Objective:To investigate the interaction of p53 with docetaxel and berberine and their anticancer activities against oral squamous cell carcinoma.Methods:The interaction between p53 with docetaxel and berberine was in...Objective:To investigate the interaction of p53 with docetaxel and berberine and their anticancer activities against oral squamous cell carcinoma.Methods:The interaction between p53 with docetaxel and berberine was investigated and their mechanisms of action against oral squamous cell carcinoma were studied.Toxicity studies were performed to determine any toxic impact of the drugs on the vital organs of tested animals.Results:In silico results revealed the molecular interaction of docetaxel and berberine with p53 and the molecules were found to be potential p53 inducers.Docetaxel and berberine inhibited the proliferation of cancer cells in a concentration-dependent manner.Flow cytometry analysis revealed that docetaxel and berberine at IC50 concentrations upregulated the expression of p53 in oral squamous cell carcinoma cells,thus triggering apoptotic cell death.In addition,no toxicity was observed in the liver and kidney tissues of mice after docetaxel and berberine treatment.Conclusions:Docetaxel and berberine significantly suppressed the proliferation of oral cancer cells by activating p53 expression and causing apoptotic cell death.Both compounds can be potential agents for the treatment of oral cancer,with little to no toxicity at the tissue level.展开更多
Objective:To evaluate the antimalarial activity of noscapine against Plasmodium falciparum 3D7 strain(Pf3D7),its clinical isolate(Pf140/SS),and Plasmodium berghei ANKA(PbA).Methods:Using ring-stage survival assay,phen...Objective:To evaluate the antimalarial activity of noscapine against Plasmodium falciparum 3D7 strain(Pf3D7),its clinical isolate(Pf140/SS),and Plasmodium berghei ANKA(PbA).Methods:Using ring-stage survival assay,phenotypic assessments,and SYBR-green-based fluorescence assay,the antimalarial activities of noscapine were assessed compared with dihydroartemisinin(DHA)in in vivo and in vitro studies.In addition,hemolysis and cytotoxicity tests were carried out to evaluate its safety.RT-PCR assay was also conducted to determine the effect of noscapine on papain-like cysteine protease Plasmodium falciparum falcipain-2(PfFP-2).Results:The antimalarial efficacy of noscapine against Pf3D7 and Pf140/SS was comparable to DHA,with IC50 values of(7.68±0.88)and(5.57±0.74)nM/mL,respectively,and>95%inhibition of PbA infected rats.Noscapine also showed a safe profile,as evidenced by low hemolysis and cytotoxicity even at high concentrations.Moreover,PfFP-2 expression was significantly inhibited in both noscapine-treated Pf3D7 and Pf140/SS(P<0.01).Conclusions:Noscapine has antimalarial properties comparable to standard antimalarial DHA with better safety profiles,which may be further explored as a therapeutic candidate for the treatment of malaria.展开更多
Nephrolithiasis is a common clinical disorder, and calcium oxalate (CaOx) is the principal crystalline component in approximately 75% of all renal stones. It is widely believed that proteins act as inhibitors of cryst...Nephrolithiasis is a common clinical disorder, and calcium oxalate (CaOx) is the principal crystalline component in approximately 75% of all renal stones. It is widely believed that proteins act as inhibitors of crystal growth and aggregation. Acidic amino acids present in these proteins play a significant role in the inhibition process. In this study, interaction of cal-cium oxalate with human phosphate cytidylyltrans-ferase 1(CCT), a novel calcium oxalate crystal growth inhibitor purified from human renal stone matrix has been elucidated in silico and involvement of acidic amino acids in the same. As only sequence of CCT is available, henceforth its 3-D structure was modeled via Homology modeling using Prime module of Schrodinger package. Molecular dynamic simulation of modeled protein with solvation was done by mac-romodel (Schrodinger). The quality of modeled pro-tein was validated by JCSG protein structure valida-tion (PROCHECK & ERRAT) server. To analyze the interaction of modeled protein CCT with calcium oxalate along with role played by acidic amino acids, ‘Docking simulation’ was done using MOE–Dock. Interaction between calcium oxalate and CCT was also studied by substituting acidic amino acid in the active sites of the protein with neutral and positively charged amino acids. The in silico analysis showed the bond formation between the acidic amino acids and calcium atom, which was further substantiated when substitution of these acidic amino acids with alanine, glycine, lysine, arginine and histidine com-pletely diminished the interaction with calcium ox-alate.展开更多
