Several methods are presently used to study SAR. 5- Structure-Activity Relationships (SAR). A structure-activity relationship (SAR) is a statement of the effect of structure change on biological activity within a congeneric series (a family) of compounds. Methods of Studying Structure-Activity Relationships. Both the affinity of a drug for its receptor and its intrinsic activity are determined by its chemical structure. Several methods are presently used to study SAR.

Structure Activity Relationships (SAR) AIM - Identify which functional groups are important for binding and/or activity METHOD Alter, remove or mask a functional group Test the analogue for activity Conclusions depend on the method of testing in vitro - tests for binding interactions with target in vivo - tests for target binding interactions and/or pharmacokinetics If in vitro activity drops, it implies group is important for binding If in vivo activity unaffected, it implies group is not important

NOTES ON ANALOGUES Modifications may disrupt binding by electronic / steric effects Easiest analogues to make are those made from lead compound Possible modifications may depend on other groups present Some analogues may have to be made by a full synthesis (e.g. replacing an aromatic ring with a cyclohexane ring) Allows identification of important groups involved in binding Allows identification of the pharmacophore

6. Identification of the active part: Only a small part of the lead compound may be involved in the appropriate receptor interactions. The relevant groups on a molecule that interact with a receptor and are responsible for the activity are collectively known as the pharmacophore. The other atoms in the lead molecule, referred to as auxophore.

PHARMACOPHORE Defines the important groups involved in binding Defines the relative positions of the binding groups Need to know Active Conformation Important to Drug Design Important to Drug Discovery

Auxophore There are three types of auxophore: Essential to maintain the integrity of the molecule and hold the pharmacophoric groups in their appropriate positions. Interfere with the binding of the pharmacophore to the receptor and need to be removed from the lead compound

Some atoms of the auxophore may be dangling in the space within the receptor and are neither binding to the receptor nor preventing the pharmacophoric atoms from binding. [these atoms can be modified without loss of potency]. Also it can be modified to solve pharmacokinetic problems [absorption, distribution, metabolism, and excretion]

Pharmacophoric descriptors are including : Pharmacophore It is that portion of the molecule containing the essential organic functional groups that directly interact with the receptor active site and therefore confers upon the molecule the biologic activity of interest. Pharmacophoric descriptors are including :  H-bond sites Hydrophobic and electrostatic interaction sites Ring centers and virtual points  Distances, 3D relationship

Sulphonamides pharmacophore sulfanilamide sulfamethoxazole sulfadiazine sulfisoxazole Sulphonamides p-aminobenzoic acid pharmacophore

Quinolones & fluoroquinolones ciprofloxacin ofloxacin moxifloxacin nalidixic acid

L = lipophilic site; A = H-bond acceptor; Pharmacophore Dopamine L = lipophilic site; A = H-bond acceptor; D = H-bond donor; PD = protonated H-bond donor

Identification of the active part ( Pharmacophore) Simplification of the original lead compound is especially appropriate for polycyclic natural substances. In this process, systemic synthesis and evaluation of simpler analogues of the lead molecule is performed. Simplification of cocaine molecule led to introduction of many local anaesthetic drugs and discovery of benzoic acid ester moiety as a pharmacophore for such activity. The main result of this methodology is the identification of the pharmacophore group.

6.1 Structural (2D) Pharmacophore Defines minimum skeleton connecting important binding groups HO O NMe HO

HO O MORPHINE NMe MOR025.WAV HO

HO O MORPHINE NMe HO IMPORTANT GROUPS FOR ANALGESIC ACTIVITY MOR025.WAV HO

ANALGESIC PHARMACOPHORE FOR OPIATES MOR025.WAV

HO HO O H3C NMe NMe CH3 METAZOCINE MORPHINE HO NMe LEVORPHANOL MOR025.WAV NMe LEVORPHANOL

HO HO O H3C NMe NMe CH3 HO METAZOCINE MORPHINE HO NMe LEVORPHANOL MOR025.WAV NMe LEVORPHANOL

6.2 3D Pharmacophore Defines relative positions in space of important binding groups Example

