Biocatalytic Retrosynthesis Nicholas J. Turner School of Chemistry & Manchester Institute of Biotechnology, University of Manchester, UK ROBOX/Carbazymes Summer School Certosa di Pontignano, Siena, IT 3 rd – 6 th October 2017
Biocatalytic Retrosynthesis
Nicholas J. Turner
School of Chemistry & Manchester Institute of Biotechnology, University of Manchester, UK
ROBOX/Carbazymes Summer School
Certosa di Pontignano, Siena, IT 3rd – 6th October 2017
3 Approaches to (un)natural product synthesis
Biosynthesis Organic
Synthesis Biocatalysis
• Natural products • Biosynthetic pathways • Enzyme mechanism • Specialised enzymes
• New reagents • New catalysts • Retrosynthesis • Synthetic strategy
• Engineered biocatalysts • Broad specificity • Systems biocatalysis • Synthetic biology
Biosynthetic retrosynthesis
Biosynthetic retrosynthesis
Biosynthetic retrosynthesis
Biosynthetic retrosynthesis
Biosynthetic retrosynthesis
Diversity of natural products
1. All steps subjected to catalysis
2. No protecting groups
3. Relatively simple transformations (oxidation, reduction, hydrolysis)
4. Cascades used to build molecular complexity
Nature Chem. Biol., 2013, 9, 285-288; Angew. Chem. Int. Ed., 2017, 56, in press (with Erick Carreira)
Biocatalytic retrosynthesis
Design-Build-Test: Development of a cascade
S.P. France, L. Hepworth, N.J. Turner & S.L. Flitsch, ACS Catal., 2017, 7, 710-724.
What makes a good cascade?
1. ‘One Pot’ – all transformations compatible
2. High selectivity/orthogonality of biocatalysts – no cross reactivity
3. Intrinsic pre-organisation of reaction sequences
4. Thermodynamics favourable
5. Comparable kinetics – no accumulation of reactive intermediates
6. Whole cells to avoid need for co-factors and enzyme isolation
A B C
Cat 1 Cat 2
S.P. France, L. Hepworth, N.J. Turner & S.L. Flitsch, ACS Catal., 2017, 7, 710-724.
Biocatalytic toolbox
(Asymmetric) biocatalytic amine toolbox
Need new biocatalysts for (C-C) formation in addition to (C-N)
Biocatalytic toolbox
(S)-DIP-Cl @ -20oC
MLK-II MLK-III
D. Rozzell and J. Liang, Speciality Chemicals Magazine, 2008, 36.
Montelukast
Replaces (S)-DIP-Cl @ -20oC
D. Rozzell and J. Liang, Speciality Chemicals Magazine, 2008, 36.
MLK-II MLK-III
Montelukast
Montelukast
Biocatalytic Process
100g/L Catalytic
45 oC 99.3%
Direct filtration >99.9%
6 IPA, H2O, toluene
Biodegradable enzyme, cofactor
D. Rozzell and J. Liang, Speciality Chemicals Magazine, 2008, 36.
(S)-DIP-Cl Process
100g/L 1.8 eq DIP-Cl
-25 oC Not provided
Extraction with high dilution 99.2% (after recryst.)
30-50 DCM, THF
Non-biodegradable borate salts Other inorganics, 3.6 eq. pinene
Parameter
Ketone Concentration Catalytic/Stoichiometric
Temperature Conversion
Product Isolation Enantiomeric Excess
Solvent/MLK-III (L/Kg) Solvents Used
Other Waste Generation
Comparison of biocatalytic and (S)-DIP-Cl process metrics for MLK-II to MLK-III
DSM
tonne-scale production
• 7-step process • Cost reduction and IP issues became important
PAL mediated synthesis of perindopril
PAL mediated synthesis of perindopril
Anti-hypertensive
DSM
96% yield; 99% e.e.
tonne-scale production
B. de Lange et al., ChemCatChem, 2011, 3, 289.
K.B. Hansen et al., J. Am. Chem. Soc., 2009, 131, 8798.
