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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
2
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 :
5
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
6
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
[email protected] • 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
7
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
8
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)
9
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
10
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
11
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
14
Snapshot of SAR around aryl imidazole (MMV023227)
Challenge:• Improve metabolic stability of compounds while improving activity
15
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
16
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
20
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
21
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
22
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
23
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
24
Together WE can – come join the community
Preclinical Candidate MedicinalChemistry
ParasitologyBiochemistry
DMPK
Invitrotoxicology
Structural Biology
Invivotoxicology Predictive
modelling
Committed funders of MMV
26
SAR around aryl piperazine (MMV024406) - recap
Challenges:• High h microsomal clearance
• High CYP inhibition
27
SAR around aryl piperazine - MMV024408(series 1a)
Challenge:• High h microsomal clearance
28
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
29
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
30
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
31
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