Potential inhibitors of SARS-CoV-2 (COVID 19) spike protein of the delta and delta plus variant: In silico studies of medicinal plants of North-East India.
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ABSTRACT:
SUBMITTER: Solo P
PROVIDER: S-EPMC8530778 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The objective of this study was to identify the genes differentially expressed in non small cell lung carcinoma associated with prevalent risk factor such as smoking and betel quid chewing in high-risk north eastern Indian population. The tumor biopsies and matched normal tissue from distant site were collected in RNA later, snap-frozen in liquid nitrogen and stored at -70°C until processed. Data of clinicopathologic parameters were obtained from patients’ clinical and pathologic report. Institutional human ethics committee approved the study.
2012-01-31 | GSE30118 | GEO
Project description:Hepatitis viral infection is a leading cause of chronic hepatitis, cirrhosis, and hepatocellular carcinoma (HCC). Over one million people are estimated to be persistently infected with hepatitis C virus (HCV) worldwide. As capsid core protein is the key element in spreading HCV; hence, it is considered to be the superlative target of antiviral compounds. Novel drug inhibitors of HCV are in need to complement or replace the current treatments such as pegylated interferon's and ribavirin as they are partially booming and beset with various side effects. Our study was conducted to predict 3D structure of capsid core protein of HCV from northern part of India. Core, the capsid protein of HCV, handles the assembly and packaging of HCV RNA genome and is the least variable of all the ten HCV proteins among the six HCV genotypes. Therefore, we screened four phytochemicals inhibitors that are known to disrupt the interactions of core and other HCV proteins such as (a) epigallocatechin gallate (EGCG), (b) ladanein, (c) naringenin, and (d) silybin extracted from medicinal plants; targeted against active site of residues of HCV-genotype 3 (G3) (Q68867) and its subtypes 3b (Q68861) and 3g (Q68865) from north India. To study the inhibitory activity of the recruited flavonoids, we conducted a quantitative structure-activity relationship (QSAR). Furthermore, docking interaction suggests that EGCG showed a maximum number of hydrogen bond (H-bond) interactions with all the three modeled capsid proteins with high interaction energy followed by naringenin and silybin. Thus, our results strongly correlate the inhibitory activity of the selected bioflavonoid. Finally, the dynamic predicted capsid protein molecule of HCV virion provides a general avenue to target structure-based antiviral compounds that support the hypothesis that the screened inhibitors for viral capsid might constitute new class of potent agents but further confirmation is necessary using in vitro and in vivo studies.
| S-EPMC4076477 | biostudies-literature
Project description:The objective of this study was to identify the genes differentially expressed in non small cell lung carcinoma associated with prevalent risk factor such as smoking and betel quid chewing in high-risk north eastern Indian population. The tumor biopsies and matched normal tissue from distant site were collected in RNA later, snap-frozen in liquid nitrogen and stored at -70°C until processed. Data of clinicopathologic parameters were obtained from patients’ clinical and pathologic report. Institutional human ethics committee approved the study. Total RNA was isolated from tumor biopsies and matched normal of five patients. Total RNA from normal tissue from three patients was pooled in one slide and normal tissue from another two patients was pooled in another slide. Individual slide were used for each tumor samples. Isolation Kit: RNeasy mini Kit (Qiagen) Scanner Used: AFFYMETRIX, 428 Array
2012-01-31 | E-GEOD-30118 | biostudies-arrayexpress
Project description:Medicinal plants have widely been used in the traditional treatment of ailments and have been proven effective. Their contribution still holds an important place in modern drug discovery due to their chemical, and biological diversities. However, the poor documentation of traditional medicine, in developing African countries for instance, can lead to the loss of knowledge related to such practices. In this study, we present the Eastern Africa Natural Products Database (EANPDB) containing the structural and bioactivity information of 1870 unique molecules isolated from about 300 source species from the Eastern African region. This represents the largest collection of natural products (NPs) from this geographical region, covering literature data of the period from 1962 to 2019. The computed physicochemical properties and toxicity profiles of each compound have been included. A comparative analysis of some physico-chemical properties like molecular weight, H-bond donor/acceptor, logPo/w , etc. as well scaffold diversity analysis has been carried out with other published NP databases. EANPDB was combined with the previously published Northern African Natural Products Database (NANPDB), to form a merger African Natural Products Database (ANPDB), containing ∼6500 unique molecules isolated from about 1000 source species (freely available at http://african-compounds.org). As a case study, latrunculins A and B isolated from the sponge Negombata magnifica (Podospongiidae) with previously reported antitumour activities, were identified via substructure searching as molecules to be explored as putative binders of histone deacetylases (HDACs).
