DNA methyltransferase 1 (DNMT1) overexpression is associated with aberrant methylation and tumorigenesis, making its detection vital for tumor diagnosis. In this study, RG108 derivatives bearing cysteine-targeted covalent moieties were constructed as warheads for the DNMT1 detectors. Following affinity assessment by surface plasmon resonance, warheads containing a 2-fluoroacrylamido moiety were selected for preparing fluorescein-labeled probes 20a and 20b. In-gel fluorescence scanning and competitive assays confirmed that the probes can covalently bind to DNMT1 at the S-adenosyl-l-homocysteine site. Probe 20b showed concentration- and time-dependent fluorescence in HeLa cells and demonstrated detection performance comparable to DNMT1 antibody with superior nuclear membrane permeability across diverse cell lines. Notably, the relative fluorescence unit ratios of probe 20b to 4′,6-diamidino-2′-phenylindole in clinical cervical exfoliated cells showed significant differences among normal cells, low-grade squamous intraepithelial lesion cells, high-grade squamous intraepithelial lesion cells, and cancer cells, indicating its great potential as a tumor diagnostic agent.
{"title":"Development of Covalent Small-Molecule Fluorescent Probes for DNA Methyltransferase 1 Detection in Cancer Cells and Cervical Exfoliated Cells","authors":"Peijia Jin, Qunxian Cheng, Xiaoqian Hong, Qingmiao Jia, Jingyi Liu, Ling Xu, Qian Zhang","doi":"10.1021/acs.jmedchem.5c03529","DOIUrl":"https://doi.org/10.1021/acs.jmedchem.5c03529","url":null,"abstract":"DNA methyltransferase 1 (DNMT1) overexpression is associated with aberrant methylation and tumorigenesis, making its detection vital for tumor diagnosis. In this study, RG108 derivatives bearing cysteine-targeted covalent moieties were constructed as warheads for the DNMT1 detectors. Following affinity assessment by surface plasmon resonance, warheads containing a 2-fluoroacrylamido moiety were selected for preparing fluorescein-labeled probes <b>20a</b> and <b>20b</b>. In-gel fluorescence scanning and competitive assays confirmed that the probes can covalently bind to DNMT1 at the <i>S</i>-adenosyl-<span>l</span>-homocysteine site. Probe <b>20b</b> showed concentration- and time-dependent fluorescence in HeLa cells and demonstrated detection performance comparable to DNMT1 antibody with superior nuclear membrane permeability across diverse cell lines. Notably, the relative fluorescence unit ratios of probe <b>20b</b> to 4′,6-diamidino-2′-phenylindole in clinical cervical exfoliated cells showed significant differences among normal cells, low-grade squamous intraepithelial lesion cells, high-grade squamous intraepithelial lesion cells, and cancer cells, indicating its great potential as a tumor diagnostic agent.","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":"17 1","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147478743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-17DOI: 10.1021/acs.jmedchem.6c00224
Chaofan Xu, Neeta Abraham, Nupur Bansal, Philippe N. Bolduc, Patrick Cullen, Thomas M. Carlile, Yirui Chen, Colin K. Choi, Rachelle Driscoll, Eric Stefan, Christina M. Gallo, Zhen Gao, Catherine L. Guardado, Guilherme Guimaraes, James Harvey, Sarah Huff, Dann Huh, Jessica Hurt, Melissa M. Kemp, Kwang Soo Lee, Joon Lee, Mukesh Lulla, Soumya Negi, Marta Nevalainen, Emily A. Peterson, Thomas J. Purgett, Joseph C. Santoro, Daniel R. Smith, Andreas Weihofen, Zain Yousaf, Magnus Pfaffenbach
Huntington’s disease (HD) is a progressive neurodegenerative disorder caused by a CAG-repeat expansion in the Huntington gene (HTT). Herein, we describe the discovery of a series of HTT pre-mRNA-splicing modulators that promote the inclusion of a cryptic stop codon that in turn lowers levels of mutant Huntington protein (mHTT). Optimization of the starting thienopyridine amide core resulted in the discovery of the potent, CNS-penetrant, selective, and orally bioavailable HTT-splicing modulator BIO-6553. This lead compound is structurally distinct from existing splicing modulators, demonstrated significant HTT-lowering in both human cells and mouse YAC128 models, and has an attractive off-target profile from RASL- and RNA-seq analysis.
