Short Courses - 2023 Archive

2023 ARCHIVES

2023 Dinner Short Courses* (In-Person Only)

Short courses at Drug Discovery Chemistry are designed to be instructional, interactive, and provide in-depth information on a specific topic with opportunities for Q&A throughout. The courses include introductions for those new to the fields and those looking to learn more, as well as explanations on more technical aspects than time allows during our main conference presentations. Instructors are drawn from industry and academics alike, and many are recognized authorities in the fields or have teaching experience.

Dinner short courses will take place on Monday evening, April 10 and Wednesday evening, April 12 and be offered IN-PERSON ONLY.

*Premium Pricing or separate registration required

Monday, April 10, 2023 6:00 - 8:30 pm

SC1: Protein Degraders: A Focus on PROTACs from a Beyond Rule of Five Space Perspective

Detailed Agenda

This course focuses on proteolysis targeting chimeras (PROTACs) and will cover topics relevant to developing them as oral therapeutics. Topics to be covered in this first part of the course will include their physicochemical properties and how these influence solubility and permeability and assays to determine polarity. We will also examine some aspects of transporters and how drug-PROTAC interactions may arise.

John Erve, PhD, President, Jerve Scientific Consulting

Instructor:

John Erve, PhD, President, Jerve Scientific Consulting

Topics to be Covered:

Comparison of Rule of 5 and Beyond Rule of 5 space
Importance of intramolecular hydrogen bonds for solubility and permeability
Determining chameleonicity and its importance for PROTACs
Transporters and potential drug-drug interactions (DDIs)

Who Should Attend:

Scientists in the field of proteolysis targeting chimeras (PROTACs) who would like to deepen their understanding of these molecules and the physicochemical attributes that may contribute to their success as oral drugs. ADME scientists and medicinal chemists wishing to understand PROTACs from a drug safety and metabolism perspective. Graduate students and academic scientists interested in learning more about this rapidly developing new drug modality.

SC2: Fragment-Based Drug Design: Advancing Tools and Technologies

Detailed Agenda

This course aims to introduce the fundamentals of Fragment-Based Lead Discovery (FBLD) to attendees. The first section will focus on the concepts of using fragments for hit generation. Special emphasis will be placed on practical pitfalls and the many ways to advance fragments to leads and drugs. The second part of the course will discuss the variety of fragment screening methods and when they are best applied. The composition of fragment libraries will also be discussed in detail. The attendees should come away from this course with a solid understanding of what FBLD is and how to apply it.

Ben J. Davis, PhD, Research Fellow, Biology, Vernalis R&D Ltd.

Daniel A. Erlanson, PhD, Senior Vice President, Innovation and Discovery, Frontier Medicines Corporation

Instructors:

Ben J. Davis, PhD, Research Fellow, Biology, Vernalis R&D Ltd.

Daniel A. Erlanson, PhD, Senior Vice President, Innovation and Discovery, Frontier Medicines Corporation

Topics to be Covered:

Pros and cons of fragment-based approaches
What makes a good fragment; properties of a good fragment library
Finding, validating, and characterizing low-affinity ligands
The importance of using orthogonal screening methods
What to do with a fragment – growing, linking, and more

INSTRUCTOR BIOGRAPHIES:

Ben J. Davis, PhD, Research Fellow, Biology, Vernalis R&D Ltd.

Dr. Ben Davis is a Research Fellow at Vernalis Research, a biotech company based in Cambridge UK which has been at the forefront of fragment-based approaches since 1998. An NMR spectroscopist and biophysicist by training, his current research focus is the development of biophysics and FBLD methods for challenging therapeutic targets and systems. Dr Davis studied for his PhD in protein folding and molecular interactions with Professor Alan Fersht at Cambridge University, and then studied the interactions of small molecules with proteins and RNA. He has over 20 years’ experience in the drug discovery industry. He has contributed to seven books over the last decade and is an author on more than forty scientific publications. He is a frequent speaker at scientific conferences and has been running FBLD training workshops since 2007.

