocus has met this demand with its ongoing development of SoftFocus® libraries of novel compounds that have aided core area research in kinases, GPCRs and ion channels. Our discussion will highlight our history of success and review our continued strategies to tackle today’s challenging and emerging targets.


1:15 Chairperson’s Remarks

Chudi Ndubaku, Ph.D., Senior Scientist, Discovery Chemistry, Genentech

1:20 Novel Tetra-Ubiquitin Substrates of Different Linkages for more Biologically Relevant Deubiquitinylase Assays utilizing AlphaLISA Technology

Cardillo_DanielDaniel Cardillo, MSc, Application Scientist, Global Discovery Applications, PerkinElmer

Many current DUB assays utilize artificial substrates that don’t mimic well the natural substrates that these proteases act upon in cells. In the strive for better compounds to put forth into the clinic more researchers are turning to developing screening assays that better recapitulate the natural environment of the target molecule. Here we demonstrate novel, more biologically relevant biochemical DUB assays utilizing tetra-ubiquitin substrates of all 8 possible natural linkages and utilizing AlphaLISA® technology.

1:35 Homology Models of the HIV-1 Attachment Inhibitor BMS-626529 Bound to GP120 Suggest a Unique Mechanism of Action

David LangleyDavid Langley, Ph.D., Senior Scientist, Computational Chemistry, Bristol-Myers Squibb Co

BMS-626529 is a HIV-1 attachment inhibitor (AI) in clinical development that is administered as the prodrug BMS-663068. It binds with HIV-1 gp120 and inhibit both CD4-induced and CD4-independent formation of the “open state” four-stranded gp120 bridging sheet, and the subsequent formation and exposure of the chemokine co-receptor binding site. This unique mechanism of action prevents the initial interaction of HIV-1 with the host CD4+ T cell, and subsequent HIV-1 binding and entry. Our proposed binding models clarify the novel mechanism of BMS-626529, supporting its ongoing clinical development.

2:05 Non-Catalytic Site Integrase Inhibitors: Interrogating a PPI Target via Virtual and Fragment Screening

Douglas C. BeshoreDouglas C. Beshore, Ph.D., Project Leader, Exploratory Chemistry, Merck Research Laboratories

The quest for novel mechanisms for the treatment of HIV remains a world-wide public health objective. An emerging mechanism is centered around the disruption of the lens epithelial growth factor (LEDGF/p75)-HIV Integrase (IN) interaction, which has been shown to inhibit viral replication. Targeting this protein-protein interaction with small molecules (LEDGINs) that binds to the LEDGF/p75 binding pocket of IN via virtual and fragment-based strategies will be presented.

2:35 Refreshment Break in the Exhibit Hall with Poster Viewing


3:20 FEATURED PRESENTATION: Site-Directed Ligand Discovery for PPI and Allosteric Enzymes

Michelle ArkinMichelle Arkin, Ph.D., Associate Professor, Pharmaceutical Chemistry, University of California, San Francisco

Protein-protein interactions and allosterically regulated enzymes have been challenging but important targets for probe- and drug discovery, especially in the inflammation field. We and others have found that fragment-based lead discovery can provide chemical starting points and furthermore serve as insightful probes of protein conformation. The Tethering method of fragment discovery links thiol-containing compounds to specific cysteine residues and therefore serves as a site-directed approach to interrogating ‘cryptic’ allosteric sites and protein interfaces.

3:50 FEATURED PRESENTATION: Allosteric Inhibitors of Interleukin-2-inducible T-cell Kinase (ITK)

Ravi G. Kurumbail, Ph.D., Research Fellow and Structural Biology Laboratory Head, Pfizer

Interleukin-2-inducible T-cell kinase (ITK) is a critical mediator of T cell signaling and hence an attractive target for T-cell mediated inflammatory diseases. We have discovered allosteric Type III inhibitors of ITK that also bind to its ATP site. Through classical medicinal chemistry approaches, we have been successful in further optimization of these compounds that leads to selective inhibition of the inactive form of ITK. We will describe how an integrated biophysical technology platform coupled with classical enzymology studies enabled the discovery of allosteric ITK inhibitors.

4:20 Session Break


4:30 Plenary Keynote Introduction

Gregg Siegal, Ph.D., CEO, ZoBio


Chemotype Coverage in Fragment, Phenotypic, & Deorphanization Screens

Brian K. ShoichetBrian K. Shoichet, Ph.D., Professor, Department of Pharmaceutical Chemistry, University of California, San Francisco

The numbing size of chemical space shouldn’t prevent us from asking what screening libraries are missing relative to what we know to be biologically relevant. I explore the impact of chemotype representation on inhibitor discovery, fragment-based screens, whole organism phenotypic screens, and screens to deorphanize enzymes and GPCRs. Each case is framed by rough calculation and illustrated by specific experimental results. The libraries that result differ as much as the goals of the screen, but specific limits and optimization strategies emerge.

5:30 Welcome Reception in the Exhibit Hall with Poster Viewing

6:30 Close of Day

Wednesday, April 22

7:30 am Continental Breakfast Breakout Discussions

In this session, attendees choose a specific roundtable discussion to join. Each group has a moderator to ensure focused conversations around key issues within the topic. The small group format allows participants to informally meet potential collaborators, share examples from their work and discuss ideas with peers. Check our website in February to see the full listing of breakout topics and moderators.

