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Items: 1 to 50 of 286

1.

Population Scale Retrospective Analysis Reveals Potential Risk of Cholestasis in Pregnant Women Taking Omeprazole, Lansoprazole, and Amoxicillin.

Zhang Y, Shi D, Abagyan R, Dai W, Dong M.

Interdiscip Sci. 2019 Jun;11(2):273-281. doi: 10.1007/s12539-019-00335-w. Epub 2019 May 20.

PMID:
31106388
2.

Extended Multitarget Pharmacology of Anticancer Drugs.

Shi D, Khan F, Abagyan R.

J Chem Inf Model. 2019 Jun 24;59(6):3006-3017. doi: 10.1021/acs.jcim.9b00031. Epub 2019 May 3.

PMID:
31025863
3.
4.

2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 1. Identification of an Allosteric Binding Site.

Bestgen B, Krimm I, Kufareva I, Kamal AAM, Seetoh WG, Abell C, Hartmann RW, Abagyan R, Cochet C, Le Borgne M, Engel M, Lomberget T.

J Med Chem. 2019 Feb 28;62(4):1803-1816. doi: 10.1021/acs.jmedchem.8b01766. Epub 2019 Feb 18.

PMID:
30689953
5.

2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 2. Structure-Based Optimization and Investigation of Effects Specific to the Allosteric Mode of Action.

Bestgen B, Kufareva I, Seetoh W, Abell C, Hartmann RW, Abagyan R, Le Borgne M, Filhol O, Cochet C, Lomberget T, Engel M.

J Med Chem. 2019 Feb 28;62(4):1817-1836. doi: 10.1021/acs.jmedchem.8b01765. Epub 2019 Feb 13.

PMID:
30689946
6.

Molecular Basis of Action of a Small-Molecule Positive Allosteric Modulator Agonist at the Type 1 Cholecystokinin Holoreceptor.

Desai AJ, Mechin I, Nagarajan K, Valant C, Wootten D, Lam PCH, Orry A, Abagyan R, Nair A, Sexton PM, Christopoulos A, Miller LJ.

Mol Pharmacol. 2019 Mar;95(3):245-259. doi: 10.1124/mol.118.114082. Epub 2018 Dec 27.

PMID:
30591538
7.

Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3.

Lam PC, Abagyan R, Totrov M.

J Comput Aided Mol Des. 2019 Jan;33(1):35-46. doi: 10.1007/s10822-018-0139-5. Epub 2018 Aug 9.

PMID:
30094533
8.

In silico discovery of small molecules that inhibit RfaH recruitment to RNA polymerase.

Svetlov D, Shi D, Twentyman J, Nedialkov Y, Rosen DA, Abagyan R, Artsimovitch I.

Mol Microbiol. 2018 Oct;110(1):128-142. doi: 10.1111/mmi.14093. Epub 2018 Oct 2.

9.

Protein-RNA Docking Using ICM.

Arnautova YA, Abagyan R, Totrov M.

J Chem Theory Comput. 2018 Sep 11;14(9):4971-4984. doi: 10.1021/acs.jctc.8b00293. Epub 2018 Aug 9.

PMID:
30016588
10.

Population scale retrospective analysis reveals distinctive antidepressant and anxiolytic effects of diclofenac, ketoprofen and naproxen in patients with pain.

Makunts T, Cohen IV, Lee KC, Abagyan R.

PLoS One. 2018 Apr 18;13(4):e0195521. doi: 10.1371/journal.pone.0195521. eCollection 2018.

11.

Hedgehog pathway and smoothened inhibitors in cancer therapies.

Chahal KK, Parle M, Abagyan R.

Anticancer Drugs. 2018 Jun;29(5):387-401. doi: 10.1097/CAD.0000000000000609. Review.

PMID:
29537987
12.

Identification of new benzamide inhibitor against α-subunit of tryptophan synthase from Mycobacterium tuberculosis through structure-based virtual screening, anti-tuberculosis activity and molecular dynamics simulations.

Naz S, Farooq U, Ali S, Sarwar R, Khan S, Abagyan R.

