Literature Seminar
2012.5.7. Yuya Morita (M1)

Application of Bioisosteres in Drug Design
O

O
H

F

N

O

N
N
N

OH
H

Contents
1. Introduction~What are Bioisosteres?
~Drug-like Concepts
2. Application of Isosteres in Drug Design~Fluorine as an Isostere of Hydrogen~Carboxylic Acid Isosteres~Phenol Isosteres~Amide and Ester Isosteres~Phenyl Ring Isosteres
3. Oxetanes in Drug Discovery~Physicochemical Properties of Oxetanes~Oxetanes as Isosteres~Preparation of Oxetanes
4. Summary

1. Introduction

What are bioisosteres?

Isostere• The isostere concept was formulated by Irving Langmuir in 1919.
J. Am. Chem. Soc. 1919, 41, 1543
The octet theory of valence indicates that if compounds
having the same number of atoms have also the same
total number of electrons, the electrons may arrange
themselves in the same manner. In this case the compounds
or groups of atoms are said to be isosteric.
Such compounds should show remarkable similarity inphysical properties, that is, in those properties which do not
involve a separation of the atoms in the molecule.
Irving Langmuir

Isosteres were initially defined as
those compounds or groups of atoms
that have the same number andarrangement of electrons.

• A further extension to this concept of isosteres came about in 1925 with Grimm's
Hydride Displacement Law.
"Atoms anywhere up to four places in the periodic system before an inert gas change
their properties by uniting with one to four hydrogen atoms, in such a manner that theresulting combinations behave like pseudoatoms, which are similar to elements in thegroups one to four places respectively, to their right."• Erlenmeyer further broadened Grimm's classification in 1932.
Isosteres were redefined as atoms, ions, and molecules in which the peripheral layerof electrons can be considered identical.

Bioisostere
The emergence of the concept of bioisoteres as structurally distinct compounds recognizedsimilarly by biological systems has its origins in a series of studies published by Erlenmeyerin the 1930s.
The term "bioisostere" was introduced by Harris Friedman in 1950 who defined it ascompounds eliciting a similar biological effect.
More recently this definition of bioisosteres has been broadened by Burger as"Compounds or groups that possess near-equal molecular shapes andvolumes, approximately the same distribution of electrons, and which
exhibit similar physical properties."
Prog. Drug Res. 1991, 37, 287

Erlenmeyer showed that antibodies were unable to discriminate between
phenyl and thienyl rings or O, NH, and CH2 in the context of artificial antigens.

the changes induced by the application of bioisosteres
The design of bioisosteres introduces structural changes that can be beneficial ordeleterious depending on the context.
size, shape, electronic distribution, polarizability
dipole, polarity, lipophilicity, pKa

In the contemporary practice of
medicinal chemistry
The development and application of bioisosteres have been adopted as a fundamental
tactical approach useful to address a number of aspects associated with the designand development of drug candidates.
improving potency, enhancing selectivity, altering physical properties
reducing or redirecting metabolism, eliminating or modifying toxicophores
acquiring novel intellectual property

Classical and Nonclassical Bioisosteres
Chem. Rev. 1996, 96, 3147

classical bioisostereClassical bioisosteres represent the results of an early appreciation of the concept
and encompass structurally simple atoms or groups.
1) monovalent atoms or groups
D and HF and HNH2 and OH
RSH and ROH
F, OH, NH2 and CH3
Cl, Br, SH and OH
2) divalent atoms or groups
C=C, C=N, C=O, C=S–CH2–, –NH–, –O–, –S–3) trivalent atoms or groups–CH=, –N=4) tetrasubstituted atoms
R4C, R4Si, R4N+
5) ring equivalentN,

nonclassical bioisostereNonclassical bioisosteres are structually distinct, usually comprise different
number of atoms and exhibit different steric and electronic properties.

