DAHLIA WEISS 334 N Claremont Street San Mateo, CA 94401 USA		dahlia.weiss at gmail.com http://www.rationaldrugdesign.org https://www.linkedin.com/in/dahliaweiss/
Key words: Structure based drug design; Computational chemistry; Structural biology
CURRENT Position
Senior Principal Scientist, Protein Homeostasis Modelling Group Leader Bristol-Myers-Squibb, Redwood City, CA				2020-
Education
Ph.D.	Structural Biology / Chemistry		2009
Department of Chemistry, Stanford University, USA
Advisor: Professor M Levitt, Computational Structural Biology lab
Joint B.S. Magna cum laude	Chemistry and Biology		2001
Department of Chemistry and Department of Biology, Tel Aviv University, Israel
Publications AND PATENTS
1. WO2021168197 Bifunctional degraders of interleukin-1 receptor-associated kinases and therapeutic use thereof (2021) 2. WO2020081450 Bifunctional compounds for degrading btk via ubiquitin proteosome pathway (2020) 3. WO2021021761 Urea, amide, and substituted heteroaryl compounds for cbl-b inhibition (2021) 4. WO2020210508 3-substituted piperidine compounds for cbl-b inhibition, and use of a cbl-b inhibitor in combination with a cancer vaccine and/or oncolytic virus (2020) 5. WO2020236654 Cyano cyclobutyl compounds for cbl-b inhibition and uses thereof (2020) 6. WO2020264398 Substituted benzyl-triazole compounds for cbl-b inhibition, and further uses thereof (2020) 7. DR Weiss, J Karpiak, XP Huang, MF Sassanno, J Lyu, BL Roth, BK Shoichet; Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets Journal of medicinal chemistry 61 (15), 6830-6845 (2018) 8. M Korczynska, MJ Clark, C Valant, J Xu, E Von Moo, S Albold, DR Weiss,...,RK Sunahara ; Structure-based discovery of selective positive allosteric modulators of antagonists for the M2 muscarinic acetylcholine receptor Proceedings of the National Academy of Sciences 115 (10) E2419-E2428 (2018) 9. DR Weiss, A Bortolato, B Tehan, JS Mason; GPCR-Bench: A Benchmarking Set and Practitioners’ Guide for G Protein-Coupled Receptor Docking Journal of chemical information and modeling 56 (4),642-651 (2016) 10. A Bortolato, F Deflorian, DR Weiss, JS Mason; Decoding the Role of Water Dynamics in Ligand–Protein Unbinding: CRF1R as a Test Case Journal of chemical information and modeling 55 (9), 1857-1866 (2015) 11. Bennet, KA; Doré, AS, Christopher, JA; Weiss, DR; Marshall, FH; Structures of mGluRs shed light on the challenges of drug development of allosteric modulators Current Opinion in Pharmacology 20:1–7 (2015) 12. Silva, DA; Weiss, DR; Avila, FD; Da, LT; Levitt, M; Wang, D; Huang, X;  Millisecond dynamics of RNA polymerase II translocation at atomic resolution Proceedings of the National Academy of Sciences 111 (21) : 7665-7670 (2014) 13. Weiss, DR; Koehl, P;  Morphing Methods to Visualize Coarse-Grained Protein Dynamics Protein Dynamics : 271-282 (2014) 14. Coleman, RG; Sterling, T; Weiss, DR;  SAMPL4 & DOCK3. 7: lessons for automated docking procedures Journal of Computer-Aided Molecular Design : 41883 (2014) 15. Weiss, DR*; Ahn, SK*; Sassano, MF; Kleist, A; Zhu, X; Strachan, R; Roth, BL; Lefkowitz, RJ; Shoichet, BK;  Conformation Guides Molecular Efficacy in Docking Screens of Activated β-2 Adrenergic G Protein Coupled Receptor ACS chemical biology (8) : 1018-1026 (2013)    16. Kruse, AC*; Weiss, DR*; Rossi, M; Hu, J; Hu, K; Eitel, K; Gmeiner, P; Wess, J; Kobilka, BK; Shoichet, BK;  Muscarinic Receptors as Model Targets and Antitargets for Structure-Based Ligand Discovery Molecular pharmacology (84) : 528-540 (2013)      17. Mason, JS*; Bortolato, A*; Weiss, DR*; Deflorian, F; Tehan, B; Marshall, FH;  High end GPCR design: crafted ligand design and druggability analysis using protein structure, lipophilic hotspots and explicit water networks In Silico Pharmacology (1) : 23 (2013)      18. Mysinger, MM*; Weiss, DR*; Ziarek, JJ*; Gravel, S; Doak, AK; Karpiak, J; Heveker, N; Shoichet, BK; Volkman, BF;  Structure-based ligand discovery for the protein–protein interface of chemokine receptor CXCR4 Proceedings of the National Academy of Sciences (109) : 5517-5522 (2012)    19. Bray, JK; Weiss, DR; Levitt, M;  Optimized Torsion-Angle Normal Modes Reproduce Conformational Changes More Accurately Than Cartesian Modes Biophysical journal (101) : 2966 (2011) 20. Huang, X; Wang, D; Weiss, DR; Bushnell, DA; Kornberg, RD; Levitt, M;  RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription Proceedings of the National Academy of Sciences (107) : 15745-15750 (2010) 21. Weiss, DR; Levitt, M;   Can morphing methods predict intermediate structures? Journal of molecular biology (385) : 665-674 (2009) 22. Weiss, DR; Raschke, TM; Levitt, M;  How hydrophobic buckminsterfullerene affects surrounding water structure The Journal of Physical Chemistry B (112) : 2981-2990 (2008) *equal contributors
PAST Research Interests
Senior Scientist, Modelling group leader, Nurix Inc, San Francisco, USA 2015-2020 E2 conjugating enzymes and E3 ligases control protein stability and protein fate through the Ubiquitin Proteasome System (UPS). Small molecule enhancers and inhibitors of E2 and E3 enzymes provide an innovative path to regulate key actors in cell fate through modulation of the UPS. I am leading the predictive design of bifunctional molecules for targeted protein degradation, applying protein-protein docking and prediction of ternary complex formation, and advanced ADME prediction for Beyond Ro5 space. Senior Scientist, Computer Aided Drug Design, Heptares Therapeutics Limited, UK 2013-2015 G-protein coupled receptors (GPCRs), are the largest superfamily of proteins in the human body and are the targets of >30% of all marketed drugs. At Heptares Therapeutics, I applied computer aided drug design to challenging GPCR targets as part of the drug discovery team. I led the development of new computational methods for use of water structure in docking and lead optimization, MD simulation, Free Energy Perturbation in GPCRs and prediction of drug binding kinetics.
Post-doctoral research, Shoichet lab, Pharmaceutical Chemistry, University of California, San Francisco, USA 2009-2013
I applied virtual screening and GPCR homology modeling for the discovery of new chemical matter for GPCR targets, including the rational design of selectivity for receptor subtypes and ligand efficacy.
Visiting scholar, INRIA, French National Institute for Research in Computer Science and Control,  France 2008
Geometries of waters at protein-protein interfaces in the dynamic setting
I applied computational geometry techniques to study the interaction and dynamics of water in the protein-protein interface.
Ph.D. Studies, Levitt Lab, Department of Chemistry, Stanford University, USA 2003-2009
Coarse graining of protein dynamics
Protein dynamics important to biological function often happen on a time scale that is unattainable through detailed simulation methods such as molecular dynamics (MD). We developed a novel interpolation method to study transitions between known crystal structures that does not extrapolate motion linearly and can therefore move around high energy barriers. The interpolation method I developed is now used in several methods as a starting point for long-time-scale simulation.
Simulated behavior of nanoscale hydrophobic solutes in water
Using MD simulation, we studied details of the water structure surrounding a single molecule of Buckminsterfullerene (C60). We showed ordering of water in both the first and second hydration shell, and an increase of hydrogen bonding within shells, with important implications for nanomaterials.
