Archives of biochemistry and biophysics最新文献

{"title":"Characterization of the lysine decarboxylase activity of human ornithine decarboxylase and identification of lysine-like inhibitors","authors":"Jessica Georgina Filisola-Villaseñor ,&nbsp;Samuel Álvarez-Almazán ,&nbsp;Omar Granados-Portillo ,&nbsp;Alicia Cruz-Jiménez ,&nbsp;Gustavo G. Medina-Mendoza ,&nbsp;Dan Israel Zavala-Vargas ,&nbsp;J. Armando Luján-Montelongo ,&nbsp;Edgar Morales-Ríos ,&nbsp;Viridiana Olin-Sandoval","doi":"10.1016/j.abb.2025.110646","DOIUrl":"10.1016/j.abb.2025.110646","url":null,"abstract":"<div><div>Ornithine decarboxylase (ODC) catalyzes the first step in the polyamines (PAs) biosynthesis pathway. These biomolecules are polycations that participate in many cellular processes. However, the non-physiological increase of human ODC (HsODC) expression can lead to the accumulation of PAs, and consequently, to the development of various types of cancer. Despite several inhibitors of HsODC have been proposed for cancer treatment, only the administration of difluoromethylornithine (DFMO) has been accepted as a drug for preventing the relapse of neuroblastoma. Thus, the search for other HsODC inhibitors continues. Previously, an alternative <span>l</span>-lysine decarboxylase activity was described in yeast and rat ODC. In this work, we expressed and purified the recombinant HsODC. Then, we kinetically characterized the ornithine and lysine decarboxylase (LDC) activities of the enzyme with V_max/K_M of 25.4 and 0.353 mL min⁻¹ mg protein⁻¹, respectively. Then, we selected 30 lysine-analogues from 300 candidate ligands for HsODC by molecular docking. The binding of these thirty molecules to HsODC was evaluated through thermal shift assays (TSA), obtaining nine binding molecules. Finally, the HsODC kinetic inhibition assays demonstrated that 7 compounds can inhibit this enzyme <em>in vitro</em> (with Ki ranging from 3.8 nM to 523.5 μM). With our results, we suggest these compounds as candidates to be explored as HsODC inhibitors in cell lines and <em>in vivo</em> models.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"775 ","pages":"Article 110646"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145414938","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":"Clinical value of serum miR-943 as a diagnostic and prognostic biomarker for acute cerebral infarction and its mechanism of action via targeting BDNF","authors":"Sheng Lin,&nbsp;Junbin Chen","doi":"10.1016/j.abb.2025.110667","DOIUrl":"10.1016/j.abb.2025.110667","url":null,"abstract":"<div><h3>Background</h3><div>Dysregulated microRNAs are implicated in the acute cerebral infarction (ACI) pathogenesis.</div></div><div><h3>Aim</h3><div>This study investigated the clinical significance and mechanisms of miR-943 in ACI.</div></div><div><h3>Methods</h3><div>Serum miR-943 levels were measured using RT-qPCR in 132 ACI patients and 135 healthy controls (HC). Diagnostic potential was evaluated by ROC analysis. Prognosis was assessed using 90-day mRS scores. Correlations with clinical parameters were analyzed using Pearson's/Spearman's tests. Multivariate logistic regression identified outcome predictors. Bioinformatic prediction and experimental validation (dual-luciferase, RIP assays) identified miR-943 targets. An OGD/R model in BV-2 microglia simulated ischemia-reperfusion. Effects of miR-943 inhibitors and si-BDNF on viability (CCK-8), apoptosis (flow cytometry), and inflammation (ELISA) were assessed.</div></div><div><h3>Results</h3><div>ACI patients exhibited significantly elevated serum miR-943 expression and reduced BDNF levels versus HC. miR-943 showed high diagnostic value (AUC = 0.909, sensitivity 85.6 %, specificity 83.7 %). MiR-943 expression correlated positively with SBP, DBP, FBG, Hcy, NIHSS score, and infarct volume. Patients with a poor prognosis exhibited significantly higher miR-943 expression levels. Multivariate analysis identified high expression of miR-943 as an independent risk factor for poor outcome. BDNF was validated as a direct miR-943 target gene. OGD/R increased miR-943 expression, suppressed proliferation, promoted apoptosis, and enhanced the expression of inflammatory factors in BV-2 cells. Inhibiting miR-943 expression reversed these detrimental effects, enhancing proliferation and reducing apoptosis/inflammation. Critically, BDNF knockdown abolished the protective effects of miR-943 inhibition.</div></div><div><h3>Conclusion</h3><div>Serum miR-943 is a promising diagnostic and prognostic biomarker for ACI. It exerts pathological effects by post-transcriptionally suppressing BDNF. Targeting the miR-943/BDNF axis represents a potential therapeutic strategy.