Water Networks in Drug Design

Water Networks in Drug Design

Leah Frye, PhD

Basel Life Science Week

2015

Outline

• Introduction to importance of understanding water networks

• Locations of waters and energetics of the waters in drug design – Potency – Selectivity

• Effect of ligand binding on water energetics – implications for ligand design

• Free energy perturbation (FEP) calculations

• Real world examples

Why Is Water Important?

• Water is everywhere in biological systems

• Apo protein binding sites are mostly filled with water

• Water is a direct competitor in ligand binding

• Locations of all waters in active site not provided by crystallography

• Water energetics cannot be determined from structure alone

• Displacement of high energy (unhappy) waters can lead to big potency gains

Thermodynamic Decomposition of Ligand/Protein Binding

Solvated Ligand Solvated Apo

Protein

Desolvated Ligand

Solvated Ligand in Bioactive

Conformation

Ligand-Induced Desolvated Protein

Binding Site

Solvated Protein in Ligand-Induced

Conformation

Protein/Ligand/Water Complex

DGbind = DGi=1

5

å i( )

∆G( 5 ) ∆H reward ∆Srot / t rans penalty

∆G( 1 ) ∆Hconf penalty ∆Sconf penalty

∆G( 3 ) ∆H penalty ∆S reward

∆G( 2 ) ∆Hconf penalty ∆Sconf penalty

∆G( 4 ) ∆H ? ∆S ? WaterMap

WaterMap Background

• Predicts locations and energetics of active site waters –Molecular dynamics simulation with explicit waters

• Protein is rigid

– Identifies regions where water molecules most often reside: hydration sites

• Not limited to crystallographic waters

– Entropic and enthalpic properties, as well as DG, of each hydration site are calculated using statistical methods • Lazaridis T. et al. J. Phys. Chem. B 1998, 102, 3531-3541

Young, T., et al. PNAS 2007, 104, 808 Abel, R., et al. J. Am. Chem. Soc. 2008, 130, 2817

Apo WaterMap Example: SYK (3FQS)

Water site DG range: -6.35 – 6.83 kcal/mol

X-ray ligand

Hydration Sites and Crystallographic Waters

Thrombin (2UUF)

– 1.26 Å resolution

– 41 crystal waters vs.

115 hydration sties

within the active site

– >90% of crystal

waters have hydration

sites within 2.0 Å

= hydration site

= crystal water

WaterMap and Potency

• WaterMap computes the entropy and enthalpy of “hydration sites”

• These can be used to rationalize SAR, drive potency, and tune selectivity – Green = stable – Red = unstable

• Provides a “map”

Stable

(happy)

waters

Unstable

(unhappy)

water

Thrombin

S1 pocket

Abel, R., et al. ChemMedChem 2011, 6, 1049

Hydration Sites and Drug Design: Thrombin

3 stable waters with favorable enthalpy

most unstable water in binding site

A


Thrombin

S1 pocket

Thrombin WaterMap Scoring

B



10,000 nM 9,010 nM

A B C



B



10,000 nM 9,010 nM

654 nM

A

D

B C

Avoiding a stable water



B



10,000 nM 9,010 nM

654 nM 89 nM

A

D E

B C

Partial displacement



B



10,000 nM 9,010 nM

654 nM 89 nM 3 nM

A

D E F

B C

Full displacement


WaterMap in Drug Design

• Provides a clear roadmap for ligand design – Which regions of active site are most important for potency – Which regions should be avoided, if possible – What type of functionality to place in each region

• Displace hydration site with hydrophobic group when enthalpic term high

• Replace hydration site when entropic term high and enthalpic term near zero

– Optimal directionality of H-bond donors and acceptors

Water Energetics and Selectivity

• Comparison of WaterMaps of different proteins can provide guidance for the design of selective compounds

McInnes, C., et al., Chem Biol, 2004. 11, 525

CDK2 and CDK4 (homology model)

High-energy water is displaced by MeNH- in CDK4 but not CDK2

N

N

HN

N

HN

S

N

CH3

R1

Kinase Inhibition (uM)

R1 IC50(CDK4) IC50(CDK2) Selectivity

Me- 0.64 1.1 1.7

MeNH- 0.007 0.22 31.4

Apo WaterMap Summary

• Advantages – Single simulation – Predictive for buried, fully displaced waters

• Limitations – Energetics of water rearrangement is not accounted for

• Complex water networks – Protein rigid – Does not include ligand desolvation – Doesn’t rigorously address interactions between ligand and protein

