An Integrated Approach To Drug Discovery Using Parallel Synthesis - Presentation Transcript
An integrated approach to drug discovery using parallel synthesis Graham F Smith Sandwich Chemistry Pfizer Global Research and Development
Overview Enabled Hit Follow Up & Productive lead Discovery File Enrichment Chemo informatics High Throughput Chemistry HTS
File Enrichment – our early thoughts
Drug discovery fails more often than it succeeds
Some very difficult drug targets
Fewer targets than before
Some targets in the past, the industry has succeeded but Pfizer hasn’t
One possible cause
Industry file said to be approx 3,000,000 in 1999
Pfizer’s was approx 500,000
Narrow range of structural types
George M Milne Jr (Pfizer), Annual Reports in Medicinal Chemistry, 2003, 38, 383-396
Rationale for file enrichment
70% of PGRD project leads originate as HTS hits
Quality of drug candidate is reflected in quality of the lead matter
One significant source of Discovery and Development attrition is chemical in nature
Screening file attributes will drive downstream processes, efficiency and overall success in Medicinal Chemistry
Taking attrition early is good BUT suffering attrition on approaches early can be costly,
Therefore having more series options critical
Testing the mechanism is the key
Gunther Wess (Aventis), Drug Discovery Today, 7 (10), 2002, 533-535.
File enrichment strategy: consider attrition from outset
We know what chemotypes are more likely to fail in development
We know clinical candidates are similar to leads
Build this knowledge into library design
make and screen drug-like or lead-like compounds
hit lead candidate drug
Beautiful compound concept parallel chemistry no toxicophores rule of 5 compliant pure and stable Pfizer exclusive Lipinski, C.A. Chris Lipinski Discusses Life and Chemistry after the Rule of Five. Drug Discovery Today 2003 , 8 , 12-16.
File Enrichment Initiative
Aim to make a 3,000,000 compound pure compound file by compound design and acquisition
Hits enabled by having established parallel chemistry protocols
The largest screening file of any pharmaceutical company
More hits on difficult targets – better choices on easier targets
Faster / cheaper lead discovery in Pfizer enabled for the long term
File Enrichment 1 – “the big four”
Neurogen
Informatics based design and synthesis technology
Predicts the next // chemistry compound to make
ArQule
Broad experience of high throughput parallel chemistry
Delivering ~500,000 compounds and associated protocols
Evotec
Ultra High Throughput Screening uHTS
Aurora
Ultra High Throughput Screening uHTS
The Evotec ultra high throughput screening system
Capacity to analyse >100,000 compounds per day
Assay volume of 1 l - saving in reagent and compound usage
2080 wells on a single assay plate
File Enrichment 2002-2006
ArQule
800,000
Developing ~200 new chemistry protocols
Tripos
440,000 compounds
12,000 privileged monomers
Chembridge
500,000 compounds
4,000 privileged monomers
Chem RX (Discovery partners )
500,000 compounds
Evotec Technology
Developed in collaboration
Created uHTS centres of emphasis
1 mergers and 1 acquisition with associated legacy compound file acquisition
Warner Lambert
Pharmacia
Alan Procter (Pfizer), Drug Discovery and Development, December, 2003 See various collaboration press releases ~$1 Billion FE investment
File Enrichment – managing diversity La Jolla Groton Ann Arbor Sandwich Generation of ideas for library protocols Global Ideas overlap resolution La Jolla Groton Ann Arbor Sandwich Prioritization of ideas for development Library chemistry development Library idea Management Tool La Jolla Library production and purification
Hit Follow Up (2006…)
A strategic modification of File Enrichment contracts
Hit Follow-up – (HF)
Med Chem Support
Emphasis on Pfizer design
Pfizer monomers and protocols
Custom synthesis of key monomers and templates
Development and optimisation of // chemistry
Fast turnaround a contractual priority
Compound supplied enough for project screening and Pfizer global HTS activities
Supported by local Pfizer Parallel Chemistry
Core expertise
Overview Enabled Hit Follow Up & Productive lead Discovery File Enrichment Chemo informatics High Throughput Chemistry HTS
Enhancing Chemo-informatics
Enable designs
Monomers
Protocols
Chemical Knowledge
Enumeration
Filtering
Prioritise lead series
Share Designs
Visualise large libraries
Use common desktop tools which aid collaboration
The Pfizer Global Virtual Library - PGVL
All resources connected in one application
All Pfizer Monomers stored in one location
All Pfizer // synthesis reactions and protocols
Stored in one location
With enumeration and structure checking
With knowledge of prior parallel chemistry reactions
All Pfizer in silico properties available
Filtering, clustering tools and visualisation
All parallel chemistry HTS Hit Follow up work comes from within this tool
A research sharing and visualisation tool
Links to Excel, Spotfire etc.
