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Items: 1 to 50 of 54

1.

A Synopsis of Contemporary Anesthesia Airway Management.

Bohringer C, Duca J, Liu H.

Transl Perioper Pain Med. 2019;6(1):5-16. Epub 2019 Jan 15.

2.

Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening.

Chen L, Cruz A, Ramsey S, Dickson CJ, Duca JS, Hornak V, Koes DR, Kurtzman T.

PLoS One. 2019 Aug 20;14(8):e0220113. doi: 10.1371/journal.pone.0220113. eCollection 2019.

3.

A small-molecule inhibitor of C5 complement protein.

Jendza K, Kato M, Salcius M, Srinivas H, De Erkenez A, Nguyen A, McLaughlin D, Be C, Wiesmann C, Murphy J, Bolduc P, Mogi M, Duca J, Namil A, Capparelli M, Darsigny V, Meredith E, Tichkule R, Ferrara L, Heyder J, Liu F, Horton PA, Romanowski MJ, Schirle M, Mainolfi N, Anderson K, Michaud GA.

Nat Chem Biol. 2019 Jul;15(7):666-668. doi: 10.1038/s41589-019-0303-9. Epub 2019 Jun 17.

PMID:
31209353
4.

PathwayMap: Molecular Pathway Association with Self-Normalizing Neural Networks.

Jiménez J, Sabbadin D, Cuzzolin A, Martínez-Rosell G, Gora J, Manchester J, Duca J, De Fabritiis G.

J Chem Inf Model. 2019 Mar 25;59(3):1172-1181. doi: 10.1021/acs.jcim.8b00711. Epub 2019 Jan 10.

PMID:
30586501
5.

Using Membrane Partitioning Simulations To Predict Permeability of Forty-Nine Drug-Like Molecules.

Dickson CJ, Hornak V, Bednarczyk D, Duca JS.

J Chem Inf Model. 2019 Jan 28;59(1):236-244. doi: 10.1021/acs.jcim.8b00744. Epub 2018 Dec 26.

PMID:
30540467
6.

Building New Bridges between In Vitro and In Vivo in Early Drug Discovery: Where Molecular Modeling Meets Systems Biology.

Pearlstein RA, McKay DJJ, Hornak V, Dickson C, Golosov A, Harrison T, Velez-Vega C, Duca J.

Curr Top Med Chem. 2017;17(23):2642-2662. doi: 10.2174/1568026617666170414152311. Review.

PMID:
28413952
7.

"Addition" and "Subtraction": Selectivity Design for Type II Maternal Embryonic Leucine Zipper Kinase Inhibitors.

Chen X, Giraldes J, Sprague ER, Shakya S, Chen Z, Wang Y, Joud C, Mathieu S, Chen CH, Straub C, Duca J, Hurov K, Yuan Y, Shao W, Touré BB.

J Med Chem. 2017 Mar 9;60(5):2155-2161. doi: 10.1021/acs.jmedchem.7b00033. Epub 2017 Feb 24.

PMID:
28186750
8.

Collaborating to improve the use of free-energy and other quantitative methods in drug discovery.

Sherborne B, Shanmugasundaram V, Cheng AC, Christ CD, DesJarlais RL, Duca JS, Lewis RA, Loughney DA, Manas ES, McGaughey GB, Peishoff CE, van Vlijmen H.

J Comput Aided Mol Des. 2016 Dec;30(12):1139-1141. doi: 10.1007/s10822-016-9996-y. Epub 2016 Dec 24.

PMID:
28013427
9.

Structure-Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling.

Dickson CJ, Hornak V, Pearlstein RA, Duca JS.

J Am Chem Soc. 2017 Jan 11;139(1):442-452. doi: 10.1021/jacs.6b11215. Epub 2016 Dec 21.

PMID:
27951634
10.

Uncoupling the Structure-Activity Relationships of β2 Adrenergic Receptor Ligands from Membrane Binding.

