Hui Wang , Li Liu , Zhoudong Zhang , Chencheng Li , Kai Wang , Jingjing Gao , Qinghua Hu , Weipeng Wang , Huanqiu Li
{"title":"Insights of affinity-based probes for target identification in drug discovery","authors":"Hui Wang , Li Liu , Zhoudong Zhang , Chencheng Li , Kai Wang , Jingjing Gao , Qinghua Hu , Weipeng Wang , Huanqiu Li","doi":"10.1016/j.ejmech.2025.117711","DOIUrl":"10.1016/j.ejmech.2025.117711","url":null,"abstract":"<div><div>Identifying molecular targets of physiologically active organic compounds remains a major challenge in contemporary biomedical research and drug discovery. In recent years, the development of activity-based protein profiling (ABPP) techniques has proven to be superior to classical molecular target identification methods. ABPP can be classified into activity-based probes (AcBPs) and affinity-based probes (AfBPs). AfBPs bind to target proteins through reversible non-covalent interactions, thus minimizing the impact on the natural biological functions of the protein. The development of AfBPs has great potential for studying drug targets, optimizing drugs, and improving therapeutic efficacy. As a result, there has been a dramatic increase in research and development focused on affinity probes with the use of a wide range of AfBPs such as biotin probes, FITC probes, BRET probes, and radiolabeled probes. This tutorial describes the process of designing and synthesizing different types of AfBPs from biologically active compounds, and then utilizing the probes to identify the target proteins. It also provides insights for subsequent drug discovery and development.</div></div>","PeriodicalId":314,"journal":{"name":"European Journal of Medicinal Chemistry","volume":"293 ","pages":"Article 117711"},"PeriodicalIF":6.0,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143915794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xuehong Qiao , Menghan Cui , Zhiwei Yu , Ling Ma , Hailong Liu , Xingxing Yang , Yuan Chen , Dahong Li , Jinjing Che , Linxiang Zhao , Ruibin Su , Xuhong Ren , Shan Cen , Bin Lin , Xinhua He
{"title":"Thiol esters as chemical warheads of SARS-CoV-2 main protease (3CLpro) peptide-like inhibitors","authors":"Xuehong Qiao , Menghan Cui , Zhiwei Yu , Ling Ma , Hailong Liu , Xingxing Yang , Yuan Chen , Dahong Li , Jinjing Che , Linxiang Zhao , Ruibin Su , Xuhong Ren , Shan Cen , Bin Lin , Xinhua He","doi":"10.1016/j.ejmech.2025.117709","DOIUrl":"10.1016/j.ejmech.2025.117709","url":null,"abstract":"<div><div>Peptide-like 3CLpro covalent binding inhibitors are the most effective antiviral drugs for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Their covalent warheads were designed based on the addition reaction activity of the aldehyde (ketone) carbonyl or its derivative structures. These addition reactions between the warheads and the thiol of the 3CLpro are reversible, and the resulting hemimonothioacetals are chemically unstable. Herein, after DFT calculation, we designed thiol ester warheads using the principle of ester exchange reaction. Then, the warhead fluorescence probe binding experiment suggested these adducts of thiol ester warheads and 3CLpro protein are more stable than the hemimonothioacetals mentioned earlier. Therefore, new 3CLpro inhibitors were subsequently designed through a structure-based drug design method employing those thiol ester warheads. Those 3CLpro inhibitors demonstrated potent 3CLpro inhibitory activities and anti-coronavirus HCoV-OC43 activities. Among them, <strong>B16</strong> stands out as the most promising, demonstrating not only the strongest anti-coronavirus HCoV-OC43 activity but also being a moderate inhibitor of CYP3A4, suggesting that <strong>B16</strong> does not require co-administration with ritonavir in the treatment of SARS-CoV-2 infection. This work demonstrates the significant potential of thiol esters as novel chemical warheads in designing covalent binding inhibitors for 3CLpro and beyond.</div></div>","PeriodicalId":314,"journal":{"name":"European Journal of Medicinal Chemistry","volume":"293 ","pages":"Article 117709"},"PeriodicalIF":6.0,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143910325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Renjie Lin , Jiajia Han , Yun He , Lin Xie , Tianyu Gao , Yaoming Chen , Ye Zhong , Qiang Ding , Kui Cheng , Xingang Yao , Zhipeng Chen
