►
Description
Open project meeting for Open Source Antibiotics Series 1, the Mur Ligases.
Full Project: https://github.com/opensourceantibiotics/murligase
Relevant GitHub Issue: https://github.com/opensourceantibiotics/murligase/issues/88
On the call: Professor Matthew Todd, Dr Edwin Tse, Yuhang Wang, Dr Daniel Gedder (UCL), Dr Adrian Lloyd and Dr Laura Diaz Saez (University of Warwick), Dr Joe Eyermann (Northeastern University), Dr Chris Swain (Cambridge MedChem Consulting), Dr Jan Abendroth (UCB Biosciences), Dr Bart Staker (SSGCID), Prof Jan Jensen (Uni Copenhagen), Roman (observer, not sure of institution).
B
A
An
issue
up
I
think
everyone's
seen
it,
and
we
can
look
at
that
in
a
minute,
but
I
just
want
to
make
sure
we
have
a
chance
to
get
through
everything
and
the
first
thing
I
think
it
would
be
great
to
hear
about
if
you
are
happy
to
talk
through
your
slide
deck
Adrian
yeah.
Certainly
that
would
be
a
primary
interest
to
everyone.
I
think.
C
C
C
D
D
So
if
you've
got
continuous
data,
which
we
generate,
the
amount
of
data
and
the
processing
we're
required
to
generate
an
initial
rate,
which
is
the
quantitative
estimate
of
enzyme
activity
is
quite
onerous.
I
mean
actual
fact.
If
we're
talking
about
the
analysis
of
20
compounds
and
we
consider
that
we're
doing
roughly
quadruplicates
and
quaduplicate
controls
for
each
it
has
been
taking
a
ridiculous
amount
of
time
up
to
one
to
two
days
to
analyze
the
data
set.
D
So
what
we've
done
we
we've
have
in
the
lab
well
had
in
the
lab
a
post-grad
called
Hector
Newman,
who
now
has
a
job.
A
bicycle
and
Hector
knows
his
way
around
Matlab,
and
so
what
he's
done
he's
devised
a
program
whereby,
and
so,
if
you
look
on
the
left
hand
the
right
hand
side
of
the
screen
on
the
red
traces,
what
it
does.
D
It
takes
the
first
five
points
and
it
calculates
by
linear
regression,
a
slope
and
it
calculates
the
correlation
coefficient
and
then
it
extends
its
width
of
analysis
to
points
one
to
six
and
one
to
seven,
then
one
to
eight
and
so
on
and
all
the
way
to
the
end
of
the
previous
curve.
And
it's
looking
for
linear
regions
and
what
it
does.
D
So
what
we've
done?
We've
tried
to
verify
the
what
we
do
by
long
hand
equates
to
what
Matlab
tells
us
and
on
the
y-axis
we
have
percentage
inhibition
calculated
from
data
generated
by
Matlab
for
compounds,
25
23
to
45,
Vietnam,
atom-wise,
Library
and
Analysis
of
the
same
data,
long
Hound,
and
we
get
quite
a
decent
agreement
between
the
two.
So
perfect
agreement
will
be
a
line
of
45
degrees
going
through
the
origin
and
a
slope
of
one,
and
we
are
quite
happy
with
that.
We're
quite
happy
that
Matlab
is
cup.
D
D
We
have
bars
in
blue,
which
are
the
actual
activity,
the
inhibition,
we're
detecting
against
pseudomonas
mercy
and
bear
in
mind
that
the
assays
we
do
are
coupled
assays.
What
we've
also
done
is
we've
also,
as
I
say,
the
coupling
system
to
look
at
the
impact
of
the
atom-wise
compounds
on
the
crafting
system
and
in
some
cases
they
are
significant.
D
So
a
good
result,
for
example,
would
be
a
very,
very
high
Blue
Bar,
with
a
much
much
lower,
Red
Bar
associated
with
it,
which
would
imply
that
the
coupling
enzymes
aren't
particularly
affected.
So
because
we
were
seeing
an
impact
of
the
atomized
compounds
on
the
coupling
system.
We
had
a
look
at
that
in
detail.
Next
slide,
please!
D
D
So
we've
actually
tightened
back
the
amount
of
coupling
enzyme
in
these
assays
to
see
what
we
can
get
away
with.
