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Chen SY, Chiang IC, Chen YY, Hsu YH, Yen GC. Recent advances in the potential of Phyllanthus emblica L. and its related foods for combating metabolic diseases through methylglyoxal trapping. Food Res Int 2024; 194:114907. [PMID: 39232532 DOI: 10.1016/j.foodres.2024.114907] [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: 06/19/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 09/06/2024]
Abstract
Methylglyoxal (MG) serves as the primary precursor for the nonenzymatic glycation of proteins and DNA, leading to advanced glycation end products (AGEs). Regular intake of dietary MG is strongly correlated with low-grade inflammation, potentially accelerating the pathogenesis of metabolic diseases, including obesity, diabetes, cancers, liver diseases, Alzheimer's disease, cardiovascular diseases, aging, and bone loss. Although pharmaceutical agents (pimagedine and candesartan) have been developed to inhibit MG formation, they often come with serious side effects (nausea, diarrhea, headache, gastrointestinal disturbance, symptomatic hypotension, abnormal renal and liver function tests, development of antinuclear antibody, pernicious-like anemia, and hyperkalemia), highlighting the need for an efficient and safe approach to scavenging MG. Phyllanthus emblica Linn fruit, a nutritious edible fruit, and medicinal plant contains over 300 bioactive compounds. Among twenty-three herbals, 100 μg/mL of the aqueous extract of Phyllanthus emblica fruit (APF) exhibits the highest potency in trapping MG, achieving an 87.3 % reduction under d-fructose induced BSA-AGEs formation. However, there are few reports detailing APF and its related foods' specific impact on disease prevention through MG trapping. This review summarizes the mechanisms through which MG is linked to the development of metabolic diseases and provides several strategies for reducing MG levels using APF and its bioactive compounds. The potential antiglycation properties of APF may offer new applications in the food industry and pharmacological research.
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Affiliation(s)
- Sheng-Yi Chen
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Road, Taichung 40227, Taiwan
| | - I-Chen Chiang
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Road, Taichung 40227, Taiwan
| | - Ying-Ying Chen
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Road, Taichung 40227, Taiwan
| | - Yi-Hsien Hsu
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Road, Taichung 40227, Taiwan
| | - Gow-Chin Yen
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Road, Taichung 40227, Taiwan; Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan.
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2
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Piech S, Brüschweiler S, Westphalen J, Siess KM, García Murias J, Konrat R, Bigenzahn JW, Superti-Furga G. Identification and Characterization of Novel Small-Molecule Enhancers of the CUL3 LZTR1 E3 Ligase KRAS Complex. ACS Chem Biol 2024. [PMID: 39194017 DOI: 10.1021/acschembio.4c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
The RAS family of GTPases is among the most frequently mutated proteins in human cancer, creating a high clinical demand for therapies that counteract their signaling activity. An important layer of regulation that could be therapeutically exploited is the proteostatic regulation of the main RAS GTPases KRAS, NRAS, and HRAS, as well as the closely related members, MRAS and RIT1, by the leucine zipper-like transcriptional regulator 1 cullin 3 RING E3 ubiquitin ligase complex (CUL3LZTR1). Genetic inactivation of LZTR1, as observed in different cancer entities and Noonan syndrome leads to enhanced RAS GTPase abundance and altered MAPK pathway activation state. Novel therapeutic approaches to interfere with hyperactive RAS signaling, thereby complementing existing treatments, are highly sought after. Motivated by the growing arsenal of molecular glue degraders, we report the identification of novel chemical fragments that enhance the protein-protein interaction (PPI) of the KRAS-LZTR1 complex. We established a split-luciferase-based reporter assay that monitors the RAS GTPase-LZTR1 interaction in a scalable format, capable of capturing chemical, as well as mutational perturbations. Using this screening system, in combination with a small fragment library, we identified two fragments, C53 and Z86, that enhance the interaction of the KRAS-LZTR1 complex in a dose-dependent manner. Further orthogonal validation experiments using proximity biotinylation (BioID), thermal shift assays, and NMR spectroscopy demonstrated fragment-dependent enhanced recruitment of endogenous LZTR1 and physical engagement of KRAS. The two fragments, which potentiate the KRAS-LZTR1 interaction, serve as starting points for fragment-based drug discovery. Additionally, the assay we introduced is amenable to high-throughput screening to further explore the pharmacological modulation of the CUL3LZTR1-RAS GTPase complex.
