Publications

2008

• Delmas J, Chen Y, Prati F, Robin F, Shoichet BK, Bonnet R. Structure and dynamics of CTX-M enzymes reveal insights into substrate accommodation by extended-spectrum beta-lactamases. J Mol Biol 375 (1), 192-201 (2008). [Pubmed | DOI]

• Feng BY, Toyama BH, Wille H, Colby DW, Collins SR, May BC, Prusiner SB, Weissman J, Shoichet BK. Small-molecule aggregates inhibit amyloid polymerization. Nat Chem Biol 4 (3), 197-9 (2008). [Pubmed | DOI | Download PDF]

• Morandi S, Morandi F, Caselli E, Shoichet BK, Prati F. Structure-based optimization of cephalothin-analogue boronic acids as beta-lactamase inhibitors. Bioorg Med Chem 16 (3), 1195-205 (2008). [Pubmed | DOI]

2007

• Chen Y, Bonnet R, Shoichet BK. The Acylation Mechanism of CTX-M beta-Lactamase at 0.88 A Resolution. J Am Chem Soc 129 (17), 5378-5380 (2007). [Pubmed | DOI]

• Coan KE, Shoichet BK. Stability and equilibria of promiscuous aggregates in high protein milieus. Mol Biosyst 3 (3), 208-13 (2007). [Pubmed | DOI]

• Feng BY, Simeonov A, Jadhav A, Babaoglu K, Inglese J, Shoichet BK, Austin CP. A High-Throughput Screen for Aggregation-Based Inhibition in a Large Compound Library. J Med Chem 50 (10), 2385-2390 (2007). [Pubmed | DOI | Download screening results]

Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM. Structure-based activity prediction for an enzyme of unknown function. Nature 448 (7155), 775-9 (2007). [Pubmed | DOI]

• Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotech 25 (2), 197-206 (2007). [Pubmed | DOI | Download PDF]

• Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA. Predicting Absolute Ligand Binding Free Energies to a Simple Model Site. J Mol Biol 371 (4), 1118-1134 (2007). [Pubmed | DOI]

• Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC. Stability for Function Trade-Offs in the Enolase Superfamily 'Catalytic Module'. Biochemistry 46 (23), 6688-95 (2007). [Pubmed | DOI]

• Shoichet BK. No free energy lunch. Nat Biotechnol 25 (10), 1109-10 (2007). [Pubmed | DOI]

• 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 (23), 5644-54 (2007). [Pubmed | DOI]

• Wyrembak PN, Babaoglu K, Pelto RB, Shoichet BK, Pratt RF. O-Aryloxycarbonyl Hydroxamates: New beta-Lactamase Inhibitors That Cross-Link the Active Site. J Am Chem Soc 129 (31), 9548-9 (2007). [Pubmed | DOI]

2006

• Babaoglu K, Shoichet BK. Deconstructing fragment-based inhibitor discovery. Nat Chem Biol 2 (12), 720-3 (2006). [Pubmed | DOI | Download PDF]

• Brenk R, Vetter SW, Boyce SE, Goodin DB, Shoichet BK. Probing molecular docking in a charged model binding site. J Mol Biol 357 (5), 1449-70 (2006). [Pubmed | DOI | Download PDF]

• Chen Y, Minasov G, Roth TA, Prati F, Shoichet BK. The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution. J Am Chem Soc 128 (9), 2970-6 (2006). [Pubmed | DOI | Download PDF]

• Feng BY, Shoichet BK. Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures. J Med Chem 49 (7), 2151-4 (2006). [Pubmed | DOI | Download PDF]

• Feng BY, Shoichet BK. A detergent-based assay for the detection of promiscuous inhibitors. Nature Protocols 1, 550-3 (2006). [Pubmed | DOI | Download PDF]

• 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 (49), 15882-891 (2006). [Pubmed | DOI | Download PDF]

• Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem 49 (23), 6789-801 (2006). [Pubmed | DOI | Download PDF]

• Leach AR, Shoichet BK, Peishoff CE. Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. J Med Chem 49 (20), 5851-5 (2006). [Pubmed | DOI]

• 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 (49), 15892-902 (2006). [Pubmed | DOI]

• Shoichet BK. Screening in a spirit haunted world. Drug Discov Today 11 (13-14), 607-15 (2006). [Pubmed | DOI | Download PDF]

• Shoichet BK. Interpreting Steep Dose-Response Curves in Early Inhibitor Discovery. J Med Chem 49 (25), 7274-7277 (2006). [Pubmed | DOI | Download PDF]