In
other
words,
what
degree
of
inhibition
the
assay
will
tolerate
and
quite
easily,
if
we
see
coupling
enzyme
inhibition
of
the
order
of
50
to
60
percent,
essentially
there's
no
significant
impact
on
the
rate
of
merliger's
Mercy
activity.
So
with
that
in
hand,
we
also
consider
the
possibility
that
the
atomized
compounds
themselves
might
actually
be
quenching
fluorescents,
because
we're
running
a
fluorescence
assay.
D
So
we
actually
filed
the
atomized
compounds
against
their
impact
upon
the
fluorescence
of
the
terminal
step
in
our
Cascade,
which
generates
the
fluorophore,
Reser,
roof
and
and
I
can
tell
you
that
there
is
no
quenching
really
in
any
of
the
compounds
that
atom
mice
have
supplied
so
excited
to
say.
The
fluorescence
we're
measuring
is
a
representation
of
what's
actually
happening
to
the
enzyme
activity
in
the
well.
D
So
we've
on
the
right
hand,
side
of
the
top
I've
taken
one
part
of
the
data
I
showed
in
the
previous
slide.
Just
as
an
example,
the
Asterix
is
below
the
compound
labels
on
the
x-axis
are
those
hits
whereby
we're
seeing
a
level
of
inhibition
of
the
coupling
system
that
is
so
insignificant
in
those
hits
which
give
us
greater
than
70
in
the
kitchen.
But
we
can
essentially
ignore
it
and
I've
listed
those
those
atomized
compounds
that
have
that
property
with
respect
to
Mercy.
D
D
D
So
on
the
right
hand,
side
are
the
a
compendium
of
data
which
basically
shows
those
compounds
that
show
greater
than
70
inhibition.
At
one
millimolar
and
of
the
16
Mercy
compounds,
we've
got,
nine
are
singly
targeted,
just
Mercy
two
are
doubly
targeted,
three
triply
so
and
two
quadruple
targets
that
it
is
to
say
against
all
of
the
large
ages
that
we've
tried.
D
C
D
D
D
D
So
what
essentially
we're
seeing
is
some
compounds,
particularly
aw17
are
particularly
potent
against,
for
example,
Cola,
pseudomona's
mercy
and
E
other
compounds
less.
So
what
we
are
also
seeing
is
a
degree
of
sigmoidicity
in
some
of
these
traces,
which
is
suggested
with
perhaps
more
than
one
mode
of
interaction.
D
D
We
have
seen
significant
impact
some
of
these
compounds
on
the
coupling
system.
Again,
we
are
working
at
high
concentration,
we
are
working
with
fragments,
I
would
imagine
that
and
it
is
a
bit
of
warning
shot
across
the
balance,
because
these
compounds
are
inhibiting
things
like
xanthinopsidase
and
hrp,
and
so
on.
D
A
A
A
D
Mean
yeah
I
mean
we'll
be
following
up,
certainly
with
some
motive
action
work.
Looking
at
what
these
things
compete
against
and
so
on,
because
I
gather
some
of
these
compounds
actually
supposedly
our
dollars
directly
and
actual
fact.
If
they
do
act,
our
historically
one
of
the
oh
phenomena,
you
often
see
with
allosteric
interactions,
is
sigmaticity.
F
D
D
A
D
Essentially,
if
we're
looking
at
the
system
itself,
we
give
the
same
concentration
of
inorganic
phosphates
as
we
have
substrate
in
there,
so
about
20,
odd
micromolar.
We
dilute
down
the
coupling
enzymes,
so
we
can
measure
initial
rates
because
usually
they're
present
in
vast
excess,
and
then
we
measure
the
rates
of
conversion
of
generational
fluorescence
from
phosphate.
Okay,.
D
D
It's
still
the
case
that
if
we
were
able
to
do
these
as
discontinuously,
there
will
be
a
significant
saving
in
terms
of
time
and
material.
So
that
is
something
we're
still
Keen
to
solve
and
we'll
be
doing
when
we
can
do
that,
then
screening
entire
libraries,
as
opposed
to
select
versions
based
upon
one
complete
screen,
is
going
to
be
a
little
easier.
A
A
C
D
G
D
A
A
A
E
A
A
A
Essentially
they
want
a
witch
compounds,
gave
hits
by
which
method
and
and
to
submit
that
back
to
them
in
the
format
that
they
want
to
see,
and
it's
always
a
bit
of
a
introduces
a
bit
of
a
roadblock
when
people
ask
for
data
back
in
prescribed
formats
But.
