Degradation by Design: New Cyclin K Degraders from Old CDK Inhibitors

ACS Chemical Biology, Journal Year: 2024, Volume and Issue: 19(1), P. 173 - 184

Published: Jan. 9, 2024

Small molecules that induce protein degradation hold the potential to overcome several limitations of currently available inhibitors. Monovalent or molecular glue degraders, in particular, enable benefits without disadvantages high weight and resulting challenge drug development are associated with bivalent like Proteolysis Targeting Chimeras. One key designing monovalent degraders is how build degrader activity─how can we convert an inhibitor into a degrader? If activity requires very specific features, it will be difficult find new challenging optimize those toward drugs. Herein, demonstrate unexpectedly wide range modifications degradation-inducing group cyclin K CR8 tolerated, including both aromatic nonaromatic groups. We used these findings pan-CDK inhibitors dinaciclib AT-7519 Cyclin leading novel dinaciclib-based compound improved compared confirm mechanism degradation. These results suggest general design principles generated for optimization degraders.

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: 6(5), P. 788 - 799

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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The current status and future prospects for therapeutic targeting of KEAP1-NRF2 and β-TrCP-NRF2 interactions in cancer chemoresistance

Free Radical Biology and Medicine, Journal Year: 2022, Volume and Issue: 192, P. 246 - 260

Published: Sept. 28, 2022

Drug resistance is one of the biggest challenges in cancer treatment and limits potential to cure patients. In many tumors, sustained activation protein NRF2 makes tumor cells resistant chemo- radiotherapy. Thus, blocking inappropriate activity cancers has been shown reduce models disease. There a growing scientific interest inhibitors. However, compounds developed so far are not target-specific associated with high degree toxicity, hampering clinical applications. Compounds that can enhance binding its ubiquitination-facilitating regulator proteins, either KEAP1 or β-TrCP, have increase degradation may be value as chemosensitising agents treatment. Approaches based on molecular glue-type mechanisms, which ligands stabilise ternary complex between partner β-catenin by stabilising interaction β-TrCP. This strategy could applied rationally discover degradative β-TrCP-NRF2 KEAP1-NRF2 protein-protein enhancers. We proposing novel approach selectively suppress tumors. It recent methodology promising new addition arsenal anticancer agents.

Language: Английский

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Single-Molecule-Based, Label-Free Monitoring of Molecular Glue Efficacies for Promoting Protein–Protein Interactions Using YaxAB Nanopores

ACS Nano, Journal Year: 2024, Volume and Issue: 18(45), P. 31451 - 31465

Published: Nov. 1, 2024

Modulating protein–protein interactions (PPIs) is an attractive strategy in drug discovery. Molecular glues, bifunctional small-molecule drugs that promote PPIs, offer approach to targeting traditionally undruggable targets. However, the efficient discovery of molecular glues has been hampered by current limitations conventional ensemble-averaging-based methods. In this study, we present a YaxAB nanopore for probing efficacy inducing PPIs. Using nanopores, demonstrate single-molecule-based, label-free monitoring protein complex formation between mammalian target rapamycin (mTOR) and FK506-binding proteins (FKBPs) triggered glue, rapamycin. Owing its wide entrance adjustable pore size, combination with potent electro-osmotic flow (EOF), single funnel-shaped enables simultaneous detection single-molecule-level quantification multiprotein states, including proteins, binary complexes, ternary complexes induced Notably, nanopores could sensitively discriminate or analogues, despite subtle size differences ∼122 ∼116 Da, respectively. Taken together, our results provide proof-of-concept label-free, ultrasensitive screening structure–activity relationship (SAR) analysis which will contribute low-cost, highly discovery, rational design modality drugs, such as glues.

Language: Английский

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Discovery of a small molecule that selectively destabilizes Cryptochrome 1 and enhances life span in p53 knockout mice

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Nov. 8, 2022

Abstract Cryptochromes are negative transcriptional regulators of the circadian clock in mammals. It is not clear how reducing level endogenous CRY1 mammals will affect rhythm and relation such a decrease with apoptosis. Here, we discovered molecule (M47) that destabilizes Cryptochrome 1 (CRY1) both vitro vivo. The M47 selectively enhanced degradation rate by increasing its ubiquitination resulted period length U2OS Bmal1 -d Luc cells. In addition, subcellular fractionation studies from mice liver indicated increased nucleus. Furthermore, M47-mediated reduction oxaliplatin-induced apoptosis Ras-transformed p53 null fibroblast Systemic repetitive administration median lifespan −/− ~25%. Collectively our data suggest promising to treat forms cancer depending on mutation.

