Resarch Articles
2024
216. Dogan, B., Durdagi, S. Investigating the effect of Glu238 protonation state on the conformational heterogeneity of CCR5 by Extended Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. 2024 (accepted)
215. Tunc, H., Yilmaz, S.; Darendeli Kiraz, B. N.; Sari, M.; Kotil, E.S.; Sensoy, O.; Durdagi, S. Improving predictive efficacy for drug resistance in novel HIV-1 protease inhibitors through transfer learning mechanisms. Journal of Chemical Information and Modeling. 2024 (accepted)
214. Yilmaz, Y.B.; Gungor, T.; Donmez, S.; Atalay, H.N.; Siyah, P.; Durdagi, S.; Ay, M.; Tumer Boyunegmez, T. Synthesis, in silico and bio-evaluation of new isothiocyanate derivatives with respect to COX inhibition and H2S release profiles. RSC Medicinal Chemistry. 2024 (accepted)
213. Koksallar Alkan, F.; Caglayan, A.B.; Alkan, H.K.; Benson, E.; Gunduz, Y.E.; Sensoy, O.; Durdagi, S.; Zarbaliyev, E.; Dyson, G.; Assad, H.; Shull, A.; Shi, H.; Ozturk, G.; Korkaya, H. Dual activity of Minnelide chemosensitize basal/triple negative breast cancer stem cells and regression programs immunosuppressive tumor microenvironment. Scientific Reports. 2024, 14(1), 22487.
212. Kahveci, K., Duzgun, M.B., Atis, A.E., Yilmaz, A., Shahraki, A., Coskun, B., Iyison, N.B., Durdagi, S. Discovering allotastatin type-C receptor specific agonists. Nature Communications. 2024, 15, 3965. DOI:10.1038/s41467-024-48156-w
211. Aydın, S., Yavuz, E., Ghazy, S., Celebi, A., Kilic, T., Avsar, T., Durdagi, S. Synthesis of Tryptamine-Thoazolidin-4-one Derivatives and the Combined in silico and in vitro Evaluation of their Biological Activity and Cytotoxicity. ACS Omega. 2024 (accepted)
210. Tapera, M., Dogan, E., Sahin, K., Gözkamene, G.A., Kekeçmuhammed, H., Sandal, S., Coker Gurkan, A., Bora, R.E., Anber, A., Durdagi, S., Zorlu, Y., Sarıpınar, E. Imidazole-based hydrazones as potent anti-colon cancer agents: Design, synthesis, biological evaluation and computational studies. Journal of Molecular Structures. 2024 (accepted)
209. Calis, S., Dogan, B., Celebi, A., Yapicier, O., Kilic, T., Turanli, E.T., Avsar, T., Durdagi, S. BAU-243: A novel BCL-2 inhibitor inducing autophagic cell death in glioblastoma, unveiled through multistep virtual screening, comprehensive in vitro and in vivo animal model evaluation. Cancer Research. 2024, 84(7).
208. Teiar, R.; Sane, F.; Erol, I.; Nekoua, M.P.; Lecouturier, D.; Boukherroub, R.; Durdağı, S.; Hober, D.; Drider, D. EnterociN DD14 can inhibit the infection of eukaryotic cells with enveloped viruses. Archives of Microbiology. 2024, 206(6), 269. DOI: 10.1007/s00203-024-04002-7.
207. Mavroedi, P., Zorba, L.P., Tzouras, N.V., Neofotistos, S.P., Georgiou, N., Sahin, K., Durdagi, S., Vougioukalakis, G.C., Mavromoustakos, T. Are terminal alkynes necessary for MAO-A/MAO-B inhibition? A new scaffold is revealed. Molecules 2024, 29, 2486.
206. Sayyah, E., Oktay, L., Tunc, H., Durdagi, S. Developing Dynamic Structure-based Pharmacophore and ML-Trained QSAR Models for the Discovery of Novel Resistance-Free RET Tyrosine Kinase Inhibitors. ChemMedChem 2024 (accepted)
205. Ikram, S., Sayyah, E., Durdagi, S. Identifying Potential SOS1 Inhibitors via Virtual Screening of Multiple Small Molecule Libraries against KRAS-SOS1 Interface. ChemBioChem 2024, 25(12):e202400008. DOI:10.1002/cbic.202400008.
