Resarch Articles
2023
196. Sukkar, B; Oktay. L.; Sahaboglu, A.; Moayedi, A.; Zenouri, S.; Al-Maghout, T.; Canto, A.; Miranda, M.; Durdagi, S.; Hosseinzadeh, Z. Inhibition of altered Orai1 channels in Muller cells protects photoreceptors in retinal degeneration. Glia. 2023, 71(11):2511-2526.
195. Haddad, S.; Oktay, L.; Erol, I.; Sahin, K.; Durdagi, S. Utilizing Heteroatom Types and Numbers from Extensive Ligand Libraries to Develop Novel hERG Blocker QSAR Models Using Machine Learning-Based Classifiers. ACS Omega 2023, 8(43):40864-40877.
2022
194. Calis, Seyma; Dogan, Berna; Durdagi, Serdar; Yapicier, Ozlem; Kilic, Turker; Turanli, Eda Tahir; Avsar, Timucin. A novel BH3 mimetic Bcl-2 inhibitor promotes autophagic cell death and reduces in vivo Glioblastoma tumor growth, Cell Death Discovery, 2022 (accepted).
193. Doğan, Nuriye; Yavuz, Sevtap Çağlar; Sahin, Kader; Orhan, Muge Didem; Kekeçmuhammed, Hüseyin; Calis, Seyma; Küpe, Fatma Öztürk; Avsar, Timucin; Akkoc, Senem; Taper, Michael; Sahin, Onur; Kilic, Turker; Durdagi, Serdar; Saripinar, Emin. Synthesis, Characterization, Biological Activity and Molecular Modeling Studies of Novel Aminoguanidine Derivatives, ChemistrySelect, 2022 (accepted).
192. Tunc, Huseyin; Durdagi, Serdar; Kotil, Seyfullah Enes. The drug-isolate-fold change-based artificial neural network model predicts the resistance profiles of the HIV-1 protease inhibitors , Journal of Chemical Information and Modeling, 2022 (submitted).
191. Erol, Ismail; Kotil, Seyfullah Enes; Ortakci, Fatih; Durdagi, Serdar. Exploring the binding capacity of lactic acid bacteria derived bacteriocins against RBD of SARS-CoV-2 Omicron variant by molecular simulations, Journal of Biomolecular Structure and Dynamics, 2022. (submitted)
190. Durdagi, Serdar; Sahaboglu, Ayse; Dogan, Berna; Erol, Ismail; Rosmus, Dennis-Dominik; Lange, Clemens; Sukkar, Basma; Bhavsar, Shefalee K.; Castor, Tatian; Sopjani, Mentor; Wieghofer, Peter; Hosseinzadeh, Zohreh. Interplay between sensitivity of hERG Kv11.1 potassium channel to Janus Kinase 2 and stimulation of retinoblastoma Y79 cells migration , Nature Communications, 2022. (submitted)
189. Sukkar, Basma; Sahaboglu, Ayse; Oktay, Lalehan; Moayedi, Aylin; Zenouri, Shima; Al-Maghout, Tamer; Cantó, Antolin; Miranda, María; Durdagi, Serdar; Hosseinzadeh, Zohreh. Altered Orai1 calcium channel activity within stressed Müller glial cells and degenerated mouse retina , Nature Communications, 2022. (submitted)
188. Dinc, Bircan; Dogan, Berna; Durdagi, Serdar. Usage of Differential Scanning Calorimetry (DSC) in High Throughput Ligand Screening Assays: A Game Changer in the Field , Biophysical Journal, 2022. (submitted)
187. Selcuk, Berkay; Erol, Ismail; Durdagi, Serdar; Adebali, Ogun. Evolutionary association of receptor-wide amino acids with G protein–coupling selectivity in aminergic GPCRs, Life Science Alliance, 5(10), 2022. DOI:10.26508/lsa.202201439
186. Onder, Ferah Comert; Siyah, Pinar; Durdagi, Serdar; Ay, Mehmet; Ozpolat, Bulent. Novel etodolac derivatives as eukaryotic elongation factor 2 kinase (eEF2K) inhibitors for targeted cancer therapy , RSC Medicinal Chemistry, 13(7), 840-849, 2022.
185. Tapera, Michael; Kekeçmuhammed, Hüseyin; Sahin, Kader; Krishna, Vagolu Siva; Lherbet, Christian; Homberset, Håvard; Chebaiki, Mélina; Tønjum, Tone; Mourey, Lionel; Zorlu, Yunus; Durdagi, Serdar; Sarıpınar, Emin. Synthesis, characterization, anti-tuberculosis activity and molecular modeling studies of thiourea derivatives bearing aminoguanidine moiety , Journal of Molecular Structure, 2022. DOI: 10.1016/j.molstruc.2022.133899
184. Aksoydan, Busecan; Durdagi, Serdar. Virtual Drug Repurposing Study for the CGRPR Identifies Pentagastrin and Leuprorelin as Putative Candidates , Journal of Molecular Graphics and Modelling, 116, 2022. DOI:10.1016/j.jmgm.2022.108254
183. Mansoor, Samman; Kayik, Gulru; Durdagi, Serdar; Sensoy, Ozge. Mechanistic insight into the impact of a bivalent ligand on the structure and dynamics of a GPCR oligomer , Computational and Structural Biotechnology Journal, 20, 925-936, 2022.
182. Durdagi, Serdar; Orhan, Muge Didem; Aksoydan, Busecan; Calis, Seyma; Dogan, Berna; Sahin, Kader; Shahraki, Aida; Iyison, Necla Birgul; Avsar, Timucin. Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS-CoV-2: A Combined in silico and in vitro Study , Molecular Informatics, 41(2), 2022. DOI: 10.1002/minf.202100062
181. Onder, Ferah Comert; Sahin, Kader; Senturk, Murat; Durdagi, Serdar; Ay, Mehmet. Identifying highly effective coumarin-based novel cholinesterase inhibitors by in silico and in vitro studies, Journal of Molecular Graphics and Modelling, 115, 2022. DOI: 10.1016/j.jmgm.2022.108210
180. Aksoydan, Busecan; Durdagi, Serdar. Molecular simulations reveal the impact of RAMP1 on ligand binding and dynamics of calcitonin gene-related peptide receptor (CGRPR) heterodimer, Computers in Biology and Medicine, 141, 2022. DOI: 10.1016/j.compbiomed.2021.105130
179. Bayrak, Cetin; Yildizhan, Gulsah; Kilinc, Namik; Durdagi, Serdar; Menzek, Abdullah. Synthesis and Aldose Reductase Inhibition Effects of Novel N-Benzyl-4-Methoxyaniline Derivatives, 19(1), 2022. DOI: 10.1002/cbdv.202100530
178. Dogan, Kubra; Erol, Ebru; Orhan, Muge Didem; Degirmenci, Zehra; Kan, Tugce; Gungor, Aysen; Yasa, Belkis; Avsar, Timucin; Cetin, Yuksel; Durdagi, Serdar; Guzel, Mustafa. Instant determination of the artemisinin from various Artemisia annua L. extracts by LC-ESI-MS/MS and their in-silico modelling and in vitro antiviral activity studies against SARS-CoV-2, Phytochemical Analysis, 33(2), 303-319, 2022.
177. Balli, Oyku Irem; Uversky, Vladimir N.; Durdagi, Serdar; Coskuner-Weber, Orkid. Challenges and limitations in the studies of glycoproteins: A computational chemist s perspective, Proteins-Structure Function and Bioinformatics, 90(2), 322-339, 2022.
176. Cetin, Yuksel; Aydinlik, Seyma; Kan, Tugce; Gungor, Aysen; Avsar, Timucin; Durdagi, Serdar. Review on In silico Methods, High-throughput Screening Techniques, and Cell Culture Based In Vitro Assays for SARS-CoV-2, Current Medicinal Chemistry, 2022. DOI: 10.2174/0929867329666220627121416.
175. Durdagi, Serdar; Avsar, Timucin; Orhan, Muge Didem; Serhatli, Muge; Balcioglu, Bertan Koray; Ozturk, Hasan Umit; Kayabolen, Alisan; Cetin, Yuksel; Aydinlik, Seyma; Bagci-Onder, Tugba; Tekin, Saban; Demirci, Hasan; Guzel, Mustafa; Akdemir, Atilla; Calis, Seyma; Oktay, Lalehan; Tolu, Ilayda; Butun, Yasar Enes; Erdemoglu, Ece; Olkan, Alpsu; Tokay, Nurettin; Isik, Seyma; Ozcan, Aysenur; Acar, Elif; Buyukkilic, Sehriban; Yumak, Yesim. The neutralization effect of montelukast on SARS-CoV-2 is shown by multiscale in silico simulations and combined in vitro studies, Molecular Therapy, 30(2), 963-974, 2022.
