De Winter, H. | bioRxiv Science

bioRxiv2026

Chemical tools to Detect and Inhibit IgA1 Proteases in Haemophilus influenzae

Non-encapsulated ("non-typeable") Haemophilus influenzae is a major cause of mucosal infections such as otitis media, conjunctivitis, and exacerbations of chronic obstructive pulmonary disease. Rising antibiotic resistance has increased interest in anti-virulence strategies that reduce pathogenicity without exerting selective pressure for resistance. A key virulence factor of H. influenzae is immunoglobulin A1 protease (IgA1P), a secreted serine protease that promotes colonization by cleaving human IgA1 at the hinge region and enabling immune evasion. Despite its therapeutic promise, progress has been limited by the lack of chemical tools to probe IgA1P activity in its native biological environment. Here, we report the first activity-based probes that enable direct detection of active IgA1Ps in complex samples and H. influenzae clinical isolates. Competitive activity-based screening using these probes identified novel IgA1P inhibitors, and structure-activity relationship guided optimization yielded a potent lead IgA1P inhibitor. This inhibitor preserves IgA1 at the bacterial surface, demonstrating effective inhibition of IgA1P activity in its native context and chemical disruption of an IgA1P-dependent immune-evasion mechanism. Together, these chemical tools establish a versatile platform for elucidating IgA1Ps role in H. influenzae colonization and virulence, and for validating IgA1Ps as diagnostic markers and antivirulence targets.

microbiology↗

bioRxiv2024

Allosteric inhibition of trypanosomatid pyruvate kinases by a camelid single-domain antibody

African trypanosomes are the causative agents of neglected tropical diseases affecting both humans and livestock. Disease control is highly challenging due to an increasing number of drug treatment failures. African trypanosomes are extracellular, blood-borne parasites that mainly rely on glycolysis for their energy metabolism within the mammalian host. Trypanosomal glycolytic enzymes are therefore of interest for the development of trypanocidal drugs. Here, we report the serendipitous discovery of a camelid single-domain antibody (sdAb aka Nanobody) that selectively inhibits the enzymatic activity of trypanosomatid (but not host) pyruvate kinases through an allosteric mechanism. By combining enzyme kinetics, biophysics, structural biology, and transgenic parasite survival assays, we provide a proof-of-principle that the sdAb-mediated enzyme inhibition negatively impacts parasite fitness and growth.

biochemistry↗

bioRxiv2021

Genomic and phenotypic characterization of experimentally selected resistant Leishmania donovani reveals a role for dynamin-1 like protein in the mechanism of resistance to a novel anti-leishmanial compound

The implementation of prospective drug resistance (DR) studies in the R&D pipelines is a common practice for many infectious diseases, but not for Neglected Tropical Diseases. Here, we explored and demonstrated the importance of this approach, using as paradigms Leishmania donovani, the etiological agent of Visceral Leishmaniasis (VL), and TCMDC-143345, a promising compound of the GSK Leishbox to treat VL. We experimentally selected resistance to TCMDC-143345 in vitro and characterized resistant parasites at genomic and phenotypic levels. We found that it took more time to develop resistance to TCMDC-143345 than to other drugs in clinical use and that there was no cross resistance to these drugs, suggesting a new and unique mechanism. By whole genome sequencing, we found two mutations in the gene encoding the L. donovani dynamin-1-like protein (LdoDLP1) that were fixed at highest drug pressure. Through phylogenetic analysis, we identified LdoDLP1 as a family member of the dynamin-related proteins, a group of proteins that impacts the shapes of biological membranes by mediating fusion and fission events, with a putative role in mitochondrial fission. We found that L. donovani lines genetically engineered to harbor the two identified LdoDLP1 mutations were resistant to TCMDC-143345 and displayed altered mitochondrial properties. By homology modeling, we showed how the two LdoDLP1 mutations may influence protein structure and function. Taken together, our data reveal a clear involvement of LdoDLP1 in the adaptation/resistance of L. donovani to TCMDC-143345. ImportanceHumans and their pathogens are continuously locked in a molecular arms race during which the eventual emergence of pathogen drug resistance (DR) seems inevitable. For neglected tropical diseases (NTDs), DR is generally studied retrospectively, once it has already been established in clinical settings. We previously recommended to keep one step ahead in the host-pathogen arms race and implement prospective DR studies in the R&D pipeline, a common practice for many infectious diseases, but not for NTDs. Here, using Leishmania donovani, the etiological agent of Visceral Leishmaniasis (VL), and TCMDC-143345, a promising compound of the GSK Leishbox to treat VL, as paradigms, we experimentally selected resistance to the compound and proceeded to genomic and phenotypic characterization of DR parasites. The results gathered in the present study suggest a new DR mechanism involving the L. donovani dynamin-1 like protein (LdoDLP1) and demonstrate the practical relevance of prospective DR studies.

microbiology↗