Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf ·...

48
Bioisosteres of Common Functional Groups N N O OH N O OH N Cl Cl Hydroxyzine Ian Perry MacMillan Group Meeting May 16 th , 2019

Transcript of Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf ·...

Page 1: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Bioisosteres of Common Functional Groups

N

NO

OHN

OOH

N

ClCl

Hydroxyzine

Ian PerryMacMillan Group Meeting

May 16th, 2019

Page 2: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Introduction to Isosterism

Irving Langmuir

JACS 1919: “The Arrangement of Electrons in Atoms and Molecules”

JACS 1919: “Isomorphism, Isosterism and Covalence

1932 Nobel Prize in Chemistry for Discoveries in Surface Chemistry

OC

ON

N

OO

CN

N

NN

HH

CO

HH

Langmuir, I. J. Am. Chem. Soc., 1919, 41, 1543

NN

HH

CO

HH

Page 3: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Introduction to Bioisosterism

Friedman, H. L. NASNRS., 1951, 206, 358

1951: H. L. Friedman coins “Bioisostere” - Molecules or groups “which fit the broadest definition of isosteres and have the same type of biological activity.”

1932: Erlenmeyer Demonstrates Bioisosterism of some of Langmuir’s Isosteres - Antibodies were found to not discriminate in the binding of several artificial antigens

O

NH

peptide

HN

NH

peptide

H2C

NH

peptide

Erlenmeyer, H., Berger, E., Biochem Z. 1932, 252, 22

Page 4: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Talk Outline

examples of bioisostereism are abundant in medicinal chemistry, this talk is not comprehensive. For a more detailed review, see:

Meanwell, N. A. J. Med. Chem. 2011, 54, 2529

Part 2 - Nonclassical Bioisosteres

Common examples of Nonclassical Bioisosteres

Strained (hetero)cycles as Bioisosteres

Bioisosteres of Aromatic Rings

Part 1 - Classical Bioisosteres

3 case studies of isosteric atom substitution:

Procaine vs. Procainamide

Haloperidol vs. Silahaloperidol

The importance of Celebrex-CH3

examples of bioisosterism are abundant in medicinal chemistry, this talk is not comprehensive. For a more detailed review, see:

Meanwell, N. A. J. Med. Chem. 2011, 54, 2529

Page 5: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Case Study in Classical Bioisosteres: Procaine vs. Procainamide

Imming, P., Sinning, C., Meyer, A. Nat. Rev. Drug Discov. 2006, 6, 126

H2N

O

ONEt2

procaine

H2N

O

NH

NEt2

procainamide

substitution ofa divalent atom

Nav channel blocker

Analgesic

Metabolsim viaester hydrolysis

(pseudocholinesterase)

H2N

O

OH

Nav channel blocker

Analgesic

Metabolsim viaAcylation or oxidation

(P450)

NH

O

NH

NEt2

Me

O

OH

Page 6: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Case Study in Classical Bioisosteres: Haloperidol vs. Sila-haloperidol

Tacke, R. et al. ChemMedChem 2008, 3, 152

haloperidolAntipsychotic

N

HOO

F

Cl3

Janssen, P. A. J., J. Med. Chem. 1958, 1, 105

Developed for the treatment of neuropsychiatric disorders

Alleviates allucinations and delusions associated with chizophrenia

Irreversible side effects associated with long-term use

NO

F

3

Cl

aromatizationN

O

F

3

Cl

neurotoxin associated with dyskinesia

HPP+

Alleviates hallucinations and delusions associated with schizophrenia

Page 7: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Case Study in Classical Bioisosteres: Haloperidol vs. Sila-haloperidol

Tacke, R. et al. ChemMedChem 2008, 3, 152

haloperidolAntipsychotic

N

HOO

F

Cl3

Janssen, P. A. J., J. Med. Chem. 1958, 1, 105

SiN

O

F

3

Cl

no detected neurotoxic metabolites

SiN

HOO

F

Cl3

Silahaloperidol

substitution of carbon for silicon has limited effecton pharmacokinetic properties

strong Si-OH bond and weak Si=C bond disfavorselimination compared to carbon analogue

Page 8: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Case Study in Classical Bioisosteres: Haloperidol vs. Sila-haloperidol

