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Wang D, Wang Y. Identification of protein partners for small molecules reshapes the understanding of nonalcoholic steatohepatitis and drug discovery. Life Sci 2024; 356:123031. [PMID: 39226989 DOI: 10.1016/j.lfs.2024.123031] [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: 05/31/2024] [Revised: 08/16/2024] [Accepted: 08/30/2024] [Indexed: 09/05/2024]
Abstract
AIMS Nonalcoholic steatohepatitis (NASH) is the severe subtype of nonalcoholic fatty diseases (NAFLD) with few options for treatment. Patients with NASH exhibit partial responses to the current therapeutics and adverse effects. Identification of the binding proteins for the drugs is essential to understanding the mechanism and adverse effects of the drugs and fuels the discovery of potent and safe drugs. This paper aims to critically discuss recent advances in covalent and noncovalent approaches for identifying binding proteins that mediate NASH progression, along with an in-depth analysis of the mechanisms by which these targets regulate NASH. MATERIALS AND METHODS A literature search was conducted to identify the relevant studies in the database of PubMed and the American Chemical Society. The search covered articles published from January 1990 to July 2024, using the search terms with keywords such as NASH, benzophenone, diazirine, photo-affinity labeling, thermal protein profiling, CETSA, target identification. KEY FINDINGS The covalent approaches utilize drugs modified with diazirine and benzophenone to covalently crosslink with the target proteins, which facilitates the purification and identification of target proteins. In addition, they map the binding sites in the target proteins. By contrast, noncovalent approaches identify the binding targets of unmodified drugs in the intact cell proteome. The advantages and limitations of both approaches have been compared, along with a comprehensive analysis of recent innovations that further enhance the efficiency and specificity. SIGNIFICANCE The analyses of the applicability of these approaches provide novel tools to delineate NASH pathogenesis and promote drug discovery.
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Affiliation(s)
- Danyi Wang
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, China
| | - Yibing Wang
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, China.
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Zheng X, Zhu H, Zhao X, Wang J, Li Q, Zhao X. Emerging affinity methods for protein-drug interaction analysis. J Pharm Biomed Anal 2024; 249:116371. [PMID: 39047466 DOI: 10.1016/j.jpba.2024.116371] [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: 05/30/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
The study of protein-drug interaction plays a crucial role in understanding drug mechanisms, identifying new drug targets and biomarkers, and facilitating drug development and disease treatment. In recent years, significant progress has been made in various protein-drug interaction research methods due to the rapid development and in-depth application of mass spectrometry, nuclear magnetic resonance, Raman spectroscopy, and other technologies. The progress has enhanced the sensitivity, precision, accuracy, and applicability of analytical methods, enabling the establishment of drug-protein interaction networks. This review discusses various emerging research methods, such as native mass spectrometry, infrared spectroscopy, nuclear magnetic resonance and spectrum, biosensor technologies employing surface enhanced Raman, electrochemistry, and magneto resistive signals, as well as affinity magnetic levitation and affinity chromatography. The article also delves into the principles, applications, advantages, and limitations of these technologies.
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Affiliation(s)
- Xinxin Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Huiting Zhu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xue Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jing Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qian Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xinfeng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.
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Yu H, Chen Y, Wang Y, Fu W, Xu R, Liu J, Chen Y, Liu X, Wu Y, Xu T. Integrated Thermal Proteome Profiling and Affinity Ultrafiltration Mass Spectrometry (iTPAUMS): A Novel Paradigm for Elucidating the Mechanism of Action of Natural Products. Anal Chem 2024; 96:15980-15990. [PMID: 39252608 DOI: 10.1021/acs.analchem.4c03398] [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: 09/11/2024]
Abstract
Natural products (NPs) are foundational to drug discovery, offering a rich repertoire of molecular diversity with multifaceted modes of action against a broad array of targets. Despite their potential, deconvoluting the intricate mechanism of action (MoA) of NPs, characterized by their multicomponent, multitarget, and multilevel interactions, remains a formidable challenge. Here, we introduce an innovative pipeline called integrated thermal proteome profiling and affinity ultrafiltration mass spectrometry (iTPAUMS). This approach combines the high-throughput capacity of thermal proteome profiling (TPP) with the specificity of affinity ultrafiltration mass spectrometry (AUMS), creating a powerful toolkit for elucidating complex MoAs of NPs. Significantly, our investigation represents a pioneering application of TPP to delineate the target group of NPs mixtures and overcome the long-standing obstacle of mapping specific component-target interactions through AUMS. Our findings demonstrate the utility of iTPAUMS in constructing a comprehensive component-target atlas, providing a robust analytical foundation for unraveling the intricate pharmacological landscapes of NPs and advancing drug discovery.
