new compound sets identified from high throughput ... · new compound sets identified from high...

New Compound Sets Identified from High Throughput Phenotypic

Screening against Three Kinetoplastid Parasites: An Open Resource

Imanol Peña1, M. Pilar Manzano

2, Juan Cantizani

2, Albane Kessler

2, Julio Alonso-Padilla

3,

Ana I. Bardera1, Emilio Alvarez

1, Gonzalo Colmenarejo

1, Ignacio Cotillo

2, Irene Roquero

1,

Francisco de Dios-Anton1, Vanessa Barroso

1, Ana Rodriguez

3, David W. Gray

4, Miguel

Navarro5, Vinod Kumar

6, Alexander Sherstnev

7, David Drewry

8, James R. Brown

6, Jose M.

Fiandor2 & J. Julio Martin

1*

1Molecular Discovery Research, Tres Cantos Medicines Development Campus,

GlaxoSmithKline, Tres Cantos, Spain. 2Diseases of the Developing World (DDW), Tres

Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain. 3Department

of Microbiology, Division of Parasitology, New York University School of Medicine, New

York, NY, USA. 4Drug Discovery Unit, Division of Biological Chemistry and Drug

Discovery, University of Dundee, Dundee, UK. 5Instituto de Parasitología y Biomedicina

"López-Neyra" Consejo Superior de Investigaciones Cientificas, Granada, Spain.

6Computational Biology, Quantitative Sciences, GlaxoSmithKline, Collegeville, PA, USA.

7Computational Biology, Quantitative Sciences, GlaxoSmithKline, Medicines Research

Center, Stevenage, Hertfordshire, UK. 8Chemical Sciences, Molecular Discovery Research,

GlaxoSmithKline, Research Triangle Park, NC, USA.

*Corresponding author ([email protected])

mailto:[email protected]

Supplementary Information

Figure 3. Neighbor-joining phylogenetic tree of combined human and Trypanosoma

brucei str. 927 kinomes.

Human kinase targets with putative compounds are colored and prefixed (T_red); all human

kinases are colored black. T. brucei kinases are colored and prefixed for the RNAi

phenotypes death (D_blue), arrest (A_dark green) or slow (S_orange) according to Table 1 in

Jones et al.22

. All other T. brucei kinases are colored violet. A few key clusters of human

target and essential T. brucei kinases are labeled. The size and color of circles on the nodes

represent support in 1000 bootstrap replicates.

22. Jones, N.G. et al. Regulators of Trypanosoma brucei cell cycle progression and differentiation

identified using a kinome-wide RNAi screen. PLoS Pathog. 10, e1003886 (2014)

Note: the figure below is a high resolution version of Figure 3 in the main

manuscript. It can be zoomed in at your convenience

Bootstrap values99.7%

0%VRK1

Tb927.3.2060

T_PLK

3

CDK7

T_CDK2

T_MAP3K5

TSSK

2

T_GSK

3B

Tb927.9.2240

SPEG

T_CDK16

MAP3K4

TYRO3

PKN1

MUSK

T_BTK

Tb927.3.4860

Tb927.6.2030

MAP4K3

T_MAP3K7

ADRBK1

TAOK1

T_CL

K2

BRSK2

LIMK2

Tb927.5.4430

EPHB2

T_STK4

RSK4

_DO

M2

T_AKT2

Tb92

7.2.27

20

CDK17

IRAK3

RIPK4

Tb927.9.10040

T_RIPK1

T_PAK7

STK3

8L

Tb927.10.10870

GRK7

T_MAPKAPK2

CDC7

BLK

KSR1

TIE1

ZAK

PBK

Tb927.4.5310

TRIB1

FGR

D_Tb927.4.5180

A_Tb927.9.10920

NEK6

T_AKT3

BRSK1

FGFR3

MAP2K4

STK32A

LTK

GCN2_DOM2

D_Tb92

7.11.1

2310

Tb927.11.10520

A_Tb927.8.5730

Tb92

7.11

.124

20

Tb92

7.4.

