{"title":"Modeling disruption of Apis mellifera (honey bee) odorant-binding protein function with high-affinity binders","authors":"Berin Karaman Mayack","doi":"10.1002/jmr.3008","DOIUrl":"10.1002/jmr.3008","url":null,"abstract":"<p>Chemical toxins pose a great threat to honey bee health because they affect memory and cognition, diminish immunity, and increase susceptibility to infection, resulting in decreased colony performance, reproduction, and survival. Although the behavioral effects of sub-lethal chemical exposure on honey bees have been intensively studied, how xenobiotics affect olfaction, at the molecular level, still needs to be elucidated. In the present work, in silico tools, such as molecular docking, binding free energy calculations, and molecular dynamics simulations are used to predict if environmental chemicals have stronger binding affinities to honey bee antennal odorant-binding protein 14 (OBP14) than the representative floral odors citralva, eugenol, and the fluorescent probe 1-<i>N</i>-phenylnaphthylamine. Based on structural analysis, 21 chemicals from crop pesticides, household appliances, cosmetics, food, public health-related products, and other sources, many of which are pervasive in the hive environment, have higher binding affinities than the floral odors. These results suggest that chemical exposures are likely to interfere with the honey bee's sense of smell and this disruptive mechanism may be responsible for the lower associative learning and memory based on olfaction found in bees exposed to pesticides. Moreover, bees mainly rely on olfactory cues to perceive their environment and orient themselves as well as to discriminate and identify their food, predators, nestmates, and diseased individuals that need to be removed with hygienic behavior. In summary, sub-lethal exposure to environmental toxins can contribute to colony collapse in several ways from the disruption of proper olfaction functioning.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 5","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9731491","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}
{"title":"An immunoinformatics and structural vaccinology study to design a multi-epitope vaccine against Staphylococcus aureus infection","authors":"Rahul Chatterjee, Soumya Ranjan Mahapatra, Jyotirmayee Dey, Kiran Raj Takur, Vishakha Raina, Namrata Misra, Mrutyunjay Suar","doi":"10.1002/jmr.3007","DOIUrl":"10.1002/jmr.3007","url":null,"abstract":"<p><i>Staphylococcus aureus</i> has been widely reported to be majorly responsible for causing nosocomial infections worldwide. Due to an increase in antibiotic-resistant strains, the development of an effective vaccine against the bacteria is the most viable alternative. Therefore, in the current work, an effort has been undertaken to develop a novel peptide-based vaccine construct against <i>S aureus</i> that can potentially evoke the B and T cell immune responses. The fibronectin-binding proteins are an attractive target as they play a prominent role in bacterial adherence and host cell invasion and are also well conserved among rapidly mutating pathogens. Therefore, highly immunogenic linear B lymphocytes (LBL), cytotoxic T lymphocytes (CTL), and helper T lymphocytes (HTL) epitopes were identified from the antigenic fibronectin-binding proteins A and B (FnBPA and FnBPB) of <i>S aureus</i> using immunoinformatics approaches. The selected peptides were confirmed to be non-allergenic, non-toxic, and with a high binding affinity to the majority of human leukocyte antigens (HLA) alleles. Consequently, the multi-peptide vaccine construct was developed by fusing the screened epitopes (three LBL, five CTL, and two HTL) together with the suitable adjuvant and linkers. In addition, the tertiary conformation of the peptide construct was modeled and later docked to the Toll-like receptor 2. Subsequently, a molecular dynamics simulation of 100 ns was employed to corroborate the stability of the designed vaccine-receptor complex. Besides exhibiting high immunogenicity and conformational stability, the developed vaccine was observed to possess wide population coverage of 99.51% worldwide. Additional in vivo and in vitro validation studies would certainly corroborate the designed vaccine construct to have improved prophylactic efficacy against <i>S aureus</i>.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 4","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9117017","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}
Jianping Shu, Juelin Li, Shaozhou Wang, Jing Lin, Li Wen, Haiyang Ye, Peng Zhou