J Biomol Struct Dyn. 2019 Mar;37(4):1043-1053. doi: 10.1080/07391102.2018.1448303. Epub 2018 Mar 13.

PMID:
29502488
13.

Revisiting Antipsychotic Drug Actions Through Gene Networks Associated With Schizophrenia.

Kauppi K, Rosenthal SB, Lo MT, Sanyal N, Jiang M, Abagyan R, McEvoy LK, Andreassen OA, Chen CH.

Am J Psychiatry. 2018 Jul 1;175(7):674-682. doi: 10.1176/appi.ajp.2017.17040410. Epub 2018 Mar 2.

14.

CYP51 is an essential drug target for the treatment of primary amoebic meningoencephalitis (PAM).

Debnath A, Calvet CM, Jennings G, Zhou W, Aksenov A, Luth MR, Abagyan R, Nes WD, McKerrow JH, Podust LM.

PLoS Negl Trop Dis. 2017 Dec 28;11(12):e0006104. doi: 10.1371/journal.pntd.0006104. eCollection 2017 Dec.

15.

Multi-targeting Drug Community Challenge.

Schlessinger A, Abagyan R, Carlson HA, Dang KK, Guinney J, Cagan RL.

Cell Chem Biol. 2017 Dec 21;24(12):1434-1435. doi: 10.1016/j.chembiol.2017.12.006. No abstract available.

16.

The anthelmintic praziquantel is a human serotoninergic G-protein-coupled receptor ligand.

Chan JD, Cupit PM, Gunaratne GS, McCorvy JD, Yang Y, Stoltz K, Webb TR, Dosa PI, Roth BL, Abagyan R, Cunningham C, Marchant JS.

Nat Commun. 2017 Dec 5;8(1):1910. doi: 10.1038/s41467-017-02084-0.

17.
18.

Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens.

Naz S, Ngo T, Farooq U, Abagyan R.

PeerJ. 2017 Sep 19;5:e3765. doi: 10.7717/peerj.3765. eCollection 2017.

19.

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.

Lam PC, Abagyan R, Totrov M.

J Comput Aided Mol Des. 2018 Jan;32(1):187-198. doi: 10.1007/s10822-017-0058-x. Epub 2017 Sep 8.

20.

Phenotypic, chemical and functional characterization of cyclic nucleotide phosphodiesterase 4 (PDE4) as a potential anthelmintic drug target.

Long T, Rojo-Arreola L, Shi D, El-Sakkary N, Jarnagin K, Rock F, Meewan M, Rascón AA Jr, Lin L, Cunningham KA, Lemieux GA, Podust L, Abagyan R, Ashrafi K, McKerrow JH, Caffrey CR.

PLoS Negl Trop Dis. 2017 Jul 13;11(7):e0005680. doi: 10.1371/journal.pntd.0005680. eCollection 2017 Jul.

21.

Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV.

Zheng Y, Han GW, Abagyan R, Wu B, Stevens RC, Cherezov V, Kufareva I, Handel TM.

Immunity. 2017 Jun 20;46(6):1005-1017.e5. doi: 10.1016/j.immuni.2017.05.002.

22.

Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor.

Shi D, Svetlov D, Abagyan R, Artsimovitch I.

Nucleic Acids Res. 2017 Sep 6;45(15):8835-8843. doi: 10.1093/nar/gkx523.

23.

A Thiazole Orange Derivative Targeting the Bacterial Protein FtsZ Shows Potent Antibacterial Activity.

Sun N, Lu YJ, Chan FY, Du RL, Zheng YY, Zhang K, So LY, Abagyan R, Zhuo C, Leung YC, Wong KY.

Front Microbiol. 2017 May 11;8:855. doi: 10.3389/fmicb.2017.00855. eCollection 2017.

24.

Population scale data reveals the antidepressant effects of ketamine and other therapeutics approved for non-psychiatric indications.

Cohen IV, Makunts T, Atayee R, Abagyan R.

Sci Rep. 2017 May 3;7(1):1450. doi: 10.1038/s41598-017-01590-x. Erratum in: Sci Rep. 2017 Dec 5;7(1):17268.