2021
174. Tareq, Zeyad; Durdagi, Serdar. Ab initio and comparative 3D modeling of FAM222A-encoded protein and target-driven-based virtual screening for the identification of novel therapeutics against Alzheimer s disease, Computers in Biology and Medicine, 2021 (submitted)
173. Özil, Musa; Balaydın, Halis T.; Dogan, Berna; Şentürk, Murat; Durdagi, Serdar. "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", European Journal of Medicinal Chemistry, 2021 (submitted)
172. Kanan, Duaa; Kanan, Tarek; Dogan, Berna; Erol, Ismail, Durdagi, Serdar. "A drug repurposing study for the discovery of potential USP7 inhibitors" ACS Pharmacology & Translational Science, 2021 (submitted)
171. Guven, Omur; Gul, Mehmet; Ayan, Esra; Johnson, J. Austin; Cakilkaya, Baris; Usta, Gozde; Ertem, Fatma Betul; Tokay, Nurettin; Yuksel, Busra; Gocenler, Oktay; Buyukdag, Cengizhan; Botha, Sabine; Ketawala, Gihan; Su, Zhen; Hayes, Brandon; Poitevin, Frederic; Batyuk, Alexander; Yoon, Chun Hong; Kupitz, Christopher; Durdagi, Serdar; Sierra, Raymond G.; DeMirci, Hasan. Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography , Crystals, 11(12), 2021. DOI: 10.3390/cryst11121579
170. Durdagi, Serdar; Dag, Cagdas; Dogan, Berna; Yigin, Merve; Avsar, Timucin; Buyukdag, Cengizhan; Erol, Ismail; Ertem, Fatma Betul; Calis, Seyma; Yildirim, Gunseli; Orhan, Muge D.; Guven, Omur; Aksoydan, Busecan; Destan, Ebru; Sahin, Kader; Besler, Sabri O.; Oktay, Lalehan; Shafiei, Alaleh; Tolu, Ilayda; Ayan, Esra; Yuksel, Busra; Peksen, Ayse B.; Gocenler, Oktay; Yucel, Ali D.; Can, Ozgur; Ozabrahamyan, Serena; Olkan, Alpsu; Erdemoglu, Ece; Aksit, Fulya; Tanisali, Gokhan; Yefanov, Oleksandr M.; Barty, Anton; Tolstikova, Alexandra; Ketawala, Gihan K.; Botha, Sabine; Dao, E. Han; Hayes, Brandon; Liang, Mengning; Seaberg, Matthew H.; Hunter, Mark S.; Batyuk, Alex; Mariani, Valerio; Su, Zhen; Poitevin, Frederic; Yoon, Chun Hong; Kupitz, Christopher; Sierra, Raymond G.; Snell, Edward H.; DeMirci, Hasan. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing , Structure, 29(12), 1382, 2021. DOI: 10.1016/j.str.2021.07.007
169. Oguz, Mehmet; Dogan, Berna; Durdagi, Serdar; Bhatti, Asif Ali; Karakurt, Serdar; Yilmaz, Mustafa. Investigation of supramolecular interaction of quercetin with N,N-dimethylamine-functionalized p-sulfonated calix[4,8]arenes using molecular modeling and their in vitro cytotoxic response towards selected cancer cells , New Journal of Chemistry, 45(39), 18443-18452, 2021.
168. Sahin, Kader; Saripinar, Emin; Durdagi, Serdar. Combined 4D-QSAR and target-based approaches for the determination of bioactive Isatin derivatives , SAR and QSAR in Environmental Research, 32(10), 769-792, 2021.
167. Ozten, Ozge; Kurt, Belma Zengin; Sonmez, Fatih; Dogan, Berna; Durdagi, Serdar. Synthesis, molecular docking and molecular dynamics studies of novel tacrine-carbamate derivatives as potent cholinesterase inhibitors , Bioorganic Chemistry, 115, 2021. DOI: 10.1016/j.bioorg.2021.105225
166. Oktay, Lalehan; Erdemoglu, Ece; Tolu, Ilayda; Yumak, Yesim; Ozcan, Aysenur; Acar, Elif; Buyukkilic, Sehriban; Olkan, Alpsu; Durdagi, Serdar. Binary-QSAR guided virtual screening of FDA approved drugs and compounds in clinical investigation against SARS-CoV-2 main protease , Turkish Journal of Biology, 45(4), 459, 2021. DOI: 10.3906/biy-2106-61
165. Erol, Ismail; Kotil, Seyfullah Enes; Fidan, Ozkan; Yetiman, Ahmet E.; Durdagi, Serdar; Ortakci, Fatih. In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2 , Probiotics and Antimicrobial Proteins, 2021.DOI:10.1007/s12602-021-09879-0
164. Avsar, Timucin; Yigit, Berfu Nur; Turan, Gizem; Altunsu, Deniz; Calis, Seynna; Kurt, Bahar; Kilic, Turker; Ergun, M. Yavuz; Durdagi, Serdar; Acar, Melih. Development of imidazolone based angiotensin II receptor type I inhibitor small molecule as a chemotherapeutic agent for cell cycle inhibition , All Life, 14(1), 678-690, 2021.
163. Gungor, Tugba; Ozleyen, Adem; Yilmaz, Yakup Berkay; Siyah, Pinar; Ay, Mehmet; Durdagi, Serdar; Tumer, Tugba Boyunegmez. New nimesulide derivatives with amide/sulfonamide moieties: Selective COX-2 inhibition and antitumor effects , European Journal of Medicinal Chemistry, 221, 2021. DOI: 10.1016/j.ejmech.2021.113566
162. Onder, Ferah Comert; Durdagi, Serdar; Kahraman, Nermin; Uslu, Tugce Nur; Kandemir, Hakan; Atici, Esen Bellur; Ozpolat, Bulent; Ay, Mehmet. Novel inhibitors of eukaryotic elongation factor 2 kinase: In silico, synthesis and in vitro studies , Bioorganic Chemistry, 116, 2021. DOI: 10.1016/j.bioorg.2021.105296
161. Sahin, Kader; Orhan, Muge Didem; Avsar, Timucin; Durdagi, Serdar. Hybrid In Silico and TR-FRET-Guided Discovery of Novel BCL-2 Inhibitors , ACS Pharmacology & Translational Science, 4(3), 1111-1123, 2021.
160. Onder, Ferah Comert; Kahraman, Nermin; Atici, Esen Bellur; Cagir, Ali; Kandemir, Hakan; Tatar, Gizem; Tok, Tugba Taskin; Kara, Goknur; Karliga, Bekir; Durdagi, Serdar; Ay, Mehmet; Ozpolat, Bulent. Target-Driven Design of a Coumarinyl Chalcone Scaffold Based Novel EF2 Kinase Inhibitor Suppresses Breast Cancer Growth In Vivo , ACS Pharmacology & Translational Science, 4(2), 926-940, 2021.
159. Akbayrak, Ibrahim Yagiz; Caglayan, Sule Irem; Durdagi, Serdar; Kurgan, Lukasz; Uversky, Vladimir N.; Ulver, Burak; Dervisoglu, Havvanur; Haklidir, Mehmet; Hasekioglu, Orkun; Coskuner-Weber, Orkid. Structures of MERS-CoV macro domain in aqueous solution with dynamics: Impacts of parallel tempering simulation techniques and CHARMM36m and AMBER99SB force field parameters , Proteins-Structure Function and Bioinformatics, 89(10), 1289-1299, 2021.
158. Shahraki, Aida; Isbilir, Ali; Dogan, Berna; Lohse, Martin J.; Durdagi, Serdar; Birgul-Iyison, Necla. Structural and Functional Characterization of Allatostatin Receptor Type-C of Thaumetopoea pityocampa, a Potential Target for Next-Generation Pest Control Agents , Journal of Chemical Information and Modeling, 61(2), 715-728, 2021.
157. Ikram, Saima; Ahmad, Fawad; Ahmad, Jamshaid; Durdagi, Serdar. 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, 105, 2021. DOI: 10.1016/j.jmgm.2021.107876
156. Sucu, Bilgesu Onur; Koc, Elif Beyza; Ipek, Ozgecan Savlug; Mirat, Afranur; Almas, Furkan; Guzel, Melike Aybala; Dogan, Berna; Uludag, Damla; Karakas, Nihal; Durdagi, Serdar; Guzel, Mustafa. Design and 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, 113, 2022. DOI: 10.1016/j.jmgm.2022.108160
155. Kanan, Tarek; Kanan, Duaa; Al Shardoub, Ebrahim Jaafar; Durdagi, Serdar. Transcription factor NF-kappa B as target for SARS-CoV-2 drug discovery efforts using inflammation-based QSAR screening model , Journal of Molecular Graphics and Modelling, 108, 2021. DOI: 10.1016/j.jmgm.2021.107968
154. Siyah, Pinar; Akgol, Sezer; Durdagi, Serdar; Kocabas, Fatih. Identification of first-in-class plasmodium OTU inhibitors with potent anti-malarial activity , Biochemical Journal, 478(18), 3445-3466, 2021.
153. Ikram, Saima; Ahmad, Fawad; Ahmad, Jamshaid; Durdagi, Serdar. 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, 105, 2021. DOI: 10.1016/j.jmgm.2021.107876
152. Dogan, Berna; Durdagi, Serdar. Drug Re-Positioning Studies for Novel HIV-1 Inhibitors Using Binary QSAR Models and Multi-Target-DrivenIn Silico Studies , Molecular Informatics, 40(2), 2021. DOI: 10.1002/minf.202000012
151. Sahin, Kader; Saripinar, Emin; Durdagi, Serdar. Combined 4D-QSAR and target-based approaches for the determination of bioactive Isatin derivatives , SAR and QSAR in Environmental Research, 32(10), 769-792, 2021.