Enables choice from ~10,000,000,000,000 potential products
This virtual space grows with each new chemistry protocol and monomer discovered
PGVL ~ (PGRL) 2
HTS Hit triage protocol – Pipeline Pilot Raw data
Compound Name
% inhibition
Structures
Physical properties (Mw, clogP, etc)
Potential false positives/negatives
(Bayesian statistics)
Library protocol if any
Custom substructures (known series etc)
Clustering of actives by Murcko frame
Known aggregators, reactive groups
Ligand efficiency
M Murcko (Vertex), J. Med. Chem. 1999, 42, 5095-5099 A L Hopkins (Pfizer), Drug Discovery Today. 2004 May 15;9(10):430-1
Pipeline Pilot tree HTS Actives HTS Hits
HTS library output multiple lead options for most targets
Global Protocol database intranet access All Parallel Chemistry searchable in one place All 9 PGRD site use this tool All File enrichment research captured in the global database A link from compound to parallel synthesis protocol
Architecture based on Formal Reactions Protocols are associated into Formal Reactions VRXN-2-00001 Reductive amination as a family of protocols aldehydes nucleophilic amines Two protocols of broadest scope cover the largest range of potential ---- thus potential for re-use: Capturing these is what really builds the asset in global Chemical Knowledge Bases VRXN-2-00001 is defined by the Formal Reaction scheme and spans the space covered by all suitable amines & aldehydes in the linked inventory db
Formal Reactions as Families of Protocols 21 VRXN-3-00029 4 VRXN-3-00007 2 VRXN-2-00081 3 VRXN-2-00018 7 VRXN-2-00017 9 VRXN-2-00016 8 VRXN-2-00013 15 VRXN-2-00011 39 VRXN-2-00010 12 VRXN-2-00009 9 VRXN-2-00007 16 VRXN-2-00005 4 VRXN-2-00004 11 VRXN-2-00002 13 VRXN-2-00001 Source (each color represents one of the Pfizer R&D sites) # of explicit protocols within reaction family Name of Formal Reaction (broad scope rxns)
Chemist’s Desktop
Access to 543 (and growing) Formal Reactions
Scope & Limitations for the thousands of Protocols under those Formal Reactions is scientific basis for
Round-the-clock automated monomer mining
PGVL server-side automated search engine system uses thousands of stored query components running on Pipeline Pilot
Linked to global inventory
Search engine defines the precise VL for each protocol and (by concatenation) the overall VL for each Formal Reaction
PGVL exceeds 10 trillion compounds 10 13 +
PGVL Hub, an internally developed application
PGVL Hub on the Chemist’s Desktop
Access to virtual libraries from the desktop Suitable monomers retrieved for each reaction protocol Properties calculated Inventory and location searched Clustering and filtering pre and post enumeration
Spotfire Design analysis
Overview Enabled Hit Follow Up & Productive lead Discovery File Enrichment Chemo informatics High Throughput Chemistry HTS
HTS at Pfizer 10 years ago
A 500,000 screening file
Of mixed quality and purity
Early days of parallel chemistry and automation in chemistry and purification
Typical HTS gave 10% of lead matter being parallel chemistry friendly
Crude informatics tools for HTS follow up
Mostly Excel
The parallel chemistry friendly hits given more effort and therefore typically start more projects
Singleton hits - higher chemistry cost and risk
Parallel chemistry hits already have SAR, starting materials and high speed method
HTS at Pfizer now
uHTS capacity with Evotec and other platforms
Automated triage process based on
Clustering of actives and analysis of near neighbours
Hot monomer analysis
Parallel chemistry protocols
In Silico predicted physicochemical and ADME properties
Several libraries initiated on priority series
Several series / chemotypes progressed to reduce risk of project attrition
Monomer and template synthesis initiated where needed
Protocol development where needed
HTS at Pfizer now – cont.
