►
Description
Open project meeting for Open Source Antibiotics Series 1, the Mur Ligases.
Full Project: https://github.com/opensourceantibiot...
Relevant GitHub Issue: https://github.com/opensourceantibiotics/murligase/issues/99
On the call: Prof. Matthew Todd, Yuhang Wang, Yiwei Wang (UCL), Prof Chris Dowson (chair), Dr Adrian Lloyd and Dr Laura Diaz Saez (University of Warwick), Dr Joe Eyermann, Dr Lori Ferrins (Northeastern University), Bart Staker (SSGCID), Jan Abendroth (UCB Pharma).
A
Okay,
so
Tuesday
13th
of
June,
open
source
antibiotics
more
like
A's
meeting.
There
is
an
agenda
online,
which
you
hang
very
kindly
posted
and
I
just
tweaked
a
little
bit
I
guess
there
are
still.
You
know
the
same
major
items
that
we're
dealing
with
and
the
the
big
one
was
the
ongoing
swing
of
the
enemy
compounds
and
Adrian.
You
shared
a
slide
deck
very
kindly
the
other
day.
C
D
B
C
C
Right,
okay,
so
it's
I've
basically
done
absolutely
done
with
their
enemy
library,
with
the
student
Administration,
that's
for
enzyme
and
gone
through
and
not
carefully
at
everything
that
we've
done
so.
Basically,
in
the
beginning,
we
received
the
enemy
Library,
all
676
members
of
it,
the
practice
fragments,
distribute.
E
C
C
C
Okay,
so
in
the
figure
I've
labeled
a
is
the
entire
Library
data,
in
other
words,
percentage
inhibition
for
all
compounds
the
red
bar
towards
the
right
hand.
Side
of
that
is
the
response
of
our
standard
at
PCP,
and
then
what
we
did
is
we
triaged
the
any
compound
that
gives
an
inhibition
of
greater
than
50
percent.
C
C
Now,
if
you
look
at
the
right
hand,
side
with
the
two
histograms,
the
one
in
purple,
which
looks
at
the
response
of
the
discontinuous
assay
that
we
used
in
the
library
to
loss
of
coupling
enzyme
activity,
essentially
that
assay
has
an
issue
with
any
loss
of
coupling
enzyme
activity,
because
that
is
reflected
in
the
final
result
furiously
enough.
If
you
run
the
assay
continuously,
which
you
can
do,
then
the
impact
of
loss
of
coupling
enzyme
activity
is
a
lot
lot
less.
C
The
impact
of
the
compounds
on
the
inhibition
of
the
coupling
system,
the
bars
in
blue,
are
the
actual
Murdy
University
Commerce
data
that
we
got
and
what
was
very
clear
is
that
of
all
the
screening
that
we've
done
only
11
or
so
compounds.
Could
we
actually
say
hand
on
heart,
were
not
artifacts
of
coupling
enzyme,
inhibition
that
left
about
113
compounds
whose
activity
may
or
may
not
be
impacted
on
D,
and
that's
an
awful
lot
of
chemical
Equity
to
throw
away.
E
C
F
C
We,
which
may
or
may
not
be
inhibited
by
the
compounds
we
were
testing
them
against,
and
the
fourth
point
is
that,
in
an
asset
with
emotional
components,
the
more
components
you
have,
the
more
liability
you
have
to
interference
in
any
of
those
coupling
steps
and
also
the
fifth
point
is
the
situation
is
exacerbated
by
the
nature
of
the
library,
so
the
compounds
of
fragments.
So
it
appears
that
to
expect
clean
discrimination,
Nation
against
of
Target
activity
is
probably
asking
a
little
much
for
molecules
of
this
sort
of
size.
C
So
what
we
did
is
we
basically
sixth
Point
sort
of
simpler
method
of
passay,
of
the
fragments
that
we
suspected
might
actually
be
meredy
inhibitors,
no,
essentially,
what
we
can
do
if
we
just
run
the
assay
with
perineucaiposterone.
Well,
there's
no
other
coupling
enzyme
and
we
use
methylthyroidism.
Those
cleavage
biphosphate
generates
a
singular
360..
We
have
a
a
number
of
advantages:
there's
no
possibility
of
fluorescence
quenching
it's
simpler,
so
there
are
less
potential
libel
targets
for
off
Target
inhibition.
