Organic and Biochemistry

(1)

Development of Complex Curricula for Molecular Bionics and Infobionics Programs within a consortial* framework**

Consortium leader

PETER PAZMANY CATHOLIC UNIVERSITY

Consortium members

SEMMELWEIS UNIVERSITY, DIALOG CAMPUS PUBLISHER

The Project has been realised with the support of the European Union and has been co-financed by the European Social Fund ***

**Molekuláris bionika és Infobionika Szakok tananyagának komplex fejlesztése konzorciumi keretben

***A projekt az Európai Unió támogatásával, az Európai Szociális Alap társfinanszírozásával valósul meg.

PETER PAZMANY CATHOLIC UNIVERSITY SEMMELWEIS

UNIVERSITY

(2)

Application of the knowledge for synthetic and medicinal chemistry. Examples.

(A szintetikus és az orvosi kémiai tudás alkalmazása. Példák.)

Organic and Biochemistry

(Szerves és Biokémia )

semmelweis-egyetem.hu

Compiled by dr. Péter Mátyus

with contribution by dr. Gábor Krajsovszky Formatted by dr. Balázs Balogh

Organic and Biochemistry: Synthetic and medicinal chemistry

(3)

Type of the Projects

driven by

i) medicinal chemistry

ii) synthetic/mechanistic chemistry

(4)

Medicinal Chemistry

Goals

Improvement of biological activity: lead optimization - efficacy

- side effects

• Systematic SAR study

’step by step’ e.g. bioisosteric replacement

• QSAR-oriented (molecular modelling) Tools

(5)

Synthetic and mechanistic chemistry

Goals

• Scope and limitations of the synthetic method

• Structure-reactivity relationships and/or

• Mechanism proposal

(tools: kinetical, non-kinetical methods)

(6)

I. Mechanistic study: tert.-Amino effect II. Medicinal chemistry: CNS project

Case studies

(7)

Case-study I.

Mechanism proposal

i) structure-reactivity relationship ii) kinetic methods

determination of k, ΔH^#, ΔS^# iii) non-kinetic methods

spectroscopy, deuteration (labelling), cross-over, etc iv) literature overview (related reactions)

(8)

tert-Amino effect: kinetic isotope effect

k_H/k_D= 2.95 (120 °C) k_H/k_D= 2.80 (80 °C) R¹= R²= CN

R¹+ R²=

N N

O CH₃

O CH₃ O

N C N H₃

O

N CH₃

R² R¹

Ph N

N N

C H₃

O R¹

R²

CH₃ CH₃ Ph

DMSO-d₆

Δ

N C N H₃

O

N CD₃

R² R¹

Ph

D H

D D N

N N

C H₃

O R¹

R²

CD₃ CD₃ Ph

DMSO-d₆

Δ

(9)

Case-study II.

i) bioisosterism COOH

ii) patent position – literature search

iii) synthesis proposal - literature overview

N COOH

OAr

R² R¹

bioisosteric replacement

(10)

Case study II.

-bioisoterism

• hand books

• databases

N COOH

OAr

R² R¹

N H N N

- tetrazole

- hydroxamic acid Organic and Biochemistry: Synthetic and medicinal chemistry

(11)

Literature search

• First step!

• Target compound

• Analogue

purpose: i) medicinal chemistry ? ii) synthesis ?

ad i) survey on therapeutic class ad ii) chemical relationship

Databases

• Chemical Abstracts, Xfire, others - formula

- substructure - fragment, etc

(12)

Search for

i) target compound ii) model compound(s)

N H N N N

R³ R²

N H N N N

H

R² N N

N H

R²

N Prot

N H N N X

N N N X

Pr

a)

b)

(13)

Production of Compounds for Biological Assays

■ Design of the compound (medicinal chemistry)

■ Synthesis strategy

■ Selection of synthetic methods, based on

• Comprehensive knowledge

• Careful analysis of literature

• Creativity

▲ time scale: the possible shortest

- number and quality of steps

- availability of starting compounds - applicability to own system

▲ economical aspects

■ Design the full process time/amounts

■ Perform the synthesis do it at the right scale

- reaction conditions - isolation/purification

■ Prove the structure and quality

(14)

Ar¹ NR¹R² O Ar²

* ^Ar

1 Cl

O Ar²

*

Ar¹ Cl

OH

* ^Ar¹ ^Cl

O

provide it in enantiomerically pure form!

resolution?

asymmetric synthesis (stereoselective reduction)?

