2023 ARCHIVES

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Dinner Short Courses* (In-Person Only)

Short courses at Discovery on Target 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.

Short courses will be offered IN-PERSON ONLY.

*Premium Pricing or separate registration required

Monday, September 25, 2023  5:00 - 7:30 pm

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

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) and 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.

INSTRUCTOR BIOGRAPHIES:

John Erve, PhD, President, Jerve Scientific Consulting

John Erve is from Chicago and studied Chemistry (BS, MS) at the University of Chicago and earned a PhD in Toxicology at Oregon State University. Following postdoctoral work at Vanderbilt (1995-1999) he joined BD-Biosciences (Woburn, MA) as a Study Director. In 2002, he joined AstraZeneca (Sweden) where he characterized reactive metabolites. In 2004 he joined Wyeth (Collegeville, PA) as a Principal Scientist responsible for metabolite identification. In 2010, John joined Novartis (Cambridge, MA) as a Lab Head in Analytical Sciences. John returned to drug metabolism at Elan Pharmaceuticals (San Francisco, CA) in 2012 and later formed Jerve Scientific Consulting, Inc to help small biotech companies in the Bay area with their drug discovery efforts. John was a certified D.A.B.T. from 2004 to 2019.

 

SC2: Chemical Biology for Covalent Discovery, Phenotypic Screening, and Target Deconvolution

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


Topics to be Covered:         

  • Chemical biology assays and probes for target engagement and mechanistic understanding
  • Chemoproteomic methods and reagents for covalent ligand drug discovery
  • Comparison of various chemical biology approaches (mass spectrometry, affinity-bead methods, thermal profiling and more) 
  • Use of quantitative mass spectrometry-based proteomics and global proteomics
  • Cysteine profiling and covalent inhibitors for target discovery and occupancy
  • Case studies highlighting use of proteomics for target engagement and deconvolution​

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.

 

SC3: Best Practices for Targeting GPCRs, Ion Channels, and Transporters with Monoclonal Antibodies

Complex membrane proteins represent the majority of protein classes addressed by therapeutic drugs. Significant opportunities exist for targeting complex membrane proteins with antibodies, but it has been challenging. This course will examine emerging technologies and strategies for enabling the successful isolation of specific and functional antibodies against GPCRs, ion channels, and transporters, and highlight progress via case studies.
Ross Chambers, PhD, Vice President, Antibody Discovery, Integral Molecular, Inc.
Riley Payne, PhD, Director, Antibody Discovery, Integral Molecular, Inc.

Instructor:

Ross Chambers, PhD, Vice President, Antibody Discovery, Integral Molecular, Inc.

Riley Payne, PhD, Director, Antibody Discovery, Integral Molecular, Inc.


Topics to be Covered:  ​

  • Overview of different classes of membrane proteins, including structure, mechanism, and their role in disease
  • Membrane protein biochemistry and antigen preparation strategies
  • Use of mRNA and DNA for eliciting immune responses against membrane proteins
  • Antibody discovery and methods to enable isolation of functional antibodies
  • Review of mechanisms relevant to complex membrane proteins (GPCRs, ion channels, transporters), in vitro assays for measuring the detailed binding and function of antibodies
  • Review of promising membrane protein targets and antibodies in development

INSTRUCTOR BIOGRAPHIES:

Ross Chambers, PhD, Vice President, Antibody Discovery, Integral Molecular, Inc.

Ross Chambers is the Vice President of Antibody Discovery at Integral Molecular. He pioneered the use of DNA immunization for antibody production and developed Integral Molecular’s MPS system for isolating antibodies. Dr. Chambers earned his PhD from the University of Otago, New Zealand, and did post-doctoral studies at UC Davis and Berkeley. Before joining Integral Molecular, he was the Director of R&D at SDIX and directed the discovery of thousands of commercial antibodies.

Riley Payne, PhD, Director, Antibody Discovery, Integral Molecular, Inc.

PhD in Cell and Molecular Biology from the University of Pennsylvania with 10+ years industry experience in biotechnology/drug discovery. Demonstrated history of leadership in process development, protein engineering, therapeutic antibody discovery, and lead characterization.

 

SC4: Fragment-Based Drug Design: Advancing Tools and Technologies

This course aims to introduce the fundamentals of Fragment-Based Lead Discovery (FBLD). The first section focuses 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 discusses the variety of fragment screening methods and when they are best applied. Fragment libraries will also be discussed.
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/).

Wednesday, September 27, 2023  5:30 - 8:00 pm

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

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
Prasoon Chaturvedi, PhD, Vice President & Head, DMPK, C4 Therapeutics, Inc.

Instructors:

John Erve, PhD, President, Jerve Scientific Consulting

Prasoon Chaturvedi, PhD, Vice President & Head, DMPK, C4 Therapeutics, Inc.


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) and 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.​


INSTRUCTOR BIOGRAPHIES:

John Erve, PhD, President, Jerve Scientific Consulting

John Erve is from Chicago and studied Chemistry (BS, MS) at the University of Chicago and earned a PhD in Toxicology at Oregon State University. Following postdoctoral work at Vanderbilt (1995-1999) he joined BD-Biosciences (Woburn, MA) as a Study Director. In 2002, he joined AstraZeneca (Sweden) where he characterized reactive metabolites. In 2004 he joined Wyeth (Collegeville, PA) as a Principal Scientist responsible for metabolite identification. In 2010, John joined Novartis (Cambridge, MA) as a Lab Head in Analytical Sciences. John returned to drug metabolism at Elan Pharmaceuticals (San Francisco, CA) in 2012 and later formed Jerve Scientific Consulting, Inc to help small biotech companies in the Bay area with their drug discovery efforts. John was a certified D.A.B.T. from 2004 to 2019.

Prasoon Chaturvedi, PhD, Vice President & Head, DMPK, C4 Therapeutics, Inc.

Prasoon Chaturvedi, Ph.D., currently leads the DMPK efforts in the protein degrader space as Vice President, DMPK, at C4 Therapeutics in Watertown, MA. Over the last two decades, Prasoon has worked with numerous cutting-edge technologies to drive drug development endeavors in multiple therapeutic areas including infectious disease, oncology, hematology, cardiovascular, inflammation, and rare diseases leading to multiple successful IND, CTA, and NDA filings and has made key DMPK contributions for several marketed drugs including NUZYRA and ONPATTRO. Prasoon holds a Ph.D. from IIT, Roorkee (India), and did his postdoctoral training at E.K. Shriver Center of Harvard Medical School, MA.

 

SC6: Synthetic Biology Applications for Drug Discovery and Therapy

Synthetic biology is defined as a precise, scalable, programmable and sustainable approach to manipulate and control genetic and cellular activities. It is a versatile biological tool that can tackle many different cellular engineering problems, in drug discovery to bioprocessing and therapeutic development. This course will help chemists and biologists understand what synthetic biology is, what is involved, and how it’s being applied today. Instructors will offer case studies to highlight its growing potential and use, while discussing inherent challenges and limitations. Along with insightful talks, the course also offers time for discussion and brainstorming with experts in the field.
Akos Nyerges, PhD, Research Fellow, Laboratory of Dr. George Church, Department of Genetics, Harvard Medical School
Ron Weiss, PhD, Professor, Biological Engineering, Massachusetts Institute of Technology
William Chen, MD, PhD, Assistant Professor, Sanford School of Medicine, University of South Dakota
Charles Chen, PhD, Senior Scientist, Advanced Drug Delivery, Pharmaceutical Sciences, AstraZeneca Pharmaceuticals, R&D

Instructors:

Akos Nyerges, PhD, Research Fellow, Laboratory of Dr. George Church, Department of Genetics, Harvard Medical School

Ron Weiss, PhD, Professor, Biological Engineering, Massachusetts Institute of Technology

William Chen, MD, PhD, Assistant Professor, Sanford School of Medicine, University of South Dakota

Formulation Strategy in Drug Delivery: From Small Molecules to Macromolecules to Living Microorganisms

Charles Chen, PhD, Senior Scientist, Advanced Drug Delivery, Pharmaceutical Sciences, AstraZeneca Pharmaceuticals, R&D


Topics to be Covered:

  • Exploiting the intricacies of cell regulation and developing gene circuits to modulate it
  • Designing synthetic biology tools for manipulating prokaryotic and eukaryotic cells
  • Case study: Synthetic biology for drug development
  • Case study: Synthetic biology for designing programmable organoids for drug screening
  • Case study: Synthetic biology for cellular phenotype perturbation
  • Case study: Synthetic biology for therapeutic protein production
  • Case study: Computer-guided membrane-active peptide evolution
  • Case study: Formulations using synthetic biology for peptide and non-viral nucleic acid delivery
  • Understanding the inherent limitations in programming mammalian cells​​

INSTRUCTOR BIOGRAPHIES:

Akos Nyerges, PhD, Research Fellow, Laboratory of Dr. George Church, Department of Genetics, Harvard Medical School

Akos Nyerges has a long-standing interest in synthetic biology, directed evolution, and genetic code engineering. He earned his PhD in Hungary and currently is a postdoctoral researcher with Professor George M. Church at Harvard Medical School. His PhD focused on developing tools to perform precise genome engineering in human pathogenic bacteria and hosts for microbial fermentation. During his research and in multiple collaborative projects, Akos developed a broad-host-range genome editing system, pORTMAGE, and later, DIvERGE, a tool for broad-host-range in vivo directed evolution. As a postdoctoral researcher, he is developing technologies for bottom-up genome construction and genetic code engineering. With his research, Akos aims to understand the design principles of functional genomes and construct synthetic genomes with functions not available in current organisms. In his talk, he will share how precise genome engineering tools can help us generate vast libraries of biomolecules, better understand enzyme-inhibitor interactions, and construct organisms that fundamentally differ from existing living organisms, including current hosts for bioproduction.

Ron Weiss, PhD, Professor, Biological Engineering, Massachusetts Institute of Technology

Ron Weiss is Professor in the Department of Biological Engineering and in the Department of Electrical Engineering and Computer Science at the Massachusetts Institute of Technology, and is the Director of the Synthetic Biology Center at MIT. Professor Weiss is one of the pioneers of synthetic biology. He has been engaged in synthetic biology research since 1996 when he was a graduate student at MIT and where he helped set up a wet-lab in the Electrical Engineering and Computer Science Department. After completion of his PhD, Weiss joined the faculty at Princeton University, and then returned to MIT in 2009 to take on a faculty position in the Department of Biological Engineering and the Department of Electrical Engineering and Computer Science. The research pursued by Weiss since those early days has placed him in a position of leadership in the field, as evidenced both by publications from his lab as well as a variety of awards and other forms of recognition. He pursued several aspects of synthetic biology, including synthesis of gene networks engineered to perform in vivo analog and digital logic computation. The Weiss lab also published seminal papers in synthetic biology focused on programming cell aggregates to perform coordinated tasks using engineered cell-cell communication with chemical diffusion mechanisms such as quorum sensing. Several of these manuscripts were featured in a recent Nature special collection of a select number of synthetic biology papers reflecting on the first 10 years of synthetic biology. While work in the Weiss lab began mostly with prokaryotes, during the last 5 years a majority of the research in the lab shifted to mammalian synthetic biology. The lab focuses both on foundational research, e.g., creating general methods to improve our ability to engineering biological systems, as well as pursuing specific health related applications where synthetic biology provides unique capabilities.http://groups.csail.mit.edu/synbio/

William Chen, MD, PhD, Assistant Professor, Sanford School of Medicine, University of South Dakota

Dr. Chen is a surgeon, engineer, and multidisciplinary scientist with a career vision to improve human health. Dr. Chen is currently an Assistant Professor at the University of South Dakota (USD). He received his MD degree and medical training (internship and surgical residency) in Taiwan before pursuing an academic path. Dr. Chen obtained his Master’s in Biotechnology at the University of Pennsylvania and PhD in Bioengineering at the University of Pittsburgh. He finished his first postdoctoral fellowship in Biomaterial and Regenerative Medicine at the University of Pittsburgh. Dr. Chen finished his NIH-sponsored joint postdoctoral fellowship at Massachusetts Institute of Technology (MIT) and Massachusetts General Hospital (MGH) under the co-mentorship of Dr. Timothy Lu (MIT) and Dr. Anthony Rosenzweig (MGH). He then served as a Research Scientist at MIT for more than 2 years prior to joining USD. Dr. Chen’s research is focused on the development of platform technologies for cardiovascular regenerative medicine using genetic engineering and synthetic and systems biology approaches.

Charles Chen, PhD, Senior Scientist, Advanced Drug Delivery, Pharmaceutical Sciences, AstraZeneca Pharmaceuticals, R&D

Dr. Charles Chen is a Senior Scientist at AstraZeneca working on designing and synthesizing novel lipids and focusing on non-viral nucleic acid delivery. Before joining AstraZeneca, Charles started his research journey when he was an undergraduate student and found his passion in drug development. Charles got his PhD in Chemistry at King’s College London under the supervision of Professor Martin Ulmschneider. In 2019, Charles moved to Boston in the US and did a 2-year postdoc training at the Massachusetts Institute of Technology and Massachusetts General Hospital, co-supervised by Professors Timothy Lu and Joanna Yeh. Charles’ combinational approaches have shown promising outcomes in antibiotics and cancer chemotherapy.

 

SC7: DNA-Encoded Libraries

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

Instructors:

Svetlana Belyanskaya, PhD, former Vice President, Biology, Anagenex

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


Topics to be Covered:

  • DNA-Encoded Library (DEL) screening platforms
  • Common selection strategies for identifying novel hits from DEL campaigns
  • Parameters for building a library collection
  • Strategic considerations in using DEL selection data to accelerate hit-to-lead steps in drug discovery

INSTRUCTOR BIOGRAPHIES:

Svetlana Belyanskaya, PhD, former 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: Generative and Predictive AI Modeling for Designing Small Molecule and Peptide Drugs

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 new therapeutic modalities. That is, instead of traditional inhibitors, we can now design 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 and peptide drug design.
Parthiban Srinivasan, PhD, Professor, Data Science and Engineering, Indian Institute of Science Education and Research, Bhopal
Stephanie Ashenden, PhD, Senior Informatician, Artificial Intelligence & Machine Learning, AstraZeneca
Victor Guallar, PhD, Professor, Barcelona Supercomputing Center and Nostrum Biodiscovery
Nicholas Nystrom, PhD, CTO, Peptilogics, Inc.

