Benjamin E. Deprez, Debayan Dey, Natalia Zelinskaya, Erika E. Csatary, Qimin Winnie Yang, Minhua Nie, Graeme L. Conn, William M. Wuest
One of the major mechanisms of resistance to ribosome-targeting antibiotics is the modification of ribosomal RNA (rRNA). Specific methyltransferase enzymes, for example, confer high-level resistance to aminoglycosides by selectively methylating the 16S rRNA in the ribosomal decoding center. These enzymes have been detected globally and pose a threat to the continued use of aminoglycosides. Compound 1, a dehydroamino amide inhibitor of the m1A1408 methyltransferase NpmA, was previously disclosed and identified using high-throughput virtual screening. Here, the synthesis and biological evaluation of rationally designed analogs of 1 has been reported. Guided by molecular docking, additional putative inhibitors of NpmA, as well as the functionally related m7G1405 methyltransferase RmtB, varying in each region of the original scaffold are disclosed. A modular, fragment-based synthesis enables access to 17 analogs, which exhibits mixed activity against NpmA and RmtB, including several that are selective for RmtB. The structure–activity relationship determined for the dehydroamino amide series will guide continued research against this target class with the aim of developing a toolkit for selective- or pan-16S rRNA methyltransferase inhibition.
{"title":"Design, Synthesis, and Evaluation of Novel Inhibitors of Aminoglycoside-Resistance 16S Ribosomal RNA Methyltransferases","authors":"Benjamin E. Deprez, Debayan Dey, Natalia Zelinskaya, Erika E. Csatary, Qimin Winnie Yang, Minhua Nie, Graeme L. Conn, William M. Wuest","doi":"10.1002/cmdc.202500889","DOIUrl":"10.1002/cmdc.202500889","url":null,"abstract":"<p>One of the major mechanisms of resistance to ribosome-targeting antibiotics is the modification of ribosomal RNA (rRNA). Specific methyltransferase enzymes, for example, confer high-level resistance to aminoglycosides by selectively methylating the 16S rRNA in the ribosomal decoding center. These enzymes have been detected globally and pose a threat to the continued use of aminoglycosides. Compound <b>1</b>, a dehydroamino amide inhibitor of the m<sup>1</sup>A1408 methyltransferase NpmA, was previously disclosed and identified using high-throughput virtual screening. Here, the synthesis and biological evaluation of rationally designed analogs of <b>1</b> has been reported. Guided by molecular docking, additional putative inhibitors of NpmA, as well as the functionally related m<sup>7</sup>G1405 methyltransferase RmtB, varying in each region of the original scaffold are disclosed. A modular, fragment-based synthesis enables access to 17 analogs, which exhibits mixed activity against NpmA and RmtB, including several that are selective for RmtB. The structure–activity relationship determined for the dehydroamino amide series will guide continued research against this target class with the aim of developing a toolkit for selective- or pan-16S rRNA methyltransferase inhibition.</p>","PeriodicalId":147,"journal":{"name":"ChemMedChem","volume":"21 4","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145706847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Assessing if compounds with intracellular targets reach their site of action is crucial for success in drug development. Cell type-specific uptake goes beyond permeability studies, typically mimicking crossing the gut, the lung, or the blood–brain barrier. A medium- to high-throughput cellular accumulation protocol in 96-well format is presented using six compounds, evaluating optimal conditions varying several parameters, such as incubation time, compound concentration, and extraction protocol. An optimized assay protocol for cellular accumulation of distinct chemical classes is a compromise: No one-extraction-protocol-fits-all exists; equally, some compounds need longer incubation periods to reach maximal intracellular concentration. Reliable high performance liquid chromatography with tandem mass spectrometry based quantification of cellular accumulation for all six compounds to the nM range is achieved with a short 1 h incubation. Intracellular concentrations per cell count are determined in A549ACE+TMPRSS2 cells, taking nonspecific binding into account. Hence, this approach adds valuable information during the pre-screening of compounds with intracellular targets. Finally, optimal assay conditions are emphasized as essential for predicting activity in vitro and in vivo, based on biochemical information and intracellular concentrations. In summary, the workflow for cellular accumulation determination can serve two scenarios: 1) Pre-selection of compounds for screening purposes or 2) systematic optimization of conditions to advance compounds with intracellular targets.
