Ferroptosis, a cell death regulation process dependent on iron levels, represents a promising therapeutic target in cancer treatment. However, the scarcity of potent ferroptosis inducers hinders advancement in this area. This study addresses this gap by screening the PubChem database for compounds with favorable ADMET properties to identify potential GPX4 inhibitors. A structure-based virtual screening was conducted to compare binding affinities of selected compounds to that of RSL3. The candidates—isochondrodendrine, hinokiflavone, irinotecan, and ginkgetin—were further analyzed through molecular dynamics (MD) simulations to assess their stability within the GPX4-ligand complexes. The computed binding free energies for RSL3, isochondrodendrine, hinokiflavone, irinotecan and ginkgetin were −80.12, −107.31, −132.03, and −137.52 and −91.11 kJ/mol, respectively, indicating their significantly higher inhibitory effects compared to RSL3. These findings highlight the potential for developing novel GPX4 inhibitors to promote ferroptosis, warranting further experimental validation.
{"title":"Computational discovery of novel GPX4 inhibitors from herbal sources as potential ferroptosis inducers in cancer therapy","authors":"Mohammad Mahdi Mokhtari Tabar , Abdolmajid Ghasemian , Amin Kouhpayeh , Esmaeil Behmard","doi":"10.1016/j.abb.2024.110231","DOIUrl":"10.1016/j.abb.2024.110231","url":null,"abstract":"<div><div>Ferroptosis, a cell death regulation process dependent on iron levels, represents a promising therapeutic target in cancer treatment. However, the scarcity of potent ferroptosis inducers hinders advancement in this area. This study addresses this gap by screening the PubChem database for compounds with favorable ADMET properties to identify potential GPX4 inhibitors. A structure-based virtual screening was conducted to compare binding affinities of selected compounds to that of RSL3. The candidates—isochondrodendrine, hinokiflavone, irinotecan, and ginkgetin—were further analyzed through molecular dynamics (MD) simulations to assess their stability within the GPX4-ligand complexes. The computed binding free energies for RSL3, isochondrodendrine, hinokiflavone, irinotecan and ginkgetin were −80.12, −107.31, −132.03, and −137.52 and −91.11 kJ/mol, respectively, indicating their significantly higher inhibitory effects compared to RSL3. These findings highlight the potential for developing novel GPX4 inhibitors to promote ferroptosis, warranting further experimental validation.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110231"},"PeriodicalIF":3.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142738212","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 : 2024-11-26DOI: 10.1016/j.abb.2024.110229
Mahmoud Abdelnaser , Mina Ezzat Attya , Mahmoud A. El-Rehany , Moustafa Fathy
Sepsis is a fatal condition, with an annual incidence of more than 48 million cases as well as 11 million deaths resulting from it. Moreover, sepsis continues to rank as the fifth most prevalent cause of mortality globally. The objective of this study is to investigate if Clemastine (CLM) pretreatment protects against acute kidney injury (AKI) caused by cecal ligation and puncture (CLP) via modulating Toll-like receptor-4 (TLR-4), Myeloid differentiation primary response 88 (MYD-88), nuclear factor kappa B (NF-κB), Bcl-2-associated X (Bax), B-cell lymphoma-2 (Bcl-2), and caspase-3 signaling pathways. CLM markedly attenuated sepsis-caused molecular, biochemical, and histopathological alterations. CLM downregulated the levels of the proinflammatory markers, suppressed the expression of cleaved caspase-3, TLR-4 and MYD-88 as well as inactivating NF-κB p-P65 and p-P38 proteins, inhibited Bax, NF-κB, and caspase-3 genes expression, and augmented α-Klotho protein expression as well as Bcl-2 gene expression. Finally, CLM pretreatment protected against acute kidney injury by preventing TLR-4/p-P38 pathway-mediated apoptotic cell death in rats.