C
C
E
B
C
C
C
C
C
Inhibited,
the
company
and,
on
that
basis
and
the
PMP
couple
most
of
those
compounds
were
actually
made
it
through.
In
other
words,
the
coupling
enzyme
inhibition
was
less
than
50
percent,
so
we
were
looking
at
genuine
murder
activity,
and
that
leaves
us
with
11
compounds.
On
the
left
hand,
side
in
addition
to
j06,
m02
and
lo6,
which
I
believe
are
actually
genuinely
active.
C
The
enemy
Library
bites
did
present
its
own
set
of
issues,
for
example,
compound
precipitation
reaction
with
the
components
of
the
assay,
the
amplex
red
assay
substitution
to
a
special
photo
metric.
One
didn't
get
us
out
of
jail
completely.
They
were
still
significant
absorbance
issues
with
many
compounds.
C
The
other
thing,
and
it
was
it
shouldn't
have
been,
but
it
was
a
surprise
to
me
is
how
wildly
indiscriminate
many
of
the
enemy
compounds
actually
are,
and
that
is
telling,
because
it
really
really
made
it
a
real
issue-
the
amplex
red
assay,
to
discriminate
against
things
that
were
truly
murder
us
now.
You
might
think
that
I'm
not
a
fan
of
the
fluorescent
anymore,
but.
C
In
the
right
place
at
the
right
time,
it
doesn't
have
his
own
compound
and
we've
been
working
with
with
Mercy.
There
is
no
issue
at
all
they're,
very
in
those
assays.
Those
compounds
are
selective
enough
to
use
even
in
the
work
I've
talked
about
here,
it
may
have
might
have
been
able,
it
might
have
been
possible
to
employ
the
fluorescent
assay
we'd
originally
intended
to
use
an
ATP
analog,
because
that
would
buy
more
weekly.
C
C
Having
gone
through
the
exercise,
what
we're
now
doing
on
the
ic50s
on
the
hits
that
we've
got
with
the
mesg
PMP
assay,
we
don't
have
the
facility
to
use
the
Malachi
green
assay,
because
the
problems
that
it's
acidity
creates
India
the
actual
assay
with
this
particular.
If
we
were
going
to
do
anything
more
with
it,
we
might
be
looking
at
using
things
like
they
ADP
glow,
luminous.
A
That
thank
you
very
much
all
right.
So
personal
question
is,
if
I
may
so
you're
doing
of
the
14
compounds
which,
for
which
you
have
high
confidence,
you're
doing
ic50s.
Is
that
right?
Yes,
that's
right
and
just
to
raise
two
other
questions.
One
is
these
are,
of
course,
the
enamine
collection
of
600
and
something
compounds
we've,
given
that
we
are
making
and
shipping
compounds
related
to
the
atom-wise.
That
I
just
wondered
if
you
were
able
to
also
to
evaluate
the
atomized
compounds
in
this
way.
C
Of
the
original
atomized
data
was
good,
it
was
done
with
the
application
identity
of
of
Target
coupling
enzyme.
Inhibition
was
much
much
much
lower
a
long
way.
So,
interestingly
enough,
the
atomized
library
from
that
perspective
and
the
enzymatic
perspective
was
actually
a
far
easier
thing
to
deal
with
and
the
hits
that
we
got.
We
are
confident
of
it's
just
that
here
in
the
context
of
this
Library,
the
members
of
it
are
far
more
multi-potent.
A
The
the
molecular
weights
here
are
a
little
bit
smaller
than
some
of
the
atomized
ones,
I
suppose
just
a
little
bit
not
much
okay
and
and
then
before
I
I
stopped
talking,
because
I'm
sure
other
people
might
want
to
ask
you.
Questions
I
mean
so
you're
trying
to
work,
and
it's
it's
fantastic
and
it
clarifies
an
awful
lot.
A
C
The
it's
a
in
a
way,
I'm
tempted
to
say
no
simply
because
quite
often,
because
spr
looks
at
Frank
bonding
as
opposed
to
actual
inhibition
of
an
enzyme
activity,
you
can
get
binding
without
inhibition,
I
mean
it
really
depends
what
you're
after.
But
if,
if
January,
we
are
after
active
site,
focused
molecules
that
have
an
inhibitory
potency,
then,
to
my
mind,
unfortunately,
it
has
to
be
kind
of
this
way
around.
E
G
G
B
F
E
G
E
G
E
E
F
Want
you
want
High,
you
want
High
numbers
and
the
mirror
D
column
and
you
want
low
numbers
in
the
PNP
column,
pardon
yeah
exactly
so
right.
