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1
Biomimetics
Chemomimetics How?
2
USING EVOLUTIONARY DESIGN TO EXPAND
GENETICALLY ENCODED CHEMISTRY
FAPESP SEMINAR
São Paulo, April 15th 2014
WWW.PROVIVI.COM
CO
MP
AN
Y OV
ERV
IEW
Who We Are
Our breakthrough technology was developed in the Arnold lab at Caltech
― Pedro Coelho, Ph.D.
• Co-founder and CEO
• Winner of Demetriades and McCoy awards for best PhD thesis in biotechnology and chemistry at Caltech
― Prof. Frances Arnold, Ph.D.
• Co-founder and board member
• Pioneer of “directed evolution”
• Elected to all three National Academies in the U.S.A. (Sciences, Engineering, Medicine)
• Co-founder of Gevo, Inc. (NASDAQ:GEVO)
― Peter Meinhold, Ph.D.
• Co-founder and CTO
• Named one of world’s top innovators under the age of 35 by MIT’s Technology Review magazine
• Co-founder of Gevo, Inc. (NASDAQ:GEVO)
4
CO
MP
AN
Y OV
ERV
IEW
Provivi
We engineer biocatalysts to perform synthetic chemical functions
Unique Solutions in Agchem Mission
5
“To use the power of synthetic
biology to make products with
improved performance”
Strategy
End-user solutions driven
Initial Focus: Agchem
1. Synthetic pyrethrum,
currently sourced from
flowers in Africa
2. Cyclopropyl isosteres to
create products with
improved performance
3. High efficacy enantiopure
pesticides
First Nature Identical Pyrethrum
Advantages:
• Very safe broad spectrum insecticide
• Non-persistent. Fast photolysis
• Few cases of resistance reported
• Ideal for household and post-harvest crop
protection
6
CO
MM
ERC
IAL T
AR
GET
chrysanthemate
pryrethrolone
Challenges:
• Unstable supply chain. Chrysanthemum
farmed mainly in East Africa and Australia
• Complex mixture of six esters
• Biosynthesis in plant not fully elucidated
• Significantly more expensive than
pyrethroids and allethrin
Cyclopropyl Isosteres for Improved Products
7
UN
IQU
E SO
LUTIO
NS
Bioorg. Med. Chem. Lett. 18, 4118 (2008) (Bristol-Myers Squibb) Bioorg. Med. Chem. Lett. 17, 828 (2007) (Merck)
Bioorg. Med. Chem. Lett. 19, 1575 (2009) (Japan Tobacco)
O
NC
O N
N
COOH
COOH
COOH
t1/2 (rat) = 0.7 h
trans t1/2 (rat) = 5.9 h
cis t1/2 (rat) = 7.4 h
Inreased metabolic stability
ATR
AZIN
E
8
• 1950–1993 non-biodegradable; accummulated in soil
• From 1993 onwards, fast degradation was observed
9
?
ATR
AZIN
E CH
LOR
OH
YDR
OLA
SE
10
J. L. Seffernick et al., Rapid Evolution of Bacterial Catabolic Enzymes: A Case Study with Atrazine Chlorohydrolase. Biochemistry 40, 12747 (2001)
9 amino acid mutations (98% sequence identity)
The introduction of synthetic compounds drives the evolution of novel catabolic activities
ATR
AZIN
E CH
LOR
OH
YDR
OLA
SE
“NA
TUR
A NO
N FA
CIT SA
LTUS”
11
DN
A
NO
NN
ATU
RA
L CA
TALYSIS
Computational design
Mechanism-based modeling
e.g. diels-alder, retro-aldol, Kemp
12
Hybrid Bio-TM catalysts
Artificial co-factor in a host protein
e.g. hydrogenation, C-H activation
D. Baker et al., PLoS One 6, e19230 (2011) T. R. Ward, Acc. Chem. Res. 44, 47 (2011)
Do Novel Reactions Require New Active Sites?
DN
A
NO
NN
ATU
RA
L CA
TALYSIS
13
novel reactions
novel enzymes old enzymes
?
1. “enzymes evolve because they have evolved” 2. high performance in vivo
DN
A
NO
NN
ATU
RA
L CA
TALYSIS
14
nonnatural reactions
old scaffold (e.g. P450s)
natural reactions
C–H C–OH
C=C epoxide
R2S R2SO R2SO2
RCOH RH + CO2
RCH2CH2R’ RHC=CHR’
natural selection + biological reagents
directed evolution + synthetic reagents
C=C cyclopropanes
C–H C–NHR
(por.+)FeIV=O
Fe=X (X = O, NR, CR2)
Isoelectronic
15
O, NR, and CR2 Transfers Share Mechanistic Features
1. Do P450s show promiscuous cyclopropanation activity?
2. Is there an evolutionary pathway for improving the novel activity?
REA
CTIO
N D
ISCO
VER
Y
Heme Proteins Show Promiscuous Activity
for Olefin Cyclopropanation
16 P. S. Coelho, E. M. Brustad, A. Kannan, F. H. Arnold, Science 339, 307 (2013)
* Diastereomeric ratios and enantiomeric excess were determined by GC analysis. † (R,S) – (S,R). ‡ (R,R) – (S,S). § Bioconversion conducted at 0.1 M citrate buffer pH = 4.0.