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"775 ","pages":"Article 110667"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145407760","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":"MiR-133a encapsulated in hyaluronic acid nanoparticles alleviates sepsis-induced cardiomyopathy by decreasing M1 macrophage polarization via the SOCS3/JAK/STAT3 pathway","authors":"Changrui Zheng ,&nbsp;Yuqiang Gao ,&nbsp;Xuehan Wei ,&nbsp;Xiaohong Huang ,&nbsp;Dayan Wu ,&nbsp;Jia Tian","doi":"10.1016/j.abb.2025.110673","DOIUrl":"10.1016/j.abb.2025.110673","url":null,"abstract":"<div><h3>Background</h3><div>Sepsis-induced cardiomyopathy (SIC) is a reversible myocardial dysfunction driven by excessive inflammation, with M1 macrophage polarization as a major contributor. This study explored the regulatory role of the miR-133a/SOCS3 axis in macrophage polarization and myocardial injury and assessed a hyaluronic acid (HA)–based nanogel for targeted miR-133a delivery.</div></div><div><h3>Methods</h3><div>RAW264.7 macrophages were stimulated with LPS and co-cultured with H9C2 cardiomyocytes, followed by transfection with miR-133a mimics/inhibitor or SOCS3 overexpression plasmids. The direct binding between miR-133a and SOCS3 was verified by dual-luciferase reporter assay. A cecal ligation and puncture (CLP) rat model was used to assess <em>in vivo</em> therapeutic effects after intravenous administration of free or HA-encapsulated miR-133a. Macrophage polarization was measured by flow cytometry and qRT-PCR; inflammatory cytokines by ELISA; protein expression (SOCS3, JAK/STAT3 pathway, iNOS, CD206) by Western blot and immunohistochemistry; apoptosis by TUNEL; and myocardial injury by H&amp;E staining.</div></div><div><h3>Results</h3><div>MiR-133a was significantly downregulated in LPS-treated macrophages and in SIC blood samples, with levels inversely correlated to SOCS3. MiR-133a overexpression suppressed M1 polarization, cytokine production, and SOCS3 expression, while enhancing M2 polarization; these effects were reversed by SOCS3 overexpression. In co-culture, miR-133a reduced cardiomyocyte inflammation and apoptosis through SOCS3/JAK/STAT3 inhibition. In CLP rats, HA–miR-133a achieved greater myocardial accumulation than free mimics, attenuated histopathological damage, lowered cytokine levels, iNOS, and phosphorylated JAK3/STAT3, and increased CD206 expression.</div></div><div><h3>Conclusion</h3><div>MiR-133a alleviates SIC by inhibiting SOCS3/JAK/STAT3 signaling and promoting M2 polarization. HA-based targeted delivery enhances stability, tissue uptake, and therapeutic efficacy, representing a promising SIC therapy.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"775 ","pages":"Article 110673"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145556104","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":"Structure-based drug repurposing and experimental validation of inhibitors targeting LigaseD from Mycobacterium tuberculosis","authors":"Ayushi Saini,&nbsp;Aishik Sil,&nbsp;Satyajit Beura,&nbsp;Amit Kumar Das","doi":"10.1016/j.abb.2025.110645","DOIUrl":"10.1016/j.abb.2025.110645","url":null,"abstract":"<div><div><em>Mycobacterium tuberculosis</em> (Mtb) remains a major global health threat due to its survival under host-induced stress and the rise of drug-resistant strains. One critical factor contributing to this resilience is its ability to efficiently repair DNA damage. To survive double-stranded DNA breaks, Mtb utilizes two pathways: homologous recombination (HR) and non-homologous end joining (NHEJ). During dormancy, when HR is less active, Mtb predominantly relies on NHEJ, a pathway involving Ku and LigaseD. LigaseD catalyses DNA ligation through its ligase domain (LigDom), which comprises two subdomains: the NTase, harboring the ATP-binding site essential for adenylation, and the OB domain, which interacts with DNA. LigDom is highly conserved and exhibits low mutation rates in resistant strains, making it an attractive drug target. Using a structure-based drug repurposing approach, FDA-approved drugs were screened, identifying L-756423 as a potent inhibitor with a lowest binding free energy. Molecular dynamics simulation of the L-756423 bound LigDom complex reveals a stable domain structure with significant fluctuations in the interdomain region, suggesting movement in the OB domain that may support efficient binding. To validate these findings, Indinavir, a clinically approved HIV protease inhibitor with structural similarity to L-756423, was selected for experimental testing. Indinavir induces conformational flexibility in LigDom, and also competitively inhibits ATP binding thus blocking the adenylation. Functional microbiological assays confirmed that under oxidative stress, when NHEJ is critical, indinavir-treated cells displayed reduced survival, consistent with impaired DNA repair. These findings indicate that L-756423/Indinavir may hold therapeutic potential against latent tuberculosis and provide a rationale for further experimental investigation.