{"title":"Design, synthesis and biological evaluation of dapsone derivatives with broad-spectrum antiviral activity","authors":"Renjie Lin , Jiajia Han , Yun He , Lin Xie , Tianyu Gao , Yaoming Chen , Ye Zhong , Qiang Ding , Kui Cheng , Xingang Yao , Zhipeng Chen","doi":"10.1016/j.ejmech.2025.117717","DOIUrl":"10.1016/j.ejmech.2025.117717","url":null,"abstract":"<div><div>Inhibition of STAT2 degradation has emerged as a promising strategy for flaviviruses. The NS5 protein of the ZIKV and DENV-2 inhibits the IFN-Ⅰ antiviral response by degrading STAT2, thereby evading the host's immune defense. Therefore, the development of novel agents capable of inhibiting STAT2 degradation <em>via</em> targeted modulation constitutes a pivotal therapeutic strategy for controlling viral infections. In this study, HEK293T<sup>STAT2−mCherry-Flag/rtTA−HA-NS5</sup> cells were used as reporter tools. Through screening the ZINC drug-like database, the lead compound <strong>ZINC000060514583</strong> was obtained and structurally modified to yield the optimized compounds <strong>SMU-1k</strong>, which significantly inhibited the degradation of STAT2. We verified its activity against ZIKV and DENV-2 through Western blotting, RT-qPCR, plaque formation assays, and immunofluorescence experiments. The results showed that <strong>SMU-1k</strong> significantly inhibited the expression of NS5 protein and restored the level of STAT2 to a certain extent. Additionally, the EC<sub>50</sub> values of <strong>SMU-1k</strong> against ZIKV and DENV-2 were 7.08 ± 0.06 μM and 3.96 ± 0.11 μM, respectively, which helped to alleviate the cytopathic effects caused by ZIKV and DENV-2 infection. Here, we have successfully characterized a novel small-molecule compound that selectively blocks STAT2 proteasomal degradation while exhibiting potent dual antiviral efficacy against both ZIKV and DENV-2, thereby revealing a promising lead candidate for developing broad-spectrum antiviral therapeutics.</div></div>","PeriodicalId":314,"journal":{"name":"European Journal of Medicinal Chemistry","volume":"293 ","pages":"Article 117717"},"PeriodicalIF":6.0,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143910326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiaofei Gao , Yu Cao , Hangyan Li , Faming Yu , Jianjun Xi , Jiankang Zhang , Rangxiao Zhuang , Yizhou Xu , Linhao Xu
{"title":"Mechanisms underlying altered ubiquitin-proteasome system activity during heart failure and pharmacological interventions","authors":"Xiaofei Gao , Yu Cao , Hangyan Li , Faming Yu , Jianjun Xi , Jiankang Zhang , Rangxiao Zhuang , Yizhou Xu , Linhao Xu","doi":"10.1016/j.ejmech.2025.117725","DOIUrl":"10.1016/j.ejmech.2025.117725","url":null,"abstract":"<div><div>Heart failure (HF) is a refractory disease with a global prevalence that is continuously increasing. The mechanisms underlying the pathogenesis of HF are multi-faceted, intricate, and not yet fully elucidated. Appropriate levels of protein turnover are essential for maintaining cardiac homeostasis and, accordingly, compromised protein degradation systems can significantly contribute to heart disease. The ubiquitin-proteasome system (UPS) modulates the structure and function of cardiac cells by facilitating the degradation of signaling and structural proteins. Research in the preceding decade has focused on elucidating the role of the UPS in the context of cardiovascular physiology and pathophysiology. A comprehensive understanding of the UPS status and the underlying mechanisms contributing to its potential dysregulation in HF is imperative for developing targeted therapeutic interventions. Previous research has identified several novel interventions involving components of the UPS and several have been adapted for HF therapy. In this review, we summarize the mechanisms underlying altered UPS activity in HF and provide an outline of UPS regulators that affect the progression of HF. Additionally, the potential for small molecules to intervene in UPS function in HF is discussed.