Nonclassical bioisosteres have been devided into two subgroups.
1) cyclic and noncyclic isosteres2) exchangeable group isosterism in which the properties of discrete functional
elements are emulated
N N
N
N

O
CO2H
R1

OH

H
O
R2

CO2H

R3

O

S

N
N O

MAOMM
(methyleneaminoxy)-methyl moiety

R

H
Carboxylic Acid Isosteres

Drug-like Concepts
The application of guidelines linked to the concept of drug-likeness, such as the "rule of five",has gained wide acceptance as an approach to reduce attrition in drug discovery anddevelopment.
Lipinski's Rule of Five

Adv. Drug. Del. Rev. 1997, 23, 3
Lipinski's rule states that, poor absorption or permeability is more likely when...
• the molecular weight is greater than 500 daltons• the clogP(the calculated 1-octanol-water partition coefficient) is greater than 5• the number of hydrogen-bond donors(OH, NH) is more than 5• the number of hydrogen-bond acceptors(O, N) is more than 10

Lipophilicity in Drug Discovery

Expert Opin. Drug Discov. 2010, 5, 235

The role of lipophilicity in determining the overall quality of candidate drug molecules is ofparamount importance. Recent developments suggest that, as well as determining pre-clinical
ADMET (absorption, distribution, metabolism, excretion and toxicology) properties,
compounds of optimal lipophilicity might have increased chances of success in development.
Solubility
logP > 3
logP < 3

only 1% were soluble (having kinetic solubility > 250 µg/mL)
50% were soluble

Permeability
logP > 1.7 for MW 350 - 400
logP > 3.4 for MW 450 - 500

logP > 3.1 for MW 400 - 450
to achieve high permeability
logP > 4.5 for MW > 500

Clearance and Metabolism
With respect to metabolic stability, logD < 3 is desirable.
On the other hand, reducing logD leads to increasing renal clearance.
50% of the compounds that showed net renal secretion had calculated logD < 0
50% of the compounds that showed net renal reabsorption had calculated logD > 1.2
Bioavailability
Bioavailability can be considered to be a composite of the effect of solubility,
permeability and metabolic stability.
It has been suggested that the optimal range is 0 < logP < 3, 1 < logD < 3
Toxicity
In principle, more lipophilic compounds might be expected to be more promiscuous, that is,lack of selectivity. So more lipophilic compounds are likely to be more toxic.
• hERG potencies diminish significantly as logD increases• the risk of a compound causing phospholipidosis increases if logP2 + pKa2 is > 90
for a base with a pKa of 9, logP < 3 is desirable.
• the average CYP inhibition are significantly lower for compounds with logP < 3(A) shows the regions of lipophilicity where good overall compounds are distributed(B) shows where properties are compromised for logD(orange) and logP(light blue)2. Application of Isosteres in Drug Design
Fluorine as an Isostere of Hydrogen
The unique properties of fluorine have led to its widespread application in drug design as an
isostere for hydrogen, since incorporation of fluorine can productively modulate a range ofproperties of interest to medicinal chemists.
ChemBioChem 2004, 5, 637
Metabolic stability

The effect on the pKa

block the metabolically labile site with a fluorine
substituent, hoping that the small fluorine atom
will not impair the binding to the target protein

As the most electronegative atom, fluorine hasa very strong effect on the acidity or basicity ofnearby functional groups.

The effect on molecular lipophilicity
A survey of 293 pairs of molecules that differed only by a F-for-H exchange revealed that the
average lipophilicity(logD) increased by 0.25 log units. But there are quite a number of cases(shown below) for which an H to F substitution decreases lipophilicity.
A close inspection of these cases revealed that
all compounds were found to have at least one
low-energy conformer with an O  F distancesmaller than 3.1 Å.

