G-quadruplexes (G4s) are non-canonical secondary structures of nucleic acids that play crucial roles in gene expression, and their dysregulation has been implicated in various diseases. Therefore, development of G4-binding molecules, including peptides and proteins, is required to modulate G4-dependent biological processes for therapeutic purposes. In this study, a novel G4-binding peptide with high affinity for the G4 structure was developed using directed evolution based on mRNA display. The identified peptide, LP7, exhibited a preferential affinity for parallel G4 structures. Dimerization of LP7 significantly enhanced its binding to hTERC rG4 by approximately 70-fold, with a Kd of 7 nM. Analysis of the sequence-activity relationship revealed that both the basic and aromatic amino acid residues of the peptide are critical for its binding affinity to G4. Functional assays confirmed that LP7 inhibits reverse transcription in a G4-dependent manner by binding to the rG4 region. This study demonstrates the successful application of the mRNA display platform for discovering novel G4-binding peptides. A detailed characterization of LP7 provides valuable insights into the molecular interactions that govern G4 recognition. These findings highlight the potential of G4-binding peptides as tools for targeting and regulating G4-mediated gene functions, offering a promising avenue for the development of G4-dependent therapeutic strategies in the future.
g -四联体（G4s）是核酸的非规范二级结构，在基因表达中起着至关重要的作用，其失调与多种疾病有关。因此，需要开发g4结合分子，包括肽和蛋白质，来调节g4依赖的生物过程以达到治疗目的。本研究采用基于mRNA展示的定向进化方法，开发了一种与G4结构具有高亲和力的新型G4结合肽。所鉴定的肽LP7对平行G4结构表现出优先亲和力。LP7的二聚化使其与hTERC rG4的结合增强了约70倍，Kd为7 nM。序列-活性关系分析表明，该肽的碱性和芳香氨基酸残基对其与G4的结合亲和力至关重要。功能分析证实，LP7通过与rG4区域结合，以g4依赖的方式抑制逆转录。本研究证明了mRNA展示平台在发现新的g4结合肽方面的成功应用。LP7的详细表征为控制G4识别的分子相互作用提供了有价值的见解。这些发现突出了g4结合肽作为靶向和调节g4介导的基因功能的工具的潜力，为未来开发依赖g4的治疗策略提供了一条有希望的途径。
{"title":"Discovery and characterization of a high-affinity G-quadruplex binding peptide via mRNA display","authors":"Naka Kudo Ida , Yoshimasa Kawaguchi , Shiroh Futaki , Miki Imanishi","doi":"10.1016/j.bmc.2025.118543","DOIUrl":"10.1016/j.bmc.2025.118543","url":null,"abstract":"<div><div>G-quadruplexes (G4s) are non-canonical secondary structures of nucleic acids that play crucial roles in gene expression, and their dysregulation has been implicated in various diseases. Therefore, development of G4-binding molecules, including peptides and proteins, is required to modulate G4-dependent biological processes for therapeutic purposes. In this study, a novel G4-binding peptide with high affinity for the G4 structure was developed using directed evolution based on mRNA display. The identified peptide, <strong>LP7</strong>, exhibited a preferential affinity for parallel G4 structures. Dimerization of <strong>LP7</strong> significantly enhanced its binding to hTERC rG4 by approximately 70-fold, with a <em>K</em><sub>d</sub> of 7 nM. Analysis of the sequence-activity relationship revealed that both the basic and aromatic amino acid residues of the peptide are critical for its binding affinity to G4. Functional assays confirmed that <strong>LP7</strong> inhibits reverse transcription in a G4-dependent manner by binding to the rG4 region. This study demonstrates the successful application of the mRNA display platform for discovering novel G4-binding peptides. A detailed characterization of <strong>LP7</strong> provides valuable insights into the molecular interactions that govern G4 recognition. These findings highlight the potential of G4-binding peptides as tools for targeting and regulating G4-mediated gene functions, offering a promising avenue for the development of G4-dependent therapeutic strategies in the future.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"135 ","pages":"Article 118543"},"PeriodicalIF":3.0,"publicationDate":"2025-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145957411","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 : 2025-12-27DOI: 10.1016/j.bmc.2025.118542
Anna Rita Tondo , Marialuigia Fantacuzzi , Simone Carradori , Ilaria D'Agostino , Andrea Angeli , Claudiu T. Supuran , Clemente Capasso , Nicola Gambacorta , Luca Piemontese , Antonio Laghezza , Orazio Nicolotti , Paolo Tortorella , Mariangela Agamennone
Antimicrobial resistance (AMR) is one of the world's most pressing health problems and requires immediate action from the scientific community. Pseudomonas aeruginosa is a particularly concerning bacterium due to its high level of resistance, especially among hospitalized and immunocompromised individuals. We recently investigated PsCA3, one of three P. aeruginosa β‑carbonic anhydrases (β-CAs), as a potential new pharmacological target for developing innovative antibacterial drugs. In this study, we applied a consensus structure-based virtual screening approach to select the most promising PsCA3 inhibitors from an in-house library of 607 small molecules. Twenty-one diverse compounds were selected and experimentally validated through enzyme inhibition assays, which assessed the ability of all ligands to block PsCA3 activity while sparing human α‑carbonic anhydrases (hCAs). Next, we focused on the benzoxazinone/dihydroquinolinone scaffold, testing fifteen additional analogues and expanding the set of assayed microbial β-CAs. Notably, we identified new, potent ligands based on unexplored scaffolds that can effectively target microbial β-CAs at micromolar/submicromolar concentrations with remarkable selectivity over human CAs.
{"title":"Targeting microbial β-CAs: bridging in silico screening with in vitro validation","authors":"Anna Rita Tondo , Marialuigia Fantacuzzi , Simone Carradori , Ilaria D'Agostino , Andrea Angeli , Claudiu T. Supuran , Clemente Capasso , Nicola Gambacorta , Luca Piemontese , Antonio Laghezza , Orazio Nicolotti , Paolo Tortorella , Mariangela Agamennone","doi":"10.1016/j.bmc.2025.118542","DOIUrl":"10.1016/j.bmc.2025.118542","url":null,"abstract":"<div><div>Antimicrobial resistance (AMR) is one of the world's most pressing health problems and requires immediate action from the scientific community. <em>Pseudomonas aeruginosa</em> is a particularly concerning bacterium due to its high level of resistance, especially among hospitalized and immunocompromised individuals. We recently investigated PsCA3, one of three <em>P. aeruginosa</em> β‑carbonic anhydrases (β-CAs), as a potential new pharmacological target for developing innovative antibacterial drugs. In this study, we applied a consensus structure-based virtual screening approach to select the most promising PsCA3 inhibitors from an in-house library of 607 small molecules. Twenty-one diverse compounds were selected and experimentally validated through enzyme inhibition assays, which assessed the ability of all ligands to block PsCA3 activity while sparing human α‑carbonic anhydrases (<em>h</em>CAs). Next, we focused on the benzoxazinone/dihydroquinolinone scaffold, testing fifteen additional analogues and expanding the set of assayed microbial β-CAs. Notably, we identified new, potent ligands based on unexplored scaffolds that can effectively target microbial β-CAs at micromolar/submicromolar concentrations with remarkable selectivity over human CAs.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"134 ","pages":"Article 118542"},"PeriodicalIF":3.0,"publicationDate":"2025-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145881201","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 : 2025-12-25DOI: 10.1016/j.bmc.2025.118541
Gui-Ping Gao , Quan-Ke Li , Jin-Cheng Ma , Zhi-Jun Zhang , Shao-Yong Zhang , Ying-Qian Liu
Indole, an aromatic heterocyclic compound formed by the fusion of a benzene ring with a pyrrole ring, is widely distributed in the secondary metabolites of plants, animals, and marine organisms. Owing to its unique physicochemical properties and high structural modifiability, indole derivatives can engage in specific interactions with various biological targets, demonstrating a broad spectrum of bioactivities including anticancer, anti-inflammatory, antiviral, and antibacterial effects. Consequently, indole holds an indispensable position in innovative drug discovery and development. This review provides a comprehensive summary of the primary strategies employed in the discovery of indole derivatives. These encompass structure optimization approaches inspired by natural products, such as structure simplification, diversity-oriented synthesis (DOS), biology-oriented synthesis (BIOS), the “pseudo-natural product” (PNP) strategy, and bioinspired synthesis based on biosynthetic building blocks. Additionally, strategies like scaffold hopping, molecular hybridization, drug repurposing, and multicomponent reactions (MCRs) for constructing indole-based molecules are discussed. Particular emphasis is placed on target structure-based discovery strategies for indole derivatives, including ligand-based structure modification, molecular docking-assisted high-throughput virtual screening, and fragment-based drug design (FBDD). Furthermore, the application of emerging techniques such as phenotypic screening, DNA-encoded library (DEL) technology, and free energy perturbation (FEP) calculations in indole-based drug research and development is highlighted. This review aims to systematically organize the multi-dimensional R&D framework for indole derivatives, analyze the specific value of each strategy in addressing drug discovery challenges, and provide a theoretical foundation and methodological support for the rational design and development of novel indole-based drugs. It is anticipated that this work will further enhance the efficiency and innovation level in the development of this class of compounds.
