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Items: 1 to 50 of 56

1.

Superior Performance of the SQM/COSMO Scoring Functions in Native Pose Recognition of Diverse Protein-Ligand Complexes in Cognate Docking.

Ajani H, Pecina A, Eyrilmez SM, Fanfrlík J, Haldar S, Řezáč J, Hobza P, Lepšík M.

ACS Omega. 2017 Jul 31;2(7):4022-4029. doi: 10.1021/acsomega.7b00503. Epub 2017 Jul 27.

2.

Chalcogen Bonding in Protein-Ligand Complexes: PDB Survey and Quantum Mechanical Calculations.

Kříž K, Fanfrlík J, Lepšík M.

Chemphyschem. 2018 Oct 5;19(19):2540-2548. doi: 10.1002/cphc.201800409. Epub 2018 Jul 13.

PMID:
30003638
3.

Affinity switching of the LEDGF/p75 IBD interactome is governed by kinase-dependent phosphorylation.

Sharma S, Čermáková K, De Rijck J, Demeulemeester J, Fábry M, El Ashkar S, Van Belle S, Lepšík M, Tesina P, Duchoslav V, Novák P, Hubálek M, Srb P, Christ F, Řezáčová P, Hodges HC, Debyser Z, Veverka V.

Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):E7053-E7062. doi: 10.1073/pnas.1803909115. Epub 2018 Jul 11.

PMID:
29997176
4.

Imidazo[1,2-c]pyrimidin-5(6H)-one as a novel core of cyclin-dependent kinase 2 inhibitors: Synthesis, activity measurement, docking, and quantum mechanical scoring.

Ajani H, Jansa J, Köprülüoğlu C, Hobza P, Kryštof V, Lyčka A, Lepsik M.

J Mol Recognit. 2018 Sep;31(9):e2720. doi: 10.1002/jmr.2720. Epub 2018 Apr 23.

PMID:
29687635
5.

Discovery of N2-(4-Amino-cyclohexyl)-9-cyclopentyl- N6-(4-morpholin-4-ylmethyl-phenyl)- 9H-purine-2,6-diamine as a Potent FLT3 Kinase Inhibitor for Acute Myeloid Leukemia with FLT3 Mutations.

Gucký T, Řezníčková E, Radošová Muchová T, Jorda R, Klejová Z, Malínková V, Berka K, Bazgier V, Ajani H, Lepšík M, Divoký V, Kryštof V.

J Med Chem. 2018 May 10;61(9):3855-3869. doi: 10.1021/acs.jmedchem.7b01529. Epub 2018 Apr 30.

PMID:
29672049
6.

Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes.

Pecina A, Brynda J, Vrzal L, Gnanasekaran R, Hořejší M, Eyrilmez SM, Řezáč J, Lepšík M, Řezáčová P, Hobza P, Majer P, Veverka V, Fanfrlík J.

Chemphyschem. 2018 Apr 5;19(7):873-879. doi: 10.1002/cphc.201701104. Epub 2018 Feb 19.

PMID:
29316128
7.

Synthesis of α-Branched Acyclic Nucleoside Phosphonates as Potential Inhibitors of Bacterial Adenylate Cyclases.

Frydrych J, Skácel J, Šmídková M, Mertlíková-Kaiserová H, Dračínský M, Gnanasekaran R, Lepšík M, Soto-Velasquez M, Watts VJ, Janeba Z.

ChemMedChem. 2018 Jan 22;13(2):199-206. doi: 10.1002/cmdc.201700715. Epub 2018 Jan 8.

PMID:
29235265
8.

General and Modular Strategy for Designing Potent, Selective, and Pharmacologically Compliant Inhibitors of Rhomboid Proteases.

Tichá A, Stanchev S, Vinothkumar KR, Mikles DC, Pachl P, Began J, Škerle J, Švehlová K, Nguyen MTN, Verhelst SHL, Johnson DC, Bachovchin DA, Lepšík M, Majer P, Strisovsky K.

Cell Chem Biol. 2017 Dec 21;24(12):1523-1536.e4. doi: 10.1016/j.chembiol.2017.09.007. Epub 2017 Oct 26.

9.

Structural characterization of CAS SH3 domain selectivity and regulation reveals new CAS interaction partners.

