1
|
Chen G, Wang W, Guan B, Zhang G, Zhang Z, Lin L, Han X, Xu T, Hu C, Pang M, Zhao X, Zhou Y, Li R. Cycloastragenol reduces inflammation in CLP-induced septic MICE by suppressing TLR4 signaling pathways. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2025; 142:156645. [PMID: 40319834 DOI: 10.1016/j.phymed.2025.156645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/26/2024] [Accepted: 01/05/2025] [Indexed: 05/07/2025]
Abstract
BACKGROUND Aggressive systemic inflammation due to activation of macrophage-derived excessive immune responses is a critical cause of sepsis leading to clinical death. The effect of cycloastragenol (CAG) on cecal ligation and puncture (CLP)-induced systemic inflammation in mice with sepsis and the underlying mechanism are still unknown. PURPOSE Here, we firstly investigated the ameliorative functions of CAG in CLP-induced systemic inflammation in sepsis and LPS-mediated inflammatory response, and the impact of Toll-like receptor 4 (TLR4) pathway on the anti-inflammatory effects of CAG. METHODS The in vitro effect of CAG on RAW264.7 cells and THP-1-derived macrophages induced by LPS was detected with quantitative polymerase chain reaction (qPCR), enzyme-linked immunosorbent assay (ELISA), and Western blotting (WB) assays. In addition, the association of TLR4-MD2 complex with CAG was measured through molecular docking, molecular dynamics (MD) simulation, surface plasmon resonance imaging (SPRi), cellular thermal shift assay (CETSA), immunofluorescence and WB. A specific inhibitor of TLR4 receptor TAK-242 and a TLR4-encoding adenovirus were adopted for verifying the functions of CAG. Meanwhile, the in vivo effects of CAG on cardiopulmonary structure, inflammatory factors and survival of CLP-induced septic mice were analyzed through hematoxylin and eosin staining, qPCR, ELISA, and survival analysis. RESULTS CAG hindered the LPS-induced production of inflammatory mediators like TNF-α, IL-6 and IL-1β within macrophages in vitro. It also inhibited MAPK and NF-κB pathway activation induced by binding of LPS to TLR4 receptor. As suggested by molecular docking results, the MD2-CAG binding energy was -9.53 kcal/mol. During the MD simulation, CAG could tightly bind to the binding pocket of MD2. SPRi revealed that the equilibrium dissociation constant (KD) value for CAG and TLR4 was 5.24× 10-9 M. Moreover, CAG enhanced the thermal stability of TLR4 by approximately 2.68 °C. It further inhibited the binding between LPS-488 and cell membrane receptors. These inhibitory effects of CAG could be partly reversed by TLR4 overexpression and could not increase by specifically blocking TLR4. In vivo, CAG attenuated cardiopulmonary injury and inflammation and improved survival in septic mice dose-dependently. CONCLUSION CAG exerts its anti-inflammatory activity through suppressing MAPK and NF-κB pathway activation caused by TLR4 activation and inhibiting inflammatory factor production dose-dependently.
Collapse
Affiliation(s)
- Guanghong Chen
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, China; Postdoctoral Research Station of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, China; Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou, Guangdong, 510405, China
| | - Wanyu Wang
- Department of Neurosurgery, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Baoyi Guan
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, China; Postdoctoral Research Station of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, China; Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou, Guangdong, 510405, China
| | - Guoyong Zhang
- school of Traditional Chinese Medicine, Department of Traditional Chinese Medicine, Nanfang Hospital (ZengCheng Branch), Southern Medical University, Guangzhou, 510515, China
| | - Zhimin Zhang
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, China; Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou, Guangdong, 510405, China
| | - Liwen Lin
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, China; Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou, Guangdong, 510405, China
| | - Xin Han
- school of Traditional Chinese Medicine, Department of Traditional Chinese Medicine, Nanfang Hospital (ZengCheng Branch), Southern Medical University, Guangzhou, 510515, China
| | - Tong Xu
- school of Traditional Chinese Medicine, Department of Traditional Chinese Medicine, Nanfang Hospital (ZengCheng Branch), Southern Medical University, Guangzhou, 510515, China
| | - Changlei Hu
- school of Traditional Chinese Medicine, Department of Traditional Chinese Medicine, Nanfang Hospital (ZengCheng Branch), Southern Medical University, Guangzhou, 510515, China
| | - Mingjie Pang
- school of Traditional Chinese Medicine, Department of Traditional Chinese Medicine, Nanfang Hospital (ZengCheng Branch), Southern Medical University, Guangzhou, 510515, China
| | - Xinjun Zhao
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, China.
| | - Yingchun Zhou
- school of Traditional Chinese Medicine, Department of Traditional Chinese Medicine, Nanfang Hospital (ZengCheng Branch), Southern Medical University, Guangzhou, 510515, China.
| | - Rong Li
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, China.
| |
Collapse
|
2
|
Peng S, Zhang W, Sun Q, Zhang W, Chen Y, Lv Z, Fang Z, Wei X, Lu T, Chen G, Jiao Y. Discovery of THB Derivates as Ferroptosis Inhibitors for the Treatment of Acute Kidney Injury by Targeting VDAC. J Med Chem 2025. [PMID: 40402184 DOI: 10.1021/acs.jmedchem.5c00280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2025]
Abstract
Acute kidney injury (AKI), a clinical syndrome marked by high morbidity and mortality, remains a significant challenge due to the lack of effective therapeutic options. The accumulation of Fe2+ and reactive oxygen species (ROS) in injured renal cells, which triggers ferroptosis, play a key driver in the pathogenesis of AKI. In this study, tetrahydroberberine (THB), a natural product, was identified as a ferroptosis inhibitor that targeted the voltage-dependent anion channel (VDAC). Through structural optimization, a series of THB derivatives were developed, among which 34a exhibited about 100-fold enhanced ferroptosis inhibitory activity. Moreover, 34a significantly reduced ROS, Fe2+ and restored glutathione (GSH) below 20 nM. In vivo experiments confirmed that 34a effectively alleviated folic acid-induced AKI, accompanied by a reduction in key kidney injury markers. These results highlight the potential of 12-amino THB derivatives as novel ferroptosis inhibitors and provide promising therapeutic strategies for AKI treatment.
Collapse
Affiliation(s)
- Shengkuan Peng
- School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Wenhao Zhang
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Qiaoyi Sun
- School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Wenqiang Zhang
- School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Yadong Chen
- School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Zhicheng Lv
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Zhihang Fang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Xian Wei
- Department of Pharmacy, Youjiang Medical University for Nationalities, Baise 533000, P. R. China
| | - Tao Lu
- School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Guo Chen
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Yu Jiao
- School of Science, China Pharmaceutical University, Nanjing 211198, P. R. China
| |
Collapse
|
3
|
Kohnken R, Fossey S, Buck WR, Segreti J, Treadway J, Green J, Koshman YE, Zafiratos M, Mittelstadt S, Blomme E, Foley CM. ABBV-712-induced cardiac pathology in rats is related to off-target-driven acute vasodilation, tachycardia, and increased cardiac contractility. Toxicol Sci 2025; 205:233-244. [PMID: 40214157 DOI: 10.1093/toxsci/kfaf021] [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] [Indexed: 04/30/2025] Open
Abstract
Following an observation of myocardial toxicity in rats with an experimental TYK2 inhibitor (ABBV-712), investigative studies were performed to identify the mechanism. Telemetry-instrumented rats were administered ABBV-712 with or without atenolol to investigate effects of co-dosing on hemodynamic parameters and cardiac pathology. In vitro studies included cytotoxicity assessment in human-induced pluripotent stem cell-derived cardiomyocytes and relaxation of isolated rat aorta. Off-target pharmacology was evaluated by binding and inhibition screening assays. Finally, TYK2 knockout mice were administered ABBV-712 to evaluate hemodynamics as compared with wild-type animals. ABBV-712 resulted in decreased mean arterial pressure and increased heart rate in rats that was prevented by pre-dosing atenolol. ABBV-712-induced myocardial necrosis was also prevented by atenolol, suggesting a mechanistic link between hemodynamic changes and cardiac pathology. The pathology was unrelated to direct cytotoxicity on cardiomyocytes as demonstrated in vitro and was shown to be a compound-related effect on vascular relaxation mediated by the endothelium. The toxicity was considered an off-target effect, as demonstrated by similar hemodynamic responses between TYK2 knockout and wild-type mice administered ABBV-712, as well as by the lack of hemodynamic alterations in the knockout mouse. Inhibition of identified off-targets was unlikely to be the cause of the hemodynamic changes. In conclusion. a novel TYK2 inhibitor was associated with decreased mean arterial pressure, increased heart rate, and secondary myocardial necrosis in rats. These effects were unrelated to TYK2 inhibition. This report is an example of a cross-functional mechanistic investigation into the pharmacologic cause of an identified cardiovascular toxicity.
Collapse
Affiliation(s)
- Rebecca Kohnken
- Safety Pharmacology, AbbVie Inc., North Chicago, IL 60064, United States
| | - Stacey Fossey
- Investigative Toxicology and Pathology, AbbVie Inc., North Chicago, IL 60064, United States
| | - Wayne R Buck
- Investigative Toxicology and Pathology, AbbVie Inc., North Chicago, IL 60064, United States
| | - Jason Segreti
- Safety Pharmacology, AbbVie Inc., North Chicago, IL 60064, United States
| | - Jessica Treadway
- Safety Pharmacology, AbbVie Inc., North Chicago, IL 60064, United States
| | - Jonathon Green
- Safety Pharmacology, AbbVie Inc., North Chicago, IL 60064, United States
| | - Yevgeniya E Koshman
- Investigative Toxicology and Pathology, AbbVie Inc., North Chicago, IL 60064, United States
| | - Mark Zafiratos
- Safety Pharmacology, AbbVie Inc., North Chicago, IL 60064, United States
| | - Scott Mittelstadt
- Preclinical Safety, AbbVie Inc., North Chicago, IL 60064, United States
| | - Eric Blomme
- Development Biologic Sciences, AbbVie Inc., North Chicago, IL 60064, United States
| | - Charles M Foley
- Safety Pharmacology, AbbVie Inc., North Chicago, IL 60064, United States
| |
Collapse
|
4
|
Song J. Applications of the Cellular Thermal Shift Assay to Drug Discovery in Natural Products: A Review. Int J Mol Sci 2025; 26:3940. [PMID: 40362180 PMCID: PMC12072176 DOI: 10.3390/ijms26093940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 04/21/2025] [Accepted: 04/21/2025] [Indexed: 05/15/2025] Open
Abstract
Natural products play a crucial role in drug discovery because of their structural diversity and biological activity. However, identifying their molecular targets remains a challenge. Traditional target identification approaches such as affinity-based protein profiling and activity-based protein profiling are limited by the need for chemical modification or reactive groups in natural products. The emergence of label-free techniques offers a powerful alternative for studying drug-target engagement in a physiological context. In particular, the cellular thermal shift assay (CETSA) exploits ligand-induced protein stabilization-a phenomenon where ligand binding enhances a protein's thermal stability by reducing conformational flexibility-to assess drug binding without requiring chemical modifications. CETSA's integration with advanced mass spectrometry and high-throughput platforms has dramatically expanded proteome coverage and sensitivity, enabling the simultaneous quantification of thousands of proteins and the identification of low-abundance targets in native cellular environments. This review highlights the application of key CETSA-based methods to target identification in natural products including Western blot-based CETSA, isothermal dose-response CETSA, mass spectrometry-based CETSA, and high-throughput CETSA. Case studies are presented that demonstrate their effectiveness in uncovering the mechanisms of action of different drugs. The current limitations of CETSA-based strategies are also explored, and future improvements to optimize their potential for drug discovery are discussed. Integrating CETSA with complementary approaches can enhance the target identification accuracy and efficiency for natural products and ultimately advance development of therapeutic applications.
