Pub Date : 2025-10-11DOI: 10.1016/j.bpc.2025.107535
Katrina Brandmier, Kerney Jebrell Glover
Caveolin-1 (Cav1) is an integral membrane protein essential for the formation of caveolae, plasma microdomains implicated in signal transduction and mechanoprotection. Cav1 is comprised of three major alpha helices, but the topology these helices adopt remains unclear. Proline 110 is located between helix 1 and helix 2, and is hypothesized to enable Cav1 to adopt an intramembrane turn crucial for the cytosolic topology of Cav1. To assess the structural role of Proline 110, we utilized Förster resonance energy transfer (FRET) between native tryptophan (W128) and site-specifically labeled dansyl fluorophores to monitor conformational changes induced by the mutation of Proline 110 to Alanine (P110A). Static light scattering confirmed that all FRET constructs behaved monomerically, ensuring intramolecular energy transfer measurements. Our results show a significant decrease in FRET efficiency upon the P110A mutation consistent with a large conformational change. These findings support the critical role of P110 in maintaining the native topology of Cav1 and highlights the structural sensitivity of the intramembrane turn.
{"title":"Proline 110 is necessary for maintaining a compact helical arrangement in caveolin-1","authors":"Katrina Brandmier, Kerney Jebrell Glover","doi":"10.1016/j.bpc.2025.107535","DOIUrl":"10.1016/j.bpc.2025.107535","url":null,"abstract":"<div><div>Caveolin-1 (Cav1) is an integral membrane protein essential for the formation of caveolae, plasma microdomains implicated in signal transduction and mechanoprotection. Cav1 is comprised of three major alpha helices, but the topology these helices adopt remains unclear. Proline 110 is located between helix 1 and helix 2, and is hypothesized to enable Cav1 to adopt an intramembrane turn crucial for the cytosolic topology of Cav1. To assess the structural role of Proline 110, we utilized Förster resonance energy transfer (FRET) between native tryptophan (W128) and site-specifically labeled dansyl fluorophores to monitor conformational changes induced by the mutation of Proline 110 to Alanine (P110A). Static light scattering confirmed that all FRET constructs behaved monomerically, ensuring intramolecular energy transfer measurements. Our results show a significant decrease in FRET efficiency upon the P110A mutation consistent with a large conformational change. These findings support the critical role of P110 in maintaining the native topology of Cav1 and highlights the structural sensitivity of the intramembrane turn.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107535"},"PeriodicalIF":2.2,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145312022","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}
Sodium dodecyl sulfate (SDS) is one of the most widely used detergents. Here, we discuss current knowledge regarding applications of SDS and its modes of interaction with proteins, particularly at low concentrations. SDS at 1–2 %, which is well above the critical micelle concentration, is commonly used to extract fully denatured and dissociated proteins and SDS polyacrylamide gel electrophoresis (SDS-PAGE) in various applications, especially proteomics. In contrast, low concentration SDS may have been relatively underutilized. Here, we demonstrate the use of 0.1 % SDS for decellularization and protein fractionation. Why is 0.1 % SDS unique? The interaction between SDS and proteins is complex and depends on both the conditions and the proteins involved. At 0.1 %, the effects of SDS appear to be intermediate between negligible and extensive binding, highlighting its potential for novel applications. Two milder anionic detergents, Sarkosyl and sodium N-lauroyglutamate, whose effects are similar in certain applications to those of low concentration SDS, were briefly discussed.