(15)

Drug-Receptor Interactions

Thermodynamics

D + R DR DR* response

D + R K

_as

DR K

_DR

DRG* response

K

_i

= [ligand] [receptor] / [ligand·receptor]

(16)

Drug-Receptor Interactions

PRODUCTIVE

1. Electrostatic interactions εr

q_iq_j

2. Inductive interactions a) in ligand or receptor

b) between ligand and receptor α α

r⁶ r⁴

~ ~

3. Non-polar interactions α₁α₂

r⁴

I₁I₂ I₁+I₂ 4. Hydrogen bond

5. Hydrophobic interactions

COSTS 1. Entropic

losses of rotational, translational and conformational freedom

2. Enthalpic - desolvation

- higher energy conformation ΔG = ΔH - TΔS = -RTlnK_as

(17)

ΔH

_DW

ΔS

_int

ΔS

_rt

ΔH

_RW

ΔS

_W

ΔS

_vib

ΔH

_DR

(18)

K

_i

= 10

^-9

M = 1 nM ΔG = -51 kJ/mol

(19)

Configuration Conformation

(20)

HO

H

CH₂ O H

N CH₃

CH₃

H HO

HO

O

CH₂ H

N CH₃

CH₃ H H

Donor-acceptor interaction

H-bond

Ionic interaction Ionic interaction

H-bond Donor-acceptor

interaction

A B

Interaction capacities of the natural R-(+)-epinephrine and its S-(-) antipode. (A) The combination of the donor-acceptor interaction, the hydrogen bond and the ionic interaction will generate energies of the order 12-17 kcal/mol, which corresponds to binding constans of 10^-9to 10^-12 M. (B) The loss of the hydrogen bond interaction represents to approximately 3 kcal/mol; this isomer should therefore possess an approximately 100-fold lower affinity.

(21)

Stereoselectivity in the Pharmacologic Action of Some Chiral Antiarrhythmic Drugs

Relative activity Biological response

Drug (ratio) (species)

Disopyramide S(+)>>R(-) Prolongation of QT intervals (human)

Encainide (+)=(-) Action potential parameters of cardiac Purkinje fibers (dog)

Flecainide S(+)=R(-) Prevention of chloroform-induced ventricular fibrillation (mouse) Prevention of ouabain-induced ventricular tachycardia (dog)

Mexiletine R(-)>S(+) Prevention of ventricular tachycardia (dog)

R(-)>S(+)(2:1) Tonic block of skeletal muscle sodium channels (frog) Propafenone R(-)=S(+) Sodium channel blocking activity (human)

R(-)=S(+) Antiarrhythmic effect in cardiac Purkinje fibers (dog) S(+)>R(-) (100:1) Beta blocking effect on lymphocytes (human)

Tocainide R(-)>S(+) (4:1) Sodium channel blocking activity (human) R(-)>>S(+) Analgesic effects (mouse)

Verapamil S(-)>R(+) (10:1) Calcium channel blocking activity (human)

S(-)=R(+) Inhibition of aortic contractions by α₁-agonists (rabbit) S(-)=R(+) Reduction of multidrug resistance to vincristine (human)

(22)

C H₃

H₂NSO₂

CHCH₂NHCH₂CH₂ OH

O

CH₃O

Pharmacodynamic Activity of the Enantiomers of Amosulalol

Eutomer pA2 Eudismic

Receptor Tissue (enantiomer) ratio

β₁ Rat atrium 7.71 (-) 48

β₂ Guinea pig trachea 7.38 (-) 47

α₁ Rabbit aorta 8.31 (+) 14

α₂ Rat vas deferens 5.36 (+) 3

Amosulalol

(23)

RRRRRR RRRRRR RRRRRR RRRRRR

SRSRSR SRSRSR SRSRSR SRSRSR

SSSRSR RRSRSR

SRRSSR RSRRSR

(a) (b) (c)

Schematic representation of the molecular arrangements in three types of racemates:

(a) enantiomeric or homochiral crystal (same chirality); (b) racemic or heterochiral crystal (paired enantiomers);

(c) pseudoracemate or solid solution (randomly arranged enantiomers).

