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Items: 42

1.

A review of transcranial electrical stimulation methods in stroke rehabilitation.

Solomons CD, Shanmugasundaram V.

Neurol India. 2019 Mar-Apr;67(2):417-423. doi: 10.4103/0028-3886.258057. Review.

2.

Cyclic Peptide Design Guided by Residual Dipolar Couplings, J-Couplings, and Intramolecular Hydrogen Bond Analysis.

Farley KA, Che Y, Navarro-Vázquez A, Limberakis C, Anderson D, Yan J, Shapiro M, Shanmugasundaram V, Gil RR.

J Org Chem. 2019 Apr 19;84(8):4803-4813. doi: 10.1021/acs.joc.8b02811. Epub 2019 Jan 15.

PMID:
30605335
3.

TRPA1 ankyrin repeat six interacts with a small molecule inhibitor chemotype.

Tseng WC, Pryde DC, Yoger KE, Padilla KM, Antonio BM, Han S, Shanmugasundaram V, Gerlach AC.

Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):12301-12306. doi: 10.1073/pnas.1808142115. Epub 2018 Nov 14.

4.

Delineating the role of cooperativity in the design of potent PROTACs for BTK.

Zorba A, Nguyen C, Xu Y, Starr J, Borzilleri K, Smith J, Zhu H, Farley KA, Ding W, Schiemer J, Feng X, Chang JS, Uccello DP, Young JA, Garcia-Irrizary CN, Czabaniuk L, Schuff B, Oliver R, Montgomery J, Hayward MM, Coe J, Chen J, Niosi M, Luthra S, Shah JC, El-Kattan A, Qiu X, West GM, Noe MC, Shanmugasundaram V, Gilbert AM, Brown MF, Calabrese MF.

Proc Natl Acad Sci U S A. 2018 Jul 31;115(31):E7285-E7292. doi: 10.1073/pnas.1803662115. Epub 2018 Jul 16.

5.

Inducing protein-protein interactions with molecular glues.

Che Y, Gilbert AM, Shanmugasundaram V, Noe MC.

Bioorg Med Chem Lett. 2018 Aug 15;28(15):2585-2592. doi: 10.1016/j.bmcl.2018.04.046. Epub 2018 Apr 19. Review.

PMID:
29980357
6.

Novel Methods for Prioritizing "Close-In" Analogs from Structure-Activity Relationship Matrices.

Zhang L, Johnson K, Starr J, Milbank J, Kuhn AM, Poss C, Stanton RV, Shanmugasundaram V.

J Chem Inf Model. 2017 Jul 24;57(7):1667-1676. doi: 10.1021/acs.jcim.7b00055. Epub 2017 Jul 13.

PMID:
28657313
7.

Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter.

Harrigan MP, McKiernan KA, Shanmugasundaram V, Denny RA, Pande VS.

Sci Rep. 2017 Apr 4;7(1):632. doi: 10.1038/s41598-017-00256-y.

8.

Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation.

Wan S, Bhati AP, Skerratt S, Omoto K, Shanmugasundaram V, Bagal SK, Coveney PV.

J Chem Inf Model. 2017 Apr 24;57(4):897-909. doi: 10.1021/acs.jcim.6b00780. Epub 2017 Apr 4.

9.

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
10.

Molecular Basis for Inhibition of the Na+/Citrate Transporter NaCT (SLC13A5) by Dicarboxylate Inhibitors.

Pajor AM, de Oliveira CA, Song K, Huard K, Shanmugasundaram V, Erion DM.

Mol Pharmacol. 2016 Dec;90(6):755-765. Epub 2016 Sep 28.

PMID:
27683012
11.

Discovery of a Selective Covalent Inhibitor of Lysophospholipase-like 1 (LYPLAL1) as a Tool to Evaluate the Role of this Serine Hydrolase in Metabolism.