Ultimately,
if
we
can
fill
that
in
which
I
think
we
can
now,
we
can
send
that
back
to
them
and
they
can
do
some
magic
on
that
and
see
if
anything,
pops
out,
I
guess.
A
The
reason
why
it's
quite
interesting
is
because
they're
there
are
a
number
of
hits
against
Mercy
there,
and
there
were,
of
course,
a
number
of
Crystal
structures
and
I.
Don't
know
how
many
compounds
gave
us
sort
of
what
you
might
term
a
hit
on
the
spr
Laura
was
it?
Was
it
a
handful
or
was
it?
You
know
a
decent
number
like
we're
like
we're,
seeing
on
the
screen.
A
A
H
A
D
Well,
the
next
logical
things
to
do
would
be
to
actually
start
from
an
enzyme.
Entomologist
point
of
view
is
to
look
at
the
load
of
actions
so,
in
other
words,
to
look
at
the
impact
of
ATP
concentrations
under
the
substrates,
which
will
give
us
an
idea
with
respect
to
what
binding
sites,
if
anything
actually
targeting
and
if
we,
if
we
know
that,
if
we're
really
lucky,
we
might
even
get
ordered
bonding
out
of
this.
D
A
A
E
A
F
I
I
The
second
one
I
have
the
compound
with
the
double
bond.
I'm
sure
need
to
do
the
dial
synthesis
to
have
the
dial
compound.
The
final
one
and
the
last
one
I
also
bought
new
chemicals,
because
I
was
doing
some
reaction.
That
was
not
working,
so
I
actually
bought
the
bromine
immutasol
and
some
boronic
acid
producer
coupling
and
then
do
the
next
steps
and
she
worked
in
the
seats
of
those
two
okay.
F
All
the
blue
ones
are
already
with
Laura
the
last
pink
one
in
the
UCL
cop
say
is
finished,
so
that's
ready
and
then
that
middle
one
in
the
TCS
is
also
finished.
Sorry,
the
next
box
between
the
two
groups
yeah
that
one
is
also
finished
and
ready
the
abandoned
one.
It's
I
did
the
reaction
for
the
reductive
ammunition
that
it
worked,
but
I
haven't
been
able
to
isolate
it.
F
A
A
C
A
D
C
A
C
A
B
C
B
B
A
B
A
A
A
B
B
A
Okay,
all
right,
if,
if
anyone's
got
any
immediate
suggestions
for
which
protein
this
goes
for
then
please
say
now.
Otherwise
it
will
dig
up
the
what
this
compound
has
already
been
crystallized
with
and
and
we'll
suggest
changes.
I
mean
you
know,
I
I'm,
pretty
sure
that
this
compound
was
one
that
had
low
levels
of
activity
against
Murdy
and
my
am
I
am
I
right.
So
there's
there
was
very
little
inhibition
by
the
compound
az5595.
Is
that
right?
A
H
Well,
not
with
mere
D,
but
I
guess
you
know
maybe
ask
Anita
bakter
I
mean
I'm,
not
sure
you
know
what
the
point
is
for
these
compounds
and
also
the
urea
compounds
haven't
been
tested
against
any
place
in
terms
of
spr
or
anything
like
that.
So
I
think
it's
a
real
shot
in
the
dark,
but
yeah
you
can
try
them.
Maybe
that's
something
I
don't
know
if
you
guys
are
doing
the
Nano
DSF.
C
H
C
H
H
H
You
know
what
the
value
is
of
doing
crystallography
on
this
compounds
at
this
point,
unless
you,
unless
you
had
some
insight
on
you,
know
another
you're
like
Ace
right
now,
we
know
you're,
these
don't
bind
them
you're
D.
We
have
that
data
right,
so
I'm,
not
sure
what
else
you
know.
It's
been
profiled,
whether
it's
you
know
E
and
F.
There's
been
any
profiling
against
enf
for
any
of
these
compounds
that
Warwick
or
not.
C
H
A
B
A
B
So,
with
these
layups
with
these
overlapes,
we
can
see
you
can
see
the
their
modes
of
binding
were
pretty
similar,
especially
the
three
main
key
Hydro
bondings,
with
the
asparaging
and
taurusing
and
with
the
perizzle
parts
of
the
molecules.
