Brian Shoichet, CV
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`
`
`January, 2016
`
`University of California
`Brian Shoichet, Curriculum Vitae
`
`Brian Shoichet, Ph.D.
`Professor, Step VII, Dept. of Pharmaceutical Chemistry
`
`University of California, San Francisco
`1700 4th St., Byers Hall Rm 508D
`San Francisco, CA 94158-2550
`e-mail: bshoichet@gmail.com
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`Canada, Born: 06/27/63
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`US Permanent Resident
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`Massachusetts Institute of Technology
`B.Sc. in Chemistry; B.Sc. in History
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`University of California, San Francisco
`Ph.D. in Pharmaceutical Chemistry, Advisor Professor Irwin Kuntz
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`Name:
`Position
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`Address
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`Citizenship
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`Education
`1981-1985
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`1986-1991
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`Postdoctoral Research
`1992
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`University of California, San Francisco, Professor Irwin Kuntz
`1993-1996
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`Institute of Molecular Biology, Eugene, Oregon, Professor Brian Matthews
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`Principal Positions Held:
`1996-2002
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`Assistant Professor of Molecular Pharmacology & Biological Chemistry
`2002-2003
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`Associate Professor (tenured), Mol. Pharmacology & Biological Chemistry
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`Northwestern University
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`2003-2005
`2005-2013
`2011-2012
`2012-2013
`2013-2014
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`2013-2014
`2014-Present
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`2014-Present
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`Keywords:
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`Associate Professor of Pharmaceutical Chemistry
`Professor (Step VII) of Pharmaceutical Chemistry
`Vice Chair, Dept. of Pharmaceutical Chemistry, UCSF
`Director, California Institute for Quantitative Biology of UCSF (QB3)
`Adjunct Professor of Pharmaceutical Chemistry (WOS)
`University of California, San Francisco
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`Professor, Faculty of Pharmacy
`Adjunct Professor, Faculty of Pharmacy (Courtesy Appt)
`University of Toronto
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`Professor of Pharmaceutical Chemistry, Step VII
`University of California, San Francisco
`
`Molecular recognition, drug discovery, structure-based inhibitor discovery,
`computational chemical biology, systems pharmacology, molecular docking,
`promiscuous inhibition, G-Protein Coupled Receptors.
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`Honors & Awards
`1993-1996
`Damon Runyon-Walter Winchell Cancer Research Fellow
`1997-1999
`PhRMA Foundation Career Development Award
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`1998-2003
`National Science Foundation CAREER Award
`2001
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`Dean’s Award for Teaching Excellence (Northwestern University)
`2004
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`Astra Lectureship, University of Ottawa
`2006-2007
`Novartis Chemistry Lecturer (Cambridge, Basel, Vienna, Horsham, Tsukuba, Emeryville)
`Swiss Universities 3e Cycle en Chimie (Lausanne, Bern, Friborg, Geneva)
`2008
`2009
`Abbott Lectureship, Yale University
`2011
`Society for Biomolecular Sciences Accomplishment Award
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`FUSTIBAL Ex. 1009
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`

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`Brian Shoichet, CV
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`
`
`January, 2015
`
`Topliss Lectureship, University of Michigan
`Distinguished Scientist Seminar, University of Pittsburgh
`Distinguished Scientist Lectureship, University of Ohio School of Pharmacy
`Center for Mol. Innovation in Drug Discovery, Northwestern University, Annual Keynote
`Cambridge Healthtech 10th Annual Drug Discovery Chemistry, Plenary Keynote.
`Arthur Broom Lecture, University of Utah School of Pharmacy.
`International Chair of Therapeutic Innovation, CNRS, Paris.
`Molecular Graphics & Modeling Society, Erlangen, Germany. Plenary Keynote.
`Partnership for Excellence in Structural Biology Annual Symposium, UConn. Keynote
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`2011
`2013
`2014
`2014
`2015
`2015
`2015
`2016
`2016
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`Professional & Scientific Activity
`Editorial Service
`1993-present
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`Ad hoc reviewer for J. Mol. Biol., Proc. Natl. Acad. Sci., Chemistry & Biology,
`Protein Sci., Proteins, J. Am. Chem. Soc., J. Med. Chem., J. Chem. Inf. Modeling,
`Protein Eng., J.Biol. Chem., Nature Biotech., Nature Struct. Biol., Nature Chemical
`Biology, Nature Chemistry, Nature, and Science.
`Editorial Board of Journal Of Computer-Aided Molecular Design
`Editorial advisory board of PharmSci, Amer. Assoc. of Pharmaceutical Sciences
`Faculty of 1000 (Ligand-Macromolecular Interactions & Inhibitor Design)
`Editor-in-Chief of Journal Of Computer-Aided Molecular Design
`International Advisory Board Molecular Biosciences, Royal Soc. Chem.
`Editorial Advisory Board Journal of Medicinal Chemistry
`Editorial Advisory Board, Journal of Chemical Information & Modeling
`Editorial Advisory Board, ACS Chemical Biology
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`1999-2000
`1999-2003
`2001-2003
`2001-2003
`2005-present
`2005-2010
`2016-2017
`2016-2017
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`Conferences & Sessions Organized
`1998
`Midwest Enzyme Chemistry Conference, Northwestern University.
