Tag Archives: in silico

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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© 2022 Journal of Pharmacy & Pharmacognosy Research (JPPRes)

Multi-epitope spike glycoprotein vaccine for SARS-CoV-2

J. Pharm. Pharmacogn. Res., vol. 10, no. 3, pp. 445-458, May-June 2022.

Original Article

Development of a multi-epitope spike glycoprotein vaccine to combat SARS-CoV-2 using the bioinformatics approach

[Desarrollo de una vacuna de glicoproteína spike multiepítopo para combatir el SARS-CoV-2 utilizando el enfoque bioinformático]

Aamir Shehzad1, Christijogo Sumartono2, Jusak Nugraha3, Helen Susilowati4, Andi Yasmin Wijaya4, Hafiz Ishfaq Ahmad5, Muhammad Kashif6, Wiwiek Tyasningsih7, Fedik Abdul Rantam1,4*

1Virology and Immunology Laboratory, Division of Microbiology, Faculty of Veterinary Medicine, Airlangga University, Surabaya, East Java, 60115, Indonesia.

2Anasthesiology and Reanimation Department, Dr. Soetomo Gerneral Hospital and Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.

3Clinical Pathology Department, Dr. Soetomo Gerneral Hospital and Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.

4Research Center for Vaccine Technology and Development, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.

5Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki, Punjab, Pakistan.

6Department of Biomedical Engineering, Science and Technology, Universitas Airlangga, Surabaya, Indonesia.

7Bacteriology and Mycology Laboratory, Department of Microbiology, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, 60132, Indonesia.

*E-mail: fedik-a-r@fkh.unair.ac.id

Abstract

Context: The current COVID-19 pandemic has significantly impacted health and socio-economic status worldwide. The only way to combat this situation is to develop an effective vaccine and immunize people around the globe.

Aims: To construct a multi-epitope spike glycoprotein-based vaccine from the SARS-CoV-2 Surabaya isolate using a bioinformatics approach.

Methods: The spike protein was submitted to IEDB, VaxiJen, AllerTOP, and ToxinPred webservers to predict antigenic, non-allergic, non-toxic, B- and T-cell epitopes. To develop a multi-epitope vaccine, an adjuvant cholera toxin B subunit was linked to B-cell and B-cell with T-cell through EAAAK and GPGPG linkers, respectively. The designed vaccine 3D structure development, refinement, and validation were done through PHYRE2, Galaxy Refine, and RAMPAGE webservers. Moreover, the Cluspro-2.0 webserver was used for the molecular docking of the vaccine designed with TLR3. The vaccine+TLR3 complex was docked with Surfactant protein A as a control to validate the docking results. Finally, immune-simulation and in silico cloning of the vaccine were carried out by C-ImmSim webserver and SnapGene software, respectively.

Results: A multi-epitopic vaccine containing B and T-cell was developed using 392 amino acids with a molecular weight of 40825.59 Da. The docking and immunogenicity results of the vaccine met all established parameters for constructing a quality vaccine. Furthermore, the optimized sequence of the vaccine was successfully cloned in expression vector pET 28 a (+) that yielded a colon of 2724 bp.

Conclusions: The vaccine’s immunogenicity demonstrates its effectiveness against SARS-CoV-2 infection. Further confirmatory testing may therefore be performed as soon as possible in the public interest.

Keywords: in silico; public health; SARS-CoV-2; spike protein; TLR3-receptor.

Resumen

Contexto: La actual pandemia de COVID-19 ha afectado significativamente la salud y el estado socioeconómico en todo el mundo. La única forma de combatir esta situación es desarrollar una vacuna eficaz e inmunizar a las personas en todo el mundo.

Objetivos: Construir una vacuna basada en glicoproteína de pico de múltiples epítopos a partir del aislado SARS-CoV-2 Surabaya utilizando un enfoque bioinformático.