2005

Brenk R, Irwin JJ, Shoichet BK. Here be dragons: docking and screening in an uncharted region of chemical space. J Biomol Screen 10 (7), 667-74 (2005). [Pubmed | DOI | Download PDF]

• Chen Y, Delmas J, Sirot J, Shoichet B, Bonnet R. Atomic Resolution Structures of CTX-M beta-Lactamases: Extended Spectrum Acti vities from Increased Mobility and Decreased Stability. J Mol Biol 348 (2), 349-62 (2005). [Pubmed | DOI | PDB 1YLT | PDB 1YLJ | PDB 1YLP | PDB 1YLW | Download PDF]

• Chen Y, Shoichet B, Bonnet R. Structure, function, and inhibition along the reaction coordinate of CTX-M beta-lactamases. J Am Chem Soc 127 (15), 5423-34 (2005). [Pubmed | DOI | Download PDF]

Feng BY, Shelat A, Doman TN, Guy RK, Shoichet BK. High-throughput assays for promiscuous inhibitors. Nature Chem Biol 1 (3), 146-8 (2005). [Pubmed | DOI | Download PDF]

• Graves AP, Brenk R, Shoichet BK. Decoys for Docking. J Med Chem 48 (11), 3714 - 372 (2005). [Pubmed | DOI | PDB 1XEP | Download PDF]

• Irwin JJ, Raushel FM, Shoichet BK. Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry 44 (37), 12316-28 (2005). [Pubmed | DOI | Download PDF]

• Irwin JJ, Shoichet BK. ZINC - A Free Database of Commercially Available Compounds for Virtual Screening. J Chem Inf Model 45 (1), 177-82 (2005). [Pubmed | DOI | Supporting Info | Download PDF]

• Lorber DM, Shoichet BK. Hierarchical docking of databases of multiple ligand conformations. Curr Top Med Chem 5 (8), 739-49 (2005). [Pubmed | Download PDF]

• Thomas VL, Golemi-Kotra D, Kim C, Vakulenko SB, Mobashery S, Shoichet BK. Structural consequences of the inhibitor-resistant Ser130Gly substitution in TEM beta-lactamase. Biochemistry 44 ( 26), 9330-9338 (2005). [Pubmed | DOI | Download PDF]

• Tondi D, Morandi F, Bonnet R, Costi MP, Shoichet BK. Structure-Based Optimization of a Non-beta-lactam Lead Results in Inhibitors That Do Not Up-Regulate beta-Lactamase Expression in Cell Culture. J Am Chem Soc 127 (13), 5423-34 (2005). [Pubmed | DOI | PDB 1XGJ | PDB 1XGI | Download PDF]

2004

• Ferrari AM, Wei BQ, Costantino L, Shoichet BK. Soft Docking and Multiple Receptor Conformations in Virtual Screening. J Med Chem 47 (21), 5076 -84 (2004). [Pubmed | DOI | Download PDF]

Horn J, Shoichet BK. Allosteric Inhibition through Core Disruption. J Mol Biol 336 (5), 1283-91 (2004). [Pubmed | DOI | PDB 1PZP | PDB 1PZO | Download PDF]

• Shoichet BK. Virtual Screening of Chemical Libraries (Review). Nature 432, 40-43 (2004). [Pubmed | DOI | Download free Pubmedcentral version]

• Wei BQ, Weaver L, Ferrari AM, Matthews BM, Shoichet BK. Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol 337 (5), 1161-82 (2004). [Pubmed | DOI | Supplementary Material | PDB 1OV5 | PDB 1OV7 | PDB 1OVH | PDB 1OVJ | PDB 1OVK | PDB 1OWY | PDB 1OWZ | Download PDF]

2003

• Atreya CE, Johnson EF, Irwin JJ, Dow A, Massimine KM, Coppens I, Stempliuk V, Beverley S, Joiner KA, Shoichet BK, 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 (16), 14092-100 (2003). [Pubmed | DOI | Faculty of 1000 | Download PDF]

• McGovern SL, Helfand BT, Feng B, Shoichet BK. A Specific Mechanism of Nonspecific Inhibition. J Med Chem 46 (20), 4265-72 (2003). [Pubmed | DOI | Download PDF]

• McGovern SL, Shoichet BK. Kinase inhibitors: not just for kinases anymore. J Med Chem 46 (8), 1478-83 (2003). [Pubmed | DOI | In Brief | Faculty of 1000 | Download PDF]