{"title":"Systematic analysis and comparison of peptide specificity and selectivity between their cognate receptors and noncognate decoys","authors":"Jianping Shu, Juelin Li, Shaozhou Wang, Jing Lin, Li Wen, Haiyang Ye, Peng Zhou","doi":"10.1002/jmr.3006","DOIUrl":"10.1002/jmr.3006","url":null,"abstract":"<p>Protein–peptide interactions (PpIs) play an important role in cell signaling networks and have been exploited as new and attractive therapeutic targets. The affinity and specificity are two unity-of-opposite aspects of PpIs (and other biomolecular interactions); the former indicates the absolute binding strength between the peptide ligand and its cognate protein receptor in a PpI, while the latter represents the relative recognition selectivity of the peptide ligand for its cognate protein receptor in a PpI over those noncognate decoys that could be potentially encountered by the peptide in cell. Although the PpI binding affinity has been widely investigated over the past decades, the peptide recognition specificity (and selectivity) still remains largely unexplored to date. In this study, we classified PpI specificity into three types: (i) class-I specificity: peptide selectivity for its cognate wild-type protein receptor over the noncognate mutant decoys of this receptor, (ii) class-II specificity: peptide selectivity for its cognate protein receptor over other noncognate decoys that are homologous with this receptor, and (iii) class-III specificity: peptide selectivity for its cognate protein receptor over other noncognate decoys that are the cognate receptors of other peptides. We performed affinity and selectivity analysis for the three types of PpI specificity and revealed that the PpIs generally exhibit a moderate or modest specificity; peptide selectivity increases in the order: class-I < class-II < class-III. All the three types of PpI specificity were observed to have no statistically significant correlation with peptide length and hydrophobicity, but the class-I and class-II specificities can be influenced considerably by peptide secondary structures; the high specificity is preferentially associated with ordered structure types as compared to undefined structure types. In addition, the mutation distribution (for class-I specificity), sequence conservation (for class-II specificity), and structural similarity (for class-III specificity) seem also to address effects on peptide selectivity.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2022-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9402956","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}
{"title":"Interactions between polycyclic musks and human lactoferrin: Multi-spectroscopic methods and docking simulation","authors":"Mengjie Shi, Jinfeng He, Minhua Xu, Xiaolian Lin, Hongyan Liu, Tiemin Jiang, Zhongsheng Yi","doi":"10.1002/jmr.3005","DOIUrl":"10.1002/jmr.3005","url":null,"abstract":"<p>Galaxolide (1,3,4,6,7,8-hexahydro-4,6,6,7,8-hexamethylcyclopenta-γ-2-benzopyrane; HHCB) and Tonalide (7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4-tetrahydronaphthalene; AHTN) are “pseudo-persistent” pollutants that can cause DNA damage, endocrine disruption, organ toxicity, and reproductive toxicity in humans. HHCB and AHTN are readily enriched in breast milk, so exposure of infants to HHCB and AHTN is of concern. Here, the molecular mechanisms through which HHCB and AHTN interact with human lactoferrin (HLF) are investigated using computational simulations and spectroscopic methods to identify indirectly how HHCB and AHTN may harm infants. Molecular docking and kinetic simulation studies indicated that HHCB and AHTN can interact with and alter the secondary HLF structure. The fluorescence quenching of HLF by HHCB, AHTN was static with the forming of HLF-HHCB, HLF-AHTN complex, and accompanied by non-radiative energy transfer and that 1:1 complexes form through interaction forces. Time-resolved fluorescence spectroscopy indicated that binding to small molecules does not markedly change the HLF fluorescence lifetime. Three-dimensional fluorescence spectroscopy indicated that HHCB and AHTN alter the peptide chain backbone structure of HLF. Ultraviolet-visible absorption spectroscopy, simultaneous fluorescence spectroscopy, Fourier-transform infrared spectroscopy, and circular dichroism spectroscopy indicated that HHCB and AHTN change the secondary HLF conformation. Antimicrobial activity experiments indicated that polycyclic musks decrease lactoferrin activity and interact with HLF. These results improve our understanding of the mechanisms involved in the toxicities of polycyclic musks bound to HLF at the molecular level and provide theoretical support for mother-and-child health risk assessments.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 4","pages":""},"PeriodicalIF":2.7,"publicationDate":"2022-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9471020","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}
Esra Palabıyık, Ayşe Nurseli Sulumer, Handan Uguz, Bahri Avcı, Seda Askın, Hakan Askın, Yeliz Demir