204. Ghazy, S., Oktay, L., Durdagi, S. A novel algorithm for the virtual screening of extensive small molecule libraries against ERCC1/XPF protein-protein interaction for the identification of therapeutic resistance-bypassing small anticancer molecules. Turk. J. Biol. 2024 (accepted)
203. Kekecmuhammed, H., Tapera, M., Sahin, K., Ozturk Sever, B., Anber, A.M., Bora, R.E., Avsar, T., Kilic, T., Gunger, E., Saripinar, E., Coker-Gurkan, A., Durdagi, S. The suppressive effect of novel hydrazones-tethered imidazoles in HCT-116 and HT-29 colorectal cancer cells: Synthesis, biological activity, and molecular modeling studies. ChemistrySelect 2024 (accepted)
202. Cakmak, R., Basaran, E., Sahin, K., Senturk, M., Durdagi, S. Synthesis of Novel Hydrazide-Hydrazone Compounds and in vitro and in silico Investigation of their Biological Activities against AChE, BChE, and hCA I and II. ACS Omega. 2024, 9, 18, 20030-20041.
201. Ozil, M., Balaydin, H.T., Dogan, B., Senturk, M., Durdagi, S. Efficient, rapid, and high-yield synthesis of aryl Schiff base derivatives and their in vitro and in silico inhibition studies of hCA I, hCA II, AChE, and BuChE. Arch. Pharm. 2024, e2300266. DOI: 10.1002/ardp.202300266.
200. Sambur, E., Oktay, L., Durdagi, S. Covalent docking-driven virtual screening of extensive small-molecule libraries against Bruton tyrosine kinase for the identification of highly selective and potent novel therapeutic candicates. J. Mol. Graph. Model. 2024, 130, 108762. DOI: 10.1016/j.jmgm.2024.108762.
2023
199. Tunc, H.; Dogan, B., Darendereli,Kiraz, B.N., Sari, M., Durdagi, S., Kotil, S. Prediction of HIV-1 protease resistance using genotypic, phenotypic, and molecular information with artificial neural networks. PeerJ. 2023, 11:e14987. DOI: 10.7717/peerj.14987.
198. Atalay, N., Akcan, E.K., Gul, M., Ayan, E., Destan, E., Ertem, F.B., Tokay, N., Cakilkaya, B., Nergiz, Z., Karakadioglu, G., Kepceoglu, A., Yapici, I., Tosun, B., Baldir, N., Yildirim, G., Johnson, J.A., Guven, O., Shafie, A., Arslan, N.E., Yilmaz, M., Kulakman, C., Paydos, S.S., Cinal, Z.S., Sabanoglu, K., Pazarceviren, A., Yilmaz, A., Canbay, B., Asci, B., Kartal, E., Tavli, S., Caliseki, M., Goc, G., Mermer, A., Yesilay, G., Altuntas, S., Tateishi, H., Otsuka, M., Fujita, M., Tekin, S., Ciftci, H., Durdagi, S., Dinler Doganay, G., Karaca, E., Kaplan Turkoz, B., Kabasakal, B.V., Kati, A., Demirci, H. Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source "Turkish DeLight". Turk. J. Biol.. 2023, 47(1):1-13.
197. Gul, M,; Ayan, E., Johnson, J.A., Shafiei, A., Kepceoglu, A., Yilmaz, M., Ertem, F.B., Yapici, I., Tosun, B., Baldir, N., Tokay, N., Nergiz, Z., Kadakadioglu, G., Paydos, S.S., Kulakman, C., Ferah, C.K., Guven, O., Atalay, N., Akcan, E.K., Cetinok, H., Arslan, N.E., Sabanoglu, K., Asci, B., Tavli, S., Gumusboga, H., Altuntas, S., Otsuka, M., Fujita, M., Teki, N.S., Ciftci, H., Durdagi, S., Karaca, E., Kaplan Turkoz, B., Kabasakal, B.V., Kati, A., Demirci, H. Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source. Scientific Reports. 2023, 13(1):8123. DOI: 10.1038/s41598-023-33989-0.
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