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3. Super-rapid race for saving lives by developing COVID-19 vaccines

Author

Uttarilli Anusha, Amalakanti Sridhar, Kommoju Phaneeswara-Rao, Sharma Srihari, Goyal Pankaj, Manjunath Gowrang Kasaba, Upadhayay Vineet, Parveen Alisha, Tandon Ravi, Prasad Kumar Suranjit, Dakal Tikam Chand, Ben Shlomo Izhar, Yousef Malik, Neerathilingam Muniasamy, and Kumar Abhishek

Subjects
covid-19, sars-cov-2, vaccine development, Biotechnology, TP248.13-248.65
Abstract

The pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected millions of people and claimed thousands of lives. Starting in China, it is arguably the most precipitous global health calamity of modern times. The entire world has rocked back to fight against the disease and the COVID-19 vaccine is the prime weapon. Even though the conventional vaccine development pipeline usually takes more than a decade, the escalating daily death rates due to COVID-19 infections have resulted in the development of fast-track strategies to bring in the vaccine under a year’s time. Governments, companies, and universities have networked to pool resources and have come up with a number of vaccine candidates. Also, international consortia have emerged to address the distribution of successful candidates. Herein, we summarize these unprecedented developments in vaccine science and discuss the types of COVID-19 vaccines, their developmental strategies, and their roles as well as their limitations.

Published
2021
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6. In silicostudies disclose the underlying link between binding affinity and redox potential in laccase isoforms

Author

Takur, Kiran Raj, Kohli, Mayank, Pande, Kajal, Malik, Ashish, Deshmukh, Apoorva, Kayal, Abhijit, Kommoju, Phaneeswara Rao, and Kulkarni, Naveen

Abstract

AbstractLaccases are copper-containing enzymes belonging to the family of multicopper oxidases (MCOs). All MCOs use molecular oxygen to oxidize a wide range of organic compounds by radical catalysis. One of the key fundamental properties of laccases is having high or low redox potentials depending on the active site organization. Several experimental studies have been done to rationalize the high and low redox potential laccases (LRPL), however, molecular understanding is still lacking. In this work, we explored the proteomic profile of laccases produced in the fungal cultures, specifically induced with lignocellulosic biomass such as rice straw. This study was undertaken to explain the differences in the high redox and low redox potential values of different laccases using in-silico approaches. Proteomic profiling and structural and sequence analysis revealed a low level of similarity among them. Docking analyses and molecular dynamics simulation analysis revealed that high redox potential laccases (HRPL) are having good binding affinity compared to low or medium redox potential laccases (MRPL). The stability of these complexes was further analyzed based on reactive distances, active site volume comparison and a number of tunnel formations that were observed to be significantly higher for HRPL. Our results indicate that the number of tunnel formations calculated from the simulation’s trajectories and available water molecules at the T3 site directly correlates with the laccases’ redox potentials. This study will be helpful and provide valuable inputs for the designing of new laccases to improve lignin degradation.Communicated by Ramaswamy H. Sarma

Published
2023
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8. Factors that affect oxygen activation and coupling of the two redox cycles in the aromatization reaction catalyzed by NikD, an unusual amino acid oxidase

Author

Kommoju, Phaneeswara-Rao, Bruckner, Robert C., Ferreira, Patricia, Carrell, Christopher J., Mathews, F. Scott, and Jorns, Marilyn Schuman

Subjects
Bioflavonoids -- Chemical properties, Flavones -- Chemical properties, Flavonoids -- Chemical properties, Gene mutations -- Analysis, Heterocyclic aromatic compounds -- Structure, Heterocyclic aromatic compounds -- Chemical properties, Oxidases -- Chemical properties, Tyrosine -- Chemical properties, Enzyme binding -- Analysis, Catalysis -- Analysis, Biological sciences, Chemistry
Abstract

A remarkable aromatization reaction comprising two redox cycles and at least one isomerization step observed in NikD, a flavoprotein oxidase that catalyzes the oxidation of piperideine-2-carboxylate (P2C) to picolinate is described. The mutation of Tyr258 in picolinate ring which caused subtle changes in active site dynamics promoted release of the reactive dihydropicolinate intermediate and disrupted the efficient synchronization of oxygen activation observed with wild-type nikD.

Published
2009

9. Probing the role of active site residues in NikD, an unusual amino acid oxidase that catalyzes an aromatization reaction important in nikkomycin biosynthesis

Author

Kommoju, Phaneeswara-Rao, Bruckner, Robert C., Ferreira, Patricia, and Jorns, Marilyn Schuman

Subjects
Binding sites (Biochemistry) -- Physiological aspects, Binding sites (Biochemistry) -- Research, Oxidases -- Physiological aspects, Oxidases -- Research, Biosynthesis -- Research, Antifungal agents -- Research, Biological sciences, Chemistry
Abstract

Stopped-flow studies of the reductive half-reaction with wild-type nikD and piperideine 2-carboxylate (P2C) was carried out gain insight into the ability of the enzyme to oxidize the enamine tautomer of P2C but not distinguish among several possible paths for the initial two-electron oxidation step. The results provides evidence that nikD oxidized the bond between N(1) and C(6) in the enamine tautomer of P2C to rule out alternative paths that require an active site base to mediate the oxidation of a carbon?carbon bond.

Published
2009

10. Heterologer expression der L-aminosauren Oxydase vom calloselasma rhodostoma und Induction der apoptose

Author

Kommoju, Phaneeswara Rao

Subjects
Einschlusskörper [gnd], Pichia pastoris, ddc:570, apoptosis, Pichia pastoris [gnd], Apoptosis [gnd], inclusion bodies, Heterologe Genexpression [gnd], Heterologous expression
Abstract

It has been proposed that L-amino acid oxidases (LAAOs) from different snake venoms interact with the cell membrane receptors to induce many of their toxic effect. This interaction could be mediated by the terminal sialic acids of the N-linked glycan moieties. However no clear and direct evidence has been proposed so far. One of the glycan moieties of LAAO from Calloselasma rhodostoma (CRLAAO) is located near the vicinity of the substrate entry channel, which also serves for the release of the products including the cytotoxic H2O2. To verify the above-mentioned hypothesis, one should have to compare the modes of action by glycosylated and unglycosylted LAAOs. Attempts were made to obtain unglycosylated LAAO either by enzymatic (PNGase-F) treatment or by heterologous expression in E.coli. But no soluble active LAAO could be obtained in either case. Moreover expression in Baculovirus and mammalian expression systems led to secretion of either very little and (or) inactive recombinant enzyme. Expression in Pichia pastoris was successful to some extent in that the active recombinant LAAO could be expressed and purified to near homogeneity. Further standardizations are required inorder to improve the expression yields for characterization of the recombinant enzyme. As an alternative method desialylated native LAAO was also prepared by treatment with neuraminidase and this enzyme was used in the cell culture studies. It was shown that sialic acids have a role in binding of LAAO to the cell surface and internalization, which might be a mechanism to potentiate the effects of H2O2 by enhancing its local concentration. Once being internalized LAAO might further exert toxic effects by generating hydrogen peroxide and metabolizing amino acids and/or other factors important for cell survival. The possible sialic acid receptors mediating the binding of this toxic LAAO are yet to be identified.

Published
2006

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