Arella, D. | Search bioRxiv

bioRxiv2024

Development of DuoMYC: a synthetic cell penetrant miniprotein that efficiently inhibits the oncogenic transcription factor MYC

The master regulator transcription factor MYC is implicated in numerous human cancers, and its targeting is a long-standing challenge in drug development. MYC is a typical undruggable target, with no binding pockets on its DNA binding domain and extensive intrinsically disordered regions. Rather than trying to target MYC directly with classical modalities, here we engineer synthetic cell penetrating miniproteins that can bind to MYCs target DNA, the enhancer box (E-Box), with a high affinity and block MYC-driven transcription. We obtained the miniproteins via structure-based design and a combination of solid phase peptide synthesis and site-specific crosslinking. Our lead variant, DuoMYC, binds to E-Box DNA with high affinity (KD = 118 nM) and molecular dynamic simulations provide insights into the structural features leading to the high stability of that DNA binding complex. DuoMYC displays an excellent stability in human serum and is able to enter cells and inhibit MYC-driven transcription with submicromolar potency (IC50 = 464 nM) as shown by reporter gene assay. Notably, DuoMYC surpasses the efficacy of several other recently developed MYC inhibitors. Our results highlight the potential of engineered synthetic protein therapeutics for addressing challenging intracellular targets. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=46 SRC="FIGDIR/small/583305v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@16e2687org.highwire.dtl.DTLVardef@a3a33eorg.highwire.dtl.DTLVardef@132784borg.highwire.dtl.DTLVardef@77bdfc_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2020

Codon usage bias in prokaryotic genomes and environmental adaptation

In each genome synonymous codons are used with different frequencies; this phenomenon is known as codon usage bias. The preferred codons tend to correspond to the most highly expressed tRNAs. It had been known that codon usage bias can influence the cellular fitness and that might be associated with the lifestyle of the organism. To test the impact of environments on genome evolution we studied the relationship between codon usage bias and the phenotypic traits of 615 prokaryotic organisms. Principal component analysis revealed that prokaryotes with a specific phenotypic characteristic and living in similar environmental conditions have similar codon preferences, accessed by the Relative Synonymous Codon Usage (RSCU), and a similar tRNA availability gauged by the tRNA gene copy number (tGCN). In addition, by measuring the average tRNA adaptation index (tAI) for each genome, we discovered that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, exhibit lower extents of translational efficiency, consistent with their need to adapt to different environments. This is the first large-scale study that examines the role of translational efficiency in the environmental adaptation of prokaryotes. Our results show that synonymous codon choices might be under strong translational selection, adapting the codons to the tRNA pool to different extents depending on the organisms lifestyle needs.

bioinformatics↗