Scientists at the Massachusetts Institute of Technology (MIT) have developed an antimicrobial peptide (AMP) that is derived from a 12 amino acid toxin produced by a species of South American wasp. The team used a rational peptide design strategy to fine tune the structure and properties of the wasp peptide, and generate an AMP candidate that was nontoxic to human cells at doses used to completely clear infections in mice caused by the bacterium Pseudomonas aeruginosa, a common cause of respiratory and urinary tract infections in people.
“After four days, that compound can completely clear the infection, and that was quite surprising and exciting because we don’t typically see that with other experimental antimicrobials or other antibiotics that we’ve tested in the past with this particular mouse model,” said Cesar de la Fuente-Nunez, Ph.D., a researcher at the MIT Synthetic Biology Center’s Synthetic Biology Group. “We’ve repurposed a toxic molecule into one that is a viable molecule to treat infections. By systematically analyzing the structure and function of these peptides, we’ve been able to tune their properties and activity.”
The researchers reported on their research in Nature Communications Biology, in a paper titled “Structure-function-guided exploration of the antimicrobial peptide polybia-CP identifies activity determinants and generates synthetic therapeutic candidates.”
Drug-resistant infections represent a growing global health concern. Each year in developed countries including the U.S. about 2 million people become infected with antibiotic-resistant bacteria, resulting in at least 23,000 deaths, the authors write. Antimicrobial peptides represent a promising alternative to traditional antibiotics for treating drug-resistant infections, as they offer effective strategies against difficult-to-treat infections including a group of organisms known as the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp).
AMPs also offer “a unique diversity” of peptide sequences, and while molecules with certain basic sequences have been selected through evolution, making even minor changes to these sequences offers “unprecedented biological function,” the researchers write.
Wasps, bees, spiders, and scorpions are among the insects and arachnids that produce a class of AMPs known as linear amphipathic AMPs, which work by disrupting bacterial cell membranes. The South African social wasp Polybia paulista produces a variety of peptides in its venom, including a 12-residue cationic amphipathic AMP, polybia-CP (Pol-CP-NH2), which takes on a helical structure when it comes into contact with the membranes of microorganisms. “Pol-CP-NH2 is a chemotactic peptide from the venom of a tropical species of wasp that presents 12 residues typical of peptides found in these wasp species,” the authors explained.
Working with colleagues in the U.S and Brazil, the MIT team reasoned that the peptide was small enough to allow them to manipulate the residues and generate variants that could be tested for antibacterial potency, but without harming human cells.
The team’s first step was to create a few dozen variants of the polybia–CP peptide and measure the effects that the changes had on features such as helical structure and hydrophobicity, which is a key determinant of peptide interaction with membranes. These initial variants were tested against Gram-negative and Gram-positive bacterial strains and different fungi, so that their structures and physicochemical properties could be compared with antimicrobial potency.
The structure-activity relationships identified then helped to direct another round of peptide design, through which the scientists optimally changed the proportion of hydrophobic amino acids and positively charged amino acids, while conserving a cluster of amino acids that were required for the molecules’ overall function.
The resulting peptides were then tested for efficacy against a larger panel of Gram-positive and Gram-negative bacteria, and against the fungal strains. The peptides were also evaluated for stability and for toxicity against laboratory-grown human kidney cells. Promising peptides from both rounds of design were then evaluated in an in vivo mouse model of Pseudomonas aeruginosa skin infection. Of the peptides tested, the most potent and nontoxic to the mice completely cleared the infection after just four days.
“Our study is an example of how to design small cationic amphipathic peptides to optimize biological activities and selectivity,” the authors stated. “… we describe a systematic structure-activity relationship design approach aimed at revealing the sequence requirements for antimicrobial activity of a natural wasp venom AMP and several of its derivatives. Through single-residue substitutions guided by identified physicochemical activity determinants, we generated peptide antibiotics with anti-infective potential in a mouse model.”
The researchers are continuing to create peptide variants that might be effective antimicrobial candidates at even lower doses, and hope that their basic approach might also be used to optimize other peptides. “We envision that the principles and approaches exploited here can be applied to other structure-activity studies in order to rationalize and better understand the role of physicochemical features and which approaches fit better to each family of peptides,” they stated.
Dr. de la Fuente-Nunez will be joining a faculty at the University of Pennsylvania next year and plans to apply the same approach to other types of naturally occurring antimicrobial peptides. “I do think some of the principles that we’ve learned here can be applicable to other similar peptides that are derived from nature,” he said. “Things like helicity and hydrophobicity are very important for a lot of these molecules, and some of the rules that we’ve learned here can definitely be extrapolated.”