Biochemistry and Pharmacology - Research Publications

Permanent URI for this collection

Search Results

Now showing 1 - 10 of 71
  • Item
    No Preview Available
    Pharmacologic hyperstabilisation of the HIV-1 capsid lattice induces capsid failure
    Faysal, KMR ; Walsh, JC ; Renner, N ; Marquez, CL ; Shah, VB ; Tuckwell, AJ ; Christie, MP ; Parker, MW ; Turville, SG ; Towers, GJ ; James, LC ; Jacques, DA ; Bocking, T (eLIFE SCIENCES PUBL LTD, 2024-02-13)
    The HIV-1 capsid has emerged as a tractable target for antiretroviral therapy. Lenacapavir, developed by Gilead Sciences, is the first capsid-targeting drug approved for medical use. Here, we investigate the effect of lenacapavir on HIV capsid stability and uncoating. We employ a single particle approach that simultaneously measures capsid content release and lattice persistence. We demonstrate that lenacapavir's potent antiviral activity is predominantly due to lethal hyperstabilisation of the capsid lattice and resultant loss of compartmentalisation. This study highlights that disrupting capsid metastability is a powerful strategy for the development of novel antivirals.
  • Item
    No Preview Available
    Distinct Assemblies of Heterodimeric Cytokine Receptors Govern Stemness Programs in Leukemia
    Kan, WL ; Dhagat, U ; Kaufmann, KB ; Hercus, TR ; Nero, TL ; Zeng, AGX ; Toubia, J ; Barry, EF ; Broughton, SE ; Gomez, GA ; Benard, BA ; Dottore, M ; Shing, KS ; Boutzen, H ; Samaraweera, SE ; Simpson, KJ ; Jin, L ; Goodall, GJ ; Begley, CG ; Thomas, D ; Ekert, PG ; Tvorogov, D ; D'Andrea, RJ ; Dick, JE ; Parker, MW ; Lopez, AF (AMER ASSOC CANCER RESEARCH, 2023-08-04)
    UNLABELLED: Leukemia stem cells (LSC) possess distinct self-renewal and arrested differentiation properties that are responsible for disease emergence, therapy failure, and recurrence in acute myeloid leukemia (AML). Despite AML displaying extensive biological and clinical heterogeneity, LSC with high interleukin-3 receptor (IL3R) levels are a constant yet puzzling feature, as this receptor lacks tyrosine kinase activity. Here, we show that the heterodimeric IL3Rα/βc receptor assembles into hexamers and dodecamers through a unique interface in the 3D structure, where high IL3Rα/βc ratios bias hexamer formation. Importantly, receptor stoichiometry is clinically relevant as it varies across the individual cells in the AML hierarchy, in which high IL3Rα/βc ratios in LSCs drive hexamer-mediated stemness programs and poor patient survival, while low ratios mediate differentiation. Our study establishes a new paradigm in which alternative cytokine receptor stoichiometries differentially regulate cell fate, a signaling mechanism that may be generalizable to other transformed cellular hierarchies and of potential therapeutic significance. SIGNIFICANCE: Stemness is a hallmark of many cancers and is largely responsible for disease emergence, progression, and relapse. Our finding that clinically significant stemness programs in AML are directly regulated by different stoichiometries of cytokine receptors represents a hitherto unexplained mechanism underlying cell-fate decisions in cancer stem cell hierarchies. This article is highlighted in the In This Issue feature, p. 1749.
  • Item
    Thumbnail Image
    Bromodomain and extraterminal protein-targeted probe enables tumour visualisation in vivo using positron emission tomography
    Dickmann, CGF ; McDonald, AFF ; Huynh, N ; Rigopoulos, A ; Liu, Z ; Guo, N ; Osellame, LDD ; Gorman, MAA ; Parker, MWW ; Gan, HKK ; Scott, AMM ; Ackermann, U ; Burvenich, IJG ; White, JMM (ROYAL SOC CHEMISTRY, 2023-03-09)
    Bromodomain and extraterminal (BET) proteins, a family of epigenetic regulators, have emerged as important oncology drug targets. BET proteins have not been targeted for molecular imaging of cancer. Here, we report the development of a novel molecule radiolabelled with positron emitting fluorine-18, [18F]BiPET-2, and its in vitro and preclinical evaluation in glioblastoma models.
  • Item
    No Preview Available
    Covalent Inhibition by a Natural Product-Inspired Latent Electrophile
    Byun, DPP ; Ritchie, J ; Jung, Y ; Holewinski, R ; Kim, H-R ; Tagirasa, R ; Ivanic, J ; Weekley, CMM ; Parker, MWW ; Andresson, T ; Yoo, E (AMER CHEMICAL SOC, 2023-05-15)
    Strategies to target specific protein cysteines are critical to covalent probe and drug discovery. 3-Bromo-4,5-dihydroisoxazole (BDHI) is a natural product-inspired, synthetically accessible electrophilic moiety that has previously been shown to react with nucleophilic cysteines in the active site of purified enzymes. Here, we define the global cysteine reactivity and selectivity of a set of BDHI-functionalized chemical fragments using competitive chemoproteomic profiling methods. Our study demonstrates that BDHIs capably engage reactive cysteine residues in the human proteome and the selectivity landscape of cysteines liganded by BDHI is distinct from that of haloacetamide electrophiles. Given its tempered reactivity, BDHIs showed restricted, selective engagement with proteins driven by interactions between a tunable binding element and the complementary protein sites. We validate that BDHI forms covalent conjugates with glutathione S-transferase Pi (GSTP1) and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1), emerging anticancer targets. BDHI electrophile was further exploited in Bruton's tyrosine kinase (BTK) inhibitor design using a single-step late-stage installation of the warhead onto acrylamide-containing compounds. Together, this study expands the spectrum of optimizable chemical tools for covalent ligand discovery and highlights the utility of 3-bromo-4,5-dihydroisoxazole as a cysteine-reactive electrophile.
  • Item
    No Preview Available
    Translating the biology of B common receptor- engaging cytokines into clinical medicine
    Pant, H ; Hercus, TR ; Tumes, DJ ; Yip, KH ; Parker, MW ; Owczarek, CM ; Lopez, AF ; Huston, DP (MOSBY-ELSEVIER, 2023-02)
    The family of cytokines that comprises IL-3, IL-5, and GM-CSF was discovered over 30 years ago, and their biological activities and resulting impact in clinical medicine has continued to expand ever since. Originally identified as bone marrow growth factors capable of acting on hemopoietic progenitor cells to induce their proliferation and differentiation into mature blood cells, these cytokines are also recognized as key mediators of inflammation and the pathobiology of diverse immunologic diseases. This increased understanding of the functional repertoire of IL-3, IL-5, and GM-CSF has led to an explosion of interest in modulating their functions for clinical management. Key to the successful clinical translation of this knowledge is the recognition that these cytokines act by engaging distinct dimeric receptors and that they share a common signaling subunit called β-common or βc. The structural determination of how IL-3, IL-5, and GM-CSF interact with their receptors and linking this to their differential biological functions on effector cells has unveiled new paradigms of cell signaling. This knowledge has paved the way for novel mAbs and other molecules as selective or pan inhibitors for use in different clinical settings.
  • Item
    No Preview Available
    Structural biology of cell surface receptors implicated in Alzheimer's disease
    Hermans, SJ ; Nero, TL ; Morton, CJ ; Gooi, JH ; Crespi, GAN ; Hancock, NC ; Gao, C ; Ishii, K ; Markulic, J ; Parker, MW (SPRINGERNATURE, 2022-02)
    Alzheimer's disease is a common and devastating age-related disease with no effective disease-modifying treatments. Human genetics has implicated a wide range of cell surface receptors as playing a role in the disease, many of which are involved in the production or clearance of neurotoxins in the brain. Amyloid precursor protein, a membrane-bound signaling molecule, is at the very heart of the disease: hereditary mutations in its gene are associated with a greatly increased risk of getting the disease. A proteolytic breakdown product of amyloid precursor protein, the neurotoxic Aβ peptide, has been the target for many drug discovery efforts. Antibodies have been designed to target Aβ production with some success, although they have not proved efficacious in clinical trials with regards to cognitive benefits to date. Many of the recently identified genes associated with late-onset Alzheimer's disease risk are integral to the innate immune system. Some of these genes code for microglial proteins, such as the strongest genetic risk factor for the disease, namely APOE, and the cell surface receptors CD33 and TREM2 which are involved in clearance of the Aβ peptide from the brain. In this review, we show how structural biology has provided key insights into the normal functioning of these cell surface receptors and provided a framework for developing novel treatments to combat Alzheimer's disease.
  • Item
    No Preview Available
    Cholesterol-dependent cytolysins: The outstanding questions
    Johnstone, BA ; Joseph, R ; Christie, MP ; Morton, CJ ; McGuiness, C ; Walsh, JC ; Bocking, T ; Tweten, RK ; Parker, MW (WILEY, 2022-12)
    The cholesterol-dependent cytolysins (CDCs) are a major family of bacterial pore-forming proteins secreted as virulence factors by Gram-positive bacterial species. CDCs are produced as soluble, monomeric proteins that bind specifically to cholesterol-rich membranes, where they oligomerize into ring-shaped pores of more than 30 monomers. Understanding the details of the steps the toxin undergoes in converting from monomer to a membrane-spanning pore is a continuing challenge. In this review we summarize what we know about CDCs and highlight the remaining outstanding questions that require answers to obtain a complete picture of how these toxins kill cells.
  • Item
    Thumbnail Image
    A novel phosphocholine-mimetic inhibits a pro-inflammatory conformational change in C-reactive protein
    Zeller, J ; Shing, KSCT ; Nero, TL ; McFadyen, JD ; Krippner, G ; Bogner, B ; Kreuzaler, S ; Kiefer, J ; Horner, VK ; Braig, D ; Danish, H ; Baratchi, S ; Fricke, M ; Wang, X ; Kather, MG ; Kammerer, B ; Woollard, KJ ; Sharma, P ; Morton, CJ ; Pietersz, G ; Parker, MW ; Peter, K ; Eisenhardt, SU (WILEY, 2023-01-11)
    C-reactive protein (CRP) is an early-stage acute phase protein and highly upregulated in response to inflammatory reactions. We recently identified a novel mechanism that leads to a conformational change from the native, functionally relatively inert, pentameric CRP (pCRP) structure to a pentameric CRP intermediate (pCRP*) and ultimately to the monomeric CRP (mCRP) form, both exhibiting highly pro-inflammatory effects. This transition in the inflammatory profile of CRP is mediated by binding of pCRP to activated/damaged cell membranes via exposed phosphocholine lipid head groups. We designed a tool compound as a low molecular weight CRP inhibitor using the structure of phosphocholine as a template. X-ray crystallography revealed specific binding to the phosphocholine binding pockets of pCRP. We provide in vitro and in vivo proof-of-concept data demonstrating that the low molecular weight tool compound inhibits CRP-driven exacerbation of local inflammatory responses, while potentially preserving pathogen-defense functions of CRP. The inhibition of the conformational change generating pro-inflammatory CRP isoforms via phosphocholine-mimicking compounds represents a promising, potentially broadly applicable anti-inflammatory therapy.
  • Item
    Thumbnail Image
    Heparin Inhibits SARS-CoV-2 Replication in Human Nasal Epithelial Cells
    Lee, LYY ; Suryadinata, R ; McCafferty, C ; Ignjatovic, V ; Purcell, DFJ ; Robinson, P ; Morton, CJ ; Parker, MW ; Anderson, GP ; Monagle, P ; Subbarao, K ; Neil, JA (MDPI, 2022-12)
    SARS-CoV-2 is the causative agent of the COVID-19 pandemic. Vaccination, supported by social and public health measures, has proven efficacious for reducing disease severity and virus spread. However, the emergence of highly transmissible viral variants that escape prior immunity highlights the need for additional mitigation approaches. Heparin binds the SARS-CoV-2 spike protein and can inhibit virus entry and replication in susceptible human cell lines and bronchial epithelial cells. Primary infection predominantly occurs via the nasal epithelium, but the nasal cell biology of SARS-CoV-2 is not well studied. We hypothesized that prophylactic intranasal administration of heparin may provide strain-agnostic protection for household contacts or those in high-risk settings against SARS-CoV-2 infection. Therefore, we investigated the ability of heparin to inhibit SARS-CoV-2 infection and replication in differentiated human nasal epithelial cells and showed that prolonged exposure to heparin inhibits virus infection. Furthermore, we establish a method for PCR detection of SARS-CoV-2 viral genomes in heparin-treated samples that can be adapted for the detection of viruses in clinical studies.
  • Item
    Thumbnail Image
    Single-molecule analysis of the entire perfringolysin O pore formation pathway
    Mc Guinness, C ; Walsh, JC ; Bayly-Jones, C ; Dunstone, MA ; Christie, MP ; Morton, CJ ; Parker, MW ; Bocking, T (eLIFE SCIENCES PUBL LTD, 2022-08-24)
    The cholesterol-dependent cytolysin perfringolysin O (PFO) is secreted by Clostridium perfringens as a bacterial virulence factor able to form giant ring-shaped pores that perforate and ultimately lyse mammalian cell membranes. To resolve the kinetics of all steps in the assembly pathway, we have used single-molecule fluorescence imaging to follow the dynamics of PFO on dye-loaded liposomes that lead to opening of a pore and release of the encapsulated dye. Formation of a long-lived membrane-bound PFO dimer nucleates the growth of an irreversible oligomer. The growing oligomer can insert into the membrane and open a pore at stoichiometries ranging from tetramers to full rings (~35 mers), whereby the rate of insertion increases linearly with the number of subunits. Oligomers that insert before the ring is complete continue to grow by monomer addition post insertion. Overall, our observations suggest that PFO membrane insertion is kinetically controlled.