Elucidating the Structure-Function Relationships of Enterococcus faecium Nicotinate-Nucleotide Adenylyltransferase through X-Ray Crystallography, Computational Modelling and Binding Studies
| dc.contributor.author | Jeje, Olamide Adetomi | |
| dc.contributor.co-supervisor | Pandian, Ramesh | |
| dc.contributor.supervisor | Achilonu, Ikechukwu A. | |
| dc.date.accessioned | 2024-11-01T07:29:32Z | |
| dc.date.available | 2024-11-01T07:29:32Z | |
| dc.date.issued | 2024 | |
| dc.description | A Thesis Submitted in fulfillment of the requirements for the degree of Doctor of Philosophy in Molecular and Cell Biology in the Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa, 2024 | |
| dc.description.abstract | Nicotinate nucleotide adenylyltransferase (NNAT) is a vital enzyme at the heart of NAD biosynthesis, catalysing a crucial reaction that leads to the formation of pyridine dinucleotides. NAD+ is an essential coenzyme in numerous metabolic processes, DNA repair, and cellular signalling. Given its pivotal role, NNAT has emerged as a compelling drug target, particularly for its potential to disrupt the survival mechanisms of bacterial pathogens. By inhibiting NNAT, it is possible to undermine the metabolic integrity of these pathogens, making NNAT a promising focal point in the fight against bacterial infections and antibiotic resistance. However, understanding the structure-function relationship of Enterococcus faecium NNAT (EfNNAT) has remained elusive. Hence, this study aimed to address this gap bycharacterising EfNNAT and validating its potential as a druggable target. EfNNAT was overexpressed and purified using the Escherichia coli system and IMAC purification technique. Subsequently, biophysical characterisation was performed, followed by the determination of the three-dimensional structure in both apo and liganded forms using X-ray crystallography. High-throughput virtual screening, along with SP and XP docking, was conducted using a library of synthesizable flavonoids. Molecular dynamic simulation and fluorescence studies were employed to establish and validate the binding of identified inhibitors to EfNNAT. Successful expression and purification of EfNNAT yielded approximately 101 mg per 7.8 g of wet E. coli cells, with a purity exceeding 98%. High-resolution crystal structures of EfNNAT in native, adenine-bound, and NMN-bound forms were determined at 1.90 Å, 1.82 Å, and 1.84 Å, respectively. These structures provided insights into EfNNAT's substrate preference and revealed a potential allosteric site at the dimer interface of the NMN-bound structure. Virtual screening identified quercetin 3-O-beta-D-glucose- 7-O-beta-D-gentiobioside as the only potential inhibitor from the flavonoid library used. A 500 ns atomistic molecular dynamics simulation showed the compound interacted through hydrogen bonding and water bridges, albeit unstable within the receptor. ANS and mant-ATP fluorescence spectroscopy confirmed quercetin binding, while thermal shift assay revealed minimal impact of the inhibitor on the protein stability and structure. This study establishes a pipeline from expression and purification to structure solution and potential inhibitor identification for EfNNAT, validating its druggability. The mechanistic insights offer a foundation for advancing drug discovery efforts targeting EfNNAT and other bacterial NNAT enzymes. | |
| dc.description.sponsorship | MRC | |
| dc.description.submitter | MM2024 | |
| dc.faculty | Faculty of Science | |
| dc.identifier | https://orcid.org/ 0000-0003-2625-9144 | |
| dc.identifier.citation | Jeje, Olamide Adetomi . (2024). Elucidating the Structure-Function Relationships of Enterococcus faecium Nicotinate-Nucleotide Adenylyltransferase through X-Ray Crystallography, Computational Modelling and Binding Studies [PhD thesis, University of the Witwatersrand, Johannesburg]. WireDSpace. | |
| dc.identifier.uri | https://hdl.handle.net/10539/42156 | |
| dc.language.iso | en | |
| dc.publisher | University of the Witwatersrand, Johannesburg | |
| dc.rights | © 2024 University of the Witwatersrand, Johannesburg. All rights reserved. The copyright in this work vests in the University of the Witwatersrand, Johannesburg. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of University of the Witwatersrand, Johannesburg. | |
| dc.rights.holder | University of the Witwatersrand, Johannesburg | |
| dc.school | School of Molecular and Cell Biology | |
| dc.subject | Enterococcus faecium | |
| dc.subject | Nicotinate-Nucleotide Adenylyltransferase (NNAT) | |
| dc.subject | Drug target | |
| dc.subject | Antibiotics | |
| dc.subject | Multi-drug resistance bacteria | |
| dc.subject | Nosocomial infection | |
| dc.subject | Drug discovery | |
| dc.subject | Potential inhibitors | |
| dc.subject | Virtual screening | |
| dc.subject | Computational modelling | |
| dc.subject | UCTD | |
| dc.subject | Crystal structure | |
| dc.subject.other | SDG-4: Quality education | |
| dc.title | Elucidating the Structure-Function Relationships of Enterococcus faecium Nicotinate-Nucleotide Adenylyltransferase through X-Ray Crystallography, Computational Modelling and Binding Studies | |
| dc.type | Thesis |