Molecular dynamics simulations in designing DARPins as phosphorylation-specific protein binders of ERK2

Gautam, Vertika and Nimmanpipug, Piyarat and Zain, Sharifuddin Md and Abd Rahman, Noorsaadah and Lee, Vannajan Sanghiran (2021) Molecular dynamics simulations in designing DARPins as phosphorylation-specific protein binders of ERK2. Molecules, 26 (15). ISSN 1420-3049, DOI

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Extracellular signal-regulated kinases 1 and 2 (ERK1/2) play key roles in promoting cell survival and proliferation through the phosphorylation of various substrates. Remarkable antitumour activity is found in many inhibitors that act upstream of the ERK pathway. However, drug-resistant tumour cells invariably emerge after their use due to the reactivation of ERK1/2 signalling. ERK1/2 inhibitors have shown clinical efficacy as a therapeutic strategy for the treatment of tumours with mitogen-activated protein kinase (MAPK) upstream target mutations. These inhibitors may be used as a possible strategy to overcome acquired resistance to MAPK inhibitors. Here, we report a class of repeat proteins-designed ankyrin repeat protein (DARPin) macromolecules targeting ERK2 as inhibitors. The structural basis of ERK2-DARPin interactions based on molecular dynamics (MD) simulations was studied. The information was then used to predict stabilizing mutations employing a web-based algorithm, MAESTRO. To evaluate whether these design strategies were successfully deployed, we performed all-atom, explicit-solvent molecular dynamics (MD) simulations. Two mutations, Ala -> Asp and Ser -> Leu, were found to perform better than the original sequence (DARPin E40) based on the associated energy and key residues involved in protein-protein interaction. MD simulations and analysis of the data obtained on these mutations supported our predictions.

Item Type: Article
Funders: Ministry of Higher Education (MOHE) through Fundamental Research Grant Scheme (FP125-2019A), Distinguished Research Professor Grant of the National Research Council of Thailand (NRCT 808/2563), Office of National Higher Education Science Research and Innovation Policy Council, Program Management Unit for Human Resources & Institutional Development, Research and Innovation (B05F630102), National Science and Technology Development Agency (NSTDA)
Uncontrolled Keywords: Molecular dynamics simulations; Extracellular regulated kinase; DARPins; MAESTRO
Subjects: Q Science > QD Chemistry
Q Science > QH Natural history > QH301 Biology
Divisions: Faculty of Science > Department of Chemistry
Depositing User: Ms Zaharah Ramly
Date Deposited: 22 Jun 2022 07:47
Last Modified: 22 Jun 2022 07:47

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