Literature summary for 2.7.7.60 extracted from

Ghavami, M.; Merino, E.F.; Yao, Z.K.; Elahi, R.; Simpson, M.E.; Fernandez-Murga, M.L.; Butler, J.H.; Casasanta, M.A.; Krai, P.M.; Totrov, M.M.; Slade, D.J.; Carlier, P.R.; Cassera, M.B.
Biological studies and target engagement of the 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD)-targeting antimalarial agent (1 R,3 S)-MMV008138 and analogs (2018), ACS Infect. Dis., 4, 549-559 .

Application

Application	Comment	Organism
drug development	PfIspD enzyme inhibitor MMV008138 does not target the human IspD, reinforcing MMV008138 as a prototype of a distinct class of species-selective IspD-targeting antimalarial agents	Plasmodium falciparum

Inhibitors

Inhibitors	Comment	Organism
(1R,3S)-1-(2,3,4-trifluorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(2,4-dibromophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(2,4-dichlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide	-	Plasmodium falciparum
(1R,3S)-1-(2,4-dichlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(2,4-dichlorophenyl)-N,N-dimethyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide	about 5% inhibition at 0.001 mM	Plasmodium falciparum
(1R,3S)-1-(2,4-dichlorophenyl)-N-ethyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide	-	Plasmodium falciparum
(1R,3S)-1-(2,4-dichlorophenyl)-N-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide	-	Plasmodium falciparum
(1R,3S)-1-(2,4-difluorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(2-bromo-4,5-difluorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(2-bromo-4-chlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(2-bromo-4-chlorophenyl)-N-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide	-	Plasmodium falciparum
(1R,3S)-1-(2-bromo-4-iodophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(2-chloro-4-fluorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(2-chloro-4-fluorophenyl)-N-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide	-	Plasmodium falciparum
(1R,3S)-1-(2-chloro-4-hydroxyphenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(2-chloro-4-methoxyphenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(2-chloro-4-methylphenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(2-chloro-4-methylphenyl)-N-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide	-	Plasmodium falciparum
(1R,3S)-1-(2-chlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(2-fluoro-4-iodophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(3,4-dimethoxyphenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(3-chloropyridin-4-yl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(4-bromo-2-chlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(4-bromo-2-chlorophenyl)-N-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide	-	Plasmodium falciparum
(1R,3S)-1-(4-carboxy-2-chlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(4-chloro-2,6-difluorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(4-chloro-2-fluorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(4-chloro-2-methoxyphenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(4-chloro-2-methylphenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(4-chlorophenyl)-1-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(4-chlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-(4-fluoro-2-iodophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-methyl-1-phenyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-phenyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-[(2,4-dichlorophenyl)methyl]-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-[2,4-bis(dimethoxymethyl)phenyl]-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-[2,4-bis(trifluoromethyl)phenyl]-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-1-[2,4-di(propan-2-yl)phenyl]-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
(1R,3S)-MMV008138	(1R,3S)-MMV008138 targets the enzyme 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) in the MEP pathway. The Malaria Box compound MMV008138 targets the apicoplast and that parasite growth inhibition by this compound can be reversed by supplementation of IPP. The compound inhibits Plasmodium falciparum Dd2 strain growth with an IC50 value of 250 nM	Plasmodium falciparum
(1S,3S)-1-(5-chlorothiophen-2-yl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid	-	Plasmodium falciparum
1-(2,4-dichlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole	about 7% inhibition at 0.001 mM	Plasmodium falciparum
1-[(1R,3S)-1-(2,4-dichlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indol-3-yl]-2-hydroxyethan-1-one	-	Plasmodium falciparum
fosmidomycin	about 4% inhibition at 0.01 mM	Plasmodium falciparum
additional information	inhibitor design and inhibition structure-activity relationships analysis, overview. In addition to (1R,3S)-configuration, potent growth inhibition requires 2',4'-disubstitution of the D-ring, featuring at least one electron-withdrawing substituent. Neither (1R,3S)-1-phenyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid (bearing an unsubstituted phenyl ring) nor (1R,3S)-1-[2,4-di(propan-2-yl)phenyl]-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid (bearing 2',4'-dimethyl substitution) inhibit Plasmodium falciparum growth at 0.01 mM. The 2'-chloro substituted analogue (1R,3S)-1-(2-chlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid shows weak growth inhibition, and (1R,3S)-1-(2-chloro-4-methylphenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid (2'-chloro-4'-methyl substituted) nearly recapitulates the potency of (1R,3S)-MMV008138. The carboxy substituent at C3 of the C-ring also proves to be essential, replacement with CO2Me (3a) or H (11a) abrogates growth inhibition potency. But weak growth inhibition is restored with the first amide analogue (1R,3S)-1-(2,4-dichlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide, and methyl amide derivative (1R,3S)-1-(2,4-dichlorophenyl)-N-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide proves equipotent to (1R,3S)-MMV008138. Not inhibitory: (1R,3S)-1-(3,4-dichlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid, methyl (1R,3S)-1-(2,4-dichlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate.	Plasmodium falciparum

