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Items: 1 to 50 of 199

1.

The Recognition of Unrelated Ligands by Individual Proteins.

Pottel J, Levit A, Korczynska M, Fischer M, Shoichet BK.

ACS Chem Biol. 2018 Aug 10. doi: 10.1021/acschembio.8b00443. [Epub ahead of print]

PMID:
30095890
2.

Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets.

Weiss DR, Karpiak J, Huang XP, Sassano MF, Lyu J, Roth BL, Shoichet BK.

J Med Chem. 2018 Aug 9;61(15):6830-6845. doi: 10.1021/acs.jmedchem.8b00718. Epub 2018 Jul 24.

PMID:
29990431
3.

Structure of the D2 dopamine receptor bound to the atypical antipsychotic drug risperidone.

Wang S, Che T, Levit A, Shoichet BK, Wacker D, Roth BL.

Nature. 2018 Mar 8;555(7695):269-273. doi: 10.1038/nature25758. Epub 2018 Jan 24.

4.

Structure-based discovery of selective positive allosteric modulators of antagonists for the M2 muscarinic acetylcholine receptor.

Korczynska M, Clark MJ, Valant C, Xu J, Moo EV, Albold S, Weiss DR, Torosyan H, Huang W, Kruse AC, Lyda BR, May LT, Baltos JA, Sexton PM, Kobilka BK, Christopoulos A, Shoichet BK, Sunahara RK.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2419-E2428. doi: 10.1073/pnas.1718037115. Epub 2018 Feb 16.

5.

Prediction of enzymatic pathways by integrative pathway mapping.

Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, Shoichet BK, Sali A.

Elife. 2018 Jan 29;7. pii: e31097. doi: 10.7554/eLife.31097.

6.

Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs.

McCorvy JD, Butler KV, Kelly B, Rechsteiner K, Karpiak J, Betz RM, Kormos BL, Shoichet BK, Dror RO, Jin J, Roth BL.

Nat Chem Biol. 2018 Feb;14(2):126-134. doi: 10.1038/nchembio.2527. Epub 2017 Dec 11.

7.

Structure-Based Design and Discovery of New M2 Receptor Agonists.

Fish I, Stößel A, Eitel K, Valant C, Albold S, Huebner H, Möller D, Clark MJ, Sunahara RK, Christopoulos A, Shoichet BK, Gmeiner P.

J Med Chem. 2017 Nov 22;60(22):9239-9250. doi: 10.1021/acs.jmedchem.7b01113. Epub 2017 Nov 13.

PMID:
29094937
8.

D4 dopamine receptor high-resolution structures enable the discovery of selective agonists.

Wang S, Wacker D, Levit A, Che T, Betz RM, McCorvy JD, Venkatakrishnan AJ, Huang XP, Dror RO, Shoichet BK, Roth BL.

Science. 2017 Oct 20;358(6361):381-386. doi: 10.1126/science.aan5468.

9.

Discovery of new GPCR ligands to illuminate new biology.

Roth BL, Irwin JJ, Shoichet BK.

Nat Chem Biol. 2017 Nov;13(11):1143-1151. doi: 10.1038/nchembio.2490. Epub 2017 Oct 18.

10.

Reverse translation of adverse event reports paves the way for de-risking preclinical off-targets.

Maciejewski M, Lounkine E, Whitebread S, Farmer P, DuMouchel W, Shoichet BK, Urban L.

Elife. 2017 Aug 8;6. pii: e25818. doi: 10.7554/eLife.25818.

11.

Testing inhomogeneous solvation theory in structure-based ligand discovery.

Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK.

Proc Natl Acad Sci U S A. 2017 Aug 15;114(33):E6839-E6846. doi: 10.1073/pnas.1703287114. Epub 2017 Jul 31.

12.

Leveraging Colloidal Aggregation for Drug-Rich Nanoparticle Formulations.

Ganesh AN, Logie J, McLaughlin CK, Barthel BL, Koch TH, Shoichet BK, Shoichet MS.

Mol Pharm. 2017 Jun 5;14(6):1852-1860. doi: 10.1021/acs.molpharmaceut.6b01015. Epub 2017 May 19.

13.

A New Spin on Antibody-Drug Conjugates: Trastuzumab-Fulvestrant Colloidal Drug Aggregates Target HER2-Positive Cells.

Ganesh AN, McLaughlin CK, Duan D, Shoichet BK, Shoichet MS.