Language: Английский

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Experimental Conditions to Retrieve Intrinsic Cooperativity α Directly from Single Binding Assay Data Exemplified by the Ternary Complex Formation of FKBP12, MAPRE1 and Macrocyclic Molecular Glues

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(7), P. 2936 - 2936

Published: March 24, 2025

The incorporation of disease-relevant targets into ternary complexes in a compound-dependent manner by utilizing an assisting chaperone has become common modality as far bifunctional complex-forming compounds are concerned. In contrast, examples formed molecular glues much rarer. Due to their lack significant binary (independent) target affinity, identification cannot yet be achieved rational methods and is, therefore, more challenging. However, it is precisely for that reason (given the associated advantages) systematic application drug discovery recently attracted particular interest. contrast compounds, retrieve part thermodynamic stability through newly induced chaperone-target or glue-target interactions occur only complex. These lead enhanced ligand binding-termed intrinsic cooperativity α-which can retrieved via apparent either monitoring binding protein. this publication, advantage measuring (to determine α) weaker protein discussed illustrated using example between FKBP12, MAPRE1 macrocyclic derived from rapamycin motif FKBP12. Furthermore, impact following three parameters on illustrated: (1) concentration protein, (2) excess counter (3) affinity glue combination with degree α. From this, experimental conditions α one assay without need comprehensive mathematical model covering all simultaneous events under non-saturating highlighted. framework requires capable at least estimating very weak affinities. If not possible reasons, but assays both proteins available within normal bandwidth stronger too high, how curve presence used overcome missing Kd weakly

Language: Английский

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Targeting pyruvate kinase M2 for the treatment of kidney disease

Frontiers in Pharmacology, Journal Year: 2024, Volume and Issue: 15

Published: June 7, 2024

Pyruvate kinase M2 (PKM2), a rate limiting enzyme in glycolysis, is cellular regulator that has received extensive attention and regards as metabolic of metabolism energy. Kidney highly metabolically active organ, glycolysis the important energy resource for kidney. The accumulated evidences indicates enzymatic activity PKM2 disturbed kidney disease progression treatment, especially diabetic acute injury. Modulating post-translational modification determines its nuclear translocation serves an interventional approach to regulate PKM2. Emerging show participate treatment through modulating regulation, podocyte injury, fibroblast activation proliferation, macrophage polarization, T cell regulation. Interestingly, activators (TEPP-46, DASA-58, mitapivat, TP-1454) inhibitors (shikonin, alkannin, compound 3k 3h) have exhibited potential therapeutic property disease, which pleiotropic effects In future, deep investigation urgently needed determine effect activator/inhibitor benefit patients. information this review highlights functions biomarker target diseases.

Language: Английский

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Development of Novel Silicon-Based Hydrophobic Tags (SiHyT) for Targeted Proteins Degradation

Journal of Medicinal Chemistry, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 2, 2024

Recent advances in targeted protein degradation (TPD) have propelled it to the forefront of small molecular drug discovery. Among these, hydrophobic tagging (HyT) strategies garnered significant interest. Carbon-based tags been recognized as effective Hyts for degrading a variety target proteins. In this study, we introduce novel class potential EGFR degraders first time, which combine Gefitinib with silicon-based (SiHyT). The most promising candidate, degrader 7, links simple TBDPS silyl ether, has shown efficacy mutant EGFRs via ubiquitin-proteosome system (UPS) both vitro and vivo. Notably, 7 exhibits enhanced oral bioavailability owing its superior metabolic stability compared traditional carbon-based Hyts. Mechanistically, was revealed that disrupts by dissociating EGFR-HSP90 complex recruiting E3 ligase, RNF149. More importantly, potent selective PD-L1 BTK were discovered successfully utilizing SiHyT strategy. development these innovative compounds could broaden repertoire HyTs, enhancing future design TPD agents.

Language: Английский

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Conformational diversity and protein–protein interfaces in drug repurposing in Ras signaling pathway

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Jan. 12, 2024

Abstract We focus on drug repurposing in the Ras signaling pathway, considering structural similarities of protein–protein interfaces. The interfaces formed by physically interacting proteins are found from PDB if available and via PRISM (PRotein Interaction Structural Matching) otherwise. coverage these interactions has been increased 21 to 92% using PRISM. Multiple conformations each protein used include dynamics diversity. Next, we find FDA-approved drugs bound structurally similar results suggest that HIV protease inhibitors tipranavir, indinavir, saquinavir may bind EGFR ERBB3/HER3 interface. Tipranavir indinavir also ERBB2/HER2 Additionally, a Alzheimer's disease can RAF1 BRAF Hence, propose methodology be potentially for cancer dataset interface clusters rather than pockets systematic way.

Language: Английский

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The Multienzyme Complex Nature of Dehydroepiandrosterone Sulfate Biosynthesis

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(4), P. 2072 - 2072

Published: Feb. 8, 2024

Dehydroepiandrosterone (DHEA), a precursor of steroid sex hormones, is synthesized by 17-alpha-hydroxylase/17,20-lyase (CYP17A1) with the participation microsomal cytochrome b5 (CYB5A) and P450 reductase (CPR), followed sulfation two cytosolic sulfotransferases, SULT1E1 SULT2A1, for storage transport to tissues in which its synthesis not available. The involvement CYP17A1 SULTs these successive reactions led us consider possible interaction DHEA-producing redox partners. Text mining analysis, protein–protein network gene co-expression analysis were performed determine relationships between CYP isoforms. For first time, using surface plasmon resonance, we detected interactions SULT2A1 or SULT1E1. also interacted CYB5A CPR. parameters SULT2A1/CYP17A1 SULT2A1/CYB5A complexes seemed be modulated 3′-phosphoadenosine-5′-phosphosulfate (PAPS). Affinity purification, combined mass spectrometry (AP-MS), allowed identify spectrum potential protein partners, including CYB5A. We showed that enzymatic activity increased presence only mixture. structures CYP17A1/SULT1E1 CYB5A/SULT1E1 predicted. Our data provide novel fundamental information about organization CYP-dependent macromolecular complexes.

Language: Английский

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