{"title":"SDS protein interactions","authors":"Tsutomu Arakawa , Daisuke Ejima , Tomoto Ura , Teruo Akuta , Masamichi Oh-Ishi","doi":"10.1016/j.bpc.2025.107534","DOIUrl":"10.1016/j.bpc.2025.107534","url":null,"abstract":"<div><div>Sodium dodecyl sulfate (SDS) is one of the most widely used detergents. Here, we discuss current knowledge regarding applications of SDS and its modes of interaction with proteins, particularly at low concentrations. SDS at 1–2 %, which is well above the critical micelle concentration, is commonly used to extract fully denatured and dissociated proteins and SDS polyacrylamide gel electrophoresis (SDS-PAGE) in various applications, especially proteomics. In contrast, low concentration SDS may have been relatively underutilized. Here, we demonstrate the use of 0.1 % SDS for decellularization and protein fractionation. Why is 0.1 % SDS unique? The interaction between SDS and proteins is complex and depends on both the conditions and the proteins involved. At 0.1 %, the effects of SDS appear to be intermediate between negligible and extensive binding, highlighting its potential for novel applications. Two milder anionic detergents, Sarkosyl and sodium N-lauroyglutamate, whose effects are similar in certain applications to those of low concentration SDS, were briefly discussed.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107534"},"PeriodicalIF":2.2,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145290894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-06DOI: 10.1016/j.bpc.2025.107533
Hari K.C. , Kumar Neupane , Khadka B. Chhetri , Rojina Ojha , Raj K. Acharya
Holy basil (Ocimum tenuiflorum) is primarily found in Nepal and India. In Ayurveda, it is commonly used as a traditional medicine to reduce pain, swelling, and various diseases. It has gained significant attention for its potential anti-inflammatory properties. One of the key targets associated with inflammation is Cyclooxygenase-2 (COX-2), an enzyme responsible for prostaglandin synthesis during the inflammatory response. In this study, we selected twenty flavonoids in the Holy Basil plant. These compounds were screened through Lipinski’s Rule of Five, followed by ADMET prediction. Virtual screening was conducted on the selected compounds against the COX-2 enzyme as a receptor using molecular docking techniques. Molecular docking study provides valuable insights at the molecular level into the interactions between Holy Basil compounds and COX-2. Furthermore, density functional computations were carried out utilizing the B3LYP method with the 6-311G basis, which is set to gain insight into the structural and electronic properties of the compounds. This study showcases the potential of flavonoids such as rhamnetin, Luteolin and kaempferol to act as anti-inflammatory agents, sparking further interest and research in this area.
圣罗勒（Ocimum tenuflorum）主要产于尼泊尔和印度。在阿育吠陀，它通常被用作一种传统药物来减轻疼痛、肿胀和各种疾病。它因其潜在的抗炎特性而受到广泛关注。与炎症相关的关键靶点之一是环氧化酶-2 (COX-2)，一种在炎症反应中负责前列腺素合成的酶。本研究从罗勒植物中提取了20种黄酮类化合物。这些化合物通过Lipinski 's Rule of Five进行筛选，然后进行ADMET预测。利用分子对接技术对选定的COX-2酶受体进行虚拟筛选。分子对接研究在分子水平上对罗勒化合物与COX-2的相互作用提供了有价值的见解。此外，利用6-311G基的B3LYP方法进行密度泛函计算，以深入了解化合物的结构和电子性质。这项研究展示了鼠李素、木犀草素和山奈酚等类黄酮作为抗炎剂的潜力，激发了这一领域的进一步兴趣和研究。
{"title":"Molecular docking and density functional theory studies of flavonoids of Holy basil plant against COX-2 enzyme","authors":"Hari K.C. , Kumar Neupane , Khadka B. Chhetri , Rojina Ojha , Raj K. Acharya","doi":"10.1016/j.bpc.2025.107533","DOIUrl":"10.1016/j.bpc.2025.107533","url":null,"abstract":"<div><div>Holy basil (Ocimum tenuiflorum) is primarily found in Nepal and India. In Ayurveda, it is commonly used as a traditional medicine to reduce pain, swelling, and various diseases. It has gained significant attention for its potential anti-inflammatory properties. One of the key targets associated with inflammation is Cyclooxygenase-2 (COX-2), an enzyme responsible for prostaglandin synthesis during the inflammatory response. In this study, we selected twenty flavonoids in the Holy Basil plant. These compounds were screened through Lipinski’s Rule of Five, followed by ADMET prediction. Virtual screening was conducted on the selected compounds against the COX-2 enzyme as a receptor using molecular docking techniques. Molecular docking study provides valuable insights at the molecular level into the interactions between Holy Basil compounds and COX-2. Furthermore, density functional computations were carried out utilizing the B3LYP method with the 6-311G basis, which is set to gain insight into the structural and electronic properties of the compounds. This study showcases the potential of flavonoids such as rhamnetin, Luteolin and kaempferol to act as anti-inflammatory agents, sparking further interest and research in this area.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107533"},"PeriodicalIF":2.2,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145263230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-26DOI: 10.1016/j.bpc.2025.107531
Michael T. Harnish, Bill Pham, Avery B. Arons, Yingjie Xu, Elias J. Fernandez, Tongye Shen
Nuclear receptors (NRs) are multidomain, ligand-activated transcription factors that play critical physiological roles. While the structured DNA-binding domain (DBD) and ligand-binding domain (LBD) have been well characterized, the function of intrinsically disordered regions—such as the hinge between the LBD and DBD—remains unclear. To illuminate the role of the hinge, we conducted five-microsecond molecular dynamics simulations of thyroid hormone receptor (TRα) alone versus bound to DNA. We reveal that DNA binding induces a significant structural change in the hinge region (helical to unwound coil), with a potentially important role in the regulation of TRα activity. Previously, hinge helicity has been reported to drive oligomerization and the consequent inhibition of coactivator binding, and such DNA-induced transition may promote TR activation. Protein-DNA binding is found to be multivalent and contains the direct interaction of the hinge with the DNA minor groove in addition to the canonical recognition helix of the DBD with the major groove. Furthermore, the poly-Arg segment of the hinge has a direct and significant influence on DNA conformation. This interaction promotes a bent DNA phosphate backbone, which might further contribute to the protein-DNA recognition. On a global scale, DNA binding induces a “closed-to-open” conformational change thus reducing direct DBD-LBD interactions, which corroborates previous calorimetric binding studies. Overall, our results provide insight into the mechanism of DNA recognition and the resulting conformational dynamics of the TRα-DNA complex.
