Structure-based Drug Design 陸志豪 [email protected] 分子系統生物醫學研究所...

Structure-based Drug Design

陸志豪[email protected]

分子系統生物醫學研究所

教材來源 : 國立交通大學楊進木博士http://gemdock.life.nctu.edu.tw

陸志豪助理教授

[email protected]

國立交通大學生物資訊所博士

結構生物資訊、計算生物學、演化式計算與機器學習

蛋白質區域結構模組與功能預測蛋白質結構與動力學的相關研究蛋白質與分子的交互作用相關研究

學歷

專長

研究領域

Outline

Current state of drug discovery Structure-based drug discovery Molecular docking Method of iGEMDOCK

Practice of virtual screening Prepare protein binding site Prepare compounds library Molecular docking Post-screening analysis

http://gemdock.life.nctu.edu.tw/dock/

World‘s Top-10 Selling Drugs 2010

氣喘

http://knol.google.com/k/krishan-maggon/top-ten-twenty-best-selling-drugs-2010/3fy5eowy8suq3/141#

Rank Drug Companies IndicationsSales

$ billion

1 LipitorPfizer, Astellas

降血脂 11.8

2 PlavixBristol Myers Squibb,

Sanofi Aventis抗血栓 9.4

3 RemicadeJ&J, Merck,

Mitsubishi Tanabe關節炎 , 脊柱炎… 8

4 Advair Glaxo Smith Kline 氣喘 7.96

5 EnbrelAmgen, Pfizer,

Takeda關節炎 , 脊柱炎… 7.4

6 Avastin Roche 肺癌，結腸癌，腎癌… 6.87 Abilify Otsuka, BMS 精神病 6.88 Rituxan Roche 非霍奇金淋巴瘤 , 白血病 6.7

9 Humira Abbott關節炎 , 脊柱炎 , 克羅恩

病…6.5

10 Diovan Novartis 高血壓 6.1

Patents: Advair

Manufacturer: GlaxoSmithKlineFDA approval: 2000Patent expiry: Feb. 12, 2008

US $6 billion/year: 15% income for GlaxoSmithKline

http://images.businessweek.com/ss/08/02/0206_generic_drugs/index_01.htm

氣喘

Drug Development Life Cycle

Years

0 2 4 6 8 10 12 14 16

Discovery (Lead discovery, Lead optimization, Toxicity prediction)Discovery (Lead discovery, Lead optimization, Toxicity prediction)

Preclinical Testing(Lab and Animal Testing)

Phase I(20-80 Healthy Volunteers used to check for safety and dosage)

Phase II(36-300 Patient Volunteers used to check for efficacy and side effects)

Phase III(300-3000 Patient Volunteers used to monitor reactions to long-term drug use)

FDA Review & Approval

Post-Marketing Testing

Identify lead compounds Structure-based screening ligand-based screening High-throughput screening

Lead optimization: QSAR

$600-800 US Million!$600-800 US Million!

7 – 15 Years!

2 to 10 Years2 to 10 Years

Classification of Drug Development

Protein

(receptor) S

tructu

re

Compound structure Known Unknown

Known

Unknow

n

Structure-based Drug Design (SBDD)

SBDD or de novo design

High-Throughput Screening(HTS)

Compound similarity searchO

O

O

O

O

O

query Similar compounds

OO

DDT 2002

Comparison of SBDD and HTS

Yellow: virtual screening (SBDD)Blue: high-throughput screening (HTS)Yellow: virtual screening (SBDD)Blue: high-throughput screening (HTS)

HTSSBDD

• Lipinski's Rule of Five• There are more than 5 H-bond donors.

• The molecular weight is over 500.

• The LogP is over 5.

• There are more than 10 H-bond acceptors. Curr. opin. Chem. Biol. 2002, 439

SBDD: high hit rateSBDD: high hit rate

Drugs derived from SBDD

Drug Discovery Today, 10, 895, 2005

克流感克流感

瑞樂沙瑞樂沙

To identify drugs that inhibit target proteins involved in diseases and have therapeutic effect against diseases Drugs often have stronger binding affinities than natural

compounds

Mechanism of drug actions

Target protein

A pathway of disease

ProteinProtein

Natural compound

Drug

xx x x

Structure-based Drug Design

Virtual screening using molecular docking

iGEMDOCK

Virtual screening using molecular docking

iGEMDOCK

Post-screening analysisiGEMDOCK, SiMMapPost-screening analysisiGEMDOCK, SiMMap

Compound database

Compound databaseProteinProtein

BioassayBioassay

Lead optimizationSiMMap, QSAR

Lead optimizationSiMMap, QSAR

What is the Molecular Docking ?