{"title":"Strategic approaches to the discovery of biologically active indole derivatives: a comprehensive review","authors":"Gui-Ping Gao , Quan-Ke Li , Jin-Cheng Ma , Zhi-Jun Zhang , Shao-Yong Zhang , Ying-Qian Liu","doi":"10.1016/j.bmc.2025.118541","DOIUrl":"10.1016/j.bmc.2025.118541","url":null,"abstract":"<div><div>Indole, an aromatic heterocyclic compound formed by the fusion of a benzene ring with a pyrrole ring, is widely distributed in the secondary metabolites of plants, animals, and marine organisms. Owing to its unique physicochemical properties and high structural modifiability, indole derivatives can engage in specific interactions with various biological targets, demonstrating a broad spectrum of bioactivities including anticancer, anti-inflammatory, antiviral, and antibacterial effects. Consequently, indole holds an indispensable position in innovative drug discovery and development. This review provides a comprehensive summary of the primary strategies employed in the discovery of indole derivatives. These encompass structure optimization approaches inspired by natural products, such as structure simplification, diversity-oriented synthesis (DOS), biology-oriented synthesis (BIOS), the “pseudo-natural product” (PNP) strategy, and bioinspired synthesis based on biosynthetic building blocks. Additionally, strategies like scaffold hopping, molecular hybridization, drug repurposing, and multicomponent reactions (MCRs) for constructing indole-based molecules are discussed. Particular emphasis is placed on target structure-based discovery strategies for indole derivatives, including ligand-based structure modification, molecular docking-assisted high-throughput virtual screening, and fragment-based drug design (FBDD). Furthermore, the application of emerging techniques such as phenotypic screening, DNA-encoded library (DEL) technology, and free energy perturbation (FEP) calculations in indole-based drug research and development is highlighted. This review aims to systematically organize the multi-dimensional R&D framework for indole derivatives, analyze the specific value of each strategy in addressing drug discovery challenges, and provide a theoretical foundation and methodological support for the rational design and development of novel indole-based drugs. It is anticipated that this work will further enhance the efficiency and innovation level in the development of this class of compounds.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"135 ","pages":"Article 118541"},"PeriodicalIF":3.0,"publicationDate":"2025-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146075208","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 : 2025-12-20DOI: 10.1016/j.bmc.2025.118536
Lin Qiu , Wenjuan Zhou , Hong Chen , Hao Jiang , Jiawen Lang , Zhimin Xing , Madison Heady , Robert J. Gropler , Caroline Guglielmetti , Joel S. Perlmutter , Zhude Tu
Sphingosine-1-phosphate receptor 2 (S1PR2) plays an important role in demyelinating central nervous system (CNS) disease, such as multiple sclerosis (MS). To identify a suitable PET radiotracer for imaging S1PR2 in the brain, we synthesized thirteen new phthalazinyl-indazole containing S1PR2 ligands and determined their S1PR2 binding potencies in vitro. A racemic carboxylic acid and its enantiomeric isomers, (±)-5d, (−)-5d, (+)-5d, and 3-fluoropropoxyl analogues 5e, and (±)-5f are potent with IC50 values of 33.4, 13.4, 12.1, 27.7, and 16.4 nM for S1PR2, respectively. These compounds selectively bind S1PR2 over other S1PRs with IC50s >1000 nM. Three tracers (±)-[18F]5d, (−)-[18F]5d, (+)-[18F]5d were radiosynthesized with radiochemical yields of 38 %, 20 %, and 20 %, respectively, high radiochemical purity (>95 %), and high molar activity (>39 GBq/μmol, decay corrected to EOS). In addition, (±)-[18F]7a, a methyl ester pro-drug tracer of (±)-[18F]5d, was designed and synthesized with a radiochemical yield of 38 %, high radiochemical purity (>95 %), and high molar activity (>37 GBq/μmol, decay corrected to EOS). Our PET studies indicated (±)-[18F]5d had low mouse brain uptake with 0.35 %ID/g at 40–60 min post-injection, however, the pro-drug tracer (±)-[18F]7a had 11-fold higher brain uptake (4.10 %ID/g) than that of (±)-[18F]5d at 40–60 min post-injection. Ex vivo biodistribution revealed (±)-[18F]5d had consistently low brain uptake and no defluorination in vivo in SD rats. The radiometabolic analysis confirmed that (±)-[18F]7a was metabolized fast to form (±)-[18F]5d in rat plasma, and (±)-[18F]5d was ∼30 % of the total radioactivity at 45 min post-injection in rat brain. (±)-[18F]5d demonstrated relatively stable in nonhuman primate plasma in vivo. Furthermore, a PET brain study of (±)-[18F]7a showed that cuprizone-fed mice had reduced radioactive brain uptake compared with control mice, suggesting downregulation of S1PR2 expression in the brain of this demyelinating disease mouse model. Together, (±)-[18F]7a is a potential pro-drug PET radiotracer for imaging S1PR2 expression in the brain supporting further optimization of an S1PR2-specific radiotracer with appropriate in vivo radiolabeled metabolism kinetics.
