Malaria Libre

3rd project meeting11th September 2020

• Please keep cameras and microphones switched off

• Switch on the microphone during your turn for discussion

• Type your request for questions/ discussion point in the chat box

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3

Agenda

• Introductory session – if new members join

• Status of action items from last meeting

• Project update

• Discussion – Medicinal Chemistry, compound registration

• ESAC review meeting: discussion points

• How to contribute- new members?

MMV: Partnerships for health impact

Discover, develop and deliver safe, effective and affordable antimalarial medicineshttps://www.mmv.org/research-development/mmv-supported-projects

New way of working :

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Malaria Libre - New way of working

MalariaLibre

Open access

No patents

Suggestions are best form

of criticism

Opportunity to seek free

expertise

Not owned by any

lab

Data is public

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Malaria

Libre

People

resources

ProcessesInformation

sharing

• Open access to datahttps://www.mmv.org/mmv-open/malaria-libre/malaria-libre-

data-repository

• Suggestions:

post on LinkedIn

or email to

malaria.libre@mmv.org • Centrally coordinated and community developed

• Simple processes

• Periodic discussions

• Focussed efforts to targeted deliverables

• Core team to support the project(1st tier assays, synthesis)

• Engage scientists from industry and academia in

fortnightly/monthly discussions

• Expand network

Malaria Libre – Connect and Integrate

Objective: Identification of preclinical candidate(s)

Criteria for stage up : https://www.mmv.org/research-development/information-scientists

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Status of last meeting’s action items

Action items Responsible team/group Status

Design and Synthesis of analogues CDRI(Sanjay, PP, Kishore);

Gloria; TCGLS

CDRI – slowed down due to COVID;

Gloria to initiate – confirm?

TCGLS ongoing

Primary screening(3D7 screening) LDH assay: TCGLS

SYBR assay: CDRI (in house

compounds)

TCGLS: ongoing

CDRI : to initiate after 15th Aug – Kiran sent 5

compounds for assay

synchronisation(MMV024408-

03,MMV1803992-01,MMV1804317-

01,MMV1804344-01,MMV1804508-01)

Cytotoxicity(HepG2) TCGLS ongoing

Screening of representative

compounds in ring stage assay

Shailja(JNU)Sent 2 compounds (MMV1803899-01

MMV1804508-01)Screening of representative

compounds in clinical isolates

Shailja(JNU)

In vitro ADME profiling(Tier 1) TCGLS ongoing

Life cycle assays Volunteers/done through MMV

network

Select compounds

MMV690095 and MMV1803899 sent to STPH for profiling in resistant panel

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Workflow

Synthesis in individual labs &TCGLS

Registration of compounds in MMV database : Science

Cloud*

Purity >90%

Send the compounds to TCGLS for 3D7LDH and

HepG2 assay**

Data updated on webpages

Tier 1 ADME assays @TCGLSScreening in panel of

strains (Shailja)

*

**CDRI to screen compounds synthesised in house in 3D7SYBR and K1

Blood stage specificity assay(Shailja)

1-2 compounds/scaffoldto understand the potential

1-2 compounds/scaffoldto understand the potential

In vivo PK(FNDR, TCGLS)mouse and rat

Tier1 assays: solubility, logD, h mic, rhep

CYP inhibition, PPB, blood/plasma partitioning

hERG(manual patch clamp)Ames(2 strain)in case of aniline

In vivo Pharmacology models

Invitro PRR

Early lead compound(s)

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SAR around aryl piperazine - recap

High h microsomal clearance

High CYP inhibition

Pf NF54/3D7(µM): 0.26, 0.42

eLogD: 3.7

Clint(hmic,mL/min/mg): 20.6

Caco2: 2.1

Sol (PBSbuffer, µM) <2.5

CYP 1A2, 2C9, 2D6, 3A4

% Inhibition@10 µM: 45,69,72,84

-, 0.43

4.3

18.1

ND

7.2

IC50>30µM

High h microsomal clearance

Series 1aSeries 1c

MMV024406 MMV024408

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Strategy around aryl piperazine - MMV024408(series 1a)