• McGovern SL, Shoichet BK. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem 46 (14), 2895-907 (2003). [Pubmed | DOI | Supporting Info | Download PDF]

• Meroueh SO, Minasov G, Lee W, Shoichet BK, Mobashery S. Structural aspects for evolution of beta-lactamases from penicillin-binding proteins. J Am Chem Soc 125 (32), 9612-8 (2003). [Pubmed | DOI | Download PDF]

• Morandi F, Caselli E, Morandi S, Focia PJ, Blazquez J, Shoichet BK, Prati F. Nanomolar inhibitors of AmpC beta-lactamase. J Am Chem Soc 125 (3), 685-95 (2003). [Pubmed | DOI | PDB 1MXO | PDB 1MY8 | News In Brief]

• Roth TA, Minasov G, Morandi S, Prati F, Shoichet BK. Thermodynamic cycle analysis and inhibitor design against beta-lactamase. Biochemistry 42 (49), 14483-91 (2003). [Pubmed | DOI | Download PDF]

• Seidler J, McGovern SL, Doman TN, Shoichet BK. Identification and Prediction of Promiscuous Aggregating Inhibitors among Known Drugs. J Med Chem 46 (21), 4477-86 (2003). [Pubmed | DOI | Supporting Info | newsinbrief | Download PDF]

• Soelaiman S, Wei BQ, Bergson P, Lee YS, Shen Y, Mrksich M, Shoichet BK*, Tang WJ*. Structure-based inhibitor discovery against adenylyl cyclase toxins from pathogenic bacteria that cause anthrax and whooping cough. J Biol Chem 278 (28), 25990-7 (2003). [Pubmed | DOI | Download PDF]

• Wang X, Minasov G, Blazquez J, Caselli E, Prati F, Shoichet BK. Recognition and resistance in TEM beta-lactamase. Biochemistry 42 (28), 8434-44 (2003). [Pubmed | DOI | Download PDF]

2002

• Beadle BM, Shoichet BK. Structural basis for imipenem inhibition of class C beta-lactamases. Antimicrob Agents Chemother 46 (12), 3978-80 (2002). [Pubmed | DOI | PDB 1LL5 | Download PDF]

• Beadle BM, Shoichet BK. Structural bases of stability-function tradeoffs in enzymes. J Mol Biol 321 (2), 285-96 (2002). [Pubmed | DOI | PDB 1L0D | PDB 1L0E | PDB 1L0F | PDB 1L0G | Download PDF]

• Beadle BM, Trehan I, Focia PJ, Shoichet BK. Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase. Structure (Camb) 10 (3), 413-24 (2002). [Pubmed | DOI | Erratum | Download PDF]

• Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, Stallings WC, Connolly DT, Shoichet BK. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem 45 (11), 2213-21 (2002). [Pubmed | DOI | NRDD Highlight | Faculty of 1000 | Download PDF]

• Lorber DM, Udo MK, Shoichet BK. Protein-protein docking with multiple residue conformations and residue substitutions. Protein Science 11, 1393-1408 (2002). [Pubmed | DOI | Supplemental Data | Download PDF]

• McGovern SL, Caselli E, Grigorieff N, Shoichet BK. A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening. J Med Chem 45 (8), 1712-22 (2002). [Pubmed | DOI | Supporting Information | C & EN News of the Week | NRDD Highlight | ESI Special Topics | Download PDF]

• Minasov G, Wang X, Shoichet BK. An ultrahigh resolution structure of TEM-1 ß-lactamase suggests a role for Glu166 as the general base in acylation. J Am Chem Soc 124 (19), 5333-40 (2002). [Pubmed | DOI | PDB 1M40 | Download PDF]

Powers RA, Morandi F, Shoichet BK. Structure-based discovery of a novel, non-covalent inhibitor of AmpC ß-lactamase. Structure 10 (7), 1013-23 (2002). [Pubmed | DOI | PDB 1L2S | Download PDF]

• Powers RA, Shoichet BK. Structure-based approach for binding site identification on AmpC ß-lactamase. J Med Chem 45 (15), 3222-34 (2002). [Pubmed | DOI | Supporting Info | PDB 1KDS | PDB 1KDW | PDB 1KE0 | PDB 1KE3 | PDB 1KE4 | Download PDF]

• Shoichet BK, McGovern SL, Wei B, Irwin JJ. Lead discovery using molecular docking (Review). Current Opinion in Chemical Biology 6, 439-46 (2002). [Pubmed | DOI | Download PDF]