Daniel A. Erlanson, PhD, Senior Vice President, Innovation and Discovery, Frontier Medicines Corporation

Dr. Daniel A. Erlanson is the VP of Chemistry for Frontier Medicines, which is using covalent fragments, machine learning, and chemoproteomics to target proteins often thought undruggable. Prior to Frontier he co-founded Carmot Therapeutics, where he contributed to two clinical-stage molecules. Before Carmot, Dr. Erlanson spent a decade developing fragment-based discovery technologies and leading medicinal chemistry projects at Sunesis Pharmaceuticals. Dr. Erlanson was an NIH postdoctoral fellow with James A. Wells at Genentech, earned his PhD in chemistry from Harvard University in the laboratory of Gregory L. Verdine, and his BA in chemistry from Carleton College. He has co-edited two books on fragment-based drug discovery and is an inventor on more than a dozen issued patents and an author of more than forty scientific publications. He also runs a blog devoted to fragment-based drug discovery, Practical Fragments (http://practicalfragments.blogspot.com/).

SC3: Chemical Biology for Phenotypic Screening and Target Deconvolution

Detailed Agenda

This course is designed to provide an overview and best practices in the use of chemical biology probes and assays that have been developed for applications in early drug discovery. Chemists and biologists working in lead generation, assay development, phenotypic screening, target discovery and deconvolution, target engagement and mechanism-of-action (MoA) studies will all benefit from attending this course. The instructors will share their knowledge and expertise around the use of various technologies and chemistries and there will be time for open discussion and exchange of ideas.

Paul Brennan, PhD, Professor, Nuffield Department of Medicine, University of Oxford

Brent Martin, PhD, Vice President, Chemical Biology, Scorpion Therapeutics

Andrew Zhang, PhD, Director, Chemical Biology, AstraZeneca

Instructors:

Paul Brennan, PhD, Professor, Nuffield Department of Medicine, University of Oxford

Brent Martin, PhD, Vice President, Chemical Biology, Scorpion Therapeutics

Andrew Zhang, PhD, Director, Chemical Biology, AstraZeneca

INSTRUCTOR BIOGRAPHIES:

Paul Brennan, PhD, Professor, Nuffield Department of Medicine, University of Oxford

Paul Brennan received his PhD in organic chemistry from UC Berkeley. Following post-doctoral research at Cambridge University, Paul spent eight years working in the pharmaceutical industry at Amgen and Pfizer. In 2011, Paul joined the Structural Genomics Consortium at the University of Oxford. Over the course of his career, Paul has worked on most major drug classes of drug targets: kinases, GPCRs, ion-channels, metabolic enzymes, and epigenetic proteins. Paul is currently Professor of Medicinal Chemistry and CSO of the Alzheimer’s Research UK Oxford Drug Discovery Institute in the Centre for Medicines Discovery at the University of Oxford. His research is focused on finding new treatments for dementia.

Brent Martin, PhD, Vice President, Chemical Biology, Scorpion Therapeutics

Brent Martin received his Ph.D. in Pharmacology at the University of California in San Diego developing new chemical strategies for correlated fluorescence and electron microscopy. He then carried out postdoctoral studies at the Scripps Research Institute developing new strategies for activity-based profiling, high-throughput screening, and chemical proteomics. As faculty member at the University of Michigan in Ann Arbor, he continued expanding the scope of activity-based profiling methods, while also establishing new bioconjugation reactions to detect and profile protein lipidation, redox modifications, and cysteine occupancy. Brent is the recipient of the NCI Howard Temin K99/R00 award in Cancer Research, the NIH Director’s New Innovator Award, and the NIGMS MIRA Established Investigator Award. He then moved to industry to lead the Chemical Biology at Janssen and is currently Vice President and Head of Chemical Biology at Scorpion Therapeutics.

Andrew Zhang, PhD, Director, Chemical Biology, AstraZeneca

Andrew Zhang is a Team Leader in the Chemical Biology Department at AstraZeneca. He joined AstraZeneca in 2013 with research interests in target deconvolution, particularly using chemical proteomics and orthogonal methods for identifying target engagement events and profiling selectivity. He is now leading the proteomics efforts around profiling the selectivity and mechanism of small molecule protein degraders. Andrew trained at the interface of chemistry and molecular and cell biology, obtaining a B.S. in Chemistry and a B.A. in Molecular and Cell Biology from the University of California, Berkeley, followed by Ph.D. studies with Professor David Spiegel at Yale University around small molecule immunomodulators. Prior to joining AstraZeneca, Andrew carried out postdoctoral trainings with the Drug Discovery Group at the Ontario Institute for Cancer Research (Toronto, Canada) with Dr. Rima Al-awar.