{"title":"Conformational transition of a polycationic hinge domain contributes to DNA binding","authors":"Michael T. Harnish, Bill Pham, Avery B. Arons, Yingjie Xu, Elias J. Fernandez, Tongye Shen","doi":"10.1016/j.bpc.2025.107531","DOIUrl":"10.1016/j.bpc.2025.107531","url":null,"abstract":"<div><div>Nuclear receptors (NRs) are multidomain, ligand-activated transcription factors that play critical physiological roles. While the structured DNA-binding domain (DBD) and ligand-binding domain (LBD) have been well characterized, the function of intrinsically disordered regions—such as the hinge between the LBD and DBD—remains unclear. To illuminate the role of the hinge, we conducted five-microsecond molecular dynamics simulations of thyroid hormone receptor (TRα) alone versus bound to DNA. We reveal that DNA binding induces a significant structural change in the hinge region (helical to unwound coil), with a potentially important role in the regulation of TRα activity. Previously, hinge helicity has been reported to drive oligomerization and the consequent inhibition of coactivator binding, and such DNA-induced transition may promote TR activation. Protein-DNA binding is found to be multivalent and contains the direct interaction of the hinge with the DNA minor groove in addition to the canonical recognition helix of the DBD with the major groove. Furthermore, the poly-Arg segment of the hinge has a direct and significant influence on DNA conformation. This interaction promotes a bent DNA phosphate backbone, which might further contribute to the protein-DNA recognition. On a global scale, DNA binding induces a “closed-to-open” conformational change thus reducing direct DBD-LBD interactions, which corroborates previous calorimetric binding studies. Overall, our results provide insight into the mechanism of DNA recognition and the resulting conformational dynamics of the TRα-DNA complex.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107531"},"PeriodicalIF":2.2,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145263229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-24DOI: 10.1016/j.bpc.2025.107532
Laila Zaatouf, Thierry Drujon, Astrid Walrant, Emmanuelle Sachon, Dror E. Warschawski
Staphylococcus aureus (S. aureus) is a Gram-positive pathogenic bacterium and a major cause of nosocomial infections. Between 20 % and 50 % of S. aureus strains are resistant to a wide range of antibiotics. DMS-DA6-NH2 (DA6) is a novel antimicrobial peptide (AMP) that exhibits high efficacy against various bacterial strains, particularly S. aureus, by disrupting its membrane through an as-yet-unknown mechanism. We employed in vivo2H solid state Nuclear Magnetic Resonance (NMR) to investigate the mode of action of AMPs on deuterated bacteria. This technique provides insights into membrane order and its changes with increasing AMP concentration. Our results enabled us to compare the mechanism of DA6 with those of AMPs with established modes of action. We found that DA6 induces pore formation in the membrane of S. aureus. This protocol serves as a template for determining the mechanisms of action of other peptides, an essential step for developing and patenting such drugs for the treatment of human diseases.