Dickson CJ, Hornak V, Velez-Vega C, McKay DJ, Reilly J, Sandham DA, Shaw D, Fairhurst RA, Charlton SJ, Sykes DA, Pearlstein RA, Duca JS.

J Med Chem. 2016 Jun 23;59(12):5780-9. doi: 10.1021/acs.jmedchem.6b00358. Epub 2016 Jun 7.

PMID:
27239696
11.

Toward the Validation of Maternal Embryonic Leucine Zipper Kinase: Discovery, Optimization of Highly Potent and Selective Inhibitors, and Preliminary Biology Insight.

Touré BB, Giraldes J, Smith T, Sprague ER, Wang Y, Mathieu S, Chen Z, Mishina Y, Feng Y, Yan-Neale Y, Shakya S, Chen D, Meyer M, Puleo D, Brazell JT, Straub C, Sage D, Wright K, Yuan Y, Chen X, Duca J, Kim S, Tian L, Martin E, Hurov K, Shao W.

J Med Chem. 2016 May 26;59(10):4711-23. doi: 10.1021/acs.jmedchem.6b00052. Epub 2016 May 17.

PMID:
27187609
12.

Implications of Dynamic Occupancy, Binding Kinetics, and Channel Gating Kinetics for hERG Blocker Safety Assessment and Mitigation.

Pearlstein RA, MacCannell KA, Erdemli G, Yeola S, Helmlinger G, Hu QY, Farid R, Egan W, Whitebread S, Springer C, Beck J, Wang HR, Maciejewski M, Urban L, Duca JS.

Curr Top Med Chem. 2016;16(16):1792-818. Review.

PMID:
26975508
13.

Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen-Hydrogen Correlations.

Velez-Vega C, McKay DJ, Kurtzman T, Aravamuthan V, Pearlstein RA, Duca JS.

J Chem Theory Comput. 2015 Nov 10;11(11):5090-102. doi: 10.1021/acs.jctc.5b00439. Epub 2015 Oct 21.

14.

Antibodies to influenza nucleoprotein cross-react with human hypocretin receptor 2.

Ahmed SS, Volkmuth W, Duca J, Corti L, Pallaoro M, Pezzicoli A, Karle A, Rigat F, Rappuoli R, Narasimhan V, Julkunen I, Vuorela A, Vaarala O, Nohynek H, Pasini FL, Montomoli E, Trombetta C, Adams CM, Rothbard J, Steinman L.

Sci Transl Med. 2015 Jul 1;7(294):294ra105. doi: 10.1126/scitranslmed.aab2354.

PMID:
26136476
15.

Elevated Lactate Secondary to Gastrointestinal Beriberi.

Duca J, Lum CJ, Lo AM.

J Gen Intern Med. 2016 Jan;31(1):133-6. doi: 10.1007/s11606-015-3326-2. Epub 2015 Apr 16.

16.

Time-averaged distributions of solute and solvent motions: exploring proton wires of GFP and PfM2DH.

Velez-Vega C, McKay DJ, Aravamuthan V, Pearlstein R, Duca JS.

J Chem Inf Model. 2014 Dec 22;54(12):3344-61. doi: 10.1021/ci500571h. Epub 2014 Nov 26.

PMID:
25405925
17.

Modulating the interaction between CDK2 and cyclin A with a quinoline-based inhibitor.

Deng Y, Shipps GW Jr, Zhao L, Siddiqui MA, Popovici-Muller J, Curran PJ, Duca JS, Hruza AW, Fischmann TO, Madison VS, Zhang R, McNemar CW, Mayhood TW, Syto R, Annis A, Kirschmeier P, Lees EM, Parry DA, Windsor WT.

Bioorg Med Chem Lett. 2014 Jan 1;24(1):199-203. doi: 10.1016/j.bmcl.2013.11.041. Epub 2013 Nov 23.

PMID:
24332088
18.

