A bioinformatic approach of hydroxyapatite and polymethylmethacrylate composite exploration as dental implant biomaterial

Abstract

Context: The most common biomaterial used for dental implants is titanium. However, the release of metal ions and the risk of allergic reactions to metals that may occur in some patients cannot be avoided. Hydroxyapatite-polymethylmethacrylate (HA-PMMA) composite biomaterials are proposed to have potential as dental implant biomaterials due to their mechanical, chemical, and biological properties. HA-PMMA may induce osseointegration, biocompatible, less allergic reactions, and no metal ions released. In addition, HA-PMMA can be obtained from Indonesia’s abundant natural resources. Aims: To explore HA-PMMA composites through molecular docking as a biomaterial candidate for dental implants in silico. Methods: Structure data format (sdf), molecular weight, and identity number (CID) of HA-PMMA ligand samples were obtained from PubChem database and minimized through OpenBabel. 3D structure, selection method, resolution, atom count, weight, sequence length, and ID protein BMP2, BMP4, BMP7, alkaline phosphatase (AP), osteonectin, osteopontin, and osteocalcin on RCSB-PDB native ligand and water sterilization on PyMol were carried out with the aim of to maximize the formation of binding affinity during molecular docking simulations. Results: HA-PMMA composites can enhance the activity of proteins associated with osseointegration such as BMP-2/4/7, AP, osteocalcin, osteonectin, and osteopontin in silico. HA-PMMA composites have the strongest binding to osteonectin and are predicted to enhance the AP activity in silico. Conclusions: HA-PMMA composites are potential candidates for dental implant biomaterials with the osteointegration ability through binding with BMP-2/4/7, AP, osteocalcin, osteonectin, and osteopontin in silico.

Bioactive Compounds from Purslane (Portulaca oleracea L.) and Star Anise (Illicium verum Hook) as SARS-CoV-2 Antiviral Agent via Dual Inhibitor Mechanism: In Silico Approach

“…29 The bond affinity value that used in this study is the smallest because it indicates the presence of additional stability and higher inhibition activity performed by the ligand towards the protein target. 30,31 The presence of bond types, amino acids on the active side, and amino acid residues on the ligands affects the affinity of the bond between the ligands and receptors. 12 The more hydrogen bonds, the more stable the ligand-protein interaction.…”

“…The negative binding energy generated by hydrogen bonds aids stabilizes the binding between luteolin and TMPRSS2. 30 Pi-pi T shaped interaction is the interaction of electron pi clouds between two aromatic groups in the form of T. 34 The presence of pi-pi T shaped interaction affects the protein stability and flexibility and is important in drug intercalation and supramolecular chemistry. 35,36 PLpro has catalytic triads and important catalytic residues.…”

In Silico Screening of Bioactive Compounds from Syzygium cumini L. and Moringa oleifera L. Against SARS-CoV-2 via Tetra Inhibitors

“…Hydrogen bonds cause the resulting binding affinity to be more negative, thus stabilizing the interaction of myricetin and ellagic acid with the SARS-CoV-2 RBD spike. 34 Furthermore, the presence of weak hydrophobic interactions such as Pi-alkyl, Pi-sigma, and vdw bonds aids the stability and turnover of interactions between ligands and target proteins in cellular processes. 35 SARS-CoV-2 helicase is involved in RNA replication.…”

Molecular docking of polyether ether ketone and nano-hydroxyapatite as biomaterial candidates for orthodontic mini-implant fabrication

“…The screening docking method is used to determine the activity of the ligand against the target protein by referring to the binding affinity produced (Ramadhani et al, 2022). Weak binding interactions are formed when the ligand binds to the target protein domain to contribute to triggering a biological response (Prahasanti et al, 2021). The results showed that the type of chemical interaction formed consisted of hydrogen, van der Waals, pi, and alkyl.…”

“…The 3D structure of the protein-ligand complex was displayed using the PyMol 2.5 version software. Proteins were displayed through the structure of cartoons and transparent surfaces, while sticks for ligands were selected for staining on both molecules (Prahasanti et al, 2021).…”