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Affiliation(s)
- Hengyuan Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yang Chen
- Department of Clinical Pharmacy, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Xihu University School of Medicine, Hangzhou 310006, China
| | - Yichen Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Weiliang Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rui Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jie Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Shandong C.P. Freda Pharmaceutical Co., Ltd., Jinan 250104, China
- Engineering Research Center for Medicines of Orthopedic Pain of Shandong Province, Jinan 250104, China
| | - Yong Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, Wenzhou 325800, China
| | - Xuesong Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, Wenzhou 325800, China
| | - Yongjiang Wu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tengfei Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, Wenzhou 325800, China
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Wang XR, Zhong H, Ma SS, Huang YH, Xu WH, Wang Y. Discovery of petroselinic acid with in vitro and in vivo antifungal activity by targeting fructose-1,6-bisphosphate aldolase. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 133:155948. [PMID: 39153276 DOI: 10.1016/j.phymed.2024.155948] [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: 05/09/2024] [Revised: 07/29/2024] [Accepted: 08/08/2024] [Indexed: 08/19/2024]
Abstract
BACKGROUND The incidence of invasive fungal diseases (IFDs), represented by Candida albicans infection, is increasing year by year. However, clinically available antifungal drugs are very limited and encounter challenges such as limited efficacy, drug resistance, high toxicity, and exorbitant cost. Therefore, there is an urgent need for new antifungal drugs. PURPOSE This study aims to find new antifungal compounds from plants, preferably those with good activity and low toxicity, and reveal their antifungal targets. METHODS In vitro antifungal activities of compounds were investigated using broth microdilution method, spot assay, hyphal growth assay and biofilm formation assay. Synergistic effects were assessed using broth microdilution checkerboard technique. In vivo antifungal activities were evaluated using Galleria mellonella and murine candidiasis models. Cytotoxicity of compounds was investigated using Cell Counting Kit-8 (CCK-8). Discovery and validation of antifungal targets of compounds were conducted by using monoallelic knockout library of C. albicans, haploinsufficiency profiling (HIP), thermal shift assay (TSA), enzyme inhibitory effect assay, molecular docking, and in vitro and in vivo antifungal studies. RESULTS 814 plant products were screened, among which petroselinic acid (PeAc) was found as an antifungal molecule. As a rare fatty acid isolated from coriander (Coriandrum sativum), carrot (Daucus carota) and other plants of the Apiaceae family, PeAc had not previously been found to have antifungal effects. In this study, PeAc was revealed to inhibit the growth of various pathogenic fungi, exhibited synergistic effects with fluconazole (FLC), inhibited the formation of C. albicans hyphae and biofilms, and showed antifungal effects in vivo. PeAc was less toxic to mammalian cells. Fructose-1,6-bisphosphate aldolase (Fba1p) was identified as a target of PeAc by using HIP, TSA, enzyme inhibitory effect assay and molecular docking methods. PeAc exerted antifungal effects more effectively on fba1Δ/FBA1 than wild-type (WT) strain both in vitro and in vivo. CONCLUSIONS PeAc is an effective and low toxic antifungal compound. The target of PeAc is Fba1p. Fba1p is a promising target for antifungal drug development.
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Affiliation(s)
- Xin-Rong Wang
- School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Hua Zhong
- School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Shan-Shan Ma
- School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Ya-Hui Huang
- School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Wei-Heng Xu
- School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Yan Wang
- School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, China.
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Zhang YM, Li T, Xu CC, Qian JY, Guo H, Zhang X, Zhan ZJ, Lu JJ. Uncover the anticancer potential of lycorine. Chin Med 2024; 19:121. [PMID: 39245716 PMCID: PMC11382518 DOI: 10.1186/s13020-024-00989-9] [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: 05/29/2024] [Accepted: 08/22/2024] [Indexed: 09/10/2024] Open
Abstract
BACKGROUND Natural products have a long history in drug discovery. Lycorine is an alkaloid derived from Amaryllidaceae plants, demonstrating significant pharmacological potential. Lycorine and its hydrochloride salt, lycorine hydrochloride, have shown outstanding anticancer effects both in vitro and in vivo. PURPOSE This review aims to comprehensively summarize recent research advancements regarding the anticancer potential of lycorine and lycorine hydrochloride. It intends to elucidate current research limitations, optimization strategies, and future research directions to guide clinical translation. METHODS Various databases, e.g., Web of Science, PubMed, and Chinese National Knowledge Infrastructure, are systematically searched for relevant articles using keywords such as lycorine, cancer, pharmacokinetics, and toxicity. The retrieved literature is then categorized and summarized to provide an overview of the research advancements in the anticancer potential of lycorine and lycorine hydrochloride. RESULTS Lycorine and lycorine hydrochloride demonstrate significant anticancer activities against various types of cancer both in vitro and in vivo, employing diverse mechanisms such as inducing cell cycle arrest, triggering cellular senescence, regulating programmed cell death, inhibiting angiogenesis, suppressing metastasis, and modulating immune system. Furthermore, pharmacokinetic profiles and toxicity data are summarized. Additionally, this review discusses the druggability, limitations, optimization strategies, and target identification of lycorine, offering insights for future preclinical studies. CONCLUSION The anticancer effects and safety profile of lycorine and lycorine hydrochloride suggest promising potential for clinical applications. Further research on their in-depth mechanisms and optimization strategies targeting their limitations will enhance the understanding and druggability of lycorine and lycorine hydrochloride.
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Affiliation(s)
- Yan-Ming Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao SAR, 999078, China
| | - Ting Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao SAR, 999078, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macao SAR, 999078, China
| | - Chun-Cao Xu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao SAR, 999078, China
| | - Jia-Yu Qian
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Hongwei Guo
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Xiaolei Zhang
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Zha-Jun Zhan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China.
| | - Jin-Jian Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao SAR, 999078, China.