{"title":"Discovery and in vivo evaluation of a fluorine-18 pro-drug tracer for imaging sphingosine-1-phosphate receptor 2 in the brain","authors":"Lin Qiu , Wenjuan Zhou , Hong Chen , Hao Jiang , Jiawen Lang , Zhimin Xing , Madison Heady , Robert J. Gropler , Caroline Guglielmetti , Joel S. Perlmutter , Zhude Tu","doi":"10.1016/j.bmc.2025.118536","DOIUrl":"10.1016/j.bmc.2025.118536","url":null,"abstract":"<div><div>Sphingosine-1-phosphate receptor 2 (S1PR2) plays an important role in demyelinating central nervous system (CNS) disease, such as multiple sclerosis (MS). To identify a suitable PET radiotracer for imaging S1PR2 in the brain, we synthesized thirteen new phthalazinyl-indazole containing S1PR2 ligands and determined their S1PR2 binding potencies <em>in vitro</em>. A racemic carboxylic acid and its enantiomeric isomers, (±)-<strong>5d</strong>, (−)-<strong>5d</strong>, (+)-<strong>5d</strong>, and 3-fluoropropoxyl analogues <strong>5e</strong>, and (±)-<strong>5f</strong> are potent with IC<sub>50</sub> values of 33.4, 13.4, 12.1, 27.7, and 16.4 nM for S1PR2, respectively. These compounds selectively bind S1PR2 over other S1PRs with IC<sub>50</sub>s >1000 nM. Three tracers (±)-[<sup>18</sup>F]<strong>5d</strong>, (−)-[<sup>18</sup>F]<strong>5d</strong>, (+)-[<sup>18</sup>F]<strong>5d</strong> were radiosynthesized with radiochemical yields of 38 %, 20 %, and 20 %, respectively, high radiochemical purity (>95 %), and high molar activity (>39 GBq/μmol, decay corrected to EOS). In addition, (±)-[<sup>18</sup>F]<strong>7a</strong>, a methyl ester pro-drug tracer of (±)-[<sup>18</sup>F]<strong>5d</strong>, was designed and synthesized with a radiochemical yield of 38 %, high radiochemical purity (>95 %), and high molar activity (>37 GBq/μmol, decay corrected to EOS). Our PET studies indicated (±)-[<sup>18</sup>F]<strong>5d</strong> had low mouse brain uptake with 0.35 %ID/g at 40–60 min post-injection, however, the pro-drug tracer (±)-[<sup>18</sup>F]<strong>7a</strong> had 11-fold higher brain uptake (4.10 %ID/g) than that of (±)-[<sup>18</sup>F]<strong>5d</strong> at 40–60 min post-injection. <em>Ex vivo</em> biodistribution revealed (±)-[<sup>18</sup>F]<strong>5d</strong> had consistently low brain uptake and no defluorination <em>in vivo</em> in SD rats. The radiometabolic analysis confirmed that (±)-[<sup>18</sup>F]<strong>7a</strong> was metabolized fast to form (±)-[<sup>18</sup>F]<strong>5d</strong> in rat plasma, and (±)-[<sup>18</sup>F]<strong>5d</strong> was ∼30 % of the total radioactivity at 45 min post-injection in rat brain. (±)-[<sup>18</sup>F]<strong>5d</strong> demonstrated relatively stable in nonhuman primate plasma <em>in vivo</em>. Furthermore, a PET brain study of (±)-[<sup>18</sup>F]<strong>7a</strong> showed that cuprizone-fed mice had reduced radioactive brain uptake compared with control mice, suggesting downregulation of S1PR2 expression in the brain of this demyelinating disease mouse model. Together, (±)-[<sup>18</sup>F]<strong>7a</strong> is a potential pro-drug PET radiotracer for imaging S1PR2 expression in the brain supporting further optimization of an S1PR2-specific radiotracer with appropriate <em>in vivo</em> radiolabeled metabolism kinetics.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"134 ","pages":"Article 118536"},"PeriodicalIF":3.0,"publicationDate":"2025-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145831780","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 : 2025-12-18DOI: 10.1016/j.bmc.2025.118527
Sachin M. Thorat , Summon Koul , Sachin Kote , Ramakrishna G. Bhat
1,3,4-Thiadiazoles are known to exhibit a wide array of biological activities such as diuretic, antifungal, anticonvulsant and anticancer properties. Since 1,3,4-thiadiazoles are structurally considered as bio-isosteres of pyrimidine, this structural framework along with its capability to bind to various biological targets has led to the development of many FDA approved drugs. The current work focuses on the identification of an initial hit from an existing library of thiadiazoles and its optimization to a potential lead molecule. The compounds were evaluated for in-vitro cytotoxicity in four human cancer cell lines namely HepG2, MCF7, HCT116 and A549 as well as in Vero cell lines. Four compounds 11h–11k showed potency comparable with or better than the positive control Erlotinib and exemplary selectivity towards normal cells. These compounds were then screened to assess their inhibitory potential in wild type and mutated EGFR (T790M). Compound 11j was found to be potent in these assays. Further computational approach driven SAR around this compound led to the identification of a more potent compound 14h that showed sub-micromolar potency in wild type EGFR with much improved potency against T790M. Apoptotic effect of 14h was investigated using annexin V-FITC/PI dual staining assay in which 14h was found to trigger apoptotic pathways effectively with a significantly higher proportion of cells undergoing both early and late apoptotic events, underscoring its potential as a therapeutic agent targeting programmed cell death. Western blot analysis of 14h indicates that it primarily impairs EGFR phosphorylation, supporting its potential as a targeted modulator of EGFR signalling.
