In silico identification of potential antigenic proteins and promiscuous CTL epitopes in Mycobacterium tuberculosis

Cell-mediated immunity is critical for the control of Mycobacterium tuberculosis infection. We hypothesized that those proteins of M. tuberculosis (MTB) that do not have homologs in humans as well as human gut flora, would mount a good antigenic response in man, and employed a bioinformatics approach to identify MTB antigens capable of inducing a robust cell-mediated immune response in humans. In the first step we identified 624 MTB proteins that had no homologs in humans. Comparison of this set of proteins with the proteome of 77 different microbes that comprise the human gut flora narrowed down the list to 180 proteins unique to MTB. Twenty nine of the 180 proteins are known to be associated with dormancy. Since dormancy associated proteins are known to harbor CTL epitopes, we selected four representative unique proteins and subjected them to epitope analysis using ProPred1. Nineteen novel promiscuous epitopes were identified in the four proteins. Population coverage for 7 of the 19 shortlisted epitopes including Rv3852 (58-KPAEAPVSL, 112-VPLIVAVTL, 118-VTLSLLALL and 123-LALLLIRQL), Rv2706c (66-RPLSGVSFL) Rv3466 (8- RIVEVFDAL and 38-RSLERLECL) was >74%. These novel promiscuous epitopes are conserved in other virulent MTB strains, and can therefore be further investigated for their immunological relevance and usefulness as vaccine candidates.     

The effect of Mycobacterium tuberculosis CRISPR-associated Cas2 (Rv2816c) on stress response genes expression,morphology and macrophage survival of Mycobacterium smegmatis

Clustered regularly interspaced short palindromic repeats (CRISPR) are present in the genome of 40% bacteria and 90% archaea. CRISPR and accompanying Cas proteins constitute an adaptive immune system against disruptive mobile genetic elements. Two CRISPRs and 9 genes encoding CRISPR-associated proteins have been found in the genome of Mycobacterium tuberculosis. The CRISPR-associated Cas2 is an endoribonuclease required for the acquisition of new spacers. In this study, Cas2 encoded by Rv2816c was expressed in Mycobacterium smegmatis lacking CRISPR-Cas system and its role in stress responses of M. smegmatis in vitro and within macrophages was studied. We found that Cas2 mediated M. smegmatis stress response changes were associated with the altered expression of sigma factors which involved in mycobacterial stress response and virulence. We also found that Cas2 decreased the survival of M. smegmatis within macrophages. This study provides new insights on the role of Cas2.     

Epitope based recombinant BCG vaccine elicits specific Th1 polarized immune responses in BALB/c mice

Developing an efficacious vaccine is one of the highest priorities in tuberculosis research. A vaccine based on T cell epitopes representing multiple antigens is an ideal approach to generate effective cellular immunity against the disease. In the present study, we have selected four T cell epitopes from four well defined Mycobacterium tuberculosis antigens, Ag85C (Rv2903c), 10-kDa culture filtrate protein (CFP-10) (Rv3874), PPE68 (Rv3873) and INV (Rv1478). The epitope encoding genes were grafted into a Cpn 10 based epitope delivery system. The cpn 10-epitope chimeras were further cloned and expressed in BCG to obtain four rBCGs (BCG::CFP, BCG::FBP, BCG::PPE and BCG::INV). Both cellular and humoral immune responses induced by these r-BCG strains were evaluated in BALB/c mice after subcutaneous injection of a single dose of 1×10(6)CFU of the individual rBCGs. Compared to the parent BCG immunized animals the splenocytes derived from rBCG vaccinated groups showed greater antigen specific proliferation, characterized with higher IFN-γ response and reduced IL-4 secretion. Also rBCG vaccination was able to induce specific humoral immune response with an enhanced IgG2a/IgG1 ratio. The rBCGs therefore favor an epitope specific Th1 type response, which is known to be important for mycobacterial immunity. Further when two of the rBCGs (BCG::CFP and BCG::FBP) were tested for their protective efficacy both the rBCGs were comparable to BCG in a H37Rv challenge study performed in guinea pigs.     