Ahn K, Boehm M, Brown MF, Calloway J, Che Y, Chen J, Fennell KF, Geoghegan KF, Gilbert AM, Gutierrez JA, Kalgutkar AS, Lanba A, Limberakis C, Magee TV, O'Doherty I, Oliver R, Pabst B, Pandit J, Parris K, Pfefferkorn JA, Rolph TP, Patel R, Schuff B, Shanmugasundaram V, Starr JT, Varghese AH, Vera NB, Vernochet C, Yan J.

ACS Chem Biol. 2016 Sep 16;11(9):2529-40. doi: 10.1021/acschembio.6b00266. Epub 2016 Jul 19.

PMID:
27391855
12.

Discovery of a Highly Selective Glycogen Synthase Kinase-3 Inhibitor (PF-04802367) That Modulates Tau Phosphorylation in the Brain: Translation for PET Neuroimaging.

Liang SH, Chen JM, Normandin MD, Chang JS, Chang GC, Taylor CK, Trapa P, Plummer MS, Para KS, Conn EL, Lopresti-Morrow L, Lanyon LF, Cook JM, Richter KE, Nolan CE, Schachter JB, Janat F, Che Y, Shanmugasundaram V, Lefker BA, Enerson BE, Livni E, Wang L, Guehl NJ, Patnaik D, Wagner FF, Perlis R, Holson EB, Haggarty SJ, El Fakhri G, Kurumbail RG, Vasdev N.

Angew Chem Int Ed Engl. 2016 Aug 8;55(33):9601-5. doi: 10.1002/anie.201603797. Epub 2016 Jun 29.

13.

Monitoring the Progression of Structure-Activity Relationship Information during Lead Optimization.

Shanmugasundaram V, Zhang L, Kayastha S, de la Vega de León A, Dimova D, Bajorath J.

J Med Chem. 2016 May 12;59(9):4235-44. doi: 10.1021/acs.jmedchem.5b01428. Epub 2015 Nov 16.

PMID:
26569348
14.

Chemical and computational methods for the characterization of covalent reactive groups for the prospective design of irreversible inhibitors.

Flanagan ME, Abramite JA, Anderson DP, Aulabaugh A, Dahal UP, Gilbert AM, Li C, Montgomery J, Oppenheimer SR, Ryder T, Schuff BP, Uccello DP, Walker GS, Wu Y, Brown MF, Chen JM, Hayward MM, Noe MC, Obach RS, Philippe L, Shanmugasundaram V, Shapiro MJ, Starr J, Stroh J, Che Y.

J Med Chem. 2014 Dec 11;57(23):10072-9. doi: 10.1021/jm501412a. Epub 2014 Nov 26.

PMID:
25375838
15.

Multiparameter optimization in CNS drug discovery: design of pyrimido[4,5-d]azepines as potent 5-hydroxytryptamine 2C (5-HT₂C) receptor agonists with exquisite functional selectivity over 5-HT₂A and 5-HT₂B receptors.

Storer RI, Brennan PE, Brown AD, Bungay PJ, Conlon KM, Corbett MS, DePianta RP, Fish PV, Heifetz A, Ho DK, Jessiman AS, McMurray G, de Oliveira CA, Roberts LR, Root JA, Shanmugasundaram V, Shapiro MJ, Skerten M, Westbrook D, Wheeler S, Whitlock GA, Wright J.

J Med Chem. 2014 Jun 26;57(12):5258-69. doi: 10.1021/jm5003292. Epub 2014 Jun 17.

PMID:
24878222
16.

Siderophore receptor-mediated uptake of lactivicin analogues in gram-negative bacteria.

Starr J, Brown MF, Aschenbrenner L, Caspers N, Che Y, Gerstenberger BS, Huband M, Knafels JD, Lemmon MM, Li C, McCurdy SP, McElroy E, Rauckhorst MR, Tomaras AP, Young JA, Zaniewski RP, Shanmugasundaram V, Han S.

J Med Chem. 2014 May 8;57(9):3845-55. doi: 10.1021/jm500219c. Epub 2014 Apr 21.

