Pub Date : 2025-02-01DOI: 10.1016/j.abb.2024.110284
Amira M. Elshamy , Asmaa F. El Tantawy , Eman H. Basha , Eman F. Eltabaa , Heba M. Arakeeb , Ahmed S. Ahmed , Amal M. Abdelsattar , Rowida Raafat Ibrahim , Omnia Safwat El Deeb , Asmaa M. Eid , Shaimaa S. Mashal , Mohamed A. Safa , Amany Mohamed Shalaby , Hoda A. Ibrahim
Background
Bleomycin (BLM), an anticancer medication, can exacerbate pulmonary fibrosis by inducing oxidative stress and inflammation. Anti-inflammatory, anti-fibrotic, and antioxidant properties are exhibited by ganoderic acid A (GAA).
Aim
So, we aim to assess GAA's protective impact on lung fibrosis induced via BLM.
Method
Forty mice were randomly classified into four groups. Lung fibrosis was induced by injection of BLM intraperitoneally (15 mg/kg body weight). GAA was given by oral gavage (25 mg/kg body weight). Lung tissue MDA, TAC, and GSH were assessed spectrophotometrically. As well, TGFβ, p38 MAPK, TNF-α, IL-1β, and CAV1 levels were measured by enzyme-linked immunosorbent assay. Gene expression of tumor growth factor beta (TGF-β), Smad2, Smad3, and glutamate-cysteine ligase (GCL) were also evaluated.
Results
GAA had significantly improved biochemical biomarkers as well as histopathology of the lung. The protective impact of GAA may be linked to the upregulation of GCL gene expression and subsequent GSH levels. In addition, the GAA-treated group showed a significant decrement in the levels of TGF-β, Smad2&3, P38 MAPK, TNF-α, IL1β, and MDA compared to BLM induced lung fibrosis group. GAA has a protective impact on lung fibrosis induced by BLM via downregulation of TGF-β and upregulation of CAV1 level and GCL expression which may play a critical role in the improvement of the pathogenesis of lung fibrosis induced via BLM.
{"title":"Ganoderic acid a potential protective impact on bleomycin (BLM) -induced lung fibrosis in albino mice: Targeting caveolin 1/TGF-β/ Smad and P38MAPK signaling pathway","authors":"Amira M. Elshamy , Asmaa F. El Tantawy , Eman H. Basha , Eman F. Eltabaa , Heba M. Arakeeb , Ahmed S. Ahmed , Amal M. Abdelsattar , Rowida Raafat Ibrahim , Omnia Safwat El Deeb , Asmaa M. Eid , Shaimaa S. Mashal , Mohamed A. Safa , Amany Mohamed Shalaby , Hoda A. Ibrahim","doi":"10.1016/j.abb.2024.110284","DOIUrl":"10.1016/j.abb.2024.110284","url":null,"abstract":"<div><h3>Background</h3><div>Bleomycin (BLM), an anticancer medication, can exacerbate pulmonary fibrosis by inducing oxidative stress and inflammation. Anti-inflammatory, anti-fibrotic, and antioxidant properties are exhibited by ganoderic acid A (GAA).</div></div><div><h3>Aim</h3><div>So, we aim to assess GAA's protective impact on lung fibrosis induced via BLM.</div></div><div><h3>Method</h3><div>Forty mice were randomly classified into four groups. Lung fibrosis was induced by injection of BLM intraperitoneally (15 mg/kg body weight). GAA was given by oral gavage (25 mg/kg body weight). Lung tissue MDA, TAC, and GSH were assessed spectrophotometrically. As well, TGFβ, p38 MAPK, TNF-α, IL-1β, and CAV1 levels were measured by enzyme-linked immunosorbent assay. Gene expression of tumor growth factor beta (TGF-β), Smad2, Smad3, and glutamate-cysteine ligase (GCL) were also evaluated.</div></div><div><h3>Results</h3><div>GAA had significantly improved biochemical biomarkers as well as histopathology of the lung. The protective impact of GAA may be linked to the upregulation of GCL gene expression and subsequent GSH levels. In addition, the GAA-treated group showed a significant decrement in the levels of TGF-β, Smad2&3, P38 MAPK, TNF-α, IL1β, and MDA compared to BLM induced lung fibrosis group. GAA has a protective impact on lung fibrosis induced by BLM via downregulation of TGF-β and upregulation of CAV1 level and GCL expression which may play a critical role in the improvement of the pathogenesis of lung fibrosis induced via BLM<strong>.</strong></div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110284"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142908695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.abb.2024.110241
Egor A. Turovsky , Egor Y. Plotnikov , Alexander V. Simakin , Sergey V. Gudkov , Elena G. Varlamova
