Pub Date : 2025-10-28DOI: 10.1016/j.bmc.2025.118471
Pedro Augusto Lemos Santana, Rafael Christian de Matos, Ana Flávia Alvarenga Bitencourt, Vinícius Gonçalves Maltarollo, Marta Marques Gontijo de Aguiar, Renes Resende Machado, Renata Barbosa de Oliveira
The endocannabinoid system plays a critical role in regulating pathophysiological processes and represents a promising target for novel therapies aimed at neurodegenerative disorders. Anandamide (AEA) mediates its therapeutic effects, particularly in pain modulation; however, its clinical potential is constrained by rapid degradation via fatty acid amide hydrolase (FAAH). The keto-oxazolopyridine derivative OL-135 is a potent FAAH inhibitor (IC50 = 4.7 nM). In this study, molecular docking simulations using three distinct protocols were performed to evaluate the binding modes of 44 arylfuran analogs of OL-135 at the FAAH enzyme binding site. These analyses identified several promising candidates, including analogs 2 and 24, which were subsequently synthesized, characterized, and tested in experimental models of pain and inflammation in mice. Carrageenan-induced pain and paw edema were used to investigate the antinociceptive and anti-inflammatory activities. Also, hot plate test was employed to evaluate the antinociceptive activity. Compound 2 significantly reduced mechanical allodynia and acute paw edema induced by carrageenan. Compounds 2 and 24 (5, 25 and 100 mg/Kg, i.p.) reduced the nociceptive response in model of nociceptive pain (hot plate). The activity of compound 2 (100 mg/Kg) in the model of nociceptive pain was attenuated by previous administration of AM251 (4 and 8 mg/Kg, i.p.). Importantly, compound 2 demonstrated no adverse effects on key biochemical parameters indicative of cardiotoxicity, hepatotoxicity, or nephrotoxicity. These findings underscore the potential of arylfuran analogs as analgesic and anti-inflammatory agents, paving the way for further development of therapeutic molecules.
{"title":"Design of arylfurans as potential FAAH inhibitors: therapeutic potential in pain management","authors":"Pedro Augusto Lemos Santana, Rafael Christian de Matos, Ana Flávia Alvarenga Bitencourt, Vinícius Gonçalves Maltarollo, Marta Marques Gontijo de Aguiar, Renes Resende Machado, Renata Barbosa de Oliveira","doi":"10.1016/j.bmc.2025.118471","DOIUrl":"10.1016/j.bmc.2025.118471","url":null,"abstract":"<div><div>The endocannabinoid system plays a critical role in regulating pathophysiological processes and represents a promising target for novel therapies aimed at neurodegenerative disorders. Anandamide (AEA) mediates its therapeutic effects, particularly in pain modulation; however, its clinical potential is constrained by rapid degradation via fatty acid amide hydrolase (FAAH). The keto-oxazolopyridine derivative OL-135 is a potent FAAH inhibitor (IC<sub>50</sub> = 4.7 nM). In this study, molecular docking simulations using three distinct protocols were performed to evaluate the binding modes of 44 arylfuran analogs of OL-135 at the FAAH enzyme binding site. These analyses identified several promising candidates, including analogs <strong>2</strong> and <strong>24</strong>, which were subsequently synthesized, characterized, and tested in experimental models of pain and inflammation in mice. Carrageenan-induced pain and paw edema were used to investigate the antinociceptive and anti-inflammatory activities. Also, hot plate test was employed to evaluate the antinociceptive activity. Compound <strong>2</strong> significantly reduced mechanical allodynia and acute paw edema induced by carrageenan. Compounds <strong>2</strong> and <strong>24</strong> (5, 25 and 100 mg/Kg, i.p.) reduced the nociceptive response in model of nociceptive pain (hot plate). The activity of compound 2 (100 mg/Kg) in the model of nociceptive pain was attenuated by previous administration of AM251 (4 and 8 mg/Kg, i.p.). Importantly, compound <strong>2</strong> demonstrated no adverse effects on key biochemical parameters indicative of cardiotoxicity, hepatotoxicity, or nephrotoxicity. These findings underscore the potential of arylfuran analogs as analgesic and anti-inflammatory agents, paving the way for further development of therapeutic molecules.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"132 ","pages":"Article 118471"},"PeriodicalIF":3.0,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145413938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-27DOI: 10.1016/j.bmc.2025.118469
Rong Li , Wei-Feng Zhang , Hui Lei , Fan-Bo Meng , Wenyi Liu , Rui Xiong , Hang Zhang , Yanjun Wang , Yingying Jiang , Guo-Bo Li , Li-Jiao Wang , Lingling Yang , Hua-Li Wang