{"title":"Discovery and Optimization of Thienopyrazine RNA-Splicing Modulators for the Treatment of Huntington’s Disease","authors":"Chaofan Xu, Neeta Abraham, Nupur Bansal, Philippe N. Bolduc, Patrick Cullen, Thomas M. Carlile, Yirui Chen, Colin K. Choi, Rachelle Driscoll, Eric Stefan, Christina M. Gallo, Zhen Gao, Catherine L. Guardado, Guilherme Guimaraes, James Harvey, Sarah Huff, Dann Huh, Jessica Hurt, Melissa M. Kemp, Kwang Soo Lee, Joon Lee, Mukesh Lulla, Soumya Negi, Marta Nevalainen, Emily A. Peterson, Thomas J. Purgett, Joseph C. Santoro, Daniel R. Smith, Andreas Weihofen, Zain Yousaf, Magnus Pfaffenbach","doi":"10.1021/acs.jmedchem.6c00224","DOIUrl":"https://doi.org/10.1021/acs.jmedchem.6c00224","url":null,"abstract":"Huntington’s disease (HD) is a progressive neurodegenerative disorder caused by a CAG-repeat expansion in the Huntington gene (HTT). Herein, we describe the discovery of a series of HTT pre-mRNA-splicing modulators that promote the inclusion of a cryptic stop codon that in turn lowers levels of mutant Huntington protein (mHTT). Optimization of the starting thienopyridine amide core resulted in the discovery of the potent, CNS-penetrant, selective, and orally bioavailable HTT-splicing modulator BIO-6553. This lead compound is structurally distinct from existing splicing modulators, demonstrated significant HTT-lowering in both human cells and mouse YAC128 models, and has an attractive off-target profile from RASL- and RNA-seq analysis.","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":"87 1","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147466046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-17DOI: 10.1021/acs.jmedchem.5c01803
Benjamin D Horning,Cian Kingston,Gabriel M Simon,Matthew P Patricelli,David S Weinstein,Brian N Cook
Covalent modalities represent an important component of the modern medicinal chemist's toolbox for pursuing challenging targets in drug discovery. By taking a "covalent-first" approach to identifying druggable pockets on challenging-to-drug targets, we and others have expanded accessible target space and driven fragment-like hits to clinical-stage molecules. The field has long recognized intrinsic warhead reactivity as a key parameter to monitor, typically addressed by determining kinact and KI values, which are impractically time-intensive and can be misleading regarding reactivity. Here we present an alternative way to normalize potency for electrophilicity utilizing glutathione (GSH) consumption data, which enables us to extract target-specific improvements in potency, a metric we term ligand reactivity efficiency (LRE). Our hope is that the details of our approach and this metric will simplify the rational design of covalent drugs for fellow practitioners in the field.
