Journal of Biomolecular Structure & Dynamics最新文献_第4页

Elevating the rice blast disease immunity through CPKA protein targeting in Magnaporthe oryzae (M. oryzae) with natural compounds.

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-01-02 DOI: 10.1080/07391102.2024.2446665

Nimai Charan Mahanandia, Satyaranjan Biswal, Dwijesh Chandra Mishra, Sudhir Srivastava, Krishna Kumar Chaturvedi, Sneha Murmu, Anu Sharma, Girish Kumar Jha, Mohammad Samir Farooqi

{"title":"Elevating the rice blast disease immunity through CPKA protein targeting in Magnaporthe oryzae (M. oryzae) with natural compounds.","authors":"Nimai Charan Mahanandia, Satyaranjan Biswal, Dwijesh Chandra Mishra, Sudhir Srivastava, Krishna Kumar Chaturvedi, Sneha Murmu, Anu Sharma, Girish Kumar Jha, Mohammad Samir Farooqi","doi":"10.1080/07391102.2024.2446665","DOIUrl":"https://doi.org/10.1080/07391102.2024.2446665","url":null,"abstract":"Rice blast disease, instigated by Magnaporthe oryzae (M. oryzae), significantly impedes global rice production. Targeting the M. oryzae signaling protein, cAMP-Protein Kinase A (CPKA), which facilitates appressorium development and host penetration, this study explores the potential inhibitory effects of natural compounds. Virtual screening, molecular docking and text mining approaches were used to find the nimonol and curcumin that inhibit the CPKA protein. The MM-PBSA method was used to do the molecular dynamics (MD) simulation and the binding free energy analysis of the molecule. Their binding free energies (ΔGbind) of -78.81 kJ/mol and -117.65 kJ/mol, respectively, point to the potential efficacy of the CPKA-nimonol and CPKA-curcumin complexes as inhibitors. The inhibitory effects have been further verified by various MD analysis. This study emphasizes the need to conduct further study on the CPKA protein and gives important insights into the possibility of natural compounds as M. oryzae inhibitors.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-16"},"PeriodicalIF":2.7,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914959","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}

引用次数: 0

HDAC inhibition by Nigella sativa L. sprouts extract in hepatocellular carcinoma: an approach to study anti-cancer potential. Nigella sativa L.芽提取物对肝细胞癌HDAC的抑制作用：一种研究抗癌潜力的方法。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-01-01 Epub Date: 2023-11-10 DOI: 10.1080/07391102.2023.2279283

Abdullah Algaissi, Heena Tabassum, Elhan Khan, Sonam Dwivedi, Mohtashim Lohani, Nizar A Khamjan, Abdullah Farasani, Iffat Zareen Ahmad

{"title":"HDAC inhibition by Nigella sativa L. sprouts extract in hepatocellular carcinoma: an approach to study anti-cancer potential.","authors":"Abdullah Algaissi, Heena Tabassum, Elhan Khan, Sonam Dwivedi, Mohtashim Lohani, Nizar A Khamjan, Abdullah Farasani, Iffat Zareen Ahmad","doi":"10.1080/07391102.2023.2279283","DOIUrl":"10.1080/07391102.2023.2279283","url":null,"abstract":"A wide variety of natural products have been widely used in chemoprevention therapy because they have antioxidant, anti-inflammatory, and anticancer activity. In the present study, we shed light on the 5th day germinated sprouts of N. sativa seeds and evaluated them against HDAC inhibition and antioxidant activity. The extract from the seed and sprout was extracted and characterised by LC-MS/MS, FTIR, and NMR to reveal its chemical composition, especially thymol (THY) and thymoquinone (TQ). Hepatocellular carcinoma (HCC) is a global health concern as it is a major lifestyle disease. Hence, incorporating herbal-based therapeutic compounds into everyday routines has become an attractive alternative for preventing hepatic diseases. Histone deacetylase (HDAC) inhibition (HDACi) is emerging as a promising therapeutic strategy for managing various carcinomas including HCC. Therefore, the 5th day of N. sativa can be used as a potential anticancer agent by inhibiting HDAC activity, as it is reported to have an important role in the management of oxidative stress. The bioactive compound of N. sativa, i.e. thymoquinone, also showed a good binding affinity with the HDAC protein (3MAX) with a stable interaction in an in silico study as compared to the standard drug (Trichostatin A) and thymol.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-19"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72209459","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}

