# High-throughput profiling of proteases with phage and arrays

> **NIH NIH R43** · TANGO BIOSCIENCES, INC. · 2023 · $256,776

## Abstract

Proteases represent an important class of enzymes in all eukaryotic cells where they play
critical roles in activating and destroying proteins during cell growth, development, cell signaling,
apoptosis, and autophagy. Misregulation, however, can lead to disease; for example, cancer
cells often secrete metalloproteases that degrade the extracellular matrix, permitting cancers
cells to metastasize and take root at various locations in the body. Proteases work by recogniz-
ing linear regions, typically 6 to 8 residues, in their substrates and hydrolyzing a peptide bond,
thereby fragmenting their substrate into N-terminal and C-terminal fragments. Understanding
the range of peptide sequences cleaved by a protease, termed the "proteolysis signature" or
"substrate profile", has many scientific implications and practical benefits. One powerful method
for determining the proteolysis signature or substrate profile of a recombinant protease is
through the use of combinatorial peptide libraries. In this effort, there are two specific aims. In
Aim #1, we will develop an improved phage vector for protease site identification by allowing for
more efficient cleavage of recognized sequences, more even representation of amino acids,
and identification of longer recognition sequences (up to 10 AA).The vectors will carry the
kanamycin resistance gene and a second copy of gene III that is tagged at the N-terminus with
the AviTag and has the same cloning site cassette at three different locations. After the vectors
have been demonstrated to be suitable as substrates for two model proteases, oligonucleotides
will be ordered with a 10-mer region randomized with 19 trinucleotide phosphoramidites at equal
frequency encoding 19 amino acids (excluding cysteine) for cloning into each site and large (>
1010) libraries created. The OmpT gene in the bacterial strain, XL1-Blue, will be knocked out by
homologous recombination to eliminate the loss of phage-displayed peptides in the libraries that
carry dibasic residues. In Aim #2, Tango will evaluate the utility of the new libraries with two
commercially available proteases, the human metalloprotease, ADAM15, and the Escherichia
coli protease, DegP. Virions will be captured on neutravidin-coated magnetic beads, released
with each protease, and the output will be sequenced by Next Generation Sequencing (NGS).
Nimble Therapeutics will then synthesize two million peptides on arrays, corresponding to 10 or
more copies of each peptide sequence discovered by NGS, along with systematic amino acid
replacements of any motifs identified among the selected peptides. The peptides will carry a
peptide tag at their C-termini, which binds to fluorescent streptavidin, and a PEG linker at their
N-termini to distance them it away from the array surface. Arrays will be incubated with the pro-
tease, incubated with fluorescent streptavidin, and scans will reveal which spots lose fluores-
cence due to proteolysis. To confirm that such peptides are t...

## Key facts

- **NIH application ID:** 10602245
- **Project number:** 1R43AI174404-01
- **Recipient organization:** TANGO BIOSCIENCES, INC.
- **Principal Investigator:** BRIAN KENNETH KAY
- **Activity code:** R43 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $256,776
- **Award type:** 1
- **Project period:** 2023-05-01 → 2025-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10602245

## Citation

> US National Institutes of Health, RePORTER application 10602245, High-throughput profiling of proteases with phage and arrays (1R43AI174404-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10602245. Licensed CC0.

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