2460

CDK19

KSR2

Tb927.6.1780

IRAK2

ACVRL1

MAPK15

CAMK1G

MERTK

D_Tb927.3.690

MKNK1

WN

K1

EPHA3

KALRN

CAMK2A

NRBP1

TTK

TXK

T_AURKA

CDK8

CDC4

2BPG

CDK13

D_Tb927.11.790

T_FES

EPHB6

A_Tb927.11.4470

TTN

BMX

TEX14

Tb92

7.8.11

00

S_Tb927.10.7780

T_AKT1

MAP3K8

MST1R

MSK

1_DO

M2

T_JAK 3

T_PLK

1

Tb927.9.12400

NEK4

AMHR2

PRPF

4B

Tb927.11.8150

NEK5

D_Tb927.10.5140

D_Tb9

27.3

.244

0

Tb927.2.1820

FER

Tb927.7.3580

Tb927.11.14270

Tb927.11.15010

T_H

IPK2

GRK5

MO

S

Tb927.11.7210

TNK2

MAP3K14

S_Tb

927.

11.5

340

PKDCC

Tb927.10.3230

ERBB4

EPHA2

A_Tb92

7.9.14

430

Tb927.7.5220

PRKD2

BUB1

PLK2

MAST3

MAST1

CDKL5

PRKCH

A_Tb927.10.13780

T_PRKCQ

CSK

PXK

Tb927.11.8170

T_WEE1

D_T

b927

.5.8

00

Tb927.11.16790

Tb927.10.14780

T_PRKCE

MYLK3

NPR1

Tb927.11.9190

Tb92

7.10

.239

0

CSNK2A

2

Tb927.4.2500

ERN

2

Tb92

7.5.

3160

MAK

CDK12

CDK5

NEK9

CAMK2D

T_D

YRK1

A

Tb927.11.6990

PRKYS_

Tb92

7.7.

5770

ULK1

Tb927.8.6810

Tb92

7.10.1

4770

A_Tb

927.

6.49

70

T_MAPK14

Tb92

7.6.51

00

STK3

8

TEK

MAPKAPK3

CDK9

Tb927.8.870

ACVR1

NTRK2

DCLK1

ULK4

STK10

Tb927.3.1570

TGFBR2

MAPK6

Tb927.7.6680

RPS6KA2

MAPK3

EPHA7

TYK2

MAS

TL

PRKACB

Tb927.10.13480

MAPK13

PNCK

T_PAK4

MAST4

GAK

CAMK2B

MATK

Tb92

7.5 .

2820

TESK2

CSN

K1E

T_IRAK1

RPS6KA4

D_Tb927.10.4990

Tb92

7.11

.716

0

MAR

K4

T_PI

M1

NPR2

Tb927.8.1670

PRKCZ

Tb927.7.3650

T_MAPK9

FGFR2

FRK

MAPK4

HSER

T_CAMKK2

T_CHUK

Tb927.3.319 0

ULK2

CDK15

PRKD3

T_SYK

MST4

MAPK1

TBCK

TAOK2

EPHA6

S_Tb927.4.3420

T_INSR

Tb92

7.8.

1780

S_Tb927.7.7360

EPHA1

OXSR1

FLT1

Tb92

7.11

.314

0

ROCK

2

ARAF

Tb927.4.3770

CSN

K1G

1

MAP

KAPK

5

NRBP2

NEK3

STKLD1

STK3

ROS1

Tb927.5.3320

Tb927.10.5950

NTRK1

Tb92

7.8.

7450

T_PRKCA

S_Tb

927.

9.49

10

MSK

2_DO

M2

EPHA10

PDGFRA

ILK

CAMK1

CDK11A

MEL

K

PKN3

T_PAK6

Tb92

7.9.

9320

MAP2K3

WN

K2

MYO3B

INSRR

CDKL4

MAST2

PRKG1

EPHB4

Tb927.10.10350

RSK3

_DOM

2

STK32B

Tb927.10.1380

Tb92

7.10

.960

0

ABL2

T_LYN

Tb927.11.9290

MAP3K9

T_TGFBR1

STK36

T_ACVR2B

Tb927.11.11110

T_CL

K1

PHKG1

PLK4

Tb92

7.7.

4090

STK25

T_EIF2AK2

MAP3K11

T_PAK2

T_CH

EK1

TAOK3

T_LCK

Tb927.10.1910

T_RIPK2

AXL

Tb927.10.12040

Tb927.9.1570

STK35

Tb927.8.5500

A_Tb927.7.6220

MAP3K15

MAP3K3

RAF1

PRKCB

D_Tb

927.

