Biology subjects

Wintjens, R.

Publications and source records attributed to Wintjens, R..

3 recordsLinked to original sources

bioRxiv2025

AI-guided competitive docking for virtual screening and compound efficacy prediction

Machine learning has transformed how we predict protein structures and interactions, but its full potential in drug discovery is only beginning to be realized. In this study, we demonstrate that advanced deep learning tools --such as AlphaFold3 and Boltz-1/2-- not only predict protein-ligand interactions with high accuracy but can also separate active drug compounds from inactive ones. We present a straightforward strategy called pairwise competitive docking, which ranks drug candidates by directly comparing how well they bind to a proteins target site. When applied to both bacterial and human enzymes, this method produced rankings that closely matched experimental results. We further show how this approach can guide the design of improved antibiotics and speed up the discovery of promising drug candidates from large chemical libraries. Overall, our findings highlight how machine learning can make structure-based drug design faster, more reliable, and more cost-effective.

bioinformatics↗

bioRxiv2025

Exploiting Vitamin B6 Dependency: BVL3572S Inhibits HisC and AlaA to Kill Mycobacterium tuberculosis

Tuberculosis remains the leading cause of death from a single infectious agent worldwide, and the growing prevalence of multi-drug resistant Mycobacterium tuberculosis (Mtb) underscores the urgent need for antibiotics with novel mechanisms of action. Here, we characterize BVL3572S, a hydroxamic acid-containing compound that is bactericidal and potently inhibits the growth of both extracellular and intracellular Mtb. Integrated transcriptomic, genetic, and biochemical analyses identified the pyridoxal phosphate (PLP)-dependent aminotransferases HisC (Rv1600) and AlaA (Rv0337c; formerly AspC) as the primary molecular targets of BVL3572S, thereby simultaneously impacting L-histidine and L-alanine biosynthesis. Spontaneous resistance mutants harbored mutations in hisC or alaA. Target engagement was further supported by overexpression studies: AlaA overexpression increased resistance in the presence of L-His whereas HisC overexpression paradoxically increased susceptibility. X-ray crystallography revealed a covalent adduct between PLP and BVL3572S within the HisC active site. The short occupancy of this adduct suggests a futile cycle that sequesters PLP. Isotopic labeling revealed widespread perturbation of amino acid biosynthesis, consistent with PLP starvation. The stepwise resistance observed upon supplementation with L-His and L-Ala together or with PLP alone suggests inhibition of multiple targets. Genome-scale CRISPRi and Tn-seq analyses additionally indicated disruptions in central metabolism, cell envelope integrity, and redox balance, possibly due to PLP depletion cascades. Consistent with its inhibition of AlaA, BVL3572S displayed strong synergy with D-cycloserine, a second-line antitubercular drug targeting D-alanine synthesis and impacting peptidoglycan synthesis, highlighting the potential of this compound in combination therapy. Collectively, our findings establish BVL3572S as a promising lead compound acting through a previously unexploited, multitarget mechanism that induces broad metabolic stress in Mtb, offering a novel therapeutic strategy against drug-resistant tuberculosis.

microbiology↗

bioRxiv2022

Putative SET-domain methyltransferases in Cryptosporidium parvum and histone methylation during infection

Cryptosporidium parvum is a major cause of an intestinal pathology called cryptosporidiosis which affects humans and other vertebrates. Despite being declared as a public health problem by World Health Organization (WHO) since 2006, pathogenesis caused by this parasite remains poorly understood. More recently, C. parvum has been linked with oncogenesis. In particular, the mechanisms involved in the processes of gene expression regulation are completely unexplored in Cryptosporidium. In the current study, we took the opportunity to investigate a dynamic epigenetic modification called histone lysine methylation during the life cycle of the parasite. We successfully identified putative SET-domain containing proteins, lysine methyltransferases (KMTs), which catalyze the methylation of different lysine residues. Phylogenetic analysis classified them into distinct subfamilies namely CpSET1, CpSET2, CpSET8, CpKMTox and CpAKMT. Structural analysis further characterized CpSET1, CpSET2 and CpSET8 to be histone lysine methyltransferases (HKMTs). Their functional significance was predicted by using site-specific methyl-lysine antibodies during development of the parasite (CpSET1:H3K4; CpSET2:H3K36; CpSET8:H4K20). In particular, the SET domain of CpSET8 showcased methyltransferase activity confirming the existence of functional HKMTs in Cryptosporidium. Moreover, the consequence of C. parvum infection on the host lysine methylation events highlights the inherit potential of the parasite to exploit the host epigenetic regulation to its advantage. Thus, this study is the first one to provide insights on epigenetics mechanisms occurring throughout the parasites life cycle and during the interaction with its host. As Cryptosporidium is a protozoan that significantly affects the health of both humans and animals, a better understanding of its developmental processes within the definitive host may highlight novel infection control strategies. Author SummaryCryptosporidium species have a very compact genome (~9.2 Mb) unlike its apicomplexan homologs such as Toxoplasma (~63 Mb). Moreover, the lack of large families of transcriptional factors requires them to heavily rely on chromatin remodeling components for its gene regulation. Thus, study and identification of novel elements which contribute to chromatin dynamics could assist a better understanding of the biology of this parasite. In the current study we investigated histone lysine methylation, a dynamic epigenetic modification which regulates gene activation as well as repression. More importantly, characterizing the enzymes which bring about this regulation, provides potential new druggable targets to attack the parasite.

microbiology↗