{"title":"Clemastine mitigates sepsis-induced acute kidney injury in rats; the role of α-Klotho/TLR-4/MYD-88/NF-κB/ Caspase-3/ p-P38 MAPK signaling pathways","authors":"Mahmoud Abdelnaser , Mina Ezzat Attya , Mahmoud A. El-Rehany , Moustafa Fathy","doi":"10.1016/j.abb.2024.110229","DOIUrl":"10.1016/j.abb.2024.110229","url":null,"abstract":"<div><div>Sepsis is a fatal condition, with an annual incidence of more than 48 million cases as well as 11 million deaths resulting from it. Moreover, sepsis continues to rank as the fifth most prevalent cause of mortality globally. The objective of this study is to investigate if Clemastine (CLM) pretreatment protects against acute kidney injury (AKI) caused by cecal ligation and puncture (CLP) via modulating Toll-like receptor-4 (TLR-4), Myeloid differentiation primary response 88 (MYD-88), nuclear factor kappa B (<em>NF-κB),</em> Bcl-2-associated X (<em>Bax), B-cell lymphoma-2 (Bcl-2), and caspase-3</em> signaling pathways. CLM markedly attenuated sepsis-caused molecular, biochemical, and histopathological alterations. CLM downregulated the levels of the proinflammatory markers, suppressed the expression of cleaved caspase-3, TLR-4 and MYD-88 as well as inactivating NF-κB p-P65 and p-P38 proteins, inhibited <em>Bax, NF-κB,</em> and <em>caspase-3</em> genes expression, and augmented α-Klotho protein expression as well as <em>Bcl-2</em> gene expression. Finally, CLM pretreatment protected against acute kidney injury by preventing TLR-4/p-P38 pathway-mediated apoptotic cell death in rats.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"763 ","pages":"Article 110229"},"PeriodicalIF":3.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142745523","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 : 2024-11-26DOI: 10.1016/j.abb.2024.110232
Madhulika Shrivastava, Arun Goyal
Arabinoxylan, a complex hemicellulose, can be degraded to its constituent sugars by concerted action of hemicellulases like α-l-arabinofuranosidase, endo-β-1,4-xylanase and xylosidase. In this study, a novel bifunctional α-l-arabinofuranosidase/endo-β-1,4-xylanase (BoGH43_35) of glycoside hydrolase family 43 subfamily 35 from Bacteroides ovatus was characterized by computational and experimental approaches. Sequence analysis identified Asp34 and Glu251 as the conserved catalytic residues. Structure analysis of BoGH43_35 disclosed 5-bladed β-propeller fold adopted by the N-terminal GH43 catalytic module followed by two independently folded carbohydrate-binding modules family 6 (CBM6A and CBM6B), displaying jellyroll type β-sandwich fold. Molecular Dynamics simulation of BoGH43_35 for 200 ns showed RMSD 0.35 nm, confirming structural stability and compactness of modeled structure. Molecular docking of BoGH43_35 with arabino-xylooligosaccharides and xylooligosaccharides by using AutoDock 4.2.7 demonstrated most favourable binding with arabinose (−5.01 kcal/mol) followed by arabinoxylobiose (−4.35 kcal/mol), xylotriose (−4.65 kcal/mol), xylotetraose (−4.18 kcal/mol) and xylobiose (−3.66 kcal/mol) showing affinity with both types of oligosaccharides. RMSD value of BoGH43_35-arabinose complex decreased to 0.28 nm upon MD simulation from 0.35 nm for only BoGH43_35, indicating stability of enzyme-substrate complex throughout the trajectory. The binding analysis of BoGH43_35 with wheat arabinoxylan by fluorescence spectroscopy gave Ka, 3.1 × 102 M−1, ΔG -14.2 kJ mole−1 and number of binding sites 2.2. Dynamic light scattering of BoGH43_35 showed hydrodynamic radius (Rh) of 4.0 nm, slightly higher than the radius of gyration (2.69 nm) from MD simulation. Additionally, zeta potential measurements (−9.3 mV at 0.5 mg/mL and −9.4 mV at 1.0 mg/mL) denoted its fair resistance towards aggregation in aqueous solution.
{"title":"Unveiling the structural and functional perspectives of a bifunctional α-l-arabinofuranosidase/endo-β-1,4-xylanase (BoGH43_35) from Bacteroides ovatus","authors":"Madhulika Shrivastava, Arun Goyal","doi":"10.1016/j.abb.2024.110232","DOIUrl":"10.1016/j.abb.2024.110232","url":null,"abstract":"<div><div>Arabinoxylan, a complex hemicellulose, can be degraded to its constituent sugars by concerted action of hemicellulases like α-<span>l</span>-arabinofuranosidase, endo-β-1,4-xylanase and xylosidase. In this study, a novel bifunctional α-<span>l</span>-arabinofuranosidase/endo-β-1,4-xylanase (<em>Bo</em>GH43_35) of glycoside hydrolase family 43 subfamily 35 from <em>Bacteroides ovatus</em> was characterized by computational and experimental approaches. Sequence analysis identified Asp34 and Glu251 as the conserved catalytic residues. Structure analysis of <em>Bo</em>GH43_35 disclosed 5-bladed β-propeller fold adopted by the N-terminal GH43 catalytic module followed by two independently folded carbohydrate-binding modules family 6 (CBM6A and CBM6B), displaying jellyroll type β-sandwich fold. Molecular Dynamics simulation of <em>Bo</em>GH43_35 for 200 ns showed RMSD 0.35 nm, confirming structural stability and compactness of modeled structure. Molecular docking of <em>Bo</em>GH43_35 with arabino-xylooligosaccharides and xylooligosaccharides by using AutoDock 