`2001
`Computational Structural Biology (Session on Docking), FSU, Tallahasse FL
`2001
`Docking & Testing Session, ACS National Meeting, Chicago IL
`2002
`Structure-based drug design, Cambridge HealthTech Institute, Boston MA
`2003
`Structure-based drug design, Cambridge HealthTech Institute, Boston MA
`2005
`NIH Meeting on Docking & Scoring, Washington DC (co-chair)
`2006
`Structure-Based Drug Design Keystone Conference, Whistler BC (co-chair)
`2007
`Gordon Research Conference in Computer-Aided Drug Discovery, New Hampshire
`(vice chair)
`ASBMB National Meeting, New Orleans LA (co-chair), April 18-22
`Gordon Research Conference in Computer-Aided Drug Discovery, New Hampshire
`(chair). July 19-24
`Nature Chem. Biol. Drug Discovery Meeting, Boston MA (co-chair)
`Gordon Research Conference in Biomolecular Interactions and Methods, session
`chair in drug discovery (January, Galveston Tx)
`Scientific Advisory Board of the 21st EuroQSAR Symposium
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`2009
`2009
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`2009
`2010
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`2015-2016
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`Scientific Advisory Boards, Consulting & Companies Founded
`1998-2003
`SAB Synergix, Cue Biotech, Ctr for Molecular Design (Univ of Toronto)
`2001-2003
`Consultant for Pharmacia Corp.; Procter & Gamble Pharmaceuticals
`2001-2004
`Consultant for Protein Pathways, Cytoclonal Pharma, Syrrx, Epix Medical
`2002-2008
`Consultant for Structural GenomiX
`2004-present
`SAB, NIH RoadMap Chemical Libraries and Screening Initiative
`2005
`Consultant for Scios; Consultant for Novartis
`2005-2006
`Consultant for Boehringer Ingelheim
`2006-2007
`Consultant for CropSolutions Inc.
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`Brian Shoichet, CV
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`January, 2015
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`2006-2008
`2007-2009
`2008-2009
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`2009-2012
`2012
`2009-2011
`2008-2012
`2009-present
`2014
`2015
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`2009
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`SAB for Buck Institute.
`Consultant for Eli Lilly & Co.
`SAB for Chicago Tri-Institutional Center for Chemical Methods and Library
`Development
`Scientific Advisory Group for Corning Life Sciences
`Consultant for Alios Pharma
`Consultant for Anacor Pharma
`Consultant for Vitae Pharmaceuticals
`Consultant for ZoBio Pharma
`Consultant for Astra Zeneca
`External Advisory Board, University of Pittsburgh Drug Discovery Institute
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`Founder, SeaChange Pharmaceuticals
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`Research Program
`An overarching goal of our lab is bringing chemical reagents to biology, using a combination of
`computational simulation and experiment. Using a protein-centric approach, we search for new ligands
`that complement protein structures. This typically involves molecular docking and the development of
`model experimental systems to experimentally test new algorithms that we develop. A new direction
`adopts a ligand-centric approach that seeks new targets for known drugs. Whereas this lacks the
`physical foundation of the structure-based docking, it returns to an older, pharmacological view of
`biological relationships, bringing to it a quantitative model. A biological focus for both areas is the
`discovery of reagents to modulate GPCRs.
`
`As part of our research, we have introduced free computational & experimental community
`resources:
`1. The ZINC database of commercially available, dockable molecules: http://zinc.docking.org.
`2. The DUD benchmark of 40 targets, 3000 ligands & 97000 decoys: http://dud.docking.org.
`3. DOCK Blaster, a web-based community tool for docking: http://blaster.docking.org.
`4. SEA, a chemoinformatics method for predicting targets for ligands: http://sea.docking.org.
`5. Procedures and reagents for counterscreening for promiscuous aggregation.
`6. Libraries of ligands and decoys for model binding sites for testing docking:
`http://shoichetlab.compbio.ucsf.edu/take-away.php.
`
`Six recent papers representative of the interests of my laboratory:
`MJ Keiser, V Setola, JJ Irwin et al., BK Shoichet* & BL Roth*. Predicting new molecular targets
`for known drugs. Nature, 462, 175-81 (2009).
`
` J
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` Carlsson et al. BL Roth* & BK Shoichet*. Comparing structure-based ligand discovery from a
`homology model and the crystal structure of the dopamine D3 receptor. Nature Chem. Biol. 7, 769-78
`(2011).
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` Laggner, et al., BL Roth,* RT Peterson* & BK Shoichet*. Chemical Informatics and Target
`Identification in a Zebrafish Phenotypic Screen. Nature Chem. Biol., 8, 144-146 (2012).
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` Lounkine†, et al., BK Shoichet* & L Urban* Large Scale Prediction and Testing of Drug Activity
`on Side-Effect Targets. Nature 486, 361-7. (2012).