Objective: Improve potency(3D7LDH IC50<100nM)

Address poor metabolic stability and solubility

• Lower log D

• Modifications of metabolic hot spots

MMVIDPf3D7 IC50 uM

MMV 024408

0.43Confirm the role of phenyl ring for potency

Reduce log D

Introduction of linker – impact on potency

Explore ring size to improve potency/ insertion

of hetero atom to reduce logD; replace amide

by heterocycles to improve metabolic stability,

substituted cyclopropyl groups

Reverse amide- potency improvement?

heterocycles

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SAR around aryl piperazine - MMV024408(series 1a)

1804685

3.18

1804634

3.50

MMVIDPf3D7 LDH IC50 uM

1804684

2.56

1804459

1.13

1804508

0.19

1804345

1.17

1846946

>25

1846944

8.33

1846945

5.67

1846943

0.63

1804743

0.42

1804742

1.26

1846891

1.25

024408

0.43

MMV1804508 shows improvement in activity

1847005

RA

1847006

RA

Earlier compounds

This month’s compounds

1804319

7.82

MMV 024408

Reverse amide- potency improvement?

Ongoing at CDRI

Future Plans around aryl piperazine series 1a

isosteres of amide

stability and potency

Synthesis lined up at TCGLS

Improving metabolic stability

Improvement in potency?

Few analogs

Synthesis on going at TCGLS

Modulation of pKa to modulate activity

Synthesis ongoing at TCGLSNH2, Me

Strategy around aryl piperazine - MMV024406(series 1c)

Reverse amide- moving away from anilines

Ongoing at CDRI

1803899

0.37

Yet to start

MMVIDPf3D7 LDH IC50 uM

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Snapshot of SAR around aryl imidazole (MMV023227)

Challenge:• Improve metabolic stability of compounds while improving activity

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Addressing poor metabolic stability of MMV023227

[O]

[O]

[O] MMV023227

MMV1794034

MMV893302

MMV1804344

MMV892881

MMV ID 023227 1794034 892881 893302 893303 1804344

Pf3D7(SYBR/LDH,IC50 uM)

0.46/1.1 0.86/- 0.72/- 0.92/- 0.7/2.4 -/1.4

HLM, Clint 205 246 54 98 70.3 ND

r hep,Clint 206 163 ND 22.4 13.4 ND

MMV893303

Putative metabolites

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MMV 892881 Synthesise and characterise 5-7

diverse compounds to confirm SAR

and DMPK properties wrt to

MMV023227

MMV 884798

2 analogs in amides indicate a

reverse pattern as compared to amines and

ethers - synthesise 4-5 diverse compounds with

low log D

Modifications to improve potency

To be initiated at TCGLS

Explore role of linker length

Ongoing at CDRI

Aza indoles and substituted

phenyl

Substitution with CH2OH

Oxazole/thiazole

Plans around aryl imidazole scaffold

Few representative compounds

X= O,NH; R= H,F

Proposal by Clint Veale – aryl piperazine

Proposal by Clint Veale – aryl imidazole

N

N N N

O

NH

Cl

Cl

N

NH

Cl

O

NH

O

NH

O

N

N

ClON

NHCl

N

ON

NHCl

Cl

N N N

N NN

NN

X

N N

O

CN

N

CN

N

Cl

N

N

N NCN

N N

CN

N N O* *

O

NH

Also

explore

for LHS

N N N

N N N

NN

N*

N N N

*

Only for

SAR

Proposal by R. Venkat – aryl piperazine

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NH

N

NH

O

NHX

X

O

NHX

X

NX

X X

O

X

X

X X

NH

X

NH2

N

X

X

X

X

NH

X

X

NH

NH

NH

O O

N

X

N

X

X = CH2, O, NMe

N

NH

N

N

XX = CH

2, O, NMe

For LHS

NH

NH

Proposal by R Venkat – aryl imidazole

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Action items

Action items Responsible team/group Status

Design and Synthesis of analogues CDRI(Sanjay, PP, Kishore);

Gloria; TCGLS; Clint; Ram

CDRI – slowed down due to COVID;

Gloria to initiate – confirm?