150. Kanan, Duaa; Kanan, Tarek; Dogan, Berna; Orhan, Muge Didem; Avsar, Timucin; Durdagi, Serdar. An Integrated in silico Approach and in vitro Study for the Discovery of Small-Molecule USP7 Inhibitors as Potential Cancer Therapies , ChemMedChem, 16(3), 555-567, 2021.
2020
149. Sariguney, Ahmet Burak; Oktay, Lalehan; Ekici, Deniz; Durdagi, Serdar. Synthesis, carbonic anhydrase inhibitory activity, anticancer activity and molecular docking studies of new imidazolyl hydrazone derivatives , Bioorganic and Medicinal Chemistry, 2020 (submitted)
148. Ahmad, Jamshaid; Ikram, Saima; Bin Hafeez, Ahmer; Durdagi, Serdar. Physics-driven identification of clinically approved and investigation drugs against human neutrophil serine protease 4 (NSP4): A virtual drug repurposing study , Journal of Molecular Graphics and Modelling, 101, 2020. DOI: 10.1016/j.jmgm.2020.107744
147. Durdagi, Serdar. An Integrated Computational Approach for the Discovery of Ubiquitin Specific Protease 7 (USP7) Inhibitors as Potential Cancer Therapies , Biophysical Journal, 118(3), 47A-47A, 2020.
146. Durdagi, Serdar. Virtual drug repurposing study against SARS-CoV-2 TMPRSS2 target , Turkish Journal of Biology, 44(3), 185, 2020. DOI: 10.3906/biy-2005-112
145. Onder, Ferah Comert; Durdagi, Serdar; Sahin, Kader; Ozpolat, Bulent; Ay, Mehmet. Design, Synthesis, and Molecular Modeling Studies of Novel Coumarin Carboxamide Derivatives as eEF-2K Inhibitors , Journal of Chemical Information and Modeling, 60(3), 1766-1778, 2020.
144. Sahin, Kader; Durdagi, Serdar. Identifying new piperazine-based PARP1 inhibitors using text mining and integrated molecular modeling approaches , Journal of Biomolecular Structure & Dynamics, 39(2), 681-690, 2021.
143. Is, Yusuf Serhat; Aksoydan, Busecan; Senturk, Murat; Yurtsever, Mine; Durdagi, Serdar. Integrated Binary QSAR-Driven Virtual Screening and In Vitro Studies for Finding Novel hMAO-B-Selective Inhibitors , Journal of Chemical Information and Modeling, 60(8), 4047-4055, 2020.
142. Iyison, Necla Birgul; Sinmaz, Merve Gizem; Sahbaz, Burcin Duan; Shahraki, Aida; Aksoydan, Busecan; Durdagi, Serdar. In silico characterization of adipokinetic hormone receptor and screening for pesticide candidates against stick insect, Carausius morosus , Journal of Molecular Graphics and Modelling, 101, 2020. DOI: 10.1016/j.jmgm.2020.107720
141. Tutumlu, Gurbet; Dogan, Berna; Avsar, Timucin; Orhan, Muge Didem; Calis, Seyma; Durdagi, Serdar. Integrating Ligand and Target-Driven Based Virtual Screening Approaches With in vitro Human Cell Line Models and Time-Resolved Fluorescence Resonance Energy Transfer Assay to Identify Novel Hit Compounds Against BCL-2 , Frontiers in Chemistry, 8, 2020. DOI: 10.3389/fchem.2020.00167
140. Unver, Yasemin; Unluer, Dilek; Direkel, Sahin; Durdagi, Serdar. Bis benzothiophene Schiff bases: synthesis and in silico-guided biological activity studies , Turkish Journal of Chemistry, 44(4), 1164, 2020. DOI: 10.3906/kim-2004-78
139. Kurt, Belma Zengin; Durdagi, Serdar; Celebi, Gulsen; Salmas, Ramin Ekhteiari; Sonmez, Fatih. Synthesis, anticholinesterase activity and molecular modeling studies of novel carvacrol-substituted amide derivatives , Journal of Biomolecular Structure & Dynamics, 38(3), 841¬-859, 2020.
138. Kuskucu, Mert; Akyildiz, Vildan; Kulmany, Agnes; Ergun, Yavuz; Zencir, Sevil.; Zupko, Istvan; Durdagi, Serdar; Zaka, Mehreen; Sahin, Kubra; Orhan, Hilmi; Topcu, Zeki. 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, 29(2), 189-198, 2020.
137. Sahin, Kader; Durdagi, Serdar. Combined ligand and structure-based virtual screening approaches for identification of novel AChE inhibitors , Turkish Journal of Biology, 44(3), 574-588, 2020.
136. Sahaboglu, Ayse; Miranda, Maria; Canjuga, Denis; Avci-Adali, Meltem; Savytska, Natalia; Secer, Enver; Abigail Feria-Pliego, Jessica; Kayik, Gulru; Durdagi, Serdar. Drug repurposing studies of PARP inhibitors as a new therapy for inherited retinal degeneration , Cellular and Molecular Life Sciences, 77(11), 2199-2216, 2020.
135. Kulabas, Seda Savranoglu; Onder, Ferah Comert; Yilmaz, Yakup Berkay; Ozleyen, Adem; Durdagi, Serdar; Sahin, Kader; Ay, Mehmet; Tumer, Tugba Boyunegmez. In vitro and in silico studies of nitrobenzamide derivatives as potential anti-neuroinflammatory agents , Journal of Biomolecular Structure & Dynamics, 38(15), 4655-4668, 2020.
134. Ikram, Saima; Ahmad, Jamshaid; Durdagi, Serdar. Screening of FDA approved drugs for finding potential inhibitors against Granzyme B as a potent drug-repurposing target , Journal of Molecular Graphics and Modelling, 95, 2020. DOI:10.1016/j.jmgm.2019.107462
133. Oguz, Mehmet; Bhatti, Asif Ali; Dogan, Berna; Karakurt, Serdar; Durdagi, Serdar; Yilmaz, Mustafa. 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 & Dynamics, 38(13), 3801-3813, 2020.
132. Gunay, Beril Colak; Yurtsever, Mine; Durdagi, Serdar. Elucidation of interaction mechanism of hERGI potassium channel with scorpion toxins BeKm-1 and BmTx3b , Journal of Molecular Graphics and Modelling, 96, 2020. DOI:10.1016/j.jmgm.2019.107504
131. Sahin, Kader; Durdagi, Serdar. 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, 7(2): 383-404, 2020. DOI: 10.18596/jotcsa.701243
130. Sahin, Kader; Zengin Kurt, Belma; Sonmez, Fatih; Durdagi, Serdar. Novel AChE and BChE inhibitors using combined virtual screening, text mining and in vitro binding assays , Journal of Biomolecular Structure & Dynamics, 38(11), 3342-3358, 2020.
129. Turan, Raife Dilek; Albayrak, Esra; Uslu, Merve; Siyah, Pinar; Alyazici, Lamia Yazgi; Kalkan, Batuhan Mert; Aslan, Galip Servet; Yucel, Dogacan; Aksoz, Merve; Tuysuz, Emre Can; Meric, Neslihan; Durdagi, Serdar; Gulbas, Zafer; Kocabas, Fatih. Development of Small Molecule MEIS Inhibitors that modulate HSC activity , Scientific Reports, 10(1), 2020. DOI: 10.1038/s41598-020-64888-3
128. Ikram, Saima; Ahmad, Jamshaid; Rehman, Irshad-Ur; Durdagi, Serdar. Potent novel inhibitors against hepatitis C virus NS3 (HCV NS3 GT-3a) protease domain , Journal of Molecular Graphics and Modelling, 101, 2020. DOI:10.1016/j.jmgm.2020.107727
2019
127. Durdagi, Serdar; Erol, Ismail; Salmas, Ramin Ekhteiari; Aksoydan, Busecan; Kantarcioglu, Isik. Oligomerization and cooperativity in GPCRs from the perspective of the angiotensin AT1 and dopamine D2 receptors , Neuroscience Letters, 700, 2019. DOI: 10.1016/j.neulet.2018.04.028
126. Orhan, Ilkay Erdogan; Deniz, F. Sezer Senol; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Epifano, Francesco; Genovese, Salvatore; Fiorito, Serena. Combined molecular modeling and cholinesterase inhibition studies on some natural and semisynthetic O-alkylcoumarin derivatives , Bioorganic Chemistry, 84, 355-362, 2019.
125. Zaka, Mehreen; Abbasi, Bilal Haider; Durdagi, Serdar. Novel tumor necrosis factor-alpha (TNF-alpha) 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, 37(9), 2464-2476, 2019.
124. Kiriakidi, Sofia; Kolocouris, Antonios; Liapakis, George; Ikram, Saima; Durdagi, Serdar; Mavromoustakos, Thomas. Effects of Cholesterol on GPCR Function: Insights from Computational and Experimental Studies , Direct Mechanisms in Cholesterol Modulation of Protein Function, 1135, 89-103, 2019.