Tacke, R. et al. ChemMedChem 2008, 3, 152

Haloperidol

N

HOO

F

Cl3

Janssen, P. A. J., J. Med. Chem. 1958, 1, 105

SiN

HOO

F

Cl3

Silahaloperidol

HN

O Br

Cl

Mg0

NH

HO

Cl

Cl

OCl

F

ClO

PhF

short and convergent synthesis from readily available feedstock materials

Page 9: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Case Study in Classical Bioisosteres: Haloperidol vs. Sila-haloperidol

Tacke, R. et al. ChemMedChem 2008, 3, 152Janssen, P. A. J., J. Med. Chem. 1958, 1, 105

SiN

HOO

F

Cl3

Silahaloperidol

SiMeO OMe

OMeMeO H2NOO

F

12 steps, 7% overall yield

SiOPG

II

Cl

F

NH2OO

F

NOO

SiOPG

Cl

key silacycle formation

incorporation of non-native functionality as bioisosteres often involves lengthy syntheses

Page 10: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Case Study in Classical Bioisosteres: Celecoxib

Penning, T. D., J. Med. Chem. 1997, 40, 1347

NSAID developed by Pfizer

Selective COX-2 inhibitor

Marketed for the treatment of Arthritis

SNH2

O O

NN

F3C

H

SNH2

O O

NN

F3C

F

SNH2

O O

NN

F3C

CF3

SNH2

O O

NN

F3C

OMe

µM level IC50 for COX-2 in all cases

high specificity for COX-2 vs. COX-1

SNH2

O O

NN

F3C

CF3

SNH2

O O

NN

F3C

Cy

SNH2

O O

NN

F3C

CF2H

SNH2

O O

NN

F3C

CF3

SNH

O O

NN

F3C

Me

n-pentylSNH2

O O

NN

F3CBr

SNH2

O O

NN

F3C

CD3

SNH2

O O

NN

F3C

CO2H

FF

SNH2

O O

NN

F3C

CO2Me

NHBoc

SNH2

O O

NN

F3C

N NPh

SNH2

O O

NN

F3C

O

SNH2

O O

NN

F3C

Me

Page 11: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Case Study in Classical Bioisosteres: Celecoxib

Penning, T. D., J. Med. Chem. 1997, 40, 1347

SNH2

O O

NN

F3C

H

HH

SNH2

O O

NN

F3C

F

FF

fluorine atom substitution

Increased metabolic stability?

SNH2

O O

NN

F3C

H

SNH2

O O

NN

F3C

F

SNH2

O O

NN

F3C

CF3

SNH2

O O

NN

F3C

OMe

undesirably long half life (>200 hours!)

For an excellent review on rational incorporation of fluorine as a hydrogen isostere, see:Meanwell, N. A. J. Med. Chem. 2018, 61, 5822

isosteric substitution that removes benzylic metabolic handle results in undesirable pharmacokinetic properties

Page 12: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Part 2 - Nonclassical Bioisosteres

Common examples of Nonclassical Bioisosteres

Strained (hetero)cycles as Bioisosteres

Bioisosteres of Aromatic Rings

Talk Outline

examples of bioisostereism are abundant in medicinal chemistry, this talk is not comprehensive. For a more detailed review, see:

Meanwell, N. A. J. Med. Chem. 2011, 54, 2529

Part 1 - Classical Bioisosteres

3 case studies of isosteric atom substitution:

Procaine vs. Procainamide

Haloperidol vs. Silahaloperidol

The importance of Celebrex-CH3

examples of bioisosterism are abundant in medicinal chemistry, this talk is not comprehensive. For a more detailed review, see:

Meanwell, N. A. J. Med. Chem. 2011, 54, 2529

Page 13: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

O

OH

Introduction to Nonclassical Bioisosteres

Ballatore, C., Huryn, D. M. & Smith, A. B. ChemMedChem 2013, 8, 385

Unlike their classical counterparts, nonclassical bioisosteres do not conform to Langmuir’s broad definition of “isostere.”

Nonclassical bioisosteres are groups capable of emulating the steric or electronic profile of the original functional group

N

NBu

Cl

OH

IC50 [µM] dose [mg/kg]

NH

NNN

losartan scaffoldhigh blood pressure

0.23

0.019

3

0.8

pKa

4.2

4.5

Page 14: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Introduction to Nonclassical Bioisosteres

Am. J. Med., 1976, 10, 1107

Unlike their classical counterparts, nonclassical bioisosteres do not conform to Langmuir’s broad definition of “isostere.”