• Problem: Given two biological molecules determines:1. Whether the two molecules “interact”2. Formulated as a force field minimization process

• Goal: Retrieve molecules that can interact with query protein structure

Scoring function

Algorithm

Search

Evaluate

-30-2

Ene

rgy

Conformation

Three Components of Docking

Representation of receptor binding site (blue) and ligand

(red)

Sampling of configuration space of the ligand-receptor complex

(Search methods)

Evaluation of ligand-receptor Interactions

(Scoring methods)

PDB

ZINC, NCI, FDA...

configurations of the complex

-sco

res

Protein-ligand complex

?

GASA

Types of Scoring Functions Physics-based

nonbonded interaction terms as the score, sometimes in combination with solvation terms

Empirical multivariate regression methods to fit

coefficients of physically motivated structural functions by using a training set of ligand-receptor complexes with measured binding affinity

Knowledge-based statistical atom pair potentials derived from

structural databases as the score

Consensus scoring functions approach-6

-1

4

9

14

19

Distance (r)

Ener

gy

V 6

V 5

V 3V 4V 2V 1

2 0- 0 . 46 . 04 . 53 . 63 . 3S t e r i c ( v a n - d e r )

2 0- 2 . 53 . 63 . 12 . 62 . 3H - b o n d ( p o l a r )

V 6V 5V 4V 3V 2V 1I n t e r a c t i v e t y p e

E l e c t r o s t a t i c

S t e r i c

H - b o n d

Empirical

Physics-based

Docking Software GEMDOCK (Yang & Chen 2004)iGEMDOCK (Yang & HSU 2011)

DOCK: (Kuntz et al. 1982)DOCK 4.0 (Ewing & Kuntz 1997)AutoDOCK (Goodsell & Olson 1990)AutoDOCK 3.0 (Morris et al. 1998) GOLD (Jones et al. 1997)FlexX: (Rarey et al. 1996) GLIDE: (Friesner et al. 2004)ADAM (Mizutani et al. 1994)CDOCKER (Wu et al. 2003)CombiDOCK (Sun et al. 1998)DIVALI (Clark & Ajay 1995)DockVision (Hart & Read 1992)FLOG (Miller et al. 1994) Hammerhead (Welch et al. 1996)LIBDOCK (Diller & Merz 2001)MCDOCK (Liu & Wang 1999)PRO_LEADS (Baxter et al. 1998)

SDOCKER (Wu et al. 2004)QXP (McMartin & Bohacek 1997)Validate (Head et al. 1996)

de novo design toolsLUDI (Boehm 1992), BUILDER (Roe & Kuntz 1995)SMOG (DeWitte et al. 1997)CONCEPTS (Pearlman & Murcko 1996)DLD/MCSS (Stultz & Karplus 2000)Genstar (Rotstein & Murcko 1993)Group-Build (Rotstein & Murcko 1993)Grow (Moon & Howe 1991)HOOK (Eisen et al. 1994)Legend (Nishibata & Itai 1993)MCDNLG (Gehlhaar et al. 1995)SPROUT (Gillet et al. 1993)

研究成果 : iGEMDOCK 電腦輔助藥物設計

GEMDOCK 相關論文被引用次數超過 150 次GEMDOCK 在實際應用上，與國內外超過十實驗室合作，發現 20 個潛力藥物

Easy use, high accuracy, and automatic Easy use, high accuracy, and automatic

-6

-1

4

9

14

19

Distance (r)

Ener

gy

V 6

V 5

V 3V 4V 2V 1

2 0- 0 . 46 . 04 . 53 . 63 . 3S t e r i c ( v a n - d e r )

2 0- 2 . 53 . 63 . 12 . 62 . 3H - b o n d ( p o l a r )

V 6V 5V 4V 3V 2V 1I n t e r a c t i v e t y p e

E l e c t r o s t a t i c

S t e r i c

H - b o n d

iGEMDOCK: Fitness Function

van der Waals Energy Electrostatic Energy H-Bond Dihedral Parameter

dihed

kk

lig

i

lig

ij

Bijra mArFE ij

10

1 2int cos1

lig

i

pro

j ij

jiBijinter r

qqrFE ij

1 124

0.332

•Ebind = Einter + Eintra + Epenal

An example of van der Waals force:Gecko climbs on the glasshttp://en.wikipedia.org/wiki/Van_der_Waals_force