Collapse
Affiliation(s)
- Jayoung Song
- Department of Pharmacology, College of Medicine, Dankook University, Cheonan 31116, Republic of Korea
| |
Collapse
|
5
|
Lemke MC, Avala NR, Rader MT, Hargett SR, Lank DS, Seltzer BD, Harris TE. MAST Kinases' Function and Regulation: Insights from Structural Modeling and Disease Mutations. Biomedicines 2025; 13:925. [PMID: 40299535 PMCID: PMC12024977 DOI: 10.3390/biomedicines13040925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Revised: 04/01/2025] [Accepted: 04/03/2025] [Indexed: 04/30/2025] Open
Abstract
Background/Objectives: The MAST kinases are ancient AGC kinases associated with many human diseases, such as cancer, diabetes, and neurodevelopmental disorders. We set out to describe the origins and diversification of MAST kinases from a structural and bioinformatic perspective to inform future research directions. Methods: We investigated MAST-lineage kinases using database and sequence analysis. We also estimate the functional consequences of disease point mutations on protein stability by integrating predictive algorithms and AlphaFold. Results: Higher-order organisms often have multiple MASTs and a single MASTL kinase. MAST proteins conserve an AGC kinase domain, a domain of unknown function 1908 (DUF), and a PDZ binding domain. D. discoideum contains MAST kinase-like proteins that exhibit a characteristic insertion within the T-loop but do not conserve DUF or PDZ domains. While the DUF domain is conserved in plants, the PDZ domain is not. The four mammalian MASTs demonstrate tissue expression heterogeneity by mRNA and protein. MAST1-4 are likely regulated by 14-3-3 proteins based on interactome data and in silico predictions. Comparative ΔΔG estimation identified that MAST1-L232P and G522E mutations are likely destabilizing. Conclusions: We conclude that MAST and MASTL kinases diverged from the primordial MAST, which likely operated in both biological niches. The number of MAST paralogs then expanded to the heterogeneous subfamily seen in mammals that are all likely regulated by 14-3-3 protein interaction. The reported pathogenic mutations in MASTs primarily represent alterations to post-translational modification topology in the DUF and kinase domains. Our report outlines a computational basis for future work in MAST kinase regulation and drug discovery.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Thurl E. Harris
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22903, USA; (M.C.L.)
| |
Collapse
|
6
|
Huang M, Wu Y, Wei X, Cheng L, Fu L, Yan H, Wei W, Li B, Ru H, Mo X, Tang W, Su Z, Yan L. Trifluridine/tipiracil induces ferroptosis by targeting p53 via the p53-SLC7A11 axis in colorectal cancer 3D organoids. Cell Death Dis 2025; 16:255. [PMID: 40188162 PMCID: PMC11972347 DOI: 10.1038/s41419-025-07541-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 02/15/2025] [Accepted: 03/14/2025] [Indexed: 04/07/2025]
Abstract
Trifluridine/Tipiracil (FTD/TPI, TAS102) has been approved for the treatment of patients with colorectal cancer (CRC) for its promising anticancer activity enabled by its incorporation into double strands during DNA synthesis. However, the mechanisms underlying the anticancer targets of FTD/TPI remain not fully understood. Here we report our observation of the activation of ferroptosis in CRC by FTD/TPI. Mechanistically, FTD/TPI directly promotes the ubiquitination and degradation of MDM2, thereby stabilizing the p53. Nuclear accumulation of p53 subsequently downregulates SLC7A11 expression, leading to ferroptosis. Furthermore, we observed that FTD/TPI combined with sulfasalazine (SAS), a system Xc- inhibitor, works in a synergistic manner to induce ferroptosis and further inhibit the proliferation of CRC cells. Finally, we confirmed the synergistic effect of SAS and FTD/TPI on patient-derived organoids in vitro and patient-derived xenograft mouse models in vivo. Our findings are the first to reveal that FTD/TPI induces ferroptosis via the p53-SLC7A11 axis and that SAS enhances the sensitivity and therapeutic effect of FTD/TPI. These findings suggest that the synergistic effect of FTD/TPI and SAS may represent a new therapeutic strategy for patients with CRC.
Collapse
Affiliation(s)
- Maosen Huang
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Yancen Wu
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Xiaoxia Wei
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Linyao Cheng
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Lihua Fu
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Haochao Yan
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Wene Wei
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Bo Li
- Liaoning Provincial Engineering Laboratory of Anti-tumor Immunity and Molecular Theranostics Technology, Collaborative Innovation Center for Age-related Disease, Life Science Institute of Jinzhou Medical University, Jinzhou, 121001, Liaoning, China
| | - Haiming Ru
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Xianwei Mo
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Weizhong Tang
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Zijie Su
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China.
| | - Linhai Yan
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China.
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning, 530021, Guangxi Zhuang Autonomous Region, China.
| |
Collapse
|
7
|
Li J, Bao J, Liu Y, Chen M, Chen Y, Tuolihong L, Jiang F, Xie S, Lyu F, Sun Y, Cao Y, Chen H, Chen Z, Zeng Z. Lentinan enhances microbiota-derived isoursodeoxycholic acid levels to alleviate hepatic ischemia-reperfusion injury in mice. Int J Biol Macromol 2025; 304:140717. [PMID: 39920949 DOI: 10.1016/j.ijbiomac.2025.140717] [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: 12/16/2024] [Revised: 01/28/2025] [Accepted: 02/04/2025] [Indexed: 02/10/2025]
Abstract
Hepatic ischemia-reperfusion injury (HIRI) is an essential clinical concern caused by liver transplantation, resection, trauma, and shock that must be addressed immediately. Although the mechanisms underlying HIRI are well-documented, effective prevention and treatment strategies are still lacking. Inflammation is a central mechanism of HIRI, with macrophages playing a crucial role in initiating and amplifying the inflammatory response. Numerous plant polysaccharides exhibit substantial anti-inflammatory and hepatoprotective properties. However, the function of Lentinan (LNT) in HIRI has not been fully explored. Thus, this study aims to investigate the preventive potential of LNT in HIRI. Here, we reveal that oral administration of LNT considerably reduces hepatic inflammation and improves liver pathology in mice with HIRI by modulating gut microbiota. Specifically, LNT considerably increased microbiota-derived isoursodeoxycholic acid (IsoUDCA). Further experiments showed that IsoUDCA alleviates hepatic injury by suppressing macrophage inflammation. Mechanistically, IsoUDCA directly binds to and activates the neuron-derived clone 77 (Nur77) transcription factor, inhibiting the NF-κB signaling pathway in macrophages. Our findings shed light on the significant role of the LNT-microbiota-IsoUDCA-Nur77 axis in attenuating macrophage inflammation during HIRI, offering novel insights into potential therapeutic targets and avenues for preventing HIRI.
Collapse
Affiliation(s)
- Jiaxin Li
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China; Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jingna Bao
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China; Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yihong Liu
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China; Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Meiling Chen
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yuqi Chen
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lina Tuolihong
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Fuhui Jiang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shihao Xie
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Fengyuan Lyu
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Ye Sun
- Department of Critical Care Medicine, Yuebei People's Hospital, Shaoguan 512000, Guangdong, China
| | - Yan Cao
- Department of Critical Care Medicine, Yuebei People's Hospital, Shaoguan 512000, Guangdong, China
| | - Huarong Chen
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong.
| | - Zhongqing Chen
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Zhenhua Zeng
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| |
Collapse
|
8
|
Obisesan OA, Ofori S, Orobator ON, Sharma H, Groetecke E, Awuah SG. Discovery of a Pyrazolopyridinone-Based MYC Inhibitor That Selectively Engages Intracellular c-MYC and Disrupts MYC-MAX Heterodimerization. J Med Chem 2025; 68:6233-6251. [PMID: 40077826 DOI: 10.1021/acs.jmedchem.4c02556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2025]
Abstract
c-MYC is an oncogenic transcription factor that plays a crucial role in the regulation of downstream targets involved in proliferation, apoptosis, differentiation, metabolism, signaling, and immune response processes whose deregulation leads to the progression of different pathologies. The development of selective and potent small-molecule inhibitors of c-MYC remains a grand challenge in chemical biology and medicine due to its undruggability, derived from extensive intrinsic disorder. In this study, we identified a novel dihydro pyrazolo pyridinone scaffold, MY05, that selectively targets c-MYC in cells and disrupts MYC-MAX interaction. MY05 engages intracellular c-MYC, modulates c-MYC thermal stability, reduces c-MYC transcriptional targets, and inhibits proliferation in cancer cells and tumor growth in mice. In summary, we identified a novel compound that directly interacts with c-MYC to disrupt the transcriptional program.
Collapse
Affiliation(s)
- Oluwatosin A Obisesan
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Samuel Ofori
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Owamagbe N Orobator
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Himanshi Sharma
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Emma Groetecke
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Samuel G Awuah
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
- Center for Pharmaceutical Research and Innovation, Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Markey NCI Comprehensive Cancer Center, University of Kentucky, Lexington, Kentucky 40536, United States
- University of Kentucky Bioelectronics and Nanomedicine Research Center, Lexington, Kentucky 40506, United States
| |
Collapse
|
9
|
Wang J, Zhou M, Zhou Q, Sun G, Zhang Y, Tao F, Ye M. Beta-sitosterol regulates PTGS1 to inhibit gastric cancer cell proliferation and angiogenesis. Prostaglandins Other Lipid Mediat 2025; 177:106964. [PMID: 39863019 DOI: 10.1016/j.prostaglandins.2025.106964] [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: 11/04/2024] [Revised: 01/13/2025] [Accepted: 01/21/2025] [Indexed: 01/27/2025]
Abstract
BACKGROUND Gastric cancer (GC) is the third leading culprit of cancer-related deaths around the world. Beta-sitosterol (BS) is an important phytosterol that has been proven to have anti-proliferative effects on GC and other tumors. However, mechanisms and targets of BS in cancer are rarely explored. METHODS In this investigation, the targets of BS in the treatment of GC were analyzed by network pharmacology. Molecular docking and cellular thermal shift assay were introduced to validate the binding relationship between BS and PTGS1. The impacts of BS on GC cell viability, half maximal inhibitory concentration, proliferation ability, apoptosis level, and angiogenesis ability were detected by using Cell Counting Kit-8, clone formation assay, flow cytometry, and angiogenesis experiment, respectively. In addition, the expression levels of angiogenic factors (VEGF, FGF, PAI-1) were detected by using western blot. RESULTS In this project, through cell experiments, PTGS1 was identified as a protein that directly binds to BS. In vitro cell experiments revealed that BS promoted apoptosis and inhibited GC cell proliferation and angiogenesis. Importantly, treatment with BS attenuated the promoting influence of PTGS1 overexpression on GC cell proliferation and angiogenesis. CONCLUSION This investigation highlighted PTGS1 as the target of BS in GC cells. BS can regulate PTGS1 to inhibit GC cell proliferation and angiogenesis, providing new evidence for the potential use of BS as a therapeutic agent for GC.
Collapse
Affiliation(s)
- Jindao Wang
- Department of Endoscopy Center, Shaoxing People's Hospital, Shaoxing 312000, China
| | - Minghui Zhou
- Department of Gastrointestinal Surgery, Shaoxing People's Hospital, Shaoxing 312000, China
| | - Qiuli Zhou
- Department of Gastrointestinal Surgery, Shaoxing People's Hospital, Shaoxing 312000, China
| | - Guangyang Sun
- Department of Gastrointestinal Surgery, Shaoxing People's Hospital, Shaoxing 312000, China
| | - Yu Zhang
- Department of Gastrointestinal Surgery, Shaoxing People's Hospital, Shaoxing 312000, China
| | - Feng Tao
- Department of Gastrointestinal Surgery, Shaoxing People's Hospital, Shaoxing 312000, China
| | - Minfeng Ye
- Department of Gastrointestinal Surgery, Shaoxing People's Hospital, Shaoxing 312000, China.
| |
Collapse
|
10
|
Mackinnon SR, Zarganes-Tzitzikas T, Adams CJ, Brennan PE, Yue WW. Luminescence-based complementation assay to assess target engagement and cell permeability of glycolate oxidase (HAO1) inhibitors. Biochimie 2025; 228:71-81. [PMID: 39151880 DOI: 10.1016/j.biochi.2024.08.011] [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: 06/10/2024] [Revised: 08/05/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Glycolate oxidase (HAO1) catalyses the synthesis of glyoxylate, a common metabolic intermediate that causes renal failure if accumulated. HAO1 inhibition is an emerging treatment for primary hyperoxaluria, a rare disorder of glyoxylate metabolism. Here we report the first cell-based measurement of inhibitor uptake and engagement with HAO1, by adapting the cellular thermal shift assay (CETSA) based on Nano luciferase complementation and luminescence readout. By profiling the interaction between HAO1 and four well-characterised inhibitors in intact and lysed HEK293T cells, we showed that our CETSA method differentiates between low-permeability/high-engagement and high-permeability/low-engagement ligands and is able to rank HAO1 inhibitors in line with both recombinant protein methods and previously reported indirect cellular assays. Our methodology addresses the unmet need for a robust, sensitive, and scalable cellular assay to guide HAO1 inhibitor development and, in broader terms, can be rapidly adapted for other targets to simultaneously monitor compound affinity and cellular permeability.
