Serdar Durdagi - Publications

Affiliations: 
Bahcesehir University, School of Medicine, Department of Biophysics 
Area:
computer-aided drug design, virtual screening, molecular docking, MD simulations, protein engineering, computational modeling, protein-protein and protein-ligand interactions

58 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 DurdaĞi S. Virtual drug repurposing study against SARS-CoV-2 TMPRSS2 target. Turkish Journal of Biology = Turk Biyoloji Dergisi. 44: 185-191. PMID 32595355 DOI: 10.3906/biy-2005-112  0.338
2020 Turan RD, Albayrak E, Uslu M, Siyah P, Alyazici LY, Kalkan BM, Aslan GS, Yucel D, Aksoz M, Tuysuz EC, Meric N, Durdagi S, Gulbas Z, Kocabas F. Development of Small Molecule MEIS Inhibitors that modulate HSC activity. Scientific Reports. 10: 7994. PMID 32409701 DOI: 10.1038/S41598-020-64888-3  0.328
2020 Sahin K, Durdagi S. Identifying new piperazine-based PARP1 inhibitors using text mining and integrated molecular modeling approaches. Journal of Biomolecular Structure & Dynamics. 1-10. PMID 32048546 DOI: 10.1080/07391102.2020.1715262  0.303
2019 Gunay BC, Yurtsever M, Durdagi S. Elucidation of interaction mechanism of hERG1 potassium channel with scorpion toxins BeKm-1 and BmTx3b. Journal of Molecular Graphics & Modelling. 96: 107504. PMID 31901677 DOI: 10.1016/j.jmgm.2019.107504  0.314
2019 Ikram S, Ahmad J, Durdagi S. Screening of FDA approved drugs for finding potential inhibitors against Granzyme B as a potent drug-repurposing target. Journal of Molecular Graphics & Modelling. 107462. PMID 31786094 DOI: 10.1016/j.jmgm.2019.107462  0.317
2019 Sahin K, Zengin Kurt B, Sonmez F, Durdagi S. Novel AChE and BChE Inhibitors Using Combined Virtual Screening, Text mining and In Vitro Binding Assays. Journal of Biomolecular Structure & Dynamics. 1-24. PMID 31462153 DOI: 10.1080/07391102.2019.1660218  0.304
2018 Erol I, Aksoydan B, Kantarcioglu I, Durdagi S. Application of Multiscale Simulation Tools on GPCRs. An Example with Angiotensin II Type 1 Receptor. Methods in Molecular Biology (Clifton, N.J.). 1824: 431-448. PMID 30039423 DOI: 10.1007/978-1-4939-8630-9_26  0.317
2018 Aksoydan B, Kantarcioglu I, Erol I, Salmas RE, Durdagi S. Structure-based design of hERG-neutral antihypertensive oxazalone and imidazolone derivatives. Journal of Molecular Graphics & Modelling. 79: 103-117. PMID 29156380 DOI: 10.1016/j.jmgm.2017.10.011  0.349
2017 Kayık G, Tüzün NŞ, Durdagi S. Structural investigation of vesnarinone at the pore domains of open and open-inactivated states of hERG1 Kchannel. Journal of Molecular Graphics & Modelling. 77: 399-412. PMID 28963955 DOI: 10.1016/j.jmgm.2017.08.017  0.44
2017 Aksoydan B, Kantarcioglu I, Erol I, Salmas RE, Durdagi S. Structure-based design of hERG-neutral antihypertensive oxazalone and imidazolone derivatives. Journal of Molecular Graphics & Modelling. 77: 240-249. PMID 28957753 DOI: 10.1016/j.jmgm.2017.08.004  0.349
2017 Akıncıoğlu A, Kocaman E, Akıncıoğlu H, Salmas RE, Durdagi S, Gülçin İ, Supuran CT, Göksu S. The synthesis of novel sulfamides derived from β-benzylphenethylamines as acetylcholinesterase, butyrylcholinesterase and carbonic anhydrase enzymes inhibitors. Bioorganic Chemistry. 74: 238-250. PMID 28866249 DOI: 10.1016/J.Bioorg.2017.08.012  0.313
2017 Durdagi S, Erol I, Salmas RE, Patterson M, Noskov SY. First universal pharmacophore model for hERG1 K(+) channel activators: acthER. Journal of Molecular Graphics & Modelling. 74: 153-170. PMID 28499268 DOI: 10.1016/J.Jmgm.2017.03.020  0.666
2017 Salmas RE, Seeman P, Aksoydan B, Erol I, Kantarcioglu I, Stein M, Yurtsever M, Durdagi S. Analysis of the Glutamate Agonist LY404,039 Binding to Non-Static Dopamine Receptor D2 Dimer Structures and Consensus Docking. Acs Chemical Neuroscience. PMID 28272861 DOI: 10.1021/Acschemneuro.7B00070  0.316
2017 Bukiya AN, Durdagi S, Noskov S, Rosenhouse-Dantsker A. Cholesterol up-regulates neuronal G protein-gated inwardly rectifying potassium (GIRK) channel activity in the hippocampus. The Journal of Biological Chemistry. 292: 6135-6147. PMID 28213520 DOI: 10.1074/Jbc.M116.753350  0.587
2017 Kayık G, Tüzün NŞ, Durdagi S. Investigation of PDE5/PDE6 and PDE5/PDE11 selective potent tadalafil-like PDE5 inhibitors using combination of molecular modeling approaches, molecular fingerprint-based virtual screening protocols and structure-based pharmacophore development. Journal of Enzyme Inhibition and Medicinal Chemistry. 32: 311-330. PMID 28150511 DOI: 10.1080/14756366.2016.1250756  0.302
2017 Kayık G, Tüzün NŞ, Durdagi S. In silico design of novel hERG-neutral sildenafil-like PDE5 inhibitors. Journal of Biomolecular Structure & Dynamics. 35: 2830-2852. PMID 27581752 DOI: 10.1080/07391102.2016.1231634  0.436
2017 Ekhteiari Salmas R, Unlu A, Bektaş M, Yurtsever M, Mestanoglu M, Durdagi S. Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: combination of in silico and in vitro studies. Journal of Biomolecular Structure & Dynamics. 35: 1899-1915. PMID 27315035 DOI: 10.1080/07391102.2016.1199328  0.302
2016 Wang Y, Guo J, Perissinotti LL, Lees-Miller J, Teng G, Durdagi S, Duff HJ, Noskov SY. Role of the pH in state-dependent blockade of hERG currents. Scientific Reports. 6: 32536. PMID 27731415 DOI: 10.1038/Srep32536  0.685
2016 Özgeriş B, Göksu S, Polat Köse L, Gülçin İ, Salmas RE, Durdagi S, Tümer F, Supuran CT. Acetylcholinesterase and carbonic anhydrase inhibitory properties of novel urea and sulfamide derivatives incorporating dopaminergic 2-aminotetralin scaffolds. Bioorganic & Medicinal Chemistry. 24: 2318-29. PMID 27068142 DOI: 10.1016/J.Bmc.2016.04.002  0.337
2015 Strom TA, Durdagi S, Ersoz SS, Salmas RE, Supuran CT, Barron AR. Fullerene-based inhibitors of HIV-1 protease. Journal of Peptide Science : An Official Publication of the European Peptide Society. 21: 862-70. PMID 26767741 DOI: 10.1002/Psc.2828  0.434
2015 Salmas RE, Mestanoglu M, Yurtsever M, Noskov SY, Durdagi S. Molecular Simulations of Solved Co-crystallized X-Ray Structures Identify Action Mechanisms of PDEδ Inhibitors. Biophysical Journal. 109: 1163-8. PMID 26340817 DOI: 10.1016/J.Bpj.2015.08.001  0.58
2015 Salmas RE, Unlu A, Yurtsever M, Noskov SY, Durdagi S. In silico investigation of PARP-1 catalytic domains in holo and apo states for the design of high-affinity PARP-1 inhibitors. Journal of Enzyme Inhibition and Medicinal Chemistry. 1-9. PMID 26083304 DOI: 10.3109/14756366.2015.1005011  0.618
2015 Akıncıoğlu A, Akıncıoğlu H, Gülçin İ, Durdagi S, Supuran CT, Göksu S. Discovery of potent carbonic anhydrase and acetylcholine esterase inhibitors: novel sulfamoylcarbamates and sulfamides derived from acetophenones. Bioorganic & Medicinal Chemistry. 23: 3592-602. PMID 25921269 DOI: 10.1016/J.Bmc.2015.04.019  0.303
2015 Guo J, Cheng YM, Lees-Miller JP, Perissinotti LL, Claydon TW, Hull CM, Thouta S, Roach DE, Durdagi S, Noskov SY, Duff HJ. NS1643 interacts around L529 of hERG to alter voltage sensor movement on the path to activation. Biophysical Journal. 108: 1400-13. PMID 25809253 DOI: 10.1016/J.Bpj.2014.12.055  0.512
2015 Salmas RE, Yurtsever M, Stein M, Durdagi S. Modeling and protein engineering studies of active and inactive states of human dopamine D2 receptor (D2R) and investigation of drug/receptor interactions. Molecular Diversity. 19: 321-32. PMID 25652238 DOI: 10.1007/S11030-015-9569-3  0.331
2014 Guo J, Durdagi S, Changalov M, Perissinotti LL, Hargreaves JM, Back TG, Noskov SY, Duff HJ. Structure driven design of novel human ether-a-go-go-related-gene channel (hERG1) activators. Plos One. 9: e105553. PMID 25191697 DOI: 10.1371/Journal.Pone.0105553  0.679
2014 Göksu S, Naderi A, Akbaba Y, Kalın P, Akıncıoğlu A, Gülçin İ, Durdagi S, Salmas RE. Carbonic anhydrase inhibitory properties of novel benzylsulfamides using molecular modeling and experimental studies. Bioorganic Chemistry. 56: 75-82. PMID 25159522 DOI: 10.1016/J.Bioorg.2014.07.009  0.323
2014 Buturak B, Durdagi S, Noskov SY, Ildeniz AT. Designing of multi-targeted molecules using combination of molecular screening and in silico drug cardiotoxicity prediction approaches. Journal of Molecular Graphics & Modelling. 50: 16-34. PMID 24699019 DOI: 10.1016/J.Jmgm.2014.02.007  0.565
2014 Durdagi S, Randall T, Duff HJ, Chamberlin A, Noskov SY. Rehabilitating drug-induced long-QT promoters: in-silico design of hERG-neutral cisapride analogues with retained pharmacological activity. Bmc Pharmacology & Toxicology. 15: 14. PMID 24606761 DOI: 10.1186/2050-6511-15-14  0.627
2014 Rosenhouse-Dantsker A, Noskov S, Durdagi S, Logothetis DE, Levitan I. Identification of Novel Cholesterol Binding Regions in the Transmembrane Domain of Kir2.1 Biophysical Journal. 106: 747a. DOI: 10.1016/J.Bpj.2013.11.4117  0.621
2014 Durdagi S, Patterson M, Noskov SY. Development and Validation Studies of Universal Pharmacophore Models for hERG Channel Openers Biophysical Journal. 106: 15a. DOI: 10.1016/J.Bpj.2013.11.137  0.681
2013 Rosenhouse-Dantsker A, Noskov S, Durdagi S, Logothetis DE, Levitan I. Identification of novel cholesterol-binding regions in Kir2 channels. The Journal of Biological Chemistry. 288: 31154-64. PMID 24019518 DOI: 10.1074/Jbc.M113.496117  0.635
2013 Talaz O, Cavdar H, Durdagi S, Azak H, Ekinci D. 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. Bioorganic & Medicinal Chemistry. 21: 1477-82. PMID 23121721 DOI: 10.1016/J.Bmc.2012.09.027  0.322
2013 Durdagi S, Randal T, Duff HJ, Noskov SY. Rehabilitation Studies for withdrawn Drugs from the Market: Derivation of Non-hERG1 Channel Blocker Cisapride Analogues using Multi-Faceted Approaches Biophysical Journal. 104: 266a. DOI: 10.1016/J.Bpj.2012.11.1495  0.62
2012 Durdagi S, Deshpande S, Duff HJ, Noskov SY. Modeling of open, closed, and open-inactivated states of the hERG1 channel: structural mechanisms of the state-dependent drug binding. Journal of Chemical Information and Modeling. 52: 2760-74. PMID 22989185 DOI: 10.1021/Ci300353U  0.657