Glutaminyl cyclase isoforms (gQC and sQC) are zinc-dependent metalloenzymes that catalyze the formation of N-terminal pyroglutamate (pE) in peptides and proteins. In human malignancies, gQC drives tumor immune evasion by enhancing CD47 pyroglutamylation, thereby amplifying its “don't eat me” signaling through interactions with SIRPα on immune cells. This establishes QC (particularly gQC isoform) as a compelling therapeutic target for cancer immunotherapy. In this study, we describe the structure-guided design and SAR optimization of a novel series of benzimidazole-based QC inhibitors aimed at disrupting the CD47-SIRPα immune checkpoint in breast cancer. Among these, compound 30 was identified as a potent dual inhibitor of both gQC and sQC, exhibiting nanomolar inhibitory activity with IC50 values of 0.59 μM (gQC) and 0.83 μM (sQC). Molecular docking and 100 ns molecular dynamics simulations revealed that compound 30 with the catalytic zinc ion and forms multiple stabilizing hydrogen bonds within the QC active site, with simulations further confirming the stability of the binding mode. Biological evaluation demonstrated that compound 30 selectively disrupted the CD47-SIRPα interaction, significantly enhancing macrophage-mediated phagocytosis of tumor cells. These findings highlight compound 30 as a promising lead compound and validate QC catalytic inhibition as a potential therapeutic strategy to counteract immune evasion in breast cancer.
{"title":"Design, synthesis and biological evaluation of novel glutaminyl cyclase inhibitors targeting the CD47-SIRPα axis in breast cancer cells","authors":"Rong Li , Wei-Feng Zhang , Hui Lei , Fan-Bo Meng , Wenyi Liu , Rui Xiong , Hang Zhang , Yanjun Wang , Yingying Jiang , Guo-Bo Li , Li-Jiao Wang , Lingling Yang , Hua-Li Wang","doi":"10.1016/j.bmc.2025.118469","DOIUrl":"10.1016/j.bmc.2025.118469","url":null,"abstract":"<div><div>Glutaminyl cyclase isoforms (gQC and sQC) are zinc-dependent metalloenzymes that catalyze the formation of <em>N</em>-terminal pyroglutamate (pE) in peptides and proteins. In human malignancies, gQC drives tumor immune evasion by enhancing CD47 pyroglutamylation, thereby amplifying its “don't eat me” signaling through interactions with SIRPα on immune cells. This establishes QC (particularly gQC isoform) as a compelling therapeutic target for cancer immunotherapy. In this study, we describe the structure-guided design and SAR optimization of a novel series of benzimidazole-based QC inhibitors aimed at disrupting the CD47-SIRPα immune checkpoint in breast cancer. Among these, compound <strong>30</strong> was identified as a potent dual inhibitor of both gQC and sQC, exhibiting nanomolar inhibitory activity with IC<sub>50</sub> values of 0.59 μM (gQC) and 0.83 μM (sQC). Molecular docking and 100 ns molecular dynamics simulations revealed that compound <strong>30</strong> with the catalytic zinc ion and forms multiple stabilizing hydrogen bonds within the QC active site, with simulations further confirming the stability of the binding mode. Biological evaluation demonstrated that compound <strong>30</strong> selectively disrupted the CD47-SIRPα interaction, significantly enhancing macrophage-mediated phagocytosis of tumor cells. These findings highlight compound <strong>30</strong> as a promising lead compound and validate QC catalytic inhibition as a potential therapeutic strategy to counteract immune evasion in breast cancer.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"132 ","pages":"Article 118469"},"PeriodicalIF":3.0,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145413940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-26DOI: 10.1016/j.bmc.2025.118456
Mengmeng Yao , Yan Wu , Xinlan Hu , Chunyu Feng , Jie Xu , Zhuo Chen , Qianbin Li
Renal fibrosis, a progressive pathology in chronic kidney disease (CKD), is primarily driven by HIPK2 (homeodomain-interacting protein kinase 2)-mediated activation of the TGF-β/Smad3 and NF-κB signaling pathways, leading to excessive extracellular matrix deposition and inflammation. Current therapeutic strategies targeting HIPK2 show limited efficacy, highlighting the need for more effective inhibitors. We developed compound c4 through rational optimization of the lead compound CHR-6494. This derivative exhibits potent dual activities, with IC50 values of 0.68 ± 0.18 μM for HIPK2 inhibition and 0.15 ± 0.02 μM for anti-proliferative effects in NRK-49F cells. Molecular dynamics simulations confirmed the stable binding of the c4-HIPK2 complex. Functional assays in TGF-β-stimulated NRK-49F cells and TNF-α-stimulated HK-2 cells demonstrated that c4, even at low concentrations, significantly downregulated fibrosis markers (Collagen I, Fibronectin, α-SMA) and inflammatory mediators (p-P65, IL-6), while suppressing fibrotic responses (cell proliferation, migration). These findings establish c4 as a promising HIPK2 kinase inhibitor for developing effective anti-fibrotic therapies targeting HIPK2 in CKD.