| S-EPMC7685152 | biostudies-literature
Project description:Background: Cancer is a major cause of mortality worldwide with increasing numbers by the years. In North Africa, the number of cancer patients is alarming. Also shocking is that a huge number of cancer patients only have access to traditional medicines due to several factors, e.g., economic difficulties. In fact, medicinal plants are widely used for the treatment of several pathologies, including cancer. Truthfully, herbalists and botanists in North African countries prescribe several plants for cancer treatment. Despite the popularity and the potential of medicinal plants for the treatment of cancer, scientific evidence on their anticancer effects are still scarce for most of the described plants. Objective: Bearing in mind the lack of comprehensive and systematic studies, the aim of this review is to give an overview of studies, namely ethnobotanical surveys and experimental evidence of anticancer effects regarding medicinal plants used in North Africa for cancer therapy. Method: The research was conducted on several popular search engines including PubMed, Science Direct, Scopus and Web of Science. The research focused primarily on English written papers published between the years 2000 and 2016. Results: This review on plants traditionally used by herbalists in North Africa highlights that Morocco and Algeria are the countries with most surveys on the use of medicinal plants in folk medicine. Among the plethora of plants used, Nigella sativa and Trigonella foenum-graecum are the most referred ones by herbalists for the treatment of cancer. Moreover, a plethora of scientific evidence qualifies them as candidates for further drug development. Furthermore, we report on the underlying cellular and molecular mechanisms. Conclusion: Overall, this review highlights the therapeutic potential of some medicinal plants as anticancer agents. The North African flora offers a rich source of medicinal plants for a wide array of diseases, including cancer. The elucidation of their modes of action represents an indispensable condition for the rational development of new drugs for cancer treatment. Furthermore, testing the anticancer activity in vivo and in clinical trials are warranted to explore the full therapeutic potential of North African plants for cancer therapy.
| S-EPMC5483438 | biostudies-other
Project description:Intra-species genetic variability assessment is an effective tool in formulating genetic improvement and germplasm conservation strategies. Houttuynia cordata Thunb. is a semidomesticated medicinal herb consumed widely in traditional diet in North-Eastern India. In the present study, an effort has been made to assess the genetic diversity of H. cordata Thunb. from Brahmaputra valley of North-East India. A total of 545 genotypes from 18 populations of H. cordata Thunb. from four different regions, i.e. North-East, North-West, South-East and South-West, with respect to river Brahmaputra were collected and population genetic diversity and structure were analysed using ISSR molecular markers. Population genetic structure analysis using unweighted pair group method with averages (UPGMA)-based hierarchical cluster analysis, principal coordinate analysis (PCoA) and model-based clustering in STRUCTURE program revealed that the population of H. cordata Thunb. grouped according to regional distribution and forms four genetically distinct clusters. The analysis of molecular variance showed that differentiation among regions was significant with 60% genetic variation among region, 3% genetic variation among population within region and 37% genetic variation within population. We found wide variation in Nei's gene diversity (Hj) ranging from 0.07782 in Margherita population to 0.13634 in Barapani population. Furthermore, Nei's gene diversity within population (Nei's Hs) and total gene diversity (Ht) were found to be 0.1081 and 0.1769 respectively. The genetic differentiation among 18 population was high (Fst = 0.3894; p < 0.001) with relatively restricted gene flow (Nm = 0.6564). Based on the result of this study, we suggest ex situ conservation could be an appropriate measure to adequately capture the total genetic diversity of H. cordata Thunb. populations of North-East India by selecting few individuals from different populations.Supplementary informationThe online version contains supplementary material available at 10.1007/s11105-020-01260-9.
