drug discovery: generating drug candidates to novel targets
TRANSCRIPT
Discovery and development timeline
Source: Tufts University 3
* Risky Success rate is low Even “Big Pharma” isn’t perfect
* Takes a lot of time * Very expensive
The Future
Pharma
VC/ Virtual COs
Academia Not for profit Scien)fic Ins)tu)ons
Engines of New Drug Development
PRECLINICAL DEVELOPMENT
CLINICAL DEVELOPMENT AND REGULATORY
MANUFACTURING, SALES AND DISTRIBUTION
DRUG DISCOVERY
Pharma
VC/IPO Backed
Academia, Scien)fic Ins)tu)ons
The Recent Past
TARGET IDENTIFICATION BASIC RESEARCH
Drug Discovery and Development Stages and milestones
Assay Development
High Throughput Screening
Hit to Lead Lead
Optimization Pre-clinical
Development Candidate Seeking
Assay Hit Validated Lead
Optimized Lead
Clinical Candidate
(NME)
Lead Validated
Hit (Probes)
Target
IND Ready NME
Clinic
Research Inves)gator 1
Research Inves)gator 2
Research Inves)gator 3
Research Inves)gator 4
New poten)al concepts for future
therapies
Clinical trials with new therapies
Conrad Prebys Center for Chemical Genomics
Translating Biomedical Research Discoveries
Advancing molecular medicine
Small Molecule Drug Discovery
Engine
Transla)on Biomedical Research
7
Animal Resources Animal Care & Procedures In Vivo Analysis Cardiometabolic Phenotyping Model Organisms
Cell Imaging & Analysis Histology and Molecular Pathology Cell Imaging Flow Cytometry
Genomics DNA Analysis Microarray & QPCR HT DNA sequencing
Proteomics & Metabolomics Proteomics Metabolomics
Medicinal Chemistry & Pharmacology Medicinal Chemistry SAR by NMR Experimental Pharmacology
Structural Biology Crystallography NMR Protein ProducIon & Analysis
Bioinforma)cs & Data Management BioinformaIcs CheminformaIcs 3D Modeling (CADD)
High throughput screening Assay Development Libraries and HT Screening Ultra-‐HTS High Content Screening CheminformaIcs
Func)onal Genomics siRNA/shRNA screening Viral Vectors
Stem Cells Embryonic Stem Cells Electrophysiology
Shared Resources
Superior Technology Infrastructure empowers world-class science
Drug Discovery -‐ CPCCG
SBMRI Drug Discovery Capabilities • State of the art uHTS
• HTS and High Content Screening • Chemical library >900,000 compounds
• Diversity of screening platforms • Industry trained (Pharma and Biotech) staff (> 70 FTE) • Established Drug Discovery teams (biologists and chemists) plus
technical Core Groups • Medicinal Chemistry • In Vitro/In Vivo Pharmacology (ADME/PK) • Experience outsourcing (Chemistry/PK/Tox)
• Extensive HTL and LO experience • Preclinical development experience • Project management (Fully implemented web based system
tracks all projects – timelines, $, resources, milestones etc.)