{"title":"Design, synthesis, and in vitro anti-renal fibrotic effects of imidazopyridazine-based homeodomain-interacting protein kinase 2 inhibitors","authors":"Mengmeng Yao , Yan Wu , Xinlan Hu , Chunyu Feng , Jie Xu , Zhuo Chen , Qianbin Li","doi":"10.1016/j.bmc.2025.118456","DOIUrl":"10.1016/j.bmc.2025.118456","url":null,"abstract":"<div><div>Renal fibrosis, a progressive pathology in chronic kidney disease (CKD), is primarily driven by HIPK2 (homeodomain-interacting protein kinase 2)-mediated activation of the TGF-β/Smad3 and NF-κB signaling pathways, leading to excessive extracellular matrix deposition and inflammation. Current therapeutic strategies targeting HIPK2 show limited efficacy, highlighting the need for more effective inhibitors. We developed compound <strong>c4</strong> through rational optimization of the lead compound CHR-6494. This derivative exhibits potent dual activities, with IC<sub>50</sub> values of 0.68 ± 0.18 μM for HIPK2 inhibition and 0.15 ± 0.02 μM for anti-proliferative effects in NRK-49F cells. Molecular dynamics simulations confirmed the stable binding of the <strong>c4</strong>-HIPK2 complex. Functional assays in TGF-β-stimulated NRK-49F cells and TNF-α-stimulated HK-2 cells demonstrated that <strong>c4</strong>, even at low concentrations, significantly downregulated fibrosis markers (Collagen I, Fibronectin, α-SMA) and inflammatory mediators (p-P65, IL-6), while suppressing fibrotic responses (cell proliferation, migration). These findings establish <strong>c4</strong> as a promising HIPK2 kinase inhibitor for developing effective anti-fibrotic therapies targeting HIPK2 in CKD.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"132 ","pages":"Article 118456"},"PeriodicalIF":3.0,"publicationDate":"2025-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145413939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-25DOI: 10.1016/j.bmc.2025.118451
Ali M. Alaseem , Summya Rashid , J. Puneetha , M. Arockia Babu , Glowi Alasiri , Thakur Gurjeet Singh , Yogita Tyagi , Mohammad Suhail Akhter , Anand Mohan Singh , Nisha Bansal
c-Src is the non-receptor kinase commonly overexpressed in numerous cancer isoforms. As potential anticancer target, these receptors are difficult to target with drugs because of their continuous shuttling between cellular and nuclear compartments and role in relaying of vital signals for gene expression, cell growth, and survival. Besides this high structural homology to other kinases, the involvement of compensatory pathways and the availability of multiple domains within the same proteins further complicate the targeting by drugs. The toxicity and resistance issue with the handful of c-Src inhibitors available, which are again non-selective in approach, further complicate this process. Considering the gap, we employed a drug identification strategy for a plausible c-Src inhibition and its anticancer potential. We selected 500,000 small molecules from the ChemBridge commercial library (database) for the virtual screening. These molecules were filtered via the development of a pharmacophore model, in silico pharmacokinetics (ADME) analysis, and high-throughput virtual screening (HTVS). The top-ranked molecules based on the docking scores, which represent computational binding affinity between a protein and a ligand, were selected and eventually led to 29 best docked molecules. The visual inspection further resulted in refinement of 4 molecules (5280699, 9797370, 11200016, and 71736582), demonstrating protein–ligand interactions the most at the c-Src kinase binding site. To validate their optimal binding, we carried out 200 ns MD simulations on these four selected proteins–ligand complexes. MD analysis revealed that the inhibitors 11200016 and 71736582 were found to be exceptionally stable at the c-Src kinase binding site, meeting the essential prerequisite. The top hit, 71736582, was further corroborated biologically. 71736582 portrayed excellent anticancer potential towards various cancer cell lines (A549, MDAMB-231, HCT-116, DU-145, and PC-3). It was found to inhibit the c-Src-mediated kinase activity (IC50: 517 nM) in comparison to the positive control, bosutinib (IC50: 408 nM). The compound was also able to increase the oxidative stress and induce apoptosis in the colorectal cancer cells employed. The study thus may pave the way for exploration of the top identified ligands further to develop and establish their potential as c-Src kinase inhibitors with anticancer potential.
