University of Jyväskylä, Finland August 2012 University of ...

Sh

ort C

ou

rse:

So

lutio

n S

tructu

re Determ

inatio

n

In O

rgan

ic Ch

emistry an

d C

hem

ical Bio

log

y

Sam

uel H

. Gellm

anU

niversity o

f Wisco

nsin

– Mad

ison

, US

A

Au

gu

st 2012U

niversity o

f Jyväskylä, Fin

land

V. Fo

ldam

ers

FO

LDA

ME

RS

-- Oligom

ers that adopt compact,

predictable and well-defined conform

ations

A

new strategy for controlling

molecular shape and function

Proteins: W

orkhorse Molecules in B

iology

Proteins: W

orkhorse Molecules in B

iologyS

equence (1D)

Shape (3D

) F

unction…

Tyr – His – A

la – Leu – Phe – Leu – G

ly – Lys…Pepsin (P

DB

6AP

R)

NH

HNNH

O

O

OR

R

NH

+ H3 N

NH

O

O

OR

R

O -

H2 O

Martick, S

cott C

ell 126:309 (2006)

Proteins vs. R

NA

: Backbone V

ariation is Possible

OO

Base

OPO

OO - H

O

HNNH

O

O

R

van d

en B

erg et al. E

mb

o J 14:4123 (1995)

Biopolym

er Folding S

imulated

with S

imple Lattice m

odels

22

= h

ydro

ph

ob

ic

= p

olar

Dill et al. P

rotein

Scien

ce 4:561 (1995)

Foldam

er Exam

ples: Extended P

eptidic Backbones

-Pep

tides:

Gervay, F

leetO

AcO

OA

c

HN

OO

AcO

OA

c

HNHN

OO

-Pep

tides:

-Pep

tides: NH

NHNH

OO

OS

eebach

, Gellm

an, G

un

g,

Died

erichsen

, DeG

rado

, Fleet,

Fü

löp

, Win

kler, Berkessel,

Sch

epartz,...

NH

HN

OS

chreib

er ("vinylo

go

us p

eptid

es"), S

eebach

, Han

essian, G

ellman

, S

mith

...

RR

O

NH

OR

R

-Pep

tides:

Gervay, F

leetO

AcO

OA

c

HN

OO

AcO

OA

c

HNHN

OO

-Pep

tides:

-Pep

tides: NH

NHNH

OO

OS

eebach

, Gellm

an, G

un

g,

Died

erichsen

, DeG

rado

, Fleet,

Fü

löp

, Win

kler, Berkessel,

Sch

epartz,...

NH

HN

OS

chreib

er ("vinylo

go

us p

eptid

es"), S

eebach

, Han

essian, G

ellman

, S

mith

...

RR

O

NH

OR

R

Foldam

er Exam

ples: Extended P

eptidic Backbones

Foldam

er Exam

ples: Nucleotide A

nalogues

Nielsen

, Acc. C

hem

. Res.

32:624 (1999)

Pep

tide-N

ucleic A

cids (P

NA

s):

NNH

O

Base

Ph

osp

ho

roth

ioates:

Millig

an, M

atteucci &

Martin

J. Med

. Ch

em. 36:1923 (1993)

O

NNH

O

Base

O

OO

Base

OPO

S -

OO

Base

OPO

S -

O

OO

Base

OPO

O -

OO

Base

OPO

O -

O

DN

A:

Foldam

er Exam

ples

Helical P

epto

ids:

Dill, Z

uckerm

ann

, Co

hen

, Barro

n, K

irshen

bau

m,

Blackw

ell, Ko

dad

ek, Ap

pella...

NN

O

OR

R

HN O

O

O

N

OO

H

O

R

R

RR

Aro

matic O

ligo

amid

es

Ham

ilton

, Go

ng

, Hu

c,...

NN

HH

N

OO

HN

NH

OO

MeO

2 CC

O2 M

e

Arom

atic Foldam

er Design: H

uc et al.

Huc et al. J. A

m. C

hem. S

oc. 2007, 129, 11348.

Foldam

er Exam

ples: Beyond C

arboxamides

-Am

ino

xy Acid

Olig

om

ers:

Su

lfon

amid

e Olig

om

ers:

Urea O

ligo

mers:

Gen

nari, L

iskamp

Yan

g

SNH

SNH

SNH

OO

OR

R'

NH

ONH

ONH

OO

O

OO

RR

'

NHNH

HNHN

NHNH

OR

OR

'

OG

uich

ard

O

Foldam

er Exam

ples: Purely H

ydrocarbon Backbones

Mo

ore

m-P

hen

ylene-eth

ynylen

e Olig

om

ers:

