Biology subjects

Ahmed, F. H.

Publications and source records attributed to Ahmed, F. H..

4 recordsLinked to original sources

bioRxiv2026

Data-Efficient Exploration of Enzyme Function Using Family-Specific Machine Learning

Enzymes are essential biocatalysts across diverse industries, driving demand for high-performing variants. Foundation models are attractive for guiding enzyme discovery, but often lack the resolution to model subtle variations driving function within homologous families. Navigating these rugged functional landscapes to identify elite variants remains challenging and experimentally costly, even when guided by such models. Here we show that coupling dense, family-specific experimental screening with targeted, sequence-based deep learning provides a data-efficient discovery strategy. We experimentally screened 1,513 natural homologues from an esterase superfamily (>7,500 assays) and used this functional landscape to train task-specific models that predict activity, thermostability, and substrate specificity from sequence alone. Prospective experimental validation of previously untested sequences demonstrated that these task-specific models significantly outperformed generalist pre-trained and physics-based models in enriching for target traits. Residue-level attribution further indicated that the models captured sequence patterns consistent with underlying structural features. Finally, retrospective simulations showed that iterative retraining compresses the search space, discovering 60% of top-tier hits using nearly half the samples required by pre-trained baseline models. Together, these results highlight that machine learning can provide mechanistic insight, and that integrating targeted data acquisition with iterative machine learning provides a more data-efficient discovery strategy than relying on generic model scale.

bioengineering↗

bioRxiv2023

The complex inhibitory mechanism of glycomimetics with human heparanase

Heparanase (HPSE) is the only mammalian endo-{beta}-glucuronidase known to catalyse the degradation of heparan sulfate. Dysfunction of HPSE activity has been linked to several disease states, resulting in HPSE becoming the target of numerous therapeutic programs, yet no drug has passed clinical trials to date. Pentosan polysulfate sodium (PPS) is a heterogeneous FDA-approved drug for the treatment of interstitial cystitis and a known HPSE inhibitor. However, due to its heterogeneity, characterisation of its mechanism of HPSE inhibition is challenging. Here we show that inhibition of HPSE by PPS is complex, involving multiple overlapping binding events, each influenced by factors such as oligosaccharide length and inhibitor-induced changes in protein secondary structure. The present work advances our molecular understanding of the inhibition of HPSE, which will aid the development of therapeutics for the treatment of a broad range of pathologies associated with enzyme dysfunction including cancer, inflammatory disease and viral infections.

biochemistry↗

bioRxiv2022

A F420-dependent single domain chemogenetic tool for protein de-dimerization

Protein-protein interactions (PPIs) mediate many fundamental cellular processes and their control through optically or chemically responsive protein domains has a profound impact on basic research and some clinical applications. Most available chemogenetic methods induce the association, i.e., dimerization or oligomerization, of target proteins, and the few available dissociation approaches either break large oligomeric protein clusters or heteromeric complexes. Here, we have exploited the controlled dissociation of a dimeric oxidoreductase from mycobacteria (MSMEG_2027) by its native cofactor, F420, which is not present in mammals, as a bioorthogonal monomerization switch. We found that in the absence of F420, MSMEG_2027 forms a unique domain-swapped dimer that occludes the cofactor binding site. Substantial remodelling of the intertwined N-terminal helix upon F420 binding results in the dissolution of the dimer. We then show that MSMEG_2027 can be expressed as fusion proteins in human cells and apply it as a tool to induce and release MAPK/ERK signalling downstream of a chimeric fibroblast growth factor receptor 1 (FGFR1) tyrosine kinase. This F420-dependent chemogenetic de-dimerization tool is stoichiometric, based on a single domain and presents a novel mechanism to investigate protein complexes in situ.

synthetic biology↗

bioRxiv2019

The evolution of nitroimidazole antibiotic resistance in Mycobacterium tuberculosis

Our inability to predict whether certain mutations will confer antibiotic resistance has made it difficult to rapidly detect the emergence of resistance, identify pre-existing resistant populations and manage our use of antibiotics to effective treat patients and prevent or slow the spread of resistance. Here we investigated the potential for resistance against the new antitubercular nitroimidazole prodrugs pretomanid and delamanid to emerge in Mycobacterium tuberculosis, the causative agent of tuberculosis (TB). Deazaflavin-dependent nitroreductase (Ddn) is the only identified enzyme within M. tuberculosis that activates these prodrugs, via an F420H2-dependent reaction. We show that the native menaquinone-reductase activity of Ddn is important in aerobic respiration and essential for emergence from dormancy, which suggests that for resistance to spread and pose a threat to human health, the native activity of Ddn must be at least partially retained. We tested 75 unique mutations, including all known sequence polymorphisms identified among ~15,000 sequenced M. tuberculosis genomes. Several mutations abolished pretomanid activation in vitro, without causing complete loss of the native activity. We confirmed that a transmissible M. tuberculosis isolate from the hypervirulent Beijing family already possesses one such mutation and is resistant to pretomanid, even though it was never exposed to pretomanid. Notably, delamanid was still effective against this strain, which is consistent with structural analysis that indicates delamanid and pretomanid bind to Ddn differently. We suggest that the mutations identified in this work be monitored for informed use of delamanid and pretomanid treatment and to slow the emergence of resistance.

molecular biology↗