Iterations of library design are synthesised to address series issues versus project criteria
Designs include global and project specific in silico models
Measures of success: Sandwich
96% of projects using parallel synthesis
138 libraries of >96 compounds each across the Sandwich discovery portfolio in 2003
Can identify multiple series to pursue from most HTS
Several leads from HTS & parallel synthesis currently in lead to CAN phase and early development
33% of clinical candidates resulted from FE enabled hits
applying multiple libraries (including structure based drug design) & traditional medicinal chemistry synthesis
Overview Enabled Hit Follow Up & Productive lead Discovery File Enrichment Chemo informatics High Throughput Chemistry HTS
IKK2 inhibitors from HTS hits to multiple project leads
Weak HTS hits from early FE library
2 active custom templates
5.6 billion potential analogues
4880 library inactives in HTS
6 rounds of library synthesis
Potent IKK2 inhibition in acidic, basic and neutral series found
The Hardware – 1st generation 6 x 2M Tecan Genesis 8 x Waters LCMS+ELSD 2 x Bohdan Weighing Stations 12 x Gilson 215 based HPLC systems
Assorted plate types
Assorted plate types continued
Tecan Genesis with Argon Blanketing
Prep HPLC stacking to save space
Barcode based fraction tracking
Crystal Structure of UK-411,930 bound to CDK2 - SBLD 2.3A resolution data SRS, Daresbury. Key pyrazole Donor Acceptor Donor interaction
Overview of Closed-loops for IKK Activity goes up with library iteration Number of actives increases with library iteration 0 10 20 30 40 50 60 0 1 2 3 4 5&6 Closed-loop iteration % of compounds active at 10 M 1 10 100 1000 10000 activity of most potent compound (nM)
Novel low MWt PDE-5 inhibitors from closed loop chemistry on HTS hits
Most potent compounds confirmed as functional antagonists
Keating, T.A. & Armstrong, R.W. (1995) "Molecular diversity via a convertible isocyanide in the Ugi four-component condensation," J. Am. Chem. Soc. 117 : 7842-7843
File enrichment library issue
Cyclisation of anthranilic acid derivatives formed using Ugi chemistry 1 provided targeted Benzdiazepinedione
Use of 2-aminonicotinic acid yielded non-cyclised by-products
R = Ph 2 avoids use of volatile, smelly isonitrile and yields 4-phenylcyclohexanone, readily separable from products by HPLC.
1) Ugi et al. Chem. Ber., 1961, 94, 2802, Armstrong et al. J. Am. Chem. Soc. 1996, 118 , 2574 2) Martens et al. Bio-organic & Medicinal Chemistry 2000, 8, 1343
Resolution of Oxytocin library actives
Resolution of library actives provided compounds meeting the target potency and selectivity criteria
Series accepted as leads for further development.