4.2.7 demonstrated most favourable binding with arabinose (−5.01 kcal/mol) followed by arabinoxylobiose (−4.35 kcal/mol), xylotriose (−4.65 kcal/mol), xylotetraose (−4.18 kcal/mol) and xylobiose (−3.66 kcal/mol) showing affinity with both types of oligosaccharides. RMSD value of <em>Bo</em>GH43_35-arabinose complex decreased to 0.28 nm upon MD simulation from 0.35 nm for only <em>Bo</em>GH43_35, indicating stability of enzyme-substrate complex throughout the trajectory. The binding analysis of <em>Bo</em>GH43_35 with wheat arabinoxylan by fluorescence spectroscopy gave <em>K</em><sub><em>a</em></sub>, 3.1 × 10<sup>2</sup> M<sup>−1</sup>, ΔG -14.2 kJ mole<sup>−1</sup> and number of binding sites 2.2. Dynamic light scattering of <em>Bo</em>GH43_35 showed hydrodynamic radius (<em>R</em><sub><em>h</em></sub>) of 4.0 nm, slightly higher than the radius of gyration (2.69 nm) from MD simulation. Additionally, zeta potential measurements (−9.3 mV at 0.5 mg/mL and −9.4 mV at 1.0 mg/mL) denoted its fair resistance towards aggregation in aqueous solution.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110232"},"PeriodicalIF":3.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749804","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 : 2024-11-25DOI: 10.1016/j.abb.2024.110230
Jialong Yang , Shenchuyue Ni , An Wang , Kaitao Wang , Jiapeng Deng , Zijie Li , Yizhen Cai , Yiqi Chen , Guodong Chen , Dingsheng Lin
Skin flaps are often used for repair and reconstruction, including oral cavity and palate. However, postoperative flap necrosis limited applications. Myrtenol, a plant-derived bicyclic monoterpene, has pharmacological effects including inhibiting apoptosis and promoting autophagy. But any impact on skin flaps survival remains unclear. Thus, we established modified McFarlane flaps on 24 Sprague-Dawley rats and applied myrtenol. They were randomly divided into low-dose myrtenol (L-Myr), high-dose myrtenol (H-Myr), inhibitor and control groups. On postoperative day 7, flap survival rate was increased and Laser Doppler images showed blood circulation improvement under myrtenol treatment. Hematoxylin and eosin staining (H&E) results indicated that it increased micro vessel density (MVD) and decreased neutrophil numbers. Besides, kits detection showed that it improved anti-oxidant stress factors activities and reduced pro-oxidant stress factors contents. Moreover, immunofluorescence and Western blot results demonstrated that it upregulated the expression of pro-angiogenic factors, anti-apoptotic proteins, pro-autophagic proteins, mitogen-activated protein kinase 1/2 (MEK1/2) and extracellular signal-regulated kinases 1/2 (ERK1/2) and downregulated the expression of pro-inflammatory cytokines, pro-apoptotic proteins and anti-autophagic proteins. The specific inhibitor U0126 of MEK/ERK pathway partially reversed these effects. Overall, Myrtenol promoted angiogenesis, reduced oxidative stress, ameliorated inflammation, inhibited apoptosis and upregulated autophagy via MEK/ERK pathway to promote flap survival.
{"title":"Myrtenol promotes skin flap survival by inhibiting apoptosis and promoting autophagy via the MEK/ERK pathway","authors":"Jialong Yang , Shenchuyue Ni , An Wang , Kaitao Wang , Jiapeng Deng , Zijie Li , Yizhen Cai , Yiqi Chen , Guodong Chen , Dingsheng Lin","doi":"10.1016/j.abb.2024.110230","DOIUrl":"10.1016/j.abb.2024.110230","url":null,"abstract":"<div><div>Skin flaps are often used for repair and reconstruction, including oral cavity and palate. However, postoperative flap necrosis limited applications. Myrtenol, a plant-derived bicyclic monoterpene, has pharmacological effects including inhibiting apoptosis and promoting autophagy. But any impact on skin flaps survival remains unclear. Thus, we established modified McFarlane flaps on 24 Sprague-Dawley rats and applied myrtenol. They were randomly divided into low-dose myrtenol (L-Myr), high-dose myrtenol (H-Myr), inhibitor and control groups. On postoperative day 7, flap survival rate was increased and Laser Doppler images showed blood circulation improvement under myrtenol treatment. Hematoxylin and eosin staining (H&E) results indicated that it increased micro vessel density (MVD) and decreased neutrophil numbers. Besides, kits detection showed that it improved anti-oxidant stress factors activities and reduced pro-oxidant stress factors contents. Moreover, immunofluorescence and Western blot results demonstrated that it upregulated the expression of pro-angiogenic factors, anti-apoptotic proteins, pro-autophagic proteins, mitogen-activated protein kinase 1/2 (MEK1/2) and extracellular signal-regulated kinases 1/2 (ERK1/2) and downregulated the expression of pro-inflammatory cytokines, pro-apoptotic proteins and anti-autophagic proteins. The specific inhibitor U0126 of MEK/ERK pathway partially reversed these effects. Overall, Myrtenol promoted angiogenesis, reduced oxidative stress, ameliorated inflammation, inhibited apoptosis and upregulated autophagy via MEK/ERK pathway to promote flap survival.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"763 ","pages":"Article 110230"},"PeriodicalIF":3.8,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142723765","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 : 2024-11-25DOI: 10.1016/j.abb.2024.110227