So
you
have
a
bunch
of
compounds
there
that
you
know
if
you
look
at
like
m17,
it's
86
inhibition
at
500
micro
mower,
you
guys
for
your
D,
but
it's
only
inhibiting
the
PNP
assay
at
seven
percent,
so
that
I
think
my
interpretation
of
that
is
that
that's
the
very
that's
quote
as
selective
your
D
inhibitor.
G
E
F
F
G
You
know
and
then
once
we
got
that,
then
those
we
can
definitely
test
them.
If
it's
a
small
number
of
compounds,
I
can
even
try
to
do
competition
essays
on
the
SBR
and
or
include
ATP,
for
example,
or
what
amp
PNP
and
things
like
that
on
the
buffers,
because
then
it's
a
really
slow
volume
ancestories
and
things
like
that.
G
G
C
F
G
Because
I
was
just
talking
about
the
spirit,
because
you
were
mentioning
it,
you
know
you
wanted
my
opinion
on
that
area.
Well,
if
we
wanted
to
measure
anybody,
because
for
for
crystallography
and
things
like
that,
it's
more
important
The
Binding
than
the
inhibition,
because
we
want
to
saturate
completely.
G
C
C
F
Yeah
I
I
would
say,
take
these
and
go
after
either.
You
know
ideally
mercy
and
mirror
e
and
to
see
if
you
get
any
inhibition,
I
guess
you're.
Seeing
from
your
excuse
me
from
your
C
from
your
e
yeah,
I
would
say:
just
I
mean
you.
This
is
Herculean
effort.
You've
done
I
mean
it's
just
I
I
can't
emphasize
that
enough
about
how
persistent
you've
been
and
I
know
it's.
It's
been
just
an
amazing
amount
of
effort
to
get
to
this
point.
F
A
Yeah
but
I
I
agree
if
you,
if
you
redid
everything
available,
if
you
do
that,
you
run
the
risk
of
missing
compounds
that
are
active
against
Mercia
Mercy
selectively,
but
I
think
the
risk
of
that
is
small
compared
to
the
amount
of
work
will
be
involved
in
re-screening
everything
that
makes
sense
to
go
after
the
these
existing
compounds.
Yeah.
E
G
The
ssgc
is
is
doing
with
the
a06,
but
in
my
experience
this
campus,
so
I
can't
get
into
high
concentrations
for
microstellation
experiments.
So
if
we
get
more
potent
compounds,
I
will
have
to
add
less
compound
onto
my
crystallization
trials
and
maybe
keeping
that
into
account
for
the
follow-up
compounds
May,
introducing
something
that
might
make
them
a
little
bit
more
soluble
for
the
experiments.
That
would
be
amazing.
E
G
B
F
A
G
A
All
right
great
and
then
there
were
some
some
ones
we
couldn't
buy.
Anything
of
so
yiwa's
made
some
variants
and
it's
continued
to
do
that
and
Eve
has
made
some
variants
of
this
one.
So
again,
these
are
atomized
compounds
that
we
liked
and
had
shipped
of
last
two
competition
compounds
so
yeah.
Those
are
those
are
now
with
you.
Ua
is
looking
at
some
other
variances,
which
should
be
better
more
more
soluble
to
some
extent.
So
that's
the
next
round
of
compound
she's
going
to
make.
E
A
All
right,
just
by
the
way,
with
the
competition
ones,
these
are
the
last
two.
You
know
that
is
a
discrete
piece
of
work
and
I.
Think
as
we
as
we
mentioned
before.
If
we
investigated
those
compounds
and
collated
together
all
the
methods
that
people
used
and
if
we
have
identified
anything
that
is
binding,
we
can
quickly
get
a
paper
out
on
that
because
it's
a
completely
self-contained
piece
of
work.
A
Also,
thinking
about
you
know
Publications
from
this
group
as
a
way
of
convincing
people
to
to
fund
the
next
step,
and
that
could
be
one
of
them,
obviously
crystallography
paper
being
another
and
you
hang's
exploration
of
the
AZ
compounds
being
another.
If
we
can
get
some
of
these
over
the
line
that.
A
H
There
you
go
yeah,
that's
been
shipped
off
from
me
to
Scott
now,
and
then
they
have
the
myrrh.
We
also
have
the
mer
D
proteins
for
crystallography.