• Holo WaterMaps can be useful when water networks are involved – Holo WaterMaps: simulation run with ligand present

Holo Watermaps: PI3K Selectivity

• Highest energy water molecule in site resides near point of substitution

+6.0


• Energetics of water similar for beta and delta

• Water molecule is displaced by R-enantiomer

• Equal gain in potency for beta and delta +6.0

R


• S-enantiomer: Holo watermap for delta isoform exhibits higher energy hydration site than beta isoform with S-Me compound

• Selectivity: 20x beta to delta

+5.9 +6.7

Beta Delta

Holo WaterMaps

• Advantages – Better representation of true solvation thermodynamics upon

binding – Often provides insight into complex water networks and solvent-

exposed regions

• Disadvantages – More computationally intensive

• Separate simulation for each ligand

– Protein rigid – Does not include ligand desolvation – Doesn’t rigorously address interactions between ligand and protein

Free Energy Perturbations (FEP)

DDGbinding = DG1 – DG2 = DGA – DGB

A

B

1 2

Predicts relative free energies of binding

• Over 300 perturbations tested w/ identical protocol

– RMSE ≈ 1.1 kcal/mol

|ΔΔGFEP – ΔΔGExpt.| (kcal/mol)

Pe

rce

nta

ge

46.2%

24.8%

15.4%

7.4% 6.2%

0%

5%

10%

15%

20%

25%

30%

35%

40%

45%

50%

< 0.6 0.6-1.2 1.2-1.8 1.8-2.4 >2.4

Schrödinger FEP Retrospective Accuracy

-15

-14

-13

-12

-11

-10

-9

-8

-7

-6

-5

-4

-15 -14 -13 -12 -11 -10 -9 -8 -7 -6 -5 -4

BACE

CDK2

JNK1

MCL1

P38

PTB1B

THROM

TYK2

ΔG

FEP

(kc

al/m

ol)

ΔG Expt. (kcal/mol) L Wang, et al. J. Am. Chem. Soc. 2015, 137, 2695

FEP

• Advantages – Takes into account all aspects of binding energy equation – Flexible protein and ligand – Better quantification of ligand-protein interactions – In the majority of cases, allows for rank ordering of compounds

within error range

• Disadvantages – Computationally intensive – Limitation on type of perturbations that are amenable – Not applicable to diverse sets of ligands

Recent Collaboration

Round Number of synthesized

compounds*

Ki of best compound

VS --- 2 µM

1 4 82 nM

2 10 14 nM

*Does not include standards, synthetic intermediates and by-products

• Virtual screen (VS) with Glide SP and WScore

• Two rounds of optimization • WaterMap for design • FEP+ to prioritize for

synthesis

25

Acetyl CoA Carboxylase (ACC): Master Regulator of Fatty

Acid Synthesis & Oxidation

Acetyl

-CoA

ACC

Inhibit

or

ACC1

Malonyl-

CoA

Malonyl

-CoA

Fatty acid synthesis Fatty acid oxidation

ACC2

26

Fatty Liver Spectrum Disorders: Substantial Unmet Medical

Need

% of Population 70-83%1 3-5%2 5-20% of

NASH Patients3

1 in 200 NASH

Patients3

Prevalence

(US)4 9-16M 0.5-3.2M 45-80K6

Annual HCC

Incidence (US)5 15K

1. Arthur J. McCullough, Cleveland Clinic at the AASLD – FDA Workshop on NASH, Sep 5, 2013

2. AASLD Practice Guidelines for NAFLD, 2012 3. Schuppan et al., Liver International, 2010

4 US Census Bureau, 2013 estimate: 317 million 5. Venook et al. The Oncologist 2010;15(suppl 4):5–13

6. Will develop NASH-related HCC over time Graphic: Cohen et al., Science . 2011 June 24; 332(6037): 1519–1523

Normal Liver

Simple

Steatosis

NASH

Cirrhosis Hepatocellular

Carcinoma

12 - 27%1

ND-630

Liver : Muscle 100:1

ND-654

Liver : Muscle 2700:1

27

WaterMap Identified Unexploited Potency Opportunities

High-energy waters in soraphen allosteric binding site

6.0

1.0

2.0

3.0

4.0

5.0

∆G kcal/mol

28

From Binding Mode to Man in 42 Months

0 12

Months

Milestone

Achieved

Confirm Binding

Mode (X-ray) In Vivo Target

Engagement

16

In vivo Efficacy

42

Safety

First in human

5,000 Ideas

175

Total synthesized compounds

8,000 nM <10 nM Potency

ACC1, ACC2

[1.3MM] 10,000

225

<1 nM

Schrödinger Drug Discovery Group

• Ramy Farid • Mark Murco • Leah Frye • Jeremy Greenwood • Mark Brewer • Lidia Cristian • Mats Svensson • Sathesh Bhat • Shaughn Robinson • Josh Kennedy-Smith • Carolyn McQuaw • Shawn Watts • Mee Shelley