Given a protein sequence, how can we identify whether it is a metalloprotein or not? If it is, which main functional class and subclasses it belongs to? This is an important biological question because they are closel...Given a protein sequence, how can we identify whether it is a metalloprotein or not? If it is, which main functional class and subclasses it belongs to? This is an important biological question because they are closely related to the biological function of an uncharacterized protein. Particularly, with the avalanche of protein sequences generated in the post genomic era and since conventional techniques are time consuming and expensive, it is highly desirable to develop an automated method by which one can get a fast and accurate answer to these questions. Here, a top-down predictor, called MetalloPred, is developed which consists of 3 level of hierarchical classification using cascade of neural networks from sequence derived features. The 1st layer of the prediction engine is for identifying a query protein as metalloprotein or not;the 2nd layer for the main functional class;and the 3rd layer for the sub-functional class. The overall success rates for all the three layers are higher than 60% that were obtained through rigorous cross-validation tests on the very stringent benchmark datasets in which none of the proteins has 30% sequence identity with any other in the same class or subclass. MetalloPred achieved good prediction accuracies and could nicely complement experimental approaches for identification of metal binding proteins. MetalloPred is freely available to be used in-house as a standalone and is accessible at http://www.juit.ac.in/assets/Metallopred/.展开更多
Despite its efficacy against malaria, the relatively low yield （0.01%-0.8%） of artemisinin in Artemisia annua is a serious limitation to the commercialization of the drug. A better understanding of the biosynthetic ...Despite its efficacy against malaria, the relatively low yield （0.01%-0.8%） of artemisinin in Artemisia annua is a serious limitation to the commercialization of the drug. A better understanding of the biosynthetic pathway of artemisinin and its regulation by both exogenous and endogenous factors is essential to improve artemisinin yield. Increasing evidence has shown that microRNAs （miRNAs） play multiple roles in various biological processes. In this study, we used previously known miRNAs from Arabidopsis and rice against expressed sequence tag （EST） database of A. annua to search for potential miRNAs and their targets in A. annua. A total of six potential rniRNAs were predicted, which belong to the miR414 and miR1310 families. Furthermore, eight potential target genes were identified in this species. Among them, seven genes encode proteins that play important roles in artemisinin biosynthesis, including HMG-CoA reductase （HMGR）, amorpha-4,11-diene synthase （ADS）, farnesyl pyrophosphate synthase （FPS） and cytochrome P450. In addition, a gene coding for putative AINTEGUMENTA, which is involved in signal transduction and development, was also predicted as one of the targets. This is the first in silico study to indicate that miRNAs target genes encoding enzymes involved in artemisinin biosynthesis, which may help to understand the miRNA-mediated regulation of artemisinin biosynthesis in A. annua.展开更多
文摘Objective:To investigate the interaction of p53 with docetaxel and berberine and their anticancer activities against oral squamous cell carcinoma.Methods:The interaction between p53 with docetaxel and berberine was investigated and their mechanisms of action against oral squamous cell carcinoma were studied.Toxicity studies were performed to determine any toxic impact of the drugs on the vital organs of tested animals.Results:In silico results revealed the molecular interaction of docetaxel and berberine with p53 and the molecules were found to be potential p53 inducers.Docetaxel and berberine inhibited the proliferation of cancer cells in a concentration-dependent manner.Flow cytometry analysis revealed that docetaxel and berberine at IC50 concentrations upregulated the expression of p53 in oral squamous cell carcinoma cells,thus triggering apoptotic cell death.In addition,no toxicity was observed in the liver and kidney tissues of mice after docetaxel and berberine treatment.Conclusions:Docetaxel and berberine significantly suppressed the proliferation of oral cancer cells by activating p53 expression and causing apoptotic cell death.Both compounds can be potential agents for the treatment of oral cancer,with little to no toxicity at the tissue level.
