Stepwise prediction and statistical screening: B-cell epitopes on neuraminidase of human avian H5N1 virus

The B-cell epitopes of virus are associated with the antiviral drug and the vaccine screening. As the nucleotide sequences of neuraminidase （NA） of stain GD-01-06 were sequenced, we predicted the a-helix and β-fold structure and the indexes of the flexible regions of secondary structure of NA with methods of the Hydrophilicity plot by Kyte-Doolittle, the Surface probability plot by Emini and the An- tigenic index by Jameson-Wolf, and then screened statistically the parameters to predict B-cell epi- topes by the Hierarchical cluster and the Bivariate correlation and the quartiles with SPSS 13.0. The impact of variation of amino acids in NA on its epitopes was analyzed. The predictive results were evaluated by Wu＇s Antigenic Index and SWISS-MODEL. We found that the most possible epitopes on NA were located within or nearby its N-terminal Nos. 120--137, 81--84, 408--415, 273--282, 429--432, 356--368, 46--55, 146--155, 341 --350 and 198--209, which were the dominant regions of NA epitopes. Peptide 120--137 including the glycoprotein domain （NGT126 128） was first chosen as the B-cell epitopes on NA. NA in H5N1 strain isolated after 2003 lacked in No. 53 amino acid （I）, resulting in an increase in the surface flexible region of NA in GD-01-06 and an enlargement to their epitope regions （VEP48-48→ VEPISNTNFL46-55）. Conclusively, prediction of the B-cell epitopes on the NA based on multiple pa- rameters is useful for researches on the molecular immunology and drug screening and immuno-prophylaxis. A deletion of No. 53 amino acid （I） in NA in strain GD-01-06 might increase its anti- genicity.     

环己烯类神经氨酸酶抑制剂的三维定量构效关系研究

环己烯类神经氨酸酶抑制剂是目前效果最好的流感病毒抑制剂.选取26个典型的环己烯类神经氨酸酶抑制剂,应用比较分子力场分析(CoMFA)方法,研究它们与神经氨酸酶(NA)的相互作用,建立了环己烯类NA抑制剂与NA的三维定量构效关系(3D-QSAR)模型.该模型的最佳非交叉验证系数R2为0.991,交叉验证系数R2cv为0.760,检测值F为521.53,标准偏差SEE为0.098,立体场、静电场的贡献分别为74.6%、25.4%,最佳主成分为4,这表明模型具有很强的稳定性和预测能力.用该模型对随机挑选的3个化合物进行预测,得到了满意的结果.     

Antigenic epitope peptides of influenza H3N2 virus neuraminidase gene based on experiments

The neuraminidase (NA) in viral surface is one of the main subtype-specific antigen of influenza type A viruses.Neuraminidase is an enzyme to break the bonds between hemagglutinin (HA) and sialic acid to release newly formed viruses from infected cells.In this study,the H3N2 subtype virus NA genes were sequenced and NA proteins were screened for B-cell epitopes and assessed based on immunoinformatics.Based on this results,four peptides DR6,EY7,VG8 and RE8 (covering amino acid residues 151-156,368-374,398-405 and 428-435,respectively) of the NA protein were synthesized artificially.These peptides were used to immunize New Zealand rabbits subcutaneously to raise antisera.Experimental results showed that these four peptides were capable of eliciting antibodies against H3N2 viruses in a specific and sensitive feature,detected in vitro by enzyme-linked immunosorbent assay.Moreover,hemadsorption anti-releasing effects took place in three three-antisera-mixtures at a dilution of 1:40.Alignment using NA gene database showed that amino acid residues in these four epitope peptides were substituted at specific sites in all the NAs sequenced in this study.It was suggested that these NA epitope peptides might be used in combination with HA proteins as vaccine antigens.     

Molecular simulation study of the binding mechanism of [α-PTi<Subscript>2</Subscript>W<Subscript>10</Subscript>O<Subscript>40</Subscript>]<Superscript>7−</Superscript> for its promising broad-spectrum inhibitory activity to FluV-A neuraminidase

Polyoxometalate (POM) has promising antiviral activities. It shows broad-spectrum inhibiting ability, high efficiency, and low tox-icity. Experimental assays show that titanium containing polyoxotungstates have anti-influenza-virus activity. In this paper, the bind-ing mechanisms of five isomers of di-Ti-substituted polyoxotungstate, [α-1,2-PTi₂W₁₀O₄₀]^7– (α-1,2), [α-1,6-PTi₂W₁₀O₄₀]^7– (α-1,6), [α-1,5-PTi₂W₁₀O₄₀]^7– (α-1,5), [α-1,4-PTi₂W₁₀O₄₀]^7– (α-1,4) and [α-1,11-PTi₂W₁₀O₄₀]^7– (α-1,11), to five subtypes of influenza virus A neuraminidase (FluV-A NA) were investigated in the context of aqueous solution by using molecular docking and molecular dynamics studies. The results show that the isomer α-1,2 is superior to other isomers as a potential inhibitor to neuraminidase. The positively charged arginine residues around the active site of NA could be induced by negatively charged POM to adapt themselves and could form salt bridge interactions and hydrogen bond interactions with POM. The binding free energies of POM/NA complexes range from –5.36 to –8.31 kcal mol^–1. The electrostatic interactions are found to be the driving force during the binding process of POM to NA. The conformational analysis shows that POM tends to bind primarily with N1 and N8 at the edge of the active pocket, which causes the conformational change of the pincers structure comprising residue 347 and loop 150. Whereas, the active pockets of N2, N9 and N4 are found to be more spacious, which allows POM to enter into the active pockets directly and anchor there firmly. This study shows that negatively charged ligand as POM could induce the reorganization of the active site of NA and highlights POM as a promising inhibitor to NA despite the ever increasing mutants of NA.     

