Molecular docking of polyether ether ketone and nano-hydroxyapatite in orthodontics

J. Pharm. Pharmacogn. Res., vol. 10, no. 4, pp. 676-686, July-August 2022.

Original Article

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

[Acoplamiento molecular de poliéter éter cetona y nano-hidroxiapatita como biomateriales candidatos para la fabricación de mini-implantes de ortodoncia]

I Gusti Aju Wahju Ardani1,2, Alexander Patera Nugraha1,2,3*, Monika Nilam Suryani1, Ryan Hafidz Putra Pamungkas1, Devani Githa Vitamamy1, Rizky Alif Susanto1, Riyanarto Sarno4, Aziz Fajar4, Viol Dhea Kharisma5, Albertus Putera Nugraha6, Tengku Natasha Eleena binti Tengku Ahmad Noor7,8

1Orthodontics Department, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia.

2Dental Implant Research Group, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia.

3Graduate Student of Dental Health Science, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia.

4Department of Informatics, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia.

5Department of Biology, Faculty of Mathematics and Natural Science, Universitas Brawijaya, Malang, Indonesia.

6Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.

7Membership of Faculty of Dental Surgery, Royal College of Surgeons, Edinburgh University, United Kingdom.

8Malaysian Armed Forces Dental Officer, 609 Armed Forces Dental Clinic, Kem Semenggo, Kuching, Sarawak, Malaysia.

*E-mail: alexander.patera.nugraha@fkg.unair.ac.id

Abstract

Context: Modified polyether ether ketone (PEEK) by adding nano-hydroxyapatite (HA) material on its fixture for mini-implant fabrication may increase resistance force through osseointegration.

Aims: To analyze the binding molecular docking of PEEK incorporated with HA as a biomaterial candidate for orthodontic mini-implant fabrication through a bioinformatic approach, an in silico study.

Methods: 3D ligand structure consisting of HA, PEEK and target proteins consisting of osteopontin, osteocalcin, osteonectin, bone morphogenetic protein 4 (BMP4), bone morphogenetic protein 2 (BMP2), bone morphogenetic protein 7 (BMP7), alkaline phosphatase (ALP),  runt-related transcription factor 2 (RUNX2), Insulin growth factor-1 (IGF-1), osterix, tartrate-resistant acid phosphatase (TRAP), collagen alpha-1 (COL1A1) obtained from RCSB-PDB. It was analyzed the binding affinity of a single HA, PEEK, and HA + PEEK complex to twelve target proteins related to osseointegration. The types of chemical interactions produced by the ligands in the target protein domain consisted of Van der Waals, hydrogen, hydrophobic, pi, and alkyl.

Results: The blind docking simulation succeeded in identifying the most negative binding affinity; it was found in the HA + PEEK molecular complex compared to HA and PEEK in the single condition. The type of chemical interaction formed consisted of hydrogen, van der Waals, pi, and alkyl. HA+PEEK showed the most negative binding affinity with ALP and IGF-1, as much as -8.7 binding affinity.

Conclusions: The molecular docking of PEEK with HA exhibited a prominent binding affinity with osteogenic markers like ALP and IGF-1 in silico, allowing it to have a higher potential than nano-HA or PEEK as a single biomaterial for osseointegration as the fabrication of mini-implants that may support orthodontic treatment.

Keywords: dentistry; good health and well-being; in silico; medicine; temporary anchorage device.

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Resumen

Contexto: La poliéter éter cetona modificada (PEEK) puede aumentar la fuerza de resistencia a través de la osteointegración mediante la adición de material de nanohidroxiapatita (HA) para la fabricación de mini-implantes.

Objetivos: Analizar el acoplamiento molecular de PEEK incorporado con HA como candidato a biomaterial para la fabricación de miniimplantes de ortodoncia a través de un enfoque bioinformático, un estudio in silico.

Métodos: Estructura de ligando 3D que consiste en HA, PEEK y proteínas diana como osteopontina, osteocalcina, osteonectina, proteína morfogenética ósea 4 (BMP4), proteína morfogenética ósea 2 (BMP2), proteína morfogenética ósea 7 (BMP7), fosfatasa alcalina (ALP) , factor de transcripción relacionado con runt 2 (RUNX2), factor de crecimiento de insulina-1 (IGF-1), osterix, fosfatasa ácida tartrato resistente (TRAP), colágeno alfa-1 (COL1A1) obtenido de RCSB-PDB. Fue analizada la afinidad de unión del complejo único HA, PEEK y HA + PEEK a doce proteínas diana relacionadas con la osteointegración. Los tipos de interacciones químicas producidas por los ligandos en el dominio de la proteína objetivo consistieron en Van der Waals, hidrógeno, hidrofóbico, pi y alquilo.

Resultados: La simulación a ciegas de acoplamiento logró identificar la afinidad de unión más negativa. Esta se encontró en el complejo molecular HA + PEEK en comparación con HA y PEEK de forma individual. El tipo de interacción química formada consistió en hidrógeno, van der Waals, pi y alquilo. HA+PEEK mostró la afinidad de unión más negativa con ALP e IGF-1, con una afinidad de unión de -8,7.

Conclusiones: El acoplamiento molecular de PEEK con HA exhibió una afinidad de unión prominente con marcadores osteogénicos como ALP e IGF-1 in silico, lo que le permite tener un mayor potencial que HA o PEEK como biomaterial único para la osteointegración como la fabricación de mini-implantes que puedan soportar el tratamiento de ortodoncia.

Palabras Clave: buena salud y bienestar; dispositivo de anclaje temporal; in silico; odontología; medicina.

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Citation Format: Ardani IGAW, Nugraha AP, Suryani NM, Pamungkas RH, Vitamamy DG, Susanto RA, Sarno R, Fajar A, Kharisma VD, Nugraha AP, Noor TNEBTA (2022) Molecular docking of polyether ether ketone and nano-hydroxyapatite as biomaterial candidates for orthodontic mini-implant fabrication. J Pharm Pharmacogn Res 10(4): 676–686.
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