The effect on molecular conformation
α-fluorinated carbonyl derivatives favor a conformation in which the C-F and C=O bonds adopt a transorientation to align the dipoles in an antiperiplanar.
~0.4 kcal/mol

The modestly prefered(~0.4 kcal/mol) conformation of benzyl
fruoride projects the C-F bond orthogonal to the aryl ring, stabilized
by donation of electron density from the aryl π-orbital into the σ*C-F
antibonding orbital.
The electrostatic interaction between F(δ - ) and NH(δ+) has
a effect on conformational preferences
O
R1

NH
N

HN

N

O
N
N

O

O
R
O 1
N
H

NH
N
R2

When R1=H and R2=F
~3 kcal/mol favored

O

O

R2

N

O

N
N

When R1=F and R2=H
~3 kcal/mol favoredCarboxylic Acid Isosteres
Isosteres of carboxylic acid have been studied extensively.
These studies have typically focused on...
• enhancing potency• reducing polarity• increasing lipophilicity(improve membrane permeability)• enhancing pharmacokinetic properties• reducing the potential for toxicity

application (Angiotensin II receptor antagonists)
nBu

N
Cl

N

OH
N

pKa
logP
IC50

5.0
4.5
4.5
1.2
19 nM 200 nM

N
Et
N

N

O

Ph

O

O S NH

H
N

N N
N

NH

O
N
OH

N

MK-996

resistance toward glucuronidation

Losartan

Phenol Isosteres
Phenol and catechol isosteres were typically designed to ovecome pharmacokinetic andtoxicological limitations.

A range of useful surrogates are well-established.
The structural diversity, electronic properties,
lipophilicity, and size of these functionalities varies
widely, providing ample flexibility to customize for a
special application.

application (Non-selective β-adrenoceptor agonists)
OH
HO
HO

H
N

MeO2S

H
N

OH

H
N

HO
resistance toward COMT(catechol O-methyl transferase)Amide and Ester IsosteresAmide isosteres have typically been of interest as a means of modulating polarity andbioavailability, while ester isosteres have frequently been developed to address metabolism
issues since esters can be repidly cleaved in vivo.

trifluoroethylamines as amide isosteresAmide isosteres have been focused on in the context of peptidemimetics.
Many amide replacements are known which retain the geometry of the amide bond or
maintain the hydrogen bond-accepting properties of the amide. However, there are few
functional groups, which are capable of preserving the hydrogen bond-donating propertiesof the amide.
In this situation, trifluoroethylamines were identified as amide isosteres.
O

CF3
N
H

N
H

• reducing the basicity of the amine without compromising the ability of the NH tofunction as a H-bond donor• CF3CH(R)NHR' bond is close to the 120o observed with an amide• C-CF3 bond is as polar as C=O bondapplication (inhibitors of cathepsin K)
Bioorg. Med. Chem. 2005, 15, 4741

The replacement of an amide with atrifluoroethylamine leads to high potency,
high selectivity and metabolic stability.
The role of the CF3 group was exploredin a brief SAR study. (right Table)
And compound 6 has been modeled intoa Cat K crystal structure.

• Low basicity allows the excellent H-bond to Gly66.
• The CF3 group attached to an sp3 carbon orients itself perpendicular to the aromatic ringand stabilizes the aromatic ring in its bioactive conformation.
• The sp3 hybridized nitrogen allows the simultaneous formation of an optimal H-bond.

Phenyl Ring Isosteres
Application of the bicyclo[1.1.1]pentane motif as a nonclassical phenyl ring bioisosterein the design of a potent and orally active γ-secretase inhibitor
J. Med. Chem. 2012, 55, 3414

The rationale for the use of the disubsituted
bicyclo[1.1.1]pentane motif as a bioisostere
for the central fluorophenyl ring derived fromgeneric spatial features.
• comparable dihedral angles• similar distances between substituents

SAR studies into other fluorophenyl replacements indicate the intrinsic advantage of thebicyclo[1.1.1]pentane moiety over conventional phenyl ring isosteres with respect toachieving an optimal balance of properties.
For further application of bicyclo[1.1.1]pentane skeleton to drug discovery
Scalable synthesis of 1-bicyclo[1.1.1]pentylamine was developed.
The key reaction is hydrohydrazination reaction.
Org. Lett. 2011, 13, 4746
• successfully scaled to 20 g
• overall yield improved to 62%• a 50-fold reduction in costMn-catalyzed hydrohydrazination:
J. Am. Chem. Soc. 2006, 128, 11693

The previous syntheses• low yield• complications for scale-up (toxic, explosive...)• using reversed phase chromatography

3. Oxetanes in Drug Discovery
Oxetanes have recently gained attention as attractive, stable, and less lipophilicmolecular for drug discovery.

