Understanding Mutations in Human SARS-CoV-2 Spike Glycoprotein: A Systematic Review & Meta-Analysis.

Genetic variant(s) of concern (VoC) of SARS-CoV-2 have been emerging worldwide due to mutations in the gene encoding spike glycoprotein. We performed comprehensive analyses of spike protein mutations in the significant variant clade of SARS-CoV-2, using the data available on the Nextstrain server. We selected various mutations, namely, A222V, N439K, N501Y, L452R, Y453F, E484K, K417N, T478K, L981F, L212I, N856K, T547K, G496S, and Y369C for this study. These mutations were chosen based on their global entropic score, emergence, spread, transmission, and their location in the spike receptor binding domain (RBD). The relative abundance of these mutations was mapped with global mutation D614G as a reference. Our analyses suggest the rapid emergence of newer global mutations alongside D614G, as reported during the recent waves of COVID-19 in various parts of the world. These mutations could be instrumentally imperative for the transmission, infectivity, virulence, and host immune system's evasion of SARS-CoV-2. The probable impact of these mutations on vaccine effectiveness, antigenic diversity, antibody interactions, protein stability, RBD flexibility, and accessibility to human cell receptor ACE2 was studied in silico. Overall, the present study can help researchers to design the next generation of vaccines and biotherapeutics to combat COVID-19 infection.

Redox interactome in malaria parasite Plasmodium falciparum.

The malaria-causing parasite Plasmodium falciparum is a severe threat to human health across the globe. This parasite alone causes the highest morbidity and mortality than any other species of Plasmodium. The parasites dynamically multiply in the erythrocytes of the vertebrate hosts, a large number of reactive oxygen species that damage biological macromolecules are produced in the cell during parasite growth. To relieve this intense oxidative stress, the parasite employs an NADPH-dependent thioredoxin and glutathione system that acts as an antioxidant and maintains redox status in the parasite. The mutual interaction of both redox proteins is involved in various biological functions and the survival of the erythrocytic stage of the parasite. Since the Plasmodium species is deficient in catalase and classical glutathione peroxidase, so their redox balance relies on a complex set of five peroxiredoxins, differentially positioned in the cytosol, mitochondria, apicoplast, and nucleus with partly overlapping substrate preferences. Moreover, Plasmodium falciparum possesses a set of members belonging to the thioredoxin superfamily, such as three thioredoxins, two thioredoxin-like proteins, one dithiol, three monocysteine glutaredoxins, and one redox-active plasmoredoxin with largely redundant functions. This review paper aims to discuss and encapsulate the biological function and current knowledge of the functional redox network of Plasmodium falciparum.

Identification and characterization of a novel prolyl oligopeptidase in filarial parasite Setaria cervi.

A 75 kDa serine protease having prolyl oligopeptidase activity has been purified from Setaria cervi, a bovine filarial parasite. The MALDI-MS/MS analysis of the purified protein revealed 6 peptides showing nearest match S9A (prolyl oligopeptidase) family protein from Plesiocystis pacifica. The ScPOP was found to be unique compared to mammalian POP with respect to its kinetic properties. To elucidate its role, filarial parasites were exposed to specific inhibitor of POP, Z-Pro-prolinal (ZPP) for 8 h. The inhibition of POP induced calcium signaling via phospholipase c stimulation which further triggered mitochondrial mediated apoptosis in filarial parasites.

Inhibition of Setaria cervi protein tyrosine phosphatases by Phenylarsine oxide: A proteomic and biochemical study.

