Chemists at Texas A&M University are taking a p[h]age from bacteria’s playbook in order to beat viruses at their own game and develop new drugs to fight cancer and a host of other human diseases in the process.
For decades, scientists have relied on phage display — a technique used to identify novel peptide ligands, or peptides that bind to other proteins or molecules — as a versatile tool in a variety of applications ranging from drug discovery to materials science. A team led by Texas A&M chemist and 2018 Texas A&M Presidential Impact Fellow Dr. Wenshe R. Liu has learned a new trick from an old master, bacteria, successfully harnessing its ability to make short peptides containing noncanonical amino acids (ncAAs) that equip them with special properties, such as enzyme degradation resistance and targeted protein binding capabilities.
Using a clever strategy to “trick” the system so that only viruses containing peptides with ncAAs are capable of reproducing, the Liu research group has found a way to stack the phage display library construction deck, effectively expanding the genetic code of bacteriophages and paving the way for new peptide-based therapeutics. Their findings are published Friday (March 13) in the journal Nature Communications.
“Utilizing unnatural amino acids, we greatly expand the utility of phage display for identifying new peptide therapeutics,” Liu said.
Since joining the Texas A&M Department of Chemistry faculty in 2007, Liu and his chemical biology-based research group has focused on using organic chemistry tools to better understand biological systems. Specifically, they have developed or perfected genetic code expansion techniques to enable and manipulate protein functionalization. Such techniques allow scientists to expand beyond the canonical 20 amino acids found in Nature to create additional ones containing diverse chemical functional groups. Liu says this work has opened the door for an array of novel protein research, including one of his group’s specialties — phage display, which makes it possible to target essential components and pathways within many different diseases, from cancer and AIDS to cardiovascular disease and autoimmune disorders.
“Phage display is an efficient method to identify peptides for therapeutic interventions,” said Liu, holder of the Gradipore Chair in Chemistry at Texas A&M. “However, a phage display peptide library has limited structure motifs and functional groups, because only 20 natural amino acids can be used to generate a library. We continue to work to expand the chemical diversity of a phage display library by incorporating multiple noncanonical amino acids and chemically modifying them to extend functional diversities. Screening this unnatural phage display library against therapeutic targets helps us to identify highly potent inhibitors — work that is highly likely to result in new probes and inhibitors of proteins involved in cancer.”
Phage display is one of several tools that scientist rely on to find new peptides with potential use as drugs to treat diseases, explains 2018 Texas A&M chemistry Ph.D. graduate Dr. Jeffery M. Tharp, a postdoctoral associate at Yale University and lead author on the team’s current paper, the third thus far representing his Ph.D. thesis work at Texas A&M. In addition, it is one of the first from the Texas A&M Drug Discovery Laboratory, founded by Liu and fellow Texas A&M chemists in 2018.
“Phage display uses viruses, or phages, to ‘fish out’ specific peptides from a pool of millions of different peptide variants; however, it is very difficult to use this technique to find peptides containing ncAAs,” Tharp added. “In our paper, we developed a new method of phage display that allows for easy retrieval of potential peptide drugs containing diverse ncAAs. In addition, we used our new technique to identify novel peptides containing ncAAs that are very strong inhibitors of sirtuin 2 — an enzyme that is involved in regulating human lifespan and is a promising drug target for the treatment of human cancers.”
The Liu group collaborated with the Laboratory for Molecular Simulation (LMS), including Texas A&M chemistry Ph.D. candidate and LMS interim manager Andreas Ehnbom and Texas A&M High Performance Research Computing Associate Director Dr. Lisa M. Pérez, who performed the molecular dynamics simulations that enabled the team to understand the selectivity involved for specific peptides.
“The beauty of this work, at least in my mind, is that it crosses multiple disciplines of chemistry — synthetic chemistry, chemical biology and computations,” Ehnbom said.
Tharp notes that the founders of phage display were awarded the 2018 Nobel Prize in Chemistry in recognition of the technique’s versatility, relative ease of use and effectiveness across myriad disciplines. In combination with the resulting new molecules, he predicts the Liu group’s new method will be similarly useful for all applications of phage display.
“This technique allows ncAAs with unique structures to be incorporated into the phage peptides, which can help identify more potent peptide drugs,” Tharp added. ”In addition, we can include reactive ncAAs into the phage peptides, which can potentially be used to make better materials and drug delivery systems.”
Tharp says the team will continue to use their new phage display technique to search for other peptides containing ncAAs that inhibit enzymes related to human disease while continuing to develop other methods that expand its utility.
The team’s research was funded by the National Institutes of Health (Grant No. R01CA161158), the Cancer Prevention and Research Institute of Texas (Grant No. RP170797), the Welch Foundation (Grant No. A-1715) and National Science Foundation (Grant Nos. CHE-1566601, 1664866 and 1900549).
The team’s paper, “An Amber Obligate Active Site-Directed Ligand Evolution Technique for Phage Display,” can be viewed online along with related figures and captions.
To learn more about the Liu group and related research, visit https://www.chem.tamu.edu/rgroup/liu/.
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Contact: Shana K. Hutchins, (979) 862-1237 or email@example.com; Dr. Jeffery M. Tharp, (812) 878-5988 or firstname.lastname@example.org; or Dr. Wenshe Liu, (979) 845-1746 or email@example.com