Ischemic stroke is the cause of high mortality and disability Worldwide. The material costs of stroke treatment and recovery are constantly increasing, making the search for effective and more cost-effective treatment approaches an urgent task for modern biomedicine. In this study, iron nanoparticles doped with selenium nanoparticles, FeNP@SeNPs, which are three-layered structures, were created and characterized using physical methods. Fluorescence microscopy, inhibitor and PCR analyzes were used to determine the signaling pathways involved in the activation of the Ca2+ signaling system of cortical astrocytes and the protection of cells from ischemia-like conditions (oxygen-glucose deprivation and reoxygenation). In particular, when using magnetic selenium nanoparticles together with electromagnetic stimulation, an additional pathway for nanoparticle penetration into the cell is activated through the activation of TRPV4 channels and the mechanism of their endocytosis is facilitated. It has been shown that the use of magnetic selenium nanoparticles together with magnetic stimulation represents an advantage over the use of classical selenium nanoparticles, as the effective concentration of nanoparticles can be reduced many times over.
{"title":"New magnetic iron nanoparticle doped with selenium nanoparticles and the mechanisms of their cytoprotective effect on cortical cells under ischemia-like conditions","authors":"Egor A. Turovsky , Egor Y. Plotnikov , Alexander V. Simakin , Sergey V. Gudkov , Elena G. Varlamova","doi":"10.1016/j.abb.2024.110241","DOIUrl":"10.1016/j.abb.2024.110241","url":null,"abstract":"<div><div>Ischemic stroke is the cause of high mortality and disability Worldwide. The material costs of stroke treatment and recovery are constantly increasing, making the search for effective and more cost-effective treatment approaches an urgent task for modern biomedicine. In this study, iron nanoparticles doped with selenium nanoparticles, FeNP@SeNPs, which are three-layered structures, were created and characterized using physical methods. Fluorescence microscopy, inhibitor and PCR analyzes were used to determine the signaling pathways involved in the activation of the Ca<sup>2+</sup> signaling system of cortical astrocytes and the protection of cells from ischemia-like conditions (oxygen-glucose deprivation and reoxygenation). In particular, when using magnetic selenium nanoparticles together with electromagnetic stimulation, an additional pathway for nanoparticle penetration into the cell is activated through the activation of TRPV4 channels and the mechanism of their endocytosis is facilitated. It has been shown that the use of magnetic selenium nanoparticles together with magnetic stimulation represents an advantage over the use of classical selenium nanoparticles, as the effective concentration of nanoparticles can be reduced many times over.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110241"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142754470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.abb.2024.110269
Anna Koczurowska , David Ruiz Carrillo , María García Alai , Małgorzata Zakłos-Szyda , Grzegorz Bujacz , Agnieszka J. Pietrzyk-Brzezinska
The HprSR constitutes the bacterial two-component regulatory system engaged by Escherichia coli to reduce the damaging effects of reactive chlorine and oxygen species present in its cytosol. Hypochlorous acid (HOCl) has been shown to be the molecule capable of activating of the HprSR system. HOCl is produced upon pathogen invasion by phagocytic cells of the human innate immune system, particularly neutrophils, to take advantage of its powerful antimicrobial attributes. Therefore, comprehensive studies concerning bacterial sensing and regulatory HprSR system are indispensable in understanding and effectively eliminating pathogens. Here we present the first crystal structure, solved at 1.7 Å resolution, of the HprS cytoplasmic domains arranged as a homodimer. In both protomers, the catalytic ATP-binding domain contains a non-hydrolysable ATP analog coordinated by a magnesium ion. This structure allowed us to provide a detailed characterization of kinase-substrate interaction. Furthermore, the structural data are supported by biophysical studies of kinase interaction with cognate response regulator HprR and substrate ATP. The kinase activity is also assessed in the presence or absence of HprR.
