Drug Discovery: Generating Drug Candidates to Novel Targets

Sanford-Burnham Center for Chemical Genomics

Pharmaceu)cal drugs – chemicals

Lipitor

Nexium

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




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.)

8

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

Partnering with the government and industry to find new medicines

S|B’s Internal Pipeline

Assay Feasibility

Preliminary HTS Data


Hit to Lead Lead

Op)miza)on


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


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

Acoustic Dispense 2.5 nL droplets

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

M. Quintavalle et al. (2011), Science Signaling 4(183):ra49

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


Hit to Lead Lead

Op)miza)on Pre-‐clinical Development

Candidate Seeking


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

Hit to Lead Workflow and Key Assays

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


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

NIH GRANTS -‐ HTS

CTRI – Drug Discovery Seed Grants

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


Hit to Lead Lead

Optimization Pre-clinical

Development Candidate Seeking


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

NIH GRANTS -‐ HTL

Drug Discovery: Generating Drug Candidates to Novel Targets

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