Journal of Molecular Recognition最新文献_第7页

In silico identification and analysis of potential inhibitors for acid phosphatase, HppA from Helicobacter pylori 幽门螺杆菌酸性磷酸酶HppA潜在抑制剂的计算机鉴定和分析

IF 2.7 4区生物学

Journal of Molecular Recognition Pub Date : 2023-08-08 DOI: 10.1002/jmr.3049

Rinki Sisodia, Pooja Anjali Mazumdar, Chaithanya Madhurantakam

引用次数: 0

Investigation of the effects of some pesticides on carbonic anhydrase isoenzymes 几种农药对碳酸酐酶同工酶影响的研究

IF 2.7 4区生物学

Journal of Molecular Recognition Pub Date : 2023-08-08 DOI: 10.1002/jmr.3048

Aybike Baltacı, Kubra Cıkrıkcı, Nahit Gençer

{"title":"Investigation of the effects of some pesticides on carbonic anhydrase isoenzymes","authors":"Aybike Baltacı, Kubra Cıkrıkcı, Nahit Gençer","doi":"10.1002/jmr.3048","DOIUrl":"10.1002/jmr.3048","url":null,"abstract":"The aim of this study was to investigate the inhibitory effects of some pesticides known to have harmful effects on human health on carbonic anhydrase isoenzymes. Therefore, carbonic anhydrase isoenzymes (hCA I and II) were purified from human erythrocytes. The isoenzymes were purified from human erythrocytes by using an affinity column that has the chemical structure of Sepharose-4B-4-(6-amino-hexyloxy)-benzenesulfonamide. The purity of the isoenzymes was checked by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDSPAGE). It was determined that the pesticides used in this study inhibit hCA I and hCA II isoenzymes at different levels in vitro. It was determined that the strongest inhibitor for the hCA I enzyme was Carbofuran (IC50:6.52 μM; Ki: 3.58 μM) and the weakest one was 1-Naphtol (IC50:16.55 μM; Ki: 14.4 μM) among these pesticides. It was also found that the strongest inhibitor for the hCA II enzyme was coumatetralil (IC50:5.06 μM; Ki: 1.62 μM) and the weakest one was Dimethachlor (IC50 14.6 μM; Ki: 8.44 μM).","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 9","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10381030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Cry11Aa and Cyt1Aa exhibit different structural orders in crystal topography Cry11Aa和Cyt1Aa在晶体形貌上表现出不同的结构顺序

IF 2.7 4区生物学

Journal of Molecular Recognition Pub Date : 2023-07-20 DOI: 10.1002/jmr.3047

Shu-wen W. Chen, Jean-Marie Teulon, Jean-Luc Pellequer

引用次数: 0

Investigation of the binding interactions mechanism between zein with chrysin by multispectroscopic techniques 用多光谱技术研究玉米蛋白与菊花素的结合作用机理

IF 2.7 4区生物学

Journal of Molecular Recognition Pub Date : 2023-07-16 DOI: 10.1002/jmr.3046

Xue Gao, Ruiquan Qi, Ye Cheng, Junliang Chen, Yin He, Yitong Mao, Xiangyu Cao

{"title":"Investigation of the binding interactions mechanism between zein with chrysin by multispectroscopic techniques","authors":"Xue Gao, Ruiquan Qi, Ye Cheng, Junliang Chen, Yin He, Yitong Mao, Xiangyu Cao","doi":"10.1002/jmr.3046","DOIUrl":"10.1002/jmr.3046","url":null,"abstract":"As a natural carrier protein, zein was intensively studied for the construction of a flavonoid delivery system. Chrysin has presented superior tumor-resistant, anti-inflammatory, and anti-oxidation potentials among the flavonoid candidates in clinical practice. However, due to inadequate research, the binding mechanism and structural affinity of zein to chrysin are still indeterminate. Therefore, multispectral methods were employed to explore the molecular interaction of zein and chrysin in this work. These techniques showed that chrysin reduced the intrinsic fluorescence of zein via a static process and that the interaction between zein and chrysin was mainly driven spontaneously by hydrophobic forces. Additionally, the experimental results revealed the changed microenvironment in the vicinity of tyrosine and affected secondary structure in the presence of chrysin, indicating zein's conformation were altered by chrysin. This work provided comprehensive insight into the combination of plant-derived protein (zein) and flavonoids (chrysin) and helped rationalize the protection, transportation, and release of chrysin through a zein-based delivery system.","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 8","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9857218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Molecular modeling and rational design of disulfide-stapled self-inhibitory peptides to target IL-17A/IL-17RA interaction 靶向IL-17A/IL-17RA相互作用的二硫自抑制肽的分子建模和合理设计

