The drug, called ATX-MS-1467, has now been tested in humans for the first time - in six Secondary Progressive Multiple Sclerosis (SPMS) patients in a Phase I/IIa trial - and the results so far are encouraging.
No safety issues have been unearthed and one patient also showed good clinical improvement in their symptoms.
The immune system attacks proteins it sees as dangerous and helps protect us from a myriad of pathogens.
Occassionally these attacks can be devastating if it mistakenly sees proteins in our own body as dangerous and sets about destroying them.
This autoimmune reaction leads to numerous diseases, such as Type I diabetes.
In the case of MS, the immune system wipes out the myelin sheath around nerve cells - an insulating layer that allows the cells to effectively conduct electrical signals.
This causes the nerves to die and the symptoms of MS to appear, including visual problems, weakness, difficulties with balance and speech, severe fatigue, pain, impaired mobility and often disability.
According to the MS International Federation, around 2.5 million people suffer from the incurable, progressive disease.
Current therapies aim to reduce the inflammation around the nerve cells to offset further damage or, alternatively, to suppress the immune system.
However, these broad approaches also suffer from significant side-effects such as an increased susceptibility to infections and a greater risk of cancer.
Apitope has taken a different approach with their peptide based vaccine that seeks to retune the immune system so it no longer overreacts to proteins in the myelin sheath.
One of these proteins in called myelin basic protein (MBP).
This protein is chopped up inside a cell into different peptide strips.
Some of these strips or epitopes then bind to a protein called major histocompatability complex (MHC) class II and are carried to the surface of the cell where they are presented to the immune system.
Dr Keith Martin, CEO of Apitope, explained to DrugResearcher.com that if certain danger signals are present, then the MBP peptide epitopes can 'switch on' T cells and cause an inflammatory response that damages the myelin.
However, and this is where the Apitope vaccine comes in, if the epitope is presented to the immune system in the absence of these danger signals, a different subset of T cells are switched on (called regulatory T cells) and instead of causing damage, these can suppress the immune system reaction to the epitope in question and thus make it more 'tolerant' to myelin.
They do this through producing interleukin-10 (IL-10), an anti-inflammatory cytokine.
One key part of this is to ensure the vaccine is only injected at sites where there are no danger signals.
So, the clinicians doing the trial inject the drug in the periphery of the body and the regulatory T cells produced can then travel to the central nervous system (CNS) and begin to retune the immune system there.
One problem remained however.
Not all fragments of MBP are capable of causing the immune system to become tolerant to the protein.
For example, the MBP peptide made up of amino acids 89 to 101 can induce an immune response both in terms of priming for T cell reactivity and inducing autoimmune encephalomyelitis (EAE) - the commonly used animal model for MS.
However, the same peptide does not induce tolerance.
So which peptides do and which don't?
After much research, David Wraith, a Professor of Experimental Pathology at the University of Bristol, found the answer.
He discovered that only peptide fragments that are the right size and shape to be presented to the immune system without further processing can go on to induce tolerance.
The discovery led to the spin out of the company and also gave it its name and the name of this class of potential drug - Antigen Processing Independent epiTOPES or Apitopes.
Prof. Wraith became the chief scientific officer at Apitope.
First, the team use bioinformatics to design peptides that will bind to MHC strongly and, crucially, ones that can also adopt the right shape to bind.
"If the peptide isn't the right shape, then it won't trigger a response," said Martin.
"If they are in the right conformation, they won't require processing [and therefore will induce immune system tolerance]."
He added that in the case of MS, Apitope identified five different peptide epitopes that looked like they would work and then proceeded to test them in a number of in vitro assays.
After that process, four remained and these are what make up ATX-MS-1467.
The advantage to having four is that there are different subtypes of MHC class II molecules and these four can bind to different ones, such that the "vast majority" of MS patients will be theoretically responsive to the drug.
The initial signs are that the vaccine is effective.
Given that the myelin sheath also contains other proteins that are thought to induce the immune system to attack, such as myelin oligodendrocyte glycoprotein (MOG), and proteolipid protein (PLP), this is perhaps surprising at first.
So how does a vaccine based only on MBP peptides also prevent these other proteins from sending the immune system into overdrive?
The answer is 'bystander suppression'.
The epitopes for a given protein antigen (in this case MBP) can also induce tolerance to other epitopes from the same antigen, and even epitopes from other antigens, such as MOG and PLP.
"Essentially, the activity of the mixture is greater than the sum of its parts," explained Martin.
Indeed, one patient on the trial has shown "remarkable improvement in her eyesight" , explained Prof. Wraith.
"Since the optic nerve is acutely sensitive to inflammation and optic neuritis is often one of the first symptoms of MS, this early indication of efficacy is very encouraging.
It suggests that treatment with ATX-MS-1467 can suppress the inflammation associated with MS," he continued.
The next step is to continue to monitor the six patients who have completed dosing in the Phase I/IIa trial so that a three month safety follow-up can be conducted.
If the drug gets the all clear, Apitope will then continue with a Phase IIb proof-of-concept trial.
If that proves successful, the firm will then look to partner the programme with a larger pharma company, although Martin said the company would be willing to partner earlier if the opportunity arose.
Way before this drug makes it anywhere near the market though, Apitope hope to begin generating revenues thanks to a MS diagnostic test they have developed.
Martin said that early diagnosis in MS is crucial as treatments that seek to slow down or halt the progression of the disease are obviously best given before the disease has had the chance to do too much damage.
Even with existing treatments, there is evidence to suggest patients would have much better outcomes if they were diagnosed earlier he said.
Unfortunately, the current process of diagnosing the disease can take a while, leaving patients untreated while the disease damages their nerves.
Apitope have developed a blood test that can diagnose the disease much more quickly.
The test is still undergoing regulatory tests but Martin said that Apitope hopes it will be available to doctors by the end of 2009.
The same test also has the potential to be extended as a tool for other autoimmune diseases such as rheumatoid arthritis and lupus.
Apitope's approach is also applicable to other immune hypersensitivity reactions and the firm has a programme to identify apitopes to prevent Factor VIII inhibitor formation, which can cause haemophilia.
Martin said that he is confident the company will gain orphan drug status for this programme from the US Food and Drug Administration (FDA), although they haven't applied for it yet.
This is important as the faster regulatory process for orphan drugs means that, if necessary, Apitope could bring that drug to market without a partner.
Scientists at Apitope are also conducting preclinical tests on Type I diabetes and allergy peptides.
The MS project remains the most advanced however, and it is this research that will make or break Apitope's approach to peptide induced tolerance.
A great number of people with autoimmune diseases will be waiting with baited breath.