chemoinformatics in drug design
DESCRIPTION
Chemoinformatics in Drug Design. Irene Kouskoumvekaki, Associate Professor, Computational Chemical Biology, CBS, DTU-Systems Biology. Biological Sequence Analysis, May 6, 2011. Computational Chemical Biology group. Tudor Oprea Guest Professor. Olivier Taboureau Associate Professor. - PowerPoint PPT PresentationTRANSCRIPT
Chemoinformatics in Drug Design
Biological Sequence Analysis, May 6, 2011
Irene Kouskoumvekaki,Associate Professor,Computational Chemical Biology,CBS, DTU-Systems Biology
2 CBS, Department of Systems Biology
Computational Chemical Biology group
Irene Kouskoumvekaki
Associate Professor
Olivier Taboureau
Associate Professor
Sonny Kim Nielsen
PhD student Kasper Jensen
PhD student
Tudor Oprea
Guest Professor
Ulrik Plesner
master student
5 CBS, Department of Systems Biology
Definition:Chemoinformatics
Gathering and systematic use of chemical information, and application of this information to predict the behavior of unknown compounds in silico.
data prediction
6 CBS, Department of Systems Biology
Definition:A drug candidate…
... is a (ligand) compound that binds to a biological target (protein, enzyme, receptor, ...) and in this way either initiates a process (agonist) or inhibits it (antagonist)
The structure/conformation of the ligand is complementary to the space defined by the protein’s active site
The binding is caused by favorable interactions between the ligand and the side chains of the amino acids in the active site. (electrostatic interactions, hydrogen bonds, hydrophobic contacts...)
7 CBS, Department of Systems Biology
In vitro / In silico studies
Drug Discovery
Clinical studies
Animal studies
9 CBS, Department of Systems Biology
The Drug Discovery Process
MKTAALAPLFFLPSALATTVYLA
GDSTMAKNGGGSGTNGWGEYL
ASYLSATVVNDAVAGRSAR…(etc)
We know the structure of the biological target
We identify/predict the binding pocket
Challenge:
To design an organic molecule that would bind strong enough to the biological target and modute it’s activity.
New drug candidate
10 CBS, Department of Systems Biology
What is it?Alzheimer's is a disease that causes failure of brain
functions and dementia. It starts with bad memory and disability to function in common everyday activities.
Example: – Alzheimer’s disease
How do you get it?Alzheimer's disease is the result of malfunctioning
neurons at different parts of the brain. This, in turn, is due to an inbalance in the concentration of neurotranmitters.
11 CBS, Department of Systems Biology
How can we treat it?
Example: – Alzheimer’s disease
Acetylkolin neurotransmitter
Drug against Alzheimer’s
12 CBS, Department of Systems Biology
Old School Drug discovery process
Screening collection
HTS
Actives
103 actives106 cmp.
Follow-up
Hits
1-10 hits
Lead series
0-3 lead series
Hit-to-lead
Clinical trials
Drug candidate
0-1
Lead-to-drug
High rate of false positives !!!
15 CBS, Department of Systems Biology
Drug discovery in the 21st Century
Diverse set of molecules tested in the lab
in vitro in silico + in vitro
Computational methods to select subsets (to be tested in the lab) based on prediction of drug-likeness, solubility, binding, pharmacokinetics, toxicity, side effects, ...
16 CBS, Department of Systems Biology
The Lipinski ‘rule of five’ for drug-likeness prediction
Octanol-water partition coefficient (logP) ≤ 5 Molecular weight ≤ 500 # hydrogen bond acceptors (HBA) ≤ 10 # hydrogen bond donors (HBD) ≤ 5
If two or more of these rules are violated, the compound might
have problems with oral bioavailability.(Lipinski et al., Adv. Drug Delivery Rev., 23, 1997, 3.)
18 CBS, Department of Systems Biology
Major Aspects of Chemoinformatics
•Information Acquisition and Management: Methods for collecting data (mainly experimental). Development of databases for storage and retrieval of information.
•Information Use: Data analysis, correlation and model building.
•Information Application: Prediction of molecular properties relevant to chemical and biochemical sciences.
19 CBS, Department of Systems Biology
Major Aspects of Chemoinformatics
•Information Acquisition and Management: Methods for collecting data (mainly experimental). Development of databases for storage and retrieval of information.
•Information Use: Data analysis, correlation and model building.
•Information Application: Prediction of molecular properties relevant to chemical and biochemical sciences.
22 CBS, Department of Systems Biology
0
2,000,000
4,000,000
6,000,000
8,000,000
10,000,000
12,000,000
14,000,000
16,000,000
18,000,000
20,000,000
May-05 Sep-05 Jan-06 May-06 Sep-06 Jan-07 May-07 Sep-07
Compound
Substance
Growth In PubChem Substances & Compounds
Recent count: Substance: 72,156,631 Compound: 28,807,320 Rule of 5: 20,692,980
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Structural representation of molecules
Structural representation of molecules
25 CBS, Department of Systems Biology
Major Aspects of Chemoinformatics
•Information Acquisition and Management: Methods for collecting data (mainly experimental). Development of databases for storage and retrieval of information.
