Identification of Phytochemicals from Arabian Peninsula Medicinal Plants as Strong Binders to SARS-CoV-2 Proteases (3CLPro and PLPro) by Molecular Docking and Dynamic Simulation Studies.

We provide promising computational (in silico) data on phytochemicals (compounds 1-10) from Arabian Peninsula medicinal plants as strong binders, targeting 3-chymotrypsin-like protease (3CLPro) and papain-like proteases (PLPro) of SARS-CoV-2. Compounds 1-10 followed the Lipinski rules of five (RO5) and ADMET analysis, exhibiting drug-like characters. Non-covalent (reversible) docking of compounds 1-10 demonstrated their binding with the catalytic dyad (CYS145 and HIS41) of 3CLPro and catalytic triad (CYS111, HIS272, and ASP286) of PLPro. Moreover, the implementation of the covalent (irreversible) docking protocol revealed that only compounds 7, 8, and 9 possess covalent warheads, which allowed the formation of the covalent bond with the catalytic dyad (CYS145) in 3CLPro and the catalytic triad (CYS111) in PLPro. Root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and radius of gyration (Rg) analysis from molecular dynamic (MD) simulations revealed that complexation between ligands (compounds 7, 8, and 9) and 3CLPro and PLPro was stable, and there was less deviation of ligands. Overall, the in silico data on the inherent properties of the above phytochemicals unravel the fact that they can act as reversible inhibitors for 3CLPro and PLPro. Moreover, compounds 7, 8, and 9 also showed their novel properties to inhibit dual targets by irreversible inhibition, indicating their effectiveness for possibly developing future drugs against SARS-CoV-2. Nonetheless, to confirm the theoretical findings here, the effectiveness of the above compounds as inhibitors of 3CLPro and PLPro warrants future investigations using suitable in vitro and in vivo tests.

Covalent Inhibitors from Saudi Medicinal Plants Target RNA-Dependent RNA Polymerase (RdRp) of SARS-CoV-2.

COVID-19, a disease caused by SARS-CoV-2, has caused a huge loss of human life, and the number of deaths is still continuing. Despite the lack of repurposed drugs and vaccines, the search for potential small molecules to inhibit SARS-CoV-2 is in demand. Hence, we relied on the drug-like characters of ten phytochemicals (compounds 1-10) that were previously isolated and purified by our research team from Saudi medicinal plants. We computationally evaluated the inhibition of RNA-dependent RNA polymerase (RdRp) by compounds 1-10. Non-covalent (reversible) docking of compounds 1-10 with RdRp led to the formation of a hydrogen bond with template primer nucleotides (A and U) and key amino acid residues (ASP623, LYS545, ARG555, ASN691, SER682, and ARG553) in its active pocket. Covalent (irreversible) docking revealed that compounds 7, 8, and 9 exhibited their irreversible nature of binding with CYS813, a crucial amino acid in the palm domain of RdRP. Molecular dynamic (MD) simulation analysis by RMSD, RMSF, and Rg parameters affirmed that RdRP complexes with compounds 7, 8, and 9 were stable and showed less deviation. Our data provide novel information on compounds 7, 8, and 9 that demonstrated their non-nucleoside and irreversible interaction capabilities to inhibit RdRp and shed new scaffolds as antivirals against SARS-CoV-2.

Myristica fragrans bio-active ester functionalized ZnO nanoparticles exhibit antibacterial and antibiofilm activities in clinical isolates.