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` Lin, MF Sassano, BL Roth* and BK Shoichet*. A Pharmacological Organization of G Protein-
`coupled Receptors. Nature Methods 10, 140-6 (2013).
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`London N, et al., Shoichet BK* & Taunton J*. Covalent docking of large libraries for the discovery
`of chemical probes. Nature Chem Biol. 10, 1066-72 (2014).
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`Peer Reviewed Publications (166 total, Total Cites 22,316, Google Scholar H-index 79)
`1. Sowdhamini, R.; Srinivasan, N.; Shoichet, BK.; Santi, DV.; Ramakrishnan, C & Balaram, P*;
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`Brian Shoichet, CV
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`January, 2015
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`Stereochemical Modeling of Disulfide Bridges. Protein Engineer., 3(2): 95-103 (1989).
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`2. BK Shoichet & ID Kuntz.* Protein docking and complementarity. J. Mol. Biol. 221, 327-346 (1991)
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`3. Shoichet, BK, Bodian, DL & Kuntz, ID*; Molecular Docking Using Shape Descriptors. J. Comput
`Chem. 13, 380-397 (1992).
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`4. Meng, E.C.; Shoichet, B.K. & Kuntz, I.D.*; Automated Docking with Grid-Based Energy Evaluation.
`Journal of Computational Chemistry 13, 504-524. (1992).
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`5. Shoichet, B.K.; Stroud, R.M.; Santi, D.V.; Kuntz, I.D* & Perry, K.M.; Structure Based Inhibitor
`Discovery in Thymidylate Synthase. Science 259, 1445-1449 (1993).
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`6. BK Shoichet & ID Kuntz.* Matching chemistry and shape in molecular docking, Protein. Engineer, 6,
`723-32 (1993).
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`7. U. Schellenberger, VS Francis, P. Balaram, BK Shoichet, & DV Santi.* Designed deletion of an
`entire domain of Lactobacillus thymidylate synthase gives a catalytically active enzyme.
`Biochemistry, 33, 5623-5629 (1994).
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`8. Shoichet, B.K; Baase, W.A.; Kuroki, R. & Matthews, B.W.*; A Relationship Between Protein Stability
`and Protein Function. Proc. Nat. Acad. Sci. 92, 452-456 (1995).
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`9. Zhang, X.J.; Baase, W.A.; Shoichet, B.K.; Wilson, K. & Matthews, B.W.*; Incremental Enhancement
`of Protein Stability by the Combination of Point Mutations in T4 Lysozyme. Protein Engineer 8,
`1017-1022 (1995).
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`10. Strynadka, NCJ, Eisenstein, M, Katchalski-Katzir, E, Shoichet, BK, et al. & James, MNG*; Molecular
`Docking Programs Successfully Predict the Binding of a Beta-Lactamase Inhibitory Protein to the
`TEM-1 Beta-Lactamase. Nat. Struct. Biol. 3, 233-239 (1996).
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`11. Gassner, N.C., Baase, W.A., Linstrom, J.D., Shoichet, B.K. & Matthews, B.W*. Isolation and
`Characterization of Multiple Methionine Mutants of T4 Lysozyme with a Simplified Core. Techniques
`in Protein Chemistry, VII 851-863 (1997).
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`12. Lorber, D.A. & Shoichet, B.K.*, Flexible Ligand Docking Using Conformational Ensembles. Protein
`Science, 7, 938-950 (1998).
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`13. Morosini, M.-I.; Negri, M.-C.; Shoichet, B.; M.-R. Baquero; Baquero, F. and Blazquez, J.*; An
`extended-spectrum AmpC-type (cid:533)-lactamase obtained by in vitro antibiotic selection. FEMS
`Microbiology Letters, 165, 85-90 (1998).
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`14. Weston, GS.; Blasquez, J; Baquero, F, and Shoichet, BK*; Structure-based Enhancement of
`Boronic Acid Based Inhibitors of AmpC (cid:533)-lactamase. J. Med. Chem., 41: 4577-4586 (1998).
`15. KC Usher, LC Blaszczak, GS Weston, BK Shoichet* & SJ Remington*; The three dimensional
`structure of AmpC (cid:533)-lactamase from Escherichia coli bound to a transition state analog: possible
`implications for the oxyanion hypothesis and for inhibitor design. Biochemistry 37,16082-16092 (1998).
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`16. Shoichet, B.K.*; Leach, A. & Kuntz, I.D*; Ligand Solvation Effects in Molecular Docking. Proteins
`34, 4-16, (1999).
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`17. BM Beadle, WA Baase, D. Wilson, NR Gilkes & BK Shoichet* Comparing the Thermodynamic
`Stabilities of a Thermophilic and a Mesophilic Enzyme. Biochemistry 38, 2570-2576 (1999).
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`18. Stout, T.J.; Tondi, D., Rinaldi, M., Barlocco, D., Pecorari, P., Santi, D.V., Kuntz, I.D., Stroud*, R.M.,
`Shoichet, B.K.* & Costi, M.P.* Structure-Based Design of Inhibitors Specific for Bacterial
`Thymidylate Synthase. Biochemistry 38, 1607-1617 (1999).