11.1

2410

OBSCN

Tb927.8.4260

PRKX

SIK1

MAP3K2

T_EIF2AK3

PRKACG

ERN

1

T_SI

K2

SGK3

Tb92

7.10

.143

00

STK40

RSK1

_DO

M2

MA

P2 K7

MYLK

Tb927.6.2980

T_TBK1

RPS6KL1

ERBB3

TSSK

1B

CDK14

Tb927.10.1460

T_D

YRK3

Tb927.9.2350

Tb92

7.5.

790

CLK4

STK32C SBK3

T_EGFR

PTK2B

PTK7

Tb927.10.5930

BMP2

K

HIP

K1

MAPK11

WEE2

T_ALK

NRK

Tb927.10.14420

Tb927.8.3550

Tb927.7.1900

Tb927.10.3340

Tb927.4.4590

DSTYK

EPHB3

PIM

2

PDGFRB

TTBK

1

Tb92

7.6.

3110

Tb92

7.8.37

70

ERBB2

Tb92

7.2.

4200

Tb927.3.1850

Tb927.10.13490

T_CS

NK1

D

Tb92

7.3.46

70

GRK6

TYK2_DO

M2

RPS6KA3

TSSK

6

STRADB

DYR

K1B

MAP3K13

RPS6KA6

S_Tb927.9.11030

Tb927.6.2450

STK33

AAK1

FGFR4

CHEK2

DYR

K4

T_PRKCDDAPK2

RSK2

_DO

M2

T_PD

K1

GRK1

TTBK

2

DYR

K2

MAP3K6

Tb927.6.3430

Tb927.3.5650

Tb92

7.3.

1610

MO

K

T_RET

DM

PK

TSSK

4

CASK

Tb92

7.7.63

10

ROR1

LRRK1

PRKD1

CAMK2G

VRK2

Tb927.3.3290

PRKG2

SGK494

D_Tb927.10.2040

A_Tb927.9.6560

GRK4

EPHA8

NLK

Tb92

7.4.

1700

Tb927.8.7110

T_IKBKB

D_Tb927.10.5310

ROR2

T_JAK1

ADRBK2

CSN

K1G

3

Tb92

7.4.

4970

SBK1

STYK1

CDKL

3

SGK223

BMPR1B

CDK1

T_KDR

T_AURKC

SBK2

RPS6KB2

NU

AK2

Tb927.9.2140

T_PI

M3

FLT3

MKNK2CS

NK1

A1L

D_Tb927.8.7220

SGK2

S_Tb927.10.1070

T_PRKACA

Tb927.11.9270

LATS

1

T_ZAP70

SRMS

PTK6

NEK7

NEK1

Tb927.1.1530

TSSK

3

PSKH2

T_SGK1

NU

AK1

Tb92

7.9.

1500

SCYL3

DCLK3

T_LRRK2

Tb92

7.10

.160

30

EIF2AK4

CDK4

SCYL2

CDK10

A_T

b927

.10.

4940

CDC 4

2BPB

MYO3A

MYLK4

SPEG_DOM2

T_ITK

UHMK1

HCK

MAP3K10

Tb927.8.5390

PRKAA1

Tb92

7.11

.894

0

FGFR1

LMTK2

Tb92

7.7.2

420

WN

K3

CLK3

SLK

PKN2

LIMK1

Tb927. 10.460

MAP2K6

FLT4

PRKCI

MYLK2

YES1

TESK1

DAPK1

DAPK3

Tb927.2.2120

T_CSN

K2A1

GSK3A

NEK

10

JAK1_DO

M2

SIK3

T_MAPK10

MAP3K1

MAP4K2

CAMK4

AATK

Tb92

7.10

.150

20

Tb927.8.1690

TRIO

Tb927.2.5230

MAP3K12

T_PAK1

Tb927.10.16160

CDK3

Tb92

7.7.