• Trehan I, Morandi F, Blaszczak LC, Shoichet BK. Using steric hindrance to design new inhibitors of class C ß-lactamases. Chem Biol 9 (9), 971-80 (2002). [Pubmed | DOI | PDB 1LL9 | PDB 1LLB | Download PDF]

• Wang X, Minasov G, Shoichet BK. The structural bases of antibiotic resistance in the clinically-derived mutant ß-lactamases TEM-30, TEM-32, and TEM-34. J Biol Chem 277 (35), 32149-56 (2002). [Pubmed | DOI | PDB 1LHY | PDB 1LI0 | PDB 1LI9 | Download PDF]

Wang X, Minasov G, Shoichet BK. Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol 320 (1), 85-95 (2002). [Pubmed | DOI | PDB 1JWP | PDB 1JWV | PDB 1JWZ | Download PDF]

• Wang X, Minasov G, Shoichet BK. Non-covalent interaction energies in covalent complexes: TEM-1 ß-lactamase and ß-lactams. Proteins 47 (1), 86-96 (2002). [Pubmed | DOI | PDB 1JVJ | Download PDF]

• Wei BQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK. A model binding site for testing scoring functions in molecular docking. J Mol Biol 322, 339-55 (2002). [Pubmed | DOI | PDB 1LGU | PDB 1LGW | PDB 1LGX | PDB 1LI2 | PDB 1LI3 | PDB 1LI6 | Download PDF]

2001

• Beadle BM, Nicholas RA, Shoichet BK. Interaction energies between beta-lactam antibiotics and E. coli penicillin-binding protein 5 by reversible thermal denaturation. Protein Sci 10 (6), 1254-9 (2001). [Pubmed | DOI]

Caselli E, Powers RA, Blasczcak LC, Wu CY, Prati F, Shoichet BK. Energetic, structural, and antimicrobial analyses of beta-lactam side chain recognition by beta-lactamases. Chem Biol 8 (1), 17-31 (2001). [Pubmed | DOI | PDB 1FSW | PDB 1FSY]

• Powers RA, Caselli E, Focia PJ, Prati F, Shoichet BK. Structures of ceftazidime and its transition-state analogue in complex with AmpC beta-lactamase: implications for resistance mutations and inhibitor design. Biochemistry 40 (31), 9207-14 (2001). [Pubmed | DOI | PDB 1IEL | PDB 1IEM]

• Su AI, Lorber DM, Weston GS, Baase WA, Matthew BW, Shoichet BK. Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation. Proteins 42, 279-93 (2001). [Pubmed | DOI | Supplementary Material]

• Tondi D, Powers RA, Caselli E, Negri M, Blazquez J, Costi MP, Shoichet BK. Structure-based design and in-parallel synthesis of inhibitors of AmpC ß-lactamases. Chem Biol 8 (6), 593-611 (2001). [Pubmed | DOI | PDB 1GA9]

• Trehan I, Beadle BM, Shoichet BK. Inhibition of AmpC ß-lactamase through a destabilizing interaction in the active site. Biochemistry 40 (27), 7992-9 (2001). [Pubmed | DOI | PDB 1I5Q]

2000

• Patera A, Blaszczak LC, Shoichet BK. Crystal structures of substrate and inhibitor complexes with AmpC ß-lactamase: possible implications for substrate-assisted catalysis. J Am Chem Soc 122 (43), 10504-12 (2000). [DOI | PDB 1FCM | PDB 1FCN | PDB 1FCO]

• Shoichet BK, Bussiere DE. Macromolecular crystallography and lead discovery: possibilities and limitations (Review). Current Opinion in Drug Discovery & Development 3, 408-22 (2000).

1999

• Beadle BM, Baase WA, Wilson DB, Gilkes NR, Shoichet BK. Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme. Biochemistry 38, 2570-2576 (1999). [Pubmed | DOI]

• Beadle BM, McGovern SL, Patera A, Shoichet BK. Functional analyses of AmpC ß-lactamase through differential stability. Protein Sci 8 (9), 1816-24 (1999). [Pubmed]

• Powers RA, Blazquez J, Weston GS, Morosini MI, Baquero F, Shoichet BK. The complexed structure and antimicrobial activity of a non-β-lactam inhibitor of AmpC β-lactamase. Protein Science 8, 2330-2337 (1999). [Pubmed | DOI]

