Pub Date : 2025-11-25DOI: 10.1016/j.jinorgbio.2025.113162
Yan Zhao , Xinyu Ma , Qingchuan Zheng
Triazolam (TRZ) is a representative benzodiazepine sedative-hypnotic drug that has gradually been abused due to the increasing societal pressures. To further provide a theoretical basis for the rationale use of TRZ and obtain more information for its metabolic process, in this study, human CYP3A4 was employed as the metabolic enzyme to investigate the metabolic mechanism of TRZ by multiple computational methods. Here, three types of substrate-binding conformations related to the diversity of TRZ metabolites are identified (pose A, pose B and pose C). The “sandwich” structure and the π-π stacking between TRZ and F304/porphyrin ring may be the key factors in dominating three substrate-binding conformations. Furthermore, we discovered pose A is the predominant binding mode, with Cα-H serving as the key metabolic site and CYP3A4-catalyzed Cα-H hydroxylation follows a hydrogen abstraction-rebound mechanism. More importantly, in hydroxylation process, the spin states of iron can regulate the metabolic reaction rate of TRZ and the highest rate of metabolism (5.96 s−1) is found in the quartet spin states. Based on our findings, it can be suggested that rational incorporating aromatic groups into TRZ could improve its metabolic stability. Meanwhile, the transition of the heme iron from a low-spin to a high-spin state appears to accelerate TRZ metabolism, potentially leading to the accumulation of α-OH triazolam in vivo, which may pose risks to human health. These results could enhance our understanding of CYP3A4-mediated regioselective metabolism of TRZ and provide a theoretical foundation and new perspective for studies on the metabolism of other triazole drugs.
{"title":"Impact of electrostatic distribution in CYP3A4 on the regioselectivity of triazolam metabolism and regulation of its metabolic rate by the iron spin states: Insights from MD simulations and QM calculations","authors":"Yan Zhao , Xinyu Ma , Qingchuan Zheng","doi":"10.1016/j.jinorgbio.2025.113162","DOIUrl":"10.1016/j.jinorgbio.2025.113162","url":null,"abstract":"<div><div>Triazolam (TRZ) is a representative benzodiazepine sedative-hypnotic drug that has gradually been abused due to the increasing societal pressures. To further provide a theoretical basis for the rationale use of TRZ and obtain more information for its metabolic process, in this study, human CYP3A4 was employed as the metabolic enzyme to investigate the metabolic mechanism of TRZ by multiple computational methods. Here, three types of substrate-binding conformations related to the diversity of TRZ metabolites are identified (pose A, pose B and pose C). The “sandwich” structure and the π-π stacking between TRZ and F304/porphyrin ring may be the key factors in dominating three substrate-binding conformations. Furthermore, we discovered pose A is the predominant binding mode, with Cα-H serving as the key metabolic site and CYP3A4-catalyzed Cα-H hydroxylation follows a hydrogen abstraction-rebound mechanism. More importantly, in hydroxylation process, the spin states of iron can regulate the metabolic reaction rate of TRZ and the highest rate of metabolism (5.96 s<sup>−1</sup>) is found in the quartet spin states. Based on our findings, it can be suggested that rational incorporating aromatic groups into TRZ could improve its metabolic stability. Meanwhile, the transition of the heme iron from a low-spin to a high-spin state appears to accelerate TRZ metabolism, potentially leading to the accumulation of α-OH triazolam in vivo, which may pose risks to human health. These results could enhance our understanding of CYP3A4-mediated regioselective metabolism of TRZ and provide a theoretical foundation and new perspective for studies on the metabolism of other triazole drugs.</div></div>","PeriodicalId":364,"journal":{"name":"Journal of Inorganic Biochemistry","volume":"276 ","pages":"Article 113162"},"PeriodicalIF":3.2,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145617585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-24DOI: 10.1016/j.jinorgbio.2025.113155
Dariusz Wyrzykowski , Katarzyna Chmur , Jakub Brzeski , Artur Sikorski , Olga Tovchiga , Justyna Budka , Iwona Inkielewicz-Stępniak , Aleksandra Tesmar
This research aimed to compare the crystal structure, physicochemical, and biological properties of novel (acetylacetonate)(thiodiacetato)oxidovanadium(IV) complex salts, namely [QH][VO(acac)(tda)] (1) and [(acr)H][VO(acac)(tda)] (2) (acac = acetylacetonate, tda2− = thiodiacetate, Q = quinoline, acr = acridine) with previously reported oxydiacetate (oda−) analogues: [QH][VO(acac)(oda)] (3) and [(acr)H][VO(acac)(oda)](H2O)2 (4). A combination of experimental data, including X-ray crystallography, IR spectroscopy, potentiometric measurements and ESI-MS, and density functional theory (DFT) calculations enables thorough characterization of the complexes in the solid state and in solution. It has been demonstrated that the observed differences in the nature of VS (thioether) and VO (ether) dative bonds have only a slight impact on orbital energy levels and spin density distribution. At the same time, these minor differences do not significantly affect the thermodynamic stability of the complexes: logß1110 {[VO(acac)(tda)]−} = 16.91 and logß1110 {[VO(acac)(oda)]−} = 16.45. Additionally, the calculated thermodynamic parameters for the formation of these complexes (∆H, T∆S, ∆G in kcal mol−1, at 298 K) are −66.72, −16.38, and − 50.34 for [VO(acac)(tda)]−, and − 68.47, −15.64, and − 52.82 for [VO(acac)(oda)]−, respectively. The biological evaluations showed promising selective cytotoxic activity of the investigated complex salts against the human osteosarcoma cell line MG-63. The mechanism of biological action of these complexes appears to involve disruption of cell cycle regulation and induction of apoptosis. The counterions (acridine and quinoline) alone do not significantly affect cell cycle distribution, suggesting that the cytotoxic and cell cycle effects are primarily due to the [VO(acac)(tda)]− and [VO(acac)(oda)]− species.