Collapse
Affiliation(s)
- Sabrina R Mackinnon
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Tryfon Zarganes-Tzitzikas
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford, UK
| | - Cassandra J Adams
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building (NDMRB), University of Oxford, Oxford, UK
| | - Paul E Brennan
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building (NDMRB), University of Oxford, Oxford, UK.
| | - Wyatt W Yue
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
| |
Collapse
|
11
|
Qi Y, Gong H, Wang Z, Song X, Shen Z, Wu L, Gu Y, Wang W, Li X, Zhang M, Xu Z, Qiu J, Wen H, Xu Z, Shi N, Li X, Zhao Q. Discovery of novel oxindole derivatives as TRPA1 antagonists with potent analgesic activity for pain treatment. Bioorg Chem 2025; 154:108088. [PMID: 39721146 DOI: 10.1016/j.bioorg.2024.108088] [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: 09/17/2024] [Revised: 12/18/2024] [Accepted: 12/20/2024] [Indexed: 12/28/2024]
Abstract
Transient Receptor Potential Ankyrin 1 (TRPA1) is a non-selective cation channel involved in detecting harmful stimuli and endogenous ligands, primarily expressed in sensory neurons. Due to its role in pain and itch, TRPA1 is a potential drug target. We identified an oxindole core structure via high-throughput screening, modified it, and tested the modified compounds in vitro and in vivo. Calcium influx assays in primary dorsal root ganglion (DRG) cells and TRPA1-overexpressing HEK-293 T cells identified best compound ZQMT-10. ZQMT-10 demonstrated strong interaction with TRPA1 in the CETSA and MST assays. Oral administration of ZQMT-10 in C57BL/6J mice significantly reduced abnormal responses in the cold plate test. ZQMT-10 alleviated pain induced by AITC application on the mouse paw or by intracolonic administration, while also increasing the pain threshold and relieving persistent inflammatory pain. These results suggest ZQMT-10 as a promising TRPA1-targeted therapeutic agent.
Collapse
Affiliation(s)
- Yiming Qi
- College of Pharmacy, Dalian Medical University, Dalian 116044, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang 110840, People's Republic of China
| | - Hao Gong
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Zhiya Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Xiaoxuan Song
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Zixian Shen
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Limeng Wu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Yujia Gu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Weiyi Wang
- Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Xinyu Li
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Mingzuo Zhang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Zonghe Xu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Jingsong Qiu
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang 110840, People's Republic of China
| | - Han Wen
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Zihua Xu
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang 110840, People's Republic of China
| | - Nuo Shi
- College of Pharmacy, Dalian Medical University, Dalian 116044, People's Republic of China
| | - Xiang Li
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang 110840, People's Republic of China.
| | - Qingchun Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang 110840, People's Republic of China.
| |
Collapse
|
12
|
Ogasawara D, Konrad DB, Tan ZY, Carey KL, Luo J, Won SJ, Li H, Carter TR, DeMeester KE, Njomen E, Schreiber SL, Xavier RJ, Melillo B, Cravatt BF. Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes. Cell Chem Biol 2024; 31:2138-2155.e32. [PMID: 39547236 PMCID: PMC11837778 DOI: 10.1016/j.chembiol.2024.10.005] [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: 05/31/2024] [Revised: 09/09/2024] [Accepted: 10/18/2024] [Indexed: 11/17/2024]
Abstract
Chemical proteomics enables the global analysis of small molecule-protein interactions in native biological systems and has emerged as a versatile approach for ligand discovery. The range of small molecules explored by chemical proteomics has, however, remained limited. Here, we describe a diversity-oriented synthesis (DOS)-inspired library of stereochemically defined compounds bearing diazirine and alkyne units for UV light-induced covalent modification and click chemistry enrichment of interacting proteins, respectively. We find that these "photo-stereoprobes" interact in a stereoselective manner with hundreds of proteins from various structural and functional classes in human cells and demonstrate that these interactions can form the basis for high-throughput screening-compatible NanoBRET assays. Integrated phenotypic screening and chemical proteomics identified photo-stereoprobes that modulate autophagy by engaging the mitochondrial serine protease CLPP. Our findings show the utility of DOS-inspired photo-stereoprobes for expanding the ligandable proteome, furnishing target engagement assays, and facilitating the discovery and characterization of bioactive compounds in phenotypic screens.
Collapse
Affiliation(s)
- Daisuke Ogasawara
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - David B Konrad
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Zher Yin Tan
- Immunology Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kimberly L Carey
- Immunology Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jessica Luo
- Immunology Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sang Joon Won
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Haoxin Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Trever R Carter
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kristen E DeMeester
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Evert Njomen
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ramnik J Xavier
- Immunology Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
13
|
Li P, Wang T, Qiu H, Zhang R, Yu C, Wang J. 6-Gingerol Inhibits De Novo Lipogenesis by Targeting Stearoyl-CoA Desaturase to Alleviate Fructose-Induced Hepatic Steatosis. Int J Mol Sci 2024; 25:11289. [PMID: 39457074 PMCID: PMC11508832 DOI: 10.3390/ijms252011289] [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: 09/26/2024] [Revised: 10/18/2024] [Accepted: 10/18/2024] [Indexed: 10/28/2024] Open
Abstract
Metabolic-associated fatty liver disease (MAFLD), also known as non-alcoholic fatty liver disease (NAFLD), is a worldwide liver disease without definitive or widely used therapeutic drugs in clinical practice. In this study, we confirm that 6-gingerol (6-G), an active ingredient of ginger (Zingiber officinale Roscoe) in traditional Chinese medicine (TCM), can alleviate fructose-induced hepatic steatosis. It was found that 6-G significantly decreased hyperlipidemia caused by high-fructose diets (HFD) in rats, and reversed the increase in hepatic de novo lipogenesis (DNL) and triglyceride (TG) levels induced by HFD, both in vivo and in vitro. Mechanistically, chemical proteomics and cellular thermal shift assay (CETSA)-proteomics approaches revealed that stearoyl-CoA desaturase (SCD) is a direct binding target of 6-G, which was confirmed by further CETSA assay and molecular docking. Meanwhile, it was found that 6-G could not alter SCD expression (in either mRNA or protein levels), but inhibited SCD activity (decreasing the desaturation levels of fatty acids) in HFD-fed rats. Furthermore, SCD deficiency mimicked the ability of 6-G to reduce lipid accumulation in HF-induced HepG2 cells, and impaired the improvement in hepatic steatosis brought about by 6-G treatment in HFD supplemented with oleic acid diet-induced SCD1 knockout mice. Taken together, our present study demonstrated that 6-G inhibits DNL by targeting SCD to alleviate fructose diet-induced hepatic steatosis.
Collapse
Affiliation(s)
- Pan Li
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Medical University, Chongqing 400016, China; (P.L.); (T.W.)
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China;
| | - Tingting Wang
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Medical University, Chongqing 400016, China; (P.L.); (T.W.)
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China;
| | - Hongmei Qiu
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China;
| | - Ruoyu Zhang
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, Chongqing Medical University, Chongqing 400016, China;
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China
| | - Chao Yu
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Medical University, Chongqing 400016, China; (P.L.); (T.W.)
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China;
| | - Jianwei Wang
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, Chongqing Medical University, Chongqing 400016, China;
| |
Collapse
|
14
|
Zhou L, Qi Z, Wang X, Li Z, Feng W, Wang N, Li X, Ning X, Xing Y, Jiang X, Xu Z, Zhao Q. Discovery of a novel Xanthone derivative P24 for anti-AD via targeting sTGFBR3. Eur J Med Chem 2024; 276:116729. [PMID: 39088998 DOI: 10.1016/j.ejmech.2024.116729] [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: 06/26/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/03/2024]
Abstract
Soluble transforming growth factor beta receptor 3 (sTGFBR3) antagonist is a new focus in the research and development of Alzheimer's disease (AD) drugs. Our previous studies have identified sTGFBR3 as a promising new target for AD, with few targeted antagonists identified. In this study, we performed structural modeling of sTGFBR3 using AlphaFold2, followed by high-throughput virtual screening and surface plasmon resonance assays. which collectively identified Xanthone as potential compounds for targeting sTGFBR3. After optimizing the sTGFBR3-Xanthone complex using molecular dynamics (MD) simulations, we prepared a series of novel Xanthone derivatives and evaluated their anti-inflammatory activity, toxicity, and structure-activity relationship in BV2 cell model induced by lipopolysaccharides (LPS) or APP/PS1/tau mouse brain extract (BE). Several derivatives with the most potent anti-inflammatory activity were tested for blood-brain barrier permeability and sTGFBR3 affinity. Derivative P24, selected for its superior properties, was further evaluated in vitro. The results indicated that P24 increased the activation of TGF-β signaling and decreased the activation of IκBα/NF-κB signaling by targeting sTGFBR3, thereby regulating the inflammation-phagocytosis balance in microglia. Moreover, the low acute toxicity, long half-life, and low plasma clearance of P24 suggest that it can be sustained in vivo. This property may render P24 a more effective treatment modality for chronic diseases, particularly AD. The study demonstrates P24 serve as potential novel candidates for the treatment of AD via antagonizing sTGFBR3.
Collapse
Affiliation(s)
- Lijun Zhou
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China; Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Zhentong Qi
- Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xinpeng Wang
- Department of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China
| | - Zhenshu Li
- Department of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China
| | - Wenzhen Feng
- Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Nan Wang
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xinzhu Li
- Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xinyue Ning
- Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Yu Xing
- Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xiaowen Jiang
- School of Traditional Chinese Medicine, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Zihua Xu
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China; Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Qingchun Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China; Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.
| |
Collapse
|
15
|
Zhao Z, Zhao L, Kong C, Zhou J, Zhou F. A review of biophysical strategies to investigate protein-ligand binding: What have we employed? Int J Biol Macromol 2024; 276:133973. [PMID: 39032877 DOI: 10.1016/j.ijbiomac.2024.133973] [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: 04/30/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
The protein-ligand binding frequently occurs in living organisms and plays a crucial role in the execution of the functions of proteins and drugs. It is also an indispensable part of drug discovery and screening. While the methods for investigating protein-ligand binding are diverse, each has its own objectives, strengths, and limitations, which all influence the choice of method. Many studies concentrate on one or a few specific methods, suggesting that comprehensive summaries are lacking. Therefore in this review, these methods are comprehensively summarized and are discussed in detail: prediction and simulation methods, thermal and thermodynamic methods, spectroscopic methods, methods of determining three-dimensional structures of the complex, mass spectrometry-based methods and others. It is also important to integrate these methods based on the specific objectives of the research. With the aim of advancing pharmaceutical research, this review seeks to deepen the understanding of the protein-ligand binding process.
Collapse
Affiliation(s)
- Zhen Zhao
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Tsinghua East Road, Beijing 100083, China.
| | - Liang Zhao
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, 11 Fucheng Road, Beijing 100048, China.
| | - Chenxi Kong
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Tsinghua East Road, Beijing 100083, China
| | - Jingxuan Zhou
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Tsinghua East Road, Beijing 100083, China.
| | - Feng Zhou
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Tsinghua East Road, Beijing 100083, China.
| |
Collapse
|
16
|
Emery-Corbin SJ, Yousef JM, Adhikari S, Sumardy F, Nhu D, van Delft MF, Lessene G, Dziekan J, Webb AI, Dagley LF. Improved drug target deconvolution with PISA-DIA using an extended, overlapping temperature gradient. Proteomics 2024; 24:e2300644. [PMID: 38766901 DOI: 10.1002/pmic.202300644] [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: 12/19/2023] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Thermal proteome profiling (TPP) is a powerful tool for drug target deconvolution. Recently, data-independent acquisition mass spectrometry (DIA-MS) approaches have demonstrated significant improvements to depth and missingness in proteome data, but traditional TPP (a.k.a. CEllular Thermal Shift Assay "CETSA") workflows typically employ multiplexing reagents reliant on data-dependent acquisition (DDA). Herein, we introduce a new experimental design for the Proteome Integral Solubility Alteration via label-free DIA approach (PISA-DIA). We highlight the proteome coverage and sensitivity achieved by using multiple overlapping thermal gradients alongside DIA-MS, which maximizes efficiencies in PISA sample concatenation and safeguards against missing protein targets that exist at high melting temperatures. We demonstrate our extended PISA-DIA design has superior proteome coverage as compared to using tandem-mass tags (TMT) necessitating DDA-MS analysis. Importantly, we demonstrate our PISA-DIA approach has the quantitative and statistical rigor using A-1331852, a specific inhibitor of BCL-xL. Due to the high melt temperature of this protein target, we utilized our extended multiple gradient PISA-DIA workflow to identify BCL-xL. We assert our novel overlapping gradient PISA-DIA-MS approach is ideal for unbiased drug target deconvolution, spanning a large temperature range whilst minimizing target dropout between gradients, increasing the likelihood of resolving the protein targets of novel compounds.
