Archives of biochemistry and biophysics最新文献

{"title":"Assessing the role of Berberine as an inhibitor of advanced glycation end products (AGEs) formation using in vitro and molecular interaction studies.","authors":"Yusra Ahmad, Faisal Nabi, Sana Siddiqui, Rizwan Hasan Khan, Shagufta Moin","doi":"10.1016/j.abb.2025.110292","DOIUrl":"https://doi.org/10.1016/j.abb.2025.110292","url":null,"abstract":"<p><p>Glycation and aggregation of proteins have garnered more interest in recent years. Glycation leads to the formation of protein aggregates and advanced glycation ends (AGEs) that play crucial roles within several pathological conditions. The objective of our study is to gain a deeper understanding of the formation of AGEs and aggregates of human serum albumin (HSA) in the presence of methylglyoxal and the protective effects of the phytochemical berberine. HSA was incubated with methylglyoxal and different concentrations of berberine for 7-14 days at 35-37 °C. Methylglyoxal resulted in the formation of AGEs, fibrillar aggregates, and hydrophobic protein patches in HSA, as was evident from AGE fluorescence, ThT and ANS fluorescence studies. It also disrupted the secondary structure of HSA shown by CD spectroscopy. All these parameters were restored towards native HSA in the glycated HSA + berberine samples. Molecular docking was employed to identify the critical HSA residues implicated in the HSA-berberine interaction and also to determine the spontaneous binding of berberine on the HSA sub-domain favoring the thermodynamic binding. The binding energy between HSA-berberine was found to be -9.1 kcal/mol. Various types of forces like hydrophobic interactions, polar forces, hydrogen bonds, etc are were at play between the HSA and berberine interaction. Since MGO level is increased in pathological conditions such as type II diabetes, there is a chance that increased MGO concentration could cause glycation of HSA, leading to decreased levels of HSA, as observed in pathological circumstances. The binding of berberine to lysine and arginine residues might be linked to its antiglycation potential as these amino acids play an important role in the glycation of proteins. Nevertheless, additional inquiries are needed to substantiate this claim. Thus, our study characterizes AGEs and aggregates of clinically important protein HSA.</p>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":" ","pages":"110292"},"PeriodicalIF":3.8,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142963675","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}

{"title":"Structural and functional insights into UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) from Brucella ovis","authors":"Martha Minjárez-Sáenz ,&nbsp;Maribel Rivero ,&nbsp;Víctor Correa-Pérez ,&nbsp;Sergio Boneta ,&nbsp;Paula Suárez ,&nbsp;Víctor Polo ,&nbsp;Sheila J. Sadeghi ,&nbsp;Inmaculada Yruela ,&nbsp;Marta Martínez-Júlvez ,&nbsp;Milagros Medina","doi":"10.1016/j.abb.2025.110288","DOIUrl":"10.1016/j.abb.2025.110288","url":null,"abstract":"<div><div>The peptidoglycan biosynthetic pathway involves a series of enzymatic reactions in which UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) plays a crucial role in catalyzing the conversion of UDP-N-acetylglucosamine-enolpyruvate (UNAGEP) to UDP-N-acetylmuramic acid. This reaction relies on NADPH and FAD and, since MurB is not found in eukaryotes, it is an attractive target for the development of antimicrobials. MurB from <em>Brucella ovis</em>, the causative agent of brucellosis in sheep, is characterized here. The FAD cofactor in MurB of <em>B. ovis</em> is reduced to the hydroquinone state without semiquinone stabilization with an estimated <em>E</em>_ox/hq of −260 mV. MurB from <em>B. ovis</em> catalyzes the oxidation of NADPH in a slow process that is positively influenced by the presence of the second product, UNAGEP. The crystallographic structure of the MurB_ox:UNAGEP complex confirms its folding into three domains and the binding of UNAGEP, positioning its enolpyruvyl group for hydride transfer from FAD. MurB shows a complex thermal unfolding pathway that is influenced by UNAGEP and NADP⁺, confirming its ability to bind both molecules. Molecular dynamics (MD) simulations predict that the nicotinamide of NADP⁺ is more stable at the active site than the enolpyruvyl of UNAGEP, and suggests that MurB can simultaneously accommodate NADPH and UNAGEP in the substrate channel, increasing overall protein-ligand flexibility. Sequence and evolutionary analyses show that MurB from <em>B. ovis</em> conserves all motifs predicted to be involved in catalysis within the Type IIa family.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"765 ","pages":"Article 110288"},"PeriodicalIF":3.8,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142969509","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}

