EFMC ISMC 2016

Manchester, UK

August 2016

THE NTD DRUG DISCOVERY BOOSTER A NOVEL APPROACH FOR HIT TO LEAD CHEMISTRYBenjamin G. Perry,1 Charles E. Mowbray,1 Nao-aki Watanbe,2 Atsushi Inoue,2 Chiaki Fujikoshi, 3 Shuji Yonezawa,3 Mitsuyuki Shimada,4

Sachiko Itono,4 Yuichiro Akao,4 Ieuan Roberts,5 Garry Pairaudeau,5 Thierry Kogej,6 Ola Engkvist,6 Stacie Canan,7 Kevin Condroski,7

David Shum,8 Constantin Radu,8

1) DNDi, 15 Chemin Louis Dunant, Geneva, Switzerland; 2) Eisai Co Ltd., Tsukuba, Japan; 3) Shionogi & Co Ltd. Osaka, Japan; 4)Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan; 5) AstraZeneca plc, 310 Science Park, Milton Road, Cambridge, CB4 0WG, UK; 6) AstraZeneca plc. Pepparedsleden 1, 431 50, Mölndal, Sweden; 7) Celgene Corporation, 10300 Campus Point Dr, San Diego, CA 92121, United States; 8) Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil Bundang-gu, Seongnam-si, Gyeonggi-do 463-400 Rep. of Korea

About DNDiDrugs for Neglected Diseases initiative (DNDi) is a collaborative, patients’ needs-driven, non-profit drug research and development (R&D) organization that is developing new treatments for neglected diseases. Since its formation in 2003, DNDi has focussed on late stage optimization of formulations and combinations of existing drugs for clinical development in neglected populations and regions for neglected diseases, but has also invested in discovery of new chemical entities for kinetoplastid diseases where existing tools are inadequate and drug repurposing opportunities have been exhausted.

Visceral leishmaniasis and Chagas disease: an unmet need

Between 900,000-1,300,000 people are afflicted with leishmaniasis each year following the bite of sandflies infected with various species of leishmania parasites such as Leishmaniadonovani. This leads to 20,000-30,000 deaths largely due to the visceral form of the disease (Visceral Leishmaniasis, Kala-azar). Existing treatments for VL still fall short of the safe, effective, and field-adapted medicines one would hope to find in the 21st century. The bite of notorious triatomine insects or ‘kissing bugs’ can transmit the Trypansoma cruziparasite and has resulted in 6-7 million infected individuals and thousands of deaths per year from the resulting Chagas disease. The unpredictable and lengthy onset time linked to development of serious cardiovascular, digestive, and other symptoms makes Chagas disease a huge public health issue and a ticking time bomb for millions of infected patients. The available treatments for Chagas disease are even more limited than for leishmaniasis, and so safe, effective, short course treatments are urgently needed to help the large number of chronically infected patients.

Funding for this

work provided by:

Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul

Seed 1

2015 2016

Seed 2

Seed 3

Seed 4

Seed 5

Seed 6

Booster Timelines and process

In silico screening

In vitro screening

Data analysis

Submit to another booster iteration

Booster Concept & Consortium

Step 1: DNDi shares the chemical structure of a “seed” compound with a pharmaceutical company consortium who search their corporate compound collections for analogues by ‘in silico screening’

Step 2: The companies share in silico screening results with DNDi. DNDi selects up to 96 compounds from each company for in vitro testing against L. donovani, T. cruzi and parallel assessments of cytotoxicity

Step 3: DNDi analyses dataset, identifies emerging structure activity relationships and chooses the most improved hit compound for resubmission and a further iteration of the Booster in silico and in vitro screening steps.

Step 4: After 1-3 Booster iterations DNDiconstructs a hit series of compounds from within the data (20-40 structurally related compounds). The hit series is then progressed towards in vivo proof of concept and lead optimization, in collaboration between DNDiand some / all of the consortium members.