Synthesis, characterisation and biological activity of novel 4-thiazolidinones, 1,3,4-oxadiazoles and some related compounds

Two novel series of 4-thiazolidinone derivatives, namely 2-substituted-3-([4-(4-methoxybenzoylamino)benzoyl]amino)-4-thiazolidinones (7a-e) and 2-[4-(4-methoxybenzoylamino)benzoylhydrazono]-3-alkyl-4-thiazolidinones (5a-c) together with 2-[4-(4-methoxybenzoylamino)phenyl]-5-(substituted phenyl)amino-1,3,4-oxadiazoles (6a-c) have been synthesised as title compounds. N(1)-[4-(4-methoxybenzoylamino)benzoyl]-N(2)-substituted methylene hydrazines (3a-e) and 1-[4-(4-methoxybenzoylamino)benzoyl]-4-substituted phenyl thiosemicarbazides (4a-f) were also prepared and used as intermediate to give the title compounds. All synthesised compounds were screened for their antimycobacterial activity against Mycobacterium tuberculosis H37Rv and antimicrobial activities against various bacteria and fungi. Compounds 7a and 7b were found as the most active derivatives demonstrating 90 and 98% inhibition of mycobacterial growth of M. tuberculosis H37Rv in the primary screen at 6.25 microg mL(-1), respectively. However, level II assay revealed that the MIC values were not less than 6.25 microg mL(-1). None of the compounds showed significant antimicrobial activity against the microorganisms used whereas 3a and 7a inhibited the growth of several bacteria and fungi.     

Overview on mechanisms of isoniazid action and resistance in Mycobacterium tuberculosis

Isoniazid (INH) is one of the most active compounds used to treat tuberculosis (TB) worldwide. In addition, INH has been used as a prophylactic drug for individuals with latent Mycobacterium tuberculosis (MTB) infection to prevent reactivation of disease. Importantly, the definition of multidrug resistance (MDR) in TB is based on the resistance of MTB strains to INH and rifampicin (RIF). Despite its simple chemical structure, the mechanism of action of INH is very complex and involves several different concepts. Many pathways pertaining to macromolecular synthesis are affected, notably mycolic acid synthesis. The pro-drug INH is activated by catalase-peroxidase (KatG), and the active INH products are targeted by enzymes namely, enoyl acyl carrier protein (ACP) reductase (InhA) and beta-ketoacyl ACP synthase (KasA). In contrast, INH is inactivated by arylamine N-acetyltransferases (NATs). Consequently, the molecular mechanisms of INH resistance involve several genes in multiple biosynthetic networks and pathways. Mutation in the katG gene is the major cause for INH resistance, followed by inhA, ahpC, kasA, ndh, iniABC,fadE, furA, Rv1592c and Rv1772. The recent association of efflux genes with INH resistance has also gained considerable attention. Interestingly, substitutions have also been observed in nat, fabD, and accD recently in resistant isolates. Understanding the mechanisms operating behind INH action and resistance would enable better detection of INH resistance. This information would aid novel drug design strategies. Herein we review all mechanisms known to potentially contribute to the complexity of INH action and mechanisms of resistance in MTB, with insights into methods for detection of INH resistance as well as their limitations.     

Elicitation of efficient, protective immune responses by using DNA vaccines against tuberculosis

DNA vaccination is an effective method for elicitation of strong humoral as well as cellular immune responses. DNA vaccines expressing mycobacterial antigens ESAT-6 (Rv3875), alpha-crystallin (Rv2031c) and superoxide dismutase A (Rv3846) were evaluated for their immune responses in Balb/c mice and protective efficacy in guinea pigs. Immunization of mice with the DNA vaccines expressing superoxide dismutase A and alpha-crystallin resulted in markedly higher levels of IFN-gamma as compared to the levels of IL-10. The DNA vaccine expressing ESAT-6 elicited a mixed Th1/Th2 response. Immunization of guinea pigs with these DNA vaccines and subsequent challenge of animals with Mycobacterium tuberculosis H(37)Rv, showed that DNA vaccine expressing superoxide dismutase imparted the maximum protection as observed by a 50 and 10 folds reduction in bacillary load in spleens and lungs, respectively, in comparison to immunization with vector control.     