{"title":"Antimicrobial peptide mechanism of action on S. aureus membranes determined by in vivo solid-state NMR","authors":"Laila Zaatouf, Thierry Drujon, Astrid Walrant, Emmanuelle Sachon, Dror E. Warschawski","doi":"10.1016/j.bpc.2025.107532","DOIUrl":"10.1016/j.bpc.2025.107532","url":null,"abstract":"<div><div><em>Staphylococcus aureus (S. aureus)</em> is a Gram-positive pathogenic bacterium and a major cause of nosocomial infections. Between 20 % and 50 % of <em>S. aureus</em> strains are resistant to a wide range of antibiotics. DMS-DA6-NH<sub>2</sub> (DA6) is a novel antimicrobial peptide (AMP) that exhibits high efficacy against various bacterial strains, particularly <em>S. aureus</em>, by disrupting its membrane through an as-yet-unknown mechanism. We employed <em>in vivo</em> <sup>2</sup>H solid state Nuclear Magnetic Resonance (NMR) to investigate the mode of action of AMPs on deuterated bacteria. This technique provides insights into membrane order and its changes with increasing AMP concentration. Our results enabled us to compare the mechanism of DA6 with those of AMPs with established modes of action. We found that DA6 induces pore formation in the membrane of <em>S. aureus.</em> This protocol serves as a template for determining the mechanisms of action of other peptides, an essential step for developing and patenting such drugs for the treatment of human diseases.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107532"},"PeriodicalIF":2.2,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145155943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-22DOI: 10.1016/j.bpc.2025.107530
Yuval Ben-Abu
Recent work by Ben Abu and Wolfson introduces the concept of ‘energetic memory’ in ion channels, providing a mechanistic framework for ultrasound neuromodulation. This discussion examines how K2P (two-pore domain potassium) channels serve as primary mediators of mechanosensitive memory due to their small size (0.5 μm radius), constitutive activity, and critical physiological roles. In contrast, larger Kv channels (5 μm) show intermediate sensitivity while Na+ channels (50 μm) remain largely unaffected, creating size-dependent responses. Nanoindentor experiments demonstrate sustained membrane hyperpolarization following mechanical compression, validating the theoretical predictions. The energetic memory model explains ultrasound therapy's clinical efficacy through preferential K2P channel compression, energy system adaptation, and prolonged recovery phases. This framework enables rational optimization of therapeutic protocols and extends to other mechanically-based interventions, fundamentally expanding our understanding of neural plasticity beyond traditional electrical mechanisms.
Ben Abu和Wolfson最近的工作介绍了离子通道中“能量记忆”的概念，为超声神经调节提供了一个机制框架。本文探讨了K2P（双孔结构域钾）通道如何由于其小尺寸（0.5 μm半径）、本构活性和关键的生理作用而成为机械敏感记忆的主要介质。相比之下，较大的Kv通道（5 μm）表现出中等灵敏度，而Na+通道（50 μm）基本不受影响，产生尺寸相关的响应。纳米压痕实验证明了机械压缩后膜的持续超极化，验证了理论预测。能量记忆模型通过优先压缩K2P通道、能量系统适应和延长恢复期来解释超声治疗的临床疗效。该框架能够合理优化治疗方案，并扩展到其他基于机械的干预措施，从根本上扩展了我们对传统电机制之外的神经可塑性的理解。
{"title":"K2P channels and ultrasound neuromodulation: A mechanosensitive memory perspective","authors":"Yuval Ben-Abu","doi":"10.1016/j.bpc.2025.107530","DOIUrl":"10.1016/j.bpc.2025.107530","url":null,"abstract":"<div><div>Recent work by Ben Abu and Wolfson introduces the concept of ‘energetic memory’ in ion channels, providing a mechanistic framework for ultrasound neuromodulation. This discussion examines how K2P (two-pore domain potassium) channels serve as primary mediators of mechanosensitive memory due to their small size (0.5 μm radius), constitutive activity, and critical physiological roles. In contrast, larger Kv channels (5 μm) show intermediate sensitivity while Na<sup>+</sup> channels (50 μm) remain largely unaffected, creating size-dependent responses. Nanoindentor experiments demonstrate sustained membrane hyperpolarization following mechanical compression, validating the theoretical predictions. The energetic memory model explains ultrasound therapy's clinical efficacy through preferential K2P channel compression, energy system adaptation, and prolonged recovery phases. This framework enables rational optimization of therapeutic protocols and extends to other mechanically-based interventions, fundamentally expanding our understanding of neural plasticity beyond traditional electrical mechanisms.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107530"},"PeriodicalIF":2.2,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145155941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-22DOI: 10.1016/j.bpc.2025.107529
Jing Zhang, Qiang Ma, Honghui Wang, Bin Chen, Yan Li, Yingmin Liao