O NMe HO MOR028.WAV

MOR028.WAV

O N Ar MOR028.WAV

O N Ar 11.3o 150o 18.5o 7.098 A 2.798 A 4.534 A MOR028.WAV

6.3 The Active Conformation Need to identify the active conformation in order to identify the 3D pharmacophore Conformational analysis - identifies possible conformations and their activities Conformational analysis is difficult for simple flexible molecules with large numbers of conformations Compare activity of rigid analogues Locked bonds

6.4 Pharmacophores from Target Binding Sites 2 A S P SER PHE Binding site H-bond donor or acceptor aromatic center basic or positive H-bond donor or acceptor basic or positive center Pharmacophore aromatic center

QSAR is mathematical relationships linking chemical structure and pharmacological activity in a quantitative manner for a series of compounds. Methods which can be used in QSAR include various regression and pattern recognition techniques.

Adrenergic blocking activity of b-halo-b-arylamines Examples: Adrenergic blocking activity of b-halo-b-arylamines Log 1 C æ è ö ø = 1.22 p - 1.59 s + 7.89 Conclusions: Activity increases if p is + (i.e. hydrophobic substituents) Activity increases if s is negative (i.e. e-donating substituents)

7. DRUG DESIGN - OPTIMISING BINDING INTERACTIONS AIM - To optimise binding interactions with target REASONS To increase activity and reduce dose levels To increase selectivity and reduce side effects STRATEGIES The approaches for molecular modification can be classified as: I. General approach II. Special approach

I. General approach 1- Molecular disjunction (molecular dissociation, dissection or simplification)

2- Molecular conjunctive approaches Association of two or more molecules to give more complex analogues of the lead molecules with improved pharmacokinetic and pharmacodynamic properties represents typical process of conjunctive strategy. Molecular association processes comprise :- Molecular addition Molecular replication Molecular hybridization

a. Molecular addition Molecular addition involves association of different molecules through weak forces such electrostatic attraction or hydrogen bonding. e.g. Electrostatic attraction in the urinary antiseptic methenamine mandelate.

b. Molecular replication Molecular replication involves association of identical molecules through covalent bond formation (identical twin drug).

c. Molecular hybridization Molecular hybridization involves association of two different molecules through covalent bond formation ( non identical twin drug).

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II. Special approach 1. Variation of alkyl substituents. 2. Extention of the structure. 3. Ring closure or ring opening 4. Ring expansion and ring contraction 5. Homologation and chain branching 6. Introduction of unsaturation center 7. Introduction, removal or replacement of bulky groups 8. Introduction of chiral center 9. Conformation restriction (molecular rigidification) 10. Isosteres and bioisosteres

1 . Vary Alkyl Substituents Rationale : Alkyl group in lead compound may interact with hydrophobic region in binding site Vary length and bulk of group to optimise interaction

1. Vary Alkyl Substituents Rationale : Vary length and bulk of alkyl group to introduce selectivity Binding region for N Receptor 1 Receptor 2

1 . Vary Alkyl Substituents Rationale: Vary length and bulk of alkyl group to introduce selectivity Example: Selectivity of adrenergic agonists and antagonists for b-adrenoceptors over a-adrenoceptors

1. Vary Alkyl Substituents Adrenaline Salbutamol (Ventolin) (Anti-asthmatic) Propranolol (b-Blocker)

a-Adrenoceptor H-Bonding region Ionic bonding Van der Waals

a-Adrenoceptor ADRENALINE

a-Adrenoceptor

b-Adrenoceptor ADRENALINE

b-Adrenoceptor SALBUTAMOL

b-Adrenoceptor

a-Adrenoceptor SALBUTAMOL

a-Adrenoceptor SALBUTAMOL

a-Adrenoceptor SALBUTAMOL

a-Adrenoceptor SALBUTAMOL

a-Adrenoceptor SALBUTAMOL

a-Adrenoceptor SALBUTAMOL

a-Adrenoceptor SALBUTAMOL

a-Adrenoceptor

1. Vary Alkyl Substituents Notes on synthetic feasibility of analogues Feasible to remove alkyl substituents on heteroatoms and replace with other alkyl substituents Difficult to modify alkyl substituents on the carbon skeleton of a lead compound. Full synthesis is usually required

