Person: SARIYAR AKBULUT, BERNA
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SARIYAR AKBULUT
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Publication Open Access Piperidine-based natural products targeting type IV pili antivirulence: a computational approach(2023-03-01) SARIYAR AKBULUT, BERNA; ÖZBEK SARICA, PEMRA; Ozcan A., Keskin O., Sariyar Akbulut B., Özbek Sarica P.© 2022 Elsevier Inc.Type IV (T4) pilus is among the virulence factors with a key role in serious bacterial diseases. Specifically, in Neisseria meningitidis and Pseudomonas aeruginosa, it determines pathogenicity and causes infection. Here, a computational approach has been pursued to find piperidine-based inhibitor molecules against the elongation ATPase of T4 pili in these two selected pathogens. Using the modeled structures of the PilF and PilB ATPases of N. meningitidis and P. aeruginosa, virtual library screening via molecular docking has returned inhibitor molecule candidates. The dynamics of the best three binders have further been investigated in detail via molecular dynamic simulations. Among these, ligands with COCONUT IDs CNP0030078 and CNP0051517 were found to have higher potential in the inhibition of ATPases based on molecular dynamic simulation analysis and biological activity information. The obtained results will guide future efforts in antivirulence drug development against T4 pili of N. meningitidis and P. aeruginosa.Publication Open Access Identification of novel inhibitors of the ABC transporter BmrA(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2020-12) SARIYAR AKBULUT, BERNA; Sercinoglu, Onur; Senturk, Duygu; Kaya, Fatma Ece Altinisik; Avci, Fatma Gizem; Frlan, Rok; Tomasic, Tihomir; Ozbek, Pemra; Orelle, Cedric; Jault, Jean-Michel; Akbulut, Berna SariyarThe resistance of microbes to commonly used antibiotics has become a worldwide health problem. A major underlying mechanism of microbial antibiotic resistance is the export of drugs from bacterial cells. Drug efflux is mediated through the action of multidrug resistance efflux pumps located in the bacterial cell membranes. The critical role of bacterial efflux pumps in antibiotic resistance has directed research efforts to the identification of novel efflux pump inhibitors that can be used alongside antibiotics in clinical settings. Here, we aimed to find potential inhibitors of the archetypical ATP-binding cassette (ABC) efflux pump BmrA of Bacillus subtilis via virtual screening of the Mu.Ta.Lig. Chemotheca small molecule library. Molecular docking calculations targeting the nucleotide-binding domain of BmrA were performed using AutoDock Vina. Following a further drug-likeness filtering step based on Lipinski's Rule of Five, top 25 scorers were identified. These ligands were then clustered into separate groups based on their contact patterns with the BmrA nucleotide-binding domain. Six ligands with distinct contact patterns were used for further in vitro inhibition assays based on intracellular ethidium bromide accumulation. Using this methodology, we identified two novel inhibitors of BmrA from the Chemotheca small molecule library.Publication Metadata only Screening of FDA-Approved Natural Drugs as Anti-Virulence Agents Against Pseudomonas aeruginosa and Neisseria meningitides.(2022-06-30) KULA, CEYDA; ÖZBEK SARICA, PEMRA; SARIYAR AKBULUT, BERNA; Özcan A., Kula C., Avcı F. G., Keskin Özkaya Z. Ö., Özbek Sarıca P., Sarıyar Akbulut B.Publication Open Access A review on the mechanistic details of OXA enzymes of ESKAPE pathogens(2023-01-01) SARIYAR AKBULUT, BERNA; ÖZBEK SARICA, PEMRA; Avci F. G., Tastekil I., Jaisi A., ÖZBEK SARICA P., SARIYAR AKBULUT B.The production of beta-lactamases is a prevalent mechanism that poses serious pressure on the control of bacterial resistance. Furthermore, the unavoidable and alarming increase in the transmission of bacteria producing extended-spectrum beta-lactamases complicates treatment alternatives with existing drugs and/or approaches. Class D beta-lactamases, designated as OXA enzymes, are characterized by their activity specifically towards oxacillins. They are widely distributed among the ESKAPE bugs that are associated with antibiotic resistance and life-threatening hospital infections. The inadequacy of current beta-lactamase inhibitors for conventional treatments of \"OXA\" mediated infections confirms the necessity of new approaches. Here, the focus is on the mechanistic details of OXA-10, OXA-23, and OXA-48, commonly found in highly virulent and antibiotic-resistant pathogens Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter spp. to describe their similarities and differences. Furthermore, this review contains a specific emphasis on structural and computational perspectives, which will be valuable to guide efforts in the design/discovery of a common single-molecule drug against ESKAPE pathogens.Publication Metadata only Investigation of the Inhibition of Pseudomonas aeruginosa Type IV Pili Elongation ATPases to Prevent Biofilm Formation.(2022-11-04) KULA, CEYDA; ÖZBEK SARICA, PEMRA; SARIYAR AKBULUT, BERNA; Kula C., Avcı F. G., Keskin Özkaya Z. Ö., Özbek Sarıca P., Sarıyar Akbulut B.