Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (2019-nCoV), is a positive-sense, single-stranded RNA coronavirus. The virus is the causative agent of coronavirus disease 2019 (COVID-19) and is contagious through human-to-human transmission. The present study reports sequence analysis, complete coordinate tertiary structure prediction and in silico sequence-based and structure-based functional characterization of full SARS-CoV-2 proteome based on the NCBI reference sequence NC_045512 (29903 bp ss-RNA) which is identical to GenBank entry MN908947 and MT415321. The proteome includes 12 major proteins namely orf1ab polyprotein (includes 15 proteins), surface glycoprotein, ORF3a protein, envelope protein, membrane glycoprotein, ORF6 protein, ORF7a protein, orf7b, ORF8, Nucleocapsid phosphoprotein and ORF10 protein. Each protein of orf1ab polyprotein group has been studied separately. A total of 25 polypeptides have been analyzed out of which 15 proteins are not yet having experimental structures and only 10 are having experimental structures with known PDB IDs. Out of 15 newly predicted structures six (6) were predicted using comparative modeling and nine (09) proteins having no significant similarity with so far available PDB structures were modeled using ab-initio modeling. Structure verification using recent tools QMEANDisCo 4.0.0 and ProQ3 for global and local (per-residue) quality estimates indicate that the all-atom model of tertiary structure of high quality and may be useful for structure-based drug designing targets. The study has identified nine major targets (spike protein, envelop protein, membrane protein, nucleocapsid protein, 2’-O-ribose methyltransferase, endoRNAse, 3’-to-5’ exonuclease, RNA-dependent RNA polymerase and helicase) for which drug design targets could be considered. There are other 16 nonstructural proteins (NSPs), which may also be percieved from the drug design angle. The protein structures have been deposited to ModelArchive. Tunnel analysis revealed the presence of large number of tunnels in NSP3, ORF 6 protein and membrane glycoprotein indicating a large number of transport pathways for small ligands influencing their reactivity.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a single-stranded RNA genome that encodes 14 open reading frames (ORFs), eight of which encode accessory proteins that allow the virus to infect the host and promote virulence. The genome expresses around 29 structural and nonstructural protein products. The accessory proteins of SARS-CoV-2 are not essential for virus replication but do affect viral release, stability, and pathogenesis and finally contribute to virulence. This paper has attempted the structure prediction and functional analysis of two such accessory proteins, 9b and ORF14, in the absence of experimental structures. Sequence analysis, structure prediction, functional characterization, and evolutionary analysis based on the UniProtKB reviewed the amino acid sequences of SARS-CoV-2 9b (P0DTD2) and ORF14 (P0DTD3) proteins. Modeling has been presented with the introduction of hybrid comparative and ab initio modeling. QMEANDisCo 4.0.0 and ProQ3 for global and local (per residue) quality estimates verified the structures as high quality, which may be attributed to structure-based drug design targets. Tunnel analysis revealed the presence of 1-2 highly active tunneling sites, perhaps which will able to provide certain inputs for advanced structure-based drug design or to formulate potential vaccines in the absence of a complete experimental structure. The evolutionary analysis of both proteins of human SARS-CoV-2 indicates close relatedness to the bat coronavirus. The whole-genome phylogeny indicates that only the new bat coronavirus followed by pangolin coronaviruses has a close evolutionary relationship with the novel SARS-CoV-2.

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Background: Tea is a natural beverage made from the tender leaves of the tea plant (Camellia sinensis Kuntze). Being of a perennial and monoculture nature in terms of its cultivation system, it provides a stable micro-climate for various insect pests, which cause substantial loss of crop. With the escalating cost of insect pest management and increasing concern about the adverse effects of the pesticide residues in manufactured tea, there is an urgent need to explore other avenues for pest management strategies.Aim: Integrated pest management (IPM) in tea invites an multidisciplinary approach owing to the high pest diversity in the perennial tea plantation system. In this review, we have highlighted current developments of nanotechnology for crop protection and the prospects of nanoparticles (NPs) in plant protection, emphasizing the control of different major pests of tea plantations.Methods: A literature search was performed using the ScienceDirect, Web of Science, Pubmed, and Google Scholar search engines with the following terms: nanotechnology, nanopesticides, tea, and insect pest. An article search concentrated on developments after 1988.Results: We have described the impact of various pests in tea production and innovative approaches on the use of various biosynthesized and syntheric nanopesticides against specific insect pest targets. Simultaneously, we have provided support for NP-based technology and their different categories that are currently employed for the management of pests in different agro-ecosystems. Besides the broad categories of active ingredients (AI) of synthetic insecticides, pheromones and natural resource-based molecules have pesticidal activity and can also be used with NPs as a carriers as alternatives to traditional pest control agents. Finally, the merits and demerits of incorporating NP-based nanopesticides are also illustrated.Conclusions: Nanopesticides for plant protection is an emerging research field, and it offers new methods to design active ingredients amid nanoscale dimensions. Nanopesticide-based formulations have a potential and bright future for the development of more effective and safer pesticide/biopesticides.

Background Entomopathogens are pathogenic to insect pests. Several types of naturally occurring, viz. fungus, bacteria, viruses, and nematodes, infect a range of insect pests and help manage crop growth. They offer several advantages over chemical pesticides, including being precise, safe, and ecologically sustainable. Agricultural systems are streamlined, and changes to natural ecosystems occur. Viruses, bacteria are host-specific, while fungi have a greater host range, and they may infect both soil-dwelling and aboveground pests. Main body The study highlights the current state of knowledge on entomopathogenic microorganisms (EM) (entomopathogenic fungi, nematodes, viruses, bacteria, etc.) as it relates to their current usage as biological pest management. It is essential to enhance our understanding of the ecology of EM and their role in nature to use a variety of biological control techniques against insect hosts. This article may help to comprehend their accomplishments in the significant field. Some recent researches indicated common patterns in interactions between insect pests and EM. Conclusion More focus has been placed on the use of natural enemies like entomopathogens for pest control in recent years. EM expands possibilities for insect control. Eco-friendly alternatives to existing agricultural pesticides are being developed which are utilized to control insect pests and support agricultural sustainability.

<p>This paper has attempted into the structure prediction and functional analysis of two such accessory proteins, 9b and ORF14, in the absence of experimental structures. Sequence analysis, structure prediction, functional characterization, and evolutionary analysis based on the UniProtKB reviewed the amino acid sequences of SARS-CoV-2 9b (P0DTD2) and ORF14 (P0DTD3) proteins. Modeling has been presented with the introduction of hybrid comparative and <i>ab-initio</i> modeling. The evolutionary analysis of both the proteins of human SARS-CoV-2 indicates close relatedness to the bat coronavirus.</p> <p> </p>

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