SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel coronavirus for which no known effective antiviral drugs are available. In the present study, to accelerate the discovery of potential drug candidates, bioinformatics-based in silico drug discovery approaches are utilized. We performed multiple sequence alignments of the Spike (S) protein with 75 sequences of different viruses from the Orthocoronavirinae subfamily. This provided us with insights into the evolutionarily conserved domains that can be targeted using drugs or specific antibodies. Further, we analyzed the mechanism of SARS-CoV-2 core proteins, i.e., S and RdRp (RNA-dependent RNA polymerase), to elucidate how the virus infection can utilize hemoglobin to decrease the blood oxygen level. Moreover, after a comprehensive literature survey, more than 60 antiviral drugs were chosen. The candidate drugs were then ranked based on their potential to interact with the Spike and RdRp proteins of SARS-CoV-2. The present multidimensional study further advances our understanding of the novel viral molecular targets and potential of computational approaches for therapeutic assessments. The present study can be a steppingstone in the selection of potential drug candidates to be used either as a treatment or as a reference point when designing a new drug/antibody/inhibitory peptide/vaccine against SARS-CoV-2.

The present research investigates the tuber proteome of the ‘medicinal’ plant Jerusalem artichoke (abbreviated as JA) (Helianthus tuberosus L.) using a high-throughput proteomics technique. Although JA has been historically known to the Native Americans, it was introduced to Europe in the late 19th century and later spread to Japan (referred to as ‘kiku-imo’) as a folk remedy for diabetes. Genboku Takahashi research group has been working on the cultivation and utilization of kiku-imo tuber as a traditional/alternative medicine in daily life and researched on the lowering of blood sugar level, HbA1c, etc., in human subjects (unpublished data). Understanding the protein components of the tuber may shed light on its healing properties, especially related to diabetes. Using three commercially processed JA tuber products (dried powder and dried chips) we performed total protein extraction on the powdered samples using a label-free quantitate proteomic approach (mass spectrometry) and catalogued for the first time a comprehensive protein list for the JA tuber. A total of 2967 protein groups were identified, statistically analyzed, and further categorized into different protein classes using bioinformatics techniques. We discussed the association of these proteins to health and disease regulatory metabolism. Data are available via ProteomeXchange with identifier PXD030744.

Higher temperature conditions during the final stages of rice seed development (seed filling and maturation) are known to cause damage to both rice yield and rice kernel quality. The western and central parts of Japan especially have seen record high temperatures during the past decade, resulting in the decrease of rice kernel quality. In this study, we looked at the rice harvested from a town in the central Kanto-plains (Japan) in 2010. The daytime temperatures were above the critical limits ranging from 34 to 38 °C at the final stages of seed development and maturity allowing us to investigate high-temperature effects in the actual field condition. Three sets of dry mature rice seeds (commercial), each with specific quality standards, were obtained from Japan Agriculture (JA Zen-Noh) branch in Ami-town of Ibaraki Prefecture in September 2010: grade 1 (top quality, labeled as Y1), grade 2 (medium quality, labeled as Y2), and grade 3 (out-of-grade or low quality, labeled as Y3). The research objective was to examine particular alterations in genome-wide gene expression in grade 2 (Y2) and grade 3 (Y3) seeds compared to grade 1 (Y1). We followed the high-temperature spike using a high-throughput omics-approach DNA microarray (Agilent 4 × 44 K rice oligo DNA chip) in conjunction with MapMan bioinformatics analysis. As expected, rice seed quality analysis revealed low quality in Y3 > Y2 over Y1 in taste, amylose, protein, and fatty acid degree, but not in water content. Differentially expressed gene (DEG) analysis from the transcriptomic profiling data revealed that there are more than one hundred upregulated (124 and 373) and downregulated (106 and 129) genes in Y2 (grade 2 rice seed) and Y3 (grade 3 rice seed), respectively. Bioinformatic analysis of DEGs selected as highly regulated differentially expressed (HRDE) genes revealed changes in function of genes related to metabolism, defense/stress response, fatty acid biosynthesis, and hormones. This research provides, for the first time, the seed transcriptome profile for the classified low grades (grade 2, and out-of-grade; i.e., grade 3) of rice under high-temperature stress condition.