{"title":"Design, synthesis, and biological evaluation of 2-amino-1,3,4-thiadiazoles as new potential EGFR inhibitors for treatment of cancer","authors":"Sachin M. Thorat , Summon Koul , Sachin Kote , Ramakrishna G. Bhat","doi":"10.1016/j.bmc.2025.118527","DOIUrl":"10.1016/j.bmc.2025.118527","url":null,"abstract":"<div><div>1,3,4-Thiadiazoles are known to exhibit a wide array of biological activities such as diuretic, antifungal, anticonvulsant and anticancer properties. Since 1,3,4-thiadiazoles are structurally considered as bio-isosteres of pyrimidine, this structural framework along with its capability to bind to various biological targets has led to the development of many FDA approved drugs. The current work focuses on the identification of an initial hit from an existing library of thiadiazoles and its optimization to a potential lead molecule. The compounds were evaluated for in-vitro cytotoxicity in four human cancer cell lines namely HepG2, MCF7, HCT116 and A549 as well as in Vero cell lines. Four compounds <strong>11h</strong>–<strong>11k</strong> showed potency comparable with or better than the positive control Erlotinib and exemplary selectivity towards normal cells. These compounds were then screened to assess their inhibitory potential in wild type and mutated EGFR (T790M). Compound <strong>11j</strong> was found to be potent in these assays. Further computational approach driven SAR around this compound led to the identification of a more potent compound <strong>14h</strong> that showed sub-micromolar potency in wild type EGFR with much improved potency against T790M. Apoptotic effect of <strong>14h</strong> was investigated using annexin V-FITC/PI dual staining assay in which <strong>14h</strong> was found to trigger apoptotic pathways effectively with a significantly higher proportion of cells undergoing both early and late apoptotic events, underscoring its potential as a therapeutic agent targeting programmed cell death. Western blot analysis of <strong>14h</strong> indicates that it primarily impairs EGFR phosphorylation, supporting its potential as a targeted modulator of EGFR signalling.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"134 ","pages":"Article 118527"},"PeriodicalIF":3.0,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145831748","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 : 2025-12-18DOI: 10.1016/j.bmc.2025.118535
Ahmed Abd El-Hamed El-Rahmany , Nadia A. Khalil , Mohamed S. Nafie , Wagdy M. Eldehna , Hatem A. Abdel-Aziz , Marwa S.A. Hassan
Five new series of pyrazolo[1,5-a]pyrimidine derivatives were synthesized as potential anti-cancer agents targeting the CDK2 enzyme. Their cytotoxic activity was evaluated against colon cancer (HCT-116) and breast cancer (MDA-MB-231) cell lines. Among the tested compounds, 7-(4-bromophenyl)-2-(methylthio)pyrazolo[1,5-a]pyrimidine-3‑carbonitrile (13g), 7-(2,4-dichlorophenyl)-2-(methylthio)pyrazolo[1,5-a]pyrimidine-3‑carbonitrile (13j), 7-[1-(4-fluorophenyl)-5-methyl-1H-1,2,3-triazol-4-yl)-2-(methylthio)pyrazolo[1,5-a] pyrimidine-3‑carbonitrile (21c), and 7-(6-bromo-2-oxo-2H-chromen-3-yl)-2-(methylthio)pyrazolo[1,5-a] pyrimidine-3‑carbonitrile (26b) exhibited strong growth inhibition in HCT-116 cells, comparable to the reference drug roscovitine. Compounds 13g and 21c were identified as the most potent candidates against HCT-116 cells, with IC₅₀ values of 0.45 μM and 0.09 μM, respectively, compared to roscovitine (IC₅₀ = 0.07 μM). Moreover, compounds 13g, 13j, 21c, and 26b also displayed low toxicity toward normal WI-38 fibroblast cells, indicating superior selectivity. CDK2 inhibition assay for the most potent compounds 13g, 13j, and 21c, demonstrated promising IC50 values ranging from 18 to 150 nM, compared to roscovitine (IC50 = 140 nM). Further biological evaluation revealed that compound 21c (IC₅₀ = 18 nM) triggered G1-phase cell cycle arrest and promoted more apoptosis than necrosis in HCT-116 cells (total apoptosis: 32.96 % compared to 0.63 % in the control). RT-PCR analysis indicated that apoptosis was mediated through both intrinsic and extrinsic pathways, accompanied by downregulation of the anti-apoptotic gene BCL-2 (0.7-fold change). Molecular docking studies supported these results, showing favorable interactions of compound 21c within the CDK2 active site. Overall, compound 21c emerges as a promising lead candidate for the development of selective CDK2 inhibitors exhibiting potent anti-cancer activity and low toxicity toward normal cells.