O
Physicochemical Properties of Oxetanes
What makes the oxetane a potentially attractive structual motif for drug discovery?
High polarity and outstanding ability to function as an acceptor of hydrogen bonds.
Metabolic and chemical stability.
Why the oxetane shows the high affinity for hydrogen bonds?
1. For cyclic ethers, a decrease in the ring size is accompanied by a diminution in thecorresponding endocyclic C-O-C angle. This has the effect of exposing the oxygen
atom more effectively to hydrogen-bond donors.
2. An increase in the s character of the nonbonding orbitals of the electron lone pairs
renders these less available to engage in hydrogen bonding.
Several studies suggest that only oxiranes experience a significant change in the
hybridization associated with the electron lone pairs on the oxygen atom.

The balance of the two effects makes oxetanes optimal among the cyclic ethers
as acceptors of hydrogen bonds.
O

H

O

F

n
base

acid
pKHB

O

H

O

n

F
complex
Figure: strength of association with 4-fluorophenol in cyclic ethers against ring-size

pKHB shows the thermodynamic hydrogen-bond basicity.
Base + 4-FC6H4OH

4-FC6H4OH • • • Base

Kf = [Hydrogen-bond complex] / [Base][4-FC6H4OH]
pKHB = -log10 (dissociation constant of the complex) = log10 Kf
pKHB scale of ethers: Eur. J. Org. Chem. 1998, 925

Oxetanes as Isosteres
Isosteres of gem-dimethy groups
Initially oxetanes were studied as potential surrogates for gem-dimethyl groups, thus
allowing the introduction of enhanced polarity with a similar molecular volume.
Oxetanes have the ability to graft bulky
substituents onto a scaffold of interest
without increasing the lipophilicity.
Having high lipophilicity leads to low aqueous
solubility and fast metabolic degradation.

Isosteres of carbonyl groups
There are liabilities associated with carbonyl groups that stem from their susceptibility to
enzymatic modification and to the epimerization of adjacent stereogenic centers, as well as
their inherent electrophilic reactivities and their potential for covalent binding.
So oxetanes are used as chemically and metabolically stable isosteres of carbonyl groups.
The oxetane oxygen atom expresses
a similar capacity to the C=O moiety toaccept a hydrogen bond.
pKHB for oxetane is 1.36
pKHB for cyclopentanone is 1.27

pKHB scale of carbonyl groups: J. Chem. Soc., Perkin T rans. 1998, 101

pKHB

Figure: affinity of oxetane and different carbonyl compounds to act as acceptors for hydrogen bonds

Influence on the basicity of proximal amines
While the oxygen atom of an oxetane can donate electron density as a Lewis base,the oxetane motif itself acts as an electron-withdrawing group on neighboring functionalgroups. This distant-dependent inductive effect of the oxetane can be used to temper thebasicity of a proximal amine.
Angew. Chem. Int. Ed. 2006, 45, 7736

Lower the basicity !

Influence on lipophilicity and solubility
Having seen that the presence of an oxetane can markedly influence the basicity of aproximal amine, it is important to assess its influence on the lipophilicity of the underlying
scaffold.
Angew. Chem. Int. Ed. 2008, 47, 4512
It is shown that an oxetane-containing
molecule is typically much less lipophilic than
the respective gem-dimethyl analogue, andthat the corresponding carbonyl compounds
are even more hydrophilic.
logP = intrinsic lipophilicity of the neutral basen.d. = not determined because of chemical instability

Lower the lipophilicity !
The themodynamic solubilities measured in buffered solutions at pH9.9 are shown below.
O

α NMe2

NMe2
tBu

Solibility

O

tBu

<1

β

NMe2

tBu

57

25

O

γ
tBu

O

Solubility

4100

NMe2

δ

NMe2

NMe2
Me

tBu

270

O

4400

Highten the solubility !

