10 Tips for Designing Peptides

These peptides, like the parent compound AC253, acted as antagonists at the AMY receptor. They were also resistant to protein breakdown, and crossed the blood-brain barrier easily when injected into the abdominal cavity, to localize in the hippocampus, which is crucial in memory. These peptides protected the brain against beta-amyloid injury, and normalized the AD-associated impairment of the memory-associated long-term potentiation of nerve impulses in the hippocampus. They improved memory testing results, and reduced the level of inflammation in the brain. These effects appear to be mediated via the blockade of AMY receptors. For instance, inhibition of microglial AMY receptors reduce the activation of the inflammasome NLRP3. This reduces the secretion of inflammatory chemicals in the surrounding brain tissue, which offers another mechanism for lower amyloid production. In addition, these peptides increase the rate of outflow of amyloid beta from the brain, which also contributes to a lower level of amyloid after treatment. These marked changes all occurred within a relatively short span of treatment. A very important additional finding was that treatment with these peptides brought about improvement in mice which were showing signs of well-established AD in the brain as well as in their behavior. This is unique in that most therapies fail to affect the progress of AD once it has begun to manifest clinically. Peptides also have fewer off-target effects. Small molecules are easy to administer, inexpensive to make and cross the blood-brain barrier more rapidly. For this reason, the team resorted to computational tools and artificial intelligence to come up with a new small molecular drug based on these peptides. This can be taken orally, and is similar in size and structure to the medications used for medical conditions like high blood pressure. An optimized version is being developed to enable human trials to be conducted. The work so far has taken about two decades, building step upon painstaking step to come up with the right solution. However, says Jhamandas, “Occasionally you come across a discovery that has the potential to change the game in a very fundamental way, like hitting a home run, and I'm very excited that we are really on to something here.” Short amylin receptor antagonist peptides improve memory deficits in Alzheimer’s disease mouse model. Rania Soudy, Ryoichi Kimura, Aarti Patel, Wen Fu, Kamaljit Kaur, David Westaway, Jing Yang & Jack Jhamandas. Scientific Reports, volume 9, Article number: 10942 (2019). https://doi.org/10.1038/s41598-019-47255-9. https://www.nature.com/articles/s41598-019-47255-9

To precisely define self and non-self peptides and, in turn, self-similarity, we must first improve our understanding of the adaptive immune cascade and its constituent components. In brief, the fundamental unit of adaptive immune recognition comprises the major histocompatibility complex (MHC) molecules (called the human leukocyte antigen [HLA] in humans), the peptide being presented (and, in turn, identified as self or non-self), and the T cell receptor.

Some bacterial species produce antimicrobial peptides known as bacteriocins that have been used in the food industry as preservatives. For example, nisin, which is produced by Lactococcus lactis, has broad-spectrum bactericidal activity and has been used as a food preservative throughout the world. Nisin is effective in controlling Gram-positive bacteria such as Clostridioides difficile. In combination with other compounds like ethylene diamine tetra-acetic acid and cinnamaldehyde, nisin has been effective in controlling enterotoxigenic Gram-negative bacteria such as Escherichia coli. Previous studies have used chicken and mouse models to demonstrate the in vivo efficacy of nisin on the microbiome, whereas nisin efficacy has been proven in ex vivo experiments on the human microbiome. To date, no studies have assessed the in vivo effects of nisin in large mammals.

Conventional pharmacological studies on spices have traditionally focused on secondary metabolites like polyphenols, alkaloids, and terpenes. More recently, food science research has also examined spice proteins and their enzymatic hydrolysates, using proteomic methods such as liquid chromatography–tandem mass spectrometry (LC-MS/MS) to identify short bioactive peptide sequences released from larger precursor proteins.6 Once released during food processing, fermentation, or gastrointestinal digestion, these functional peptides can act as metabolic regulators, antimicrobials, or antioxidants.1 Functional peptides refer to specific protein fragments that, once released from their parent proteins, exert biological activities.1,2 In the context of foods, these activities are most often demonstrated using in vitro biochemical or cell-based assays, and their physiological relevance depends on bioavailability and dose.2 Unlike intact proteins, which can have the potential to be allergenic or difficult to absorb due to their complex tertiary structures, functional peptides may exhibit improved bioaccessibility, and some small peptides can cross the intestinal epithelial barrier via peptide transport systems. However, absorption efficiency varies substantially by peptide sequence and digestive conditions.6 Nutriomics and mechanistic investigations have established that the bioactivity of a peptide is dictated by its physicochemical properties, particularly its amino acid composition, molecular weight, and net charge. For example, the presence of hydrophobic amino acids like proline, leucine, and valine often correlates with high antioxidant and enzyme-inhibitory activity.2,3 Smaller peptides, typically those less than three kilodaltons (kDa) in size, exhibit greater stability against proteolytic degradation in the gastrointestinal tract.3 Moreover, cationic peptides are particularly effective as antimicrobial agents through their electrostatic interactions with bacterial membranes.3

It has been noted in around 20 percent of the world population suffers from some form of pain or the other. In many individuals, pain may be relieved initially with pain medications, but soon tolerance develops, and there is a decrease in the efficacy of pain relievers. One of the main symptoms of IBS seen commonly in many sufferers is chronic abdominal pain. Professor Lewis said, "All pains are complex, but gut pain is particularly challenging to treat and affects around 20 percent of the world's population. Current drugs are failing to produce effective pain relief in many patients before side effects limit the dose that can be administered." Professor Brierley echoed this statement saying, "Internal organs have a complex network of sensory nerves that have a wide array of voltage-gated ion channels and receptors to detect stimuli... The hypersensitivity of these nerves in disease often contributes to the development of pain."