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macao SAR, 999078, China.
- Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Macao SAR, 999078, China.
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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.
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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.
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Shen X, Yang H, Yang Y, Zhu X, Sun Q. The cellular and molecular targets of natural products against metabolic disorders: a translational approach to reach the bedside. MedComm (Beijing) 2024; 5:e664. [PMID: 39049964 PMCID: PMC11266934 DOI: 10.1002/mco2.664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024] Open
Abstract
Metabolic disorders, including obesity, dyslipidemia, diabetes, nonalcoholic fatty liver disease, and metabolic syndrome, are characterized by insulin resistance, abnormalities in circulating cholesterol and lipid profiles, and hypertension. The most common pathophysiologies of metabolic disorders are glucose/lipid metabolism dysregulation, insulin resistance, inflammatory response, and oxidative stress. Although several agents have been approved for the treatment of metabolic disorders, there is still a strong demand for more efficacious drugs with less side effects. Natural products have been critical sources of drug research and discovery for decades. However, the usefulness of bioactive natural products is often limited by incomplete understanding of their direct cellular targets. In this review, we highlight the current understanding of the established and emerging molecular mechanisms of metabolic disorders. We further summarize the therapeutic effects and underlying mechanisms of natural products on metabolic disorders, with highlights on their direct cellular targets, which are mainly implicated in the regulation of glucose/lipid metabolism, insulin resistance, metabolic inflammation, and oxidative stress. Finally, this review also covers the clinical studies of natural products in metabolic disorders. These progresses are expected to facilitate the application of these natural products and their derivatives in the development of novel drugs against metabolic disorders.
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Affiliation(s)
- Xiaofei Shen
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan ProvinceHospital of Chengdu University of Traditional Chinese MedicineChengdu University of Traditional Chinese MedicineChengduChina
| | - Hongling Yang
- Department of Nephrology and Institute of NephrologySichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Sichuan Clinical Research Centre for Kidney DiseasesChengduChina
| | - Yang Yang
- Department of Respiratory and Critical Care MedicineSichuan Provincial People's HospitalUniversity of Electronic Science and TechnologyChengduChina
| | - Xianjun Zhu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical GeneticsSichuan Provincial People's HospitalUniversity of Electronic Science and TechnologyChengduChina
| | - Qingxiang Sun
- Department of Respiratory and Critical Care MedicineSichuan Provincial People's HospitalUniversity of Electronic Science and TechnologyChengduChina
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Nie Y, Yan J, Huang X, Jiang T, Zhang S, Zhang G. Dihydrotanshinone I targets ESR1 to induce DNA double-strand breaks and proliferation inhibition in hepatocellular carcinoma. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 130:155767. [PMID: 38833789 DOI: 10.1016/j.phymed.2024.155767] [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: 12/24/2023] [Revised: 02/28/2024] [Accepted: 03/28/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Due to its high incidence and elevated mortality, hepatocellular carcinoma (HCC) has emerged as a formidable global healthcare challenge. The intricate interplay between gender-specific disparities in both incidence and clinical outcomes has prompted a progressive recognition of the substantial influence exerted by estrogen and its corresponding receptors (ERs) upon HCC pathogenesis. Estrogen replacement therapy (ERT) emerged for the treatment of HCC by administering exogenous estrogen. However, the powerful side effects of estrogen, including the promotion of breast cancer and infertility, hinder the further application of ERT. Identifying effective therapeutic targets for estrogen and screening bioactive ingredients without E2-like side effects is of great significance for optimizing HCC ERT. METHODS In this study, we employed an integrative approach, harnessing data from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, clinical paraffin sections, adenoviral constructs as well as in vivo studies, to unveil the association between estrogen, estrogen receptor α (ESR1) and HCC. Leveraging methodologies encompassing molecular dynamics simulation and cellular thermal shift assay (CETSA) were used to confirm whether ESR1 is a molecular target of DHT. Multiple in vitro and in vivo experiments were used to identify whether i) ESR1 is a crucial gene that promotes DNA double-strand breaks (DSBs) and proliferation inhibition in HCC, ii) Dihydrotanshinone I (DHT), a quinonoid monomeric constituent derived from Salvia miltiorrhiza (Dan shen) exerts anti-HCC effects by regulating ESR1 and subsequent DSBs, iii) DHT has the potential to replace E2. RESULTS DHT could target ESR1 and upregulate its expression in a concentration-dependent manner. This, in turn, leads to the downregulation of breast cancer type 1 susceptibility protein (BRCA1), a pivotal protein involved in the homologous recombination repair (HRR) process. The consequence of this downregulation is manifested through the induction of DSBs in HCC, subsequently precipitating a cascade of downstream events, including apoptosis and cell cycle arrest. Of particular significance is the comparative assessment of DHT and isodose estradiol treatments, which underscores DHT's excellent HCC-suppressive efficacy without concomitant perturbation of endogenous sex hormone homeostasis. CONCLUSION Our findings not only confirm ESR1 as a therapeutic target in HCC management but also underscores DHT's role in upregulating ESR1 expression, thereby impeding the proliferation and invasive tendencies of HCC. In addition, we preliminarily identified DHT has the potential to emerge as an agent in optimizing HCC ERT through the substitution of E2.