Collapse
Affiliation(s)
- Samantha J Emery-Corbin
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jumana M Yousef
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Subash Adhikari
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Fransisca Sumardy
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- ACRF Chemical Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Duong Nhu
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- ACRF Chemical Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Mark F van Delft
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Blood Cells and Blood Cancer Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Guillaume Lessene
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- ACRF Chemical Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Victoria, Australia
| | - Jerzy Dziekan
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Andrew I Webb
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Laura F Dagley
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
17
|
Schwalm MP, Saxena K, Müller S, Knapp S. Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells. Nat Protoc 2024; 19:2317-2357. [PMID: 38637703 DOI: 10.1038/s41596-024-00979-z] [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: 09/08/2023] [Accepted: 01/31/2024] [Indexed: 04/20/2024]
Abstract
The rational development of small-molecule degraders (e.g., proteolysis targeting chimeras) remains a challenge as the rate-limiting steps that determine degrader efficiency are largely unknown. Standard methods in the field of targeted protein degradation mostly rely on classical, low-throughput endpoint assays such as western blots or quantitative proteomics. Here we applied NanoLuciferase- and HaloTag-based screening technologies to determine the kinetics and stability of small-molecule-induced ternary complex formation between a protein of interest and a selected E3 ligase. A collection of live-cell assays were designed to probe the most critical steps of the degradation process while minimizing the number of required expression constructs, making the proposed assay pipeline flexible and adaptable to the requirements of the users. This approach evaluates the underlying mechanism of selective target degraders and reveals the exact characteristics of the developed degrader molecules in living cells. The protocol allows scientists trained in basic cell culture and molecular biology to carry out small-molecule proximity-inducer screening via tracking of the ternary complex formation within 2 weeks of establishment, while degrader screening using the HiBiT system requires a CRISPR-Cas9 engineered cell line whose generation can take up to 3 months. After cell-line generation, degrader screening and validation can be carried out in high-throughput manner within days.
Collapse
Affiliation(s)
- Martin P Schwalm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
| | - Krishna Saxena
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
| |
Collapse
|
18
|
Graham K, Lienau P, Bader B, Prechtl S, Naujoks J, Lesche R, Weiske J, Kuehnlenz J, Brzezinka K, Potze L, Zanconato F, Nicke B, Montebaur A, Bone W, Golfier S, Kaulfuss S, Kopitz C, Pilari S, Steuber H, Hayat S, Kamburov A, Steffen A, Schlicker A, Buchgraber P, Braeuer N, Font NA, Heinrich T, Kuhnke L, Nowak-Reppel K, Stresemann C, Steigemann P, Walter AO, Blotta S, Ocker M, Lakner A, von Nussbaum F, Mumberg D, Eis K, Piccolo S, Lange M. Discovery of YAP1/TAZ pathway inhibitors through phenotypic screening with potent anti-tumor activity via blockade of Rho-GTPase signaling. Cell Chem Biol 2024; 31:1247-1263.e16. [PMID: 38537632 DOI: 10.1016/j.chembiol.2024.02.013] [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: 09/18/2023] [Revised: 01/08/2024] [Accepted: 02/27/2024] [Indexed: 07/21/2024]
Abstract
This study describes the identification and target deconvolution of small molecule inhibitors of oncogenic Yes-associated protein (YAP1)/TAZ activity with potent anti-tumor activity in vivo. A high-throughput screen (HTS) of 3.8 million compounds was conducted using a cellular YAP1/TAZ reporter assay. Target deconvolution studies identified the geranylgeranyltransferase-I (GGTase-I) complex as the direct target of YAP1/TAZ pathway inhibitors. The small molecule inhibitors block the activation of Rho-GTPases, leading to subsequent inactivation of YAP1/TAZ and inhibition of cancer cell proliferation in vitro. Multi-parameter optimization resulted in BAY-593, an in vivo probe with favorable PK properties, which demonstrated anti-tumor activity and blockade of YAP1/TAZ signaling in vivo.
Collapse
Affiliation(s)
- Keith Graham
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Philip Lienau
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Benjamin Bader
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Stefan Prechtl
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Jan Naujoks
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Ralf Lesche
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Joerg Weiske
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Julia Kuehnlenz
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Krzysztof Brzezinka
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Lisette Potze
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Francesca Zanconato
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Barbara Nicke
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Anna Montebaur
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Wilhelm Bone
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Sven Golfier
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Stefan Kaulfuss
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Charlotte Kopitz
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Sabine Pilari
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Holger Steuber
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Sikander Hayat
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Atanas Kamburov
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Andreas Steffen
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Andreas Schlicker
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Philipp Buchgraber
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Nico Braeuer
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Nuria Aiguabella Font
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Tobias Heinrich
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Lara Kuhnke
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Katrin Nowak-Reppel
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Carlo Stresemann
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Patrick Steigemann
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Annette O Walter
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Simona Blotta
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Matthias Ocker
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Ashley Lakner
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Franz von Nussbaum
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany
| | - Dominik Mumberg
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Knut Eis
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany
| | - Stefano Piccolo
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy; IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Martin Lange
- Bayer AG, Pharmaceuticals, Research & Development, Muellerstr. 178, 13353 Berlin, Germany; Nuvisan ICB GmbH, Muellerstr. 178, 13353 Berlin, Germany.
| |
Collapse
|
19
|
Monticelli M, Hay Mele B, Wright DM, Guerriero S, Andreotti G, Cubellis MV. Exploring ligand interactions with human phosphomannomutases using recombinant bacterial thermal shift assay and biochemical validation. Biochimie 2024; 222:123-131. [PMID: 38458414 DOI: 10.1016/j.biochi.2024.02.011] [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: 02/02/2024] [Accepted: 02/26/2024] [Indexed: 03/10/2024]
Abstract
PMM2-CDG, a disease caused by mutations in phosphomannomutase-2, is the most common congenital disorder of glycosylation. Yet, it still lacks a cure. Targeting phosphomannomutase-2 with pharmacological chaperones or inhibiting the phosphatase activity of phosphomannomutase-1 to enhance intracellular glucose-1,6-bisphosphate have been proposed as therapeutical approaches. We used Recombinant Bacterial Thermal Shift Assay to assess the binding of a substrate analog to phosphomannomutase-2 and the specific binding to phosphomannomutase-1 of an FDA-approved drug - clodronate. We also deepened the clodronate binding by enzyme activity assays and in silico docking. Our results confirmed the selective binding of clodronate to phosphomannomutase-1 and shed light on such binding.
Collapse
Affiliation(s)
- Maria Monticelli
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy
| | - Bruno Hay Mele
- Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy
| | - Demi Marie Wright
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy; Institute of Chemistry and Biochemistry, Freie Universität Berlin, D-14195, Berlin, Germany
| | - Simone Guerriero
- Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy
| | - Giuseppina Andreotti
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy.
| | - Maria Vittoria Cubellis
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy; Stazione Zoologica "Anton Dohrn", Villa Comunale, Naples, Italy
| |
Collapse
|
20
|
Ni Z, Shi Y, Liu Q, Wang L, Sun X, Rao Y. Degradation-Based Protein Profiling: A Case Study of Celastrol. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308186. [PMID: 38664976 PMCID: PMC11220716 DOI: 10.1002/advs.202308186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/28/2024] [Indexed: 07/04/2024]
Abstract
Natural products, while valuable for drug discovery, encounter limitations like uncertainty in targets and toxicity. As an important active ingredient in traditional Chinese medicine, celastrol exhibits a wide range of biological activities, yet its mechanism remains unclear. In this study, they introduced an innovative "Degradation-based protein profiling (DBPP)" strategy, which combined PROteolysis TArgeting Chimeras (PROTAC) technology with quantitative proteomics and Immunoprecipitation-Mass Spectrometry (IP-MS) techniques, to identify multiple targets of natural products using a toolbox of degraders. Taking celastrol as an example, they successfully identified its known targets, including inhibitor of nuclear factor kappa B kinase subunit beta (IKKβ), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PI3Kα), and cellular inhibitor of PP2A (CIP2A), as well as potential new targets such as checkpoint kinase 1 (CHK1), O-GlcNAcase (OGA), and DNA excision repair protein ERCC-6-like (ERCC6L). Furthermore, the first glycosidase degrader is developed in this work. Finally, by employing a mixed PROTAC toolbox in quantitative proteomics, they also achieved multi-target identification of celastrol, significantly reducing costs while improving efficiency. Taken together, they believe that the DBPP strategy can complement existing target identification strategies, thereby facilitating the rapid advancement of the pharmaceutical field.
Collapse
Affiliation(s)
- Zhihao Ni
- MOE Key Laboratory of Protein SciencesSchool of Pharmaceutical SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijing100084China
| | - Yi Shi
- MOE Key Laboratory of Protein SciencesSchool of Pharmaceutical SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijing100084China
| | - Qianlong Liu
- MOE Key Laboratory of Protein SciencesSchool of Pharmaceutical SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijing100084China
| | - Liguo Wang
- MOE Key Laboratory of Protein SciencesSchool of Pharmaceutical SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijing100084China
| | | | - Yu Rao
- MOE Key Laboratory of Protein SciencesSchool of Pharmaceutical SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijing100084China
- Changping LaboratoryBeijing102206China
| |
Collapse
|
21
|
Kairys V, Baranauskiene L, Kazlauskiene M, Zubrienė A, Petrauskas V, Matulis D, Kazlauskas E. Recent advances in computational and experimental protein-ligand affinity determination techniques. Expert Opin Drug Discov 2024; 19:649-670. [PMID: 38715415 DOI: 10.1080/17460441.2024.2349169] [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: 03/18/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Modern drug discovery revolves around designing ligands that target the chosen biomolecule, typically proteins. For this, the evaluation of affinities of putative ligands is crucial. This has given rise to a multitude of dedicated computational and experimental methods that are constantly being developed and improved. AREAS COVERED In this review, the authors reassess both the industry mainstays and the newest trends among the methods for protein - small-molecule affinity determination. They discuss both computational affinity predictions and experimental techniques, describing their basic principles, main limitations, and advantages. Together, this serves as initial guide to the currently most popular and cutting-edge ligand-binding assays employed in rational drug design. EXPERT OPINION The affinity determination methods continue to develop toward miniaturization, high-throughput, and in-cell application. Moreover, the availability of data analysis tools has been constantly increasing. Nevertheless, cross-verification of data using at least two different techniques and careful result interpretation remain of utmost importance.
Collapse
Affiliation(s)
- Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| |
Collapse
|
22
|
Zhao H, Kumar P, Sobreira TJP, Smith M, Novick S, Johansson A, Luchniak A, Zhang A, Woollard KJ, Larsson N, Kawatkar A. Integrated Proteomics Characterization of NLRP3 Inflammasome Inhibitor MCC950 in Monocytic Cell Line Confirms Direct MCC950 Engagement with Endogenous NLRP3. ACS Chem Biol 2024; 19:962-972. [PMID: 38509779 DOI: 10.1021/acschembio.3c00777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Inhibition of the NLRP3 inflammasome is a promising strategy for the development of new treatments for inflammatory diseases. MCC950 is a potent and selective small-molecule inhibitor of the NLRP3 pathway and has been validated in numerous species and disease models. Although the capacity of MCC950 to block NLRP3 signaling is well-established, it is still critical to identify the mechanism of action and molecular targets of MCC950 to inform and derisk drug development. Quantitative proteomics performed in disease-relevant systems provides a powerful method to study both direct and indirect pharmacological responses to small molecules to elucidate the mechanism of action and confirm target engagement. A comprehensive target deconvolution campaign requires the use of complementary chemical biology techniques. Here we applied two orthogonal chemical biology techniques: compressed Cellular Thermal Shift Assay (CETSA) and photoaffinity labeling chemoproteomics, performed under biologically relevant conditions with LPS-primed THP-1 cells, thereby deconvoluting, for the first time, the molecular targets of MCC950 using chemical biology techniques. In-cell chemoproteomics with inlysate CETSA confirmed the suspected mechanism as the disruption of inflammasome formation via NLRP3. Further cCETSA (c indicates compressed) in live cells mapped the stabilization of NLRP3 inflammasome pathway proteins, highlighting modulation of the targeted pathway. This is the first evidence of direct MCC950 engagement with endogenous NLRP3 in a human macrophage cellular system using discovery proteomics chemical biology techniques, providing critical information for inflammasome studies.