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`19. Tondi, D., Slomczsynska, U., Watterson, D.M., Costi, M.P., Ghelli, S & Shoichet, B.K.*, Structure-
`Based Discovery and In-Parallel Elaboration of Novel inhibitors of Thymidylate Synthase. Chemistry
`& Biology 6, 319-331 (1999).
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`Brian Shoichet, CV
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`20. Beadle, B.M., McGovern, S.L., Patera, A. & Shoichet, B.K.* Functional Analyses of AmpC (cid:533)-
`Lactamase Through Differential Stability. Protein Science 8, 1816-1824 (1999).
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`21. Powers, R.A., Blazquez, J., Weston G.S., Morosini, M.I., Baquero F. & Shoichet, B.K.* The
`Complexed Structure and Anti-Microbial Activity of a Non- (cid:533)-Lactam Inhibitor of AmpC (cid:533)-lactamase.
`Protein Science, 8, 2330-2337 (1999).
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`22. A Patera, LC Blaszczak & BK Shoichet.* Crystal structures of substrate and inhibitor complexes
`with AmpC (cid:533)-lactamase: possible implications for substrate-assisted catalysis. J. Am. Chem. Soc.
`122, 10504-10512 (2000).
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`23. E Caselli, RA Powers, LC Blaszczak, CY Wu, F Prati & BK Shoichet.* Energetic, structural & anti-
`microbial analyses of (cid:533)-lactam side chain recognition by (cid:533)-lactamases. Chem.& Biol 8, 10-17 (2001).
`24. Su, A.I, Lorber, D.M., Weston, G.S., Baase, W.A, Matthews, B.W. & Shoichet, B.K.* Docking
`Molecules by Families to Increase the Diversity of Hits in Database Screens: Computational Strategy
`and Experimental Evaluation. Proteins 42:279–293 (2001).
`25. Beadle, BM, Nicholas, RA & Shoichet, BK* Interaction energies between (cid:533)-lactam antibiotics and a
`penicillin binding protein by reversible thermal denaturation. Protein Science 10, 1254-9 (2001)
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`26. D Tondi, RA Powers, MC Negri, E Caselli, J Blazquez, MP Costi* & BK Shoichet* Structure-based
`design & in-parallel synthesis of inhibitors of AmpC (cid:533)-lactamase. Chem. & Biol. 8, 593-611 (2001).
`27. Trehan, I, Beadle, B.M., & Shoichet, B.K.* Inhibition of AmpC (cid:533)-Lactamase Through a Destabilizing
`Interaction in the Active Site. Biochemistry 40, 7992-7999 (2001).
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`28. Powers, R.A., Caselli, E., Focia, P., Prati, F. & Shoichet, B.K.* The Structures of Ceftazidime and
`its Transition-State Analog Bound to AmpC (cid:533)-lactamase: Implications for Inhibition, Mechanism and
`Resistance. Biochemistry 40, 9207-14 (2001).
`29. Wang, X., Minasov, G. & Shoichet, B.K.* Interaction Energies in Covalent Complexes: TEM-1 (cid:533)-
`lactamase and (cid:533)-lactams. Proteins 47, 86-96 (2002).
`30. Lorber, D.M., Udo, M.K., & Shoichet, B.K.* Protein-Protein Docking with Multiple Ligand Residue
`Conformations and Multiple Residue Identities. Protein Science, 11, 1393-1408 (2002).
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`31. BM Beadle, I Trehan, P Focia & BK Shoichet.* Structural milestones in the pathway of an amide
`hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC (cid:69)-lactamase. Structure
`10, 413-424 (2002).
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`32. SL McGovern, E Caselli, N Grigorieff & BK Shoichet* A common mechanism underlying promiscuous
`inhibitors from virtual and high-throughput screening. J. Med. Chem. 45, 1712-1722 (2002).
`33. G. Minasov, X. Wang. & B.K. Shoichet* An ultra-high resolution structure of TEM-1 (cid:69)-lactamase
`suggests a role for Glu166 as the general base in acylation. J. Am. Chem. Soc. 124, 5333-40 (2002)
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`34. Doman, T.N*, McGovern, S.L., Witherbee, B.J., Kasten, T.P., Kurumbail, R., Stallings, W.C.,
`Connolly, D.T., & Shoichet, B.K.* Molecular Docking and High-Throughput Screening for Novel
`Inhibitors of Protein Tyrosine Phosphatase-1B. J. Med. Chem. 45, 2213-2221 (2002).
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`35. Wang, X., Minasov, G., & Shoichet, B.K.* Evolution of an Antibiotic Resistance Enzyme Constrained
`by Stability and Activity Trade-Offs. J. Mol. Biol. 320, 85-95 (2002).
`36. Powers, R.A. & Shoichet, B.K.* Mapping the Active Site of AmpC (cid:533)-Lactamase for Hot-Spots. J.
`Med. Chem. 35, 3222-3234 (2002).