{"title":"Structural and biophysical characterization of the cytoplasmic domains of HprS kinase and its interactions with the cognate regulator HprR","authors":"Anna Koczurowska , David Ruiz Carrillo , María García Alai , Małgorzata Zakłos-Szyda , Grzegorz Bujacz , Agnieszka J. Pietrzyk-Brzezinska","doi":"10.1016/j.abb.2024.110269","DOIUrl":"10.1016/j.abb.2024.110269","url":null,"abstract":"<div><div>The HprSR constitutes the bacterial two-component regulatory system engaged by <em>Escherichia coli</em> to reduce the damaging effects of reactive chlorine and oxygen species present in its cytosol. Hypochlorous acid (HOCl) has been shown to be the molecule capable of activating of the HprSR system. HOCl is produced upon pathogen invasion by phagocytic cells of the human innate immune system, particularly neutrophils, to take advantage of its powerful antimicrobial attributes. Therefore, comprehensive studies concerning bacterial sensing and regulatory HprSR system are indispensable in understanding and effectively eliminating pathogens. Here we present the first crystal structure, solved at 1.7 Å resolution, of the HprS cytoplasmic domains arranged as a homodimer. In both protomers, the catalytic ATP-binding domain contains a non-hydrolysable ATP analog coordinated by a magnesium ion. This structure allowed us to provide a detailed characterization of kinase-substrate interaction. Furthermore, the structural data are supported by biophysical studies of kinase interaction with cognate response regulator HprR and substrate ATP. The kinase activity is also assessed in the presence or absence of HprR.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110269"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.abb.2024.110271
Adriana Tomkova , Erik Cizmar , Daniel Jancura , Marian Fabian
In aerobic organisms, cellular respiration is associated with electron transfer through a respiratory system of membrane-bound complexes. This electron flow is terminated by the reduction of dioxygen to water by respiratory oxidases. Cytochrome c oxidase (CcO) is a widely distributed heme-copper-oxygen reductase (HCO) found in all mitochondria and some bacteria. However, the sequential reduction of O2 to water in CcO generates a protein-based radical at the catalytic heme a3-CuB site. To avoid the potential damage from the radical, CcO has apparently developed protective mechanisms. Protection by transfer of the highly oxidizing equivalent over considerable distances away from the catalytic site by redox-active Tyr/Trp chains has been previously demonstrated in bovine CcO. However, the rate of the radical migration from the catalytic center has not yet been determined for any HCO. In this work, we show that the radical escapes from the catalytic center of the ferryl PM intermediate of bovine CcO within minutes, which is much longer than the time of its functional reduction during cellular respiration. Apparently, this high stability has evolved to avoid the dissipation of energy released during the oxygen reduction with substrate electrons.