2nd generation process
Januvia (Sitagliptin)
oral anti-diabetic DPP-4 inhibitor
Sitagliptin
Januvia (Sitagliptin)
oral anti-diabetic DPP-4 inhibitor
C.J. Savile et al., Science, 2010, 329, 305.
(R)-selective transaminase ‘substrate walking’ to evolve larger binding pocket
3rd generation process
• Increased yield (by 13%) • Higher e.e. • Higher productivity (by 53%) • Reduced waste (by 19%)
92% yield >99.95% e.e.
Sitagliptin
Retrosynthesis of lipitor side-chain
Sustainable low cost production of medicines for 3rd world
‘A process for the preparation of substituted prolyl peptides and similar peptidomimetics EP 2539320 A1’.
Synthesis of telaprevir (hepatitis C)
Reagents and conditions: a) MAO-N, 100 mM KPO4, pH = 8.0, 37 °C, then: b)
1,2, CH2Cl2, 50%; c) K2CO3, MeOH; d) Dess-Martin, CH2Cl2, 50% over 2 steps.
telaprevir
Multi-component synthesis of telaprevir
A. Znabet, R. Orru, N.J. Turner et al., Chem. Commun., 2010, 7918.
83:17
Galactose oxidase (GOase)
J.B. Rannes et al., J. Am. Chem. Soc., 2011, 133, 8436-8439.
B. Yuan et al., Angew. Chem. Int Ed., 2010, 49, 7010; S. Staniland, et al. Chem. Eur. J. 2014, 20, 13084.
Chiral auxilliary based on diarylether
Lipase catalysed desymmetrisation Asymmetric oxidation Asymmetric reduction
B. Yuan, J. Clayden, N.J. Turner et al., Angew. Chem. Int Ed., 2010, 49, 7010.
Desymmetrisation of diaryl ethers
Origin of selectivity
B. Yuan, J. Clayden, N.J. Turner et al., Angew. Chem. Int Ed., 2010, 49, 7010.
(+)-P
Entry KRED conv [%] ee [%] Config
1 102 21 7 R
2 105 4 >99 R
3 107 5 >99 R
4 108 100 96 S
5 110 59 99 S
6 111 5 >99 R
7 112 100 98 S
8 113 93 95 S
9 119 100 94 S
10 123 22 16 S
11 124 73 68 S
12 130 100 >99 R
DKR of racemic quinoline N-oxide
S. Staniland, N.J. Turner, J. Clayden et al., Angew. Chem. Int. Ed. 2016, 55, 10755.
Tandem GOase/PaoABC oxidation
Susanne, Herter, Shane McKenna, Will Birmingham, Andrew Carnell
Tandem GOase/XDH oxidation
B. Bechi, S. Herter, S. McKenna, C. Riley, S. Leimkühler, N. J. Turner and A.J. Carnell, Green
Chem. 2014, 16, 4524.
Dibenz[c,e]azepines – biocatalytic retrosynthesis
• Possess carbon centred and axial chirality (atropisomers)
• Potentially interesting applications as chiral ligands
• Can possess biological activity e.g. Azapetine is a vasodilator.
Azapetine S. L. Pira, T. W. Wallace and J. P. Graham, Org. Lett., 2009, 11, 1663-1666.
Scott France
Dibenz[c,e]azepines
Scott France
Dibenz[c,e]azepines
Scott France
Cascade reactions with IREDs
ω-TA - IRED tandem reactions
S.P. France, S. Hussain, F. Leipold, A. Hill et al., ACS Catal., 2016, 6, 3753.
S.P. France, S. Hussain, F. Leipold, A. Hill et al., ACS Catal., 2016, 6, 3753.
Cascade reactions with IREDs
CAR - ω-TA - IRED tandem reactions
O’Reilly et al., Angew. Chem. Int. Ed. 2014, 53, 10714 - 10717 (VIP).
S.P. France, S. Hussain, F. Leipold, A. Hill et al., ACS Catal., 2016, 6, 3753.
D. Gahloth et al., Nature Chem. Biol, 2017, 13, in press: (CAR structure).
In vitro generation of chiral piperidines
S.P. France, S. Hussain, F. Leipold, A. Hill et al., ACS Catal., 2016, 6, 3753.