引用次数: 0

Virtual screening, pharmacokinetics & MD simulation study of active phytoconstituents of Ficus Carica Linn. against PPAR-γ in diabetes mellitus. 无花果有效成分的虚拟筛选、药代动力学及分子动力学模拟研究。抗PPAR-γ在糖尿病中的作用。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-01-01 Epub Date: 2023-11-10 DOI: 10.1080/07391102.2023.2279286

Shridhar Deshpande N, Prarambh S R Dwivedi, B C Revanasiddappa

{"title":"Virtual screening, pharmacokinetics & MD simulation study of active phytoconstituents of Ficus Carica Linn. against PPAR-γ in diabetes mellitus.","authors":"Shridhar Deshpande N, Prarambh S R Dwivedi, B C Revanasiddappa","doi":"10.1080/07391102.2023.2279286","DOIUrl":"10.1080/07391102.2023.2279286","url":null,"abstract":"F. carica is a small tree and commonly used as a traditional medicine against several disorders. Diabetes is currently treated with insulin and oral hypoglycemic medicines such as sulphonyl urea derivatives, bigunides, thiazolidinediones and alpha-glucosidase inhibitors. Peroxisome proliferator-activated receptor gamma (PPAR-γ) agonists were found to be very much beneficial in the management of diabetes by inhibiting hepatic gluconeogenesis. The aim of this study is to evaluate the bioactive phytoconstituents from Ficus carica Linn. against the target PPAR-γ agonist by in silico docking approach. We investigated 68 phytoconstituents as potential inhibitors of PPAR-γ agonists and the top 24 phytoconstituents were further selected for molecular docking studies. Drug ability, side effects, and ADMET analysis were determined by using MolSoft, toxtree freeware, and ADMET SAR web server, respectively. The phytoconstituents were docked with the target PPAR-γ (PDB ID: 4Y29, 1.98 Å) receptor. Quercetin-3-o-rutinoside possessed the highest G score -14.22 kcal/mol, followed by Angelicin with a G score of -13.56 kcal/mol. All the other phytoconstituents displayed good pharmacokinetic and toxicological parameters with values within the permissible limits. The ligand-protein interaction was calculated by molecular dynamic (MD) simulation study. Subsequently, the binding free energy of the Quercetin-3-o-rutinosideand Pioglitazone complex was calculated using MMPBSA analysis. The results indicated that some of the phytoconstituents from Ficus carica have potency as an anti-diabetic agents. So, these bioactive phytoconstituents like Quercetin-3-o-glucoside, 5-O-caffeoylquinic acids may act as a good agonist for PPAR-γ.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"36-52"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72209467","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}

引用次数: 0

Epitopes mapping for identification of potential cross-reactive peptide against leptospirosis. 用于鉴定针对钩端螺旋体病的潜在交叉反应肽的表位定位。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-01-01 Epub Date: 2023-11-10 DOI: 10.1080/07391102.2023.2279285

