Molecular modeling and simulation studies of SELEX-derived high-affinity DNA aptamers to the Ebola virus nucleoprotein

D R Martin; A T Mutombwera; A M Madiehe; M O Onani; M Meyer; R Cloete

doi:10.1080/07391102.2024.2302922

Molecular modeling and simulation studies of SELEX-derived high-affinity DNA aptamers to the Ebola virus nucleoprotein

J Biomol Struct Dyn. 2024 Jan 13:1-18. doi: 10.1080/07391102.2024.2302922. Online ahead of print.

Authors

D R Martin^{1

2}, A T Mutombwera³, A M Madiehe^{1

4}, M O Onani⁵, M Meyer¹, R Cloete²

Affiliations

¹ Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa.
² South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Bellville, South Africa Cape Town, South Africa.
³ Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa.
⁴ Nanobiotechnology Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa.
⁵ Department of Chemistry, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa.

PMID: 38217874
DOI: 10.1080/07391102.2024.2302922

Abstract

Ebola viral disease (EVD) is a highly infectious and potentially fatal illness with a case fatality rate ranging from 25% to 90%. To effectively control its spread, there is a need for rapid, reliable and lowcost point-of-care (P OC) diagnostic tests. While various EVD diagnostic tests exist, few are P OC tests, and many are not cost-effective. The use of antibodies in these tests has limitations, prompting the exploration of aptamers as potential alternatives. Various proteins from the Ebola virus (EBOV) proteome, including EBOV nucleoprotein (NP), are considered viable targets for diagnostic assays. A previous study identified three aptamers (Apt1. Apt2 and Apt3) with high affinity for EBOV NP using systemic evolution of ligands by exponential enrichment (SELEX). This study aimed to employ in silico methods, such as Phyre2, RNAfold, RNAComposer, HADDOCK and GROMACS, to model the structures of EBOV NP and the aptamers, and to investigate their binding. The in silico analysis revealed successful binding of all the three aptamers to EBOV NP, with a suggested ranking of Apt1 > Apt2 > Apt3 based on binding affinity. Microscale thermophoresis (MST) analysis confirmed the binding, providing dissociation constants of 25 ± 2.84, 56 ± 2.76 and 140 ±3.69 nM for Apt1, Apt2 and Apt3, respectively. The study shows that the findings of the in silico analysis was in agreement with the MST analysis. Inclusion of these in silico approaches in diagnostic assay development can expedite the selection of candidate aptamers, potentially overcoming challenges associated with aptamer application in diagnostics.Communicated by Ramaswamy H. Sarma.

Keywords: Ebola virus; Ebola virus nucleoprotein; aptamers; diagnostics; microscale thermophoresis; molecular docking; molecular dynamic simulations; molecular modeling; sELEX.