{"title":"Thiodiacetate vs. oxydiacetate: physicochemical and biological properties of new heteroligand (acetylacetonate)oxidovanadium(IV) complexes","authors":"Dariusz Wyrzykowski , Katarzyna Chmur , Jakub Brzeski , Artur Sikorski , Olga Tovchiga , Justyna Budka , Iwona Inkielewicz-Stępniak , Aleksandra Tesmar","doi":"10.1016/j.jinorgbio.2025.113155","DOIUrl":"10.1016/j.jinorgbio.2025.113155","url":null,"abstract":"<div><div>This research aimed to compare the crystal structure, physicochemical, and biological properties of novel (acetylacetonate)(thiodiacetato)oxidovanadium(IV) complex salts, namely [QH][VO(acac)(tda)] (<strong>1</strong>) and [(acr)H][VO(acac)(tda)] (<strong>2</strong>) (acac = acetylacetonate, tda<sup>2−</sup> = thiodiacetate, Q = quinoline, acr = acridine) with previously reported oxydiacetate (oda<sup>−</sup>) analogues: [QH][VO(acac)(oda)] (<strong>3</strong>) and [(acr)H][VO(acac)(oda)](H<sub>2</sub>O)<sub>2</sub> (<strong>4</strong>). A combination of experimental data, including X-ray crystallography, IR spectroscopy, potentiometric measurements and ESI-MS, and density functional theory (DFT) calculations enables thorough characterization of the complexes in the solid state and in solution. It has been demonstrated that the observed differences in the nature of <em>V</em><img>S (thioether) and V<img>O (ether) dative bonds have only a slight impact on orbital energy levels and spin density distribution. At the same time, these minor differences do not significantly affect the thermodynamic stability of the complexes: log<em>ß</em><sub>1110</sub> {[VO(acac)(tda)]<sup>−</sup>} = 16.91 and log<em>ß</em><sub>1110</sub> {[VO(acac)(oda)]<sup>−</sup>} = 16.45. Additionally, the calculated thermodynamic parameters for the formation of these complexes (∆<em>H</em>, T∆<em>S</em>, ∆<em>G</em> in kcal mol<sup>−1</sup>, at 298 K) are −66.72, −16.38, and − 50.34 for [VO(acac)(tda)]<sup>−</sup>, and − 68.47, −15.64, and − 52.82 for [VO(acac)(oda)]<sup>−</sup>, respectively. The biological evaluations showed promising selective cytotoxic activity of the investigated complex salts against the human osteosarcoma cell line MG-63. The mechanism of biological action of these complexes appears to involve disruption of cell cycle regulation and induction of apoptosis. The counterions (acridine and quinoline) alone do not significantly affect cell cycle distribution, suggesting that the cytotoxic and cell cycle effects are primarily due to the [VO(acac)(tda)]<sup>−</sup> and [VO(acac)(oda)]<sup>−</sup> species.</div></div>","PeriodicalId":364,"journal":{"name":"Journal of Inorganic Biochemistry","volume":"276 ","pages":"Article 113155"},"PeriodicalIF":3.2,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145600641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-24DOI: 10.1016/j.jinorgbio.2025.113158
Jia-yu Xu , Xue-bin Bi , Sha-sha Luo, Yue Huang, Chen-yu Wang, Chang-chun Wen, Rui-xue Liu, Yan-cheng Liu, Hong Liang
This research presents the design, synthesis, structural characterization, and evaluation of the anticancer activities of three new pyrimidylanthrahydrazone cobalt(II) complexes: 1) 9-MPMAH-Co, 2) 9-FPMAH-Co, and 3) 9-PMAH-Co. Single-crystal X-ray diffraction analysis confirmed that all three complexes adopt a hexacoordinate mononuclear geometry. However, differences in their coordination modes were observed due to variations in the ligand substituents (-CH3, -F, -H). Spectroscopic DNA interaction studies indicated that all three cobalt complexes exhibit varying levels of DNA intercalation. Topoisomerase I inhibition assays revealed that 9-PMAH-Co demonstrates significant enzyme inhibition at a low concentration of 1 μM. In vitro antiproliferative assays confirmed that 9-PMAH-Co exhibits potent cytotoxic activity against SK-OV-3 and HeLa-229 cancer cell lines, with IC₅₀ values of 4.99 ± 0.18 μM and 8.09 ± 1.13 μM, respectively, while showing reduced toxicity toward normal liver cells (HL-7702) compared to cisplatin. Further investigation through cell cycle analysis indicated that 9-PMAH-Co induces G2/M phase arrest in SK-OV-3 cells, with a population increase to 91.37 % (Δ = 76.59 %). Studies on the structural-activity relationship suggest that the synergistic interactions between the ligand substituents and the cobalt center play a crucial role in modulating biological activity, highlighting 9-PMAH-Co as a promising lead compound for the development of targeted anticancer agents.