IF 2.7 4区生物学

Journal of Molecular Recognition Pub Date : 2023-07-06 DOI: 10.1002/jmr.3045

Weihua Huang, Yang Zhou, Chunhua Pan, Xin Zhang, Huijun Zhao, Lili Shen

{"title":"Molecular modeling and rational design of disulfide-stapled self-inhibitory peptides to target IL-17A/IL-17RA interaction","authors":"Weihua Huang, Yang Zhou, Chunhua Pan, Xin Zhang, Huijun Zhao, Lili Shen","doi":"10.1002/jmr.3045","DOIUrl":"10.1002/jmr.3045","url":null,"abstract":"Interleukin-17A (IL-17A) is a pro-inflammatory cytokine implicated in diverse autoimmune and inflammatory disorders such as psoriasis and Kawasaki disease. Mature IL-17A is a homodimer that binds to the extracellular type-III fibronectin D1:D2-dual domain of its cognate IL-17 receptor A (IL-17RA). In this study, we systematically examined the structural basis, thermodynamics property, and dynamics behavior of IL-17RA/IL-17A interaction and computationally identified two continuous hotspot regions separately from different monomers of IL-17A homodimer that contribute significantly to the interaction, namely I-shaped and U-shaped segments, thus rendered as a peptide-mediated protein–protein interaction (PmPPI). Self-inhibitory peptides (SIPs) are derived from the two segments to disrupt IL-17RA/IL-17A interaction by competitively rebinding to the IL-17A-binding pocket on IL-17RA surface, which, however, only have a weak affinity and low specificity for IL-17RA due to lack of the context support of intact IL-17A protein, thus exhibiting a large flexibility and intrinsic disorder when splitting from the protein context and incurring a considerable entropy penalty when rebinding to IL-17RA. The U-shaped segment is further extended, mutated and stapled by a disulfide bridge across its two strands to obtain a number of double-stranded cyclic SIPs, which are partially ordered and conformationally similar to their native status at IL-17RA/IL-17A complex interface. Experimental fluorescence polarization assays substantiate that the stapling can moderately or considerably improve the binding affinity of U-shaped segment-derived peptides by 2–5-fold. In addition, computational structural modeling also reveals that the stapled peptides can bind in a similar mode with the native crystal conformation of U-shaped segment in IL-17RA pocket, where the disulfide bridge is out of the pocket for avoiding intervene of the peptide binding.","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 8","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10233512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Issue Information 问题信息

IF 2.7 4区生物学

Journal of Molecular Recognition Pub Date : 2023-07-01 DOI: 10.1111/tops.12619

引用次数: 0

Human serum albumin subdomain IB is physiologically adapted for payloading homopterocarpin to human aldehyde dehydrogenase: Combinatorial in vitro and in silico approaches 人血清白蛋白亚结构域IB在生理上适合于向人醛脱氢酶装载同叶紫红素:体外和计算机组合方法

IF 2.7 4区生物学

Journal of Molecular Recognition Pub Date : 2023-06-29 DOI: 10.1002/jmr.3043

Michael E. Ayenero, Gbemi E. Akinwusi, Adejoke N. Kolawole, Babatunde A. Falese, Idowu J. Olawuni, Ayodele O. Kolawole