Biosynthesis of chiral piperidines via PKS
H. Peng, et al., ACS Chem. Biol., 2016, 11, 3278-3283.
• Can we develop guidelines for route design for synthetic
chemists (biocatalytic retrosynthesis).
• How many different biocatalyst classes do we have/need to be able to do real organic synthesis? 50 /250.
• How many distinct retrosynthetic disconnections? (ca. 250).
• Where are the gaps in biocatalysis – which reactions are under-represented in the biocatalysis toolbox (C-C bond formation)?
• Need biocatalysts with broad substrate scope that are active and stable under the conditions of a chemical process (fit
• biocatalyst to process rather than vice-versa).
• Need to increase application of biocatalysis in medicinal chemistry.
Challenges for biocatalysis
Engineered Biocatalysts for Chiral Amine Synthesis
Nicholas J. Turner
School of Chemistry & Manchester Institute of Biotechnology, University of Manchester, UK
ROBOX/Carbazymes Summer School
Certosa di Pontignano, Siena, IT 3rd – 6th October 2017
Protein Evolution
Biocatalysts Synthesis Mechanism-based Discovery
Design – Evolution - Synthesis
Design features: • Activity • Selectivity • Specificity • Stability
Sequence-based Discovery
(Bioinformatics)
Amines in organic chemistry
Amine biocatalysis
ACS Catal, 2016, 6, 3753; ACIE, 2014, 53, 2447.
Transaminase
Januvia (Sitagliptin)
oral anti-diabetic DPP-4 inhibitor
C.J. Savile et al., Science, 2010, 329, 305.
(R)-selective transaminase ‘substrate walking’ to evolve larger binding pocket
3rd generation process
• Increased yield (by 13%) • Higher e.e. • Higher productivity (by 53%) • Reduced waste (by 19%)
92% yield >99.95% e.e.
Sitagliptin
DKR with transaminases
J. Limanto et al., Org. Lett., 2014, 16, 2716.
C.K. Cheung et al., OPRD, 2014, 18, 215.
DKR with transaminases
Z. Peng et al., Org. Lett., 2014, 16, 860 (Pfizer).
A
The PAL (ammonia lyase) and PAM (ammonia
mutase) toolbox
A = Wild-type PcPAL / RgPAL
B
A
Wu et al., Angew Chem Int Ed 2012, 51, 482.
B = Directed evolution of TcPAM
The PAL (ammonia lyase) and PAM (ammonia
mutase) toolbox
B
A
C
,
C = Combining AvPAL, deaminase and chemical reduction steps
The PAL (ammonia lyase) and PAM (ammonia
mutase) toolbox
Parmeggiani et al., Angew Chem Int Ed, 2015, 54, 4608.
B
D
A
C
The PAL (ammonia lyase) and PAM (ammonia
mutase) toolbox
A = Wild-type PcPAL / RgPAL
B = Directed evolution of TcPAM
C = Combining AvPAL, deaminase and chemical reduction steps
D = Rational Design of EncP
(S)-selective MIO-dependent amination of
cinnamate derivatives by EncP
N.J. Weise et al., J. Am. Chem. Soc., 2015, 137, 12977-12983.
(a)
(b)
EncP whole cells
4M (NH4)2SO4, 55oC
Cinnamate β-Phenylalanine α-Phenylalanine
EncPwt 56 : 44 EncPR299K 88 : 12 EncPE293Q 43 : 57 EncPE293M 18 : 82
Rationally designed point mutations: regioselectivity amenable to shifting in both directions
EncP variants with altered regioselectivity
N.J. Weise et al., J. Am. Chem. Soc., 2015, 137, 12977-12983.
N.J. Weise et al., J. Am. Chem. Soc., 2015, 137, 12977-12983.
0
20
40
60
80
100
1a 1b 1c 1d 1e 1f 1g 1h 1i 1j 1k 1l 1m 1n 1o 1p 1q 1r 1s 1t 1u 1v
0
20
40
60
80
100
1a 1b 1c 1d 1e 1f 1g 1h 1i 1j 1k 1l 1m 1n 1o 1p 1q 1r 1s 1t 1u 1v
0
20
40
60
80
100
1a 1b 1c 1d 1e 1f 1g 1h 1i 1j 1k 1l 1m 1n 1o 1p 1q 1r 1s 1t 1u 1v
>95
>95
75
83
>95
>95
>95
>95
n.d.