Rong Li, Ying Huang
Glutaredoxins (Grxs) are small, heat-stable proteins that serve as multi-functional glutathione （GSH）-dependent thiol transferases. Recent studies have elucidated their role in regulating cellular iron and copper homeostases. In Schizosaccharomyces pombe, five Grxs (Grx1-5) have been identified. Among them， Grx4 and its homologs possess a C-terminal glutaredoxin domain (GRX) and an N-terminal thioredoxin-like domain (TRX). The functional roles of the GRX and TRX domains in Grx4 were investigated by constructing strains that express a truncated Grx4 under the regulation of either a constitutive cam1 promoter or its native promoter. Our findings indicated that two autophagy-related (Atg) protein 8 (Atg8)-interacting motifs (AIM), FLKI and FQEI, in the TRX domain of Grx4 are sufficient to induce autophagic degradation under nitrogen- and iron-starvation, respectively. Moreover, the expression level of a vacuolar ferrous iron transporter Pcl1 was altered in Δatg5 or Δatg8 strains under iron starvation,suggesting that autophagy is required for maintaining iron homeostasis in S. pombe. Further investigations revealed that Grx4 is required for cellular survival and endoplasmic reticulum (ER) autophagy (ER-phagy) during dithiothreitol (DTT) treatment, implying a potential correlation between Grxs and ER-stress. Additionally, loss of Grx4 disrupts nuclear integrity during ER stress, highlighting the versatility and importance of further investigations into the functions of Grx4.
{"title":"Schizosaccharomyces pombe Grx4 is subject to autophagic degradation under nitrogen- and iron- starvation and ER-stress","authors":"Rong Li, Ying Huang","doi":"10.1016/j.abb.2024.110227","DOIUrl":"10.1016/j.abb.2024.110227","url":null,"abstract":"<div><div>Glutaredoxins (Grxs) are small, heat-stable proteins that serve as multi-functional glutathione （GSH）-dependent thiol transferases. Recent studies have elucidated their role in regulating cellular iron and copper homeostases. In <em>Schizosaccharomyces pombe</em>, five Grxs (Grx1-5) have been identified. Among them， Grx4 and its homologs possess a C-terminal glutaredoxin domain (GRX) and an N-terminal thioredoxin-like domain (TRX). The functional roles of the GRX and TRX domains in Grx4 were investigated by constructing strains that express a truncated Grx4 under the regulation of either a constitutive <em>cam1</em> promoter or its native promoter. Our findings indicated that two autophagy-related (Atg) protein 8 (Atg8)-interacting motifs (AIM), FLKI and FQEI, in the TRX domain of Grx4 are sufficient to induce autophagic degradation under nitrogen- and iron-starvation, respectively. Moreover, the expression level of a vacuolar ferrous iron transporter Pcl1 was altered in Δ<em>atg5</em> or Δ<em>atg8</em> strains under iron starvation,suggesting that autophagy is required for maintaining iron homeostasis in <em>S. pombe</em>. Further investigations revealed that Grx4 is required for cellular survival and endoplasmic reticulum (ER) autophagy (ER-phagy) during dithiothreitol (DTT) treatment, implying a potential correlation between Grxs and ER-stress. Additionally, loss of Grx4 disrupts nuclear integrity during ER stress, highlighting the versatility and importance of further investigations into the functions of Grx4.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110227"},"PeriodicalIF":3.8,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142738227","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 : 2024-11-24DOI: 10.1016/j.abb.2024.110228
Saniye G. Kaya , Andrej Hovan , Marco W. Fraaije
Light-Oxygen-Voltage (LOV) domains are the protein-based light switches used in nature to trigger and regulate various processes. They allow light signals to be converted into metabolic signaling cascades. Various LOV-domain proteins have been characterized in the last few decades and have been used to develop light-sensitive tools in cell biology research. LOV-based applications exploit the light-driven regulation of effector elements to activate signaling pathways, activate genes, or locate proteins within cells. A relatively new application of an engineered small LOV-domain protein called miniSOG (mini singlet oxygen generator) is based on the light-induced formation of reactive oxygen species (ROS). The first miniSOG was engineered from a LOV domain from Arabidopsis thaliana. This engineered 14 kDa light-responsive flavin-containing protein can be exploited as protein tag for the light-triggered localized production of ROS. Such tunable ROS production by miniSOG or similarly redesigned LOV-domains can be of use in studies focused on subcellular phenomena but may also allow new light-fueled catalytic processes. This review provides an overview of the discovery of LOV domains and their development into tools for cell biology. It also highlights recent advancements in engineering LOV domains for various biotechnological applications and cell biology studies.