Chemical starting points for drug discovery against kinetoplastid parasites are scarce, and maximum value needs to be taken from those that are identified. The Booster process engages collaborative cycles of in silico screening and in vitro testing to maximize this value extraction through SAR elaboration and scaffold hopping.The Booster consortium consists of Astrazeneca plc, Celgene Corporation, Eisai Co. Ltd, Shionogi & Co Ltd. and Takeda Pharmaceutical Company Ltd.

Chemical Diversity SpaceAnalysis of the chemical diversity was achieved using the RDKit plug-in for the KNIME data analytics platform. • Chemical fingerprints (1024-bit Morgan

circular, 2 bond radius) were calculated and condensed by Principal Component Analysis (PCA) into 4 dimensions.

• Physicochemical properties (75 distinct properties including SlogP, molecular refractivity, %sp3…) were calculated and condensed by PCA into 4 dimensions.

• Visualizing the PCA dimensions in 2D or 3D space using DataWarrior (openmolecules.org) allows analysis of the chemical diversity space.

• The closer 2 molecules are in space the more «chemically similar» they are.

Results

Seed

L. donovani a T.cruzi a

OutcomeSeed DataIC50 (SI)

% Enrichment b

IC50

Best compoundIC50 (SI)

Seed DataIC50(SI)

% Enrichment b

IC50

Best compoundIC50 (SI)

120.1 µM

(2.5)23.2%

0.1 µM(>500)

>50 µM(1)

61.7%0.07 µM(>500)

Hit Series identified for L.donovani & T.cruzi

22.99 µM

(7.9)1.3%

4.15 µM(12)

8.4%0.24 µM

(208)New Scaffold identified for T.cruzi

35.8 µM

(8.6)0.7%

5.8 µM(8.6)

14.7%3.51 µM

(14)New Scaffold identified for T.cruzi

43.95 µM

(13)0.3%

1.12 µM(45)

2.1% None

5>50 µM

(1)17.1%

3.84 µM(13)

0.31 µM(161)

2.2% Hit Series identified for L.donovani

64.37 µM

(12)0.6%

6.62 µM(7.6)

10.7%0.1 µM(>50)

New Scaffold identified for T.cruzi

a) All data based on total parasite clearance read-out; b) % of compounds in screen with improvement in IC50 over parent seed compound

High Content imaging assayWe employ a high content imaging assay in 384 well plate format, with a 10-concentration dose response curve. Each well enables three distinct readouts:

a) Total parasite Clearance (IC50 for clearance of parasites from the well)b) Total infected cell clearance: IC50 for total clearance of parasite from each cell)c) Cytotoxicity against the host cell line (CC50; Host cell lines are THP1 for L.donovani and U2OS for T.cruzi)

In parallel we perform an identical cytotoxicity CC50

measurement on the non-infected host cell line.

Cell ratio (%)_Counter

Cell ratio (%)

Inhibition-norma.inf.ratio (%)

Norm.act.-Num.para (%)

X axis: Compound (uM)

Y axis: Ratio (%)

0.1 1 10-40

0

40

80

120

160

0.1 1 10-40

0

40

80

120

160

50 uM1.5 uM0.1 uM

Seed 1

Representative example of Booster process : Seed 1

Compound partner BCompound partner A

Compound partner DCompound partner C

Compound from first Booster iterationCompound from second Booster iterationInitial seedMost improved compound from first iteration

L.donovani IC50 µM0.1 µM 50 µM

THP1 CC50 µM0.1 µM 50 µMInitial seed compound

1st in silico screen based on seed

In vitro analysis identifies most improved hit

New in silico screen based on

In vitro analysis deepens SAR

around

Hit Series of 38 closely related

analogues (Different scaffold

to parent seed)

Conclusion

• The Booster concept - collaborative cycles of in silico screening across a broad range of pharmaceutical companies libraries - is an efficient and effective alternative to hit-to-lead exploration.

• The Booster process permits both Structure-Activity-Relationship elaboration and scaffold hopping exploration.

• The Booster process demonstrates the power of pharmaceutical company collaboration in the pre-competitive space, and the subsequent benefits for neglected disease drug discovery. research

IC50 µMSI

(para)a (Inf)b

L.donovani 20.1 27.2 2.5

T.cruzi >50 >50 1

Starr International Foundation: