Inna, K. V. | Search bioRxiv

bioRxiv2025

Fleming: An AI Agent for Antibiotic Discovery in Mycobacterium Tuberculosis

Antibiotic development is challenged by high costs and failure rates. Artificial intelligence (AI) holds promise to overcome these challenges by predicting inhibitory properties of novel compounds, generating new candidates, and contextualizing property predictions in the biological background. Fleming is an integrative AI agent that explores novel chemical space to identify lead compounds meeting multiple criteria. The discriminative and generative AI models for Mycobacterium tuberculosis (Mtb) inhibition were trained on a set of 114,900 diverse compounds and fragments based on in vitro growth inhibition. We combined both models as well as molecular optimization, ADMET prediction and literature search functions to make Fleming an integrated agent for Mtb preclinical lead identification. Fleming has 17% higher discrimination between known Mtb leads and leads for other diseases than a generic LLM agent along with 13% higher discrimination than molecular property prediction alone on challenging ADMET tasks. Fleming demonstrates an 83% in vitro hit rate of predicted inhibition and a 100% hit rate of de novo generative design. Flemings generative designs also demonstrate an 83% rate of favorable ADMET profiles. Fleming is an integrative AI agent able to explore new regions of the chemical space to select lead compounds that simultaneously meet several desirable criteria.

bioinformatics↗

bioRxiv2020

A Sec14-like Phosphatidylinositol Transfer Protein Paralog Defines a Novel Class of Heme-binding Proteins With An Unusual Heme Coordination Mechanism

Yeast Sfh5 is an unusual member of the Sec14-like phosphatidylinositol transfer protein (PITP) family. Whereas PITPs are defined by their abilities to transfer phosphatidylinositol between membranes in vitro, and to stimulate phosphoinositide signaling in vivo, Sfh5 does not exhibit these activities. Rather, Sfh5 is a redox-active penta-coordinate high spin FeIII heme-binding protein with an unusual heme-binding arrangement that involves a co-axial tyrosine/histidine coordination strategy and a complex electronic structure connecting the open shell iron d-orbitals with three aromatic ring systems. That Sfh5 is not a PITP is supported by demonstrations that heme is not a readily exchangeable ligand, and that phosphatidylinositol-exchange activity is resuscitated in heme binding-deficient Sfh5 mutants. The collective data identify Sfh5 as the prototype of a new class of fungal hemoproteins, and emphasize the versatility of the Sec14-fold as scaffold for translating the binding of chemically distinct ligands to the control of diverse sets of cellular activities.

biochemistry↗

bioRxiv2018

A DNA-binding protein tunes septum placement during Bacillus subtilis sporulation

Bacillus subtilis is a soil bacterium capable of differentiating into a spore form resistant to desiccation, UV radiation, and heat. Early in spore development the cell possesses two copies of a circular chromosome, anchored to opposite cell poles via DNA proximal to the origin of replication (oriC). As sporulation progresses an FtsZ ring (Z-ring) assembles close to one pole and directs septation over one chromosome. The polar division generates two cell compartments with differing chromosomal contents. The smaller \"forespore\" compartment initially contains only 25-30% of one chromosome and this transient genetic asymmetry is required for differentiation. At the population level, the timely assembly of polar Z-rings and the precise capture of the chromosome in the forespore both require RefZ, a DNA-binding protein synthesized early in sporulation. To mediate precise capture of the chromosome RefZ must bind to specific DNA motifs (RBMs) that are localized near the poles around the time of septation, suggesting RefZ binds to the RBMs to affect positioning of the septum relative to the chromosome. RefZs mechanism of action is unknown, however, cells artificially induced to express RefZ during vegetative growth cannot assemble Z-rings or divide, leading to the hypothesis that RefZ-RBM complexes mediate precise chromosome capture by modulating FtsZ function. To investigate this possibility, we isolated 10 RefZ loss-of-function (rLOF) variants unable to inhibit cell division when expressed during vegetative growth, yet were still capable of binding RBM-containing DNA. Sporulating cells expressing the rLOF variants in place of wild-type RefZ phenocopy a {Delta}refZ mutant, suggesting that RefZ mediates chromosome capture through an FtsZ-dependent mechanism. To better understand the molecular basis of RefZs activity, the crystal structure of RefZ was solved and wild-type RefZ and the rLOF variants were further characterized. Our data suggest that RefZs oligomerization state and specificity for the RBMs are critical determinants influencing RefZs ability to affect FtsZ dynamics in vivo. We propose that RBM-bound RefZ complexes function as a developmentally regulated nucleoid occlusion system for fine-tuning the position of the septum relative to the chromosome during sporulation.\n\nAuthor SummaryThe Gram-positive bacterium B. subtilis can differentiate into a dormant cell type called a spore. Early in sporulation the cell divides near one pole, generating two compartments: a larger mother cell and a smaller forespore (future spore). Only approximately 30 percent of one chromosome is initially captured in the forespore compartment at the time of division and this genetic asymmetry is critical for sporulation to progress. Precise chromosome capture requires RefZ, a sporulation protein that binds to specific DNA motifs (RBMs) positioned at the pole near the site of cell division. How RefZ functions at the molecular level is not fully understood. Here we show that RefZ-RBM complexes facilitate chromosome capture by acting through the major cell division protein FtsZ.

microbiology↗