Biophysical chemistry最新文献

{"title":"From Markovian to Non-Markovian: Advancing ion channel rate process theory","authors":"Yuval Ben-Abu","doi":"10.1016/j.bpc.2025.107484","DOIUrl":"10.1016/j.bpc.2025.107484","url":null,"abstract":"<div><div>Ion channels are essential membrane proteins that control ionic flow and cellular electrical activity. While traditional Markovian models have provided insights into channel gating, they fail to capture the memory-dependent dynamics of real ion channel behavior. This manuscript presents a novel semi non-Markovian framework for understanding ion channel gating processes. Using continuous time and discrete state space models for two and three-state systems, we derive Volterra convolution-type integral equations governing channel dynamics. Through Laplace transform analysis, we reveal asymptotic behaviors and previously hidden asymmetries between opening and closing rates. Our approach successfully predicts asymmetrical gating kinetics, characterizes infinite-state processes, and elucidates dynamic state creation—capabilities beyond conventional Markovian models. This breakthrough moves from phenomenological descriptions toward understanding the fundamental physics of ion channel gating, with significant implications for drug discovery and therapeutic development targeting ion channel dysfunction. This work establishes a new paradigm in ion channel research, providing the mathematical framework needed to unlock the full complexity of these critical cellular processes.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107484"},"PeriodicalIF":3.3,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144366883","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":"Next-generation antibacterial cryogels: Berberine-infused smart membranes with molecular docking-guided targeting of MRSA and MDR E. coli","authors":"Metin Yildirim ,&nbsp;Mehmet Cimentepe ,&nbsp;Kemal Dogan ,&nbsp;Adem Necip ,&nbsp;Madina Amangeldinova","doi":"10.1016/j.bpc.2025.107481","DOIUrl":"10.1016/j.bpc.2025.107481","url":null,"abstract":"<div><div>Multidrug-resistant (MDR) bacteria have become a significant global concern in recent years, necessitating the development of innovative strategies to combat these pathogens. Berberine, a bioactive alkaloid found in <em>Berberis vulgaris</em>, <em>Berberis aquifolium</em>, <em>Coptis chinensis</em>, <em>Coptis japonica</em>, and <em>Hydrastis canadensis</em>, exhibits a broad spectrum of biological activities, including antibacterial effects. However, its low aqueous solubility limits its bioavailability, restricting its therapeutic potential. Poly(2-hydroxyethyl methacrylate) (pHEMA)-based cryogel membranes, known for their biocompatibility and ease of synthesis, have been widely utilized in biomedical applications, particularly in wound healing. In this study, berberine was successfully incorporated into pHEMA cryogel membranes and characterized using FT-IR spectroscopy. Biocompatibility assessments were conducted using L929 fibroblast cells, and MTT assay results confirmed that cell viability remained above 88 %, indicating good biocompatibility. The antibacterial properties of the prepared membranes against MDR <em>E. coli</em> and MRSA were evaluated using the disk diffusion and time-kill methods. According to the time-kill assay, high-dose berberine-loaded cryogel membranes (BM2) exhibited inhibition rates of 87.2 % against MRSA and 96.8 % against MDR <em>E. coli</em>. The antibacterial and antibiofilm effects of the membranes were further validated by SEM imaging, which revealed that berberine effectively disrupted bacterial biofilms. To gain insight into the molecular mechanisms underlying antibacterial activity, molecular docking studies were performed on key bacterial proteins involved in essential physiological processes, including the OmpA transmembrane domain (PDB ID: <span><span>1BXW</span><svg><path></path></svg></span>), <em>E. coli</em> DNA gyrase B (PDB IDs: <span><span>4WUB</span><svg><path></path></svg></span>, <span><span>6KZX</span><svg><path></path></svg></span>, <span><span>6KZV</span><svg><path></path></svg></span>), <em>E. coli</em> hydrogenase (PDB ID: <span><span>5LMM</span><svg><path></path></svg></span>), penicillin-binding protein 3 (PBP3; PDB ID: <span><span>3VSL</span><svg><path></path></svg></span>), and PBP2a from MRSA (PDB IDs: <span><span>1MWT</span><svg><path></path></svg></span>, <span><span>4CJN</span><svg><path></path></svg></span>, <span><span>5M18</span><svg><path></path></svg></span>, <span><span>6Q9N</span><svg><path></path></svg></span>). The strongest interaction was observed between berberine and 6KZX, with a docking score of −7.898 kcal/mol, whereas the weakest interaction was noted with 4CJN, with a docking score of −3.743 kcal/mol. These findings highlight the potential of berberine-loaded pHEMA cryogel membranes as a promising antibacterial platform for combating MDR bacterial infections, particularly for wound healing applications.