{"title":"Normalizing Covalent Potency for Electrophilicity with Ligand Reactivity Efficiency.","authors":"Benjamin D Horning,Cian Kingston,Gabriel M Simon,Matthew P Patricelli,David S Weinstein,Brian N Cook","doi":"10.1021/acs.jmedchem.5c01803","DOIUrl":"https://doi.org/10.1021/acs.jmedchem.5c01803","url":null,"abstract":"Covalent modalities represent an important component of the modern medicinal chemist's toolbox for pursuing challenging targets in drug discovery. By taking a \"covalent-first\" approach to identifying druggable pockets on challenging-to-drug targets, we and others have expanded accessible target space and driven fragment-like hits to clinical-stage molecules. The field has long recognized intrinsic warhead reactivity as a key parameter to monitor, typically addressed by determining kinact and KI values, which are impractically time-intensive and can be misleading regarding reactivity. Here we present an alternative way to normalize potency for electrophilicity utilizing glutathione (GSH) consumption data, which enables us to extract target-specific improvements in potency, a metric we term ligand reactivity efficiency (LRE). Our hope is that the details of our approach and this metric will simplify the rational design of covalent drugs for fellow practitioners in the field.","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":"77 1","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147471836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alzheimer's disease impairs the cognitive domain of learning and memory through synaptic dysfunction. Memory formation requires gene expression to facilitate synaptic plasticity. When HDAC2 is inhibited, elevated histone acetylation promotes the gene expressions critical for synaptic plasticity and thus facilitates memory formation. However, simultaneous inhibition of HDAC1 and HDAC2 leads to hematologic toxicity. As the two isoforms have high homology, it is a challenge to identify selective HDAC2 inhibitors. Here, we report the development of novel cellular assays to determine HDAC2 potency and selectivity over HDAC1. Our HTS campaign using cellular assays for both isoforms identified 6 as a selective hit compound. With optimization efforts focusing on balancing cellular potency, selectivity, and mitigating BCRP recognition, we discovered compound 11, which exhibited significant in vivo efficacy in elevating histone acetylation levels and enhancing LTP. Importantly, 11 showed no significant hematological toxicity in human blood cells derived from simultaneous inhibition of HDAC1 and HDAC2.
{"title":"Discovery of Highly Selective HDAC2 Inhibitors in Cells That Elevate Histone Acetylation In Vivo without Adverse Effects from Dual Inhibition of HDAC1 and 2.","authors":"Naoyuki Suzuki,Hidekuni Yamakawa,Ken Yoshihara,Kazuki Niidome,Kosuke Anan,Kenji Takaya,Kensuke Kouki,Kazuki Fujimoto,Hiroko Ono,Takaya Izumi,Kazuhiro Unemura,Mana Ito,Takuya Hatta,Yasuto Kido,Naotaka Horiguchi,Ken-Ichi Kusakabe","doi":"10.1021/acs.jmedchem.5c02022","DOIUrl":"https://doi.org/10.1021/acs.jmedchem.5c02022","url":null,"abstract":"Alzheimer's disease impairs the cognitive domain of learning and memory through synaptic dysfunction. Memory formation requires gene expression to facilitate synaptic plasticity. When HDAC2 is inhibited, elevated histone acetylation promotes the gene expressions critical for synaptic plasticity and thus facilitates memory formation. However, simultaneous inhibition of HDAC1 and HDAC2 leads to hematologic toxicity. As the two isoforms have high homology, it is a challenge to identify selective HDAC2 inhibitors. Here, we report the development of novel cellular assays to determine HDAC2 potency and selectivity over HDAC1. Our HTS campaign using cellular assays for both isoforms identified 6 as a selective hit compound. With optimization efforts focusing on balancing cellular potency, selectivity, and mitigating BCRP recognition, we discovered compound 11, which exhibited significant in vivo efficacy in elevating histone acetylation levels and enhancing LTP. Importantly, 11 showed no significant hematological toxicity in human blood cells derived from simultaneous inhibition of HDAC1 and HDAC2.","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":"12 1","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147471835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
CD38 is an established biomarker for the diagnosis and treatment of various malignancies, including multiple myeloma. Accurate assessment of CD38 expression holds significant clinical value for optimizing CD38-targeted therapies. This study developed a series of small-molecule radiotracers for in vivo assessment of CD38 expression and monitoring of therapeutic response. All 68Ga-labeled radiotracers exhibited high radiochemical purity and stability both in vitro and in vivo. PET/CT imaging showed that 68Ga-NOTA-MK0159 uptake in multiple myeloma models correlated positively with CD38 expression and could be blocked by excess MK-0159. Notably, daratumumab did not block the uptake of 68Ga-NOTA-MK0159 under the experimental conditions of this study, suggesting the probe’s potential for assessing CD38 expression during daratumumab therapy. Preclinical studies demonstrated that 68Ga-NOTA-MK0159 enables noninvasive whole-body assessment of CD38 in multiple myeloma, which may guide personalized treatment and monitor CD38 expression during daratumumab therapy.