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Affiliation(s)
- Yunmeng Nie
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310000, China
| | - Junbin Yan
- The Second Affiliated Hospital of Zhejiang Chinese Medical University (The Xin Hua Hospital of Zhejiang Province), No. 318 Chaowang Road, Hangzhou, Zhejiang 310000, China
| | - Xueru Huang
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310000, China
| | - Tao Jiang
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310000, China
| | - Shuo Zhang
- The Second Affiliated Hospital of Zhejiang Chinese Medical University (The Xin Hua Hospital of Zhejiang Province), No. 318 Chaowang Road, Hangzhou, Zhejiang 310000, China; Key Laboratory of Traditional Chinese Medicine for the treatment of Intestine-Liver of Zhejiang Province, Hangzhou 310000, China.
| | - Guangji Zhang
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310000, China; Key Laboratory of Blood-Stasis-Toxin Syndrome of Zhejiang Province, Hangzhou, Zhejiang 310053, China; Traditional Chinese Medicine 'Preventing Disease' Wisdom Health Project Research Center of Zhejiang, Hangzhou 310053, China.
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Zou M, Zhou H, Gu L, Zhang J, Fang L. Therapeutic Target Identification and Drug Discovery Driven by Chemical Proteomics. BIOLOGY 2024; 13:555. [PMID: 39194493 DOI: 10.3390/biology13080555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/07/2024] [Accepted: 07/19/2024] [Indexed: 08/29/2024]
Abstract
Throughout the human lifespan, from conception to the end of life, small molecules have an intrinsic relationship with numerous physiological processes. The investigation into small-molecule targets holds significant implications for pharmacological discovery. The determination of the action sites of small molecules provide clarity into the pharmacodynamics and toxicological mechanisms of small-molecule drugs, assisting in the elucidation of drug off-target effects and resistance mechanisms. Consequently, innovative methods to study small-molecule targets have proliferated in recent years, with chemical proteomics standing out as a vanguard development in chemical biology in the post-genomic age. Chemical proteomics can non-selectively identify unknown targets of compounds within complex biological matrices, with both probe and non-probe modalities enabling effective target identification. This review attempts to summarize methods and illustrative examples of small-molecule target identification via chemical proteomics. It delves deeply into the interactions between small molecules and human biology to provide pivotal directions and strategies for the discovery and comprehension of novel pharmaceuticals, as well as to improve the evaluation of drug safety.
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Affiliation(s)
- Mingjie Zou
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Haiyuan Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Letian Gu
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Jingzi Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Lei Fang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
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Jiang X, Shon K, Li X, Cui G, Wu Y, Wei Z, Wang A, Li X, Lu Y. Recent advances in identifying protein targets of bioactive natural products. Heliyon 2024; 10:e33917. [PMID: 39091937 PMCID: PMC11292521 DOI: 10.1016/j.heliyon.2024.e33917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 08/04/2024] Open
Abstract
Background Natural products exhibit structural complexity, diversity, and historical therapeutic significance, boasting attractive functions and biological activities that have significantly influenced drug discovery endeavors. The identification of target proteins of active natural compounds is crucial for advancing novel drug innovation. Currently, methods for identifying targets of natural products can be categorized into labeling and label-free approaches based on whether the natural bioactive constituents are modified into active probes. In addition, there is a new avenue for rapidly exploring the targets of natural products based on their innate functions. Aim This review aimed to summarize recent advancements in both labeling and label-free approaches to the identification of targets for natural products, as well as the novel target identification method based on the natural functions of natural products. Methods We systematically collected relevant articles published in recent years from PubMed, Web of Science, and ScienceDirect, focusing on methods employed for identifying protein targets of bioactive natural products. Furthermore, we systematically summarized the principles, procedures, and successful cases, as well as the advantages and limitations of each method. Results Labeling methods allow for the direct labeling of target proteins and the exclusion of indirectly targeted proteins. However, these methods are not suitable for studying post-modified compounds with abolished activity, chemically challenging synthesis, or trace amounts of natural active compounds. Label-free methods can be employed to identify targets of any natural active compounds, including trace amounts and multicomponent mixtures, but their reliability is not as high as labeling methods. The structural complementarity between natural products and their innate receptors significantly increase the opportunities for finding more promising structural analogues of the natural products, and natural products may interact with several structural analogues of receptors in humans. Conclusion Each approach presents benefits and drawbacks. In practice, a combination of methods is employed to identify targets of natural products. And natural products' innate functions-based approach is a rapid and selective strategy for target identification. This review provides valuable references for future research in this field, offering insights into techniques and methodologies.