Métodos: La proteína de pico se envió a los servidores web IEDB, VaxiJen, AllerTOP y ToxinPred para predecir epítopos antigénicos, no alérgicos, no tóxicos, de células B y T. Para desarrollar una vacuna multiepítopo, se unió una subunidad B de la toxina del cólera adyuvante a la célula B y una célula B a una célula T a través de conectores EAAAK y GPGPG, respectivamente. El desarrollo, el refinamiento y la validación de la estructura 3D de la vacuna diseñada se realizaron a través de los servidores web PHYRE2, Galaxy Refine y RAMPAGE. Además, se utilizó el servidor web Cluspro-2.0 para el acoplamiento molecular de la vacuna diseñada con TLR3. El complejo vacuna + TLR3 se acopló con la proteína A del tensioactivo como control para validar los resultados del acoplamiento. Finalmente, la inmunosimulación y la clonación in silico de la vacuna se llevaron a cabo mediante el servidor web C-ImmSim y el software SnapGene, respectivamente.

Resultados: Se desarrolló una vacuna multiepitópica que contenía células B y T utilizando 392 aminoácidos con un peso molecular de 40825,59 Da. Los resultados de acoplamiento e inmunogenicidad de la vacuna cumplieron con todos los parámetros establecidos para construir una vacuna de calidad. Además, la secuencia optimizada de la vacuna se clonó con éxito en el vector de expresión pET 28 a (+) que produjo un colon de 2724 pb.

Conclusiones: La inmunogenicidad de la vacuna demuestra su eficacia contra la infección por SARS-CoV-2. Por lo tanto, se pueden realizar más pruebas de confirmación lo antes posible en interés público.

Palabras Clave: in silico; proteína de punta; receptor TLR3; salud pública; SARS-CoV-2.

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Citation Format: Shehzad A, Sumartono C, Nugraha J, Susilowati H, Wijaya AY, Ahmad HI, Kashif M, Tyasningsih W, Rantam FA (2022) Development of a multi-epitope spike glycoprotein vaccine to combat SARS-CoV-2 using the bioinformatics approach. J Pharm Pharmacogn Res 10(3): 445–458.
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© 2022 Journal of Pharmacy & Pharmacognosy Research (JPPRes)

Hydroxyapatite-polymethylmethacrylate dental implant in silico


J Pharm Pharmacogn Res 9(5): 746-754, 2021.

Original article

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

[Un enfoque bioinformático de la exploración con compuestos de hidroxiapatita y polimetilmetacrilato como biomaterial de implantes dentales]

Chiquita Prahasanti1, Alexander Patera Nugraha1,2*, Viol Dhea Kharisma3, Arif Nur Muhammad Ansori4, Rini Devijanti Ridwan1, Tansza Permata Setiana Putri1, Nastiti Faradilla Ramadhani5, Ida Bagus Narmada1,2, I Gusti Aju Wahju Ardani1,2, Tengku Natasha Eleena Binti Ahmad Noor6

1Dental Implant Research Group, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia.

2Department of Orthodontic, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia.

3Department of Biology, Faculty of Mathematic and Natural Science, Brawijaya University, Malang Indonesia.

4Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia.

5Graduate Student of Dental Health Science, Universitas Airlangga, Surabaya, Indonesia.

6Dental Officer of 609 Armed Forces Dental Clinic, Kuching, Sarawak, Malaysia.

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

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.

Keywords: biomaterials; composite; human well-being; hydroxyapatite-polymethylmethacrylate; in silico; osseointegration.

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Resumen

Contexto: El biomaterial más común utilizado para implantes dentales es el titanio. Con este no se evita la liberación de iones metálicos y el riesgo de reacciones alérgicas a los metales que pueden ocurrir en algunos pacientes. Se propone que los biomateriales compuestos de hidroxiapatita-polimetilmetacrilato (HA-PMMA) tienen un potencial como biomateriales de implantes dentales debido a sus propiedades mecánicas, químicas y biológicas. HA-PMMA puede inducir osteointegración, reacciones biocompatibles, menos alérgicas y sin liberación de iones metálicos.