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Affiliation(s)
- Sophie Piech
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Josepha Westphalen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Julio García Murias
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Robert Konrat
- MAG-LAB GmbH, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, 1030 Vienna, Austria
| | - Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna Austria
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3
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Njomen E, Hayward RE, DeMeester KE, Ogasawara D, Dix MM, Nguyen T, Ashby P, Simon GM, Schreiber SL, Melillo B, Cravatt BF. Multi-tiered chemical proteomic maps of tryptoline acrylamide-protein interactions in cancer cells. Nat Chem 2024:10.1038/s41557-024-01601-1. [PMID: 39138346 DOI: 10.1038/s41557-024-01601-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/12/2024] [Indexed: 08/15/2024]
Abstract
Covalent chemistry is a versatile approach for expanding the ligandability of the human proteome. Activity-based protein profiling (ABPP) can infer the specific residues modified by electrophilic compounds through competition with broadly reactive probes. However, the extent to which such residue-directed platforms fully assess the protein targets of electrophilic compounds in cells remains unclear. Here we evaluate a complementary protein-directed ABPP method that identifies proteins showing stereoselective reactivity with alkynylated, chiral electrophilic compounds-termed stereoprobes. Integration of protein- and cysteine-directed data from cancer cells treated with tryptoline acrylamide stereoprobes revealed generally well-correlated ligandability maps and highlighted features, such as protein size and the proteotypicity of cysteine-containing peptides, that explain gaps in each ABPP platform. In total, we identified stereoprobe binding events for >300 structurally and functionally diverse proteins, including compounds that stereoselectively and site-specifically disrupt MAD2L1BP interactions with the spindle assembly checkpoint complex leading to delayed mitotic exit in cancer cells.
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Affiliation(s)
- Evert Njomen
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
| | | | | | | | - Melissa M Dix
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | | | | | | | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Bruno Melillo
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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4
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McDuffie EL, Panettieri RA, Scott CP. G 12/13 signaling in asthma. Respir Res 2024; 25:295. [PMID: 39095798 PMCID: PMC11297630 DOI: 10.1186/s12931-024-02920-0] [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: 06/14/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024] Open
Abstract
Shortening of airway smooth muscle and bronchoconstriction are pathognomonic for asthma. Airway shortening occurs through calcium-dependent activation of myosin light chain kinase, and RhoA-dependent calcium sensitization, which inhibits myosin light chain phosphatase. The mechanism through which pro-contractile stimuli activate calcium sensitization is poorly understood. Our review of the literature suggests that pro-contractile G protein coupled receptors likely signal through G12/13 to activate RhoA and mediate calcium sensitization. This hypothesis is consistent with the effects of pro-contractile agonists on RhoA and Rho kinase activation, actin polymerization and myosin light chain phosphorylation. Recognizing the likely role of G12/13 signaling in the pathophysiology of asthma rationalizes the effects of pro-contractile stimuli on airway hyperresponsiveness, immune activation and airway remodeling, and suggests new approaches for asthma treatment.
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Affiliation(s)
- Elizabeth L McDuffie
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Reynold A Panettieri
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, NJ, USA
| | - Charles P Scott
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.
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Sternicki LM, Poulsen SA. Fragment-based drug discovery campaigns guided by native mass spectrometry. RSC Med Chem 2024; 15:2270-2285. [PMID: 39026646 PMCID: PMC11253872 DOI: 10.1039/d4md00273c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/19/2024] [Indexed: 07/20/2024] Open
Abstract
Native mass spectrometry (nMS) is well established as a biophysical technique for characterising biomolecules and their interactions with endogenous or investigational small molecule ligands. The high sensitivity mass measurements make nMS particularly well suited for applications in fragment-based drug discovery (FBDD) screening campaigns where the detection of weakly binding ligands to a target biomolecule is crucial. We first reviewed the contributions of nMS to guiding FBDD hit identification in 2013, providing a comprehensive perspective on the early adoption of nMS for fragment screening. Here we update this initial progress with a focus on contributions of nMS that have guided FBDD for the period 2014 until end of 2023. We highlight the development of nMS adoption in FBDD in the context of other biophysical fragment screening techniques. We also discuss the roadmap for increased adoption of nMS for fragment screening beyond soluble proteins, including for guiding the discovery of fragments supporting advances in PROTAC discovery, RNA-binding small molecules and covalent therapeutic drug discovery.