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Affiliation(s)
- Xuan Jiang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Kinyu Shon
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiaofeng Li
- Department of Biochemistry and Molecular Biology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Guoliang Cui
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yuanyuan Wu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhonghong Wei
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Aiyun Wang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiaoman Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yin Lu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, 210023, China
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11
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Rao J, Wang T, Wang K, Qiu F. Integrative analysis of metabolomics and proteomics reveals mechanism of berberrubine-induced nephrotoxicity. Toxicol Appl Pharmacol 2024; 488:116992. [PMID: 38843998 DOI: 10.1016/j.taap.2024.116992] [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: 02/13/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
Berberrubine (BRB), a main metabolite of berberine, has stronger hypoglycemic and lipid-lowering activity than its parent form. We previously found that BRB could cause obvious nephrotoxicity, but the molecular mechanism involved remains unknown. In this study, we systematically integrated metabolomics and quantitative proteomics to reveal the potential mechanism of nephrotoxicity caused by BRB. Metabolomic analysis revealed that 103 significant- differentially metabolites were changed. Among the mentioned compounds, significantly upregulated metabolites were observed for phosphorylcholine, sn-glycerol-3-phosphoethanolamine, and phosphatidylcholine. The top three enriched KEGG pathways were the mTOR signaling pathway, central carbon metabolism in cancer, and choline metabolism in cancer. ERK1/2 plays key roles in all three metabolic pathways. To further confirm the main signaling pathways involved, a proteomic analysis was conducted to screen for key proteins (such as Mapk1, Mapk14, and Caspase), indicating the potential involvement of cellular growth and apoptosis. Moreover, combined metabolomics and proteomics analyses revealed the participation of ERK1/2 in multiple metabolic pathways. These findings indicated that ERK1/2 regulated the significant- differentially abundant metabolites determined via metabolomics analysis. Notably, through a cellular thermal shift assay (CETSA) and molecular docking, ERK1/2 were revealed to be the direct binding target involved in BRB-induced nephrotoxicity. To summarize, this study sheds light on the understanding of severe nephrotoxicity caused by BRB and provides scientific basis for its safe use and rational development.
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Affiliation(s)
- Jinqiu Rao
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China
| | - Tianwang Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China
| | - Kai Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China.
| | - Feng Qiu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China.
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12
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Chen S, Li Y, Wu E, Li Q, Xiang L, Qi J. Arctigenin from Fructus arctii Exhibits Antiaging Effects via Autophagy Induction, Antioxidative Stress, and Increase in Telomerase Activity in Yeast. Antioxidants (Basel) 2024; 13:684. [PMID: 38929123 PMCID: PMC11200627 DOI: 10.3390/antiox13060684] [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: 05/15/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Aging is often accompanied by irreversible decline in body function, which causes a large number of age-related diseases and brings a huge economic burden to society and families. Many traditional Chinese medicines have been known to extend lifespan, but it has still been a challenge to isolate a single active molecule from them and verify the mechanism of anti-aging action. Drugs that inhibit senescence-associated secretory phenotypes (SASPs) are called "senomorphics". In this study, arctigenin (ATG), a senomorphic, was screened from the Chinese medicine Fructus arctii using K6001 yeast replicative lifespan. Autophagy, oxidative stress, and telomerase activity are key mechanisms related to aging. We found that ATG may act through multiple mechanisms to become an effective anti-aging molecule. In exploring the effect of ATG on autophagy, it was clearly observed that ATG significantly enhanced autophagy in yeast. We further verified that ATG can enhance autophagy by targeting protein phosphatase 2A (PP2A), leading to an increased lifespan. Meanwhile, we evaluated the antioxidant capacity of ATG and found that ATG increased the activities of the antioxidant enzymes, thereby reducing reactive oxygen species (ROS) and malondialdehyde (MDA) levels to improve the survival of yeast under oxidative stress. In addition, ATG was able to increase telomerase activity by enhancing the expression of EST1, EST2, and EST3 genes in yeast. In conclusion, ATG exerts anti-aging effects through induction of autophagy, antioxidative stress, and enhancement of telomerase activity in yeast, which is recognized as a potential molecule with promising anti-aging effects, deserving in-depth research in the future.
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Affiliation(s)
- Siqi Chen
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu 610068, China;
| | - Yajing Li
- College of Pharmaceutical Sciences, Zhejiang University, Yu Hang Tang Road 866, Hangzhou 310058, China; (Y.L.); (E.W.)
| | - Enchan Wu
- College of Pharmaceutical Sciences, Zhejiang University, Yu Hang Tang Road 866, Hangzhou 310058, China; (Y.L.); (E.W.)
| | - Qing Li
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu 610068, China;
| | - Lan Xiang
- College of Pharmaceutical Sciences, Zhejiang University, Yu Hang Tang Road 866, Hangzhou 310058, China; (Y.L.); (E.W.)
| | - Jianhua Qi
- College of Pharmaceutical Sciences, Zhejiang University, Yu Hang Tang Road 866, Hangzhou 310058, China; (Y.L.); (E.W.)