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"775 ","pages":"Article 110645"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145407871","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":"Thermotolerance induced by non-lethal heat shock at 40 °C is activated by mitochondrial ROS and is Nrf2-dependent","authors":"Georges Hraoui,&nbsp;Mélanie Grondin,&nbsp;Khadija Rezki,&nbsp;Diana A. Averill-Bates","doi":"10.1016/j.abb.2025.110649","DOIUrl":"10.1016/j.abb.2025.110649","url":null,"abstract":"<div><div>Hyperthermia is generally administered as an adjuvant to chemotherapy/radiotherapy and sensitizes tumors to these anticancer treatments. Repeated heat treatments (≥42 °C) cause development of transient thermotolerance, an adaptive survival response. This response can be mediated by upregulation of cellular defense pathways and remains unclear. We aim to clarify the mechanistic explanations behind activation of this response. <em>In vitro</em>, thermotolerance can be induced by mild heat stress at 40 °C and protects cells against subsequent lethal heat shock (≥42 °C). When HeLa cells were heated at 42 °C, cellular and mitochondrial superoxide and peroxide levels increased. Treatment with mitochondrial antioxidant MitoQ, or NADPH oxidase (NOX) inhibitor apocynin, decreased levels of reactive oxygen species (ROS) and apoptotic cell death, indicating that mitochondria and NOX are important sources of ROS at 42 °C. Mild heat stress at 40 °C increased production of ROS, which are thought to activate the adaptive response, and reduce subsequent cell death at 42 °C. Our results show that heat-derived ROS are linked to expression of master antioxidant regulator Nrf2. When Nrf2 was overexpressed or knocked down, Nrf2 expression was directly associated with protective ability of the adaptive response induced by mild heat stress (40 °C). Mitochondrial ROS were found to be essential in mediating Nrf2-dependent thermotolerance, because MitoQ treatment prior to exposure to 40 °C reduced Nrf2 levels and dissipated the subsequent protective effect of thermotolerance against toxicity at 42 °C. Our study demonstrates that specific sources of ROS had biologically different implications in activating Nrf2, underlining potential therapeutic targets that may contribute to thermotolerance in anticancer treatments.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"775 ","pages":"Article 110649"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145414939","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":"Substrate stiffness attenuates cardiomyocyte depolarization slope via sodium channel kinetics modulation","authors":"Yuan Zhu ,&nbsp;Sheng-an Su ,&nbsp;Jixie Le ,&nbsp;Yutao Xi ,&nbsp;Meixiang Xiang","doi":"10.1016/j.abb.2025.110668","DOIUrl":"10.1016/j.abb.2025.110668","url":null,"abstract":"<div><h3>Background</h3><div>The excessive deposition of extracellular matrix (ECM) components in cardiac tissue increases myocardial stiffness, contributing to diastolic dysfunction and arrhythmia risk. While this clinical association is established, the underlying electromechanical mechanisms remain elusive.</div></div><div><h3>Methods</h3><div>Using human and neonatal rat cardiomyocytes cultured on tunable 3D PDMS substrates replicating infarcted rat heart decellularized ECM (dECM) stiffness, we systematically investigated how ECM-mediated mechanical changes alter action potentials and sodium current dynamics, as well as Nav1.5 expression. 3D PDMS substrates were fabricated with stiffness values spanning the mechanical range of infarcted rat heart dECM (Young's modulus: ∼20–400 kPa; elastic modulus: ∼5–30 pN/nm). Human induced pluripotent stem cell-derived cardiomyocytes (15-day culture), neonatal rat cardiomyocytes (3-day culture) and human embryonic kidney 293 (24-h culture) cells stably expressing human Nav1.5 were cultured on the these PDMS substrates. Stiffness-dependent cellular electrophysiological effects were assessed using patch-clamp recordings. The gene and protein level changes were assessed by real-time quantitative polymerase chain reaction and immune blot.</div></div><div><h3>Results</h3><div>We found that evaluated substrate stiffness levels progressively reduced the AP upstroke slope, resulted in proarrhythmic AP morphologies characterized by increased AP instability and triangulation. Electrophysiological analysis revealed this mechanical modulation occurred through distinct sodium channel kinetic alterations: (1) a significant rightward-shifted voltage-dependent activation curve, and (2) a faster transition from a closed state to inactivation occurred, while maintaining unchanged current density, steady-state inactivation properties, and recovery time across stiffness conditions. This effect may arise from a conformation change in Nav1.5, since the expression and distribution of Nav1.5 has not altered across three PDMS groups.