Gliotoxin (GT) is a redox-active natural product produced by some fungal species that contributes to the virulence of the human pathogen Aspergillus fumigatus. It contains a characteristic disulphide bridge responsible for the deleterious effects of this molecule. GT also displays antifungal properties, however the mechanisms of cytotoxicity behind it has not been fully characterised. The work presented here investigates A. niger as a model organism to understand GT cytotoxicity and reveal new metabolic systems, as it does not produce GT. Comparative proteomics revealed that exposure of A. niger to exogenous GT resulted in a significant (p < 0.05) dysregulation of hundreds of proteins involved in several cellular processes, especially metabolism. Two putative S-adenosylmethionine (SAM)-dependent methyltransferases showed de novo abundance under GT conditions. In addition an increase in abundance of proteins involved in the methionine cycle was also observed. Analysis of methionine-related metabolites revealed significant increases in the levels of methionine and adenosine, in correlation with proteomic data. Moreover, proteomic data revealed a significant increase in the abundance of hydrolytic enzymes, including glycoside hydrolases (n = 22) and peptidases (n = 16) which have important applications in the biotechnology industry. A significant dysregulation of proteins involved in amino acid metabolism coupled to an increase in the levels of selected amino acids appeared to occur in A. niger under GT conditions. Furthermore this thesis reveals a novel protection mechanism in A. niger against GT which is mediated by one the methyltransferases (MTases) identified on the proteomic data. This MTase (referred as MT-II) is responsible for bisthiobis(methylthio)gliotoxin (BmGT) formation and deletion of MT-II led to increased GT sensitivity in A. niger. The applications of other fungal natural products like siderophores (Fusarinine C), are also evaluated herein. The development and validation of a Fusarinine C based enzyme-linked immunosorbent assay (ELISA) was carried out. Results showed the potential applications of this ELISA in the diagnosis of aspergillus related diseases. Overall, this work highlights the different roles and applications fungal natural products have.