123. Kanan, Tarek; Kanan, Duaa; Erol, Ismail; Yazdi, Samira; Stein, Matthias; Durdagi, Serdar. Targeting the NF-kappa B/I kappa B alpha complex via fragment-based E-Pharmacophore virtual screening and binary QSAR models , Journal of Molecular Graphics and Modelling, 86, 264-277, 2019.
122. Cavdar, Huseyin; Senturk, Murat; Guney, Murat; Durdagi, Serdar; Kayik, Gulru; Supuran, Claudiu T.; Ekinci, Deniz. Inhibition of acetylcholinesterase and butyrylcholinesterase with uracil derivatives: kinetic and computational studies , Journal of Enzyme Inhibition and Medicinal Chemistry, 34(1), 429-437, 2019.
121. Mollica, Adriano; Zengin, Gokhan; Durdagi, Serdar; Salmas, Ramin Ekhteiari; Macedonio, Giorgia; Stefanucci, Azzurra; Dimmito, Marilisa Pia; Novellino, Ettore. Combinatorial peptide library screening for discovery of diverse alpha-glucosidase inhibitors using molecular dynamics simulations and binary QSAR models , Journal of Biomolecular Structure & Dynamics, 37(3), 726-740, 2019.
120. Cavusoglu, Kubra; Senturk, Murat; Durdagi, Serdar. Determination of in Vitro and in Silico Effects of Some Uracil Derivatives on Carbonic Anhydrase I Isoenzyme , ACTA Physiologica, 227, 122-122, 2019.
119. Aydin, Gulsah; Paksoy, Maide Nur; Orhan, Muge Didem; Avsar, Timucin; Yurtsever, Mine; Durdagi, Serdar. Proposing novel MDM2 inhibitors: Combined physics-driven high-throughput virtual screening and in vitro studies , Chemical Biology & Drug Design, 96(1), 684-700, 2020.
118. Sahaboglu, Ayse; Miranda, Maria; Durdagi, Serdar; Kayik, Gulru; Zrenner, Eberhart. PARP inhibitors: The protective ways on retinal degeneration , Investigative Ophthalmology & Visual Science, 60(9), 2019.
117. Onder, Ferah Comert; Ay, Mehmet; Durdagi, Serdar; Ozpolat, Bulent; Kantarcioglu, Isik. New and potent small molecule as EF2K inhibitor: A novel EF2K inhibitor , Cancer Research, 79(13_Supplement), 4787-4787, 2019.
116. Erol, Ismail; Cosut, Bunyemin; Durdagi, Serdar. Toward Understanding the Impact of Dimerization Interfaces in Angiotensin II Type 1 Receptor , Journal of Chemical Information and Modeling, 59(10), 4314-4327, 2019.
115. Durdagi, Serdar; Erol, Ismail; Dogan, Berna; Sen, Taha Berkay. Integration of Text Mining and Binary QSAR Models for Novel Anti-Hypertensive Antagonist Scaffolds , Biophysical Journal, 116(3), 478A- 478A, 2019.
114. Kurt, Belma Zengin; Dag, Aydan; Dogan, Berna; Durdagi, Serdar; Angeli, Andrea; Nocentini, Alessio; Supuran, Claudiu T.; Sonmez, Fatih. 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, 87, 838-850, 2019.
113. Ntountaniotis, Dimitrios; Andreadelis, Ioannis; Kellici, Tahsin F.; Karageorgos, Vlasios; Leonis, Georgios; Christodoulou, Eirini; Kiriakidi, Sofia; Becker-Baldus, Johanna; Stylos, Evgenios K.; Chatziathanasiadou, Maria V.; Chatzigiannis, Christos M.; Damalas, Dimitrios E.; Aksoydan, Busecan; Javornik, Uros; Valsami, Georgia; Glaubitz, Clemens; Durdagi, Serdar; Thomaidis, Nikolaos S.; Kolocouris, Antonios; Plavec, Janet; Tzakos, Andreas G.; Liapakis, George; Mavromoustakos, Thomas. Host-Guest Interactions between Candesartan and Its Prodrug Candesartan Cilexetil in Complex with 2-Hydroxypropyl-beta-cyclodextrin: On the Biological Potency for Angiotensin II Antagonism , Molecular Pharmaceutics, 16(3), 1255-1271, 2019.
112. Durdagi, Serdar; Dogan, Berna; Erol, Ismail; Kayik, Gulru; Aksoydan, Busecan. Current status of multiscale simulations on GPCRs , Current Opinion in Structural Biology, 55, 93-103, 2019.
111. Cavdar, Huseyin; Senturk, Murat; Guney, Murat; Durdagi, Serdar; Kayik, Gulru; Ekinci, Deniz. Kinetic and in silico studies of some uracil derivatives on acetylcholinesterase and butyrylcholinesterase enzymes , Journal of Enzyme Inhibition and Medicinal Chemistry, 34(1), 429-437, 2019.
2018
110. Erdemli, Mehmet Erman; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Akgul, Hasan; Demirkol, Mehmet; Aksungur, Zeynep; Selamoglu, Zeliha. Biochemical changes induced by grape seed extract and low level laser therapy administration during intraoral wound healing in rat liver: an experimental and in silico study , Journal of Biomolecular Structure & Dynamics, 36(4), 993-1008, 2018.
109. Salmas, Ramin Ekhteiari; Is, Yusuf Serhat; Durdagi, Serdar; Stein, Matthias; Yurtsever, Mine. A QM protein-ligand investigation of antipsychotic drugs with the dopamine D2 Receptor (D2R) , Journal of Biomolecular Structure & Dynamics, 36(10), 2668-2677, 2018.
108. Salmas, Ramin Ekhteiari; Durdagi, Serdar; Gulhan, Mehmet Fuat; Duruyurek, Merve; Abdullah, Huda I.; Selamoglu, Zeliha. 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, 36(3), 609-620, 2018.
107. Aksoydan, Busecan; Kantarcioglu, Isik; Erol, Ismail; Salmas, Ramin Ekhteiari; Durdagi, Serdar. Structure-based design of hERG-neutral antihypertensive oxazalone and imidazolone derivatives , Journal of Molecular Graphics and Modelling, 79, 103-117, 2018.
106. Mirza, Shaher Bano; Lee, Regina Ching Hua; Chu, Justin Jang Hann; Salmas, Ramin Ekhteiari; Mavromoustakos, Thomas; Durdagi, Serdar. 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, 79, 88-102, 2018.
105. Durdagi, Serdar; Aksoydan, Busecan; Erol, Ismail; Kantarcioglu, Isik; Ergun, Yavuz; Bulut, Gulay; Acar, Melih; Avsar, Timucin; Liapakis, George; Karageorgos, Viasios; Salmas, Ramin E.; Sergi, Baris; Alkhatib, Sara; Turan, Gizem; Yigit, Berfu Nur; Cantasir, Kutay; Kurt, Bahar; Kilic, Turker. 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, 145, 273-290, 2018.
104. Rodrigues, Maria Joao; Slusarczyk, Sylwester; Pecio, Lukasz; Matkowski, Adam; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Pereira, Catarina; Varela, Joao; Barreira, Luisa; Custodio, Luisa. In vitro and in silico approaches to appraise Polygonum maritimum. L. as a source of innovative products with anti-ageing potential , Industrial Crops and Products, 111, 391-399, 2018.
103. Salmas, Ramin Ekhteiari; Seeman, Philip; Stein, Matthias; Durdagi, Serdar. Structural Investigation of the Dopamine-2 Receptor Agonist Bromocriptine Binding to Dimeric D2(High)R and D2(Low)R States , Journal of Chemical Information and Modeling, 58(4), 826-836, 2018.
102. Is, Yusuf Serhat; Durdagi, Serdar; Aksoydan, Busecan; Yurtsever, Mine. Proposing Novel MAO-B Hit Inhibitors Using Multidimensional Molecular Modeling Approaches and Application of Binary QSAR Models for Prediction of Their Therapeutic Activity, Pharmacokinetic and Toxicity Properties , ACS Chemical Neuroscience, 9(7), 1768-1782, 2018.
101. Erol, Ismail; Aksoydan, Busecan; Kantarcioglu, Isik; Durdagi, Serdar. Application of Multiscale Simulation Tools on GPCRs. An Example with Angiotensin II Type 1 Receptor , Rational Drug Design Methods and Protocols, 1824, 431-448, 2018.
100. Durdagi, Serdar; ul Qamar, Muhammad Tahir; Salmas, Ramin Ekhteiari; Tariq, Quratulain; Anwar, Farooq; Ashfaq, Usman Ali. Investigating the molecular mechanism of staphylococcal DNA gyrase inhibitors: A combined ligand-based and structure-based resources pipeline , Journal of Molecular Graphics and Modelling, 85, 122-129, 2018.
99. Zaka, Mehreen; Abbasi, Bilal Haider; Durdagi, Serdar. Proposing novel TNF alpha direct inhibitor Scaffolds using fragment-docking based e-pharmacophore modeling and binary QSAR-based virtual screening protocols pipeline , Journal of Molecular Graphics and Modelling, 85, 111-121, 2018.