{"title":"Retraction notice to “Role of sulfurous mineral water and sodium hydrosulfide as potent inhibitors of fibrosis in the heart of diabetic rats” [Archiv. Biochem. Biophys. 506 (2011) 48–57]","authors":"Mohamed M. El-Seweidy ,&nbsp;Nermin A.H. Sadik ,&nbsp;Olfat G. Shaker","doi":"10.1016/j.abb.2024.110174","DOIUrl":"10.1016/j.abb.2024.110174","url":null,"abstract":"","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"762 ","pages":"Article 110174"},"PeriodicalIF":3.8,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142563883","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}

{"title":"Corrigendum to “Aldose reductase with quinolone antibiotics interaction: In vitro and in silico approach of its relationship with diabetic complications” [Arch. Biochem. Biophys. 761 (2024) 110161]","authors":"Cüneyt Türkeş","doi":"10.1016/j.abb.2024.110211","DOIUrl":"10.1016/j.abb.2024.110211","url":null,"abstract":"","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"762 ","pages":"Article 110211"},"PeriodicalIF":3.8,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613542","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}

{"title":"Biochemical and structural insights into pinoresinol hydroxylase from Pseudomonas sp","authors":"Teresa Benedetta Guerriere ,&nbsp;Marco W. Fraaije ,&nbsp;Andrea Mattevi","doi":"10.1016/j.abb.2024.110247","DOIUrl":"10.1016/j.abb.2024.110247","url":null,"abstract":"<div><div>The vanillyl alcohol oxidase/<em>p</em>-cresol methylhydroxylase (VAO/PCMH) flavoprotein family comprises a broad spectrum of enzymes capable of catalyzing the oxidative bioconversions of various substrates. Among them, pinoresinol hydroxylase (PinH) from the 4-alkylphenol oxidizing subgroup initiates the oxidative degradation of (+)-pinoresinol, a lignan important for both lignin structure and plant defense. In this study, we present a detailed biochemical and structural characterization of PinH from <em>Pseudomonas</em> sp., with focus on its substrate specificity and product formation. PinH was expressed in <em>E. coli</em> and purified as FAD-containing, soluble protein. The flavoenzyme catalyzes the hydroxylation of both (+)-pinoresinol and eugenol. Structural analysis reveals its dimeric form, non-covalent flavin binding, and a large active site. AlphaFold models of the PinH-cytochrome complex demonstrate cytochrome's dual role in electron transfer and modulating PinH's conformation. A distinctive feature of PinH is a large cavity that hosts its multi-ring (+)-pinoresinol substrate. The capability of converting bulky lignans is particularly attractive for biotechnological applications aimed at producing high-value compounds from phenolic precursors. These insights expand our knowledge on the structure and mechanism of the VAO/PCMH flavoenzyme family members.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110247"},"PeriodicalIF":3.8,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142754468","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}

