The key to a powerful antibiotic's formation now clear

Date:
February 2, 2022
Source:
Penn State
Summary:
According to new research, the enzyme tokK helps synthesize a chain
of methyl groups that allows potent antibiotics called carbapenems
to circumvent antibiotic resistance.



FULL STORY ==========================================================================
A powerful class of antibiotics called carbapenems can circumvent
antibiotic resistance thanks to a particular chain of atoms in their
structure. Now, a team of researchers from Penn State and Johns Hopkins University have imaged an enzyme involved in the creation of this chain
to better understand how it forms -- and perhaps replicate the process
to improve future antibiotics. A paper describing the process appears
Feb. 2 in the journal Nature.


========================================================================== Carbapenems are naturally occurring potent, broad-spectrum antibiotics
that belong to a larger group called beta-lactam antibiotics that
also includes penicillin. Carbapenems are often used as a last
resort to treat bacterial infections, including hospital-acquired and ventilator-associated bacterial pneumonia -- an increasing problem during
the COVID-19 pandemic. Certain carbapenems have a side chain that includes
two or three methyl groups -- a carbon atom and three hydrogen atoms --
that help them thwart antibiotic resistance.

"In many cases, bacteria can evolve resistance to beta-lactam antibiotics
by degrading a structure in the antibiotic called the 'beta-lactam
ring,' which renders it ineffective," said Squire Booker, a biochemist
at Penn State, investigator with the Howard Hughes Medical Institute,
and an author of the paper. "But the addition of the methyl groups in
the side chain prevents this degradation, making carbapenems powerful
clinical tools. In this study, we imaged a protein called TokK that we
know facilitates the synthesis of the side chain in order to reconstruct
the initial chemical steps in this process." TokK is a type of radical
SAM (S-adenosylmethionine) enzyme that is involved in the process of methylation -- adding a methyl group. In this case, TokK helps facilitate
the addition of three methyl groups to the antibiotic, building the side
chain that is so critical in this antibiotic.

The researchers found that, like most radical SAM enzymes, TokK first uses
one if its iron-sulfur clusters to convert a SAM molecule into a "free radical," which propels the reaction forward. The radical then takes a
hydrogen atom from the under-construction antibiotic. TokK then donates
a methyl group from a part of its structure called methyl-cobalamin to
the vacant spot on the antibiotic where the hydrogen was removed. This methylation process is repeated three times, ultimately producing the
side chain with three methyl groups.

"TokK acts like a scaffold in this process, bringing together the methyl- cobalamin, a SAM molecule, and the antibiotic into an ideal position
for transfer of the methyl group to occur," said Hayley Knox, a graduate student at Penn State and an author of the paper. "The second methyl group
is actually attached much more quickly than we would expect based on the energetics. We think that this is because the components are already so
well aligned from the first step." Cobalamin, also known as vitamin
B12, helps facilitate a variety of enzyme- driven reactions. However,
this type of "radical chemistry" is uncommon in known reactions where
cobalamin is involved, suggesting that cobalamin may play a different
role than anticipated in many reactions.

"Typically, we think of methylcobalamin as being involved in what we call 'polar chemistry' rather than 'radical chemistry,'" said Booker. "But here
we found that TokK, and we think many other cobalamin-dependent radical
SAM enzymes, use radical chemistry. It turns out that cobalamin is much
more versatile than we had previously appreciated." This improved understanding of how the side chain in carbapenems is created could
provide important insight for how to replicate this process and
potentially improve antibiotics.

"Multiple methylations by a radical SAM enzyme are unusual, although
not unprecedented, and have created a 'library' of two- and three-carbon variants of the carbapenem core in nature," said Craig Townsend, Alsoph
H. Corwin Professor of Chemistry at Johns Hopkins and an author of
the paper. "Two methyl groups may be optimal for antibiotic activity,
but one wonders if engineering of TokK to incorporate four or more of
these groups could lead to further improvements in the running battle
against bacterial resistance." This work was funded by the National
Institutes of Health, the Penn State Eberly College of Science, and the
Howard Hughes Medical Institute.

========================================================================== Story Source: Materials provided by Penn_State. Original written by Gail McCormick. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Hayley L. Knox, Erica K. Sinner, Craig A. Townsend, Amie K. Boal,
Squire
J. Booker. Structure of a B12-dependent radical SAM
enzyme in carbapenem biosynthesis. Nature, 2022; DOI:
10.1038/s41586-021-04392-4 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/02/220202134712.htm

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