{"title":"Assessment of hypolipidemic and anti-inflammatory properties of walnut (Juglans regia) seed coat extract and modulates some metabolic enzymes activity in triton WR-1339-induced hyperlipidemia in rat kidney, liver, and heart","authors":"Esra Palabıyık, Ayşe Nurseli Sulumer, Handan Uguz, Bahri Avcı, Seda Askın, Hakan Askın, Yeliz Demir","doi":"10.1002/jmr.3004","DOIUrl":"10.1002/jmr.3004","url":null,"abstract":"<p>Atherosclerosis and cognitive impairment are both influenced by hyperlipidemia. Due to their high margin of safety and low cost, natural chemicals have recently attracted particular attention in the context of the treatment of disease. Hence, the purpose of this study was to investigate the possible amendatory impact of ethanol extract walnut (<i>Juglans regia</i>) seed coat (E-WSC) on some metabolic enzymes (glutathione reductase (GR), paraoxonase-1 (PON1), aldose reductase (AR), sorbitol dehydrogenase (SDH), acetylcholinesterase (AChE), glutathione S-transferase (GST), and butyrylcholinesterase (BChE)) activity in the liver, kidney, and heart of rats with Triton WR-1339-induced hyperlipidemia. Rats were divided into five groups: control group, HL-Control group (Triton WR-1339 400 mg/kg, i.p administered group), E- WSC + 150 (150 mg/kg,o.d given group), E- WSC + 300 (E- WSC 300 mg/kg, o.d given group) and HL+ E-WSC + 300 (Group receiving E- WSC 300 mg/kg, o.d 30 min prior to administration of Triton WR-1339 400 mg/kg, i.p). In HL-Control, AR, SDH, and BChE enzyme activity was significantly increased in all tissues compared to the control, while the activity of other studied enzymes was significantly decreased. The effects of hyperlipidemia on balance were improved and alterations in the activity of the investigated metabolic enzymes were prevented by E-WSC. As a result, promising natural compounds that can be used as adjuvant therapy in the treatment of cognitive disorders and hyperlipidemia may be found in E-WSC powder.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2022-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10855509","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}
{"title":"Insights into the interaction between the kusaginin and bovine serum albumin: Multi-spectroscopic techniques and computational approaches","authors":"Fengwen Huang, Chen Chen","doi":"10.1002/jmr.3003","DOIUrl":"10.1002/jmr.3003","url":null,"abstract":"Kusaginin, as a phenylethanoid glycoside, which has exhibited wide antioxidant and antimicrobial properties. The molecular mechanism underlying the broad biological activities of kusaginin has not yet been well documented. In this paper, the interaction of kusaginin with bovine serum albumin (BSA) has been explored by fluorescence spectra, UV‐vis absorption spectra, and circular dichroism (CD) spectra along with computational approaches. The fluorescence experiments showed that kusaginin could strongly quench the intrinsic fluorescence of BSA through both dynamic and static quenching mechanisms. The thermodynamic analysis suggested that hydrophobic force was the main force in stabilizing the BSA‐kusaginin complex. In addition, conformation changes of BSA were observed from three‐dimensional and synchronous fluorescence spectra, UV spectra, and CD spectra under experimental conditions. All these experimental results have been complemented and validated by the molecular docking and dynamic simulation studies, which revealed that kusaginin was bound on the hydrophobic cavity in subdomain IIA of BSA and formed a stable BSA‐kusaginin complex. Finally, density functional theory (DFT) calculation further implied that hydrogen bonds also support stabilizing the BSA‐kusaginin complex. This research may aid in understanding the pharmacological characteristics of kusaginin and provide a vital reference modeling for the design of analogues drugs.","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9401383","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}
{"title":"Lipase activity inhibited by aloenin A: Glycoside from Aloe vera (L.) Burm. f.—In vitro and molecular docking studies","authors":"Neha Deora, Krishnan Venkatraman","doi":"10.1002/jmr.3002","DOIUrl":"10.1002/jmr.3002","url":null,"abstract":"<p>Obesity is taking over many parts of the world and has been identified as the second leading cause of preventable death, with a dramatic increase in prevalence over the last two decades. Pancreatic <i>lipase</i> is a lipid-digesting enzyme that plays an important role in fat metabolism. Inhibiting pancreatic <i>lipase</i> is an attractive target for obesity treatment. Phytochemicals or bioactive compounds/extracts isolated from medicinal plants offer a promising platform for the development of pancreatic <i>lipase</i> inhibitors. This study aims to characterize and investigate the effect of aloenin A, glycoside found in <i>Aloe vera</i>, as a possible inhibitor of pancreatic <i>lipase</i> in vitro and in silico. <i>A. vera</i> extract had an IC50 value of 0.5472 μg/ml, whereas aloenin A had an IC50 value of 14.95 μg/mL and was found to inhibit in a competitive manner. These findings were supported by molecular docking studies, which revealed that aloenin A binds to the substrate binding site with a binding energy of − 7.16 kcal/mol, and this binding site is stabilized by three hydrogen bonds contributed by Phe<sup>77</sup> and Asp<sup>79</sup>. Our findings suggest that the anti-hyperlipidemic effects of <i>A. vera</i> on pancreatic <i>lipase</i> can be attributed in part to the presence of aloenin A.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2022-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10751645","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}