{"title":"Engineering of LOV-domains for their use as protein tags","authors":"Saniye G. Kaya , Andrej Hovan , Marco W. Fraaije","doi":"10.1016/j.abb.2024.110228","DOIUrl":"10.1016/j.abb.2024.110228","url":null,"abstract":"<div><div>Light-Oxygen-Voltage (LOV) domains are the protein-based light switches used in nature to trigger and regulate various processes. They allow light signals to be converted into metabolic signaling cascades. Various LOV-domain proteins have been characterized in the last few decades and have been used to develop light-sensitive tools in cell biology research. LOV-based applications exploit the light-driven regulation of effector elements to activate signaling pathways, activate genes, or locate proteins within cells. A relatively new application of an engineered small LOV-domain protein called miniSOG (mini singlet oxygen generator) is based on the light-induced formation of reactive oxygen species (ROS). The first miniSOG was engineered from a LOV domain from <em>Arabidopsis thaliana</em>. This engineered 14 kDa light-responsive flavin-containing protein can be exploited as protein tag for the light-triggered localized production of ROS. Such tunable ROS production by miniSOG or similarly redesigned LOV-domains can be of use in studies focused on subcellular phenomena but may also allow new light-fueled catalytic processes. This review provides an overview of the discovery of LOV domains and their development into tools for cell biology. It also highlights recent advancements in engineering LOV domains for various biotechnological applications and cell biology studies.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"763 ","pages":"Article 110228"},"PeriodicalIF":3.8,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142723766","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 : 2024-11-22DOI: 10.1016/j.abb.2024.110225
Qing Li , Yi-Yue Zhang , Dan Peng , Hong-Rui Liu , Lin Wu , Ting-Ting Tang , Xiu-Ju Luo
Iron overload-dependent ferroptosis is believed to contribute to the brain injury of ischemia/reperfusion (I/R), whereas toll-like receptor 4 (TLR4) can exert pro-ferroptosis effect via inhibiting the glutathione peroxidase 4 (GPX4) level, but the mechanisms behind these phenomenon are not fully elucidated. Tumor necrosis factor receptor correlated factor 3-interaction Jun amino-terminal kinase [JNK]-activating modulator (T3JAM) can activate specific molecule and its downstream signaling pathways, including TLR4. This study aims to explore whether targeting T3JAM can reduce I/R-induced ferroptosis in brain via downregulating TLR4. A Sprague Dawley (SD) rat model of cerebral I/R injury was established by 2 h-ischemia plus 24 h-reperfusion, which displayed brain injury (increases in neurological deficit score and infarct volume) and upregulation of T3JAM and TLR4, concomitant with the increased ferroptosis, reflected by increases in the levels of transferrin receptor protein 1 (TfR1), total iron, Fe2+ and lipid peroxidation (LPO) while decreases in the levels of ferroportin (FPN) and GPX4. Consistently, similar results were achieved in the cultured HT22 cells subjected to 8h-oxygen-glucose deprivation plus 12 h-reoxygenation (OGD/R), and knockdown of T3JAM reversed these phenomena. Moreover, Telaprevir, an anti-hepatitis C virus (HCV) drug, could also provide beneficial effect on alleviating ischemic brain injury via inhibition of T3JAM. Based on these observations, we conclud that inhibition of T3JAM can reduce I/R-induced brain cell ferroptosis through downregulating TLR4 and that T3JAM could be a potential target for identifying novel or existing drugs (such as Telaprevir) to treat cerebral I/R injury.