M.S. Studies, Department of Biochemistry, Tel Aviv University, Israel
The Anti-Codon Nuclease active site
We used multiple sequence alignment and secondary structure predictions to study a t-RNA nuclease with anti-HIV potential. Predicted mutations were experimentally shown to alter cleavage patterns, with possible therapeutic applications.
B.S. Studies, Department of Biotechnology, Tel Aviv University, Israel
Kinetics of self-assembly in amyloidal fibrils: Biophysical studies
We used biophysical measurements (CD and ELISA) to characterize the kinetics of self-assembly in amyloid fibrils.
Awards and Honors
NIH NRSA for Individual Postdoctoral Fellows, F32 GM093580-01, UCSF Following a successful grant application, I was awarded NIH funding for 3 years.			2009-2012
SimBios, NIH Center for Biomedical Computation, Full fellowship, Stanford SimBios is an NIH funded center, awarding up to 3 full doctoral fellowships each year.			2007-2009
Program in Mathematics and Molecular Biology, Full fellowship, Stanford The PMMB is a national research and training consortium funded by a Burroughs Wellcome Fund Interfaces grant (now discontinued), granting ten doctoral awards each year.			2006-2007
Wise Scholarship for Masters Studies, Full fellowship, Tel Aviv University			2001-2003
Magna cum laude, B.S. Studies, Chemistry and Biology			2001
TEACHING EXPERience
Head Teaching Assistant Computational Structural Biology   Stanford University			2005-2006
Teaching Assistant and Laboratory Instructor General Chemistry; Organic Chemistry Stanford University General Chemistry, Tel Aviv University			2001-2005
LEADERSHIP
President, Israeli Student Organization			2005-2007
I served as president of the Israeli Student Organization at Stanford for two years, created and managed a budget of over $8000, oversaw a mailing list and website, and organized events for over 150 members.
IT Administrator, Biox Super Computing Cluster			2004-2005
I supported a parallel computer cluster of 300 dual processors (600 CPUs), and 1TB network attached storage. As part of the IT admin team, I added and maintained hundreds of user accounts, answered user queries, weighed in on policy decisions and maintained FAQs.
Non-Commissioned Officer, Israeli Defense Forces			1997-1999
I served in the Israeli army in a diplomatic capacity. I corresponded regularly with high-level foreign dignitaries, organized meetings, and resolved problems in real time. As a NCO, I set priorities and tasks for subordinate soldiers, directed the archiving of classified information and supervised proper protocol with foreign agencies.
Invited Talks And workshops (Selection)
American Chemical Society National Meeting, San Diego, USA “Computational Modelling Workflow to Characterize the Structure of Bi-functional Degrader-Protein-Protein Ternary Complex”			August 2019
American Chemical Society National Meeting, San Francisco, USA “GPCR drug-binding kinetics: Insights from explicit water network modeling”			August 2014
KNCV Medicinal Chemistry, Utrecht, Netherlands “Water molecules in drug target structures”			March 2014
Royal Society of Chemistry and Biochemical Society, London, UK “Tools and Strategies to Find Chemical Probes for Your Protein - The Role of Computer-Aided Drug Discovery”			November 2013
American Chemical Society National Meeting, New Orleans, USA “G-protein coupled receptors in virtual screening: Functional fidelity and selectivity”			April 2013
Uppsala University, Sweden, “Multiresolution Molecular Simulation Workshop”			June 2011
Duke University, USA “Docking: Dockblaster and SEA”			Sept 2011
University of Science and Technology, Hong Kong, “Virtual screening of B2 Adrenergic Receptor”			April 2010
San Jose State University, USA, “Hydrophobic hydration”			Feb 2010
University of New Orleans, USA, “Non-linear morphing”			Jan 2009
Stockholm University, Sweden, “Can morphing predict intermediate structures?”			April 2008