• Dragon Cirovic • Sarah Boyce • Markus Dahlgren • Jonathan Gable • Kyle Konze • Nick Boyles • Amy Rask • Mary Beth Grimes • Kyle Marshall • Josh Staker • David Casio • Will Richards

• Robert Abel • Jennifer Knight • Goran Krilov • Lingle Wang • Sayan Mondal • Tyler Day • Jeff Bell • Shulu Feng

• Byungchan Kim

Schrödinger Drug Discovery Group

• Ramy Farid • Mark Murco • Leah Frye • Jeremy Greenwood • Mark Brewer • Lidia Cristian • Mats Svensson • Sathesh Bhat • Shaughn Robinson • Josh Kennedy-Smith • Carolyn McQuaw • Shawn Watts • Mee Shelley

• Dragon Cirovic • Sarah Boyce • Markus Dahlgren • Jonathan Gable • Kyle Konze • Nick Boyles • Amy Rask • Mary Beth Grimes • Kyle Marshall • Josh Staker • David Casio • Will Richards

• Robert Abel • Jennifer Knight • Goran Krilov • Lingle Wang • Sayan Mondal • Tyler Day • Jeff Bell • Shulu Feng

• Byungchan Kim

Acknowledgements Applications Sciences Thijs Beuming Daniel Cappel Roy Kimura Michelle Hall Daniel Robinson Madhavi Sastry Woody Sherman Devleena Shivakumar Thomas Steinbrecher Dora Warshaviak Sanofi (PI3K) Thomas Bertrand Frank Halley Andreas Karlsson Magali Mathieu Herve Minoux Laurent Schio

Leadership Ramy Farid Mark Murcko Scientific Development Yuqing Deng Ed Harder Teng Lin Levi Pierce Justin Xiang Yujie Wu Friesner Lab @ Columbia

Scientific Advisors Bruce Berne John Chodera (new) Rich Friesner Bill Jorgensen Ron Levy David Mobley (new) Vijay Pande (new) D. E. Shaw Research Michael Bergdorf Justin Gullingsrud Ross Lippert Charles Rendleman Huafeng Xu

Acknowledgements: Nimbus

32

BD & Strategy

World-Class

Medicinal

Chemists

Outstanding

Biology

Expertise

Daniel Lynch –

Executive Chairman

BMS, ImClone,

Stromedix, Avila

Jonathan Montagu –

VP, Business

Development &

Operations

Concert, J&J, Chiron,

Biogen Idec

Ron Wester, PhD –

Head of Chemistry

23 years medicinal

chemistry at Pfizer

Donna Romero, PhD –

Head, Nimbus Iris

(IRAK4)

20 years at Pfizer

Craig Masse, PhD –

Head Nimbus Zeus

(Tyk2)

Amgen, Concert

Pharmaceuticals

Gerry Harriman, PhD –

Head, Nimbus Apollo

(ACC)

VP, Chemistry at Galenea,

Millennium

Rosana Kapeller, MD, PhD –

Chief Scientific Officer

Aileron, Millennium, Dana-

Farber

William Westlin, PhD –

Head Preclinical Research

& Early Dev.

Avila, Praecis, Pharmacia

James Harwood, PhD –

Biochemistry

Pfizer

http://www.mlnm.com/index.asp

Incorporation of Water Energetics Into Docking: WScore

• Novel scoring function – Integrates water energetics (WaterMap) – Very ‘hard’, empirical scoring function – Designed to improve hit rates – Scoring function based on physics of binding – Employs multi-structure protein ensembles when possible

• Advantages of WScore – Hit identification – Understanding physics of protein-ligand binding – Recovery of a diverse set of chemotypes in screening

WScore Superior To Glide SP In Early Enrichment

0

0.2

0.4

0.6

0.8

1

WScore

Glide SP

WScore Superior To Glide SP In Overall Enrichment

0

0.2

0.4

0.6

0.8

1

WScore

Glide SP

Documents

Water Networks in Drug Design