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107481"},"PeriodicalIF":3.3,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144306232","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":"Raman spectroscopic signatures of amyloid fibrils: Insights into structural and biochemical changes in human tissues","authors":"N.S. Mohd Nor Ihsan ,&nbsp;S.F. Abdul Sani ,&nbsp;L.M. Looi ,&nbsp;Dharini Pathmanathan ,&nbsp;P.L. Cheah ,&nbsp;S.F. Chiew ,&nbsp;D.A. Bradley","doi":"10.1016/j.bpc.2025.107480","DOIUrl":"10.1016/j.bpc.2025.107480","url":null,"abstract":"<div><div>Amyloid fibrils, characterized by β-sheet-rich protein aggregates, are closely associated with various diseases. Understanding the structural and biochemical changes in amyloid formation requires detailed characterization of their Raman spectroscopic signatures. This study evaluated the application of Raman spectroscopy, utilizing a 532-nm laser excitation source, for differentiating amyloid from normal tissues. Raman spectroscopy effectively identifies protein secondary structures and distinguishes normal tissues from amyloid-containing tissues, offering potential for real-time diagnosis. A total of 13 amyloid tissue samples (heart, kidney, and thyroid) and 9 normal controls were analyzed. Key spectral differences were observed in the amide I (∼1660 cm⁻¹) and amide III (∼1300 cm⁻¹) regions, characteristic of β-sheet structures in amyloid fibrils. Spatially resolved Raman spectra revealed molecular heterogeneity between amide and lipid components in amyloid deposits. Ratiometric analysis further supported this, demonstrating significant differences in the amide-to-lipid ratio (with attributed significant peak intensities at 1660 cm⁻¹ for amide I and 1440 cm⁻¹ for lipids) between amyloid and control tissues. Statistical analysis (Mann-Whitney <em>U</em> test, <em>p</em> = 0.006) confirmed significant differences in amide group intensities between amyloid and control tissues. These findings highlight Raman spectroscopy as a promising tool for real-time identification and characterization of amyloid deposits, with potential clinical applications in diagnosing amyloid-related diseases.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107480"},"PeriodicalIF":3.3,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144254174","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":"Concentration-dependent structural transition of huntingtin protein in Huntington's disease","authors":"Ji-Na Yoo ,&nbsp;Ha-Neul Kim ,&nbsp;Su-Yeon Choi ,&nbsp;Yuxi Lin ,&nbsp;Young-Ho Lee ,&nbsp;Min-Duk Seo","doi":"10.1016/j.bpc.2025.107473","DOIUrl":"10.1016/j.bpc.2025.107473","url":null,"abstract":"<div><div>Huntington's disease (HD) is a genetic neurodegenerative disorder caused by the abnormal expansion of the polyglutamine (polyQ) tract (&gt; 35Q) in the first exon of the huntingtin (Htt), HttEx1. This N-terminal fragment tends to form fibrillar inclusions, which constitute a key pathological hallmark of HD. Although polyQ expansion is commonly understood to be a primary cause of HttEx1 pathology, the molecular mechanism of aggregations of non-pathogenic polyQ tract with the N-terminally flanking region of N17 in HttEx1 (HttEx1-17Q) remains largely unknown. In this study, we exclusively investigated the effect of the protein concentration on the structural transition of HttEx1-17Q and its relation to the amyloid fibril formation by employing biophysical techniques including nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM), atomic force microscopy (AFM), and thioflavin T (ThT) fluorescence. Complementary analyses showed that monomeric HttEx1-17Q undergoes a multiple structural transition from largely unfolded structures to β structures <em>via</em> helical structures in a concentration-dependent manner in the early stages of aggregation. This structural rearrangement accelerates kinetically the formation of short amyloid fibrils of HttEx1-17Q by facilitating nucleation. Our findings provide new insights into the amyloid formation of HttEx1 by highlighting the critical role of a structural conversion into an amyloidogenic structure, of which mechanism is helpful to understand amyloidogenesis of other amyloid-forming molecules.