{"title":"Three cobalt(II) complexes containing pyrimidylanthrahydrazone ligands: Synthesis, crystal structure, DNA binding, anticancer activity and structure-activity relationship","authors":"Jia-yu Xu , Xue-bin Bi , Sha-sha Luo, Yue Huang, Chen-yu Wang, Chang-chun Wen, Rui-xue Liu, Yan-cheng Liu, Hong Liang","doi":"10.1016/j.jinorgbio.2025.113158","DOIUrl":"10.1016/j.jinorgbio.2025.113158","url":null,"abstract":"<div><div>This research presents the design, synthesis, structural characterization, and evaluation of the anticancer activities of three new pyrimidylanthrahydrazone cobalt(II) complexes: <strong>1</strong>) 9-MPMAH-Co, <strong>2</strong>) 9-FPMAH-Co, and <strong>3</strong>) 9-PMAH-Co. Single-crystal X-ray diffraction analysis confirmed that all three complexes adopt a hexacoordinate mononuclear geometry. However, differences in their coordination modes were observed due to variations in the ligand substituents (-CH<sub>3</sub>, -F, -H). Spectroscopic DNA interaction studies indicated that all three cobalt complexes exhibit varying levels of DNA intercalation. Topoisomerase I inhibition assays revealed that 9-PMAH-Co demonstrates significant enzyme inhibition at a low concentration of 1 μM. <em>In vitro</em> antiproliferative assays confirmed that 9-PMAH-Co exhibits potent cytotoxic activity against SK-OV-3 and HeLa-229 cancer cell lines, with IC₅₀ values of 4.99 ± 0.18 μM and 8.09 ± 1.13 μM, respectively, while showing reduced toxicity toward normal liver cells (HL-7702) compared to cisplatin. Further investigation through cell cycle analysis indicated that 9-PMAH-Co induces G2/M phase arrest in SK-OV-3 cells, with a population increase to 91.37 % (Δ = 76.59 %). Studies on the structural-activity relationship suggest that the synergistic interactions between the ligand substituents and the cobalt center play a crucial role in modulating biological activity, highlighting 9-PMAH-Co as a promising lead compound for the development of targeted anticancer agents.</div></div>","PeriodicalId":364,"journal":{"name":"Journal of Inorganic Biochemistry","volume":"276 ","pages":"Article 113158"},"PeriodicalIF":3.2,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145666590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-24DOI: 10.1016/j.jinorgbio.2025.113161
Iogann Tolbatov , Alessandro Marrone
Auranofin (AF) is a clinically approved gold(I) metallodrug with recognized anti-inflammatory and anticancer properties, whose mechanism of action relies on the covalent binding at key selenoproteins and thiols causing their irreversible deactivation. While the final covalent binding event is well-documented, the initial non-covalent recognition phase that precedes it, and which likely governs the drug's selectivity, remains poorly characterized by experimental methods. To address this gap, we employed density functional theory (DFT) calculations to systematically investigate the weak, pre-covalent interactions between auranofin (AF) or its chlorido derivative, Au(PEt3 )Cl (AFCl), with model protein residues. Our results reveal distinct non-covalent interactions preferences for each drug: AF shows a stronger affinity for charged amino acid residues, while AFCl exhibits a marked preference for aromatic and some charged residues. We demonstrate that these initial non-covalent interactions induce a significant redistribution of electron density. This effect alters the local electronic properties of the gold center and its bond to the labile ligand, effectively priming the drug for subsequent covalent attack. We then utilized the computationally derived geometric assets to perform a comprehensive motif search within the Protein Data Bank (PDB) database, which identified ten protein targets with significant therapeutic relevance. This bioinformatic analysis provided a general picture of how these gold compounds navigate their biological environment and led to the identification of targets. This pre-covalent interaction with protein is not a random anchoring process but a crucial preparatory step for the targeted attachment of gold-based drugs.