Definition of Atom Types in iGEMDOCK

Atom type Heavy atom name

Donor Primary and secondary amines, sulfur, and metal atoms

Acceptor Oxygen and nitrogen with no bound hydrogen

Both Structural water and hydroxyl groups

Nonpolar Other atoms (such as carbon and phosphorus)

Formal charge

Atom name

Receptor:

0.5 N atom in His (ND1 & NE2) and Arg (NH1 & NH2)

-0.5 O atom in Asp (OD1 & OD2) and Glu (OE1 & OE2)

1.0 N atom in Lys (NZ)

2.0 metal ions (MG, MN, CA, ZN, FE, and CU)

0 other atoms

Ligand:

0.5 N atom in –C(NH2)2+

-0.5 O atom in -COO-, -PO2-, -PO3

-, -SO3-, and -SO4

-

1.0 N atom in -NH3+ and -N+(CH3)3

0 other atoms

ASP

both

THR

HIS

-0.5

-0.524

0.332ij

ji

r

qq

Rotatable bonds

Docking Problem

Optimization steps1. Fix the location of the receptor, Initialize the orientation and conformation

2. Adapt the orientation and conformation of ligand

3. Evaluate the interaction energy and select the configuration

4. Repeatedly execute step 2 and 3

center

(x1, x2, x3):3-dimensional location relating to the center of receptor(x4, x5, x6): rotational angles of ligand relating to axes(x7, …, xn): twisting angles of rotatable bonds in the ligand

The Evolution Approach of iGEMDOCK

-30

-2

Ene

rgy

Conformation

Population: 2 Generation: 3 Population: 2 Generation: 3

Power of evolution

-30Ene

rgy

Conformation

1

1

0

1

0...

1

1

0

0

0...

1

1

1

1

0...

MutationMutation Crossover

0

1

1

0

1...

1

1

1

0

1...

0

1

1

1

0...

GEMDCOK – Docking Evaluation (100 complexes)

On 100 complexes

79% 66% 69%Proteins 2004

GEMDOCK Datasethttp://gemdock.life.nctu.edu.tw/dock/download.php

J.-M. Yang* and C.-C. Chen, “GEMDOCK: A generic evolutionary method for molecular

docking,” Proteins, 55, 288-304, 2004

Old drugs New Use ( 舊藥新用 )

Reasons It takes too long and costs too much to bring new drugs

to market. Nobel laureate James Black (1988)

the most fruitful basis for the discovery of a new drug is to start with an old drug.

for their discoveries of important principles for drug treatment

Old drugs New Use ( 舊藥新用 )

Examples: 舊藥新用的成功案例治療癌症常用藥「顆粒球生長激素」

可刺激骨髓細胞游移到大腦、分化成神經細胞，取代受損或死亡的腦神經細胞，達到治療老年痴呆症的效果 ( 院士沈哲鯤 )

就利用該藥治療老年痴呆症，向美國、台灣、中國大陸和歐盟等地提出應用專利申請

葛蘭素史克公司（ GSK ） Seroxat: 原本是丹麥人於 1970 年發現的一種用來抗抑鬱的藥 2001 年 (32 億美元 ) ， 2004 年又名列收入最高的 50 種處方藥加拿大 Apotex 公司經過研究，發現其可以治療強迫症、後外傷性

壓迫症輝瑞的 minoxidil

治療高血壓的口服藥發現能刺激毛髮生長，成為治療人類禿頭症的局部用藥

Compound databasesTarget protein:

1kim

>100,000 compoundsPrepared binding siteof the target protein

iGEMDOCKiGEMDOCK

Ranking

Molecular recognition

Steps of virtual screening

O

N

N

O

O

O

O

Post-screening analysis

Preparation

of docking

databases

Docking

program

Thymidine kinase (TK)

TK a drug target for the therapy of herpes simplex virus type-1

1kim

DNA synthesis

Thymidine kinase

The role of TK

ATP ADPThymidine Thymidine

5’-phosphate

Thymidine kinase

The reaction of TK

Thymidine: Drug design by modifying from substrate

O

N

N

O

O

O

O

Inhibitor

Blue is different

O

OH

O

N

HN

O

I

OH

O

OH

O

N

HN

O

OH

Preparation of protein binding site from Protein Data Bank (PDB)