Optimization of potency and pharmacokinetics of tricyclic indole derived inhibitors of HCV NS5B polymerase. Identification of ester prodrugs with improved oral pharmacokinetics.

Venkatraman S, Velazquez F, Gavalas S, Wu W, Chen KX, Nair AG, Bennett F, Huang Y, Pinto P, Jiang Y, Selyutin O, Vibulbhan B, Zeng Q, Lesburg C, Duca J, Heimark L, Huang HC, Agrawal S, Jiang CK, Ferrari E, Li C, Kozlowski J, Rosenblum S, Shih NY, Njoroge FG.

Bioorg Med Chem. 2014 Jan 1;22(1):447-58. doi: 10.1016/j.bmc.2013.11.007. Epub 2013 Nov 13.

PMID:
24275348
19.

Discovery of an irreversible HCV NS5B polymerase inhibitor.

Zeng Q, Nair AG, Rosenblum SB, Huang HC, Lesburg CA, Jiang Y, Selyutin O, Chan TY, Bennett F, Chen KX, Venkatraman S, Sannigrahi M, Velazquez F, Duca JS, Gavalas S, Huang Y, Pu H, Wang L, Pinto P, Vibulbhan B, Agrawal S, Ferrari E, Jiang CK, Li C, Hesk D, Gesell J, Sorota S, Shih NY, Njoroge FG, Kozlowski JA.

Bioorg Med Chem Lett. 2013 Dec 15;23(24):6585-7. doi: 10.1016/j.bmcl.2013.10.060. Epub 2013 Nov 6.

PMID:
24252545
20.

LMX1B mutations cause hereditary FSGS without extrarenal involvement.

Boyer O, Woerner S, Yang F, Oakeley EJ, Linghu B, Gribouval O, Tête MJ, Duca JS, Klickstein L, Damask AJ, Szustakowski JD, Heibel F, Matignon M, Baudouin V, Chantrel F, Champigneulle J, Martin L, Nitschké P, Gubler MC, Johnson KJ, Chibout SD, Antignac C.

J Am Soc Nephrol. 2013 Jul;24(8):1216-22. doi: 10.1681/ASN.2013020171. Epub 2013 May 16.

21.

Structure-based design and optimization of 2-aminothiazole-4-carboxamide as a new class of CHK1 inhibitors.

Huang X, Cheng CC, Fischmann TO, Duca JS, Richards M, Tadikonda PK, Reddy PA, Zhao L, Siddiqui MA, Parry D, Davis N, Seghezzi W, Wiswell D, Shipps GW Jr.

Bioorg Med Chem Lett. 2013 May 1;23(9):2590-4. doi: 10.1016/j.bmcl.2013.02.108. Epub 2013 Mar 7.

PMID:
23535330
22.

Discovery of novel tricyclic indole derived inhibitors of HCV NS5B RNA dependent RNA polymerase.

Venkatraman S, Velazquez F, Gavalas S, Wu W, Chen KX, Nair AG, Bennett F, Huang Y, Pinto P, Jiang Y, Selyutin O, Vibulbhan B, Zeng Q, Lesburg C, Duca J, Huang HC, Agrawal S, Jiang CK, Ferrari E, Li C, Kozlowski J, Rosenblum S, Shih NY, Njoroge FG.

Bioorg Med Chem. 2013 Apr 1;21(7):2007-17. doi: 10.1016/j.bmc.2013.01.024. Epub 2013 Jan 23.

PMID:
23434368
23.

Noticing the unnoticed: bridging structural data and drug design.

Duca JS, Karki RG.

Future Med Chem. 2012 Oct;4(15):1869-71. doi: 10.4155/fmc.12.163. No abstract available.

PMID:
23088265
24.

Discovery of a Novel Series of CHK1 Kinase Inhibitors with a Distinctive Hinge Binding Mode.

Huang X, Cheng CC, Fischmann TO, Duca JS, Yang X, Richards M, Shipps GW Jr.

