Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: July 13, 2023

Abstract Targeted protein degradation via “hijacking” of the ubiquitin-proteasome system using proteolysis targeting chimeras (PROTACs) has evolved into a novel therapeutic modality. The design PROTACs is challenging; multiple steps involved in PROTAC-induced make it difficult to establish coherent structure-activity relationships. Herein, we characterize PROTAC-mediated ternary complex formation and by employing von Hippel–Lindau (VHL) recruiting for two different target proteins, SMARCA2 BRD4. Ternary-complex attributes activity parameters are evaluated varying components PROTAC’s architecture. Ternary binding affinity cooperativity correlates well with potency initial rates degradation. Additionally, develop ternary-complex structure modeling workflow calculate total buried surface area at interface, which agreement measured affinity. Our findings predictive framework guide potent degraders.

Language: Английский

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Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods

Journal of Chemical Information and Modeling, Journal Year: 2023, Volume and Issue: 63(17), P. 5408 - 5432

Published: Aug. 21, 2023

The therapeutic approach of targeted protein degradation (TPD) is gaining momentum due to its potentially superior effects compared with inhibition. Recent advancements in the biotech and pharmaceutical sectors have led development compounds that are currently human trials, some showing promising clinical results. However, use computational tools TPD still limited, as it has distinct characteristics traditional drug design methods. involves creating a ternary structure (protein-degrader-ligase) responsible for biological function, such ubiquitination subsequent proteasomal degradation, which depends on spatial orientation interest (POI) relative E2-loaded ubiquitin. Modeling this necessitates unique blend initially developed small molecules (e.g., docking) biologics protein-protein interaction modeling). Additionally, degrader molecules, particularly heterobifunctional degraders, generally larger than conventional molecule drugs, leading challenges determining drug-like properties like solubility permeability. Furthermore, catalytic nature makes occupancy-based modeling insufficient. consists multiple interconnected yet steps, POI binding, E3 ligase interactions, ubiquitination, along properties. A comprehensive set needed address dynamic induced proximity complex implications ubiquitination. In Perspective, we discuss current state TPD. We start by describing series steps involved process experimental methods used characterize them. Then, delve into detailed analysis employed also present an integrative proven successful impact project decisions. Finally, examine future prospects areas greatest potential impact.

Language: Английский

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Biolayer interferometry and its applications in drug discovery and development

TrAC Trends in Analytical Chemistry, Journal Year: 2024, Volume and Issue: 176, P. 117741 - 117741

Published: May 2, 2024

Biolayer interferometry (BLI) is an optical 'dip-and-read' biosensor method for real-time, label-free analysis of biomolecular interactions. It can be used kinetic analyses, analyte detection and quantitation with mid- to high throughput. Here, we review how BLI support diverse activities in the broad field drug design development, ranging from fragment compound library screening, structure-activity relationship selectivity analyses small-molecule leads, cell line development production biopharmaceutics, optimization surveillance bioprocess, characterization quality control biologic substances. We discuss strengths drawbacks compare it other well-established methods techniques. With advances sensitivity, has established itself as a robust versatile tool interrogating molecular interactions structures, expanding world biological molecules small synthetic compounds.

Language: Английский

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Mass Spectrometry Analysis of Chemically and Collisionally Dissociated Molecular Glue- and PROTAC-Mediated Protein Complexes Informs on Disassembly Pathways

Journal of the American Society for Mass Spectrometry, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 15, 2025

Molecular glues (MGs) and proteolysis-targeting chimeras (PROTACs) are used to modulate protein–protein interactions (PPIs), via induced proximity between compounds that have little or no affinity for each other naturally. They promote either reversible inhibition selective degradation of a target protein, including ones deemed undruggable by traditional therapeutics. Though native MS (nMS) is capable analyzing multiprotein complexes, the behavior these artificially in gas phase still not fully understood, number publications over past few years rather limited. Here, we studied two MG-induced complexes mTORFRB FKBP12 as well PROTAC-induced complex FKBP51FK1 von Hippel-Lindau E3 ligase (VHL). Native combined with collision-induced dissociation (CID) provided way measuring only formation but also their pathways. Both protein seem eject preferably centrally located small (compared mass proteins) ligand upon CID, than dissociating peripheral subunit, often observed naturally occurring complexes. In contrast, chemically solution generated complementary data disrupting PPI surface, which resulted more diverse spectra preserved stronger solution.

Language: Английский

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Identification and characterization of ternary complexes consisting of FKBP12, MAPRE1 and macrocyclic molecular glues

RSC Chemical Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Many disease-relevant and functionally well-validated targets are difficult to drug. Their poorly defined 3D structure without deep hydrophobic pockets makes the development of ligands with low molecular weight high affinity almost impossible. For these targets, incorporation into a ternary complex may be viable alternative modulate in most cases inhibit their function. Therefore, we interested methods identify characterize glues. In protein array screen 50 different macrocyclic FKBP12 against 2500 randomly selected proteins, glue compound was found recruit dimeric called MAPRE1 compound-dependent manner. The corresponding characterized by TR-FRET proximity assay native MS spectroscopy. Insights were obtained 2D NMR spectroscopy finally an X-ray structure, which revealed as 2 : exhibiting multiple interactions that occur exclusively lead significant cooperativity α. Using rationally guided synthesis series analogues led driven improvement stability complex. Furthermore, formation confirmed cellular NanoBiT assays, whose A max values correlate those from assay. experiments showed functional impact (inhibition) glues on interaction its intracellular partners.

Language: Английский

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Proteomic approaches advancing targeted protein degradation

Trends in Pharmacological Sciences, Journal Year: 2023, Volume and Issue: 44(11), P. 786 - 801

Published: Sept. 29, 2023

Targeted protein degradation (TPD) is an emerging modality for research and therapeutics. Most TPD approaches harness cellular ubiquitin-dependent proteolytic pathways. Proteolysis-targeting chimeras (PROTACs) molecular glue (MG) degraders (MGDs) represent the most advanced approaches, with some already used in clinical settings. Despite these advances, still faces many challenges, pertaining to both development of effective, selective, tissue-penetrant understanding their mode action. In this review, we focus on progress made addressing challenges. particular, discuss utility application recent proteomic as indispensable tools enable insights into degrader development, including target engagement, selectivity, efficacy, safety,

Language: Английский

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Rapid PROTAC Discovery Platform: Nanomole-Scale Array Synthesis and Direct Screening of Reaction Mixtures

ACS Medicinal Chemistry Letters, Journal Year: 2023, Volume and Issue: 14(12), P. 1882 - 1890

Published: Nov. 11, 2023

Precise length, shape, and linker attachment points are all integral components to designing efficacious proteolysis targeting chimeras (PROTACs). Due the synthetic complexity of these heterobifunctional degraders difficulty computational modeling aid PROTAC design, exploration structure–activity relationships remains mostly empirical, which requires a significant investment time resources. To facilitate rapid hit finding, we developed capabilities for parallel synthesis purification by harnessing an array preformed E3-ligand-linker intermediates. In next iteration this approach, rapid, nanomole-scale methodology using amide coupling that enables direct screening nonpurified reaction mixtures in cell-based degradation assays, as well logD EPSA measurements. This approach greatly expands accelerates SAR (5 days instead several weeks) avoids laborious solvent-demanding mixtures, thus making it economical more sustainable finding.

Language: Английский

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A paradigm shift: analytical ultracentrifugation as a multi-attribute platform method in targeted protein degradation

European Biophysics Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 17, 2025

Language: Английский

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In silico modeling of targeted protein degradation

European Journal of Medicinal Chemistry, Journal Year: 2025, Volume and Issue: 289, P. 117432 - 117432

Published: Feb. 20, 2025

Language: Английский

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A Comprehensive Primer and Review of PROTACs and Their In Silico Design

Computer Methods and Programs in Biomedicine, Journal Year: 2025, Volume and Issue: 264, P. 108687 - 108687

Published: Feb. 27, 2025

Language: Английский

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