•Information Use: Data analysis, correlation and model building.
•Information Application: Prediction of molecular properties relevant to chemical and biochemical sciences.
26 CBS, Department of Systems Biology
Beyond the Lipinski Rule of 5...
•Chemometrics: The application of mathematical or statistical methods to chemical data (simple, linear methods)e.g. Principal Component Analysis
•Machine Learning: The design and development of algorithms and techniques that allow computers to learn (complex, non-linear algorithms)e.g. Artificial Neural Networks, K-means clustering
27 CBS, Department of Systems Biology
Major Aspects of Chemoinformatics
•Information Acquisition and Management: Methods for collecting data (mainly experimental). Development of databases for storage and retrieval of information.
•Information Use: Data analysis, correlation and model building.
•Information Application: Prediction of molecular properties relevant to chemical and biochemical sciences.
28 CBS, Department of Systems Biology
Prediction of Solubility, ADME & Toxicity
Solid
drug
Dissolution
Solubility
Drug in
solution
Membrane
transfer
Absorption
Absorbed
drug
Liver extraction Systemic
circulation
Metabolism
32 CBS, Department of Systems Biology
Virtual Screening Flavors
1D1D filters
e.g. Lipinskis Rule of Five
LIGAND-BASED
TARGET-BASED
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Molecular similarity on the Chemical Space
• Similar Property Principle – Molecules having similar structures and properties are expected to exhibit similar biological activity. (Not always true!)
• Thus, molecules that are located closely together in the chemical space are often considered to be functionally related.
34 CBS, Department of Systems Biology
Ligand-based VS: Fingerprints
– widely used similarity search tool– consists of descriptors encoded as bit strings– Bit strings of query and database are compared using
similarity metric such as Tanimoto coefficient
MACCS fingerprints: 166 structural keys
that answer questions of the type:
• Is there a ring of size 4?
• Is at least one F, Br, Cl, or I present?
where the answer is either
TRUE (1) or FALSE (0)
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Structure-based Virtual Screening: Docking
Given a protein and a database of ligands, docking scores determine which ligands are most likely to bind.
Binding pocket of target Library of small compounds
39 CBS, Department of Systems Biology
Energy of binding
Binding pocket of target Library of small compounds
-10 kcal/mol
+1 kcal/mol
-1 kcal/mol
+10 kcal/mol
ΔG = ΔH - TΔS
vdW
Hbond
Desolvation E
Electrostatic E
Torsional free E
40 CBS, Department of Systems Biology
“Docking” and “Scoring”
•Docking involves the prediction of the binding mode of individual molecules
– Goal: new ligand orientation closest in geometry to the observed X-ray structure (Conformations of ligands in complexes often have very similar geometries to minimum-energy conformations of the isolated ligand)
•Scoring ranks the ligands using some function related to the free energy of association of the two partners, looking at attractive and repulsive regions and taking into account steric and hydrogen bonding interactions
– Goal: new ligand score closest in value to the docking score of the X-ray structure
41 CBS, Department of Systems Biology
Docking algorithms
•Most exhaustive algorithms:– Accurate prediction of a binding pose
•Most efficient algorithms– Docking of small ligand databases in reasonable time
•Rapid algorithms– Virtual high-throughput screening of millions of
compounds
42 CBS, Department of Systems Biology
Scoring functions
•Molecular mechanics force field-based
Score is estimated by summing the strength of intermolecular van der Waals and electrostatic interactions between all atoms of the ligand-target complex
-CHARMM, AMBER
•Empirical-based
Based on summing various types of interactions between the two binding partners (hydrogen bonds, hydrophobic, …)
- ChemScore, GlideScore, AutoDock
•Knowledge-based
Based on statistical observations of intermolecular close contacts from large 3D databases, which are used to derive potentials or mean forces
-PMF, DrugScore
43 CBS, Department of Systems Biology
Ligand-based VSgood enrichment of candidate
molecules from the screening of large databases with less computational efforts
×too coarse to pick up subtle differences induced by small structural variations in the ligands
many options for model refinement
Structure-based VSbetter fit for analyzing smaller
sets of compounds, especially in retrospective analysis
include all possible interactions thus allowing the detection of unexpected binding modes
×Changing parameters for docking algorithms and scores is demanding
Mutants are being developed:
• pharmacophore methods with information about the target’s binding site
• docking programs that incorporate pharmacophore constraints
Combination of pharmacophore, docking and molecular dynamics (MD) screens
45 CBS, Department of Systems Biology
Public Web Chemoinformatics Toolshttp://pasilla.health.unm.edu/
http://pasilla.health.unm.edu/
48 CBS, Department of Systems Biology D. Vidal et al, Ligand-based Approaches to In Silico Pharmacology, Chemoinformatics and Computational Chemical Biology, Ed J. Bajorath, Springer, 2011