Collapse
Affiliation(s)
- Heng Zhao
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, 02451 Waltham, Massachusetts, United States
| | - Praveen Kumar
- Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, 02451 Waltham, Massachusetts, United States
| | | | - Mackenzie Smith
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, 02451 Waltham, Massachusetts, United States
| | - Steven Novick
- Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, 02451 Waltham, Massachusetts, United States
| | - Anders Johansson
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43183 Mölndal, Sweden
| | - Anna Luchniak
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, 43183 Mölndal, Sweden
| | - Andrew Zhang
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, 02451 Waltham, Massachusetts, United States
| | - Kevin J Woollard
- Bioscience Renal, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, CB2 OAA Cambridge, U.K
| | - Niklas Larsson
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, 43183 Mölndal, Sweden
| | - Aarti Kawatkar
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, 02451 Waltham, Massachusetts, United States
| |
Collapse
|
23
|
Zhang H, Ouyang H, Zhang J, Lin L, Wei M, Lu B, Ji L. Exploring the efficacy and mechanism of Glycyrrhizae Radix et Rhizoma in improving collagen-induced arthritis in mice. JOURNAL OF ETHNOPHARMACOLOGY 2024; 322:117554. [PMID: 38092318 DOI: 10.1016/j.jep.2023.117554] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/07/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Rheumatoid arthritis (RA), a chronic auto-immune disease, will cause serious joint damage and disability. Glycyrrhizae Radix et Rhizoma (GRR) is commonly included in many anti-RA formulas used in the clinical practice in China. AIM OF THE STUDY To elucidate the alleviation of GRR and its active compounds on RA and the possible engaged mechanism. MATERIALS AND METHODS The clinical score, paw swelling degree and pain threshold were detected in the collagen-induced arthritis (CIA) in DBA/1 mice. The ankle joints of mice were observed by using X-Ray, hematoxylin-eosin (H&E), masson's trichrome (Masson), and safranin O and fast green (Safranin O) staining. The potential targets of GRR were predicted by network pharmacology and further verified by using enzyme-linked immunosorbent assay (ELISA) and western-blot. Real-time polymerase chain reaction (Real-time PCR) and wound healing assay were conducted in synovial MH7A cells. The interaction between active compounds and potential targets predicted by molecular docking was confirmed by using cellular thermal shift assay (CETSA). RESULTS GRR (615 mg/kg) obviously alleviated CIA in mice. Network pharmacology implied that GRR might affect angiogenesis and inflammation, among which vascular endothelial growth factor-A (VEGF-A), tumor necrosis factor-α (TNFα), interleukin-1β (IL-1β), IL-6 and phosphorylated protein kinase B (AKT) might be the key targets involved in this process. GRR decreased AKT phosphorylation and reduced the elevated levels of TNFα, VEGF-A, IL-1β and IL-6. Next, in vitro results demonstrated that glycyrrhetinic acid (GA) and isoliquiritigenin (ISL) were two active compounds that inhibited TNFα-induced synovial cell angiogenesis and inflammation. Moreover, GA and ISL actually improved RA in CIA mice. The results of molecular docking and CETSA displayed that ISL and GA might interact with TNF receptor-1 (TNFR1), toll-like receptor-4 (TLR4) and VEGF receptor-2 (VEGFR2), thereby contributing to their inhibition on angiogenesis and inflammation. CONCLUSION GRR and two active compounds, including ISL and GA, alleviated RA via inhibiting angiogenesis and inflammation.
Collapse
Affiliation(s)
- Hong Zhang
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Hao Ouyang
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; Department of Hepatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Jinyu Zhang
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Li Lin
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Mengjuan Wei
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Bin Lu
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Lili Ji
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| |
Collapse
|
24
|
Lu JQ, Luo ZY, Sun C, Wang SM, Sun D, Huang RJ, Yang X, Ding Y, Wang G. Baicalin administration could rescue high glucose-induced craniofacial skeleton malformation by regulating neural crest development. Front Pharmacol 2024; 15:1295356. [PMID: 38515837 PMCID: PMC10955141 DOI: 10.3389/fphar.2024.1295356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024] Open
Abstract
Hyperglycemia in pregnancy can increase the risk of congenital disorders, but little is known about craniofacial skeleton malformation and its corresponding medication. Our study first used meta-analysis to review the previous findings. Second, baicalin, an antioxidant, was chosen to counteract high glucose-induced craniofacial skeleton malformation. Its effectiveness was then tested by exposing chicken embryos to a combination of high glucose (HG, 50 mM) and 6 μM baicalin. Third, whole-mount immunofluorescence staining and in situ hybridization revealed that baicalin administration could reverse HG-inhibited neural crest cells (NCC) delamination and migration through upregulating the expression of Pax7 and Foxd3, and mitigate the disordered epithelial-mesenchymal transition (EMT) process by regulating corresponding adhesion molecules and transcription factors (i.e., E-cadherin, N-cadherin, Cadherin 6B, Slug and Msx1). Finally, through bioinformatic analysis and cellular thermal shift assay, we identified the AKR1B1 gene as a potential target. In summary, these findings suggest that baicalin could be used as a therapeutic agent for high glucose-induced craniofacial skeleton malformation.
Collapse
Affiliation(s)
- Jia-Qi Lu
- The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
- Division of Histology and Embryology, International Joint Laboratory for Embryonic Development and Prenatal Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Zhi-Yan Luo
- The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
- Division of Histology and Embryology, International Joint Laboratory for Embryonic Development and Prenatal Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Chengyang Sun
- Division of Histology and Embryology, International Joint Laboratory for Embryonic Development and Prenatal Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Si-Miao Wang
- Division of Histology and Embryology, International Joint Laboratory for Embryonic Development and Prenatal Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Dixiang Sun
- Department of Pathology, Mengyin County Hospital of Traditional Chinese Medicine, Linyi, China
| | - Ruo-Jing Huang
- The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Xuesong Yang
- Division of Histology and Embryology, International Joint Laboratory for Embryonic Development and Prenatal Medicine, School of Medicine, Jinan University, Guangzhou, China
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, Jinan University, Guangzhou, China
| | - Yong Ding
- The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Guang Wang
- Division of Histology and Embryology, International Joint Laboratory for Embryonic Development and Prenatal Medicine, School of Medicine, Jinan University, Guangzhou, China
- Key Laboratory for Regenerative Medicine of the Ministry of Education of China, Jinan University, Guangzhou, China
| |
Collapse
|
25
|
Gooran N, Kopra K. Fluorescence-Based Protein Stability Monitoring-A Review. Int J Mol Sci 2024; 25:1764. [PMID: 38339045 PMCID: PMC10855643 DOI: 10.3390/ijms25031764] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.
Collapse
Affiliation(s)
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland;
| |
Collapse
|
26
|
Monticelli M, Wright DM, Cubellis MV, Andreotti G. ReBaTSA: A simplified CeTSA protocol for studying recombinant mutant proteins in bacterial extracts. Biochim Biophys Acta Gen Subj 2024; 1868:130526. [PMID: 38049040 DOI: 10.1016/j.bbagen.2023.130526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023]
Abstract
INTRODUCTION The study of protein stability is crucial to biochemistry and relies on different methodologies. Recently, the Cellular Thermal Shift Assay has been introduced to study protein stability in whole cells. METHODS We report a novel application of CeTSA named ReBaTSA. This Recombinant Bacterial TSA was performed using clear extracts from bacteria expressing a recombinant protein, incubated at different temperatures, centrifuged and analyzed via SDS-PAGE. RESULTS AND CONCLUSIONS We demonstrated the feasibility and reliability of this simplified approach. We validated the method using the protein phosphomannomutase-2 and its common mutants, which were compared in the presence or the absence of a known ligand.
Collapse
Affiliation(s)
- Maria Monticelli
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy
| | - Demi Marie Wright
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; Institute of Chemistry and Biochemistry, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Maria Vittoria Cubellis
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy; Stazione Zoologica "Anton Dohrn", Villa Comunale, Naples, Italy.
| | - Giuseppina Andreotti
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
| |
Collapse
|
27
|
Shu Y, Yang R, Wen H, Dong Q, Chen Z, Xiang Y, Wu H. Myricetin reduces neutrophil extracellular trap release in a rat model of rheumatoid arthritis, which is associated with a decrease in disease severity. Innate Immun 2024; 30:66-78. [PMID: 38780369 PMCID: PMC11165658 DOI: 10.1177/17534259241255439] [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: 11/13/2023] [Revised: 04/01/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
Rheumatoid arthritis (RA) is a chronic disease characterized by joint inflammation and severe disability. However, there is a lack of safe and effective drugs for treating RA. In our previous study, we discovered that myricetin (MC) and celecoxib have a synergistic effect in the treatment of RA. We conducted in vitro and in vivo experiments to further investigate the effects and mechanisms of action of MC. Our findings demonstrated that MC treatment effectively reduced the release of neutrophil extracellular traps (NETs) and alleviated the inflammatory response in RA. Mechanistic studies showed that MC prevents the entry of PADI4 and MPO into the cell nucleus, thereby protecting DNA from decondensation. In a rat arthritis model, MC improved histological changes in ankle joints and suppressed NET-related signaling factors. In conclusion, MC protects the ankle joints against arthritis by inhibiting MPO and PADI4, thereby reducing NET release. The pharmacological mechanism of MC in RA involves the inhibition of NET release.
Collapse
Affiliation(s)
- Yiqin Shu
- Medical College of Hubei Enshi College, Enshi, China
| | - Rui Yang
- Medical College of Hubei Enshi College, Enshi, China
- Institute of anti-rheumatism Tujia Medicine, Enshi, China
| | - Huijie Wen
- Medical College of Hubei Enshi College, Enshi, China
| | - Qiannan Dong
- Medical College of Hubei Enshi College, Enshi, China
- Institute of anti-rheumatism Tujia Medicine, Enshi, China
| | - Zhiqi Chen
- Medical College of Hubei Enshi College, Enshi, China
| | - Yang Xiang
- Medical College of Hubei Enshi College, Enshi, China
- Institute of anti-rheumatism Tujia Medicine, Enshi, China
- Hubei Provincial Key Laboratory of Rheumatic Disease Development and Intervention, Enshi, China
| | - Hao Wu
- Medical College of Hubei Enshi College, Enshi, China
- Institute of anti-rheumatism Tujia Medicine, Enshi, China
- Hubei Provincial Key Laboratory of Rheumatic Disease Development and Intervention, Enshi, China
| |
Collapse
|
28
|
Wang J, Yang C, Xu H, Fan X, Jia L, Du Y, Liu S, Wang W, Zhang J, Zhang Y, Wang X, Liu Z, Bao J, Li S, Yang J, Wu C, Tang J, Chen G, Wang L. The Interplay Between HIF-1α and EZH2 in Lung Cancer and Dual-Targeted Drug Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303904. [PMID: 38072662 PMCID: PMC10870044 DOI: 10.1002/advs.202303904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/26/2023] [Indexed: 02/17/2024]
Abstract
Interactions between oncogenic proteins contribute to the phenotype and drug resistance. Here, EZH2 (enhancer of zest homolog 2) is identified as a crucial factor that mediates HIF-1 (hypoxia-inducible factor) inhibitor resistance. Mechanistically, targeting HIF-1 enhanced the activity of EZH2 through transcription activation of SUZ12 (suppressor of zest 12 protein homolog). Conversely, inhibiting EZH2 increased HIF-1α transcription, but not the transcription of other HIF family members. Additionally, the negative feedback regulation between EZH2 and HIF-1α is confirmed in lung cancer patient tissues and a database of cell lines. Moreover, molecular prediction showed that a newly screened dual-target compound, DYB-03, forms multiple hydrogen bonds with HIF-1α and EZH2 to effectively inhibit the activity of both targets. Subsequent studies revealed that DYB-03 could better inhibit migration, invasion, and angiogenesis of lung cancer cells and HUVECs in vitro and in vivo compared to single agent. DYB-03 showed promising antitumor activity in a xenograft tumor model by promoting apoptosis and inhibiting angiogenesis, which could be almost abolished by the deletion of HIF-1α and EZH2. Notably, DYB-03 could reverse 2-ME2 and GSK126-resistance in lung cancer. These findings clarified the molecular mechanism of cross-regulation of HIF-1α and EZH2, and the potential of DYB-03 for clinical combination target therapy.