</div></div>","PeriodicalId":314,"journal":{"name":"European Journal of Medicinal Chemistry","volume":"292 ","pages":"Article 117725"},"PeriodicalIF":6.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143905511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Progression and expansion of ALK inhibitors against NSCLC: A dual target approach","authors":"Shreya Kumari , Mymoona Akhter , Ghanshyam Das Gupta , Kalicharan Sharma","doi":"10.1016/j.ejmech.2025.117722","DOIUrl":"10.1016/j.ejmech.2025.117722","url":null,"abstract":"<div><div>ALK gene is a member of the tyrosine kinase receptor family found on chromosome 2 (2p23) that plays an important role in the progression of the non-small cell lung cancer (NSCLC). Since the ALK inhibitors such as Crizotinib, Ceritinib, Brigatinib, Alectinib and Lorlatinib, was endorsed for the treatment of advanced NSCLC linked to ALK gene rearrangement. But eventually, patients become resistant to the medication, which will result in treatment failure. However, treatment for NSCLC could be greatly advanced by the development of dual inhibitors that target ALK in addition to other oncogenic pathways like ROS1, c-MET, EGFR, etc. These strategies seek to improve therapy efficacy, address resistance mechanisms, and provide treatment alternatives for patients with intricate molecular profiles. The aim of this review is to summarize the introduction to ALK and the synergy between ALK and other anti-tumor targets, recent developments in the synthesis of various dual inhibitors of the ALK. We also thoroughly discussed their design concepts, structure–activity relationships (SARs), preclinical and clinical data as well as <em>in silico</em> studies to provide ideas for further development of novel ALK based dual inhibitors.</div></div>","PeriodicalId":314,"journal":{"name":"European Journal of Medicinal Chemistry","volume":"293 ","pages":"Article 117722"},"PeriodicalIF":6.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143905540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Design and synthetic approaches to thalidomide based small molecule degraders","authors":"Ajeet Kumar , Gulshan Kumar , Nidhi Kalia , Priya Ranjan Sahoo","doi":"10.1016/j.ejmech.2025.117700","DOIUrl":"10.1016/j.ejmech.2025.117700","url":null,"abstract":"<div><div>Thalidomide has been used as a repurposed drug for treating multiple myeloma since 1997. Several novel anticancer drugs containing thalidomide active moiety has been discovered since then. Many thalidomide drug candidates with tuned linker size have been instrumental in inhibiting histone deacetylase, kinase, transcription factors etc. and facilitate selective degradation of E3 ligase and other enzymes. Here we are focused on small molecule degraders that are being tailored with tweaking synthetic architectures around thalidomide chemical motif towards the development of promising drug candidates. Interesting biomedical applications of thalidomide-based degraders with recent developments including pharmacokinetic profiles, protein stability, activity studies, degradation assays, and antitumor response are elucidated.</div></div>","PeriodicalId":314,"journal":{"name":"European Journal of Medicinal Chemistry","volume":"293 ","pages":"Article 117700"},"PeriodicalIF":6.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143905539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cong Bian , Tianqi Wang , Meng Wu , Xin Li , Shuwen Zhao , Xiao Zheng , Yonghua Liu , Jinming Zhou , Xiaofang Chen , Laixing Hu