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Affiliation(s)
- Louise M Sternicki
- Griffith Institute for Drug Discovery, Griffith University Nathan Brisbane Queensland 4111 Australia
- ARC Centre for Fragment-Based Design Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University Nathan Brisbane Queensland 4111 Australia
- ARC Centre for Fragment-Based Design Australia
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Hoffer L, Charifi-Hoareau G, Barelier S, Betzi S, Miller T, Morelli X, Roche P. ChemoDOTS: a web server to design chemistry-driven focused libraries. Nucleic Acids Res 2024; 52:W461-W468. [PMID: 38686808 PMCID: PMC11223810 DOI: 10.1093/nar/gkae326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
In drug discovery, the successful optimization of an initial hit compound into a lead molecule requires multiple cycles of chemical modification. Consequently, there is a need to efficiently generate synthesizable chemical libraries to navigate the chemical space surrounding the primary hit. To address this need, we introduce ChemoDOTS, an easy-to-use web server for hit-to-lead chemical optimization freely available at https://chemodots.marseille.inserm.fr/. With this tool, users enter an activated form of the initial hit molecule then choose from automatically detected reactive functions. The server proposes compatible chemical transformations via an ensemble of encoded chemical reactions widely used in the pharmaceutical industry during hit-to-lead optimization. After selection of the desired reactions, all compatible chemical building blocks are automatically coupled to the initial hit to generate a raw chemical library. Post-processing filters can be applied to extract a subset of compounds with specific physicochemical properties. Finally, explicit stereoisomers and tautomers are computed, and a 3D conformer is generated for each molecule. The resulting virtual library is compatible with most docking software for virtual screening campaigns. ChemoDOTS rapidly generates synthetically feasible, hit-focused, large, diverse chemical libraries with finely-tuned physicochemical properties via a user-friendly interface providing a powerful resource for researchers engaged in hit-to-lead optimization.
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Affiliation(s)
- Laurent Hoffer
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Univ, Marseille 13273, France
| | | | - Sarah Barelier
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Univ, Marseille 13273, France
| | - Stéphane Betzi
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Univ, Marseille 13273, France
| | - Thomas Miller
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Univ, Marseille 13273, France
| | - Xavier Morelli
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Univ, Marseille 13273, France
| | - Philippe Roche
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Univ, Marseille 13273, France
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Zhao Y, Hadavi D, Dijkgraaf I, Honing M. Coupling of surface plasmon resonance and mass spectrometry for molecular interaction studies in drug discovery. Drug Discov Today 2024; 29:104027. [PMID: 38762085 DOI: 10.1016/j.drudis.2024.104027] [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: 03/11/2024] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Various analytical technologies have been developed for the study of target-ligand interactions. The combination of these technologies gives pivotal information on the binding mechanism, kinetics, affinity, residence time, and changes in molecular structures. Mass spectrometry (MS) offers structural information, enabling the identification and quantification of target-ligand interactions. Surface plasmon resonance (SPR) provides kinetic information on target-ligand interaction in real time. The coupling of MS and SPR complements each other in the studies of target-ligand interactions. Over the last two decades, the capabilities and added values of SPR-MS have been reported. This review summarizes and highlights the benefits, applications, and potential for further research of the SPR-MS approach.
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Affiliation(s)
- Yuandi Zhao
- Maastricht Multimodal Molecular Imaging (M4i) Institute, Maastricht University, Maastricht, the Netherlands
| | - Darya Hadavi
- Maastricht Multimodal Molecular Imaging (M4i) Institute, Maastricht University, Maastricht, the Netherlands.