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`37. Powers, R.A., Morandi, F. & Shoichet, B.K.* Structure-based discovery of a novel, non-covalent
`inhibitor of AmpC (cid:533)-lactamase. Structure 10, 1013-1023 (2002)
`38. B.M. Beadle and B.K. Shoichet.* Structural bases of stability-function trade-offs in enzymes. J.
`Mol. Biol. 321, 285-296 (2002)
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`Brian Shoichet, CV
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`39. Wang, X. Minasov, G. & Shoichet, B.K.* Inhibitor Resistance Mechanisms Revealed by TEM-30,
`TEM-32, and TEM-34 structures. J. Biol. Chem. 277, 32149-32156 (2002)
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`40. Trehan, I., Morandi, F. & Shoichet, B.K.* Using Steric Hindrance to Design New Inhibitors of Class
`C (cid:69)-Lactamases. Chemistry & Biology 9, 971-980 (2002).
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`41. BQ Wei, WA Baase, L Weaver, BW Matthews* & BK Shoichet*. A Model Binding Site for Testing
`Scoring Functions in Molecular Docking. J. Mol. Biol. 322, 339-355 (2002).
`42. B.M. Beadle and B.K. Shoichet.* A structural basis for imipenem inhibition of class C (cid:533)-lactamases.
`Antimicrobial Agents in Chemotherapy 46(12), (Dec, 2002).
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`43. F. Morandi, E. Caselli, S. Morandi, P.J. Focia, J. Blazquez, B.K. Shoichet* and F. Prati*. Nanomolar
`inhibitors of AmpC (cid:69)-lactamase. J. Am. Chem. Soc, 125, 685-695 (2003).
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`44. S.L. McGovern & B.K. Shoichet.* Kinase Inhibitors: not just for kinases anymore. J. Med. Chem.
`46, 1478-1483 (2003).
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`45. CE Atreya, EF Johnson, JJ Irwin, et al. BK Shoichet & Anderson KS*. A molecular docking strategy
`identifies eosin B as a non-active site inhibitor of protozoal bifunctional thymidylate synthase-
`dihydrofolate reductase. J Biol Chem. 278, 14092-100 (2003)
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`46. S. Soelaiman, BQ Wei, et al, BK Shoichet* & W-J Tang*. Structure-based inhibitor discovery against
`adenylyl cyclase toxins from pathogenic bacteria that cause anthrax and whooping cough. J. Biol.
`Chem. 278, 25990-7 (2003).
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`47. S.L. McGovern & B.K. Shoichet.* Information decay in molecular docking screens with decreasing
`definition of the receptor binding site. J. Med. Chem., 46, 2895-2907 (2003).
`48. X. Wang, G. Minasov & B.K. Shoichet.* Recognition and Resistance in TEM (cid:69)-lactamase.
`Biochemistry 42, 8434-8444 (2003).
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`49. SO Meroueh, G Minasov, W Lee, BK Shoichet, S Mobashery.* Structural aspects for evolution of
`beta-lactamases from penicillin-binding proteins. J Am Chem Soc. 125, 9612-8 (2003)
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`50. SL McGovern, B. Helfand, B. Feng & BK Shoichet.* A Specific Mechanism for Non-Specific
`Inhibition. J. Med. Chem. 46, 4265-72 (2003).
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`51. J. Seidler, SL McGovern, TN Doman & BK Shoichet.* Identification and Prediction of Promiscuous
`Drugs. J. Med. Chem. 46, 4477-4486 (2003)
`52. T. Roth, G. Minasov & BK Shoichet.* Thermodynamic Cycle Analysis & Inhibitor Design Against (cid:69)-
`lactamase. Biochemistry 42, 14483-91 (2003).
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`53. J Horn & BK Shoichet* Allosteric inhibition through core disruption. J. Mol. Biol. 336, 1283-91 (2004)
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`54. BQ Wei, L Weaver, AM Ferrari, BW Matthews* & BK Shoichet.* Testing a flexible-receptor docking
`algorithm in a model binding site. J. Mol. Biol. 337, 1161-82 (2004).
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`55. AM Ferrari, BQ Wei, L. Costantino & BK Shoichet.* Soft docking and multiple receptor conformations
`in virtual screening. J. Med. Chem. 47, 5076-84 (2004).
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`56. JJ Irwin* & BK Shoichet.* ZINC - A Free Database of Commercially Available Compounds for Virtual
`Screening. J Chem Inf Comput Sci. 45, 177-82 (2005)
`57. Y Chen, J Delmas, J Sirot, BK Shoichet* & R Bonnet.* Atomic resolution structures of CTX-M (cid:69)-
`lactamases: extended spectrum activities from increased mobility and decreased stability. J. Mol.
`Biol 348, 349-62 (2005).
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`58. Y Chen, BK Shoichet* & Richard Bonnet.* Structure, function & inhibition along the reaction
`coordinate of CTX-M (cid:69)-lactamases. J. Am. Chem. Soc. 127, 5423-34 (2005).
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`59. D Tondi, F Morandi, R Bonnet, MPCosti & BK Shoichet.* Structure-based optimization of a non-(cid:533)-
`lactam lead results in inhibitors that do not up-regulate (cid:533)-lactamase expression in cell culture. J. Am.
