Serdar Durdagi

Serdar Durdagi

UNVERIFIED PROFILE

Are you Serdar Durdagi?   Register this Author

Register author
Serdar Durdagi

Serdar Durdagi

Publications by authors named "Serdar Durdagi"

Are you Serdar Durdagi?   Register this Author

100Publications

1747Reads

44Profile Views

Inhibition of acetylcholinesterase and butyrylcholinesterase with uracil derivatives: kinetic and computational studies.

J Enzyme Inhib Med Chem 2019 Dec;34(1):429-437

f Department of Agricultural Biotechnology , Agriculture Faculty, Ondokuz Mayis University , Samsun , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/14756366.2018.1543288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327988PMC
December 2019

Novel tumor necrosis factor-α (TNF-α) inhibitors from small molecule library screening for their therapeutic activity profiles against rheumatoid arthritis using target-driven approaches and binary QSAR models.

J Biomol Struct Dyn 2019 Jun 23;37(9):2464-2476. Epub 2018 Dec 23.

a Department of Biophysics, School of Medicine, Computational Biology and Molecular Simulations Laboratory , Bahcesehir University (BAU) , Istanbul , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/07391102.2018.1491423DOI Listing
June 2019

Oligomerization and cooperativity in GPCRs from the perspective of the angiotensin AT1 and dopamine D2 receptors.

Neurosci Lett 2019 05 20;700:30-37. Epub 2018 Apr 20.

Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Bioengineering Program, Graduate School of Natural and Applied Sciences, Bahcesehir University, Istanbul, Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.neulet.2018.04.028DOI Listing
May 2019

Current status of multiscale simulations on GPCRs.

Curr Opin Struct Biol 2019 May 10;55:93-103. Epub 2019 May 10.

Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.sbi.2019.02.013DOI Listing
May 2019

Application of Multiscale Simulation Tools on GPCRs. An Example with Angiotensin II Type 1 Receptor.

Methods Mol Biol 2018 ;1824:431-448

Department of Biophysics, Computational Biology and Molecular Simulations Laboratory, School of Medicine, Bahcesehir University, Istanbul, Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-8630-9_26DOI Listing
March 2019

Combined molecular modeling and cholinesterase inhibition studies on some natural and semisynthetic O-alkylcoumarin derivatives.

Bioorg Chem 2019 Mar 26;84:355-362. Epub 2018 Nov 26.

Dipartimento di Farmacia, Università "G. d'Annunzio" Chieti-Pescara, Via dei Vestini 31, 66100 Chieti Scalo, CH, Italy.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S00452068183116
Publisher Site
http://dx.doi.org/10.1016/j.bioorg.2018.11.044DOI Listing
March 2019

Synthesis, anticholinesterase activity and molecular modeling studies of novel carvacrol-substituted amide derivatives.

J Biomol Struct Dyn 2019 Mar 5:1-19. Epub 2019 Mar 5.

d Pamukova Vocational High School , Sakarya University of Applied Sciences , Sakarya , Turkey.

View Article

Download full-text PDF

Source
https://www.tandfonline.com/doi/full/10.1080/07391102.2019.1
Publisher Site
http://dx.doi.org/10.1080/07391102.2019.1590243DOI Listing
March 2019

Combinatorial peptide library screening for discovery of diverse α-glucosidase inhibitors using molecular dynamics simulations and binary QSAR models.

J Biomol Struct Dyn 2019 Feb 22;37(3):726-740. Epub 2018 Feb 22.

e Dipartimento di Farmacia , Università di Napoli "Federico II" , Via D. Montesano, Naples 49, 80131 , Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/07391102.2018.1439403DOI Listing
February 2019

Targeting the NF-κB/IκBα complex via fragment-based E-Pharmacophore virtual screening and binary QSAR models.

J Mol Graph Model 2019 Jan 5;86:264-277. Epub 2018 Oct 5.

Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey; Neuroscience Program, Institute of Health Sciences, Bahcesehir University, Istanbul, Turkey. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S10933263183063
Publisher Site
http://dx.doi.org/10.1016/j.jmgm.2018.09.014DOI Listing
January 2019

Effects of Cholesterol on GPCR Function: Insights from Computational and Experimental Studies.

Adv Exp Med Biol 2019 ;1135:89-103

Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-3-030-14265-0_5DOI Listing
January 2019

Proposing novel TNFα direct inhibitor Scaffolds using fragment-docking based e-pharmacophore modeling and binary QSAR-based virtual screening protocols pipeline.

J Mol Graph Model 2018 Oct 24;85:111-121. Epub 2018 Aug 24.

Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey; Neuroscience Program, Institute of Health Sciences, Bahcesehir University, Istanbul, Turkey. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmgm.2018.07.007DOI Listing
October 2018

Investigating the molecular mechanism of staphylococcal DNA gyrase inhibitors: A combined ligand-based and structure-based resources pipeline.

J Mol Graph Model 2018 Oct 27;85:122-129. Epub 2018 Jul 27.

Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S10933263183046
Publisher Site
http://dx.doi.org/10.1016/j.jmgm.2018.07.010DOI Listing
October 2018

A QM protein-ligand investigation of antipsychotic drugs with the dopamine D2 Receptor (D2R).

J Biomol Struct Dyn 2018 Aug 22;36(10):2668-2677. Epub 2017 Aug 22.

a Department of Chemistry , Istanbul Technical University , Istanbul , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/07391102.2017.1365772DOI Listing
August 2018

Structural Investigation of the Dopamine-2 Receptor Agonist Bromocriptine Binding to Dimeric D2R and D2R States.

J Chem Inf Model 2018 04 29;58(4):826-836. Epub 2018 Mar 29.

Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine , Bahcesehir University , Istanbul 34349 , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jcim.7b00722DOI Listing
April 2018

Biochemical changes induced by grape seed extract and low level laser therapy administration during intraoral wound healing in rat liver: an experimental and in silico study.

J Biomol Struct Dyn 2018 Mar 5;36(4):993-1008. Epub 2017 Apr 5.

f Faculty of Arts and Science, Department of Biotechnology , Omer Halisdemir University , Nigde , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/07391102.2017.1305297DOI Listing
March 2018

Structure-based design of hERG-neutral antihypertensive oxazalone and imidazolone derivatives.

J Mol Graph Model 2018 01 18;79:103-117. Epub 2017 Oct 18.

Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmgm.2017.10.011DOI Listing
January 2018

In silico design of novel hERG-neutral sildenafil-like PDE5 inhibitors.

J Biomol Struct Dyn 2017 Oct 6;35(13):2830-2852. Epub 2016 Oct 6.

b Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/07391102.2016.1231634DOI Listing
October 2017

Structure-based design of hERG-neutral antihypertensive oxazalone and imidazolone derivatives.

J Mol Graph Model 2017 10 12;77:240-249. Epub 2017 Aug 12.

Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmgm.2017.08.004DOI Listing
October 2017

Discovery of selective dengue virus inhibitors using combination of molecular fingerprint-based virtual screening protocols, structure-based pharmacophore model development, molecular dynamics simulations and in vitro studies.

J Mol Graph Model 2017 10 9;77:338. Epub 2017 Aug 9.

Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmgm.2017.08.006DOI Listing
October 2017

Structural investigation of vesnarinone at the pore domains of open and open-inactivated states of hERG1 K channel.

J Mol Graph Model 2017 10 6;77:399-412. Epub 2017 Sep 6.

Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul, Turkey. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmgm.2017.08.017DOI Listing
October 2017

Effects of propolis, caffeic acid phenethyl ester, and pollen on renal injury in hypertensive rat: An experimental and theoretical approach.

Cell Biochem Funct 2017 Aug 22;35(6):304-314. Epub 2017 Aug 22.

Department of Medical Biology, Faculty of Medicine, Omer Halisdemir University, Nigde, Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/cbf.3277DOI Listing
August 2017

Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: combination of in silico and in vitro studies.

J Biomol Struct Dyn 2017 Jul 17;35(9):1899-1915. Epub 2016 Jul 17.

a Department of Biophysics, School of Medicine , Bahcesehir University , Istanbul , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/07391102.2016.1199328DOI Listing
July 2017

The signaling pathway of dopamine D2 receptor (D2R) activation using normal mode analysis (NMA) and the construction of pharmacophore models for D2R ligands.

J Biomol Struct Dyn 2017 Jul 27;35(9):2040-2048. Epub 2016 Jul 27.

a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/07391102.2016.1206487DOI Listing
July 2017

Analysis of the Glutamate Agonist LY404,039 Binding to Nonstatic Dopamine Receptor D2 Dimer Structures and Consensus Docking.

ACS Chem Neurosci 2017 06 22;8(6):1404-1415. Epub 2017 Mar 22.

Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University , 34349 Istanbul, Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acschemneuro.7b00070DOI Listing
June 2017

First universal pharmacophore model for hERG1 K channel activators: acthER.

J Mol Graph Model 2017 06 5;74:153-170. Epub 2017 Apr 5.

Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmgm.2017.03.020DOI Listing
June 2017

Identification of novel serotonin reuptake inhibitors targeting central and allosteric binding sites: A virtual screening and molecular dynamics simulations study.

J Mol Graph Model 2017 06 22;74:193-202. Epub 2017 Mar 22.

Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmgm.2017.02.001DOI Listing
June 2017

Biological Insights of the Dopaminergic Stabilizer ACR16 at the Binding Pocket of Dopamine D2 Receptor.

ACS Chem Neurosci 2017 04 20;8(4):826-836. Epub 2017 Jan 20.

Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University , Istanbul, Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acschemneuro.6b00396DOI Listing
April 2017

Cholesterol up-regulates neuronal G protein-gated inwardly rectifying potassium (GIRK) channel activity in the hippocampus.

J Biol Chem 2017 04 17;292(15):6135-6147. Epub 2017 Feb 17.

From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607,

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/jbc.M116.753350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5391746PMC
April 2017

Atomistic molecular dynamics simulations of typical and atypical antipsychotic drugs at the dopamine D2 receptor (D2R) elucidates their inhibition mechanism.

J Biomol Struct Dyn 2017 Mar 6;35(4):738-754. Epub 2016 Apr 6.

a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/07391102.2016.1159986DOI Listing
March 2017

Investigation of inhibition of human glucose 6-phosphate dehydrogenase by some 99mTc chelators by in silico and in vitro methods.

J Enzyme Inhib Med Chem 2016 3;31(sup1):141-147. Epub 2016 May 3.

d School of Medicine, Bahcesehir University , Istanbul , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/14756366.2016.1178735DOI Listing
February 2017

Synthesis, anticholinesterase activity and molecular modeling study of novel carbamate-substituted thymol/carvacrol derivatives.

Bioorg Med Chem 2017 02 26;25(4):1352-1363. Epub 2016 Dec 26.

Pamukova Vocational High School, Sakarya University, 54900 Sakarya, Turkey. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmc.2016.12.037DOI Listing
February 2017

Kinetic and docking studies of cytosolic/tumor-associated carbonic anhydrase isozymes I, II and IX with some hydroxylic compounds.

J Enzyme Inhib Med Chem 2016 Dec 4;31(6):1214-20. Epub 2015 Dec 4.

d Polo Scientifico, Laboratorio Di Chimica Bioinorganica, Università Degli Studi Di Firenze , Florence , Italy .

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3109/14756366.2015.1114930DOI Listing
December 2016

Discovering novel carbonic anhydrase type IX (CA IX) inhibitors from seven million compounds using virtual screening and in vitro analysis.

J Enzyme Inhib Med Chem 2016 7;31(3):425-33. Epub 2015 May 7.

c Department of Biophysics , School of Medicine, Bahçeşehir University , Istanbul , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3109/14756366.2015.1036049DOI Listing
November 2016

Mutated form (G52E) of inactive diphtheria toxin CRM197: molecular simulations clearly display effect of the mutation to NAD binding.

J Biomol Struct Dyn 2016 Nov 2;34(11):2462-8. Epub 2016 Feb 2.

b Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/07391102.2015.1119060DOI Listing
November 2016

Kinetic and in silico studies of hydroxy-based inhibitors of carbonic anhydrase isoforms I and II.

J Enzyme Inhib Med Chem 2016 13;31(1):31-7. Epub 2015 Feb 13.

e School of Health, Gumushane University , Gumushane , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3109/14756366.2014.1003216DOI Listing
October 2016

In silico investigation of PARP-1 catalytic domains in holo and apo states for the design of high-affinity PARP-1 inhibitors.

J Enzyme Inhib Med Chem 2016 17;31(1):112-20. Epub 2015 Jun 17.

d Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3109/14756366.2015.1005011DOI Listing
October 2016

Role of the pH in state-dependent blockade of hERG currents.

Sci Rep 2016 10 12;6:32536. Epub 2016 Oct 12.

Centre for Molecular Simulation, Department of Biological Sciences, Faculty of Science, University of Calgary, 2500 University Drive, Calgary T2N 1N4, Alberta, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep32536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5059635PMC
October 2016

Virtual screening of eighteen million compounds against dengue virus: Combined molecular docking and molecular dynamics simulations study.

J Mol Graph Model 2016 05 25;66:99-107. Epub 2016 Mar 25.

Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmgm.2016.03.008DOI Listing
May 2016

Acetylcholinesterase and carbonic anhydrase inhibitory properties of novel urea and sulfamide derivatives incorporating dopaminergic 2-aminotetralin scaffolds.

Bioorg Med Chem 2016 05 2;24(10):2318-29. Epub 2016 Apr 2.

Dipartimento di Chimica Ugo Schiff, Universita degli Studi di Firenze, Sesto Fiorentino (Firenze), Italy; Neurofarba Department, Section of Pharmaceutical and Nutraceutical Sciences, Universita degli Studi di Firenze, Sesto Fiorentino (Florence), Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmc.2016.04.002DOI Listing
May 2016

Binding Interactions of Dopamine and Apomorphine in D2High and D2Low States of Human Dopamine D2 Receptor Using Computational and Experimental Techniques.

ACS Chem Neurosci 2016 Feb 22;7(2):185-95. Epub 2015 Dec 22.

Departments of Pharmacology and Psychiatry, University of Toronto , 260 Heath Street West, Unit 605, M5P 3L6, Toronto, Ontario Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acschemneuro.5b00271DOI Listing
February 2016

Recent developments of carbonic anhydrase inhibitors as potential drugs.

Biomed Res Int 2015 2;2015:174178. Epub 2015 Mar 2.

Institute of Biostructure and Bioimaging (IBB), The Italian National Research Council, Via Mezzocannone 16, 80134 Naples, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1155/2015/174178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4363540PMC
December 2015

Interaction of carbonic anhydrase isozymes I, II, and IX with some pyridine and phenol hydrazinecarbothioamide derivatives.

Bioorg Med Chem Lett 2015 Dec 13;25(23):5636-41. Epub 2015 Oct 13.

University of Florence, Neurofarba Department, Via Ugo Schiff 6, Polo Scientifico, 50019 Sesto Fiorentino, Firenze, Italy. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmcl.2015.10.021DOI Listing
December 2015

Carbonic anhydrase inhibitors: Design, synthesis, kinetic, docking and molecular dynamics analysis of novel glycine and phenylalanine sulfonamide derivatives.

Bioorg Med Chem 2015 Dec 23;23(23):7353-8. Epub 2015 Oct 23.