| | - Ingrid Dijkgraaf
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands; Department of Radiology and Nuclear Medicine, MUMC+, The Netherlands
| | - Maarten Honing
- Maastricht Multimodal Molecular Imaging (M4i) Institute, Maastricht University, Maastricht, the Netherlands
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Zhang C, Liu Y, Li G, Yang Z, Han C, Sun X, Sheng C, Ding K, Rao Y. Targeting the undruggables-the power of protein degraders. Sci Bull (Beijing) 2024; 69:1776-1797. [PMID: 38614856 DOI: 10.1016/j.scib.2024.03.056] [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: 01/27/2024] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 04/15/2024]
Abstract
Undruggable targets typically refer to a class of therapeutic targets that are difficult to target through conventional methods or have not yet been targeted, but are of great clinical significance. According to statistics, over 80% of disease-related pathogenic proteins cannot be targeted by current conventional treatment methods. In recent years, with the advancement of basic research and new technologies, the development of various new technologies and mechanisms has brought new perspectives to overcome challenging drug targets. Among them, targeted protein degradation technology is a breakthrough drug development strategy for challenging drug targets. This technology can specifically identify target proteins and directly degrade pathogenic target proteins by utilizing the inherent protein degradation pathways within cells. This new form of drug development includes various types such as proteolysis targeting chimera (PROTAC), molecular glue, lysosome-targeting Chimaera (LYTAC), autophagosome-tethering compound (ATTEC), autophagy-targeting chimera (AUTAC), autophagy-targeting chimera (AUTOTAC), degrader-antibody conjugate (DAC). This article systematically summarizes the application of targeted protein degradation technology in the development of degraders for challenging drug targets. Finally, the article looks forward to the future development direction and application prospects of targeted protein degradation technology.
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Affiliation(s)
- Chao Zhang
- Changping Laboratory, Beijing 102206, China
| | - Yongbo Liu
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Guangchen Li
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Zhouli Yang
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Chi Han
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiuyun Sun
- Changping Laboratory, Beijing 102206, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China.
| | - Ke Ding
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Yu Rao
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Changping Laboratory, Beijing 102206, China.
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Wu Z, Chen S, Wang Y, Li F, Xu H, Li M, Zeng Y, Wu Z, Gao Y. Current perspectives and trend of computer-aided drug design: a review and bibliometric analysis. Int J Surg 2024; 110:3848-3878. [PMID: 38502850 PMCID: PMC11175770 DOI: 10.1097/js9.0000000000001289] [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: 11/08/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
AIM Computer-aided drug design (CADD) is a drug design technique for computing ligand-receptor interactions and is involved in various stages of drug development. To better grasp the frontiers and hotspots of CADD, we conducted a review analysis through bibliometrics. METHODS A systematic review of studies published between 2000 and 20 July 2023 was conducted following the PRISMA guidelines. Literature on CADD was selected from the Web of Science Core Collection. General information, publications, output trends, countries/regions, institutions, journals, keywords, and influential authors were visually analyzed using software such as Excel, VOSviewer, RStudio, and CiteSpace. RESULTS A total of 2031 publications were included. These publications primarily originated from 99 countries or regions led by the U.S. and China. Among the contributors, MacKerell AD had the highest number of articles and the greatest influence. The Journal of Medicinal Chemistry was the most cited journal, whereas the Journal of Chemical Information and Modeling had the highest number of publications. CONCLUSIONS Influential authors in the field were identified. Current research shows active collaboration between countries, institutions, and companies. CADD technologies such as homology modeling, pharmacophore modeling, quantitative conformational relationships, molecular docking, molecular dynamics simulation, binding free energy prediction, and high-throughput virtual screening can effectively improve the efficiency of new drug discovery. Artificial intelligence-assisted drug design and screening based on CADD represent key topics that will influence future development. Furthermore, this paper will be helpful in better understanding the frontiers and hotspots of CADD.