Vibhisha Vaghasia, Kumari Snehkant Lata, Saumya Patel, Jayashankar Das

{"title":"Epitopes mapping for identification of potential cross-reactive peptide against leptospirosis.","authors":"Vibhisha Vaghasia, Kumari Snehkant Lata, Saumya Patel, Jayashankar Das","doi":"10.1080/07391102.2023.2279285","DOIUrl":"10.1080/07391102.2023.2279285","url":null,"abstract":"Leptospira, the pathogenic helical spirochetes that cause leptospirosis, is an emerging zoonotic disease with effective dissemination tactics in the host and can infect humans and animals with moderate or severe illnesses. Thus, peptide-based vaccines may be the most effective strategy to manage the immune response against Leptospira to close these gaps. In the current investigation, highly immunogenic proteins from the proteome of Leptospira interorgan serogroup Icterohaemorrhagie serovar Lai strain 56601 were identified using immunoinformatic methods. It was discovered that the conserved and most immunogenic outer membrane Lepin protein was both antigenic and non-allergenic by testing 15 linear B-cells and the ten best T-cell (Helper-lymphocyte (HTL) with the most significant number of HLA-DR binding alleles and the eight cytotoxic T lymphocyte (CTL)) epitopes. Furthermore, a 3D structural model of CTL epitopes was created using the Pep-Fold3 platform. Using the Autodock 4.2 docking server, research was conducted to determine how well the top-ranked CTL peptide models attach to HLA-A*0201 (PDB ID: 4U6Y). With HLA-A*0201, the epitope SSGTGNLHV binds with a binding energy of -1.29 kcal/mol. Utilizing molecular dynamics modeling, the projected epitope-allele docked complex structure was optimized, and the stability of the complex system was assessed. Therefore, this epitope can trigger an immunological response and produce effective Leptospira vaccine candidates. Overall, this study offers a unique vaccination candidate and may encourage additional research into leptospirosis vaccines.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"20-35"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72209458","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}

引用次数: 0

Antimicrobial activity prediction, inter- and intramolecular charge transfer investigation, reactivity analysis and molecular docking studies of adenine derivatives. 腺嘌呤衍生物的抗菌活性预测、分子间和分子内电荷转移研究、反应性分析和分子对接研究。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-01-01 Epub Date: 2023-11-18 DOI: 10.1080/07391102.2023.2281636

C Geetha Priya, B R Venkatraman, I Arockiaraj, S Sowrirajan, N Elangovan, Mohammad Shahidul Islam, Sakkarapalayam M Mahalingam

{"title":"Antimicrobial activity prediction, inter- and intramolecular charge transfer investigation, reactivity analysis and molecular docking studies of adenine derivatives.","authors":"C Geetha Priya, B R Venkatraman, I Arockiaraj, S Sowrirajan, N Elangovan, Mohammad Shahidul Islam, Sakkarapalayam M Mahalingam","doi":"10.1080/07391102.2023.2281636","DOIUrl":"10.1080/07391102.2023.2281636","url":null,"abstract":"The utilization of the density functional theory (DFT) methodology has developed as a highly efficient method for investigating molecular structure and vibrational spectra, and it is increasingly being employed in various applications relating to biological systems. This study focuses on conducting investigations, both experimental and computed, to analyze the molecular structure, electronic properties and features of (E)-4-(((9H-purin-6-yl)imino)methyl)-2-methoxyphenol (ANVA). The expression ANVA should be rewritten as follows: the compound is a derivative of adenine (primary amine), specifically a vanillin (aldehyde). The present study reports the synthesis, characterization, DFT, docking and antimicrobial activity of ANVA. The optimization of the molecular structure was conducted, and the determination of its structural features was performed using DFT with the B3LYP/cc-pVDZ method. The vibrational assignments were determined in detail by analyzing the potential energy distribution. A strong correlation was observed between the spectra that were observed and the spectra that were calculated. The calculation of intramolecular charge transfer was performed using natural bond orbital analysis. In addition, several computational methods were employed, including highest occupied molecular orbital-least unoccupied molecular orbital analysis, molecular electrostatic potential calculations, non-linear optical, reduced density gradient, localization orbital locator and electron localization function analysis. This paper examines the present use of adenine derivatives in combatting bacterial and fungal infections, as well as the inclusion of spectral and quantum chemical calculations in the discussion.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"372-385"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136397593","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}

引用次数: 0

Multi-spectroscopic and thermodynamic profiles on HSA binding of Cassia fistula leaf based potential antibacterial and anticancer silver nanoparticles. 决明子瘘叶基潜在抗菌抗癌银纳米颗粒HSA结合的多光谱和热力学特征。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-01-01 Epub Date: 2023-11-21 DOI: 10.1080/07391102.2023.2283148