{"title":"Design, synthesis and activity evaluation of benzene sulfonamide derivatives as novel androgen receptor antagonist","authors":"Cong Bian , Tianqi Wang , Meng Wu , Xin Li , Shuwen Zhao , Xiao Zheng , Yonghua Liu , Jinming Zhou , Xiaofang Chen , Laixing Hu","doi":"10.1016/j.ejmech.2025.117712","DOIUrl":"10.1016/j.ejmech.2025.117712","url":null,"abstract":"<div><div>The androgen receptor (AR) is a critical therapeutic target for the endocrine treatment of prostate cancer (PCa). Current AR antagonists, which primarily target the hormone binding pocket (HBP) within the ligand-binding domain (LBD), are often limited by the emergence of resistance mutations, calling for novel strategies of AR inhibition. In this study, a series of substituted benzene sulfonamide derivatives were designed and synthesized based on IMB-A6, a lead compound previously identified by our group to target the activation function 2 (AF2) region of AR-LBD. These compounds were evaluated for AR inhibitory activity using a dual-luciferase reporter assay, with selected derivatives further assessed for their anti-proliferative effects against the LNCaP cell line. Notably, compounds <strong>8a</strong> and <strong>3l</strong> also exhibited significant inhibitory activity against the AR F876L mutant. Additionally, the pharmacokinetic (PK) profile of <strong>8a</strong> was evaluated in male Sprague-Dawley (SD) rats. <em>In vivo</em> studies using the LNCaP xenograft model revealed that oral administration of <strong>8a</strong> (30 mg/kg, BID) effectively suppressed tumor growth with tumor growth inhibition (TGI) rate of 48.20 %. Molecular docking studies of <strong>8a</strong> binding to the AF2 region were conducted. <strong>8a</strong> represents the first reported example of an orally effective AR inhibitor derived from AF2-targeting research, offering a promising therapeutic strategy to overcome resistance mutations in PCa treatment.</div></div>","PeriodicalId":314,"journal":{"name":"European Journal of Medicinal Chemistry","volume":"294 ","pages":"Article 117712"},"PeriodicalIF":6.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143905512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Discovery of Quinazoline Derivatives as RIPK3 Inhibitors That Switch Cell Death from Necroptosis to Apoptosis for Psoriasis Treatment","authors":"Ya-Ling Hong, Zheng-Xing Wu, Jia-Xing Jiang, Yi-Meng Sun, Jia-Hai Ma, Jia-Xin Ai, Yu Wang, Duo Ma, Jing Zhang, Chang-Qi Yang, Yi-Xiang Li, Chong Li, Qing-Ling Chen, Xin-Hua Liu, Xue-Song Liu, Jun-Ting Ma, Ming-Ming Liu, Jing-Bo Shi","doi":"10.1016/j.ejmech.2025.117716","DOIUrl":"https://doi.org/10.1016/j.ejmech.2025.117716","url":null,"abstract":"In this study, we employed a structure-based approach and step-by-step structural optimization to identify a series of quinazoline derivatives as potent receptor interacting protein kinase 3 (RIPK3) inhibitors. Among these, compound <strong>32</strong> emerged as the most effective inhibitor, with strong inhibition of RIPK3 (IC<sub>50</sub> = 27 nM) and necroptosis (EC<sub>50</sub> = 0.45 μM). Biological evaluation showed that compound <strong>32</strong> binds directly to RIPK3, inhibiting the phosphorylation of both RIPK3 and its downstream substrate, MLKL, thus suppressing necroptosis. Additionally, compound <strong>32</strong> induces Caspase-8/3-mediated apoptosis, resulting in moderate anti-proliferative effects. By converting inflammatory necroptosis to non-inflammatory apoptosis, compound <strong>32</strong> not only exerts anti-inflammatory effects but also reduces inflammatory hyperplasia. More importantly, compared to the known RIPK3 inhibitor HS-1371, compound <strong>32</strong> significantly lower toxicity in vivo in mice. In an IMQ-induced