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Identification of SARS-CoV-2 inhibitors from extracts of Houttuynia cordata Thunb.

ABSTRACT: Houttuynia cordata Thunb., a perennial herb belonging to the Saururaceae family is a well-known ingredient of Traditional Chinese medicine (TCM) with several therapeutic properties. During the severe acute respiratory syndrome (SARS) outbreak in China, it was one of the approved ingredients in SARS preventative formulations and therefore, the plant may contain novel bioactive chemicals that can be used to suppress the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus for which there are currently no effective drugs available. Like all RNA viruses, SARS-CoV-2 encode RNA-dependent RNA polymerase (RdRp) enzyme which aids viral gene transcription and replication. The present study is aimed at understanding the potential of bioactive compounds from H. cordata as inhibitors of the SARS-CoV-2 RdRp enzyme. We investigated the drug-likeness of the plant's active constituents, such as alkaloids, polyphenols, and flavonoids, as well as their binding affinity for the RdRp enzyme. Molecular docking experiments show that compounds 3 (1,2,3,4,5-pentamethoxy-dibenzo-quinolin-7-one), 14 (7-oxodehydroasimilobine), and 21 (1,2-dimethoxy-3-hydroxy-5-oxonoraporphine) have a high affinity for the drug target and that the complexes are maintained by hydrogen bonds with residues like Arg553, Cys622 and Asp623, as well as hydrophobic interactions with other residues. The lead compounds' complexes with the target enzyme remained stable throughout the molecular dynamics simulation. Analysis of molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics generalized Born surface area (MM-GBSA) revealed the key residues contributing considerably to binding free energy. Thus, the findings reveal the potential of H. cordata bioactive compounds as anti-SARS-CoV-2 drug candidate molecules against the target enzyme.

SUBMITTER: Bahadur Gurung A

PROVIDER: S-EPMC8420092 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Houttuynia cordata Thunb (H. cordata; Saururaceae) is widely distributed in Asian regions. It plays an important role in traditional health care and disease treatment, as its aboveground stems and leaves have a long medicinal history in China and are used in the treatment of pneumonia and lung abscess. In clinical treatment, it can usually be combined with other drugs to treat dysentery, cold, fever, and mumps; additionally, H. cordata is an edible plant. This review summarizes detailed information on the phytochemistry and pharmacological effects of H. cordata. By searching the keywords "H. cordata and lung", "H. cordata and heart", "H. cordata and liver", and "H. cordata and inflammation" in PubMed, Web of Science and ScienceDirect, we screened out articles with high correlation in the past ten years, sorted out the research contents, disease models and research methods of the articles, and provided a new perspective on the therapeutic effects of H. cordata. A variety of its chemical constituents are characteristic of medicinal plants, the chemical constituents were isolated from H. cordata, including volatile oils, alkaloids, flavonoids, and phenolic acids. Flavonoids and volatile oils are the main active components. In pharmacological studies, H. cordata showed organ protective activity, such as reducing the release of inflammatory factors to alleviate lung injury. Moreover, H. cordata regulates immunity, enhances the immune barriers of the vagina, oral cavity, and intestinal tract, and combined with the antibacterial and antiviral activity of its extract, effectively reduces pathogen infection. Furthermore, experiments in vivo and in vitro showed significant anti-inflammatory activity, and its chemical derivatives exert potential therapeutic activity against rheumatoid arthritis. Antitumour action is also an important pharmacological activity of H. cordata, and studies have shown that H. cordata has a notable effect on lung tumour, liver tumour, colon tumour, and breast tumour. This review categorizes the biological activities of H. cordata according to modern research papers, and provides insights into disease prevention and treatment of H. cordata.

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 Information:The online version contains supplementary material available at 10.1007/s11105-020-01260-9.

Project description:BackgroundHouttuynia cordata Thunb. is an important traditional medical herb in China and other Asian countries, with high medicinal and economic value. However, a lack of available genomic information has become a limitation for research on this species. Thus, we carried out high-throughput transcriptomic sequencing of H. cordata to generate an enormous transcriptome sequence dataset for gene discovery and molecular marker development.Principal findingsIllumina paired-end sequencing technology produced over 56 million sequencing reads from H. cordata mRNA. Subsequent de novo assembly yielded 63,954 unigenes, 39,982 (62.52%) and 26,122 (40.84%) of which had significant similarity to proteins in the NCBI nonredundant protein and Swiss-Prot databases (E-value <10(-5)), respectively. Of these annotated unigenes, 30,131 and 15,363 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. In addition, 24,434 (38.21%) unigenes were mapped onto 128 pathways using the KEGG pathway database and 17,964 (44.93%) unigenes showed homology to Vitis vinifera (Vitaceae) genes in BLASTx analysis. Furthermore, 4,800 cDNA SSRs were identified as potential molecular markers. Fifty primer pairs were randomly selected to detect polymorphism among 30 samples of H. cordata; 43 (86%) produced fragments of expected size, suggesting that the unigenes were suitable for specific primer design and of high quality, and the SSR marker could be widely used in marker-assisted selection and molecular breeding of H. cordata in the future.ConclusionsThis is the first application of Illumina paired-end sequencing technology to investigate the whole transcriptome of H. cordata and to assemble RNA-seq reads without a reference genome. These data should help researchers investigating the evolution and biological processes of this species. The SSR markers developed can be used for construction of high-resolution genetic linkage maps and for gene-based association analyses in H. cordata. This work will enable future functional genomic research and research into the distinctive active constituents of this genus.

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Identification of SARS-CoV-2 inhibitors from extracts of Houttuynia cordata Thunb.

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