The rubber antioxidant, N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine (6-PPD), as an emerging pollutant, is receiving more and more attention recently. This study investigated the intermolecular interactions of 6-PPD with two key biological macromolecules, human serum albumin (HSA) and alpha-glucosidase (AG), to understand the transport and toxic effects of 6-PPD. Using multiple spectroscopic methods and molecular docking technology, the results demonstrated that 6-PPD could bind to both HSA and AG, thereby inducing fluorescence quenching and conformational changes in both proteins. The binding constants were determined to be (5.93 ± 0.20) × 105 and (3.17 ± 0.15) × 104 L mol−1 respectively for HSA-6-PPD and AG-6-PPD systems at 298 K, revealing strong binding affinities. Molecular docking identified specific binding sites and non-covalent interactions of the two systems. MD and Energy decomposition analysis revealed the dynamics conformational changes of the complexes and identified van der Waals and electrostatic interactions as primary binding drivers for both systems, while polar solvation energy impeded complex formation. TYR161, ILE142, and TYR138 dominated HSA-6-PPD stabilization, whereas AG-6-PPD was driven by hydrophobic interactions with TRP1369 and VAL1373, with ARG1377 incurring substantial desolvation penalties. Synchronous fluorescence and circular dichroism spectroscopy indicated that 6-PPD binding did not disrupt the microenvironment of Tyr and Trp residues in HSA and AG, while induced structural alterations in HSA and AG that could affect their physiological function. In-vitro tests showed that 6-PPD inhibited AG activity in a dose-dependent manner, with an IC50 of 8.22 ± 0.44 μmol L−1. ADMET and PASS online tools was used to predict physicochemical properties and multiorgan toxicity. This work provided insights into the transport and molecular toxicity of 6-PPD, highlighting the adverse biological effects associated with this common rubber additive.
{"title":"Molecular insights into the transport and toxicity of 6-PPD: Interactions with human serum albumin and alpha-glucosidase","authors":"Jing Zhang, Qiang Ma, Honghui Wang, Bin Chen, Yan Li, Yingmin Liao","doi":"10.1016/j.bpc.2025.107529","DOIUrl":"10.1016/j.bpc.2025.107529","url":null,"abstract":"<div><div>The rubber antioxidant, <em>N</em>-(1,3-dimethylbutyl)-<em>N</em>′-phenyl-<em>p</em>-phenylenediamine (6-PPD), as an emerging pollutant, is receiving more and more attention recently. This study investigated the intermolecular interactions of 6-PPD with two key biological macromolecules, human serum albumin (HSA) and alpha-glucosidase (AG), to understand the transport and toxic effects of 6-PPD. Using multiple spectroscopic methods and molecular docking technology, the results demonstrated that 6-PPD could bind to both HSA and AG, thereby inducing fluorescence quenching and conformational changes in both proteins. The binding constants were determined to be (5.93 ± 0.20) × 10<sup>5</sup> and (3.17 ± 0.15) × 10<sup>4</sup> L mol<sup>−1</sup> respectively for HSA-6-PPD and AG-6-PPD systems at 298 K, revealing strong binding affinities. Molecular docking identified specific binding sites and non-covalent interactions of the two systems. MD and Energy decomposition analysis revealed the dynamics conformational changes of the complexes and identified van der Waals and electrostatic interactions as primary binding drivers for both systems, while polar solvation energy impeded complex formation. TYR161, ILE142, and TYR138 dominated HSA-6-PPD stabilization, whereas AG-6-PPD was driven by hydrophobic interactions with TRP1369 and VAL1373, with ARG1377 incurring substantial desolvation penalties. Synchronous fluorescence and circular dichroism spectroscopy indicated that 6-PPD binding did not disrupt the microenvironment of Tyr and Trp residues in HSA and AG, while induced structural alterations in HSA and AG that could affect their physiological function. <em>In-vitro</em> tests showed that 6-PPD inhibited AG activity in a dose-dependent manner, with an IC<sub>50</sub> of 8.22 ± 0.44 μmol L<sup>−1</sup>. ADMET and PASS online tools was used to predict physicochemical properties and multiorgan toxicity. This work provided insights into the transport and molecular toxicity of 6-PPD, highlighting the adverse biological effects associated with this common rubber additive.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107529"},"PeriodicalIF":2.2,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145155942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-10DOI: 10.1016/j.bpc.2025.107526
Tooba Khalid , Hafiz Abdul Rafey , Adnan Amin , Muhammad Kamran , Muhammad Kazim Zargaham , Samir Anis Ross , Shah-Iram Niaz