{"title":"Targeting inhibition of T3JAM reduces brain cell ferroptosis in rat following ischemia/reperfusion via a mechanism involving prevention of TLR4-mediated iron overload","authors":"Qing Li , Yi-Yue Zhang , Dan Peng , Hong-Rui Liu , Lin Wu , Ting-Ting Tang , Xiu-Ju Luo","doi":"10.1016/j.abb.2024.110225","DOIUrl":"10.1016/j.abb.2024.110225","url":null,"abstract":"<div><div>Iron overload-dependent ferroptosis is believed to contribute to the brain injury of ischemia/reperfusion (I/R), whereas toll-like receptor 4 (TLR4) can exert pro-ferroptosis effect via inhibiting the glutathione peroxidase 4 (GPX4) level, but the mechanisms behind these phenomenon are not fully elucidated. Tumor necrosis factor receptor correlated factor 3-interaction Jun amino-terminal kinase [JNK]-activating modulator (T3JAM) can activate specific molecule and its downstream signaling pathways, including TLR4. This study aims to explore whether targeting T3JAM can reduce I/R-induced ferroptosis in brain via downregulating TLR4. A Sprague Dawley (SD) rat model of cerebral I/R injury was established by 2 h-ischemia plus 24 h-reperfusion, which displayed brain injury (increases in neurological deficit score and infarct volume) and upregulation of T3JAM and TLR4, concomitant with the increased ferroptosis, reflected by increases in the levels of transferrin receptor protein 1 (TfR1), total iron, Fe<sup>2+</sup> and lipid peroxidation (LPO) while decreases in the levels of ferroportin (FPN) and GPX4. Consistently, similar results were achieved in the cultured HT22 cells subjected to 8h-oxygen-glucose deprivation plus 12 h-reoxygenation (OGD/R), and knockdown of T3JAM reversed these phenomena. Moreover, Telaprevir, an anti-hepatitis C virus (HCV) drug, could also provide beneficial effect on alleviating ischemic brain injury via inhibition of T3JAM. Based on these observations, we conclud that inhibition of T3JAM can reduce I/R-induced brain cell ferroptosis through downregulating TLR4 and that T3JAM could be a potential target for identifying novel or existing drugs (such as Telaprevir) to treat cerebral I/R injury.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"763 ","pages":"Article 110225"},"PeriodicalIF":3.8,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708521","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 : 2024-11-22DOI: 10.1016/j.abb.2024.110223
Kirankumar Nalla , Biji Chatterjee , Jagadeesha Poyya , Aishwarya Swain , Krishna Ghosh , Archana Pan , Chandrashekhar G. Joshi , Bramanandam Manavathi , Santosh R. Kanade
Purpose
Histone methyltransferases are enzymes that selectively methylate lysine or arginine residues on both histone and non-histone proteins, categorized into lysine methyltransferases and arginine methyltransferases. Notably, EZH2 and PRMT5 are known for catalyzing trimethylation of H3 at K27 and symmetric dimethylation of H4 at R3, respectively. These methylation events are recognized as characteristic histone-repressive marks in cancer. The over expression of PRMT5 and EZH2 were reported in various cancers and recognized as a drug target. The study aims to explore the inhibitory potential of phytocompound, Epigallocatechin-3-gallate (EGCG), against PRMT5 and EZH2 in the breast cancer model.
Methods
Screening of an array of phytocompounds was conducted through a combination of in-silico and in-vitro assays. Interactions between EGCG and human PRMT5: MEP50 and EZH2 were evaluated using molecular docking. Binding efficiency was validated, by Surface Plasmon Resonance studies and inhibitory potential was accessed by in vitro methylation followed by western blots, ELISA, and cell-based assays. In-vivo efficacy of EGCG was carried on cell line derived mice xenograft model.
Results
EGCG demonstrated robust interactions with PRMT5:MEP50 complex and EZH2, particularly within the SAM binding site. Surface Plasmon Resonance analysis revealed strong binding affinity in nanomolar concentrations, particularly with PRMT5-MEP50 compared to EZH2. In-vitro assays confirmed EGCG's ability to inhibit PRMT5 and EZH2, leading to a decrease in their catalytic products, namely H4R3me2s and H3K27me3, respectively. EGCG treatment induced both autophagy and apoptosis invitro. In-vivo studies demonstrated significant reductions in tumor size and the proliferation marker ki67, accompanied by a decrease in histone repressive marks.
Conclusion
The findings suggest that EGCG effectively inhibits PRMT5 and EZH2, underscoring its potential for combined therapeutic strategies in cancer treatment.