Topic: How/When to Embark on a Covalent Inhibitor Strategy

Moderator: Chudi Ndubaku, Ph.D., Senior Scientist, Discovery Chemistry, Genentech

  • Include as part of the hit identification process?
  • Substrate-based approaches
  • PK considerations
  • Types of targets most or least amenable (ubiquitinated proteins?)

Topic: Using Kinetic and Thermodynamic data to Drive Medicinal Chemistry

Moderator: Edward R. Zartler, Ph.D., President & CSO, Quantum Tessera Consulting

  • Is kinetic and/or thermodynamic data useful for med chem decisions?
  • Entropy or Enthalpy?
  • Different PPI targets
  • Fast on, fast off, does any of it matter if you have rapid clearance?

Topic: Challenges in Targeting PPIs

Moderator: Joe Patel, Ph.D., FBLG Specialist, Discovery Sciences, AstraZeneca

  • Screening methods, biophysics verses biochemical and their pros/cons
  • Lipinski dilemma, how to keep hits lean and mean?
  • Is covalent the right way to gain a foothold?


8:40 Chairperson’s Remarks

Michelle Arkin, Ph.D., Associate Professor, Pharmaceutical Chemistry, University of California, San Francisco

8:45 Development of Small Molecule Inhibitors of Epstein-Barr Virus-Associated Diseases

Troy MessickTroy Messick, Ph.D., Staff Scientist,Virology,TheWistar Institute

EBV is a DNA tumor virus that causes 1-2% of human cancers. Our therapeutic approach targets EBNA1, a multifunctional protein critical for viral replication and genome maintenance. We used a fragment-based approach to develop a small molecule lead series that selectively inhibits the DNA-binding activity of EBNA1, has activity in cell based assays, and provides tumor growth inhibition in xenograft studies. These data establish proof-of-concept for targeting EBNA1—a protein previously thought to be undruggable.

9:15 Targeting the NPM1 and FOXM1 Interaction as a Novel Anticancer Therapy

Andrei GartelAndrei Gartel, Ph.D., Associate Professor, Medicine, University of Illinois, Chicago

Targeting FOXM1, a transcription factor whose gene is one of the most over-expressed in liver cancer, in mono- or combination therapy has shown promising therapeutic benefits in current research. We found, via mass spectrometric analysis, that FOXM1 interacts with the chaperone, nucleophosmin (NPM1), which is ubiquitously expressed in mammalian cells. FOXM1- NPM1 interaction is also required for sustaining the level and localization of FOXM1. We report the first NPM1 peptide that inhibits FOXM1 in cancer cells, paving the way to develop specific FOXM1 inhibitors.


9:45 Coffee Break in the Exhibit Hall with Poster Viewing


10:30 Targeting MCL1 for the Treatment of Cancer

Michael H. Serrano-WuMichael H. Serrano-Wu, Ph.D., Director, Medicinal Chemistry, Center for the Development of Therapeutics, Broad Institute

MCL1 is highly expressed in many tumor types and high expression levels of MCL1 contribute to tumor development and resistance to chemotherapy. Recently we discovered that the top biomarker for MCL1 dependency is the low expression levels of BCL-xL, and high expression levels of BCL-xL predicted resistance to MCL1 modulation. Here, we describe our multi-prong strategy towards discovering selective MCL1 inhibitors which includes direct-binding and cellular assays for complementary molecular approaches to targeting diverse aspects of MCL1 biology.

11:00 Discovery and Structure-Based Optimization of Novel Small Molecule Mcl-1 Inhibitors

Zaneta Nikolovska-ColeskaZaneta Nikolovska-Coleska, Ph.D., Assistant Professor, Pathology, University of Michigan Medical School

This talk presents our HTS identification and subsequent structure-based optimization of inhibitors of the interactions between Mcl1 and pro-apoptotic proteins. With our small-molecule inhibitor, we validated Mcl-1 as a potential therapeutic target for pancreatic cancer (Mol Cancer Ther, 2014) and furthermore demonstrate that Mcl-1 inhibitors can act as radiosensitizers in pancreatic cancer by inducing apoptosis (Translational Oncology, 2015). Furthermore, using model cell lines dependent upon specific anti-apoptotic BCL-2 family members, we have shown the on target effects of our selective Mcl-1 inhibitors.

11:30 Modulators of PUMA: BCL2 Interactions Discovered Using High-Throughput BRET2 and Mammalian-2-Hybrid Assays

Mary Ellen DiganMary Ellen Digan, Ph.D., Senior Research Investigator I, Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Inc.

PUMA is a key initiator of DNA-damage-induced mitochondrial apoptosis which acts by neutralizing all five anti-apoptotic BCL2 family members via protein-protein interactions mediated by its BH3-domain. Inhibitors of PUMA-induced apoptosis have been proposed as treatments for therapy-induced oral and intestinal mucositis in patients with p53-mutated tumors. This presentation, the first oral disclosure of the use of mammalian-two-hybrid assays in high throughput screening mode, describes an entirely cell-based hit prosecution process based on a BRET2 screen. Full-length proteins were used and we maintained their native mitochondrial location and stayed close to their endogenous protein levels.

12:00 pm Close of Track