3880

CSF1R

BMPR2

Tb927.11.5860

DCLK2

HUNK

PAK3

PIN

K1

Tb927.3.2690

STLK5

CSN

K1G

2

PSKH1

MAPK7

A_Tb927.9.12880

Tb927.3.3080

Tb92

7.10

.350

PRKCG

CDK20

CDKL1

STK31

Tb927.10.5940

STK16

ICK

CDK18

Tb927.11.7010

Tb92

7.3.

1630

LMTK3

NEK11

T_IGF1R

RNA

SEL

MET

T_IRAK4

S_Tb927.11.1180

Tb927.9.3120

ULK3

GSG2

Tb927.10.15880

Tb927.10.14800

EPHB1

MAPK12

POMK

Tb92

7.8.

5950

T_CAMKK1

PASK

RYK

STK24

MA

P2K2

TNIK

MAR

K3

TRIB3

Tb92

7.10

.527

0

CDKL2

Tb927.6.4220

NEK8

JAK2_DO

M2

S_Tb927.9.11100

TEC

WN

K4

D_Tb927.11.8220

Tb927.10.3900

MAR

K1

ACVR1B

T_NEK 2

NIM

1K

T_SRC

T_RO

CK1

ACVR1C

A_Tb927.11.2040

D_Tb927

.2.4510

SNRKM

AP4K5

MA

P2K5

Tb927.4.5390

Tb927.11.6690

SRPK

2SR

PK1

Tb927.10.13010

Tb927.8.6930

Tb92

7 .3 .

3 920

T_PTK2

T_H

IPK3

MAP4K1

PEAK1

BUB1

B

STK17A

EIF2AK1

T_DDR2

T_RIPK3

GU

CY2F

T_PRKAA2

Tb927.5.3150

LATS

2

Tb927.10.1940

TNK1

T_RPS6KA1

ANKK1

TNNI3K

T_M

APK8

T_MAP4K4

S_Tb

927.

7.27

50

T_FYN

CIT

EPHA5

CDK6

STK17B

JAK3_DO

M2VRK3

Tb927.3.4560

PKMYT1

STK11

T_IKBKE

BMPR1A

MA

P2K1

DDR1

EPHA4

T_BRAF

Tb92

7.7.

960

RPS6KA5

MAR

K2

TLK2

MLKL

Tb927.1.3130

Tb92

7.2.24

30

RPS6KC1

NTRK3

GU

CY2D

TRIB2

S_Tb

927.

7.32

10

PHKG2

STK39

Tb927.6.2250CS

NK1

A1

PDIK1L

S_Tb927.11.14070

T_AURKB

SCYL1

COT

Tb92

7.5.

1650

TLK1

S_Tb927.9.1670

Tb927.8.6490

S_Tb927.10.15300

T_JAK2

OBSCN_DOM2

CDC4

2BPA

T_RPS6KB1

KIAA1804

HIP

K4

MINK1

ABL1

T_ACVR2A

SRPK

3

CAMK1D

KIT

MAP3K

CDK

CSNK2A

CSNK1A

PRKAA

PIM/CHEK

AURK

Supplementary Information

Figure 4. Pathway network analysis of combined and individual kinetoplastid

target hypotheses.

Pathways were assigned using KEGG and visualized using Cytoscape42

. Proteins of

three species are grouped and colored according to general functional groups (kinases,

proteases, other enzymes and cytochromes).

42. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular

interaction networks. Genome Res. 13, 2498–504 (2013).