J. S. M

oo

re et al., Ch

em. R

ev. 101:3893 (2001)A

Field

Gu

ide to

Fo

ldam

ers

NHNH

NHNH

NHNH

OO

OO

OO

NH

HNNH

HNNH

HN

O

O

O

O

O

O

-Peptides

Seebach et al.; G

ung et al.; Fleet et al.; D

eGrado et al.; D

iederichsen et al.; Ichikawa et al.;

Winkler, K

lein et al.; Martinek, F

ülöp et al.; Kessler et al.; S

chepartz et al.; Berkessel et al.;

Sharm

a, Kunw

ar et al., Chandrasekhar, Jagadeesh, Jagannadh et al.; H

ofmann et al.;

Wu et al.; V

an Gunsteren et al.; Jorgensen et al.; B

runsveld et al., Ortuño et al.;…

Extrapolation from

-P

eptides: -P

eptides

-Peptides w

ith Acyclic R

esidues (3)

H2 N

NHNH

NHNH

NHOH

OO

OO

OO

D. S

eebach et al. Helv. C

him. A

cta 1996, 79, 913 and 2043.D

. Seebach and J. L. M

atthews C

hem. C

omm

un. 1997, 2015.

14-helix in organic solvents

NH

O

NH

O

NH

O

NH

OR

R'

NH

R'''

HH

OR

''H

14-atom

H-b

on

ded

ring

s

-Peptides w

ith Acyclic R

esidues (3)

H2 N

NHNH

NHNH

NHOH

OO

OO

OO

D. S

eebach et al. Helv. C

him. A

cta 1996, 79, 913 and 2043.D

. Seebach and J. L. M

atthews C

hem. C

omm

un. 1997, 2015.

NH

O

NH

O

NH

O

NH

OR

R'

NH

R'''

HH

OR

''H

CH

(i) -- CH

(i+3) NO

E

14-helix in organic solvents

-Peptide S

econdary Structure: S

tabilize Helix w

ithC

yclic -A

mino A

cid Residues?

14-Helix

(Crystal stru

cture)

Appella, C

hristianson et al.JACS

1996, 118, 13071.

tBuO

NH

O

NH

NH

O

NHNH

O

NH

OCH2 Ph

O

O

O

O

14-atom

ring

H-b

on

d

NO

E P

atterns for the -P

eptide 14-Helix

NH

NH

OO

O

NHNH

OO

O

O

H

H

H

H

H

H

H

H

NO

ES

Y d

ata (CD

3 OH

, 5˚C, tm

ix = 400 ms)

(Joe B

archi an

d X

iaolin

Hu

ang

, NIH

)

sequ

ence

con

form

ation

Barch

i et al., J. Am

. Ch

em. S

oc. 122:2711 (2000)

Qualitative Indication of 14-H

elix Stability from

S

low H

/D E

xchange ( 1H N

MR

)

tBuO

NH

O

NHNH

O

NHNH

ONH

OBn

OO

OO

Appella, C

hristianson et al.JACS

1996, 118, 13071.

CD

3 OD

tBuO

OBn

O

NHNH

OO

No

n-fo

lded

con

trol (*):

-Peptide S

econdary Structure: C

ontrol over Helix

Shape via C

hoice of Cyclic C

onstraint

12-Helix

Appella,

Christianson et al.,

Nature 1997, 387, 381.

HN

O

HN

O

HN

O

HN

O

HN

O

BocNH

HN

O

HN

O

OCH2 Ph

O

12-atom

ring

H-b

on

d

HN

O

HN

O

HN

O

HN

O

HN

O

HN

O

OC

H2 P

h

OO

H

H

H

H

HH

HH

HH

HH

RO

ES

Y D

ata (pyrid

ine-d

5 and

CD

3 OH

)

(Joe B

archi an

d X

iaolin

Hu

ang

, NIH

)

Ap

pella et al., N

ature 387:381 (1997)

Barch

i et al., J. Am

. Ch

em. S

oc. 122:2711 (2000)

NO

E P

atterns for the -P

eptide 12-Helix

-Peptide vs.

-Peptide H

elices

-helix

310 -helix

12-helix14-helix

NHNH

NHNH

NHNH

NH

OO

OO

OO

O

NH2

CO2 H

NH2

CO2 H

NH

HNNH

HNNH

HN

O

O

O

O

O

O

RR

R

RR

Sheet S

econdary Structure in

-Peptides?

Krauthäuser et al. JA

CS

1997, 119, 11719.C

hung et al. JAC

S 1998, 120, 10555.

See also:

Seebach et al. A

ngew. C

hem. Int. E

d. 1999, 38, 1595.M

artinek et al. Angew

. Chem

. Int. Ed. 2002, 41, 1718.