`Chem. Soc. 127, 4632-9 (2005).
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`60. AP Graves, R Brenk & BK Shoichet*. Decoys for Docking. J. Med. Chem. 48, 3714-28 (2005).
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`61. VL Thomas, D Golemi-Kotra, C Kim, SB Vakulenko, S Mobashery & BK Shoichet.* Structural
`Consequences of the Inhibitor-Resistant Ser130Gly Substitution in TEM (cid:533)-Lactamase. Biochemistry
`44, 9330-9338 (2005).
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`62. BY Feng, A Shelat, TN Doman, RK Guy, BK Shoichet*. High-throughput assays for promiscuous
`inhibitors. Nature Chem. Biol. 1, 146 - 148 (2005)
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`63. R Brenk, JJ Irwin & BK Shoichet*. Here be dragons: docking and screening in an uncharted region
`of chemical space. J Biomol Screen. 10, 667-74 (2005).
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`64. JJ Irwin, FM Raushel & BK Shoichet*. Virtual Screening against Metalloenzymes for Inhibitors and
`Substrates. Biochemistry 44, 12316-28 (2005)
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`65. DM. Lorber and Brian K. Shoichet* Hierarchical Docking of Databases of Multiple Ligand
`Conformations. Current Topics Med. Chem. 5, 739-749 (2005).
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`65. R Brenk, S Vetter, SE Boyce, DB Goodin & BK Shoichet.*. Probing molecular docking in a charged
`model binding site. J. Mol. Biol. 357, 1449-70 (2006).
`66. Y Chen, G Minasov, TA Roth, F Prati & BK Shoichet.* The Deacylation Mechanism of AmpC (cid:533)-
`lactamase at Ultra-High Resolution. J. Am. Chem. Soc. 128, 2970-6 (2006).
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`67. BY Feng & BK Shoichet.* Synergy and Antagonism of Promiscuous Inhibition in Multiple-Compound
`Mixtures. J. Med. Chem. 49, 2151-4 (2006).
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`68. BK Shoichet. Interpreting Steep Dose-Response Curves in Early Inhibitor Discovery. J Med
`Chem. 49, 7274-7277 (2006).
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`69. K Babaoglu & BK Shoichet.* Deconstructing Fragment-based Inhibitor Discovery. Nat. Chem. Biol
`2, 720-3 (2006).
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`70. Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ*, Shoichet BK.* Predicting substrates by
`docking high-energy intermediates to enzyme structures. J Am Chem Soc. 128,15882-91 (2006).
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`71. Nowlan C, Li Y, Hermann JC, Evans T, Carpenter J, Ghanem E, Shoichet BK, Raushel FM.
`Resolution of Chiral Phosphate, Phosphonate, and Phosphinate Esters by an Enantioselective
`Enzyme Library. J Am Chem Soc. 128,15892-902 (2006).
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`72. Niu Huang, Brian K. Shoichet* & John J. Irwin.* Benchmarking Sets for Molecular Docking. J. Med.
`Chem. 49, 6789-801(2006).
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`73. KE Coan & BK Shoichet*. Stability and equilibria of promiscuous aggregates in high protein milieus.
`Mol Biosyst. 3, 208-13 (2007).
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`74. MJ Keiser, BL Roth, BN Armbruster, P Ernsberger, JJ Irwin, BK Shoichet*. Relating protein
`pharmacology by ligand chemistry. Nat Biotech 25 (2), 197-206 (2007).
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`75. BY Feng, A Simeonov, A Jadhav, K Babaoglu, J Inglese, BK Shoichet* & CP. Austin.* A High-
`throughput Screen for Aggregation-based Inhibition in a Large Compound Library. J. Med. Chem.
`50, 2385-90 (2007)
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`76. Chen Y, Bonnet R, Shoichet BK*. The Acylation Mechanism of CTX-M beta-Lactamase at 0.88 A
`Resolution. J Am Chem Soc 129, 5378-5380 (2007).
`77. JC Hermann, R Mart(cid:531)-Arbona, AA Fedorov, E Federov, SC Almo, BK Shoichet*, FM Raushel.
`Structure-based activity prediction for an enzyme of unknown function. Nature (2007).
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`78. DL Mobley, AP Graves, JD Chodera, AC McReynolds, BK Shoichet*, KA Dill.* Predicting absolute
`ligand binding free energies to a simple model site. J Mol Biol. 371, 1118-34 (2007).
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`79. A Venturelli, D Tondi1,2, L Cancian, F Morandi G. Cannazza, B Segatore, B Prati, G Amicosante, BK
`Shoichet & MP Costi*. Optimizing Cell Permeation of an Antibiotic Resistance Inhibitor for Improved
`Efficacy. J. Med. Chem. 15, 5644-54 (2007).
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`80. S Morandi, F Morandi, BK Shoichet, E Caselli & F Prati*. Structure-based optimization of
`cephalothin-analog boronic acids as (cid:533)-lactamase inhibitors. Bioorg. Med. Chem. Let. in press (2007).
`81. Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC. Stability for Function Trade-Offs in
`the Enolase Superfamily 'Catalytic Module'. Biochemistry 46, 6688-95 (2007).