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Target ID
Assay Dev. HTS Pre-‐
Clinical Ph. I Ph. III Hit to Lead Ph. II Ph. IV
Lead Op)miz-‐a)on
Disease Target
NDA
IND
Drug Development Pipeline – Major Trans-‐NIH Ac)vi)es
Rare Diseases Clinical Research Network (RDCRN)
AIDS Clinical Trials Group (ACTG)
Interna)onal Network for Strategic Ini)a)ves in Global HIV Trials (INSIGHT)
Interna)onal Maternal Pediatric Adolescent AIDS Clinical Trials Group (IMPAACT)
Mechanisms, Models, Measurement, and Management in Pain Research
SHIFT Award: Small Businesses Helping Inves)gators to Fuel the Transla)on of Scien)fic Discoveries (SBIR)
Center for Human Immunology, Autoimmunity, Inflamma)on (CHI)
Preclinical and transla)onal studies of PET radiopharmaceu)cals
NIH Chemical Genomics Center
Therapeu)cs for Rare and Neglected Diseases (TRND)
Blueprint Neurotherapeu)cs Grand Challenge
Molecular Libraries Program RAID
Bioengineering Research Partnerships
Nanoscience and Nanotechnology in Biology and Medicine
Knock-‐out Mouse Project (KOMP)
Interna)onal Coopera)ve Biodiversity Groups
9
PAR-‐12-‐058 /059/060
S|B’s Internal Pipeline
Assay Feasibility
Preliminary HTS Data
High Throughput Screening
Hit to Lead Lead
Op)miza)on
Assay Hit Validated Lead
Op)mized Lead
Lead Validated
Hit (Probes)
Target
CV
Oncology
Neurology
Oncology
ID
ID
Oncology
Oncology
Oncology Bcl-‐2 Family (Sabutoclax)
Oncology
Oncology
Inflamma)on
Neurology
Oncology
CV
Licensed
Therapeu)c Area
Inflamma)on
SBMRI Library Screens (2011/12)
Assay Feasibility
Addic)on
20 High Throughput screens In past 12 months for Sanford-‐Burnham PI’s projects
Assay Feasibility
Preliminary HTS Data
High Throughput Screening
Hit to Lead
Cancer
Autoimmunity
CV
An)bio)c
Cancer
Cancer
Cancer
Bipolar
BiPolar
Cancer
CV/Metabolic
Neurology
Autoimmunity
Cancer
Cancer
Cancer/occular
Cancer
Cancer
Cancer
World Class Lead Discovery Capabili)es >$25 million capital
• 5 Fully Integrated Robo)c Liquid Handling Systems (HRE unipod and tripod /1536 format), acousIc liquid dispensing (BC Biomek 2-‐bridge FX 8/384 format)
– MulIple plate readers, Ip box & plate hotels, CO2 Incubators, etc.
• 4 Fully integrated HCS Systems – RoboIcs arms, Ip wash & cell dispense, plate hotel
& incubator – IN Cell housed in sterile room
• Off-‐line Instruments & Worksta)on – 6 Plate readers, 2 Plate washers, 3 Bulk reagent
dispensers – Plate WorkstaIon: Plate sealer, barcode labeler, 384/1536 liquid handler – Liquid Handler WorkstaIon 96/384/1536 – High Content Microscope – GPRC -‐ Hamamatsu FDSS-‐7000
13
CPCCG uHTS Facility (Florida) • Robot runs several screens simultaneously,
permieng complex scheduling • Swap out device “on the fly” & dock “off-‐line” • “Touchless” compound transfer (50 nL) for 1° HTS
& cherry-‐picking • Perkin Elmer Opera HCS + Acapella solware
Echo (5 total)
HRE Dispenser Or Combi
Carousels (500 plates each)
Handoff Press Lid hotel
Incubator x 3
Opera Waste
V-‐spin x2
Viewlux
FLIPR Envision
MicroDocks
5-‐Echos w/ On-‐Board library 3-‐Arms (Staubli RX-‐160L) 5 Readers
1 min/plate 1500 plate capacity
> 1 MM datapts / day
AddiIonal docks allow Off-‐system devices to Communicate w/Cellario™ scheduler & data acquisiIon modules
Tasks by Colors: Project team Biology Cheminforma)cs Chemistry Compound Management
Hit to Lead/probe Module : Workflow
Triage Scaffolds
Confirmed Hits
QC & RegistraIon
Analogs By Chemistry
Clustering
Purchase
RegistraIon
Inventory & Aliquot Inventory & Aliquot
SBMRI library
HTS posiIves
Cherry picks
>2500 hits
<2500 hits
promiscuous compounds? (Cbis/PubChem)
In-house CP confirmation
Drop
Single-concentration confirmation
SAR panel QC
QC
Synthesis/PurificaIon
SAR panel
Chemical LEAD
SAR panel
2o assays 2o assays
Is it Lead? yes
no sufficient SAR? yes
no
yes
no
High Throughput Screens and chemical probes (early drug leads)
107 HTS Screens of large chemical libraries have been completed by SBMRI Probe Discovery : Probes to explore biology in vitro (cellular/biochemical systems) Drug Discovery : StarIng points for Hit-‐to-‐Lead effort to explore and validate target in vivo Target Discovery: Chemicals to idenIfy new targets/pathways relevant to biology/disease
53 Biochemical Screens
(22 probes)
44 Cell-‐based Pathway Screens
(15 probes)
2005-‐2011 107 Library Screens 48 Probes Iden)fied
12 High Content Screens (11 probes)
How were new medicines discovered ?
