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Liu Y, Goebel GL, Kanis L, Hastürk O, Kemker C, Wu P. Aminothiazolone Inhibitors Disrupt the Protein-RNA Interaction of METTL16 and Modulate the m 6A RNA Modification. JACS AU 2024; 4:1436-1449. [PMID: 38665670 PMCID: PMC11040665 DOI: 10.1021/jacsau.3c00832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 04/28/2024]
Abstract
Targeting RNA-binding and modifying proteins via small molecules to modulate post-transcriptional modifications have emerged as a new frontier for chemical biology and therapeutic research. One such RNA-binding protein that regulates the most prevalent eukaryotic RNA modification, N6-methyladenosine (m6A), is the methyltransferase-like protein 16 (METTL16), which plays an oncogenic role in cancers by cofunctioning with other nucleic acid-binding proteins. To date, no potent small-molecule inhibitor of METTL16 or modulator interfering with the METTL16-RNA interaction has been reported and validated, highlighting the unmet need to develop such small molecules to investigate the METTL16-involved regulatory network. Herein, we described the identification of a series of first-in-class aminothiazolone METTL16 inhibitors via a discovery pipeline that started with a fluorescence-polarization (FP)-based screening. Structural optimization of the initial hit yielded inhibitors, such as compound 45, that showed potent single-digit micromolar inhibition activity against the METTL16-RNA binding. The identified aminothiazolone inhibitors can be useful probes to elucidate the biological function of METTL16 upon perturbation and evaluate the therapeutic potential of METTL16 inhibition via small molecules at the post-transcriptional level.
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Affiliation(s)
- Yang Liu
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Dortmund 44227, Germany
| | - Georg L. Goebel
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Dortmund 44227, Germany
| | - Laurin Kanis
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Dortmund 44227, Germany
| | - Oguz Hastürk
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Dortmund 44227, Germany
| | - Claus Kemker
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Dortmund 44227, Germany
| | - Peng Wu
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
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Raja R, Sundararaj R, Kandasamy R. Identification of small molecule inhibitors against Lin28/let-7 to suppress tumor progression and its alleviation role in LIN28-dependent glucose metabolism. Med Oncol 2024; 41:118. [PMID: 38630184 DOI: 10.1007/s12032-024-02350-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/04/2024] [Indexed: 04/19/2024]
Abstract
The reciprocal suppression of an RNA-binding protein LIN28 (human abnormal cell lineage 28) and miRNA Let-7 (Lethal 7) is considered to have a prime role in hepatocellular carcinoma (HCC). Though targeting this inhibition interaction is effective for therapeutics, it causes other unfavorable effects on glucose metabolism and increased insulin resistance. Hence, this study aims to identify small molecules targeting Lin28/let-7 interaction along with additional potency to improve insulin sensitivity. Of 22,14,996 small molecules screened by high throughput virtual screening, 6 molecules, namely 41354, 1558, 12437, 23837, 15710, and 8319 were able to block the LIN28 interaction with let-7 and increase the insulin sensitivity via interacting with PPARγ (peroxisome proliferator-activated receptors γ). MM-GBSA (Molecular Mechanics-Generalized Born Surface Area) analysis is used to re-score the binding affinity of docked complexes. Upon further analysis, it is also seen that these molecules have superior ADME (Absorption, Distribution, Metabolism, and Excretion) properties and form stable complexes with the targets for a significant period in a biologically simulated environment (Molecular Dynamics simulation) for 100 ns. From our results, we hypothesize that these identified 6 small molecules can be potential candidates for HCC treatment and the glucose metabolic disorder caused by the HCC treatment.
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Affiliation(s)
- Rachanaa Raja
- Centre for Excellence in Nanobio Translational Research, Department of Pharmaceutical Technology, University College of Engineering, Anna University (BIT Campus), Tiruchirappalli, Tamil Nadu, India
| | - Rajamanikandan Sundararaj
- Centre for Drug Discovery, Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - Ruckmani Kandasamy
- Centre for Excellence in Nanobio Translational Research, Department of Pharmaceutical Technology, University College of Engineering, Anna University (BIT Campus), Tiruchirappalli, Tamil Nadu, India.