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13
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Lin Y, Chen X, Lin L, Xu B, Zhu X, Lin X. Sesamolin serves as an MYH14 inhibitor to sensitize endometrial cancer to chemotherapy and endocrine therapy via suppressing MYH9/GSK3β/β-catenin signaling. Cell Mol Biol Lett 2024; 29:63. [PMID: 38698330 PMCID: PMC11067147 DOI: 10.1186/s11658-024-00583-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/24/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Endometrial cancer (EC) is one of the most common gynecological cancers. Herein, we aimed to define the role of specific myosin family members in EC because this protein family is involved in the progression of various cancers. METHODS Bioinformatics analyses were performed to reveal EC patients' prognosis-associated genes in patients with EC. Furthermore, colony formation, immunofluorescence, cell counting kit 8, wound healing, and transwell assays as well as coimmunoprecipitation, cycloheximide chase, luciferase reporter, and cellular thermal shift assays were performed to functionally and mechanistically analyze human EC samples, cell lines, and a mouse model, respectively. RESULTS Machine learning techniques identified MYH14, a member of the myosin family, as the prognosis-associated gene in patients with EC. Furthermore, bioinformatics analyses based on public databases showed that MYH14 was associated with EC chemoresistance. Moreover, immunohistochemistry validated MYH14 upregulation in EC cases compared with that in normal controls and confirmed that MYH14 was an independent and unfavorable prognostic indicator of EC. MYH14 impaired cell sensitivity to carboplatin, paclitaxel, and progesterone, and increased cell proliferation and metastasis in EC. The mechanistic study showed that MYH14 interacted with MYH9 and impaired GSK3β-mediated β-catenin ubiquitination and degradation, thus facilitating the Wnt/β-catenin signaling pathway and epithelial-mesenchymal transition. Sesamolin, a natural compound extracted from Sesamum indicum (L.), directly targeted MYH14 and attenuated EC progression. Additionally, the compound disrupted the interplay between MYH14 and MYH9 and repressed MYH9-regulated Wnt/β-catenin signaling. The in vivo study further verified sesamolin as a therapeutic drug without side effects. CONCLUSIONS Herein, we identified that EC prognosis-associated MYH14 was independently responsible for poor overall survival time of patients, and it augmented EC progression by activating Wnt/β-catenin signaling. Targeting MYH14 by sesamolin, a cytotoxicity-based approach, can be applied synergistically with chemotherapy and endocrine therapy to eventually mitigate EC development. This study emphasizes MYH14 as a potential target and sesamolin as a valuable natural drug for EC therapy.
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Affiliation(s)
- Yibin Lin
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, Fujian, China
| | - Xiao Chen
- Department of Intensive Care Unit, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, Fujian, China
- Department of Intensive Care Unit, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, Fujian, China
| | - Linping Lin
- Hunan Institute of Engineering, Xiangtan, 411100, Hunan, China
| | - Benhua Xu
- Department of Radiation Oncology, Fujian Medical University Union Hospital, Xinquan Road 29, Gulou District, Fuzhou, 350001, Fujian, China.
| | - Xiaofeng Zhu
- Department of Oral Maxillo-Facial Surgery, The First Affiliated Hospital, Fujian Medical University, No. 20 Chazhong Road, Taijing District, Fuzhou, 350005, Fujian, China.
- Department of Oral Maxillo-Facial Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
| | - Xian Lin
- Shenzhen Key Laboratory of Inflammatory and Immunology Diseases, No. 1120 Lianhua Road, Futian District, Shenzhen, 518036, Guangdong, China.
- Peking University Shenzhen Hospital, Shenzhen, 518036, Guangdong, China.
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14
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Chen Y, Jin T, Zhang M, Hong B, Jin B, Hu C, Wang J, Chen Y, Zhang L, Wang Y, Huang L. Flavokawain B inhibits NF-κB inflammatory signaling pathway activation in inflammatory bowel disease by targeting TLR2. Toxicol Appl Pharmacol 2024; 486:116922. [PMID: 38583725 DOI: 10.1016/j.taap.2024.116922] [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: 12/03/2023] [Revised: 03/11/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Inflammatory bowel disease (IBD) is characterized by recurrent inflammatory reactions in the intestinal mucosa, including ulcerative colitis (UC) and Crohn's disease (CD). The expression of Toll-like receptor 2 (TLR2) has been observed to increase during the progression of IBD. Flavokawain B (FKB), a natural chalcone with potent anti-inflammatory activity, exerts its effects through inhibition of the NF-κB pathway. In this study, we aimed to investigate the effects and mechanisms of FKB targeting TLR2 in IBD. C57BL/6 J mice were treated with 2.5% dextran sulfate sodium (DSS) for 7 days, with administration of FKB or TLR2 inhibitor C29 starting on day 2 to establish the model of IBD. In vitro, bone marrow-derived macrophages (BMDMs) were stimulated with the TLR2 agonist Pam3CSK4 to explore the therapeutic effect of FKB and its pharmacological mechanism. Compared with the model group, the FKB-treated group showed significant reductions in colitis-related injuries in the IBD mouse model, including weight gain, increased colon length and reduced inflammation. FKB decreased the formation of TLR2-MyD88 complex by targeting TLR2, leading to suppression of downstream NF-κB signaling pathway. Similar therapeutic effects were observed in the C29-treated group. Additionally, in vitro data suggested that FKB exerted its anti-inflammatory effect by targeting TLR2 and inhibiting Pam3CSK4-induced activation of the NF-κB pathway. The anti-inflammatory effects of FKB were demonstrated through drug affinity responsive target stability assay and cellular thermal shift assay, revealing its binding affinity to TLR2. By inhibiting the activation of the TLR2/NF-κB signaling pathway, FKB effectively prevented DSS-induced IBD and exhibited promising potential as a therapeutic candidate for IBD treatment.