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
0.0093	-	CTP	pH 7.4, 37°C	Plasmodium falciparum
0.012	-	2-C-methyl-D-erythritol 4-phosphate	pH 7.4, 37°C	Plasmodium falciparum

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Plasmodium falciparum

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
CTP + 2-C-methyl-D-erythritol 4-phosphate	Plasmodium falciparum	-	diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol	-	?

Organism

Organism	UniProt	Comment	Textmining
Plasmodium falciparum	Q8I273	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
CTP + 2-C-methyl-D-erythritol 4-phosphate	-	Plasmodium falciparum	diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol	-	?
additional information	the fluorimetric assay directly measures diphosphate	Plasmodium falciparum	?	-	-

Synonyms

Synonyms	Comment	Organism
IspD	-	Plasmodium falciparum
Pf IspD	-	Plasmodium falciparum

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
37	-	assay at	Plasmodium falciparum

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
7.6	-	2-C-methyl-D-erythritol 4-phosphate	pH 7.4, 37°C	Plasmodium falciparum
11.7	-	CTP	pH 7.4, 37°C	Plasmodium falciparum

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.4	-	assay at	Plasmodium falciparum

Ki Value [mM]

Ki Value [mM]	Ki Value maximum [mM]	Inhibitor	Comment	Organism	Structure
0.000007	0.000013	(1R,3S)-MMV008138	pH 7.4, 37°C	Plasmodium falciparum

IC50 Value

IC50 Value	IC50 Value Maximum	Comment	Organism	Inhibitor
0.000021	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(4-bromo-2-chlorophenyl)-N-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide
0.000031	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2-bromo-4-chlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.000031	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2-bromo-4-chlorophenyl)-N-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide
0.000034	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(4-bromo-2-chlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.000044	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2,4-dichlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.000057	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2,4-dichlorophenyl)-N-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide
0.000082	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2-chloro-4-methylphenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.000084	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2,4-dibromophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.0001	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2-chloro-4-fluorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.00013	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2-fluoro-4-iodophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.00014	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(4-chloro-2-fluorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.00014	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(4-fluoro-2-iodophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.00023	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2,4-difluorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.00026	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(4-chloro-2-methylphenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.00028	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2-chloro-4-fluorophenyl)-N-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide
0.00036	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2-chloro-4-methylphenyl)-N-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide
0.00051	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(4-chlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.001	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2,4-dichlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide
0.001	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2,4-dichlorophenyl)-N-ethyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide
0.001	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-(2-chlorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.001	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-[2,4-di(propan-2-yl)phenyl]-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.005	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-phenyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.005	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-[2,4-bis(dimethoxymethyl)phenyl]-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
0.005	-	pH 7.4, 37°C	Plasmodium falciparum	(1R,3S)-1-[2,4-bis(trifluoromethyl)phenyl]-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid

General Information

General Information	Comment	Organism
physiological function	enzyme 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) acts in the MEP pathway and converts MEP and cytidine triphosphate (CTP) to cytidine diphosphate methylerythritol (CDP-ME) and diphosphate	Plasmodium falciparum

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism	Structure
633.3	-	2-C-methyl-D-erythritol 4-phosphate	pH 7.4, 37°C	Plasmodium falciparum
1258.1	-	CTP	pH 7.4, 37°C	Plasmodium falciparum