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107473"},"PeriodicalIF":3.3,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144230942","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":"Redox-dependent structural and thermal stability of HMGB1: A thermodynamic analysis","authors":"Weronika Malicka ,&nbsp;Marten Kagelmacher ,&nbsp;Michel W. Jaworek ,&nbsp;Roland Winter ,&nbsp;Leïla Bechtella ,&nbsp;Kevin Pagel ,&nbsp;Beate Koksch ,&nbsp;Andreas Herrmann ,&nbsp;Jens Dernedde ,&nbsp;Thomas Risse ,&nbsp;Matthias Ballauff ,&nbsp;Marina Pigaleva","doi":"10.1016/j.bpc.2025.107472","DOIUrl":"10.1016/j.bpc.2025.107472","url":null,"abstract":"<div><div>HMGB1 is a highly conserved nuclear protein with functions that depend on its biological environment, which are linked to structural differences in the protein. Inside the cell, HMGB1 adopts a reduced form, regulating DNA transcription. In contrast, in the extracellular environment, it exists in a form with a closed disulfide bridge within the A-box motif playing a role in inflammation. We analyzed the stability of HMGB1 in these two redox states using differential scanning fluorimetry (nanoDSF), which enables high-precision thermal unfolding measurements with minimal protein quantities — something not previously feasible for HMGB1. The A-box domain was found to unfold reversibly in both redox forms, unlike the B-box. Surprisingly, the reduced form showed lower thermal stability but higher enthalpy of unfolding, indicating that it is enthalpically favorable and suggesting a significant difference in entropy contributions. For full-length HMGB1, both redox variants displayed similar thermal stability. However, only the reduced form was able to refold after unfolding; the disulfide form could not return to its native structure. Additionally, the reduced full-length variant exhibited a decrease in unfolding enthalpy, likely due to the destabilizing effect of its negatively charged C-terminal tail. Overall, the redox state has a strong influence on HMGB1's thermodynamic behavior. These thermodynamic differences can be linked to the protein's dual functionality: enhanced flexibility is beneficial for DNA transcription inside the nucleus. At the same time, increased conformational stability is advantageous for extracellular protein-protein recognition pathways.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107472"},"PeriodicalIF":3.3,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144312702","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":"Effect of pyrimethanil on aβ42 aggregation mechanisms revealed at single entity level and molecular dynamic simulations","authors":"Nathan Meyer ,&nbsp;Nicolas Arroyo ,&nbsp;Lois Roustan ,&nbsp;Jean-Marc Janot ,&nbsp;Véronique Perrier ,&nbsp;Joan Torrent ,&nbsp;Fabien Picaud ,&nbsp;Sebastien Balme","doi":"10.1016/j.bpc.2025.107471","DOIUrl":"10.1016/j.bpc.2025.107471","url":null,"abstract":"<div><div>This study investigated the impact of pyrimethanil, a fungicide, on the aggregation of amyloid-β 42 (aβ42) peptides in vitro. The findings demonstrated that pyrimethanil accelerated aβ42 aggregation kinetics, as evidenced by thioflavin T (ThT) fluorescence assays in both tube and microplate experiments. A combination of single molecule techniques and molecular dynamics simulations is used to elucidate the complex effects of pyrimethanil on aβ42 aggregation mechanism. Nanopore experiments indicated that pyrimethanil promoted the formation of small oligomers (6-13.5 nm) during the lag phase, which were not detected under control conditions. Confocal fluorescence spectroscopy revealed that pyrimethanil induced the formation of larger β-sheet structured aggregates. In the presence of preformed seeds, pyrimethanil exhibited a dual role by fragmenting existing fibrils into smaller species and enhancing aggregation, likely through combined effects with the newly formed smaller seeds. Molecular dynamics simulations confirmed that pyrimethanil has a higher affinity for fibrils than monomers and weakens monomer-fibril interactions. Overall, this study elucidates the complex effects of pyrimethanil on aβ42 aggregation, involving promotion of primary nucleation, fibril fragmentation, and modulation of monomer-fibril interactions. These findings provide important mechanistic insights into how environmental factors like pesticides may influence amyloid aggregation processes relevant to Alzheimer's disease.