So
these
three
interactions
are
very
important
and
they
are
all
behaving
the
same.
B
The
other
two
still
use
the
perizzle
part
to
to
buy
with
the
history.
So
it's
a
bit
different,
but
mostly
is
fine
and
what
adds
up
to
it
is
I.
Did
the
rmsd
calculation
so
individually
right
to
lie
and
in
Primal
and
lie?
Align
the
ID
of
against
6x9n
gets
a
value
of
0.27
and
8
dof
against
6s
9f
like
it
gives
the
value
of
0.29
so,
which
is
quite
good
just
think.
B
Just
in
case
we
had
a
bit
of
bias
generated
during
the
process.
I
align
the
car
I
align
the
compounds
individually
as
well.
The
AZ
compounds
four
against
either
5
and
I5
gives
the
value
of
3.1
3.2
around
each
and
the
azer
compounds
four
against
either
compounds
eight
zero.
Seven
four
gives
the
value
of
around
2.6,
so
there
are
decent
I.
Think,
from
my
point
of
view,
I
think
it's
decent
genome
too
see.
Okay,
they
are
the
bunny
mode,
are
pretty
much
similar.
A
A
A
And
the
issues
that
we
had
the
new
CMS
Mercy
structure
and
I
guess
we
wanted
to
confirm
that
that
structure
has
gone
through
peer
review
and
there
was
a
further
structure
with
another
Azo
compound
I.
Think
you
mentioned
last
time.
I
just
wondered
if
you
remembered
a
month
ago
now
you
know
whether
this
had
been
taken
on
yeah.
A
G
G
So
these
are
two
of
the
three
AZ
compounds
that
have
been
sent
to
us.
Well,
this
one
I
should
say
the
density
here
or
the
right
part
as
it's
displayed
here
is
quite
good
and
I
could
see,
or
it
looks
like
the
density
for
this
bicycle
here
is
a
bit
wobbly
or
it's
a
bit
thin.
So
it
seems
like
there
are
a
few
interactions
that
this
ring
by
by
cyclic
ring
is
doing
you
switch
over
to
the
other
chain.
G
G
G
So
as
soon
as
that
process
has
been
done,
I
would
publish
it.
There
was
a
discussion
a
while
back
as
to
how
to
cite
or
which
authors
should
be
connected
to
this
deposition,
and
if
you
guys
could
give
me
some
clarity
on
who
should
be
apart
from
the
stand-up
list
of
authors
that
we
have
within
SSG
CID
I'm
very
happy
to
follow
that
there
were
some
folks
at
AstraZeneca
Maybe
that
might
have
to
be
included,
but
yeah.
That's.
C
G
Look
I'll
do
that
yep
and
the
third
easy
compound
that
is
still
pending.
I
have
crystals
if
I
they're
a
little
bit
small
yet
but
I'm
quite
optimistic.
That
I
can
collect
data
in
a
week
or
two
I
can
still
do
that
in-house
I
don't
have
the
option
to
collect
at
a
synchrotron,
but
I
can
do
that
in
my
20
spare
time
and
I
can.
If
we
get
good
data,
I
can
refine
the
structure
on
my
commute
and
provide
it
to
you
with
some
delay,
but
it
might
still
happen.
C
A
D
C
C
B
Oh
sorry,
I
just
one
more
question
about
the
about
the
general
procedures.
Sorry,
the
general
procedures
we
are
using
like,
for
example,
the
what
Young
has
been
doing
and
what
Laura
has
been
doing
like
is
that
is
there
like
a
general
procedure
we
can
refer
to
because
I'm
I'm
currently
doing
sorry
I'm,
currently
doing
writing
for
the
upgrade
and
thesis.
A
Any
help
yeah,
so
you
hang
for
his
thesis,
which
is
going
to
go
in
a
month
or
so.
We'll
just
needs
to
either
refer
to
an
existing
publication
where
procedures
for
biological
essays
or
crystallography
have
been
described
or
may
need
help
with
just
some
words
to
go
into
the
sporting
information,
making
it
clear
that
the
work's
been
done
by
somebody
else,
but
but
giving
a
little
bit
of
detail.
So
his
examiners
are
able
to
understand
what
was
done
so
if
he,
if
he
can
so
and
eventually
it
costs
one
year
for
a
full
paper.