Больше хороших молекул: скаффолд-ориентированный синтез для биомедицинских

приложений

Lecture 2. 1st Year Graduate students. 2016

Picture of the day

Once again: main points from the previous (intro) lecture

• medicinal chemistry

• drug target

• target identification

• target validation

• from validated target to pre-clinical candidate in ____ months

• any individual and pure organic compound is good for screening: TRUE/FALSE

• Lipinsky “RULE OF FIVE”

Quotation from the course synopsis

Основной дидактической целью курса является выработка у слушателей трех важнейших навыков: • понимания сложностей и особенностей принятия решений в многопараметрической медицинско-химической оптимизации • способности критически оценивать встречающиеся в литературе результаты • навыков дизайна собственных исследовательских проектов по разработке и оптимизации новых химических серий в различных терапевтических областях, на различных биологических мишенях + LOTS AND LOTS OF MEDCHEM AND DRUG DISCOVERY LINGO IDEA FOR A LECTURE: «Англоязычная терминология в медицинской химии и drug discovery: перспективы использования в русскоязычной практике»

Chemistry space projection on Biology space

Понятие скаффолда (scaffold)

SO

OR

R'

Скаффолд (темплат, хемотип)

Selective COX-2

inhibitors

O

SO

O

O

NN

SO

ONH2

F3C

ON

SO

ONH2

SBr

S OO

F

Vioxx(Merck)

Dup-679 Bextra (Pfizer)

Celebrex (Pfizer) 2013 sales >US$2.5B

WITHDRAWN

WITHDRAWN

Расположение периферии в пространстве Свойства соединения, «слабые места» Первоочередная основа для защиты интеллектуальной

собственности

Периферия

Принципы отбора синтетических идей в работу

Biological relevance

Novelty of scaffold

Novelty of chemistry

Elegance of synthetic approach

New environment for a known pharmacophore

Реакция Уги: от дипептоидов к разнообразным гетероциклам

NH2R1

O

R2

R3

R4OH

O

-CN+

R5

+N+H

R1

R3

R2

N+C-R5

R4

-O O

R3 R2

NH

R1N

O

R4

OR5

R4 N

O

R1

R3 R2HN

OR5• Суррогатные замены

• Бифункциональные реагенты

• Пост-конденсационные модификации

* *

* *

- H2O

Mumm rearrangement Многокомпонентная реакция

NH2

NH2

PhCHOt-BuNC N

NH2

Ph-C

N+

H+

NH

HN Ph

NH

DDQ, benzene

HClMeOH

r. t., 18 h

N

N Ph

NH

51% over 2 steps

2 X

HCl

dioxaner.t.

93%

N

N Ph

N

N Ph

NH2

N

NH

n-PrCHOt-BuNC

TMSClN

N Ph

NC-

N+

LA

69%

Krasavin et al. Synlett 2008, 645; JOC 2009, 74, 2627

2 МКР подряд ?

* *

NCNH

ONH2

O

TFA, dioxaner. t., 18 h

82%

NC

NH

NNH

O

O

NF3C O 0.5M HCl

MeOH60 oC, 18 h

74%

N

HNO

NH2

HNO

aq. K2CO3MeOH60 oC, 18 h

N

HNO

CF3

HNO

NC

69%NH

NNH

O

O

NF3C O

H+

NH

HN

NH

O

O

N F3CO

H+

- H2O

Krasavin et al. Tetrahedron Lett. 2010, 51, 4095

DOS – синтез, ориентированный на разнообразие

* *

OCHO H2N

NC HO

O

NHPh

O

+ O N

OPhHNOC

NHO

MeOH

r. t.

O N

O

ONH

O NHPh

68%

N

O

ONH

O NHPh

85% H3PO4 85% H3PO4

100 oC, 2 h88%

NN

O

O

O

OO

H

Krasavin et al. J. Org. Chem. 2006, 71, 9544

X

Тандем «реакция Уги – внутримолекулярное присоединение»

Мы в Википедии!

* *

S SO

SO O

SO

EWG

SO

EWG

OEWG

[O] [O]

[O]

- SO2

[O]

k1(DA) k2(DA)

k1(DA) >> k2(DA)

EWG EWG

Thiophene-S-oxide: IMDA and aromatization in one step?