Long Acting Beta 2 agonists
Beta2 0.74 nM EC50 HTS hit
Parallel synthesis friendly project strategy
Enabled rapid progress of the project
Partnering TA with PMC group
Protected head groups
Optimised for potency and duration
Salmeterol like potency and DOA found
Exciting potential for long DOA in humans
mGluR1 antagonist
A number of weak and simple HTS hits identified
Both side of amide were optimised to give some potent amide analogues
Amides were high logD and high CL
Chose to diversify chemistry into PGVL space
6000 FE analogues were available for screening
The available VL was still huge
4.2 Billion products
mGluR1 Leads optimised within PGVL
Within a larger VL the logD and Cl properties could be better optimised
Several 1000s of analogues were easily made in the program
Progress was rapid and used outsourcing at Tripos, Bude, UK
Compounds with good potency and low Cl were obtained
Project identified tools for further development
Dafydd Owen* et al , Bioorganic Medicinal Chemistry Letter, 2006 In Press.
Maraviroc - Faster to CAN with parallel synthesis UK-107,543 (HTS hit) 400 nM CCR5 blocker no antiviral activity CYP450 inhibitor UK-427,857 antiviral IC 90 1 nM selective no CYP450 inhibition jun00 dec97 Dorr et al , Antimicrob Agents Chemother ., 2005 , 49 , 11 Armour & Wood, Progress in Medicinal Chemistry , 2005 , 43 , 239, WO2003084954 965 analogues
CCR5 antagonist - Maraviroc
Most final products made by HSA
Maraviroc first made in a filter tube with solid phase reagent
Blood rotator used for agitation
Crude products purified by prep HPLC
OA FractionLynx
NEP Parallel Chemistry Strategy
Initially retain a small R1(S1‘) based on known Candoxatrilat SAR
start with nPr and start racemic for expediency
Rapid exploration of R2 using parallel chemistry (1ml 96wp)
diverse set of amines based on Desired drug properties
Crude products sent for prep HPLC purification
As SAR emerges, incorporate chiral and diverse R1 S1'
NEP inhibitor SAR
Successful and rapid SAR exploration
UK-447,841 discovered
Short half life prn dose regimen required T1/2 7-10h
High absorption (F)
David C. Pryde et al , J. Med. Chem. 2005 WO2002002513 R2 dNEP (nM) MWt. LogD Caco-2 24 339 0.5 9/14 R1 6 393 -0.2 - 100 375 1.0 6/10 n Pr Me (CH 2 ) 2 OMe (CH 2 ) 2 OMe (CH 2 ) 2 OMe (CH 2 ) 2 OMe 4 333 0.8 21/21 3 379 0.5 12/17 0.5 396 1.0 12/14
Overview Enabled Hit Follow Up & Productive lead Discovery File Enrichment Chemo informatics High Throughput Chemistry HTS
Conclusions
HTS hit follow up is supported by huge global resources
FE created a 3MM compound pure parallel chemistry rich file
Global Chemo informatics resources able to quickly mine 1 trillion potential molecules
Contract research to support early stage lead optimisation and SAR generation
Acknowledgements
Everyone!
Additional Slides
Pfizer Overview
Industry pressures
Pfizer Overview
World’s leading healthcare company
Biggest investor in R&D worldwide
2004 R&D investment: $7.5 billion
The largest foreign owned R&D investor in the UK
122,000 employees across 60 sites in 31 countries
sales in over 150 countries:
12,000 R&D employees worldwide
2,700 people in R&D in UK
6900 Pfizer UK employees
Biggest supplier of medicines to the NHS
INDUSTRY AVERAGES:
100 Screens Produce 12 Candidates
1 in 12 survival rate during development
Only 1 of 4 products shows significant profit
12 years from idea to market
12-13 years of market exclusivity
Up to $800 million investment per product
Pre-Clin Phase I Phase II Phase III Registration MARKET Animal Toxicity, Chemical Stability, Superior Compound Human PK, Toleration, Formulation Efficacy, Safety Differentiation , Dose Long-term Safety Approval?
An Integrated Approach To Drug Discovery Using Para more
An Integrated Approach To Drug Discovery Using Parallel Synthesis. The history of parallel chemistry for lead discovery at Pfizer Sandwich from begining to outsourcing less
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