David C. Swinney and Jason Anthony (2011) Nature Drug Discovery 10, 508-‐519
1999-‐2008 259 Drugs approved by FDA 75 First-‐in-‐class drugs
157 Follower drugs
Image-‐Based GPCR Screens Assay Provider / PI: • Larry Barak, Duke Univ. & Mary Abood, Temple Univ.
GPCR Projects & Goals: • Iden)fy small molecule agonist /antagonists for:
– Orphan GPCR GPR55 (agonist & antagonist) – Orphan GPCR GPR35 (antagonist) – GPCR Neurotensin-‐1 (agonist)
Background/Disease Relevance: • Addic)ve behavior and drug abuse
GPR35 GPR55 NTR1
3 Novel GPR35 Antagonists
SN
S
HN
O
OH
COOH
N N
NNN
N Cl
S
F
F
O
O
NH
NNHN N
MLS-‐0205231
GPR35 IC50 = 20.1 nM GPR55 IC50 = 21,700 nM 1,080-‐fold selecIve
MLS-‐0013034
GPR35 IC50 = 2220 nM GPR55 IC50 > 32,000 nM
>15-‐fold selecIve
Probe Criteria: GP35 IC50 < 5uM
SelecIvity against GPR55 antagonist >10x
MLS-‐0300303
GPR35 IC50 = 160 nM GPR55 IC50 ~ 9,080 nM
~57-‐fold selecIve
• Imaging takes ~ 2h 10 min/plate, 25 days to image 270 plates conInuously • Images/data uploaded to Columbus™ • Data uploaded/analyzed in CBIS™ • % RedistribuIon (pits & vesicles); cytoxicity (nuclei & morphology); & cell staIsIcs
obtained from same sample
NTR1 -‐ HCS was taken to a new level in 1536-‐well format – a 1st for SBCCG
β-‐Arres)n HCS Screen in 1536-‐wells
GPR35 b-‐arres)n (GFP) + nuclei (DAPI) nuclei (DAPI) only
San Diego
Orlando
uHTS System
HCS/HTM Systems
HTS Systems / Liquid Handlers
Image Host
HCS Temp Storage ~12TB
Opera QEHS IC200 InCell1000 Eidaq100 Opera QEHS Celigo
HCS Assay Plates (96, 384, 1536)
Assay Images Assay Data
Data & Images
Data
Visualize Images & Data (Linked) across Plates and Screens, Export
Images, Export Data
CBIS Cheminforma)cs
Database
HTS/HCS Analyzer
Acapella – 2D HCS
Volocity – 3D / Time
Columbus Image-‐Data Storage & Image (Re-‐)Analysis
Systems: Wide-‐field, Confocal, Live Cell; Objec)ves: 3.5x to 40x (60x), 0.15 to 0.95 NA
Scien)st Collaborators Images
HCS Infrastructure at SBMRI
24
Assay Development
High Throughput Screening
Hit to Lead Lead
Op)miza)on Pre-‐clinical Development
Candidate Seeking
Assay Hit Validated Lead
Op)mized Lead
Clinical Candidate (NME)
Lead Validated
Hit (Probes)
Target
IND Ready NME
Potent, selec)ve Oral inhibitors of TNAP Indica)ons – GACI, Vascular Calcifica)on
Example 1 : Hit to lead optimization Non-‐specific Alkaline Phosphatase : TNAP
Chemical probes to explore physiological and pathological calcifica)on
Up-‐regulated TNAP acIvity leads to decreased extracellular [PPi] and the deposiIon of hydroxyapaIte in the vasculature media
Inhibitors of TNAP may be used to treat and prevent medial calcificaIon and inappropriate bone deposiIon (cancer) + rare diseases e.g. ACDC, Fibrodysplasia Ossificans Progressiva, Hyperphosphatasia
