Biology subjects

Darragh, A. C.

Publications and source records attributed to Darragh, A. C..

3 recordsLinked to original sources

bioRxiv2024

Comprehensive Characterization of BTK Inhibitor Specificity, Potency, and Biological Effects: Insights into Covalent and Non-covalent Mechanistic Signatures

AbstractUncovering a drugs mechanism of action and possible adverse effects are critical components in drug discovery and development. Moreover, it provides evidence for why some drugs prove more effective than others, and how to design better drugs altogether. Here we demonstrate the utility of a high- throughput in vitro screening platform along with a comprehensive panel to aid in the characterization of fifteen BTK inhibitors that are either approved by the FDA or presently under clinical evaluation. To compare the potency of these drugs, we measured the binding affinity of each to wild-type BTK, as well as a clinically relevant resistance mutant of BTK (BTK C481S). In doing so, we discovered a considerable difference in the selectivity and potency of these BTK inhibitors to the wild-type and mutant proteins. Some of this potentially contributes to the adverse effects experienced by patients undergoing therapy using these drugs. Overall, non-covalent BTK inhibitors showed stronger potency for both the wild-type and mutant BTK when compared with that of covalent inhibitors, with the majority demonstrating a higher specificity and less off-target modulation. Additionally, we compared biological outcomes for four of these inhibitors in human cell-based models. As expected, we found different phenotypic profiles for each inhibitor. However, the two non-covalent inhibitors had fewer off-target biological effects when compared with the two covalent inhibitors. This and similar in-depth preclinical characterization of drug candidates can provide critical insights into the efficacy and mechanism of action of a compound that may affect its safety in a clinical setting. Table of Contents/Abstract Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/611550v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@744cf2org.highwire.dtl.DTLVardef@167cf2forg.highwire.dtl.DTLVardef@5326c4org.highwire.dtl.DTLVardef@1163b29_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2022

A GATA factor radiation in Caenorhabditis rewired the endoderm specification network

Although similar developmental regulatory networks can produce diverse phenotypes, different networks can also produce the same phenotype. In theory, as long as development can produce an acceptable end phenotype, the details of the process could be shielded from selection, leading to the possibility of developmental system drift, where the developmental mechanisms underlying a stable phenotype continue to evolve. Many examples exist of divergent developmental genetics underlying conserved traits. However, studies that elucidate how these differences arose and how other features of development accommodated them are rarer. In Caenorhabditis elegans, six transcription factors that bind motifs with a GATA core sequence (GATA factors) comprise the zygotic part of the endoderm specification network. Here we show that the core of this network - five of the genes - originated within the genus during a brief but explosive radiation of this gene family and that at least three of them evolved from a single ancestral gene with at least two different spatio-temporal expression patterns. Based on analyses of their evolutionary history, gene structure, expression, and sequence, we explain how these GATA factors were integrated into this network. Our results show how gene duplication fueled the developmental system drift of the endoderm network in a phylogenetically brief period in developmentally canalized nematodes.

evolutionary biology↗

bioRxiv2022

Radiation and diversification of GATA-domain-containing proteins in the genus Caenorhabditis

Transcription factors are defined by their DNA-binding domains (DBDs). The binding affinities and specificities of a transcription factor to its DNA binding sites can be used by an organism to fine-tune gene regulation and so are targets for evolution. Here we investigate the evolution of GATA-type transcription factors (GATA factors) in the Caenorhabditis genus. Based upon comparisons of their DBDs, these proteins form 13 distinct groups. This protein family experienced a burst of gene duplication in several of these groups along two short branches in the species tree, giving rise to subclades with very distinct complements of GATA factors. By comparing extant gene structures, DBD sequences, genome locations, and selection pressures we reconstructed how these duplications occurred. Although the paralogs have diverged in various ways, the literature shows that at least eight of the DBD groups bind to similar G-A-T-A DNA sequences. Thus, despite gene duplications and divergence among DBD sequences, most Caenorhabditis GATA factors appear to have maintained similar binding preferences, which could create the opportunity for developmental system drift. We hypothesize that this limited divergence in binding specificities contributes to the apparent disconnect between the extensive genomic evolution that has occurred in this genus and the absence of significant anatomical changes.

evolutionary biology↗