{"title":"Human serum albumin subdomain IB is physiologically adapted for payloading homopterocarpin to human aldehyde dehydrogenase: Combinatorial in vitro and in silico approaches","authors":"Michael E. Ayenero, Gbemi E. Akinwusi, Adejoke N. Kolawole, Babatunde A. Falese, Idowu J. Olawuni, Ayodele O. Kolawole","doi":"10.1002/jmr.3043","DOIUrl":"10.1002/jmr.3043","url":null,"abstract":"The in vitro interactions of homopterocarpin, a potent antioxidant and anti-ulcerative isoflavonoid, with human serum albumin (HSA) and human aldehyde dehydrogenase (hALDH) were explored using various spectroscopic methods, in silico and molecular dynamic (MD) studies. The result showed that homopterocarpin quenched the intrinsic fluorescences of HSA and hALDH. The interactions were entropically favorable, driven primarily by hydrophobic interactions. The proteins have one binding site for the isoflavonoid. This interaction increased the proteins hydrodynamic radii by over 5% and caused a slight change in HSA surface hydrophobicity Homopterocarpin preferentially binds to HSA subdomain IB with a binding affinity of −10.1 kcal/mol before interaction stoke with hALDH (–8.4 kcal/mol). HSA-homopterocarpin complex attained pharmacokinetic-pharmacodynamics reversible equilibration time faster than ALDH-homopterocarpin. However, the probable and eventual therapeutic effect of homopterocarpin is the mixed inhibition ALDH activity having a Ki value of 20.74 μM. The MD results revealed the stabilization of the complex in HSA–homopterocarpin and ALDH–homopterocarpin from their respective spatial structures of the complex. The findings of this research will provide significant benefits in understanding the pharmacokinetics characteristics of homopterocarpin at the clinical level.","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 8","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9853590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Construction of a prognostic model based on genes associated with mitochondrial energy metabolic pathway in colon adenocarcinoma and its clinical significance 基于线粒体能量代谢途径相关基因的结肠癌预后模型的构建及其临床意义。

IF 2.7 4区生物学

Journal of Molecular Recognition Pub Date : 2023-06-15 DOI: 10.1002/jmr.3044

Xiangcheng Zhang, Ce Liang, Bingchuan Zhou, Liming Pang

{"title":"Construction of a prognostic model based on genes associated with mitochondrial energy metabolic pathway in colon adenocarcinoma and its clinical significance","authors":"Xiangcheng Zhang, Ce Liang, Bingchuan Zhou, Liming Pang","doi":"10.1002/jmr.3044","DOIUrl":"10.1002/jmr.3044","url":null,"abstract":"Mitochondria are the main sites of oxidative metabolism and energy release of sugars, fats and amino acids in the body. According to studies, malignant tumor occurrence and development have been linked to abnormal mitochondrial energy metabolism (MEM). However, the feasible role of abnormal MEM in colon adenocarcinoma (COAD) is poorly understood. In this work, we obtained COAD patient data from The Cancer Genome Atlas (TCGA) as the training set, and GSE103479 from Gene Expression Omnibus (GEO) as the validation set. Combined with the mitochondrial energy metabolic pathway (MEMP)-related genes in Kyoto Encyclopedia of Genes and Genomes (KEGG) database, a risk prognostic model was constructed by utilizing Cox regression analysis to identify 6 feature genes (CYP4A11, PGM2, PKLR, PPARGC1A, CPT2 and ACAT2) that were significantly associated with MEMP in COAD. By stratifying the samples based on riskscore, two distinct groups, namely the high- and low-risk groups, were identified. The model demonstrated accurate assessment of the prognosis risk in COAD patients and exhibited independent prognostic capability, as evidenced by the survival curve and receiver operating characteristic (ROC) curve analysis. A nomogram was plotted based on clinical information and riskscore. We proved it could predict the survival time of COAD patients effectively combined with the calibration curve of risk prediction. Subsequently, based on the immune evaluation and mutation frequency analysis performed on COAD patients, patients in high-risk group had observably higher immune scores, immune activity and PDCD1 expression level than low-risk group. In general, the prognostic model developed using MEMP-related genes served as a valuable biomarker for forecasting the prognosis of COAD patients, which offered a reference for the prognosis evaluation and clinical cure of COAD patients.","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 8","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9833063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Comprehensive analysis on the diagnostic role of circulatory exosome-based miR-92a-3p for osteoblastic metastases in prostate adenocarcinoma 基于循环外泌体的miR-92a-3p在前列腺癌成骨细胞转移诊断中的综合分析