25.

Inhibition of PDE5A1 guanosine cyclic monophosphate (cGMP) hydrolysing activity by sildenafil analogues that inhibit cellular cGMP efflux.

Subbotina A, Ravna AW, Lysaa RA, Abagyan R, Bugno R, Sager G.

J Pharm Pharmacol. 2017 Jun;69(6):675-683. doi: 10.1111/jphp.12693. Epub 2017 Feb 17.

26.

Structural basis of ligand interaction with atypical chemokine receptor 3.

Gustavsson M, Wang L, van Gils N, Stephens BS, Zhang P, Schall TJ, Yang S, Abagyan R, Chance MR, Kufareva I, Handel TM.

Nat Commun. 2017 Jan 18;8:14135. doi: 10.1038/ncomms14135.

27.

From Homology Models to a Set of Predictive Binding Pockets-a 5-HT1A Receptor Case Study.

Warszycki D, Rueda M, Mordalski S, Kristiansen K, Satała G, Rataj K, Chilmonczyk Z, Sylte I, Abagyan R, Bojarski AJ.

J Chem Inf Model. 2017 Feb 27;57(2):311-321. doi: 10.1021/acs.jcim.6b00263. Epub 2017 Jan 18.

28.

Orphan receptor ligand discovery by pickpocketing pharmacological neighbors.

Ngo T, Ilatovskiy AV, Stewart AG, Coleman JL, McRobb FM, Riek RP, Graham RM, Abagyan R, Kufareva I, Smith NJ.

Nat Chem Biol. 2017 Feb;13(2):235-242. doi: 10.1038/nchembio.2266. Epub 2016 Dec 19.

29.

Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists.

Zheng Y, Qin L, Zacarías NV, de Vries H, Han GW, Gustavsson M, Dabros M, Zhao C, Cherney RJ, Carter P, Stamos D, Abagyan R, Cherezov V, Stevens RC, IJzerman AP, Heitman LH, Tebben A, Kufareva I, Handel TM.

Nature. 2016 Dec 15;540(7633):458-461. doi: 10.1038/nature20605. Epub 2016 Dec 7.

30.

Correction to Environmental Photochemistry of Altrenogest: Photoisomerization to a Bioactive Product with Increased Environmental Persistence via Reversible Photohydration.

Wammer KH, Anderson KC, Erickson PR, Kliegman S, Moffatt ME, Berg SM, Heitzman JA, Pflug NC, McNeill K, Martinovic-Weigelt D, Abagyan R, Cwiertny DM, Kolodziej EP.

Environ Sci Technol. 2016 Sep 20;50(18):10292. doi: 10.1021/acs.est.6b04213. Epub 2016 Sep 8. No abstract available.

PMID:
27604407
31.

Molecular Properties of Drugs Interacting with SLC22 Transporters OAT1, OAT3, OCT1, and OCT2: A Machine-Learning Approach.

Liu HC, Goldenberg A, Chen Y, Lun C, Wu W, Bush KT, Balac N, Rodriguez P, Abagyan R, Nigam SK.

J Pharmacol Exp Ther. 2016 Oct;359(1):215-29. doi: 10.1124/jpet.116.232660. Epub 2016 Aug 3.

32.

An Organic Anion Transporter 1 (OAT1)-centered Metabolic Network.

Liu HC, Jamshidi N, Chen Y, Eraly SA, Cho SY, Bhatnagar V, Wu W, Bush KT, Abagyan R, Palsson BO, Nigam SK.

J Biol Chem. 2016 Sep 9;291(37):19474-86. doi: 10.1074/jbc.M116.745216. Epub 2016 Jul 20.

33.

SIRT2- and NRF2-Targeting Thiazole-Containing Compound with Therapeutic Activity in Huntington's Disease Models.

Quinti L, Casale M, Moniot S, Pais TF, Van Kanegan MJ, Kaltenbach LS, Pallos J, Lim RG, Naidu SD, Runne H, Meisel L, Rauf NA, Leyfer D, Maxwell MM, Saiah E, Landers JE, Luthi-Carter R, Abagyan R, Dinkova-Kostova AT, Steegborn C, Marsh JL, Lo DC, Thompson LM, Kazantsev AG.

