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PharmacophorePharmacophore--based Drug designbased Drug design

Ping-Chiang Lyu

Institute of Bioinformatics and Structural Biology,Institute of Bioinformatics and Structural Biology,Department of Life Science,Department of Life Science,

National National TsingTsing HuaHua University University

96/08/07

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Outline

Part I: AnalysisThe analytical process and underlying principles of the pharmacophore-based drug design approach

Part II: DesignThere are four methods for designing new molecules in a pharmacophore-based drug design approach.

Part III: Examples

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Part I: Part I: AnalysisAnalysis

1.1. IntroductionIntroduction

2.2. Analytical ProcessAnalytical Process

3.3. Principles of AnalysisPrinciples of Analysis

4.4. Managing HypothesesManaging Hypotheses

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1. IntroductionPharmacophore-Based Drug Design

Pharmacophore based drug design allows the creation of new lead molecules based on already known biologically active molecules.

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1. IntroductionOperational Strategy: Molecular Mimicry

This approach consists of mimicking the structural features of a reference compound. The central question is which elements should be

mimicked in order to obtain biologically active molecules? Should all the elements be mimicked or only a part of

the reference compound?

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1. IntroductionAnalogy with Keys

Similar to a key that activates a mechanical lock, some of the elements of a biologically active molecule are essential while others are not.

Handle Teeth

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1. IntroductionActive Molecules are Complicated Keys

The following example shows a molecule with a "handle" containing two essential functional groups (carbonyl and N-H) as well as an element of the "teeth" (phenyl group) that is not essential. The pharmacophore is defined by all the structural

elements that are essential for the specified biological activity.

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1. IntroductionDefinition 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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2. Analytical ProcessIncludes the following three steps:

1. Data Collection

2. Analysis

3. Design

Gathering all relevant information

In depth analyses of the information

The design of new molecules based on the analysis

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2. Analytical ProcessExample:Two following compounds showed good biological activities in a given project

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2. Analytical ProcessIdentification of the Bioactive Conformation

The conformational analysis of the two molecules show that they have 972 and 648 preferred conformersrespectively.

The question is which one of these conformers is the bioactive form.

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2. Analytical ProcessBioactive Conformation: Geometry

The example shown here illustrates the case of methotrexate where the conformation of the free molecule is shown in red, and in blue when the molecule is bound to its biological target.

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2. Analytical ProcessBioactive Conformation: Energy

The difference of energy between the bioactiveconformation of a molecule and the global minimumconformation of the isolated molecule is generallyless than 12 kJ/mol (3 kcal/mol).

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2. Analytical ProcessReduction of the Complexity

This observation allows us to filter and reject a great number of conformations that cannot represent the bioactive geometry. At this stage the

number of conformations is greatly reduced.

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2. Analytical ProcessBioactive Conformations Must be Superimposable

After having eliminated high energy conformers, we can now consider to identify in the remaining set of low energy conformations, the probable bioactive geometry of our molecules.

Both compounds bind to the same active site of the biological receptor, we can hypothesizethat their bioactive conformations must share common 3D features.

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2. Analytical ProcessSystematic Superimposition of Conformers

To identify the probable bioactive conformations of the two molecules, all pairs of conformers are superimposed.

The conformers that are present in this superimposition are the probable bioactive conformations of the two molecules.

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2. Analytical ProcessResults with High Informational Content

The superimposition of the molecules reveals the common structural moieties and differences, information of central importance for further design of new lead compounds.

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2. Analytical ProcessIn Summary

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3. Principles of AnalysisSix Rules for Analyses

Common Structural Features: Rule 1

Multiple Hypotheses: Rule 2

Inactive Molecules: Rule 3

Closely Related Molecules: Rule 4

Molecules With No Common Features: Rule 5

Mapping the Receptor: Rule 6

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3. Principles of AnalysisRule 1- Common Structural Features

Initial Data:We have two biologically active molecules with the same mechanism of action.

Hypothesis:We can identify common structural features and assume that they are all essential for the biological activities.

Rule: By comparing active 'keys', we can figure out how the 'lock' functions.

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3. Principles of AnalysisRule 2- Multiple Hypotheses

Initial Data:We have two biologically active molecules with the same mechanism of action.

Hypothesis:We can identify common structural features but we are not sure if they are all indispensable for the biological activities.

Rule: One has to consider in parallel several working hypotheses.

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3. Principles of AnalysisRule 3- Inactive Molecules

Initial Data:We have two active and two inactive compounds.

Hypothesis:We deduce that several elements need to be present simultaneously in order to have activities.

Rule: The more different keys, the more refined the working hypothesis will be.

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3. Principles of AnalysisRule 4- Closely Related Molecules

Initial Data:We have two active molecules whose chemical structures are very closely related.

Hypothesis:Closely related analogs allow no constructive deduction to be made. The available data is of poor informational content.

Rule: Biologically active analog molecules often result in redundant information.

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3. Principles of AnalysisRule 5- Molecules With No Common Features

Initial Data:We have two active molecules but their chemical structures are not related chemically.

Hypothesis:No link can be found between their structures. As such, this information cannot be utilized.

Rule: Active molecules with no common similarities cannot be utilized for original design.

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3. Principles of AnalysisRule 6- Mapping the Receptor

Initial Data:We have two closely related molecules, one is active and the other is inactive.

