Tag Archives: antivenom

Epitope prediction of candoxin protein from Malayan krait

J. Pharm. Pharmacogn. Res., vol. 10, no. 6, pp. 1046-1057, November-December 2022.

DOI: https://doi.org/10.56499/jppres22.1469_10.6.1046

Original Article

Virtual prediction of potential immunogenic epitope of candoxin protein from Malayan krait (Bungarus candidus) venom

[Predicción virtual del epítopo inmunogénico potencial de la proteína candoxina del veneno de krait malayo (Bungarus candidus)]

Rahmat Grahadi1,2, Fatchiyah Fatchiyah1,2, Nia Kurniawan1*

1Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Jl. Veteran, 65145, Malang, Indonesia.

2Research Center of Smart Molecules of Natural Genetic Resources (SMONAGENES), Brawijaya University, Malang, Indonesia.

*E-mail: wawan@ub.ac.id

Abstract

Context: Malayan krait (Bungarus candidus) is a snake that is considered highly venomous snake and widely distributed across Southeast Asia. Envenomation by this snake is characterized by facial weakness, paralysis, respiratory muscle weakness, and in most cases, it renders the victim dead. Unfortunately, there is only one antivenom for neutralizing venom that is only available from the Thai Red Cross Society.

Aims: To predict the epitopes from candoxin protein of B. candidus venom that could be a candidate for vaccine-based antivenom.

Methods: :  In this study, IEDB and SYFPHEITHI databases were utilized to predict candoxin epitope sequences and determine their immunogenicity, conservancy, and population coverage. Next, the epitopes were modeled, and the binding interactions between epitopes and MHC-II were analyzed. The epitope that binds into the active site of human and murine MHC-II proceeded to the next step. Then, the allergenic properties of the chosen epitope were assessed to ensure its safety. Lastly, the physicochemical characteristics prediction and molecular dynamics simulation were conducted to verify the epitope’s stability when produced in vivo.

Results: The results showed that epitope 47-CFKESWREARGTRIE-61 has the best binding interaction when compared to others. This epitope was confirmed that did not show potential allergenic properties. The physicochemical properties and molecular dynamics simulation demonstrated that this epitope was stable.

Conclusions: The results of this study will be useful in developing a novel antivenom for Bungarus candidus using a vaccine-based method.

Keywords: animal toxin; antivenom; neurotoxin; vaccine.

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Resumen

Contexto: La krait malaya (Bungarus candidus) es una serpiente que se considera altamente venenosa y está ampliamente distribuida en el sudeste asiático. El envenenamiento por esta serpiente se caracteriza por debilidad facial, parálisis, debilidad de los músculos respiratorios y, en la mayoría de los casos, provoca la muerte de la víctima. Desafortunadamente, solo hay un antiveneno para neutralizar el veneno que solo está disponible en la Sociedad de la Cruz Roja Tailandesa.

Objetivos: Predecir los epítopos de la proteína candoxina del veneno de B. candidus que podrían ser candidatos a antiveneno vacunal.

Métodos: En este estudio, se utilizaron las bases de datos IEDB y SYFPHEITHI para predecir las secuencias de epítopos de candoxina y determinar su inmunogenicidad, conservación y cobertura poblacional. A continuación, se modelaron los epítopos y se analizaron las interacciones de unión entre los epítopos y el MHC-II. El epítopo que se une al sitio activo del MHC-II humano y murino pasó al siguiente paso. Luego, se evaluaron las propiedades alergénicas del epítopo elegido para garantizar su seguridad. Por último, se realizó la predicción de las características fisicoquímicas y la simulación de la dinámica molecular para verificar la estabilidad del epítopo cuando se produce in vivo.

Resultados: Los resultados mostraron que el epítopo 47-CFKESWREARGTRIE-61 tiene la mejor interacción de unión en comparación con otros. Se confirmó que este epítopo no presentaba propiedades alergénicas potenciales. La simulación de propiedades fisicoquímicas y dinámica molecular demostró que este epítopo era estable.

Conclusiones: Los resultados de este estudio serán útiles para desarrollar un nuevo antiveneno para Bungarus candidus utilizando un método basado en vacunas.

Palabras Clave: antiveneno; neurotoxina; toxina animal; vacuna.

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Citation Format: Grahadi R, Fatchiyah F, Kurniawan N (2022) Virtual prediction of potential immunogenic epitope of candoxin protein from Malayan krait (Bungarus candidus) venom. J Pharm Pharmacogn Res 10(6): 1046–1057. https://doi.org/10.56499/jppres22.1469_10.6.1046
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