Cheap, potent pathway to pandemic therapeutics

Date:
February 15, 2021
Source:
University of Pittsburgh
Summary:
By capitalizing on a convergence of chemical, biological and
artificial intelligence advances, scientists have developed an
unusually fast and efficient method for discovering tiny antibody
fragments with big potential for development into therapeutics
against deadly diseases.



FULL STORY ==========================================================================
By capitalizing on a convergence of chemical, biological and artificial intelligence advances, University of Pittsburgh School of Medicine
scientists have developed an unusually fast and efficient method for discovering tiny antibody fragments with big potential for development
into therapeutics against deadly diseases.


==========================================================================
The technique, published today in the journal Cell Systems, is the same
process the Pitt team used to extract tiny SARS-CoV-2 antibody fragments
from llamas, which could become an inhalable COVID-19 treatment for
humans. This approach has the potential to quickly identify multiple
potent nanobodies that target different parts of a pathogen -- thwarting variants.

"Most of the vaccines and treatments against SARS-CoV-2 target the
spike protein, but if that part of the virus mutates, which we know it
is, those vaccines and treatments may be less effective," said senior
author Yi Shi, Ph.D., assistant professor of cell biology at Pitt. "Our approach is an efficient way to develop therapeutic cocktails consisting
of multiple nanobodies that can launch a multipronged attack to neutralize
the pathogen." Shi and his team specialize in finding nanobodies --
which are small, highly specific fragments of antibodies produced by
llamas and other camelids.

Nanobodies are particularly attractive for development into therapeutics because they are easy to produce and bioengineer. In addition, they
feature high stability and solubility, and can be aerosolized and inhaled, rather than administered through intravenous infusion, like traditional antibodies.

By immunizing a llama with a piece of a pathogen, the animal's immune
system produces a plethora of mature nanobodies in about two months. Then
it's a matter of teasing out which nanobodies are best at neutralizing the pathogen - - and most promising for development into therapies for humans.

That's where Shi's "high-throughput proteomics strategy" comes into play.



========================================================================== "Using this new technique, in a matter of days we're typically able to
identify tens of thousands of distinct, highly potent nanobodies from the immunized llama serum and survey them for certain characteristics, such
as where they bind to the pathogen," Shi said. "Prior to this approach,
it has been extremely challenging to identify high-affinity nanobodies."
After drawing a llama blood sample rich in mature nanobodies, the
researchers isolate those nanobodies that bind specifically to the
target of interest on the pathogen. The nanobodies are then broken
down to release small "fingerprint" peptides that are unique to each
nanobody. These fingerprint peptides are placed into a mass spectrometer,
which is a machine that measures their mass. By knowing their mass,
the scientists can figure out their amino acid sequence -- the protein
building blocks that determine the nanobody's structure. Then, from the
amino acids, the researchers can work backward to DNA -- the directions
for building more nanobodies.

Simultaneously, the amino acid sequence is uploaded to a computer
outfitted with artificial intelligence software. By rapidly sifting
through mountains of data, the program "learns" which nanobodies bind
the tightest to the pathogen and where on the pathogen they bind. In the
case of most of the currently available COVID-19 therapeutics, this is
the spike protein, but recently it has become clear that some sites on
the spike are prone to mutations that change its shape and allow for
antibody "escape." Shi's approach can select for binding sites on the
spike that are evolutionarily stable, and therefore less likely to allow
new variants to slip past.

Finally, the directions for building the most potent and diverse
nanobodies can then be fed into vats of bacterial cells, which act as
mini factories, churning out orders of magnitude more nanobodies compared
to the human cells required to produce traditional antibodies. Bacterial
cells double in 10 minutes, effectively doubling the nanobodies with them, whereas human cells take 24 hours to do the same.

"This drastically reduces the cost of producing these therapeutics,"
said Shi.

Shi and his team believe their technology could be beneficial for more
than just developing therapeutics against COVID-19 -- or even the next pandemic.

"The possible uses of highly potent and specific nanobodies that can be identified quickly and inexpensively are tremendous," said Shi. "We're exploring their use in treating cancer and neurodegenerative diseases. Our technique could even be used in personalized medicine, developing specific treatments for mutated superbugs for which every other antibiotic has
failed." Additional researchers on this publication are Yufei Xiang and Jianquan Xu, Ph.D., both of Pitt; Zhe Sang of Pitt and Carnegie Mellon University; and Lirane Bitton and Dina Schneidman-Duhovny, Ph.D., both
of the Hebrew University of Jerusalem.

This research was supported by the UPMC Aging Institute, National
Institutes of Health grant 1R35GM137905-01, Israel Science Foundation
grant 1466/18, the Ministry of Science and Technology of Israel and
the Hebrew University of Jerusalem Center for Interdisciplinary Data
Science Research.


========================================================================== Story Source: Materials provided by University_of_Pittsburgh. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Yufei Xiang, Zhe Sang, Lirane Bitton, Jianquan Xu, Yang Liu, Dina
Schneidman-Duhovny, Yi Shi. Integrative proteomics
identifies thousands of distinct, multi-epitope, and
high-affinity nanobodies. Cell Systems, Feb. 15, 2021; DOI:
10.1016/j.cels.2021.01.003 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/02/210215110323.htm

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