ACS Appl Mater Interfaces. 2017 Apr 12;9(14):12195-12202. doi: 10.1021/acsami.6b15987. Epub 2017 Mar 28.

14.

In silico design of novel probes for the atypical opioid receptor MRGPRX2.

Lansu K, Karpiak J, Liu J, Huang XP, McCorvy JD, Kroeze WK, Che T, Nagase H, Carroll FI, Jin J, Shoichet BK, Roth BL.

Nat Chem Biol. 2017 May;13(5):529-536. doi: 10.1038/nchembio.2334. Epub 2017 Mar 13.

15.

Crystal Structure of an LSD-Bound Human Serotonin Receptor.

Wacker D, Wang S, McCorvy JD, Betz RM, Venkatakrishnan AJ, Levit A, Lansu K, Schools ZL, Che T, Nichols DE, Shoichet BK, Dror RO, Roth BL.

Cell. 2017 Jan 26;168(3):377-389.e12. doi: 10.1016/j.cell.2016.12.033.

16.

Internal Structure and Preferential Protein Binding of Colloidal Aggregates.

Duan D, Torosyan H, Elnatan D, McLaughlin CK, Logie J, Shoichet MS, Agard DA, Shoichet BK.

ACS Chem Biol. 2017 Jan 20;12(1):282-290. doi: 10.1021/acschembio.6b00791. Epub 2016 Dec 16.

17.

Design, Synthesis, and Biological Evaluation of Novel Tetrahydroprotoberberine Derivatives (THPBs) as Selective α1A-Adrenoceptor Antagonists.

Guo D, Li J, Lin H, Zhou Y, Chen Y, Zhao F, Sun H, Zhang D, Li H, Shoichet BK, Shan L, Zhang W, Xie X, Jiang H, Liu H.

J Med Chem. 2016 Oct 27;59(20):9489-9502. Epub 2016 Oct 12.

PMID:
27709945
18.

Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics.

Lee H, Fischer M, Shoichet BK, Liu SY.

J Am Chem Soc. 2016 Sep 21;138(37):12021-4. doi: 10.1021/jacs.6b06566. Epub 2016 Sep 12.

19.

A Molecular Basis for Innovation in Drug Excipients.

Irwin JJ, Pottel J, Zou L, Wen H, Zuk S, Zhang X, Sterling T, Shoichet BK, Lionberger R, Giacomini KM.

Clin Pharmacol Ther. 2017 Mar;101(3):320-323. doi: 10.1002/cpt.458. Epub 2016 Sep 28. Review.

PMID:
27557422
20.

Structure-based discovery of opioid analgesics with reduced side effects.

Manglik A, Lin H, Aryal DK, McCorvy JD, Dengler D, Corder G, Levit A, Kling RC, Bernat V, Hübner H, Huang XP, Sassano MF, Giguère PM, Löber S, Da Duan, Scherrer G, Kobilka BK, Gmeiner P, Roth BL, Shoichet BK.

Nature. 2016 Sep 8;537(7619):185-190. doi: 10.1038/nature19112. Epub 2016 Aug 17.

21.

Identification of Novel Smoothened Ligands Using Structure-Based Docking.

Lacroix C, Fish I, Torosyan H, Parathaman P, Irwin JJ, Shoichet BK, Angers S.

PLoS One. 2016 Aug 4;11(8):e0160365. doi: 10.1371/journal.pone.0160365. eCollection 2016.

22.

Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction.

O'Meara MJ, Ballouz S, Shoichet BK, Gillis J.

PLoS One. 2016 Jul 28;11(7):e0160098. doi: 10.1371/journal.pone.0160098. eCollection 2016.

23.

Advances in Computational Medicinal Chemistry: A Reflection on the Evolution of the Field and Perspective Going Forward.

Shoichet BK, Walters WP, Jiang H, Bajorath J.

J Med Chem. 2016 May 12;59(9):4033-4. doi: 10.1021/acs.jmedchem.6b00511. Epub 2016 Apr 7. No abstract available.

PMID:
27054949
24.

In Vitro and In Vivo Characterization of the Alkaloid Nuciferine.

Farrell MS, McCorvy JD, Huang XP, Urban DJ, White KL, Giguere PM, Doak AK, Bernstein AI, Stout KA, Park SM, Rodriguiz RM, Gray BW, Hyatt WS, Norwood AP, Webster KA, Gannon BM, Miller GW, Porter JH, Shoichet BK, Fantegrossi WE, Wetsel WC, Roth BL.