{"title":"CD38-Targeted Small-Molecule PET Radiotracer for Noninvasive Tumor Evaluation and Preliminary Therapy Monitoring in Multiple Myeloma","authors":"Chunyu Duan, Shibo Guo, Peng Xu, Wei Han, Yu Lu, Zhide Guo, Peng Fu, Gang Liu, Changjiu Zhao","doi":"10.1021/acs.jmedchem.5c03340","DOIUrl":"https://doi.org/10.1021/acs.jmedchem.5c03340","url":null,"abstract":"CD38 is an established biomarker for the diagnosis and treatment of various malignancies, including multiple myeloma. Accurate assessment of CD38 expression holds significant clinical value for optimizing CD38-targeted therapies. This study developed a series of small-molecule radiotracers for in vivo assessment of CD38 expression and monitoring of therapeutic response. All <sup>68</sup>Ga-labeled radiotracers exhibited high radiochemical purity and stability both in vitro and in vivo. PET/CT imaging showed that <sup>68</sup>Ga-NOTA-MK0159 uptake in multiple myeloma models correlated positively with CD38 expression and could be blocked by excess MK-0159. Notably, daratumumab did not block the uptake of <sup>68</sup>Ga-NOTA-MK0159 under the experimental conditions of this study, suggesting the probe’s potential for assessing CD38 expression during daratumumab therapy. Preclinical studies demonstrated that <sup>68</sup>Ga-NOTA-MK0159 enables noninvasive whole-body assessment of CD38 in multiple myeloma, which may guide personalized treatment and monitor CD38 expression during daratumumab therapy.","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":"36 1","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147462116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-16DOI: 10.1021/acs.jmedchem.5c03050
Enrique Madruga, Alfonso Garcia-Rubia, Carlos Sanchez-Nuñez, Loreto Martinez-Gonzalez, Ana María Fernandez-Escamilla, Isabel Lastres-Becker, Carmen Gil, Ana Martinez
A major challenge in modern medicine is developing new therapies for aging-related diseases such as neurodegenerative disorders, whose prevalence increases with longer life expectancy. Although kinase inhibitors have achieved clinical success, their development for central nervous system (CNS) disorders remains limited due to the complexity of kinase networks and poor blood–brain barrier (BBB) permeability. Serum/glucocorticoid-regulated kinase 1 (SGK1) participates in multiple signaling pathways but remains an underexplored target in neurodegeneration. Following a mixed ligand- and structure-based virtual screening, we have previously identified a brain-penetrant SGK1 inhibitor. A medicinal chemistry program based on hit expansion and optimization for BBB permeability reported here has generated a new family of SGK1 inhibitors as chemical probes that enable the investigation of SGK1’s role in neurological disorders and serve as promising starting points for drug development. These findings highlight SGK1 as a potential therapeutic target for neurodegenerative diseases, such as Alzheimer’s disease.
