Show Abstract ▼

Abstract: Plant lectins are carbohydrate-binding proteins with diverse biological functions and growing biomedical relevance due to their ability to recognize specific glycan structures. Here, we report the high-resolution crystallographic structure of a lectin from D. altissima seeds (DAL), resolved by X-ray diffraction at 2.21 Å (PDB ID: 7LJG). The structure reveals a homodimeric fold consistent with other lectins from the Dioclea genus, reinforcing its conserved molecular architecture. Other lectins reported within the Dioclea genus share the conserved β-sandwich fold typical of this group, while DAL exhibits unique amino acid substitutions at the carbohydrate-binding site that may influence its flexibility and interaction with other proteins. To explore DAL's potential antiviral activity against SARS-CoV-2, we performed molecular docking and molecular dynamics simulations targeting the main viral protease (Mpro). The results indicated that DAL forms a stable complex with Mpro, engaging key residues within the active site and exhibiting stronger predicted binding affinity than Nirmatrelvir, the currently approved COVID-19 therapeutic. Together, these findings highlight DAL as a promising scaffold for antiviral drug development, bridging structural insights and computational analysis to guide future experimental exploration.

Open Access

Show Abstract ▼

Abstract: Evasion of apoptosis is a hallmark of cancer. Deregulation of BCL-XL, a member of the BCL-2 family of proteins, has been linked to the development of various tumor types. This study presents the design and synthesis of BCL-XL inhibitors with novel mono- and bicyclic cores. The new structural features were optimized to combine high binding efficiency with the opening of diverse novel vectors for additional modifications. The lead compounds exhibited picomolar affinities and significant cellular potency in the BCL-XL-dependent MOLT-4 cell line, which also translated into marked tumor growth inhibition in a xenograft study. These findings highlight the potential of BCL-XL inhibitors as therapeutic agents in cancer treatment by targeting the apoptotic intrinsic pathway.

Show Abstract ▼

Abstract: The prevalence of multi-drug resistant strains of bacteria on a global scale demands the development and implementation of novel antibacterial therapeutics. DNA gyrase is a type IIA topoisomerase enzyme involved in the regulation and maintenance of DNA topology in bacteria. Targeting DNA gyrase as inhibitors, the fluoroquinolones have become one of the most prescribed antibiotic classes globally. However, due to the emergence of fluoroquinolone resistant bacterial strains, numerous resistance mechanisms to these antibiotics have been observed. Two novel, first-in-class antibiotics have recently achieved U.S Food and Drug Administration (FDA) approval; zoliflodacin, a spiropyrimidinetrione (SPT), and gepotidacin, a Novel Bacterial Topoisomerase Inhibitor (NBTI). These approvals mark a significant shift in antibacterial drug development, as they are the first new classes of antibiotics targeting DNA gyrase approved in decades. Protein X-ray crystallography played a vital role in the lead-compound development of gepotidacin, with six crystal structures published in the Protein Data Bank (PDB). Protocols detailing DNA gyrase crystallisation in complex with DNA and antibiotics favour the microbatch under-oil method, and no structure-based fragment screening programs had been done on the S. aureus GyrB27:A56 fusion truncateCORE construct for the discovery of novel compounds. Furthermore, DNA gyrase crystals are often twinned resulting in complications in structure solution and molecular refinement. In this thesis, a 2.78 Å resolution crystal structure (PDB ID 8BP2) showed two molecules of zoliflodacin binding to an S. aureus DNA gyrase - DNA cleavage complex. Structural analysis showed zoliflodacin binds more directly with conserved GyrB residues, rather than through the water-metal ion bridge to highly mutated GyrA residues, observed in fluoroquinolone structures. Furthermore, a 2.58 Å resolution crystal structure was determined (PDB ID 9FZ6), whereby anomalous difference Fourier maps enabled the modelling of three novel manganese binding sites. Investigations into crystal twinning using the nanofocus beamline VMXm at Diamond Light Source (DLS) demonstrated that multiple complete datasets can be solved from a single, large macromolecular crystal. Extensive crystallisation optimisation saw the development of a new crystallisation protocol for the S. aureus DNA gyrase - DNA complex, through sitting drop vapour diffusion, enhancing the reliability of growing highly diffracting crystals. By achieving a robust, high-throughput crystallisation protocol, the first structure-based fragment screening campaign at XChem (DLS) on the S. aureus GyrB27:A56 fusion truncateCORE construct was completed, soaking over 500 crystals with small drug-like fragments for structure determination. Following extensive refinement and model building, four fragment hits were observed in notable binding pockets; three within the thiophene pocket and one in the GyrA dimer interface pocket.

Open Access

Show Abstract ▼

Abstract: Achiral bivalent ligands capable of simultaneous occupation of both hormone binding sites of transthyretin generate a substantial and complex induced near ultraviolet circular dichroism spectrum during protein binding, revealing the dynamics of this process. Reduced temperature and pH slow the interaction and reveal two phases consistent with formation of an encounter complex and progression of the interaction through the core of the transthyretin tetramer. The x-ray structure of the protein-ligand complex confirms the endpoint of the binding trajectory and shows evidence of plasticity in the structure, with substantial disturbances of some mainchain and sidechains within and adjacent to the binding channel. This study highlights the effective complementarity of CD and x-ray investigations.

Open Access

Show Abstract ▼

Abstract: Classical molecules encoded by the major histocompatibility complex (MHC) are central to immune responses. Compared to typical mammals, the chicken MHC is small and simple, determining life or death from economically important pathogens like avian influenza virus and Marek’s disease virus (MDV). Several genes within the tightly linked chicken MHC have been suggested to determine resistance and susceptibility to MDV, but it was a surprise to find that the dominantly expressed class II molecule from the resistant B2 haplotype employed a novel peptide-binding mode with a decamer core sequence compared to the susceptible B19 haplotype with a typical nonamer core. We examined the crystal structure of the dominantly expressed class II molecule from another resistant haplotype, B21, which is extremely frequent in commercial chicken flocks, to find that it bound the same MDV peptide with both nonamer and decamer cores, revealing an unexpected plasticity of binding that potentially increases the immune response to this devastating pathogen.