Collapse
Affiliation(s)
- Jianmin Wang
- School of Life Science and BiopharmaceuticsShenyang Pharmaceutical UniversityShenyang110016P. R. China
- Benxi Institute of Pharmaceutical ResearchShenyang Pharmaceutical UniversityBenxi117004P. R. China
| | - Cheng Yang
- School of Life Science and BiopharmaceuticsShenyang Pharmaceutical UniversityShenyang110016P. R. China
- Benxi Institute of Pharmaceutical ResearchShenyang Pharmaceutical UniversityBenxi117004P. R. China
| | - Huashen Xu
- Key Laboratory of Structure‐Based Drug Design & Discovery of Ministry of EducationSchool of Pharmaceutical EngineeringShenyang Pharmaceutical UniversityShenyang110016P. R. China
| | - Xinyu Fan
- Department of PharmacyShengjing Hospital of China Medical UniversityShenyang110004P. R. China
| | - Lina Jia
- School of Life Science and BiopharmaceuticsShenyang Pharmaceutical UniversityShenyang110016P. R. China
- Benxi Institute of Pharmaceutical ResearchShenyang Pharmaceutical UniversityBenxi117004P. R. China
| | - Yang Du
- Key Laboratory of Structure‐Based Drug Design & Discovery of Ministry of EducationSchool of Pharmaceutical EngineeringShenyang Pharmaceutical UniversityShenyang110016P. R. China
| | - Shougeng Liu
- School of Life Science and BiopharmaceuticsShenyang Pharmaceutical UniversityShenyang110016P. R. China
- Benxi Institute of Pharmaceutical ResearchShenyang Pharmaceutical UniversityBenxi117004P. R. China
| | - Wenjing Wang
- School of Life Science and BiopharmaceuticsShenyang Pharmaceutical UniversityShenyang110016P. R. China
- Benxi Institute of Pharmaceutical ResearchShenyang Pharmaceutical UniversityBenxi117004P. R. China
| | - Jie Zhang
- School of Life Science and BiopharmaceuticsShenyang Pharmaceutical UniversityShenyang110016P. R. China
- Benxi Institute of Pharmaceutical ResearchShenyang Pharmaceutical UniversityBenxi117004P. R. China
| | - Yu Zhang
- School of Life Science and BiopharmaceuticsShenyang Pharmaceutical UniversityShenyang110016P. R. China
- Benxi Institute of Pharmaceutical ResearchShenyang Pharmaceutical UniversityBenxi117004P. R. China
| | - Xiaoxue Wang
- School of Life Science and BiopharmaceuticsShenyang Pharmaceutical UniversityShenyang110016P. R. China
- Benxi Institute of Pharmaceutical ResearchShenyang Pharmaceutical UniversityBenxi117004P. R. China
| | - Zhongbo Liu
- School of PharmacyShenyang Pharmaceutical UniversityShenyang110016P. R. China
| | - Jie Bao
- Research Program in Systems OncologyFaculty of MedicineUniversity of HelsinkiHelsinki00290Finland
| | - Songping Li
- School of Life Science and BiopharmaceuticsShenyang Pharmaceutical UniversityShenyang110016P. R. China
| | - Jingyu Yang
- School of Life Science and BiopharmaceuticsShenyang Pharmaceutical UniversityShenyang110016P. R. China
- Benxi Institute of Pharmaceutical ResearchShenyang Pharmaceutical UniversityBenxi117004P. R. China
| | - Chunfu Wu
- School of Life Science and BiopharmaceuticsShenyang Pharmaceutical UniversityShenyang110016P. R. China
- Benxi Institute of Pharmaceutical ResearchShenyang Pharmaceutical UniversityBenxi117004P. R. China
| | - Jing Tang
- Research Program in Systems OncologyFaculty of MedicineUniversity of HelsinkiHelsinki00290Finland
| | - Guoliang Chen
- Key Laboratory of Structure‐Based Drug Design & Discovery of Ministry of EducationSchool of Pharmaceutical EngineeringShenyang Pharmaceutical UniversityShenyang110016P. R. China
| | - Lihui Wang
- School of Life Science and BiopharmaceuticsShenyang Pharmaceutical UniversityShenyang110016P. R. China
- Benxi Institute of Pharmaceutical ResearchShenyang Pharmaceutical UniversityBenxi117004P. R. China
| |
Collapse
|
29
|
Luchinat E, Barbieri L, Davis B, Brough PA, Pennestri M, Banci L. Ligand-Based Competition Binding by Real-Time 19F NMR in Human Cells. J Med Chem 2024; 67:1115-1126. [PMID: 38215028 PMCID: PMC10823471 DOI: 10.1021/acs.jmedchem.3c01600] [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: 08/30/2023] [Revised: 12/17/2023] [Accepted: 12/26/2023] [Indexed: 01/14/2024]
Abstract
The development of more effective drugs requires knowledge of their bioavailability and binding efficacy directly in the native cellular environment. In-cell nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for investigating ligand-target interactions directly in living cells. However, the target molecule may be NMR-invisible due to interactions with cellular components, while observing the ligand by 1H NMR is impractical due to the cellular background. Such limitations can be overcome by observing fluorinated ligands by 19F in-cell NMR as they bind to the intracellular target. Here we report a novel approach based on real-time in-cell 19F NMR that allows measuring ligand binding affinities in human cells by competition binding, using a fluorinated compound as a reference. The binding of a set of compounds toward Hsp90α was investigated. In principle, this approach could be applied to other pharmacologically relevant targets, thus aiding the design of more effective compounds in the early stages of drug development.
Collapse
Affiliation(s)
- Enrico Luchinat
- Dipartimento
di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum—Università di Bologna, Piazza Goidanich 60, Cesena 47521, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Letizia Barbieri
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Ben Davis
- Vernalis
Research, Granta Park, Great Abington, Cambridge CB21 6GB, U.K.
| | - Paul A. Brough
- Vernalis
Research, Granta Park, Great Abington, Cambridge CB21 6GB, U.K.
| | - Matteo Pennestri
- Pharmaceutical
Business Unit, Bruker UK Limited, Banner Lane, Coventry CV4 9GH, U.K.
| | - Lucia Banci
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
- Centro
di Risonanze Magnetiche—CERM, Università
degli Studi di Firenze, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
- Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, Sesto Fiorentino 50019, Italy
| |
Collapse
|
30
|
Pang Z, Cravatt BF, Ye L. Deciphering Drug Targets and Actions with Single-Cell and Spatial Resolution. Annu Rev Pharmacol Toxicol 2024; 64:507-526. [PMID: 37722721 DOI: 10.1146/annurev-pharmtox-033123-123610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Recent advances in chemical, molecular, and genetic approaches have provided us with an unprecedented capacity to identify drug-target interactions across the whole proteome and genome. Meanwhile, rapid developments of single-cell and spatial omics technologies are revolutionizing our understanding of the molecular architecture of biological systems. However, a significant gap remains in how we align our understanding of drug actions, traditionally based on molecular affinities, with the in vivo cellular and spatial tissue heterogeneity revealed by these newer techniques. Here, we review state-of-the-art methods for profiling drug-target interactions and emerging multiomics tools to delineate the tissue heterogeneity at single-cell resolution. Highlighting the recent technical advances enabling high-resolution, multiplexable in situ small-molecule drug imaging (clearing-assisted tissue click chemistry, or CATCH), we foresee the integration of single-cell and spatial omics platforms, data, and concepts into the future framework of defining and understanding in vivo drug-target interactions and mechanisms of actions.
Collapse
Affiliation(s)
- Zhengyuan Pang
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California, USA;
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA;
| | - Li Ye
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California, USA;
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| |
Collapse
|
31
|
Gervasoni S, Manelfi C, Adobati S, Talarico C, Biswas AD, Pedretti A, Vistoli G, Beccari AR. Target Prediction by Multiple Virtual Screenings: Analyzing the SARS-CoV-2 Phenotypic Screening by the Docking Simulations Submitted to the MEDIATE Initiative. Int J Mol Sci 2023; 25:450. [PMID: 38203621 PMCID: PMC10779154 DOI: 10.3390/ijms25010450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Phenotypic screenings are usually combined with deconvolution techniques to characterize the mechanism of action for the retrieved hits. These studies can be supported by various computational analyses, although docking simulations are rarely employed. The present study aims to assess if multiple docking calculations can prove successful in target prediction. In detail, the docking simulations submitted to the MEDIATE initiative are utilized to predict the viral targets involved in the hits retrieved by a recently published cytopathic screening. Multiple docking results are combined by the EFO approach to develop target-specific consensus models. The combination of multiple docking simulations enhances the performances of the developed consensus models (average increases in EF1% value of 40% and 25% when combining three and two docking runs, respectively). These models are able to propose reliable targets for about half of the retrieved hits (31 out of 59). Thus, the study emphasizes that docking simulations might be effective in target identification and provide a convincing validation for the collaborative strategies that inspire the MEDIATE initiative. Disappointingly, cross-target and cross-program correlations suggest that common scoring functions are not specific enough for the simulated target.
Collapse
Affiliation(s)
- Silvia Gervasoni
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (S.A.); (A.P.)
- Department of Physics, Università di Cagliari, I-09042 Monserrato, Italy
| | - Candida Manelfi
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy; (C.M.); (C.T.); (A.D.B.); (A.R.B.)
| | - Sara Adobati
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (S.A.); (A.P.)
| | - Carmine Talarico
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy; (C.M.); (C.T.); (A.D.B.); (A.R.B.)
| | - Akash Deep Biswas
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy; (C.M.); (C.T.); (A.D.B.); (A.R.B.)
| | - Alessandro Pedretti
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (S.A.); (A.P.)
| | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (S.A.); (A.P.)
| | - Andrea R. Beccari
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy; (C.M.); (C.T.); (A.D.B.); (A.R.B.)
| |
Collapse
|
32
|
Wu T, Hornsby M, Zhu L, Yu JC, Shokat KM, Gestwicki JE. Protocol for performing and optimizing differential scanning fluorimetry experiments. STAR Protoc 2023; 4:102688. [PMID: 37943662 PMCID: PMC10663957 DOI: 10.1016/j.xpro.2023.102688] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023] Open
Abstract
Differential scanning fluorimetry (DSF) is a widely used technique for determining the apparent melting temperature (Tma) of a purified protein. Here, we present a protocol for performing and optimizing DSF experiments. We describe steps for designing and performing the experiment, analyzing data, and optimization. We provide benchmarks for typical Tmas and ΔTmas, standard assay conditions, and upper and lower limits of commonly altered experimental variables. We also detail common pitfalls of DSF and ways to avoid, identify, and overcome them.
Collapse
Affiliation(s)
- Taiasean Wu
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael Hornsby
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 941583, USA
| | - Lawrence Zhu
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joshua C Yu
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 941583, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
33
|
Lindberg MF, Deau E, Miege F, Greverie M, Roche D, George N, George P, Merlet L, Gavard J, Brugman SJT, Aret E, Tinnemans P, de Gelder R, Sadownik J, Verhofstad E, Sleegers D, Santangelo S, Dairou J, Fernandez-Blanco Á, Dierssen M, Krämer A, Knapp S, Meijer L. Chemical, Biochemical, Cellular, and Physiological Characterization of Leucettinib-21, a Down Syndrome and Alzheimer's Disease Drug Candidate. J Med Chem 2023; 66:15648-15670. [PMID: 38051674 DOI: 10.1021/acs.jmedchem.3c01888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Leucettinibs are substituted 2-aminoimidazolin-4-ones (inspired by the marine sponge natural product Leucettamine B) developed as pharmacological inhibitors of DYRK1A (dual-specificity, tyrosine phosphorylation-regulated kinase 1A), a therapeutic target for indications such as Down syndrome and Alzheimer's disease. Leucettinib-21 was selected as a drug candidate following extensive structure/activity studies and multiparametric evaluations. We here report its physicochemical properties (X-ray powder diffraction, differential scanning calorimetry, stability, solubility, crystal structure) and drug-like profile. Leucettinib-21's selectivity (analyzed by radiometric, fluorescence, interaction, thermal shift, residence time assays) reveals DYRK1A as the first target but also some "off-targets" which may contribute to the drug's biological effects. Leucettinib-21 was cocrystallized with CLK1 and modeled in the DYRK1A structure. Leucettinib-21 inhibits DYRK1A in cells (demonstrated by direct catalytic activity and phosphorylation levels of Thr286-cyclin D1 or Thr212-Tau). Leucettinib-21 corrects memory disorders in the Down syndrome mouse model Ts65Dn and is now entering safety/tolerance phase 1 clinical trials.
Collapse
Affiliation(s)
- Mattias F Lindberg
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
| | - Emmanuel Deau
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
| | - Frédéric Miege
- Edelris, Bâtiment Bioserra 1, 60 Avenue Rockefeller, 69008 Lyon, France
| | - Marie Greverie
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
| | - Didier Roche
- Edelris, Bâtiment Bioserra 1, 60 Avenue Rockefeller, 69008 Lyon, France
| | - Nicolas George
- Oncodesign, 25-27 Avenue du Québec, 91140 Villebon-sur-Yvette, France
| | - Pascal George
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
| | - Laura Merlet
- Team SOAP, CRCI2NA, Nantes Université, Inserm, CNRS, Université d'Angers, 8 Quai Moncousu, 44007 Nantes Cedex 1, France
- Equipe Labellisée Ligue Contre le Cancer, 75013 Paris, France
| | - Julie Gavard
- Team SOAP, CRCI2NA, Nantes Université, Inserm, CNRS, Université d'Angers, 8 Quai Moncousu, 44007 Nantes Cedex 1, France
- Equipe Labellisée Ligue Contre le Cancer, 75013 Paris, France
- Institut de Cancérologie de l'Ouest (ICO), Boulevard Professeur Jacques Monod, 44800 Saint-Herblain, France
| | | | - Edwin Aret
- Symeres, Peelterbaan 2, 6002 NK Weert, The Netherlands
| | - Paul Tinnemans
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - René de Gelder
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jan Sadownik
- Symeres, Peelterbaan 2, 6002 NK Weert, The Netherlands
| | | | | | | | - Julien Dairou
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS, 45 rue des Saints Pères, 75006 Paris, France
| | - Álvaro Fernandez-Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08036, Spain
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08036, Spain
| | - Andreas Krämer
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von Laue Strasse 15, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von Laue Strasse 15, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Laurent Meijer
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
| |
Collapse
|
34
|
Hansel CS, Lanne A, Rowlands H, Shaw J, Collier MJ, Plant H. High-throughput differential scanning fluorimetry (DSF) and cellular thermal shift assays (CETSA): Shifting from manual to automated screening. SLAS Technol 2023; 28:411-415. [PMID: 37598756 DOI: 10.1016/j.slast.2023.08.004] [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: 04/13/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/22/2023]
Abstract
Biophysical affinity screening is increasingly being adopted as a high-throughput hit finding technique in drug discovery. Automation is highly beneficial to high-throughput screening (HTS) since a large number of compounds need to be reproducibly tested against a biological target. Herein, we describe how we have automated two biophysical affinity screening methods that rely on a thermal shift in protein melting temperature upon small molecule binding: differential scanning fluorimetry (DSF) and the cellular thermal shift assay (CETSA).
