Ping-Chiang Lyu. Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University.

Transcription

1 Pharmacophore-based Drug design Ping-Chiang Lyu Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University 96/08/07 Outline Part I: Analysis The analytical process and underlying principles of the pharmacophore-based drug design approach Part II: Design There are four methods for designing new molecules in a pharmacophore-based drug design approach. Part III: Examples 2 1

2 Part I: Analysis 1. Introduction 2. Analytical Process 3. Principles of Analysis 4. Managing Hypotheses 3 1. Introduction Pharmacophore-Based Drug Design Pharmacophore based drug design allows the creation of new lead molecules based on already known biologically active molecules. 4 2

3 1. Introduction Operational 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? 5 Analogy with Keys 1. Introduction 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 6 3

4 1. Introduction Active 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 Introduction 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. 8 4

5 2. Analytical Process Includes the following three steps: 1. Data Collection Gathering all relevant information 2. Analysis In depth analyses of the information 3. Design The design of new molecules based on the analysis 9 2. Analytical Process Example: Two following compounds showed good biological activities in a given project 10 5

6 2. Analytical Process Identification of the Bioactive Conformation The conformational analysis of the two molecules show that they have 972 and 648 preferred conformers respectively. The question is which one of these conformers is the bioactive form Analytical Process Bioactive 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. 12 6

7 2. Analytical Process Bioactive Conformation: Energy The difference of energy between the bioactive conformation of a molecule and the global minimum conformation of the isolated molecule is generally less than 12 kj/mol (3 kcal/mol) Analytical Process Reduction 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. 14 7

8 2. Analytical Process Bioactive 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 hypothesize that their bioactive conformations must share common 3D features Analytical Process Systematic 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. 16 8

9 2. Analytical Process Results 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. 17 In Summary 2. Analytical Process 18 9

10 3. Principles of Analysis Six 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 Principles of Analysis Rule 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

11 3. Principles of Analysis Rule 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 Principles of Analysis Rule 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

12 3. Principles of Analysis Rule 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 Principles of Analysis Rule 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

13 3. Principles of Analysis Rule 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 Managing Hypotheses Tracking & Reconsidering Hypotheses Incorrect Hypotheses: be careful Too 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 26 13

14 Part II: Design The Four Design Methods 1. Chemical modification 2. Database searching 3. De-Novo design 4. Manual design Chemical modification Bioisosteric Replacements Molecules that are designed by bioisosteric replacements are expected to have similar biological properties

15 Rigid Analogs 1. Chemical modification Dopamine has two trans rotameric forms that can be incorporated in different structurally constrained systems Chemical modification Alteration of Ring Size The central seven membered 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

16 1. Chemical modification Ring 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 Chemical modification Homologation of Alkyl Chains The hydrogen atom connected to the nitrogen of apomorphine was 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

17 1. Chemical modification Alteration of Stereochemistry Retroprogesterone is an example of a synthetic analog that is more active than the natural progesterone Database searching 3D Database Searching 3D database searching enables one to identify existing molecules that match a pharmacophore hypothesis. Pharmacophore Query 34 17

18 2. Database searching 3D 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 De-Novo design Algorithm Based Approaches 36 18

19 3. De-Novo design Example Manual design Importance 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

20 4. Manual design Design 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 Part III: Examples 1. ACE Inhibitors The angiotensin-converting enzyme (ACE) plays a central role in the control of blood pressure through various effects of angiotensin II, which is a potent pressor peptide. 2. Serotonin Antagonists It is suggested that antagonists at the serotonin receptor would have desirable therapeutic potential as anxiolytic agents

21 1. ACE Inhibitors Therapeutic Utility of ACE Inhibitors ACE inhibitors have the potential to specifically block the formation of angiotensin II and thus reduce high blood pressure. 41 The ACE Enzyme 1. ACE Inhibitors ACE is a carboxypeptidase enzyme that catalyzes the cleavage of two amino acids from the C-terminal of the Angiotensin I substrate, generating the octapeptide Angiotensin II. Its active site contains a Zinc atom. ACE inhibitors are useful antihypertensive agents

22 1. ACE Inhibitors Discovery of the First ACE Inhibitor Captopril is the first ACE-inhibitor that was discovered. Based on the structure of captopril, new analogs were designed ACE Inhibitors Pharmacophore 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)

23 1. ACE Inhibitors Design 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 Serotonin Antagonists Conformational study of Serotonin Antagonists Conformational study and superimposition of 4 serotonin receptor ligands (R-methiothepin, spiperone, S-propranolol and buspirone) reveal that they share a common pharmacophore

24 2. Serotonin Antagonists Superimposition of Serotonin Receptor Antagonists Superimposition of the amino and aromatic moieties of methiothepin, propranolol, spiperone and buspirone. pharmacophore Serotonin Antagonists Pharmacophore for Serotonin Antagonists The minimum pharmacophoric elements of serotonin ligand receptors consist of a phenyl ring and a nitrogen atom

25 2. Serotonin Antagonists The Design of MDL The pharmacophore model was used to design new serotonin receptor ligands. MDL is an example of a designed compound, which showed a nanomolar affinity for the serotonin receptor in vivo. 49 謝謝! 清華大學生物資訊中心 Bioinformatics Center, NTHU 50 25