Gemperle J, Hexnerová R, Lepšík M, Tesina P, Dibus M, Novotný M, Brábek J, Veverka V, Rosel D.

Sci Rep. 2017 Aug 14;7(1):8057. doi: 10.1038/s41598-017-08303-4.

10.

B-Hπ: a nonclassical hydrogen bond or dispersion contact?

Fanfrlík J, Pecina A, Řezáč J, Sedlak R, Hnyk D, Lepšík M, Hobza P.

Phys Chem Chem Phys. 2017 Jul 19;19(28):18194-18200. doi: 10.1039/c7cp02762a.

PMID:
28555227
11.

Binary twinned-icosahedral [B21H18]- interacts with cyclodextrins as a precedent for its complexation with other organic motifs.

Eyrilmez SM, Bernhardt E, Dávalos JZ, Lepšík M, Hobza P, Assaf KI, Nau WM, Holub J, Oliva-Enrich JM, Fanfrlík J, Hnyk D.

Phys Chem Chem Phys. 2017 May 17;19(19):11748-11752. doi: 10.1039/c7cp01074e.

PMID:
28453021
12.

The Role of Cysteine Residues in Catalysis of Phosphoenolpyruvate Carboxykinase from Mycobacterium tuberculosis.

Machová I, Hubálek M, Lepšík M, Bednárová L, Pazderková M, Kopecký V Jr, Snášel J, Dostál J, Pichová I.

PLoS One. 2017 Jan 30;12(1):e0170373. doi: 10.1371/journal.pone.0170373. eCollection 2017.

13.

SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein-Ligand Poses.

Pecina A, Haldar S, Fanfrlík J, Meier R, Řezáč J, Lepšík M, Hobza P.

J Chem Inf Model. 2017 Feb 27;57(2):127-132. doi: 10.1021/acs.jcim.6b00513. Epub 2017 Jan 17.

PMID:
28045518
14.

Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines.

Hylsová M, Carbain B, Fanfrlík J, Musilová L, Haldar S, Köprülüoğlu C, Ajani H, Brahmkshatriya PS, Jorda R, Kryštof V, Hobza P, Echalier A, Paruch K, Lepšík M.

Eur J Med Chem. 2017 Jan 27;126:1118-1128. doi: 10.1016/j.ejmech.2016.12.023. Epub 2016 Dec 11.

PMID:
28039837
15.

Synthesis, structural characterization, docking, lipophilicity and cytotoxicity of 1-[(1R)-1-(6-fluoro-1,3-benzothiazol-2-yl)ethyl]-3-alkyl carbamates, novel acetylcholinesterase and butyrylcholinesterase pseudo-irreversible inhibitors.

Pejchal V, Štěpánková Š, Pejchalová M, Královec K, Havelek R, Růžičková Z, Ajani H, Lo R, Lepšík M.

Bioorg Med Chem. 2016 Apr 1;24(7):1560-72. doi: 10.1016/j.bmc.2016.02.033. Epub 2016 Feb 26.

PMID:
26947959
16.

The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein-ligand interactions and implicit COSMO solvation.

Pecina A, Meier R, Fanfrlík J, Lepšík M, Řezáč J, Hobza P, Baldauf C.

Chem Commun (Camb). 2016 Feb 25;52(16):3312-5. doi: 10.1039/c5cc09499b.

PMID:
26821703
17.

Myristoylation drives dimerization of matrix protein from mouse mammary tumor virus.

Doležal M, Zábranský A, Dostál J, Vaněk O, Brynda J, Lepšík M, Hadravová R, Pichová I.

Retrovirology. 2016 Jan 5;13:2. doi: 10.1186/s12977-015-0235-8.

18.

Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis.

Dostál J, Pecina A, Hrušková-Heidingsfeldová O, Marečková L, Pichová I, Řezáčová P, Lepšík M, Brynda J.

Acta Crystallogr D Biol Crystallogr. 2015 Dec 1;71(Pt 12):2494-504. doi: 10.1107/S1399004715019392. Epub 2015 Nov 27.

PMID:
26627656
19.

Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization.

Kohagen M, Lepšík M, Jungwirth P.

J Phys Chem Lett. 2014 Nov 20;5(22):3964-9. doi: 10.1021/jz502099g. Epub 2014 Nov 3.

PMID:
26276478
20.