NH2

CO2 H

H

CO2 H

NH2

H

CO2 H

HR H

R*

NH2

H2 N

CO2 H

R*R

Fo

r helices…

Fo

r sheets…

C-C

~ gau

che

C-C

~ anti

A

-Peptide R

everse Turn

N

N

OO

HN

O

N

N

OO

HN

O

L. C

hristian

son

, Y. Ch

un

g

IR D

ata in C

H2 C

l2 (N-H

Stretch

Reg

ion

)

A M

inimal

-Peptide H

airpin: O

ne Residue in E

ach Strand and a R

everse Turn

Ph

H

O

O

N

O

N

NH

OO

N

NH

OSPh

Chung, C

hristianson, Stanger, P

owell, G

ellman J. A

m. C

hem. S

oc. 1998, 120, 10555.

Minim

al -P

eptide Hairpin: N

OE

Data (C

D2 C

l2 )

Ph

OH

OH

N

ON

NSPh

H

O

N

N

O

HH

Alternative

-Peptide R

everse Turns

Seeb

ach et al., A

ng

ew. C

hem

. In

t. Ed

. En

gl. 1999, 38, 1595.

Ph

OH

OH

N

ON

NS

Ph

H

O

N

N

O

Stran

d resid

ues: K

rauth

äuser et al.,

J. Am

. Ch

em. S

oc. 1997, 119, 11719.

Reverse tu

rn: C

hu

ng

et al., J. A

m. C

hem

. So

c. 1998, 120, 10555.

OH

NCO

2 HN

H3 +

O

O

NH

HN

O

NH

O

NH

NH

3 +

14-Helix F

ormation by a

-Peptide H

examer in W

ater(T

he Ultim

ate Challenge in P

eptide Folding…

)

+ H3 N

+ H3 N

O

O

O

NH

3 +

NH

O

BnO

NH

NH

O

Ph

NH

O

NH

NH

OC

H3

O

vs.

(crystal)

(2D N

MR

)

Backbone overlay: rm

sd = 0.27 Å

Appella, B

archi, Durell, G

ellman J. A

m. C

hem. S

oc. 1999, 121, 2309.

tBuO

NH

O

NH

NH

O

NHNH

O

NH

OCH2 Ph

O

O

O

O

Synthesis R

equired…

OM

e

OO

OM

e

OH

OO

OM

e

NH

Cbz

OO

IN

HC

bz

O

OM

eH

O

NH

Cb

z

O

OM

eB

ocHN

NH

Cb

z

O

OM

eB

ocH

N

CH

2 Cl2

NaH

CO

3

NH

Cbz

O

OHN

HC

bz

O

OM

eB

ocHN

1. DB

U, P

hH

, R

eflux

2. NaO

Me, 0 °C

1. MsC

l, NE

t32. B

u4 + N

3 -

I2 , KI

3. PB

u3 , H

2 O

4. Bo

c2 O

Pig

Liver

Esterase

pH

8.0

1. EtO

CO

Cl

2. NaN

3

3. Ph

H, R

eflux

4. Bn

OH

, Reflu

x5. N

aOH

, MeO

H

1. H2 , P

d-C

2. Cb

z-Cl, N

Et3

NaO

Me,

MeO

H, R

eflux

Appella et al. J. O

rg. Chem

. 2000, 65, 4766

Cyclic vs. A

cyclic Residues:

Dram

atic Conform

ational Effects in W

ater(C

ircular Dichroism

)

+ H3 N

+ H3 N

O

O

O

NH

3 +

NH

O

BnO

NH

NH

O

Ph

NH

O

NH

NH

OC

H3

O

O

O

O

NH

3 +

NH

O

BnO

NH

NH

3 +

NH

ONH

O

NH

3 +

NH

NH

OC

H3

O

+ H3 N

+ H3 N

+ H3 N

O

O

O

NH

O

BnO

NH

NH

ONH

O

NH

NH

OC

H3

O

O

O

O

NH

3 +

NH

O

BnO

NH

3 +

NH

Ph

NH

3 +

NH

ONH

O

NH

NH

OC

H3

O

Appella, B

archi, Durell, G

ellman J. A

m. C

hem. S

oc. 1999, 121, 2309.

A P

reorganized 14-Helix S

hows H

igh Therm

al Stability

OO

O+ H

3 N

+ H3 N

+ H

3 N

NH

O

BnO

NHNH

O

NH

O

NHNH

OC

H3

O

O+ H

3 N

NH

O

BnO

NH

O

OC

H3

25oC

45oC

65oC

80oC

25oC

Ion Pairing A

llows 14-H

elix Form

ation in Water

Without C

yclic Residues

i-Pr

+

+ H3 N

NHNH

OO

O

CO

2 -

-

i-Pr

2

Seebach et al. J. C

hem. S

oc., Chem

. Com

mun., 2001, 649.

+

i-Pr

NHNH

NH

OO

O

-

-+

NHO

-

O

-

+

+ H3 N

-

CO

2 -

+ H3 N

+-C

heng & D

eGrado J. A

m. C

hem. S

oc., 2001, 123, 5162.+

NHNH

OO

O

NHNH

NH*

OO

O

NH

O

CO

2 -

NHC

O2 -

NH

3 +N

H3 +

CO

2 -

+ H3 N

NH

OC

O2 -

HO

CH

3

CH

3

CH

3

CH

3

CH

3

Circular D

ichroism: C

yclic Residues D

iminish

Environm

ental Effects on F

olding

-25

-20

-15

-10 -5 0 5

10

15

19

02

00

21

02

20

23

02

40

25

02

60

Wa

ve

len

gth

(nm

)

[ ] (103 deg cm2 decimol-1)

MeO

H

pH

7

pH

2

pH

12

H2 N

NHNH

NHNH

OO

OO

O

NHNH

NH

2

OO

- O2 C

+ H3 N

+ H3 N

- O2 C

T. R. R

aguse / Seebach sequence

Circular D

ichroism: C

yclic Residues D

iminish

Environm

ental Effects on F

olding

-25

-20

-15

-10 -5 0 5

10

15

19

02

00

21

02

20

23

02

40

25

02

60

Wa

ve

len

gth

(nm

)

[ ] (103 deg cm2 decimol-1)

MeO

H

pH

7

pH

2

pH

12

-25

-20

-15

-10 -5 0 5

10

15

19

02

00

21

02

20

23

02

40

25

02

60

Wa

ve

len

gth

(nm

)

[ ] (103 deg cm2 decimol-1)

MeO

H

pH

7

pH

2

pH

12

H2 N

NHNH

NHNH

OO

OO

O

NHNH

NH

2

OO

- O2 C

+ H3 N

+ H3 N

- O2 C

H2 N

O

NHNH

OO

NH

O

NHNH

OO

NH

O

NH

2

- O2 C

- O2 C

+ H3 N

+ H3 N

T. R. R

aguse

NO

Es D

emonstrate 14-H

elix Form

ation in Solution

H2 N

O

NHNH

OO

NH

O

NHNH

OO

NH

O

NH

2

- O2 C

- O2 C

+ H3 N

+ H3 N

H

H

H

H

H

H

HH

HH

H2 N

O

NHNH

OO

NH

O

NHNH

OO

NH

O

NH

2

- O2 C

- O2 C

+ H3 N

+ H3 N

H

H

H

H

H

H

HH

HH

Meth

ano

l

Water, p

H 7R

aguse, Lai, Gellm

an J. Am

. Chem

. Soc. 2003, 125, 5592.

i,i+3 NO

Es

12-Helix F

ormation in W

ater by Hexam

ers (RO

ES

Y)

OS

O

OS

O

OS

O

OCH3

NN

HN

ON

HN

ON

N

HN

O

HN

O

N

HN

O

NH2

O

HN

OH2

H2

H2

++

+

Lee, Syud, W

ang, Gellm

an J. Am

. Chem

. Soc. 2001, 123, 7721.

H

H

H

H

HH

HH

HH

HH

N

HN

ON

HN

ON

HN

O

HN

O

HN

O

NH2

O

HN

OH2

H2

H2

++

+

Wang, E

spinosa, Gellm

an J. Am

. Chem

. Soc. 2000, 122, 4821.

i,i+2 NO

Es

Will the 12-H

elix Tolerate A

cyclic Residues?

HN

O

HN

O

HNHN

O

HN

OO

NH2

ON

HN

O

R

NH3

HN

O

NH3

++

+ H2

Will the 12-H

elix Tolerate A

cyclic Residues?

Yes.

LePlae, F

isk, Porter, W

eisblum, G

ellman J. A

m. C

hem. S

oc. 2002, 124, 6820

HN

O

HN

O

HNHN

O

HN

OO

NH2

O

H

H

H

H

NH

HH

H

HHN

OH

HR

NH3

HN

O

H

NH3

HH

++

+H2

Num

erous NO

Es betw

een sequentially non-adjacent residues (C

D3 O

H), all characteristic of the 12-helix

New

Foldam

ers:H

omogeneous vs. H

eterogeneous Backbones

Hom

ogeneous Backbones: A

ll residues in the same class

(e.g., conventional peptides, DN

A, R

NA

, -peptides,

-peptides)

Heterogeneous B

ackbones: Residues of different classes

(e.g., …?)

/-P

eptide Foldam

ers?

