2021
186. Berkay Selcuk, Ismail Erol, Serdar Durdagi, Ogun Adebali. "Receptor-wide Determinants of G Protein Coupling Selectivity in Aminergic GPCRs" Molecular Systems Biology 2021 (submitted)
185. Serdar Durdagi*, Timucin Avsar, Muge Didem Orhan, Muge Serhatli, Bertan Koray Balcioglu, Hasan Umit Ozturk, Alisan Kayabolen, Yuksel Cetin, Seyma Aydinlik, Tugba Bagci-Onder, Saban Tekin, Hasan Demirci, Mustafa Guzel, Atilla Akdemir, Seyma Calis, Lalehan Oktay, Ilayda Tolu, Yasar Enes Butun, Ece Erdemoglu, Alpsu Olkan, Nurettin Tokay, Şeyma Işık, Aysenur Ozcan, Elif Acar, Sehriban Buyukkilic, Yesim Yumak. "The neutralization effect of Montelukast on SARS-CoV-2 is shown by multiscale in silico simulations and combined in vitro studies" Molecular Therapy 2021 (accepted)
184. 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. Structure 2020 (accepted)
183. Musa Özil, Halis T. Balaydın, Berna Dogan, Murat Şentürk, Serdar Durdagi*. "Fast and effective 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" ACS Chemical Neuroscience 2021 (submitted)
182. Yuksel Cetin, Seyma Aydinlik, Tugce Kan, Aysen Gungor, Timucin Avsar, Serdar Durdagi*. "Review on In silico Methods, High-throughput Screening Techniques, and Cell Culture Based In Vitro Assays for SARS-CoV-2" ACS Infectious Diseases 2021 (submitted)
181. 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. New Journal of Chemistry 2020 (accepted)
180. Kader Sahin, Emin Saripinar, Serdar Durdagi*. Determination of Bioactive Pharmacophore Groups in Isatin Derivatives with Combined 4D-QSAR and Target-driven Approaches" SAR and QSAR Environmental Research (accepted)
179. Ozge Ozten, Belma Zengin Kurt, Fatih Sonmez, Berna Dogan, Serdar Durdagi*. "Synthesis, molecular docking and molecular dynamics studies of novel tacrine-carbamate derivatives as potent cholinesterase inhibitors" Bio-organic Chemistry 2021 (accepted)
178. Lalehan Oktay, Ece Erdemoğlu, İlayda Tolu, Yeşim Yumak, Ayşenur Özcan, Elif Acar, Şehriban Büyükkılıç, Alpsu Olkan, Serdar Durdağı*. Binary-QSAR guided virtual screening of FDA approved drugs and compounds in clinical investigation against SARS-CoV-2 main protease. Turk. J. Biol. 2021 (accepted)
177. Kubra Dogan, Ebru Erol, Muge Didem Orhan, Zehra Değirmenci,
Tugce Kan, Aysen Gungor, Belkis Yasa, Timucin Avsar, Yuksel
Cetin, Serdar Durdagi, Mustafa Guzel. "Ultra-Rapid Determination of the Artemisinin from Diverse Artemisia annua Extracts and Their in Silico Modeling & in Vitro Anti-Viral Studies Against SARS-CoV-2" Phytochemical Analysis 2021 (accepted)
176. Ferah Comert Onder; Kader Sahin; Murat Senturk; Serdar Durdagi*, Mehmet Ay. "Identifying Highly Effective Coumarin-based Novel Cholinesterase Inhibitors by in silico and in vitro Studies" Chemical Biology &Drug Design 2021 (submitted)
175. Ismail Erol; Ozkan Fidan; Ahmet Yetiman; Enes Kotil; Serdar Durdagi*; Fatih Ortakci. "Role of postbiotics from lactic acid bacteria against SARS-CoV-2" Probiotics and Antimicrobial Proteins 2021 (accepted)
174. Oyku Irem Balli, Serdar Durdagi, Vladimir N. Uversky, Orkid Coskuner-Weber. "Current Challenges and Limitations in the Studies of Glycoproteins: A Computational Chemist’s Perspective" Proteins: Structure, Function, and Bioinformatics 2021 (accepted)
173. Timucin Avsar, Berfu Nur Yigit, Gizem Turan, Deniz Altunsu, Seyma Calis, Bahar Kurt, Turker Kilic, M. Yavuz Ergun, Serdar Durdagi* Melih Acar. "Development of Imidazolone Based Angiotensin II Receptor Type I Inhibitor Small Molecule As A Chemotherapeutic Agent For Cell Cycle Inhibition" All Life 2021 (accepted)
172. Busecan Aksoydan, Serdar Durdagi*. "Virtual Drug Repurposing Study for the CGRPR Identifies Pentagastrin and Leuprorelin as Putative Candidates" Molecular Informatics 2021 (submitted)
171. Tuğba Güngör, Adem Özleyen, Yakup Berkay Yılmaz, Pinar Siyah, Mehmet Ay, Serdar Durdagi, Tuğba Boyuneğmez Tümer. "New Nimesulide Derivatives with Amide/Sulfonamide Moieties: Selective COX-2 Inhibiton and Antitumor Effects" European Journal of Medicinal Chemistry 2021 (accepted)
170. Kubra Dogan, Ebru Erol, Muge Didem Orhan, Zehra Değirmenci, Tugce Kan, Aysen Gungor, Belkis Yasa, Timucin Avsar, Yuksel Cetin, Serdar Durdagi, Mustafa Guzel. "Instant Determination of the Artemisinin from Various Artemisia annua L. Extracts by LC-ESI-MS/MS and Their in-Silico Modelling & in Vitro Anti-Viral Activity Studies Against SARS-CoV-2" Phytochemical Analysis 2021 (accepted)
169. Ferah Comert Onder, Serdar Durdagi, Nermin Kahraman, Tugce Nur Uslu, Hakan Kandemir, Esen Bellur Atici, Bulent Ozpolat, Mehmet Ay. "Novel inhibitors of Eukaryotic Elongation Factor 2 Kinase: In silico, synthesis, and in vitro studies" Bioorganic Chemistry 2021 (accepted)
168. 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 2021 (accepted)
167. Ferah Comert Onder, Nermin Kahraman, Esen Bellur Atici, Ali Cagir, Hakan Kandemir, Gizem Tatar, Tugba Taskin Tok, Bekir Karliga, Serdar Durdagi, Mehmet Ay and Bulent Ozpolat. "Target-driven design of a coumarinyl chalcone scaffold based novel EF2 Kinase inhibitor suppresses breast cancer growth in vivo" ACS Pharmacology & Translational Science 2021 (accepted)
166. Hind Aljanabi, Barbaros Nalbantoglu, Murat Senturk,
Serdar Durdagi*. "Drug Repurposing Effort for the Novel AChE and BChE Targets: A Combined in silico and in vitro Study"
ACS Chemical Neuroscience 2021 (submitted)
165. Ibrahim Yagiz Albayrak,
Serdar Durdagi, Sule Irem Cagayan, Lukasz Kurgan, Vladimir N. Uversky, Burak Ulver, Havvanur Dervisoglu, Mehmet Haklidir, Orkun Hasekioglu, Orkid Coskuner-Weber. “Structures of MERS-CoV Macro Domain in Aqueous Solution with Dynamics: Impacts of Simulation Techniques and CHARMM36m and AMBER99SB Force Field Parameters”
Proteins: Structure, Function, and Bioinformatics 2021
(accepted)
164. 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, 2021 (accepted)
163. Saima Ikram, 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. Journal of Molecular Graphics and Modelling, 2021 (accepted)
162. Bilgesu Onur Sucu; Elif Beyza Koc; Ozgecan Savlug Ipek; Afranur Mirat; Furkan Almas; Melike Aybala Guzel; Berna Dogan; Damla Uludag; Nihal Karakas; Serdar Durdagi, Mustafa Guzel. "Synthesis of Novel Caffeic Acid Phenethyl Ester (CAPE) Derivatives and Their Biological Activity Studies in Glioblastoma Multiforme (GBM) Cancer Cell Lines" Journal of Molecular Graphics and Modelling, 2021 (submitted)
161. Tarek Kanan, Duaa Kanan, Ibrahim Jaffar, Serdar Durdagi*. Transcription Factor NF-κB as Target for SARS-CoV-2 Drug Discovery Efforts Using Inflammation-based QSAR Screening Model. Journal of Molecular Graphics and Modelling 2021 (accepted).
160. Pinar Siyah, Sezer Akgol, Serdar Durdagi, Fatih Kocabas. "Identification of viral OTU-like plasmodium parasite proteases and development of antimalarial DUB inhibitors: An integrated in silico, in vitro, and in vivo study" Biochemical Journal 2020 (accepted)2020
159. Samman Mansoor, Gulru Kayik, Serdar Durdagi, and Ozge Sensoy. "A bivalent ligand with an affinity-generating linkermodulates dynamics within adenosine A2Areceptor-dopamine 2 receptor tetramer"Journal of Chemical Information and Modeling 2020 (submitted)
158. Busecan Aksoydan and Serdar Durdagi* "The impact of RAMP1 on ligand binding and stability of the CGRP Receptor heterodimer structure is explained by atomic simulations" Molecular Informatics 2020 (submitted)
157. Cetin Bayrak, Gulsah Yildizhan, Namik Kilinc, Serdar Durdagi, Abdullah Menzek. Synthesis and aldose reductase inhibition effects of novel N-benzyl-4-methoxyaniline derivatives. Bioorganic and Medicinal Chemistry Letters 2020 (submitted)
156. 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)
155. 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.
154. 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 2020 (accepted)
153. Serdar Durdagi*. Virtual drug repurposing study against SARS-1 CoV-2 TMPRSS2 target. Turkish Journal of Biology. 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7314512/
152. 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: A Combined In Silico and In Vitro Study. Molecular Informatics 2020 (accepted)
151. 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
149. 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/
148. 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)
147. 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).
146. 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)
145. 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
144. 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)
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)
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 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
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 2016
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.
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