{"title":"Pharmacophore-based high-throughput virtual screening (HTVS) to identify new c-Src kinase inhibitors with anticancer potential","authors":"Ali M. Alaseem , Summya Rashid , J. Puneetha , M. Arockia Babu , Glowi Alasiri , Thakur Gurjeet Singh , Yogita Tyagi , Mohammad Suhail Akhter , Anand Mohan Singh , Nisha Bansal","doi":"10.1016/j.bmc.2025.118451","DOIUrl":"10.1016/j.bmc.2025.118451","url":null,"abstract":"<div><div>c-Src is the non-receptor kinase commonly overexpressed in numerous cancer isoforms. As potential anticancer target, these receptors are difficult to target with drugs because of their continuous shuttling between cellular and nuclear compartments and role in relaying of vital signals for gene expression, cell growth, and survival. Besides this high structural homology to other kinases, the involvement of compensatory pathways and the availability of multiple domains within the same proteins further complicate the targeting by drugs. The toxicity and resistance issue with the handful of c-Src inhibitors available, which are again non-selective in approach, further complicate this process. Considering the gap, we employed a drug identification strategy for a plausible c-Src inhibition and its anticancer potential. We selected 500,000 small molecules from the ChemBridge commercial library (database) for the virtual screening. These molecules were filtered via the development of a pharmacophore model, in silico pharmacokinetics (ADME) analysis, and high-throughput virtual screening (HTVS). The top-ranked molecules based on the docking scores, which represent computational binding affinity between a protein and a ligand, were selected and eventually led to 29 best docked molecules. The visual inspection further resulted in refinement of 4 molecules (5280699, 9797370, 11200016, and 71736582), demonstrating protein–ligand interactions the most at the c-Src kinase binding site. To validate their optimal binding, we carried out 200 ns MD simulations on these four selected proteins–ligand complexes. MD analysis revealed that the inhibitors 11200016 and 71736582 were found to be exceptionally stable at the c-Src kinase binding site, meeting the essential prerequisite. The top hit, 71736582, was further corroborated biologically. 71736582 portrayed excellent anticancer potential towards various cancer cell lines (A549, MDAMB-231, HCT-116, DU-145, and PC-3). It was found to inhibit the c-Src-mediated kinase activity (IC<sub>50</sub>: 517 nM) in comparison to the positive control, bosutinib (IC<sub>50</sub>: 408 nM). The compound was also able to increase the oxidative stress and induce apoptosis in the colorectal cancer cells employed. The study thus may pave the way for exploration of the top identified ligands further to develop and establish their potential as c-Src kinase inhibitors with anticancer potential.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"132 ","pages":"Article 118451"},"PeriodicalIF":3.0,"publicationDate":"2025-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145399252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The escalating threat of multidrug-resistant (MDR) pathogens necessitates the development of antibacterial agents with novel mechanisms of action. In this study, indole-chalcones and their 4,5-dihydroisoxazole derivatives were synthesized and characterized using various analytical and spectral techniques. Single-crystal X-ray diffraction (SC-XRD) confirmed the structural integrity of the optimized compounds. Antibacterial screening against MDR-ESKAPE pathogens identified two compounds, 24 (E-3-(1-cyclopentyl-1H-indol-3-yl)-1-(2,4-dichlorophenyl)prop-2-en-1-one) and 27 (E-3-(1-cyclopentyl-1H-indol-3-yl)-1-(4-hydroxyphenyl)prop-2-en-1-one) as the most potent candidates. Notably, compound 24 exhibited the lowest minimum inhibitory concentration (MIC) of 19.53 μg/mL against both bacterial strains, demonstrating strong activity against Gram-positive (Staphylococcus aureus) and Gram-negative (Pseudomonas aeruginosa) pathogens. To elucidate the mechanistic basis of their antibacterial action, flow cytometry was conducted, revealing that compound 24 induced extensive membrane damage, resulting in over 89.8 % bacterial cell death, thereby demonstrating its potent bactericidal properties. Molecular docking analyses of compound 24 and 27 against S. aureus and P. aeruginosa DNA gyrase