{"title":"Brain Permeable SGK1 Inhibitors: A Promising Therapeutic Strategy for Neurodegenerative Diseases","authors":"Enrique Madruga, Alfonso Garcia-Rubia, Carlos Sanchez-Nuñez, Loreto Martinez-Gonzalez, Ana María Fernandez-Escamilla, Isabel Lastres-Becker, Carmen Gil, Ana Martinez","doi":"10.1021/acs.jmedchem.5c03050","DOIUrl":"https://doi.org/10.1021/acs.jmedchem.5c03050","url":null,"abstract":"A major challenge in modern medicine is developing new therapies for aging-related diseases such as neurodegenerative disorders, whose prevalence increases with longer life expectancy. Although kinase inhibitors have achieved clinical success, their development for central nervous system (CNS) disorders remains limited due to the complexity of kinase networks and poor blood–brain barrier (BBB) permeability. Serum/glucocorticoid-regulated kinase 1 (SGK1) participates in multiple signaling pathways but remains an underexplored target in neurodegeneration. Following a mixed ligand- and structure-based virtual screening, we have previously identified a brain-penetrant SGK1 inhibitor. A medicinal chemistry program based on hit expansion and optimization for BBB permeability reported here has generated a new family of SGK1 inhibitors as chemical probes that enable the investigation of SGK1’s role in neurological disorders and serve as promising starting points for drug development. These findings highlight SGK1 as a potential therapeutic target for neurodegenerative diseases, such as Alzheimer’s disease.","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":"44 1","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147462172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-16DOI: 10.1021/acs.jmedchem.5c03280
Antonio Linero-Artiaga, Marie Svitelova, Vojtěch Novohradský, Venancio Rodríguez, Lenka Markova, Jana Kasparkova, Christoph Janiak, José Ruiz, Viktor Brabec
This study explores the therapeutic potential of seven bis-cyclometalated Ir(III) complexes (1–7), derived from the 2,2′-(benzothiazolyl)benzimidazole scaffold, as highly promising next-generation photoactivatable agents for type I and type II-guided photodynamic therapy (PDT) in lung and colorectal cancers. Their high phototoxicity in 2D and 3D cancer cell models, achieving IC50 values in the nanomolar region, was closely linked to the generation of singlet oxygen and type I reactive oxygen species (ROS) and the photooxidation of NADH, with complex 4 identified as the strongest ROS inducer and the most photocytotoxic complex. Notably, the iridium complexes proved to maintain their phototoxicity in hypoxic conditions. Using 3D spheroids, complex 4 demonstrated deep tissue penetration sought to overcome PDT limitations in solid tumors. Overall, the synthesized complexes showcase high efficacy and favorable pharmacological profiles, positioning them as promising candidates for the ROS-guided photodynamic treatment of cancers, including those located within hypoxic environments.
{"title":"Novel 2-(2′-Benzothiazolyl)-benzimidazole-Based Iridium(III) Photocatalysts Exhibit Antiproliferative Effects in 2D and 3D Cancer Cells to Bypass Hypoxia-Induced Resistance","authors":"Antonio Linero-Artiaga, Marie Svitelova, Vojtěch Novohradský, Venancio Rodríguez, Lenka Markova, Jana Kasparkova, Christoph Janiak, José Ruiz, Viktor Brabec","doi":"10.1021/acs.jmedchem.5c03280","DOIUrl":"https://doi.org/10.1021/acs.jmedchem.5c03280","url":null,"abstract":"This study explores the therapeutic potential of seven bis-cyclometalated Ir(III) complexes (<b>1–7</b>), derived from the 2,2′-(benzothiazolyl)benzimidazole scaffold, as highly promising next-generation photoactivatable agents for type I and type II-guided photodynamic therapy (PDT) in lung and colorectal cancers. Their high phototoxicity in 2D and 3D cancer cell models, achieving IC<sub>50</sub> values in the nanomolar region, was closely linked to the generation of singlet oxygen and type I reactive oxygen species (ROS) and the photooxidation of NADH, with complex <b>4</b> identified as the strongest ROS inducer and the most photocytotoxic complex. Notably, the iridium complexes proved to maintain their phototoxicity in hypoxic conditions. Using 3D spheroids, complex <b>4</b> demonstrated deep tissue penetration sought to overcome PDT limitations in solid tumors. Overall, the synthesized complexes showcase high efficacy and favorable pharmacological profiles, positioning them as promising candidates for the ROS-guided photodynamic treatment of cancers, including those located within hypoxic environments.","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":"93 1","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147462173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-16DOI: 10.1021/acs.jmedchem.5c03315
Shuang Chen,Muchen Yu,Manming Xu,Sergio Decherchi,Magdalena A. Taracila,Andrea M. Hujer,Christopher R. Bethel,Robert A. Bonomo,Shozeb Haider
The global spread of β-lactamase-mediated resistance poses a threat to β-lactam antibiotics. Boron-based β-lactamase inhibitors (BLIs) represent a promising class of reversible covalent inhibitors, yet the molecular basis of their recognition and dissociation remains poorly understood. Using Pseudomonas-derived cephalosporinase-3 (PDC-3) as a model, we employed enhanced sampling strategies with machine learning and steady-state kinetic assays to investigate the binding and unbinding dynamics of LP06, a boronate BLI. We identify three binding pathways, governed by hydrophobic recognition motifs and a conserved arginine anchor that together steer the ligand toward the precovalent state. Sequence alignment of nearly 7000 class C β-lactamases supports the conservation of these determinants, and structural analyses suggest that R349 may act as a shared anchoring point across serine β-lactamases. Additionally, hydrogen-bonding interactions were found to delay productive binding by stabilizing nonproductive conformations. Our findings provide fundamental insights into β-lactamase inhibition and establish design principles for next-generation β-lactamase inhibitors.