Objetivos: Explorar los implantes HA-PMMA a través del acoplamiento molecular como biomaterial candidato para implante dental in silico.

Métodos: Formato de datos de estructura (sdf), peso molecular y número de identidad (CID) de muestras de ligando HA-PMMA se obtuvieron de PubChem y se minimizaron a través de OpenBabel. Estructura 3D, método de selección, resolución, recuento de átomos, peso, longitud de secuencia e identificación de proteínas BMP2, BMP4, BMP7, fosfatasa alcalina (AP), osteonectina, ostepontina y osteocalcina en ligando nativo RCSB-PDB y esterilización de agua en PyMol fueron desarrollados con el objetivo de maximizar la formación de afinidad de unión durante las simulaciones de acoplamiento molecular.

Resultados: Los implantes de HA-PMMA pueden potenciar la actividad de proteínas asociadas con la osteointegración como BMP-2/4/7, AP, osteocalcina, osteonectina y osteopontina in silico. Los implantes de HA-PMMA se unen fuertemente a la osteonectina y podrían mejorar la actividad AP in silico.

Conclusiones: Los implantes de HA-PMMA son candidatos potenciales para implantes dentales con capacidad de osteointegración por la unión con BMP-2/4/7, AP, osteocalcina, osteonectina y osteopontina in silico.

Palabras Clave: bienestar humano; biomateriales; hidroxiapatita-polimetilmetacrilato; implante; in silico; osteointegración.

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Citation Format: Prahasanti C, Nugraha AP, Kharisma VD, Ansori ANM, Ridwan RD, Putri TPS, Narmada IB, Ardani IGAW, Ramadhani NF, Noor TNEBA (2021) A bioinformatic approach of hydroxyapatite and polymethylmethacrylate composite exploration as dental implant biomaterial. J Pharm Pharmacogn Res 9(5): 746–754.

© 2021 Journal of Pharmacy & Pharmacognosy Research (JPPRes)

Characterization in vitro and in silico of Q10 NLCs


J Pharm Pharmacogn Res 9(5): 573-583, 2021.

Original article

Development, characterization in vitro and in silico of coenzyme Q10 loaded myristic acid with different liquid lipids nanostructured lipid carriers

[Desarrollo, caracterización in vitro e in silico de coenzima Q10 cargado de ácido mirístico con diferentes lípidos líquidos portadores de lípidos nanoestructurados]

Ni Luh Dewi Aryani1,4, Siswandono2, Wdji Soeratri3*, Dian Yulyandani Putri4, Pingky Dwi Puspitasarini4

1Doctoral Program of Pharmaceutical Sciences, Faculty of Pharmacy, Airlangga University, Surabaya, Indonesia.

2Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Airlangga University, Surabaya, Indonesia.

3Department of Pharmaceutics, Faculty of Pharmacy, Airlangga University, Surabaya, Indonesia.

4Department of Pharmaceutics, Faculty of Pharmacy, University of Surabaya, Surabaya, Indonesia.

*E-mail: widji-s@ff.unair.ac.id

Abstract

Context: Nanostructured lipid carriers can enhance skin penetration of active substances. Coenzyme Q10 is a lipophilic antioxidant, that has poor skin penetration. This limitation is overcome by nanostructured lipid carriers.

Aims: To developed coenzyme Q10 nanostructured lipid carriers using myristic acid with various liquid lipids as lipid matrix by in vitro studies and in silico approach for explaining the interaction of coenzyme Q10-lipid at the molecular level.

Methods: The coenzyme Q10 nanostructured lipid carriers were prepared using myristic acid as solid lipid with oleic acid, isopropyl myristate, and isopropyl palmitate as liquid lipids using the high shear homogenization method. Then, they were evaluated in physicochemical characteristics by dynamic light scattering, differential scanning calorimetry, Fourier transforms infrared, scanning electron microscopy, spectrophotometry ultraviolet-visible, and pH meter. Furthermore, the in silico studies were conducted using AutoDock 4.2.