Medial calcifica)on
Vascular smooth muscle cells
NPPs
R03 MH077602-‐01 (J. Luis Millán : SANFORD BURNHAM)
TNAP Inhibitor Program: Probe ML028
• High clearance and poor AUC in rodent • Modest cell based activity • Focus on developing diverse, novel
leads with improved drug properties
1
10
100
1000
10000
100000
0 5 10 15 20 25
Con
cent
ratio
n (n
g/m
L)
Time (h)
Mean IV
Mean PO
Mouse PK profile ML028 (2 mpk IV/10 mpk PO)
ML028
TNAP IC50= 15 nM VSMC assay IC50= ~ 3 µM
Plasma stability= 97% @ 1 hr Rat microsomal stability= 26% @ 1hr
logP= 3.5
N
HNS
O
O O
O
IV PO Clp = 45 mL/min/kg Cmax = 791 ng/mL (2.3 µM) Vdss = 0.284 L/kg AUC = 1125 ng.hr/mL t1/2 = 0.15 hr t1/2 = 0.9 hr
%F = 31
Key PK Parameters
Lead Op)miza)on to IND Drug Discovery )meline
Lead Op)miza)on Pre-‐clinical Development
Candidate Seeking
Clinical Candidate
NME
IND Ready NME
Lead In Vivo POC
Op)mized Lead(s)
~0.5 -‐ 2yrs Yr 1 Yr 0.5 Yr
GMP Scale up Formula)on
GLP Toxicology/CV ADMET
Clinical Plan, Inves)gator Brochure etc.
Medicinal Chemistry – Potency, drug like proper)es, I.P.
Pharmacology, PK, ADME
In vitro and In Vivo Biology – Efficacy, PK,PD, Biomarkers
Back Up Chemical series
Non GLP Chem. Scale up
Tolerance – Tox Non GLP CV safety
Lead Op)miza)on of TNAP probe
Parameter Ideal Profile ML028 SBI-‐425 IC50 in TNAP enzymaIc assay – nM (human)) <100 15
IC50 whole blood assay (pH7.5) µM (mouse/human) <1 6.8
IC50 in mineralizaIon of cultured VSMCs -‐ µM 5 3 ND
Microsomal stability (HLM, RLM) % remaining @1 hr >75% 26
t1/2 (rodent) -‐ hr >1 0.9
PO bioavailability (rodent) > 50% 31%
Clearance (rodent) -‐ mL/min/kg <30 45
Plasma Protein binding < 95% >98%
Exposure (AUC, rodent) -‐ ng.mL/kg 3,000 1125
Solubility -‐ µg/ml >10 <10 >10
HERG binding – “clean” at dose (µM) >50 ND >10
IC50 P450 inhibiIon 5 major isozymes (µM) >10 <10 >10
SelecIvity over other targets (IAP,PLAP) -‐ fold >10 >100
Assay Development
High Throughput Screening
Hit to Lead Lead
Op)miza)on Pre-‐clinical Development
Candidate Seeking
Probe ML028
LEAD SBI-425
Op)mized Lead SBI-‐425 Met or Exceeded All “Ideal” Profile for Parameter
Values of a Lead for Pre-‐clinical tes)ng
Exploratory Pharmacology
Pharma quality in vitro and in vivo ADME/T PK plauorm
RouZne assays conducted: • Cell Permeability
• CYP450 Inhibi)on profiling
• Hepa)c microsome stability
• Plasma protein binding
• Plasma stability
• In vitro tox: cytotoxicity/hepatotoxicity/cardiotoxicity • Rapid PK assessment -‐ R.A.C.E. (mouse or rat)
• Comprehensive PK analysis
• Drug distribu)on analysis
• Drug metabolite analysis
31
Recent announcement NIH screening and Hit-‐to-‐Lead Grants