(24)

NH₂ HO

HO

NH₂ HO

HO H₂N

O OH

HN

O OH

HN O

OH

HO

NH₂ O OH O

NH₂ O OH N

O HO

NH₂ O OH O

N H₃C

OH

HN N

NH₂

HN N

NH₂ H₃C

HN N

NH

NH₂

HO

NH NH₂

GABA

glutamic acid

histamine 4-methylhistamine

serotonin RU 27849

Conformationally restricred receptor agonists

adrenaline

(25)

ΔG = TΔS _r,t + n _DOF E _DOF + n _x E _x

TΔS_r,trepresents the unfavourable entropy term for a ligand binding to its receptor, assumed to be constant, and estimated to be 14 kcal mol^-1 n_DOF represents the internal degrees of conformational freedom, rotatable

bonds in the ligand

E_DOF represents the average entropy loss on binding per rotatable bond n_x represents the number of times that the functional group X appears

in the ligand

E_x represents the derived average intrinsic binding energy for group X.

(26)

Intrinsic bindings energies (kcal mol

^-1

)

Group Energy Range Group Energy Range

Charged Neutral

N⁺ 11.5 10.4-15.0 C=O 3.4 3.2-4.0

PO₄^2- 10.0 7.7-10.6 OH 2.5 2.5-4.0 COO^- 8.2 7.3-10.3 halogen 1.3 0.2-2.0

N 1.2 0.8-1.8

O, S 1.1 0.7-7.0

C (sp³) 0.8 0.1-1.0

DOF -0.7 -7.0 to-1.0 C (sp²) 0.7 0.6-0.8 Organic and Biochemistry: Synthetic and medicinal chemistry

(27)

H O H Asp 176

O

N⁺ H H O H

H

Asp 38

O O

P O O O^-

Gln 195

Asp 38

O

O O

N

N N

N NH₂

H H

Gly 36 Gly 192 Cys 35

His 48

Thr 51 Tyr 169

Tyr 34

(28)

Synthetic Chemistry

methods

sequence of steps

solvent optimization (mechanism-based) temperature

reagent (catalyst)

(29)

N H

N

Cl

Cl O

N N

Cl

Nu O

R

N H

N

Cl

Cl O

N N

Cl

Cl O

R N

N

Cl

Nu O

Nu: R

RX base

N H

N

Cl

Cl O

N H

N

Cl

Nu O

N N

Cl

Nu O

Nu: RX R

base

Sequence of reactions

Two options

A)

B)

(30)

Proper selection of solvent

N N

Cl

Cl O

R

N N

Nu

Cl O

R

N N

Cl

Nu O

R

apolar aprotic

polar Nu

(Nu:)

N N R

O

CH₃ CHO

N

N H R

O

N N

O R

KOBu^tert

DMF

KOBu^tert THF

(31)

N N

O R

H

R¹

R²

N N

O

R R¹

R²

N

C O R

N

R¹

R²

N O

N R

R¹

R²

N O

HN R

R¹

R²

base H⁺

-H⁺ N N

O

CH₃

R CHO

KOtBu DMF 80 °C 10 min

N O

N H R

R = BOM R = Bn

67%

47%

HRMS, IR

1H-NMR, ¹³C-NMR COSY, HSQC, HMBC X-ray

Ring closure I: using a strong base in DMF

Mechanism proposal: deprotonation-ring opening-ring closure

Rearrangement!

Precedent in the literature??

(32)

Becker, R. Ger. Pat. DE 3308297(1984)

30% NaOCH₃

DMSO rt 20 h

N N

O

OCH₃

OCH₃ N

H O

N

N O

HN Ph

OCH₃

OCH₃ CH₃O

N

HN Ph

OCH₃

OCH₃ O

CH₃O

CH₃O N

O

NH

OCH₃

OCH₃ Ph

CH₃O HN

O

N

OCH₃

Ph CH₃O

HN O

N

OCH₃

Ph

Ring contraction+N-phenyl migration Our mechanism proposal

Part I: deprotonation-ring opening-ring closure- Part II: ring opening-ring closure

I) rearrangement to 5-imino-1-phenylpyrroline

II) in the presence of a good nucleophile, another rearrangement occurs to 5-phenyliminopyrroline

80 % (our own result)

Pyridazine → pyrroline rearrangement: one published example

(33)

N N

O

CH₃

R CHO

N N

O Bn

CH₃CHO

46-94%

THF Base

Δ

THF Cs₂CO₃

Δ

N N

O R

N N

O Bn

94%

R = BOM R = Bn

Ring closure II: using the base in THF

HRMS, IR

1H-NMR, ¹³C-NMR COSY, HSQC, HMBC X-ray

No rearrangement!

i) change the solvent

ii) change the base

(34)

44%

KOtBu DMF 80 °C 10 min

N O

N H N

N O

N N

O

30% NaOCH₃ DMSO

rt

N H

N O

+

40% 45%

starting material

Two roles of the base in side reactions:

Rearrangement or debenzylation

(35)

• Be competent:

excellent knowledge about all aspects of the field

• Be well-prepared for every day

• Be competitive in your knowledge

• Be enthusiastic

The researcher - characteristics

(36)

Synthetic Chemistry

C – C bond formation C – X bond formation

(37)

C–C bond formation

- C–C cross coupling reactions (Pd-catalysed) - olefin metathesis

- cycloaddition 1,3-dipolar Diels-Alder

C–X bond formation

- C–O–C Mitsunobu

- C–N Buchwald-Hartwig

(38)

(39)

R² R¹

R³

H R⁴ X

R² R¹

R³ R⁴

+ cat.[Pd⁰L_n]

base R⁴= aryl, benyzl, vinyl X = Cl, Br, I, OTf

R¹ BY₂ + R² X cat.[Pd⁰L_n]

base R¹ R²

R¹= alkyl, alkynyl, aryl, vinyl

R²= alkyl, alkynyl, aryl, benzyl, vinyl X = Br, Cl, I, OP(=O)(OR)₂, OTf, OTs

R¹ SnR₃ + R² X cat.[Pd⁰L_n]

R¹ R² R¹= alkyl, alkynyl, aryl, vinyl

R²= alkyl, alkynyl, aryl, benzyl, vinyl X = Br, Cl, I, OAc, OP(=O)(OR) , OTf Heck Reaction

Suzuki Reaction

Stille Reaction

(40)

R² X

+ cat.[Pd⁰L_n]

cat. CuX,base

+ cat.[Pd⁰L_n]

base

X = Br, Cl, OCOR, OCO₂R, SO₂R, P(=O)(OR)₂ NuH =β-dicarbonyls, β-ketosulfones, enamines, enolates

R¹ ZnR² + R³ X cat.[Pd⁰L_n]

R¹ R³ Sonogashira Reaction

Tsuji-Trost Reaction

Negishi Reaction

R¹= alkyl, aryl, vinyl R²= aryl, benzyl, vinyl X = Br, Cl, I, OTf

R¹ H R¹ R²

R¹= alkyl, alkynyl, aryl, vinyl R³ = acyl, aryl, benzyl, vinyl X = Br, I, OTf, OTs

X NuH Nu

(41)

The typical, textbook catalytic cycle of the Heck reaction.

HPdXL₂ ArPdXL₂

Pd⁰L₂

oxidative addition

syn addition β-hidride

elimination

ArX Pd(OAc)₂+nPPh₃

? NEt₃

HNEt₃⁺X

PdXL₂ R Ar H Ar R

R

(42)

The catalytic cycle involving anionic intermediates as proposed by Amatore and Jutand for the Heck reaction.

Ar R

PdXL₂ R Ar

H ArPd(OAc)(PPh₃)₂ ArPd(PPh₃)₂⁺ + AcO^-

HOAc

+ H⁺ NEt₃ X^- NEt₃

HNEt₃⁺

ArX

HPd(OAc)(PPh₃)₂ ArPdX(OAc)(PPh₃)₂

R Pd⁰(PPh₃)₂(OAc) Pd(OAc)₂(PPh₃)₂ Pd(OAc)₂+ n PPh₃

PPh₃ (O)PPh₃ + H⁺ -

-

(43)

P Pd

C Br

Y

P Pd

C Br

Y AcO

P Pd

C Br

Y AcO

Br Ar

P Pd

C Br

Y Ar

Br

P Pd

C Br

Br Ar

Y P

Pd

C Br

Br H

Ar

Y

Pd Br

R R

R = o-MeC₆H₄

palladacycle complex:

palladacycle complex -HBr

+ AcO^- + AcBr

- AcO^-

The Pd(II)-Pd(IV) catalytic cycle outlined by Shaw for the Heck reaction.

(44)

A catalytic Heck cycle illustrating the presence of anionic palladium intermediates akin to those proposed by Amatore/Jutand.

Pd BuO₂C

Ph

I

I Ph Pd

I I

CO₂Bu

I Pd

I

Et₃N + Et₃NHI

Ph CO₂Bu

Pd I

PhI

Ph Pd I

I

CO₂Bu dimer or

Pd cluster

- -

-

PhI, I^- H₂O, ^-OAc H₂O Pd

O

-

I₂ -

(45)

The general catalytic cycle for the homeopathic Heck reaction as proposed by de Vries in 2006.