• Shoichet BK, Leach AR, Kuntz ID. Ligand solvation in molecular docking. Proteins 34, 4-16 (1999). [Pubmed | DOI]

• Stout TJ, Tondi D, Rinaldi M, Barlocco D, Pecorari P, Santi DV, Kuntz ID, Stroud RM, Shoichet BK, Costi MP. Structure-based design of inhibitors specific for bacterial thymidylate synthase. Biochemistry 38, 1607-1617 (1999). [Pubmed | DOI | PDB 1TSL]

• Tondi D, Slomczynska U, Costi MP, Watterson DM, Ghelli S, Shoichet BK. Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase. Chem Biol 6 (5), 319-31 (1999). [Pubmed | DOI]

1998

• Lorber DM, Shoichet BK. Flexible ligand docking using conformational ensembles. Protein Science 7, 938-950 (1998). [Pubmed | DOI]

• Morosini MI, Negri MC, Shoichet B, Baquero MR, Baquero F, Blazquez J. An extended-spectrum AmpC-type β-lactamase obtained by in vitro antibiotic selection. FEMS Microbiology Letters 165, 85-90 (1998). [Pubmed | DOI]

• Usher KC, Blaszczak LC, Weston GS, Shoichet BK, Remington SJ. Three-dimensional structure of AmpC β-lactamase from Escherichia coli bound to a transition-state analogue: possible implications for the oxyanion hypothesis and for inhibitor design. Biochemistry 37, 16082-1609 (1998). [Pubmed | DOI | PDB 2BLS]

• Weston GS, Blazquez J, Baquero F, Shoichet BK. Structure-based enhancement of boronic acid-based inhibitors of AmpC β-lactamase. Journal of Medicinal Chemistry 41, 4577-4586 (1998). [Pubmed | DOI]

1997

• Shoichet BK. Receptor Preorganization for Activity and its Role in Identifying Ligand-Binding Sites on Proteins. In Practical Application of Computer-Aided Drug Design (ed. Charifson PS), pp. 195-226 (Marcel Dekker Inc, New York, 1997).

1996

• Shoichet BK, Kuntz ID. Predicting the structure of protein complexes: a step in the right direction (Review). Chemistry & Biology 3, 151-6 (1996). [Pubmed]

• Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MN. Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase. Nature Structural Biology 3, 233-239 (1996). [Pubmed | DOI]

1995

• Shoichet BK, Baase WA, Kuroki R, Matthews BW. A relationship between protein stability and protein function. Proc Natl Acad Sci U S A 92 (2), 452-6 (1995). [Pubmed | PDF | PDB 253L | PDB 254L | PDB 255L]

• Zhang XJ, Baase WA, Shoichet BK, Wilson KP, Matthews BW. Enhancement of protein stability by the combination of point mutations in T4 lysozyme is additive. Protein Engineering 8, 1017-1022 (1995). [Pubmed | DOI]

1994

• Kuntz ID, Meng EC, Shoichet BK. Structure-based molecular design. Accounts of Chemical Research 27, 117-123 (1994). [DOI]

• Schellenberger U, Balaram P, Francis VS, Shoichet BK, Santi DV. Partial restoration of activity to Lactobacillus casei thymidylate synthase following inactivation by domain deletion. Biochemistry 33, 5623-5629 (1994). [Pubmed | DOI]

1993

• Shoichet BK, Kuntz ID. Matching chemistry and shape in molecular docking. Protein Engineering 6, 723-732 (1993). [Pubmed | DOI]

• Shoichet BK, Stroud RM, Santi DV, Kuntz ID, Perry KM. Structure-based discovery of inhibitors of thymidylate synthase. Science 259, 1445-1450 (1993). [Pubmed | DOI]

1992

• Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid-based energy evaluation. Journal of Computational Chemistry 13, 505-524 (1992). [DOI]

• Shoichet BK, Bodian DL, Kuntz ID. Molecular docking using shape descriptors. Journal of Computational Chemistry 13, 380-397 (1992). [DOI]

1991

• Shoichet BK, Kuntz ID. Protein docking and complementarity. Journal of Molecular Biology 221, 327-346 (1991). [Pubmed | DOI]

1989

• Sowdhamini R, Srinivasan N, Shoichet B, Santi DV, Ramakrishnan C, Balaram P. Stereochemical modeling of disulfide bridges: criteria for introduction into proteins by site-directed mutagenesis. Protein Engineering 3, 95-103 (1989). [Pubmed | DOI]