Nonclassical bioisosteres are groups capable of emulating the steric or electronic profile of the original functional group

HO

Me

H

H H

OH

estrogenprimary female sex hormone

OH

HO

Me

Me

diethyl stilbestrol“synthetic estrogen”

Prescribed to pregnant women1940-1970

Thought to prevent miscarriagesin pregnant women with low estrogen

Use discontinued after DES linked todevelopment of clear cell carcinoma

by women exposed in utero

Page 15: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Bioisosteres of Common Functional Groups

OH

O

NH

NNN NO

OH

OO

OH

O

SO O

NH2

OMe Me

O

NH

H H

FF

O

NH

CF3

NH

F

NH

O

Me

Me

CF3 SF5

HN

NH

HN

O

HN

…and many more

Page 16: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

HN

HN

HN

HN

Escaping Flatland

Lovering, F., Bikker, J. & Humblet, C., J. Med. Chem. 2009, 52, 6752

Incorporating highly saturated fragments in drug discovery correlates with clinical success

Greater three-dimensionality imparts higher specificity in binding

N

& enantiomers

Aside from synthetic accessibility, is there a caveat to increased sp3 character?

Page 17: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Escaping Flatland

Bolleddula, J. et al. Drug Metab. Rev. 2014, 46, 379

NHN

easily synthetically accessed

high likelihood ofclinical success

HNO

H2N O

NO

more pathwaysavailable for

oxidative metabolism

HNH

H

NN N

NFe

MeMeR

RMe MeO

cytochrome P450 amine oxidase

Page 18: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Escaping Flatland

Bolleddula, J. et al. Drug Metab. Rev. 2014, 46, 379Vitaku, E., Smith, D. T., Njardarson, J. T. J. Med. Chem. 2014, 57, 10257

Despite metabolic instability, saturated heterocycles remain some of the most utilized functionality in medicinal chemistry

Most frequiently used saturated nitrogen heterocycles in FDA approved pharmaceuticals

NH N

H

HN

NH HN O

HN

NH

HN

N

HN

72 59 37 13 12 11 10

number of approved drugs containing each saturated heterocyclic core

expanding the scope of saturated heterocycles toward molecules of increased metabolic stability could greatly impact the rate of success in drug development

expanding the scope of accessible functionality toward saturated heterocycles of increased metabolic stability could greatly impact the rate of success in drug development

Page 19: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Spirocyclic Azetidines as Bioisosteres of Nitrogen Heterocycles

O

HN

O

HN

HN

HN

HN

NH

HN

NH

HN

2, 3 & 4-substituted piperidine analogues

2 & 3 substituted morpholine analogues

2 & 3 substituted piperazine analogues

X

HN

2-azaspiro[3.3]heptanecore

Page 20: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

6-oxa-2-azabicyclo[3.3]heptane in an MCHr1 Antagonist

Johansson, A. et al. J. Med. Chem. 2016, 59, 2497

High throughput screening at AstraZeneca generated compound 1 for lead optimization

Melanin concentrating hormone receptor 1 (MCHr1)has been linked to regulation of appetite.

Small molecule antagonists of this receptor have been shown to prevent obesity

compound 1 - antagonist of MCHr1

O

NN

O

N N

O Cl

Page 21: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

6-oxa-2-azabicyclo[3.3]heptane in an MCHr1 Antagonist

Johansson, A. et al. J. Med. Chem. 2016, 59, 2497

low tolerance for structural modification

basic, benzylic aminecritical for MCHr1 activity

high degree of piperidine lipophilicitylimited degrees of freedom in exploring SAR

O

NN

O

N N

O R

azetidine substitution had limited effect on activity, but allowed for greater freedom in exploring benzylic amine functionality

O

NN

O

N N

O Cl

reduction of HERG activity (off target binding resulting in cardiac arrhythmia) is a priority

Page 22: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

6-oxa-2-azabicyclo[3.3]heptane in an MCHr1 Antagonist

Johansson, A. et al. J. Med. Chem. 2016, 59, 2497

low tolerance for structural modification

basic, benzylic aminecritical for MCHr1 activity

high degree of piperidine lipophilicitylimited degrees of freedom in exploring SAR

O

NN

O

N N

O R

azetidine substitution had limited effect on activity, but allowed for greater freedom in exploring benzylic amine functionality