Maidul Beg, Anukul Maji, Mt Nasima Aktara, Somenath Kundu, Samaresh Paria, Basudev Shit, Asima Dhal, Md Maidul Islam, Maidul Hossain

{"title":"Multi-spectroscopic and thermodynamic profiles on HSA binding of Cassia fistula leaf based potential antibacterial and anticancer silver nanoparticles.","authors":"Maidul Beg, Anukul Maji, Mt Nasima Aktara, Somenath Kundu, Samaresh Paria, Basudev Shit, Asima Dhal, Md Maidul Islam, Maidul Hossain","doi":"10.1080/07391102.2023.2283148","DOIUrl":"10.1080/07391102.2023.2283148","url":null,"abstract":"Here, a simple, one step, lucrative and green synthesis of Cassia fistula leaf extract inspired antibacterial silver nanoparticles (CF-SNPs) was provided. Characterization of these CF-SNPs were achieved by using various spectroscopic techniques for instance Ultraviolet Visible (UV-Vis) Spectroscopy, Fourier-Transform Infrared (FTIR) Spectroscopy, Dynamic Light Scattering (DLS), Transmission Electron Microscopy (TEM) and Energy Dispersive X-ray (EDX). The effective antibacterial action of the CF-SNPs was checked against Escherichia coli (E. Coli) DH5-Alpha where MIC was 1.6 nM. Anticancer dynamism of the CF-SNPs was also tested in opposition to skin melanoma, A375 cell lines in which 4.4 nM was IC50. The binding proneness of HSA towards CF-SNPs was investigated by means of UV-Vis Spectroscopy, Fluorescence Spectroscopy, Time Resolved Fluorescence Spectroscopy, Circular Dichroism (CD) Spectroscopy, Dynamic Light Scattering, and Isothermal Titration Colorimetry (ITC). CD spectroscopy established minor secondary structural exchange of HSA in HSA-CF-SNPs complex. ITC and Time Resolved Fluorescence Spectroscopy verified the static type quenching mechanism involved in HSA-CF-SNPs complex. The binding constant was 3.45 × 108 M-1 at 298.15K from ITC study. The thermodynamic parameters showed that the interaction was occurred spontaneously by the hydrophilic forces and hydrogen bonding.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"521-533"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138291026","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}

引用次数: 0

Plasmepsin II inhibitory potential of phytochemicals isolated from African antimalarial plants: a computational approach. 从非洲抗疟植物中分离的植物化学物质的Plasmepsin II抑制潜力:计算方法。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-01-01 Epub Date: 2023-11-15 DOI: 10.1080/07391102.2023.2283146

Kolade O Faloye, Manish Kumar Tripathi, Emmanuel G Fakola, Awodayo O Adepiti, Stephen A Adesida, Ibukun O Oyeleke, Praise A Adebayo, Adeola E Aregbesola, Samson O Famuyiwa, Olawale F Akinyele

{"title":"Plasmepsin II inhibitory potential of phytochemicals isolated from African antimalarial plants: a computational approach.","authors":"Kolade O Faloye, Manish Kumar Tripathi, Emmanuel G Fakola, Awodayo O Adepiti, Stephen A Adesida, Ibukun O Oyeleke, Praise A Adebayo, Adeola E Aregbesola, Samson O Famuyiwa, Olawale F Akinyele","doi":"10.1080/07391102.2023.2283146","DOIUrl":"10.1080/07391102.2023.2283146","url":null,"abstract":"Plamepsin II has been identified as a therapeutic target in the Plasmodium falciparum's life cycle and may lead to a drastic reduction in deaths caused by malaria worldwide. Africa flora is rich in medicinal qualities and possesses both simple and complex bioactive phytochemicals. This study utilized computational approaches like molecular docking, molecular dynamics simulation, quantum chemical calculations and ADMET to evaluate the plasmepsin II inhibitory properties of phytochemicals isolated from African antimalarial plants. Molecular docking was carried out to estimate the binding affinity of 229 phytochemicals whereby ekeberin A, dichamanetin, 10-hydroxyusambaresine, chamuvaritin and diuvaretin were selected. Further, RMSD and RMSF plots from the 100 ns simulation results showed that the screened phytochemicals were stable in the enzyme's binding pocket. The quantum chemical calculation revealed that all the phytochemicals are strong electrophiles, while ekeberin A was identified as the most stable and dichamanetin as the most reactive. Also, ADMET studies established the drug candidacy of the phytochemicals. Thus, these phytochemicals could act as good antimalarial agents after extensive in vitro and in vivo studies.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"505-520"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134648993","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}