{"title":"A Streamlined High Performance Liquid Chromatography with Tandem Mass Spectrometry Based Workflow for Rapid Screening of Cellular Accumulation of Small Molecules","authors":"Alina Metzen, Katharina Rox","doi":"10.1002/cmdc.202500753","DOIUrl":"10.1002/cmdc.202500753","url":null,"abstract":"<p>Assessing if compounds with intracellular targets reach their site of action is crucial for success in drug development. Cell type-specific uptake goes beyond permeability studies, typically mimicking crossing the gut, the lung, or the blood–brain barrier. A medium- to high-throughput cellular accumulation protocol in 96-well format is presented using six compounds, evaluating optimal conditions varying several parameters, such as incubation time, compound concentration, and extraction protocol. An optimized assay protocol for cellular accumulation of distinct chemical classes is a compromise: No one-extraction-protocol-fits-all exists; equally, some compounds need longer incubation periods to reach maximal intracellular concentration. Reliable high performance liquid chromatography with tandem mass spectrometry based quantification of cellular accumulation for all six compounds to the nM range is achieved with a short 1 h incubation. Intracellular concentrations per cell count are determined in A549<sup>ACE+TMPRSS2</sup> cells, taking nonspecific binding into account. Hence, this approach adds valuable information during the pre-screening of compounds with intracellular targets. Finally, optimal assay conditions are emphasized as essential for predicting activity in vitro and in vivo, based on biochemical information and intracellular concentrations. In summary, the workflow for cellular accumulation determination can serve two scenarios: 1) Pre-selection of compounds for screening purposes or 2) systematic optimization of conditions to advance compounds with intracellular targets.</p>","PeriodicalId":147,"journal":{"name":"ChemMedChem","volume":"21 4","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12913241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145706871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Monika Marcinkowska, Mariana Antunes, Kinga Piórecka, Catarina Pinto Reis, Jan Kurjata, Włodzimierz Stańczyk, Barbara Klajnert-Maculewicz
Female cancers, primarily breast, cervical, and ovarian cancers, remain a major public health challenge, with rising incidence and high mortality. Cisplatin has long been a cornerstone of anticancer therapy, yet its clinical use is limited by low selectivity, severe side effects, drug resistance, and relapse. Thus, more effective and selective therapeutic strategies are needed. In this study, we evaluated the cytotoxicity and mechanisms of action of three cisplatin derivatives (C-cisplatin, D-cisplatin, and Ac-cisplatin) and their complexes with generation 2 polyamidoamine (PAMAM G2) dendrimers. All drug–dendrimer complexes were prepared at a 10:1 molar ratio and tested on two cancer cell lines—HeLa (cervical cancer) and MCF-7 (breast cancer)—and one non-cancer human microvascular endothelial cell line (HMEC-1). Complex formation was confirmed by zeta potential measurements. Cytotoxicity was assessed for both free and complexed drugs. To explore potential mechanisms of action, mitochondrial membrane potential and reactive oxygen species (ROS) levels were evaluated. Flow cytometry was then used to determine dominant cell-death pathways. The complexes demonstrated cytotoxicity comparable to or greater than cisplatin and showed improved selectivity toward cancer cells. Among them, D-cisplatin complexed with PAMAM G2 was the most promising candidate, exhibiting the highest selectivity toward HeLa cells.
{"title":"Cisplatin Derivatives and Their Complexes with PAMAM Dendrimers—A Way to Improve the Efficacy of Anticancer Drugs","authors":"Monika Marcinkowska, Mariana Antunes, Kinga Piórecka, Catarina Pinto Reis, Jan Kurjata, Włodzimierz Stańczyk, Barbara Klajnert-Maculewicz","doi":"10.1002/cmdc.202500881","DOIUrl":"10.1002/cmdc.202500881","url":null,"abstract":"<p>Female cancers, primarily breast, cervical, and ovarian cancers, remain a major public health challenge, with rising incidence and high mortality. Cisplatin has long been a cornerstone of anticancer therapy, yet its clinical use is limited by low selectivity, severe side effects, drug resistance, and relapse. Thus, more effective and selective therapeutic strategies are needed. In this study, we evaluated the cytotoxicity and mechanisms of action of three cisplatin derivatives (C-cisplatin, D-cisplatin, and Ac-cisplatin) and their complexes with generation 2 polyamidoamine (PAMAM G2) dendrimers. All drug–dendrimer complexes were prepared at a 10:1 molar ratio and tested on two cancer cell lines—HeLa (cervical cancer) and MCF-7 (breast cancer)—and one non-cancer human microvascular endothelial cell line (HMEC-1). Complex formation was confirmed by zeta potential measurements. Cytotoxicity was assessed for both free and complexed drugs. To explore potential mechanisms of action, mitochondrial membrane potential and reactive oxygen species (ROS) levels were evaluated. Flow cytometry was then used to determine dominant cell-death pathways. The complexes demonstrated cytotoxicity comparable to or greater than cisplatin and showed improved selectivity toward cancer cells. Among them, D-cisplatin complexed with PAMAM G2 was the most promising candidate, exhibiting the highest selectivity toward HeLa cells.</p>","PeriodicalId":147,"journal":{"name":"ChemMedChem","volume":"21 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145706810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gareth Arnott, Jonah Ruskin, Antonin Knirsch, Aditya Vardhan, Adam Huczyński, Travis Dudding, Thomas Lectka
Imagine a divalent metal ion (such as Zn(II)) binding to a folded ionophore such as salinomycin. The resulting complex is superacidified, shooting a proton at an unbound salinomycin molecule and cleaving it into two parts. However, when potassium ion is prebound to salinomycin, no superacidic protons are generated by this complex, whereas the protons generated by the divalent metal ion complex just bounce off. More details can be found in the Research Article by Adam Huczyński, Travis Dudding, Thomas Lectka, and co-workers (DOI: 10.1002/cmdc.202500783).