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1. Sogukomerogullari HG, Başaran E, Çakmak R, Muhammed MT, Akkoc S. Novel transition metal (II) complexes of hydrazones as potential antitumor agents: Synthesis, characterization, DFT computations, cytotoxic activities, molecular docking and simulation studies. Inorganica Chimica Acta. 2025;581:122634. doi: 10.1016/j.ica.2025.122634
2. Bimoussa A, Hachim ME, Laamari Y, Geesi MH, Muhammed MT, Alamri MA, et al. Computational assessment of the reactivity and anticancer activity of 1,2,3-triazole-thiazolidinones derivatives: An approach combining DFT calculations, molecular dynamics simulations, molecular docking, and ADMET. Journal of Molecular Structure. 2025;1321:139756. doi: 10.1016/j.molstruc.2024.139756
3. Saeed S, Shahzadi I, Zahoor AF, Al-Mutairi AA, Kamal S, Faisal S, et al. Exploring theophylline-1,2,4-triazole tethered N-phenylacetamide derivatives as antimicrobial agents: unraveling mechanisms via structure-activity relationship, in vitro validation, and in silico insights. Frontiers in Chemistry. 2024;12. doi: 10.3389/fchem.2024.1372378
4. S KK, K J, K A, C P, R M. Exploration of Solvent Effects, Structural and Spectroscopic Properties, Chemical Shifts, Bonding Nature, Reactive Sites and Molecular Docking Studies on 3-Chloro-2,6-Difluoropyridin-4-Amine as a Potent Antimicrobial Agent. International Research Journal of Multidisciplinary Technovation. 2024;:109. doi: 10.54392/irjmt2419
5. Basaran E, Sogukomerogullari HG, Muhammed MT, Akkoc S. Synthesis of Novel Cu(II), Co(II), Fe(II), and Ni(II) Hydrazone Metal Complexes as Potent Anticancer Agents: Spectroscopic, DFT, Molecular Docking, and MD Simulation Studies. ACS Omega. 2024;. doi: 10.1021/acsomega.4c06202
6. Kothinti RR, Basavegowda L, Bhoomandla S, Gosu NR, Muppavarapu S, Allaka TR, et al. Design, Synthesis, and Biological Evaluation of New Benzo[b]Oxepine‐Based 1,2,3‐Triazole Derivatives: Molecular Docking, DFT Analysis, In Silico Pharmacokinetics, and Identification of Antimicrobial Pharmacophore Sites. Chemistry & Biodiversity. 2025;. doi: 10.1002/cbdv.202500520
7. Kızılyıldırım S, Kandemir T, Kendir G, Muhammed MT, Köroğlu A, Köksal F, et al. The antibacterial effect mechanisms of Laurus nobilis extracts on carbapenem-resistant Acinetobacter baumanii isolates. Food Bioscience. 2024;59:104011. doi: 10.1016/j.fbio.2024.104011
8. Erdoğan �, Erbaş S, Muhammed MT, Onem E, Soyocak A, Ak A. Isolation and characterization of thymoquinone from Nigella sativa essential oil: antioxidant and antibacterial activities, molecular modeling studies, and cytotoxic effects on lung cancer A549 cells . Journal of Essential Oil Bearing Plants. 2024;27(3):787. doi: 10.1080/0972060X.2024.2352418
9. Ergüç A, Albayrak G, Muhammed MT, Karakuş F, Arzuk E. Mitochondrial toxicity of selected natural compounds: in vitro assessment and in silico molecular docking and dynamics simulation . Drug and Chemical Toxicology. 2025;48(1):199. doi: 10.1080/01480545.2024.2412775
10. Mavvaji M, Muhammed MT, Akkoc S. Synthesis, Cytotoxic Activity, Docking and MD Simulation ofN,N‐Disubstituted New Benzimidazolium Salts. ChemistrySelect. 2023;8(43). doi: 10.1002/slct.202303053
11. Mateev E, Karatchobanov V, Dedja M, Diamantakos K, Mateeva A, Muhammed MT, et al. Novel Pyrrole Derivatives as Multi-Target Agents for the Treatment of Alzheimer’s Disease: Microwave-Assisted Synthesis, In Silico Studies and Biological Evaluation. Pharmaceuticals. 2024;17(9):1171. doi: 10.3390/ph17091171
12. Mavvaji M, Muhammed MT, Onem E, Aslan HG, Alhag SK, Akkoc S. Synthesis, Cytotoxic Activity, Antiquorum Sensing Effect, Docking and Md Simulation of Novel 1,3‐Disubstituted 2‐Mercapto‐1H‐Benzo[D]Imidazolium Chlorides. Journal of Biochemical and Molecular Toxicology. 2025;39(4). doi: 10.1002/jbt.70248
13. Mateev E, Muhammed MT, Irfan A, Sharma S, Georgieva M, Zlatkov A. Hydrazide-hydrazones as novel antioxidants - in vitro, molecular docking and DFT studies. Pharmacia. 2024;71:1. doi: 10.3897/pharmacia.71.e133114
14. Irfan A, Faisal S, Ahmad S, Saif MJ, Zahoor AF, Khan SG, et al. An Exploration of the Inhibitory Mechanism of Rationally Screened Benzofuran-1,3,4-Oxadiazoles and-1,2,4-Triazoles as Inhibitors of NS5B RdRp Hepatitis C Virus through Pharmacoinformatic Approaches. Biomedicines. 2023;11(11):3085. doi: 10.3390/biomedicines11113085
15. Kızılyıldırım S, Kandemir T, Kendir G, Muhammed MT, Köroğlu A, Ozogul F. Antibacterial activity of avocado extract (Persea americana Mill.) against aminoglycoside-resistant Klebsiella pneumoniae strains. Food Bioscience. 2024;60:104523. doi: 10.1016/j.fbio.2024.104523
16. Irfan A, Zahoor AF, Boulaamane Y, Javed S, Hameed H, Maurady A, et al. Computational exploration of acefylline derivatives as MAO-B inhibitors for Parkinson’s disease: insights from molecular docking, DFT, ADMET, and molecular dynamics approaches. Frontiers in Chemistry. 2024;12. doi: 10.3389/fchem.2024.1449165
17. Konyar D, Muhammed MT. MOLECULAR DOCKING AND MOLECULAR DYNAMICS SIMULATIONS INHIBITION AGAINST OF HUMAN TELOMERASE BY NUCLEOSIDE AND NON-NUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITORS (NRTIs/NNRTIs). Ankara Universitesi Eczacilik Fakultesi Dergisi. 2024;48(2):18. doi: 10.33483/jfpau.1444259
18. Laamari Y, Muhammed MT, Irfan A, Oubella A, Alossaimi MA, Geesi MH, et al. New isoxazoline‐linked 1,3,4‐thiadiazole derivatives: Synthesis, antiproliferative activity, molecular docking, molecular dynamics and DFT. Journal of Molecular Structure. 2025;1319:139368. doi: 10.1016/j.molstruc.2024.139368