在需氧生物中，细胞呼吸与电子通过膜结合复合物的呼吸系统传递有关。这种电子流通过呼吸氧化酶将二氧还原为水而终止。细胞色素c氧化酶（Cytochrome c oxidase, CcO）是一种广泛分布于所有线粒体和一些细菌中的血红素-铜-氧还原酶（HCO）。然而，在CcO中O2连续还原成水，在催化血红素a3-CuB位点产生一个基于蛋白质的自由基。为了避免自由基的潜在损害，CcO显然发展了保护机制。通过氧化还原活性的Tyr/Trp链将高度氧化的等价物转移到离催化位点相当远的地方进行保护，此前已在牛CcO中得到证实。然而，对于任何HCO，自由基从催化中心迁移的速率尚未确定。在这项工作中，我们证明了自由基在几分钟内从牛CcO的铁基PM中间体的催化中心逃逸，这比它在细胞呼吸过程中的功能还原时间要长得多。显然，这种高稳定性是为了避免氧与衬底电子还原过程中释放的能量耗散。
{"title":"High stability of the radical at the catalytic center of cytochrome c oxidase","authors":"Adriana Tomkova , Erik Cizmar , Daniel Jancura , Marian Fabian","doi":"10.1016/j.abb.2024.110271","DOIUrl":"10.1016/j.abb.2024.110271","url":null,"abstract":"<div><div>In aerobic organisms, cellular respiration is associated with electron transfer through a respiratory system of membrane-bound complexes. This electron flow is terminated by the reduction of dioxygen to water by respiratory oxidases. Cytochrome <em>c</em> oxidase (CcO) is a widely distributed heme-copper-oxygen reductase (HCO) found in all mitochondria and some bacteria. However, the sequential reduction of O<sub>2</sub> to water in CcO generates a protein-based radical at the catalytic heme <em>a</em><sub>3</sub>-Cu<sub>B</sub> site. To avoid the potential damage from the radical, CcO has apparently developed protective mechanisms. Protection by transfer of the highly oxidizing equivalent over considerable distances away from the catalytic site by redox-active Tyr/Trp chains has been previously demonstrated in bovine CcO. However, the rate of the radical migration from the catalytic center has not yet been determined for any HCO. In this work, we show that the radical escapes from the catalytic center of the ferryl <strong>P</strong><sub><strong>M</strong></sub> intermediate of bovine CcO within minutes, which is much longer than the time of its functional reduction during cellular respiration. Apparently, this high stability has evolved to avoid the dissipation of energy released during the oxygen reduction with substrate electrons.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110271"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.abb.2024.110276
Lorenzo Basile , Chiara Poli , Lars L. Santema , Răzvan C. Lesenciuc , Marco W. Fraaije , Claudia Binda
Bacterial monoamine oxidases (MAOs) are FAD-dependent proteins catalyzing a relevant reaction for many industrial biocatalytic applications, ranging from production of enantiomerically pure building blocks for pharmaceutical synthesis to biosensors for monitoring food and beverage quality. The thermostable MAO enzyme from Thermoanaerobacterales bacterium (MAOTb) is about 36 % identical to both putrescine oxidase and human MAOs and can be efficiently produced in Escherichia coli. MAOTb preferentially acts on n-alkyl monoamines but shows detectable activity also on polyamines and aromatic monoamines. The crystal structures of MAOTb in complex with putrescine, benzylamine, spermidine and n-heptylamine at resolution ranging from 1.6 to 2.3 Å resolution revealed the binding mode of substrates to the enzyme. The MAOTb active site is highly conserved in the inner part of the cavity in front of the flavin ring (re face), where the presence of two tyrosine residues creates the substrate amine binding site that is found also in human MAOs. Instead, more distantly from the flavin, the entrance of the catalytic site is much more open in MAOTb and features a different arrangement of amino acids. Site-directed mutagenesis targeting residues Ala168, Thr199 and Val324 allowed the identification of key residues in ligand binding to alter substrate specificity. The A168D variant showed a higher activity on putrescine than wild-type, whereas by replacing either Thr199 or Val324 to Trp a marked enhancement in kcat/KM values was found on n-alkyl-monoamines and on aromatic amines.
