Biology subjects

Zhao, E. M.

Publications and source records attributed to Zhao, E. M..

5 recordsLinked to original sources

bioRxiv2026

AI-enabled discovery of small molecules targeting complementary pathways for hair follicle rejuvenation

Hair thinning arises from multi-faceted dysfunction within the hair follicle, driven by both intrinsic cellular pathways and pathways responding to extrinsic hormonal and microenvironmental cues. Here, we present an AI-enabled discovery framework to discover small molecules that promote hair follicle rejuvenation. This framework integrates graph neural networks trained on phenotypic screening data with structure-based virtual screening to prioritize compounds that modulate complementary biological pathways. Through AI-enabled screening, hit-to-lead optimization, and medicinal chemistry, we identified four compounds that increase follicle dermal papilla cell viability, stabilize hypoxia signaling by inhibiting prolyl hydroxylase domain protein 2 (PHD2), and suppress androgen-mediated follicular miniaturization by inhibiting 5-reductases (5-ARs). RNA sequencing analyses confirmed pathway engagement, and functional validation across primary cells and a 3D hair follicle organoid model demonstrated high activity and cellular specificity. The lead compounds were incorporated into a water-based formulation, where they demonstrated robust solubility and combinatorial efficacy to increase sprouting length of follicle organoids. These results establish an AI-enabled platform for discovering multi-pathway modulators of hair follicle rejuvenation.

bioengineering↗

bioRxiv2025

Development of high-affinity, single-domain protein binders for neutralizing household allergens

Feline, canine, and human dust mite allergens drive significant IgE-mediated allergies in the household environment. Here, we describe the discovery and characterization of novel protein binders, termed AVA, which efficiently bind and disrupt major allergens from cats (Fel d 1), dogs (Can f 1, Can f 2), and dust mites (Der p 1, Der p 2). Leveraging camelid single-domain variable-heavy chain (VHH) antibodies, we identified and optimized VHH sequences with robust affinity towards the individual allergens. AVA disrupted critical allergen substructures (Fel d 1) and catalytic functions (Der p 1) in molecular dynamics simulations and in in vitro assays, respectively. Paired with robust thermostability and non-toxic in vitro viability profiles, AVA represents a promising approach for downstream household allergen mitigation.

bioengineering↗

bioRxiv2020

Optogenetic Amplification Circuits for Light-Induced Metabolic Control

Dynamic control of microbial metabolism is an effective strategy to improve chemical production in fermentations. While dynamic control is most often implemented using chemical inducers, optogenetics offers an attractive alternative due to the high tunability and reversibility afforded by light. However, a major concern of applying optogenetics in metabolic engineering is the risk of insufficient light penetration at high cell densities, especially in large bioreactors. Here, we present a new series of optogenetic circuits we call OptoAMP, which amplify the transcriptional response to blue light by as much as 21.8-fold compared to the basal circuit (OptoEXP). These circuits show as much as a 41-fold induction between dark and light conditions, efficient activation at light doses as low as ~1%, and strong homogeneous light-induction in bioreactors of at least 5L, with limited illumination at cell densities above 40 OD600. We demonstrate the ability of OptoAMP circuits to control engineered metabolic pathways in novel three-phase fermentations using different light schedules to control enzyme expression and improve production of lactic acid, isobutanol, and naringenin. These circuits expand the applicability of optogenetics to metabolic engineering.

synthetic biology↗

bioRxiv2019

Optogenetic lac operon to control chemical and protein production in Escherichia coli with light

Control of the lac operon with IPTG has been used for decades to regulate gene expression in E. coli for countless applications, including metabolic engineering and recombinant protein production. However, optogenetics offers unique capabilities such as easy tunability, reversibility, dynamic induction strength, and spatial control that are difficult to obtain with chemical inducers. We developed an optogenetic lac operon in a series of circuits we call OptoLAC. With these circuits, we control gene expression from various IPTG-inducible promoters using only blue light. Applying them to metabolic engineering improves mevalonate and isobutanol production by 24% and 27% respectively, compared to IPTG induction, in light-controlled fermentations scalable to at least 2L bioreactors. Furthermore, OptoLAC circuits enable light control of recombinant protein production, reaching yields comparable to IPTG induction, but with enhanced tunability of expression and spatial control. OptoLAC circuits are potentially useful to confer light controls over other cell functions originally engineered to be IPTG-inducible.

synthetic biology↗

bioRxiv2019

Optogenetic control of protein binding using light-switchable nanobodies

A growing number of optogenetic tools have been developed to control binding between two engineered protein domains. In contrast, relatively few tools confer light-switchable binding to a generic target protein of interest. Such a capability would offer substantial advantages, enabling photoswitchable binding to endogenous target proteins in vivo or light-based protein purification in vitro. Here, we report the development of opto-nanobodies (OptoNBs), a versatile class of chimeric photoswitchable proteins whose binding to proteins of interest can be enhanced or inhibited upon blue light illumination. We find that OptoNBs are suitable for a range of applications: modulating intracellular protein localization and signaling pathway activity and controlling target protein binding to surfaces and in protein separation columns. This work represents a first step towards programmable photoswitchable regulation of untagged, endogenous target proteins.\n\nHighlightsO_LIOpto-Nanobodies (OptoNBs) enable light-regulated binding to a wide range of protein targets.\nC_LIO_LIWe identify an optimized LOV domain and two loop insertion sites for light-regulated binding.\nC_LIO_LIOptoNBs function in vivo: when expressed in cells and fused to signaling domains, OptoNBs enable light-activated and light-inhibited Ras/Erk signaling.\nC_LIO_LIOptoNBs function in vitro: Target proteins can be reversibly bound to OptoNB-coated beads and separated through size-exclusion chromatography.\nC_LI

biochemistry↗