Open Synthesis Network Project 1 Lead series for Visceral Leishmaniasis

Project Background Lead series originating from screening of Pfizer internal collection SCYX0001780041 identified as initial hit: To date, > 1,000 analogues have been made around this series Some of the key exploration has been published (Mowbray et.al. J.Med.Chem 2015 link) Lead candidates have been identified and are undergoing advanced profiling SCYX0001780041 L.donovani IC50: 5.8 µM Open Source Chemistry

Open Source Chemistry Opportunity DNDi have a clear need for back-up molecules within the series DNDi have identified certain chemical avenues that require further exploration These avenues have been broken down into various “work packages” exploring different areas of the scaffold Open Source Chemistry

Open Source Chemistry Opportunity Each Work Package provides concise data set around related molecules (20-30 compounds) Each Work Package provides a list of target molecules that DNDI would like to have synthesized and tested for potency Within each Work Package there is the scope for participants to propose and synthesize their own analogues, alongside the analogues suggested by DNDi New proposed molecules will need to by cleared and confirmed by DNDi beforehand in order to avoid duplication Open Source Chemistry

Work packages for chemistry investigation Open alkyl chain ureas A Functionality scan of pyridine D ß-Proline analogues E Cyclized core Piperazine ureas Fluorinated pyrazole analogues & other targets C B F Open Source Chemistry

Work packages for chemistry investigation Open alkyl chain ureas A Functionality scan of pyridine D ß-Proline analogues E Cyclized core Piperazine ureas Fluorinated pyrazole analogues & other targets C B F Open Source Chemistry

Work package A Open Source Chemistry Open alkyl chain ureas Work package A Handful of acyclic alkyl ureas have been made; activity observed but deprioritized DNDi will provide data set of compounds made within this sub-series (approx. 30) Stability in rodent microsomes seems to be an issue / area for improvement. Balance of ClogP is key for keeping potency and achieving metabolic stability Focus of work package: Improve potency and improve rodent microsomal stability via exploration / combination approach: Examples of target compounds: Library scans (suitable for parallel synthesis from common intermediate) For list of DNDi targets, see associated sdf file Open Source Chemistry

Work package A Open Source Chemistry Open alkyl chain ureas Work package A Handful of acyclic alkyl ureas have been made; activity observed but deprioritized DNDi will provide data set of compounds made within this sub-series (approx. 30) Stability in rodent microsomes seems to be an issue / area for improvement. Balance of ClogP is key for keeping potency and achieving metabolic stability Focus of work package: Improve potency and improve rodent microsomal stability via exploration / combination approach: Examples of target compounds: Alkylation and other derivatization around urea (May require some bespoke synthetic investigation) For list of DNDi targets, see associated sdf file Open Source Chemistry

Work packages for chemistry investigation Open alkyl chain ureas A Functionality scan of pyridine D ß-Proline analogues E Cyclized core Piperazine ureas Fluorinated pyrazole analogues & other targets C B F Open Source Chemistry

Work package B Open Source Chemistry Piperazine ureas Work package B Examples of piperazine and homopiperazine ureas have been made (approx. 35 analogues), with activity observed. Data set of existing piperazines and other compounds will be provided Metabolic stability and optimization of potency needs to be addresses DNDI000296578 L.Infantum IC50: 0.45 µM HLM 51 µL/min/mg.pr DNDI0002491055 L.Infantum IC50: 0.732 µM HLM 51 µL/min/mg.pr Examples of target compounds: Further exploration of this sub-series: (Library analoging, approximately 30-40 compounds, relatively straightforward synthesis) For list of DNDi targets, see associated sdf file Open Source Chemistry

Work package B Open Source Chemistry Piperazine ureas Work package B Examples of piperazine and homopiperazine ureas have been made (approx. 35 analogues), with activity observed. Data set of existing piperazines and other compounds will be provided Metabolic stability and optimization of potency needs to be addresses DNDI000296578 L.Infantum IC50: 0.45 µM HLM 51 µL/min/mg.pr DNDI0002491055 L.Infantum IC50: 0.732 µM HLM 51 µL/min/mg.pr Examples of target compounds: Combine with substituted pyrazole & triazole (Straightforward synthesis) For list of DNDi targets, see associated sdf file Open Source Chemistry

Work packages for chemistry investigation Open alkyl chain ureas A Functionality scan of pyridine D ß-Proline analogues E Cyclized core Piperazine ureas Fluorinated pyrazole analogues & other targets C B F Open Source Chemistry

Work package C Open Source Chemistry Cyclized core Work package C Cyclization of the core to give a partially saturated [5.6] system has demonstrated some potential but is relatively unexplored Relevant data set will be provided (4 compounds) Exploration of this chemical sub-series may require development of target-specific chemistry Examples of target compounds: For list of DNDi targets, see associated sdf file Open Source Chemistry

Work packages for chemistry investigation Open alkyl chain ureas A Functionality scan of pyridine D ß-Proline analogues E Cyclized core Piperazine ureas Fluorinated pyrazole analogues & other targets C B F Open Source Chemistry

Functionality scan of pyridine Work package D Replacement of 2-pyridyl on left-hand side (LHS) has been investigated, but not necessarily for more advanced right hand sides (RHS) Relevant data set will be provided (approx. 20 compounds) New chemistry could be developed to allow parallel synthesis; otherwise this requires bespoke synthesis for each analogue (approx. 4 steps) Examples of target compounds: For list of DNDi targets, see associated sdf file Open Source Chemistry

Work packages for chemistry investigation Open alkyl chain ureas A Functionality scan of pyridine D ß-Proline analogues E Cyclized core Piperazine ureas Fluorinated pyrazole analogues & other targets C B F Open Source Chemistry

Work package E Open Source Chemistry ß-Proline analogues Work package E ß-Proline analogues showed some promise but have been deprioritized in favour of pyrrolidine ureas, mainly due to issues of metabolic stability Data set of 15-20 compounds can be provided Ideally suited to synthesis of single building block followed by analoguing through parallel synthesis DNDI0003084291 L.Infantum IC50: 0.60 µM MRC5 CC50 >64 µM PMM CC50 >64 µM Examples of target compounds: Further investigation + other ring variations? For list of DNDi targets, see associated sdf file Open Source Chemistry

Work packages for chemistry investigation Open alkyl chain ureas A Functionality scan of pyridine D ß-Proline analogues E Cyclized core Piperazine ureas Fluorinated pyrazole analogues & other targets C B F Open Source Chemistry

Fluorinated pyrazole analogues & other targets Work package F Substitution of the 4-position of the pyrazole has been shown to be advantageous, however certain analogues have yet to be synthesized: Expected to be Synthetically challenging Examples of target compounds: For list of DNDi targets, see associated sdf file Open Source Chemistry