{"title":"Altering substrate specificity of a thermostable bacterial monoamine oxidase by structure-based mutagenesis","authors":"Lorenzo Basile , Chiara Poli , Lars L. Santema , Răzvan C. Lesenciuc , Marco W. Fraaije , Claudia Binda","doi":"10.1016/j.abb.2024.110276","DOIUrl":"10.1016/j.abb.2024.110276","url":null,"abstract":"<div><div>Bacterial monoamine oxidases (MAOs) are FAD-dependent proteins catalyzing a relevant reaction for many industrial biocatalytic applications, ranging from production of enantiomerically pure building blocks for pharmaceutical synthesis to biosensors for monitoring food and beverage quality. The thermostable MAO enzyme from <em>Thermoanaerobacterales</em> bacterium (MAO<sub>Tb</sub>) is about 36 % identical to both putrescine oxidase and human MAOs and can be efficiently produced in <em>Escherichia coli</em>. MAO<sub>Tb</sub> preferentially acts on <em>n</em>-alkyl monoamines but shows detectable activity also on polyamines and aromatic monoamines. The crystal structures of MAO<sub>Tb</sub> in complex with putrescine, benzylamine, spermidine and <em>n-</em>heptylamine at resolution ranging from 1.6 to 2.3 Å resolution revealed the binding mode of substrates to the enzyme. The MAO<sub>Tb</sub> active site is highly conserved in the inner part of the cavity in front of the flavin ring (<em>re</em> face), where the presence of two tyrosine residues creates the substrate amine binding site that is found also in human MAOs. Instead, more distantly from the flavin, the entrance of the catalytic site is much more open in MAO<sub>Tb</sub> and features a different arrangement of amino acids. Site-directed mutagenesis targeting residues Ala168, Thr199 and Val324 allowed the identification of key residues in ligand binding to alter substrate specificity. The A168D variant showed a higher activity on putrescine than wild-type, whereas by replacing either Thr199 or Val324 to Trp a marked enhancement in <em>k</em><sub><em>cat</em></sub>/K<sub>M</sub> values was found on <em>n</em>-alkyl-monoamines and on aromatic amines.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110276"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lysine-specific demethylase 1 (LSD1) is a key regulator in cancer epigenetic, and its activity is reliant on flavin adenine dinucleotide (FAD) as a cofactor. In this study, we investigated the correlation between LSD1 and FAD synthase isoform 2 (FADS2) protein levels in pancreatic ductal adenocarcinoma (PDAC) cell lines. We first assessed LSD1 protein and mRNA levels in mutant p53-expressing PANC-1 and MiaPaCa2 cells and p53-null AsPc-1 cells, compared to human pancreatic ductal epithelial (HPDE) controls. Our results confirmed elevated LSD1 protein levels in PANC-1 and MiaPaCa2, but not in AsPc-1, despite mRNA overexpression across all cell lines. Similarly, FADS2 levels were significantly upregulated in PANC-1 and MiaPaCa2, but not in AsPc-1, highlighting a possible link between FADS2 expression and p53 gain-of-function mutations. These results prompted us to better investigate the functional relationship between FADS2 and LSD1 by performing in cellulo protein-protein interaction analyses. Our results indicate a direct interaction between LSD1 and FADS2, while no significant interaction was observed between LSD1 and FADS1. These findings reinforce the role of FAD synthesis and its delivery to LSD1 as critical events in cancer progression and shed light on potential implications of FADS2-LSD1 dynamics as targeted therapies in cancer.
{"title":"Supplying LSD1 with FAD in pancreatic cancer: A matter of protein-protein interaction?","authors":"Alessia Nisco , Angela Sposato , Marilena Ardone , Piero Leone , Rosa Angela Cardone , Lara Console , Cesare Indiveri , Katia Zanier , Maria Barile","doi":"10.1016/j.abb.2025.110291","DOIUrl":"10.1016/j.abb.2025.110291","url":null,"abstract":"<div><div>Lysine-specific demethylase 1 (LSD1) is a key regulator in cancer epigenetic, and its activity is reliant on flavin adenine dinucleotide (FAD) as a cofactor. In this study, we investigated the correlation between LSD1 and FAD synthase isoform 2 (FADS2) protein levels in pancreatic ductal adenocarcinoma (PDAC) cell lines. We first assessed LSD1 protein and mRNA levels in mutant p53-expressing PANC-1 and MiaPaCa2 cells and p53-null AsPc-1 cells, compared to human pancreatic ductal epithelial (HPDE) controls. Our results confirmed elevated LSD1 protein levels in PANC-1 and MiaPaCa2, but not in AsPc-1, despite mRNA overexpression across all cell lines. Similarly, FADS2 levels were significantly upregulated in PANC-1 and MiaPaCa2, but not in AsPc-1, highlighting a possible link between FADS2 expression and p53 gain-of-function mutations. These results prompted us to better investigate the functional relationship between FADS2 and LSD1 by performing <em>in cellulo</em> protein-protein interaction analyses. Our results indicate a direct interaction between LSD1 and FADS2, while no significant interaction was observed between LSD1 and FADS1. These findings reinforce the role of FAD synthesis and its delivery to LSD1 as critical events in cancer progression and shed light on potential implications of FADS2-LSD1 dynamics as targeted therapies in cancer.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110291"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142942954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.abb.2024.110263