Stepwise prediction and statistical screening:B-cell epitopes on neuraminidase of human avian H_5N_1 virus

The B-cell epitopes of virus are associated with the antiviral drug and the vaccine screening. As the nucleotide sequences of neuraminidase (NA) of stain GD-01-06 were sequenced, we predicted the α-helix and β-fold structure and the indexes of the flexible regions of secondary structure of NA with methods of the Hydrophilicity plot by Kyte-Doolittle, the Surface probability plot by Emini and the Antigenic index by Jameson-Wolf, and then screened statistically the parameters to predict B-cell epitopes by the Hierarchical cluster and the Bivariate correlation and the quartiles with SPSS 13.0. The impact of variation of amino acids in NA on its epitopes was analyzed. The predictive results were evaluated by Wu’s Antigenic Index and SWISS-MODEL. We found that the most possible epitopes on NA were located within or nearby its N-terminal Nos. 120―137, 81―84, 408―415, 273―282, 429―432, 356―368, 46―55, 146―155, 341―350 and 198―209, which were the dominant regions of NA epitopes. Peptide 120―137 including the glycoprotein domain (NGT126―128) was first chosen as the B-cell epitopes on NA. NA in H5N1 strain isolated after 2003 lacked in No. 53 amino acid (I), resulting in an increase in the surface flexible region of NA in GD-01-06 and an enlargement to their epitope regions (VEP46―48→ VEPISNTNFL46―55). Conclusively, prediction of the B-cell epitopes on the NA based on multiple parameters is useful for researches on the molecular immunology and drug screening and immuno-prophylaxis. A deletion of No. 53 amino acid (I) in NA in strain GD-01-06 might increase its antigenicity.     

黄酮类神经氨酸酶抑制剂的QSAR研究

HQSAR、CoMFA和CoMSIA用于研究38个黄酮类神经氨酸酶抑制剂（NIs）的定量-结构活性关系（QSAR）,控制其抑制神经氨酸酶（NA）的生物活性,为新药设计提供理论依据和参考信息．HQSAR建模获得R^2、Q^2、Rtest^2和Qext^2分别为0.881、0．834、0．918和0．831．基于药效团叠合,进行CoMFA和CoMSIA建模分析,得到模型的R^2、Q^2、Rtext^2和Qext^2分别为0．988和0．978,0．741和0．802,0．697和0．643,0．604和0．580．而且,氢键对活性的贡献最大,其次是疏水、静电和立体因素．HQSAR结果与CoMFA和CoMSIA结果一致．     

神经氨酸苷酶抑制剂研究进展

神经氨酸苷酶(NA)是流感病毒的一种主要表面糖蛋白,在病毒致病过程中起重要作用.本文对以NA为药物靶点,设计的各种NA抑制剂作以综述.     

Special features of the 2009 pandemic swine-origin influenza A H1N1 hemagglutinin and neuraminidase

Since the 2009 pandemic H1N1 swine-origin influenza A virus (09 S-OIV) has reminded the world about the global threat of the ever changing influenza virus,many questions regarding the detailed re-assortment of influenza viruses yet remain unanswered.Influenza A virus is the causative agent of the pandemic flu and contains 2 major antigenic glycoproteins on its surface:(i) hemagglutinin (HA);and (ii) neuraminidase (NA).The structures of the 09 S-OIV HA and NA proteins (09H1 and 09N1) have recently been resolved in our laboratory and provide some clues as to why the 09 S-OIV re-assortment virus is highly infectious with severe consequences in humans.For example,the 09H1 is highly similar to the HA of the 1918 influenza A pandemic virus in overall structure and especially in regards to its 5 defined antibody binding epitopes.For 09N1,its most distinctive feature is the lack of a 150-loop active site cavity,which was previously predicted to be present in all N1 NAs,and we hypothesize that the 150-loop may play a important role in the substrate specificity (α2,3 or α2,6 linked sialic acid receptors) and enzymatic mechanism of influenza NA.Combination of the HA and NA with special characteristics for the 09 S-OIV might contribute to its high increased transmissibility in humans.     

Trypanosoma cruzi: metabolic labeling of trypomastigote sialoglycolipids

Summary Trypomastigote forms (infective) ofTrypanosoma cruzi incorporate (³H)-palmitic acid and D-(³H)-galactose into glycolipids. Palmitic acid-labeled acidic glycolipids were partially hydrolyzed with neuraminidase. The labeling of these compounds when the intact cell surface was labeled with galactose oxidase plus NaB³H₄ indicates the membrane location of the sialoglycolipids.This investigation received financial support from SECYT and CONICET to RML; CNPq, FINEP, and UNDP/World Bank/ WHOSSpecial Programme for Research and Training in Tropical Diseases to WC; and FAPESP to BZ and WC. ASC is a fellow from FAPESP.