Diabetes and the related comorbidities have been associated with elevated levels of advanced glycation end products (AGEs). The biochemical process of advanced glycation, is believed to be playing a pivotal role in the development of complications. Since there exists a great deal of promise for natural products offering antidiabetic potential, we studied advanced glycation inhibition and anti-diabetic profile of Phytolacca latbenia (Moq). on fractions and the sorted compounds based on the QSAR and molecular docking analysis. The top two bioactive compounds; Kaempferol and Esculentoside G, were further evaluated for the MD simulation studies at 150 ns run, compared with the standard. Among the tested compounds, Kaempferol presented significant binding energies in MM-GBSA (−48.63 Kcal/mol) and MD simulation studies (73 %) with transcriptional regulator 4F5S. Molecular docking studies revealed that kaempferol formed three hydrogen bonds with Val342, Ser343 and Ser453, along with Pi-Pi stacking and Pi-cation interactions with Trp213 and Arg217 residues of the 4F5S protein. Kaempferol also displayed significant α-glucosidase inhibition (IC50 0.042 ± 2.31 μg/ml) compared to the acarbose (IC50 0.036 ± 0.31 μg/ml). Almost all of the selected compounds demonstrated adherence to the safety requirements established by ADMET investigation. Liquid–liquid partitioning of the crude methanolic extract with solvents of increasing polarity yielded five solvent fractions;the ethyl acetate fraction (ETOA) obtained by liquid–liquid partitioning of the crude extract with ethyl acetate and water proclaimed substantial results in both the non-oxidative (61 %) and oxidative (58 %) antiglycation assays for thiol group estimation. The ethylacetae fraction (ETOA) demonstrated comparatively strong antioxidant activity, with an IC₅₀ value of 13.25 ± 0.69 μg/ml as determined by the DPPH assay. In α-glucosidase assay, Aqueous fraction demonstrated a considerable inhibition with IC50 value of 0.108 ± 0.32 μg /ml compared to the standard (IC50 0.083 ± 0.43 μg/ml). The safety assessment revealed a slight decline in HeLa cell viability, dropping from 82 % at a 2.5 % concentration to 69 % at a 10 % concentration over 24 h, relative to the control.Therefore, Phytolacca latbenia (Moq). and its phytocompounds tested inhibit α-glucosidase and Advanced glycation end product-the process that underlie diabetic complications and may therefore holds great promise as therapeutic agent, with no toxicity concern,against diabetes and related comorbidities.
{"title":"In silico and in vitro characterization of Phytolacca latbenia (Moq.): QSAR, phytochemical, and toxicological insights into antiglycation and antidiabetic potential","authors":"Tooba Khalid , Hafiz Abdul Rafey , Adnan Amin , Muhammad Kamran , Muhammad Kazim Zargaham , Samir Anis Ross , Shah-Iram Niaz","doi":"10.1016/j.bpc.2025.107526","DOIUrl":"10.1016/j.bpc.2025.107526","url":null,"abstract":"<div><div>Diabetes and the related comorbidities have been associated with elevated levels of advanced glycation end products (AGEs). The biochemical process of advanced glycation, is believed to be playing a pivotal role in the development of complications. Since there exists a great deal of promise for natural products offering antidiabetic potential, we studied advanced glycation inhibition and anti-diabetic profile of <em>Phytolacca latbenia (Moq)</em>. on fractions and the sorted compounds based on the QSAR and molecular docking analysis. The top two bioactive compounds; Kaempferol and Esculentoside G, were further evaluated for the MD simulation studies at 150 ns run, compared with the standard. Among the tested compounds, Kaempferol presented significant binding energies in MM-GBSA (−48.63 Kcal/mol) and MD simulation studies (73 %) with transcriptional regulator 4F5S. Molecular docking studies revealed that kaempferol formed three hydrogen bonds with Val342, Ser343 and Ser453, along with Pi-Pi stacking and Pi-cation interactions with Trp213 and Arg217 residues of the 4F5S protein. Kaempferol also displayed significant α-glucosidase inhibition (IC<sub>50</sub> 0.042 ± 2.31 μg/ml) compared to the acarbose (IC<sub>50</sub> 0.036 ± 0.31 μg/ml). Almost all of the selected compounds demonstrated adherence to the safety requirements established by ADMET investigation. Liquid–liquid partitioning of the crude methanolic extract with solvents of increasing polarity yielded five solvent fractions;the ethyl acetate fraction (ETOA) obtained by liquid–liquid partitioning of the crude extract with ethyl acetate and water proclaimed substantial results in both the non-oxidative (61 %) and oxidative (58 %) antiglycation assays for thiol group estimation. The ethylacetae fraction (ETOA) demonstrated comparatively strong antioxidant activity, with an IC₅₀ value of 13.25 ± 0.69 μg/ml as determined by the DPPH assay. In α-glucosidase assay, Aqueous fraction demonstrated a considerable inhibition with IC<sub>50</sub> value of 0.108 ± 0.32 μg /ml compared to the standard (IC<sub>50</sub> 0.083 ± 0.43 μg/ml). The safety assessment revealed a slight decline in HeLa cell viability, dropping from 82 % at a 2.5 % concentration to 69 % at a 10 % concentration over 24 h, relative to the control.Therefore, <em>Phytolacca latbenia (Moq)</em>. and its phytocompounds tested inhibit α-glucosidase and Advanced glycation end product-the process that underlie diabetic complications and may therefore holds great promise as therapeutic agent, with no toxicity concern,against diabetes and related comorbidities.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107526"},"PeriodicalIF":2.2,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145097050","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}
Silver nanoparticles (AgNPs) synthesized through green chemistry approaches offer a sustainable alternative to conventional methods, with potential applications in various biological fields. In this study, we report the synthesis of AgNPs using terpenoids derived from Ipomoea hederifolia L. (Convolvulaceae). The AgNPs (AgNPs-T) were characterized using UV–Vis spectroscopy, which revealed a surface plasmon resonance (SPR) peak at 452 nm, confirming successful synthesis. Fourier-transform infrared spectroscopy (FTIR) analysis identified functional groups such as hydroxyl and carbonyl that facilitated the reduction of silver ions and acted as stabilizing agents. Transmission electron microscopy (TEM) showed that the AgNPs-T were spherical in shape, with sizes ranging from 4 to 20 nm, and were well-dispersed due to the presence of capping agents from the plant extract. The biological activities of AgNPs-T were evaluated, showcasing potent antibacterial activity against several human pathogenic bacteria. Additionally, AgNPs-T exhibited significant antibiofilm and anti-quorum sensing activities, disrupting biofilm formation and inhibiting bacterial communication. The nanoparticles also demonstrated strong antioxidant properties by scavenging DPPH radicals in a dose-dependent manner. Moreover, cytotoxicity studies using the MTT assay revealed that AgNPs-T exerted dose-dependent anticancer effects against breast cancer (MCF-7) cells. These findings suggest that Ipomoea hederifolia-derived AgNPs possess multifunctional biological activities, making them promising candidates for applications in antimicrobial, antioxidant, and anticancer therapies.
{"title":"Sustainable synthesis and functional profiling of Ipomoea hederifolia-derived terpenoids-assisted silver nanoparticles: Mechanistic insights into anticancer, antioxidant, antibiofilm, and anti-quorum sensing activities","authors":"Khushboo Makwana , Reem Binsuwaidan , Mohd Adnan , Nawaf Alshammari , Mitesh Patel","doi":"10.1016/j.bpc.2025.107524","DOIUrl":"10.1016/j.bpc.2025.107524","url":null,"abstract":"<div><div>Silver nanoparticles (AgNPs) synthesized through green chemistry approaches offer a sustainable alternative to conventional methods, with potential applications in various biological fields. In this study, we report the synthesis of AgNPs using terpenoids derived from <em>Ipomoea hederifolia</em> L. (Convolvulaceae). The AgNPs (AgNPs-T) were characterized using UV–Vis spectroscopy, which revealed a surface plasmon resonance (SPR) peak at 452 nm, confirming successful synthesis. Fourier-transform infrared spectroscopy (FTIR) analysis identified functional groups such as hydroxyl and carbonyl that facilitated the reduction of silver ions and acted as stabilizing agents. Transmission electron microscopy (TEM) showed that the AgNPs-T were spherical in shape, with sizes ranging from 4 to 20 nm, and were well-dispersed due to the presence of capping agents from the plant extract. The biological activities of AgNPs-T were evaluated, showcasing potent antibacterial activity against several human pathogenic bacteria. Additionally, AgNPs-T exhibited significant antibiofilm and anti-quorum sensing activities, disrupting biofilm formation and inhibiting bacterial communication. The nanoparticles also demonstrated strong antioxidant properties by scavenging DPPH radicals in a dose-dependent manner. Moreover, cytotoxicity studies using the MTT assay revealed that AgNPs-T exerted dose-dependent anticancer effects against breast cancer (MCF-7) cells. These findings suggest that <em>Ipomoea hederifolia</em>-derived AgNPs possess multifunctional biological activities, making them promising candidates for applications in antimicrobial, antioxidant, and anticancer therapies.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107524"},"PeriodicalIF":2.2,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145019315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-04DOI: 10.1016/j.bpc.2025.107525