SC4: Generative and Predictive AI Modeling for Protein Inhibitors and Degraders

Detailed Agenda

Drug discovery has always been experimenting with new approaches to find novel molecules with desirable properties. Currently, we are witnessing three approaches in the spotlight. The first one is a new set of AI techniques for designing and predicting in silico molecules. The next trend is exploring the massive search space of biomolecules and designing peptides with desirable properties. The third trend is the emergence of a new therapeutic modality itself. That is, instead of designing traditional inhibitors, now we can dream about designing molecular glues and PROTACs as target degraders. With these recent developments, this course will cover various AI techniques applied in generative and predictive models for small molecule inhibitors and peptide design. We hope this course will shed light on AI driven molecular design and how that can be applied for PROTACs degrader design.

Petrina Kamya, PhD, Head of AI Platforms and President of Insilico Medicine, Canada

Parthiban Srinivasan, PhD, Professor, Data Science and Engineering, Indian Institute of Science Education and Research

Instructors:

Petrina Kamya, PhD, Head of AI Platforms and President of Insilico Medicine, Canada

Parthiban Srinivasan, PhD, Professor, Data Science and Engineering, Indian Institute of Science Education and Research

Topics to be covered:

Small molecule inhibitors and degraders as target modulators
AI methods for generating small molecules
Chemical space exploration and exploitation
Deep learning based predictive models
Inhibitors and degraders design using these AI techniques

Who Should Attend:

Attendance is recommended for drug discovery researchers wishing to understand the current state of AI in drug discovery. This will enable them to what to expect from AI in their organization. Also this course is recommended for graduate students and academic scientists interested in learning more about this rapidly developing new drug modality and how AI could be leveraged.

Wednesday, April 12, 2023 6:15 - 8:45 pm

SC5: Protein Degraders: A Focus on PROTACs from an ADME-Tox Perspective

Detailed Agenda

This course focuses on proteolysis targeting chimeras (PROTACs) and will cover topics relevant to developing them as oral therapeutics. Topics to be covered in this second part of the course will include an examination of the assays used to determine ADME properties and the challenges that PROTACs pose. We will also look at the metabolism of PROTACs including how the linker affects stability and pharmacokinetics. The unique mechanism of action of PROTACs gives rise to some drug safety issues not seen in small molecules, which will be discussed. Finally, we will explore the possible relevance of circadian rhythm to protein degradation and PROTACs.

John Erve, PhD, President, Jerve Scientific Consulting

Matthew Hoffmann, PhD, Senior Director, Drug Metabolism & Pharmacokinetics, Bristol Myers Squibb Co.

Instructors:

John Erve, PhD, President, Jerve Scientific Consulting

Matthew Hoffmann, PhD, Senior Director, Drug Metabolism & Pharmacokinetics, Bristol Myers Squibb Co.

Topics to be Covered:

Measuring ADME properties in vitro and in vivo and specific challenges
Metabolism of PROTACs and influence of linker length on stability
Case study of optimizing a PROTAC
Safety issues unique to PROTACs
Circadian rhythm considerations

Who Should Attend:

Scientists in the field of proteolysis targeting chimeras (PROTACs) who would like to deepen their understanding of these molecules and the physicochemical attributes that may contribute to their success as oral drugs. ADME scientists and medicinal chemists wishing to understand PROTACS from a drug safety and metabolism perspective. Graduate students and academic scientists interested in learning more about this rapidly developing new drug modality.

SC6: Principles of Drug Design: Ligand-Receptor Interactions and More

Detailed Agenda

This course provides an overview of protein-ligand interactions and drug design principles. The presentation is targeted to medicinal chemists. The course starts by covering hydrophobic, H-bonding and electrostatic interactions. Then the course moves into coverage of specialized topics such as conformation analysis, pi-stack, cation-pi, halogen bonding, protein-protein interface, and covalent inhibition. Medicinal chemistry case studies are incorporated.

Maricel Torrent, PhD, Principal Research Scientist, Computational Drug Discovery, AbbVie, Inc.

Instructor:

Maricel Torrent, PhD, Principal Research Scientist, Computational Drug Discovery, AbbVie, Inc.

