Rhizosphere of a halotolerant plant Suaeda fruticosa from saline desert of Little Rann of Kutch, Gujarat (India) was explored for isolation of PGPR form the rare ecological niche having4.33% salinity. Total 85 isolates from the rhizosphere belonging to different species were isolated. Out of 85 isolates, 23 could solubilize phosphate and 11 isolates produced IAA. Seven isolates showed both the traits of phosphate solubilization and IAA production. All isolates which showed either of IAA production or phosphate solubilization or both were further screened for other PGP traits like production of ammonia, siderophore, chitinase, HCN and assessment of their antifungal activity. Out of all the screened isolates, Bacillus licheniformis strain A2 showed most prominent PGP traits in vitro and it was tested in vivo for growth promotion of Groundnut (Arachis hypogaea) under saline soil condition. In presence of soil supplemented with 50 mM NaCl, B. licheniformis treated plants showed increase in fresh biomass, total length and root length by 28%, 24% and 17% and in absence of NaCl it was 43%, 31% and 39% respectively.
The non-structural protein (nsp)-3 of SARS-CoV2 coronavirus is sought to be an essential target protein which is also named as papain-like protease (PLpro). This protease cleaves the viral polyprotein, but importantly in human host it also removes ubiquitin-like interferon-stimulated gene 15 protein (ISG15) from interferon responsive factor 3 (IRF3) protein which ultimately downregulates the production of type I interferon leading to weakening of immune response. GRL0617 is the most potent known inhibitor for PLpro that was initially developed for SARS outbreak of 2003. The PLpro of SARS-CoV and CoV2 share 83% sequence identity but interestingly have several identical conserved amino acids that suggests GRL0617 to be an effective inhibitor for PLpro of SARS-CoV2. GRL0617 is a naphthalene-based molecule and interacts with Tyr268 of SARS-CoV2-PLpro (and Tyr269 of SARS-CoV-PLpro). To identify PLpro inhibitors, we prepared a library of secondary metabolites from fungi with aromatic nature and docked them with PLpro of SARS-CoV and SARS-CoV2. We found six hits which interacts with Tyr268 of SARS-CoV2-PLpro (and Tyr269 of SARS-CoV-PLpro). More surprisingly the top hit, Fonsecin, has naphthalene moiety in its structure, which recruits Tyr268 of SARS-CoV2-PLpro (and Tyr269 of SARS-CoV-PLpro) and has binding energy at par with control (GRL0617). Molecular dynamics (MD) simulation showed Fonsecin to interact with Tyr268 of SARS-CoV2-PLpro more efficiently than control (GRL0617) and interacting with a greater number of amino acids in the binding cleft of PLpro.
Graphic abstract
The novel SARS-CoV-2 is the etiological agent causing the Coronavirus disease 2019 (COVID-19), which continues to become an inevitable pandemic outbreak. Over a short span of time, the structures of therapeutic target proteins for SARS-CoV-2 were identified based on the homology modelled structure of similar SARS-CoV transmission of 2003. Since the onset of the disease, the research community has been looking for a potential drug lead. Out of all the known resolved structures related to SARS-CoV, Main protease (M
pro
) is considered an attractive anti-viral drug target on the grounds of its role in viral replication and probable non-interactive competency to bind to any viral host protein. To the best of our knowledge, till date only one compound has been identified and tested
in-vivo
as a potent inhibitor of M
pro
protein, addressed as N3 (PubChem Compound CID: 6323191) and is known to bind irreversibly to M
pro
suppressing its activity. Using computational approach, we intend to identify a probable natural fungal metabolite to interact and inhibit M
pro
. After screening various small molecules for molecular docking and dynamics simulation, we propose Pyranonigrin A, a secondary fungal metabolite to possess potent inhibitory potential against the Main protease (M
pro
) expressed in SARS-CoV-2 virus.
Bacterium Pseudomonas spp. olive green (OG) was isolated from marine water, yet, it was characterized as plant growth promoting bacterium (PGPB). Multiple plant growth promoting traits of OG isolate were determined in vitro. It was tested positive for Indole-3-acetic acid (IAA) production with 29 mg ml (1 of IAA yield, phosphate solubilization with 34 mg ml (1 solubilization of Tri-calcium-phosphate and it showed maximum of 32 mg ml (1 of ammonia production. OG isolate was affirming siderophore production, hydrocyanic acid (HCN) production and catalase production. 16S rRNA gene sequence comparison was used to identify the isolate which showed its closest neighbor to be Pseudomonas fluoroscens strain BCPBMS-1. Efficacy of this PGPB was tested on the seedling growth of two test plants chickpea and green gram. Both the test plants treated with OG-based talc bioformulation showed significant growth promotion. Chickpea showed enhanced overall fresh biomass by 24%, overall dry biomass by 27% was observed after 15 days of seeded in pots. Green gram showed enhanced overall dry biomass by 28% was observed after 10 days of seeded in pots.
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