Pd BuO₂C

Ph

I

I Ph Pd

I I

CO₂Bu

I Pd

I

Et₃N + Et₃NHI

Ph CO₂Bu

Pd I

PhI

Ph Pd I

I

CO₂Bu

- -

-

PhI, I^- H₂O, ^-OAc

Pd O

O

-

Pd(OAc)₂

I₂ -

I Pd

I

I I

Pd I

I

-

2 H₂O

(46)

Pd BuO₂C

Ph

I

I Ph Pd

I I

CO₂Bu

I Pd

I

Et₃N + Et₃NHI

Ph CO₂Bu

Pd I

PhI

Ph Pd I

I

CO₂Bu

- -

-

PhI, I^- H₂O, ^-OAc

Pd O

O

-

Pd(OAc)₂

I2 -

I Pd

I

I I

Pd I

I

-

2 H₂O

-I I^-

I^- I^-

-I

-I I^-

I^- Na⁺

Na⁺ Na⁺

Na⁺ Na⁺ Na⁺

Na⁺ Na⁺

The general catalytic cycle for the homeopathic Heck reaction as proposed by de Vries in 2006.

(47)

The typical, textbook catalytic cycle for the Suzuki reaction.

Pd⁰

oxidative addition reductive

elimination

R¹ Pd^IIR² R¹ Pd^IIX

R¹ X R¹ R²

X-

[OR³]- transmetalation

(R⁴)₂BOR³

R²B(R⁴)₂

(48)

H

R

Pd(L) X

R

oxidative addition

N H

Ph

H Pd(L)

Ar

N H

Ph

N

Ph H Pd(L) Ar

N H

Ph Pd(L)

Ar

N H

Ph Ar Base

Base

reductive elimination

N

Ph

Pd(L) Ar

reductive

elimination N

Ph

Ar X = Br

"hard"

X = I

"soft"

electrophilic substitution

+

Proposed pathways to account the selectivity observed in the Pd-catalysed arylation of 2-phenylindole by aryl bromides or iodides.

(49)

OH OH OH OH OH

SiO₂ OH

3-(2-aminoethyl- amino)propyltri- methyloxysilane

O O O

Si NH NH₂

O O O

Si NH NH₂

O O O

Si HN NH₂

Pd(II)

O O O

Si HN NH₂

Pd(OAc)₂

SiO₂ SiO₂

[Pd] Catalyst

X R

+ R H R

R [Pd] Cat. (1 mol %)

K₂CO₃, EtOH, Reflux No Phosphine!

No Copper!

No Amine!

Recoverable Palladium Cat.!

Organic and Biochemistry

Application of the knowledge for synthetic and medicinal chemistry. Examples.

Organic and Biochemistry

Compiled by dr. Péter Mátyus

with contribution by dr. Gábor Krajsovszky Formatted by dr. Balázs Balogh

Type of the Projects

driven by

i) medicinal chemistry

ii) synthetic/mechanistic chemistry

Medicinal Chemistry

Synthetic and mechanistic chemistry

Case-study I.

tert-Amino effect: kinetic isotope effect

Case-study II.

i) bioisosterism COOH

ii) patent position – literature search

iii) synthesis proposal - literature overview

Case study II.

Literature search

Production of Compounds for Biological Assays

Drug-Receptor Interactions

D + R DR DR* response

D + R K

DR K

DRG* response

K

= [ligand] [receptor] / [ligand·receptor]

Drug-Receptor Interactions

ΔH

ΔS

ΔS

ΔH

ΔS

ΔS

ΔH

K

= 10

M = 1 nM ΔG = -51 kJ/mol

Configuration Conformation

Pharmacodynamic Activity of the Enantiomers of Amosulalol

RRRRRR RRRRRR RRRRRR RRRRRR

SRSRSR SRSRSR SRSRSR SRSRSR

SSSRSR RRSRSR

SRRSSR RSRRSR

(a) (b) (c)

ΔG = TΔS r,t + n DOF E DOF + n x E x

Intrinsic bindings energies (kcal mol

)

Synthetic Chemistry

Sequence of reactions

Two options

Proper selection of solvent

Ring closure I: using a strong base in DMF

Rearrangement!

Pyridazine → pyrroline rearrangement: one published example

Ring closure II: using the base in THF

No rearrangement!

Two roles of the base in side reactions:

Rearrangement or debenzylation

The researcher - characteristics

Synthetic Chemistry

C–C bond formation

C–X bond formation

ΔG = TΔS _r,t + n _DOF E _DOF + n _x E _x