Citations¶
Core papers cited across the Open Enzyme research library. Full text and abstracts are stored in reference/papers/ in the project repository.
Uricase & Gut-Lumen Enzyme Therapy¶
Pierzynowska K et al. (2020)
Oral Treatment With an Engineered Uricase (ALLN-346) in a Mouse Model of Hyperuricemia.
Frontiers in Medicine, 7, 569215.
PMID: 33330529 · DOI: 10.3389/fmed.2020.569215
Oral uricase reduces serum uric acid 44% in hyperuricemic mice. Direct precedent for gut-lumen degradation strategy.
Gao X et al. (2025)
Dynamic uric acid biosensor-driven urate oxidase expression in engineered probiotic E. coli Nissle 1917 (PULSE system).
Cell Reports Medicine, October 2025.
PMID: 41038159
HucR repressor-based uric acid sensor enables on-demand enzyme expression. Proof-of-concept for responsive gut-lumen therapy.
Wang Y et al. (2025)
Systematic engineering of Saccharomyces boulardii for uric acid degradation; achieved 365.32 ± 20.54 μmol/h/OD using V. vulnificus uricase + chimeric UapA transporter.
ACS Synthetic Biology, 2025.
PMID: 40340401
Benchmark for yeast-based uricase expression. Sets the bar for Open Enzyme's S. cerevisiae track.
Balico LJ & Gaucher EA (2025)
CRISPR-based insertion of reconstructed ancestral uricase gene into human hepatocytes restores urate oxidase activity and prevents fructose-driven fat accumulation.
Scientific Reports, 2025.
PMID: 40681749
Confirms the fructose-uricase-fat-storage link. Parallel gene therapy track to the engineered probiotic approach.
Oda M et al. (2002)
Loss of Urate Oxidase Activity in Hominoids and its Evolutionary Implications.
Molecular Biology and Evolution, 19(5), 640–653.
PMID: 11961098 · DOI: 10.1093/oxfordjournals.molbev.a004123
Foundational paper establishing the two nonsense mutations and aberrant splice site that silenced UOX ~15 Mya.
Kratzer JT et al. (2014)
Evolutionary history and metabolic insights of ancient mammalian uricases.
Proceedings of the National Academy of Sciences, 111(10), 3763–3768.
PMID: 24550457 · DOI: 10.1073/pnas.1320393111
Resurrection of ancestral uricases; kinetics and stability data. Informs engineering targets.
NLRP3 Inflammasome¶
He H et al. (2018)
Oridonin is a covalent NLRP3 inhibitor with strong anti-inflammasome activity.
Nature Communications, 9, 2550.
PMID: 29959312 · DOI: 10.1038/s41467-018-04947-6
Identifies Cys279 in the NACHT domain as the covalent binding site. IC50 0.5–2 µM. Specific to NLRP3.
Hu JJ et al. (2020)
FDA-approved drug disulfiram inhibits pyroptosis by blocking gasdermin D pore formation.
Nature Immunology, 21, 736–745.
PMID: 32367036 · DOI: 10.1038/s41590-020-0669-6
Disulfiram blocks GSDMD at Cys191/Cys192 at nanomolar concentrations. Chokepoint 5 in the NLRP3 map.
Youm YH et al. (2015)
The ketone metabolite β-hydroxybutyrate blocks NLRP3 inflammasome-mediated inflammatory disease.
Nature Medicine, 21, 263–269.
PMID: 25686106 · DOI: 10.1038/nm.3804
BHB directly inhibits NLRP3 without affecting NLRC4 or AIM2. Mechanism: prevents K⁺ efflux and ASC oligomerization.
Huang Y et al. (2018)
Tranilast directly targets DDOST/OST48 to inhibit NLRP3 inflammasome activation.
EMBO Molecular Medicine, 10(4), e8689.
PMID: 29531021 · DOI: 10.15252/emmm.201708689
Japan/Korea-approved drug (1982) repositioned as NLRP3 inhibitor. Direct NACHT domain binding.
Protein Engineering¶
Rahbar MR et al. (2025)
Disulfide bond engineering improves stability and activity of Aspergillus flavus uricase.
Scientific Reports, 15.
PMID: 40419569
Direct experimental basis for the SB-1/BAL-1/OPT-1 disulfide engineering strategy.
Expression & Codon Optimization¶
Demissie ZA et al. (2025)
Codon optimization strategies for heterologous protein expression in S. cerevisiae.
Journal of Microbiology and Biotechnology, PMC12010093.
PMC12010093
Peng B et al. (2015)
Characterization of commonly used promoters and terminators for S. cerevisiae expression.
Microbial Cell Factories, PMC4480987.
PMC4480987
Lin-Cereghino GP et al. (2013)
Secretion of recombinant proteins using alpha-mating factor prepro signal.
Gene, PMC3628533.
PMC3628533