{"title":"Epigallocatechin-3-gallate inhibit the protein arginine methyltransferase 5 and enhancer of Zeste homolog 2 in breast cancer both in vitro and in vivo","authors":"Kirankumar Nalla , Biji Chatterjee , Jagadeesha Poyya , Aishwarya Swain , Krishna Ghosh , Archana Pan , Chandrashekhar G. Joshi , Bramanandam Manavathi , Santosh R. Kanade","doi":"10.1016/j.abb.2024.110223","DOIUrl":"10.1016/j.abb.2024.110223","url":null,"abstract":"<div><h3>Purpose</h3><div>Histone methyltransferases are enzymes that selectively methylate lysine or arginine residues on both histone and non-histone proteins, categorized into lysine methyltransferases and arginine methyltransferases. Notably, EZH2 and PRMT5 are known for catalyzing trimethylation of H3 at K27 and symmetric dimethylation of H4 at R3, respectively. These methylation events are recognized as characteristic histone-repressive marks in cancer. The over expression of PRMT5 and EZH2 were reported in various cancers and recognized as a drug target. The study aims to explore the inhibitory potential of phytocompound, Epigallocatechin-3-gallate (EGCG), against PRMT5 and EZH2 in the breast cancer model.</div></div><div><h3>Methods</h3><div>Screening of an array of phytocompounds was conducted through a combination of <em>in-silico</em> and <em>in-vitro</em> assays. Interactions between EGCG and human PRMT5: MEP50 and EZH2 were evaluated using molecular docking. Binding efficiency was validated, by Surface Plasmon Resonance studies and inhibitory potential was accessed by <em>in vitro</em> methylation followed by western blots, ELISA, and cell-based assays. <em>In-vivo</em> efficacy of EGCG was carried on cell line derived mice xenograft model.</div></div><div><h3>Results</h3><div>EGCG demonstrated robust interactions with PRMT5:MEP50 complex and EZH2, particularly within the SAM binding site. Surface Plasmon Resonance analysis revealed strong binding affinity in nanomolar concentrations, particularly with PRMT5-MEP50 compared to EZH2. <em>In-vitro</em> assays confirmed EGCG's ability to inhibit PRMT5 and EZH2, leading to a decrease in their catalytic products, namely H4R3me2s and H3K27me3, respectively. EGCG treatment induced both autophagy and apoptosis <em>invitro</em>. <em>In-vivo</em> studies demonstrated significant reductions in tumor size and the proliferation marker ki67, accompanied by a decrease in histone repressive marks.</div></div><div><h3>Conclusion</h3><div>The findings suggest that EGCG effectively inhibits PRMT5 and EZH2, underscoring its potential for combined therapeutic strategies in cancer treatment.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"763 ","pages":"Article 110223"},"PeriodicalIF":3.8,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142709018","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 : 2024-11-19DOI: 10.1016/j.abb.2024.110219
Kuldeep Jangid, Jai Krishna Mahto, K Amith Kumar, Preeti Dhaka, Anchal Sharma, Amaan Tariq, Ashwani Kumar Sharma, Pravindra Kumar
The shikimate pathway, essential for aromatic amino acid biosynthesis, is absent in animals, making its enzymes promising targets for developing antimicrobials. 3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) catalyzes the first committed step, which serves as the primary checkpoint for regulating the flow within the pathway, regulated by its end products (Phe, Tyr and Trp). Previously, we identified chlorogenic acid (CGA), an ester of caffeic and quinic acid, as an inhibitor of DAHPS from Bacillus subtilis, prompting us to investigate quinic acid as a potential inhibitor of Providencia alcalifaciens DAHPS (PaDAHPS). Here, we report the crystal structures of phenylalanine-sensitive DAHPS from Providenciaalcalifaciens in complex with phenylalanine (Phe) and quinic acid (QA) at resolutions of 2.5 Å and 2.68 Å, respectively. Structural analysis reveals that QA binds to the same site as Phe, with biophysical assays showing a similar binding affinity (KD = 42 μM for QA and KD = 32 μM for Phe). In vitro inhibition studies demonstrated that QA and Phe inhibit PaDAHPS activity, with appKi values of 382 μM and 132 μM, respectively. Additionally, QA inhibited the growth of several bacterial species, including Pseudomonas aeruginosa, Moraxella catarrhalis, Providencia alcalifaciens, Staphylococcus aureus, Escherichia coli with minimum inhibitory concentrations (MICs) ranging from 2.5 to 5 mg/ml. These findings identify quinic acid as a promising scaffold for developing novel antimicrobial agents targeting the shikimate pathway, providing potential therapeutic strategies for bacterial infections.
{"title":"Structural and biochemical analyses reveal quinic acid inhibits DAHP synthase a key player in shikimate pathway","authors":"Kuldeep Jangid, Jai Krishna Mahto, K Amith Kumar, Preeti Dhaka, Anchal Sharma, Amaan Tariq, Ashwani Kumar Sharma, Pravindra Kumar","doi":"10.1016/j.abb.2024.110219","DOIUrl":"10.1016/j.abb.2024.110219","url":null,"abstract":"<div><div>The shikimate pathway, essential for aromatic amino acid biosynthesis, is absent in animals, making its enzymes promising targets for developing antimicrobials. 3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) catalyzes the first committed step, which serves as the primary checkpoint for regulating the flow within the pathway, regulated by its end products (Phe, Tyr and Trp). Previously, we identified chlorogenic acid (CGA), an ester of caffeic and quinic acid, as an inhibitor of DAHPS from <em>Bacillus subtilis,</em> prompting us to investigate quinic acid as a potential inhibitor of <em>Providencia alcalifaciens</em> DAHPS (<em>Pa</em>DAHPS). Here, we report the crystal structures of phenylalanine-sensitive DAHPS from <em>P</em><em>rovidencia</em> <em>alcalifaciens</em> in complex with phenylalanine (Phe) and quinic acid (QA) at resolutions of 2.5 Å and 2.68 Å, respectively. Structural analysis reveals that QA binds to the same site as Phe, with biophysical assays showing a similar binding affinity (<em>K</em><sub><em>D</em></sub> = 42 μM for QA and <em>K</em><sub><em>D</em></sub> = 32 μM for Phe). <em>In vitro</em> inhibition studies demonstrated that QA and Phe inhibit <em>Pa</em>DAHPS activity, with <sup>app</sup><em>K</em><sub><em>i</em></sub> values of 382 μM and 132 μM, respectively. Additionally, QA inhibited the growth of several bacterial species, including <em>Pseudomonas aeruginosa, Moraxella catarrhalis, Providencia alcalifaciens, Staphylococcus aureus, Escherichia coli</em> with minimum inhibitory concentrations (MICs) ranging from 2.5 to 5 mg/ml. These findings identify quinic acid as a promising scaffold for developing novel antimicrobial agents targeting the shikimate pathway, providing potential therapeutic strategies for bacterial infections.