Pratyasha Bhowal , David Jameson , Rajat Banerjee
Given the high prevalence of Chagas disease in the Americas, we targeted the unique arginyl-tRNA synthetase of its causative agent Trypanosoma cruzi. Among their many possible uses, naphthalene-derived fluorescent ligands, such as ANS and bis-ANS, may be employed in pharmacokinetic research. Although ANS and bis-ANS have become prominent fluorescent probes for protein characterization, the structural and spectroscopic characteristics of protein-ANS/bis-ANS complexes remain largely unknown. Both fluorescent dyes bind to either the folded or partially folded hydrophobic regions of proteins. Additionally, they serve to identify molten globule-like intermediates. These probes have been used to study the folding problems of protein structures and the mechanisms of protein-protein interactions. ANS and bis-ANS exhibited significant enhancement and blue shift in their emission spectra upon binding to TcArgRS, the primary enzyme responsible for attaching l-arginine to its corresponding tRNA. Through fluorescence spectroscopy and computational studies, we concluded that bis-ANS binds more tightly to TcArgRS and that ATP affects bis-ANS fluorescence signal. Thus, these probes are useful resources for studying the intricate intermolecular relationships between proteins in terms of their structure, function, and mechanism. Our study provides a framework for identifying the hydrophobic regions present in TcArgRS. The utilization of hydrophobic patches on proteins for drug targeting is noteworthy because they can assist in identifying regions on the surface of proteins that are likely to interact with ligands. These patches help identify hotspot residues that play a vital role in determining binding affinity. Drugs are mainly small and hydrophobic in nature, and they target protein surfaces which have complementary properties. In this study, we elucidated the potential of TcArgRS as a target for combating trypanosomal diseases and extending life expectancy.
{"title":"Investigating the binding of fluorescent probes to a trypanosomal-tRNA synthetase: A fluorescence spectroscopic and molecular dynamics study","authors":"Pratyasha Bhowal , David Jameson , Rajat Banerjee","doi":"10.1016/j.abb.2024.110263","DOIUrl":"10.1016/j.abb.2024.110263","url":null,"abstract":"<div><div>Given the high prevalence of Chagas disease in the Americas, we targeted the unique arginyl-tRNA synthetase of its causative agent <em>Trypanosoma cruzi</em>. Among their many possible uses, naphthalene-derived fluorescent ligands, such as ANS and bis-ANS, may be employed in pharmacokinetic research. Although ANS and bis-ANS have become prominent fluorescent probes for protein characterization, the structural and spectroscopic characteristics of protein-ANS/bis-ANS complexes remain largely unknown. Both fluorescent dyes bind to either the folded or partially folded hydrophobic regions of proteins. Additionally, they serve to identify molten globule-like intermediates. These probes have been used to study the folding problems of protein structures and the mechanisms of protein-protein interactions. ANS and bis-ANS exhibited significant enhancement and blue shift in their emission spectra upon binding to <em>Tc</em>ArgRS, the primary enzyme responsible for attaching <span>l</span>-arginine to its corresponding tRNA. Through fluorescence spectroscopy and computational studies, we concluded that bis-ANS binds more tightly to <em>Tc</em>ArgRS and that ATP affects bis-ANS fluorescence signal. Thus, these probes are useful resources for studying the intricate intermolecular relationships between proteins in terms of their structure, function, and mechanism. Our study provides a framework for identifying the hydrophobic regions present in <em>Tc</em>ArgRS. The utilization of hydrophobic patches on proteins for drug targeting is noteworthy because they can assist in identifying regions on the surface of proteins that are likely to interact with ligands. These patches help identify hotspot residues that play a vital role in determining binding affinity. Drugs are mainly small and hydrophobic in nature, and they target protein surfaces which have complementary properties. In this study, we elucidated the potential of <em>Tc</em>ArgRS as a target for combating trypanosomal diseases and extending life expectancy.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110263"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Neurodegenerative diseases are now significant chronic progressive neurological conditions that affect individuals' physical health. Oxidative stress is crucial in the development of these diseases. Among the various neurodegenerative diseases, mitochondrial damage has become a major factor in oxidative stress and disease advancement. During this process, oxidative stress and mitophagy plays an important role. In this paper, we introduced the role of mitophagy and oxidative stress in detail, and expounded the relationship between them. In addition, we summarized the pathogenesis of some neurodegenerative diseases and the mechanism of three antioxidants. The former includes AD, PD, HD and ALS, while the latter includes carnosine, adiponectin and resveratrol. Provide goals and directions for further research and treatment of neurodegenerative diseases.