ACS Med Chem Lett. 2012 Jan 20;3(2):123-8. doi: 10.1021/ml200249h. eCollection 2012 Feb 9.

25.

A novel class of highly potent irreversible hepatitis C virus NS5B polymerase inhibitors.

Chen KX, Lesburg CA, Vibulbhan B, Yang W, Chan TY, Venkatraman S, Velazquez F, Zeng Q, Bennett F, Anilkumar GN, Duca J, Jiang Y, Pinto P, Wang L, Huang Y, Selyutin O, Gavalas S, Pu H, Agrawal S, Feld B, Huang HC, Li C, Cheng KC, Shih NY, Kozlowski JA, Rosenblum SB, Njoroge FG.

J Med Chem. 2012 Mar 8;55(5):2089-101. doi: 10.1021/jm201322r. Epub 2012 Feb 22.

PMID:
22247956
26.

Synthesis of new 4,5-dihydrofuranoindoles and their evaluation as HCV NS5B polymerase inhibitors.

Velázquez F, Venkatraman S, Lesburg CA, Duca J, Rosenblum SB, Kozlowski JA, Njoroge FG.

Org Lett. 2012 Jan 20;14(2):556-9. doi: 10.1021/ol203177g. Epub 2012 Jan 5.

PMID:
22220815
27.

Structure-activity relationship (SAR) development and discovery of potent indole-based inhibitors of the hepatitis C virus (HCV) NS5B polymerase.

Chen KX, Vibulbhan B, Yang W, Sannigrahi M, Velazquez F, Chan TY, Venkatraman S, Anilkumar GN, Zeng Q, Bennet F, Jiang Y, Lesburg CA, Duca J, Pinto P, Gavalas S, Huang Y, Wu W, Selyutin O, Agrawal S, Feld B, Huang HC, Li C, Cheng KC, Shih NY, Kozlowski JA, Rosenblum SB, Njoroge FG.

J Med Chem. 2012 Jan 26;55(2):754-65. doi: 10.1021/jm201258k. Epub 2012 Jan 6.

PMID:
22148957
28.

II. Novel HCV NS5B polymerase inhibitors: discovery of indole C2 acyl sulfonamides.

Anilkumar GN, Selyutin O, Rosenblum SB, Zeng Q, Jiang Y, Chan TY, Pu H, Wang L, Bennett F, Chen KX, Lesburg CA, Duca J, Gavalas S, Huang Y, Pinto P, Sannigrahi M, Velazquez F, Venkatraman S, Vibulbhan B, Agrawal S, Ferrari E, Jiang CK, Huang HC, Shih NY, George Njoroge F, Kozlowski JA.

Bioorg Med Chem Lett. 2012 Jan 1;22(1):713-7. doi: 10.1016/j.bmcl.2011.10.041. Epub 2011 Oct 20.

PMID:
22104146
29.

Gazing into the crystal ball; the future of computer-aided drug design.

Martin E, Ertl P, Hunt P, Duca J, Lewis R.

J Comput Aided Mol Des. 2012 Jan;26(1):77-9. doi: 10.1007/s10822-011-9487-0. Epub 2011 Nov 17. No abstract available.

PMID:
22089332
30.

I. Novel HCV NS5B polymerase inhibitors: discovery of indole 2-carboxylic acids with C3-heterocycles.

Anilkumar GN, Lesburg CA, Selyutin O, Rosenblum SB, Zeng Q, Jiang Y, Chan TY, Pu H, Vaccaro H, Wang L, Bennett F, Chen KX, Duca J, Gavalas S, Huang Y, Pinto P, Sannigrahi M, Velazquez F, Venkatraman S, Vibulbhan B, Agrawal S, Butkiewicz N, Feld B, Ferrari E, He Z, Jiang CK, Palermo RE, McMonagle P, Huang HC, Shih NY, Njoroge G, Kozlowski JA.

Bioorg Med Chem Lett. 2011 Sep 15;21(18):5336-41. doi: 10.1016/j.bmcl.2011.07.021. Epub 2011 Jul 19.

PMID:
21840715
31.

Discovery of pyrazolo[1,5-a]pyrimidine-based CHK1 inhibitors: a template-based approach--part 1.

Dwyer MP, Paruch K, Labroli M, Alvarez C, Keertikar KM, Poker C, Rossman R, Fischmann TO, Duca JS, Madison V, Parry D, Davis N, Seghezzi W, Wiswell D, Guzi TJ.

Bioorg Med Chem Lett. 2011 Jan 1;21(1):467-70. doi: 10.1016/j.bmcl.2010.10.113. Epub 2010 Oct 27.

PMID:
21094608
32.

Discovery of pyrazolo[1,5-a]pyrimidine-based CHK1 inhibitors: a template-based approach--part 2.

Labroli M, Paruch K, Dwyer MP, Alvarez C, Keertikar K, Poker C, Rossman R, Duca JS, Fischmann TO, Madison V, Parry D, Davis N, Seghezzi W, Wiswell D, Guzi TJ.

Bioorg Med Chem Lett. 2011 Jan 1;21(1):471-4. doi: 10.1016/j.bmcl.2010.10.114. Epub 2010 Oct 28.

PMID:
21094607
33.

Inhibitors of hepatitis C virus polymerase: synthesis and characterization of novel 2-oxy-6-fluoro-N-((S)-1-hydroxy-3-phenylpropan-2-yl)-benzamides.

Cheng CC, Shipps GW Jr, Yang Z, Kawahata N, Lesburg CA, Duca JS, Bandouveres J, Bracken JD, Jiang CK, Agrawal S, Ferrari E, Huang HC.

Bioorg Med Chem Lett. 2010 Apr 1;20(7):2119-24. doi: 10.1016/j.bmcl.2010.02.054. Epub 2010 Feb 18.

PMID:
20219368
34.

Clinical resistance to vicriviroc through adaptive V3 loop mutations in HIV-1 subtype D gp120 that alter interactions with the N-terminus and ECL2 of CCR5.

Ogert RA, Hou Y, Ba L, Wojcik L, Qiu P, Murgolo N, Duca J, Dunkle LM, Ralston R, Howe JA.

Virology. 2010 Apr 25;400(1):145-55. doi: 10.1016/j.virol.2010.01.037. Epub 2010 Feb 21.

35.

Recent advances on structure-informed drug discovery of cyclin-dependent kinase-2 inhibitors.

Duca JS.

Future Med Chem. 2009 Nov;1(8):1453-66. doi: 10.4155/fmc.09.102. Review.

PMID:
21426059
36.

Thermodynamics of nucleotide and inhibitor binding to wild-type and ispinesib-resistant forms of human kinesin spindle protein.

Sheth PR, Basso A, Duca JS, Lesburg CA, Ogas P, Gray K, Nale L, Mannarino AF, Prongay AJ, Le HV.

Biochemistry. 2009 Nov 24;48(46):11045-55. doi: 10.1021/bi900946r.

PMID:
19824700
37.

Pyrazolo[1,5-a]pyrimidine-based inhibitors of HCV polymerase.

Popovici-Muller J, Shipps GW Jr, Rosner KE, Deng Y, Wang T, Curran PJ, Brown MA, Siddiqui MA, Cooper AB, Duca J, Cable M, Girijavallabhan V.

Bioorg Med Chem Lett. 2009 Nov 15;19(22):6331-6. doi: 10.1016/j.bmcl.2009.09.087. Epub 2009 Sep 25.

PMID:
19819138
38.

Structure-function analysis of human immunodeficiency virus type 1 gp120 amino acid mutations associated with resistance to the CCR5 coreceptor antagonist vicriviroc.