Note: the figure below is a high resolution version of Figure 4 in the

main manuscript. It can be zoomed in at your convenience

TCMDC-143397

TCMDC-143076

TCMDC-143633

TCMDC-143280

TCMDC-143239 TCMDC-143246

TCMDC-143391

TCMDC-143224


TCMDC-143248

TCMDC-143433

TCMDC-143182

TCMDC-143221

TCMDC-143396

TCMDC-143249

TCMDC-143086

TCMDC-143072

TCMDC-143563

TCMDC-143314

TCMDC-143349

TCMDC-143387

TCMDC-143281

TCMDC-143144

TCMDC-143180

TCMDC-143410

TCMDC-143181

TCMDC-143191

TCMDC-143429

TCMDC-143414

TCMDC-142900

TCMDC-143629

TCMDC-143630

TCMDC-143420

TCMDC-143113

TCMDC-143627

TCMDC-143517

TCMDC-143170

TCMDC-125825

TCMDC-143122

TCMDC-143302

TCMDC-143379


TCMDC-143636

TCMDC-143368

TCMDC-143386

TCMDC-143323

TCMDC-143356

TCMDC-143369

TCMDC-143377

TCMDC-143596

TCMDC-143176

TCMDC-143254

TCMDC-143513

TCMDC-143634

TCMDC-143402

TCMDC-143458

TCMDC-143339

TCMDC-143635

TCMDC-143374

TCMDC-143316

TCMDC-143401

TCMDC-143364

TCMDC-143515

TCMDC-143352

TCMDC-143380

TCMDC-143560


TCMDC-143257

TCMDC-143360





Tbr::XP_828183::isocitrate_dehydrogenase

Tbr::XP_847430::fatty_acid_desaturase

Tbr::XP_843994::phosphatidylinositol 4-kinase_alpha

Tbr::XP_847451::phosphatidylinositol_3-kinase

Tbr::XP_845793::silent_information_regulator_2

Tbr::XP_827629::casein_kinase_II

Tbr::XP_845218::cysteine_peptidase_precursor

Tbr::XP_845010::calcium-translocating P-type_ATPase

Tbr::XP_844977::poly(ADP-ribose)_polymerase

Tbr::XP_827786::3'_5'-cyclic_nucleotide phosphodiesterase

Tbr::XP_843664::cytochrome_P450



Tbr::XP_828695::lanosterol_14-alpha-demethylase

TCMDC-143638

TCMDC-142497

TCMDC-143533

TCMDC-143240

TCMDC-143582

TCMDC-143572

Ribosome_biogenesis_in_eukaryotes

African_trypanosomiasis

Oxidative_phosphorylation

Base_excision_repair

Ldo::CBZ32662::phosphatidylinositol_3-kinase_2,_putative

Ldo::CBZ34909::silent_information_regulator_2,_putative

Ldo::CBZ33416::phosphodiesterase,_putative

Ldo::CBZ35939::serine/threonine_protein_kinase,_putative

Butanoate_metabolism

Ldo::CBZ37910::hypothetical_protein

Ldo::CBZ33293::hypothetical_protein

Ldo::CBZ35881::phosphatidylinositol kinase_domain_protein,_putative

Endocytosis

Tcr::XP_819938::phosphodiesterase Tcr::XP_821198::serine/threonine_protein_kinase

Tcr::XP_816094::silent_information_regulator_2 Tcr::XP_805828::phosphatidylinositol_3-kinase_2

Chagas_disease_(American_trypanosomiasis)

Tcr::XP_808854::mitogen-activated_protein_kinase

Tcr::XP_821599::isocitrate_dehydrogenase

Tcr::XP_809016::phosphatidylinositol kinase_domain_protein

Tcr::XP_821219::lanosterol_14-alpha-demethylase

Tcr::XP_811840::NAD(P)-dependent_oxidoreductase

Synthesis_and_degradation_of_ketone_bodies

Biosynthesis_of_secondary_metabolites

Phagosome

Phosphatidylinositol_signaling_system

Metabolic_pathways

Fatty_acid_metabolism

Inositol_phosphate_metabolism

Biosynthesis_of_unsaturated_fatty_acids

Purine_metabolism Biosynthesis_of_amino_acids

Nicotinate_and_nicotinamide_metabolism

Carbon_metabolism

2-Oxocarboxylic_acid_metabolism

Peroxisome

Citrate_cycle_(TCA_cycle)

Regulation_of_autophagy

Steroid_biosynthesis

Glutathione_metabolism

Ldo::CBZ32712::stearic_acid_desaturase,_putative

Other_Enzymes Proteases

Ldo::CBZ32152::isocitrate_dehydrogenase_[NADP], mitochondrial_precursor,_putative

Kinases

Ldo::CBZ34597::phosphatidylinositol_3-kinase,_putative

Cytochromes

L. donovani

T. brucei

T. cruzi


TCMDC-143627

TCMDC-143517



TCMDC-143086


TCMDC-143281

TCMDC-143349


TCMDC-143170

TCMDC-143396

TCMDC-143391

TCMDC-143239

TCMDC-142900

TCMDC-143180

TCMDC-143144

TCMDC-143420

TCMDC-143429

TCMDC-143397

TCMDC-143181

TCMDC-143630

TCMDC-143633

Metabolic_pathways


Carbon_metabolism


Peroxisome


Biosynthesis_of_amino_acids

Purine_metabolism




Phagosome





Endocytosis

"Ld::CBZ33416::phosphodiesterase,_putative"

