DIPARTIMENTO DI SCIENZE FARMACEUTICHE β-AMINO ACIDS AS TOOL FOR THE ...

213 Pages·2014·7.86 MB·English

UNIVERSITA’ DEGLI STUDI DI MILANO
DIPARTIMENTO DI
SCIENZE FARMACEUTICHE

DOCTORATE SCHOOL IN CHEMICAL SCIENCES AND
TECHNOLOGIES
Doctorate course in Pharmaceutical Sciences – XXVII Cycle
AREA 03 SCIENZE CHIMICHE SSD-CHIM/06


-AMINO ACIDS AS TOOL FOR THE PREPARATION
OF FOLDAMERS AND NANOMATERIALS

Ph.D. Thesis presented by: Andrea BONETTI
R09727

SUPERVISOR: Prof.ssa Maria Luisa GELMI
COORDINATOR: Prof. Ermanno VALOTI

Anno Accademico 2013-2014
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Possano le tue scelte riflettere le tue speranze,
non le tue paure.
N. Mandela

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Table of contents
Abbreviations ........................................................................................................................................ 5
Chapter 1 –General Introduction ............................................................................................................ 7
1 Beta Aminoacids, Beta Peptides and Hybrid Peptides: Synthesis, Conformational Analisys and
Applications. .................................................................................................................................................. 8
1.1 Acyclic-Amino Acids Nomenclature and conformational properties ............................................. 9
1.2 Conformational Properties of cyclic-Amino Acids .............................................................................. 12
1.3 StandardSynthetic Methodologies for the preparation of -Amino Acids ........................................... 13
1.4 -Oligopeptides and -Hybrid Oligopeptides Conformation overview ............................................ 16
1.4.1 -Oligopeptides Secondary Structures. ......................................................................................... 17
1.4.2 -Hybrid OligopeptidesFoldamers: Secondary Structures. ........................................................ 22
1.5 Applications of  -peptides or  -Foldamers ...................................................................................... 26
1.5.1 Biological and Pharmaceutical Applications .................................................................................. 26
1.5.2 Nanomaterial Applications ............................................................................................................. 29
1.6 Aim of my Ph.D thesis ............................................................................................................................ 30
Chapter 2 – syn/anti Switching by Specific Heteroatom–Titanium Coordination in the Mannich-Like
Synthesis of 2,3-Diaryl-β-amino Acid Derivatives .................................................................................. 41
2. Introduction ............................................................................................................................................. 42
2.1 Results ................................................................................................................................................... 43
2.2 Discussion .............................................................................................................................................. 52
2.3 1H NMR discussion for 2,3-Diaryl--aminoesters 3 and 4 ..................................................................... 54
2.4 Complete set of NMR data for the Mannich-like reaction of 1d and 1i with imine 2c ......................... 55
2.5. Conclusions ........................................................................................................................................... 68
2.6 Reference ............................................................................................................................................... 69
Chapter 3 – 2,3-Diaryl-β-amino acid for the preparation of  Foldamers and Nanomaterials ............... 88
3. Introduction ............................................................................................................................................. 89
3.1 Result and Discussion ............................................................................................................................ 90
3.1.1 Chemistry ........................................................................................................................................ 90
3.2 Dipeptides 3a-(D1) and 3b-(D2) characterization. ................................................................................ 93
3.2.1 Solid state (X-ray analysis). ............................................................................................................. 93
3.2.2 In solution characterization ............................................................................................................ 95
3.3 Self organization studies on Dipeptides 3a-D1 and 3b-D2 .................................................................... 98
3.3.1 Proteolytic and Thermal stability of 3b-D2 Nanotubes .................................................................. 99
3.4 NMR Characterization of tetrapeptides and hexapeptides of D1 and D2 series. ............................... 100
3.4.1 Tetrapeptides 6a-(D1) and 6b-(D2) .............................................................................................. 101
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3.4.2 Characterization of hexapeptides 8a-(D1) and 8b-(D2) ............................................................... 107
3.5.Conclusion ........................................................................................................................................... 113
3.6 References ........................................................................................................................................... 115
Chapter 4 –Tetrahydroisoquinoline-4-carboxylic acid/-Alanine, a -Peptide Reverse Turn that Promotes
Hairpin formation .............................................................................................................................. 133
4.Introduction ............................................................................................................................................ 134
4.1 Results and discussion ......................................................................................................................... 136
4.1.1 Synthesis of amino acid 1 and its N-Boc derivative 5. .................................................................. 136
4.2 Studies on enzymatic resolution of N-Boc derivative 5. ...................................................................... 137
4.2.1 Pronase ......................................................................................................................................... 141
4.3 Preparation of model tetrapeptides. Fmoc-NH-(L)Ala-TIC-Ala-(L)Val-OBn and Ac-NH-(L)Ala-TIC-Ala-
(L)Val-NH . ................................................................................................................................................. 144
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4.4 NMR Characterization ......................................................................................................................... 147
4.5 References ........................................................................................................................................... 153
Chapter 5 – Rhodium catalyzed transformation of -(-diazo carbonyl)-piperidine derivatives ............ 170
5.Introduction ............................................................................................................................................ 171
5.1 Rhodium catalysts: an overview on their synthetic applications ........................................................ 171
5.1.1 H-CR1R2R3 insertion ....................................................................................................................... 174
5.1.2 H-NR1R2 insertion .......................................................................................................................... 175
5.1.3 Ylide Formation and Subsequent Reactions ................................................................................. 176
5.1.4. Reactions with Aromatics: Benzene and Its Derivatives ............................................................. 177
5.1.5. Chemoselectivity and regioselectivity ......................................................................................... 179
5.2 Aim of the work ................................................................................................................................... 179
5.3 Results and Discussion ......................................................................................................................... 180
5.3.1 Starting materials preparation. .................................................................................................... 180
5.3.3 Discussion ..................................................................................................................................... 190
5.3 Reference ............................................................................................................................................. 195

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Abbreviations

AA. amino acid
Ac. acetyl
ACC. aminocyclopropanecarboxylic acid
ACHC. 2-aminocyclohexanecarboxylic acid
ACPC. aminocyclopentanecarboxylic acid
Aib. Aminoisobutyric acid
Ala. alanine
APC. aminopyrrolidinecarboxylic acid
Bn. benzyl
Boc. tert-butyloxycarbonyl
Cbz. benzyloxycarbonyl
CD. circular dichroism
COSY. correlation spectroscopy
DBU. 1,8-Diazabicyclo[5.4.0]undec-7-ene
DCHC. 2,5-diaminocyclohexanecarboxylic acid
DCM. dichloromethane
DIPEA. diisopropylethylamine
DMAP. N,N-dimethylaminopyridine
DMF. N,N-dimethylformamide
DMSO. dimethylsulfoxide
ee. enantiomeric eccess
eq. equivalents
ESI.electrosprayionisation
Fmoc.Fluorenylmethyloxycarbonyl
hAla. Homoalanine
HMBC. Heteronuclear Multiple Bond Correlation
HOAc.acetic acid
HSQC. Heteronuclear Single Quantum Coherence
hVal. Homovaline
iBu.isobutyl
IR.infra-red
Me. methyl
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MS. mass spectrometry
Nip. Nipecotic acid
NMM. N-methylmorpholine
NMR.nuclear magnetic resonance
NOE.nuclearOverhauser effect
NOESY.nuclearOverhauser effectspectroscopy
Nt. Nanotube
PBS. Phosphate buffer solution
pfb. perfluorobutirrate
Ph. phenyl
Ppm. parts per million
Pro. proline
ROESY.rotating frame NOESY
Rt. room temperature
SPPS.solid phase peptide synthesis
Bu.tert-butyl
t
TEA. Triethyamine
TEM.transmission electronmicroscopy
TFA.trifluoroacetic acid
THF.tetrahydrofurane
TIC. tetrahydroisoquinoline
TOCSY.total correlationspectroscopy
tpa. tetraphenylacetate
Val. valine

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Chapter 1 –General Introduction

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1 Beta Aminoacids, Beta Peptides and Hybrid Peptides: Synthesis,
Conformational Analisys and Applications.
-Amino acids are analogues of -amino acids (AAs) in which the amino group is linked to the
beta-carbon instead of the alpha-carbon (Figure 1).

Figure 1. Alpha and Beta amino acids
Differently from proteinogenicamino acids, that are costituent of all enzymes which control the
metabolism in living matter and are thus an essential prerequisite for life, amino acids are present
in few natural products, such as peptides, cyclopeptides, glycopeptides, alkaloids or terpenoids.
Therefore, these compounds are often characterized by potent biological and physiological activities
that are often crucially based on their structures. As a consequence, many natural products with
aamino acids (AAs) moiety are potential lead structures for the development of new drugs
(Figure 2).

Figure 2. Bio-active compounds containing -amino acids moiety

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Moreover, the incorporation of amino acids into peptides instead of amino acids increases
the stability against degradation by mammalian peptidases. This enhanced stability is caused by a
lack of enzymes which induce the cleavage of peptidic bond. Therefore amino acids are
important tools in the development of drugs as single molecules or for the preparation of peptides
capable of withstanding hydrolytic degradation for prolonged periods of time. For all these reasons,
in recent years,the focus on the synthesis of new amino acids is exponentially increased, making
this field of great interest and strong expansion (Figure 3).
Figure 3
1.1 Acyclic-Amino Acids Nomenclature and conformational properties
The nomenclature for -AAs generaly takes in consideration three types of acyclic amino acids,
depending on whether the sobstitution of side chain takes place, (i.e.C C or both). Recently,
 
Seebach and co-workers 1 proposed the terms and amino acids, where the numbers indicate
the position of the side chain substitution with respect to the carboxylic function, in order to
distinguish positional isomer (Figure 4).As regards as aminoacidscarringsubstitutionat
bothC andC () the number of possibleregioandstereoisomers becomesgreaterthan and
 
-AAswhere only enantioisomersare possible. -AAs, may exist as apair of diastereisomers
generally namedsynandantidepending on the stereoisomeric relationshipof the substituents (Figure
4). Furthermore, position C2 and C3can be doubly substituted, giving rise to more complex and
constrained-AAs.
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Figure 4
Concerning the use of -AAs in peptide synthesis, it is of relevance to analyze the amino acid
conformation in terms of the main chain torsional angles assigned as φ, θ, and ψ according to the
convention of Balaram2(Figure 5).

Figure 5
The effects of the substituents on the local conformation of a -amino acidare summarized in Figure
6. The unsubstituted-amino acid, (i.e. -alanine), is highly flexible, as for Glycine in the -amino
acids. Substituents at position 2 or 3 favor a gauche conformation around the C2-C3 bond3.

Figure 6. Effects of the substituents on the local conformation of a -amino acid
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