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Affiliation(s)
- Zhenhui Wu
- School of Pharmacy, Jiangxi University of Chinese Medicine
- School of Clinical Medicine, Jiangxi University of Chinese Medicine, Nanchang
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
| | - Shupeng Chen
- School of Clinical Medicine, Jiangxi University of Chinese Medicine, Nanchang
| | - Yihao Wang
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
| | - Fangyang Li
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
| | - Huanhua Xu
- School of Pharmacy, Jiangxi University of Chinese Medicine
| | - Maoxing Li
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
| | - Yingjian Zeng
- School of Clinical Medicine, Jiangxi University of Chinese Medicine, Nanchang
| | - Zhenfeng Wu
- School of Pharmacy, Jiangxi University of Chinese Medicine
| | - Yue Gao
- School of Pharmacy, Jiangxi University of Chinese Medicine
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
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Lin Y, Chen X, Lin L, Xu B, Zhu X, Lin X. Sesamolin serves as an MYH14 inhibitor to sensitize endometrial cancer to chemotherapy and endocrine therapy via suppressing MYH9/GSK3β/β-catenin signaling. Cell Mol Biol Lett 2024; 29:63. [PMID: 38698330 PMCID: PMC11067147 DOI: 10.1186/s11658-024-00583-9] [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: 11/06/2023] [Accepted: 04/24/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Endometrial cancer (EC) is one of the most common gynecological cancers. Herein, we aimed to define the role of specific myosin family members in EC because this protein family is involved in the progression of various cancers. METHODS Bioinformatics analyses were performed to reveal EC patients' prognosis-associated genes in patients with EC. Furthermore, colony formation, immunofluorescence, cell counting kit 8, wound healing, and transwell assays as well as coimmunoprecipitation, cycloheximide chase, luciferase reporter, and cellular thermal shift assays were performed to functionally and mechanistically analyze human EC samples, cell lines, and a mouse model, respectively. RESULTS Machine learning techniques identified MYH14, a member of the myosin family, as the prognosis-associated gene in patients with EC. Furthermore, bioinformatics analyses based on public databases showed that MYH14 was associated with EC chemoresistance. Moreover, immunohistochemistry validated MYH14 upregulation in EC cases compared with that in normal controls and confirmed that MYH14 was an independent and unfavorable prognostic indicator of EC. MYH14 impaired cell sensitivity to carboplatin, paclitaxel, and progesterone, and increased cell proliferation and metastasis in EC. The mechanistic study showed that MYH14 interacted with MYH9 and impaired GSK3β-mediated β-catenin ubiquitination and degradation, thus facilitating the Wnt/β-catenin signaling pathway and epithelial-mesenchymal transition. Sesamolin, a natural compound extracted from Sesamum indicum (L.), directly targeted MYH14 and attenuated EC progression. Additionally, the compound disrupted the interplay between MYH14 and MYH9 and repressed MYH9-regulated Wnt/β-catenin signaling. The in vivo study further verified sesamolin as a therapeutic drug without side effects. CONCLUSIONS Herein, we identified that EC prognosis-associated MYH14 was independently responsible for poor overall survival time of patients, and it augmented EC progression by activating Wnt/β-catenin signaling. Targeting MYH14 by sesamolin, a cytotoxicity-based approach, can be applied synergistically with chemotherapy and endocrine therapy to eventually mitigate EC development. This study emphasizes MYH14 as a potential target and sesamolin as a valuable natural drug for EC therapy.
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Affiliation(s)
- Yibin Lin
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, Fujian, China
| | - Xiao Chen
- Department of Intensive Care Unit, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, Fujian, China
- Department of Intensive Care Unit, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, Fujian, China
| | - Linping Lin
- Hunan Institute of Engineering, Xiangtan, 411100, Hunan, China
| | - Benhua Xu
- Department of Radiation Oncology, Fujian Medical University Union Hospital, Xinquan Road 29, Gulou District, Fuzhou, 350001, Fujian, China.
| | - Xiaofeng Zhu
- Department of Oral Maxillo-Facial Surgery, The First Affiliated Hospital, Fujian Medical University, No. 20 Chazhong Road, Taijing District, Fuzhou, 350005, Fujian, China.
- Department of Oral Maxillo-Facial Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
| | - Xian Lin
- Shenzhen Key Laboratory of Inflammatory and Immunology Diseases, No. 1120 Lianhua Road, Futian District, Shenzhen, 518036, Guangdong, China.
- Peking University Shenzhen Hospital, Shenzhen, 518036, Guangdong, China.
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Huang Y, Li Z, Chen Y, Li W, Wei S, Ji Z. Synthesis and Herbicidal Activity of 2-(2-Oxo-3-pyridyl-benzothiazol-6-yloxy)hexanoic Acids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7457-7463. [PMID: 38527909 DOI: 10.1021/acs.jafc.3c08213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The discovery of a lead compound is fundamental to herbicide innovation, but the limited availability of valuable lead compounds has hindered their development in recent years. By utilizing the structural diversity-oriented inactive group strategy, 3-(2-pyridyl)-benzothiazol-2-one was identified as a promising lead scaffold for herbicides, starting from benzothiazole which is an inactive moiety commonly found in herbicides such as mefenacet, benazolin, benzthiazuron, and fenthiaprop-ethyl. To investigate the structure-activity relationship (SAR) of these chemicals, a series of 2-(2-oxo-3-pyridyl-benzothiazol-6-yloxy)hexanoic acid derivatives (VI01 ∼ VI28) were synthesized through classical nucleophilic SNAr reaction using halogenated pyridines and 6-methoxybenzothiazole-2-one. The chemical structures of all the title compounds were confirmed by NMR and MS analysis. Petri dish assays indicated that many compounds exhibited potent herbicidal activity against both broad-leaf weeds and grass weeds at 1.0 mg/L. The SAR analysis revealed that the presence of a trifluoromethyl group at the 5-position of pyridine is essential for herbicidal activity. Furthermore, carboxylic esters exhibit higher herbicidal activity compared to carboxylic amides and free acids, and the activity decreased with the extension of the carbon chain. The postemergence herbicidal activity of VI03 against 16 species of weeds was tested by pot experiments in a greenhouse. VI03 demonstrated comparable efficacy in controlling broadleaf weeds and superior efficacy in controlling grass weeds compared to carfentrazone ethyl. The present study has unveiled a novel molecular scaffold exhibiting remarkably potent herbicidal activity. These findings are anticipated to provide valuable insights for the advancement of new herbicides and offer an alternative approach for managing resistant weeds.