98. Orhan, Ilkay Erdogan; Jedrejek, Dariusz; Senol, F. Sezer; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Kowalska, Iwona; Pecio, Lukasz; Oleszek, Wieslaw. Molecular modeling and in vitro approaches towards cholinesterase inhibitory effect of some natural xanthohumol, naringenin, and acyl phloroglucinol derivatives , Phytomedicine, 42, 25-33, 2018.
97. Durdagi, Serdar; Aksoydan, Busecan; Erol, Ismail; Kantarcioglu, Isik; Ergun, Yavuz; Bulut, Gulay; Acar, Melih; Avsar, Timucin; Liapakis, George; Karageorgos, Viasios; Salmas, Ramin E.; Sergi, Baris; Alkhatib, Sara; Turan, Gizem; Yigit, Berfu Nur; Cantasir, Kutay; Kurt, Bahar; Kilic, Turker. 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, 145, 273-290, 2018.
2017
96. Kayik, Gulru; Tuzun, Nurcan S.; Durdagi, Serdar. In silico design of novel hERG-neutral sildenafil-like PDE5 inhibitors , Journal of Biomolecular Structure & Dynamics, 35(13), 2830-2852, 2017.
95. Salmas, Ramin Ekhteiari; Stein, Matthias; Yurtsever, Mine; Seeman, Philip; Erol, Ismail; Mestanoglu, Mert; Durdagi, Serdar. The signaling pathway of dopamine D2 receptor (D2R) activation using normal mode analysis (NMA) and the construction of pharmacophore models for D2R ligands , Journal of Biomolecular Structure & Dynamics, 35(9), 2040-2048, 2017.
94. Salmas, Ramin Ekhteiari; Yurtsever, Mine; Durdagi, Serdar. Atomistic molecular dynamics simulations of typical and atypical antipsychotic drugs at the dopamine D2 receptor (D2R) elucidates their inhibition mechanism , Journal of Biomolecular Structure & Dynamics, 35(4), 738-754, 2017.
93. Salmas, Ramin Ekhteiari; Unlu, Ayhan; Bektas, Muhammet; Yurtsever, Mine; Mestanoglu, Mert; Durdagi, Serdar. Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: combination of in silico and in vitro studies , Journal of Biomolecular Structure & Dynamics, 35(9), 1899-1915, 2017.
92. Salmas, Ramin Ekhteiari; Seeman, Philip; Aksoydan, Busecan; Stein, Matthias; Yurtsever, Mine; Durdagi, Serdar. Biological Insights of the Dopaminergic Stabilizer ACR16 at the Binding Pocket of Dopamine D2 Receptor , ACS Chemical Neuroscience, 8(4), 826-836, 2017.
91. Shityakov, Sergey; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Roewer, Norbert; Foerster, Carola; Broscheit, Jens. Solubility profiles, hydration and desolvation of curcumin complexed with gamma-cyclodextrin and hydroxypropyl-gamma-cyclodextrin , Journal of Molecular Structure, 1134, 91-98, 2017.
90. Kayik, Gulru; Tuzun, Nurcan S.; Durdagi, Serdar. Investigation of PDE5/PDE6 and PDE5/PDE11 selective potent tadalafil-like PDE5 inhibitors using combination of molecular modeling approaches, molecular fingerprint-based virtual screening protocols and structure-based pharmacophore development , Journal of Enzyme Inhibition and Medicinal Chemistry, 32(1), 311-330, 2017.
89. Kurt, Belma Zengin; Gazioglu, Isil; Dag, Aydan; Salmas, Ramin Ekhteiari; Kayik, Gulru; Durdagi, Serdar; Sonmez, Fatih. Synthesis, anticholinesterase activity and molecular modeling study of novel carbamate-substituted thymol/carvacrol derivatives , Bioorganic & Medicinal Chemistry, 25(4), 1352-1363, 2017.
88. Kayik, Gulru; Tuzun, Nurcan S.; Durdagi, Serdar. Structural investigation of vesnarinone at the pore domains of open and open-inactivated states of hERG1 K+ channel , Journal of Molecular Graphics and Modelling, 77, 399-412, 2017.
87. Akincioglu, Akin; Kocaman, Ebutalib; Akincioglu, Hulya; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Gulcin, Ilhami; Supuran, Claudiu T.; Goksu, Suleyman. The synthesis of novel sulfamides derived from beta-benzylphenethylamines as acetylcholinesterase, butyrylcholinesterase and carbonic anhydrase enzymes inhibitors , Bioorganic Chemistry, 74, 238-250, 2017.
86. Mirza, Shaher Bano; Salmas, Ramin Ekhteiari; Fatmi, M. Qaiser; Durdagi, Serdar. 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, 32(1), 84-98, 2017.
85. Kurt, Belma Zengin; Sonmez, Fatih; Durdagi, Serdar; Aksoydan, Busecan; Salmas, Ramin Ekhteiari; Angeli, Andrea; Kucukislamoglu, Mustafa; Supuran, Claudiu T. 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, 32(1), 1042-1052, 2017.
84. Salmas, Ramin Ekhteiari; Gulhan, Mehmet Fuat; Durdagi, Serdar; Sahna, Engin; Abdullah, Huda I.; Selamoglu, Zeliha. Effects of propolis, caffeic acid phenethyl ester, and pollen on renal injury in hypertensive rat: An experimental and theoretical approach , Cell Biochemistry and Function, 35(6), 304-314, 2017.
83. Aslancan, Reyhan; Aksoydan, Busecan; Kantarcioglu, Isik; Erol, Ismail; Salmas, Ramin Ekhteiari; Durdagi, Serdar. Investigation of chemical interactions of small peptides and vitamin substances at the developed dopamine D2 receptor models , European Psychiatry, 41(S1), S366-S366, 2017. 82. Durdagi, Serdar; Erol, Ismail; Salmas, Ramin Ekhteiari; Patterson, Matthew; Noskov, Sergei Y. First universal pharmacophore model for hERG1 K+ channel activators: acthER , Journal of Molecular Graphics and Modelling, 74, 153-170, 2017.
81. Salmas, Ramin Ekhteiari; Seeman, Philip; Aksoydan, Busecan; Erol, Ismail; Kantarcioglu, Isik; Stein, Matthias; Yurtsever, Mine; Durdagi, Serdar. Analysis of the Glutamate Agonist LY404,039 Binding to Nonstatic Dopamine Receptor D2 Dimer Structures and Consensus Docking , ACS Chemical Neuroscience, 8(6), 1404-1415, 2017.
80. Bukiya, Anna N.; Durdagi, Serdar; Noskov, Sergei; Rosenhouse-Dantsker, Avia. Cholesterol up-regulates neuronal G protein-gated inwardly rectifying potassium (GIRK) channel activity in the hippocampus , Journal of Biological Chemistry, 292(15), 6135-6147, 2017.
79. Erol, Ismail; Aksoydan, Busecan; Kantarcioglu, Isik; Salmas, Ramin E.; Durdagi, Serdar. 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, 74, 193-202, 2017.
2016
78. Salmas, Ramin Ekhteiari; Mestanoglu, Mert; Unlu, Ayhan; Yurtsever, Mine; Durdagi, Serdar. Mutated form (G52E) of inactive diphtheria toxin CRM197: molecular simulations clearly display effect of the mutation to NAD binding , Journal of Biomolecular Structure & Dynamics, 34(11), 2462-2468, 2016.
77. Durdagi, Serdar; Korkmaz, Neslihan; Isik, Semra; Vullo, Daniela; Astley, Demet; Ekinci, Deniz; Salmas, Ramin E.; Senturk, Murat; Supuran, Claudiu T. Kinetic and docking studies of cytosolic/tumor-associated carbonic anhydrase isozymes I, II and IX with some hydroxylic compounds , Journal of Enzyme Inhibition and Medicinal Chemistry, 31(6), 1214-1220, 2016.
76. Salmas, Ramin Ekhteiari; Senturk, Murat; Yurtsever, Mine; Durdagi, Serdar. 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, 31(3), 425-433, 2016.
75. Salmas, Ramin Ekhteiari; Mestanoglu, Mert; Durdagi, Serdar; Senturk, Murat; Kaya, A. Afsin; Kaya, Elif Celenk. Kinetic and in silico studies of hydroxy-based inhibitors of carbonic anhydrase isoforms I and II , Journal of Enzyme Inhibition and Medicinal Chemistry, 31(1), 31-37, 2016.
74. Kellici, Tahsin F.; Ntountaniotis, Dimitrios; Kritsi, Eftichia; Zervou, Maria; Zoumpoulakis, Panagiotis; Potamitis, Constantinos; Durdagi, Serdar; Salmas, Ramin Ekhteiari; Ergun, Gizem; Gokdemir, Ebru; Halabalaki, Maria; Gerothanassis, Ioannis P.; Liapakis, George; Tzakos, Andreas G.; Mavromoustakos, Thomas. Leveraging NMR and X-ray Data of the Free Ligands to Build Better Drugs Targeting Angiotensin II Type 1 G-Protein Coupled Receptor , Current Medicinal Chemistry, 23(1), 36-59, 2016.
73. Salmas, Ramin Ekhteiari; Unlu, Ayhan; Yurtsever, Mine; Noskov, Sergei Y.; Durdagi, Serdar. 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, 31(1), 112-120, 2016.
