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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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2
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Yan L, Sun J, Wang Y, Liu X, Hu J, Sun M, Suo X, Duan R, Yuan C. Lin28 affects the proliferation and osteogenic differentiation of human dental pulp stem cells by directly inhibiting let-7b maturation. BDJ Open 2024; 10:17. [PMID: 38443392 PMCID: PMC10914815 DOI: 10.1038/s41405-024-00194-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/23/2024] [Accepted: 01/27/2024] [Indexed: 03/07/2024] Open
Abstract
OBJECTIVE Activation of Lin28 gene under certain conditions promotes tissue damage repair. However, it remains unknown whether conditional expression of Lin28 facilitates the recovery of damaged pulp tissue. In the study, we focus on exploring the effects and possible regulatory mechanisms of Lin28 on the proliferation and differentiation of human dental pulp stem cells (hDPSCs). MATERIALS AND METHODS We adopted techniques such as the ethynyl-2'-deoxyuridine (EdU) incorporation assay, RNA-protein immunoprecipitation (RIP) analysis, and luciferase assays to study the regulation of hDPSCs by Lin28. Furthermore, gain-of-function and loss-of-function analyses were also used in explored factors regulating hDPSCs activation. RESULTS The results show that Lin28 inhibited osteogenic differentiation by directly targets pre-let-7b. Through bioinformatics sequencing and dual luciferase experiments we learned that let-7b directly targets the IGF2BP2 3'UTR. Silencing of IGF2BP2 showed a similar biological effect as overexpression of let-7b. Overexpression of IGF2BP2 counteracted the differentiation-promoting effects produced by let-7b overexpression. DISCUSSION/CONCLUSIONS In conclusion, the RNA-binding protein Lin28 regulates osteogenic differentiation of hDPSCs by inhibiting let-7 miRNA maturation. And mature let-7b directly regulated the expression of IGF2BP2 by targeting the 3'UTR region of IGF2BP2 mRNA thus further inhibiting the differentiation of hDPSCs.
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Affiliation(s)
- Liu Yan
- School of Stomatology, Xuzhou Medical University, No.209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
- Affiliated Stomatological Hospital of Xuzhou Medical University, No.130 Huaihai West Road, Xuzhou, 221000, Jiangsu, China
| | - Jing Sun
- School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Yushan Wang
- School of Stomatology, Xuzhou Medical University, No.209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Xinxin Liu
- School of Stomatology, Xuzhou Medical University, No.209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Jiayi Hu
- School of Stomatology, Xuzhou Medical University, No.209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Mengxin Sun
- School of Stomatology, Xuzhou Medical University, No.209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Xi Suo
- School of Stomatology, Xuzhou Medical University, No.209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Rongquan Duan
- School of Stomatology, Xuzhou Medical University, No.209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
| | - Changyong Yuan
- School of Stomatology, Xuzhou Medical University, No.209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
- Affiliated Stomatological Hospital of Xuzhou Medical University, No.130 Huaihai West Road, Xuzhou, 221000, Jiangsu, China.
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Tropsha A, Isayev O, Varnek A, Schneider G, Cherkasov A. Integrating QSAR modelling and deep learning in drug discovery: the emergence of deep QSAR. Nat Rev Drug Discov 2024; 23:141-155. [PMID: 38066301 DOI: 10.1038/s41573-023-00832-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2023] [Indexed: 02/08/2024]
Abstract
Quantitative structure-activity relationship (QSAR) modelling, an approach that was introduced 60 years ago, is widely used in computer-aided drug design. In recent years, progress in artificial intelligence techniques, such as deep learning, the rapid growth of databases of molecules for virtual screening and dramatic improvements in computational power have supported the emergence of a new field of QSAR applications that we term 'deep QSAR'. Marking a decade from the pioneering applications of deep QSAR to tasks involved in small-molecule drug discovery, we herein describe key advances in the field, including deep generative and reinforcement learning approaches in molecular design, deep learning models for synthetic planning and the application of deep QSAR models in structure-based virtual screening. We also reflect on the emergence of quantum computing, which promises to further accelerate deep QSAR applications and the need for open-source and democratized resources to support computer-aided drug design.
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Affiliation(s)
| | | | | | | | - Artem Cherkasov
- University of British Columbia, Vancouver, BC, Canada.
- Photonic Inc., Coquitlam, BC, Canada.
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4
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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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5
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Zamora I, Freeman MR, Encío IJ, Rotinen M. Targeting Key Players of Neuroendocrine Differentiation in Prostate Cancer. Int J Mol Sci 2023; 24:13673. [PMID: 37761978 PMCID: PMC10531052 DOI: 10.3390/ijms241813673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/02/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023] Open
Abstract
Neuroendocrine prostate cancer (NEPC) is a highly aggressive subtype of prostate cancer (PC) that commonly emerges through a transdifferentiation process from prostate adenocarcinoma and evades conventional therapies. Extensive molecular research has revealed factors that drive lineage plasticity, uncovering novel therapeutic targets to be explored. A diverse array of targeting agents is currently under evaluation in pre-clinical and clinical studies with promising results in suppressing or reversing the neuroendocrine phenotype and inhibiting tumor growth and metastasis. This new knowledge has the potential to contribute to the development of novel therapeutic approaches that may enhance the clinical management and prognosis of this lethal disease. In the present review, we discuss molecular players involved in the neuroendocrine phenotype, and we explore therapeutic strategies that are currently under investigation for NEPC.
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Affiliation(s)
- Irene Zamora
- Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain
| | - Michael R. Freeman
- Departments of Urology and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ignacio J. Encío
- Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Navarre Institute for Health Research, 31008 Pamplona, Spain
| | - Mirja Rotinen
- Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Navarre Institute for Health Research, 31008 Pamplona, Spain
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GEWALT TABEA, NOH KAWON, MEDER LYDIA. The role of LIN28B in tumor progression and metastasis in solid tumor entities. Oncol Res 2023; 31:101-115. [PMID: 37304235 PMCID: PMC10208000 DOI: 10.32604/or.2023.028105] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/16/2023] [Indexed: 06/13/2023] Open
Abstract
LIN28B is an RNA-binding protein that targets a broad range of microRNAs and modulates their maturation and activity. Under normal conditions, LIN28B is exclusively expressed in embryogenic stem cells, blocking differentiation and promoting proliferation. In addition, it can play a role in epithelial-to-mesenchymal transition by repressing the biogenesis of let-7 microRNAs. In malignancies, LIN28B is frequently overexpressed, which is associated with increased tumor aggressiveness and metastatic properties. In this review, we discuss the molecular mechanisms of LIN28B in promoting tumor progression and metastasis in solid tumor entities and its potential use as a clinical therapeutic target and biomarker.
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Affiliation(s)
- TABEA GEWALT
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - KA-WON NOH
- Institute for Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - LYDIA MEDER
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
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