{"title":"Investigations of interaction mechanism and conformational variation of serum albumin affected by artemisinin and dihydroartemisinin","authors":"Rukui Zhu, Yu Liang, Huajian Luo, Huishan Cao, Yi Liu, Shan Huang, Qi Xiao","doi":"10.1002/jmr.3000","DOIUrl":"10.1002/jmr.3000","url":null,"abstract":"<p>In this work, binding interactions of artemisinin (ART) and dihydroartemisinin (DHA) with human serum albumin (HSA) and bovine serum albumin (BSA) were investigated thoroughly to illustrate the conformational variation of serum albumin. Experimental results indicated that ART and DHA bound strongly with the site I of serum albumins via hydrogen bond (H-bond) and van der Waals force and subsequently statically quenched the intrinsic fluorescence of serum albumins through concentration-dependent manner. The quenching abilities of two drugs on the intrinsic fluorescence of HSA were much higher than the quenching abilities of two drugs on the intrinsic fluorescence of BSA. Both ART and DHA, especially DHA, caused the conformational variation of serum albumins and reduced the <i>α</i>-helix structure content of serum albumins. DHA with hydrophilic hydroxyl group bound with HSA more strongly, suggesting the important roles of the chemical polarity and the hydrophilicity during the binding interactions of two drugs with serum albumins. These results reveal the molecular understanding of binding interactions between ART derivatives and serum albumins, providing vital information for the future application of ART derivatives in biological and clinical areas.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2022-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9209486","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}
G. Pandimeena, T. Mathavan, E. James Jebaseelan Samuel, A. Milton Franklin Benial
{"title":"Quantum chemical, spectroscopic and molecular docking investigations of potential pulmonary fibrosis drug methyl 2-chloro 4-iodonicotinate","authors":"G. Pandimeena, T. Mathavan, E. James Jebaseelan Samuel, A. Milton Franklin Benial","doi":"10.1002/jmr.3001","DOIUrl":"10.1002/jmr.3001","url":null,"abstract":"<p>In this work, the methyl 2-chloro 4-iodonicotinate (MCIN) was investigated to study the structural, spectroscopic and electronic properties using density functional theory (DFT) quantum chemical calculations. The most stable structure of MCIN was optimized by DFT/B3LYP method with a LanLD2Z basis set. The optimized parameters and vibrational wavenumbers were determined. The vibrational task of the molecule was done by potential energy distribution calculations. The <sup>13</sup>C NMR spectrum of the MCIN molecule was simulated by the Gauge-Invariant-Atomic Orbital method using a dimethyl sulfoxide solution and the isotropic chemical shift values of the molecule were calculated and observed. Ultraviolet-visible spectra were simulated and observed. The pharmaceutical activity was predicted using frontier molecular orbital and natural bond orbital analysis. The reactive sites of the MCIN molecule were determined using Mulliken atomic charge distribution, molecular electrostatic potential surface and the local reactivity analysis. The molecular docking analysis confirms that the title molecule can be used in drug design for the treatment of pulmonary fibrosis.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2022-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9294595","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}
{"title":"Systematic analysis to identify novel disease indications and plausible potential chemical leads of glutamate ionotropic receptor NMDA type subunit 1, GRIN1","authors":"Tulika Bhardwaj, Irshad Ahmad, Pallavi Somvanshi","doi":"10.1002/jmr.2997","DOIUrl":"10.1002/jmr.2997","url":null,"abstract":"<p>Schizophrenia is a mental illness affecting the normal lifestyle of adults and early adolescents incurring major symptoms as jumbled speech, involvement in everyday activities eventually got reduced, patients always struggle with attention and memory, reason being both the genetic and environmental factors responsible for altered brain chemistry and structure, resulting in schizophrenia and associated orphan diseases. The network biology describes the interactions among genes/proteins encoding molecular mechanisms of biological processes, development, and diseases. Besides, all the molecular networks, protein-protein Interaction Networks have been significant in distinguishing the pathogenesis of diseases and thereby drug discovery. The present meta-analysis prioritizes novel disease indications viz. rare and orphan diseases associated with target Glutamate Ionotropic Receptor NMDA Type Subunit 1, GRIN1 using text mining knowledge-based tools. Furthermore, ZINC database was virtually screened, and binding conformation of selected compounds was performed and resulted in the identification of Narciclasine (ZINC04097652) and Alvespimycin (ZINC73138787) as potential inhibitors. Furthermore, docked complexes were subjected to MD simulation studies which suggests that the identified leads could be a better potential drug to recuperate schizophrenia.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"36 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2022-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10654222","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}