Biology subjects

Peil, L.

Publications and source records attributed to Peil, L..

4 recordsLinked to original sources

bioRxiv2026

Targeting IL-2 to inflamed tissues via oxidation-specific epitopes enables third-generation bispecific IL-2 therapeutics

Interleukin-2 (IL-2) is essential for the survival and activation of regulatory T cells (Tregs). Low-dose native IL-2 (IL-2LD) therapy restores immune regulation in vivo and has shown reproducible clinical benefit across multiple autoimmune, inflammatory, and neuroimmune diseases. Attempts to improve IL-2 through engineered variants (muteins) have mainly focused on enhancing Treg selectivity by reducing IL-2 receptor {beta}-chain binding, but this strategy profoundly diminishes biological potency, likely contributing to the limited clinical efficacy of IL-2 muteins. Here, we develop a ''third-generation IL-2'' that combines site-specific targeting and bifunctionality. We generated a bivalent fusion protein linking IL-2 to a single-chain antibody recognizing oxidation-specific epitopes (OSEs), which are abundantly expressed at inflamed sites. Targeting OSEs provides not only site-specific localization, but also true bifunctionality as both anti-OSE antibodies and IL-2LD independently show therapeutic benefit in limiting inflammation. We first show that IL-2IT has bifunctional biological activities in vitro. In vivo, IL-2IT had increased specificity for Treg over Teff activation, which we attribute to a conformation-dependent modulation of IL-2 receptor engagement. Importantly, IL-2IT provided precise delivery to inflamed tissues in models of psoriasis and colitis. Altogether, this resulted in superior therapeutic benefit in multiple clinical settings, including in atherosclerosis models. Thus, our strategy illustrates a generalizable approach to cytokine engineering that preserves native signaling while achieving spatial control. Specifically, our findings validate OSE targeting as an efficient strategy to guide therapeutics to sites of inflammation and establish OSE-IL-2 as a promising bispecific Treg engager for treating inflammation.

immunology↗

bioRxiv2025

AbDesign: Database of point mutants of antibodies with associated structures reveals poor generalization of binding predictions from machine learning models.

Antibodies are naturally evolved molecular recognition scaffolds that can bind a variety of surfaces. Their designability is crucial to the development of biologics, with computational methods holding promise in accelerating the delivery of medicines to the clinic. Modeling antibody-antigen recognition is prohibitively difficult, with data paucity being one of the biggest hurdles. Current affinity datasets comprise a small number of experimental measurements, which are often not standardized between molecules. Here, we address these issues by creating a dataset of seven antigens with two antibodies each, for which we introduce a heterogeneous set of mutations to the CDR-H3 measured by ELISA. Each of the parental complexes has a known crystal structure. We perform benchmarking of state-of-the-art affinity prediction algorithms to gauge their effectiveness. Current computational methods exhibit significant limitations in accurately predicting the effects of single-point mutations. In contrast, the older empirical, physics-based method FoldX, performs well in identifying mutants that retain binding. These findings highlight the need for more resources like the one presented here -- large, molecularly diverse, and experimentally consistent datasets.

bioinformatics↗

bioRxiv2021

Evolving a mitigation of the stress response pathway to change the basic chemistry of life

Billions of years of evolution have produced only slight variations in the standard genetic code, and the number and identity of proteinogenic amino acids have remained mostly consistent throughout all three domains of life. These observations suggest a certain rigidity of the genetic code and prompt musings as to the origin and evolution of the code. Here we conducted an adaptive laboratory evolution (ALE) to push the limits of the code restriction, by evolving Escherichia coli to fully replace tryptophan, thought to be the latest addition to the genetic code, with the analog L-{beta}-(thieno[3,2-b]pyrrolyl)alanine ([3,2]Tpa). We identified an overshooting of the stress response system to be the main inhibiting factor for limiting ancestral growth upon exposure to {beta}-(thieno[3,2-b]pyrrole ([3,2]Tp), a metabolic precursor of [3,2]Tpa, and Trp limitation. During the ALE, E. coli was able to "calm down" its stress response machinery, thereby restoring growth. In particular, the inactivation of RpoS itself, the master regulon of the general stress response, was a key event during the adaptation. Knocking out the rpoS gene in the ancestral background independent of other changes conferred growth on [3,2]Tp. Our results add additional evidence that frozen regulatory constraints rather than a rigid protein translation apparatus are Lifes gatekeepers of the canonical amino acid repertoire. This information will not only enable us to design enhanced synthetic amino acid incorporation systems but may also shed light on a general biological mechanism trapping organismal configurations in a status quo. SIGNIFICANCE STATEMENTThe (apparent) rigidity of the genetic code, as well as its universality, have long since ushered explorations into expanding the code with synthetic, new-to-nature building blocks and testing its boundaries. While nowadays even proteome-wide incorporation of synthetic amino acids has been reported on several occasions1-3, little is known about the underlying mechanisms. We here report ALE with auxotrophic E. coli that yielded successful proteome-wide replacement of Trp by its synthetic analog [3,2]Tpa accompanied with the selection for loss of RpoS4 function. Such laboratory domestication of bacteria by the acquisition of rpoS mitigation mutations is beneficial not only to overcome the stress of nutrient (Trp) starvation but also to evolve the paths to use environmental xenobiotics (e.g. [3,2]Tp) as essential nutrients for growth. We pose that regulatory constraints rather than a rigid and conserved protein translation apparatus are Lifes gatekeepers of the canonical amino acid repertoire (at least where close structural analogs are concerned). Our findings contribute a step towards understanding possible environmental causes of genetic changes and their relationship to evolution. Our evolved strain affords a platform for homogenous protein labeling with [3,2]Tpa as well as for the production of biomolecules5, which are challenging to synthesize chemically. Top-down synthetic biology will also benefit greatly from breaking through the boundaries of the frozen bacterial genetic code, as this will enable us to begin creating synthetic cells capable to utilize an expanded range of substrates essential for life.

synthetic biology↗

bioRxiv2018

Identification of RNA-associated peptides, iRAP, defines precise sites of protein-RNA interaction

ABSRACTThe identification of ever-increasing numbers of RNA species has underlined the importance of robust characterization of bona fide sites of protein-RNA interaction. UV crosslinking can be used to identify precise RNA targets for individual proteins, transcriptome-wide. Here we sought to generate reciprocal data, identifying precise sites of RNA-binding proteome-wide. The resulting technique, identification of RNA-associated peptides (iRAP), was used to locate 1331 unique RNA-interaction sites at single amino acid residue resolution in 324 S. cerevisiae proteins. Our identified RNA-interaction sites in characterized RNA-protein complex agree well with available high-resolution structures. In known RNA-interacting protiens, 317 sites fall into known and suspected RNA-interaction domains while only 21 sites fall into other annotated sequence features. Strikingly, 993 of the sites identified fall into protein regions that lack any recognizable protein domain structure or annotated sequence features. This suggests that, despite binding RNA in vivo, many of these proteins will not have defined functions in RNA metabolism.\n\nHighlights Method identifies precise RNA-binding sites across proteome\n1331 sites identified that contact RNA in 324 proteins in S. cerevisiae\nRNA binding takes place predominantly outside known protein domains

molecular biology↗