72. Kocak, Ramazan; Akin, Esra Turan; Kalin, Pinar; Talaz, Oktay; Saracoglu, Nurullah; Dastan, Arif; Gulcin, Ilhami; Durdagi, Serdar. Synthesis of Some Novel Norbornene-Fused Pyridazines as Potent Inhibitors of Carbonic Anhydrase and Acetylcholinesterase , Journal of Heterocyclic Chemistry, 53(6), 2049-2056, 2016.
71. Shityakov, Sergey; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Salvador, Ellaine; Papai, Katalin; Josefa Yanez-Gascon, Maria; Perez-Sanchez, Horacio; Puskas, Istvan; Roewer, Norbert; Foerster, Carola; Broscheit, Jens-Albert. 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, 56(10), 1914-1922, 2016.
70. Wang, Yibo; Guo, Jiqing; Perissinotti, Laura L.; Lees-Miller, James; Teng, Guoqi; Durdagi, Serdar; Duff, Henry J.; Noskov, Sergei Yu. Role of the pH in state-dependent blockade of hERG currents , Scientific Reports, 6, 2016. DOI:10.1038/srep32536
69. Durdagi, Serdar; Senturk, Murat; Guney, Murat; Ekinci, Deniz; Aksoydan, Busecan; Erol, Ismail; Kantarcioglu, Isik; Cavdar, Huseyin. 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, 283, 106-106, 2016.
68. Ozgeris, Bunyamin; Goksu, Suleyman; Kose, Leyla Polat; Gulcin, Ilhami; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Tumer, Ferhan; Supuran, Claudiu T. Acetylcholinesterase and carbonic anhydrase inhibitory properties of novel urea and sulfamide derivatives incorporating dopaminergic 2-aminotetralin scaffolds , Bioorganic & Medicinal Chemistry, 24(10), 2318-2329, 2016.
67. Mirza, Shaher Bano; Salmas, Ramin Ekhteiari; Fatmi, M. Qaiser; Durdagi, Serdar. Virtual screening of eighteen million compounds against dengue virus: Combined molecular docking and molecular dynamics simulations study , Journal of Molecular Graphics and Modelling, 66, 99-107, 2016.
66. Sahin, Ali; Senturk, Murat; Salmas, Ramin E.; Durdagi, Serdar; Ayan, Arif; Karagolge, Ali; Mestanoglu, Mert. 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, 31, 141-147, 2016.
65. Durdagi, Serdar; Salmas, Ramin Ekhteiari; Stein, Matthias; Yurtsever, Mine; Seeman, Philip. Binding Interactions of Dopamine and Apomorphine in D2High and D2Low States of Human Dopamine D2 Receptor Using Computational and Experimental Techniques , ACS Chemical Neuroscience, 7(2), 185-195, 2016.
64. Salmas, Ramin Ekhteiari; Yurtsever, Mine; Durdagi, Serdar. Protein Engineering Studies for CC Chemokine Receptor Type 2 (CCR2) , Current Enzyme Inhibition, 12(2), 110-114, 2016.
2015
63. Isik, Semra; Vullo, Daniela; Durdagi, Serdar; Ekinci, Deniz; Senturk, Murat; Cetin, Ahmet; Senturk, Esra; Supuran, Claudiu T. Interaction of carbonic anhydrase isozymes I, II, and IX with some pyridine and phenol hydrazinecarbothioamide derivatives , Bioorganic & Medicinal Chemistry Letters, 25(23), 5636-5641, 2015.
62. Fidan, Ismail; Salmas, Ramin Ekhteiari; Arslan, Mehmet; Senturk, Murat; Durdagi, Serdar; Ekinci, Deniz; Senturk, Esra; Cosgun, Sedat; Supuran, Claudiu T. Carbonic anhydrase inhibitors: Design, synthesis, kinetic, docking and molecular dynamics analysis of novel glycine and phenylalanine sulfonamide derivatives , Bioorganic & Medicinal Chemistry, 23(23), 7353-7358, 2015.
61. Strom, T. Amanda; Durdagi, Serdar; Ersoz, Suha Salih; Salmas, Ramin Ekhteiari; Supuran, Claudiu T.; Barron, Andrew R. Fullerene-based inhibitors of HIV-1 protease , Journal of Peptide Science, 21(12), 862-870, 2015.
60. Salmas, Ramin Ekhteiari; Mestanoglu, Mert; Yurtsever, Mine; Noskov, Sergei Y.; Durdagi, Serdar. Molecular Simulations of Solved Co-crystallized X-Ray Structures Identify Action Mechanisms of PDE delta Inhibitors , Biophysical Journal, 109(6), 1163-1168, 2015.
59. Salmas, Ramin Ekhteiari; Yurtsever, Mine; Durdagi, Serdar. Investigation of Inhibition Mechanism of Chemokine Receptor CCR5 by Micro-second Molecular Dynamics Simulations , Scientific Reports, 5, 2015. DOI: 10.1038/srep13180
58. Yazdi, Samira; Durdagi, Serdar; Naumann, Michael; Stein, Matthias. Structural modeling of the N-terminal signal-receiving domain of I kappa B alpha , Frontiers in Molecular Biosciences, 2, 2015. DOI: 10.3389/fmolb.2015.00032
57. Akincioglu, Akin; Akincioglu, Hulya; Gulcin, Ilhami; Durdagi, Serdar; Supuran, Claudiu T.; Goksu, Suleyman. Discovery of potent carbonic anhydrase and acetylcholine esterase inhibitors: Novel sulfamoylcarbamates and sulfamides derived from acetophenones , Bioorganic & Medicinal Chemistry, 23(13), 3592-3602, 2015.
56. Guo, Jiqing; Cheng, Yen May; Lees-Miller, James P.; Perissinotti, Laura L.; Claydon, Tom W.; Hull, Christina M.; Thouta, Samrat; Roach, Daniel E.; Durdagi, Serdar; Noskov, Sergei Y.; Duff, Henry J. NS1643 Interacts around L529 of hERG to Alter Voltage Sensor Movement on the Path to Activation , Biophysical Journal, 108(6), 1400-1413, 2015.
55. Salmas, Ramin Ekhteiari; Yurtsever, Mine; Stein, Matthias; Durdagi, Serdar. Modeling and protein engineering studies of active and inactive states of human dopamine D2 receptor (D2R) and investigation of drug/receptor interactions , Molecular Diversity, 19(2), 321-332, 2015.
54. Iqbal, Jamshed; Al-Rashida, Mariya; Durdagi, Serdar; Alterio, Vincenzo; Di Fiore, Anna. Recent developments of carbonic anhydrase inhibitors as potential drugs , BioMed Research International, 2015, 2015. DOI:10.1155/2015/174178
2014
53. Zervou, Maria; Cournia, Zoe; Potamitis, Constantinos; Patargias, George; Durdagi, Serdar; Grdadolnik, Simona Golic; Mavromoustakos, Thomas. Insights into the molecular basis of action of the AT(1) antagonist losartan using a combined NMR spectroscopy and computational approach , Biochimica et Biophysica Acta-Biomembranes, 1838(3), 1031-1046, 2014.
52. Durdagi, Serdar; Scozzafava, Gabriele; Vullo, Daniela; Sahin, Huseyin; Kolayli, Sevgi; Supuran, Claudiu T. Inhibition of mammalian carbonic anhydrases I-XIV with grayanotoxin III: solution and in silico studies , Journal of Enzyme Inhibition and Medicinal Chemistry, 29(4), 469-475, 2014.
51. Kufareva, Irina; Katritch, Vsevolod; Stevens, Raymond C.; Abagyan, Ruben; Biggin, Phil; Kim, Minsup; Park, Kichul; Jung, Sang Won; Cho, Art E.; Sands, Zara A.; Pitt, William R.; Shi, Jiye; Ostopovici-Halip, Liliana; Bologa, Cristian G.; Norn, Christoffer; Brylinski, Michal; Skolnick, Jeffrey; Keranen, Henrik; Lenselink, Bart E.; van Westen, Gerard; Overington, John P.; de Teran, Hugo Gutierrez; Isberg, Vignir; Fidom, Kimberley M.; Lehto, Thomas M.; Gloriam, David E.; Ghosh, Anirban; Sonavane, Uddhavesh; Joshi, Rajendra; Xia, Jie; Hsieh, Jui-Hua; Zhang, Liangren; Wang, Xiang Simon; Vogel, Horst; Yuan, Shuguang; Feng, X.; Chen, M.; Ambia, J.; Barth, P.; Gageat, Cedric; Stepniewski, Michal; Xhaard, Henri; Kelm, Sebastian; Pitt, William R.; Sands, Zara A.; Shi, Jiye; Larsen, Adrien; Li, Hubert; Wagner, Jeffrey; Bhattacharya, Supriyo; Vaidehi, Nagarajan; Kanou, Kazuhiko; Cvicek, Vaclav; Kim, Soo-Kyung; Trzaskowski, Bartosz; Goddard, William A., III; Abrol, Ravinder; Selvam, Balaji; Tikhonova, Irina G.; Cuzzolin, Alberto; Sabbadin, Davide; Ciancetta, Antonella; Moro, Stefano; Freyd, Thibaud; Gabrielsen, Mari; Kristiansen, Kurt; Sylte, Ingebrigt; Gaffney, Kevin J.; Petasis, Nicos A.; Latek, Dorota; Bajda, Marek; Mlynarczyk, Krzysztof; Filipek, Slawomir; Lopez, Laura; Kuiper, Michael; Beuming, Thijs; Perez-Aguilar, Jose Manuel; Wang, Ray Yu-Ruei; Park, Hahnbeom; Greisen, Per, Jr.; Song, Yifan; DiMaio, Frank; Baker, David; Shin, Woong-Hee; Heo, Lim; Lee, Gyu Rie; Seok, Chaok; Yang, Jianyi; Zhang, Yang; Ponassi, Marco; Rosano, Camillo; Cheremovskiy, Georgy; Grudinin, Sergei; Chaudhari, Rajan; Heim, Andrew J.; Li, Zhijun; Lv, Qiang; Grigorov, Martin G.; Hu, Xin; Sun, Hongmao; Shen, Min; Southall, Noel; Jadhav, Ajit; Rodriguez, David; Ranganathan, Anirudh; Carlsson, Jens; Najmanovich, Rafael; Durdagi, Serdar; de March, Claire; Diharce, Julien; Golebiowski, Jerome; Antonczak, Serge; Fiorucci, Sebastien; Nguyen, Elizabeth; Meiler, Jens; Gutcaits, Aleksandrs; Marti-Solano, Maria; Pastor, Manuel; Selent, Jana. Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges , Structure, 22(8), 1120-1139, 2014.