Phenylarsine oxide (PAO), a specific protein tyrosine phosphatase (PTP) inhibitor significantly decreased the motility and viability of Setaria cervi ultimately leading to its death. The PTP activity present in the cytosolic and detergent soluble fractions as well as on surface of these parasites was significantly inhibited by PAO. A marked alteration in protein spots abundance after proteomic analysis showed 14 down-regulated and 9 upregulated spots in the treated parasites as compared to the control. The PTP inhibition led to increase in the cytosolic and mitochondrial calpain activity in these parasites. PAO also blocked the ATP generation in the parasite depicted by reduced activity of phosphoglycerate kinase and expression of enolase. An increased ROS level, induced lipid peroxidation/protein carbonyl formation and decreased activity of different antioxidant enzymes like thioredoxin reductase, glutathione reductase and glutathione transferases was also observed in the PAO treated parasites. PAO, thus disturbs the overall homeostasis of the filarial parasite by inhibiting PTPs. Thereby suggesting that these molecules could be used as a good chemotherapeutic target for lymphatic filariasis.

Effect of CDNB on filarial thioredoxin reductase : A proteomic and biochemical approach.

Thioredoxin reductase plays a crucial role in the maintenance of cellular redox homeostasis. In this study, we have targeted TrxR in Setaria cervi, a bovine filarial parasite using its inhibitor CDNB. It caused significant decrease in the motility and viability of these parasites leading to their death. Inhibition of TrxR leads to the downregulation of the antioxidant system followed by generation of oxidative stress in these parasites. The increased ROS level induced lipid peroxidation and protein carbonyl formation which might alter the mitochondrial membrane permeability leading to release of cytochrome c. CDNB significantly downregulated the level of ced-9 and activity of tyrosine phosphatases, cytochrome c oxidase. It also upregulated ced-3, homolog of mammalian caspase 3 suggesting initiation of intrinsic pathway of apoptosis. The proteomic profile of CDNB treated parasites showed marked alteration in abundance of different protein spots with 20% downregulated and 13% unregulated spots in comparison to control parasites. We observed a downregulation in the glycolytic enzymes such as enolase, PGK, and GAPDH thereby blocking the ATP formation in the parasite. This study suggests that TrxR inhibition disrupts the cellular homeostasis thereby generating oxidative stress followed by mitochondrial mediated apoptosis in filarial parasites leading to the death of the parasites. BIOLOGICAL SIGNIFICANCE: Lymphatic filariasis is one of the most prevalent tropical diseases caused by tissue dwelling parasitic nematodes viz., Wuchereria bancrofti, Brugia malayi and Brugia timori. Currently available antifilarial drugs effectively eliminate larval stages of the parasite but are ineffective against the adult worms. Therefore, there is an urgent need for finding proteins/enzymes which play a crucial role in the persistence of these parasites. Our study for the first time reports the important role played by S. cervi TrxR in its survival. Thus, suggesting filarial TrxR as a potent chemotherapeutic target against lymphatic filariasis. This would help in screening of new compounds having macrofilaricidal activity.

MALDI mass sequencing and biochemical characterization of Setaria cervi protein tyrosine phosphatase.

A 30-kDa acid phosphatase with protein tyrosine phosphatase activity was identified in Setaria cervi (ScPTP). The enzyme was purified to homogeneity using three-step column chromatography. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) analysis of purified ScPTP yielded a total of eight peptides matching most closely to phosphoprotein phosphatase of Ricinus communis (RcPP). A hydrophilicity plot of RcPP revealed the presence of these peptides in the hydrophilic region, suggesting their antigenic nature. The substrate specificity of ScPTP with ortho-phospho-L-tyrosine and inhibition with sodium orthovanadate and ammonium molybdate affirmed it as a protein tyrosine phosphatase. ScPTP was also found to be tartrate resistant. The Km and Vmax were 6.60 mM and 83.3 µM/ml/min, respectively, with pNPP and 8.0 mM and 111 µM/ml/min, respectively, with ortho-phospho-L-tyrosine as the substrate. The Ki value with sodium orthovanadate was calculated to be 16.10 mM. Active site modification with DEPC, EDAC and pHMB suggested the presence of histidine, cysteine and aspartate at its active site. Thus, on the basis of MALDI-TOF and biochemical studies, it was confirmed that purified acid phosphatase is a PTP.