Black tea bioactives as inhibitors of multiple targets of SARS-CoV-2 (3CLpro, PLpro and RdRp): a virtual screening and molecular dynamic simulation study.

The global pandemic due to the novel Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has taken more than a million lives. Lack of definitive vaccine/drugs against this highly contagious virus has accelerated exploratory research on novel natural and synthetic inhibitors. Tea is a rich source of bioactives and known to have antiviral properties. In this study, an in silico strategy involving ADMET property screening, receptor-ligand docking and molecular dynamic (MD) simulation was employed to screen potential tea bio-active inhibitors against three selected targets (RdRp, 3CLpro and PLpro) of SARS-CoV-2. Among the 70 tea bioactives screened, theaflavin 3,3'-di-gallate (TF3), Procyanidin B2 and Theaflavin 3-gallate (TF2a) exhibited highest binding affinities towards RdRp, 3CLpro/Mpro and PLpro targets of SARS-CoV-2 with low docking scores of -14.92, -11.68 and -10.90 kcal/mol, respectively. All of them showed a substantial number of hydrogen bonds along with other interactions in and around the active sites. Interestingly, the top bioactives in our study showed higher binding affinities compared with known antiviral drugs. Further, the top protein-ligand complexes showed less conformational changes during binding when subjected to MD simulation for 100 nanoseconds. The MMPBSA results revealed that RdRp-TF3, 3CLpro-Procyanidin B2 and PLpro-TF2a complexes were stable with binding free energies of -93.59 ± 43.97, -139.78 ± 16.51 and -96.88 ± 25.39 kJ/mol, respectively. Our results suggest that theaflavin 3,3'-digallate, Theaflavin 3-gallate and Procyanidin B2 found in black tea have the potential to act as inhibitors for selected targets of SARS-CoV-2 and can be considered as drug candidates in future studies against COVID-19.

Comparative analysis of chloroplast genomes indicated different origin for Indian tea (Camellia assamica cv TV1) as compared to Chinese tea.

Based upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China adjoining area, yet specific origin of China and Assam type tea are not yet clear. Thus, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus by performing evolutionary study and comparing simple sequence repeats (SSRs) and codon usage distribution patterns among them. The Cp genome based phylogenetic analysis indicated that Indian Tea, TV1 formed a different group from that of China tea, indicating that TV1 might have undergone different domestications and hence owe different origins. The simple sequence repeats (SSRs) analysis and codon usage distribution patterns also supported the clustering order in the cp genome based phylogenetic tree.

Molecular analysis of drought tolerance in tea by cDNA-AFLP based transcript profiling.

A cDNA-AFLP approach was used to identify transcript and/or genes specifically expressed in response to drought in tea. Drought was artificially induced and whole genome transcript profiling was done at three different stages-6 days before wilting, 3 days before wilting and at wilting stage of both tolerant and susceptible cultivars, and genetic differences was thus visualized as polymorphisms in the transcriptome. The cDNA-AFLP technique allowed genes and transcripts to be identified in the tolerant genotype (TV-23) whose expression is responsive to drought stress. The cluster analysis revealed two types of clustering-type I separated the tolerant and susceptible cultivar, whereas type II separated the time point of sample and this may be grouped as early and late responsive transcripts. 108 transcript derived fragments were identified as differentially expressed in tolerant genotypes of which 89 sequences could be obtained. Fifty-nine of them showed homology in the public databases. Functional ontology showed genes related to carbohydrate metabolism, response to stress, protein modification process and translation. Cluster I includes five fragments and cluster II includes 25 fragments. Other genes strongly expressed in response to drought in tolerant genotype would help us in identifying and determining the genetic basis of mechanisms involved in conferring drought tolerance in tea.

Identification of drought tolerant progenies in tea by gene expression analysis.

Understanding the genes that govern tea plant (Camellia sinensis) architecture and response to drought stress is urgently needed to enhance breeding in tea with improved water use efficiency. Field drought is a slow mechanism and the plants go through an adaptive process in contrast to the drastic changes of rapid dehydration in case of controlled experiments. We identified a set of drought responsive genes under controlled condition using SSH, and validated the identified genes and their pattern of expression under field drought condition. The study was at three stages of water deficit stress viz., before wilting, wilting and recovery, which revealed a set of genes with higher expression at before wilting stage including dehydrin, abscissic acid ripening protein, glutathione peroxidase, cinnamoyl CoA reductase, calmodulin binding protein. The higher expression of these genes was related with increase tolerance character of DT/TS-463 before wilting, these five tolerant progenies could withstand drought stress and thus are candidates for breeding. We observed that physiological parameter like water use efficiency formed a close group with genes such as calmodulin related, DRM3, hexose transporter, hydrogen peroxide induced protein, ACC oxidase, lipase, ethylene responsive transcription factor and diaminopimelate decarboxylase, during wilting point. Our data provides valuable information for the gene components and the dynamics of gene expression in second and third leaf against drought stress in tea, which could be regarded as candidate targets potentially associated with drought tolerance. We propose that the identified five tolerant progenies on the basis of their drought tolerance can thus be utilised for future breeding programmes.

Understanding Darjeeling tea flavour on a molecular basis.

Darjeeling teas are the highest grown teas in the world and preferred for its flavour, aroma and quality. Apart from the genetic makeup of the plant, earlier reports suggest that insect infestation, particularly jassids and thrips triggers the aroma and flavour formation in Darjeeling tea. The present work encompasses the identification of the genes/transcriptomes responsible for the typical flavour of Darjeeling tea, besides understanding the role of jassids and thrips in particular, in producing the best cup character and quality. The quantitative real time PCR analysis was based on a suppression subtractive hybridisation forward library of B157 (tea clone infested with thrips), providing us transcripts related to aroma and flavour formation. We observed the expression of genes like leucine zipper, ntd, nced, geraniol synthase, raffinose synthase, trehalose synthase, amylase, farnesyl transferase, catalase, methyl transferase, linalool synthase, peroxidases, elicitor responsive proteins, linamarase, nerolidol linalool synthase 2, 12-oxophytodienoate reductase, glucosidase, MYB transcription factor, and alcohol dehydrogenase, highly regulated due to insect infestation, manufacturing stresses and mechanical injury. The first report on gene expression dynamics in thrips infested Darjeeling tea leaves can be extrapolated with increase in volatiles which is responsible for enhancing the quality of Darjeeling tea, specially the flavour and aroma of the infusion. We hope to model these responses in order to understand the molecular changes that occur during Darjeeling tea flavour formation.