{"title":"Combined computational and bioinformatic approach to uncover the pre-covalent protein interactions of auranofin and its chlorido derivative Au(PEt₃)Cl","authors":"Iogann Tolbatov , Alessandro Marrone","doi":"10.1016/j.jinorgbio.2025.113161","DOIUrl":"10.1016/j.jinorgbio.2025.113161","url":null,"abstract":"<div><div>Auranofin (AF) is a clinically approved gold(I) metallodrug with recognized anti-inflammatory and anticancer properties, whose mechanism of action relies on the covalent binding at key selenoproteins and thiols causing their irreversible deactivation. While the final covalent binding event is well-documented, the initial non-covalent recognition phase that precedes it, and which likely governs the drug's selectivity, remains poorly characterized by experimental methods. To address this gap, we employed density functional theory (DFT) calculations to systematically investigate the weak, pre-covalent interactions between auranofin (AF) or its chlorido derivative, Au(PEt<sub>3</sub> <!-->)Cl (AFCl), with model protein residues. Our results reveal distinct non-covalent interactions preferences for each drug: AF shows a stronger affinity for charged amino acid residues, while AFCl exhibits a marked preference for aromatic and some charged residues. We demonstrate that these initial non-covalent interactions induce a significant redistribution of electron density. This effect alters the local electronic properties of the gold center and its bond to the labile ligand, effectively priming the drug for subsequent covalent attack. We then utilized the computationally derived geometric assets to perform a comprehensive motif search within the Protein Data Bank (PDB) database, which identified ten protein targets with significant therapeutic relevance. This bioinformatic analysis provided a general picture of how these gold compounds navigate their biological environment and led to the identification of targets. This pre-covalent interaction with protein is not a random anchoring process but a crucial preparatory step for the targeted attachment of gold-based drugs.</div></div>","PeriodicalId":364,"journal":{"name":"Journal of Inorganic Biochemistry","volume":"276 ","pages":"Article 113161"},"PeriodicalIF":3.2,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145617587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-21DOI: 10.1016/j.jinorgbio.2025.113157
Benlian Xue, Youkun Zang, Wang Lv, Yuheng Zhang, Shuangyang Zhang, Xiaoshuang Li, Qinghua Chang, Yongjian Lu, Xicheng Liu, Zhe Liu
Although widely used clinically, the extensive nephrotoxicity and drug resistance of platinum-based metallic anticancer drugs have spurred the research and development of non‑platinum-based metallic anticancer drugs. Half-sandwich iridium(III) (IrIII) complexes have become a research hotspot in this field due to their excellent anticancer activity, structural tunability, and unique mechanism of action different from that of cisplatin. Then two half-sandwich IrIII xanthate complexes with a simple structure were prepared in this study. In vitro anti-proliferative evaluation showed that these two complexes enjoyed favorable activity towards A549 lung cancer cells in comparison to cisplatin, and could also effectively inhibit cell migration. Further research showed that Ir1 could target lysosomes (PCC: 0.85) and lead to lysosomal damage, then disturbing the cell cycle arrest (G0/G1 phase), decreasing mitochondrial membrane potential and inducing the improvement of intracellular reactive oxygen species levels. Western blotting also confirmed the existence of a lysosomal-mitochondrial apoptotic anticancer pathway. Collectively, these structurally simple yet highly active IrIII complexes provide a valuable foundation for the rational design and development of novel non‑platinum-based metallic anticancer drugs.