Milad Amiri , Mohammad Javad Masroor , S. Shirin Shahangian , Reza H. Sajedi , Bijan Ranjbar
A comprehensive understanding of the molecular mechanism underlying the Liquid-Liquid Phase Separation (LLPS) pathway of LCD-TDP43 remains a challenge in the context of its neuropathogenesis. The primary driving force behind the TDP-43 LLPS is the interplay of hydrophobic interactions reinforced by aromatic residues. This study presents a novel, convenient, sensitive, and probe-free approach using excitation-emission matrix (EEM) fluorescence to monitor the microenvironment of aromatic residues and π-π stacking interactions during different stages of the LLPS pathway. Protein local structuring and the alterations in the positions of aromatic residues, individually and collectively, were detected by this life-time 3D fingerprinting. A new intermediate state with a unique α-sheet structure in the liquid droplet state and other transient species up to amyloid fibrils was discovered by CD and FTIR analyses. This structure with an inherent tendency for transition to β-amyloids, has not previously been reported in the context of LCD-TDP43 nor other LLPS-prone proteins. Mapping of hydrophobic clustering during phase separation revealed a continuous increase, accompanied by different surrounding polarities. The formation of distinct protein species within the LLPS pathway (from monomer to fibril), along with the amyloidogenic nature of TDP-43 fibrillation, was also confirmed by AFM analysis and ThT assay. To conclude, the 3D fluorescence method introduced in this study provides an effective and straightforward approach to critical valuable insights into the key π-π interactions in the LLPS-dependent aggregation pathway of LCD-containing IDPs. The novel identification of the α-sheet non-fibrilar intermediates may provide a new perspective for elucidating the aggregation mechanism of these proteins.
{"title":"Mapping the structural changes of LCD-TDP43 during the liquid-liquid phase separation by different spectroscopic platforms","authors":"Milad Amiri , Mohammad Javad Masroor , S. Shirin Shahangian , Reza H. Sajedi , Bijan Ranjbar","doi":"10.1016/j.bpc.2025.107525","DOIUrl":"10.1016/j.bpc.2025.107525","url":null,"abstract":"<div><div>A comprehensive understanding of the molecular mechanism underlying the Liquid-Liquid Phase Separation (LLPS) pathway of LCD-TDP43 remains a challenge in the context of its neuropathogenesis. The primary driving force behind the TDP-43 LLPS is the interplay of hydrophobic interactions reinforced by aromatic residues. This study presents a novel, convenient, sensitive, and probe-free approach using excitation-emission matrix (EEM) fluorescence to monitor the microenvironment of aromatic residues and π-π stacking interactions during different stages of the LLPS pathway. Protein local structuring and the alterations in the positions of aromatic residues, individually and collectively, were detected by this life-time 3D fingerprinting. A new intermediate state with a unique α-sheet structure in the liquid droplet state and other transient species up to amyloid fibrils was discovered by CD and FTIR analyses. This structure with an inherent tendency for transition to β-amyloids, has not previously been reported in the context of LCD-TDP43 nor other LLPS-prone proteins. Mapping of hydrophobic clustering during phase separation revealed a continuous increase, accompanied by different surrounding polarities. The formation of distinct protein species within the LLPS pathway (from monomer to fibril), along with the amyloidogenic nature of TDP-43 fibrillation, was also confirmed by AFM analysis and ThT assay. To conclude, the 3D fluorescence method introduced in this study provides an effective and straightforward approach to critical valuable insights into the key π-π interactions in the LLPS-dependent aggregation pathway of LCD-containing IDPs. The novel identification of the α-sheet non-fibrilar intermediates may provide a new perspective for elucidating the aggregation mechanism of these proteins.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107525"},"PeriodicalIF":2.2,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145007648","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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号