Transcript 311-3` Copyx

10. Rigidification
Rationale :
• Endogenous lead compounds often simple and flexible
(e.g.
adrenaline)
•
Fit several targets due to different active conformations
(e.g. adrenergic receptor types and subtypes)
single bond
rotation
+
+
Flexible
chain
•
Different conformations
Rigidify molecule to limit conformations - conformational
restraint
• Increases activity (more chance of desired active conformation)
• Increases selectivity (less chance of undesired active
conformations)
Disadvantage:
• Molecule more complex and may be more difficult
to synthesise
10. Rigidification
Methods - Introduce rings
Bonds within ring systems are locked and cannot rotate freely
X
NHMe
Introducing
rings
H
N
X
NHMe
Me
N
X
CH3
X
X
X
NHMe
NMe
Test rigid structures to see which ones have retained active
conformation
10. Rigidification
Examples - Combretastatin (anticancer agent)
Rotatable
bond
OCH3
OH
Z-isomer
H3CO
H3CO
H3CO
OH
E-isomer
H3CO
OCH3
OH
OCH3
Combretastatin A-4
More active
Less active
H3CO
H3CO
OCH3
OCH3
OH
OCH3
Combretastatin
10. Rigidification
Methods - Steric Blockers
X
Introduce
steric block
Y
X
Y
X
Y
CH3
steric block
Flexible side chain
Y
X
CH3
Introduce
steric block
Y
X
H
CH3
Coplanarity allowed
Unfavourable conformation
Y
X
steric
clash
Steric
clash
CH3
Orthogonal rings
preferred
11. Isosteres and Bio-isosteres
Rationale (isosteres) :
•
Replace a functional group with a group of same valency
(isostere) e.g.
OH replaced by SH, NH2, CH3
O replaced by S, NH, CH2
•
Leads to more controlled changes in steric/electronic properties
•
May affect binding and / or stability
a-Classical Isosteres, they are divided into five classes as
illustrated in the following table:
Class 1
(monovalent)
F,Cl,Br,I
OH,SH
NH2, PH2
CH3
2
(divalent)
3
(trivalent)
4
(tetravalent)
5
(rings)
-O-S-Se-Te-
-N=
-P=
-As=
-Sb=
-CH=
=C=
=Si=
=N+=
=P=
=As=
=Sb+=
-CH=CH
-S-O-NH-
Grimm's Hydride Displacement Law
It is an early hypothesis to describe bioisosterism, the ability of certain
chemical groups to function as or mimic other chemical groups.
According to Grimm, each vertical column (of Table below) would represent a
group of isosteres.
Table 1: Grimm's Hydride Displacement Law
C
N
O
F
Ne
Na
CH
NH
OH
FH
-
CH2
NH2
OH2
FH2+
CH3
NH3
OH3+
CH4
NH4+
Examples
• 1) Classical Isosteres:
- Replacement of univalent atoms and groups
Replacement of CH3 group of the oral hypoglycemic tolbutamide,
by its monovalent isostere Cl in chloropropamide increases the
duration of action.
Interchange of divalent atoms or groups
• The replacement of -O- of procaine by -NH- in
procainamide leads to prolong antiarrhythmic action
due to the considerable stability of the amide
function over the ester function.
Introduction of trivalent atoms or groups
• Aminopyrine and its isostere are about equally active
as antipyretics.
Ring equivalents
N
H
O
S
b- Nonclassical Isosteres, they are also known and include paired
examples such as H and F,
-CO2H and –SO3H, and –CO- and –SO2-.