{"title":"New pyrazolo[1,5-a]pyrimidine derivatives as potential CDK2 inhibitors and apoptosis-driven antiproliferative agents","authors":"Ahmed Abd El-Hamed El-Rahmany , Nadia A. Khalil , Mohamed S. Nafie , Wagdy M. Eldehna , Hatem A. Abdel-Aziz , Marwa S.A. Hassan","doi":"10.1016/j.bmc.2025.118535","DOIUrl":"10.1016/j.bmc.2025.118535","url":null,"abstract":"<div><div>Five new series of pyrazolo[1,5-<em>a</em>]pyrimidine derivatives were synthesized as potential anti-cancer agents targeting the CDK2 enzyme. Their cytotoxic activity was evaluated against colon cancer (HCT-116) and breast cancer (MDA-MB-231) cell lines. Among the tested compounds, 7-(4-bromophenyl)-2-(methylthio)pyrazolo[1,5-<em>a</em>]pyrimidine-3‑carbonitrile (<strong>13</strong> <strong>g</strong>), 7-(2,4-dichlorophenyl)-2-(methylthio)pyrazolo[1,5-<em>a</em>]pyrimidine-3‑carbonitrile (<strong>13j</strong>), 7-[1-(4-fluorophenyl)-5-methyl-1<em>H</em>-1,2,3-triazol-4-yl)-2-(methylthio)pyrazolo[1,5-<em>a</em>] pyrimidine-3‑carbonitrile (<strong>21c</strong>), and 7-(6-bromo-2-oxo-2<em>H</em>-chromen-3-yl)-2-(methylthio)pyrazolo[1,5-<em>a</em>] pyrimidine-3‑carbonitrile (<strong>26b</strong>) exhibited strong growth inhibition in HCT-116 cells, comparable to the reference drug roscovitine. Compounds <strong>13</strong> <strong>g</strong> and <strong>21c</strong> were identified as the most potent candidates against HCT-116 cells, with IC₅₀ values of 0.45 μM and 0.09 μM, respectively, compared to roscovitine (IC₅₀ = 0.07 μM). Moreover, compounds <strong>13</strong> <strong>g</strong>, <strong>13j</strong>, <strong>21c</strong>, and <strong>26b</strong> also displayed low toxicity toward normal WI-38 fibroblast cells, indicating superior selectivity. CDK2 inhibition assay for the most potent compounds <strong>13</strong> <strong>g</strong>, <strong>13j</strong>, and <strong>21c</strong>, demonstrated promising IC<sub>50</sub> values ranging from 18 to 150 nM, compared to roscovitine (IC<sub>50</sub> = 140 nM). Further biological evaluation revealed that compound <strong>21c</strong> (IC₅₀ = 18 nM) triggered G1-phase cell cycle arrest and promoted more apoptosis than necrosis in HCT-116 cells (total apoptosis: 32.96 % compared to 0.63 % in the control). RT-PCR analysis indicated that apoptosis was mediated through both intrinsic and extrinsic pathways, accompanied by downregulation of the anti-apoptotic gene BCL-2 (0.7-fold change). Molecular docking studies supported these results, showing favorable interactions of compound <strong>21c</strong> within the CDK2 active site. Overall, compound <strong>21c</strong> emerges as a promising lead candidate for the development of selective CDK2 inhibitors exhibiting potent anti-cancer activity and low toxicity toward normal cells.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"134 ","pages":"Article 118535"},"PeriodicalIF":3.0,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145808835","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 : 2025-12-18DOI: 10.1016/j.bmc.2025.118528
Lidiane Gomes de Araújo , Rafael Gomes Soares , Bruno Galdino Lopes , Ana Rita de Sousa França , Karen Isabelly Santos Cardoso Brandão , Edilson Beserra de Alencar Filho , Yuri Virgílio dos Santos , Gardenia Carmen Gadelha Militão , Claudio Gabriel Lima-Junior , Rodrigo Cristiano
Two dihydroquinoline derivatives were synthesized through a modified Doebner reaction, which resulted in stable dihydroquinolines instead of the expected aromatized products. Their photophysical properties were investigated in solution, in the solid state, and in aqueous media, and their anticancer potential was evaluated. Both derivatives exhibited fluorescence and moderate cytotoxicity toward the HL-60 leukemia cell line. Quantum chemical calculations combined with the analysis of experimental 1H NMR shifts confirmed the formation of an intramolecular hydrogen bond (IHB) in the compound bearing an ortho-phenolic hydroxy group, which appears to reduce its affinity for biological targets. Molecular docking studies on common quinoline-associated targets suggested that both derivatives may act as tubulin depolymerizers and DNA intercalators. Interestingly, both compounds exhibited aggregation-induced emission (AIE), with the unsubstituted derivative exhibiting unusual solvent-dependent luminescence and stable emission near physiological pH. Overall, these findings identify dihydroquinolines as promising luminescent scaffolds with tunable optical behavior and preliminary anticancer activity, providing a foundation for future structural optimization and biological studies.
