Bioinformatics Protocols

The Bioinformatics-Protocols website contains in silico protocols intended for use in higher education teaching and academic research. The protocols were developed by Dr Nat Milton in his academic and commercial roles and are available on the Antisense Peptide page. Dr Milton's published academic research is available on the research page. The site also contains the NeuroDelta Ltd page which covers the commercial side of Dr Milton's work.

The
protocols available on this site all use website linked software freely available to academics alongside standard word-processing plus spreadsheet programs. They have been developed to use bioinformatics for in silico identification of novel protein-protein interactions. Protein-protein interactions play central roles in the biochemical functions of proteins and many of the interactions that naturally occur are still unknown. An understanding of such interactions also has potential for development of both therapeutic and diagnostic tools. The antisense peptide techniques, detailed on the protocols page of this website, are based on the idea that proteins coded by the sense and antisense strands of DNA interact with each other. A Taster Protocol page on this website has been designed to demonstrate use of the antisense peptides technique to identify a novel interaction. Antisense peptide sequences can also be used as potential ligands in laboratory based protein-protein interactions studies and potentially used as peptide aptamers in diagnostic and therapeutic settings.

An example of the use of these techniques was a study to identify Alzheimer's amyloid-ß (Aß) binding peptides that could block both neurotoxicity and fibril formation of Aß. The binding peptides were developed based on generating antisense peptides that would specifically bind the Aß 1-43 peptide using the messenger RNA (mRNA) sequence coding for the peptide as a template
[1],[2]. The Aß antisense peptide sequences and data from their generation plus characterisation are the subject of published patent applications [2] and were used to set up the NeuroDelta Ltd company for commercial exploitation of these patents. Subsequent studies by other groups demonstrated that similar Aß antisense peptides were able to prevent the toxicity of Aß [3], confirming the original observations.

The use of the Aß 1-43 antisense peptide screening lead to the identification of a catalase-Aß binding domain, plus development of compound R9 that was used to block the catalase-Aß interaction
[4],[5]. The use of the Aß 1-43 antisense peptide screening also lead to the identification of the Kissorphin (KSO) peptide [6] as an amyloid binding compound that was effective against Aß, amylin and prion protein toxicity [7],[8].


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