This review summarizes the impact of oxidative stress on neurodegenerative diseases by regulating mitophagy, provides a deeper understanding of their pathological mechanisms, and suggests potential new therapeutic targets.
{"title":"Oxidative stress of mitophagy in neurodegenerative diseases: Mechanism and potential therapeutic targets","authors":"Yixin Li, Wanying Zhang, Qihang Zhang, Yunzhe Li, Chonghui Xin, Rongze Tu, Haijing Yan","doi":"10.1016/j.abb.2024.110283","DOIUrl":"10.1016/j.abb.2024.110283","url":null,"abstract":"<div><div>Neurodegenerative diseases are now significant chronic progressive neurological conditions that affect individuals' physical health. Oxidative stress is crucial in the development of these diseases. Among the various neurodegenerative diseases, mitochondrial damage has become a major factor in oxidative stress and disease advancement. During this process, oxidative stress and mitophagy plays an important role. In this paper, we introduced the role of mitophagy and oxidative stress in detail, and expounded the relationship between them. In addition, we summarized the pathogenesis of some neurodegenerative diseases and the mechanism of three antioxidants. The former includes AD, PD, HD and ALS, while the latter includes carnosine, adiponectin and resveratrol. Provide goals and directions for further research and treatment of neurodegenerative diseases.</div><div>This review summarizes the impact of oxidative stress on neurodegenerative diseases by regulating mitophagy, provides a deeper understanding of their pathological mechanisms, and suggests potential new therapeutic targets.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110283"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142913631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.abb.2024.110242
Paul F. Fitzpatrick
The goals of this presentation are to summarize the present understanding of the mechanism of amine oxidation by flavoproteins and to examine the possibility that a member of the monoamine oxidase family catalyzes oxidation of a carbon-carbon bond. In the discussion of mechanism, the emphasis is on the protonation state of the amine substrate, since the once-controversial mechanism of oxidation appears to be resolved. The argument will be made that flavoproteins catalyzing amine oxidation preferentially bind the form of the substrate in which the reacting nitrogen is uncharged. The reaction of a member of L-6-hydroxynicotine oxidase, which has been proposed to oxidize a carbon-carbon bond in its substrate during nicotine catabolism, is then discussed. Analysis of the reaction product establishes that the enzyme catalyzes oxidation of a carbon-nitrogen. The effects of site-directed mutagenesis and analysis of the substrate specificity identify the key residues for substrate binding.
{"title":"Conservation of mechanism in flavoprotein-catalyzed amine oxidation","authors":"Paul F. Fitzpatrick","doi":"10.1016/j.abb.2024.110242","DOIUrl":"10.1016/j.abb.2024.110242","url":null,"abstract":"<div><div>The goals of this presentation are to summarize the present understanding of the mechanism of amine oxidation by flavoproteins and to examine the possibility that a member of the monoamine oxidase family catalyzes oxidation of a carbon-carbon bond. In the discussion of mechanism, the emphasis is on the protonation state of the amine substrate, since the once-controversial mechanism of oxidation appears to be resolved. The argument will be made that flavoproteins catalyzing amine oxidation preferentially bind the form of the substrate in which the reacting nitrogen is uncharged. The reaction of a member of L-6-hydroxynicotine oxidase, which has been proposed to oxidize a carbon-carbon bond in its substrate during nicotine catabolism, is then discussed. Analysis of the reaction product establishes that the enzyme catalyzes oxidation of a carbon-nitrogen. The effects of site-directed mutagenesis and analysis of the substrate specificity identify the key residues for substrate binding.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110242"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142754469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.abb.2024.110282