50. Guo, Jiqing; Durdagi, Serdar; Changalov, Mohamed; Perissinotti, Laura L.; Hargreaves, Jason M.; Back, Thomas G.; Noskov, Sergei Y.; Duff, Henry J. Structure Driven Design of Novel Human Ether-A-Go-Go-Related-Gene Channel (hERG1) Activators , Plos One, 9(9), 2014. DOI: 10.1371/journal.pone.0105553
49. Leonis, Georgios; Avramopoulos, Aggelos; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Yurtsever, Mine; Papadopoulos, Manthos G. Elucidation of Conformational States, Dynamics, and Mechanism of Binding in Human kappa-Opioid Receptor Complexes , Journal of Chemical Information and Modeling, 54(8), 2294-2308, 2014.
48. Durdagi, Serdar; Randall, Trevor; Duff, Henry J.; Chamberlin, Adam; Noskov, Sergei Y. Rehabilitating drug-induced long-QT promoters: In-silico design of hERG-neutral cisapride analogues with retained pharmacological activity , BMC Pharmacology & Toxicology, 15, 2014. DOI: 10.1186/2050-6511-15-14
47. Buturak, Birce; Durdagi, Serdar; Noskov, Sergei Yu; Ildeniz, A. Tugba Ozal. Designing of multi-targeted molecules using combination of molecular screening and in silico drug cardiotoxicity prediction approaches , Journal of Molecular Graphics and Modelling, 50, 16-34, 2014.
46. Durdagi, Serdar; Patterson, Matthew; Noskov, Sergei Y. Development and Validation Studies of Universal Pharmacophore Models for hERG Channel Openers , Biophysical Journal, 106(2),15A-15A, 2014.
45. Goksu, Suleyman; Naderi, Ali; Akbaba, Yusuf; Kalin, Pinar; Akincioglu, Akin; Gulcin, Ilhami; Durdagi, Serdar; Salmas, Ramin Ekhteiari. Carbonic anhydrase inhibitory properties of novel benzylsulfamides using molecular modeling and experimental studies , Bioorganic Chemistry, 56, 75-82, 2014.
44. Rosenhouse-Dantsker, Avia; Noskov, Sergei Y.; Durdagi, Serdar. Identification of Novel Cholesterol Binding Regions in the Transmembrane Domain of Kir2. 1. , Biophysical Journal, 106(2), 747A-747A, 2014.
2013
43. Tzoupis, Haralambos; Avramopoulos, Aggelos; Reis, Heribert; Leonis, Georgios; Durdagi, Serdar; Mavromoustakos, Thomas; Megariotis, Grigorios; Papadopoulos, Manthos G. Theoretical Studies of Interactions in Nanomaterials and Biological Systems , Towards Efficient Designing of Safe Nanomaterials: Innovative Merge of Computational Approaches and Experimental Techniques, 25, 148-185, 2013.
42. Talaz, Oktay; Cavdar, Huseyin; Durdagi, Serdar; Azak, Hacer; Ekinci, Deniz. Synthesis of 1,4-bis(indolin-1-ylmethyl)benzene derivatives and their structure-activity relationships for the interaction of human carbonic anhydrase isoforms I and II , Bioorganic & Medicinal Chemistry, 21(6), 1477-1482, 2013.
41. Ekinci, Deniz; Fidan, Ismail; Durdagi, Serdar; Kaban, Seniz; Supuran, Claudiu T. Kinetic and in silico analysis of thiazolidin-based inhibitors of alpha-carbonic anhydrase isoenzymes , Journal of Enzyme Inhibition and Medicinal Chemistry, 28(2), 370-374, 2013.
40. Kritsi, Eftichia; Potamitis, Constantinos; Durdagi, Serdar; Zoumpoulakis, Panagiotis; Grdadolnik, Simona Golic; Mavromoustakos, Thomas. Molecular insights into the AT(1) antagonism based on biophysical and in silico studies of telmisartan , Medicinal Chemistry Research, 22(10), 4842-4857, 2013.
39. Rosenhouse-Dantsker, Avia; Noskov, Sergei; Durdagi, Serdar; Logothetis, Diomedes E.; Levitan, Irena. Identification of Novel Cholesterol-binding Regions in Kir2 Channels , Journal of Biological Chemistry, 288(43), 31154-31164, 2013.
38. Mavromoustakos, Thomas; Agelis, George; Durdagi, Serdar. AT1 antagonists: a patent review (2008-2012) , Expert Opinion on Therapeutic Patents, 23(11), 1483-1494, 2013.
37. Durdagi, Serdar; Randal, Trevor; Duff, Henry J.; Noskov, Sergei Y. Rehabilitation studies for withdrawn drugs from the market: derivation of non-hERG1 channel blocker cisapride analogues using multi-faceted approaches , Biophysical Journal, 104(2), 266A-266A, 2013.
2012
36. Durdagi, Serdar; Papadopoulos, Manthos G.; Mavromoustakos, Thomas. An effort to discover the preferred conformation of the potent AMG3 cannabinoid analog when reaching the active sites of the cannabinoid receptors , European Journal of Medicinal Chemistry, 47, 44-51, 2012.
35. Balaydin, Halis Turker; Durdagi, Serdar; Ekinci, Deniz; Senturk, Murat; Goksu, Suleyman; Menzek, Abdullah. 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, 27(4), 467-475, 2012.
34. Durdagi, Serdar; Deshpande, Sumukh; Duff, Henry J.; Noskov, Sergei Y. Modeling of Open, Closed, and Open-Inactivated States of the hERG1 Channel: Structural Mechanisms of the State-Dependent Drug Binding , Journal of Chemical Information and Modeling, 52(10), 2760- 2774, 2012.
33. Agelis, George; Resvani, Amalia; Durdagi, Serdar; Spyridaki, Katerina; Tumova, Tereza; Slaninova, Jitina; Giannopoulos, Panagiotis; Vlahakos, Demetrios; Liapakis, George; Mavromoustakos, Thomas; Matsoukas, John. 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, 55, 358-374, 2012.
32. Durdagi, Serdar; Vullo, Daniela; Pan, Peiwen; Kahkonen, Niklas; Maatta, Juha A.; Hytonen, Vesa P.; Scozzafava, Andrea; Parkkila, Seppo; Supuran, Claudiu T. Protein-Protein Interactions: Inhibition of Mammalian Carbonic Anhydrases I-XV by the Murine Inhibitor of Carbonic Anhydrase and Other Members of the Transferrin Family , Journal of Medicinal Chemistry, 55(11), 5529-5535, 2012.
31. Durdagi, Serdar; Guo, Jiqing; Lees-Miller, James P.; Noskov, Sergei Y.; Duff, Henry J. 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, 342(2), 441-452, 2012.
30. Ekinci, Deniz; Cavdar, Huseyin; Durdagi, Serdar; Talaz, Oktay; Senturk, Murat; Supuran, Claudiu T. Structure-activity relationships for the interaction of 5,10-dihydroindeno[1,2-b] indole derivatives with human and bovine carbonic anhydrase isoforms I, II, III, IV and VI , European Journal of Medicinal Chemistry, 49, 68-73, 2012.
29. Agelis, George; Resvani, Amelia; Durdagi, Serdar; Tumova, Tereza; Slaninov, J.; Giannopoulos, Phillip; Spyridaki, Katerina; Liapakis, George; Vlahakos, Demetrios; Mavromoustakos, Thomas; Matsoukas, John. A Concise Synthesis, Docking Studies and Biological Evaluation of N-substituted 5-Butylimidazole Analogues as Potent Angiotensin II Receptor Blockers , Journal of Peptide Science, 18, S116-S116, 2012.
