Kurt B, Dag A, Dogan B, Durdagi S, Angeli A, Nocentini A, et al
. 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. Bioorg Chem. 2019;87:838-850 pubmed publisher
..In addition, electrostatic potential surfaces (ESP) for binding sites were also generated to understand interactions between proteins and active ligands. ..
Kanan T, Kanan D, Erol I, Yazdi S, Stein M, Durdagi S. Targeting the NF-κB/IκBα complex via fragment-based E-Pharmacophore virtual screening and binary QSAR models. J Mol Graph Model. 2018;86:264-277 pubmed publisher
Zaka M, Abbasi B, Durdagi S. Proposing novel TNFα direct inhibitor Scaffolds using fragment-docking based e-pharmacophore modeling and binary QSAR-based virtual screening protocols pipeline. J Mol Graph Model. 2018;85:111-121 pubmed publisher
Durdagi S, Tahir Ul Qamar M, Salmas R, Tariq Q, Anwar F, Ashfaq U. Investigating the molecular mechanism of staphylococcal DNA gyrase inhibitors: A combined ligand-based and structure-based resources pipeline. J Mol Graph Model. 2018;85:122-129 pubmed publisher
..These compounds can be explored as future lead optimization molecules to discover a new class of antibiotics against resistant Staphylococcus aureus strains. ..
Erol I, Aksoydan B, Kantarcioglu I, Durdagi S. Application of Multiscale Simulation Tools on GPCRs. An Example with Angiotensin II Type 1 Receptor. Methods Mol Biol. 2018;1824:431-448 pubmed publisher
..Moreover, investigating the activation mechanisms and atomistic determinants of ligand binding to GPCR targets would allow greater safety in the human life. ..
Durdagi S, Erol I, Salmas R, Aksoydan B, Kantarcioglu I. Oligomerization and cooperativity in GPCRs from the perspective of the angiotensin AT1 and dopamine D2 receptors. Neurosci Lett. 2018;: pubmed publisher
..Investigation of these above-mentioned interactions may greatly contribute to the candidate molecule screening studies and development of novel therapeutics with fewer adverse effects. ..
Durdagi S, Aksoydan B, Erol I, Kantarcioglu I, Ergun Y, Bulut G, et al
. 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 o. Eur J Med Chem. 2018;145:273-290 pubmed publisher
..Adherent cells detached from the plates and underwent cell death possibly due to apoptosis at 19d concentrations that induced cell cycle arrest. ..
Kurt B, Gazioglu I, Dag A, Salmas R, Kayık G, Durdagi S, et al
. Synthesis, anticholinesterase activity and molecular modeling study of novel carbamate-substituted thymol/carvacrol derivatives. Bioorg Med Chem. 2017;25:1352-1363 pubmed publisher
..e., Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approaches). ..
Durdagi S, Erol I, Salmas R, Patterson M, Noskov S. First universal pharmacophore model for hERG1 K+ channel activators: acthER. J Mol Graph Model. 2017;74:153-170 pubmed publisher
..The developed model is available upon request and it may serve as basis for the synthesis of novel therapeutic hERG1 activators. ..