PMID:
24694215
17.

Neighborhood-based prediction of novel active compounds from SAR matrices.

Gupta-Ostermann D, Shanmugasundaram V, Bajorath J.

J Chem Inf Model. 2014 Mar 24;54(3):801-9. doi: 10.1021/ci5000483. Epub 2014 Mar 12.

PMID:
24593807
18.

Pyridone-conjugated monobactam antibiotics with gram-negative activity.

Brown MF, Mitton-Fry MJ, Arcari JT, Barham R, Casavant J, Gerstenberger BS, Han S, Hardink JR, Harris TM, Hoang T, Huband MD, Lall MS, Lemmon MM, Li C, Lin J, McCurdy SP, McElroy E, McPherson C, Marr ES, Mueller JP, Mullins L, Nikitenko AA, Noe MC, Penzien J, Plummer MS, Schuff BP, Shanmugasundaram V, Starr JT, Sun J, Tomaras A, Young JA, Zaniewski RP.

J Med Chem. 2013 Jul 11;56(13):5541-52. doi: 10.1021/jm400560z. Epub 2013 Jun 27.

PMID:
23755848
19.

Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates.

Magee TV, Han S, McCurdy SP, Nguyen TT, Granskog K, Marr ES, Maguire BA, Huband MD, Chen JM, Subashi TA, Shanmugasundaram V.

Bioorg Med Chem Lett. 2013 Mar 15;23(6):1727-31. doi: 10.1016/j.bmcl.2013.01.067. Epub 2013 Jan 26.

PMID:
23414806
20.

Non-traditional antibacterial screening approaches for the identification of novel inhibitors of the glyoxylate shunt in gram-negative pathogens.

Fahnoe KC, Flanagan ME, Gibson G, Shanmugasundaram V, Che Y, Tomaras AP.

PLoS One. 2012;7(12):e51732. doi: 10.1371/journal.pone.0051732. Epub 2012 Dec 11.

21.

Heterocyclic methylsulfone hydroxamic acid LpxC inhibitors as Gram-negative antibacterial agents.

McAllister LA, Montgomery JI, Abramite JA, Reilly U, Brown MF, Chen JM, Barham RA, Che Y, Chung SW, Menard CA, Mitton-Fry M, Mullins LM, Noe MC, O'Donnell JP, Oliver RM 3rd, Penzien JB, Plummer M, Price LM, Shanmugasundaram V, Tomaras AP, Uccello DP.

Bioorg Med Chem Lett. 2012 Nov 15;22(22):6832-8. doi: 10.1016/j.bmcl.2012.09.058. Epub 2012 Sep 24.

PMID:
23046961
22.

Early insights into the interactions of different β-lactam antibiotics and β-lactamase inhibitors against soluble forms of Acinetobacter baumannii PBP1a and Acinetobacter sp. PBP3.

Papp-Wallace KM, Senkfor B, Gatta J, Chai W, Taracila MA, Shanmugasundaram V, Han S, Zaniewski RP, Lacey BM, Tomaras AP, Skalweit MJ, Harris ME, Rice LB, Buynak JD, Bonomo RA.

Antimicrob Agents Chemother. 2012 Nov;56(11):5687-92. doi: 10.1128/AAC.01027-12. Epub 2012 Aug 20.

23.

Novel monobactams utilizing a siderophore uptake mechanism for the treatment of gram-negative infections.

Mitton-Fry MJ, Arcari JT, Brown MF, Casavant JM, Finegan SM, Flanagan ME, Gao H, George DM, Gerstenberger BS, Han S, Hardink JR, Harris TM, Hoang T, Huband MD, Irvine R, Lall MS, Megan Lemmon M, Li C, Lin J, McCurdy SP, Mueller JP, Mullins L, Niosi M, Noe MC, Pattavina D, Penzien J, Plummer MS, Risley H, Schuff BP, Shanmugasundaram V, Starr JT, Sun J, Winton J, Young JA.

