Biology subjects

Leach, D. T.

Publications and source records attributed to Leach, D. T..

7 recordsLinked to original sources

bioRxiv2026

ChatGEM: An Agentic Architecture Enabling Interactive Simulation of Genome-Scale Metabolic Models

Genome-scale metabolic models (GEMs) are powerful tools for predicting cellular phenotypes and guiding microbial strain engineering, yet broad adoption remains challenging due to the computational expertise required. To overcome that, we present ChatGEM, an agentic platform that enables interactive GEM simulation through natural language. Built on the multi-agent ADEPT framework, ChatGEM integrates COBRApy within a retrieval-augmented generation (RAG) architecture that coordinates code generation and execution through specialized agents. Benchmarking across three tasks of increasing complexity showed that RAG-enabled code generation improved the mean overall performance score from 2.63 to 4.20 while reducing the execution time significantly starting from routine to complex tasks. Application of ChatGEM using an enzyme-constrained GEM (ecGEM) for four engineered Pseudomonas putida KT2440 strains identified the constitutive strain as the optimal chassis for succinate overproduction using a succinate leakage index - a prediction observed experimentally. Therefore, ChatGEM democratizes metabolic modeling by enabling researchers without computational expertise to perform sophisticated GEM-based analyses through natural language, and, hence, accelerating scientific discovery.

systems biology↗

bioRxiv2026

Blood Biochemical Responses to Acute Exercise: Findings from the Molecular Transducers of Physical Activity Consortium (MoTrPAC)

Exercise benefits numerous organ systems and tissues, however limited knowledge exists about its underlying molecular pathways. Identifying the exercise-induced biochemical changes that occur in the circulation may provide further insights into how exercise confers systemic health changes. Here, we perform large-scale plasma proteomic, metabolomic, and whole blood transcriptional profiling in sedentary human participants undergoing acute endurance exercise (EE), resistance exercise (RE), or a non-exercise control (CON) in up to 7 timepoints over a 24 hour period. We observe 7066 transcript, 189 protein, and 448 metabolite changes in response to EE or RE compared to CON. Our analyses reveal numerous shared biochemical responses between EE and RE modes, but also differences in immune cell responses, lipid metabolism, and pathways reflective of tissue repair and angiogenesis. Taken together, our findings highlight novel temporal and exercise mode-specific blood-based molecular responses to acute exercise, and provide a new resource for the scientific community.

systems biology↗

bioRxiv2026

Multi-Omic, Multi-Tissue Responses to Acute Exercise in Sedentary Adults: Findings from the Molecular Transducers of Physical Activity Consortium

Regular physical activity represents one of the greatest mechanisms for maintaining human health, yet the underlying molecular transducers of these benefits remain incompletely understood. Multi-omic assays now provide new opportunities to study the coordinated molecular responses of body tissues to different exercise modalities. The Molecular Transducers of Physical Activity Consortium (MoTrPAC) was established to address this need by creating a molecular map of the response to physical activity. Described here is the first human cohort of MoTrPAC: sedentary adults enrolled prior to study suspension during the COVID-19 pandemic (N=175) randomized to either endurance or resistance exercise, or non-exercise control. From these participants, we detail their global acute molecular response in skeletal muscle, adipose tissue, and blood, integrated at multiple levels: tissue, exercise modality, timepoint, and omic category. These analyses characterize key molecular pathways, identify central regulators, and implicate novel candidate exerkines in mediating multi-organ exercise effects.

systems biology↗

bioRxiv2025

Chemoproteomic elucidation of β-lactam drug targets in Mycobacterium abscessus

The pathogen Mycobacterium abscessus (Mab) can cause severe and difficult to treat chronic lung infections. Despite the rising incidence and clinical concern of Mab infections, treatment options are limited and often ineffective. Treatment is complicated by Mabs ability to persist in a non-replicative, drug-resistant state. Several {beta}-lactam antibiotics are potently bactericidal against Mab but are underutilized because their molecular mechanisms of action against Mab are incompletely understood. In the current study, we used {beta}-lactam-derived activity-based probes and chemoproteomics to report the first comprehensive list of enzymes in Mab targeted by {beta}-lactams. We compared {beta}-lactam targets across two Mab subspecies in actively replicating and non-replicative cultures, using a new carbon starvation model of persistence. We identified 17 targets that were active in every condition tested, seven of which were previously unknown to bind {beta}-lactams. Lastly, we characterized the {beta}-lactamase activity and {beta}-lactam inhibition profiles of nine Mab enzymes, demonstrating that imipenem inhibits these targets more effectively than cefoxitin. These findings provide clarity on the mechanisms of action of clinically relevant {beta}-lactams in Mab, a crucial step toward fully realizing their potential for treating infections caused by this opportunistic pathogen.