28. Durdagi, Serdar; Deshpande, Sumukh; Duff, Henry; Noskov, Sergei. Development of atomistic models for closed, open and open-inactivated states of hERG1 channel using rosetta protein modeling suite and molecular dynamics simulations , Biophysical Journal, 102(3), 679A-679A, 2012.
2011
27. Tzoupis, Haralambos; Leonis, Georgios; Durdagi, Serdar; Mouchlis, Varnavas; Mavromoustakos, Thomas; Papadopoulos, Manthos G. Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations , Journal of Computer-Aided Molecular Design, 25(10), 959-976, 2011.
26. Cakmak, Resit; Durdagi, Serdar; Ekinci, Deniz; Senturk, Murat; Topal, Giray. Design, synthesis and biological evaluation of novel nitroaromatic compounds as potent glutathione reductase inhibitors , Bioorganic & Medicinal Chemistry Letters, 21(18), 5398-5402, 2011.
25. Koukoulitsa, Catherine; Durdagi, Serdar; Siapi, Eleni; Villalonga-Barber, Carolina; Alexi, Xanthippi; Steele, Barry R.; Micha-Screttas, Maria; Alexis, Michael N.; Tsantili-Kakoulidou, Anna; Mavromoustakos, Thomas. 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 , European Biophysics Journal with Biophysics Letters, 40(7), 865-875, 2011.
24. Durdagi, Serdar; Zhao, Chunfeng; Cuervo, Javier Eduardo; Noskov, Sergei Yu. Atomistic Models for Free Energy Evaluation of Drug Binding to Membrane Proteins , Current Medicinal Chemistry, 18(17), 2601-2611, 2011.
23. Mavromoustakos, Thomas.; Durdagi, Serdar; Koukoulitsa, Cathrine; Simcic, Mihael; Papadopoulos, Manthos G.; Hodoscek, Milan; Grdadolnik, Simona Golic. Strategies in the Rational Drug Design , Current Medicinal Chemistry, 18(17), 2517-2530, 2011.
22. Durdagi, Serdar and Noskov, Sergei Y. Mechanism of K+/Na+ selectivity in potassium channels from the perspective of the non-selective bacterial channel NaK , Channels, 5(3), 198-200, 2011.
21. Mavromoustakos, Thomas; Chatzigeorgiou, Petros; Koukoulitsa, Catherine; Durdagi, Serdar. Partial Interdigitation of Lipid Bilayers , International Journal of Quantum Chemistry, 111(6), 1172-1183, 2011.
20. Durdagi, Serdar; Duff, Henry J.; Noskov, Sergei Yu. Combined Receptor and Ligand-Based Approach to the Universal Pharmacophore Model Development for Studies of Drug Blockade to the hERG1 Pore Domain , Journal of Chemical Information and Modeling, 51(2), 463-474, 2011.
19. Durdagi, Serdar; Senturk, Murat; Ekinci, Deniz; Balaydin, Halis Turker; Goksu, Suleyman; Kufrevioglu, O. Irfan; Innocenti, Alessio; Scozzafava, Andrea; Supuran, Claudiu T. Kinetic and docking studies of phenol-based inhibitors of carbonic anhydrase isoforms I, II, IX and XII evidence a new binding mode within the enzyme active site , Bioorganic & Medicinal Chemistry, 19(4), 1381-1389, 2011.
18. Durdagi, Serdar; Noskov, Sergei Y. Consistency of constructed hERG1 pore domain and pharmacophore models: A 3D-QSAR, molecular docking, and pharmacophore modeling study , Biochemistry and Cell Biology-Biochimie et Biologie Cellulaire, 89(2), 266-267, 2011.
2010
17. Politi, Aggeliki; Durdagi, Serdar; Moutevelis-Minakakis, Panagiota; Kokotos, George; Mavromoustakos, Thomas. Development of accurate binding affinity predictions of novel renin inhibitors through molecular docking studies , Journal of Molecular Graphics and Modelling, 29(3), 425-435, 2010.
16. Subbotina, Julia; Yarov-Yarovoy, Vladimir; Lees-Miller, James; Durdagi, Serdar; Guo, Jiqing; Duff, Henry J.; Noskov, Sergei Yu. Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations , Proteins-Structure Function and Bioinformatics, 78(14), 2922-2934, 2010.
15. Durdagi, Serdar; Subbotina, Julia; Lees-Miller, James; Guo, Jiqing; Duff, Henry J.; Noskov, Sergei Y. Insights into the Molecular Mechanism of hERG1 Channel Activation and Blockade by Drugs , Current Medicinal Chemistry, 17(30), 3514-3532, 2010.
14. Agelis, George; Roumelioti, Panagiota; Resvani, Amalia; Durdagi, Serdar; Androutsou, Maria-Eleni; Kelaidonis, Konstantinos; Vlahakos, Demetrios; Mavromoustakos, Thomas; Matsoukas, John. 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, 24(9), 749-758, 2010.
13. Innocenti, Alessio; Durdagi, Serdar; Doostdar, Nadjmeh; Strom, T. Amanda; Barron, Andrew R.; Supuran, Claudiu T. Nanoscale enzyme inhibitors: Fullerenes inhibit carbonic anhydrase by occluding the active site entrance , Bioorganic & Medicinal Chemistry, 18(8), 2822-2828, 2010.
2009
12. Durdagi, Serdar; Supuran, Claudiu T.; Strom, T. Amanda; Doostdar, Nadjmeh; Kumar, Mananjali K.; Barron, Andrew R.; Mavromoustakos, Thomas; Papadopoulos, Manthos G. In silico drug screening approach for the design of magic bullets: a successful example with anti-HIV fullerene derivatized amino acids , Journal of Chemical Information and Modeling, 49(5), 1139–1143, 2009.
11. Politi, Aggeliki; Durdagi, Serdar; Moutevelis-Minakakis, Panagiota; Kokotos, George; Papadopoulos, Manthos G.; Mavromoustakos, Thomas. Application of 3D QSAR CoMFA/CoMSIA and in silico docking studies on novel renin inhibitors against cardiovascular diseases , European Journal of Medicinal Chemistry, 44(9), 3703-3711, 2009.
10. Potamitis, Constantinos; Zervou, Maria; Katsiaras, Vassilis; Zoumpoulakis, Panagiotis; Durdagi, Serdar; Papadopoulos, Manthos G.; Hayes, Joseph M.; Grdadolnik, Simona Golic; Kyrikou, Ioanna; Argyropoulos, Dinutris; Vatougia, Georgia; Mavromoustakos, Thomas. Antihypertensive Drug Valsartan in Solution and at the AT(1) Receptor: Conformational Analysis, Dynamic NMR Spectroscopy, in Silico Docking, and Molecular Dynamics Simulations , Journal of Chemical İnformation and Modeling, 49(3), 726-739, 2009.
2008
09. Durdagi, Serdar; Mavromoustakos, Thomas; Chronakis, Nikos; Papadopoulos, Manthos G. 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, 16(23), 9957-9974, 2008.
08. Kapou, Agnes; Benetis, Nikolas-P.; Durdagi, Serdar; Nikolaropoulos, Sotiris; Mavromoustakos, Thomas. 3D QSAR/CoMFA and CoMSIA Studies on Antileukemic Steroidal Esters Coupled with Conformationally Flexible Nitrogen Mustards , Journal of Chemical İnformation and Modeling, 48(11), 2254-2264, 2008.
07. Durdagi, Serdar; Mavromoustakos, Thomas; Papadopoulos, Manthos G. 3D QSAR CoMFA/CoMSIA, molecular docking and molecular dynamics studies of fullerene-based HIV-1 PR inhibitors , Bioorganic & Medicinal Chemistry Letters, 18(23), 6283-6289, 2008.
06. Mavromoustakos, Thomas; Petrou, Christos; Kokkalou, Eugene; Roussis, Vassilos; Christofi, Victoria; Efthimiou, Georgios; Potamitis, Constantinos; Durdagi, Serdar; Mavromoustakos, Savvas. Ficus sycomorus sap: a psoralene source with potential for the treatment of psoriasis , Planta Medica, 74(9), 1006-1006, 2008.
05. Durdagi, Serdar; Reis, Heribert; Papadopoulos, Manthos G.; Mavromoustakos, Thomas. 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, 16(15), 7377-7387, 2008.
2007
04. Durdagi, Serdar; Papadopoulos, Manthos G.; Papahatjis, Demetris P.; Mavromoustakos, Thomas. Combined 3D QSAR and molecular docking studies to reveal novel cannabinoid ligands with optimum binding activity , Bioorganic & Medicinal Chemistry Letters, 17(24), 6754-6763, 2007.
03. Durdagi, Serdar; Kapou, Agnes; Kourouli, Therapia; Andreou, Thanos; Nikas, Spyros P.; Nahmias, Victoria R.; Papahatjis, Demetris P.; Papadopoulos, Manthos G.; Mavromoustakos, Thomas. 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, 50(12), 2875-2885, 2007.
2006
02. Salzner, Ulrike; Karalti, Ozan; Durdagi, Serdar. 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, 12(5), 687-701, 2006.
2005
01. Durdagi, Serdar; Hofer, Thomas S.; Randolf, Bernhard R.; Rode, Bernd Michael. Structural and dynamical properties of Bi3+ in water, Chemical Physics Letters, 406(1-3), 20-23, 2005