</div></div><div><h3>Conclusions</h3><div>In summary, substrate stiffening impaired cardiomyocyte depolarization and promoted conduction abnormalities via Nav1.5 dysfunction, suggesting a mechanoelectrical mechanism in ECM deposition related arrhythmogenesis.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"775 ","pages":"Article 110668"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145430219","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":"CNP inhibits T3 - induced hypertrophic growth in H9c2 cells: Impact of HDAC inhibitor","authors":"Gopinath Nagaraj,&nbsp;Elangovan Vellaichamy","doi":"10.1016/j.abb.2025.110648","DOIUrl":"10.1016/j.abb.2025.110648","url":null,"abstract":"<div><div>C-type natriuretic peptide (CNP) is a multifaceted paracrine factor that regulates vital physiological functions of the cardiovascular system. The present study was designed to investigate the anti-hypertrophic activity of CNP in the presence and absence of HDAC inhibitor Suberoylanilide hydroxamic acid (SAHA) in T₃-induced H9c2 cells. The H9c2 cells were treated with T₃ (10 nM) for 48 hours to induce hypertrophic growth. T₃ alone-treated cells exhibited an increase in cell size (p &lt; 0.001) as compared with control H9c2 cells. CNP treatment effectively reverted the increased cell size by 61 %, and also altered the expression of hypertrophic marker genes. Interestingly, a significantly enhanced anti-hypertrophic activity was noticed in CNP co-treatment with SAHA, and also a more significant decrease in the expression of hypertrophic marker genes (α-sk, and α-MHC) was also observed. Moreover, CNP treatment with SAHA effectively reversed the T₃-induced changes in the expression of <em>Npr1</em> and <em>Npr2</em> genes in H9c2 cells. In addition, CNP co-treated with SAHA reversed the T₃-induced abnormal calcium influx by normalizing of CaMKII and SERCA2a. The findings of the present study clearly show that CNP co-treatment with SAHA significantly enhances the CNP-mediated anti-hypertrophic activity, probably by restoring <em>Npr1</em> and <em>Npr2</em> gene expression and calcium influx. Taken together, we conclude that CNP in combination with SAHA represents a novel therapeutic approach for the treatment and management of cardiac hypertrophy and heart failure.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"775 ","pages":"Article 110648"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145367456","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":"BACH1 drives ferroptosis in lung ischemia-reperfusion injury through epigenetic suppression of STAT3-Mediated antioxidant defense","authors":"Ying Gu ,&nbsp;Xiuli Liu ,&nbsp;Xiaojun Zhang ,&nbsp;Ning Zhang","doi":"10.1016/j.abb.2025.110669","DOIUrl":"10.1016/j.abb.2025.110669","url":null,"abstract":"<div><h3>Background</h3><div>Lung ischemia-reperfusion injury (LIRI) is a major complication in lung transplantation, with ferroptosis as a key mechanism. The role of BACH1, a regulator of oxidative stress and iron metabolism, in LIRI-associated ferroptosis is unclear. This study explores whether BACH1 promotes LIRI via ferroptosis-related pathways.</div></div><div><h3>Methods</h3><div>The GSE9634 dataset was analyzed to identify BACH1-regulated networks in LIRI. MLE-12 alveolar epithelial cells underwent hypoxia-reoxygenation with BACH1 overexpression or knockdown, with or without PU.1/SHP1 inhibitors. Protein expression was evaluated by Western blot and immunofluorescence, and oxidative stress markers (MDA, ROS) and antioxidant enzyme activity (SOD) by ELISA. A rat LIRI model with lentiviral BACH1 modulation was used for in vivo validation, assessed via histopathology, TUNEL staining, and immunohistochemistry.</div></div><div><h3>Results</h3><div>BACH1 positively correlated with KDM4C and PU.1 but negatively with STAT3. BACH1 overexpression upregulated KDM4C, reduced H3K9me3 methylation, and activated PU.1, promoting SHP1-mediated STAT3 dephosphorylation. This suppressed antioxidant proteins (GPX4, SLC7A11, FTH1), increasing ferroptosis. PU.1/SHP1 inhibition restored STAT3 phosphorylation and antioxidant expression, reducing oxidative damage. In vivo, BACH1 overexpression worsened lung injury and apoptosis, while knockdown was protective. Immunohistochemistry showed BACH1 upregulation reduced phospho-STAT3 and SLC7A11 in injured tissue.