O

NN

O

N N

O Cl

Page 23: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

6-oxa-2-azabicyclo[3.3]heptane in an MCHr1 Antagonist

Johansson, A. et al. J. Med. Chem. 2016, 59, 2497

O

NN

O

N N

O OMe

N NMe

MeN N

MeNN

ON

HOlead

reduced metabolic stability

no reduction in hERG interaction

reduced MCHr1 potency

***

* * ** **

low receptor occupancy (efflux)

hydrogen bond donorsor acceptors improve potency

Page 24: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

6-oxa-2-azabicyclo[3.3]heptane in an MCHr1 Antagonist

Johansson, A. et al. J. Med. Chem. 2016, 59, 2497

O

NN

O

N N

O OMe

N N N N

lead

Me

OMeO

O

NO

high levels of activity, but no marked improvement in metabolic stability

Page 25: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

6-oxa-2-azabicyclo[3.3]heptane in an MCHr1 Antagonist

Golden, M. et al. Org. Proc. Res. Dev. 2016, 20, 675

O

NN

O

N N

O OMe

O

increased metabolic stability - high MCHr1 activity - moved to phase 1

synthetic route to spirocycle:

OHHO

OH OH

HBr

Δ

BrHO

Br Br

NaOH

TBA•HSO4O

BrBrBnNH2

NaOH

then HCl O

NH

Ph

Cl

Page 26: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Li, X.-Q. et al. Drug Metab. Dispos. 2016, 44, 1341

“Spiromorpholine” metabolism

O

N

Bolleddula, J. et al. Drug Metab. Rev. 2014, 46, 379

R

O

N

R

O

N

R

OH

OH

O

N

R

OH

OH

O

HN

O

NH

R

O

OH

O

N

R

O

O

N

R

O

HO

N

R

OHO

O

NOH

O

NO

O

NO R

morpholinemetabolism

metabolism of morpholine dominated by C–H oxidation

Page 27: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Li, X.-Q. et al. Drug Metab. Dispos. 2016, 44, 1341

“Spiromorpholine” metabolism

O

NN

O

N N

O OMe

O

N

HO

OH

N

O R

R

18O

18O

enz

N

R

enz

HO

18O

18O

H218O

N

R

18O

18O

enz

H18O

H16O

enz epoxide hydrolase

Page 28: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Other Analogues of Saturated Heterocycles

X

HN X = CH2X = N, O H

NHN

HN

HN

NH NH

HN

O

HN

NH

HN

HN

NH2NCl

F

N

F

OCO2H

antibacterial drugDaiichi Sankyo

N

O

N

HN

O

CN

antineurodegenerativeRoche

N

HN

O

SO

O

Cl

epoxide hydrolase inhibitorMerck

Page 29: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Other Analogues of Saturated Heterocycles

X

HN fusedbridged

X

HN

HN

X

H HX

HN

NH

XX

X

HN

X

HN

HN

X

H

H

N

HN

HN

O

N N

N

N

NO

O

PI3K inhibitorPfizer

N

N NH

HN

O

N

O

OHH

NF

Me

O

HH

Peptide deformylase inhibitorGSK

spiro, fused, and bridged bicyclic compounds - lower oxidative lability, higher conformational rigidity

Page 30: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Synthesis of Complex Isosteres of Saturated Heterocycles

HN

X

Br

Br

X

Br H2N Ph

HN HO

HO

O

OR

O

RO

BrBr

affords access to N-substituted

spiro-morpholines and spiro-piperazines

modular approachto spiro-piperidine

affords greater substitutional diversityR R R

can a more modular approach to spiroheterocycles afford a broader range of medicinally relevant isosteres?

Page 31: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Synthesis of Complex Isosteres of Saturated Heterocycles

HN NH HN NH

synthetically challenging exit vectors

N

O O

OH

NF

F

HN

Me

Gatifloxacin (BMS)antibiotic

NN

Me

N

Mirtazapine (Organon)antidepressant

OH

HN O

Bn

OHN

N

N

OHN

Me MeMe

Indinavir (Merck)antiretroviral

Page 32: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Synthesis of Complex Isosteres of Saturated Heterocycles

Guérot, C., Tchitchanov, B. H., Knust, H & Carreira, E. M. Org Lett 2011, 13, 780

N

PhPh

O

H2NS

tBu

O

N

PhPh

NSO

tBuSPh2

BF4

N

PhPh

O

KHMDS Ti(OEt)4

LiBF4, toluene

N

PhPh

O

N

PhPh

NSOtBu

R R

RR

R = Me, F

CO2Et

X

N

PhPh

O

N

PhPh

NH2

N

PhPh

OHconditions

N

PhPh

O

OH

O

HNPh

Ph

[ox]

not observedO

Page 33: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Synthesis of Complex Isosteres of Saturated Heterocycles