Some of the examples of isosteric replacement that have provided
useful drugs are include:
O
H
O
NH
N
O
H
Uracil
F
OH
NH
N
O
H
5-FU
H2N
CO2H
PABA
SH
N
N
N
N
H
N
Hypoxanthine
H2N
N
N
SO 2NH2
Sulfanilamid
N
H
6-MP
Isosterism and Bioisosterism is a lead modification
approach that has been shown to be useful to :
• Attenuate Toxicity
• Modify the activity of a lead
• May have a significant role in the alteration of metabolism of
the lead
11. Isosteres and Bio-isosteres
Useful for SAR
Me
O
NH
Me
H
OH
Propranolol (b-blocker)
•
•
•
Replacing OCH2 with CH=CH, SCH2, CH2CH2
eliminates activity
Replacing OCH2 with NHCH2 retains activity
Implies O involved in binding (HBA)
Structure based drug design (SBDD)
Strategy
Carry out drug design based on the interactions between the lead
compound and the target binding site
Procedure
• Crystallise target protein with bound ligand
(e.g. enzyme + inhibitor or ligand)
• Acquire structure by X-ray crystallography
• Identify binding site (region where ligand is bound)
• Identify binding interactions between ligand and target
(modelling)
• Identify vacant regions for extra binding interactions
(modelling)
• ‘Fit’ analogues into binding site to test binding capability
(modelling)
Structure based drug design
Design of Antihypertensives - ACE inhibitors
Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-His-Leu
Angiotensin I
•
•
•
•
•
ACE
Asp-Arg-Val-Tyr-Il e-His-Pro-Phe
+
His-Leu
Angiotensin II
ACE = Angiotensin converting enzyme
Angiotensin II
- hormone which stimulates constriction of blood vessels
- causes rise in blood pressure
ACE inhibitors - useful antihypertensive agents
ACE - membrane bound zinc metalloproteinase not easily
crystallised
Study analogous enzyme which can be crystallised
Structure based drug design
Carboxypeptidase
Peptide
3
2
1
-aa -aa -aa
Carboxypeptidase
CO2H
Inhibition
OH
OH
O
O
L-Benzylsuccinic acid
Peptide
-aa3-aa2
CO2H
+
aa1
Structure based drug design
Carboxypeptidase mechanism
S1' pocket
S1' pocket
Zn2+
Zn2+
O
O
O
R
Natural Substrate
O
H 2N
N
H
R
O
O
O
Hydrolysis
NH2
H2N
NH2
H2N
145
145
Structure based drug design
Inhibition of carboxypeptidase
S1' pocket
Zn2+
O
O
No hydrolysis
O
L-benzylsuccinic acid
O
NH2
H2N
145
Structure based drug design
Lead compounds for ACE inhibitor
OH
Glu-Trp-Pro-Arg-Pro-Gl n-Il e-Pro-Pro
OH
O
O
Teprotide
L-Benzylsuccinic acid
O
N
HO
O
CO2H
Succinyl proline
Structure based drug design
Proposed binding mode
S1 pocket
S1' pocket
O
Succinyl proline
N
O
O
CO2
H 2N
H 2N
Zn 2+
Structure based drug design
Extension and bio-isostere strategies
OH
OH
CH3
CH3
N
N
O
HS
N
O
O
CO2H
CO2H
O
O
Captopril
S1 pocket
S1' pocket
CH3
N
HS
O
CO2
H 2N
H 2N
Zn 2+
CO2H
Structure based drug design
Extension strategies
CH3
O
N
NH
O
O
O
CO2H
N
N
H
O
O
CH3
O
CO2H
O
S1' pocket
CH3
Inhibitor
O
N
N
H
O
CO2
H 2N
H 2N
Zn 2+
N
O
Enalaprilate
S1 pocket
O
N
H
CO2H
Computer-Assisted Drug Design (CADD)
In practice molecular modeling uses two approaches:
1. Direct design of active substances which can be envisaged when
the 3D structure of the target molecule is known. In this case the
macromolecule can be built with the aid of computer then the fit of
the host molecule with its receptor can be optimized. The structure
of the ligand, its substituents and confirmation can be modified and
the most favorable conditions for interaction (docking) can be
simulated on the screen.
gDock: Web Docking Tool
Sketch Structure
Docked Structure
2. Indirect design of active substances, on the other hand, constitutes
the only possible approach when the 3D structure of the target
molecule is unknown. In this situation comparison of a set of ligands
selective for a given receptor is undertaken in order to reveal the
molecular information that the compounds have in common despite
apparently different chemical formula.
6.7
4.2-4.7
4.8
5.2
5.1-7.1
8. Pharmacokinetics – drug design
Aims
•
To improve pharmacokinetic properties of lead compound
•
To optimise chemical and metabolic stability
(stomach acids / digestive enzymes / metabolic enzymes)
•
To optimise hydrophilic / hydrophobic balance
(solubility in blood / solubility in GIT / solubility through
cell membranes / access to CNS / excretion rate)
8. Pharmacokinetics – drug design
•
Drugs must be polar - to be soluble in aqueous conditions
- to interact with molecular targets
•
Drugs must be ‘lipophilic’ - to cross cell membranes
- to avoid rapid excretion
•
Drugs must have both hydrophilic and lipophilic
characteristics
•
Many drugs are weak bases with pKa’s 6-8
+H
N
H
N
H
H
-H
Crosses
membranes
Receptor interaction
& water solubility
8.1 Drug stability
8.1.1 Metabolic blockers
Rationale:
• Metabolism of drugs usually occurs at specific sites. Introduce
groups at a susceptible site to block the reaction
• Increases metabolic stability and drug lifetime
Me
O
C
Me
Me
O
Me
O
C
Me
O
Me
O
6
Me
H
Megestrol
Acetate
Oral contraceptive
- limited lifetime
C
H
H
O
H
6
Me
Metabolic
Oxidation
O
O
H
H
Me
C
Metabolism
Blocked
8.1.2 Remove / replace susceptible metabolic groups
Rationale:
• Metabolism of drugs usually occurs at specific groups.