• PAR-‐12-‐058 Solicita)on of Assays for High Throughput Screening (HTS) to Discover Chemical Probes (R01) h|p://grants.nih.gov/grants/guide/pa-‐files/PAR-‐12-‐058.html
• PAR-‐12-‐059 Solicita)on of Assays for High Throughput Screening (HTS) to Discover Chemical Probes (R21) h|p://grants.nih.gov/grants/guide/pa-‐files/PAR-‐12-‐059.html
• PAR-‐12-‐060 Solicita)on of Validated Hits for the Discovery of in vivo Chemical Probes (R01) h|p://grants.nih.gov/grants/guide/pa-‐files/PAR-‐12-‐060.html
• First round Feb 5th (RO1) & Feb 16th (R21), next round June 2012
Request for Proposals
CPCCG Contact: Thomas “T.C.” Chung, Ph.D. hHp://www.sanfordburnham.org/Talent/Pages/ThomasChung.aspx UCSD Contact: Paul Mills, Ph.D. Mills [email protected]
Drug Discovery and Development Early Stages and milestones
Assay Development
High Throughput Screening
Hit to Lead Lead
Optimization Pre-clinical
Development Candidate Seeking
Assay Hit Validated Lead
Optimized Lead
Clinical Candidate
(NME)
Lead Validated
Hit (Probes)
Target
IND Ready NME
Reagent Development
Assay Feasibility (POC)
Pilot HTS Data
HTS/uHTS Implementa)on
Development Secondary Assays
Entry to Drug Discovery or Grant Funding • Assay development & • Automated HTS feasibility • Preliminary HTS data package • Develop cascade of 2 assays & feasibility • Hit-‐follow up data & Hit validaIon workplan
Stated Review Criteria from RFP New Drug Discovery Seed Funding Program
1. Novelty of the assay. Assays proposed must be “de novo” assays – i.e.
where new reagents need to be generated to generate feasibility data. (Slight reconfiguraIons of exisIng assays or commercially available assays will not be funded).
2. Relevance to drug discovery. The target of the assay should ideally be implicated in a disease or disease process & thus have a plausible clinical applicaIon.
3. Probability that the HTS assay meet the criteria for funding by NIH Special Emphasis Panel for the PAR-‐12-‐058 (R01) or PAR 12-‐059 (R21) Grant ApplicaIons. The proposed final HTS assay should fit the criteria outlined by the respecIve FOAs. Preference will be given to those applicants that are at a more robust level of technical readiness. Applicants agree to lead an R01/R21 applicaIon & agree to work with the CPCCG team to generate the preliminary HTS data required for submission.
Proposal Profile Summary Sheet Item Summary Comments (Not an evaluaZon) PI
Posi)on/Department
Ins)tu)on
Title
Target/Type
Indica)on
Impact/Need/
Ra)onale
Assay/readiness
Prior Art/Ref cmpds
Project Title: PI: Scoring Sheet & Grid
Factor Score Comments
Significance/Impact (R01) 1
No Prior Art? 1
Biological RaIonale 2
Unmet Rx Need/IndicaIon 1
InnovaIon (approach/target/assay)?
1
Fundability (R01) & supporIng NIH IC?