B revealed strong, stable interactions in comparison to Novobiocin taken as positive control, suggesting DNA gyrase inhibition. Additionally, molecular dynamics simulations supported the stability of these protein-ligand complexes, with RMSD values below 2.0 Å and consistent hydrogen-bonding patterns throughout the simulation. These in-silico predictions were experimentally validated through an in-vitro DNA supercoiling assay, which confirmed the significant suppression of gyrase activity. The combination of extensive membrane disruption and confirmed DNA gyrase inhibition establishes a dual mechanism of action for these derivatives, particularly for compound 24, which is crucial for overcoming conventional resistance pathways. Hemolytic assays indicated no cytotoxicity, positioning indole-chalcone derivatives as promising broad-spectrum antibacterial agents.
{"title":"Expanding antimicrobial chemotypes: indole-based DNA gyrase inhibitors with potential dual mechanism against multidrug-resistant bacteria","authors":"Vidyasagar , Ritu Raj Patel , Pandey Priya Arun , Aradhana Mishra , Anshuman Chandra , Harish Shukla , Sudhir Kumar Singh , Meenakshi Singh","doi":"10.1016/j.bmc.2025.118455","DOIUrl":"10.1016/j.bmc.2025.118455","url":null,"abstract":"<div><div>The escalating threat of multidrug-resistant (MDR) pathogens necessitates the development of antibacterial agents with novel mechanisms of action. In this study, indole-chalcones and their 4,5-dihydroisoxazole derivatives were synthesized and characterized using various analytical and spectral techniques. Single-crystal X-ray diffraction (SC-XRD) confirmed the structural integrity of the optimized compounds. Antibacterial screening against MDR-ESKAPE pathogens identified two compounds, <strong>24</strong> (E-3-(1-cyclopentyl-1<em>H</em>-indol-3-yl)-1-(2,4-dichlorophenyl)prop-2-en-1-one) and <strong>27</strong> (E-3-(1-cyclopentyl-1<em>H</em>-indol-3-yl)-1-(4-hydroxyphenyl)prop-2-en-1-one) as the most potent candidates. Notably, compound <strong>24</strong> exhibited the lowest minimum inhibitory concentration (MIC) of 19.53 μg/mL against both bacterial strains, demonstrating strong activity against Gram-positive (<em>Staphylococcus aureus</em>) and Gram-negative (<em>Pseudomonas aeruginosa</em>) pathogens. To elucidate the mechanistic basis of their antibacterial action, flow cytometry was conducted, revealing that compound <strong>24</strong> induced extensive membrane damage, resulting in over 89.8 % bacterial cell death, thereby demonstrating its potent bactericidal properties. Molecular docking analyses of compound <strong>24</strong> and <strong>27</strong> against <em>S. aureus</em> and <em>P. aeruginosa</em> DNA gyrase B revealed strong, stable interactions in comparison to Novobiocin taken as positive control, suggesting DNA gyrase inhibition. Additionally, molecular dynamics simulations supported the stability of these protein-ligand complexes, with RMSD values below 2.0 Å and consistent hydrogen-bonding patterns throughout the simulation. These in-silico predictions were experimentally validated through an <em>in-vitro</em> DNA supercoiling assay, which confirmed the significant suppression of gyrase activity. The combination of extensive membrane disruption and confirmed DNA gyrase inhibition establishes a dual mechanism of action for these derivatives, particularly for compound <strong>24</strong>, which is crucial for overcoming conventional resistance pathways. Hemolytic assays indicated no cytotoxicity, positioning indole-chalcone derivatives as promising broad-spectrum antibacterial agents.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"132 ","pages":"Article 118455"},"PeriodicalIF":3.0,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145399242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-21DOI: 10.1016/j.bmc.2025.118452
Dan Wu , Yu Cao , Yubing Han , Linhao Xu , Han Han , Yaoli Shi , Jiayi Ma , Qingyi Wang , Lixin Gao , Mingzhi Wang , Jianjun Xi , Jingjing Sun , Huajian Zhu , Jiaan Shao , Bin Ju , Yizhou Xu , Yubo Zhou , Jiankang Zhang