引用次数: 0

Fighting against amyotrophic lateral sclerosis (ALS) with flavonoids: a computational approach to inhibit superoxide dismutase (SOD1) mutant aggregation. 黄酮类化合物对抗肌萎缩性侧索硬化(ALS):一种抑制超氧化物歧化酶(SOD1)突变体聚集的计算方法。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-01-01 Epub Date: 2023-11-17 DOI: 10.1080/07391102.2023.2281641

Seyed Mostafa Noorbakhsh Varnosfaderani, Melika Sadat Haeri, Ali Sam Arian, Ali Yousefi Rad, Mohammad Yazdanpour, Fatemeh Mojahedian, Mohammad Yaghoubzad-Maleki, Hamidreza Zalpoor, Payam Baziyar, Mohsen Nabi-Afjadi

{"title":"Fighting against amyotrophic lateral sclerosis (ALS) with flavonoids: a computational approach to inhibit superoxide dismutase (SOD1) mutant aggregation.","authors":"Seyed Mostafa Noorbakhsh Varnosfaderani, Melika Sadat Haeri, Ali Sam Arian, Ali Yousefi Rad, Mohammad Yazdanpour, Fatemeh Mojahedian, Mohammad Yaghoubzad-Maleki, Hamidreza Zalpoor, Payam Baziyar, Mohsen Nabi-Afjadi","doi":"10.1080/07391102.2023.2281641","DOIUrl":"10.1080/07391102.2023.2281641","url":null,"abstract":"Protein aggregation is a biological process that occurs when proteins misfold. Misfolding and aggregation of human superoxide dismutase (hSOD1) cause a neurodegenerative disease called amyotrophic lateral sclerosis (ALS). Among the mutations occurring, targeting the E21K mutation could be a good choice to understand the pathological mechanism of SOD1 in ALS, whereof it significantly reduces life hopefulness in patients. Naturally occurring polyphenolic flavonoids have been suggested as a way to alleviate the amyloidogenic behavior of proteins. In this study, computational tools were used to identify promising flavonoid compounds that effectively inhibit the pathogenic behavior of the E21K mutant. Initial screening identified Pelargonidin, Curcumin, and Silybin as promising leads. Molecular dynamics (MD) simulations showed that the binding of flavonoids to the mutated SOD1 caused changes in the protein stability, hydrophobicity, flexibility, and restoration of lost hydrogen bonds. Secondary structure analysis indicated that the protein destabilization and the increased propensity of β-sheet caused by the mutation were restored to the wild-type state upon binding of flavonoids. Free energy landscape (FEL) analysis was also used to differentiate aggregation, and results showed that Silybin followed by Pelargonidin had the most therapeutic efficacy against the E21K mutant SOD1. Therefore, these flavonoids hold great potential as highly effective inhibitors in mitigating ALS's fatal and insuperable effects.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"419-436"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136397595","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}

引用次数: 0

Temperature-dependent hydration behavior of aqueous lysine: an approach towards protein binding through dielectric spectroscopy. 水赖氨酸的温度依赖水化行为:通过介电光谱研究蛋白质结合的方法。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-01-01 Epub Date: 2023-11-20 DOI: 10.1080/07391102.2023.2281642

Suad Alwaleedy, Ravikant R Karale, Komal B Kabara, Savita Kamble, Saeed Al Hamdani, Ashok C Kumbharkhane, Arvind V Sarode

