Serdar Durdagi



  1. 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. ..
  2. 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
  3. 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
  4. 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. ..
  5. 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. ..
  6. 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. ..
  7. 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. ..
  8. 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). ..
  9. 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. ..

More Information


  1. Erol I, Aksoydan B, Kantarcioglu I, Salmas R, Durdagi S. Identification of novel serotonin reuptake inhibitors targeting central and allosteric binding sites: A virtual screening and molecular dynamics simulations study. J Mol Graph Model. 2017;74:193-202 pubmed publisher
    ..Small molecule library screening study yielded candidate compounds both at central and allosteric binding site of SERT, and further experimentation may pave the way for developing novel strong inhibitors. ..
  2. Aksoydan B, Kantarcioglu I, Erol I, Salmas R, Durdagi S. Structure-based design of hERG-neutral antihypertensive oxazalone and imidazolone derivatives. J Mol Graph Model. 2017;77:240-249 pubmed publisher
    ..Results of this study can be useful for designing of novel and safe AT1 inhibitors. ..
  3. Mirza S, Lee R, Chu J, Salmas R, Mavromoustakos T, Durdagi S. 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. J Mol Graph Model. 2017;77:338 pubmed publisher
    ..In contrast, the post-treatment of cells with these compounds after Dengue virus infection has resulted in a significant 1logPFU/ml reduction of the virus infectious titre. ..
  4. Kayık G, Tüzün N, Durdagi S. Structural investigation of vesnarinone at the pore domains of open and open-inactivated states of hERG1 K+ channel. J Mol Graph Model. 2017;77:399-412 pubmed publisher
  5. Aksoydan B, Kantarcioglu I, Erol I, Salmas R, Durdagi S. Structure-based design of hERG-neutral antihypertensive oxazalone and imidazolone derivatives. J Mol Graph Model. 2017;79:103-117 pubmed publisher
    ..Results of this study can be useful for designing of novel and safe AT1 inhibitors...