The properties of substituted 3D-aromatic neutral carboranes: the potential for σ-hole bonding.

Lo R, Fanfrlík J, Lepšík M, Hobza P.

Phys Chem Chem Phys. 2015 Aug 28;17(32):20814-21. doi: 10.1039/c5cp03617h. Epub 2015 Jul 27.

PMID:
26213995
21.

The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition.

Fanfrlík J, Ruiz FX, Kadlčíková A, Řezáč J, Cousido-Siah A, Mitschler A, Haldar S, Lepšík M, Kolář MH, Majer P, Podjarny AD, Hobza P.

ACS Chem Biol. 2015 Jul 17;10(7):1637-42. doi: 10.1021/acschembio.5b00151. Epub 2015 May 6.

PMID:
25919404
22.

Chalcogen and pnicogen bonds in complexes of neutral icosahedral and bicapped square-antiprismatic heteroboranes.

Pecina A, Lepšík M, Hnyk D, Hobza P, Fanfrlík J.

J Phys Chem A. 2015 Feb 26;119(8):1388-95. doi: 10.1021/jp511101n. Epub 2015 Feb 12.

PMID:
25635676
23.

A γ-cyclodextrin duplex connected with two disulfide bonds: synthesis, structure and inclusion complexes.

Volkov S, Kumprecht L, Buděšínský M, Lepšík M, Dušek M, Kraus T.

Org Biomol Chem. 2015 Mar 14;13(10):2980-5. doi: 10.1039/c4ob02464h.

PMID:
25616110
24.

Malonate-based inhibitors of mammalian serine racemase: kinetic characterization and structure-based computational study.

Vorlová B, Nachtigallová D, Jirásková-Vaníčková J, Ajani H, Jansa P, Rezáč J, Fanfrlík J, Otyepka M, Hobza P, Konvalinka J, Lepšík M.

Eur J Med Chem. 2015 Jan 7;89:189-97. doi: 10.1016/j.ejmech.2014.10.043. Epub 2014 Oct 16.

PMID:
25462239
25.

Carborane-based carbonic anhydrase inhibitors: insight into CAII/CAIX specificity from a high-resolution crystal structure, modeling, and quantum chemical calculations.

Mader P, Pecina A, Cígler P, Lepšík M, Šícha V, Hobza P, Grüner B, Fanfrlík J, Brynda J, Řezáčová P.

Biomed Res Int. 2014;2014:389869. doi: 10.1155/2014/389869. Epub 2014 Sep 18.

26.

Human insulin analogues modified at the B26 site reveal a hormone conformation that is undetected in the receptor complex.

Záková L, Kletvíková E, Lepšík M, Collinsová M, Watson CJ, Turkenburg JP, Jiráček J, Brzozowski AM.

Acta Crystallogr D Biol Crystallogr. 2014 Oct;70(Pt 10):2765-74. doi: 10.1107/S1399004714017775. Epub 2014 Sep 27.

27.

Role of Mason-Pfizer monkey virus CA-NC spacer peptide-like domain in assembly of immature particles.

Strohalmová-Bohmová K, Spiwok V, Lepšík M, Hadravová R, Křížová I, Ulbrich P, Pichová I, Bednárová L, Ruml T, Rumlová M.

J Virol. 2014 Dec;88(24):14148-60. doi: 10.1128/JVI.02286-14. Epub 2014 Oct 1.

28.

Substrate binding and specificity of rhomboid intramembrane protease revealed by substrate-peptide complex structures.

Zoll S, Stanchev S, Began J, Skerle J, Lepšík M, Peclinovská L, Majer P, Strisovsky K.

EMBO J. 2014 Oct 16;33(20):2408-21. doi: 10.15252/embj.201489367. Epub 2014 Sep 12.

29.

The dominant role of chalcogen bonding in the crystal packing of 2D/3D aromatics.

Fanfrlík J, Přáda A, Padělková Z, Pecina A, Macháček J, Lepšík M, Holub J, Růžička A, Hnyk D, Hobza P.

Angew Chem Int Ed Engl. 2014 Sep 15;53(38):10139-42. doi: 10.1002/anie.201405901. Epub 2014 Jul 27.

PMID:
25066639
30.

Thermodynamic and structural analysis of HIV protease resistance to darunavir - analysis of heavily mutated patient-derived HIV-1 proteases.