</div></div><div><h3>Conclusion</h3><div>BACH1 drives ferroptosis-mediated LIRI via a KDM4C/PU.1/SHP1 axis, suppressing the STAT3/GPX4/SLC7A11/FTH1 pathway. Targeting BACH1 or its effectors offers therapeutic potential for LIRI prevention.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"775 ","pages":"Article 110669"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145450684","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":"Decoding ROCK1 inhibition: A comprehensive computational analysis of key binding determinants for rational design of novel neurotherapeutics","authors":"Ashish Gupta ,&nbsp;Rituraj Purohit","doi":"10.1016/j.abb.2025.110643","DOIUrl":"10.1016/j.abb.2025.110643","url":null,"abstract":"<div><div>Rho-Associated coiled-coil kinase 1 (ROCK1) is a potential drug target against neurological disorders. In this work, we deployed molecular docking, free energy calculations, and steered molecular dynamics (SMD) to identify crucial amino acids that could act as anchor points for effective inhibitor binding at the ROCK1 active site. Molecular docking studies followed by detailed interaction analysis were conducted on previously reported ROCK1 inhibitors, including standard approved ROCK1 drugs, Netrasudil and Fasudil. The interacting amino acids were confirmed by quantifying their sole energetic contributions toward the total binding energy through free energy analysis. The stability of the protein-ligand complexes under simulation conditions was further evaluated by performing molecular dynamics simulations in triplicates. SMD simulations were used to understand the magnitude of interactions between the ROCK1. Detailed interaction analysis and free energy mapping highlighted the crucial role of G83, V90, A103, K105, M153, E154, M156, D202, L205, A215, and D216 in efficacious inhibitor binding. These amino acids significantly influenced the ROCK1-inhibitor complexes' overall binding free energy, indicating their importance in optimal inhibitor binding. The present work makes use of classical molecular mechanics-based and steered molecular dynamics simulations to provide a thorough understanding of the mechanisms underlying ROCK1 inhibition, which can be of significance in the discovery and design of potential drugs.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"775 ","pages":"Article 110643"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145370208","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":"Photorin controls the intracellular activation and bacteriotoxic effect of Photorhabdus laumondii protease S during its expression in Escherichia coli","authors":"Anastasia O. Svetlova ,&nbsp;Alexey A. Komissarov ,&nbsp;Maria A. Karaseva ,&nbsp;Ksenia N. Chukhontseva ,&nbsp;Olga V. Pobeguts ,&nbsp;Mariya A. Galyamina ,&nbsp;Igor P. Smirnov ,&nbsp;Polina D. Kuchur ,&nbsp;Anna O. Izotova ,&nbsp;Stepan V. Toshchakov ,&nbsp;Ilya V. Demidyuk","doi":"10.1016/j.abb.2025.110672","DOIUrl":"10.1016/j.abb.2025.110672","url":null,"abstract":"<div><div>An important role in the regulation of protease activity in living systems is played by their propeptides and endogenous protein inhibitors. Both are capable of repressing enzyme activity, ensuring it occurs only at the right time and/or in the right place. Therefore, propeptides and inhibitors may appear to perform the same function. However, many proteases have both, but the interplay between these two modes of regulation remains virtually unexplored. We investigated the role of the propeptide of <em>Photorhabdus laumondii</em> protealysin-like protease S (PrtS) and its emfourin-like inhibitor (ELI), photorin, in controlling intracellular enzyme activation in an <em>Escherichia coli</em> model. In the absence of the inhibitor, PrtS was found to be activated within cells due to autocatalytic cleavage of the propeptide, which led to the death of most bacteria. Along with this, a bacterial population emerges in which PrtS gene transcription is suppressed apparently due to the action of epigenetic mechanisms. Thus, the propeptide alone is unable to suppress aberrant intracellular activity of PrtS, whereas photorin protects cells from the toxic effect of PrtS and prevents inactivation of its gene. In summary, using PrtS as an example, we demonstrated for the first time that protealysin-like proteases (PLPs) which are ubiquitous in bacteria and are probably involved in pathogenesis, are toxic to bacteria. In this context, the function of ELIs, whose genes in bacterial genomes are co-localized with those of PLPs, is to protect bacteria from aberrant intracellular activity of PLPs.</div></div>","PeriodicalId":8174,"journal":{"name":"Archives of biochemistry and biophysics","volume":"775 ","pages":"Article 110672"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145526749","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}