TCGLS ongoing

Clint and Ram to initiate

Primary screening(3D7 screening) LDH assay: TCGLS

SYBR assay: CDRI (in house

compounds)

TCGLS: ongoing

CDRI : to initiate

Cytotoxicity(HepG2) TCGLS ongoing

Screening of representative

compounds in ring stage assay

Shailja(JNU)

To initiate

Screening of representative

compounds in clinical isolates

Shailja(JNU)

In vitro ADME profiling(Tier 1) TCGLS ongoing

Life cycle assays Done by MMV partners Select compounds

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ESAC review meeting – Discussion points

Project risk assessment

• What are the critical issues and how has the project tackled these? What are the key results that

demonstrate progress? What issues remain or have arisen?

• Next milestone and timeline and likelihood of achieving milestone based on cumulative risks

Issue Impact Proposed

solution

GO/NO-GO

criteria

(timeline/cost)

Likelihood of

success (H/M/L)

Aryl piperazine- low metabolic stability

medium Block metabolic soft spots, reverse amides

Identification of stable compounds

High

Aryl imidazole –moderate activity and low metabolic stability

high Invitro Met ID-Block metabolic soft spots, suitable replacement of dimethyl imidazole

Identification of stable compounds with improved activity

Medium

Limited Chemistry resources from academic institutes due to COVID situation

Medium Engagement with multiple groups across geographies; look for funding opportunities to support PIs

Medium

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Ways of contribution

• Design and synthesis of compounds to achieve the objectives

• Synthesis of compounds

• Identification of putative metabolites for both scaffolds

• Carry out experimental in vitro Met ID

• Screen front runners in lab derived strains other than 3D7; asexual intraerythrocytic blood stage

assays, mechanism of action

Details of objectives and plans: https://www.mmv.org/mmv-open/malaria-libre/malaria-

libre-data-repository

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Together WE can – come join the community

Preclinical Candidate MedicinalChemistry

ParasitologyBiochemistry

DMPK

Invitrotoxicology

Structural Biology

Invivotoxicology Predictive

modelling

Committed funders of MMV

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SAR around aryl piperazine (MMV024406) - recap

Challenges:• High h microsomal clearance

• High CYP inhibition

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SAR around aryl piperazine - MMV024408(series 1a)

Challenge:• High h microsomal clearance

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There are new ways of working

together….

1. Wells, T. N. C. et al. Nature Reviews Drug Discovery, 15, 661-662 (2016)2. Van Voorhis, W. C. et al. PLOS Pathogens, 12, e1005763 (2016)3. Williamson, A. E. et al. ACS Cent. Sci., 2, 687−701 (2016)

Open Innovation1

…..project partners sharing all information

Open Source1,3

…..shared data and open

participation

Open Science1

…..deposition of data in the public

domain

Open Access1,2

…..free access to data and materials

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MMV Compound NumberTarget Product Profile (Treatment or Chemoprevention)Target Candidate Profile List TCP claimsCompound PropertiesCompounds resynthesised (Y/N)? Y

Full analytical data (1H, MS, RT, absolute stereochemistry known).pdf reports showing data and written out

electronicallyMolecular Weight (MWt) <500Salt/ adductSample MWt (including salt or adduct)cLogP/ ALogP (Science Cloud)LogD pH 7.4 <5No. of H-bond donors <5No. of H-bond acceptors <10tPSANo. of stereogenic centres <3If chiral, racemic or single isomer? Single isomerClear SAR (Y/N)? YNo. of synthetic steps from commercial starting points Simple, short routeMaximum scale synthesised to dateSolubility PBS/ SGF/ FASSIF/ FESSIF/ pH 6 (mM) ≥10mM (PBS)Melting point MeasuredChemical stability (pH 2 and pH 8) stable

