Browsing by Author "Kadhirvel, Saraboji"

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Advances in the computational methods to understand protein folding and stability
(Inderscience Publishers, 2022-11-09T00:00:00) Srikanth, Srimari; Srinivasan, Thamarai Selvi; Prabhu, Dhamodharan; Kadhirvel, Saraboji
Understanding the molecular basis of life is important for advances in fundamental and applied biological research. Numerous and complex biological activities occur simultaneously in all living cells in a controlled manner to execute an optimal equilibrium and function. Specifically, life depends on the regular functioning of the protein molecules, which depends upon the attainment of the correct three-dimensional structure and its stability. Therefore, deducing a fundamental understanding of how proteins fold and stabilise in the native states is of great intellectual and technological significance. Similar to all natural events, protein folding is a physicochemical process that is much more complex in-vivo, with the association of chaperones and/or other co-factors. Perturbations in protein�s stability results in misfolded proteins and their aggregated forms associated with protein misfolding disorders. Interestingly, researchers are involved in developing computational methods to predict the folded state of the protein and its stabilising mechanisms, which are essential in designing biotechnologically and medicinally important protein molecules. The present review aims to explore developments in the computational procedures which aid in understanding protein folding and stability and its applications. Copyright � 2021 Inderscience Enterprises Ltd.
Computational identification and experimental validation of anti-filarial lead molecules targeting metal binding/substrate channel residues of Cu/Zn SOD1 from Wuchereria bancrofti
(Taylor and Francis Ltd., 2022-10-28T00:00:00) Sureshan, Muthusamy; Prabhu, Dhamodharan; Kadhirvel, Saraboji
Lymphatic filariasis (LF) is a neglected mosquito-borne parasitic disease, widely caused by Wuchereria bancrofti (Wb) in tropical and sub-tropical countries. During a blood meal, the filarial nematodes are transmitted to humans by the infected mosquito. To counter attack the invaded nematodes, the human immune system produces reactive oxygen species. However, the anti-oxidant enzymes of nematodes counteract the host oxidative cytotoxicity. Cu/Zn Superoxide dismutase (SOD1), a member of antioxidant enzymes and are widely used by the nematodes to sustain the host oxidative stress across its lifecycle, hence targeting SOD1 to develop suitable drug molecules would help to overcome the problems related to efficacy and activity of drugs upon different stages of nematodes. In order to find the potent inhibitors, a three-dimensional structure of Cu/Zn WbSOD1 was modelled and the structural stability was analysed through simulation studies. The structure-guided virtual screening approach has been used to identify lead molecules from the ChemBridge based on the docking score, ADMET properties and protein�ligand complex stability analysis. The identified compounds were observed to interact with the copper, metal binding residues (His48, His63, His80 and His120) and catalytically important residue Arg146, which play a crucial role in the disproportionation of incoming superoxide radicals of Cu/Zn WbSOD1. Further, in�vitro validation of the selected leads in the filarial worm Setaria digitata exhibited higher inhibition and better IC50 compared to the standard drug ivermectin. Thus, the identified leads could potentially inhibit enzyme activity, which could subsequently act as drug candidates to control LF. Communicated by Ramaswamy H. Sarma. � 2022 Informa UK Limited, trading as Taylor & Francis Group.
Discovery of plant-based phytochemical�as effective antivirals that target the non-structural protein C of the Nipah virus through computational methods
(Taylor and Francis Ltd., 2023-05-24T00:00:00) Sureshan, Muthusamy; Prabhu, Dhamodharan; Joshua, Sharon Nissi; Sasikumar, Shruti Vardhini; Rajamanikandan, Sundarraj; Govindhapriya, Muthukumar; Umadevi, Venkatachalam; Kadhirvel, Saraboji
Nipah Virus (NiV) belongs to the Paramyxoviridae family and was first identified during an outbreak in Malaysia. Some initial symptoms include mild fever, headache and sore throat, which could escalate to respiratory illness and brain inflammation. The mortality rate of NiV infection can range from 40% to 75%, which is quite high. This is mainly due to the lack of efficient drugs and vaccines. In most instances, NiV is transmitted from animals to humans. Non-Structural Proteins (C, V and W) of the Nipah virus impede the host immune response by obstructive the JAK/STAT pathway. However, Non-Structural Proteins�C (NSP-C) plays a vital role in NiV pathogenesis, which includes IFN antagonist activity and viral RNA production. In the present study, the full-length structure of NiV-NSP-C was predicted using computational modelling, and the stability of the structure was analysed using 200 ns molecular dynamic (MD) simulation. Further, the structure-based virtual screening identified five potent phytochemicals (PubChem CID: 9896047, 5885, 117678, 14887603 and 5461026) with better binding affinity against NiV-NSP-C. DFT studies clearly showed that the phytochemicals had higher chemical reactivity, and the complex MD simulation depicted that the identified inhibitors exhibited stable binding with NiV-NSP-C. Furthermore, experimental validation of these identified phytochemicals would likely control the infection of NiV. Communicated by Ramaswamy H. Sarma. � 2023 Informa UK Limited, trading as Taylor & Francis Group.