PLoS One. 2016 Mar 10;11(3):e0150602. doi: 10.1371/journal.pone.0150602. eCollection 2016.

25.

Docking Screens for Novel Ligands Conferring New Biology.

Irwin JJ, Shoichet BK.

J Med Chem. 2016 May 12;59(9):4103-20. doi: 10.1021/acs.jmedchem.5b02008. Epub 2016 Mar 15. Review.

26.

Stable Colloidal Drug Aggregates Catch and Release Active Enzymes.

McLaughlin CK, Duan D, Ganesh AN, Torosyan H, Shoichet BK, Shoichet MS.

ACS Chem Biol. 2016 Apr 15;11(4):992-1000. doi: 10.1021/acschembio.5b00806. Epub 2016 Jan 15.

27.

Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors.

Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Ortiz Torres I, Oppermann U, Shoichet BK, Fujimori DG.

J Med Chem. 2016 Feb 25;59(4):1580-98. doi: 10.1021/acs.jmedchem.5b01527. Epub 2015 Dec 23.

28.

Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65.

Huang XP, Karpiak J, Kroeze WK, Zhu H, Chen X, Moy SS, Saddoris KA, Nikolova VD, Farrell MS, Wang S, Mangano TJ, Deshpande DA, Jiang A, Penn RB, Jin J, Koller BH, Kenakin T, Shoichet BK, Roth BL.

Nature. 2015 Nov 26;527(7579):477-83. doi: 10.1038/nature15699. Epub 2015 Nov 9.

29.

Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking.

Rettenmaier TJ, Fan H, Karpiak J, Doak A, Sali A, Shoichet BK, Wells JA.

J Med Chem. 2015 Oct 22;58(20):8285-8291. doi: 10.1021/acs.jmedchem.5b01216. Epub 2015 Oct 12.

30.

The Recognition of Identical Ligands by Unrelated Proteins.

Barelier S, Sterling T, O'Meara MJ, Shoichet BK.

ACS Chem Biol. 2015 Dec 18;10(12):2772-84. doi: 10.1021/acschembio.5b00683. Epub 2015 Oct 12.

31.

Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference.

Pimentel-Elardo SM, Sørensen D, Ho L, Ziko M, Bueler SA, Lu S, Tao J, Moser A, Lee R, Agard D, Fairn G, Rubinstein JL, Shoichet BK, Nodwell JR.

ACS Chem Biol. 2015 Nov 20;10(11):2616-23. doi: 10.1021/acschembio.5b00612. Epub 2015 Sep 18.

32.

Prediction and validation of enzyme and transporter off-targets for metformin.

Yee SW, Lin L, Merski M, Keiser MJ, Gupta A, Zhang Y, Chien HC, Shoichet BK, Giacomini KM.

J Pharmacokinet Pharmacodyn. 2015 Oct;42(5):463-75. doi: 10.1007/s10928-015-9436-y. Epub 2015 Sep 3.

33.

An Aggregation Advisor for Ligand Discovery.

Irwin JJ, Duan D, Torosyan H, Doak AK, Ziebart KT, Sterling T, Tumanian G, Shoichet BK.

J Med Chem. 2015 Sep 10;58(17):7076-87. doi: 10.1021/acs.jmedchem.5b01105. Epub 2015 Aug 28.

34.

Virtual Screening for UDP-Galactopyranose Mutase Ligands Identifies a New Class of Antimycobacterial Agents.

Kincaid VA, London N, Wangkanont K, Wesener DA, Marcus SA, Héroux A, Nedyalkova L, Talaat AM, Forest KT, Shoichet BK, Kiessling LL.

ACS Chem Biol. 2015 Oct 16;10(10):2209-18. doi: 10.1021/acschembio.5b00370. Epub 2015 Aug 17.

35.

One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.

Fischer M, Shoichet BK, Fraser JS.

Chembiochem. 2015 Jul 27;16(11):1560-4. doi: 10.1002/cbic.201500196. Epub 2015 Jun 15.

36.

Homologous ligands accommodated by discrete conformations of a buried cavity.

Merski M, Fischer M, Balius TE, Eidam O, Shoichet BK.

Proc Natl Acad Sci U S A. 2015 Apr 21;112(16):5039-44. doi: 10.1073/pnas.1500806112. Epub 2015 Apr 6. Erratum in: Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):E4971.

37.

Erratum: Covalent docking of large libraries for the discovery of chemical probes.

London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermančič P, Bonnet R, Shoichet BK, Taunton J.

Nat Chem Biol. 2015 Mar;11(3):235. doi: 10.1038/nchembio0315-235b. No abstract available.

PMID:
25689339
38.

Colloidal aggregation and the in vitro activity of traditional Chinese medicines.

Duan D, Doak AK, Nedyalkova L, Shoichet BK.

ACS Chem Biol. 2015 Apr 17;10(4):978-88. doi: 10.1021/cb5009487. Epub 2015 Feb 9.

39.

Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases.

London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK.

Biochemistry. 2015 Jan 20;54(2):528-37. doi: 10.1021/bi501140k. Epub 2015 Jan 5.

40.

Covalent docking of large libraries for the discovery of chemical probes.

London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermančič P, Bonnet R, Shoichet BK, Taunton J.

Nat Chem Biol. 2014 Dec;10(12):1066-72. doi: 10.1038/nchembio.1666. Epub 2014 Oct 26. Erratum in: Nat Chem Biol. 2015 Mar;11(3):235.

41.

Functional annotation and structural characterization of a novel lactonase hydrolyzing D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate.

Korczynska M, Xiang DF, Zhang Z, Xu C, Narindoshvili T, Kamat SS, Williams HJ, Chang SS, Kolb P, Hillerich B, Sauder JM, Burley SK, Almo SC, Swaminathan S, Shoichet BK, Raushel FM.

Biochemistry. 2014 Jul 22;53(28):4727-38. doi: 10.1021/bi500595c. Epub 2014 Jul 9.

42.

Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.

Fischer M, Coleman RG, Fraser JS, Shoichet BK.

Nat Chem. 2014 Jul;6(7):575-83. doi: 10.1038/nchem.1954. Epub 2014 May 25.

43.

Targeting class A and C serine β-lactamases with a broad-spectrum boronic acid derivative.

Tondi D, Venturelli A, Bonnet R, Pozzi C, Shoichet BK, Costi MP.

J Med Chem. 2014 Jun 26;57(12):5449-58. doi: 10.1021/jm5006572. Epub 2014 Jun 16.

44.

Increasing chemical space coverage by combining empirical and computational fragment screens.

Barelier S, Eidam O, Fish I, Hollander J, Figaroa F, Nachane R, Irwin JJ, Shoichet BK, Siegal G.

ACS Chem Biol. 2014 Jul 18;9(7):1528-35. doi: 10.1021/cb5001636. Epub 2014 May 20.

45.

Prediction of substrates for glutathione transferases by covalent docking.

Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A.

J Chem Inf Model. 2014 Jun 23;54(6):1687-99. doi: 10.1021/ci5001554. Epub 2014 May 16.

46.

Substrate deconstruction and the nonadditivity of enzyme recognition.

Barelier S, Cummings JA, Rauwerdink AM, Hitchcock DS, Farelli JD, Almo SC, Raushel FM, Allen KN, Shoichet BK.

J Am Chem Soc. 2014 May 21;136(20):7374-82. doi: 10.1021/ja501354q. Epub 2014 May 12.

47.

Drug discovery: follow your lead.

Shoichet BK.

Nat Chem Biol. 2014 Apr;10(4):244-5. doi: 10.1038/nchembio.1484. No abstract available.

PMID:
24643239
48.

Colloidal drug formulations can explain "bell-shaped" concentration-response curves.

Owen SC, Doak AK, Ganesh AN, Nedyalkova L, McLaughlin CK, Shoichet BK, Shoichet MS.

ACS Chem Biol. 2014 Mar 21;9(3):777-84. doi: 10.1021/cb4007584. Epub 2014 Jan 15.

49.

In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding.

Lemieux GA, Keiser MJ, Sassano MF, Laggner C, Mayer F, Bainton RJ, Werb Z, Roth BL, Shoichet BK, Ashrafi K.

PLoS Biol. 2013 Nov;11(11):e1001712. doi: 10.1371/journal.pbio.1001712. Epub 2013 Nov 19.

50.

Ligand pose and orientational sampling in molecular docking.

Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK.

PLoS One. 2013 Oct 1;8(10):e75992. doi: 10.1371/journal.pone.0075992. eCollection 2013.

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