{"title":"Anticancer behaviour of simplified lysosome-targeted half-sandwich iridium(III) xanthate complexes towards A549 cell lines","authors":"Benlian Xue, Youkun Zang, Wang Lv, Yuheng Zhang, Shuangyang Zhang, Xiaoshuang Li, Qinghua Chang, Yongjian Lu, Xicheng Liu, Zhe Liu","doi":"10.1016/j.jinorgbio.2025.113157","DOIUrl":"10.1016/j.jinorgbio.2025.113157","url":null,"abstract":"<div><div>Although widely used clinically, the extensive nephrotoxicity and drug resistance of platinum-based metallic anticancer drugs have spurred the research and development of non‑platinum-based metallic anticancer drugs. Half-sandwich iridium(III) (Ir<sup>III</sup>) complexes have become a research hotspot in this field due to their excellent anticancer activity, structural tunability, and unique mechanism of action different from that of cisplatin. Then two half-sandwich Ir<sup>III</sup> xanthate complexes with a simple structure were prepared in this study. In vitro anti-proliferative evaluation showed that these two complexes enjoyed favorable activity towards A549 lung cancer cells in comparison to cisplatin, and could also effectively inhibit cell migration. Further research showed that <strong>Ir1</strong> could target lysosomes (PCC: 0.85) and lead to lysosomal damage, then disturbing the cell cycle arrest (G<sub>0</sub>/G<sub>1</sub> phase), decreasing mitochondrial membrane potential and inducing the improvement of intracellular reactive oxygen species levels. Western blotting also confirmed the existence of a lysosomal-mitochondrial apoptotic anticancer pathway. Collectively, these structurally simple yet highly active Ir<sup>III</sup> complexes provide a valuable foundation for the rational design and development of novel non‑platinum-based metallic anticancer drugs.</div></div>","PeriodicalId":364,"journal":{"name":"Journal of Inorganic Biochemistry","volume":"275 ","pages":"Article 113157"},"PeriodicalIF":3.2,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145601625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-20DOI: 10.1016/j.jinorgbio.2025.113156
Yajing Luo , Qixuan Yang , Yabing Gan , Caixia Dou , Haiyan Wang , Qiujun Lu , Guoxing Yin , Fuyou Du , Peng Yin
Sn2+ pollution poses significant risks to ecosystems and human health, necessitating the development of simple detection methods for accurate monitoring of Sn2+ dynamics. Here, we developed a conceptually distinct strategy that exploits the Sn2+-mediated reduction of organic azides rather than conventional chelation mechanism, and constructed a series of azide-based fluorescent probes (A–G) operating via turn-on, ratiometric, or fluorescence resonance energy transfer modality with emissions spanning blue to near-infrared for specific sensing of Sn2+. These probes exhibit exceptional selectivity for Sn2+ over Sn4+ and other biologically relevant species, sub-micromolar detection limits (as low as 13.7 nM), fast response kinetics (t1/2 < 1 min), and full aqueous compatibility. The reduction mechanism was confirmed through radical trapping and product isolation. Probe B enabled direct quantify Sn2+ in real water samples with good recovery (93.5–103.3 %). All designed probes facilitated high-contrast in-situ imaging of Sn2+ in living cells. This work provides a robust platform for deciphering the environmental fate and biological roles of Sn2+.
{"title":"A general strategy for specific sensing of Sn2+ in environmental water samples and in cells","authors":"Yajing Luo , Qixuan Yang , Yabing Gan , Caixia Dou , Haiyan Wang , Qiujun Lu , Guoxing Yin , Fuyou Du , Peng Yin","doi":"10.1016/j.jinorgbio.2025.113156","DOIUrl":"10.1016/j.jinorgbio.2025.113156","url":null,"abstract":"<div><div>Sn<sup>2+</sup> pollution poses significant risks to ecosystems and human health, necessitating the development of simple detection methods for accurate monitoring of Sn<sup>2+</sup> dynamics. Here, we developed a conceptually distinct strategy that exploits the Sn<sup>2+</sup>-mediated reduction of organic azides rather than conventional chelation mechanism, and constructed a series of azide-based fluorescent probes (<strong>A</strong>–<strong>G</strong>) operating via turn-on, ratiometric, or fluorescence resonance energy transfer modality with emissions spanning blue to near-infrared for specific sensing of Sn<sup>2+</sup>. These probes exhibit exceptional selectivity for Sn<sup>2+</sup> over Sn<sup>4+</sup> and other biologically relevant species, sub-micromolar detection limits (as low as 13.7 nM), fast response kinetics (<em>t</em><sub>1/2</sub> < 1 min), and full aqueous compatibility. The reduction mechanism was confirmed through radical trapping and product isolation. Probe B enabled direct quantify Sn<sup>2+</sup> in real water samples with good recovery (93.5–103.3 %). All designed probes facilitated high-contrast in-situ imaging of Sn<sup>2+</sup> in living cells. This work provides a robust platform for deciphering the environmental fate and biological roles of Sn<sup>2+</sup>.</div></div>","PeriodicalId":364,"journal":{"name":"Journal of Inorganic Biochemistry","volume":"275 ","pages":"Article 113156"},"PeriodicalIF":3.2,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145569217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-20DOI: 10.1016/j.jinorgbio.2025.113153
Ivana R. Scolari, Mario A. Quevedo, Paulina L. Páez, Gladys E. Granero
This paper reports the development of a complex between the antibiotic gentamicin sulfate (GEN), consisting of four major congeners, and zinc ions (Zn(II)GEN complex). The composition of the complex aligns well with the proposed molecular formula [Zn₂+(L)(3H₂O)(2SO₄2−]. The Zn(II)GEN complex significantly enhanced inhibitory and bactericidal activity against S. aureus, E faecalis, P. aeruginosa, and E. coli. Unlike gentamicin sulfate alone, the Zn(II)-GEN complex did not induce drug-resistant mutants. Molecular modeling predicted predominantly hexacoordinated complexes involving three contact points with gentamicin and three with water, which agreed with the spectroscopic studies. The complexes adopted a restricted conformation of gentamicin, resulting in its hydrophilic groups being excluded from the solvent, which is consistent with the higher permeability. Molecular Modeling studies of the Zn(II)GEN complex with 16S RNA revealed a restricted bioactive conformation with stable interactions with residues A1493, G1494, and U1495, a structural requirement for antimicrobial activity. Free energy of binding analyses show that the Zn(II)GEN complex had better pharmacodynamic properties than the pure compound. A favored bioactive conformation formed upon the complexation of gentamicin sulfate with Zn(II) increased the complex's potency against bacteria and allowed it to penetrate bacterial cells. The complex also reduces the likelihood of antimicrobial resistance. The strategy is a good starting point for research into combating bacteria.