{"title":"Structural and Kinetic Basis for the Rational Design of Next-Generation β-Lactamase Inhibitors","authors":"Shuang Chen,Muchen Yu,Manming Xu,Sergio Decherchi,Magdalena A. Taracila,Andrea M. Hujer,Christopher R. Bethel,Robert A. Bonomo,Shozeb Haider","doi":"10.1021/acs.jmedchem.5c03315","DOIUrl":"https://doi.org/10.1021/acs.jmedchem.5c03315","url":null,"abstract":"The global spread of β-lactamase-mediated resistance poses a threat to β-lactam antibiotics. Boron-based β-lactamase inhibitors (BLIs) represent a promising class of reversible covalent inhibitors, yet the molecular basis of their recognition and dissociation remains poorly understood. Using Pseudomonas-derived cephalosporinase-3 (PDC-3) as a model, we employed enhanced sampling strategies with machine learning and steady-state kinetic assays to investigate the binding and unbinding dynamics of LP06, a boronate BLI. We identify three binding pathways, governed by hydrophobic recognition motifs and a conserved arginine anchor that together steer the ligand toward the precovalent state. Sequence alignment of nearly 7000 class C β-lactamases supports the conservation of these determinants, and structural analyses suggest that R349 may act as a shared anchoring point across serine β-lactamases. Additionally, hydrogen-bonding interactions were found to delay productive binding by stabilizing nonproductive conformations. Our findings provide fundamental insights into β-lactamase inhibition and establish design principles for next-generation β-lactamase inhibitors.","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":"60 1","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147462275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality worldwide, primarily due to its low immunogenicity and immunosuppressive tumor microenvironment. Inducing immunogenic cell death (ICD), a regulated form of cell death with the capacity to enhance tumor immunogenicity and activate antitumor immune responses, has emerged as a pivotal anticancer strategy. Mixed lineage kinase domain-like pseudokinase (MLKL) is a terminal-known obligate effector in the process of necroptosis, a programmed cell death pathway. Although several ATP competitive inhibitors of MLKL were reported, these inhibitors were unable to prevent the function of MLKL, rendering MLKL seemingly "undruggable." Moreover, the majority of research on MLKL focused on its biological role in necroptosis, and the investigation of its non-necroptotic functions has rarely been reported. Here, we report the discovery of C116 as a potent and selective MLKL degrader through leveraging artificial intelligence-assisted ligand discovery combined with targeted protein degradation technology. Notably, C116 effectively induces MLKL degradation and promotes parthanatos in HCC cells. More importantly, C116 was able to induce in vivo MLKL degradation and exerts strong antitumor activities in an orthotopic HCC tumor model, positioning it as a promising starting point for the treatment of HCC and for investigating the non-necroptotic functions of MLKL.