mouse model of psoriasis, compound <strong>32</strong> significantly alleviates skin inflammation, scaling, and hyperkeratosis, without inducing notable toxicity. This study highlights a promising therapeutic strategy for inflammatory proliferative diseases, such as psoriasis, by inhibiting RIPK3 and shifting the mode of cell death from necroptosis to apoptosis.","PeriodicalId":314,"journal":{"name":"European Journal of Medicinal Chemistry","volume":"118 1","pages":""},"PeriodicalIF":6.7,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143905510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiyue Yang , Linghui Wang , Peiyu Lin , Yueni Ning , Yusi Lin , Yingying Xie , Congke Zhao , Lingli Mu , Cangcang Xu
{"title":"Discovery of Artesunate (ARS) PROTACs as GPX4 protein degraders for the treatment of bladder cancer","authors":"Xiyue Yang , Linghui Wang , Peiyu Lin , Yueni Ning , Yusi Lin , Yingying Xie , Congke Zhao , Lingli Mu , Cangcang Xu","doi":"10.1016/j.ejmech.2025.117710","DOIUrl":"10.1016/j.ejmech.2025.117710","url":null,"abstract":"<div><div>Bladder cancer is the second most prevalent malignancy of the urinary system worldwide, with high incidence and mortality rates. However, existing drugs for bladder cancer treatment often cause numerous adverse reactions. Although artesunate (ARS) exhibits anti-bladder cancer activity, its scope is rather limited and the specific targets remain unclear. Therefore, in this study, the Proteolysis-Targeting Chimera (PROTAC) technology was used to design and synthesize novel ARS derivatives. The antitumor activities of these compounds were evaluated against three human bladder cancer cell lines (T24, RT4, and J82). Of these compounds, <strong>A7</strong> exhibited 12-fold stronger antiproliferative activity against bladder cancer cells than ARS. Molecular docking, surface plasmon resonance (SPR), cellular thermal shift assay (CETSA) and western blotting studies demonstrated that <strong>A7</strong> directly targeted and degraded glutathione peroxidase 4 (GPX4) protein through the ubiquitin-proteasome system. <strong>A7</strong> further induced bladder cancer cell ferroptosis. Furthermore, <strong>A7</strong> showed potent tumor suppressive activity in a xenograft T24 nude mouse model. In conclusion, our findings indicate that <strong>A7</strong> exerts notable antitumor effects against bladder cancer <em>in vitro</em> and <em>in vivo</em>. This study highlights the tremendous potential of the PROTAC technology in enhancing the efficacy of natural products and identifying therapeutic targets, demonstrating its broad application prospects in the development of natural products-based drugs.</div></div>","PeriodicalId":314,"journal":{"name":"European Journal of Medicinal Chemistry","volume":"293 ","pages":"Article 117710"},"PeriodicalIF":6.0,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143905735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Leer Yuan, Jianing Liao, Yiyang Qin, Lvtao Cai, Minkui Zhang, Jinbiao Liao, Dan Li, Tingjun Hou, Rong Sheng
{"title":"Corrigendum to “Discovery of novel tetrahydroquinoline derivatives as potent, selective, and orally Available AR antagonists” [Eur. J. Med. Chem. 291 (2025) 117566]","authors":"Leer Yuan, Jianing Liao, Yiyang Qin, Lvtao Cai, Minkui Zhang, Jinbiao Liao, Dan Li, Tingjun Hou, Rong Sheng","doi":"10.1016/j.ejmech.2025.117707","DOIUrl":"https://doi.org/10.1016/j.ejmech.2025.117707","url":null,"abstract":"This note aims to correct an error in Table 1, Table 2, Tables 3 and 5.<ul><li><span>1.</span><span>In the version of this article initially published, there were several errors in Table 1.</span></li></ul>","PeriodicalId":314,"journal":{"name":"European Journal of Medicinal Chemistry","volume":"5 1","pages":""},"PeriodicalIF":6.7,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143901145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}