Kirichok, A. A. et al. Angew. Chem. Int. Ed. 2017, 56, 8865Kirichok, A. A. et al. Chem. Eur. J. 2018, 24, 5444

OHO

O

R

X X

X = H, OMeR = alkyl, aryl

1) SOCl2

2) DIPEA

LiHMDS

reflux

NH

XX

O R

[red]

NH

O

NH

OMeMeO

Me

Me

33% overall

N HN

O Me

MeBu

19% yield

NBu HN

OMe

Me

Bupivacaine

isosteric bupivacaine showed higher protein binding, higher LD50, faster onset, and similar activity to

bupivacaine in vivo (mouse)

5 steps

first demonstration of 1-substituted 2-aza-spiro[3.3]heptane as a 2-piperidine isostere

Mykhailiuk Group has since expanded this platformto [4.3], [5.3], and [6.3] spirocyclic azetidines

Page 34: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Synthesis of Complex Isosteres of Saturated Heterocycles

HN Br

NHR

HN

X

NHRBrBr

X

HN

YZ

spirocycles with exit vectors off of terminal heteroatoms are straightforward to synthesize from feedstock materials

n

n

pathways toward strained spirocycles with exit vectors on carbon and at orthogonal angles are limited, novel developments in this arena are in great demand

For additional examples of spiroheterocycle construction, see: Carreira,E. M. & Fessard, T. C. Chem. Rev. 2014, 114, 8257

Page 35: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Bioisosteres of Benzene Rings

Taylor, R. D., MacCoss, M. & Lawson, A. D. G. J. Med. Chem. 2014, 57, 5845

While many pharmaceutical compounds contain saturated heterocycles, many, many more contain benzene rings (>500 as of 2014)

• 6 exit vectors

• high structural rigidity

• many methods for incorporation and functionalization

2D vectorial space

Page 36: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Bioisosteres of Benzene Rings

Taylor, R. D., MacCoss, M. & Lawson, A. D. G. J. Med. Chem. 2014, 57, 5845

some guidelines for phenyl isosteres

retained structural rigidity

reduced cLogP (lipophilicity) as compared to Ph

increased sp3 incorporation without intoducing metabolic instability

Eaton, ACIE 1992

Stephan, J. Med. Chem. 2012

Page 37: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

1,4-disubstituted Benzene Bioisosteres

Nicolau, K. C. et al. ChemMedChem 2016, 11, 31

NH

NN

MeO

NH

Me

N

N

N

Imatinib - ABL1 kinase inhibitor - anticancer

4 aromatic rings, low fraction of sp3–hybridized carbon atoms

nearly insoluble in neutral aqueous media

cLogP = 4.53 (upper end of Lipinski’s rule of 5)

Page 38: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

1,4-disubstituted Benzene Bioisosteres

Nicolau, K. C. et al. ChemMedChem 2016, 11, 31

incorporated linkers:

NH

O

NH

Me

N

N

NN

NMe

Page 39: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

NH

O

NH

Me

N

N

NN

NMe

1,4-disubstituted Benzene Bioisosteres

Nicolau, K. C. et al. ChemMedChem 2016, 11, 31

fract

ion

sp3

0.2

0.5

0.4

0.3

0.25

0.35

0.45

cLogP

1.5 1.75 2.0 2.25 2.5 2.75 3.0 3.25 3.5 3.75 4.0 4.25 4.5 4.75

(imatinib)

Page 40: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

1,4-disubstituted Benzene Bioisosteres

Nicolau, K. C. et al. ChemMedChem 2016, 11, 31

>80-fold increasein solubility

50-fold increasein solubility

10-fold increasein solubility

decrease in binding affinity, potency, and target selectivity across the board

Page 41: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Bioisosteres of Benzene Rings

Stephan, A. F. et al. J. Med. Chem. 2012, 55, 3414

NO

N

F

NS

O

O

Cl

CF3

NH2O

NO

NNS

O

O

Cl

CF3

NH2O

BMS 708,163γ-secretase inhibitor(anti-Alzheimer’s)

n

equipotent to BMS 708,163improved permeability

improved aqueous solubility

fluoro substitution in parent compound not required in bicyclic analogue

Page 42: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Synthesis of Benzene Bioisosteres: [1.1.1]-bicyclopentane

EWG X

BEt3X

EWG

X2

X

X

O

Me Me

O

diacetylhv

R MgBr

Pd, ArI

R

Ar

1)

1)

de Meiere, et al. Eur. J. Org. Chem.