Metabolic and chemical stability
The influence an oxetane has on oxidative phase I metabolism has been studied andcompared with compounds having carbonyl or gem-dimethyl groups at the corresponding
position.
Angew. Chem. Int. Ed. 2008, 47, 4512
It was found that compounds bearing
oxetanes tend to have a low to modest
proclivity towards metabolic degradation,and that in many cases the corresponding
gem-dimethyl or carbonyl compounds havehigher intrinsic clearance rates in humanliver microsomes.
hCLint = intrinsic clearance rates [min-1/(mgproteinµL-1)]
n.d. = not determined because of chemical instability

Improve metabolic and chemical stability !

Oxetanes in Drugs and Natural Products

Preparation of Oxetanes
Oxetane has first been reported by Reboul in 1878.
Three general approaches to the synthesis of oxetanes are shown below.
2) Paternό-Bϋchi reaction

1) Williamson ether synthesis
R1

O

R2

R3

base

X
OH

X = leaving group

O

R3
R1

R

R2

O

hν

H

R

3) sulfonium ylides (via Corey-Chaykovsky reaction)
O
O
Me
R

H

NTs
S

O

CH2Na
R

Preparation of 3-Aryl-substituted Oxetanes
Org. Lett. 2008, 10, 3259
This nickel-mediated Suzuki coupling
provides access to a wide range of
3-aryl-substituted oxetanes.
The reaction tolerates a number ofcommon functional groups.

Catalytic Asymmetric Synthesis of 2,2-Disubstituted Oxetanes
Angew. Chem. Int. Ed. 2009, 48, 1677

ylide 35d(S)-1aOne-pot catalytic asymmetric synthesis of
2,2-disubstituted oxetanes from ketones

Chiral amplification in the second reaction
between the epoxide and the ylide occur toafford oxetanes with a higher enantioselectivity than the intermediate epoxides.

In order to get various oxetane derivatives...
Oxetane-3-one is very useful.
It can be converted to many kinds of 3,3-disubstituted oxetanes.
O

Nu

O

O

EWG

Nu

EWG
O

LG
O

O

Nu

OH

Nu

Nu'
O

Why are 3,3-disubstituted oxetanes focused on?
This stems from the aim of not augmenting the complexity by generating a stereogenic
center upon grafting an oxetane unit onto a given scaffold.
The first synthesis of oxetane-3-one in pure form and significant quantities was reported in apatent from DuPont in 1967.

• intermediate 44 was unstable...
• retro Diels-Alder reaction seemed
to be difficult to accomplish withstandard laboratory equipment...

Several syntheses of oxetane-3-one was reported; however, each has practical shortcomings,
such as the use of preparative gas-chromatographic techniques.
Consequently, a straightforward route was developed starting from dihydroxyacetone dimer.
Angew. Chem. Int. Ed. 2006, 45, 7736

4. Summary
The design and application of isosteres have inspired medicinal chemists for almost
80 years, fostering creativity directed toward solving a range of problems in drug
design, including understanding and optimizing drug — target interactions andspecificity, improving drug permeability, reducing or redirecting metabolism, andavoiding toxicity.
As an established and powerful concept in medicinal chemistry, the application of
bioisosteres will continue to play an important role in drug discovery.
Isosterism can also contribute to the productive application in the design andoptimization of catalysts in organic chemistry!!

References
review of bioisosteres: J. Med. Chem. 2011, 54, 2529
Chem. Rev. 1996, 96, 3147
fluorine in medicinal chemistry: ChemBioChem 2004, 5, 637
oxetanes in drug discovery: Angew. Chem. Int. Ed. 2010, 49, 9052