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Affiliation(s)
- Yuqian Huang
- College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi, P. R. China
| | - Zhanbin Li
- College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi, P. R. China
| | - Yu Chen
- College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi, P. R. China
| | - Wenqi Li
- College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi, P. R. China
| | - Shaopeng Wei
- College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi, P. R. China
- Shaanxi Province Key Laboratory Research & Development on Botanical Pesticides, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Zhiqin Ji
- College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi, P. R. China
- Shaanxi Province Key Laboratory Research & Development on Botanical Pesticides, Northwest A&F University, Yangling, 712100 Shaanxi, China
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Lemaitre T, Cornu M, Schwalen F, Since M, Kieffer C, Voisin-Chiret AS. Molecular glue degraders: exciting opportunities for novel drug discovery. Expert Opin Drug Discov 2024; 19:433-449. [PMID: 38240114 DOI: 10.1080/17460441.2024.2306845] [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: 10/06/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
INTRODUCTION Molecular Glue Degraders (MGDs) is a concept that refers to a class of compounds that facilitate the interaction between two proteins or molecules within a cell. These compounds act as bridge that enhances specific Protein-Protein Interactions (PPIs). Over the past decade, this technology has gained attention as a potential strategy to target proteins that were traditionally considered undruggable using small molecules. AREAS COVERED This review presents the concept of cellular homeostasis and the balance between protein synthesis and protein degradation. The concept of protein degradation is concerned with molecular glues, which form part of the broader field of Targeted Protein Degradation (TPD). Next, pharmacochemical strategies for the rational design of MGDs are detailed and illustrated by examples of Ligand-Based (LBDD), Structure-Based (SBDD) and Fragment-Based Drug Design (FBDD). EXPERT OPINION Expanding the scope of what can be effectively targeted in the development of treatments for diseases that are incurable or resistant to conventional therapies offers new therapeutic options. The treatment of microbial infections and neurodegenerative diseases is a major societal challenge, and the discovery of MGDs appears to be a promising avenue. Combining different approaches to discover and exploit a variety of innovative therapeutic agents will create opportunities to treat diseases that are still incurable.
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Affiliation(s)
| | - Marie Cornu
- Normandie University, UNICAEN, CERMN, Caen, France
| | - Florian Schwalen
- Normandie University, UNICAEN, CERMN, Caen, France
- Department of Pharmacy, Caen University Hospital, Caen, France
| | - Marc Since
- Normandie University, UNICAEN, CERMN, Caen, France
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Cebi E, Lee J, Subramani VK, Bak N, Oh C, Kim KK. Cryo-electron microscopy-based drug design. Front Mol Biosci 2024; 11:1342179. [PMID: 38501110 PMCID: PMC10945328 DOI: 10.3389/fmolb.2024.1342179] [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: 11/21/2023] [Accepted: 01/31/2024] [Indexed: 03/20/2024] Open
Abstract
Structure-based drug design (SBDD) has gained popularity owing to its ability to develop more potent drugs compared to conventional drug-discovery methods. The success of SBDD relies heavily on obtaining the three-dimensional structures of drug targets. X-ray crystallography is the primary method used for solving structures and aiding the SBDD workflow; however, it is not suitable for all targets. With the resolution revolution, enabling routine high-resolution reconstruction of structures, cryogenic electron microscopy (cryo-EM) has emerged as a promising alternative and has attracted increasing attention in SBDD. Cryo-EM offers various advantages over X-ray crystallography and can potentially replace X-ray crystallography in SBDD. To fully utilize cryo-EM in drug discovery, understanding the strengths and weaknesses of this technique and noting the key advancements in the field are crucial. This review provides an overview of the general workflow of cryo-EM in SBDD and highlights technical innovations that enable its application in drug design. Furthermore, the most recent achievements in the cryo-EM methodology for drug discovery are discussed, demonstrating the potential of this technique for advancing drug development. By understanding the capabilities and advancements of cryo-EM, researchers can leverage the benefits of designing more effective drugs. This review concludes with a discussion of the future perspectives of cryo-EM-based SBDD, emphasizing the role of this technique in driving innovations in drug discovery and development. The integration of cryo-EM into the drug design process holds great promise for accelerating the discovery of new and improved therapeutic agents to combat various diseases.