Under hypoxic stress, cardiomyocytes predominantly depend on 20S proteasome-mediated degradation to clear accumulated and misfolded proteins. The resultant proteotoxic stress from impaired protein homeostasis contributes significantly to the pathogenesis of cardiovascular disorders. Pharmacological enhancement of 20S proteasome activity thus represents a novel therapeutic paradigm for ischemic cardiomyopathy by restoring proteostasis in myocardial cells. In this study, the hit compound X-1 was identified through screening of proteasome activation profile. Subsequent structure-activity relationship optimization yielded a series of highly potent activators. Intracellular protein degradation assessment revealed that these compounds possessed abilities to alleviate endoplasmic reticulum stress, as demonstrated by the luciferase reporter system. Additionally, selected compound B3 exhibited superior cytoprotection, increasing viability of hypoxia-injured cardiomyocytes while downregulating ER stress markers CHOP and Grp78 at the protein level. AlphaFold3-predicted binding modes and 100 ns molecular dynamics simulations revealing its stabilization of the α region to induce proteasome gate opening, thereby establishing a structure-function rationale for its 20S activation mechanism.
{"title":"Discovery of novel 20S proteasome activators for hypoxic cardiomyocyte protection via endoplasmic reticulum stress alleviation","authors":"Dan Wu , Yu Cao , Yubing Han , Linhao Xu , Han Han , Yaoli Shi , Jiayi Ma , Qingyi Wang , Lixin Gao , Mingzhi Wang , Jianjun Xi , Jingjing Sun , Huajian Zhu , Jiaan Shao , Bin Ju , Yizhou Xu , Yubo Zhou , Jiankang Zhang","doi":"10.1016/j.bmc.2025.118452","DOIUrl":"10.1016/j.bmc.2025.118452","url":null,"abstract":"<div><div>Under hypoxic stress, cardiomyocytes predominantly depend on 20S proteasome-mediated degradation to clear accumulated and misfolded proteins. The resultant proteotoxic stress from impaired protein homeostasis contributes significantly to the pathogenesis of cardiovascular disorders. Pharmacological enhancement of 20S proteasome activity thus represents a novel therapeutic paradigm for ischemic cardiomyopathy by restoring proteostasis in myocardial cells. In this study, the hit compound <strong>X-1</strong> was identified through screening of proteasome activation profile. Subsequent structure-activity relationship optimization yielded a series of highly potent activators. Intracellular protein degradation assessment revealed that these compounds possessed abilities to alleviate endoplasmic reticulum stress, as demonstrated by the luciferase reporter system. Additionally, selected compound <strong>B3</strong> exhibited superior cytoprotection, increasing viability of hypoxia-injured cardiomyocytes while downregulating ER stress markers CHOP and Grp78 at the protein level. AlphaFold3-predicted binding modes and 100 ns molecular dynamics simulations revealing its stabilization of the <em>α</em> region to induce proteasome gate opening, thereby establishing a structure-function rationale for its 20S activation mechanism.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"132 ","pages":"Article 118452"},"PeriodicalIF":3.0,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145407808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The Kelch-like ECH-associated protein 1 (Keap1)–nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway is a central regulator of cellular defense mechanisms against oxidative stress. The pharmacological activation of this pathway has emerged as a promising strategy for the treatment of diseases such as neurodegeneration and inflammation. In this study, we performed a high-throughput luciferase reporter assay to screen the original compound library comprising small molecules synthesized at Kobe Pharmaceutical University. Initial screening identified KU-0016, KU-0017, and KU-0171 as moderate activators of the Nrf2 pathway. Furthermore, structural comparison revealed a common α,β-unsaturated imide motif, which led to the synthesis of KU-0017-based analogs for structure–activity relationship analysis. Among them, KU-0479 exhibited potent Nrf2 activation and low cytotoxicity. Further assays demonstrated that KU-0479 increased the intracellular glutathione (GSH) levels and protected cells from hydrogen peroxide–induced oxidative damage in a GSH-dependent manner. Moreover, LC–MS analysis confirmed the formation of mono-GSH adducts, and covalent docking simulations suggested covalent binding at the Cys151 residue of Keap1. These findings highlight KU-0479 as a synthetically accessible covalent Nrf2 activator with favorable redox-modulating properties and therapeutic potential.