Collapse
Affiliation(s)
- Catherine S Hansel
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK.
| | - Alice Lanne
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Hannah Rowlands
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Joseph Shaw
- Assay Development, Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Matthew J Collier
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Helen Plant
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| |
Collapse
|
35
|
Khramtsov YV, Ulasov AV, Slastnikova TA, Rosenkranz AA, Lupanova TN, Georgiev GP, Sobolev AS. Modular Nanotransporters Delivering Biologically Active Molecules to the Surface of Mitochondria. Pharmaceutics 2023; 15:2687. [PMID: 38140028 PMCID: PMC10748074 DOI: 10.3390/pharmaceutics15122687] [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: 11/06/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Treatment of various diseases, in particular cancer, usually requires the targeting of biologically active molecules at a selected subcellular compartment. We modified our previously developed modular nanotransporters (MNTs) for targeting mitochondria. The new MNTs are capable of binding to the protein predominantly localized on the outer mitochondrial membrane, Keap1. These MNTs possessing antiKeap1 monobody co-localize with mitochondria upon addition to the cells. They efficiently interact with Keap1 both in solution and within living cells. A conjugate of the MNT with a photosensitizer, chlorin e6, demonstrated significantly higher photocytotoxicity than chlorin e6 alone. We assume that MNTs of this kind can improve efficiency of therapeutic photosensitizers and radionuclides emitting short-range particles.
Collapse
Affiliation(s)
- Yuri V. Khramtsov
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.A.S.); (A.A.R.); (T.N.L.); (G.P.G.)
| | - Alexey V. Ulasov
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.A.S.); (A.A.R.); (T.N.L.); (G.P.G.)
| | - Tatiana A. Slastnikova
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.A.S.); (A.A.R.); (T.N.L.); (G.P.G.)
| | - Andrey A. Rosenkranz
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.A.S.); (A.A.R.); (T.N.L.); (G.P.G.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory St., 119234 Moscow, Russia
| | - Tatiana N. Lupanova
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.A.S.); (A.A.R.); (T.N.L.); (G.P.G.)
| | - Georgii P. Georgiev
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.A.S.); (A.A.R.); (T.N.L.); (G.P.G.)
| | - Alexander S. Sobolev
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.A.S.); (A.A.R.); (T.N.L.); (G.P.G.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory St., 119234 Moscow, Russia
| |
Collapse
|
36
|
Li X, Sun T, Liu J, Wei S, Yang Y, Liu J, Zhang B, Li W. Phloretin alleviates doxorubicin-induced cardiotoxicity through regulating Hif3a transcription via targeting transcription factor Fos. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 120:155046. [PMID: 37659297 DOI: 10.1016/j.phymed.2023.155046] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
BACKGROUND Doxorubicin (Dox), a chemotherapeutic agent known for its efficacy, has been associated with the development of severe cardiotoxicity, commonly referred to as doxorubicin-induced cardiotoxicity (DIC). The role and mechanism of action of phloretin (Phl) in cardiovascular diseases are well-established; however, its specific function and underlying mechanism in the context of DIC have yet to be fully elucidated. OBJECTIVE This research aimed to uncover the protective effect of Phl against DIC in vivo and in vitro, while also providing a comprehensive understanding of the underlying mechanisms involved. METHODS DIC cell and murine models were established. The action targets and mechanism of Phl against DIC were comprehensively examined by systematic network pharmacology, molecular docking, transcriptomics technologies, transcription factor (TF) prediction, and experimental validation. RESULTS Phl relieved Dox-induced cell apoptosis in vitro and in vivo. Through network pharmacology analysis, a total of 554 co-targeted genes of Phl and Dox were identified. Enrichment analysis revealed several key pathways including the PI3K-Akt signaling pathway, Apoptosis, and the IL-17 signaling pathway. Protein-protein interaction (PPI) analysis identified 24 core co-targeted genes, such as Fos, Jun, Hif1a, which were predicted to bind well to Phl based on molecular docking. Transcriptomics analysis was performed to identify the top 20 differentially expressed genes (DEGs), and 202 transcription factors (TFs) were predicted for these DEGs. Among these TFs, 10 TFs (Fos, Jun, Hif1a, etc.) are also the co-targeted genes, and 3 TFs (Fos, Jun, Hif1a) are also the core co-targeted genes. Further experiments validated the finding that Phl reduced the elevated levels of Hif3a (one of the top 20 DEGs) and Fos (one of Hif3a's predicted TFs) induced by Dox. Moreover, the interaction between Fos protein and the Hif3a promoter was confirmed through luciferase reporter assays. CONCLUSION Phl actively targeted and down-regulated the Fos protein to inhibit its binding to the promoter region of Hif3a, thereby providing protection against DIC.
Collapse
Affiliation(s)
- Xiangyun Li
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Institute of Clinical Pharmacy, Central South University, Changsha, Hunan 410011, China; School of Pharmacy, Central South University, Changsha, Hunan 410078, China
| | - Taoli Sun
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
| | - Jiaqin Liu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Institute of Clinical Pharmacy, Central South University, Changsha, Hunan 410011, China
| | - Shanshan Wei
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Institute of Clinical Pharmacy, Central South University, Changsha, Hunan 410011, China
| | - Yuanying Yang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Institute of Clinical Pharmacy, Central South University, Changsha, Hunan 410011, China
| | - Jian Liu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Institute of Clinical Pharmacy, Central South University, Changsha, Hunan 410011, China
| | - Bikui Zhang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Institute of Clinical Pharmacy, Central South University, Changsha, Hunan 410011, China; School of Pharmacy, Central South University, Changsha, Hunan 410078, China.
| | - Wenqun Li
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Institute of Clinical Pharmacy, Central South University, Changsha, Hunan 410011, China.
| |
Collapse
|
37
|
Tabana Y, Babu D, Fahlman R, Siraki AG, Barakat K. Target identification of small molecules: an overview of the current applications in drug discovery. BMC Biotechnol 2023; 23:44. [PMID: 37817108 PMCID: PMC10566111 DOI: 10.1186/s12896-023-00815-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Target identification is an essential part of the drug discovery and development process, and its efficacy plays a crucial role in the success of any given therapy. Although protein target identification research can be challenging, two main approaches can help researchers make significant discoveries: affinity-based pull-down and label-free methods. Affinity-based pull-down methods use small molecules conjugated with tags to selectively isolate target proteins, while label-free methods utilize small molecules in their natural state to identify targets. Target identification strategy selection is essential to the success of any drug discovery process and must be carefully considered when determining how to best pursue a specific project. This paper provides an overview of the current target identification approaches in drug discovery related to experimental biological assays, focusing primarily on affinity-based pull-down and label-free approaches, and discusses their main limitations and advantages.
Collapse
Affiliation(s)
- Yasser Tabana
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Dinesh Babu
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Richard Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Arno G Siraki
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|
38
|
Jesudason CD, Mason ER, Chu S, Oblak AL, Javens-Wolfe J, Moussaif M, Durst G, Hipskind P, Beck DE, Dong J, Amarasinghe O, Zhang ZY, Hamdani AK, Singhal K, Mesecar AD, Souza S, Jacobson M, Salvo JD, Soni DM, Kandasamy M, Masters AR, Quinney SK, Doolen S, Huhe H, Rizzo SJS, Lamb BT, Palkowitz AD, Richardson TI. SHIP1 therapeutic target enablement: Identification and evaluation of inhibitors for the treatment of late-onset Alzheimer's disease. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2023; 9:e12429. [PMID: 38023622 PMCID: PMC10655782 DOI: 10.1002/trc2.12429] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/29/2023] [Accepted: 09/17/2023] [Indexed: 12/01/2023]
Abstract
INTRODUCTION The risk of developing Alzheimer's disease is associated with genes involved in microglial function. Inositol polyphosphate-5-phosphatase (INPP5D), which encodes Src homology 2 (SH2) domain-containing inositol polyphosphate 5-phosphatase 1 (SHIP1), is a risk gene expressed in microglia. Because SHIP1 binds receptor immunoreceptor tyrosine-based inhibitory motifs (ITIMs), competes with kinases, and converts PI(3,4,5)P3 to PI(3,4)P2, it is a negative regulator of microglia function. Validated inhibitors are needed to evaluate SHIP1 as a potential therapeutic target. METHODS We identified inhibitors and screened the enzymatic domain of SHIP1. A protein construct containing two domains was used to evaluate enzyme inhibitor potency and selectivity versus SHIP2. Inhibitors were tested against a construct containing all ordered domains of the human and mouse proteins. A cellular thermal shift assay (CETSA) provided evidence of target engagement in cells. Phospho-AKT levels provided further evidence of on-target pharmacology. A high-content imaging assay was used to study the pharmacology of SHIP1 inhibition while monitoring cell health. Physicochemical and absorption, distribution, metabolism, and excretion (ADME) properties were evaluated to select a compound suitable for in vivo studies. RESULTS SHIP1 inhibitors displayed a remarkable array of activities and cellular pharmacology. Inhibitory potency was dependent on the protein construct used to assess enzymatic activity. Some inhibitors failed to engage the target in cells. Inhibitors that were active in the CETSA consistently destabilized the protein and reduced pAKT levels. Many SHIP1 inhibitors were cytotoxic either at high concentration due to cell stress or they potently induced cell death depending on the compound and cell type. One compound activated microglia, inducing phagocytosis at concentrations that did not result in significant cell death. A pharmacokinetic study demonstrated brain exposures in mice upon oral administration. DISCUSSION 3-((2,4-Dichlorobenzyl)oxy)-5-(1-(piperidin-4-yl)-1H-pyrazol-4-yl) pyridine activated primary mouse microglia and demonstrated exposures in mouse brain upon oral dosing. Although this compound is our recommended chemical probe for investigating the pharmacology of SHIP1 inhibition at this time, further optimization is required for clinical studies. Highlights Cellular thermal shift assay (CETSA) and signaling (pAKT) assays were developed to provide evidence of src homology 2 (SH2) domain-contaning inositol phosphatase 1 (SHIP1) target engagement and on-target activity in cellular assays.A phenotypic high-content imaging assay with simultaneous measures of phagocytosis, cell number, and nuclear intensity was developed to explore cellular pharmacology and monitor cell health.SHIP1 inhibitors demonstrate a wide range of activity and cellular pharmacology, and many reported inhibitors are cytotoxic.The chemical probe 3-((2,4-dichlorobenzyl)oxy)-5-(1-(piperidin-4-yl)-1H-pyrazol-4-yl) pyridine is recommended to explore SHIP1 pharmacology.
Collapse
Affiliation(s)
| | - Emily R Mason
- Indiana University School of Medicine Indianapolis Indiana USA
| | - Shaoyou Chu
- Indiana University School of Medicine Indianapolis Indiana USA
| | - Adrian L Oblak
- Indiana University School of Medicine Indianapolis Indiana USA
- Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis Indiana USA
| | | | | | | | | | - Daniel E Beck
- Institute for Drug Discovery Purdue University West Lafayette Indiana USA
| | - Jiajun Dong
- Department of Medicinal Chemistry and Molecular Pharmacology Purdue University West Lafayette Indiana USA
| | - Ovini Amarasinghe
- Department of Medicinal Chemistry and Molecular Pharmacology Purdue University West Lafayette Indiana USA
| | - Zhong-Yin Zhang
- Institute for Drug Discovery Purdue University West Lafayette Indiana USA
- Department of Medicinal Chemistry and Molecular Pharmacology Purdue University West Lafayette Indiana USA
| | - Adam K Hamdani
- Department of Biochemistry Purdue University West Lafayette Indiana USA
| | - Kratika Singhal
- Department of Biochemistry Purdue University West Lafayette Indiana USA
| | - Andrew D Mesecar
- Department of Biochemistry Purdue University West Lafayette Indiana USA
| | | | | | | | - Disha M Soni
- Indiana University School of Medicine Indianapolis Indiana USA
| | | | | | - Sara K Quinney
- Indiana University School of Medicine Indianapolis Indiana USA
| | - Suzanne Doolen
- University of Pittsburgh School of Medicine Pittsburgh Pennsylvania USA
| | - Hasi Huhe
- University of Pittsburgh School of Medicine Pittsburgh Pennsylvania USA
| | | | - Bruce T Lamb
- Indiana University School of Medicine Indianapolis Indiana USA
- Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis Indiana USA
| | - Alan D Palkowitz
- Indiana University School of Medicine Indianapolis Indiana USA
- Indiana Biosciences Research Institute Indianapolis Indiana USA
| | - Timothy I Richardson
- Indiana University School of Medicine Indianapolis Indiana USA
- Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis Indiana USA
- Indiana Biosciences Research Institute Indianapolis Indiana USA
| |
Collapse
|
39
|
Anderson B, Rosston P, Ong HW, Hossain MA, Davis-Gilbert ZW, Drewry DH. How many kinases are druggable? A review of our current understanding. Biochem J 2023; 480:1331-1363. [PMID: 37642371 PMCID: PMC10586788 DOI: 10.1042/bcj20220217] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
There are over 500 human kinases ranging from very well-studied to almost completely ignored. Kinases are tractable and implicated in many diseases, making them ideal targets for medicinal chemistry campaigns, but is it possible to discover a drug for each individual kinase? For every human kinase, we gathered data on their citation count, availability of chemical probes, approved and investigational drugs, PDB structures, and biochemical and cellular assays. Analysis of these factors highlights which kinase groups have a wealth of information available, and which groups still have room for progress. The data suggest a disproportionate focus on the more well characterized kinases while much of the kinome remains comparatively understudied. It is noteworthy that tool compounds for understudied kinases have already been developed, and there is still untapped potential for further development in this chemical space. Finally, this review discusses many of the different strategies employed to generate selectivity between kinases. Given the large volume of information available and the progress made over the past 20 years when it comes to drugging kinases, we believe it is possible to develop a tool compound for every human kinase. We hope this review will prove to be both a useful resource as well as inspire the discovery of a tool for every kinase.