| S-EPMC7666406 | biostudies-literature
Project description:BACKGROUND: Human African trypanosomiasis (HAT), a parasitic protozoal disease, is caused primarily by two subspecies of Trypanosoma brucei. HAT is a re-emerging disease and currently threatens millions of people in sub-Saharan Africa. Many affected people live in remote areas with limited access to health services and, therefore, rely on traditional herbal medicines for treatment. METHODS: A molecular docking study has been carried out on phytochemical agents that have been previously isolated and characterized from Nigerian medicinal plants, either known to be used ethnopharmacologically to treat parasitic infections or known to have in-vitro antitrypanosomal activity. A total of 386 compounds from 19 species of medicinal plants were investigated using in-silico molecular docking with validated Trypanosoma brucei protein targets that were available from the Protein Data Bank (PDB): Adenosine kinase (TbAK), pteridine reductase 1 (TbPTR1), dihydrofolate reductase (TbDHFR), trypanothione reductase (TbTR), cathepsin B (TbCatB), heat shock protein 90 (TbHSP90), sterol 14?-demethylase (TbCYP51), nucleoside hydrolase (TbNH), triose phosphate isomerase (TbTIM), nucleoside 2-deoxyribosyltransferase (TbNDRT), UDP-galactose 4' epimerase (TbUDPGE), and ornithine decarboxylase (TbODC). RESULTS: This study revealed that triterpenoid and steroid ligands were largely selective for sterol 14?-demethylase; anthraquinones, xanthones, and berberine alkaloids docked strongly to pteridine reductase 1 (TbPTR1); chromenes, pyrazole and pyridine alkaloids preferred docking to triose phosphate isomerase (TbTIM); and numerous indole alkaloids showed notable docking energies with UDP-galactose 4' epimerase (TbUDPGE). Polyphenolic compounds such as flavonoid gallates or flavonoid glycosides tended to be promiscuous docking agents, giving strong docking energies with most proteins. CONCLUSIONS: This in-silico molecular docking study has identified potential biomolecular targets of phytochemical components of antitrypanosomal plants and has determined which phytochemical classes and structural manifolds likely target trypanosomal enzymes. The results could provide the framework for synthetic modification of bioactive phytochemicals, de novo synthesis of structural motifs, and lead to further phytochemical investigations.
| S-EPMC3404109 | biostudies-literature
Project description:The diversified genus of Clerodendrum with its complex evolutionary history leads to taxonomic mystification. Unlike traditional taxonomic methods, DNA barcoding could be a promising tool for the identification and conservation of Clerodendrum species. This study was attempted to develop an efficient barcode locus in Clerodendrum species of North East India. We evaluated four barcode candidates (ITS2, matK, rbcL, ycf1) and its combinations in different Clerodendrum species. The reliability of barcodes to distinguish the species were calculated using genetic pairwise distances, intra- and inter-specific diversity, barcode gap, and phylogenetic tree-based methods. The results exemplify that matK posse's maximum number of variables and parsimony-informative sites (103/100), intra- (0.021 ± 0.001) and inter- (0.086 ± 0.005) specific divergences and species resolution rate (89.1%) followed by ITS2, ycf1, and rbcL. Among the combinatorial locus, ITS2 + matK showed the best species discrimination with distinctive barcode gaps. Therefore, we tentatively suggest that the combination of ITS2 + matK as core barcode for Clerodendrum and converted into quick response (QR) code. Hence, this finding indicates that DNA barcoding could provide consistent resources for species discrimination and resolve taxonomic controversies of the genus as well as set a preliminary assessment toward its biodiversity.
| S-EPMC7417596 | biostudies-literature
Project description:During the period April 1993 to July 1993, a total of 410 patients with pyrexia were screened for malarial parasite and 109 (26.5%) cases were found positive for malarial parasite. Of these 109 cases, 91 were positive for Plasmodium falciparum. Of these 91 cases, 43 patients fulfilled the study criteria as per WHO's extended field trial and were included in the analysis. These patients were treated with standard doses of chloroquine. Seven patients each (16.3%) showed RI and RII resistance and 2 patients (4.7%) showed RIII levels of chloroquine resistance.
| S-EPMC5530823 | biostudies-other
Project description:In May 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected in Asiatic lions in a zoological park in India. Sequence and phylogenetic analyses showed the SARS-CoV-2 strains were the B.1.617.2 (Delta) variant. To reduce transmission of variants of concern, surveillance of SARS-CoV-2 in wild animal populations should be increased.
| S-EPMC8462327 | biostudies-literature