72
-
n.d.
n.d.
81
>95
>95
>90
>95
>90
>95
>95
>95
n.d.
>95
-
6
>95
92
n.d.
64
n.d.
>95
>95
>95
0
-
85
>95
>95
>95
84
-
n.d.
86
ee 2 (%)
ee 3 (%)
Co
nv.
(%)
(a)
>95
>95
65
>95
n.d.
>95
>95
-
n.d.
>95
-
n.d.
n.d.
>95
>95
>95
>90
-
>90
>95
>95
n.d.
n.d.
-
-
68
n.d.
>95
-
>95
n.d.
-
>95
-
0
-
84
-
>95
-
86
-
-
-
ee 2 (%)
ee 3 (%)
Co
nv.
(%)
>95
>95
-
56
n.d.
87
n.d.
>95
-
48
-
n.d.
-
60
-
74
>80
>95
-
72
-
62
n.d.
>95
-
20
-
78
-
70
-
>95
>95
>95
0
>95
>95
>95
>95
>95
82
>95
-
>95
ee 2 (%)
ee 3 (%)
(b)
(c)
Co
nv.
(%)
WT
E293M
R299K
Phenylalanine ammonia lyase
PAL
(H359Y)
ACIE, 2015, 54, 4608.
R = o-NO2, m-NO2, p-NO2, p-CF3, p-CN yields 64-83%, ee ≥98%
Directed evolution of MAO-N
NH
NH2
NH2NH2
NH2
D1 D5 D6/D7
simple achiral
1o amines
Wild-TypeMAO-N
chiral
1o amines
chiral
1o/2o/3o amines
broad spectrum(S)-selective
amine oxidase
1st random libraryca. 150,000 clones
2nd random libraryfollowed by
'hot-spot' librariesca. 20,000 clones
'active-site' librariesca. 10,000 clones
N
H
>103 improvement in kcat
e.e. >98%
(S)-MAO-N biocatalyst toolbox
Monoamine oxidase
solifenacin
(urinary tract)
levocetirizine
(anti-histamine)
telaprevir
(hepatitis c) argatroban
(blood cloting)
JACS, 2013, 135, 10863.
Nature Chem, 2013,5, 93.
ACIEE, 2015, 54, 4608.
Engineering MAO-N for diarylaminomethanes
Rational engineering MAO-N
MAO-N D11 crystal structure
Annika Frank (University of York).
Deracemisation of API building blocks
4-chlorobenzhydrylamine:
1-phenyltetrahydroisoquinoline:
(R)-selectivity
D. Ghislieri A.P. Green, M. Pontini, et al., J. Am. Chem. Soc., 2013, 135, 10863-10869.
4 reactions: 1 x C-C; 2 x Ox; 1 x Red
Harmicine:
Conv.: 80%
ee: 99%
D. Ghislieri A.P. Green, M. Pontini, et al., J. Am. Chem. Soc., 2013, 135, 10863-10869.
Piperidines
Marta Pontini and Bas Groenendaal
Regio- and stereoselective
ω-transaminase/MAO-N cascades
E. O’Reilly et al., Angew. Chem. Int. Ed., 2014, 53, 2447-2450.
ω-TA - MAO-N tandem reaction
E. O’Reilly et al., Angew. Chem. Int. Ed., 2014, 53, 2447.
MAO-N/Berberine bridge enzyme
J. Schrittwieser, D. Ghisleri, W. Kroutil, N.J. Turner et al., Angew. Chem. Int. Ed., 2014, 53, 3731-3734.
(R)-Selective amine oxidase
A) 20 mM (R)-nicotine B) 20 mM (S)-nicotine
G. Schulz et al., J. Mol. Biol., 2005, 352, 418-428.
Glu352
Glu350
Ala374 Leu375
CASTing libraries
Ala374/Leu375: no hits Glu350/Glu352: several hits including Leu350/Asp352
(R)-Selective amine oxidase
R. Heath et al., ChemCatChem, 2014, 6, 996-1002.
Substrate specificity of Leu350/Asp352 HDNO
all >95% e.e. and (S)-enantiomers
R. Heath et al., ChemCatChem, 2014, 6, 996-1002.
Imine reductases from Streptomyces sp.