1
Inherent Impact & Ra)onale
Factor Score Comments
Assay configuraIon vs. biology 1
Assay format/detecIon 3
CriIcal reagents & controls 1
Assay performance & pilot 2
CriIcal path logic & assays 1
Assay Tech Reqs & Cri)cal Path Tes)ng Funnel
1 = Strong 2 = Moderate 1 = Weak
1 = Robust 2 = Moderate 1 = Weak
Priori)za)on Matrix Im
pact/N
eed/Ra
Ionale
Feasibility/Readiness/Logic
Tier 1 Tier 2
Tier 3 Tier 4
Tier 1 (Accept -‐ execute) • Inherently high impact/unmet need/lack of prior
art/clear Rx & scienIfic raIonale/innovaIon of approach/target and/or assay
• Meet Tech reqs /assay(s)readiness
Tier 2 (Worth Improving assay – invest effort) • SIll inherently high impact/unmet need/lack of
prior art/clear Rx/scienIfic raIonale • Improving feasibility drives to Tier 1
Tier 3 (Wait -‐ Improve impact or if very facile assay, might screen at risk)
• Seek out or monitor for improvement of impact/need/raIonale that could drive to Tier 1
• Verify if facile/cheap merits screen for borderline impact
Tier 4 (Reject – Send back to PI for improvement) • Low impact/unclear need/prior art/weak Rx &
scienIfic raIonale • Very hard to do as well, so no clear reason to
invest any Ime currently • PI should invest Ime to bolster impact 1st
• Should we do it vs. can it be done (Important? versus doable?)
Period PAR-‐12-‐058 (R01) 3-‐yrs PAR-‐12-‐059 (R21) 2-‐yrs Funding ≤$250K/yr direct modular; ≤$500K/yr detailed;
>$500K 6-‐wk prior approval ≤$275K total direct; but ≤$200K in any yr
NIH ICs no NHLBI, NIAID no NINDS, NIDDK, NHLBI, NIAID
Purpose [Significance]
PI to form collabora_ons with an established academic, nonprofit, or commercial high throughput screening (HTS) facility. SImulate research in 1) discovery & dev. of novel, small molecules for their potenIal use in studying disease treatment relevant to NIH IC, & 2) discovery &/or validtn of novel, biological targets for studies of disease mechanisms. Emphasis on assays that provide new insight into important disease targets & processes. (NOT HTS assay development see PA-‐10-‐213)
Scope [Approach, inves_gators & Environment]
1) HTS implementaIon: projects expected to already have implementable HTS assay & a large collecIon of compounds & demonstrated capability 2) Hit valida_on: cherry-‐pick retest, med chem & cheminfo hit prioriIzaIon, powder retest, QC & 3) limited SAR-‐by-‐purchase elucida_on
Tech Req [Environment, Approach & inves_gators]
1) Large curated, cmpd collecIon, 2) implementable HTS, 3) follow up assays, 4) Project management
Deadline 5 pm local Ime
5Feb /5Jun/5Oct (non-‐AIDS); 5Mar/5Jul/5Nov (non-‐AIDS renew, resub, rev); 7May/7Sep/7Jan (AIDS & AIDS related)
16Feb /16Jun/16Oct (non-‐AIDS); 16Mar/16Jul/16Nov (non-‐AIDS renew, resub, rev); 7May/7Sep/7Jan (AIDS & AIDS related)
Sci Rev Cycle I: Jun -‐ Jul; Cycle II: Oct – Nov; Cycle III: Feb -‐ Mar
Council* Cycle I: Aug or Oct; Cycle II: Jan; Cycle III: May
Start Cycle I: Sep or Dec; Cycle II: Apr; Cycle III: July
*Actual date of the Advisory Council may occur in, before, or ader the month listed **Awarding components may not always be able to honor the requested start date. See NIH the Grants Policy Statement governing pre-‐award costs prior to receiving NOA &
incurring expenses.
Maps to Purpose, Scope & Technical Requirements