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Affiliation(s)
| | | | | | | | - Changsuk Oh
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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Wu Q, Centorrino F, Guillory X, Wolter M, Ottmann C, Cossar PJ, Brunsveld L. Discovery of 14-3-3 PPI Stabilizers by Extension of an Amidine-Substituted Thiophene Fragment. Chembiochem 2024; 25:e202300636. [PMID: 37902676 DOI: 10.1002/cbic.202300636] [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: 09/17/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 10/31/2023]
Abstract
Protein-protein interaction (PPI) modulation is a promising approach in drug discovery with the potential to expand the 'druggable' proteome and develop new therapeutic strategies. While there have been significant advancements in methodologies for developing PPI inhibitors, there is a relative scarcity of literature describing the 'bottom-up' development of PPI stabilizers (Molecular Glues). The hub protein 14-3-3 and its interactome provide an excellent platform for exploring conceptual approaches to PPI modulation, including evolution of chemical matter for Molecular Glues. In this study, we employed a fragment extension strategy to discover stabilizers for the complex of 14-3-3 protein and an Estrogen Receptor alpha-derived peptide (ERα). A focused library of analogues derived from an amidine-substituted thiophene fragment enhanced the affinity of the 14-3-3/ERα complex up to 6.2-fold. Structure-activity relationship (SAR) analysis underscored the importance of the newly added, aromatic side chain with a certain degree of rigidity. X-ray structural analysis revealed a unique intermolecular π-π stacking binding mode of the most active analogues, resulting in the simultaneous binding of two molecules to the PPI binding pocket. Notably, analogue 11 displayed selective stabilization of the 14-3-3/ERα complex.
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Affiliation(s)
- Qi Wu
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Federica Centorrino
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Xavier Guillory
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Madita Wolter
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
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Li X, Wang GA, Wei Z, Wang H, Zhu X. Protein-DNA interface hotspots prediction based on fusion features of embeddings of protein language model and handcrafted features. Comput Biol Chem 2023; 107:107970. [PMID: 37866116 DOI: 10.1016/j.compbiolchem.2023.107970] [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: 08/09/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/24/2023]
Abstract
The identification of hotspot residues at the protein-DNA binding interfaces plays a crucial role in various aspects such as drug discovery and disease treatment. Although experimental methods such as alanine scanning mutagenesis have been developed to determine the hotspot residues on protein-DNA interfaces, they are both inefficient and costly. Therefore, it is highly necessary to develop efficient and accurate computational methods for predicting hotspot residues. Several computational methods have been developed, however, they are mainly based on hand-crafted features which may not be able to represent all the information of proteins. In this regard, we propose a model called PDH-EH, which utilizes fused features of embeddings extracted from a protein language model (PLM) and handcrafted features. After we extracted the total 1141 dimensional features, we used mRMR to select the optimal feature subset. Based on the optimal feature subset, several different learning algorithms such as Random Forest, Support Vector Machine, and XGBoost were used to build the models. The cross-validation results on the training dataset show that the model built by using Random Forest achieves the highest AUROC. Further evaluation on the independent test set shows that our model outperforms the existing state-of-the-art models. Moreover, the effectiveness and interpretability of embeddings extracted from PLM were demonstrated in our analysis. The codes and datasets used in this study are available at: https://github.com/lixiangli01/PDH-EH.
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Affiliation(s)
- Xiang Li
- School of Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Gang-Ao Wang
- School of Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Zhuoyu Wei
- School of Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Hong Wang
- School of Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xiaolei Zhu
- School of Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China.
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