catalyst axial ligand cat. loading
(% mol eq) TTN cis:trans*
%ee
cis†
%ee
trans‡
catalase O-Tyr 0.16 0 - - -
CPO§ S-Cys 0.40 0 - - -
HRP N-His 1.00 9 7:93 8 -7
cyt c N-His, S-Met 1.00 19 6:94 0 12
Mb N-His 1.00 43 6:94 -1 2
P450BM3 S-Cys 0.20 5 37:63 -27 -2
hemin - 0.20 73 6:94 -1 0
REA
CTIO
N D
ISCO
VER
Y
Engineered P450BM3 Variants Are Stereoselective
Cyclopropanation Catalysts
17
Screened 92 P450BM3 variants for activity and altered stereoselectivity. Top 10:
P450 % yield* TTN cis:trans† %ee cis %ee trans
WT 1 5 37:63 -10 -9
WTF87A 1.2 6 37:63 26 -6
H2A10 33.4 167 60:40 -95 -78
H2-4-D4 41.2 206 53:47 -79 -33
H2-5-F10 58.8 294 16:84 -41 -63
C2C12R1 1.6 8 36:64 45 1
C3E4R1 1.6 8 43:57 51 -7
X7R1 2.4 12 33:67 23 -4
12 R1 6.2 31 17:83 9 -2
C2E6 R1 4.6 23 27:73 25 -6
C2G9 R1 48 240 9:91 10 -2
7-11D 32 160 35:65 -22 -18 * based on EDA. † Diastereomeric ratios and enantiomeric excess were determined by GC analysis.
P. S. Coelho, E. M. Brustad, A. Kannan, F. H. Arnold, Science 339, 307 (2013)
Related to 9-10A TS F87V (inactive)
REA
CTIO
N D
ISCO
VER
Y
BM3-T268A is Highly Active
18 P. S. Coelho, E. M. Brustad, A. Kannan, F. H. Arnold, Science 339, 307 (2013)
P450 (Holo) V78 F87 T268 I263 TTN cis:trans %ee cis %ee trans
WT - - - - 5 37:63 -10 -9
WT-F87A - A - - 6 38:62 26 -6
WT-F87V - V - - 9 30:70 -33 -26
WT-T268A - - A - 323 1:99 -15 -96
WT-F87V T268A - V A - 274 32:68 -77 -99
WT-V78A F87V T268A A V A - 190 32:68 -70 -20
A single active site mutation is sufficient
Mutations outside the active-site also influence the stereochemical outcome
still trans selective!
Stereoselective Biocatalytic Cyclopropanation
19
REA
CTIO
N D
ISCO
VER
Y
P. S. Coelho, E. M. Brustad, A. Kannan, F. H. Arnold, Science 339, 307 (2013)
15.0 17.5 20.0 22.5 25.0 27.5
-4.0
-3.0
-2.0
-1.0
0.0
1.0
2.0
3.0
4.0
5.0
6.0
7.0
8.0
9.0
uV(x1,000)
Chromatogram
Hemin
P450BM3
-T268A
15.0 17.5 20.0 22.5 25.0 27.5
-0.50
-0.25
0.00
0.25
0.50
0.75
1.00
1.25
1.50
1.75
2.00
2.25
2.50
2.75
3.00
3.25
3.50
3.75
4.00
uV(x10,000)
BM3-CIS
BM3-CIS-T438S
15.0 17.5 20.0 22.5 25.0 27.5-0.50
-0.25
0.00
0.25
0.50
0.75
1.00
1.25
1.50
1.75
2.00
2.25
2.50
2.75
3.00
3.25
3.50
3.75
4.00
4.25uV(x10,000)
Ph COOEt
SS
Ph COOEt
S R
COOEt
R R
Ph
R S
COOEtPh
OEt
O
N
N
+
cis trans
15.0 17.5 20.0 22.5 25.0 27.5-0.50
-0.25
0.00
0.25
0.50
0.75
1.00
1.25
1.50
1.75
2.00
2.25
2.50
2.75
3.00
3.25
3.50
3.75
4.00
4.25uV(x10,000)
catalyst (0.2 mol%)
styrene EDAChemomimetics
Non-Natural Reactions Catalyzed in vivo
20
• No protein purification
• Novel metabolic pathways
• Biobased production of
chemicals currently made
with synthetic methods
• Expand the chemical
toolbox for in vivo studies of
cellular function
Motivation Challenges
• Biocatalyst assembly in
functional form in vivo
• Biocompatibility and
permeability of the
synthetic reagents
• Need to drive the reaction
with NAD(P)H
• Is EDA stable in the
presence of cells?
