Aiyi Asnawi, Ellin Febrina, LA Ode Aman, Fachrul Razi
Objective: Molecularly Imprinted Polymers (MIPs) have garnered significant attention as promising materials for the selective recognition of target molecules. Acetoacetate is crucial in diabetes management, especially in Type 1 diabetes and diabetic ketoacidosis (DKA), and monitoring its levels is essential for detecting potential complications. In DKA, there is a lack of insulin resistance, leading to increased production of ketone bodies, including acetoacetate. MIPs, synthetic polymers, selectively bind to target molecules like acetoacetate due to unique three-dimensional structures, which can be quantitatively measured using molecular docking and molecular dynamics simulations. The research objectives were to assess the stability of acetoacetate-MIP complexes and their impact on polyacrylamide-based polymer (PAM) using molecular docking and molecular dynamics, examining their structural and energetic stability over 100 ns. Methods: Five acrylamide-based polymers were investigated using AutoDock Vina for molecular docking and Gromacs for molecular dynamics simulations, focusing on binding affinities, hydrogen bonds, hydrophobic interactions, and complex behaviors over 100 ns. Results: Acetoacetate binds well to the polymers PAM2 and PAM5, with the maximum binding affinity being 2.738 and 2.49 kcal/mol, respectively. PAM1, PAM3, and PAM4 had significant binding affinities; however, PAM4 had a lesser binding affinity of-1.534 kcal/mol, making it less appropriate for acetoacetate-specific MIP applications. The molecular dynamics investigation discovered that PAM5 had the best total energy, indicating a relatively stable interaction environment. Conclusion: The study reveals PAM5 as a promising candidate with high binding affinity and multiple hydrogen bonds with acetoacetate, providing insights for acetoacetate-specific MIP design and molecular recognition progress. © 2023 The Authors. Published by Innovare Academic Sciences Pvt Ltd.
Department of Pharmacochemistry, Faculty of Pharmacy, Universitas Bhakti Kencana, Jl. Soekarno-Hatta No. 754, Bandung, 40617, Indonesia; Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang km. 21, Jatinangor, 45363, Indonesia; Chemistry Department, Universitas Negeri Gorontalo, Jl. Jend. Sudirman No.6, Dulalowo Tim., Kec. Kota Tengah, Kota Gorontalo, Gorontalo, 96128, Indonesia; Chemical Engineering Department, Universitas Syiah Kuala, Jl. Tgk. Syech Abdul Rauf No. 7, Darussalam, Banda Aceh, 23111, Indonesia
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