Exploring novel and potent molecules for disrupting DEPTOR-mTOR interaction through structure-steered screening, extra-exactitude molecular docking, prime binding free energy estimation and voguish molecular dynamics

Shah, Basit Amin; Ganai, Shabir Ahmad; Koul, Aabid; Mohan, Suma; Amin, Asif; Wani, Z. A.; Majeed, Umer; Rajamanikandan, Sundaraj; Farooq, Faizah; Malik, Firdose Ahmad; Shah, Naveed Nazir; Qadri, Raies A.

doi:10.1080/07391102.2021.1967785

Cited by 2 publications

(2 citation statements)

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“…Besides, VERIFY3D evaluation also favoured the model quality positively [ 37 ] as 81.45% of the residues scored over or equal to 0.2 against the standard minimum of 80% residues scoring equal to or beyond 0.2 in the 3D/1D profile. The quality of this model was further validated by PROSA plot that was found to be in accordance with the proteins having similar amino acid length [ 43 ]. Therefore, taken together, the distinct validation methods authenticated the quality of refined model for further studies.…”

Section: Discussionmentioning

confidence: 99%

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Molecular and functional characterization of protease from psychrotrophic Bacillus sp. HM49 in North-western Himalaya

et al. 2023

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In this work, a psychrotrophic bacteria producing cold-active protease, was obtained from Dachigam National Park, an ecologically significant habitat in Western Himalayas owing to its varied endemic and endangered flora and fauna. This isolate was identified as Bacillus sp. HM49 via phenotypic, Gram staining, bio-chemical and 16S rRNA gene identification. Isolate HM49 when tested for proteolytic activity revealed prominent hydrolytic zone with the most production at 20 °C and pH, 8.0 post 72 h incubation. This enzyme was purified, enhancing its specific activity to 61.15 U/mg and its characterization studies revealed it to be a cold-alkaline protease being active in a wide pH (6.0–12) and temperature (5–40 °C) range. Amplification of CAASPR gene of HM49 was performed, followed by enzyme-substrate docking studies and MMGBSA providing details about its type, molecular weight validation as well as functional applications. The purified protease of HM49 was tested for laundry applications and the enzyme was found to be compatible with majority of the detergents tested. Its potential as an eco-friendly detergent additive was further validated by wash performance test as it effectively removed recalcitrant blood stains at a low temperature of 20 °C that could be beneficial for fine garments like silk which preferably need cold washing.

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Section: Discussionmentioning

confidence: 99%

“…Default parameters were maintained while the preparation of lactose. The refined model of subtilisin like protease was made fertile for docking through Protein Preparation Wizard [ 43 ]. This component of Schrödinger suite fills missing atoms, side chains and loops.…”

Section: Methodsmentioning

confidence: 99%