Topics to be Covered:

Medicinal chemistry and structure-based drug design principles
Interpretation of atomic-level protein X-ray and modeled structures of binding mode
Understanding the relative amounts of potency gain from different types of interactions
Case studies to illustrate all the design strategies

SC7: DNA-Encoded Libraries

Detailed Agenda

This course provides an overview of DNA-Encoded Library (DEL) screening platforms, discusses common selection strategies for identifying novel hits from DEL campaigns and delves into parameters for building a library collection. The instructors will also cover strategic considerations in using DEL selection data to accelerate hit-to-lead steps in drug discovery.

Svetlana Belyanskaya, PhD, Vice President, Biology, Anagenex

Ghotas Evindar, PhD, Senior Vice President, Head of Drug Discovery, 1859, Inc.

Instructors:

Svetlana Belyanskaya, PhD, Vice President, Biology, Anagenex

Ghotas Evindar, PhD, Senior Vice President, Head of Drug Discovery, 1859, Inc.

Topics to be Covered:

Introduction to DNA-encoded libraries
Pros and cons of using DNA-encoded chemical libraries
Structure of the DNA coding region and how it has evolved over a period of time
Affinity-based selection strategy and how this could guide hit picking
Data analysis and the decision-making logic in hit confirmation
Introduction to one-bead, one-compound (OBOC) DNA-encoded libraries
Additional benefits of the new platform

INSTRUCTOR BIOGRAPHIES:

Svetlana Belyanskaya, PhD, Vice President, Biology, Anagenex

Dr. Belyanskaya is accomplished scientific leader in the field of small molecule drug discovery and an expert in DNA encoded library platform. She was involved in the development of DEL platform for 20 years. Svetlana has made significant contributions to the design and development of the DEL technology at Praecis Pharmaceuticals and, later, at GlaxoSmithKline. She was instrumental in discovering first DEL-sourced molecule to progress into clinical trials, a potent and selective inhibitor for enzyme soluble epoxide hydrolase (hsEH). At GSK, Svetlana successfully led team of scientists on multiple scientific programs. Svetlana has deep expertise in biochemistry, molecular biology, cell biology and very passionate about future development of DEL technology with goal to find novel quality leads that bring value for the treatment of diseases with unmet medical needs

Ghotas Evindar, PhD, Senior Vice President, Head of Drug Discovery, 1859, Inc.

Before recently joining 1859 Inc, Ghotas was VP and head of drug discovery at Exo Therapeutics in Watertown, MA. He has authored well over 50 publications and patents in the area of drug discovery and is committed to education surrounding DNA-encoded library (DEL) technology, leading a number of DEL roundtable discussions and courses over the last several years. He was born and raised in the Kurdish mountains before migrating to Canada. He completed his undergraduate and MSc degrees at the University of Waterloo, concentrating on synthesis and structure-activity studies of aureobasidins. He then joined Vertex Pharmaceuticals, in Cambridge, as a medicinal chemist. While at Vertex, he was instrumental in the success of P38 MAP Kinase (first and second generation), ICE-1 inhibitors (second generation), and early ZAP-70 programs. After four years at Vertex, and four clinical candidates, he moved to the University of Toronto to pursue a PhD degree in organic chemistry with focus on “Novel Approaches to Synthesis of Nitrogen Containing Heterocycles”. After completing his PhD with Dr. Robert Batey, he moved back to the Boston area to join Praecis Pharmaceuticals as a staff scientist. There he led the medicinal chemistry sphingosine-1-phosphate (S1P) receptor agonist discovery program and contributed to the inception of the novel DEL platform. Praecis was acquired by GlaxoSmithKline in 2007 and Ghotas began a 12-year journey with DNA-encoded library technology (ELT) platforms, including portfolio, library and selection design, data analysis, Hit ID, and H2L medicinal chemistry. In early 2019, Ghotas moved to Exo Therapeutics where he continues his adventures in small molecule drug discovery.

SC8: Biophysical Tools for Membrane Proteins: Drug Discovery Applications

Detailed Agenda

This course will cover NMR screening methods for membrane proteins, especially GPCRs; LCP (liquid cubic phase) crystallization applications with a few GPCR examples; and advances in Cryo-EM and nanodiscs. All these biophysical techniques will be discussed in the context of their impact on membrane-protein targeted drug discovery.

Matthew T. Eddy, PhD, Assistant Professor, Chemistry, University of Florida, Gainesville

Instructor:

Matthew T. Eddy, PhD, Assistant Professor, Chemistry, University of Florida, Gainesville

Topics to be Covered: