2020
166. Serdar Durdagi, Cagdas Dag, Berna Dogan, Merve Yigin, Timucin Avsar, Cengizhan Buyukdag, Ismail Erol, Betul Ertem, Seyma Calis, Gunseli Yildirim, Muge D. Orhan, Omur Guven, Busecan Aksoydan, Ebru Destan, Kader Sahin, Sabri O. Besler, Lalehan Oktay, Alaleh Shafiei, Ilayda Tolu, Esra Ayan, Busra Yuksel, Ayse B. Peksen, Oktay Gocenler, Ali D. Yucel, Ozgur Can, Serena Ozabrahamyan, Alpsu Olkan, Ece Erdemoglu, Fulya Aksit, Gokhan Tanisali, Oleksandr M. Yefanov, Anton Barty, Alexandra Tolstikova, Gihan K. Ketawala, Sabine Botha, E. Han Dao, Brandon Hayes, Mengning Liang, Matthew H. Seaberg, Mark S. Hunter, Alex Batyuk, Valerio Mariani, Zhen Su, Frederic Poitevin, Chun Hong Yoon, Christopher Kupitz, Raymond G. Sierra, Edward Snell, Hasan DeMirci. Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing. Nature Communications 2020 (submitted)
165. Timucin Avsar; Berfu Nur Yigit; Gizem Turan; Deniz Altunsu; Seyma Calis; Bahar Kurt; Turker Kilic; M. Yavuz Ergun; Serdar Durdagi*; Melih Acar. Development of an Imidazolone-Based Angiotensin II Receptor Type I Inhibitor as a Chemotherapeutic Agent for Cell Cycle Inhibition. ACS Chemical Biology 2020 (submitted)
164. Kader Sahin, Emin Saripinar, Serdar Durdagi. Determination of Bioactive Pharmacophore Groups in Isatin Derivatives with Combined 4D-QSAR and Target-driven Approaches and Proposing of Novel Anti-cancer Hit Molecules. Journal of Computer-Aided Molecular Design 2020 (submitted)
163. Saima Ikrama, Fawad Ahmad, Jamshaid Ahmad, Serdar Durdagi*. Screening of Small Molecule Libraries Using Combined Text Mining, Ligand- and Target-Driven Based Approaches for Identification of Novel Granzyme H Inhibitors. Molecular Informatics 2020 (submitted)
162. Ahmet Burak Sariguney, Lalehan Oktay, Deniz Ekici, Serdar Durdagi. Synthesis, molecular modelling studies and carbonic anhydrase inhibition of indole-based 4-amino-1,2,4-triazole-3-thion derivatives. Bioorganic and Medicinal Chemistry, 2020 (submitted)
161. Aida Shahraki, Ali Isbilir, Berna Dogan, Martin Lohse, Serdar Durdagi*, Necla Birgul Iyison. Structural and functional characterization of allatostatin receptor type-C of Thaumetopoea pityocampa revealed the importance of Q271 residue in G protein-dependent activation pathway. Journal of Chemical Information and Modeling (submitted)
160. Serdar Durdagi. An Integrated Computational Approach for the Discovery of Ubiquitin Specific Protease 7 (USP7) Inhibitors as Potential Cancer Therapies. Biophysical Journal 2020, 118(3), 47.
159. Musa Özil, Halis T. Balaydın, Berna Dogan, Murat Şentürk, Serdar Durdagi*. Synthesis of 5-methyl-2,4-dihydro-3H-1,2,4-triazole-3-one’s aryl Schiff base derivatives, carbonic anhydrase I, II, AChE, BuChE in vitro inhibitory and in silico studies. Journal of Medicinal Chemistry (submitted)
158. Duaa Kanan, Tarek Kanan, Berna Dogan, Muge Didem Orhan, Timucin Avsar, Serdar Durdagi*. An Integrated In Silico Approach and In Vitro Study for the Discovery of Ubiquitin Specific Protease 7 (USP7) Small Molecule Inhibitors as Potential Cancer Therapies. ChemMedChem (accepted)
157. Kader Sahin, Muge Didem Orhan, Timucin Avsar, Serdar Durdagi*. Hybrid In Silico and TR-FRET-Guided Discovery of Novel BCL-2 Inhibitors. ACS Pharmacology & Translational Science 2020 (submitted)
156. Mehmet Oguz, Berna Dogan, Serdar Durdagi*, Asif Ali Bhatti, Serdar Karakurt, Mustafa Yilmaz. In vitro Cytotoxic Assay and Numerical Investigation of Inclusion Complex of Calix[4,8]arene and Quercetin. Bioorganic Chemistry 2020 (submitted)
155. Serdar Durdagi*. Virtual drug repurposing study against SARS-1 CoV-2 TMPRSS2 target. Turkish Journal of Biology. 2020 (accepted)
154. Serdar Durdagi*, Busecan Aksoydan, Berna Dogan, Kader Sahin, Aida Shahraki, Necla Birgul-Iyison. Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS-CoV-2 Main Protease and Spike Receptor-Binding Domain Bound with ACE2 COVID19 Target Proteins: A Virtual Drug Repurposing Study. ChemMedChem 2020 (submitted)
153. Kader Sahin, Serdar Durdagi*. Combined ligand and structure-based virtual screening approaches for identification of novel AChE inhibitors. Turkish Journal of Chemistry. 44, 574-588, 2020. http://journals.tubitak.gov.tr/chem/issues/kim-20-44-3/kim-44-3-3-1911-57.pdf
152. Ferah Comert Onder; Esen Bellur Atici; Nermin Kahraman; Ali Cagir; Hakan Kandemir; Gizem Tatar; Tugba Taskin Tok; Bekir Karliga; Serdar Durdagi; Mehmet Ay; Bulent Ozpolat, Bekir Karliga. Coumarinyl Chalcone Scaffold as in vitro and in vivo Effective EF2 Kinase Inhibitor. Cancer Research and Treatment (BREA) 2020 (submitted)
151. Ferah Comert Onder, Serdar Durdagi*, Bulent Ozpolat, Mehmet Ay. Design, synthesis, eEF-2K activity and molecular modeling studies of novel coumarin carboxamide derivatives. Journal of Chemical Information and Modeling 2020 (accepted). https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b01083
150. Kader Sahin, Serdar Durdagi*. Identifying New Piperazine-based PARP1 Inhibitors Using Text Mining and Integrated Molecular Modeling Approaches. Journal of Biomolecular Structure and Dynamics 2020(accepted). https://pubmed.ncbi.nlm.nih.gov/32048546/
149. Yusuf Serhat Is, Busecan Aksoydan, Murat Senturk, Mine Yurtsever, Serdar Durdagi*. Novel MAO-B Inhibitors Using Combined Virtual Screening of Small Molecules Databases and In Vitro Analysis. Journal of Chemical Information and Modeling 2020 (accepted)
148. Necla Birgul Iyison, Merve Gizem Sinmaz, Burcin Duan Sahbaz, Aida Shahraki, Busecan Aksoydan, Serdar Durdagi*. In silico characterization of adipokinetic hormone receptor and screening for pesticide candidates against stick insect, Carausius morosus. Journal of Molecular Graphics and Modelling 2020 (accepted).
147. Berna Dogan and Serdar Durdagi*. Drug Re-Positioning Studies for Novel HIV-1 Inhibitors Using Binary QSAR Models and Multi-Target-Driven In Silico Studies. Molecular Informatics 2020 (accepted)
146. Gurbet Tutumlu, Berna Dogan, Timucin Avsar, Muge Didem Orhan, Seyma Calis, Serdar Durdagi* Integrating Ligand and Target-Driven Based Virtual Screening Approaches with in vitro human Cell Line Models to Identify Novel Hit Compounds Against BCL-2. Frontiers in Chemistry 2020 (accepted) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7160371/pdf/fchem-08-00167.pdf
145. Yasemin Unver, Diler Unluer, Sahin Direkel, Serdar Durdagi .Bis Benzothiophene Schiff Bases: Multi-Scale Molecular Modeling, Synthesis And Biological Activity Studies. Turkish Journal of Chemistry 2020 (accepted)
144. Timucin Avsar, Berfu Nur Yigit, Gizem Turan, Deniz Altunsu, Seyma Calis, Bahar Kurt, Turker Kilic, M. Yavuz Ergun, Serdar Durdagi*, and Melih Acar. Development of Imidazolone Based Angiotensin II Receptor Type I Inhibitor as Chemotherapeutic Agent for Cell Cycle Inhibition. European Journal of Medicinal Chemistry 2019 (submitted)2019
143. Kubra Cavusoglu, Murat Senturk, Serdar Durdagi. Determination of in Vitro and in Silico Effects of Some Uracil Derivatives on Carbonic Anhydrase I Isoenzyme. ACTA Physiologica 2019, 227, 122.
142. Saima Ikram, Jamshaid Ahmad, Irshad-Ur-Rehman, Serdar Durdagi*. Potent Novel Inhibitors Against Hepatitis C Virus NS3 (HCV NS3 GT-3a) Protease Domain. Journal of Molecular Graphics and Modelling 2019 (accepted)
141. Saima Ikram, Jamshaid Ahmad, Fawad Ahmad, Serdar Durdagi*. Screening of Small Molecule Libraries Using Combined Text Mining, Ligand- and Target-Driven Based Approaches for Identification of Novel Granzyme H Inhibitors. Journal of Molecular Graphics and Modelling 2019 (accepted)
140. Gulsah Aydin, Maide Nur Paksoy, Müge Didem Orhan, Timucin Avsar, Mine Yurtsever, Serdar Durdagi*. Proposing Novel MDM2 Inhibitors: Combined High Throughput Virtual Screening and In Vitro Studies. Chemical Biology &Drug Design 2019 (accepted)
139. Raife Dilek Turan, Esra Albayrak, Pinar Siyah, Lamia Yazgi Alyazici, Batuhan Mert Kalkan, Galip Servet Aslan, Dogacan Yucel, Merve Aksoz, Emre Can Tuysuz, Neslihan Meric, Serdar Durdagi, Zafer Gulbas, Fatih Kocabas. Development of Small Molecule MEIS Inhibitors that modulate HSC activity. Scientific Reports 2019 (accepted).
138. Ayse Sahaboglu, Serdar Durdagi, Gulru Kayik, Eberhart Zrenner. PARP inhibitors: The protective ways on retinal degeneration. Investigative Ophthalmology & Visual Science 2019, 60(9), 5177.
137. Kader Sahin, Belma Zengin Kurt, Fatih Sonmez, Serdar Durdagi*. Novel AChE and BChE Inhibitors Using Combined Virtual Screening, Text mining and In Vitro Binding Assays. Journal of Biomolecular Structure and Dynamics 2019 (accepted). https://pubmed.ncbi.nlm.nih.gov/31462153/
136. Kader Sahin, Serdar Durdagi*. Identifying the Novel Pyrimidine-Based CDK2 Inhibitors as Anticancer Agents Using Text-Mining and Combined Molecular Modeling Approaches, Journal of the Turkish Chemical Society Section A: Chemistry, 2020 (accepted) https://dergipark.org.tr/tr/pub/jotcsa/issue/52506/701243
135. Beril Colak Gunay, Mine Yurtsever, Serdar Durdagi*. n Silico Screening of Protein-Protein Interactions of hERG1 Potassium Ion Channels with Scorpion Toxins. Journal of Molecular Graphics and Modelling 2019 (accepted).
134. Mehmet Oguz; Asif A Bhatti; Berna Dogan; Serdar Karakurt; Serdar Durdagi. Formation of the Inclusion Complex of Water Soluble Fluorescent Calix[4]arene and Naringenin: Solubility, Cytotoxic effect and Molecular Modeling Studies. Journal of Biomolecular Structure and Dynamics 2019 (accepted)
133. Ferah Comert Onder, Mehmet Ay, Serdar Durdagi, Bulent Ozpolat, isik Kantarcioglu. New and potent small molecule as EF2K inhibitor: A novel EF2K inhibitor. Cancer Research 2019 (American Association for Cancer Research) DOI: 10.1158/1538-7445.SABCS18-4787
132. Saima Ikram, Jamshaid Ahmad, Serdar Durdagi* Screening of FDA approved drugs for finding potential inhibitor for Granzyme B as a potent drug-repurposing target. Journal of Molecular Graphics and Modelling 2019 (accepted) https://pubmed.ncbi.nlm.nih.gov/31786094/
131. Ismail Erol, Bunyemin Cosut and Serdar Durdagi*. Towards Understanding the Impact of Dimerization Interfaces in Angiotensin II type 1 receptor (AT1R). Journal of Chemical Information and Modeling 2019 (accepted) https://pubmed.ncbi.nlm.nih.gov/31429557/
130. Seda Savranoglu Kulabas, Ferah Comert Onder , Yakup Berkay Yılmaz, Serdar Durdagi, Adem Ozleyen, Mehmet Ay and Tugba Boyunegmez Tumer. Integration of in vitro and in silico Studies for Nitrobenzamide Derivatives as iNOS Inhibitors and Potential Druggable Neuroprotective Agents. Journal of Biomolecular Structure and Dynamics 2019 (accepted)
129. Ayse Sahaboglu, Maria Miranda, Natalia Savytska, Enver Secer, Jessica Feria, Gülru Kayık, Serdar Durdagi. Drug Repurposing Studies of PARP Inhibitors as a New Therapy for Inherited Retinal Degeneration Cellular and Molecular Life Sciences 2019 (accepted) https://link.springer.com/article/10.1007/s00018-019-03283-2
128. Kader Sahin, Serdar Durdagi*. Combined Ligand and Structure-based Virtual Screening Approaches for Identification of Novel AChE Inhibitors. Turkish Journal of Chemistry 2019 (submitted)