A regio- and stereoselective 1,3-dipolar cycloaddition for the synthesis of novel spiro-pyrrolothiazolyloxindoles and their antitubercular evaluation

The 1,3-dipolar cycloaddition of azomethine ylides derived from substituted isatins and 1,3-thiazolane-4-carboxylic acid to a series of 2-(arylmethylene)-2,3-dihydro-1H-inden-1-ones afforded twenty nine novel spiro-pyrrolothiazolyloxindoles regio- and stereoselectively in moderate yields. These compounds were screened for their in vitro activity against Mycobacterium tuberculosis H37Rv (MTB) using agar dilution method. Among 29 compounds screened, spiro[5.3']-5'-nitrooxindole-spiro-[6.3″]-2,3-dihydro-1H-inden-1″-one-7-(2,3-dichlorophenyl)tetrahydro-1H-pyrrolo[1,2-c][1,3]thiazole, was found to be the most active compound with MIC of 2.8?μM against MTB, being 1.67 and 2.70 times more active than ciprofloxacin and ethambutol respectively.     

Synthesis, antimicrobial, antimycobacterial and structure-activity relationship of substituted pyrazolo-, isoxazolo-, pyrimido- and mercaptopyrimidocyclohepta[b]indoles

A new class of heterocycles, specifically substituted pyrazolo-, isoxazolo- and pyrimidocyclohepta[b]indoles, has been prepared by condensation of substituted 7-(hydroxymethylene)-7,8,9,10-tetrahydrocyclohepta[b]indol-6(5H)-ones with hydrazine hydrate, hydroxylamine hydrochloride, phenylhydrazine, urea and thiourea, respectively. The structures of the compounds were established by IR, (1)H NMR, (13)C NMR, mass spectral analysis, X-ray diffraction, and the compounds have been screened for in?vitro antimicrobial and antimycobacterial against Mycobacterium tuberculosis H37Rv (MTB). Among the compounds screened, five substances were found to have an MIC of 3.12?μg/ml or greater against MTB. Structure-activity relationship (SAR) analyses and in silico drug relevant properties (HBD, HBA, PSA, c Log P, M.wt) confirmed that the compounds are potential lead compounds for future drug discovery studies.     

结核杆菌重组Rv3425蛋白的结核病血清学诊断价值的评价

[目的]评价结核分支杆菌重组Rv3425蛋白在结核病血清学诊断中的价值。[方法]以重组Rv3425作为抗原，采用酶联免疫吸附试验（ELISA）检测151份确诊结核病人、143份健康人、38份卡介苗接种阳转者和42份非结核病人血清中的抗结核抗体水平，并与结核菌素纯蛋白衍生物（PPD）、Ag85B蛋白及TB—DOT、TB-CHECK-1试剂盒的检测结果进行比较，以此来评价重组Rv3425蛋白在结核病诊断上的价值。[结果]Rv3425与PPD和Ag85B抗原一样能够诊断结核病人，但PPD不能有效区分结核病人和BCG接种者，Rv3425和Ag85B蛋白可以明确区分。[结论]虽然重组Rv3425蛋白对结核病的阳性率尚不能与试剂盒媲美，但由于其能够有效区分结核病人和BCG阳转者，在结核病诊断方面具有很大的应用价值，可以作为结核病诊断的备选抗原之一。     

A facile four-component sequential protocol in the expedient synthesis of novel 2-aryl-5-methyl-2,3-dihydro-1H-3-pyrazolones in water and their antitubercular evaluation

A series of 2-aryl-5-methyl-2,3-dihydro-1H-3-pyrazolones has been synthesized by one-pot, four-component sequential reactions of phenylhydrazine, methyl acetoacetate, aromatic aldehydes and β-naphthol in the presence of p-toluenesulphonic acid in water in good yields. These 2-aryl-5-methyl-2,3-dihydro-1H-3-pyrazolones were screened for in-vitro antimycobacterial activity against Mycobacterium tuberculosis H37Rv (MTB) using agar dilution method. Among the 15 compounds screened, 4-[(2,4-dichlorophenyl)(2-hydroxy-1-naphthyl)methyl]-2-(4-fluorophenyl)-5-methyl-2,3-dihydro-1H-3-pyrazolone displays the maximum potency with a minimum inhibitory concentration (MIC) of 1.6 μM against MTB, being 2.94 and 4.75 times more active than ciprofloxacin and ethambutol respectively.     