NNH

NH

HN

O

O

HN

O

O

NNH

NH

NH2

O

O

HN

O

O

HN

OH

H

H2 N

OH

CO2 H

2D N

MR

An

alysis (CD

3 OH

)

Nu

mero

us i --> i+2 an

d i --> i+3 N

OE

s

Hayen

, Sch

mitt, N

gassa, T

ho

masso

n, G

ellman

A

ng

ew. C

hem

. Int. E

d. 43:505 (2004)

NO

E D

ata Suggest T

wo C

onformations

Populated in S

olution

11-Helix

[C=O

(i) -- H-N

(i+3)]

14/15-Helix

[C=O

(i) -- H-N

(i+4)]

NH

NH

HN

O

O

HN

O

O

NH

NH

NH2

O

O

HN

O

O

HN

O

1111

NH

NH

HN

O

O

HN

O

O

NH

NH

NH2

O

O

HN

O

O

HN

O

15

14

/-P

eptide Helix

Modeling

11-Helix

14/15-Helix

(Molecular M

echanics: S

YB

YL / M

MF

F94s;

continuum M

eOH

model;

12 residues)M. S

chmitt

11-Helix

14/15-Helix

M. S

chmitt

??

Neither

/-P

eptide Helix A

ccounts for All N

OE

s

Am

phiphilic /

-Peptide 15-m

ers: Insight into H

elix Preference from

Physical P

roperties?

NH

NH

HNO

O

HNO

O

NN

NH

NH

HNO

O

HNO

O

HN

O

H2

NH

NH

HNO

O

HNO

O

NH

NH2

OHN

O

O

NH2

H2

+

+

+H3 N

+

H3 N

+

NH

NH

HNO

O

HNO

O

NNH

NH

HNO

O

HNO

O

NHN

O

NH

NH

HNO

O

HNO

O

NNH

NH2

OHN

O

OH2

H2

H2

+

++

H3 N

H3 N

++

NNH

NH

HNO

O

HNO

O

NH

NH

HNO

O

HNO

O

NHN

O

NH

NH

HNO

O

HNO

O

NNH

NH2

OHN

O

O

H2

H2

H2

+

++

H3 N

H3 N

++

Am

phiphilic as 11-helix

Am

phiphilic as 14/15-helix

Not am

phiphilic as either helix2 x Lys (+

)5 x Leu3 x A

PC

(+)

5 x AC

PC

M. S

chmitt

Am

phiphilic /

-Peptide 15-m

er isomers:

Axial P

rojections

11-helix14/15-helix

Am

phiphilic 11-Helix

Design

Am

phiphilic 14/15-Helix

Design

Neither H

elix Am

phiphilicD

esign

Purple =

cationicB

lack = hydrophobic

Am

phiphilic /

-Peptide 15-m

er isomers:

Reverse-P

hase HP

LC R

etention

Min

ute

s

16

18

20

22

24

26

28

30

32

34

36

38

40

42

44

mVolts

-100

-50 0

50

100

150

200

250

300

350

SP

D-1

0A

vp C

h1-2

20nm

cat1

1h-p

ure

3: 2

20 n

m, 8

nm

cat1

415h

SP

D-1

0A

vp C

h1-2

20nm

catn

eith

er-p

ure

mV

Retention Tim

e (min)

11-Helix

Design

No H

elixD

esign14/15-H

elixD

esign

Conditions: C

8 column; linear gradient 20-->

60% B

over 40 min;

A =

water, B

= C

H3 C

N (both 0.1%

CF

3 CO

2 H)

Sch

mitt, W

eisblu

m, G

ellman

J. A

m. C

hem

. So

c. 126:6848 (2004)

Stro

ng

HP

LC

reten

tion

su

gg

ests that

14/15-helix is

Preferred

?

/-P

eptide 15-mers: N

OE

Analysis

HN

O

NH

NH

HNO

O

HN

O

O

R

R

NH

HN

O

OR

NO

E p

attern exp

ected fo

r 11-helix b

ut n

ot 14/15-h

elix [no

ne o

bserved

]

NO

E p

attern exp

ected fo

r 14/15-helix b

ut n

ot 11-h

elix [4 or 5 o

f 7 ob

served]

Sch

mitt, W

eisblu

m, G

ellman

J. A

m. C

hem

. So

c. 129:417 (2007)

HN

O

HN

O

OH3 C

CH3 NH

NH

HN

O

O

H3 C

CH3

Ch

oi, G

uzei, S

pen

ce, Gellm

an

J. Am

. Ch

em. S

oc. 130 :6544 (2008)

14/15-Helix

11-Helix

/-P

eptide Crystal S

tructures Reveal Tw

o Helical C

onformations

Cyclically C

onstrained -R

esidues Strongly P

romote

/

-Peptide H

elix Form

ation

NNH

NH

HN

O

O

HN

O

O

NNH

NH

NH2

O

O

HN

O

O

HN

OH

H

H2 N

OH

CO2 H

NNH

NH

HN

O

O

HN

O

O

NNH

NH

NH2

O

O

HN

O

O

HN

OH

H

H2 N

OH

CO2 H

NH

NH

HN

O

O

HN

O

O

NH

NH

NH2

O

O

HN

O

O

HN

O

H2 N

OH

CO2 H

H2 N

H2 N

Medium

-rangeN

OE

s in CD

3 OH

Many

Many

None

Sch

mitt, C

ho

i, Gu

zei, Gellm

an J. A

m. C

hem

. So

c. 127:13130 (2005)

Cyclically C

onstrained -R

esidues Strongly P

romote

/

-Peptide H

elix Form

ation

Can w

e quantify this effect?

