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A compound that could inhibit multiple targets associated with SARS-CoV-2 infection would prove to be a drug of choice against the virus. Human receptor-ACE2, receptor binding domain (RBD) of SARS-CoV-2 S-protein, Papain-like protein of SARS-CoV-2 (PLpro), reverse transcriptase of SARS-CoV-2 (RdRp) were chosen for in silico study. A set of previously synthesized compounds ( 1 - 5 ) were docked into the active sites of the targets. Based on the docking score, ligand efficiency, binding free energy, and dissociation constants for a definite conformational position of the ligand, inhibitory potentials of the compounds were measured. The stability of the protein-ligand (P-L) complex was validated in silico by using molecular dynamics simulations using the YASARA suit. Moreover, the pharmacokinetic properties, FMO and NBO analysis were performed for ranking the potentiality of the compounds as drug. The geometry optimizations and electronic structures were investigated using DFT. As per the study, compound- 5 has the best binding affinity against all four targets. Moreover, compounds 1, 3 and 5 are less toxic and can be considered for oral consumption., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Authors.)

Density Functional Theory (DFT) and Quantitative Structure-Activity Relationship (QSAR) studies were performed on four benzimidazoles (compounds 1-4) and two benzothiazoles (compounds 5 and 6), previously synthesized by our group. The compounds were also investigated for their binding affinity and interactions with the SARS-CoV-2 M pro (PDB ID: 6LU7) and the human angiotensin-converting enzyme 2 (ACE2) receptor (PDB ID: 6 M18) using a molecular docking approach. Compounds 1, 2, and 3 were found to bind with equal affinity to both targets. Compound 1 showed the highest predictive docking scores, and was further subjected to molecular dynamics (MD) simulation to explain protein stability, ligand properties, and protein-ligand interactions. All compounds were assessed for their structural, physico-chemical, pharmacokinetic, and toxicological properties. Our results suggest that the investigated compounds are potential new drug leads to target SARS-CoV-2., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Author(s).)

A three-dimensional model of the PsbS protein was built with the help of homology-modeling methods. This protein is also known as CP22 and is associated with the protection of photosystem II of thylakoid from excess quanta of light energy absorbed by the photosynthetic apparatus. PsbS is reported to bind two molecules of zeaxanthin at low pH (<5.0) and is believed to be essential for rapid nonphotochemical quenching (qE) of chlorophyll a fluorescence in photosystem II. An attempt was made to explain the pH modulation of the conformation of protein through salt-bridges Glu(-)(122)-Lys(+)(113) and Glu(-)(226)-Lys(+)(217). Binding of two molecules of zeaxanthin in the three-dimensional model of PsbS is postulated. The molecular mechanism of photoprotection by PsbS is explained through the model.

A method has been developed to calculate and represent the geometry of alpha-helices of membrane proteins. Geometrical parameters are computed from coordinate files in the protein data bank. The axis of the helix is determined from the local centroids of tetrapeptide units of the helix. The method provides lower and upper cutoff values of the distance between backbone atoms C(i)(carbonyl carbon) and N(i+4) for allocation of a hinge in a helix. The method calculates other geometrical parameters like the length of helix, twist per residue, height per residue, kink and swivel angles. Packing of bundles of alpha-helices is represented by relative angles of inclination and distance vectors. The parameters are useful in quantitative descriptions of structural features of membrane proteins. [figure]. Representation of the organization of the helix bundle in 1rwt by helix axis Theta1( i)- Theta(n)( i), helix center Theta0( i) of i(th) helix and centroid (C) of centers the three helices. Arrow-head indicates C-terminal end of a helix.

On the basis of existing evidence, a model is proposed for the topology of carotenoids in photosystem II (PS II) of chloroplasts. suggesting their possible roles in the photoprotection and stability of PS II complex. The presence of one cis and one trans beta-carotene at reaction centre II (RC II), with different photoprotective functions, is suggested. The core antennae (CP43, CP47) are presumed to contain beta-carotene molecules in clusters. The possible molecular mechanism for formation of a quenching complex in the minor LHC II, involving zeaxanthin, chlorophyll a and the glutamic acid side chain of the light harvesting protein, is worked out. This complex is proposed to be an efficient triplet quencher, in addition to its role as a quencher of singlet chlorophyll energy. The migration of triplet energy from RC II to the quenching complex is surmised. It is suggested that the carotenoids in RC II and in different LHCs form an integrated photoprotective unit.