Transcript Single Conformation Spectroscopy of SAHA_final.pptx

Single Conformation Spectroscopy of
Suberoylanilide Hydroxamic Acid (SAHA):
A Molecule bites its tail
Di Zhang, Jacob C. Dean and Timothy S. Zwier
Zwier Research Group, Purdue University
Single Conformation Spectroscopy of SAHA
BIOLOGICAL RELEVANCE
•Vorinostat (SAHA)
• Histone deacetylase inhibitor to Class I and class II HDACs at ~50 nM
• SAHA is currently in advanced clinical trials and showed significant
anticancer activity in a broad range of cancers.
Head
Tail
C6 alkyl chain
“Tail”
“Head”
Tail
Head
FUNDAMENTAL INTEREST: Prototypical Potential Energy Surface
Two hydrogen bonding groups separated by C6 hydrocarbon chain could
form head-to-tail or tail-to-head intramolecular H-bonds
Disconnectivity diagram
•Visual summaries of all the
conformational minimum and
transition states
•Generated by Amber force field
•The end of each branch identifies
a particular conformational
minimum
•Nodal points represents transition
states in the prescribed energy
window that connect the minima
below them
•1277 minima were found
connected by 1355 transition
states
Experimental Methods
Laser desorption
1064 nm
Sample
Graphite rod
Experimental energy diagram
Molecule+ +e-
Molecule S1
IR Source fixed:
Provides l selectivity
UV Source tuned
UV Source fixed:
Provides l selectivity
IR Source tuned
Molecule S0
Δt = 200 ns
Resonant 2 photon ionization
IR-UV holeburning
Δt = 200 ns
Resonant ion-dip infrared spectroscopy
R2PI and IR-UV Holeburning Spectroscopy
X3
X3
X3
• Four conformations found
• S0-S1 origin transitions spread over ~450 cm-1
• Vibronic structure is similar
• Based on positions of electronic origins:
3 of one type, 1 of another
Resonant ion-dip Infrared Spectroscopy:
Single-conformation IR spectra
3457
3306
3256
3497
3351
3496
3339
3373
3390
3516
3497
Unit: cm-1
Amide I and Amide II region
1540
1560
1614
1621
1623
1560
1560
1622
1681
1663
1685
1668
1697
1725
1724
1725
Calculational Methods
1. Force field calculation in Amber* force field
was performed first at low computational
cost with MacroModel commercial program
suite.
2. 598 stable conformation structures were
filtered out with a given energy threshold
(50kJ mol-1).
3. DFT-B3LYP was performed first to refine the
50 geometries with lowest energy imported
from Macromodel with 6-31+G* basis set.
4. Low energy outputs from those
optimizations were then re-optimized
through dispersion correlated density
functional methods (M05-2X) with the same
basis set.
kJ/mol
Energy Level Diagram
Conformer A
Global Minimum
0 kJ/mol M05-2X
C11
C5
Tail NH to head C=O
Conformer B
5.11 kJ/mol M05-2X
C10
C5
Head NH to tail C=O
Conformer D
6.31 kJ/mol M05-2X
C10
C5
Head NH to tail C=O
Conf C
Head NH to tail OH
2.53 kJ/mol
NH-p
9.55 kJ/mol
Head NH to tail OH
6.31 kJ/mol
Energy level diagram
Conformer C?
Conformer D
Conformer B
Conformer A
Conclusions and Future Outlook
• Observed 4 conformers of SAHA
– One Tail to Head
– Two Head to Tail
– One tentative assignment: NH…pi
• Title: “A molecule bites its tail”:
– Head bites the tail
– The tail bites the head
Nearly the same energy
• Remaining work:
– Alkyl CH stretch region: Analyzing the C6 alkyl chain
– What are the barriers to isomerization?
– Can we carry out a population transfer measurement to drive
population from H→T to T→H and vice versa?
– How does this change in the presence of water molecules?
• Form bridges?
• Change the conformational preferences?
Acknowledgments
Prof. Tim Zwier
Dr. Vanessa Vaquero Vara
Dr. Ryoji Kusaka
Evan G. Buchanan
Zachary Davis
James Redwine
Jacob Dean
Deepali Mehta
Nathan Kidwell
Di Zhang
Joe Korn
Nicole Shimko
Patrick Walsh
Joseph Gord