1kim


iGEMDOCK

Ranking



Preparation

of docking

databases

Docking

program

Protein data bank (PDB)

Techniques for determining protein structures X-ray crystallography, NMR spectroscopy and electron microscopy

PDB contains information about experimentally-determined structures of biological marcomoleculeas (proteins, and DNA/RNA)

Proteins (1kim)

DNAs/RNAs (2k7e)

Biological complexes (1zrc)

X-ray

NMR

EM

http://www.pdb.org/

Search protein structures in PDB

PDB provides search by protein name, ligand, or structrue related keywords

Search example:

thymidine kinase (TK)

• Function: DNA synthesis

• Therapeutic: Anticancer and antivirus drug target

Example: X-ray structures of virus’ thymidine kinase with substrates/inhibitors

Protein name

Source spices

Experimental method

has ligands

Thymidine kinase Thymidine kinase

VirusesViruses

0.10.1 2.52.5

YesYes

Search result of “X-ray structures of virus’ thymidine kinase with substrates/inhibitors”

TK of virus

TK with ligand (substrate)

PDB ID of this structure

X-ray structure

23 structures for these keywords

Structure and related data (1kim)

The citation of this structure

Related data of this structure

The title of this structure

Visualization of biological assembly

Structure and ligand data (1kim)Ligand in this structure

Domain Annotations

Structure classification ID of 1kim

Advanced inspection for protein structure: download structure from PDB

1. Save the data on your PC2. Open the file on a structure

viewer program (swiss PDBviewer, pymol, and etc.)

Download iGEMDOCK iGEMDOCK is available at

http://gemdock.life.nctu.edu.tw/dock/igemdock.php

Install of iGEMDOCK

1. Click the zip file, iGEMDOCKv2.0.zip, and then right click2. Decompress to the user defined path

Step 1. Step 2.

Docking/Screening: 1. Prepare binding site by iGEMDOCK (Define by the ligand in the protein structure)

1. Press the button binding site2. Browse and select protein file (in \examples\

protein\1KIM.pdb)

1

2

Binding site of TK

Preparation of compounds


1kim


iGEMDOCK

Ranking



Preparation

of docking

databases

Docking

program

ZINC, a free compound database

http://zinc.docking.org/

Subset in ZINC1

Subset in ZINC2

Search compounds

Query compounds

Results of query

Molecular docking using iGEMDOCK


1kim


iGEMDOCK

Ranking



Preparation

of docking

databases

Docking

program

Execute iGEMDOCK

1. After installing the iGEMDOCK, execute the igemdock.exe in the fold “\bin\”

The environment of iGEMDOCK

Docking/screening

Post-analysis

Steps of docking/screening in iGEMDOCK

1. Protein structure/model (prepare your binding site)

2. Compounds library (load your compound set)

3. & 4. Setup parameters (output)

5. Run docking/screening

6. Analyze your predicted binding poses

55

N

N

O

OO

N

N

N

N

O

O

I

O

O

O

N

N

O

O

O

O

N

N N

N

O

N

O

OO

TK05

1ki2_GA2

TK02

1e2m_HPT

TK03

1e2n_RCA

TK01

1e2k_MCT

N

N

O

O

OO

TK04

1e2p_CCV

Thymidine Kinase (TK) Inhibitors

O

N

N

O

O

O

O

TK09 1kim_THM

Docking/Screening: 2. Prepare compounds

1. Press the button compounds2. Browse and select ligand files (in \examples\

compound\ESA and TK)

Docking/Screening: 3. Set output path

1. Press the button output2. Browse and select the path for saving

screening data, or directly key in the wanted path

Docking/Screening: 4. docking parameters

1. Setup docking parameters

Recommend parameters settings for general cases

For screening Population size :200Generations :70Number of solution :3

For more precisely dockingPopulation size :300Generations :80Number of solution :10

Docking/Screening: 5. Run docking/screening

1. Press the button start2. Run the screening jobs3. The status will show in the window4. The docked poses can be visualized in real time

Docking/Screening: After screening job finished

1. Press the button ok2. Use the post-analysis interface of

iGEMDOCK3. Or directly look for the screening result

in the fold “/output/”

iGEMDOCK provides an analysis environment with visual tool and post-analysis tool for users• Users can view the docked poses, cluster the poses by the protein-ligand interactions

• The predicted poses and scores of ligands are saved in the user defined output path