We provide a novel one-step/one-pot bio-inspired method of synthesis for Myristica fragrans leaf ester (MFLE) capped­zinc oxide nanoparticles (MFLE-ZnONPs). Antibacterial and antbiofilm efficacies of MFLE-ZnONPs were tested against the multi-drug resistant (MDR) Escherichia coli (E. coli-336), methicillin-resistant Staphylococcus aureus (MRSA-1) and methicillin-sensitive (MSSA-2) clinical isolates. Antibacterial screening using well diffusion assay revealed the cytotoxicity of MFLE-ZnONPs in the range of 500-2000 µg/ml. MFLE-ZnONPs significantly increased the zone of growth inhibition of E. coli-336 (17.0 ±â€¯0.5 to 19.25 ±â€¯1.0 mm), MSSA-2 (16.75 ±â€¯0.8 to 19.0 ±â€¯0.7 mm) and MRSA-1 (16.25 ±â€¯1.0 to 18.25 ±â€¯0.5 mm), respectively. The minimum inhibitory concentration (MIC) and minimum bactericidal concentrations (MBC) against E. coli-336, MRSA-1 and MSSA-2 were found to be 1500, 1000 and 500 µg/ml, and 2500, 2000 and 1500 µg/ml, respectively. A time and dose dependent reduction in the cell proliferation were also found at the respective MICs of tested strains. Scanning electron microscopy (SEM) of MFLE-ZnONPs-treated strains exhibited cellular damage via loss of native rod and coccoid shapes because of the formation of pits and cavities. E. coli-336 and MRSA-1 strains at their MICs (1500 and 1000 µg/ml) sharply reduced the biofilm production to 51% and 24%. The physico-chemical characterization via x-ray diffraction (XRD) ascertained the crystallinity and an average size of MFLE-ZnONPs as 48.32 ±â€¯2.5 nm. Gas chromatography-mass spectroscopy (GC-MS) analysis of MFLE-ZnONPs unravelled the involvement of two bio-active esters (1) butyl 3-oxobut-2-yl ester and (2) α-monoolein) as surface capping/stabilizing agents. Fourier transform infrared (FTIR) analysis of MFLE and MFLE-ZnONPs showed the association of amines, alkanes, aldehydes, amides, carbonyl and amines functional groups in the corona formation. Overall, our data provide novel insights on the rapid development of eco-friendly, cost-effective bio-synthesis of MFLE-ZnONPs, showing their putative application as nano-antibiotics against MDR clinical isolates.

Comparative in situ ROS mediated killing of bacteria with bulk analogue, Eucalyptus leaf extract (ELE)-capped and bare surface copper oxide nanoparticles.

This study demonstrates a simple one-pot green method for biosynthesis of terpenoids encapsulated copper oxide nanoparticles (CuONPs) using aqueous leaf extract of Eucalyptus globulus (ELE), as reducing, dispersing, and stabilizing agent. Indeed, the greater attachment and internalization of ELE-CuONPs in Gram-positive and -negative biofilm producing clinical bacterial isolates validated the hypothesis that terpenoids encapsulated CuONPs are more stable and effective antibacterial and antibiofilm agent vis-à-vis commercially available nano and micro sized analogues. Gas chromatography-mass spectroscopy (GC-MS) analysis of pristine ELE identified 17 types of terpenoids based on their mass-to-charge (m/z) ratios. Amongst them four bioactive terpenoids viz. terpineols, 2,6-octadienal-3,7-dimethyl, benzamidophenyl-4-benzoate and ß-eudesmol were found associated with the CuONPs as ELE-cap, and most likely involved in the nucleation and stabilization of ELE-CuONPs. Further, the Fourier transformed infrared (FTIR) analysis of ELE-CuONPs also implicated other functional biomolecules like proteins, sugars, alkenes, etc. with ELE terpenoids corona. Flow cytometric (FCM) data exhibited significantly enhanced intracellular uptake propensity of terpenoids encapsulated ELE-CuONPs and accumulation of intracellular reactive oxygen species (ROS), which ensued killing of planktonic cells of extended spectrum ß-lactamases (ESßL) producing Escherichia coli-336 (E. coli-336), Pseudomonas aeruginosa-621 (P. aeruginosa-621) and methicillin-resistant Staphylococcus aureus-1 (MRSA-1) clinical isolates compared to the bare surface commercial nano-CuO and bulk sized CuO. The study for the first-time demonstrated the (i) differential bio-nano interface activities due to ELE surface and varied cell wall composition of test bacterial isolates, (ii) antibacterial effect and biofilm inhibition due to disruption of proteins involved in adhesion and biofilm formation triggered by CuONPs induced intracellular oxidative stress, and (iii) indigenous terpenoids-capped bio-inspired CuONPs are more stable and effective antibacterial and antibiofilm agent as compared with commercially available nano-CuO and bulk-CuO.