Computational studies of neuroactive peptides for treating neurological disorders and disease
Creators: name: WEN, Jierong
Publisher: name: RMIT University
Year: 2024
Subjects: classificationCode: 340402
subject: Biomolecular modelling and design
classificationCode: 340407
subject: Proteins and peptides

description: Since the first synthesized conotoxin analgesic, omega-conotoxin MVIIA (ziconotide), was approved by the FDA in 2004, the potential of venom peptides has been highlighted by many studies. Alpha-conotoxins are the most widely studied subfamily due to their potency for nicotinic acetylcholine receptors (nAChRs), the abnormal function of which is related to neurological disease and disorders. On the other hand, voltage-gated ion channels, such as the T-type (Cav3) calcium channels, are also involved in cell signalling. There is at present a lack of potent inhibitors or selective probes to further investigate their specific roles in neural physiology and pathology, such as chronic pain. Furthermore, owing to the diversity of this cocktail of conopeptides, the selectivity of the conotoxins as inhibitors of neuronal proteins needs to be further understood and improved. Therefore, it is important to identify the determinants that may affect the sensitivity of the toxins to act as inhibitors of nAChRs and voltage-gated calcium channels through computational methods at the atomic level. 

In Chapter 1, the scientific literature is summarized within the scope of this study. Additionally, the literature also refined the aim of this thesis is discussed in this chapter. 

Chapter 2 provides a comprehensive overview of the principles of the applied computational approaches in this study.

Once the background and methodology involved in the present work are understood, one can apply this knowledge and skills to investigate specific research questions outlined in the subsequent chapters. 

Chapter 3 identifies the important residues of the LsIA/alpha 7 nAChR complex that affect the interactions between the toxin and the membrane protein due to C-terminal carboxylation of LsIA. Alpha 7 nAChR is involved in Alzheimer's disease, Parkinson's disease, inflammation and other disorders. The intramolecular salt-bridge established by R10 and C17 of carboxylated LsIA (LsIA#) mainly affects the reduced interactions at R10 and C17 by LsIA# with the residues, W77 and Q79, on alpha7 nAChR via cation-pi and hydrogen bond interactions. 

The effects of C-terminal modification of LsIA on interactions with alpha 3 beta 2 nAChR, involved in cardiovascular diseases, were also investigated in Chapter 4. This chapter highlights the differences in interactions between neuropeptides and nAChR inter-monomer interfaces composed of different subunits. For instance, (alpha 3)2(beta 2)3, as a heteropentameric nAChR, possesses three types of binding interfaces targeted by LsIA, namely alpha 3(+)/beta 2(-), beta 2(+)/alpha3 (-) and beta 2(+)/beta 2(-) binding sites. This chapter demonstrates the important role of LsIA#-C17 in enhancing binding interactions with alpha 3 beta 2 nAChR due to its attraction with positively charged residues, (-)K187 and (-)K82, at alpha 3(+)/beta 2(-) and beta 2(+)/alpha 3(-) interfaces respectively, rather than those on the beta 2(+)/beta 2(-)binding site. However, the effect of LsIA/LsIA#-R10 on interactions with all alpha 3 beta 2 interfaces is minor, possibly due to the electrostatic repulsion between R10 and the residues on the binding site in proximity to R10 of the toxins. 

Recently, the role of Cav3.2 in pain sensation has been proposed, and analgesic molecules targeting this ion channel have been explored as possible novel therapies for alleviating such pain. Chapter 5 provides basic insights into the binding site of Cav3.2 and the residues interacting with mu-conotoxins, which may account for the sensitivity of certain toxins, such as GIIIA and PIIIA, to the Cav channel, in contrast to GIIIB, KIIIA and GIIIC which show fewer inhibitory effects on Cav3.2. In general, these mu-conotoxins bind to the Cav3.2 via pore-blocking mechanism. However, GIIIA binds more deeply at the outer vestibule of Cav3.2, whilst PIIIA demonstrates a relatively superficial binding conformation. The partially different binding conformations may be attributed to the acidic residue, D382, on the ion channel, that makes contact with the residues GIIIA-K11 and K16 via electrostatic interactions. 

Finally, Chapter 6 summarises the main findings in this thesis and provides further research directions that need to be focused on.