Biology subjects

Klebe, G.

Publications and source records attributed to Klebe, G..

3 recordsLinked to original sources

bioRxiv2025

Natural Product-Like Fragments Unlock Novel Chemotypes for a Kinase Target - Exploring Options beyond the Flatland

In this study we utilized a high-performance soaking system of protein kinase A (PKA) to perform a crystallographic screening of a natural product-like fragment library. We resolved 36 fragment-bound structures, corresponding to a hit rate of 41%. Nine fragments bound within the ATP site, nine peripherally, and 18 interacted with both the ATP and peripheral sites. One fragment binds to the same site as the approved allosteric kinase inhibitor asciminib, while another induces an unexpected conformational change. Systematic database mining revealed that both the fragments and their natural product parents have not been previously associated with PKA or kinase activity. A scaffold/chemotype analysis further underscored their novelty. Cheminformatics analyses confirmed that these fragments occupy a distinct chemical space, enriched in saturation, spatial complexity and molecular three-dimensional character compared to kinase binders from reference datasets. These properties have previously been linked to increased selectivity, reduced CYP450 inhibition, and higher overall clinical success rates. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/659015v4_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1643255org.highwire.dtl.DTLVardef@124a28eorg.highwire.dtl.DTLVardef@2c4033org.highwire.dtl.DTLVardef@12ae4c5_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Of Problems and Opportunities - How to Treat and How to not Treat Crystallographic Fragment-Screening Data

In their recent commentary in Protein Science, Jaskolski et al. analyze three randomly picked diffraction data sets from fragment-screening group depositions from the PDB and, based on that, claim that such data are principally problematic. We demonstrate here that if such data are treated properly, none of the proclaimed criticisms persist.

scientific communication and education↗

bioRxiv2020

The importance of charge in perturbing the aromatic glue stabilizing the protein-protein interface of homodimeric tRNA-guanine transglycosylase

Bacterial tRNA-guanine transglycosylase (Tgt) is involved in the biosynthesis of the modified tRNA nucleoside queuosine present in the anticodon wobble position of tRNAs specific for aspartate, asparagine, histidine and tyrosine. Inactivation of the tgt gene leads to decreased pathogenicity of Shigella bacteria. Therefore, Tgt constitutes a putative target for Shigellosis drug therapy. Since only active as homodimer, interference with dimer-interface formation may, in addition to active-site inhibition, provide further means to disable this protein. A cluster of four aromatic residues seems important to stabilize the homodimer. We mutated residues of this aromatic cluster and analyzed each exchange with respect to dimer and thermal stability or enzyme activity applying native mass spectrometry, thermal shift assay, enzyme kinetics, and X-ray crystallography. Our structural studies indicate strong influence of pH on homodimer stability. Obviously, protonation of a histidine within the aromatic cluster promotes the collapse of an essential structural motif within the dimer interface at slightly acidic pH. TOC GraphicFor table of contents use only. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

molecular biology↗