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"763 ","pages":"Article 110219"},"PeriodicalIF":3.8,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680679","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 : 2024-11-19DOI: 10.1016/j.abb.2024.110222
Miao Liang , Wei-Kang Li , Xi-Xi Xie , Bai-Cong Lai , Jing-Jing Zhao , Ke-Wei Yu , Pei-Feng Ke , Yun-Xiu Wang , Chun-Min Kang , Xian-Zhang Huang
Cardiovascular disease is characterized by chronic inflammation and atherosclerosis (AS) is the pathological basis. Mitigating endothelial dysfunction and mononuclear cell adhesion is a crucial approach in impeding the initial advancement of AS. As an inflammation-immune regulation-related protein, 2′-5′-oligoadenylate synthetase 1 (OAS1) plays a critical role in inflammation, but its impact on endothelial dysfunction and mononuclear cell adhesion is not well understood. In this study, bioinformatic analysis revealed a significant enrichment of OAS1 in atherosclerotic plaques within human aortic sections. In addition, OAS1 was detected in atherosclerotic plaques within human aortic sections across various stages of development, with elevated expression observed in more advanced plaques. The expression of OAS1 exhibited a distinct temporal and concentration-dependent upregulation in response to lipopolysaccharide (LPS) stimulation. Notably, the deficiency of OAS1 markedly attenuated the elevation in reactive oxygen species (ROS) levels, nitric oxide (NO) concentrations, and monocyte adhesion induced by LPS. A positive correlation was observed between the levels of NFκBp65 and OAS1 in human plaques, and the deletion of OAS1 led to a down-regulation of P65 expression. Furthermore, the simultaneous knockdown of OAS1 and NFκBp65 resulted in a significant amelioration of endothelial dysfunction (including ROS, NO, and inflammation factors) and monocyte adhesion, suggesting a synergistic interaction between OAS1 and NFκBp65. These findings underscore the potential of OAS1 to modulate the extent of endothelial dysfunction and monocyte adhesion through its regulation of NFκBp65 thereby positioning it as a promising therapeutic target for the management of AS.
{"title":"OAS1 induces endothelial dysfunction and promotes monocyte adhesion through the NFκB pathway in atherosclerosis","authors":"Miao Liang , Wei-Kang Li , Xi-Xi Xie , Bai-Cong Lai , Jing-Jing Zhao , Ke-Wei Yu , Pei-Feng Ke , Yun-Xiu Wang , Chun-Min Kang , Xian-Zhang Huang","doi":"10.1016/j.abb.2024.110222","DOIUrl":"10.1016/j.abb.2024.110222","url":null,"abstract":"<div><div>Cardiovascular disease is characterized by chronic inflammation and atherosclerosis (AS) is the pathological basis. Mitigating endothelial dysfunction and mononuclear cell adhesion is a crucial approach in impeding the initial advancement of AS. As an inflammation-immune regulation-related protein, 2′-5′-oligoadenylate synthetase 1 (OAS1) plays a critical role in inflammation, but its impact on endothelial dysfunction and mononuclear cell adhesion is not well understood. In this study, bioinformatic analysis revealed a significant enrichment of OAS1 in atherosclerotic plaques within human aortic sections. In addition, OAS1 was detected in atherosclerotic plaques within human aortic sections across various stages of development, with elevated expression observed in more advanced plaques. The expression of OAS1 exhibited a distinct temporal and concentration-dependent upregulation in response to lipopolysaccharide (LPS) stimulation. Notably, the deficiency of OAS1 markedly attenuated the elevation in reactive oxygen species (ROS) levels, nitric oxide (NO) concentrations, and monocyte adhesion induced by LPS. A positive correlation was observed between the levels of NFκBp65 and OAS1 in human plaques, and the deletion of OAS1 led to a down-regulation of P65 expression. Furthermore, the simultaneous knockdown of OAS1 and NFκBp65 resulted in a significant amelioration of endothelial dysfunction (including ROS, NO, and inflammation factors) and monocyte adhesion, suggesting a synergistic interaction between OAS1 and NFκBp65. These findings underscore the potential of OAS1 to modulate the extent of endothelial dysfunction and monocyte adhesion through its regulation of NFκBp65 thereby positioning it as a promising therapeutic target for the management of AS.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"763 ","pages":"Article 110222"},"PeriodicalIF":3.8,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685773","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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