Cell Chem Biol. 2016 Jul 21;23(7):849-861. doi: 10.1016/j.chembiol.2016.05.015. Epub 2016 Jul 14.

34.

Environmental Photochemistry of Altrenogest: Photoisomerization to a Bioactive Product with Increased Environmental Persistence via Reversible Photohydration.

Wammer KH, Anderson KC, Erickson PR, Kliegman S, Moffatt ME, Berg SM, Heitzman JA, Pflug NC, McNeill K, Martinovic-Weigelt D, Abagyan R, Cwiertny DM, Kolodziej EP.

Environ Sci Technol. 2016 Jul 19;50(14):7480-8. doi: 10.1021/acs.est.6b02608. Epub 2016 Jul 11. Erratum in: Environ Sci Technol. 2016 Sep 20;50(18):10292.

35.

Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein-Protein Encounters.

Pallara C, Rueda M, Abagyan R, Fernández-Recio J.

J Chem Theory Comput. 2016 Jul 12;12(7):3236-49. doi: 10.1021/acs.jctc.6b00204. Epub 2016 Jun 28.

PMID:
27294484
36.

Towards a structural understanding of allosteric drugs at the human calcium-sensing receptor.

Leach K, Gregory KJ, Kufareva I, Khajehali E, Cook AE, Abagyan R, Conigrave AD, Sexton PM, Christopoulos A.

Cell Res. 2016 May;26(5):574-92. doi: 10.1038/cr.2016.36. Epub 2016 Mar 22.

37.

X-ray structures of thioredoxin and thioredoxin reductase from Entamoeba histolytica and prevailing hypothesis of the mechanism of Auranofin action.

Parsonage D, Sheng F, Hirata K, Debnath A, McKerrow JH, Reed SL, Abagyan R, Poole LB, Podust LM.

J Struct Biol. 2016 May;194(2):180-90. doi: 10.1016/j.jsb.2016.02.015. Epub 2016 Feb 12.

38.

Identifying ligands at orphan GPCRs: current status using structure-based approaches.

Ngo T, Kufareva I, Coleman JLj, Graham RM, Abagyan R, Smith NJ.

Br J Pharmacol. 2016 Oct;173(20):2934-51. doi: 10.1111/bph.13452. Epub 2016 Mar 5. Review.

39.

An electrostatic mechanism for Ca(2+)-mediated regulation of gap junction channels.

Bennett BC, Purdy MD, Baker KA, Acharya C, McIntire WE, Stevens RC, Zhang Q, Harris AL, Abagyan R, Yeager M.

Nat Commun. 2016 Jan 12;7:8770. doi: 10.1038/ncomms9770.

40.

Use of Cysteine Trapping to Map Spatial Approximations between Residues Contributing to the Helix N-capping Motif of Secretin and Distinct Residues within Each of the Extracellular Loops of Its Receptor.

Dong M, Lam PC, Orry A, Sexton PM, Christopoulos A, Abagyan R, Miller LJ.

J Biol Chem. 2016 Mar 4;291(10):5172-84. doi: 10.1074/jbc.M115.706010. Epub 2016 Jan 6.

41.

Molecular Mechanism of Action of Triazolobenzodiazepinone Agonists of the Type 1 Cholecystokinin Receptor. Possible Cooperativity across the Receptor Homodimeric Complex.

Desai AJ, Lam PC, Orry A, Abagyan R, Christopoulos A, Sexton PM, Miller LJ.

J Med Chem. 2015 Dec 24;58(24):9562-77. doi: 10.1021/acs.jmedchem.5b01110. Epub 2015 Dec 10.

42.

Adverse Effects of Cholinesterase Inhibitors in Dementia, According to the Pharmacovigilance Databases of the United-States and Canada.

Ali TB, Schleret TR, Reilly BM, Chen WY, Abagyan R.

PLoS One. 2015 Dec 7;10(12):e0144337. doi: 10.1371/journal.pone.0144337. eCollection 2015.