文摘Objective:To evaluate the antimalarial activity of noscapine against Plasmodium falciparum 3D7 strain(Pf3D7),its clinical isolate(Pf140/SS),and Plasmodium berghei ANKA(PbA).Methods:Using ring-stage survival assay,phenotypic assessments,and SYBR-green-based fluorescence assay,the antimalarial activities of noscapine were assessed compared with dihydroartemisinin(DHA)in in vivo and in vitro studies.In addition,hemolysis and cytotoxicity tests were carried out to evaluate its safety.RT-PCR assay was also conducted to determine the effect of noscapine on papain-like cysteine protease Plasmodium falciparum falcipain-2(PfFP-2).Results:The antimalarial efficacy of noscapine against Pf3D7 and Pf140/SS was comparable to DHA,with IC50 values of(7.68±0.88)and(5.57±0.74)nM/mL,respectively,and>95%inhibition of PbA infected rats.Noscapine also showed a safe profile,as evidenced by low hemolysis and cytotoxicity even at high concentrations.Moreover,PfFP-2 expression was significantly inhibited in both noscapine-treated Pf3D7 and Pf140/SS(P<0.01).Conclusions:Noscapine has antimalarial properties comparable to standard antimalarial DHA with better safety profiles,which may be further explored as a therapeutic candidate for the treatment of malaria.
文摘Nephrolithiasis is a common clinical disorder, and calcium oxalate (CaOx) is the principal crystalline component in approximately 75% of all renal stones. It is widely believed that proteins act as inhibitors of crystal growth and aggregation. Acidic amino acids present in these proteins play a significant role in the inhibition process. In this study, interaction of cal-cium oxalate with human phosphate cytidylyltrans-ferase 1(CCT), a novel calcium oxalate crystal growth inhibitor purified from human renal stone matrix has been elucidated in silico and involvement of acidic amino acids in the same. As only sequence of CCT is available, henceforth its 3-D structure was modeled via Homology modeling using Prime module of Schrodinger package. Molecular dynamic simulation of modeled protein with solvation was done by mac-romodel (Schrodinger). The quality of modeled pro-tein was validated by JCSG protein structure valida-tion (PROCHECK & ERRAT) server. To analyze the interaction of modeled protein CCT with calcium oxalate along with role played by acidic amino acids, ‘Docking simulation’ was done using MOE–Dock. Interaction between calcium oxalate and CCT was also studied by substituting acidic amino acid in the active sites of the protein with neutral and positively charged amino acids. The in silico analysis showed the bond formation between the acidic amino acids and calcium atom, which was further substantiated when substitution of these acidic amino acids with alanine, glycine, lysine, arginine and histidine com-pletely diminished the interaction with calcium ox-alate.
文摘Given a protein sequence, how can we identify whether it is a metalloprotein or not? If it is, which main functional class and subclasses it belongs to? This is an important biological question because they are closely related to the biological function of an uncharacterized protein. Particularly, with the avalanche of protein sequences generated in the post genomic era and since conventional techniques are time consuming and expensive, it is highly desirable to develop an automated method by which one can get a fast and accurate answer to these questions. Here, a top-down predictor, called MetalloPred, is developed which consists of 3 level of hierarchical classification using cascade of neural networks from sequence derived features. The 1st layer of the prediction engine is for identifying a query protein as metalloprotein or not;the 2nd layer for the main functional class;and the 3rd layer for the sub-functional class. The overall success rates for all the three layers are higher than 60% that were obtained through rigorous cross-validation tests on the very stringent benchmark datasets in which none of the proteins has 30% sequence identity with any other in the same class or subclass. MetalloPred achieved good prediction accuracies and could nicely complement experimental approaches for identification of metal binding proteins. MetalloPred is freely available to be used in-house as a standalone and is accessible at http://www.juit.ac.in/assets/Metallopred/.
文摘Despite its efficacy against malaria, the relatively low yield （0.01%-0.8%） of artemisinin in Artemisia annua is a serious limitation to the commercialization of the drug. A better understanding of the biosynthetic pathway of artemisinin and its regulation by both exogenous and endogenous factors is essential to improve artemisinin yield. Increasing evidence has shown that microRNAs （miRNAs） play multiple roles in various biological processes. In this study, we used previously known miRNAs from Arabidopsis and rice against expressed sequence tag （EST） database of A. annua to search for potential miRNAs and their targets in A. annua. A total of six potential rniRNAs were predicted, which belong to the miR414 and miR1310 families. Furthermore, eight potential target genes were identified in this species. Among them, seven genes encode proteins that play important roles in artemisinin biosynthesis, including HMG-CoA reductase （HMGR）, amorpha-4,11-diene synthase （ADS）, farnesyl pyrophosphate synthase （FPS） and cytochrome P450. In addition, a gene coding for putative AINTEGUMENTA, which is involved in signal transduction and development, was also predicted as one of the targets. This is the first in silico study to indicate that miRNAs target genes encoding enzymes involved in artemisinin biosynthesis, which may help to understand the miRNA-mediated regulation of artemisinin biosynthesis in A. annua.