Collapse
Affiliation(s)
- Brian Anderson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Peter Rosston
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Han Wee Ong
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Zachary W. Davis-Gilbert
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| |
Collapse
|
40
|
Deau E, Lindberg MF, Miege F, Roche D, George N, George P, Krämer A, Knapp S, Meijer L. Leucettinibs, a Class of DYRK/CLK Kinase Inhibitors Inspired by the Marine Sponge Natural Product Leucettamine B. J Med Chem 2023; 66:10694-10714. [PMID: 37487467 DOI: 10.1021/acs.jmedchem.3c00884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Dual-specificity, tyrosine phosphorylation-regulated kinases (DYRKs) and cdc2-like kinases (CLKs) recently attracted attention due to their central involvement in various pathologies. We here describe a family of DYRK/CLK inhibitors derived from Leucettines and the marine natural product Leucettamine B. Forty-five N2-functionalized 2-aminoimidazolin-4-ones bearing a fused [6 + 5]-heteroarylmethylene were synthesized. Benzothiazol-6-ylmethylene was selected as the most potent residue among 15 different heteroarylmethylenes. 186 N2-substituted 2-aminoimidazolin-4-ones bearing a benzothiazol-6-ylmethylene, collectively named Leucettinibs, were synthesized and extensively characterized. Subnanomolar IC50 (0.5-20 nM on DYRK1A) inhibitors were identified and one Leucettinib was modeled in DYRK1A and co-crystallized with CLK1 and the weaker inhibited off-target CSNK2A1. Kinase-inactive isomers of Leucettinibs (>3-10 μM on DYRK1A), named iso-Leucettinibs, were synthesized and characterized as suitable negative control compounds for functional experiments. Leucettinibs, but not iso-Leucettinibs, inhibit the phosphorylation of DYRK1A substrates in cells. Leucettinibs provide new research tools and potential leads for further optimization toward therapeutic drug candidates.
Collapse
Affiliation(s)
- Emmanuel Deau
- Perha Pharmaceuticals, Perharidy, 29680 Roscoff, France
| | | | - Frédéric Miege
- Edelris, Bâtiment Bioserra 1, 60 Avenue Rockefeller, 69008 Lyon, France
| | - Didier Roche
- Edelris, Bâtiment Bioserra 1, 60 Avenue Rockefeller, 69008 Lyon, France
| | - Nicolas George
- Oncodesign, 25-27 Avenue du Québec, 91140 Villebon-sur-Yvette, France
| | - Pascal George
- Perha Pharmaceuticals, Perharidy, 29680 Roscoff, France
| | - Andreas Krämer
- Goethe-University Frankfurt, Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Max-von Laue Str. 15, 60438 Frankfurt am Main, Germany
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von Laue Str. 9, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Goethe-University Frankfurt, Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Max-von Laue Str. 15, 60438 Frankfurt am Main, Germany
| | | |
Collapse
|
41
|
Chen W, Zhang Q, Dai X, Chen X, Zhang C, Bai R, Chen Y, Zhang K, Duan X, Qiao Y, Zhao J, Tian F, Liu K, Dong Z, Lu J. PGC-1α promotes colorectal carcinoma metastasis through regulating ABCA1 transcription. Oncogene 2023; 42:2456-2470. [PMID: 37400530 DOI: 10.1038/s41388-023-02762-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 07/05/2023]
Abstract
Colorectal cancer (CRC) is a highly aggressive cancer in which metastasis plays a key role. However, the mechanisms underlying metastasis have not been fully elucidated. Peroxisome proliferator-activated receptor gamma coactivator 1α (PGC-1α), a regulator of mitochondrial function, has been reported as a complicated factor in cancer. In this study, we found that PGC-1α was highly expressed in CRC tissues and was positively correlated with lymph node and liver metastasis. Subsequently, PGC-1α knockdown was shown to inhibit CRC growth and metastasis in both in vitro and in vivo studies. Transcriptomic analysis revealed that PGC-1α regulated ATP-binding cassette transporter 1 (ABCA1) mediated cholesterol efflux. Mechanistically, PGC-1α interacted with YY1 to promote ABCA1 transcription, resulting in cholesterol efflux, which subsequently promoted CRC metastasis through epithelial-to-mesenchymal transition (EMT). In addition, the study identified the natural compound isoliquiritigenin (ISL) as an inhibitor that targeted ABCA1 and significantly reduced CRC metastasis induced by PGC-1α. Overall, this study sheds light on how PGC-1α promotes CRC metastasis by regulating ABCA1-mediated cholesterol efflux, providing a basis for further research to inhibit CRC metastasis.
Collapse
Affiliation(s)
- Wei Chen
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
| | - Qiushuang Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
| | - Xiaoshuo Dai
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
| | - Xinhuan Chen
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
- Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, 450052, P. R. China
| | - Chengjuan Zhang
- Department of Pathology, Henan Cancer Hospital, Zhengzhou University, Zhengzhou, Henan Province, 450003, P. R. China
| | - Ruihua Bai
- Department of Pathology, Henan Cancer Hospital, Zhengzhou University, Zhengzhou, Henan Province, 450003, P. R. China
| | - Yihuan Chen
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
| | - Kai Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
| | - Xiaoxuan Duan
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
| | - Yan Qiao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
- Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, 450052, P. R. China
| | - Jimin Zhao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
- Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, 450052, P. R. China
| | - Fang Tian
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
- Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, 450052, P. R. China
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
- Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, 450052, P. R. China
| | - Ziming Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
- Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, 450052, P. R. China
| | - Jing Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China.
- Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan Province, 450001, P. R. China.
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, 450052, P. R. China.
| |
Collapse
|
42
|
Kurbatov I, Dolgalev G, Arzumanian V, Kiseleva O, Poverennaya E. The Knowns and Unknowns in Protein-Metabolite Interactions. Int J Mol Sci 2023; 24:4155. [PMID: 36835565 PMCID: PMC9964805 DOI: 10.3390/ijms24044155] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Increasing attention has been focused on the study of protein-metabolite interactions (PMI), which play a key role in regulating protein functions and directing an orchestra of cellular processes. The investigation of PMIs is complicated by the fact that many such interactions are extremely short-lived, which requires very high resolution in order to detect them. As in the case of protein-protein interactions, protein-metabolite interactions are still not clearly defined. Existing assays for detecting protein-metabolite interactions have an additional limitation in the form of a limited capacity to identify interacting metabolites. Thus, although recent advances in mass spectrometry allow the routine identification and quantification of thousands of proteins and metabolites today, they still need to be improved to provide a complete inventory of biological molecules, as well as all interactions between them. Multiomic studies aimed at deciphering the implementation of genetic information often end with the analysis of changes in metabolic pathways, as they constitute one of the most informative phenotypic layers. In this approach, the quantity and quality of knowledge about PMIs become vital to establishing the full scope of crosstalk between the proteome and the metabolome in a biological object of interest. In this review, we analyze the current state of investigation into the detection and annotation of protein-metabolite interactions, describe the recent progress in developing associated research methods, and attempt to deconstruct the very term "interaction" to advance the field of interactomics further.
Collapse
Affiliation(s)
| | | | | | - Olga Kiseleva
- Institute of Biomedical Chemistry, Moscow 119121, Russia
| | | |
Collapse
|
43
|
Khramtsov YV, Ulasov AV, Rosenkranz AA, Slastnikova TA, Lupanova TN, Georgiev GP, Sobolev AS. An Approach to Evaluate the Effective Cytoplasmic Concentration of Bioactive Agents Interacting with a Selected Intracellular Target Protein. Pharmaceutics 2023; 15:pharmaceutics15020324. [PMID: 36839653 PMCID: PMC9965106 DOI: 10.3390/pharmaceutics15020324] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
To compare the effectiveness of various bioactive agents reversibly acting within a cell on a target intracellular macromolecule, it is necessary to assess effective cytoplasmic concentrations of the delivered bioactive agents. In this work, based on a simple equilibrium model and the cellular thermal shift assay (CETSA), an approach is proposed to assess effective concentrations of both a delivered bioactive agent and a target protein. This approach was tested by evaluating the average concentrations of nuclear factor erythroid 2-related factor 2 (Nrf2) and Kelch-like ECH-associated-protein 1 (Keap1) proteins in the cytoplasm for five different cell lines (Hepa1, MEF, RAW264.7, 3LL, and AML12) and comparing the results with known literature data. The proposed approach makes it possible to analyze both binary interactions and ternary competition systems; thus, it can have a wide application for the analysis of protein-protein or molecule-protein interactions in the cell. The concentrations of Nrf2 and Keap1 in the cell can be useful not only in analyzing the conditions for the activation of the Nrf2 system, but also for comparing the effectiveness of various drug delivery systems, where the delivered molecule is able to interact with Keap1.
Collapse
Affiliation(s)
- Yuri V. Khramtsov
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Alexey V. Ulasov
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Andrey A. Rosenkranz
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory St., 119234 Moscow, Russia
| | - Tatiana A. Slastnikova
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Tatiana N. Lupanova
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Georgii P. Georgiev
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Alexander S. Sobolev
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory St., 119234 Moscow, Russia
- Correspondence:
| |
Collapse
|
44
|
Sun N, Yang T, Tang Y, Zhao Y, Wang H, Zhao S, Tan H, Li L, Fan H. Lycopene Alleviates Chronic Stress-Induced Liver Injury by Inhibiting Oxidative Stress-Mediated Endoplasmic Reticulum Stress Pathway Apoptosis in Rats. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14414-14426. [PMID: 36318656 DOI: 10.1021/acs.jafc.2c06650] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The liver is the major organ of metabolism and is extremely vulnerable to chronic stress. Lycopene (LYC) is a natural carotenoid with potent antioxidant and chronic disease potential. However, whether LYC protects against chronic restraint stress (CRS)-induced liver injury and the underlying mechanisms remain unclear. In this study, rats were restrained for 21 days for 6 h per day, with or without gavage of LYC (10 mg/kg). Serum ALT (85.99 ± 4.07 U/L) and AST (181.78 ± 7.35 U/L) and scores of liver injury were significantly increased in the CRS group. LYC significantly promoted the nuclear translocation of Nrf2, elevated the expression of antioxidant genes, and attenuated reactive oxygen radicals (ROS) levels within the liver. Cellular thermal shift assay (CETSA) and molecular docking results indicated that LYC competitively binds to Keap1 with the lowest molecule affinity of -9.0 kcal/mol. Moreover, LYC significantly relieved the hepatic endoplasmic reticulum swelling and decreased the expression of endoplasmic reticulum stress (ERS) hallmarks like GRP78, CHOP, and cleaved caspase-12. Meanwhile, LYC also mitigated CRS-induced hepatocyte apoptosis. Interestingly, every other day, the intraperitoneal injection of the Nrf2 inhibitor brusatol (0.4 mg/kg) significantly counteracted the protective effect of LYC. In conclusion, LYC protects against CRS-induced liver injury by activating the Nrf2 signaling pathway, scavenging ROS, and further attenuating ERS-associated apoptosis pathways.
Collapse
Affiliation(s)
- Ning Sun
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Tianyuan Yang
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Yulin Tang
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Yuan Zhao
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Hui Wang
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Shuping Zhao
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Haoyang Tan
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Lin Li
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Honggang Fan
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| |
Collapse
|