Ogert RA, Ba L, Hou Y, Buontempo C, Qiu P, Duca J, Murgolo N, Buontempo P, Ralston R, Howe JA.

J Virol. 2009 Dec;83(23):12151-63. doi: 10.1128/JVI.01351-09. Epub 2009 Sep 23.

39.

Discovery of 4H-pyrazolo[1,5-a]pyrimidin-7-ones as potent inhibitors of hepatitis C virus polymerase.

Deng Y, Shipps GW Jr, Wang T, Popovici-Muller J, Rosner KE, Siddiqui MA, Duca J, Cooper AB, Cable M.

Bioorg Med Chem Lett. 2009 Sep 15;19(18):5363-7. doi: 10.1016/j.bmcl.2009.07.124. Epub 2009 Aug 6.

PMID:
19682898
40.

soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts.

Lesburg CA, Duca JS.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W252-4. doi: 10.1093/nar/gkn270. Epub 2008 May 16.

41.

Cross-docking of inhibitors into CDK2 structures. 2.

Voigt JH, Elkin C, Madison VS, Duca JS.

J Chem Inf Model. 2008 Mar;48(3):669-78. doi: 10.1021/ci700428d. Epub 2008 Mar 7.

PMID:
18324800
42.

Cross-docking of inhibitors into CDK2 structures. 1.

Duca JS, Madison VS, Voigt JH.

J Chem Inf Model. 2008 Mar;48(3):659-68. doi: 10.1021/ci7004274. Epub 2008 Mar 7.

PMID:
18324799
43.

Structure-guided discovery of cyclin-dependent kinase inhibitors.

Fischmann TO, Hruza A, Duca JS, Ramanathan L, Mayhood T, Windsor WT, Le HV, Guzi TJ, Dwyer MP, Paruch K, Doll RJ, Lees E, Parry D, Seghezzi W, Madison V.

Biopolymers. 2008 May;89(5):372-9.

PMID:
17937404
44.

Versatile templates for the development of novel kinase inhibitors: Discovery of novel CDK inhibitors.

Dwyer MP, Paruch K, Alvarez C, Doll RJ, Keertikar K, Duca J, Fischmann TO, Hruza A, Madison V, Lees E, Parry D, Seghezzi W, Sgambellone N, Shanahan F, Wiswell D, Guzi TJ.

Bioorg Med Chem Lett. 2007 Nov 15;17(22):6216-9. Epub 2007 Sep 8.

PMID:
17904366
45.

Novel amplicons on the short arm of chromosome 7 identified using high resolution array CGH contain over expressed genes in addition to EGFR in glioblastoma multiforme.

Rossi MR, La Duca J, Matsui S, Nowak NJ, Hawthorn L, Cowell JK.

Genes Chromosomes Cancer. 2005 Dec;44(4):392-404.

PMID:
16110500
47.

4D-fingerprints, universal QSAR and QSPR descriptors.

Senese CL, Duca J, Pan D, Hopfinger AJ, Tseng YJ.

J Chem Inf Comput Sci. 2004 Sep-Oct;44(5):1526-39.

PMID:
15446810
48.

Binding affinities and geometries of various metal ligands in peptide deformylase inhibitors.

Madison V, Duca J, Bennett F, Bohanon S, Cooper A, Chu M, Desai J, Girijavallabhan V, Hare R, Hruza A, Hendrata S, Huang Y, Kravec C, Malcolm B, McCormick J, Miesel L, Ramanathan L, Reichert P, Saksena A, Wang J, Weber PC, Zhu H, Fischmann T.

Biophys Chem. 2002 Dec 10;101-102:239-47.

PMID:
12488004
49.

The active site of a zinc-dependent metalloproteinase influences the computed pK(a) of ligands coordinated to the catalytic zinc ion.

Cross JB, Duca JS, Kaminski JJ, Madison VS.

J Am Chem Soc. 2002 Sep 18;124(37):11004-7.

PMID:
12224947

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