Kožíšek M, Lepšík M, Grantz Šašková K, Brynda J, Konvalinka J, Rezáčová P.

FEBS J. 2014 Apr;281(7):1834-47. doi: 10.1111/febs.12743.

31.

QM/MM calculations reveal the different nature of the interaction of two carborane-based sulfamide inhibitors of human carbonic anhydrase II.

Pecina A, Lepšík M, Řezáč J, Brynda J, Mader P, Řezáčová P, Hobza P, Fanfrlík J.

J Phys Chem B. 2013 Dec 19;117(50):16096-104. doi: 10.1021/jp410216m. Epub 2013 Dec 11.

PMID:
24289143
32.

Quantum mechanics-based scoring rationalizes the irreversible inactivation of parasitic Schistosoma mansoni cysteine peptidase by vinyl sulfone inhibitors.

Fanfrlík J, Brahmkshatriya PS, Řezáč J, Jílková A, Horn M, Mareš M, Hobza P, Lepšík M.

J Phys Chem B. 2013 Dec 5;117(48):14973-82. doi: 10.1021/jp409604n. Epub 2013 Nov 21.

PMID:
24195769
33.

Modulation of aldose reductase inhibition by halogen bond tuning.

Fanfrlík J, Kolář M, Kamlar M, Hurný D, Ruiz FX, Cousido-Siah A, Mitschler A, Rezáč J, Munusamy E, Lepšík M, Matějíček P, Veselý J, Podjarny A, Hobza P.

ACS Chem Biol. 2013 Nov 15;8(11):2484-92. doi: 10.1021/cb400526n. Epub 2013 Sep 17.

PMID:
23988122
34.

Assessing the accuracy and performance of implicit solvent models for drug molecules: conformational ensemble approaches.

Kolář M, Fanfrlík J, Lepšík M, Forti F, Luque FJ, Hobza P.

J Phys Chem B. 2013 May 16;117(19):5950-62. doi: 10.1021/jp402117c. Epub 2013 May 6.

PMID:
23600402
35.

Structural integrity of the B24 site in human insulin is important for hormone functionality.

Žáková L, Kletvíková E, Veverka V, Lepsík M, Watson CJ, Turkenburg JP, Jirácek J, Brzozowski AM.

J Biol Chem. 2013 Apr 12;288(15):10230-40. doi: 10.1074/jbc.M112.448050. Epub 2013 Feb 27.

36.

Quantum mechanical scoring: structural and energetic insights into cyclin-dependent kinase 2 inhibition by pyrazolo[1,5-a]pyrimidines.

Brahmkshatriya PS, Dobeš P, Fanfrlik J, Rezáç J, Paruch K, Bronowska A, Lepšík M, Hobza P.

Curr Comput Aided Drug Des. 2013 Mar;9(1):118-29.

PMID:
23157414
37.

Structure-aided design of novel inhibitors of HIV protease based on a benzodiazepine scaffold.

Schimer J, Cígler P, Veselý J, Grantz Šašková K, Lepšík M, Brynda J, Rezáčová P, Kožíšek M, Císařová I, Oberwinkler H, Kraeusslich HG, Konvalinka J.

J Med Chem. 2012 Nov 26;55(22):10130-5. doi: 10.1021/jm301249q. Epub 2012 Oct 23.

PMID:
23050738
38.

Modulation of HIV-1 Gag NC/p1 cleavage efficiency affects protease inhibitor resistance and viral replicative capacity.

van Maarseveen NM, Andersson D, Lepšík M, Fun A, Schipper PJ, de Jong D, Boucher CA, Nijhuis M.

Retrovirology. 2012 Apr 1;9:29. doi: 10.1186/1742-4690-9-29.

39.

Aurora kinase inhibitors: progress towards the clinic.

Kollareddy M, Zheleva D, Dzubak P, Brahmkshatriya PS, Lepsik M, Hajduch M.

Invest New Drugs. 2012 Dec;30(6):2411-32. doi: 10.1007/s10637-012-9798-6. Epub 2012 Feb 18. Review.

40.

Metallacarboranes and their interactions: theoretical insights and their applicability.

Farràs P, Juárez-Pérez EJ, Lepšík M, Luque R, Núñez R, Teixidor F.

