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Boceprevir drug is a ketoamide serine protease inhibitor with a linear peptidomimetic structure that exhibits inhibition activity against 2019-nCoV main protease. This paper reports electronic properties of boceprevir and its molecular docking as well as molecular dynamics simulation analysis with protein receptor. For this, the equilibrium structure of boceprevir has been obtained by DFT at B3LYP and ωB97XD levels with 6-311+G(d,p) basis set in gas and water mediums. HOMO–LUMO and absorption spectrum analysis have been used to evaluate the boceprevir’s toxicity and photosensitivity, respectively. Molecular docking simulation has been performed to test the binding affinity of boceprevir with 2019-nCoV MPRO; which rendered a variety of desirable binding locations between the ligand and target protein’s residue positions. The optimum binding location has been considered for molecular dynamics simulation. The findings have been addressed to clarify the boceprevir drug efficacy against the 2019-nCoV MPRO.

Lamivudine (3TC), a nucleoside analogue reverse transcriptase inhibitor (NARTI) that is being widely used to treat HIV infection, has been chosen in this study to investigate its electronic properties, non-linear optical properties (NLO) and absorption spectra along with its inhibition activity with deoxycytidine kinase receptor (PDB ID: 2NOA). For DFT calculations, B3LYP and ωB97XD functionals with 6–311 + G(d,p) basis set have been employed in gas, water and methanol mediums. In molecular docking, it is observed that the binding energies of the 2NOA receptor with lamivudine allow a variety of binding sites, however, the most preferred binding site, has been taken into account for molecular dynamics (MD) simulation. The molecular docking and molecular dynamics simulation results elucidate that lamivudine exhibits better binding and stability with 2NOA protein receptor.

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Restriction enzyme analysis of the rRNA genes of Eruca sativa indicated the presence of many length variants within a single plant and also between different cultivars which is unusual for most crucifers studied so far. Two length variants of the rDNA intergenic spacer (IGS) from a single individual E. sativa (cv. Itsa) plant were cloned and characterized. The complete nucleotide sequences of both the variants (3 kb and 4 kb) were determined. The intergenic spacer contains three families of tandemly repeated DNA sequences denoted as A, B and C. However, the long (4 kb) variant shows the presence of an additional repeat, denoted as D, which is a duplication of a 224 bp sequence just upstream of the putative transcription initiation site. Repeat units belonging to the three different families (A, B and C) were in the size range of 22 to 30 bp. Such short repeat elements are present in the IGS of most of the crucifers analysed so far. Sequence analysis of the variants (3 kb and 4 kb) revealed that the length heterogeneity of the spacer is located at three different regions and is due to the varying copy numbers of repeat units belonging to families A and B. Length variation of the spacer is also due to the presence of a large duplication (D repeats) in the 4 kb variant which is absent in the 3 kb variant. The putative transcription initiation site was identified by comparisons with the rDNA sequences from other plant species.