结核分枝杆菌Rv2660c蛋白结构分析及抗原表位预测

目的 分析结核分枝杆菌Rv2660c蛋白的结构并预测其抗原表位,为研发针对结核潜伏性感染的治疗性疫苗和药物提供新的靶点。方法 用BLAST软件分析Rv2660c蛋白与人类蛋白的同源性,然后运用生物信息学方法预测其二级结构、跨膜结构、信号肽序列及T细胞和B细胞抗原表位。结果 BLAST结果显示,Rv2660c蛋白与人类蛋白同源性不高,同源性最高的人类蛋白是MAD 6蛋白,同源性仅为16%。Rv2660c蛋白无跨膜区,为胞外蛋白,不含信号肽序列;该蛋白含丰富的B细胞和T细胞抗原表位,19-35、48-54、28-44和58-73位氨基酸残基可能存在优势线性B细胞表位;56-64位和65-74位氨基酸可能存在优势辅助性T细胞表位,66-74、41-49、63-71位氨基酸可能存在优势细胞毒性T细胞表位。结论 Rv2660c蛋白含丰富抗原表位,具有较强的体液免疫和细胞免疫原性,可望作为潜伏性感染结核的治疗性疫苗和药物的作用靶点。     

Protection of mice and guinea pigs against tuberculosis induced by immunization with a single Mycobacterium tuberculosis recombinant antigen, MTB41

MTB41 is a Mycobacterium antigen that is recognized by CD4+ T cells early after experimental infection of mice with Mycobacterium tuberculosis and by PBMC from healthy PPD positive individuals. Immunization of mice with plasmid DNA encoding the MTB41 gene sequence results in the development of antigen-specific CD4+ and CD8+ T cells, and protection against challenge with virulent M. tuberculosis. In the present studies, in contrast to DNA immunization, we show, that a strong MTB41-specific CD4+ T cell response, but no MHC class I restricted cytotoxic T lymphocyte (CTL) activity is detected in the spleen cells of infected mice. Therefore, this data suggests that the induction of CD8+ T cell response to MTB41 epitopes by DNA immunization may not be relevant to protection because these epitopes are not recognized during the infectious process. We also compared the repertoire of rMTB41 epitope recognition by CD4+ T cells of M. tuberculosis-infected mice with the recognition repertoire of mice immunized with the recombinant rMTB41 protein. Both regimens of sensitization lead to the recognition of the same molecular epitope. Coincidentally, immunization with the soluble recombinant protein plus adjuvant, a regimen known to generate primarily CD4+ T cells, resulted in induction of protection comparable to BCG in two well-established animal models of tuberculosis (mice and guinea pigs).     

13个VNTR位点用于113株结核分支杆菌的基因分型研究

目的 应用数目可变串联重复序列（VNTR）分子分型技术，对北京地区113株肺结核临床分离菌株进行分型研究，探讨北京地区菌株DNA多态性和基因型特征。方法 采用PCR和琼脂糖凝胶电泳技术对结核分支杆菌13个VNTR位点进行检测，并应用Gel-Pro analyzer 3．1软件和BioNumerics3．0软件进行结果分析。结果 113株结核分支杆菌可分为4个基因型（分别为Ⅰ、Ⅱ、Ⅳ和Ⅴ型），其中Ⅰ型占92．0％（104/113），其他3型所占比例很小，分别为Ⅱ型占4．4％（5／113），Ⅳ和Ⅴ型均为1．8％（2／113），而标准菌株H37Rv在分型中为独立的一个基因型，即Ⅲ型。结论 北京地区的结核分支杆菌存在基因多态性，其主要流行型为Ⅰ型。     