{"title":"Luminescent dihydroquinolines: fluorescence in aqueous media and insights into anticancer activity","authors":"Lidiane Gomes de Araújo , Rafael Gomes Soares , Bruno Galdino Lopes , Ana Rita de Sousa França , Karen Isabelly Santos Cardoso Brandão , Edilson Beserra de Alencar Filho , Yuri Virgílio dos Santos , Gardenia Carmen Gadelha Militão , Claudio Gabriel Lima-Junior , Rodrigo Cristiano","doi":"10.1016/j.bmc.2025.118528","DOIUrl":"10.1016/j.bmc.2025.118528","url":null,"abstract":"<div><div>Two dihydroquinoline derivatives were synthesized through a modified Doebner reaction, which resulted in stable dihydroquinolines instead of the expected aromatized products. Their photophysical properties were investigated in solution, in the solid state, and in aqueous media, and their anticancer potential was evaluated. Both derivatives exhibited fluorescence and moderate cytotoxicity toward the HL-60 leukemia cell line. Quantum chemical calculations combined with the analysis of experimental <sup>1</sup>H NMR shifts confirmed the formation of an intramolecular hydrogen bond (IHB) in the compound bearing an <em>ortho</em>-phenolic hydroxy group, which appears to reduce its affinity for biological targets. Molecular docking studies on common quinoline-associated targets suggested that both derivatives may act as tubulin depolymerizers and DNA intercalators. Interestingly, both compounds exhibited aggregation-induced emission (AIE), with the unsubstituted derivative exhibiting unusual solvent-dependent luminescence and stable emission near physiological pH. Overall, these findings identify dihydroquinolines as promising luminescent scaffolds with tunable optical behavior and preliminary anticancer activity, providing a foundation for future structural optimization and biological studies.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"134 ","pages":"Article 118528"},"PeriodicalIF":3.0,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145814956","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}
Allosteric inhibitors of HIV-1 integrase offer a promising approach to block an essential process in HIV-1 replication and offer a new strategy for HIV treatment. During the course of our drug discovery investigations, we identified novel allosteric HIV-1 integrase inhibitor 1 which has a conformationally constrained spiro indane scaffold. Our subsequent medicinal chemistry efforts using a structure-based drug design focused on the efficacies of related compound 5 against not only the wild type enzyme but also enzymes with polymorphisms and resistance mutations. As a result, we identified compound 38f, which exhibited the desired efficacy against major polymorphisms and resistance mutations (EC50(WT) = 0.0040 μM, EC50(T124N) = 0.0048 μM, EC50(T125A) = 0.0038 μM, EC50(A128T) = 0.0057 μM), potent anti-HIV activity in the human serum assay (EC50(HS50%) = 0.091 μM), and preferable PK profiles in rats (Cltot = 0.017 L/h/kg, MRT = 12.5 h, BA = 71.4 %).