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Affiliation(s)
- Yi Chen
- Joint Research Center on Medicine, the Affiliated Xiangshan Hospital of Wenzhou Medical University, Ningbo, Zhejiang, China; Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Tianyang Jin
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Mengpei Zhang
- Joint Research Center on Medicine, the Affiliated Xiangshan Hospital of Wenzhou Medical University, Ningbo, Zhejiang, China
| | - Bo Hong
- Joint Research Center on Medicine, the Affiliated Xiangshan Hospital of Wenzhou Medical University, Ningbo, Zhejiang, China
| | - Bo Jin
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China; School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Chenghong Hu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China; School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jiong Wang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yue Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lingxi Zhang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yi Wang
- Joint Research Center on Medicine, the Affiliated Xiangshan Hospital of Wenzhou Medical University, Ningbo, Zhejiang, China; School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China.
| | - Lijiang Huang
- Joint Research Center on Medicine, the Affiliated Xiangshan Hospital of Wenzhou Medical University, Ningbo, Zhejiang, China.
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15
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Qin Y, Liu Q, Wang S, Wang Q, Du Y, Yao J, Chen Y, Yang Q, Wu Y, Liu S, Zhao M, Wei G, Yang L. Santacruzamate A Alleviates Pain and Pain-Related Adverse Emotions through the Inhibition of Microglial Activation in the Anterior Cingulate Cortex. ACS Pharmacol Transl Sci 2024; 7:1002-1012. [PMID: 38633586 PMCID: PMC11019733 DOI: 10.1021/acsptsci.3c00282] [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: 10/14/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 04/19/2024]
Abstract
Chronic pain is a complex disease. It seriously affects patients' quality of life and imposes a significant economic burden on society. Santacruzamate A (SCA) is a natural product isolated from marine cyanobacteria in Panama. In this study, we first demonstrated that SCA could alleviate chronic inflammatory pain, pain-related anxiety, and depression emotions induced by complete Freund's adjuvant in mice while inhibiting microglial activation in the anterior cingulate cortex. Moreover, SCA treatment attenuated lipopolysaccharide (LPS)-induced inflammatory response by downregulating interleukin 1β and 6 (IL-1β and IL-6) and tumor necrosis factor-α (TNF-α) levels in BV2 cells. Furthermore, we found that SCA could bind to soluble epoxide hydrolase (sEH) through molecular docking technology, and the thermal stability of sEH was enhanced after binding of SCA to the sEH protein. Meanwhile, we identified that SCA could reduce the sEH enzyme activity and inhibit sEH protein overexpression in the LPS stimulation model. The results indicated that SCA could alleviate the development of inflammation by inhibiting the enzyme activity and expression of sEH to further reduce chronic inflammatory pain. Our study suggested that SCA could be a potential drug for treating chronic inflammatory pain.
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Affiliation(s)
- Yan Qin
- Precision
Pharmacy and Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710038, China
| | - Qingqing Liu
- Precision
Pharmacy and Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710038, China
| | - Saiying Wang
- Precision
Pharmacy and Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710038, China
| | - Qinhui Wang
- Precision
Pharmacy and Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710038, China
| | - Yaya Du
- Precision
Pharmacy and Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710038, China
| | - Jingyue Yao
- Precision
Pharmacy and Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710038, China
| | - Yue Chen
- Precision
Pharmacy and Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710038, China
| | - Qi Yang
- Precision
Pharmacy and Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710038, China
| | - Yumei Wu
- Department
of Pharmacology, School of Pharmacy, Air
Force Medical University, Xi’an 710072, China
| | - Shuibing Liu
- Department
of Pharmacology, School of Pharmacy, Air
Force Medical University, Xi’an 710072, China
| | - Minggao Zhao
- Precision
Pharmacy and Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710038, China
| | - Gaofei Wei
- Institute
of Medical Research, Northwestern Polytechnical
University, Xi’an 710072, China
| | - Le Yang
- Precision
Pharmacy and Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710038, China
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16
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Bai L, Deng Z, Xu M, Zhang Z, Guo G, Xue X, Wang S, Yang J, Xia Z. CETSA-MS-based target profiling of anti-aging natural compound quercetin. Eur J Med Chem 2024; 267:116203. [PMID: 38342014 DOI: 10.1016/j.ejmech.2024.116203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/16/2024] [Accepted: 01/31/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND Quercetin is widely distributed in nature and abundant in the human diet, which exhibits diverse biological activities and potential medical benefits. However, there remains a lack of comprehensive understanding about its cellular targets, impeding its in-depth mechanistic studies and clinical applications. PURPOSE This study aimed to profile protein targets of quercetin at the proteome level. METHODS A label-free CETSA-MS proteomics technique was employed for target enrichment and identification. The R package Inflect was used for melting curve fitting and target selection. D3Pocket and LiBiSco tools were used for binding pocket prediction and binding pocket analysis. Western blotting, molecular docking, site-directed mutagenesis and pull-down assays were used for target verification and validation. RESULTS We curated a library of direct binding targets of quercetin in cells. This library comprises 37 proteins that show increased thermal stability upon quercetin binding and 33 proteins that display decreased thermal stability. Through Western blotting, molecular docking, site-directed mutagenesis and pull-down assays, we validated CBR1 and GSK3A from the stabilized protein group and MAPK1 from the destabilized group as direct binding targets of quercetin. Moreover, we characterized the shared chemical properties of the binding pockets of quercetin with targets. CONCLUSION Our findings deepen our understanding of the proteins pivotal to the bioactivity of quercetin and lay the groundwork for further exploration into its mechanisms of action and potential clinical applications.