IF 2.7 4区生物学

Journal of Molecular Recognition Pub Date : 2023-05-31 DOI: 10.1002/jmr.3042

Gayathri Ashok, Rohini Das, Anand Anbarasu, Sudha Ramaiah

{"title":"Comprehensive analysis on the diagnostic role of circulatory exosome-based miR-92a-3p for osteoblastic metastases in prostate adenocarcinoma","authors":"Gayathri Ashok, Rohini Das, Anand Anbarasu, Sudha Ramaiah","doi":"10.1002/jmr.3042","DOIUrl":"10.1002/jmr.3042","url":null,"abstract":"Prostate adenocarcinoma (PRAD) is the second leading cause of death in men and the key factor that attributes to the severity and higher mortality rates is the tumor's ability to promote osteoblastic metastases (OM). Currently, no blood-based biomarkers are present that bridges the crosstalk between PRAD and OM progression. Conversely, circulatory microRNAs (miRNAs) are gaining interest among the scientific community for its potential as blood-based markers for cancer detection. Using computational pipeline, this study screened exosome-based miRNA that is functionally regulating OM in PRAD. We retrieved the expression profile of miRNA, mRNA from PRAD microarray, and RNA-Seq samples deposited in global repositories and identified the differentially expressed miRNAs (DEMs) and differentially expressed genes. Thereafter, the average expression of the miRNAs was identified in extracellular vesicle specifically in exosomes. Survival analysis and clinical profiling identified functionally significant miR-92a-3p to be a key factor in OM. This was further examined by the interactions with various noncoding RNA elements, transcription factors, oncogenes, tumor suppressor genes, and protein kinases regulated by miR-92a-3p. Identifying the expression pattern, nodal metastasis, Gleason score, and hazard ratio deciphered the critical role of the targets regulated by miR-92a-3p. Further, binding association analyzed through energy, seed match and accessibility showed the miRNA-targets involved in cytokine, TGF-β, and Wnt signaling having close regulatory role in promoting OM. Our findings highlight the potent role of miR-92a-3p as blood-based diagnostic biomarker for OM. The comprehensive insights from our study can be elemental in designing diagnostic biomarker for PRAD.","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 8","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9852576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 3

Studies on the synthesis, spectroscopy, thermal properties, docking, and biology of new Schiff base and its mono- and binuclear complexes 新型希夫碱及其单核和双核配合物的合成、光谱学、热性质、对接和生物学研究

IF 2.7 4区生物学

Journal of Molecular Recognition Pub Date : 2023-05-23 DOI: 10.1002/jmr.3026

Khlood Abou-Melha

{"title":"Studies on the synthesis, spectroscopy, thermal properties, docking, and biology of new Schiff base and its mono- and binuclear complexes","authors":"Khlood Abou-Melha","doi":"10.1002/jmr.3026","DOIUrl":"10.1002/jmr.3026","url":null,"abstract":"A novel Schiff base has been synthesized from the condensation of the 3-formyl-2-hydroxybenzoic acid and 4-nitrobenzene-1,2-diamine. The new ligand was found to have two coordination sites. So, it has the capability to form mono- and binuclear complexes with different metal ions. The free ligand and its mono- and binuclear cobalt(II) complexes have been characterized by UV–Visible spectra, IR, elemental analyzes, H1 NMR, conductimetric, thermal, and magnetic measurements. Results indicated that the cobalt(II) ion is attached to the inside coordination site and the second metal ion attached to the outside coordination site. The complexes are all non-electrolytes, as demonstrated by the molar conductance tests. The thermodynamic parameters of the metal complexes are calculated using Horowitz Metzger and Coats-Redfern methods. The complexes' bonding properties have also been estimated. Molecular docking was employed to forecast the interaction of the prepared with the Candida-albicans receptor (1zap). The biological activities of these metal complexes were tested against some bacteria and fungi. It is evident from the biological screening data that the prepared Co(II) binuclear complexes exhibit predominant activity against Candida albicans, Penicillium oxalicum and Escherichia coli, while they have no activity against Micrococcus roseus and Micrococcus luteus.","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 7","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9678867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 1