• Remove susceptible group or replace it with metabolically
stable group [e.g. modification of tolbutamide (oral hypoglycemic)]
Susceptible
group
Me
O
S NH C NH CH2CH2CH2CH3
O
O
Unsusceptible
group O
Cl
S NH C NH CH2CH2CH3
O
O
TOLBUTAMIDE
Metabolism
HOOC
O
S NH C NH CH2CH2CH2CH3
O
O
Rapidly excreted - short lifetime
Metabolism
8.1.3 Shifting susceptible metabolic groups
Rationale:
•
•
•
Used if the metabolically susceptible group is important for binding
Shift its position to make it unrecognisable to metabolic enzyme
Must still be recognisable to target
Example:
Unsusceptible
group
OH
Susceptible
group
HO
OH
HO
Shift
Group
Me
CHCH2
NH
C
Me
Me
OH
Me
NH
C
Me
Me
Inactive
HO
OH
C
CH2
Me
NH C
Catechol
O-Methyl
Trans feras e
MeO
CHCH2
H
Salbutamol
Cate chol
O-Me thyl
Trans fe ras e
HO
Salbutamol
Me
Me
8.3 Drug targeting
8.3.1 Linking a biosynthetic building block
Rationale:
• Drug ‘smuggled’ into cell by carrier proteins for natural building
block (e.g. amino acids or nucleic acid bases)
• Increases selectivity of drugs to target cells and reduces toxicity to
other cells
Cl
Example:
Anticancer drugs
O
Cl
N
H3C
HN
N
Cl
Cl
Non selective alkylating agent
Toxic
•
•
•
O
H
N
Uracil Mustard
Alkylating group is attached to a nucleic acid base
Cancer cells grow faster than normal cells and have a greater
demand for nucleic acid bases
Drug is concentrated in cancer cells - Trojan horse tactic
9. Reducing drug toxicity
Rationale:
• Toxicity is often due to specific functional groups
• Remove or replace functional groups known to be toxic e.g.
 aromatic nitro groups
 aromatic amines
 bromoarenes
 hydrazines
 polyhalogenated groups
 hydroxylamines
• Vary substituents
• Vary position of substituents
9.1 Prodrugs
Definition:
Inactive compounds which are converted to active compounds in
the body.
Uses:
• Improving membrane permeability
• Prolonging activity
• Masking toxicity and side effects
• Varying water solubility
• Drug targeting
• Improving chemical stability
9.1.2 Prodrugs to mask toxicity and side effects
•
•
Mask groups responsible for toxicity/side effects
Used when groups are important for activity
Example:
Aspirin for salicylic acid
O
OH
H3C
CO2H
O
CO2H
Salicylic acid
Aspirin
•
Analgesic, but causes stomach
ulcers due to phenol group
•
•
Phenol masked by ester
Hydrolysed in body
9.1.2 Prodrugs to mask toxicity and side effects
Example:
Cyclophosphoramide for phosphoramide mustard
(anticancer agent)
NH
O
Phosphoramidase
Cl
(liver)
H2N
HO
N
N
Cl
Cl
Cyclophosphoramide
Non toxic
Orally active
Cl
P
P
O
O
•
•
Phosphoramide mustard
•
Alkylating agent
9.1.3 Prodrugs to enhance patient acceptability
• Used to reduce solubility of foul tasting orally active drugs
• Less soluble on tongue
• Less revolting taste
Example:
Palmitate ester of chloramphenicol (antibiotic)
OH
H H
N
Palmitate ester
O
O
H H
N
H
O2N
O
OH
Cl
Esterase
Cl
H
Cl
Cl
O
OH
O2N
Chloramphenicol
9.1.4 Prodrugs to increase water solubility
•
•
•
Often used for i.v. drugs
Allows higher concentration and smaller dose volume
May decrease pain at site of injection
Example:
Succinate ester of chloramphenicol (antibiotic)
HO
O
Succinate ester
O
O
H H
N
H
O2N
O
OH
OH
H H
N
Cl
Cl
Esterase
H
Cl
Cl
O
OH
O2N
Chloramphenicol
Preclinical trials
Drug Metabolism
Identification of drug metabolites in test animals
Properties of drug metabolites
Toxicology
In vivo and in vitro tests for acute and chronic
toxicity
Pharmacology
Selectivity of action at drug target
Formulation
Stability tests
Methods of delivery
Phase I trials
• first introduction of IND (investigational new drug) in humans
•
usually only healthy adult volunteers (no patients)
• purpose is to investigate metabolic and pharmacological actions
of the compound in humans
• use dose-ranging (increasing dosages) to determine what side
effects may occur
• usually 20 – 80 subjects in the trial
Phase II trials
• early controlled trials in a patient population, with limited scope,
to obtain preliminary data on efficacy
• further indication of side effects, this time in patients
• about 200-400 subjects
Phase III trials
• expanded trials in a much larger sample of patients
• more information about drug efficacy and safety
• information about benefit : risk ratio
• obtain some information to determine what should be
included in the labelling of the marketed drug