{"title":"A zinc (II) gentamicin metalloantibiotic with outstanding antimicrobial activity and reduced susceptibility to bacterial resistance mechanisms: Experimental and theoretical explorations","authors":"Ivana R. Scolari, Mario A. Quevedo, Paulina L. Páez, Gladys E. Granero","doi":"10.1016/j.jinorgbio.2025.113153","DOIUrl":"10.1016/j.jinorgbio.2025.113153","url":null,"abstract":"<div><div>This paper reports the development of a complex between the antibiotic gentamicin sulfate (GEN), consisting of four major congeners, and zinc ions (Zn(II)GEN complex). The composition of the complex aligns well with the proposed molecular formula [Zn<sup>₂+</sup>(L)(3H₂O)(2SO₄<sup>2−</sup>]. The Zn(II)GEN complex significantly enhanced inhibitory and bactericidal activity against <em>S. aureus</em>, <em>E faecalis</em>, <em>P. aeruginosa</em>, and <em>E. coli</em>. Unlike gentamicin sulfate alone, the Zn(II)-GEN complex did not induce drug-resistant mutants. Molecular modeling predicted predominantly hexacoordinated complexes involving three contact points with gentamicin and three with water, which agreed with the spectroscopic studies. The complexes adopted a restricted conformation of gentamicin, resulting in its hydrophilic groups being excluded from the solvent, which is consistent with the higher permeability. Molecular Modeling studies of the Zn(II)GEN complex with 16S RNA revealed a restricted bioactive conformation with stable interactions with residues A1493, G1494, and U1495, a structural requirement for antimicrobial activity. Free energy of binding analyses show that the Zn(<em>II</em>)GEN complex had better pharmacodynamic properties than the pure compound. A favored bioactive conformation formed upon the complexation of gentamicin sulfate with Zn(II) increased the complex's potency against bacteria and allowed it to penetrate bacterial cells. The complex also reduces the likelihood of antimicrobial resistance. The strategy is a good starting point for research into combating bacteria.</div></div>","PeriodicalId":364,"journal":{"name":"Journal of Inorganic Biochemistry","volume":"276 ","pages":"Article 113153"},"PeriodicalIF":3.2,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145600640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-19DOI: 10.1016/j.jinorgbio.2025.113154
Maria De Fenza , Linda Leone , Matilde Tancredi , Edelberto Oscar Niola , Ornella Maglio , Gerardino D'Errico , Flavia Nastri , Daniele D’Alonzo , Angela Lombardi
Natural peroxidases use 4-halophenols either as substrates in oxidative chemistry or as inhibitors. Herein, we demonstrated that Fe-mimochrome VI*a (Fe-MC6*a), a miniaturized heme-enzyme, is a versatile catalyst as it integrates both these features. We previously reported that Fe-MC6*a catalyzes the chemo- and regio-selective oxidation of 4-halophenols, providing either dehalogenation or oligomerization products, depending on the nature of the halogen atom. In particular, 4-chlorophenol (4-CP) and 4-fluorophenol (4-FP) selectively led to dehalogenation and oligomerization products, respectively. Herein, spin-trapping studies and EPR analysis confirm the ability of Fe-MC6*a into processing halophenols as substrates and provide mechanistic hypothesis for the chemo-divergent reaction outcome. Further, in multiple substrate competition assays, 4-halophenols act as competitive inhibitors of Fe-MC6*a-catalyzed dehalogenation of 2,4,6-trichlorophenol (TCP). Nonetheless, the catalyst retains appreciable turnover in such complex substrate mixtures. Taken together, the combination of substrate-specific selectivity and resilience to the total inhibition position Fe-MC6*a as a promising bioremediation catalyst for simultaneous halophenol detoxification in wastewater-treatment applications.