{"title":"Screening and identification of covalent Nrf2 activators with α,β-unsaturated imide structures","authors":"Yasuhiko Izumi , Norihiko Takeda , Shuzo Nishimoto , Honoka Niimi , Sayuri Ishizu , Natsumi Muneyasu , Yuto Takamatsu , Emi Mishiro-Sato , Keiko Kano , Kouya Yamaki , Takahiro Yamada , Yutaka Koyama , Masafumi Ueda","doi":"10.1016/j.bmc.2025.118454","DOIUrl":"10.1016/j.bmc.2025.118454","url":null,"abstract":"<div><div>The Kelch-like ECH-associated protein 1 (Keap1)–nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway is a central regulator of cellular defense mechanisms against oxidative stress. The pharmacological activation of this pathway has emerged as a promising strategy for the treatment of diseases such as neurodegeneration and inflammation. In this study, we performed a high-throughput luciferase reporter assay to screen the original compound library comprising small molecules synthesized at Kobe Pharmaceutical University. Initial screening identified KU-0016, KU-0017, and KU-0171 as moderate activators of the Nrf2 pathway. Furthermore, structural comparison revealed a common α,β-unsaturated imide motif, which led to the synthesis of KU-0017-based analogs for structure–activity relationship analysis. Among them, KU-0479 exhibited potent Nrf2 activation and low cytotoxicity. Further assays demonstrated that KU-0479 increased the intracellular glutathione (GSH) levels and protected cells from hydrogen peroxide–induced oxidative damage in a GSH-dependent manner. Moreover, LC–MS analysis confirmed the formation of mono-GSH adducts, and covalent docking simulations suggested covalent binding at the Cys151 residue of Keap1. These findings highlight KU-0479 as a synthetically accessible covalent Nrf2 activator with favorable redox-modulating properties and therapeutic potential.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"132 ","pages":"Article 118454"},"PeriodicalIF":3.0,"publicationDate":"2025-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145353155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-19DOI: 10.1016/j.bmc.2025.118453
Debora Pratesi , Francesca Clemente , Camilla Matassini , Silvia Falliano , Amelia Morrone , Rebecca Sodano , Paolo Paoli , Andrea Goti , José G. Fernández-Bolanos , Óscar López , Francesca Cardona
The design and synthesis of a novel class of selenoureido-iminosugar compounds that uniquely combine antioxidant properties with pharmacological chaperone activity are reported. These derivatives feature a 3,4,5-trihydroxypiperidine iminosugar core linked via nine- or twelve‑carbon alkyl chains to N-aryl selenoureido groups. By simultaneously targeting oxidative stress and lysosomal β-glucocerebrosidase (GCase) dysfunction, this dual-action strategy addresses two key pathological hallmarks of Gaucher disease. These compounds were evaluated for the first time on human GCase and on fibroblasts derived from Gaucher patients carrying clinically relevant GBA1 variants. Notably, one of the newly synthesized compounds significantly restored GCase activity in patient-derived cells and induced a ∼60% reduction in intracellular ROS levels, further supporting its bifunctional therapeutic potential. This study introduces an innovative dual-action molecular scaffold for addressing key pathological mechanisms in Gaucher disease and related neurodegenerative conditions.