* *

S O

S NH2

OO

COOHNH2

MeO

NC

MeOH, r. t., 20 h

OO

COOH

PhCHO

NC

O

O

S

NO

HN

MeO

O

OO

S N

OO

OO

NHO

O

m-CPBA (7 equiv.)DCM, r. t., 24 h

N

OO O

NHO

OMe29%(2 steps)

N

OO O

ONH

O

O

39%(2 steps)

Krasavin et al. Tetrahedron Lett. 2010, 51, 5657

S-ox

IMDA

S-ox

- SO2

- 2H

Thiophene containing Ugi adducts easily convert into isoindolinones

NH2

O

N NH2

O

NH2

OH2N

NH

N

H2N O

NH

ABT-888

NH

HN

F

OHN . H3PO4

AG014699

Poly(ADP-ribose)polymerase 1 (PARP1)

NAD+ bound to PARP-1

N+

R

NH2

O

NAD+

Tum

or w

eigh

t (g

)

Growth of mouse tumor xenograft

0

0.2

0.4

0.6

0.8

1

1.2

1.4

0 1 3 5 8 10 12

control Compound A (75 mpk) Compound B (75 mpk)

days

N

OO

R

N HH

R'

Isoindonlin-1-one PARP-1 inhibitors?

1. Papeo, G. M. E.; Krasavin, M.; Busel, A.; Khvat, A.; Forte, B.; Zuccotto, F. Oxo-2,3-dihydro-1H-isoindole-4-carboxamides as PARP Inhibitors.PCT Int. Appl. (2011), WO 2011006794, 69 pp.

2. Papeo, G. M. E.; Busel, A.; Casale, E.; Khvat, A.; Orsini, P.; Posteri, H.; Scolaro, A.3-Oxo-2,3-dihydro-1H-isoindole-4-carboxamides with selective PARP-1 inhibitions.PCT Int. Appl. (2011), WO 2011006803, 73 pp.

3. Papeo, G. M. E.; Borghi, D.; Caruso, M.; Posteri, H.; Krasavin, M. 3-Oxo-2,3-dihydro-1H-indazole-4-carboxamide derivatives as PARP-1 inhibitors. PCT Int. Appl. (2013) WO2013014038A1, 43 pp.

4. Papeo, G. M. E.; Orsini, P.; Scolaro, A.; Krasavin, M. Preparation of carboxamido-isoindolinone derivatives as selective PARP-1 inhibitors. (Nerviano Medical Sciences) PCT Int. Appl. (2014), 60 pp. WO20142014064149A1.

“…These compounds show high oral bioavailability, good ADME properties and high tolerability. Selection of the candidate most suitable for further development is underway…”

Cancer Res, 2012,72, Supplement 1 doi: 10.1158/1538-7445.AM2012-1775 Proceedings: AACR 103rd Annual Meeting 2012-- Mar 31-Apr 4, 2012; Chicago, IL Abstract 1775: “Characterization of new highly selective and potent PARP-1 inhibitors “

Clinical candidate?

Visit our website: www.krasavin-group.org

Nadin, A. et al. Lead-Oriented Synthesis: A New Opportunity for Synthetic Chemistry. Angew. Chem. Int. Ed. 2012, 51, 1114-1122: «… Lead-oriented synthesis (LOS) is a new but simple concept describing reactions that allow the efficient preparation of diverse sets of small, polar molecules to act as starting points for drug discovery…»

В мире так мало … идеальных лид-соединений (leadlike compounds)!

Examples of compound synthesized:

(also under µwave irradiation)

Krasavin, M. Tetrahedron Lett. 2012, 53, 2876-2880.

HN

NRR

OHetArHal (1.1 equiv.)

Pd(OAc)2 (2 mol %)BINAP (4 mol %)

Cs2CO3 (1-3 equiv.)toluene, 100 oC, 16-20 h

N

NR

HetAr

H2NCH2CH2NH2

NBS

56-96% 49-93%

N

N

NF

N

N

N

N

N

NN

N

N

N

N

O

F

N

N

NNH2

(via NO2 --> NH2)

N-Heteroaryl imidazoline synthesis

Mw & cLogP on the right track!

0,0

1,0

2,0

3,0

4,0

5,0

6,0

0,0 100,0 200,0 300,0 400,0

N-Heteroaryl imidazolines cLogP

MW

Arachidonic acid cascade in inflammation

COX

COX

COX-1 COX-2

Consitutive enzyme Inducible enzyme

Inhibition undesired Selective inhibition is

highly desirable

Selective COX-2 inhibitors (coxibs)

O

SO

O

O

NN

SO

ONH2

F3C

ON

SO

ONH2

SBr

S OO

F

Vioxx(Merck)

Dup-679 Bextra (Pfizer)

Celebrex (Pfizer) 2013 sales >US$2.5B

N

N

SO

O

Cl

COX-2 IC50 = 0.24 µMCOX-1 IC50 > 100 µM

Khanna, I. K. et al. J. Med. Chem. 1997, 1634.

New synthesis of known imidazole COX-2 inhibitors gave us an idea

N

N

SO

O

Cl

COX-2 IC50 = 0.24 µMCOX-1 IC50 > 100 µM

NH

N

4-BrC6H4SO2Me (1.1 equiv.)Pd(OAc)2 (5 mol%)BINAP (10 mol%)Cs2CO3 (1.0 equiv.)toluene, 100 oC, 16-20 h

NN

NBS

DCM, 0 oC --> rt H

O

10% Pd-C

toluene, 100 oC36 h

SOO

NN

SOO

ClCl

Cl Cl

H2NNH2

Krasavin, M. Lett. Org. Chem. 2013, 10, 235

Khanna, I. K. et al. J. Med. Chem. 1997, 1634.