Genotoxicity risks based on structure e.g. hidden anilines present?No. If "Yes" then explain and give data in safety

sectionLigand efficency (pIC50/ per heavy atom count) For info

Scifinder search performed on exact structure and simplified coreState whether novel based on Scifinder search

of exact molecule or simplified core

Early lead criteria – structural aspects

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Potency at in vitro biochemical target (Ki) (Pf, Pv, Pb, Hs) - if relevant Ki<100nM against PfSelectivity vs relevant related host target (fold) >100 foldPotency Erythrocyte assay (EC50) - (minimum 7 strains including lab derived and clinical mutants)

EC50<100nM (48h, 72h)

Free EC50 in 72h 3H NF54 erythrocyte assay NF54 72h 3H EC50 hill slopePotency Cytotoxicity assay (EC50) - (minimum two cell lines) (µM) >100 foldAsexual intraerythrocytic blood stage specificity (ring vs. Trophozoites vs. schizont) Based on microscopyIn vitro PRR (Log10), onset of action (h) and Hill Slope

Mechanism of actionNovel based on resistance panel or strategic

imperative if knownPb/ Pf liver schizont EC50 EC50<100nM for causal TCP4Pc/ Pv hypnozoite EC50 EC50<1000nM for TCP3Pf NF54 Gametocyte stage I/ III EC50 MeasuredPf NF54 Gametocyte stage V EC50 EC50<100nM for TCP5Pf Male gamete formation assay (exflagellation): incubation/ incubation and wash out/ no pre-incubation EC50s For TCP5: EC50<100nM on male and/or femalePf Female gamete formation assay: incubation/ incubation and wash out/ no pre-incubation EC50s

For TCP5: EC50<100nM on male and/or female

TCP 3 Evidence of in vitro block of relapseTCP 1 Calcualed Human MPC from in vitro data

Good to have: MIR; Pf and Pv clinical field isolate values

Early lead criteria – Pharmacology

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Stability in plasma (mouse, rat, dog, human) stable Permeability: Caco-2 (A-->B; B-->A, ER plus units Measuredin vitro met stab Clint - mouse/ rat/ dog/ human microsomes Measuredin vitro met stab Clint - mouse/ rat/ dog/ human hepatocytes MeasuredPlasma protein binding (mouse, rat, dog, human) MeasuredBlood/ plasma partitioning (mouse, rat, dog, human non-infected blood) MeasuredAlbumax Bindidng MeasuredCYP450 inhibition (CYP1A2, 2D6, 2C9, 2C19, 3A4) + those that overlap with current therapies IC50uM 3/5 >10uM and none <1uM

Mouse i.v. (dose), Clearance (ml/min/kg), t1/2, Volume (L/Kg) Measured

Mouse p.o. (dose), Tmax, Cmax, AUC, F%, t1/2F%>20% using stable suspension / solution in

acceptable vehicle

Rat i.v. (dose), Clearance (ml/min/kg), t1/2, Volume (L/Kg) Measured

Rat p.o. (dose), Tmax, Cmax, AUC, F%, t1/2F%>20% using stable suspension / solution in

acceptable vehicle

TCP1 Dose to clear 9 / 12 Logs parasites from single/ three qd dose(s) For TCP1

TCP4 Dose to give t>prophylactic concentration for 7 days from single doseFor TCP4

Predicted adult human t1/2, Cl and V hours, mL/min/Kg, L/Kg

hERG IC50 uM (manual patch clamp) >1uM; some potent examples >10uM

Early lead criteria – DMPK and Toxicity