ArticleThe journal of physical chemistry. B2010
Molecular basis of the selectivity of the immunoproteasome catalytic subunit LMP2-specific inhibitor revealed by molecular modeling and dynamics simulations.
Article in The journal of physical chemistry. B, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Current landscape of the immunoproteasome: implications for disease and therapy.Cell death discovery · 2025Review
- The dichotomous role of immunoproteasome in cancer: Friend or foe?Acta pharmaceutica Sinica. B · 2023Review
- A Nut for Every Bolt: Subunit-Selective Inhibitors of the Immunoproteasome and Their Therapeutic Potential.Cells · 2021Review
- Immunoproteasome and Non-Covalent Inhibition: Exploration by Advanced Molecular Dynamics and Docking Methods.Molecules (Basel, Switzerland) · 2021Article
- Review
- 20S Proteasome as a Drug Target in Trichomonas vaginalis.Antimicrobial agents and chemotherapy · 2019Article
- Development of Novel Epoxyketone-Based Proteasome Inhibitors as a Strategy To Overcome Cancer Resistance to Carfilzomib and Bortezomib.Journal of medicinal chemistry · 2019Article
- Cell Clearing Systems Bridging Neuro-Immunity and Synaptic Plasticity.International journal of molecular sciences · 2019Review
- A Sentinel in the Crosstalk Between the Nervous and Immune System: The (Immuno)-Proteasome.Frontiers in immunology · 2019Review
- A Marine Diterpenoid Modulates the Proteasome Activity in Murine Macrophages Stimulated with LPS.Biomolecules · 2018Article
- Blockade of the malignant phenotype by β-subunit selective noncovalent inhibition of immuno- and constitutive proteasomes.Oncotarget · 2017Article
- Mining kidney toxicogenomic data by using gene co-expression modules.BMC genomics · 2016Article
- Fundamental reaction pathway and free energy profile of proteasome inhibition by syringolin A (SylA).Organic & biomolecular chemistry · 2015Article
- Proteasome inhibitors with pyrazole scaffolds from structure-based virtual screening.Journal of medicinal chemistry · 2015Article
- Selective immunoproteasome inhibitors with non-peptide scaffolds identified from structure-based virtual screening.Bioorganic & medicinal chemistry letters · 2014Article
- Binding free energies for nicotine analogs inhibiting cytochrome P450 2A6 by a combined use of molecular dynamics simulations and QM/MM-PBSA calculations.Bioorganic & medicinal chemistry · 2014Article
- A FRET-based approach for identification of proteasome catalytic subunit composition.Molecular bioSystems · 2014Article
- Fundamental reaction pathway for peptide metabolism by proteasome: insights from first-principles quantum mechanical/molecular mechanical free energy calculations.The journal of physical chemistry. B · 2013Article
- Activity-based imaging probes of the proteasome.Cell biochemistry and biophysics · 2013Review
- Inhibitors of the immunoproteasome: current status and future directions.Current pharmaceutical design · 2013Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Given that immunoproteasome inhibitors are currently being developed for a variety of potent therapeutic purposes, the unique specificity of an α',β'-epoxyketone peptide (UK101) toward the LMP2 subunit of the immunoproteasome (analogous to β5 subunit of the constitutive proteasome) has been investigated in this study for the first time by employing homology modeling, molecular docking, molecular dynamics simulation, and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations. On the basis of the simulated binding structures, the calculated binding free energies are in qualitative agreement with the corresponding experimental data, and the selectivity of UK101 is explained reasonably. The observed selectivity of UK101 for the LMP2 subunit is rationalized by the requirement for both a linear hydrocarbon chain at the N terminus and a bulky group at the C terminus of the inhibitor, because the LMP2 subunit has a much more favorable hydrophobic pocket interacting with the linear hydrocarbon chain, and the bulky group at the C terminus has a steric clash with the Tyr 169 in β5 subunit. Finally, our results help to clarify why UK101 is specific to the LMP2 subunit of immunoproteasome, and this investigation should be valuable for rational design of more potent LMP2-specific inhibitors.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.