{"title":"Discovery and optimization of novel and potent allosteric HIV-1 integrase inhibitors with a spiro[indene] moiety","authors":"Kaoru Adachi, Tomoyuki Manabe, Takayuki Yamasaki, Akira Suma, Yosuke Ogoshi, Akihiko Takahashi, Takuya Orita, Akihiro Nomura, Tsuyoshi Adachi, Yoshitsugu Ohata, Yoshiyuki Akiyama, Susumu Miyazaki","doi":"10.1016/j.bmc.2025.118526","DOIUrl":"10.1016/j.bmc.2025.118526","url":null,"abstract":"<div><div>Allosteric inhibitors of HIV-1 integrase offer a promising approach to block an essential process in HIV-1 replication and offer a new strategy for HIV treatment. During the course of our drug discovery investigations, we identified novel allosteric HIV-1 integrase inhibitor <strong>1</strong> which has a conformationally constrained spiro indane scaffold. Our subsequent medicinal chemistry efforts using a structure-based drug design focused on the efficacies of related compound <strong>5</strong> against not only the wild type enzyme but also enzymes with polymorphisms and resistance mutations. As a result, we identified compound <strong>38</strong> <strong>f</strong>, which exhibited the desired efficacy against major polymorphisms and resistance mutations (EC<sub>50</sub>(WT) = 0.0040 μM, EC<sub>50</sub>(T124N) = 0.0048 μM, EC<sub>50</sub>(T125A) = 0.0038 μM, EC<sub>50</sub>(A128T) = 0.0057 μM), potent anti-HIV activity in the human serum assay (EC<sub>50</sub>(HS50%) = 0.091 μM), and preferable PK profiles in rats (Cl<sub>tot</sub> = 0.017 L/h/kg, MRT = 12.5 h, BA = 71.4 %).</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"134 ","pages":"Article 118526"},"PeriodicalIF":3.0,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145808885","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 : 2025-12-16DOI: 10.1016/j.bmc.2025.118522
Sihan Qiang , Ke Wang , Shanshan Wang , Zongliang Liu , Xin Yu , Zuguang Yin , Yuxin Feng , Huaiyu Wang , Huili Liu , Hongbo Wang , Yi Liu
The development of multidrug resistance (MDR) to anticancer agents following chronic treatment remains a significant obstacle in cancer chemotherapy. Overexpression of the energy-dependent drug efflux transporter P-glycoprotein (P-gp) has been identified as a major contributor to MDR. Inspired by naturally occurring MDR-reversing cyclic peptides, a series of readily accessible valine thiazole-containing derivatives were designed and synthesized as effective reversal agents against P-gp–mediated MDR based on a hybridization strategy. Structure–activity relationship (SAR) analysis demonstrated that linear valine thiazole derivatives possess greater MDR reversal activity than their macrocyclic analogs. Compound 17e displayed promising synergistic activity by significantly enhancing the therapeutic efficacy of paclitaxel (PTX) against KBV cells (IC50 = 2.8 nM, reversal fold = 288.5) without inducing obvious toxicity. 17e exhibited approximately 8-fold greater potency than verapamil (VRP), 2-fold greater potency than the third-generation P-gp inhibitor tariquidar (TAR) in KBV cells. Mechanistic studies confirmed that 17e inhibits the efflux function of P-gp in a concentration-dependent manner without affecting its expression, thereby increasing intracellular chemotherapeutic drug accumulation and causing G2/M phase arrests, which is associated with increased apoptosis. Taken together, the linear valine thiazole derivative 17e represents a promising starting scaffold for developing novel P-gp inhibitors against MDR.
{"title":"Discovery of valine thiazole-containing derivatives as potent reversers of P-glycoprotein–mediated multidrug resistance","authors":"Sihan Qiang , Ke Wang , Shanshan Wang , Zongliang Liu , Xin Yu , Zuguang Yin , Yuxin Feng , Huaiyu Wang , Huili Liu , Hongbo Wang , Yi Liu","doi":"10.1016/j.bmc.2025.118522","DOIUrl":"10.1016/j.bmc.2025.118522","url":null,"abstract":"<div><div>The development of multidrug resistance (MDR) to anticancer agents following chronic treatment remains a significant obstacle in cancer chemotherapy. Overexpression of the energy-dependent drug efflux transporter P-glycoprotein (P-gp) has been identified as a major contributor to MDR. Inspired by naturally occurring MDR-reversing cyclic peptides, a series of readily accessible valine thiazole-containing derivatives were designed and synthesized as effective reversal agents against P-gp–mediated MDR based on a hybridization strategy. Structure–activity relationship (SAR) analysis demonstrated that linear valine thiazole derivatives possess greater MDR reversal activity than their macrocyclic analogs. Compound <strong>17e</strong> displayed promising synergistic activity by significantly enhancing the therapeutic efficacy of paclitaxel (PTX) against KBV cells (IC<sub>50</sub> = 2.8 nM, reversal fold = 288.5) without inducing obvious toxicity. <strong>17e</strong> exhibited approximately 8-fold greater potency than verapamil (VRP), 2-fold greater potency than the third-generation P-gp inhibitor tariquidar (TAR) in KBV cells. Mechanistic studies confirmed that <strong>17e</strong> inhibits the efflux function of P-gp in a concentration-dependent manner without affecting its expression, thereby increasing intracellular chemotherapeutic drug accumulation and causing G<sub>2</sub>/M phase arrests, which is associated with increased apoptosis. Taken together, the linear valine thiazole derivative <strong>17e</strong> represents a promising starting scaffold for developing novel P-gp inhibitors against MDR.</div></div>","PeriodicalId":255,"journal":{"name":"Bioorganic & Medicinal Chemistry","volume":"134 ","pages":"Article 118522"},"PeriodicalIF":3.0,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145789207","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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