Szczepinska, T. | Search bioRxiv

bioRxiv2024

On the mode of anti-C. albicans activity of a bis(benzoxaborole) analogue of Tavaborole

We presented the pharmacodynamic relationship between benzoxaborole concentrations and Candida albians blastoconidial population dynamics. Bis(benzoxaborole) analogue (2) and Tavaborole (ref.) showed comparable moderate effects against C. albicans (time-kill kinetic assays). Benzoxaboroles inhibited the C. albicans growth during 72 h (fungicidal after 2 h of that time) with metabolic reduction (%R=64). Biofilm-inhibiting concentration (BIC50=2 g/mL) is the lowest concentration of bezoxaboroles that presented 50% inhibition of biofilm metabolic activity vs non-treated control. 2 displayed poor ability to inhibit morphogenesis of C. albicans. Safety and fungicidal activity are still in high demand against biofilm grown on fibroblasts and the zebrafish model in vivo. This biofilm model was used to study the interactions between the C. albicans morphogenesis and benzoxaboroles. Benzoxaboroles displayed selectivity in cytotoxic effects. 2 exhibited significantly lower embryotoxicity vs ref. IC50>128 g/mL for 2. Ref. at 256 g/mL showed approximately 80% viability of VERO E6 cells. A higher selectivity of the ref--drug to the pathogen than to the mammalian cells was observed. Contrariwise, ref. and 2 showed IC50=2 g/mL against PBMCs. Benzoxaborole antifungal development targets ergosterol binding. RNAseq data indicated that efflux pumps (MDR) in C. albicans were upregulated. Inositol-1-phosphate synthase was repressed under the benzoxaborole treatment. MDR1 upregulation by 2 was accompanied by the IFD6 (aldo-keto reductase) increase and the coordination of multiple coactivators (IFD6, TNA1 encoding putative nicotinic acid transporter). Benzoxaboroles represent a similar resistance mechanism to azoles due to the subsequent expression of MDR1 and IDF6. Docking studies confirmed the proposed interactions of benzoxaborole adenosinemonophosphate adduct with LeuRS. Moreover, C5_04480C_A (cell wall biogenesis, protein folding, modification, and destination) was negatively regulated in response to the benzoxaborole stress. Benzoxaborole-altering efflux inhibitors are important for the development of combination strategies in candidiasis. Our findings present an innovative concept that can inspire further studies for designing and building new antifungal benzoxaborole. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/605614v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@10d0037org.highwire.dtl.DTLVardef@894266org.highwire.dtl.DTLVardef@1663f05org.highwire.dtl.DTLVardef@1b3736b_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

Multi-scale phase separation by explosive percolation with single chromatin loop resolution

The 2m-long human DNA is tightly intertwined into the cell nucleus of the size of 10m. The DNA packing is explained by folding of chromatin fiber. This folding leads to the formation of such hierarchical structures as: chromosomal territories, compartments; densely packed genomic regions known as Chromatin Contact Domains (CCDs), and loops. We propose models of dynamical genome folding into hierarchical components in human lymphoblastoid, stem cell, and fibroblast cell lines. Our models are based on explosive percolation theory. The chromosomes are modeled as graphs where CTCF chromatin loops are represented as edges. The folding trajectory is simulated by gradually introducing loops to the graph following various edge addition strategies that are based on topological network properties, chromatin loop frequencies, compartmentalization, or epigenomic features. Finally, we propose the genome folding model - a biophysical pseudo-time process guided by a single scalar order parameter. The parameter is calculated by Linear Discriminant Analysis. We simulate the loop formation by using Loop Extrusion Model (LEM) while adding them to the system. The chromatin phase separation, where fiber folds into topological domains and compartments, is observed when the critical number of contacts is reached. We also observe that 80% of the loops are needed for chromatin fiber to condense in 3D space, and this is constant through various cell lines. Overall, our in-silico model integrates the high-throughput 3D genome interaction experimental data with the novel theoretical concept of phase separation, which allows us to model event-based time dynamics of chromatin loop formation and folding trajectories.

genomics↗