Bioorg Med Chem Lett. 2012 Sep 15;22(18):5989-94. doi: 10.1016/j.bmcl.2012.07.005. Epub 2012 Jul 20. Erratum in: Bioorg Med Chem Lett. 2015 Sep 15;25(18):4029.

PMID:
22892121
24.

Pyridone methylsulfone hydroxamate LpxC inhibitors for the treatment of serious gram-negative infections.

Montgomery JI, Brown MF, Reilly U, Price LM, Abramite JA, Arcari J, Barham R, Che Y, Chen JM, Chung SW, Collantes EM, Desbonnet C, Doroski M, Doty J, Engtrakul JJ, Harris TM, Huband M, Knafels JD, Leach KL, Liu S, Marfat A, McAllister L, McElroy E, Menard CA, Mitton-Fry M, Mullins L, Noe MC, O'Donnell J, Oliver R, Penzien J, Plummer M, Shanmugasundaram V, Thoma C, Tomaras AP, Uccello DP, Vaz A, Wishka DG.

J Med Chem. 2012 Feb 23;55(4):1662-70. doi: 10.1021/jm2014875. Epub 2012 Feb 8.

PMID:
22257165
25.

Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization.

Beuming T, Che Y, Abel R, Kim B, Shanmugasundaram V, Sherman W.

Proteins. 2012 Mar;80(3):871-83. doi: 10.1002/prot.23244. Epub 2011 Dec 16.

PMID:
22223256
26.

Potent inhibitors of LpxC for the treatment of Gram-negative infections.

Brown MF, Reilly U, Abramite JA, Arcari JT, Oliver R, Barham RA, Che Y, Chen JM, Collantes EM, Chung SW, Desbonnet C, Doty J, Doroski M, Engtrakul JJ, Harris TM, Huband M, Knafels JD, Leach KL, Liu S, Marfat A, Marra A, McElroy E, Melnick M, Menard CA, Montgomery JI, Mullins L, Noe MC, O'Donnell J, Penzien J, Plummer MS, Price LM, Shanmugasundaram V, Thoma C, Uccello DP, Warmus JS, Wishka DG.

J Med Chem. 2012 Jan 26;55(2):914-23. doi: 10.1021/jm2014748. Epub 2012 Jan 11.

PMID:
22175825
27.

Distinctive attributes of β-lactam target proteins in Acinetobacter baumannii relevant to development of new antibiotics.

Han S, Caspers N, Zaniewski RP, Lacey BM, Tomaras AP, Feng X, Geoghegan KF, Shanmugasundaram V.

J Am Chem Soc. 2011 Dec 21;133(50):20536-45. doi: 10.1021/ja208835z. Epub 2011 Nov 28.

PMID:
22050378
28.

Pantolactams as androgen receptor antagonists for the topical suppression of sebum production.

Sexton KE, Barrett S, Bridgwood K, Carroll M, Dettling D, Du D, Fakhoury S, Fedij V, Hu LY, Kostlan C, Pocalyko D, Raheja N, Smith Y, Shanmugasundaram V, Wade K.

Bioorg Med Chem Lett. 2011 Sep 15;21(18):5230-3. doi: 10.1016/j.bmcl.2011.07.048. Epub 2011 Jul 23.

PMID:
21831636
29.

Structural basis for effectiveness of siderophore-conjugated monocarbams against clinically relevant strains of Pseudomonas aeruginosa.

Han S, Zaniewski RP, Marr ES, Lacey BM, Tomaras AP, Evdokimov A, Miller JR, Shanmugasundaram V.

Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22002-7. doi: 10.1073/pnas.1013092107. Epub 2010 Dec 6.

30.

Molecular similarity measures.

Maggiora GM, Shanmugasundaram V.

Methods Mol Biol. 2011;672:39-100. doi: 10.1007/978-1-60761-839-3_2.

PMID:
20838964
31.

Smoothened antagonists for hair inhibition.