{"title":"Temperature-dependent hydration behavior of aqueous lysine: an approach towards protein binding through dielectric spectroscopy.","authors":"Suad Alwaleedy, Ravikant R Karale, Komal B Kabara, Savita Kamble, Saeed Al Hamdani, Ashok C Kumbharkhane, Arvind V Sarode","doi":"10.1080/07391102.2023.2281642","DOIUrl":"10.1080/07391102.2023.2281642","url":null,"abstract":"Present work reports interaction between water and amino acid lysine for understanding the physicochemical properties that will be useful in the structure formation of protein. The dielectric relaxation of aqueous lysine was systematically investigated over a temperature range spanning from 298.15 K to 278.15 K, encompassing frequencies ranging from 10 MHz to 30 GHz, and across a concentration range of 0.152 M to 0.610 M. Within this study, aqueous lysine revealed the presence of two distinct relaxation modes. The low-frequency relaxation process (l-process) is primarily associated with the relaxation of lysine molecules, whereas the high-frequency relaxation process (h-process) is attributed to water molecules interacting with lysine. Several key dielectric parameters, including static dielectric constant (εj), relaxation time (τj), dipole moment (μj), correlation factor (gj), and the number of water molecules rotationally bonded by solute molecules (Zib), were meticulously determined. These parameters were interpreted in terms of molecular interactions, hydrogen bonding, hydrophobicity, and Lys-Lys binding. Additionally, various thermodynamic parameters such as molar enthalpy (ΔHj), molar entropy (ΔSj), and molar free energy (ΔFj) were calculated to provide further insights into the system's characteristics and behavior.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"437-449"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138176221","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}

引用次数: 0

Exploring imidazo[4,5-g]quinoline-4,9-dione derivatives as Acinetobacter baumannii efflux pump inhibitor: an in silico approach. 咪唑并[4,5-g]喹啉-4,9-二酮衍生物作为鲍曼不动杆菌外排泵抑制剂的探索：一种计算机方法。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-01-01 Epub Date: 2023-11-08 DOI: 10.1080/07391102.2023.2279287

Pownraj Brindangnanam, Krishnan Ashokkumar, Sriraghavan Kamaraj, Mohane Selvaraj Coumar

{"title":"Exploring imidazo[4,5-g]quinoline-4,9-dione derivatives as Acinetobacter baumannii efflux pump inhibitor: an in silico approach.","authors":"Pownraj Brindangnanam, Krishnan Ashokkumar, Sriraghavan Kamaraj, Mohane Selvaraj Coumar","doi":"10.1080/07391102.2023.2279287","DOIUrl":"10.1080/07391102.2023.2279287","url":null,"abstract":"Antimicrobial resistance (AMR) is fast becoming a medical crisis affecting the entire global population. World Health Organization (WHO) statistics show that globally 0.7 million people are dying yearly due to the emergence of AMR. By 2050, the expected number of lives lost will be 10 million per year. Acinetobacter baumannii is a dreadful nosocomial pathogen that has developed multidrug resistance (MDR) to several currently prescribed antibiotics worldwide. Overexpression of drug efflux transporters (DETs) is one of the mechanisms of multidrug resistance (MDR) in Acinetobacter baumannii. Therefore, blocking the DET can raise the efficacy of the existing antibiotics by increasing their residence time inside the bacteria. In silico screening of five synthetic compounds against three drug efflux pump from A. baumannii has identified KSA5, a novel imidazo[4,5-g]quinoline-4,9-dione derivative, to block the efflux of antibiotics. Molecular docking and simulation results showed that KSA5 could bind to adeB, adeG, and adeJ by consistently interacting with ligand-binding site residues. KSA5 has a higher binding free energy and a lower HOMO-LUMO energy gap than PAβN, suggesting a better ability to interact and inhibit DETs. Further analysis showed that KSA5 is a drug-like molecule with optimal physicochemical and ADME properties. Hence, KSA5 could be combined with antibiotics to overcome antimicrobial resistance.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"53-72"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71481966","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}

引用次数: 0