Cyclically C

onstrained -R

esidues Strongly P

romote

/

-Peptide H

elix Form

ation

Can w

e quantify this effect?

1. Po

pu

lation

analysis is ch

alleng

ing

for

-pep

tide seco

nd

ary structu

res.

2.N

o exam

ples o

f reliable p

op

ulatio

n an

alysis for fo

ldam

er seco

nd

ary structu

res to d

ate.

Cyclically C

onstrained -R

esidues Strongly P

romote

/

-Peptide H

elix Form

ation

Can w

e quantify this effect?

1. Po

pu

lation

analysis is ch

alleng

ing

for

-pep

tide seco

nd

ary structu

res.

2.N

o exam

ples o

f reliable p

op

ulatio

n an

alysis for fo

ldam

er seco

nd

ary structu

res to d

ate.

3.U

se thio

ester exchan

ge to

add

ress the ro

le of cyclic resid

ue co

nstrain

ts?

+

KT

EK

Fo

ld+

Thioester E

xchange Design:

Packing of an

-Helix against an

/-P

eptide Helix

Price, H

adley, S

teinkru

ger, G

ellman

An

gew

. Ch

em. In

t. Ed

. 49:368 (2010)

Thioester E

xchange Design:

Packing of an

-Helix against an

/-P

eptide Helix

-Helix

/-P

eptid

e14/15-H

elix

Exam

ine site o

n

solven

t-expo

sed

side.

Hyd

rop

ho

bic C

ore

So

lvent-E

xpo

sed p

ositio

n

Thioester E

xchange Design:

Packing of an

-Helix against an

/-P

eptide Helix

Quantitative E

valuation of Residue P

reorganization to

/-P

eptide Helix S

tability (1 Site)

vs.

Quantitative E

valuation of Residue P

reorganization to

/-P

eptide Helix S

tability (5 Sites)

Tow

ard Helix B

undle Foldam

er Tertiary S

tructure?

+++

+++

+++

Pro

tein p

receden

t: DeG

rado

et al., Scien

ce 270:935 (1995)

Self-asso

ciation

to

discrete ag

greg

ate(h

ydro

ph

ob

ic drive)

(Dim

er - hexam

er)

CO

2 -

+ H3 N

Am

ph

iph

ilic helix

hyd

rop

ho

bic

hyd

rop

hilic

En

gin

eer loo

ps,

diversify seq

uen

ce, etc.

Am

phiphilic 14-Helix: A

nalytical Ultracentrifugation

(Sedim

entation Equilibrium

; 60 krpm, 10 m

M T

ris, pH 8.0)

0.3 mM

1.7 mM

NH

2

O

NHNH

O

NH+ H

3 N

OO

HO

+ H3 N

3cyclo

hexyl

cycloh

exyl

+

Detection of

-Peptide S

elf-Association by N

MR

(100 mM

acetate, pH 3.8)

0.2 mM

0.4 mM

0.8 mM

1.4 mM

1.8 mM

4.0 mM

8.0 mM

NH

2

O

NHNH

O

NH+ H

3 N

OO

HO

+ H3 N

3cyclo

hexyl

cycloh

exyl

+

Non-A

ggregating Control C

ompound

+

Ch

x

3

+

NH

2

O

NHNH

O

NH+ H

3 N

OO

+H

O

Ch

x

+ H3 N

3C

hx

Ch

xC

hx

Ch

x

NO

N-A

MP

HIP

HIL

ICO

NHNH

O

NH+ H

3 N

OO

HO

+ H3 N

AM

PH

IPH

ILIC

Ch

x

NHN

H2

O

NH

O

Ch

x+

+

Ch

x

Ch

xC

hx

Ch

x+

VS

.

Monom

er-Hexam

er Equilibrium

?

Sed

imen

tation

equ

ilibriu

m resu

lts:0.3 m

M0.6 m

M

0.8 mM

1.3 mM

1.8 mM

Raguse, Lai, LeP

lae, Gellm

an Org. Lett. 2001, 3, 3963.

Mo

no

mer

(10 mM

Tris, p

H 8, 60,000 rp

m) M

on

om

er + Hexam

er

Unim

olecular -P

eptide Folding?