Hypothesis:The inactive molecule has an additional volume that is not occupied by the active one. The inactivity is due to this extra-volume that is not accepted by the receptor site. When they have active analogs, inactive molecules bring useful information.

Rule: When an extra-volume introduced in the structure of an active molecule results in a loss of activity, this can be interpreted as a steric bump with the active site.

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4. Managing Hypotheses

Tracking & Reconsidering HypothesesIncorrect Hypotheses: be carefulToo Many Hypotheses

When one has too many hypotheses and all the hypotheses are of the same importance, it is impossible to consider all of them simultaneously.

Validating Hypotheses by Chemical Syntheses

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Part II: Part II: DesignDesign

The Four Design Methods

1.1. Chemical modificationChemical modification

2.2. Database searchingDatabase searching

3.3. DeDe--Novo designNovo design

4.4. Manual designManual design

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1. Chemical modificationBioisosteric Replacements

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

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1. Chemical modificationRigid Analogs

Dopamine has two trans rotameric forms that can be incorporated in different structurally constrained systems.

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1. Chemical modificationAlteration of Ring Size

The central sevenmembered ring was modified to six membered ring structures.

Imipramine is a tricyclic antidepressant drug. Dimetacrine has a central six-membered ring, and this drug has

an antidepressant action comparable to that of imipramine.

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1. Chemical modificationRing Suppression

The structure of doxepin has been used as a starting point for the design of non-polycyclic analogs. By cuting one of the bonds in this structure results in a

doxepin-like analog that has one ring less.

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1. Chemical modificationHomologation of Alkyl Chains

The hydrogen atom connected to the nitrogen of apomorphinewas replaced by methyl, ethyl, n-propyl and n-butyl groups. The best activity was found for the n-propyl analog, whereas

the n-butyl demonstrated a great loss in potency.

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1. Chemical modificationAlteration of Stereochemistry

Retroprogesterone is an example of a synthetic analog that is more active than the natural progesterone.

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2. Database searching3D Database Searching

3D database searching enables one to identify existing moleculesthat match a pharmacophore hypothesis.

Pharmacophore Query

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2. Database searching3D Database Searching

Shape complementarity is a very important consideration in drug-receptor interactions, it is useful to search a 3D database for similar 3D shapes with a reference molecule.

Shape Query

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3. De-Novo designAlgorithm Based Approaches

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3. De-Novo designExample

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4. Manual designImportance of the Visualization

In manual design the visualization is of central importance.It is important to see in a condensed way the molecular

objects. This stimulates the creativity for considering other solutions and checking if the solutions designed fit with the specified constraints.

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4. Manual designDesign of a Spacer: a Step-by-Step Process

The three structural moieties displayed here: phenyl, carboxyl and amino represent a pharmacophore. Assembling them in 3D into a single molecule ...

1.

2. 3.

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Part III: Part III: ExamplesExamples

1.1. ACE InhibitorsACE InhibitorsThe angiotensin-converting enzyme (ACE) plays a

central role in the control of blood pressurethrough various effects of angiotensin II, which is a potent pressor peptide.

2.2. Serotonin Antagonists Serotonin Antagonists It is suggested that antagonists at the serotonin

receptor would have desirable therapeutic potential as anxiolytic agents.

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1. ACE InhibitorsTherapeutic Utility of ACE Inhibitors

ACE inhibitors have the potential to specifically block the formation of angiotensin II and thus reduce high blood pressure.

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1. ACE InhibitorsThe ACE Enzyme

ACE is a carboxypeptidase enzyme that catalyzes the cleavage of two amino acids from the C-terminal of the Angiotensin I substrate, generating the octapeptideAngiotensin II. Its active site contains a Zinc atom. ACE inhibitors are useful antihypertensive agents.

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1. ACE InhibitorsDiscovery of the First ACE Inhibitor

Captopril is the first ACE-inhibitor that was discovered.

Based on the structure of captopril, new analogs were designed.

Based on the structure of captopril, new analogs were designed.

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1. ACE InhibitorsPharmacophore for ACE Inhibition

The three basic structural requirements essential for ACE inhibition are: a terminal carboxylate group, a carbonyl group involved in hydrogen bonding, and a moiety such as a SH group, that can bind to a Zinc atom (of the enzyme).

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1. ACE InhibitorsDesign of New ACE Inhibitors

Compounds such as the indoline and the tetrahydropyridazine derivatives displayed below are examples of molecules with antihypertensive activities that are more potent than captopril.

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2. Serotonin AntagonistsConformational study of Serotonin Antagonists

Conformational study and superimposition of 4 serotonin receptor ligands (R-methiothepin, spiperone, S-propranololand buspirone) reveal that they share a common pharmacophore.

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2. Serotonin AntagonistsSuperimposition of Serotonin Receptor Antagonists

Superimposition of the amino and aromatic moieties of methiothepin, propranolol, spiperone and buspirone.

pharmacophore

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2. Serotonin AntagonistsPharmacophore for Serotonin Antagonists

The minimum pharmacophoric elements of serotonin ligandreceptors consist of a phenyl ring and a nitrogen atom.

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2. Serotonin AntagonistsThe Design of MDL 72832

The pharmacophore model was used to design new serotonin receptor ligands. MDL 72832 is an example of a designed compound, which showed a nanomolar affinity for the serotonin receptor in vivo.

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謝謝!

清華大學生物資訊中心 Bioinformatics Center, NTHU