{"title":"Dehalogenation activity of a miniaturized peroxidase: substrate dependent functional switch","authors":"Maria De Fenza , Linda Leone , Matilde Tancredi , Edelberto Oscar Niola , Ornella Maglio , Gerardino D'Errico , Flavia Nastri , Daniele D’Alonzo , Angela Lombardi","doi":"10.1016/j.jinorgbio.2025.113154","DOIUrl":"10.1016/j.jinorgbio.2025.113154","url":null,"abstract":"<div><div>Natural peroxidases use 4-halophenols either as substrates in oxidative chemistry or as inhibitors. Herein, we demonstrated that Fe-mimochrome VI*a (Fe-MC6*a), a miniaturized heme-enzyme, is a versatile catalyst as it integrates both these features. We previously reported that Fe-MC6*a catalyzes the chemo- and regio-selective oxidation of 4-halophenols, providing either dehalogenation or oligomerization products, depending on the nature of the halogen atom. In particular, 4-chlorophenol (4-CP) and 4-fluorophenol (4-FP) selectively led to dehalogenation and oligomerization products, respectively. Herein, spin-trapping studies and EPR analysis confirm the ability of Fe-MC6*a into processing halophenols as substrates and provide mechanistic hypothesis for the chemo-divergent reaction outcome. Further, in multiple substrate competition assays, 4-halophenols act as competitive inhibitors of Fe-MC6*a-catalyzed dehalogenation of 2,4,6-trichlorophenol (TCP). Nonetheless, the catalyst retains appreciable turnover in such complex substrate mixtures. Taken together, the combination of substrate-specific selectivity and resilience to the total inhibition position Fe-MC6*a as a promising bioremediation catalyst for simultaneous halophenol detoxification in wastewater-treatment applications.</div></div>","PeriodicalId":364,"journal":{"name":"Journal of Inorganic Biochemistry","volume":"276 ","pages":"Article 113154"},"PeriodicalIF":3.2,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145682809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-14DOI: 10.1016/j.jinorgbio.2025.113152
Emil Thomsen, Parker R. Stow, Maren Cukor, Alison Butler
Bacteria often produce siderophores – small molecules with high affinity for Fe(III) – to acquire the iron that they need to grow. After transport of the Fe(III)-siderophore across the outer membrane of Gram-negative bacteria, a periplasmic binding protein (PBP) generally shuttles the Fe(III)-siderophore through the periplasm to the inner membrane. The fish pathogen Yersinia ruckeri synthesizes the oligoester tris-catecholate siderophore ruckerbactin, (DHB-LArg-LSer)3 (1), to acquire iron during infection. Its biosynthetic gene cluster encodes a single PBP, RupB, which was presumed to bind Fe(III)-ruckerbactin, however, previous fluorescence quenching titrations revealed RupB does not bind Fe(III)-ruckerbactin nor the Fe(III) complexes of its hydrolysis products – the bis- and mono-catecholate siderophores, 2 and 3, respectively – with biologically relevant affinities. Instead, RupB binds the complex of the structurally-related siderophore enterobactin, (DHB-LSer)3, which is surprising since enterobactin is not biosynthesized by Y. ruckeri. RupB inverts the chirality of the Δ-Fe(III)-enterobactin to Λ upon binding. A second PBP, YiuA, which is encoded elsewhere in the genome was established previously to bind the 1:2 Fe(III) complex of the mono-catecholate DHB-LArg-LSer (3), Fe(III)-(3)2, as well as the diastereomeric complex Fe(III)-(4)2 with nanomolar affinities, in which 4 is the monocatechol DHB-DArg-LSer. We show that YiuA recognizes similar siderophore scaffolds containing the alternative cationic amino acids (Lys, Orn), suggesting a broader role in xenosiderophore uptake. YiuA binds its substrate in the Λ isomer regardless of the chirality of the complex presented to it.
细菌经常产生铁载体——一种对铁(III)具有高亲和力的小分子——来获取它们生长所需的铁。铁(III)-铁载体通过革兰氏阴性菌的外膜运输后,周围质结合蛋白(PBP)通常将铁(III)-铁载体通过周质运送到内膜。鱼类病原体拉克氏耶尔森菌在感染过程中合成低聚酯三儿茶酚铁载体拉克巴克蛋白(dhb - lang - lser)3(1)来获取铁。它的生物合成基因簇编码一个单一的PBP, RupB,它被认为可以结合Fe(III)-ruckerbactin,然而,之前的荧光猝灭测定显示,RupB不结合Fe(III)-ruckerbactin,也不结合其水解产物的Fe(III)复合物——双儿茶酚酸和单儿茶酚酸铁载体,2和3——具有生物学上相关的亲和力。相反,RupB与结构相关的铁载体肠杆菌蛋白(DHB-LSer)3的复合物结合,这是令人惊讶的,因为肠杆菌蛋白不是由洛克氏菌生物合成的。RupB在结合后将Δ-Fe(III)-enterobactin的手性反转为Λ。第二个PBP, YiuA,在基因组的其他地方编码,先前被建立结合单儿茶酚dhb - lang - lser(3)的1:2 Fe(III)复合物,Fe(III)-(3)2,以及具有纳米亲和的非对映体复合物Fe(III)-(4)2,其中4是单儿茶酚DHB-DArg-LSer。我们发现YiuA可以识别含有替代阳离子氨基酸(Lys, Orn)的类似铁载体支架,这表明在异种铁载体摄取中具有更广泛的作用。YiuA将其底物结合在Λ同分异构体中,而不考虑提供给它的配合物的手性。