University of Florence, Neurofarba Department, Via Ugo Schiff 6, Polo Scientifico, 50019 Sesto Fiorentino (Firenze), Italy. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmc.2015.10.009DOI Listing
December 2015

Fullerene-based inhibitors of HIV-1 protease.

J Pept Sci 2015 Dec;21(12):862-70

Department of Chemistry, Rice University, Houston, TX, 77005, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/psc.2828DOI Listing
December 2015

Molecular Simulations of Solved Co-crystallized X-Ray Structures Identify Action Mechanisms of PDEδ Inhibitors.

Biophys J 2015 Sep 1;109(6):1163-8. Epub 2015 Sep 1.

Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bpj.2015.08.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576317PMC
September 2015

Investigation of Inhibition Mechanism of Chemokine Receptor CCR5 by Micro-second Molecular Dynamics Simulations.

Sci Rep 2015 Aug 24;5:13180. Epub 2015 Aug 24.

Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep13180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547396PMC
August 2015

Discovery of potent carbonic anhydrase and acetylcholine esterase inhibitors: novel sulfamoylcarbamates and sulfamides derived from acetophenones.

Bioorg Med Chem 2015 Jul 14;23(13):3592-602. Epub 2015 Apr 14.

Atatürk University, Faculty of Science, Department of Chemistry, Erzurum, Turkey. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmc.2015.04.019DOI Listing
July 2015

Structural modeling of the N-terminal signal-receiving domain of IκBα.

Front Mol Biosci 2015 23;2:32. Epub 2015 Jun 23.

Molecular Simulations and Design Group, Max Planck Institute for Dynamics and Complex Technical Systems Magdeburg, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmolb.2015.00032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477481PMC
July 2015

Modeling and protein engineering studies of active and inactive states of human dopamine D2 receptor (D2R) and investigation of drug/receptor interactions.

Mol Divers 2015 May 5;19(2):321-32. Epub 2015 Feb 5.

Department of Chemistry, Istanbul Technical University, Istanbul, Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11030-015-9569-3DOI Listing
May 2015

Inhibition of mammalian carbonic anhydrases I-XIV with grayanotoxin III: solution and in silico studies.

J Enzyme Inhib Med Chem 2014 Aug 5;29(4):469-75. Epub 2013 Aug 5.

University of Calgary, Institute for Biocomplexity and Informatics , Calgary, AB , Canada .

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3109/14756366.2013.804072DOI Listing
August 2014

Elucidation of conformational states, dynamics, and mechanism of binding in human κ-opioid receptor complexes.

J Chem Inf Model 2014 Aug 25;54(8):2294-308. Epub 2014 Jul 25.

Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Avenue, Athens, Attiki 11635, Greece.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci5002873DOI Listing
August 2014

Designing of multi-targeted molecules using combination of molecular screening and in silico drug cardiotoxicity prediction approaches.

J Mol Graph Model 2014 May 6;50:16-34. Epub 2014 Mar 6.

Computational Biology and Bioinformatics, Graduate School of Science and Engineering, Kadir Has University, Istanbul, Turkey; Department of Bioinformatics and Genetics, Kadir Has University, Istanbul, Turkey. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmgm.2014.02.007DOI Listing
May 2014

Insights into the molecular basis of action of the AT1 antagonist losartan using a combined NMR spectroscopy and computational approach.

Biochim Biophys Acta 2014 Mar 27;1838(3):1031-46. Epub 2013 Dec 27.

National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry & Biotechnology, Vas. Constantinou 48, 11635 Athens, Greece; Chemistry Department of National Capodistrian University, Zographou, Athens 15784, Greece.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbamem.2013.12.012DOI Listing
March 2014

Rehabilitating drug-induced long-QT promoters: in-silico design of hERG-neutral cisapride analogues with retained pharmacological activity.

BMC Pharmacol Toxicol 2014 Mar 8;15:14. Epub 2014 Mar 8.

Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/2050-6511-15-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016140PMC
March 2014

AT1 antagonists: a patent review (2008 - 2012).