2. Vary Aryl Substituents Vary substituents Vary substitution pattern Weak H-Bond Binding Region (H-Bond) (for Y) Strong H-Bond (increased activity)

2. Vary Aryl Substituents Vary substitution pattern to enhance binding interactions Benzopyrans Anti-arrhythmic activity best when substituent is at 7-position

2. Vary Aryl Substituents Vary substitution pattern to enhance binding strength indirectly - electronic effects Binding strength of NH2 as HBD affected by relative position of NO2 Stronger when NO2 is at para position

3. Extension - Extra Functional Groups Rationale : To explore target binding site for further binding regions to achieve additional binding interactions RECEPTOR RECEPTOR Extra functional group Unused binding region DRUG DRUG Drug Extension Binding regions Binding group

3. Extension - Extra Functional Groups Example : ACE Inhibitors Hydrophobic pocket Vacant EXTENSION Hydrophobic pocket Binding site Binding site

Extension - extra functional groups Example: Second-generation anti-impotence drugs Viagra Notes: Extension - addition of pyridine ring Increased target selectivity

Chain Extension / Contraction Rationale : Useful if a chain is present connecting two binding groups Vary length of chain to optimise interactions Weak interaction Strong interaction A B Chain extension A B RECEPTOR RECEPTOR Binding regions Binding groups A & B

Chain Extension / Contraction Example : N-Phenethylmorphine Binding group Optimum chain length = 2

4- Homologation A homologous series is a group of compounds that differ by a constant unit, generally a CH2 group

e.g., alkyltrimethylammonium analogs possess different types of activity depending on the length of alkyl group: n= 5 muscarinic agonists n= 6 or 7 partial agonists n= 8 or more muscarinic antagonists. A homologous series is a series of analogs that differ in structure by simple increment in molecular formula. These may produced by sequential chemical changes which includes increasing or decreasing the length of a carbon chain.

5. Ring Expansion / Contraction Rationale : To improve overlap of binding groups with their binding regions R Ring expansion R Hydrophobic regions

5. Ring Expansion / Contraction Vary n to vary ring size Example Binding regions Binding site Binding site

Ring Enlargement and Ring Contraction:

6 . Ring Variations Rationale : Replace aromatic/heterocyclic rings with other ring systems Often done for patent reasons General structure for NSAIDS Core scaffold

6 . Ring Variations Rationale : Example : Sometimes results in improved properties Example : Ring variation Antifungal agent Improved selectivity vs. fungal enzyme

6. Ring Variations Example - Nevirapine (antiviral agent) Additional binding group

7-Introduction, removal or replacement of bulky groups This special process is used mainly to: Convert agonist to antagonist or Prevent the enzymatic degradation This process is mainly used to convert agonist to antagonist and vice versa. Acetyl choline can cause muscle contraction Propantheline cause muscle relaxation Isopreterenol is non selective beta agonist used to treat bradycardia Prpranolol is non selective beta antagonist used to treat hypertension

Example for preventing enzymatic degradation; β-lactamase resistant penicillins Bulky group introduced near the ring prevent enzymatic degradation by ….. Methicillin

Introduction, Removal, or Replacement of Bulky groups:

8. Ring Closure and Opening :

9- Introduction of chiral centers Receptors are chiral entities and the interactions of many drugs at specific sites are chirality type of interaction. E.g. The simple addition of α-methyl group to give ACE inhibitor captopril increased by 10-folds over the des-methyl compound.