{"title":"Substrate flexibility of the catechol siderophore periplasmic binding proteins, RupB and YiuA from Yersinia ruckeri YRB","authors":"Emil Thomsen, Parker R. Stow, Maren Cukor, Alison Butler","doi":"10.1016/j.jinorgbio.2025.113152","DOIUrl":"10.1016/j.jinorgbio.2025.113152","url":null,"abstract":"<div><div>Bacteria often produce siderophores – small molecules with high affinity for Fe(III) – to acquire the iron that they need to grow. After transport of the Fe(III)-siderophore across the outer membrane of Gram-negative bacteria, a periplasmic binding protein (PBP) generally shuttles the Fe(III)-siderophore through the periplasm to the inner membrane. The fish pathogen <em>Yersinia ruckeri</em> synthesizes the oligoester tris-catecholate siderophore ruckerbactin, (DHB-<sup>L</sup>Arg-<sup>L</sup>Ser)<sub>3</sub> (1), to acquire iron during infection. Its biosynthetic gene cluster encodes a single PBP, RupB, which was presumed to bind Fe(III)-ruckerbactin, however, previous fluorescence quenching titrations revealed RupB does not bind Fe(III)-ruckerbactin nor the Fe(III) complexes of its hydrolysis products – the bis- and mono-catecholate siderophores, 2 and 3, respectively – with biologically relevant affinities. Instead, RupB binds the complex of the structurally-related siderophore enterobactin, (DHB-<sup>L</sup>Ser)<sub>3</sub>, which is surprising since enterobactin is not biosynthesized by <em>Y. ruckeri</em>. RupB inverts the chirality of the Δ-Fe(III)-enterobactin to Λ upon binding. A second PBP, YiuA, which is encoded elsewhere in the genome was established previously to bind the 1:2 Fe(III) complex of the mono-catecholate DHB-<sup>L</sup>Arg-<sup>L</sup>Ser (3), Fe(III)-(3)<sub>2</sub>, as well as the diastereomeric complex Fe(III)-(4)<sub>2</sub> with nanomolar affinities, in which 4 is the monocatechol DHB-<sup>D</sup>Arg-<sup>L</sup>Ser. We show that YiuA recognizes similar siderophore scaffolds containing the alternative cationic amino acids (Lys, Orn), suggesting a broader role in xenosiderophore uptake. YiuA binds its substrate in the Λ isomer regardless of the chirality of the complex presented to it.</div></div>","PeriodicalId":364,"journal":{"name":"Journal of Inorganic Biochemistry","volume":"275 ","pages":"Article 113152"},"PeriodicalIF":3.2,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145569218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-14DOI: 10.1016/j.jinorgbio.2025.113151
Grace Wang , Jessica Samudio , Hadia Aftab , Lily Le , Fereshteh Zandakrimi , Rebecca K. Donegan
Both Mycobacterium smegmatis and M. abscessus secrete porphyrin throughout their growth, and other species of bacteria have also been shown to secrete porphyrin with various outcomes. However, how the secretion of a heme precursor alters heme levels remains to be seen. Herein we determined that porphyrin levels and heme levels in the mycobacteria are decoupled as an increase in intracellular or extracellular porphyrin does not alter intracellular heme levels. Our findings support a model for heme biosynthesis with multiple points of regulation, further our understanding of how to alter secretion and buildup of endogenous porphyrins in the mycobacteria, and suggest that mycobacteria have a biological purpose for porphyrin secretion.
{"title":"Porphyrin secretion does not alter heme biosynthesis in the nontuberculous mycobacteria","authors":"Grace Wang , Jessica Samudio , Hadia Aftab , Lily Le , Fereshteh Zandakrimi , Rebecca K. Donegan","doi":"10.1016/j.jinorgbio.2025.113151","DOIUrl":"10.1016/j.jinorgbio.2025.113151","url":null,"abstract":"<div><div>Both <em>Mycobacterium smegmatis</em> and <em>M. abscessus</em> secrete porphyrin throughout their growth, and other species of bacteria have also been shown to secrete porphyrin with various outcomes. However, how the secretion of a heme precursor alters heme levels remains to be seen. Herein we determined that porphyrin levels and heme levels in the mycobacteria are decoupled as an increase in intracellular or extracellular porphyrin does not alter intracellular heme levels. Our findings support a model for heme biosynthesis with multiple points of regulation, further our understanding of how to alter secretion and buildup of endogenous porphyrins in the mycobacteria, and suggest that mycobacteria have a biological purpose for porphyrin secretion.</div></div>","PeriodicalId":364,"journal":{"name":"Journal of Inorganic Biochemistry","volume":"275 ","pages":"Article 113151"},"PeriodicalIF":3.2,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145555904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}