{"title":"Selenoureido-N-alkyl-3,4,5-trihydroxypiperidines: probing their dual-target role in Gaucher disease","authors":"Debora Pratesi , Francesca Clemente , Camilla Matassini , Silvia Falliano , Amelia Morrone , Rebecca Sodano , Paolo Paoli , Andrea Goti , José G. Fernández-Bolanos , Óscar López , Francesca Cardona","doi":"10.1016/j.bmc.2025.118453","DOIUrl":"10.1016/j.bmc.2025.118453","url":null,"abstract":"<div><div>The design and synthesis of a novel class of selenoureido-iminosugar compounds that uniquely combine antioxidant properties with pharmacological chaperone activity are reported. These derivatives feature a 3,4,5-trihydroxypiperidine iminosugar core linked <em>via</em> nine- or twelve‑carbon alkyl chains to <em>N</em>-aryl selenoureido groups. By simultaneously targeting oxidative stress and lysosomal β-glucocerebrosidase (GCase) dysfunction, this dual-action strategy addresses two key pathological hallmarks of Gaucher disease. These compounds were evaluated for the first time on human GCase and on fibroblasts derived from Gaucher patients carrying clinically relevant <em>GBA1</em> variants. Notably, one of the newly synthesized compounds significantly restored GCase activity in patient-derived cells and induced a ∼60% reduction in intracellular ROS levels, further supporting its bifunctional therapeutic potential. This study introduces an innovative dual-action molecular scaffold for addressing key pathological mechanisms in Gaucher disease and related neurodegenerative conditions.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"132 ","pages":"Article 118453"},"PeriodicalIF":3.0,"publicationDate":"2025-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145385652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-17DOI: 10.1016/j.bmc.2025.118448
Tao Chen , Longying Cai , Xiaofei Dong , Lifang Zhang , Xuemin Cheng , Jingsong Qu , Guanyu Yang , Sen Gao , Linfu Luo , Huiyong Ma , Shuai Xia , Guansai Liu , Jin Li , Jianyou Shi , Dengfeng Dou
To better understand how pre-installed covalent warheads affect the ligand discovery in DNA encoded library (DEL), we have designed three individual covalent DELs incorporating 7, 32 and 64 cysteine-targeting covalent warheads respectively, and screened these DELs against JAK3 purified protein. The experiments resulted 6 novel series of covalent inhibitors with drug-like properties, where the most potent compounds achieved picomolor IC50 and good selectivity against a mini panel of kinases. The mass spec study confirmed their covalent MOAs by targeting JAK3 Cys909. More importantly, we confirmed the synergistic effect of the binding moiety and warhead by comparing the activities with their close analogs, suggesting that these compounds may not able to be designed by installation of covalent warheads to reversible binders. Further analysis revealed that 7 warheads were sufficient for identifying JAK3 covalent ligands. This work deepens our understanding of the design and screening of covalent DEL, and also demonstrate the power of DEL in the identification of diverse inhibitors.
{"title":"Deep seeking covalent DNA encoded library for novel JAK3 inhibitor discovery","authors":"Tao Chen , Longying Cai , Xiaofei Dong , Lifang Zhang , Xuemin Cheng , Jingsong Qu , Guanyu Yang , Sen Gao , Linfu Luo , Huiyong Ma , Shuai Xia , Guansai Liu , Jin Li , Jianyou Shi , Dengfeng Dou","doi":"10.1016/j.bmc.2025.118448","DOIUrl":"10.1016/j.bmc.2025.118448","url":null,"abstract":"<div><div>To better understand how pre-installed covalent warheads affect the ligand discovery in DNA encoded library (DEL), we have designed three individual covalent DELs incorporating 7, 32 and 64 cysteine-targeting covalent warheads respectively, and screened these DELs against JAK3 purified protein. The experiments resulted 6 novel series of covalent inhibitors with drug-like properties, where the most potent compounds achieved picomolor IC<sub>50</sub> and good selectivity against a mini panel of kinases. The mass spec study confirmed their covalent MOAs by targeting JAK3 Cys909. More importantly, we confirmed the synergistic effect of the binding moiety and warhead by comparing the activities with their close analogs, suggesting that these compounds may not able to be designed by installation of covalent warheads to reversible binders. Further analysis revealed that 7 warheads were sufficient for identifying JAK3 covalent ligands. This work deepens our understanding of the design and screening of covalent DEL, and also demonstrate the power of DEL in the identification of diverse inhibitors.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"132 ","pages":"Article 118448"},"PeriodicalIF":3.0,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145375484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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