Expert Opin Ther Pat 2013 Nov 23;23(11):1483-94. Epub 2013 Aug 23.

University of Athens, Department of Chemistry , Panepistimiopolis Zografou 15771, Athens , Greece

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1517/13543776.2013.830104DOI Listing
November 2013

Identification of novel cholesterol-binding regions in Kir2 channels.

J Biol Chem 2013 Oct 9;288(43):31154-64. Epub 2013 Sep 9.

From the Department of Medicine, Pulmonary Section, University of Illinois, Chicago, Illinois 60612.

View Article

Download full-text PDF

Source
http://www.jbc.org/content/288/43/31154.full.pdf
Web Search
http://www.jbc.org/cgi/doi/10.1074/jbc.M113.496117
Publisher Site
http://dx.doi.org/10.1074/jbc.M113.496117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3829427PMC
October 2013

Kinetic and in silico analysis of thiazolidin-based inhibitors of α-carbonic anhydrase isoenzymes.

J Enzyme Inhib Med Chem 2013 Apr 23;28(2):370-4. Epub 2012 Nov 23.

Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3109/14756366.2012.732071DOI Listing
April 2013

Synthesis of 1,4-bis(indolin-1-ylmethyl)benzene derivatives and their structure-activity relationships for the interaction of human carbonic anhydrase isoforms I and II.

Bioorg Med Chem 2013 Mar 10;21(6):1477-82. Epub 2012 Oct 10.

Karamanoğlu Mehmetbey University, Kamil Özdağ Science Faculty, Chemistry Department, 70100 Karaman, Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmc.2012.09.027DOI Listing
March 2013

Modeling of open, closed, and open-inactivated states of the hERG1 channel: structural mechanisms of the state-dependent drug binding.

J Chem Inf Model 2012 Oct 2;52(10):2760-74. Epub 2012 Oct 2.

Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, Alberta, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci300353uDOI Listing
October 2012

Structure-guided topographic mapping and mutagenesis to elucidate binding sites for the human ether-a-go-go-related gene 1 potassium channel (KCNH2) activator NS1643.

J Pharmacol Exp Ther 2012 Aug 9;342(2):441-52. Epub 2012 May 9.

Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, Calgary, Canada.

View Article

Download full-text PDF

Source
http://jpet.aspetjournals.org/content/342/2/441.full.pdf
Web Search
http://jpet.aspetjournals.org/cgi/doi/10.1124/jpet.111.18915
Publisher Site
http://dx.doi.org/10.1124/jpet.111.189159DOI Listing
August 2012

Protein-protein interactions: inhibition of mammalian carbonic anhydrases I-XV by the murine inhibitor of carbonic anhydrase and other members of the transferrin family.

J Med Chem 2012 Jun 18;55(11):5529-35. Epub 2012 May 18.

Department of Biological Sciences, Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive, T2N 1N4, Calgary, Alberta, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jm3004587DOI Listing
June 2012

Structure-activity relationships for the interaction of 5,10-dihydroindeno[1,2-b]indole derivatives with human and bovine carbonic anhydrase isoforms I, II, III, IV and VI.

Eur J Med Chem 2012 Mar 20;49:68-73. Epub 2011 Dec 20.

Ondokuz Mayıs University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ejmech.2011.12.022DOI Listing
March 2012

An effort to discover the preferred conformation of the potent AMG3 cannabinoid analog when reaching the active sites of the cannabinoid receptors.

Eur J Med Chem 2012 Jan 15;47(1):44-51. Epub 2011 Oct 15.

Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ejmech.2011.10.015DOI Listing
January 2012

Mechanism of K+/Na+ selectivity in potassium channels from the perspective of the non-selective bacterial channel NaK.

Channels (Austin) 2011 May-Jun;5(3):198-200. Epub 2011 May 1.

Department of Biological Sciences, University of Calgary, Institute for Biocomplexity and Informatics, Calgary, AB, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/chan.5.3.15873DOI Listing
October 2011

Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations.

