The 2-methylcitrate cycle and the glyoxylate shunt in Pseudomonas aeruginosa are linked through enzymatic redundancy.

The 2-methylcitrate cycle (2-MCC) and the glyoxylate cycle are central metabolic pathways in Pseudomonas aeruginosa, enabling the organism to utilize organic acids such as propionate and acetate during infection. Here, we show that these cycles are linked through enzymatic redundancy, with isocitrate lyase (AceA) exhibiting secondary 2-methylisocitrate lyase (2-MICL) activity. Furthermore, we use a combination of structural analyses, enzyme kinetics, metabolomics, and targeted mutation of PrpB to demonstrate that whereas loss of PrpB function impairs growth on propionate, the promiscuous 2-MICL activity of AceA compensates for this by mitigating the accumulation of toxic 2-MCC intermediates.

Current state and future prospects of Horizontal Gene Transfer detection.

Artificial intelligence (AI) has been shown to be beneficial in a wide range of bioinformatics applications. Horizontal Gene Transfer (HGT) is a driving force of evolutionary changes in prokaryotes. It is widely recognized that it contributes to the emergence of antimicrobial resistance (AMR), which poses a particularly serious threat to public health.

Macrocycle-based PROTACs selectively degrade cyclophilin A and inhibit HIV-1 and HCV.

Targeting host proteins that are crucial for viral replication offers a promising antiviral strategy. We have designed and characterised antiviral PROteolysis TArgeting Chimeras (PROTACs) targeting the human protein cyclophilin A (CypA), a host cofactor for unrelated viruses including human immunodeficiency virus (HIV) and hepatitis C virus (HCV). The PROTAC warheads are based on fully synthetic macrocycles derived from sanglifehrin A, which are structurally different from the classical Cyp inhibitor, cyclosporine A.

Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders.

The ubiquitin E3 ligase cereblon (CRBN) is the target of therapeutic drugs thalidomide and lenalidomide and is recruited by most targeted protein degraders (PROTACs and molecular glues) in clinical development. Biophysical and structural investigation of CRBN has been limited by current constructs that either require co-expression with the adaptor DDB1 or inadequately represent full-length protein, with high-resolution structures of degrader ternary complexes remaining rare. We present the design of CRBN, a construct that readily expresses from E.

Crystallization of VHL-based PROTAC-induced ternary complexes.

X-ray crystal structures of PROTAC-induced ternary complexes provide invaluable insights into the critical species underpinning PROTAC mode of action, explain protein degradation selectivity profiles, and can guide rational degrader design. Nevertheless, crystallization of the ternary complexes formed by PROTACs remains an important bottleneck in employing this method. This is mainly due to the potential flexibility and heterogeneity that is inherent to a non-native protein-protein complex mediated by a small molecule, which together can hamper crystallization of the desired species.