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Traditional approach for bioactive natural product discovery
fractionation
extraction
Investigate bioactivity of extract
Identify active fraction(s) and determine structure(s) of compound(s)
Genome sequence of the model antibiotic-producer Streptomyces coelicolor M145
NH
N
HN
OMe
prodiginines
OO
O
O
OH
OH
OH
OHO
O CO2H
HO2C
actinorhodin
NH O
O HN
O
HN
HN
CO2H
O NH
O
HN
ONH
OOH
NH
OHN
R'HO2C H
NO
OH2NOC
NH
O
HN
O
NH
O
CO2H
OH
O
HO2C
OR
calcium-dependent antibiotic
O
CO2HO
methylenomycin A
Nature (2002) 417, 141-147
Cryptic biosynthetic pathways encoded within the S. coelicolor genome
DEBS – an archetypal cis-AT polyketide synthase
ACPAT
Load Module 1
DEBS1
SO
ACPKS
KR
SO
HO
AT TEACPKS
KR
SO
HO
AT
HO
Module 2 Module 3
DEBS2
ACPKS
SO
O
AT ACPKS
SO
AT
O
Module 4
KRDHER
Module 5
DEBS3
ACPKS
KR
SO
HO
AT ACPKS
KR
SO
HO
AT
HO
Module 6
HO
HO
O
HO
HO
O
HO
HO
HO
HO
OH
O
O
OH
OHO
6-deoxyerythronolide B
HO
HO
O
HO
HO
O O
O
O
OHOH
O
OH
O
O
O
O OH
OMe NMe2HO
erythromycin A
O
SCoA
O
SCoA
O
-O
+
Nature (1990) 348, 176; Science (1991) 252, 671
ACPKS
DH
ER
KR
AT
OH
ACPKS
DH
ER
KR
O
SH
AT
Posttranslational ACP modification
CoASH
ACPKS
DH
ER
KR
SCoA
O
O-
O
AT
OH S-
Acyl transferase
KS
DH
ER
KR
OH S
O
O-
O
AT ACPACPKS
DH
ER
KR
O
O-
O
AT
O S-
Prediction of AT domain substrate specificity
Haydock et al. FEBS Lett. (1995) 374, 246-248Banskota et al. J. Antibiot. (2006) 59, 168-176
Malonyl-CoA
Methylmalonyl-CoA
ACPKS
DH
ER
KR
S- S
O
O-
O
AT ACPKS
DH
ER
KR
S S
O
O-
O
O
R
AT
Ketosynthase 1
ACP
S
O
R
ACP
S-
Ketosynthase 2
ACPKS
DH
ER
KR
S S
O
O-
O
O
R
AT ACPKS
DH
ER
KR
S- S
O
R
O
AT-CO2
Keto reductase
ACPKS
DH
ER
KR
S
O
R
HO
ATACPKS
DH
ER
KR
S
O
R
O
ATNADPH
Prediction of KR domain stereospecificity
Keatinge-Clay, Chem. Biol. (2007) 14, 898-908
Dehydratase
ACPKS
DH
ER
KR
S
O
R
ATACPKS
DH
ER
KR
S
O
R
HO
AT-H2O
Enoyl reductase
ACPKS
DH
ER
KR
S
O
R
ATACPKS
DH
ER
KR
S
O
R
ATNADPH
Prediction of ER domain stereospecificity
Kwan et al., Chem. Biol. (2008) 15, 1231-1240
S
O
S
O-
S
ONADPH H+H
H
H
S
O
H
HorS R
Thioesterase 1
ACP
OH
TE
S
O HO
ACP
SH
TE
O
O O
H
ACP
O
TE
S-O HO
Thioesterase 2
ACP
SH
TE
O-O O
ACP
SH
TE
OH
O
O
ACP
SH
TE
O
O O
H