Modulation of immune responses in mice to recombinant antigens from PE and PPE families of proteins of Mycobacterium tuberculosis by the Ribi adjuvant

Three proteins of PE and PPE families of Mycobacterium tuberculosis were evaluated for their ability to induce T cell responses in mice. To enhance immunity induced by protein immunization, we tested the efficacy of adjuvant Ribi (monophosphoryl lipid A+TDM), along with three proteins of the PE/PPE family. Balb/c mice were subcutaneously injected with recombinant proteins, encoded by Rv1818c, Rv3018c and Rv3812 genes of M. tuberculosis H37Rv, formulated with Ribi or IFA for comparative study. Sera from mice immunized with Ribi revealed an increase in the specific immunoglobulin G titers by twofold against Ribi than in mice immunized with IFA. Ribi also elicited stronger delayed-type hypersensitivity and cytotoxic T-lymphocyte activity against the recombinant proteins when compared with IFA. Antigen specific IgG subclass analysis showed that Ribi tends to facilitate IgG2a production, suggesting enhancement of predominant Th1 response which in turn may facilitate increased production of protective IFN-gamma. Furthermore, Ribi preparation increased the number of T cells secreting IFN-gamma. These results indicate that Ribi acts as an effective adjuvant for immune response to antigens of M. tuberculosis. For the first time, we demonstrate that Rv3018c, Rv1818c and Rv3812 proteins of PE/PPE family are T cell antigens with vaccine potential.     

多位点可变串联重复序列技术用于西藏地区结核分枝杆菌基因分型的初步研究

目的初步探讨多位点数目可变串联重复序列(MLVA)技术在西藏地区结核分枝杆菌基因分型中的应用和初步了解西藏地区结核分枝杆菌数目可变串联重复序列(VNTR)基因型种类及其分布。方法在拉萨、山南、林芝、日喀则、那曲、昌都6个地区结核病防治中心收集结核分枝杆菌临床分离菌株,设计引物,采用PCR和琼脂糖凝胶电泳技术对结核分枝杆菌20个VNTR位点进行检测,并通过BioNumerics 4.5软件进行DNA指纹图谱多态性分析。结果共收集到217株结核分枝杆菌,分为19个不同的VNTR基因型,其中以Ⅺ型为主要基因型占87.6%(属于北京家族),其次Ⅵ型、ⅩⅤ型、ⅩⅥ型各占1.38%,Ⅰ型、Ⅶ型、ⅩⅢ型各占0.92%,12株结核分枝杆菌为单一的基因型。不同地区之间,以Ⅺ型为主要基因型,分别占各地区的86.8%、91.3%、78.95%、88.2%、95.05、89.3%。结论西藏地区的结核分枝杆菌存在明显的基因多态性,主要流行型为VNTRⅪ型(即北京家族基因型),初步研究结果显示北京家族基因型与卡介苗接种和耐药性无相关性。MLVA分型方法简单、快速,可以有效地用于结核分枝杆菌的基因分型和病原监测。     

Synthesis and antimycobacterial activities of novel 6-nitroquinolone-3-carboxylic acids

Various 1-(substituted)-1,4-dihydro-6-nitro-4-oxo-7-(sub-secondary amino)-quinoline-3-carboxylic acids were synthesized from 2,4-dichlorobenzoic acid by six step synthesis. The compounds were evaluated for antimycobacterial in vitro and in vivo against Mycobacterium tuberculosis H37Rv (MTB), multi-drug resistant Mycobacterium tuberculosis (MDR-TB) and Mycobacterium smegmatis (MC(2)) and also tested for the ability to inhibit the supercoiling activity of DNA gyrase from M. smegmatis. Among the 48 synthesized compounds, 7-(4-((benzo[d][1,3]dioxol-5-yl)methyl)piperazin-1-yl)-1-cyclopropyl-1,4-dihydro-6-nitro-4-oxoquinoline-3-carboxylic acid (8c) was found to be the most active compound in vitro with MIC of 0.08 and 0.16 microM against MTB and MDR-TB, respectively. In the in vivo animal model 8c decreased the bacterial load in lung and spleen tissues with 2.78 and 4.15-log10 protections, respectively, at the dose of 50 mg/kg body weight.     