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`82. Wyrembak PN, Babaoglu K, Pelto RB, Shoichet BK, Pratt RF. O-Aryloxycarbonyl Hydroxamates:
`New (cid:533)-Lactamase Inhibitors That Cross-Link the Active Site. J Am Chem Soc 129, 9548-9 (2007).
`83. BY Feng, BH Toyama, H Wille, DW Colby, SR Collins, BC May, SB Prusiner, J Weissman & BK
`Shoichet* Promiscuous Small-molecule Aggregates Inhibit Amyloid Polymerization. Nature Chem.
`Biol 4, 197-199 (2008).
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`84. J Delmas, Y Chen, F Prati, F Robin, BK Shoichet & R Bonnet*. Structure and dynamics of CTX-M
`enzymes reveal insights into substrate accommodation by extended-spectrum beta-lactamases. J
`Mol Biol. 375,192-201.
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`85. S Morandi, F Morandi, E Caselli, BK Shoichet, F Prati*. Structure-based optimization of cephalothin-
`analogue boronic acids as (cid:533)-lactamase inhibitors. Bioorg Med Chem 16, 1195-205 (2008)
`86. Venturelli A, Tondi D, Cancian L, Morandi F, Cannazza G, Segatore B, Prati F, Amicosante G,
`Shoichet BK, Costi MP*. Optimizing cell permeation of an antibiotic resistance inhibitor for improved
`efficacy. J Med Chem. 50, 5644-54 (2008)
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`87. K Babaoglu, A Simeonov, JJ Irwin, ME Nelson, B Feng, CJ Thomas, L Cancian, MP Costi, DA
`Maltby, A Jadhav, J Inglese, CP Austin* & BK Shoichet*. A Comprehensive mechanistic analysis of
`hits from high-throughput and docking screens against (cid:533)-Lactamase. J Med Chem 51, 2502-08
`(2008)
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`88. J. Hert, MJ Keiser, JJ Irwin, TI Oprea & BK Shoichet.* Quantifying the relationships among drug
`classes. J. Chem. Inf. Model. 48, 755-65 (2008).
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`89. AP Graves, DM Shivakumar, SE Boyce, MP Jacobson, DA Case, & BK Shoichet.* Rescoring
`docking hit lists for model cavity sites: predictions and experimental testing. J. Mol. Biol. 377, 914-34
`(2008).
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`90. KE Coan & BK Shoichet. Stoichiometry and physical chemistry of promiscuous aggregate-based
`inhibitors. J Am Chem Soc 130, 9606-12 (2008).
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`91. N Huang & BK Shoichet. Exploiting ordered waters in molecular docking. J Med Chem 51, 4862-5.
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`92. Marciano DC, et al., Shoichet BK, Palzkill T. Genetic and Structural Characterization of an L201P
`Global Suppressor Substitution in TEM-1 beta-Lactamase. J Mol Biol. Sep 16 e-pub (2008).
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`93. Y Chen and BK Shoichet* Molecular docking and ligand specificity in fragment-based inhibitor
`discovery. Nature Chem. Biol. 5, 358-64 (2009).
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`94. J Hert, JJ Irwin, C Laggner, MJ Keiser & BK Shoichet*. Quantifying Library Bias in Screening
`Success. Nature Chem. Biol. 5, 479-83 (2009).
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`95. P Kolb1,*, DM Rosenbaum2,*, JJ Irwin1, JJ Fung, BK Kobilka* & BK Shoichet*. Structure-based
`discovery of (cid:533)2-adrenergic receptor ligands. Proc. Natl. Acad. Sci. 106, 6843-8 (2009).
`96. DG Teotico, K Babaoglu, et al & BK Shoichet. Docking for fragment inhibitors of AmpC (cid:533)-lactamase:
`hit-rates, structures and chemical space. Proc. Natl. Acad. Sci. 106, 7455-60 (2009). PMC2671983
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`97. KE Coan, DA Maltby, AL Burlingame & BK Shoichet. Promiscuous Aggregate-Based Inhibitors
`Promote Enzyme Unfolding. J Med Chem 52, 2067-2075 (2009). PMCID: PMC2664636
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`98. RS Ferreira, C Bryant, KK Ang, JH McKerrow, BK Shoichet, AR Renslo. Divergent Modes of
`Enzyme Inhibition in a Homologous Structure-Activity Series. J Med Chem. 2009 Jul 28 E-pub.
`PMID: 19637873
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`99. JJ Irwin, BK Shoichet, MM Mysinger, N Huang, F Colizzi, P Wassam, Y Cao. Automated docking
`screens: a feasibility study. J Med Chem. 52 5712-20 (2009). PMID: 19719084
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`100. SE Boyce, DL Mobley, GJ Rocklin, AP Graves, KA Dill, BK Shoichet..Predicting Ligand Binding
`Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site. J Mol Biol. 394, 747-
`63 (2009). PMC2788029
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`101. Y. Chen, W Zhang, Q Shi, D Hesek, M Lee, S Mobashery, BK Shoichet. Crystal structures of
`penicillin-binding protein 6 from Escherichia coli. J Am Chem Soc. 131, 14345-54 (2009). PMID:
`19807181
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`102. H Fan, JJ Irwin, BM Webb, G Klebe, BK Shoichet*, Sali A*. Molecular Docking Screens Using
`Comparative Models of Proteins. J Chem Inf Model. 49, 2512-27 (2009). PMID: 19845314
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`103. MJ Keiser, V Setola, JJ Irwin et al., BK Shoichet* & BL Roth. Predicting new molecular targets for
`known drugs. Nature, 462, 175-81 (2009).