Can imidazolines inhibit COX-2?

N

N

SO

O

Cl

COX-2 IC50 = 0.24 µMCOX-1 IC50 > 100 µM

No substitution preferred

CH3 or CF3 increases COX-2 potency

H2NSO2 in lieu of Me sulphone preferred

Hal or MeO substitutions preferred

Searle (Pfizer) compound:

Pilot imidazoline library dsigned based on the SAR from Searle

NN

SO

R

OR'

R''

H, Me = = CH3, NH2

‘Best’ substitutions from Searle

Σ = 30 compounds LIGAND-BASED DESIGN

Pilot library synthesis

NH

N

4-BrC6H4SO2Me (1.1 equiv.)Pd(OAc)2 (5 mol%)BINAP (10 mol%)Cs2CO3 (1.0 equiv.)toluene, 100 oC, 16-20 h

NN

NBS

DCM, 0 oC --> rt H

O

SOO

R'

H2NNH2

R'

R'

R R

R

Pd(OAc)2 (5 mol%)BINAP (10 mol%)

Cs2CO3 (1.0 equiv.)toluene, 100 oC, 20 h

Br SO

ON(DMB)2

DMB =

O

O*

NN

SO

N(DMB)2

OR'

R

TFA, Et3SiH DCM, 0 oC--> r.t.

NN

SO

NH2

OR'

R

Σ = 30 compounds

R’’Ph Ar1 Ar2 Ar3 Ar4 Ar5 Ar6 Ar7 Ar8 Ar9 Ar10 Ar11 Ar12

R / R’

Me/H 7.1 6.8 8.1 2.1 3.6

Me/Me

NH2/H 6.9 3.4 2.9 7.2 2.5 9.5 6.2 6.7 0.3 1.8

NH2/Me

NN

SO

R

OR'

R''

SAR for imidazoline COX-2 inhibitors (IC50, µM)*

imidazolines clearly display a different SAR compared to Searle’s imidazoles the most active compound is comparable to Celebrex (IC50 = 0.11 µM) in terms of COX-2 inhibitory potency

* All compounds do NOT inhibit COX-1 even at 100 µM !

Animal efficacy of the lead compound

Control 3h post carageeenan injection

Plethysmometer

0

10

20

30

40

50

60

70

80

90

Control Treatment

MIKR06-27-1 3.7 mg/kg i.p.

PK profile of the lead compound

Plasma

Brain tissue

LC MS MS

Systemic exposure

Drug exposure in

CNS

Сmax = 16.6 µM (55 x IC50!) Сmax = 0.71 µM

(2 x IC50!)

CNS-expressed COX-2 is implicated as target for neuroinflammation COX-2 inhibitors that cross the BBB are needed to validate this approach

A case study of an effective drug discovery collaboration

Griffith U: project design and compound synthesis

UC Davis: biochemical testing

for COX-2/1 inhibition

MIPT: in silico modeling

Enamine/Beinta: mouse PK studies

Aristotelean U Greece: animal efficacy

Sarnpitak, P.; Mujumdar, P.; Morisseau, C.; Hwang, S. H.; Hammock, B.; Iurchenko, V.; Zozulya, S.; Gavalas, A.; Geronikaki, A.; Ivanenkov, Y.; Krasavin, M. Eur. J. Med. Chem. 2014, 84, 160-172.

1,3-Diarylindanes: guessing it right

F3C

Ar

Ar

O

CF3

TfOH20 °C, 1h

+R3

R2

R1

R2

R3

R1

R1

R2R3

F3C

Ar

R1

R2R3

Ar

OH

CF3

R3

R2R1

35-80%

cLogP ~ 6-8

NH

OHO

AEA

O

OHO

2-AG

HO

O

OH

H

H

∆9-THC

Prof. Vasiliev group (SPbSU)

1,3-Diarylindanes: guessing it right

N NHN

ON

Cl

Cl

Cl

SR141716A

N

O

JWH015

O

O

MeO

CN

OMe

LY320135

CB1 CB1 CB2

F3C

OMe

OMe

Cl

MeO

MeO

1,3-Diarylindanes: guessing it right 1 µM 10 µM

F3C

OMe

OMe

Cl

MeO

MeO

U Bern (Switzerland)

Concepts introduced or touched upon today molecular scaffold and compound’s periphery

clinically validated biological (therapeutic) target

lead-like compounds (“lead-likeness”)

potency and selectivity of drug candidate

chemistry and biology space

privileged scaffolds