Instructors:

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

Stephanie Ashenden, PhD, Senior Informatician, Artificial Intelligence & Machine Learning, AstraZeneca

Victor Guallar, PhD, Professor, Barcelona Supercomputing Center and Nostrum Biodiscovery

Nicholas Nystrom, PhD, CTO, Peptilogics, Inc.


Topics to be Covered:

  • AI methods for generating small molecule inhibitors and degraders
  • AI for peptide drug design
  • AI for chemical space exploration and exploitation
  • Deep learning based predictive models

Who Should Attend:

Attendance is recommended for drug discovery researchers wishing to understand the current state of AI in drug discovery. This course is also recommended for graduate students and academic scientists interested in learning more about new small molecule and peptide-based drug modalities and how AI could be leveraged.​​

INSTRUCTOR BIOGRAPHIES:

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

Parthiban Srinivasan, an experienced data scientist, earned his PhD from Indian Institute of Science, specializing in Computational Chemistry. After his PhD, he continued the research at NASA Ames Research Center (USA) and Weizmann Institute of Science (Israel). Then he worked at AstraZeneca in the area of Computer Aided Drug Design for Tuberculosis. Later, he headed informatics business units in Jubilant Biosys and then in GvkBio before he floated the company, Parthys Reverse Informatics and later an AI consultancy, Vingyani. Currently, he is a Professor at Indian Institute of Science Education and Research (IISER) Bhopal, teaching Data Science.

Stephanie Ashenden, PhD, Senior Informatician, Artificial Intelligence & Machine Learning, AstraZeneca

Victor Guallar, PhD, Professor, Barcelona Supercomputing Center and Nostrum Biodiscovery

Currently an ICREA Professor at the Barcelona Supercomputing Center (BSC), Dr. Guallar completed his PhD in theoretical Chemistry between the University Autonomous of Barcelona (Spain) and UC Berkeley (USA) in January 2000. After three years as a postdoctoral researcher at Columbia University (New York, USA), he was appointed assistant professor at Washington University School of Medicine (St Louis, USA), before moving his group to BSC in 2006. His laboratory (EAPM) has grown considerably since, keeping a productive international character, and developing important contributions in computational biophysics, such as the protein-ligand modeling software PELE, and biochemistry, including computational algorithms for enzyme engineering and the introduction of the first PluriZyme (enzyme with multiple actives sites).As a BSC researcher, Prof. Guallar has been awarded several important research projects, including the award of a prestigious advanced ERC grant (the youngest researcher to receive it in Spain). His research has produced over 140 papers in international journals and directed 16 PhD thesis. In addition to algorithms development (and their application), the group has recently placed importance in adding interdisciplinary fields to our research, such as visualization techniques, data mining and software optimization through machine learning algorithms. Prof. Guallar is also founder of the first spin off from BSC, Nostrum Biodiscovery, a young biotech enterprise created in 2016 which aims to collaborate with pharmaceutical and biotech companies dedicated to the development of drugs and molecules of biotechnological interest. The company currently works with clients in North America, Europe, Asia, and Oceania.

Nicholas Nystrom, PhD, CTO, Peptilogics, Inc.

Nicholas Nystrom, PhD, is CTO at Peptilogics, where he leads development of the Nautilus generative AI platform for peptide drug design. Nautilus integrates generative and predictive algorithms, computational biophysics and quantum chemistry, and in-house, custom-designed supercomputing to enable peptide drug design. Nick’s areas of expertise include machine learning, drug discovery, computer architecture, computational science, and quantum chemistry. Prior to joining Peptilogics, Nick was Chief Scientist at the Pittsburgh Supercomputing Center, where he architected the first supercomputer to converge AI and HPC. Nick designed and was PI for national supercomputers including Blacklight, Bridges, and Bridges-2, and he codesigned the Neocortex supercomputer to enable scaling AI on the world’s most powerful accelerators. Nick was PI for the Human BioMolecular Atlas Program (HuBMAP), an NIH Common Fund project that is developing a map of the human body at single-cell resolution, spanning genomic, proteomic, and imaging modalities. Nick also led research in AI for breast and lung cancer and causal discovery focusing on cancer driver mutations, lung fibrosis, and the brain causome. His PhD is in quantum chemistry.