Molecular investigation of antimicrobial peptides against Helicobacter pylori proteins using a peptide-protein docking approach

Hanafiah, Alfizah; Abd Aziz, Siti Nur Arifah; Md Nesran, Zarith Nameyrra; Wezen, Xavier Chee; Ahmad, Mohd Fadzli

doi:10.1016/j.heliyon.2024.e28128

Cited by 5 publications

(1 citation statement)

References 30 publications

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“…In the paper by Mosseri et al, molecular docking was utilized to construct a model of a WWgc fiber starting from a WW dipeptide unit [45]. The dipeptide unit was used as both a receptor and a ligand in the Haddock software [46][47][48][49][50] to predict its dimeric form through molecular docking techniques. Haddock generated a set of structures from which the most energetically favorable structure of the best cluster was selected.…”

Section: Self-assembly and Biological Properties Of The Non-natural A...mentioning

confidence: 99%

BSA Binding and Aggregate Formation of a Synthetic Amino Acid with Potential for Promoting Fibroblast Proliferation: An In Silico, CD Spectroscopic, DLS, and Cellular Study

Simonyan,

Palumbo,

Petrosyan

et al. 2024

Biomolecules

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This study presents the chemical synthesis, purification, and characterization of a novel non-natural synthetic amino acid. The compound was synthesized in solution, purified, and characterized using NMR spectroscopy, polarimetry, and melting point determination. Dynamic Light Scattering (DLS) analysis demonstrated its ability to form aggregates with an average size of 391 nm, extending to the low micrometric size range. Furthermore, cellular biological assays revealed its ability to enhance fibroblast cell growth, highlighting its potential for tissue regenerative applications. Circular dichroism (CD) spectroscopy showed the ability of the synthetic amino acid to bind serum albumins (using bovine serum albumin (BSA) as a model), and CD deconvolution provided insights into the changes in the secondary structures of BSA upon interaction with the amino acid ligand. Additionally, molecular docking using HDOCK software elucidated the most likely binding mode of the ligand inside the BSA structure. We also performed in silico oligomerization of the synthetic compound in order to obtain a model of aggregate to investigate computationally. In more detail, the dimer formation achieved by molecular self-docking showed two distinct poses, corresponding to the lowest and comparable energies, with one pose exhibiting a quasi-coplanar arrangement characterized by a close alignment of two aromatic rings from the synthetic amino acids within the dimer, suggesting the presence of π-π stacking interactions. In contrast, the second pose displayed a non-coplanar configuration, with the aromatic rings oriented in a staggered arrangement, indicating distinct modes of interaction. Both poses were further utilized in the self-docking procedure. Notably, iterative molecular docking of amino acid structures resulted in the formation of higher-order aggregates, with a model of a 512-mer aggregate obtained through self-docking procedures. This model of aggregate presented a cavity capable of hosting therapeutic cargoes and biomolecules, rendering it a potential scaffold for cell adhesion and growth in tissue regenerative applications. Overall, our findings highlight the potential of this synthetic amino acid for tissue regenerative therapeutics and provide valuable insights into its molecular interactions and aggregation behavior.

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