2012 Durdagi S, Vullo D, Pan P, Kähkönen N, Määttä JA, Hytönen VP, Scozzafava A, Parkkila S, Supuran CT. Protein-protein interactions: inhibition of mammalian carbonic anhydrases I-XV by the murine inhibitor of carbonic anhydrase and other members of the transferrin family. Journal of Medicinal Chemistry. 55: 5529-35. PMID 22578027 DOI: 10.1021/Jm3004587  0.322
2012 Durdagi S, Guo J, Lees-Miller JP, Noskov SY, Duff HJ. 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. The Journal of Pharmacology and Experimental Therapeutics. 342: 441-52. PMID 22573844 DOI: 10.1124/Jpet.111.189159  0.627
2012 Ekinci D, Cavdar H, Durdagi S, Talaz O, Sentürk M, Supuran CT. 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. European Journal of Medicinal Chemistry. 49: 68-73. PMID 22245047 DOI: 10.1016/J.Ejmech.2011.12.022  0.335
2012 Durdagi S, Papadopoulos MG, Mavromoustakos T. An effort to discover the preferred conformation of the potent AMG3 cannabinoid analog when reaching the active sites of the cannabinoid receptors. European Journal of Medicinal Chemistry. 47: 44-51. PMID 22071252 DOI: 10.1016/J.Ejmech.2011.10.015  0.381
2012 Durdagi S, Deshpande S, Duff H, Noskov S. Development of Atomistic Models for Closed, Open and Open-Inactivated States of hERG1 Channel using Rosetta Protein Modeling Suite and Molecular Dynamics Simulations Biophysical Journal. 102: 679a. DOI: 10.1016/J.Bpj.2011.11.3693  0.632
2011 Tzoupis H, Leonis G, Durdagi S, Mouchlis V, Mavromoustakos T, Papadopoulos MG. Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations. Journal of Computer-Aided Molecular Design. 25: 959-76. PMID 21969102 DOI: 10.1007/S10822-011-9475-4  0.384
2011 Çakmak R, Durdagi S, Ekinci D, Sentürk M, Topal G. Design, synthesis and biological evaluation of novel nitroaromatic compounds as potent glutathione reductase inhibitors. Bioorganic & Medicinal Chemistry Letters. 21: 5398-402. PMID 21795044 DOI: 10.1016/J.Bmcl.2011.07.002  0.413
2011 Mavromoustakos T, Durdagi S, Koukoulitsa C, Simcic M, Papadopoulos MG, Hodoscek M, Grdadolnik SG. Strategies in the rational drug design. Current Medicinal Chemistry. 18: 2517-30. PMID 21568895 DOI: 10.2174/092986711795933731  0.392
2011 Durdagi S, Zhao C, Cuervo JE, Noskov SY. Atomistic models for free energy evaluation of drug binding to membrane proteins. Current Medicinal Chemistry. 18: 2601-11. PMID 21568889 DOI: 10.2174/092986711795933641  0.611
2011 Durdagi S, Noskov SY. Mechanism of K+/Na+ selectivity in potassium channels from the perspective of the non-selective bacterial channel NaK. Channels (Austin, Tex.). 5: 198-200. PMID 21540644 DOI: 10.4161/Chan.5.3.15873  0.625
2011 Durdagi S, Şentürk M, Ekinci D, Balaydın HT, Göksu S, Küfrevioğlu Öİ, Innocenti A, Scozzafava A, Supuran CT. 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. Bioorganic & Medicinal Chemistry. 19: 1381-9. PMID 21282059 DOI: 10.1016/J.Bmc.2011.01.016  0.367
2011 Durdagi S, Duff HJ, Noskov SY. Combined receptor and ligand-based approach to the universal pharmacophore model development for studies of drug blockade to the hERG1 pore domain. Journal of Chemical Information and Modeling. 51: 463-74. PMID 21241063 DOI: 10.1021/Ci100409Y  0.657
2010 Politi A, Durdagi S, Moutevelis-Minakakis P, Kokotos G, Mavromoustakos T. Development of accurate binding affinity predictions of novel renin inhibitors through molecular docking studies. Journal of Molecular Graphics & Modelling. 29: 425-35. PMID 20855222 DOI: 10.1016/J.Jmgm.2010.08.003  0.395
2010 Subbotina J, Yarov-Yarovoy V, Lees-Miller J, Durdagi S, Guo J, Duff HJ, Noskov SY. Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations. Proteins. 78: 2922-34. PMID 20740484 DOI: 10.1002/Prot.22815  0.651
2010 Durdagi S, Subbotina J, Lees-Miller J, Guo J, Duff HJ, Noskov SY. Insights into the molecular mechanism of hERG1 channel activation and blockade by drugs. Current Medicinal Chemistry. 17: 3514-32. PMID 20738248 DOI: 10.2174/092986710792927886  0.668
2010 Innocenti A, Durdagi S, Doostdar N, Strom TA, Barron AR, Supuran CT. Nanoscale enzyme inhibitors: fullerenes inhibit carbonic anhydrase by occluding the active site entrance. Bioorganic & Medicinal Chemistry. 18: 2822-8. PMID 20363143 DOI: 10.1016/J.Bmc.2010.03.026  0.489
2010 Durdagi S, Papadopoulos MG, Zoumpoulakis PG, Koukoulitsa C, Mavromoustakos T. A computational study on cannabinoid receptors and potent bioactive cannabinoid ligands: homology modeling, docking, de novo drug design and molecular dynamics analysis. Molecular Diversity. 14: 257-76. PMID 19536636 DOI: 10.1007/S11030-009-9166-4  0.361
2010 Mavromoustakos T, Chatzigeorgiou P, Koukoulitsa C, Durdagi S. Partial interdigitation of lipid bilayers International Journal of Quantum Chemistry. 111: 1172-1183. DOI: 10.1002/Qua.22610  0.302
2009 Fotakis C, Gega S, Siapi E, Potamitis C, Viras K, Moutevelis-Minakakis P, Kokotos CG, Durdagi S, Grdadolnik SG, Sartori B, Rappolt M, Mavromoustakos T. Interactions at the bilayer interface and receptor site induced by the novel synthetic pyrrolidinone analog MMK3. Biochimica Et Biophysica Acta. 1798: 422-32. PMID 19925777 DOI: 10.1016/J.Bbamem.2009.11.009  0.35
2009 Politi A, Durdagi S, Moutevelis-Minakakis P, Kokotos G, Papadopoulos MG, Mavromoustakos T. Application of 3D QSAR CoMFA/CoMSIA and in silico docking studies on novel renin inhibitors against cardiovascular diseases. European Journal of Medicinal Chemistry. 44: 3703-11. PMID 19410337 DOI: 10.1016/J.Ejmech.2009.03.040  0.335
2009 Durdagi S, Supuran CT, Strom TA, Doostdar N, Kumar MK, Barron AR, Mavromoustakos T, Papadopoulos MG. In silico drug screening approach for the design of magic bullets: a successful example with anti-HIV fullerene derivatized amino acids. Journal of Chemical Information and Modeling. 49: 1139-43. PMID 19371030 DOI: 10.1021/Ci900047S  0.539
2008 Kapou A, Benetis NP, Durdagi S, Nikolaropoulos S, Mavromoustakos T. 3D QSAR/CoMFA and CoMSIA studies on antileukemic steroidal esters coupled with conformationally flexible nitrogen mustards. Journal of Chemical Information and Modeling. 48: 2254-64. PMID 18954137 DOI: 10.1021/Ci800240M  0.348
2008 Durdagi S, Mavromoustakos T, Papadopoulos MG. 3D QSAR CoMFA/CoMSIA, molecular docking and molecular dynamics studies of fullerene-based HIV-1 PR inhibitors. Bioorganic & Medicinal Chemistry Letters. 18: 6283-9. PMID 18951793 DOI: 10.1016/J.Bmcl.2008.09.107  0.363
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