Published Papers

2017

106. Gulru Kayik, Nurcan Senyurt Tuzun, Serdar Durdagi*: Structural Investigation of Vesnarinone at the Pore Domains of Open and Open-Inactivated States of hERG1 K+ Channel. Journal of Molecular Graphics and Modelling. 2017

105. Busecan Aksoydan, Isik Kantarcioglu, Ismail Erol, Ramin Ekhteiari Salmas, Serdar Durdagi*: Structure-based Design of hERG-Neutral Antihypertensive Oxazolone and Imidazolone Derivatives. Journal of Molecular Graphics and Modelling. 2017

104.  Akın Akıncıoğlu, Ebutalib Kocaman, Hülya Akıncıoğlu, Ramin Ekhteiari Salmas, Serdar Durdagi, İlhami Gülçin, Claudiu T. Supuran, Süleyman Göksu. The Synthesis of Novel Sulfamides Derived from beta-Benzylphenethylamines as Acetylcholinesterase, Butyrylcholinesterase and Carbonic Anhydrase Enzymes Inhibitors. Bioorganic Chemistry 2017

103. Shaher Bano Mirza, Regina Ching Hua Leed, Justin Jang Hann Chud, Ramin Ekhteiari Salmas, Thomas Mavromoustakos, Serdar Durdagi*: 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. Journal of Molecular Graphics and Modelling. 2017

102. Ramin Ekhteiari Salmas, Yusuf Serhat Is, Serdar Durdagi, Matthias Stein, Mine Yurtsever: A QM Protein-Ligand Investigation of Anti-psychotic Drugs with the Dopamine D2 Receptor (D2R)  Journal of Biomolecular Structure & Dynamics 2017

101. Belma Zengin Kurt, Fatih Sonmez, Serdar Durdagi*, Busecan Aksoydan, Ramin E. Salmas, Andrea Angeli, Mustafa Kucukislamoglu, Claudiu T. Supuran: Synthesis, Biological Activity and Multiscale Molecular Modeling Studies for Coumaryl-carboxamide Derivatives as Selective Carbonic Anhydrase IX Inhibitors. Journal of Enzyme Inhibition and Medicinal Chemistry 2017

100. Ramin Ekhteiari Salmas, Mehmet Fuat Gulhan, Serdar Durdagi, Engin Sahna, Huda I. Abdullah, Zeliha Selamoglu: Effects of Propolis, Caffeic Acid Phenethyl Ester and Pollen on Renal Injury in Hypertensive Rat: An Experimental and Theoretical Approach. Cell Biochemistry & Function 2017

99. Reyhan Aslancan, Busecan Aksoydan, Isik Kantarcioglu, Ismail Erol, Ramin E Salmas, Serdar Durdagi*: Investigation of Chemical Interactions of Small Peptides and Vitamin Substances at the Developed Dopamine D2 Receptor Models. European Psychiatry 2017

98.  Serdar Durdagi*, Ismail Erol, Ramin Ekhteiari Salmas, Matthew Patterson, Sergei Y. Noskov:  First Universal Pharmacophore Model for hERG1 K+ Channel Activators. Journal of Molecular Graphics and Modelling. 2017

97. Ramin E. Salmas, Philip Seeman, Busecan Aksodan, Ismail Erol, Isik Kantarcioglu, Matthias Stein, Mine Yurtsever, Serdar Durdagi*: Analysis of the Glutamate Agonist LY404,039 Binding to Non-Static Dopamine Receptor D2 Dimer Structures and Consensus Docking. ACS Chemical Neuroscience 2017

96. Anna N. Bukiya, Serdar Durdagi, Sergei Noskov, Avia Rosenhouse-Dantsker: Cholesterol Up-regulates Neuronal G Protein-Gated Inwardly Rectifying Potassium (GIRK) Channel Activity in the Hippocampus. Journal of Biological Chemistry 2017

95. Ismail Erol, Busecan Aksoydan, Isik Kantarcioglu, Ramin E. Salmas, Serdar Durdagi*: Identification of Novel Serotonin Reuptake Inhibitors Targeting Central and Allosteric Binding Sites: A Virtual Screening and Molecular Dynamics Simulations Study. Journal of Molecular Graphics and Modelling 2017

94. Mehmet Erman Erdemli, Ramin Ekhteiari Salmas, Serdar Durdagi, Hasan Akgul, Mehmet Demirkol, Zeynep Aksungur, and Zeliha Selamoglu: Biochemical Changes Induced by Grapeseed Extract and Low Level Laser Therapy Administration During Intraoral Wound Healing in Rat Liver: An Experimental and in Silico Study. Journal of Biomolecular Structure & Dynamics 2017

93.  Ramin Ekhteiari Salmas, Serdar Durdagi, Mehmet Fuat Gulhan, Merve Duruyurek, Huda Abdullah, Zeliha Selamoglu: The Effects of Pollen, Propolis, and Caffeic Acid Phenethyl Ester on Tyrosine Hydroxylase Activity and Total RNA Levels in Hypertensive Rats Caused by Nitric Oxide Synthase Inhibition: Experimental, Docking and Molecular Dynamic Studies. Journal of Biomolecular Structure & Dynamics 2017

2016

92. Ramin Ekhteiari Salmas, Philip Seeman, Busecan Aksoydan, Matthias Stein, Mine Yurtsever, Serdar Durdagi* : Biological Insights of the Dopaminergic Stabilizer ACR16 at the Binding Pocket of Dopamine D2 Receptor.
ACS Chemical Neuroscience
2016

91. Sergey Shityakov, Ramin Ekhteiari Salmas, Serdar Durdagi, Ellaine Salvador, Katalin Papai, Maria Yanez-Gascon, Horacio Perez-Sanchez, Istvan Puskas, Norbert Roewer, Carola Forster, Jens-Albert Broscheit: Characterization, In Vivo Evaluation and Molecular Modeling of Different Propofol-Cyclodextrin Complexes to Assess Their Drug Delivery Potential at The Blood-Brain Barrier Level. Journal of Chemical Information and Modeling (ACS) 2016 (in press)

90. Yibo Wang, Jiqing Guo, Laura Perissinotti, James Lees-Miller, Guogi Teng, Serdar Durdagi, Henry J Duff, Sergei Noskov: Role of the pH in state-dependent blockade of hERG currents. Scientific Reports (Nature)  2016 (in press).

89. Serdar Durdagi*, Murat Senturk, M Guney, Deniz Ekinci, Busecan Aksoydan, Ismail Erol, Isik Kantarcioglu, Huseyin Cavdar: Design of novel uracil derivatives as inhibitors of carbonic anhydrases I & II, acetylcholinesterase, butyrylcholinesterase, and glutathione reductase using in silico, synthesis and in vitro studies. FEBS Journal 2016, 283, 106.

88. Sergey Shityakov, Ramin Ekhteiari Salmas, Serdar Durdagi, Norbert Roewer, Carola Förster, and Jens Broscheit: Solubility profiles, hydration and desolvation of curcumin complexed with γ-cyclodextrin and hydroxypropyl-γ-cyclodextrin. Journal of Molecular Structures 2016

87. Belma Zengin Kurt, Isil Gazioglu, Aydin Dag, Ramin E. Salmas, Gulru Kayik, Serdar Durdagi*, Fatih Sonmez: Synthesis, Anticholinesterase Activity and Molecular Modeling Study of Novel Carbamate-Substituted Thymol/Carvacrol Derivatives. Bioorganic and Medicinal Chemistry 2016

86. Gulru Kayik, Nurcan Senyurt Tuzun, Serdar Durdagi*: 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 2016

85. Gulru Kayik, Nurcan Senyurt Tuzun, Serdar Durdagi*: In Silico Design of Novel hERG-neutral Sildenafil-like PDE5 Inhibitors. Journal of Biomolecular Structure and Dynamics  2016 (accepted)

84. Shaher Bano Mirza, Ramin Ekhteiari Salmas, M. Qaiser Fatmi, Serdar Durdagi*: Discovery of Klotho Peptide Antagonists Against Wnt3 and  Wnt3a Target Proteins Using Combination of Protein  Engineering, Protein-Protein Docking, Peptide Docking and  Molecular Dynamics Simulations. Journal of Enzyme Inhibition and Medicinal Chemistry 2016 (accepted)

83. Ramin Ekhteiari Salmas, Matthias Stein, Mine Yurtsever, Philip Seeman, Ismail Erol, Mert Mestanoglu, Serdar Durdagi*: The Signaling Pathway of Dopamine D2 Receptor (D2R) Activation Using Normal Mode Analysis (NMA) and the Construction of Universal Pharmacophore Models for D2R Inhibitors. Journal of Biomolecular Structure and Dynamics  2016 (accepted).

82. Ramin Ekhteiari Salmas, Ayhan Unlu, Muhammet Bektaş, Mine Yurtsever, Mert Mestanoglu, Serdar Durdagi*: 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 and Dynamics  2016 (accepted).

81. Bünyamin Özgeriş, Süleyman Göksu, Leyla Polat Köse, İlhami Gülçin, Ramin Ekhteiari Salmas, Serdar Durdagi, Ferhan Tümer, Claudiu T. Supuran: Acetylcholinesterase and Carbonic Anhydrase Inhibitory Properties of Novel Urea and Sulfamide Derivatives Incorporating Dopaminergic 2-Aminotetralin Scaffolds. Bioorganic and Medicinal Chemistry. 2016 (accepted)

80. Shaher Bano Mirza, Ramin Ekhteiari Salmas, M. Qaiser Fatmi, Serdar Durdagi*: Virtual Screening of Eighteen Million Compounds against Dengue Virus: Combined Molecular Docking and Molecular Dynamics Simulations Study. Journal of Molecular Graphics and Modelling 2016 (accepted)

79. Ali Sahin, Murat Senturk, Ramin E. Salmas, Serdar Durdagi, Arif Ayan, Ali Karagolge, Mert Mestanoglu: Investigation of inhibition of human glucose 6-phosphate dehydrogenase by some 99mTc chelators by in silico and in vitro methods. Journal of Enzyme Inhibition and Medicinal Chemistry 2016 (accepted)
 
78. Ramin E. Salmas, Mine Yurtsever, Serdar Durdagi*: Atomistic Molecular Dynamic Simulations of Typical and Atypical Anti-psychotic Drugs at the Dopamine D2 Receptor (D2R) Elucidates Their Inhibition Mechanism. Journal of Biomolecular Structure & Dynamics 2016 (accepted)

77. Serdar Durdagi*, Ramin E. Salmas, Matthias Stein, Mine Yurtsever, Philip Seeman: Binding Interactions of Dopamine and Apomorphine in D2High and D2Low States of human Dopamine D2 Receptor (D2R) using Computational and Experimental Techniques. ACS Chem. Neuroscience 2016 (accepted)

2015

76. Semra Işık, Daniela Vullo, Serdar Durdagi, Deniz Ekinci, Murat Şentürk, Ahmet Cetin, Claudiu T. Supuran: Carbonic anhydrase inhibitory and activatory properties of some pyridine and phenol hydrazinecarbothioamide derivatives. Bioorganic & Medicinal Chemistry Letters 2015 (accepted).

75. Ismail Fidan, Ramin E. Salmas, Murat Senturk, Mehmet Arslan, Serdar Durdagi, Deniz Ekinci, Cosgun, S: Carbonic anhydrase inhibitors: design, synthesis, kinetic, docking and molecular dynamics analysis of novel glycine and phenylalanine sulphonamide derivatives. Bioorganic & Medicinal Chemistry 2015 (accepted).

74. Tahsin F. Kellici, Dimitrios Ntountaniotis, Eftichia Kritsi, Maria Zervou, Panagiotis Zoumpoulakis, Constantinos Potamitis, Serdar Durdagi, Ramin Ekhteiari Salmas, Gizem Ergun, Ebru Gokdemir, Maria Halabalaki, Ioannis P. Gerothanassis, George Liapakis, Andreas Tzakos, Thomas Mavromoustakos. Leveraging NMR and X-ray Data of the Free Ligands to Build Better Drugs Targeting GPCRs: The Case of AT1R. Current Medicinal Chemistry 2015 (accepted).

73. Ramin Ekhteiari Salmas, Mert Mestanoglu, Ayhan Unlu, Mine Yurtsever, Serdar Durdagi*. Mutated Form (G52E) of Inactive Diphtheria Toxin CRM197: Molecular Simulations Clearly Display Effect of the Mutation to NAD Binding. Journal of Biomolecular Structure and Dynamics  2015 (accepted).

72. Kocak, R.; Akin, EA.; Kalin, P.; Talaz, O.; Saracoglu, N.; Dastan, A.; Gulcin, I.; Durdagi, S.*  “Synthesis of some novel norbornone-fused pyridazines as potent inhibitors of carbonic anhydrase and acetylcholineesterase” Journal of Heterocyclic Chemistry 2015 (accepted)

71. Ramin Ekhteiari Salmas, Mine Yurtsever, Serdar Durdagi*: Protein Engineering Studies for C-C Chemokine Receptor Type 2 (CCR2). Current Enzyme Inhibition 2015 (accepted).

70. T. Amanda Strom, Serdar Durdagi, Suha Salih Ersoz, Ramin Ekhteiari Salmas, Claudiu T. Supuran, Andrew R. Barron: Fullerene-based Inhibitors of HIV-1 Protease. Journal of Peptide Science 2015 (accepted).

69. Ramin Ekhteiari Salmas, Mert Mestanoglu, Mine Yurtsever, Sergei Y Noskov, Serdar Durdagi*: Molecular Simulations of Solved Co-crystallized X-ray Structures Identifies Action Mechanisms of PDEδ Inhibitors. Biophysical Journal 2015 (in press)

68. Ramin Ekhteiari Salmas, Mine Yurtsever, Serdar Durdagi*: Investigation of Inhibition Mechanism of Chemokine Receptor CCR5 by Micro-second Molecular Dynamics Simulations. Scientific Reports (Nature PG) 2015; DOI: 10.1038/srep13180.

67. Samira Yazdi, Serdar Durdagi, Michael Naumann, Matthias Stein: Structural modelling of the N-terminal signal-receiving domain of IkBa. Frontiers in Molecular Biosciences 2015; DOI: 10.3389/fmolb.2015.00032

66. Akın Akıncıoğlu, Hülya Akıncıoğlu, İlhami Gülçin, Claudiu T. Supuran, Serdar Durdagi, Süleyman Göksu: Discovery of Potent Carbonic Anhydrase and Acetylcholine Esterase Inhibitors: Novel Sulfamoylcarbamates and Sulfamides Derived from Acetophenones. Bioorganic & Medicinal Chemistry 2015;  DOI:10.1016/j.bmc.2015.04.019

65. Ramin Ekhteiari Salmas, Murat Senturk, Mine Yurtsever, Serdar Durdagi*: Discovering Novel Carbonic Anhydrase Type IX (CA IX) Inhibitors from Seven Million Compounds Using Virtual Screening and In Vitro Analysis. Journal of Enzyme Inhibition and Medicinal Chemistry 03/2015;  DOI:10.3109/14756366.2015.1036049

64. Jiqing Guo, Yen May Cheng, James P Lees-Miller, Laura L Perissinotti, Tom W Claydon, Christina M Hull, Samrat Thouta, Daniel E Roach, Serdar Durdagi, Sergei Y Noskov, Henry J Duff: NS1643 Interacts around L529 of hERG to Alter Voltage Sensor Movement on the Path to Activation. Biophysical Journal 2015; 108(6):1400-13. DOI:10.1016/j.bpj.2014.12.055

63. Ramin Ekhteiari Salmas, Mert Mestanoglu, Serdar Durdagi, Murat Sentürk, A Afşin Kaya, Elif Çelenk Kaya: Kinetic and in silico studies of hydroxy-based inhibitors of carbonic anhydrase isoforms I and II. Journal of Enzyme Inhibition and Medicinal Chemistry 2015;  DOI:10.3109/14756366.2014.1003216

62. Ramin Ekhteiari Salmas, Mine Yurtsever, Matthias Stein, Serdar Durdagi*: Modeling and protein engineering studies of active and inactive states of human dopamine D2 receptor (D2R) and investigation of drug/receptor interactions. Molecular Diversity 2015;  DOI:10.1007/s11030-015-9569-3

61. Ramin Ekhteiari Salmas, Ayhan Unlu, Mine Yurtsever, Sergei Y Noskov, Serdar Durdagi*: 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 2015. (in press)

60. Jamshed Iqbal, Mariya Al-Rashida, Serdar Durdagi, Vincenzo Alterio, Anna Di Fiore: Recent Developments of Carbonic Anhydrase Inhibitors as Potential Drugs. BioMed Research International 2015; 2015:174178. DOI:10.1155/2015/174178


2014

59. Irina Kufareva; Vsevolod Katritch; Phil Biggin; Minsup Kim; Kichul Park; Sang Won Jung; Art E. Cho; Zara A. Sands; Liliana Ostopovici-Halip; Cristian G. Bologa; Christoffer Norn ; Michal Brylinski ; Jeffrey Skolnick ; Henrik Keränen ; Bart E. Lenselink ; Gerard Van Westen ; John P. Overington ; Hugo Gutiérrez De Teráán; Vignir Isberg ; Kimberley M. Fidom ; Thomas M. Lehto ; David E. Gloriam ; Anirban Ghosh ; Uddhavesh Sonavane ; Rajendra Joshi ; Jie Xia ; Jui Hua Hsieh ; Liangren Zhang ; Xiang Simon Wang ; Horst Vogel ; Shuguang Yuan ; X. Feng ; M. Chen ; J. Ambia ; P. Barth ; Cédric Gageat ; Michal Stepniewski ; Henri Xhaard; Sebastian Kelm ; William R. Pitt ; Jiye Shi ; Adrien Larsen ; Hubert Li ; Jeffrey Wagner ; Supriyo Bhattacharya ; Nagarajan Vaidehi ; Kazuhiko Kanou ; Vaclav Cvicek ; Soo Kyung Kim ; Bartosz Trzaskowski ; William A. Goddard ; Ravinder Abrol ; Balaji Selvam ; Irina G. Tikhonova ; Alberto Cuzzolin ; Davide Sabbadin ; Antonella Ciancetta ; Stefano Moro ; Thibaud Freyd ; Mari Gabrielsen ; Kurt Kristiansen ; Ingebrigt Sylte ; Kevin J. Gaffney ; Nicos A. Petasis ; Dorota Latek ; Marek Bajda ; Krzysztof Młynarczyk ; Sławomir Filipek ; Laura López ; Michael Kuiper ; Thijs Beuming ; Jose Manuel Perez-Aguilar ; Ray Yu Ruei Wang ; Hahnbeom Park ; Per Greisen ; Yifan Song ; Frank DiMaio ; David Baker ; Woong Hee Shin; Lim Heo ; Gyu Rie Lee; Chaok Seok ; Jianyi Yang; Yang Zhang; Marco Ponassi; Camillo Rosano; Georgy Cheremovskiy ; Sergei Grudinin ; Rajan Chaudhari ; Andrew J. Heim ; Zhijun Li ; Qiang Lv ; Martin G. Grigorov ; Xin Hu ; Hongmao Sun ; Min Shen ; Noel Southall ; Ajit Jadhav ; David Rodríguez ; Anirudh Ranganathan ; Jens Carlsson ; Rafael Najmanovich ; Serdar Durdagi ; Claire De March ; Julien Diharce ; Jérôme Golebiowski ; Serge Antonczak ; Sébastien Fiorucci ; Elizabeth Nguyen ; Jens Meiler ; Aleksandrs Gutcaits ; Maria Marti-Solano ; Manuel Pastor ; Jana Selent; Raymond C. Stevens; Ruben Abagyan: Advances in GPCR Modeling evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges. Structure 2014; 22, 1120-1139.

58. Jiqing Guo, Serdar Durdagi, Mohamed Changalov, Laura L Perissinotti, Jason M Hargreaves, Thomas G Back, Sergei Y Noskov, Henry J Duff: Structure Driven Design of Novel Human Ether-A-Go-Go-Related-Gene Channel (hERG1) Activators. PLoS ONE 2014; 9(9):e105553. DOI:10.1371/journal.pone.0105553

57. Süleyman Göksu, Ali Naderi, Yusuf Akbaba, Pınar Kalın, Akın Akıncıoğlu, Ilhami Gülçin, Serdar Durdagi, Ramin Ekhteiari Salmas: Carbonic anhydrase inhibitory properties of novel benzylsulfamides using molecular modeling and experimental studies. Bioorganic Chemistry 2014; 56C:75-82. DOI:10.1016/j.bioorg.2014.07.009

56. Georgios Leonis, Aggelos Avramopoulos, Ramin Ekhteiari Salmas, Serdar Durdagi, Mine Yurtsever, Manthos G Papadopoulos: Elucidation of Conformational States, Dynamics, and Mechanism of Binding in Human κ-Opioid Receptor Complexes. Journal of Chemical Information and Modeling 2014; 54(8). DOI:10.1021/ci5002873

55. Serdar Durdagi*, Trevor Randall, Henry J Duff, Adam Chamberlin, Sergei Y Noskov: Rehabilitating drug-induced long-QT promoters: In-silico design of hERG-neutral cisapride analogues with retained pharmacological activity. BMC Pharmacology and Toxicology 2014; 15(1):14. DOI:10.1186/2050-6511-15-14

54. Birce Buturak, Serdar Durdagi, Sergei Y Noskov, A Tugba Ozal Ildeniz: Designing of multi-targeted molecules using combination of molecular screening and in silico drug cardiotoxicity prediction approaches. Journal of Molecular Graphics & Modelling 2014; 50C:16-34. DOI:10.1016/j.jmgm.2014.02.007
 
53. Serdar Durdagi, Matthew Patterson, Sergei Y. Noskov: Development and Validation Studies of Universal Pharmacophore Models for hERG Channel Openers. Biophysical Journal 2014; 106(2):15a. DOI:10.1016/j.bpj.2013.11.137

52. Süleyman Göksu, Ali Naderi, Yusuf Akbaba, Pınar Kalın, Akın Akıncıoğlu, İlhami Gülçin,
Serdar Durdagi, Ramin E. Salmas: Carbonic Anhydrase Inhibitory Properties of Novel Benzylsulfamides Using Molecular Modelling and Experimental Studies. Bioorganic Chemistry 2014
; 56: 75-82. doi: 10.1016/j.bioorg.2014.07.009

51. Avia Rosenhouse-Dantsker,
Sergei Y. Noskov, Serdar Durdagi, Diomedes E. Logothetis, Irena Levitan: Identification of Novel Cholesterol Binding Regions in the Transmembrane Domain of Kir2.1. Biophysical Journal 2014; 106(2):747a. DOI:10.1016/j.bpj.2013.11.4117 

2013

50. Maria Zervou, Zoe Cournia, Constantinos Potamitis, George Patargias, Serdar Durdagi, Simona Golic Grdadolnik, Thomas Mavromoustakos: Insights into the Molecular Basis of Action of the AT1 Antagonist Losartan Using a Combined NMR Spectroscopy and Computational Approach. Biochimica et Biophysica Acta: Biomembranes 12/2013; 1838(3). DOI:10.1016/j.bbamem.2013.12.012

49. Eftichia Kritsi, Constantinos Potamitis,
Serdar Durdagi, Panagiotis Zoumpoulakis, Simona Golic Grdadolnik, Thomas Mavromoustakos: Molecular insights into the AT1 antagonism based on biophysical and in silico studies of telmisartan. Medicinal Chemistry Research 10/2013; 22(10). DOI:10.1007/s00044-012-0464-5


48. Avia Rosenhouse-Dantsker, Sergei Noskov,
Serdar Durdagi, Diomedes E Logothetis, Irena Levitan: Identification of novel cholesterol-binding regions in Kir2 channels. Journal of Biological Chemistry 2013;  DOI:10.1074/jbc.M113.496117


47. Thomas Mavromoustakos, George Agelis, Serdar Durdagi:
AT1 antagonists: a patent review (2008 - 2012). Expert Opinion on Therapeutic Patents 2013;  DOI:10.1517/13543776.2013.830104


46.
Serdar Durdagi, Gabriele Scozzafava, Daniela Vullo, Hüseyin Sahin, Sevgi Kolayli, Claudiu T Supuran: Inhibition of mammalian carbonic anhydrases I-XIV with grayanotoxin III: solution and in silico studies. Journal of Enzyme Inhibition and Medicinal Chemistry 2013;  DOI:10.3109/14756366.2013.804072


45.
Serdar Durdagi, Trevor Randal, Henry J. Duff, Sergei Y. Noskov: Rehabilitation Studies for withdrawn Drugs from the Market: Derivation of Non-hERG1 Channel Blocker Cisapride Analogues using Multi-Faceted Approaches. Biophysical Journal 2013; 104(2):266-. DOI:10.1016/j.bpj.2012.11.1495
 

2012

44.     Deniz Ekinci, Ismail Fidan, Serdar Durdagi, Seniz Kaban, Claudiu T Supuran: Kinetic and in silico analysis of thiazolidin-based inhibitors of α-carbonic anhydrase isoenzymes.. Journal of Enzyme Inhibition and Medicinal Chemistry 11/2012;  DOI:10.3109/14756366.2012.732071
43. Oktay Talaz, Hüseyin Cavdar, Serdar Durdagi, Hacer Azak, Deniz Ekinci: 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 10/2012;  DOI:10.1016/j.bmc.2012.09.027

42.
Serdar Durdagi, Sumukh Deshpande, Henry J Duff, Sergei Y Noskov: 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 09/2012; 52(10):2760-74. DOI:10.1021/ci300353u


41. George Agelis, Amalia Resvani,
Serdar Durdagi, Katerina Spyridaki, Tereza Tůmová, Jiřina Slaninová, Panagiotis Giannopoulos, Demetrios Vlahakos, George Liapakis, Thomas Mavromoustakos, John Matsoukas: The discovery of new potent non-peptide Angiotensin II AT1 receptor blockers: A concise synthesis, molecular docking studies and biological evaluation of N-substituted 5-butylimidazole derivatives. European Journal of Medicinal Chemistry 07/2012; 55:358-74. DOI:10.1016/j.ejmech.2012.07.040


40.
Serdar Durdagi, Daniela Vullo, Peiwen Pan, Niklas Kähkönen, Juha A Määttä, Vesa P Hytönen, Andrea Scozzafava, Seppo Parkkila, Claudiu T Supuran: 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 05/2012; 55(11):5529-35. DOI:10.1021/jm3004587


39.
Serdar Durdagi, Jiqing Guo, James P Lees-Miller, Sergei Y Noskov, Henry J Duff: 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. Journal of Pharmacology and Experimental Therapeutics 05/2012; 342(2):441-52. DOI:10.1124/jpet.111.189159


38. Deniz Ekinci, Hüseyin Cavdar,
Serdar Durdagi, Oktay Talaz, Murat Sentürk, Claudiu T Supuran: 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 03/2012; 49:68-73. DOI:10.1016/j.ejmech.2011.12.022


37.     G. Agelis, A. Resvani, S. Durdagi, T. Tumova, J. Slaninov, P. Giannopoulos, K. Spyridaki, G. Liapakis, D. Vlahakos, T. Mavromoustakos, J. Matsoukas: A Concise Synthesis, Docking Studies and Biological Evaluation of N-substituted 5-Butylimidazole Analogues as Potent Angiotensin II Receptor Blockers. Journal of Peptide Science 01/2012; 18:S116-S116.

36.
Serdar Durdagi, Sumukh Deshpande, Henry Duff, Sergei Noskov: 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 01/2012; 102(3):679-. DOI:10.1016/j.bpj.2011.11.3693


2011


35. Serdar Durdagi*, Manthos G Papadopoulos, Thomas Mavromoustakos: 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 10/2011; 47(1):44-51. DOI:10.1016/j.ejmech.2011.10.015
34. Haralambos Tzoupis, Georgios Leonis, Serdar Durdagi, Varnavas Mouchlis, Thomas Mavromoustakos, Manthos G Papadopoulos: 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 10/2011; 25(10):959-76. DOI:10.1007/s10822-011-9475-4 

33. Reşit Çakmak,
Serdar Durdagi, Deniz Ekinci, Murat Sentürk, Giray Topal: Design, synthesis and biological evaluation of novel nitroaromatic compounds as potent glutathione reductase inhibitors. Bioorganic & Medicinal Chemistry Letters 09/2011; 21(18):5398-402. DOI:10.1016/j.bmcl.2011.07.002


32.
Halis Türker Balaydin, Serdar Durdagi, Deniz Ekinci, Murat Sentürk, Süleyman Göksu, Abdullah Menzek: Inhibition of human carbonic anhydrase isozymes I, II and VI with a series of bisphenol, methoxy and bromophenol compounds. Journal of Enzyme Inhibition and Medicinal Chemistry 08/2011; 27(4):467-75. DOI:10.3109/14756366.2011.596836

31. Catherine Koukoulitsa,
Serdar Durdagi, Eleni Siapi, Carolina Villalonga-Barber, Xanthippi Alexi, Barry R Steele, Maria Micha-Screttas, Michael N Alexis, Anna Tsantili-Kakoulidou, Thomas Mavromoustakos: Comparison of thermal effects of stilbenoid analogs in lipid bilayers using differential scanning calorimetry and molecular dynamics: correlation of thermal effects and topographical position with antioxidant activity. Eur. Biophysics Journal 07/2011; 40(7):865-75. DOI:10.1007/s00249-011-0705-4


30. S Durdagi*, C Zhao, J E Cuervo, S Y Noskov: Atomistic models for free energy evaluation of drug binding to membrane proteins. Current Medicinal Chemistry 06/2011; 18(17):2601-11. DOI:10.2174/092986711795933641


29. T Mavromoustakos,
S Durdagi, C Koukoulitsa, M Simcic, M G Papadopoulos, M Hodoscek, S Golic Grdadolnik: Strategies in the rational drug design. Current Medicinal Chemistry 06/2011; 18(17):2517-30. DOI:10.2174/092986711795933731


28.    
Serdar Durdagi, Sergei Y Noskov: Mechanism of K+/Na+ selectivity in potassium channels from the perspective of the non-selective bacterial channel NaK. Channels (Austin, Tex.) 05/2011; 5(3):198-200. DOI:10.4161/chan.5.3.15873


27.     Thomas Mavromoustakos, Petros Chatzigeorgiou, Catherine Koukoulitsa,
Serdar Durdagi: Partial Interdigitation of Lipid Bilayers. International Journal of Quantum Chemistry 05/2011; 111(6):1172 - 1183. DOI:10.1002/qua.22610


26.    
Serdar Durdagi*, Henry J Duff, Sergei Yu Noskov: 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 02/2011; 51(2):463-74. DOI:10.1021/ci100409y


25.    
Serdar Durdagi, Murat Şentürk, Deniz Ekinci, Halis Türker Balaydın, Süleyman Göksu, Ö İrfan Küfrevioğlu, Alessio Innocenti, Andrea Scozzafava, Claudiu T Supuran: 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 02/2011; 19(4):1381-9. DOI:10.1016/j.bmc.2011.01.016
 

2010

24.     S. Durdagi, S. Y. Noskov: Consistency of constructed hERG1 pore domain and pharmacophore models: A 3D-QSAR, molecular docking, and pharmacophore modeling study. Biochemistry and Cell Biology 04/2010

23.     Aggeliki Politi, Serdar Durdagi, Panagiota Moutevelis-Minakakis, George Kokotos, Thomas Mavromoustakos: Development of accurate binding affinity predictions of novel renin inhibitors through molecular docking studies. Journal of Molecular Graphics & Modelling 11/2010; 29(3):425-35. DOI:10.1016/j.jmgm.2010.08.003

22.     Julia Subbotina, Vladimir Yarov-Yarovoy, James Lees-Miller, Serdar Durdagi, Jiqing Guo, Henry J Duff, Sergei Yu Noskov: Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations. Proteins: Structure Function and Bioinformatics 11/2010; 78(14):2922-34. DOI:10.1002/prot.22815

21.     S Durdagi, J Subbotina, J Lees-Miller, J Guo, H J Duff, S Y Noskov: Insights into the molecular mechanism of hERG1 channel activation and blockade by drugs. Current Medicinal Chemistry 10/2010; 17(30):3514-32. DOI:10.2174/092986710792927886

20.     George Agelis, Panagiota Roumelioti, Amalia Resvani, Serdar Durdagi, Maria-Eleni Androutsou, Konstantinos Kelaidonis, Demetrios Vlahakos, Thomas Mavromoustakos, John Matsoukas: An efficient synthesis of a rationally designed 1,5 disubstituted imidazole AT(1) angiotensin II receptor antagonist: reorientation of imidazole pharmacophore groups in losartan reserves high receptor affinity and confirms docking studies. Journal of Computer-Aided Molecular Design 09/2010; 24(9):749-58. DOI:10.1007/s10822-010-9371-3

19.     Alessio Innocenti, Serdar Durdagi, Nadjmeh Doostdar, T Amanda Strom, Andrew R Barron, Claudiu T Supuran: Nanoscale enzyme inhibitors: Fullerenes inhibit carbonic anhydrase by occluding the active site entrance. Bioorganic & Medicinal Chemistry 03/2010; 18(8):2822-8. DOI:10.1016/j.bmc.2010.03.026

18.     George Agelis, Panagiota Roumelioti, Amalia Resvani, Serdar Durdagi, Maria-Eleni Androutsou, Konstantinos Kelaidonis, Demetrios Vlahakos, Thomas M. Mavromoustakos, John Matsoukas: An efficient synthesis of a rationally designed 1, 5 disubstituted imidazole AT(1) Angiotensin II Receptor Antagonist: Reorientation Of Imidazole Pharmacophore Groups in Losartan Reserves High Receptor Affinity And Confirms Docking Studies Journal Of Computer-Aided Molecular Design 01/2010; 24, 749-758. DOI: 10.1007/s10822-010-9371-3

2009

17.     C Fotakis, S Gega, E Siapi, C Potamitis, K Viras, P Moutevelis-Minakakis, C G Kokotos, S Durdagi, S Golic Grdadolnik, B Sartori, M Rappolt, T Mavromoustakos: Interactions at the bilayer interface and receptor site induced by the novel synthetic pyrrolidinone analog MMK3. Biochimica et Biophysica Acta 11/2009; 1798(3):422-32. DOI:10.1016/j.bbamem.2009.11.009

16.     Serdar Durdagi*, Manthos G Papadopoulos, Panagiotis G Zoumpoulakis, Catherine Koukoulitsa, Thomas Mavromoustakos: A computational study on cannabinoid receptors and potent bioactive cannabinoid ligands: homology modeling, docking, de novo drug design and molecular dynamics analysis. Molecular Diversity 07/2009; 14(2):257-76. DOI:10.1007/s11030-009-9166-4

15.     Serdar Durdagi*, Claudiu T Supuran, T Amanda Strom, Nadjmeh Doostdar, Mananjali K Kumar, Andrew R Barron, Thomas Mavromoustakos, Manthos G Papadopoulos: 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 05/2009; 49(5):1139-43. DOI:10.1021/ci900047s

14.     Aggeliki Politi, Serdar Durdagi, Panagiota Moutevelis-Minakakis, George Kokotos, Manthos G Papadopoulos, Thomas Mavromoustakos: Application of 3D QSAR CoMFA/CoMSIA and in silico docking studies on novel renin inhibitors against cardiovascular diseases. European Journal of Medicinal Chemistry 05/2009; 44(9):3703-11. DOI:10.1016/j.ejmech.2009.03.040

13     Agnes Kapou, Nikolas-P. Benetis, Serdar Durdagi, Sotiris Nikolaropoulos, Thomas Mavromoustakos: 3D QSAR/CoMFA and CoMSIA Studies on Antileukemic Steroidal Esters Coupled with Conformationally Flexible Nitrogen Mustards. ChemInform 04/2009; 40(15). DOI:10.1002/chin.200915221

12.     Constantinos Potamitis, Maria Zervou, Vassilis Katsiaras, Panagiotis Zoumpoulakis, Serdar Durdagi, Manthos G Papadopoulos, Joseph M Hayes, Simona Golic Grdadolnik, Ioanna Kyrikou, Dimitris Argyropoulos, Georgia Vatougia, Thomas Mavromoustakos: Antihypertensive drug valsartan in solution and at the AT1 receptor: conformational analysis, dynamic NMR spectroscopy, in silico docking, and molecular dynamics simulations. Journal of Chemical Information and Modeling 04/2009; 49(3):726-39. DOI:10.1021/ci800427s

2008

11.     Serdar Durdagi*, Thomas Mavromoustakos, Nikos Chronakis, Manthos G Papadopoulos: 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. Bioorganic & Medicinal Chemistry 01/2009; 16(23):9957-74. DOI:10.1016/j.bmc.2008.10.039 2008

10.     Agnes Kapou, Nikolas-P Benetis, Serdar Durdagi, Sotiris Nikolaropoulos, Thomas Mavromoustakos: 3D QSAR/CoMFA and CoMSIA Studies on Antileukemic Steroidal Esters Coupled with Conformationally Flexible Nitrogen Mustards. Journal of Chemical Information and Modeling 11/2008; 48(11):2254-64. DOI:10.1021/ci800240m

09.     Serdar Durdagi, Thomas Mavromoustakos, Manthos G Papadopoulos: 3D QSAR CoMFA/CoMSIA, molecular docking and molecular dynamics studies of fullerene-based HIV-1 PR inhibitors. Bioorganic & Medicinal Chemistry Letters 11/2008; 18(23):6283-9. DOI:10.1016/j.bmcl.2008.09.107

08.     T. Mavromoustakos, C. Petrou, E. Kokkalou, V. Roussis, V. Christofi, G. Efthimiou, C. Potamitis, S. Durdagi, S. Mavromoustakos: Ficus sycomorus sap: a psoralene source with potential for the treatment of psoriasis. Planta Medica 07/2008; 74(9):1006-1006. DOI:10.1055/s-0028-1084264

07.     Serdar Durdagi, Heribert Reis, Manthos G Papadopoulos, Thomas Mavromoustakos: Comparative molecular dynamics simulations of the potent synthetic classical cannabinoid ligand AMG3 in solution and at binding site of the CB1 and CB2 receptors. Bioorganic & Medicinal Chemistry 07/2008; 16(15):7377-87. DOI:10.1016/j.bmc.2008.06.019

06.     Serdar Durdagi, Manthos G Papadopoulos, Demetris P Papahatjis, Thomas Mavromoustakos: Combined 3D QSAR and molecular docking studies to reveal novel cannabinoid ligands with optimum binding activity. Bioorganic & Medicinal Chemistry letters 01/2008; 17(24):6754-63. DOI:10.1016/j.bmcl.2007.10.044


2007

05.    Serdar Durdagi, Agnes Kapou, Therapia Kourouli, Thanos Andreou, Spyros P Nikas, Victoria R Nahmias, Demetris P Papahatjis, Manthos G Papadopoulos, Thomas Mavromoustakos: The application of 3D-QSAR studies for novel cannabinoid ligands substituted at the C1' position of the alkyl side chain on the structural requirements for binding to cannabinoid receptors CB1 and CB2. Journal of Medicinal Chemistry 07/2007; 50(12):2875-85. DOI:10.1021/jm0610705
04.     S. Durdagi, C. Koukoulitsa, A. Kapou, T. Kourouli, T. Andreou, S. P. Nikas, V. R. Nahmias, D. P. Papahatjis, M. G. Papadopoulos, T. Mavromoustakos: Testing the 3D QSAR/ComFA-CoMSIA results of flexible bioactive compounds with molecular docking studies. Drugs of the Future 01/2007; 32:79-79.

03.     T. Mavromoustakos, M. Zervou, P. Zoumpoulakis, C. Potamitis, V. Katsiaras, A. Politi, E. Mantzourani, S. Durdagi, C. Koukoulitsa: Putative bioactive conformers of small molecules: A concerted approach using NMR spectroscopy and computational chemistry. Drugs of the Future 01/2007; 32:33-33. 2006


2006

02.    Ulrike Salzner, Ozan Karalti, Serdar Durdaği: Does the donor-acceptor concept work for designing synthetic metals? III. Theoretical investigation of copolymers between quinoid acceptors and aromatic donors. Journal of Molecular Modeling 08/2006; 12(5):687-701. DOI:10.1007/s00894-005-0046-2


2005

01.    Serdar Durdagi, Thomas S. Hofer, Bernhard R. Randolf, Bernd M. Rode: Structural and dynamical properties of Bi 3+ in water. Chemical Physics Letters  2005; 406(1):20-23. DOI:10.1016/j.cplett.2005.02.082


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