Cheng, D

eGrado J. A

m. C

hem. S

oc. 2002, 124, 11564

Crystal S

tructure of a -P

eptide Helix B

undle

Schepartz et al. J. A

m. C

hem. S

oc. 2007, 129, 1532.

-Peptide H

elices: Pioneering S

tudies of Helix

Form

ation in Organic S

olvents

Seeb

ach et al.

Helv. C

him

. Acta 1998, 81, 983.

Han

essian et al.

J. Am

. Ch

em. S

oc. 1998, 120, 8569.

HNH

O

HNO

Bn

O

4

HNH

O

Seeb

ach et al.

Ch

em. C

om

mu

n. 2001, 207.

HNO

H

O

3

NHO

HN

O

NHO

HN

O

14-Helix

Improved H

elix Stability w

ith Constrained

-Am

ino Acids?

HN

O

-Resid

ue w

ithcyclic co

nstrain

t

NO

2

+

H

O

NH

PhP

h

OT

MS

(20 mo

l %)N

O2

(10 mo

l %)

HO

2 C

NaB

H4

dr 16:1:1

majo

r diastereo

mer:

87% yield

, 99% ee

Jon

esO

x.

NO

2

CO

2 HH

NO

2

CH

2 OH

H

HN

O

-Resid

ue w

ithcyclic co

nstrain

t

Synthesis

Precedents:

List, Pojarliev, M

artin Org. Lett. 3:2423 (2001)

Betancort, B

arbas Org. Lett. 3 :3737 (2001)

Santanu et al. C

hem. R

ev. 107 :5471 (2007)(m

ostly nitrostyrenes)

Guo, C

hi, Alm

eida, Guzei, P

arker, Gellm

an J. A

m. C

hem. S

oc. 131:16018 (2009).

Improved H

elix Stability w

ith Constrained

-Am

ino Acids?

HN

O

Seeb

ach et al.

Helv. C

him

. Acta 1998, 81, 983.

Han

essian et al.

J. Am

. Ch

em. S

oc. 1998, 120, 8569.

HNH

O

HNO

Bn

O

4

Hom

o-oligomers of the C

onstrained -A

mino A

cid R

etain 14-Helix P

ropensity

Guo, Z

hang, Reidenbach,

Giuliano, G

uzei, Spencer, G

ellman

Angew

. Chem

. Int. Ed. 50 :5843 (2011)

New

Foldam

ers: /

-Peptide H

elix

i,i+3 H-b

on

ds

HNNH

HN

O

O

NHO

O

O

NH

O

OBn

HN

OO

HNNH

HN

O

O

O

NH

OH

H

Stru

cture-d

efin

ing

NO

Es (C

DC

l3 ):

Guo, C

hi, Alm

eida, Guzei, P

arker, Gellm

an J. A

m. C

hem. S

oc. 131 :16018 (2009).12-H

elix(C

rystal Stru

cture)

Stru

cture-d

efin

ing

NO

Es in

CD

Cl3

(no

t sho

wn

)

Guo, A

lmeida, Z

hang, Reidenbach,

Choi, G

uzei, Gellm

an J. A

m. C

hem. S

oc. 132 :7868 (2010)

i,i+3 H-b

on

ds

New

Foldam

ers: /

-Peptide H

elix

13-Helix

(Crystal S

tructu

re)

-Helix M

imicry from

//

-Peptides?

NH

HNNH

O

O

OR

R

HNNH

HN

O

O

O

RR

R

NH

OHN

O

R

R

Seven

resid

ues =

Two

turn

s of

-helix

-helix w

heel”

-Helix M

imicry from

//

-Peptides?

NH

HNNH

O

O

OR

R

HNNH

HN

O

O

O

RR

R

NH

OHN

O

R

R

NH

HN

O

O

RNH

HNNH

NH

HN

O

O

OO

O

R

R

R

Sam

e nu

mb

er of

backb

on

e atom

s as seven

resid

ues

-Helix M

imicry from

//

-Peptides?

NH

HNNH

O

O

OR

R

HNNH

HN

O

O

O

RR

R

NH

OHN

O

R

R

NH

HN

O

O

RNH

HNNH

NH

HN

O

O

OO

O

R

R

R

//

-Pep

tide

Helix w

heel?

Sam

e nu

mb

er of

backb

on

e atom

s as seven

resid

ues

-Helix M

imicry from

//

-Peptides?