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107471"},"PeriodicalIF":3.3,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144212245","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":"Influence of local ordering in the permeation of Temozolomide through the brain plasmatic membrane","authors":"Yanhong Ge ,&nbsp;Huixia Lu ,&nbsp;Jordi Martí","doi":"10.1016/j.bpc.2025.107457","DOIUrl":"10.1016/j.bpc.2025.107457","url":null,"abstract":"<div><div>Temozolomide, a small-molecule drug, is primarily used to treat glioblastoma, a tumor that attacks both the spinal cord and brain. Understanding how Temozolomide interacts with different lipids within the brain cell membrane at the atomic level can help elucidate its ability to permeate through cell membranes. In this study, we constructed a simplified brain plasma membrane model to explore the microscopic structure and dynamics of Temozolomide using all-atom microsecond-scale molecular dynamics simulations. Temozolomide is typically found in the solvent-aqueous fluid surrounding the brain membrane, but it can access the membrane interface regularly and eventually bind to lipids of the choline and cerebroside classes. To investigate the free energy barriers of Temozolomide related to its crossing of brain-like plasma membranes, we employed adaptive biasing force methods. These simulations revealed that the free energy barriers ranged between 28 and 50 kcal/mol at temperatures between 310 K and 323 K. Our findings suggest that Temozolomide cannot cross the membrane by pure diffusion at normal human body temperature, but that rising the temperature significantly increases the probability of barrier crossing. This is primarily due to the crucial role played by cholesterol and lipids of the cerebroside class. These results can be used to optimise the molecular design of Temozolomide and develop new analogs with improved pharmacokinetic properties.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"324 ","pages":"Article 107457"},"PeriodicalIF":3.3,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144169142","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":"Lysozyme thermal stability in the presence of cyclodextrins at different pH values","authors":"A. Jessica Díaz-Salazar ,&nbsp;Daniel Ondo","doi":"10.1016/j.bpc.2025.107469","DOIUrl":"10.1016/j.bpc.2025.107469","url":null,"abstract":"<div><div>In the present study, the primary action of native cyclodextrins (CDs) on lysozyme protein as binding ligand and secondary as aggregation inhibitor were probed. Thermally induced denaturation using differential scanning calorimetry (DSC) was measured in the presence of native <span><math><mi>α</mi></math></span>-, <span><math><mi>β</mi></math></span>- and <span><math><mi>γ</mi></math></span>-CDs. The denaturation process in CD absence was reversible to 60–80 % at pH<span><math><mo>≤</mo></math></span>6 with maximum <span><math><msub><mi>T</mi><mi>m</mi></msub></math></span> at pH<span><math><mo>=</mo></math></span>4. Denaturation in the presence of native <span><math><mi>α</mi></math></span>-CD at pH from 2 to 10, at the least stable and partially reversible conditions in presence of <span><math><mi>β</mi></math></span>-CD and <span><math><mi>γ</mi></math></span>-CDs at single pH 2 only, was measured. The protein thermal stability decreases in the presence of CDs, with the most evident for <span><math><mi>β</mi></math></span>-CD, followed by <span><math><mi>α</mi></math></span>-CD and almost no effect for <span><math><mi>γ</mi></math></span>-CD. The reversibility in the presence of <span><math><mi>α</mi></math></span>-CD was similar to that in its absence. The best protection performance against heat-induced denaturation was found at pH 2 for <span><math><mi>β</mi></math></span>-CD. The heat capacity data for <span><math><mi>α</mi></math></span>-CD at acidic pH were fitted by the protein-ligand binding model in the whole temperature and ligand concentration ranges studied. The decrease in thermal stability for <span><math><mi>α</mi></math></span>-CD at all pH, <span><math><mi>β</mi></math></span>- and <span><math><mi>γ</mi></math></span>-CD at pH 2 were fitted linearly as a function of ligand concentration. The CD-to-lysozyme binding parameters obtained in this work and from the literature for other CDs are briefly discussed using the concept of cyclodextrin cavity size, charge distribution, solvent accessible surface area and amino acid hydrophobicity.