Bioinformatics and Drug Design

Institute of Bioinformatics and Structural Biology,Department of Life Science,National Tsing Hua University

Chao-Sheng Cheng

Watson and Crick, May 1953(From Robert Olby, The Path to the Double Helix, 1974)

1953 DNA1962 1990

2003414

James Watson

http://www.ensembl.org/

http://www.ncbi.nlm.nih.gov/

GeneBank

Ex. Cancer related genes !!

Information ComplexityInformation Complexity

DNA

Bioinformatics

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The Size of Cell

What is Cell ?

virtual cell http://www.virtualcell.com/

Virtual Frog Dissectionhttp://www-itg.lbl.gov/Frog/

Cells Life

- Computer training of surgical skills

http://www.cellsalive.com/

http://www.virtualcell.com/

http://www.froguts.com/http://www-itg.lbl.gov/Frog/

http://brc.life.nthu.edu.tw/

http://www.mi.auc.dk/virtualbrain/

(colon cancer)

Search results for query "colon cancer": 17 hits

http://www.ncbi.nlm.nih.gov/

TGFBR2 KNOWN Colon cancer; Colorectal cancer, hereditary nonpolyposis, type 6

MFS2 PHENO Marfan-like connective tissue disorder

MLH1 KNOWN Colorectal cancer, hereditary nonpolyposis, type 2, 114500

PSORS5 PHENO Psoriasis, susceptibility to, 177900

DLEC1 KNOWN Lung cancer, 211980; Esophageal cancer

ACAA1 KNOWN Pseudo-Zellweger syndrome, 261510

DNA RNA

Demonstrate similarity among sequencesIdentify functionally important sitesStructure predictionMolecular phylogenySearch for weak but significant similarity/primer design

Consensus seq.

Conserved region

Seq. ASeq. BSeq. C

Conserved motif

One Seq. with homology to A, B, C

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HIV-1 Protease Complexed With A Tripeptide Inhibitor

Docking(binding state)

10000~20000

2~32~32~3

2~3

3~4

10~122.0~3.5

Drug Characteristic

Must be safe to use

Must be effective for the intended use

Must be stable (chemically and metabolically)

Must have a good solubility profile

Must be synthetically feasible

Must be novel (patentable)

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Computer Aided Drug Design

Target Structure

Target Structure

Ligand-based approachesLigand-based approaches Structure-based approachesStructure-based approaches

knownunknown

(Pharmacophore + QSAR) (Docking; De novo design)

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Computer Aided Drug DesignTwo different strategies:

Ligand-based (analog-based) design Relies on a set of known ligands and is particularly valuable if no

structural information about the receptor is available.

Structure-based (target-based) design Usually starts with the structure of a receptor site, such as the active

site in a protein. This structure can be generated from direct experimentation or can

be deduced from experimental structures through homology modeling

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Definition of a Pharmacophore A pharmacophore can be defined as a specific 3D

arrangement of chemical groups common to active molecules and essential to their biological activities.

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SAR: Structure-activity relationship

Bioisosteric Replacements

Molecules that are designed by bioisosteric replacements are expected to have similar biological properties.

Programs

Catalyst Sybyl Discovery Studio

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Computational ligand designTwo different strategies:

Ligand-based (analog-based) design Relies on a set of known ligands and is particularly valuable if no

structural information about the receptor is available.

Structure-based (target-based) design Usually starts with the structure of a receptor site, such as the active

site in a protein. This structure can be generated from direct experimentation or can

be deduced from experimental structures through homology modeling

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Structure-based (target-based) design

(Krumrine et al., 2003)

* Homology modeling

Homology modeling:software

Modeller: http://salilab.org/modeller/tutorial/ DeepViewer: http://ca.expasy.org/spdbv/text/disclaim.htm What If: http://swift.cmbi.ru.nl/servers/html/index.html Discovery Studio/InsightII

Homology modeling:Web-Service

SWISS-MODEL: http://swissmodel.expasy.org/ What If: http://swift.cmbi.ru.nl/servers/html/index.html CPHmodels 2.0: http://www.cbs.dtu.dk/services/CPHmodels/ PredictProtein: http://www.predictprotein.org/

Quality Check of the protein structure

ProsaII ......... check protein energy Procheck ........ check protein geometric Whatcheck.. check protein geometric

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Structure-based (target-based) design

(Krumrine et al., 2003)

Dock known chemicals from an in silico database into the receptor target site (database searching or screening). Design of novel compounds to fit into receptor target site

(de novo design).

* Homology modeling

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Design MethodsDesign Methods

1.1. DockingDocking

2.2. Database searchingDatabase searching

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Docking is an energy-based operation for exploring the binding modes of two interaction molecules.

Give the 3D structure of a protein target, compuonds can be designed to fit in a cavity, which is called "docking".

The treatment ends when a minimum of energy is obtained for the complex.