{"title":"Discovery of Novel MLKL PROTAC Degraders for the Treatment of Hepatocellular Carcinoma via Promoting Parthanatos.","authors":"Chao Chen,Kaiyuan Liu,Xinlei Wang,Ruyu Yan,Yang Dai,Yiming Li,Chaoyue Xia,Yue Zhang,Biyu Yang,Xiangli Chen,Wei Zheng,Meiyu Geng,Yaxi Yang,Xifei Jiang,Jing Ai,Bing Zhou","doi":"10.1021/acs.jmedchem.5c03302","DOIUrl":"https://doi.org/10.1021/acs.jmedchem.5c03302","url":null,"abstract":"Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality worldwide, primarily due to its low immunogenicity and immunosuppressive tumor microenvironment. Inducing immunogenic cell death (ICD), a regulated form of cell death with the capacity to enhance tumor immunogenicity and activate antitumor immune responses, has emerged as a pivotal anticancer strategy. Mixed lineage kinase domain-like pseudokinase (MLKL) is a terminal-known obligate effector in the process of necroptosis, a programmed cell death pathway. Although several ATP competitive inhibitors of MLKL were reported, these inhibitors were unable to prevent the function of MLKL, rendering MLKL seemingly \"undruggable.\" Moreover, the majority of research on MLKL focused on its biological role in necroptosis, and the investigation of its non-necroptotic functions has rarely been reported. Here, we report the discovery of C116 as a potent and selective MLKL degrader through leveraging artificial intelligence-assisted ligand discovery combined with targeted protein degradation technology. Notably, C116 effectively induces MLKL degradation and promotes parthanatos in HCC cells. More importantly, C116 was able to induce in vivo MLKL degradation and exerts strong antitumor activities in an orthotopic HCC tumor model, positioning it as a promising starting point for the treatment of HCC and for investigating the non-necroptotic functions of MLKL.","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":"9 1","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147461725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fructose-1,6-bisphosphatase (FBPase) is a key gluconeogenic enzyme and an attractive target for type 2 diabetes mellitus (T2DM); however, clinical progress has been limited by known inhibitor binding sites. Here, we report the cocrystal structure of human FBPase (HuFBPase) bound to a sulfonylurea-based inhibitor (compound 5, IC50 = 2.93 μM) at a previously unrecognized cryptic allosteric pocket. Compound 5 engages this site via π-π stacking with Y57 and extensive hydrogen-bond interactions, induces conformational rearrangement of K72 and D74, and facilitates the formation of a hydrogen-bond network with S123 that disrupts substrate catalysis. Structure-guided optimization yielded compound 29 with improved potency (IC50 = 0.75 μM). Cellular target engagement was confirmed by thermal stabilization of FBPase in LO2 cells. Notably, compound 29 exhibited hypoglycemic activity in vivo, providing the first evidence that targeting this pocket confers therapeutic benefit. Collectively, our findings establish a novel, druggable allosteric site on HuFBPase for T2DM treatment.
{"title":"Crystallographic Study Reveals a Cryptic Allosteric Site of FBPase by Sulfonylurea Inhibitors toward T2DM Treatment.","authors":"Zeyue Huang,Xiuqi Hu,Zheng Liu,Li Rao,Yanliang Ren,Wanyao Li,Hongxuan Cao,Ranna Yang,De Zhao,Yueyue Chu,Yi Zhang,Xinyue Zhu,Xiao Wang,Jian Wan","doi":"10.1021/acs.jmedchem.5c03569","DOIUrl":"https://doi.org/10.1021/acs.jmedchem.5c03569","url":null,"abstract":"Fructose-1,6-bisphosphatase (FBPase) is a key gluconeogenic enzyme and an attractive target for type 2 diabetes mellitus (T2DM); however, clinical progress has been limited by known inhibitor binding sites. Here, we report the cocrystal structure of human FBPase (HuFBPase) bound to a sulfonylurea-based inhibitor (compound 5, IC50 = 2.93 μM) at a previously unrecognized cryptic allosteric pocket. Compound 5 engages this site via π-π stacking with Y57 and extensive hydrogen-bond interactions, induces conformational rearrangement of K72 and D74, and facilitates the formation of a hydrogen-bond network with S123 that disrupts substrate catalysis. Structure-guided optimization yielded compound 29 with improved potency (IC50 = 0.75 μM). Cellular target engagement was confirmed by thermal stabilization of FBPase in LO2 cells. Notably, compound 29 exhibited hypoglycemic activity in vivo, providing the first evidence that targeting this pocket confers therapeutic benefit. Collectively, our findings establish a novel, druggable allosteric site on HuFBPase for T2DM treatment.","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":"52 1","pages":""},"PeriodicalIF":7.3,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147461724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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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