Biology subjects

Walters, M. A.

Publications and source records attributed to Walters, M. A..

3 recordsLinked to original sources

bioRxiv2024

Development of Allosteric Small Molecule APOBEC3B Inhibitors from In Silico Screening

The APOBEC3 (A3) family of enzymes are zinc metalloenzymes that catalyze the conversion of 2'- deoxycytidine to 2'-deoxyuridine in single stranded DNA. APOBEC3B (A3B), a member of the A3 family, has emerged as a key driver of genomic instability in many cancer types by mutating host DNA to drive tumorigenesis and therapy resistance. Small molecule inhibitors of A3B would extend the durability of current therapies by limiting mutations that promote tumor escape and therapy resistance. Consequently, a computer aided drug discovery (CADD) campaign was employed to identify inhibitors of A3B. Through molecular dynamics (MD) simulations and computational solvent mapping analysis, we identified a novel putative allosteric pocket on the c-terminal domain of A3B and virtually screened the ChemBridge Diversity Set ([~]110,000 small molecules) against both the active and predicted allosteric sites. High scoring compounds were selected for in vitro testing and triage, resulting in 13 candidate inhibitors. Using cysteine reactive probes, one of the original hit compounds was mapped to the computationally identified allosteric pocket. However, after resynthesis of representative chemotypes and further investigation using in vitro assays, none of the chemotypes retained inhibitory activity. Further analysis revealed that most of the inhibition observed in the primary assay was due to metal contamination in the screening sample, which resulted in the removal of the catalytic zinc from the enzyme active site. Although validated A3B inhibitors were not discovered in this study, we report a ligandable allosteric site on A3B and several cautionary insights for researchers developing small molecule inhibitors of zinc metalloenzymes. TOC graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC="FIGDIR/small/591187v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@b7e577org.highwire.dtl.DTLVardef@13a1a43org.highwire.dtl.DTLVardef@192309eorg.highwire.dtl.DTLVardef@b60a31_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Identification of CK2α' selective inhibitors by the screening of an allosteric-kinase-inhibitor-like compound library

Protein Kinase CK2 is a holoenzyme composed of two regulatory subunits (CK2{beta}) and two catalytic subunits (CK2 and CK2). CK2 controls several cellular processes including proliferation, inflammation, and cell death. However, CK2 and CK2 possess different expression patterns and substrates and therefore impact each of these processes differently. Elevated CK2 participates in the development of cancer, while increased CK2 has been associated with neurodegeneration, especially Huntingtons disease (HD). HD is a fatal disease for which no effective therapies are available. Genetic deletion of CK2 in HD mouse models has ameliorated neurodegeneration. Therefore, pharmacological inhibition of CK2 presents a promising therapeutic strategy for treating HD. However, current CK2 inhibitors are unable to discriminate between CK2 and CK2 due to their high structural homology, especially in the targeted ATP binding site. Using computational analyses, we found a potential Type IV ("D" pocket) allosteric site on CK2 that contained different residues than CK2 and was distal from the ATP binding pocket featured in both kinases. With this potential allosteric site in mind, we screened a commercial library containing [~]29,000 allosteric-kinase-inhibitor-like compounds using a CK2 activity-dependent ADP-GloTM Kinase assay. Obtained hits were counter-screened against CK2 revealing two CK2 selective compounds. These two compounds might serve as the basis for further medicinal chemistry optimization for the potential treatment of HD.

biochemistry↗

bioRxiv2022

Reference compounds for characterizing cellular injury in high-content cellular morphology assays

Robust, generalizable approaches to identify compounds efficiently with undesirable mechanisms of action in complex cellular assays remain elusive. Such a process would be useful for hit triage during high-throughput screening and, ultimately, predictive toxicology during drug development. We generated cell painting and cellular health profiles for 218 prototypical cytotoxic and nuisance compounds in U-2 OS cells in a concentration-response format. A diversity of compounds causing cellular damage produced bioactive cell painting morphologies, including cytoskeletal poisons, genotoxins, nonspecific electrophiles, and redox-active compounds. Further, we show that lower quality lysine acetyltransferase inhibitors and nonspecific electrophiles can be distinguished from more selective counterparts. We propose that the purposeful inclusion of cytotoxic and nuisance reference compounds such as those profiled in this Resource will help with assay optimization and compound prioritization in complex cellular assays like cell painting.

pharmacology and toxicology↗