Chem Soc Rev. 2012 May 7;41(9):3445-63. doi: 10.1039/c2cs15338f. Epub 2012 Feb 14.

PMID:
22334301
41.

Enzymatic activity and immunoreactivity of Aca s 4, an alpha-amylase allergen from the storage mite Acarus siro.

Pytelková J, Lepšík M, Sanda M, Talacko P, Marešová L, Mareš M.

BMC Biochem. 2012 Jan 31;13:3. doi: 10.1186/1471-2091-13-3.

42.

Structural basis for inhibition of cathepsin B drug target from the human blood fluke, Schistosoma mansoni.

Jílková A, Rezácová P, Lepsík M, Horn M, Váchová J, Fanfrlík J, Brynda J, McKerrow JH, Caffrey CR, Mares M.

J Biol Chem. 2011 Oct 14;286(41):35770-81. doi: 10.1074/jbc.M111.271304. Epub 2011 Aug 10.

43.

Inhibition of human serine racemase, an emerging target for medicinal chemistry.

Jirásková-Vaníčková J, Ettrich R, Vorlová B, Hoffman HE, Lepšík M, Jansa P, Konvalinka J.

Curr Drug Targets. 2011 Jun;12(7):1037-55. Review.

PMID:
21291385
44.

Interactions of boranes and carboranes with aromatic systems: CCSD(T) complete basis set calculations and DFT-SAPT analysis of energy components.

Sedlák R, Fanfrlík J, Hnyk D, Hobza P, Lepsík M.

J Phys Chem A. 2010 Oct 28;114(42):11304-11. doi: 10.1021/jp104411x.

PMID:
20831237
45.

Thiocyanation of closo-dodecaborate B(12)H(12)(2-). A novel synthetic route and theoretical elucidation of the reaction mechanism.

Lepsík M, Srnec M, Plesek J, Budesínský M, Klepetárová B, Hnyk D, Grüner B, Rulísek L.

Inorg Chem. 2010 Jun 7;49(11):5040-8. doi: 10.1021/ic100206y.

PMID:
20426407
46.

Design of HIV protease inhibitors based on inorganic polyhedral metallacarboranes.

Rezácová P, Pokorná J, Brynda J, Kozísek M, Cígler P, Lepsík M, Fanfrlík J, Rezác J, Grantz Sasková K, Sieglová I, Plesek J, Sícha V, Grüner B, Oberwinkler H, Sedlácek' J, Kräusslich HG, Hobza P, Král V, Konvalinka J.

J Med Chem. 2009 Nov 26;52(22):7132-41. doi: 10.1021/jm9011388.

PMID:
19874035
47.

Digestive alpha-amylases of the flour moth Ephestia kuehniella--adaptation to alkaline environment and plant inhibitors.

Pytelková J, Hubert J, Lepsík M, Sobotník J, Sindelka R, Krízková I, Horn M, Mares M.

FEBS J. 2009 Jul;276(13):3531-46. doi: 10.1111/j.1742-4658.2009.07074.x. Epub 2009 May 20.

48.

Interpretation of protein/ligand crystal structure using QM/MM calculations: case of HIV-1 protease/metallacarborane complex.

Fanfrlík J, Brynda J, Rezác J, Hobza P, Lepsík M.

J Phys Chem B. 2008 Nov 27;112(47):15094-102. doi: 10.1021/jp803528w.

PMID:
18975888
49.

Inorganic polyhedral metallacarborane inhibitors of HIV protease: a new approach to overcoming antiviral resistance.

Kozísek M, Cígler P, Lepsík M, Fanfrlík J, Rezácová P, Brynda J, Pokorná J, Plesek J, Grüner B, Grantz Sasková K, Václavíková J, Král V, Konvalinka J.

J Med Chem. 2008 Aug 14;51(15):4839-43. doi: 10.1021/jm8002334. Epub 2008 Jul 4.

PMID:
18598016
50.

Enzymatic and structural analysis of the I47A mutation contributing to the reduced susceptibility to HIV protease inhibitor lopinavir.

Sasková KG, Kozísek M, Lepsík M, Brynda J, Rezácová P, Václavíková J, Kagan RM, Machala L, Konvalinka J.

Protein Sci. 2008 Sep;17(9):1555-64. doi: 10.1110/ps.036079.108. Epub 2008 Jun 17.

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