43.

High-quality and universal empirical atomic charges for chemoinformatics applications.

Geidl S, Bouchal T, Raček T, Svobodová Vařeková R, Hejret V, Křenek A, Abagyan R, Koča J.

J Cheminform. 2015 Dec 2;7:59. doi: 10.1186/s13321-015-0107-1. eCollection 2015.

44.

Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily.

Lenoir M, Kufareva I, Abagyan R, Overduin M.

Membranes (Basel). 2015 Oct 23;5(4):646-63. doi: 10.3390/membranes5040646.

45.

P16INK4a Upregulation Mediated by SIX6 Defines Retinal Ganglion Cell Pathogenesis in Glaucoma.

Skowronska-Krawczyk D, Zhao L, Zhu J, Weinreb RN, Cao G, Luo J, Flagg K, Patel S, Wen C, Krupa M, Luo H, Ouyang H, Lin D, Wang W, Li G, Xu Y, Li O, Chung C, Yeh E, Jafari M, Ai M, Zhong Z, Shi W, Zheng L, Krawczyk M, Chen D, Shi C, Zin C, Zhu J, Mellon PL, Gao W, Abagyan R, Zhang L, Sun X, Zhong S, Zhuo Y, Rosenfeld MG, Liu Y, Zhang K.

Mol Cell. 2015 Sep 17;59(6):931-40. doi: 10.1016/j.molcel.2015.07.027. Epub 2015 Sep 10.

46.

Shared Ligands Between Organic Anion Transporters (OAT1 and OAT6) and Odorant Receptors.

Wu W, Bush KT, Liu HC, Zhu C, Abagyan R, Nigam SK.

Drug Metab Dispos. 2015 Dec;43(12):1855-63. doi: 10.1124/dmd.115.065250. Epub 2015 Sep 10.

47.

Corrigendum: Lanosterol reverses protein aggregation in cataracts.

Zhao L, Chen XJ, Zhu J, Xi YB, Yang X, Hu LD, Ouyang H, Patel SH, Jin X, Lin D, Wu F, Flagg K, Cai H, Li G, Cao G, Lin Y, Chen D, Wen C, Chung C, Wang Y, Qiu A, Yeh E, Wang W, Hu X, Grob S, Abagyan R, Su Z, Tjondro HC, Zhao XJ, Luo H, Hou R, Perry JJ, Gao W, Kozak I, Granet D, Li Y, Sun X, Wang J, Zhang L, Liu Y, Yan YB, Zhang K.

Nature. 2015 Oct 22;526(7574):595. doi: 10.1038/nature15253. Epub 2015 Aug 26. No abstract available.

PMID:
26308894
48.

Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs.

Kufareva I, Handel TM, Abagyan R.

Methods Mol Biol. 2015;1335:295-311. doi: 10.1007/978-1-4939-2914-6_19.

49.

Lanosterol reverses protein aggregation in cataracts.

Zhao L, Chen XJ, Zhu J, Xi YB, Yang X, Hu LD, Ouyang H, Patel SH, Jin X, Lin D, Wu F, Flagg K, Cai H, Li G, Cao G, Lin Y, Chen D, Wen C, Chung C, Wang Y, Qiu A, Yeh E, Wang W, Hu X, Grob S, Abagyan R, Su Z, Tjondro HC, Zhao XJ, Luo H, Hou R, Jefferson J, Perry P, Gao W, Kozak I, Granet D, Li Y, Sun X, Wang J, Zhang L, Liu Y, Yan YB, Zhang K.

Nature. 2015 Jul 30;523(7562):607-11. doi: 10.1038/nature14650. Epub 2015 Jul 22. Erratum in: Nature. 2015 Oct 22;526(7574):595.

PMID:
26200341
50.

How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction?

Geidl S, Svobodová Vařeková R, Bendová V, Petrusek L, Ionescu CM, Jurka Z, Abagyan R, Koča J.

J Chem Inf Model. 2015 Jun 22;55(6):1088-97. doi: 10.1021/ci500758w. Epub 2015 Jun 11.

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