127. Serdar Durdagi*, Ismail Erol, Berna Dogan, Taha Berkay Sen. Integration of Text Mining and Binary QSAR Models for Novel Anti-Hypertensive Antagonist Scaffolds. Biophysical Journal 2019, 116, 3, 478.126. Belma Zengin Kurt, Aydan Dag, Berna Doğan, Serdar Durdagi*, Andrea Angeli, Alessio Nocentini, Claudiu T. Supuran, Fatih Sonmez. Synthesis, Biological Activity and Multiscale Molecular Modeling Studies of Bis-coumarins as Selective Carbonic Anhydrase IX and XII Inhibitors with Effective Cytotoxicity against Hepatocellular Carcinoma. Bioorganic Chemistry 2019 (in press)
125. Belma Zengin Kurt, Serdar Durdagi*, Gulsen Celebi, Ramin Ekhteiari Salmas, Fatih Sonmez. Synthesis, Anticholinesterase Activity and Molecular Modeling Studies of Novel Carvacrol Substituted Amide Derivatives. Journal of Biomolecular Structure and Dynamics 2019 (in press)124. Ntountaniotis, Dimitrios; Andreadelis, Ioannis ; Kellici, Tahsin; Karageorgos, Vlasios; Leonis, Georgios; Christodoulou, Eirini; Kiriakidi, Sofia; Becker-Baldus, Johanna; Stylos, Evgenios; Chatziathanasiadou, Maria ; Chatzigiannis, Christos ; Damalas, Dimitrios; Durdagi, Serdar; Javornik, Uroš; Valsami, Georgia; Glaubitz, Clemens; Aksoydan, Busecan; Thomaidis, Nikolaos; Kolocouris, Antonios; Plavec, Janez; Tzakos, Andreas; Liapakis, George ; Mavromoustakos, Thomas. Host-guest interactions between candesartan and its prodrug candesartan cilexetil in complex with 2-hydroxypropyl-β-cyclodextrin: on the biological potency for Angiotensin II antagonism. Molecular Pharmaceutics 2019 (in press)123. Serdar Durdagi*, Berna Dogan, Ismail Erol, Gulru Kayik, Busecan Aksoydan. Current Satus of Multiscale Simulations on GPCRs. Current Opinion in Structural Biology 2019. (in press) https://pubmed.ncbi.nlm.nih.gov/31082696/122. Melis Kuskucu; Volkan Akyildiz; Ágnes Kulmány; Yavuz Ergün; Sevil Zencir; Istvan Zupko; Serdar Durdagi; Mehreen Zaka; Hilmi Orhan; Zeki Topcu. Structural modification of Ellipticine derivatives with alkyl groups of varying length is influential on their effects on human DNA topoisomerase II: A Combined Experimental and Computational Study. Medicinal Chemistry Research 2019 (accepted)2018
121. S. Kiriakidi, A. Kolocouris, G. Liapakis, S. Ikram, S. Durdagi*, T. Mavromoustakos. Effects of cholesterol on GPCR function. Advances in Experimental Medicine and Biology 2018 (in press)120.Ilkay Erdogan Orhan, F. Sezer Senol, Ramin Ekhteiari Salmas, Serdar Durdagi, Francesco Epifano, Salvatore Genovese, Serena Fiorito. Combined Molecular Modeling and Cholinesterase Inhibition Studies on Some Natural and Semisynthetic O-Alkylcoumarin Derivatives. Bioorganic Chemistry 2018 (in press)119. Huseyin Cavdar, Murat Senturk, Murat Guney, Serdar Durdagi, Gulru Kayik, Deniz Ekinci. Kinetic and In Silico Studies of Some Uracil Derivatives on Acetylcholinesterase and Butyrylcholinesterase Enzymes. Journal of Enzyme Inhibition and Medicinal Chemistry 2018
118. Tarek Kanan, Duaa Kanan, Ismail Erol, Samira Yazdi, Matthias Stein, Serdar Durdagi*. Targeting the NF‑κB/IκBα Complex via Fragment-Based E-Pharmacophore Virtual Screening and Binary QSAR Models. Journal of Molecular Graphics and Modelling 2018
117. Ramin Ekhteiari Salmas, Philip Seeman, Matthias Stein, Serdar Durdagi*. Structural Investigation of the Dopamine-2 Receptor (D2R) Agonist Bromocriptine Binding to Dimeric D2HighR and D2LowR States. Journal of Chemical Information and Modeling 2018
116. Yusuf Serhat Is, Serdar Durdagi*, Busecan Aksoydan, Mine Yurtsever. Proposing Novel MAO-B Hit Inhibitors Using Multidimensional Molecular Modeling Approaches and Application of Binary QSAR Models for Prediction of their Therapeutic Activity and Toxic Effects. ACS Chemical Neuroscience 2018
115. Serdar Durdagi*, Ismail Erol, Ramin Ekhteiari Salmas, Busecan Aksoydan, Isik Kantarcioglu. Oligomerization and Cooperativity in GPCRs from the Perspective of the Angiotensin AT1 and Dopamine D2 Receptors. Neuroscience Letters 2018
114. Ismail Erol, Busecan Aksoydan, Isik Kantarcioglu, Serdar Durdagi*. Application of Multiscale Simulation Tools on GPCRs. An Example with Angiotensin II Type I Receptor. Methods in Molecular Biology 2018
113. Serdar Durdagi*, Muhammad Tahir ul Qamar, Ramin Ekhteiari Salmas, Quratulain Tariq, Farooq Anwar, Usman Ali Ashfaq. Investigating the Molecular Mechanism of Staphylococcal DNA Gyrase Inhibitors: A Combined Ligand-based and Structure-based Resources Pipeline. Journal of Molecular Graphics and Modelling 2018
112. Mehreen Zaka, Bilal Haider Abbasi, Serdar Durdagi*. Proposing Novel TNFα Direct Inhibitor Scaffolds Using Fragment-Docking based e-Pharmacophore Modeling and Binary QSAR-based Virtual Screening Protocols Pipeline. Journal of Molecular Graphics and Modelling 2018
111. Mehreen Zaka, Bilal Haider Abbasi, Serdar Durdagi*. 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. Journal of Biomolecular Structure & Dynamics 2018
110. Adriano Mollica,Gokhan Zengin, Serdar Durdagi, Ramin Ekhteiari Salmas, Giorgia Macedonio, Azzurra Stefanucci, Marilisa Pia Dimmito, Ettore Novellino. Combinatorial Peptide Library Screening for Discovery of Diverse α-glucosidase Inhibitors Using Molecular Dynamics Simulations and Binary QSAR Models. Journal of Biomolecular Structure & Dynamics 2018
109. Ilkay Erdogan Orhan, Dariusz Jedrejek, F. Sezer Senol, Ramin Ekhteiari Salmas, Serdar Durdagi, Iwona Kowalska, Lukasz Pecio, Wieslaw Oleszek: Molecular Modeling and In vitro Approaches Towards Cholinesterase Inhibitory Effect of Some Natural Xanthohumol, Naringenin, and Acyl Phloroglucinol Derivatives. Phytomedicine 2018
108. Serdar Durdagi*, Busecan Aksoydan, Ismail Erol, Isik Kantarcioglu, Yavuz Ergun, Gulay Bulut, Melih Acar, Timucin Avsar, George Liapakis, Vlasios Karageorgos, Ramin E. Salmas, Barış Sergi, Sara Alkhatib, Gizem Turan, Berfu Nur Yigit, Kutay Cantasir, Bahar Kurt, and Turker Kilic: Integration of Multi-scale Molecular Modeling Approaches with Experiments for the in silico Guided Design and Discovery of Novel hERG-Neutral Antihypertensive Oxazalone and Imidazolone Derivatives and Analysis of Their Potential Restrictive Effects on Cell Proliferation. European Journal of Medicinal Chemistry 20182017
107. Maria Joao Rodriques, Sylwester Slusarczyk, Lukasz Pecio, Adam Matkowski, Ramin E. Salmas, Serdar Durdagi, Caterina G. Pereira, Joao C. Varela, Luisa A. Barreira, Lusia Custodio: In vitro and in silico approaches to appraise Polygonum maritimum L. as a soruce of innovative products with anti-aging potential. Industrial Crops and Products 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 20172016
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
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
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
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 20162015
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.
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.
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.
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.
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.
71. Ramin Ekhteiari Salmas, Mine Yurtsever, Serdar Durdagi*: Protein Engineering Studies for C-C Chemokine Receptor Type 2 (CCR2). Current Enzyme Inhibition 2015.
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.
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.
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.
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.2013.11.41172013
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.2011.11.36932011
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.2011.01.0162010
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/s10822-010-9371-32009
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 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 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 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 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 Bi3+ in water. Chemical Physics Letters 2005; 406(1):20-23. DOI:10.1016/j.cplett.2005.02.082