From
from
acetobacter
and
pseudomonas.
We
have
the
armor
E's
aren't
I
was
looking.
You
know,
trying
to
figure
out
everything
and
armor
ease
that
we've
purified
never
crystallized
like
those
aren't,
so
we're
going
to
have
to
make
new
constructs
to
get
them
our
e,
but
we
did
make
the
mer
D's
for
both
of
those,
and
so
those
will
go
into
Crystal
trials.
B
H
B
F
G
E
B
Because
we
were
just
having
this
conversation
today,
whether
you,
whether
we're
trying
to
find
something
that
looks
like
some
transition
analog
as
much
as
a
substrate,
to
try
and
capture
the
enzyme
halfway
through
it,
you
know
it's
activity,
you
know,
I,
don't
know,
I,
don't
know
why
what
we
always
fail.
You
know
it
would
be
going
for.
B
C
Have
made
transitional
state
analogs
with
the
tetrahedral
Center,
where
you'll
say,
happy
have
nucleophilic
attack
between,
and
it
turns
out
that
they
are
nanomola
molecules.
It
also
turns
out
that
they
are.
They
have
no
activity
in
a
biological
sense
at
all,
because
they're
they're
still
highly
charged
and
and
they
are
impossible
to
get
through
membranes.
G
F
So
my
my
suggestion,
I
guess
since
we're
talking
about
this
right
now
so
I
think
one
of
the
the
issue
is,
you
know,
I,
guess
Laura!
You
talk
about
the
limited
solubilities
compounds,
I
mean
like
I
know.
Every
enzyme
system
is
different,
but
I
mean
there's
been
so
much
work
done.
I've
been
involved
in
in
the
kindness
space
where
kind
most
of
the
kinase
lead
generation
which
lead
lead
material
is
highly
insoluble.
F
So
if
you
took
something
like
with
the
ribose
just
the
ribose,
so
if
you
look
at
like
the
crystal
structures,
one
of
the
of
mirror
d,
the
ribose
hydroxyl
groups,
interact
with
the
acid
group
and
kind
of
help
tie
down
the
flexible
domain,
but
that
compound
should
be
relatively
weak
binding.
So
if
you
had
crystals
with
that
bound
and
then
do
more
of
a
back
soaking
and
not
putting
so
I
guess
this
other
thing
about
I,
guess
it's
what's
a
vapor
deposition!
F
F
That
might
be
enough
to
help
stabilize
some
of
the
other
domain
and
then
can
you
back
soak
in
because
some
that
that
compound
I
don't
know
what
the
activity
of
it
was
going
to
be.
But
some
of
these
compounds
that
we
have
based
on
Adrian's
work-
these
are,
you
know,
say
100,
micro,
mower
or
15
micro.
Some
of
these
compounds
are,
in
the
you
know,
lower
micro,
mower
range,
so
I'm
just
wondering
if
you
can
compete
back
out.
F
F
G
Is
a
different
system,
crystallization
conditions
as
well.
There
are
many
factors
that
why
this
is
these
compounds
might
not
be
behaving
on
the
on
the
job.
I,
don't
know
what
is
what
systems
are
you
looking
into?
If
you
remember,
if
you
remember
later,
you
can
send
me
the
the
links
to
the
pdb
and
I
can
have
a
look,
what
other
crystallization
conditions,
but
many
times
it's
just.
They
have
a
more
or
better
solubilization
condition
for
the
crystallization.
G
Our
conditions
are
not
really
good
for
solubilizing
compounds
and
I'm
trying
to
get
new
crystallization
conditions
on
the
melee
cases,
but
I'm
not
able
to
so
it's
a
mixture
of
compass
not
being
soluble
enough
from
that
range
of
conditions,
plus
the
crystals
not
wanting
to
grow
in
something
else,
and
when
I
managed
to
grow
it
in
something
else
like
with
dr6.
The
diffraction
was
not
good
enough.
Well,
I
couldn't
collect
later
right.
A
E
B
B
E
A
B
G
So
I
also
noticed
when
I
Was
preparing
the
compounds
for
spr
in
the
previous
runs
right.
They
also
irrigate.
While
you
try
to
delete
the
mud
relatively
higher
concentrations
and
I
did
different
dilutions
to
try
to
get
no
aggregation
at
all
for
preparing
things
for
the
soaking
and
cocoa
sterilization
as
well.