"Ld::CBZ32152::isocitrate_dehydrogenase_[NADP], mitochondrial_precursor,_putative"

"Ld::CBZ34909::silent_information_regulator_2,_putative"

"Ld::CBZ35939::serine/threonine_protein_kinase,_putative"

Ld::CBZ35881::phosphatidylinositol-kinase_domain_protein

Ld::CBZ33293::hypothetical_protein

"Ld::CBZ32662::phosphatidylinositol_3-kinase_2,_putative"

Ld::CBZ37910::hypothetical_protein

Other_Enzymes

Kinases

Ld::CBZ32712::stearic_acid_desaturase,_putative

"Ld::CBZ34597::phosphatidylinositol_3-kinase,_putative"

L. donovani

Phagosome






Metabolic_pathways


Carbon_metabolism



Oxidative_phosphorylation

Base_excision_repair



African_trypanosomiasis


Peroxisome


Other_Enzymes Purine_metabolism

Cytochromes

Proteases

Ribosome_biogenesis_in_eukaryotes Kinases

TCMDC-143636

TCMDC-143638

TCMDC-143374


TCMDC-143192

TCMDC-143240

TCMDC-143316

TCMDC-143458

TCMDC-143364

TCMDC-143323

TCMDC-143386

Tbr::XP_843994::phosphatidylinositol_4-kinase_alpha



Tbr::XP_845793::silent_information_regulator_2

Tbr::XP_843664::cytochrome_P450

Tbr::XP_828695::lanosterol_14-alpha-demethylase

Tbr::XP_828183::isocitrate_dehydrogenase

TCMDC-143312

TCMDC-143390

TCMDC-143547


TCMDC-143393

TCMDC-143365

TCMDC-143515

TCMDC-143560


TCMDC-143380

Tbr::XP_845010::calcium-translocating_P-type_ATPase

Tbr::XP_847430::fatty_acid_desaturase

Tbr::XP_844977::poly(ADP-ribose)_polymerase



Tbr::XP_827629::casein_kinase_II

Tbr::XP_827786::3'_5'-cyclic_nucleotide_phosphodiesterase

TCMDC-143339


TCMDC-143360

TCMDC-143402

TCMDC-143572

TCMDC-143462

TCMDC-143370

TCMDC-143257

TCMDC-143533

TCMDC-143377

TCMDC-143368

TCMDC-143254

TCMDC-143635

TCMDC-143369

TCMDC-142497

TCMDC-143401

TCMDC-143176

T. brucei

Tcr::XP_811840::NAD(P)-dependent_oxidoreductase

Tcr::XP_816094::silent_information_regulator_2

Tcr::XP_819938::phosphodiesterase

Tcr::XP_808854::mitogen-activated_protein_kinase

Tcr::XP_809016::phosphatidylinositol-kinase_domain_protein

Tcr::XP_821219::lanosterol_14-alpha-demethylase

Tcr::XP_805828::phosphatidylinositol_3-kinase_2

Tcr::XP_821599::isocitrate_dehydrogenase

TCMDC-143221

TCMDC-143408

TCMDC-143409

TCMDC-143182

TCMDC-143224

TCMDC-143433

TCMDC-143376

TCMDC-143308

TCMDC-143302

Purine_metabolism



Chagas_disease_(American_trypanosomiasis)

Butanoate_metabolism

Synthesis_and_degradation_of_ketone_bodies

Phosphatidylinositol_signaling_system TCMDC-143414

TCMDC-143410

TCMDC-143387

TCMDC-143248

TCMDC-143191

TCMDC-143379

TCMDC-143314

Metabolic_pathways



Carbon_metabolism




Peroxisome



Kinases

Other_Enzymes

Cytochromes

Tcr::XP_821198::serine/threonine_protein_kinase

T. cruzi

new compound sets identified from high throughput ... · new compound sets identified from high...

Documents