Post-screening analysisCompound databases

Target protein:1kim


iGEMDOCK

Ranking



Preparation

of docking

databases

Docking

program

Post-analysis: 1. Load binding site (if iGEMDOCK does not pre-loaded)

If the binding site does not pre-loaded1. Press the button binding site2. Select binding site from the output3. Or re-define by user

Post-analysis: 2. Load docked poses (poses generated into “output/best_Pose” in the screening process)

1. Press the button poses2. Select docked poses from the output

Post-analysis: 3. Generate interaction profile (by iGEMDOCK scoring function)

• View the predicted pose (to check the check box and press )

• Sort the table by the wanted columns)

Post-analysis: 4. cluster analysis by the protein-ligand interactions

• View the poses in the same cluster by ClusterID•Press the button display

Cluster analysisLook for compounds in the same cluster (#3)

Post-analysis: 4. cluster analysis : the protein-ligand interaction map

67

y axis: Residues

x axis: Compounds

Energy

Negative

PositiveZero

Post-analysis: 4. cluster analysis : the protein-ligand interaction analysis

68

Rows: Compounds

Columns: Interactions between each residue and compounds

Post-analysis: 4. cluster analysis : the protein-ligand interaction analysis

69

Select residues with consensus interactions (with statistical significances)

Default: confidence interval = 95% (z=1.96)

Stacking

Hbond

Essential for catalytic mechanism

J. Bio. Chem. v276, p21692-21697, 2001.

Post-analysis: 5. save the post-analysis data

1. The data generated in the post-analysis

/output/

Summary table

1. Summary: screening ranks and energy2. Profile : interaction / compound feature table3. Selected ligands data4. Cluster data: cluster index and profile

The data generated by iGEMDOCK in the process of screening and post-analysis

The binding site used in screening

Interaction table of protein-ligand

Post-analysis result

The poses with the best energies

All of the generated poses

Profile_residue-based_interactions.txt

Summary_table.txt

…

References of iGEMDOCK

Primary References: J.-M. Yang and C.-C. Chen, "GEMDOCK: A generic evolutionary method for molecular docking",

Proteins: Structure, Function and Bioinformatics, vol. 55, pp. 288-304, 2004. J.-M. Yang, "Development and evaluation of a generic evolutionary method for protein-ligand

docking", Journal of Computational Chemistry, vol. 25, pp. 843-857, 2004. J.-M. Yang and T.-W. Shen, "A pharmacophore-based evolutionary approach for screening selective

estrogen receptor modulators", Proteins: Structure, Function and Bioinformatics,vol. 59, pp. 205-220, 2005.

J.-M. Yang, Y.-F. Chen, T.-W. Shen, B. S. Kristal, and D. F. Hsu, "Consensus Scoring Criteria for Improving Enrichment in Virtual Screening ", Journal of Chemical Information and Modeling 2005.

K.-C. Hsu, Y.-F. Chen, S.-R. Lin and J.-M. Yang, "iGEMDOCK: A Graphical Environment of enhancing GEMDOCK using pharmacological interactions and postscreening analysis ," BMC Bioinformatics, 12(Suppl 1):S33, 2011

Selected Applications: J.-M. Yang, Y.-F. Chen, Y.-Y. Tu, K.-R. Yen, and Y.-L. Yang*, “Combinatorial computation

approaches identifying tetracycline derivates as flaviviruses inhibitors”, PLoS ONE, pp. e428.1- e428.12, 2007.

E.-S. Lin, J.-M. Yang, and Y.-S. Yang, "Modeling the binding and inhibition mechanism of nucleotide and sulfotransferase using molecular docking", Journal of the Chinese Chemical Society, vol. 50, pp. 655-663, 2003. (SCI)

J.-M. Yang and T.-W. Shen, "A Pharmacophore-Based Evolutionary Approach for Screening Estrogen Receptor Antagonists",Congress of Evolutionary Computation (CEC 2004),pp. 1028-1035, 2004.

Thanks for your attention

聯絡資訊 http://gemdock.life.nctu.edu.tw/bioxgem/ 藥物設計與系統生物實驗室 (BioXGEM Lab.), 交大生物資訊所

PI: Jinn-Moon Yang ( 楊進木 ) Address: 75 PO-Ai Street, Hsinchu, Taiwan, 30050, ROC Office & Lab : 308 and 304 (Lab) in Experiment Building

Tel: 886- 3-5712121 ext.56946 E-mail: [email protected]

Structure-based Drug Design 陸志豪 [email protected] 分子系統生物醫學研究所...

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