Biology subjects

Yildiz, M. S.

Publications and source records attributed to Yildiz, M. S..

3 recordsLinked to original sources

bioRxiv2024

Synergistic and antagonistic drug-drug interactions are prevalent but not conserved across acute myeloid leukemia cell lines

Acute myeloid leukemia (AML) is the most prevalent type of leukemia in adults. Despite advancements in medicine, the standard treatment that utilizes a combination of cytarabine and daunorubicin for AML has remained the same for decades. Combination drug therapies are proven to be an effective way to achieve targeted efficacy while minimizing drug dosage along with the unintended side effects. However, a systematic survey of synergistic potential of drug-drug interactions in the context of AML pathology is currently lacking. Here we examine the interactions between 15 frequently used cancer drugs across distinct AML cell lines and demonstrate that synergistic and antagonistic drug-drug interactions are widespread but not conserved across these cell lines. Notably, enasidenib (AG-221) and venetoclax (ABT-199), recently approved anticancer agents, exhibited the highest counts of synergistic interactions and the fewest antagonistic ones. In contrast, 6-Thioguanine (6-TG), a purine analog, was involved in the highest number of antagonistic interactions. The interactions we report here cannot be attributed solely to the inherent synergistic or antagonistic natures of these three drugs, as each drug we examined was involved in several synergistic or antagonistic interactions in the cell lines we tested. Moreover, we observed that these drug-drug interactions are not conserved across cell lines, suggesting that the success of combination therapies might vary depending on AML genotypes. For instance, we found that a single mutation in the TF1 cell line could dramatically alter drug-drug interactions, even turning synergistic interactions into antagonistic ones, as seen with AG-221 and cladribine A (2CdA). Our findings provide a preclinical survey of the potential synergistic effects revealing the complexity of the problem in vitro. However, the exploitable synergistic regimes in clinical scenarios remain to be explored. We anticipate these results to be an insightful guideline for future clinical studies, aiming to refine chemotherapy regimens and ultimately enhance patient outcomes.

cancer biology↗

bioRxiv2024

Elucidating TolC Protein Dynamics: Structural Shifts Facilitate Efflux Mediated β-lactam Resistance

Efflux-mediated {beta}-lactam resistance represents a significant public health challenge, limiting the efficacy of various {beta}-lactam antibiotics against numerous clinically relevant pathogenic bacteria. Structural and functional analyses have revealed that the efflux protein TolC in several Gram-negative bacteria serves as a conduit for antibiotics, bacteriocins, and phages, affecting bacterial susceptibility and virulence. In this study, we conducted a comprehensive examination of the efflux of {beta}-lactam drugs mediated by TolC, employing extensive experimental and computational analyses. Our computational investigations into the molecular dynamics of drug-free TolC revealed critical unidirectional movements of the trimeric TolC and identified residues significantly involved in TolC opening. To corroborate these findings, we performed a whole-gene-saturation mutagenesis assay, systematically mutating each residue of TolC to 19 other amino acids and measuring the fitness effects of these mutations under {beta}-lactam-induced selection. The {beta}-lactams oxacillin, piperacillin, and carbenicillin were selected for this study because they are effluxed by the AcrAB-TolC complex with varying efficiencies. This approach clarified the similarities and differences in the efflux processes of the three {beta}-lactam antibiotics through the trimeric TolC. Further analysis of TolCs efflux mechanism for these {beta}-lactam antibiotics via steered molecular dynamics simulations revealed the existence of general and drug-specific mechanisms employed by TolC. We identified key positions at the periplasmic entry of TolC whose altered dynamics influence long-range efflux motions as allosteric modulators. Our findings provide valuable insights into the structural dynamics of TolC, establishing a foundation for understanding the key mechanisms behind multidrug resistance and principles for designing new antibiotics and antibiotic derivatives capable of circumventing the bacterial efflux mechanism.

biophysics↗

bioRxiv2023

Susceptible bacteria survive antibiotic treatment in the mammalian gastrointestinal tract without evolving resistance

In vitro systems have provided great insight into the mechanisms of antibiotic resistance. Yet, in vitro approaches cannot reflect the full complexity of what transpires within a host. As the mammalian gut is host to trillions of resident bacteria and thus a potential breeding ground for antibiotic resistance, we sought to better understand how gut bacteria respond to antibiotic treatment in vivo. Here, we colonized germ-free mice with a genetically barcoded antibiotic pan-susceptible Escherichia coli clinical isolate and then administered the antibiotic cefepime via programmable subcutaneous pumps which allowed for closer emulation of human parenteral antibiotic pharmacokinetics/dynamics. After seven days of antibiotics, we were unable to culture E. coli from feces. We were, however, able to recover barcoded E. coli from harvested gastrointestinal (GI) tissue, despite high GI tract and plasma cefepime concentrations. Strikingly, these E. coli isolates were not resistant to cefepime but had acquired mutations - most notably in the wbaP gene, which encodes an enzyme required for the initiation of the synthesis of the polysaccharide capsule and lipopolysaccharide O antigen - that increased their ability to invade and survive within intestinal cells, including cultured human colonocytes. Further, these E. coli mutants exhibited a persister phenotype when exposed to cefepime, allowing for greater survival to pulses of cefepime treatment when compared to the wildtype strain. Our findings highlight a mechanism by which bacteria in the gastrointestinal tract can adapt to antibiotic treatment by increasing their ability to persist during antibiotic treatment and invade intestinal epithelial cells where antibiotic concentrations are substantially reduced.

microbiology↗