Aidan J. Hawley, Suzeeta Bhandari , Peter W. Radulovic , Natalia Borisova , Gabrielle Henry, Tyler Holets, Christian Sabbagh, Matthew Scearbo , Gabriela Suarez , David J. Merkler
An important aspect of food security is the development of innovative insecticides, particularly ones that specifically target insect pests and exhibit minimal toxicity to mammals. The insect arylalkylamine N-acyltransferases (iAANATs) could serve as targets for novel insecticides that satisfy these criteria. There exists a wealth of structural and biochemical information for the iAANATs and iAANAT knockdown experiments show that these enzymes are critical to insect health. Herein, we have expressed, purified, and characterized two new iAANATs, one from Apis mellifera (honey bee, AmNAT1) and another from Diaphorina citri (Asian citrus psyllid, DcNAT). We discovered that diminazene, a compound used to treat livestock for trypanosomiasis and babesiosis, inhibits AmNAT1, DcNAT, and D. melanogaster DmAgmNAT with modest affinity, Ki values ranging from 0.8 μM to 200 μM. We found a series of guanidines, amidines, and a hydroxamate, structurally related to diminazene, also inhibit the iAANATs, including camostat, gabexate, nafamostate, and panobinostat. Significantly, we found DmAgmNAT is far more susceptible to inhibition by four of these five of these compounds. In particular, camostat, nafamostat, and gabexate inhibit DmAgmNAT with Ki values of 0.2–30 μM, but no inhibition of AmNAT1 and DcNAT was observed at 500 μM for any of the three. These results show that a species-specific inhibitor targeted against an iAANAT is a real possibility. Also, we report that adipoyl-CoA is a substrate for AmNAT1 and DcNAT and that succinoyl-CoA is a substrate for DcNAT. These results contribute to a growing body of data suggesting that N-dicarboxyacyl-amines are metabolites in insects and other organisms.
{"title":"The identification of insect specific iAANAT inhibitors","authors":"Aidan J. Hawley, Suzeeta Bhandari , Peter W. Radulovic , Natalia Borisova , Gabrielle Henry, Tyler Holets, Christian Sabbagh, Matthew Scearbo , Gabriela Suarez , David J. Merkler","doi":"10.1016/j.abb.2024.110282","DOIUrl":"10.1016/j.abb.2024.110282","url":null,"abstract":"<div><div>An important aspect of food security is the development of innovative insecticides, particularly ones that specifically target insect pests and exhibit minimal toxicity to mammals. The insect arylalkylamine <em>N</em>-acyltransferases (iAANATs) could serve as targets for novel insecticides that satisfy these criteria. There exists a wealth of structural and biochemical information for the iAANATs and iAANAT knockdown experiments show that these enzymes are critical to insect health. Herein, we have expressed, purified, and characterized two new iAANATs, one from <em>Apis mellifera</em> (honey bee, <em>Am</em>NAT1) and another from <em>Diaphorina citri</em> (Asian citrus psyllid, <em>Dc</em>NAT). We discovered that diminazene, a compound used to treat livestock for trypanosomiasis and babesiosis, inhibits <em>Am</em>NAT1, <em>Dc</em>NAT, and <em>D. melanogaster Dm</em>AgmNAT with modest affinity, K<sub>i</sub> values ranging from 0.8 μM to 200 μM. We found a series of guanidines, amidines, and a hydroxamate, structurally related to diminazene, also inhibit the iAANATs, including camostat, gabexate, nafamostate, and panobinostat. Significantly, we found <em>Dm</em>AgmNAT is far more susceptible to inhibition by four of these five of these compounds. In particular, camostat, nafamostat, and gabexate inhibit <em>Dm</em>AgmNAT with K<sub>i</sub> values of 0.2–30 μM, but no inhibition of <em>Am</em>NAT1 and <em>Dc</em>NAT was observed at 500 μM for any of the three. These results show that a species-specific inhibitor targeted against an iAANAT is a real possibility. Also, we report that adipoyl-CoA is a substrate for <em>Am</em>NAT1 and <em>Dc</em>NAT and that succinoyl-CoA is a substrate for <em>Dc</em>NAT. These results contribute to a growing body of data suggesting that <em>N</em>-dicarboxyacyl-amines are metabolites in insects and other organisms.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110282"},"PeriodicalIF":3.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142902338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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