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Borgelt L, Hohnen L, Pallesen JS, Hommen P, Goebel GL, Bosica F, Liu Y, O’Mahony G, Wu P. N-Biphenyl Pyrrolinones and Dibenzofurans as RNA-Binding Protein LIN28 Inhibitors Disrupting the LIN28- Let-7 Interaction. ACS Med Chem Lett 2023; 14:1707-1715. [PMID: 38116413 PMCID: PMC10726440 DOI: 10.1021/acsmedchemlett.3c00341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/27/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023] Open
Abstract
The RNA-binding protein LIN28 is a regulator of miRNA let-7 biogenesis. Inhibitors of LIN28 are highly sought after given the central role that LIN28 plays in tumorigenesis and development of cancer stem cells as well as LIN28's association with poor clinical prognosis. Although LIN28 inhibitors of different scaffolds have been reported, the potential of most LIN28 inhibiting small molecules was not fully explored since very limited structure-activity relationship (SAR) studies have been performed. We previously identified trisubstituted pyrrolinones as a new class of LIN28 inhibitors disrupting the LIN28-let-7 interaction. Here, we performed extensive SAR by evaluating 95 small molecules and identified new trisubstituted pyrrolinones featuring either an N-biphenyl or N-dibenzofuran substituent, overthrowing the existing conclusion that a salicylic acid moiety is indispensable for activity. Exchange of the negatively charged salicylic acid moiety in LIN28 inhibitors with a heterocyclic substituent is beneficial for membrane permeability, leading to increased activity in a cellular assay, and will potentially reduce toxicity.
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Affiliation(s)
- Lydia Borgelt
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn
Str. 6, Dortmund 44227, Germany
| | - Lisa Hohnen
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Biochemistry, Ruhr-University
Bochum, Universitätsstr.
150, Bochum 44801, Germany
| | - Jakob S. Pallesen
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Pascal Hommen
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn
Str. 6, Dortmund 44227, Germany
| | - Georg L. Goebel
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn
Str. 6, Dortmund 44227, Germany
| | - Francesco Bosica
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Yang Liu
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn
Str. 6, Dortmund 44227, Germany
| | - Gavin O’Mahony
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Peng Wu
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
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Hommen P, Hwang J, Huang F, Borgelt L, Hohnen L, Wu P. Chromenopyrazole-Peptide Conjugates as Small-Molecule Based Inhibitors Disrupting the Protein-RNA Interaction of LIN28-let-7. Chembiochem 2023; 24:e202300376. [PMID: 37224100 DOI: 10.1002/cbic.202300376] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 05/26/2023]
Abstract
Targeting the protein-RNA interaction of LIN28 and let-7 is a promising strategy for the development of novel anticancer therapeutics. However, a limited number of small-molecule inhibitors disrupting the LIN28-let-7 interaction with potent efficacy are available. Herein, we developed a novel LIN28-inhibiting strategy by targeting selective hotspot amino acids at the LIN28-let-7 binding interface with small-molecule-based bifunctional conjugates. Starting from reported small-molecule LIN28 inhibitors, we identified a feasible linker-attachment position after performing a structure-activity relationship exploration based on the LIN28-targeting chromenopyrazoles. In parallel, a virtual alanine scan identified hotspot residues at the protein-RNA binding interface, based on which we designed a set of peptides to enhance the interaction with the identified hotspot residues. Conjugation of the tailor-designed peptides with linker-attached chromenopyrazoles yielded a series of bifunctional small-molecule-peptide conjugates, represented by compound 83 (PH-223), as a new LIN28-targeting chemical modality. Our result demonstrated an unexplored rational design approach using bifunctional conjugates to target protein-RNA interactions.
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Affiliation(s)
- Pascal Hommen
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Jimin Hwang
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Fubao Huang
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
| | - Lydia Borgelt
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Lisa Hohnen
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstr. 150, Bochum, 44780, Germany
| | - Peng Wu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
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