Skip to content
-
Subscribe to our newsletter & never miss our best posts. Subscribe Now!
Today's News. Tomorrow's Perspective. Today's News. Tomorrow's Perspective.

Deliver fast, factual, and easy-to-understand news covering global events, technology, business, science, AI, health, entertainment, and lifestyle.

Today's News. Tomorrow's Perspective. Today's News. Tomorrow's Perspective.

Deliver fast, factual, and easy-to-understand news covering global events, technology, business, science, AI, health, entertainment, and lifestyle.

  • Home
  • Breaking News
  • Business
  • Sports
  • Health
  • Politics
  • Technology & AI
  • World
  • Home
  • Breaking News
  • Business
  • Sports
  • Health
  • Politics
  • Technology & AI
  • World
Close

Search

  • https://www.facebook.com/
  • https://twitter.com/
  • https://t.me/
  • https://www.instagram.com/
  • https://youtube.com/
Subscribe
De novo design of cysteine ​​proteases
Technology & AI

De novo design of cysteine ​​proteases

By adminvoxa
October 15, 2026 5 Min Read
Comments Off on De novo design of cysteine ​​proteases
  • Radzicka, A. & Wolfenden, R. Rates of uncatalyzed peptide bond hydrolysis in neutral solution and transition state affinities of proteases. Jam. Chemical. Soc. 1186105-6109 (1996).

    Article ADS CAS Google Scholar

  • Dyer, RP & Weiss, GA Making a difference through protease engineering. Cellular chemistry. Biol. 29177-190 (2022).

    Article CAS PubMed Google Scholar

  • Otto, H.-H. & Schirmeister, T. Cysteine ​​proteases and their inhibitors. Chemical. Round. 97133-172 (1997).

    Article CAS PubMed Google Scholar

  • Carter, P. & Wells, JA Dissecting the catalytic triad of a serine protease. Nature 332564-568 (1988.

    Article ADS CAS PubMed Google Scholar

  • Ménard, R. et al. The modification of the electrostatic environment is tolerated in the oxyanion hole of the papain cysteine ​​protease. Biochemistry 34464-471 (1995).

    Article PubMed Google Scholar

  • Verma, S., Dixit, R. & Pandey, KC Cysteine ​​proteases: modes of activation and future prospects as pharmacological targets. In front. Pharmacol. 7107 (2016).

    Article PubMed PubMed Central Google Scholar

  • Lauko, A. et al. Computational design of serine hydrolases. Science 388eadu2454 (2025).

    Article CAS PubMed PubMed Central Google Scholar

  • Kim, D. et al. Computational design of metallohydrolases. Nature 649246-253 (2026).

  • Ahern, W. et al. Scaffolding of enzymatic active sites at the atomic level using RFdiffusion2. Nat. Methods 2396-105 (2026).

    Article CAS PubMed Google Scholar

  • Bauer, MS et al. De novo design of phospho-tyrosine peptide binders. Preprint at bioRxiv https://doi.org/10.1101/2025.09.29.678898 (2025).

  • Mossessova, E. & Lima, CD Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and an essential regulatory element for cell growth in yeast. Mol. Cell 5865-876 (2000).

    Article CAS PubMed Google Scholar

  • Dauparas, J. et al. Robust deep learning-based protein sequence design using ProteinMPNN. Science 37849-56 (2022).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630493-500 (2024).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Bindels, DS et al. mScarlet: a bright monomeric red fluorescent protein for cellular imaging. Nat. Methods 1453-56 (2017).

    Article CAS PubMed Google Scholar

  • Matayoshi, ED, Wang, GT, Krafft, GA and Erickson, J. Novel fluorogenic substrates for the assay of retroviral proteases by resonance energy transfer. Science 247954-958 (1990).

    Article ADS CAS PubMed Google Scholar

  • Hofer, F., Kraml, J., Kahler, U., Kamenik, AS & Liedl, KR pKa values ​​of the catalytic site of aspartic, cysteine ​​and serine proteases: MD simulations at constant pH. J.Chem. Inf. Model. 603030-3042 (2020).

    Article CAS PubMed PubMed Central Google Scholar

  • Zhai, X. & Meek, TD Catalytic mechanism of cruzain of Trypanosoma cruzi as determined from solvent kinetic isotope effects on steady-state and pre-steady-state kinetics. Biochemistry 573176-3190 (2018).

    Article CAS PubMed PubMed Central Google Scholar

  • Daniel, RM & Danson, MJ A new understanding of how temperature affects the catalytic activity of enzymes. Biochemistry Trends. Sci 35584-591 (2010).

    Article CAS PubMed Google Scholar

  • Xu, Z. et al. Molecular basis of redox regulation of SUMO proteases: a mechanism for protecting the intermolecular disulfide bond against irreversible sulfhydryl oxidation. FASEB J. 22127-137 (2008).

    Article CAS PubMed Google Scholar

  • van Kempen, M. et al. Fast and accurate protein structure research with Foldseek. Nat. Biotechnology. 42243-246 (2024).

    Article ADS PubMed Google Scholar

  • Zhang, Y. & Skolnick, J. Scoring function for automated protein structure model quality assessment. Proteins 57702-710 (2004).

    Article CAS PubMed Google Scholar

  • Anishchenko, I. et al. Modeling protein-small molecule conformational ensembles with PLACER. Proc. Natl Acad. Sci. USA 122e2427161122 (2025).

    Article CAS PubMed PubMed Central Google Scholar

  • LaLonde, JM et al. Using Papain as a Model for Structure-Based Design of Cathepsin K Inhibitors: Crystal structures of two papain-inhibitor complexes demonstrate binding to S′ subsites. J.Med. Chemical. 414567-4576 (1998).

    Article CAS PubMed Google Scholar

  • Tsuge, H. et al. Mechanism of inhibition of specific cathepsin L inhibitors based on the crystal structure of the papain-CLIK148 complex. Biochemistry. Biophysics. Res. Common. 266411-416 (1999).

    Article ADS CAS PubMed Google Scholar

  • Moldoveanu, T., Campbell, RL, Cuerrier, D. and Davies, PL Crystal structures of calpain-E64 and -leupeptin inhibitor complexes reveal mobile loops controlling the active site. J. Mol. Biol. 3431313-1326 (2004).

    Article CAS PubMed Google Scholar

  • Falke, S. et al. Structural elucidation and antiviral activity of covalent cathepsin L inhibitors. J.Med. Chemical. 677048-7067 (2024).

    Article CAS PubMed PubMed Central Google Scholar

  • Yamamoto, A. et al. Structural basis for the development of the specific noncovalent type inhibitor of cathepsin B: crystal structure of the cathepsin B-E64c complex. Biochemistry. Biophysics. Acta 1597244-251 (2002).

    Article CAS PubMed Google Scholar

  • Pauly, TA et al. Specificity determinants of human cathepsins revealed by the crystal structures of the complexes. Biochemistry 423203-3213 (2003).

    Article CAS PubMed Google Scholar

  • Huang, L., Brinen, L.S. and Ellman, J.A. Crystal structures of reversible ketone inhibitors of Cruzan cysteine ​​protease. Bioorg. Med. Chemical. 1121-29 (2003).

    Article PubMed Google Scholar

  • Kapust, RB et al. Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic competence. Protein engineering. 14993-1000 (2001).

    Article CAS PubMed Google Scholar

  • Kenneson, JR et al. Exploring possible drug-resistant variants of the SARS-CoV-2 main protease (Mpro) with a non-covalent preclinical candidate, Mpro61. ACS Bio Med Chem Au 5215-226 (2025).

    Article CAS PubMed PubMed Central Google Scholar

  • Mei, M. et al. A combinatorial strategy for engineering HRV 3C protease to achieve free N-terminal cleavage. Int. J. Biol. Macromol. 265131066 (2024).

    Article CAS PubMed Google Scholar

  • Pearlman, DA et al. AMBER, a set of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics, and free energy calculations to simulate the structural and energetic properties of molecules. Calculate. Phys. Common. 911–41 (1995).

    Article ADS CAS Google Scholar

  • Shaffer, J.M. & Greenwald, I. SALSA, a genetically encoded biosensor for spatiotemporal quantification of Notch signal transduction in vivo. Dev. Cell 57930-944.e6 (2022).

  • Gao, XJ, Chong, LS, Kim, MS & Elowitz, MB Programmable protein circuits in living cells. Science 3611252-1258 (2018).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Roybal, KT et al. Engineering T cells with personalized therapeutic response programs using synthetic Notch receptors. Cell 167419-432 (2016).

    Article CAS PubMed PubMed Central Google Scholar

  • Barnea, G. et al. The genetic design of signaling cascades to record receptor activation. Proc. Natl Acad. Sci. USA 10564-69 (2008).

    Article ADS CAS PubMed Google Scholar

  • Coukos, R. et al. A transcriptional protein localization reporter identifies regulators of mitochondrial and ER membrane protein trafficking in high-throughput CRISPRi screens. eLife 10e69142 (2021).

    Article CAS PubMed PubMed Central Google Scholar

  • Novinec, M. & Lenarčič, B. Papain-type peptidases: structure, function and evolution. Biomol. Concepts 4287-308 (2013).

    Article CAS PubMed Google Scholar

  • Hekkelman, ML, Salmoral, D. Á, Perrakis, A. & Joosten, RP DSSP 4: FAIR annotation of protein secondary structure. Protein Sci. 34e70208 (2025).

    Article CAS PubMed PubMed Central Google Scholar

  • Bennett, NR et al. Improving de novo design of protein binders using deep learning. Nat. Common. 142625 (2023).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Kuo, C.-J., Chi, Y.-H., Hsu, JT-A. & Liang, P.-H. Characterization of the primary SARS protease and inhibitor assay using a fluorogenic substrate. Biochemistry. Biophysics. Res. Common. 318862-867 (2004).

    ADS CAS PubMed PubMed Central Google Scholar

  • Kabsch, W. Integration, scaling, space group assignment and post-refinement. Acta Crystallogr. D 66133-144 (2010).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Winn, MD et al. Presentation of the CCP4 suite and current developments. Acta Crystallogr. D 67235-242 (2011).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • McCoy, AJ et al. Phaser crystallographic software. J.Appl. Crystallogr. 40658-674 (2007).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Adams, PD et al. PHENIX: a complete Python-based system for macromolecular structure solution. In International crystallography tables 539-547 (International Union of Crystallography, 2012).

  • Emsley, P. & Cowtan, K. Coot: Modeling tools for molecular graphics. Acta Crystallogr. D 602126-2132 (2004).

    Article ADS PubMed Google Scholar

  • Williams, CJ et al. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 27293-315 (2018).

    Article CAS PubMed Google Scholar

  • Gn tech

    Post Views: 7
    Author

    adminvoxa

    Follow Me
    Other Articles
    North Korea and China open new bridge after 12 years of delay
    Previous

    North Korea and China open new bridge after 12 years of delay

    A mother went missing after she and her ex-fiancé ended up in the "People's Court." He is now accused of murder.
    Next

    A mother went missing after she and her ex-fiancé ended up in the “People’s Court.” He is now accused of murder.

    Deliver fast, factual, and easy-to-understand news covering global events, technology, business, science, AI, health, entertainment, and lifestyle.
    • About Us
    • Accessibility Statement
    • Advertise With Us
    • AI Usage & Transparency Policy
    • Contact us
    • Cookie Policy
    • Corrections Policy
    • Meet Our Team
    • Privacy Policy
      • Disclaimer
      • DMCA & Copyright Policy
      • Editorial Policy
      • Ethics Policy
      • Fact-Checking Policy
    • Terms and Conditions
    Copyright 2026 — Today's News. Tomorrow's Perspective.. All rights reserved.