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`104. Hall RS, Fedorov AA, Marti-Arbona R, Fedorov EV, Kolb P, Sauder JM, Burley SK, Shoichet BK,
`Almo SC, Raushel FM. The hunt for 8-oxoguanine deaminase. J Am Chem Soc. 132, 1762-3 (2010)
`PMID: 20088583.
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`105. Mott BT, Ferreira RS, Simeonov A, Jadhav A, Ang KK, Leister W, Shen M, Silveira JT, Doyle PS,
`Arkin MR, McKerrow JH, Inglese J, Austin CP, Thomas CJ, Shoichet BK, Maloney DJ. Identification
`and optimization of inhibitors of Trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB.
`J Med Chem., 53 52-60. (2010) PMID: 19908842.
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`106. Jadhav A, Ferreira RS, Klumpp C, Mott BT, Austin CP, Inglese J, Thomas CJ, Maloney DJ, Shoichet
`BK, Simeonov A. Quantitative analyses of aggregation, autofluorescence, and reactivity artifacts in a
`screen for inhibitors of a thiol protease. J Med Chem. 53, 37-51 (2010)
`
`107. Cummings JA, Nguyen TT, Fedorov AA, Kolb P, Xu C, Fedorov EV, Shoichet BK, Barondeau DP,
`Almo SC, Raushel FM. Structure, mechanism, and substrate profile for Sco3058: the closest
`bacterial homologue to human renal dipeptidase . Biochemistry 49, 611-22. (2010) PMID:
`20000809
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`108. Thomas VL, McReynolds AC, Shoichet BK. Structural bases for stability-function tradeoffs in
`antibiotic resistance. J Mol Biol. 396, 47-59 (2010) PMID: 19913034
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`109. Kokel D, Bryan J, Laggner C, White R, Cheung CY, Mateus R, Healey D, Kim S, Werdich AA,
`Haggarty SJ, Macrae CA, Shoichet B, Peterson RT. Rapid behavior-based identification of
`neuroactive small molecules in the zebrafish. Nat Chem Biol. 6, 231-237 (2010).PMID: 20081854
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`110. Degraw AJ, Keiser MJ, Ochocki JD, Shoichet BK*, Distefano MD.* Prediction & evaluation of protein
`farnesyltransferase inhibition by commercial drugs. J Med Chem 53, 2464-71 (2010) PMID:20180535
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`111. Carlsson J, Yoo L, Gao ZG, Irwin JJ, Shoichet BK, Jacobson KA. Structure-based discovery of A2A
`adenosine receptor ligands. J Med Chem. 53, 3748-55 (2010). PMID: 20405927
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`112. Doak AK, Wille H, Prusiner SB, Shoichet BK. Colloid formation by drugs in simulated intestinal fluid.
`J Med Chem. 53, 4259-65 (2010) PMID: 20426472.
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`113. Tondi D, Calò S, Shoichet BK, Costi MP. Structural study of phenyl boronic acid derivatives as
`AmpC beta-lactamase inhibitors. Bioorg Med Chem Lett. 20, 3416-9. (2010) PMC3166525
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`114. RS Hall, AA Fedorov, R Marti-Arbona, EV Fedorov, P Kolb, JM Sauder, SK Burley, BK Shoichet, SC
`Almo & FM Raushel. The hunt for 8-oxoguanine deaminase. J Am Chem Soc.132, 1762-3 (2010).
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`January, 2015
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`115. Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ, McKerrow JH, Maloney DJ, Irwin
`JJ, Shoichet BK. Complementarity between a docking and a high-throughput screen in discovering
`new cruzain inhibitors J Med Chem. 53 4891-905 (2010) PMC2895358.
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`116. MM Mysinger, BK Shoichet. Rapid Context-Dependent Ligand Desolvation in Molecular Docking. J.
`Chem. Inf. Modeling 50, 1561-73 (2010).
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`117. O Eidam, C Romagnoli, E Caselli, K Babaoglu, DT Pohlhaus, J Karpiak, R Bonnet, BK Shoichet* &
`Fabio Prati.* Design, Synthesis, Crystal Structures, and Antimicrobial Activity of Sulfonamide Boronic
`Acids as (cid:533)-Lactamase Inhibitors J. Med. Chem. 53, 7852-63. (2010). PMC3166525
`118. PN Yadav, AI Abbas, MS Farrell, V Setola, N Sciaky, XP Huang, WK Kroeze, LK Crawford, DA Piel,
`MJ Keiser, JJ Irwin, BK Shoichet