{"title":"Targeting histidinol-phosphate aminotransferase in Acinetobacter baumannii with salvianolic acid B: A structure-based approach to novel antibacterial strategies","authors":"Anamika Singh,&nbsp;Mansi Tanwar,&nbsp;Tej P. Singh,&nbsp;Sujata Sharma,&nbsp;Pradeep Sharma","doi":"10.1016/j.abb.2024.110233","DOIUrl":"10.1016/j.abb.2024.110233","url":null,"abstract":"<div><div>Undoubtedly, <em>Acinetobacter baumannii</em> is a major ESKAPE pathogen that poses a significant threat to public health, causing severe nosocomial infections with high mortality rates in healthcare settings. Due to the rapid development of antibiotic resistance, only a limited number of antibiotics remain effective against infections caused by multidrug-resistant (MDR) <em>Acinetobacter baumannii</em>. The discovery of new class of antibiotic molecules still lags behind the rate of growing worldwide burden of antimicrobial resistance (AMR). To expedite the discovery of new therapeutic molecules, we have focused on HisC from <em>A. baumannii</em> (<em>Ab</em>HisC), a crucial enzyme involved in the seventh step of histidine biosynthesis. This pathway is absent in humans. We have employed the advanced computational techniques to target this promising drug target. <em>Ab</em>HisC was cloned, overexpressed, and purified. Three distinct sets of libraries containing ∼60,000 natural compounds from ZINC database were screened against <em>Ab</em>HisC using Schrödinger's glide module software. Based on the docking score and glide energy, top 25 hits were further subjected to induced fit (IF) docking. Top four out of the twenty five compounds from IF docking were subjected to 100ns molecular dynamics simulations, and it was observed that salvianolic acid B (SA-B) (a naturally occurring compound) complex with <em>Ab</em>HisC, was found to be extremely stable. The glide energy and docking score of SA-B were −88.59 kcal/mol and −10.4 kcal/mol. SA-B was also found to quench the intrinsic fluorescence of tyrosine indicating its binding to the target. The dissociation constant calculated using Surface Plasmon Resonance was found to be 3.4x10⁻⁹ M. Based on these results we can conclude that SA-B can serve as the potential inhibitor of <em>Ab</em>HisC that can further form the basis of structure based drug design against this deadly pathogen.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"764 ","pages":"Article 110233"},"PeriodicalIF":3.8,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142754471","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}

{"title":"Mechanisms of p53 core tetramer stability mediated by multi-interface interactions: A molecular dynamics study","authors":"Han Zhou ,&nbsp;Shiwei Yan","doi":"10.1016/j.abb.2024.110210","DOIUrl":"10.1016/j.abb.2024.110210","url":null,"abstract":"<div><div>p53 is a tumor suppressor protein for impeding cancer development and maintaining genetic integrity. The formation of the p53 core tetramer is regulated by multiple cooperative interaction interfaces. To investigate the internal mechanisms of tetramer stability, we performed all-atom molecular dynamics simulations. Our findings indicate that the symmetric interface maintains highly conserved interactions, while the dimer–dimer interface displays notable flexibility. Additionally, we identified a novel salt bridge at the dimer–dimer interface that significantly contributes to the interaction energy. Moreover, the affinity of p53 for DNA is more than twice that of protein–protein interactions, driven primarily by five key residues that form multiple hydrogen bonds. Through independent simulations of the two dimeric models, we provide a theoretical explanation for why only the symmetric dimeric structure has been observed experimentally. The study identifies key regions and residues that contribute to stability at the inter-molecular interaction interfaces within the p53 tetramer, and highlight the important roles of each contact surface in the formation and stability of the tetramer.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"763 ","pages":"Article 110210"},"PeriodicalIF":3.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142738225","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}

{"title":"Computational discovery of novel GPX4 inhibitors from herbal sources as potential ferroptosis inducers in cancer therapy","authors":"Mohammad Mahdi Mokhtari Tabar ,&nbsp;Abdolmajid Ghasemian ,&nbsp;Amin Kouhpayeh ,&nbsp;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}

{"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 ,&nbsp;Mina Ezzat Attya ,&nbsp;Mahmoud A. El-Rehany ,&nbsp;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}

{"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,&nbsp;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>_<em>a</em>, 3.1 × 10² M⁻¹, ΔG -14.2 kJ mole⁻¹ and number of binding sites 2.2. Dynamic light scattering of <em>Bo</em>GH43_35 showed hydrodynamic radius (<em>R</em>_<em>h</em>) 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}