Results: The coenzyme Q10 nanostructured lipid carriers using myristic acid-oleic acid, myristic acid-isopropyl myristate, and myristic acid-isopropyl palmitate as lipid matrix had the mean particle size, polydispersity index, entrapment efficiency, drug loading, and pH value were less than 300 nm, less than 0.3, more than 80%, about 10%, and about 5.0, respectively. Moreover, molecular docking of coenzyme Q10 and lipid showed hydrogen and hydrophobic bonds. These results supported differential scanning calorimetry and Fourier transforms infrared results.

Conclusions: The coenzyme Q10 nanostructured lipid carriers were successfully prepared using myristic acid-oleic acid, myristic acid-isopropyl myristate, and myristic acid-isopropyl palmitate as lipid matrix as well as in silico study could be used for explaining of coenzyme Q10-lipid interaction.

Keywords: coenzyme Q10; in silico; in vitro; nanostructured lipid carriers.

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Resumen

Contexto: Los portadores de lípidos nanoestructurados pueden mejorar la penetración cutánea de sustancias activas. La coenzima Q10 es un antioxidante lipofílico, que tiene poca penetración en la piel. Esta limitación se supera mediante portadores de lípidos nanoestructurados.

Objetivos: Desarrollar portadores de lípidos nanoestructurados de coenzima Q10 utilizando ácido mirístico con varios lípidos líquidos como matriz lipídica mediante estudios in vitro y enfoque in silico para explicar la interacción de la coenzima Q10-lípido a nivel molecular.

Métodos: Los portadores de lípidos nanoestructurados de coenzima Q10 se prepararon usando ácido mirístico como lípido sólido con ácido oleico, miristato de isopropilo y palmitato de isopropilo como lípidos líquidos usando el método de homogeneización de alto cizallamiento. Luego, fueron evaluados en características fisicoquímicas por dispersión dinámica de luz, calorimetría diferencial de barrido, transformadas de Fourier infrarrojas, microscopía electrónica de barrido, espectrofotometría ultravioleta-visible y pHmetro. Además, los estudios in silico se realizaron utilizando AutoDock 4.2.

Resultados: Los portadores de lípidos nanoestructurados de coenzima Q10 que utilizaron ácido mirístico-ácido oleico, ácido mirístico-miristato de isopropilo y ácido mirístico-palmitato de isopropilo como matriz lipídica tuvieron un tamaño medio de partícula, índice de polidispersidad, eficiencia de atrapamiento, carga de fármaco y valor de pH menores. de 300 nm, menos de 0,3, más del 80%, aproximadamente el 10% y aproximadamente 5,0, respectivamente. Además, el acoplamiento molecular de la coenzima Q10 y el lípido mostró enlaces hidrófobos y de hidrógeno. Estos resultados apoyaron la calorimetría de barrido diferencial y los resultados infrarrojos transformados de Fourier.

Conclusiones: Los portadores de lípidos nanoestructurados de coenzima Q10 se prepararon con éxito utilizando ácido mirístico-ácido oleico, miristato de ácido mirístico-isopropilo y ácido mirístico-palmitato de isopropilo como matriz lipídica, así como un estudio in silico que podría usarse para explicar la interacción coenzima Q10-lípido.

Palabras Clave: coenzima Q10; in silico; in vitro; portadores de lípidos nanoestructurados.

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Citation Format: Aryani NLD, Siswandono, Soeratri W, Putri DY, Pingky DP (2021) Development, characterization in vitro and in silico of coenzyme Q10 loaded myristic acid with different liquid lipids nanostructured lipid carriers. J Pharm Pharmacogn Res 9(5): 573–583.

© 2021 Journal of Pharmacy & Pharmacognosy Research (JPPRes)