2000, 1137

Michl & Kaszynski, J. Org. Chem.1988, 53, 4593

Thirumoorthi, N. T., Chem Commun. 2015, 51, 3139

Recent reports: Anderson GroupChem. Sci., 2018, 9, 5259Org. Lett. 2019, 21, 2408

Gianatassio, R. et al. Science, 2016, 351, 241

NR

R

NMgBrR

R

R

X

Ar

X

Ar/R XIr(ppy)3

Nugent, J. et al. ChemRXiv, 2019

[1.1.1]-propellane

Page 43: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Synthesis of Benzene Bioisosteres: cubane

I2

(PhO)2P(O)N3

tBuOH

PhH, hv

Moriarty, R. M. & Khosrowshahi, J. S.JACS 1989, 111, 8944

Eaton, P. E. et alJ. Org. Chem. 1984, 49, 185.

multiple reports

Eaton, P. E. & Maggini, M. J.JACS, 1988, 110, 7230

Toriyama, F et al. JACS, 2016, 138, 11132

Bernhard, S. S. R. et alChem. Eur. J., 2018, 24, 1026

methyl-1,4-cubanedicarboxylate

CO2H

MeO2C

CO2Me

H

PIDA CO2Me

I

NHBoc

MeO2C

2) Ar2ZnFe(acac)3

Ar

MeO2C

1) TCNHPIDCC

2) ArZnClNiCl2•dCO2Mebpy

1) TCNHPIDCC

Ar

MeO2C

Pb(OAc)4Ph

MeO2C

Page 44: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Synthesis of Benzene Bioisosteres: Escaping Straightland?

incorporation of strained sp3-rich scaffolds has a major limitation: nonlinear exit vectors

180°

Page 45: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Synthesis of Benzene Bioisosteres: Escaping Straightland?nonlinear exit vectors from bicyclopentane

Padwa et al. JACS, 1968, 90, 3717

Ohv HO

>280 nmPhH, 60h

~30% yield

Dougherty & Sponsler, JOC 1984, 49, 4978

O3, DCMO

Mazal et al. Org. Lett. 2006, 8, 749

benzvalene

2 steps as reported

for propellane(3 steps)

OHO

HO

O

4 stepsHOOC COOH

COOH

COOH

BrBr

Cl

Cl PhLi, Et2O

Page 46: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Fe(CO)3

Synthesis of Benzene Bioisosteres: Escaping Straightland?nonlinear exit vectors from bicyclopentane

Barborak et al. J. Am. Chem. Soc. 1966, 88, 1328

Bashir-Hashemi, J. Am. Chem. Soc. 1988, 110, 7234

8 stepsO CO2Me

MeO2C

Cl

Cl

Fe(CO)5+

O

O

Br

Br

CANO

OBr

Br 2 stepsHO2C

HO2C

~50% yield fromquinone

CO2Me

MeO2C

N

O

iPr

iPr1) LiTMP/MgBr2

2) CO2

N(iPr)2

O

CO2H

O

(iPr)2NO

(iPr)2N

HO2C

Page 47: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Additional Benzene Bioisosteres: Ortho and Meta

rigidity, increased 3 dimensionality improved physico-chemical properties?

Mykhailiuk, P. K. Org. Biomol. Chem. 2019,17, 2839

OR

O

RO

O LDA

CH2I2 OR

O

RO

O

BrClBr

Cl

Fuchs, J. & Szeimies, G. Chem. Ber. 1992, 125, 2517

MeLi

lower stability than [1.1.1]propellane

3.0 Å

5.1 Å

3.3-3.6 Å

5.0 Å

3.2 Å

Page 48: Bioisosteres of Common Functional Groupschemlabs.princeton.edu/.../6/...2019-PDF-Unlayered.pdf · key silacycle formation ... Melanin concentrating hormone receptor 1 (MCHr1) has

Bioisosteres of Common Functional Groups

Bioisosteres are frequently employed in a medicinal chemistry setting to improve or alter physico-chemical properties of lead compounds

The abundance and diversity of bioisosteres is continuously growing as novel chemical methodsfor the installation of complex functionality are developed

While important in elucidating stucture-activity relationships, bioisosteres can often have hard-to-predict effects on the activity and properties of bioactive molecules

Synthetic strategies toward installation of novel exit vectors on spirocyclic, bridged-bicyclic, and polycyclic sp3-rich scaffolds are in high demand in the medicinal chemistry community