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Affiliation(s)
- Lin Bai
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhifen Deng
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Mengfei Xu
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhehao Zhang
- Department of Biochemistry, Faculty of Life Science, Faculty of Natural Science, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Guangyu Guo
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China; Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China; Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xinli Xue
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Shaochi Wang
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jinghua Yang
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zongping Xia
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China; Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China; Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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17
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Nie S, Chang L, Huang Y, Zhou H, Yang Q, Kong L, Li Y. β-carboline derivative Z86 attenuates colorectal cancer cell proliferation and migration by directly targeting PI3K. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:3. [PMID: 38169019 PMCID: PMC10761647 DOI: 10.1007/s13659-023-00422-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024]
Abstract
Phosphoinositide 3-kinase (PI3Ks) are lipid kinases widely involved in cell proliferation, metastasis and differentiation. Constitutive activation of the PI3K/Akt/mTOR signaling are well confirmed in colorectal cancers (CRCs). In this study, we identified isopropyl 9-ethyl-1-(naphthalen-1-yl)-9 H-pyrido[3,4-b] indole-3-carboxylate (Z86), as a novel PI3Kα inhibitor with the IC50 value of 4.28 µM. The binding of Z86 to PI3Kα was further confirmed with DARTS and CETSA assay. Immunofluorescence analysis and western blotting data demonstrated that Z86 effectively attenuated PI3K/AKT pathway. Z86 caused dramatic proliferation inhibition of CRCs through G0/G1 cycle arrest rather than apoptosis induction. Besides, the migration of CRCs was also relieved by Z86. The present study not only identified Z86 as a novel PI3Kα inhibitor with potent inhibitory efficiency on PI3K-mediated CRCs growth and migration, but also elucidated a reasonable molecular mechanism of Z86 in the Wnt signaling pathway inhibition.
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Affiliation(s)
- Shiyun Nie
- Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, People's Republic of China
| | - Lizhong Chang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, People's Republic of China
| | - Ying Huang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, People's Republic of China
| | - Heyang Zhou
- Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, People's Republic of China
| | - Qianqing Yang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, People's Republic of China
| | - Lingmei Kong
- Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, People's Republic of China.
| | - Yan Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, People's Republic of China.
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18
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Cao F, Chu C, Qin JJ, Guan X. Research progress on antitumor mechanisms and molecular targets of Inula sesquiterpene lactones. Chin Med 2023; 18:164. [PMID: 38111074 PMCID: PMC10726648 DOI: 10.1186/s13020-023-00870-1] [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: 09/23/2023] [Accepted: 12/04/2023] [Indexed: 12/20/2023] Open
Abstract
The pharmacological effects of natural product therapy have received sigificant attention, among which terpenoids such as sesquiterpene lactones stand out due to their biological activity and pharmacological potential as anti-tumor drugs. Inula sesquiterpene lactones are a kind of sesquiterpene lactones extracted from Inula species. They have many pharmacological activities such as anti-inflammation, anti-asthma, anti-tumor, neuroprotective and anti-allergic. In recent years, more and more studies have proved that they are important candidate drugs for the treatment of a variety of cancers because of its good anti-tumor activity. In this paper, the structure, structure-activity relationship, antitumor activities, mechanisms and targets of Inula sesquiterpene lactones reported in recent years were reviewed in order to provide clues for the development of novel anticancer drugs.
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Affiliation(s)
- Fei Cao
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China
| | - Chu Chu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Jiang-Jiang Qin
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, China.
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China.
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, Zhejiang, China.
| | - Xiaoqing Guan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China.
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, Zhejiang, China.
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19
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Sathe G, Sapkota GP. Proteomic approaches advancing targeted protein degradation. Trends Pharmacol Sci 2023; 44:786-801. [PMID: 37778939 DOI: 10.1016/j.tips.2023.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 10/03/2023]
Abstract
Targeted protein degradation (TPD) is an emerging modality for research and therapeutics. Most TPD approaches harness cellular ubiquitin-dependent proteolytic pathways. Proteolysis-targeting chimeras (PROTACs) and molecular glue (MG) degraders (MGDs) represent the most advanced TPD approaches, with some already used in clinical settings. Despite these advances, TPD still faces many challenges, pertaining to both the development of effective, selective, and tissue-penetrant degraders and understanding their mode of action. In this review, we focus on progress made in addressing these challenges. In particular, we discuss the utility and application of recent proteomic approaches as indispensable tools to enable insights into degrader development, including target engagement, degradation selectivity, efficacy, safety, and mode of action.
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Affiliation(s)
- Gajanan Sathe
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Gopal P Sapkota
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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