Vocal
crystallization
is
the
normal
buffers
right
and
they
are
still
not
soluble
at
high
qualitation,
so
I
can
go.
I
cannot
test
the
compounds
at
really
high
connotations
without
aggregating
the
compounds.
G
So
that
limits
a
lot
in
the
experiment,
because
when
you
have
these
macromolar
binders
and
meet
micromolar
binders,
you
want
to
have
a
big
radio
like
one
two,
three
probably
or
at
least
I
like
to
have
it.
I
have
more
success
getting
to
one
two
three
closer
to
one
to
three
than
one
to
two
one
to
two
usually
works
better
for
better
inhibitors.
G
A
I
mean
the
compounds
that
we're
shipping
are
meant
to
be
little
clouds
around
each
of
these
that
give
us
confidence
that
we're
looking
at
something
real.
So
it's
not
just
a
single
tone
of
something
strange
happening.
You
know,
we've
got
something
once
once
we
established
that
there
is
reality
there,
then
building
in
solubility,
and
things
like
that
is
yeah.
G
G
G
A
A
A
A
D
The
green
ones,
the
green
ones,
are
the
structures
we
have
already
achieved,
then
I'm
saving
it
saving
this.
What
protective
version,
and
once
we
decided
to
ship
it
it
just
departed
for
the
for
the
general.
That's
for
the
comp
count
for
Gen
17
Advance.
Familiar
with
this,
then
for
the
comforting,
2020.
Oh
sorry,
company.
D
That's
the
I've!
The
book
of
coupling
didn't
work,
but
I
managed
to
figure
out
some
other
coupling
conditions
which
may
allow
us
California
to
work
and
still
work
on
those
progress,
and
once
it's
being
achieved,
it
will
be
easy
protection
upwards
and
for
the
rigid
87
I'm
having
problem
with
getting
the
right
condition
to
to
work
as
the
the
book
of
company
doesn't
work.
Nor
did
the
Almond
couples
have
a
bit
of
problem
here.
D
Another
two
couplings,
then,
hopefully
that
will
be
done
afterwards.
Oh
that's
the
book
protected
version,
so
I
would
protect
anyway-
and
here
here
are
the
redesign
redesigned
groups
to
make
gen
accomplishing
three.
So
basically
like
a
Nitro
here
then
reduce
it
to
the
aiming
sorry
reducing
to
aiming
yeah
then
make
it
a
urea.
Then.
D
D
Then
just
start
the
coupling
then
did
the
packing.
The
last
last
page
was
the
most
tricky
one
I
almost
said:
I
almost
abandoned
it
because
it
was
two
should
be
at
first
I
didn't
manage
to
design
whole
thing,
but
later
on,
I
found
out
there's
a
potential
route
here,
because
the
the
first
starting
with
this
cheap
material
starting
material,
then
my
kids
out
aldehyde
here
then
using
the
nitromethane
so
that
it
could
be
have
that
extra
carbon.
D
A
All
right
great,
thank
you
young,
so
the
idea
is
to
try
and
get
these
compounds
complete
and
evaluated,
because
these
were
the
first
generation
of
things
that
the
animal
was
putting.
The
idea,
of
course,
is
to
then
get
data
and
then
feed
that
back
into
a
second
round
of
predictions
right,
so
we're
trying
to
you
know
Keen
to
go
into
initial
things
done
the
just
the
other
things,
because
we're
going
to
run
out
of
time
so
just
to
update
you
on
on.
A
You
hangs
currently
looking
at
oh
the
variants
of
the
of
the
AZ
compound,
which
are
intended
to
promote
accumulation
so
different
things
versus
what
we
had
done
with
the
amine
compound.
If,
if
you,
the
Warwick
guys
were
able
to
get
the
ic50s
for
versus
the
enzymes
for
newhang's
alien
compound,
then
you
can.
He
can
complete
that
part
of
his
thesis
just
just
waiting
on
the
on
the
data.
A
For
that
we
know
that
they're
not
effective
against
wild
type,
but
it'd
be
great
to
get
the
ic15s
against
the
enzymes
and
then
the
last
thing
is
in
in
talking
with
Joe,
putting
together
the
key
diagram
for
a
proposal.
The
cc4
carb
to
get
some
more
chemistry
done
and
the
Young's
been
working
hard
on
on
the
summary
diagram
of
what
we're
going
to
be
asking
them
for
and
then
we'll
we'll
put
together
a
brief
scaffold
proposal
around
there.