J Comput Aided Mol Des 2011 Oct 4;25(10):959-76. Epub 2011 Oct 4.

Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Ave, 11635 Athens, Greece.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10822-011-9475-4DOI Listing
October 2011

Design, synthesis and biological evaluation of novel nitroaromatic compounds as potent glutathione reductase inhibitors.

Bioorg Med Chem Lett 2011 Sep 13;21(18):5398-402. Epub 2011 Jul 13.

Batman University, Science and Art Faculty, Chemistry Department, Batman, Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmcl.2011.07.002DOI Listing
September 2011

Combined receptor and ligand-based approach to the universal pharmacophore model development for studies of drug blockade to the hERG1 pore domain.

J Chem Inf Model 2011 Feb 11;51(2):463-74. Epub 2011 Jan 11.

Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci100409yDOI Listing
February 2011

Kinetic and docking studies of phenol-based inhibitors of carbonic anhydrase isoforms I, II, IX and XII evidence a new binding mode within the enzyme active site.

Bioorg Med Chem 2011 Feb 14;19(4):1381-9. Epub 2011 Jan 14.

Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmc.2011.01.016DOI Listing
February 2011

Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations.

Proteins 2010 Nov;78(14):2922-34

Department of Biological Sciences, Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.22815DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939218PMC
November 2010

Development of accurate binding affinity predictions of novel renin inhibitors through molecular docking studies.

J Mol Graph Model 2010 Nov 27;29(3):425-35. Epub 2010 Aug 27.

University of Athens, Department of Chemistry, Zographou 15771, Athens, Greece.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmgm.2010.08.003DOI Listing
November 2010

Nanoscale enzyme inhibitors: fullerenes inhibit carbonic anhydrase by occluding the active site entrance.

Bioorg Med Chem 2010 Apr 15;18(8):2822-8. Epub 2010 Mar 15.

Università degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, I-50019 Sesto Fiorentino (Firenze), Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmc.2010.03.026DOI Listing
April 2010

Application of 3D QSAR CoMFA/CoMSIA and in silico docking studies on novel renin inhibitors against cardiovascular diseases.

Eur J Med Chem 2009 Sep 8;44(9):3703-11. Epub 2009 Apr 8.

Capodistrian Athens University, Department of Chemistry, Zographou, 15771 Athens, Greece.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ejmech.2009.03.040DOI Listing
September 2009

3D QSAR CoMFA/CoMSIA, molecular docking and molecular dynamics studies of fullerene-based HIV-1 PR inhibitors.

Bioorg Med Chem Lett 2008 Dec 8;18(23):6283-9. Epub 2008 Oct 8.

Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635 Athens, Greece.

View Article

Download full-text PDF

Source
http://linkinghub.elsevier.com/retrieve/pii/S0960894X0801106
Publisher Site
http://dx.doi.org/10.1016/j.bmcl.2008.09.107DOI Listing
December 2008

Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations.

Bioorg Med Chem 2008 Dec 22;16(23):9957-74. Epub 2008 Oct 22.

Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmc.2008.10.039DOI Listing
December 2008

3D QSAR/CoMFA and CoMSIA studies on antileukemic steroidal esters coupled with conformationally flexible nitrogen mustards.

J Chem Inf Model 2008 Nov;48(11):2254-64

Department of Pharmacy, University of Patras, 26500 Rio, Patras, Greece.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci800240mDOI Listing
November 2008

Comparative molecular dynamics simulations of the potent synthetic classical cannabinoid ligand AMG3 in solution and at binding site of the CB1 and CB2 receptors.

Bioorg Med Chem 2008 Aug 14;16(15):7377-87. Epub 2008 Jun 14.

Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmc.2008.06.019DOI Listing
August 2008

Combined 3D QSAR and molecular docking studies to reveal novel cannabinoid ligands with optimum binding activity.

Bioorg Med Chem Lett 2007 Dec 17;17(24):6754-63. Epub 2007 Oct 17.

Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmcl.2007.10.044DOI Listing
December 2007