TEC
HN
OLO
GY D
EVELO
PM
ENT
21
Redox “Gating” of the P450 Cycle
Redox diagram from: Daff et al., Redox control of the catalytic cycle of flavocytochrome P-450 BM3. Biochemistry 36, 13816 (1997)
NADPH
Need decent substrate binding
TEC
HN
OLO
GY D
EVELO
PM
ENT
22
Rationale for Axial Serine Ligation
1) Increase the FeIII/FeII redox
potential and therefore facilitate
NAD(P)H driven reduction
1) Reported to abolish
monooxygenation activity when
introduced in a mammalian P450.1
1 K. P. Vatsis, H. M. Peng, M. J. Coon, J. Inorg. Biochem. 91, 542 (2002) P. S. Coelho et al. Nature Chemical Biology 9, 485–487 (2013)
TEC
HN
OLO
GY D
EVELO
PM
ENT
23
C400S Does NOT Alter the Crystal Structure
X-ray structure confirms serine-heme ligation
TEC
HN
OLO
GY D
EVELO
PM
ENT
P. S. Coelho et al. Nature Chemical Biology 9, 485–487 (2013)
24
P411 Does NOT Look Like a P450
FeII-CO peak at 411 nm; no longer a “P-450”
BM3-CIS ABC-CIS
P. S. Coelho et al. Nature Chemical Biology 9, 485–487 (2013)
TEC
HN
OLO
GY D
EVELO
PM
ENT
25
Reduction Potential: Resting P411 > NADPH
ΔE° = +130 mV similar to BM3 – BM3(palmitate)
Maraia Ener
Na2S2O4 −660
−420
−290
−320
BM3
NAD(P)H
ABC
+130 mV
E°’ (mV vs NHE)
TEC
HN
OLO
GY D
EVELO
PM
ENT
P. S. Coelho et al. Nature Chemical Biology 9, 485–487 (2013)
26
NADPH Driven Cyclopropanation in vitro T
ECH
NO
LOG
Y DEV
ELOP
MEN
T
P. S. Coelho et al. Nature Chemical Biology 9, 485–487 (2013)
In vivo Cyclopropanation: The New State-of-the-Art
• P450 wild-type: 5 total turnovers
• P411 in vivo: 67,000 total turnovers
• Previous state-of-the-art (Rh): 45,000
total turnovers
• High product titer: ~ 30 g L-1
• High productivity: > 1 g L-1 h-1
• High enantioselectivity: 99% eecis
• Enzyme is active inside intact bacterial
cells. No enzyme purification is
required
27
TEC
HN
OLO
GY D
EVELO
PM
ENT
P. S. Coelho et al. Nature Chemical Biology 9, 485–487 (2013)
• Lyophilized whole cells,
buffer, substrates and
nothing else
Readily Applied to Commercial Product Synthesis
28
TEC
HN
OLO
GY D
EVELO
PM
ENT
• Levomilnacipran (Fetzima) is a selective serotonin and
norephineprine reuptake inhibitor
• Recently approved by FDA for treatment of clinical depression
• This enzymatic route presents an attractive green alternative that
compares favorably to current synthesis of levomilnacipran
Z. J. Wang et al. Angew. Chemie Int. Ed. In press
Proprietary Technology: Novel Reactions Beyond Cyclopropanation
29
TEC
HN
OLO
GY P
LATFO
RM
$10Bn Opportunity in Chiral Crop Protection Chemicals
30
SIN
GLE E
NA
NTIO
MER P
ESTICID
ES Non-chiral 70%
Single isomer 8%
Mixed Isomers
22% Chiral 30%
Note: 73% of all chiral pesticides are still sold as mixed isomers
All pesticides
Single enatiomers reduce application
rates and undesired side effects
Syngenta’s asymmetric synthesis of (S)-metolachlor
Provivi’s chiral synthesis has the potential
to enable the launch of single
enantiomers on a cost competitive unit
activity basis
Conclusions
Science:
• Old scaffolds, new reactions
• Small changes in structure, big
changes in function
• Fe can go quite far…
• Why no Ser-Heme proteins in
nature?
Provivi’s technology:
• Novel proprietary technology with
broad synthetic applications
• Provivi established a new benchmark
for olefin cyclopropanation
• Has been demonstrated on a first
commercial target
31
CO
NC
LUSIO
NS
32
Acknowledgements
• Frances Arnold
• Caltech: Jared Lewis, Eric Brustad, John
McIntosh, Jane Wang, Chris Farwel
• Provivi: Peter Meinhold, Mike Chen