Immunization with hybrid recombinant Mycobacterium tuberculosis H37Rv proteins increases the TH1 cytokine response in mice following a pulmonary instillation of irradiated mycobacteria

The aim of this research was to identify subunit immunogens that can generate enhanced CD8 T cell and TH1 responses against Mycobacterium tuberculosis. A genomic comparison of the M. tuberculosis H(37)R(V) and M. bovis BCG identified 61 proteins that are unique to H(37)R(V). Further screening of these 61 proteins using in silico analyses mimicking proteasomal digestion, transporter-associated antigen processing and H-2 antigen presentation identified 13 proteins with high densities of predicted MHC class I epitopes. Two native proteins, Rv1986c and Rv3875, were selected on the basis of their secreted or transmembrane characteristics and relatively lower frequencies of predicted MHC class II epitopes. To further enhance the CD8 T cell and TH1 responses, a hybrid protein, H32, was constructed by combining the nucleotide sequences encoding the MHC class I antigen-rich segment of Rv1986c and the entire Rv3875 sequence. The two native proteins and the hybrid were used to immunize C57BL/6 and Balb/c mice, which was followed by pulmonary instillation with irradiated M. tuberculosis H(37)R(V). All three proteins elicited elevated IFN-gamma responses, with the hybrid showing significant increases over the native proteins in both mice. This strategy of immunogen selection might be used to improve the current subunit vaccines against M. tuberculosis as well as other intra-cellular pathogens.     

结核分枝杆菌Rv3914抗原的克隆表达与纯化

目的构建结核分枝杆菌Rv3914蛋白的重组质粒,并在大肠埃希菌中表达及纯化,为结核病血清学诊断提供候选抗原。方法用PCR方法从结核分枝杆菌H37Rv基因组中扩增Rv3914基因片段,插入到pET-28b(+)载体中,构建pET28b-Rv3914重组质粒,转化大肠埃希菌E.coli BL21plysS(DE3),经IPTG诱导表达后,应用Ni-NTA亲和柱纯化重组蛋白。结果 PCR扩增出Rv3914基因序列,重组质粒经测序并经BLAST分析后发现无点突变。pET28b-Rv3914重组质粒在大肠埃希菌E.coli BL21plysS(DE3)中主要以可溶性形式表达,重组蛋白占细胞蛋白总表达量的30%以上,经Ni-NTA柱纯化后,得到纯度超过90%、相对分子质量约为14.7×103的目的蛋白质。结论高纯度结核分枝杆菌Rv3914重组蛋白的获得为研究结核互补特异性抗原组合在结核病血清诊断中的价值奠定了基础。     

Identification of novel potential antibiotics for tuberculosis by in silico structure-based drug screening

The enoyl-acyl carrier protein reductase of Mycobacterium tuberculosis (MTB) is a key enzyme of the type II fatty acid synthesis system. It is involved in the production of mycolic acid and is a known target for isoniazid, an effective antibiotic for tuberculosis treatment. The increasing prevalence of tuberculosis in many areas of the world, which is associated with the rise of drug-resistant MTB strains, presents a major global health threat. In this study, we attempted to identify novel antibiotics specifically targeting the MTB enoyl-acyl carrier protein reductase. We performed in silico structure-based drug screening using the crystal structure data for the MTB enoyl-acyl carrier protein reductase (PDB code; 2H7I) and a virtual compound library, which includes 152,102 chemicals. By a two-step screening method using DOCK (first screening) and GOLD (second screening), we identified 5 chemical compounds expected to have high binding affinity to the active center of the MTB enoyl-acyl carrier protein reductase. Moreover, we examined the antibiotic effects of these chemical compounds on model bacterial strains by in vitro experiments. We found that a chemical compound, which has a basic skeleton comprised of dibenzofuran, acetoamide, trizol, furyl and methylphenyl groups, completely inhibited the growth of Mycobacterium vanbaalenii and had no toxic effects on enterobacteria and cultured mammalian cells. Therefore, the chemical compound is likely to be useful in the research and development of new antibiotics for tuberculosis.