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"324 ","pages":"Article 107469"},"PeriodicalIF":3.3,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144169143","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":"Identification of potential Abl kinase inhibitors using virtual screening and free energy calculations for the treatment of chronic myeloid leukemia","authors":"Beom Soo Kim ,&nbsp;Wookyung Yu","doi":"10.1016/j.bpc.2025.107470","DOIUrl":"10.1016/j.bpc.2025.107470","url":null,"abstract":"<div><div>Abl kinase, particularly the Bcr-Abl fusion protein, is a critical driver of chronic myeloid leukemia (CML) and remain significant therapeutic target in hematologic malignancies. Although first-generation tyrosine kinase inhibitors (TKIs) such as Imatinib have revolutionized CML treatment, resistance due to kinase domain mutations (<em>e.g.</em>, T315I gatekeeper mutation) and side effects highlight needs for another candidate inhibitors. In this study, we employed a combined virtual screening strategy to discover novel Abl kinase inhibitors from an extensive chemical database (∼670 million compounds). Initially, shape-based similarity (USR/USRCAT) and electrostatic potential filters were used to refine the candidate compounds, followed by structure-based molecular docking against the Abl kinase domain. Top-ranked candidates were evaluated using molecular dynamics (MD) simulations and binding free energy calculations, such as MM/GBSA and free energy perturbation (FEP), to confirm stability and binding affinity. Five candidate compounds emerged with binding energies comparable to or higher than known Abl kinase inhibitors, including Imatinib and Bafetinib. Finally, based on these calculations, we selected two compounds as candidates as Abl tyrosine kinase inhibitors. Overall, the results showed the effectiveness of combining ligand-based and structure-based drug design strategies to identify new Abl kinase inhibitor leads for improved the CML therapy.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"324 ","pages":"Article 107470"},"PeriodicalIF":3.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144116176","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":"Integrative approaches to network pharmacology studies in wound healing and bone fracture recovery: A comprehensive review","authors":"Rizwan Ahamed Najimudeen ,&nbsp;Catherin Amaldoss ,&nbsp;Aarthi Raghu ,&nbsp;Alex Anand Daniel ,&nbsp;Dilip Kumar Shanmugam ,&nbsp;Prakash Pandurangan ,&nbsp;Subbaiya Ramasamy","doi":"10.1016/j.bpc.2025.107458","DOIUrl":"10.1016/j.bpc.2025.107458","url":null,"abstract":"<div><div>This review provides a comprehensive exploration of the intricate processes involved in wound healing and bone fracture recovery, delving into the phases and cellular activities that underlie these critical physiological events. The integration of network pharmacology and traditional medicine approaches in the context of wound healing and bone fracture is thoroughly examined, highlighting the potential synergies between modern scientific methodologies and age-old remedies. The Research methodology for network pharmacology studies is meticulously outlined, encompassing data mining, target identification, network construction and analysis, and validation techniques. Various Bioinformatics Databases and tools implied in the network pharmacology are tabulated. The genes responsible for wound healing and bone fracture are also tabulated. By synthesizing knowledge from diverse fields, this review offers valuable insights for advancing therapeutic interventions in wound healing and bone fracture management through network pharmacology study.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"324 ","pages":"Article 107458"},"PeriodicalIF":3.3,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144185671","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}