K. Mitsukura et al., Org. Biomol. Chem., 2010, 8, 4533.
K. Mitsukura et al., Biosci. Biotechnol. Biochem. 2011, 75, 1778–1782.
Imine reductases (IREDs)
Whole cell and isolated enzyme imine reduction
ACS Catal, 2016, 6, 3753.
ACS Catal, 2016, 6, 3880. ChemCatChem, 2013, 5, 3505.
IRED from Paenibacillus
lactis: Li et al., Adv. Synth.
Catal., 2015, 357, 1692.
Y. Asano et al, J. Bacteriol., 1989, 171, 4466.
Merck-Codexis, Biocatalysis GRC, July 2014; US WO 2013170050 A1 (2013).
Asymmetric reductive amination
H. Mihara et al., FEBS J. 2005, 272, 1117–1123.
N-methyl-L-amino acid dehydrogenase
Opine dehydrogenase
L-amino acid dehydrogenase
M. Abrahamson et al., ACIEE. 2012, 51, 3969–3972.
Relationship of RedAms to IREDs
Reductive amination with AspRedAm
AspRedAm preparative-scale reactions
Turnover number (TON) of >30,000
Turnover frequency (TOF) of up to 300 min-1
[S] up to 0.4M amine & 0.2M ketone with new homologues
G. Aleku, S.P. France et al., Nature Chem., 2017, 9, doi:10.1038/nchem.2782.
Biocatalytic
Hydrogen Borrowing Cascades
Biocatalytic asymmetric hydrogen borrowing
Biocatalytic asymmetric hydrogen borrowing
F.G. Mutti. T. Knaus, N.S. Scrutton, M. Breuer and N.J. Turner, Science, 2015, 349, 1525-1529.
Biocatalytic asymmetric hydrogen borrowing
F.G. Mutti. T. Knaus, N.S. Scrutton, M. Breuer and N.J. Turner, Science, 2015, 349, 1525-1529.
2o Amine synthesis via hydrogen borrowing?
S.L. Montgomery, J. Mangas-Sanchez et al., Angew. Chem. Int. Ed., 2017, 56, in press.
ADH/AspRedAm hydrogen borrowing
S.L. Montgomery, J. Mangas-Sanchez et al., Angew. Chem. Int. Ed., 2017, 56, in press.
ADH/AspRedAm hydrogen borrowing
0
10
20
30
40
50
60
70
80
0 20 40 60 80
Pro
du
ct
(%)
Time (hours)
pH 7.0, 20°C
pH 7.0, 30°C
pH 9.0, 20°C
pH 9.0, 30°C
For racemic 2o
alcohols need
Non-selective ADH
(ADH-306 from JM)
S.L. Montgomery, J. Mangas-Sanchez et al., Angew. Chem. Int. Ed., 2017, 56, in press.
The Landscape of Amine Biocatalysis
Tall mountains dominate the view…
AMINE OXIDASES
DEHYDROGENASES
AMMONIA LYASES ω-TRANSAMINASES IMINE
REDUCTASES REDUCTIVE
AMINASES
…but there are also tiny peaks far away!
Acknowledgements
amine biocatalysis: Rachel Heath, James Galman, Juan Mangas-Sanchez, Godwin Aleku, Sarah Montgomery, Scott France, Iustina Slabu, Bruna
Costa, Cesar Iglesias, Jeremy Ramsden, Wojciech Zawodny, Agata Brzezniak, Frank Xu
Gideon Grogan, Henry Man, Mahima Sharma (York)
and everyone else in the group … Fabio Parmeggiani, Syed Ahmed, Nick Weise, Sasha Derrington,
Chantel Jensen, Will Birmingham, Ian Rowles, Mark Corbett, Jane Kwok, Navya Menon, Michele Tavanti, Matthew Thompson