Li JJ, Shanmugasundaram V, Reddy S, Fleischer LL, Wang Z, Smith Y, Harter WG, Yue WS, Swaroop M, Li L, Ji CX, Dettling D, Osak B, Fitzgerald LR, Conradi R.

Bioorg Med Chem Lett. 2010 Aug 15;20(16):4932-5. doi: 10.1016/j.bmcl.2010.06.033. Epub 2010 Jun 11.

PMID:
20620058
32.

Rational design of a topical androgen receptor antagonist for the suppression of sebum production with properties suitable for follicular delivery.

Mitchell LH, Johnson TR, Lu GW, Du D, Datta K, Grzemski F, Shanmugasundaram V, Spence J, Wade K, Wang Z, Sun K, Lin K, Hu LY, Sexton K, Raheja N, Kostlan C, Pocalyko D.

J Med Chem. 2010 Jun 10;53(11):4422-7. doi: 10.1021/jm9018004.

PMID:
20462217
33.

Development of an in silico model for human skin permeation based on a Franz cell skin permeability assay.

Lee PH, Conradi R, Shanmugasundaram V.

Bioorg Med Chem Lett. 2010 Jan 1;20(1):69-73. doi: 10.1016/j.bmcl.2009.11.039. Epub 2009 Nov 14.

PMID:
19963379
34.

Chemotypic coverage: a new basis for constructing screening sublibraries.

Johnson M, Shanmugasundaram V, Bundy G, Chapman D, Kilkuskie R.

J Chem Inf Model. 2009 Mar;49(3):531-42. doi: 10.1021/ci800250r.

PMID:
19434894
35.

Nonfunctioning adrenocorticalcarcinoma.

Bakthavathsalam G, Shanmugasundaram VP, Prabakaran J, Venkatesh SP, Sowndaravalli DV, Jain CB.

Int Surg. 2008 Mar-Apr;93(2):81-7.

PMID:
18998286
36.

Rational design and synthesis of 4-((1R,2R)-2-hydroxycyclohexyl)-2(trifluoromethyl)benzonitrile (PF-998425), a novel, nonsteroidal androgen receptor antagonist devoid of phototoxicity for dermatological indications.

Li JJ, Iula DM, Nguyen MN, Hu LY, Dettling D, Johnson TR, Du DY, Shanmugasundaram V, Van Camp JA, Wang Z, Harter WG, Yue WS, Boys ML, Wade KJ, Drummond EM, Samas BM, Lefker BA, Hoge GS, Lovdahl MJ, Asbill J, Carroll M, Meade MA, Ciotti SM, Krieger-Burke T.

J Med Chem. 2008 Nov 13;51(21):7010-4. doi: 10.1021/jm8009316. Epub 2008 Oct 16.

PMID:
18921992
37.

Virtual screening: are we there yet?

Jalaie M, Shanmugasundaram V.

Mini Rev Med Chem. 2006 Oct;6(10):1159-67. Review.

PMID:
17073716
38.

Hit-directed nearest-neighbor searching.

Shanmugasundaram V, Maggiora GM, Lajiness MS.

J Med Chem. 2005 Jan 13;48(1):240-8.

PMID:
15634017
39.

Assessment of the consistency of medicinal chemists in reviewing sets of compounds.

Lajiness MS, Maggiora GM, Shanmugasundaram V.

J Med Chem. 2004 Sep 23;47(20):4891-6.

PMID:
15369393
40.

Strategies for the identification and generation of informative compound sets.

Lajiness MS, Shanmugasundaram V.

Methods Mol Biol. 2004;275:111-30.

PMID:
15141112
41.

Molecular similarity measures.

Maggiora GM, Shanmugasundaram V.

Methods Mol Biol. 2004;275:1-50.

PMID:
15141108
42.

Estimation of aqueous solubility of organic compounds with QSPR approach.

Gao H, Shanmugasundaram V, Lee P.

Pharm Res. 2002 Apr;19(4):497-503.

PMID:
12033386

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