Definition of Docking

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Docking Goal

1. To build the binding model between ligand and protein

2. To clarify the critical residues which involve in ligand binding

3. To engineer the protein by mutagenesis

4. To develop a drug from a compound database

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Docking Require

Ligand structure

Protein structure

Docking software

Ligand: XK-263

Protein: HIV-1 Protease (1hvr)

Software: AutoDock version 2.4

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Docking Flowchart

InputInput

OutputOutput

DockingDocking

LimitationLigand structureProtein structure

AutodockDockLudiGramm

Complex structure informationAnalysis ProSall, SWISS PDB ViewerEvaluation

For Input Data:

Protein must be high resolution!

B factors

NMR(Poorly constrained regions)

Ligand StructureChemical drawing

ChemOffice Discovery Studio/InsightII Sybyl ISIS Draw Alchemy2000 The Dundee PRODRG2 Server

Ligand Structure from database Protein Data Bank Zinc database Cambridge Structural Database CrossFire Database/Beilstein, Gmelin, EcoPharm MDL ISIS Database, (Chinese) CCDC/Relibase Protein-Ligand Structure Database National Cancer Institute SoP Computer-Aided Drug Design Center

Protein Structure

Download: Protein Data Bank: http://www.rcsb.org/pdb/home/home.do

Build the model by yourself!!

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Docking Flowchart

InputInput

OutputOutput

DockingDocking

LimitationLigand structureProtein structure

AutodockDockLudiGramm

Complex structure informationAnalysis ProSall, SWISS PDB ViewerEvaluation

ForcesReceptor and ligand flexibilitySolventBinding mode

Need to consider .

Docking Program Protein-Protein Docking

ZDOCK/RDOCK PatchDOCK DOCK GRAMM Molfit HADDOCK

Protein-Ligand Docking GOLD AutoDOCK DOCK GRAMM Molegro FlexX Discovery Studio

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Docking Flowchart

InputInput

OutputOutput

DockingDocking

LimitationLigand structureProtein structure

AutodockDockLudiGramm

Complex structure informationAnalysis ProSall, SWISS PDB ViewerEvaluation

For Output Data:

(active sites)

(Geometry)

(potential energy)

Docking Analyses

Molecular visualization Calculation of Binding Energies Score Function

Molecular Visualization

Molecular Visualization

Rasmol Chime SWISS PDB Viewer Discovery Studio/insightII Sybyl Molegro Pymol

MolMol Molscript GRASP Coot O Chimera

Protein Surface Map GRASP MS MSMS Naccess Surfnet Connolly Delphi Dms MolMol PyMol Swiss PDB Viewer Discovery Studio

Structural Alignment1. CE2. Discovery Studio/InsightII3. Swiss PDB Viewer4. MolMol5. Vector Alignment Search Tool (VAST)

Protein volume & cavity size

Voidoo GRASP SWISS PDB Viewer Volume+Access

Interaction - Ligplot

Binding Energy & Kd

MMTSB + charmm or amber SCORE DynFit Discovery Studio

Virtual screening

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2. Database searching 3D Database Searching

In practice the database approach provides an easy way to arrive at leads. It consists of a 3D computerized search of a database of synthesized or naturally occurring compounds and testing them in silico.

The result of this treatment is a list of compounds ranked by a score based on the overall match with the receptor.

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2. Database searching Databases of Molecules in 3D

Throughout the world there are thousands of chemical suppliers offering more than 3 million of organic molecules.

The advantage of using commercially available molecules in database searching is that they offer a great diversity and can be purchased and tested rapidly.

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Figure 2. (a) Binding conformations of docked

compounds at the active sites of CatK.

63Compound 38

Figure 3. (a) Plots of pIC50 versus ChemScore

energy for compounds from the training and the test sets.

(b) Proposed interaction model of inhibitor 38 in the active sites of CatK

Figure 3b represents the interaction model of the docked inhibitor 38with CatK, as generated withthe program Ligplot.

Figure 3b represents the interaction model of the docked inhibitor 38with CatK, as generated withthe program Ligplot.

Database Cambridge Structural Database CrossFire Database/Beilstein, Gmelin, EcoPharm MDL ISIS Database, (Chinese) CCDC/Relibase Protein-Ligand Structure Database National Cancer Institute SoP Computer-Aided Drug Design Center Zinc database

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Virtual Screening Program

DOCK AutoDOCK GOLD Discovery Studio Molegro FlexX

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Structure-based (target-based) design

(Krumrine et al., 2003)

Dock known chemicals from an in silico database into the receptor target site (database searching or screening). Design of novel compounds to fit into receptor target site

(de novo design).

* Homology modeling

De-Novo design

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3. De-Novo design Automated Construction Approaches

The purpose of construction programs is to discover a new chemical framework that fits to the active site of the target receptor or enzyme.

Some methods are based on an existing moiety and additional fragments are appended by a step-by-step build up procedure.

Other methods consist of assembling novel molecules from pieces that are positioned optimally in favorable regions of the active site.

Program

LigBuilder Ludi

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Bioinformatics Center, NTHU