Saw

ada, G

ellman

J. Am

. Ch

em. S

oc. 133:7336 (2011)

NH

HN

O

O

RNH

HNNH

NH

HN

O

O

OO

O

R

R

R

//

-Pep

tide h

elical con

form

ation

in H

2 O(N

OE

-restrained

dyn

amics; 12-m

er)

CD

Data S

uggest High

//

-Peptide H

elix Stability

(H2 O

vs. 1:1 H2 O

:CH

3 OH

)

//

Structure

Function

Ho

st-Defen

se Pep

tide M

imicry

NH2

OO

HN

N

HN

O

N

HN

O

HN

O

HN

O

HN

O

HN

OH2

H2

++

n

++++++++

++

++

++++

Nan

ofi

ber A

ssemb

ly

CatalysisA

ldo

lase-like activity

NH

2

O

NHNH

O

NHNH

OO

HO

+ H3 N

3

O

Lyotro

pic

liqu

id crystallin

ep

hases

(Cryo

-TE

M; H

artgerin

k, Rice)

Po

rter et al. Natu

re 404:565 (2000)M

ow

ery et al. JAC

S 129:15474 (2007)

Po

meran

tz, Ab

bo

tt, Gellm

an JA

CS

128 :8730 (2006)

OH

O

O

O

O

O

O

H

O

NHNH

O

HO

O

NH

O

NHNH2

O

NH3

O

3

Fo

ldin

g an

d

assemb

ly req

uired

An

tibacterial ran

do

m co

po

lymers

Mü

ller, Win

dso

r, Po

meran

tz, Gellm

an, H

ilvert A

ng

ew C

hem

Int E

d 48:922 (2009)

++

++

ST

RU

CT

UR

E

FU

NC

TIO

N

General P

latform for M

imicry of P

rotein-Recognition S

urfaces?

(Goal =

inhibitors of deleterious protein-protein interactions)

small

mo

lecule

fold

amer

vs.

Pro

tein A

Pro

tein B

Pro

tein A

Pro

tein B

Pro

tein B

Pro

tein B

Pro

tein A

Pro

tein A

An

/-P

eptide that Mim

ics an -helix from

HIV

Protein

gp41 and Inhibits Viral E

ntry

Ho

rne, Jo

hn

son

, Ketas, K

lasse, Lu

, Mo

ore, G

ellman

PNAS

106:14751 (2009)

HN

CH3

O

HN

NH

H2 N

NH2

+

O

ZX

N

HNC

H2

O+

HNC O

Conclusions:

Conform

ational mim

icry of proteins with foldam

ers offers m

any opportunities for solution structure determination.

Establishing

folding rules for new

backbones enables function-based engineering.

New

Shapes?

Polyproline H

elices: No H

ydrogen Bonds!

Polyproline I

3.3 residues/turn1.9 Å

rise/residue

Polyproline II

3.0 residues/turn3.1 Å

rise/residue

N

O

HN

O

N

O

HN

Ocis am

idetrans

amide

(Helix-form

ing peptoids, Arm

and et al.P

roc. Natl. A

cad. Sci. 1998, 95, 4309)

(collagen)

A

-Peptide A

nalogue of a Polyproline H

elix?

NH

CO2 H

pyrrolidine-3-carboxylic acid

The rotam

er problem:

O

N

CO2 CH3

O

N

CO2 CH3

O

N

CO2 CH3

O

O

N

CO2 CH3

O

O

N

CO2 CH3

OB

. Huck

H. C

arlson et al., Univ. M

ichigan

NO

E A

nalysis of Monom

er Consistent w

ith Expected

Rotam

er Preference

N

O

O

NO(C

DC

l3 , rm tem

p)

B. H

uck

Counting A

mide R

otamer S

tates by 13C N

MR

(C

arbonyl Region)

B. H

uck

O

N

O

OCH3

4

O

O

N

O

OCH3

4

Synthesis: 5,5

-Disubstituted M

onomers

N

1) NaB

H4

2) CH

3 I, Ag

2 OM

eO2 C

63%

OT

BS

1) TB

AF

2) TsC

l

3) NaC

NN

1) con

c. HC

l2) B

oc

2 O

3) TM

SC

HN

2

OT

BS

HO

90%

Bo

c

N

73%

CN

CH

3 O

Bo

cN

CH

3 O

Bo

c

O

OC

H3

Bo

c

Startin

g m

aterial: Oh

take et al., Bu

ll. Ch

em. S

oc. Jap

an 1999, 72, 2737.

Limited T

orsional Options

N

CH3 O

O

OO

N

OCH3O

HO

NR

O

R'

N R''

O

R'''

Sim

ulations suggest two

minim

a, -80o and -160

o

ca. -80o

N. F

isk, B. H

uck

NO

ES

Y A

nalysis of a Heterotetram

er (CD

Cl3 ):

NO

Es B

etween N

on-Adjacent R

esidues

N

O

ON

OCH3 O

OO

O

N

ON

O

F

O

1

23

4

Residue 1

Residue 3

Residue 2

Residue 4

N. F

isk, B. H

uck

Tetram

er Structures: S

imulation vs. N

MR

: -80o, -80

o, -80o

: -160o, -160

o, -160o

: -160o, -160

o, -80o

(Major, by N

MR

)