microbiology↗

bioRxiv2025

Comprehensive identification of β-lactam antibiotic polypharmacology in Mycobacterium tuberculosis

Infections with Mycobacterium tuberculosis (Mtb) cause tuberculosis (TB), which requires at least six months of treatment with multiple antibiotics. There is emergent interest in using {beta}-lactam antibiotics to improve treatment outcomes for patients. These drugs target cell wall biosynthesis, but a comprehensive list of enzymes inhibited by {beta}-lactams in Mtb is lacking. In the current study, we sought to identify and characterize Mtb enzymes inhibited by {beta}-lactam antibiotics using physiological conditions representative of both acute and chronic TB disease. We used new activity-based probes based on the {beta}-lactam antibiotic meropenem due to its approval by the World Health Organization for TB treatment. Activity-based probes label enzymes based on both substrate specificity and catalytic mechanism, enabling precise identification of drug targets. We identified previously undiscovered targets of meropenem in addition to known cell wall biosynthetic enzymes. We validated {beta}-lactam binding and hydrolysis for six newly identified targets: Rv1723, Rv2257c, Rv0309, DapE (Rv1202), MurI (Rv1338), and LipD (Rv1923). Our results demonstrate that there are at least 30 enzymes in Mtb vulnerable to inhibition by meropenem. This is many more {beta}-lactam targets than historically described, suggesting that efficacy in Mtb is a direct result of polypharmacology.

biochemistry↗

bioRxiv2025

Discovery of non-opioid receptor protein targets of fentanyl across tissues from animal models and humans using photoaffinity probes

Synthetic opioids such as fentanyl and related analogs have been widely used for pain management. However, their negative side effects, including respiratory depression and high potential for addiction, underscore the need for a deeper understanding of fentanyls interactions with proteins throughout the human body. Fentanyl analogs bind and activate opioid receptors in the central and peripheral nervous systems, triggering numerous downstream signaling pathways. Increasingly, fentanyl has been shown to interact with non-opioid receptors, and elucidation of these non-canonical fentanyl-protein interactions may provide insights into the mechanisms contributing to fentanyls adverse effects and illuminate novel countermeasure strategies. To identify proteins in mammalian tissues that may interact with fentanyl, we designed and synthesized three affinity-based probes (AfBPs) that include the fentanyl core and feature a diazirine photoaffinity group and alkyne handle for click chemistry at different positions. Molecular docking simulations predicted that these AfBPs bind the mu opioid receptor similarly to fentanyl. Affinity-based protein profiling using the FA-T1 probe in vitro in tissues from six animal species identified histamine N-methyltransferase (HNMT), endophilin-B1 (SH3GLB1), fructosamine-3-kinase (FN3K), cutA divalent cation tolerance analog (CUTA), and monoamine oxidase B (MAOB) among the top proteins that bind fentanyl in multiple species and tissue types. Molecular docking of fentanyl and remifentanil with these protein structures identified putative binding sites. The interaction of fentanyl with specific proteins was empirically assessed through protein structural analyses. These findings highlight potential fentanyl-protein interactions that may contribute to the acute and long-term impacts of fentanyl exposures.

pharmacology and toxicology↗

bioRxiv2024

Proteomic characterization of Mycobacterium tuberculosis subjected to carbon starvation

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), the leading cause of infectious-disease related deaths worldwide. TB infections present as a spectrum from active to latent disease. In the human host, Mtb faces hostile environments, such as nutrient deprivation, hypoxia, and low pH. Under these conditions, Mtb can enter a dormant, but viable, state characterized by a lack of cell replication and increased resistance to antibiotics. These dormant Mtb pose a major challenge to curing infections and eradicating TB globally. In the current study, we subjected Mtb to carbon starvation (CS), a culture condition that induces growth stasis and mimics nutrient-starved conditions associated with dormancy in vivo. We provide a detailed analysis of the proteome in CS compared to replicating samples. We observed extensive proteomic reprogramming, with 36% of identified proteins significantly altered in CS. Many enzymes involved in oxidative phosphorylation and lipid metabolism were retained or upregulated in CS. The cell wall biosynthetic machinery was present in CS, although numerous changes in the abundance of peptidoglycan, arabinogalactan, and mycolic acid biosynthetic enzymes likely result in pronounced remodeling of the cell wall. Many clinically approved anti-TB drugs target cell wall biosynthesis, and we found that these enzymes were largely retained in CS. Lastly, we compared our results to those of other dormancy models and propose that CS produces a physiologically-distinct state of stasis compared to hypoxia in Mtb.

microbiology↗