• several hundred to several thousand patient subjects
(usually multi-centre studies and very expensive)
Phase IV trials
• not always performed
• may be required to explore possible side effects in more detail or
give a better indication of efficacy
• may involve a different type of patient (different age range,
different male:female ratio)
• may investigate potential efficacy in a different therapeutic area
• number of subjects is variable depending upon the reason for the
study
Drug Discovery Process
Time and Money
50,000 - 5,000,000 compounds are
often screened to find a single drug
>1,000 “hits”
12 “leads”
6 drug candidates
Discovery & Preclinical trials
Clinical trials: Phase I, Phase II, Phase III
12 to 24 years
$300 to >$500 million
1 drug
Epidemiology
• Distribution, frequency and determinants of health
problems and diseases in human populations
• Aim: obtain, interpret and use health information and
reduce disease burden
• Practical interventions and programs
Components:
1- Disease Frequency: Rates and Ratios.
2- Disease Distribution:Patterns of the disease
distribution.
3- Disease Determinants: To identify underlying causes.
Concepts and their application
• Incidence: the number of new cases, episodes or
events occurring over a defined period of time,
commonly one year.
• Prevalence: the total number of existing cases,
episodes or events occurring at one point in time,
commonly on a particular day.
• Population at risk: is vital to know about all people
at risk of developing a disease or having a health
problem, as well as those who are currently
suffering from it.
Uses of epidemiology
• Study effects of disease states in populations over
time and predict future health needs
• Diagnose the health of the community
• Evaluate health services
• Estimate individual risk from group experience
• Identify syndromes
• Complete the clinical picture so that prevention
can be accomplished before disease is
irreversible
• Search for cause
Pharmacogenetics
The term pharmacogenetics comes from
the combination of two words:
•
Pharmacogenetics
–
•
Study of how genetic differences in a SINGLE gene
influence variability in drug response (i.e., efficacy
and toxicity)
Pharmacogenomics
–
Study of how genetic (genome) differences in
MULTIPLE genes influence variability in drug
response (i.e., efficacy and toxicity)
AIM OF PHARMACOGENETIC STUDIES
Identify and categorize the genetic factors that
underlie the differences and apply this in clinical
practice
Rational, individual therapy
Screening for those patients who carry the genes
which place them at risk in case of certain therapies
Discovering which drugs are potentially dangerous
for carriers of a given polymorphism
Establishing the frequency of pharmacogenetic
phenotypes
Non-responders and
toxic responders
Responders
treat with
convential drugs
GENETIC FACTORS:
The first observations of genetic variation in
drug response date from the 1950’s, involving
the muscle relaxant suxamethonium chloride.
One in 3500 Caucasians has less efficient variant
of the enzyme (butyrylcholinesterase) that
metabolizes suxamethonium chloride. As a
consequence, the drug’s effect is prolonged,
with slower recovery from surgical paralysis.
A. Atypical Plasma Cholinesterase
SUCCINYLCHOLINE
+
O
(H3C)3NH2CH2C O C CH2CH2
O
+
C O CH2CH2N(CH3)3
succinylmonocholine
choline
Hydrolysis by pseudocholinesterase
•a rapid acting, rapid recovery muscle relaxant - 1951
•usual paralysis lasted 2 to 6 min in patients
•occasional patient exhibited paralysis lasting hrs.
•cause identified as an “atypical” plasma cholinesterase
53
Potential Benefits of Pharmacogenetics
 Improve Drug Choices:
• Each year, many dies of adverse reactions to medicine.
• Pharmacogenomics will predict who's likely to have a
negative or positive reaction to a drug
 Safer Dosing Options
• Testing of Genomic Variation Improve Determination of
Correct Dose for Each Individual
 Improvement in Drug Development:
• Permit pharmaceutical companies to determine in which
populations new drugs will be effective
 Decrease Health Care Costs
• Reduce number of deaths & hospitalizations due to adverse
drug reactions. Reduce purchase of drugs which are
ineffective in certain individuals due to genetic variations
 Speed Up Clinical Trials for New Drugs