Molecular Basis of Specificity in Nucleic Acid-Drug Interactions: Proceedings of the Twenty-Third Jerusalem Symposium on Quantum Chemistry and Biochemistry Held in Jerusalem, Israel, May 14–17, 1990

594 Pages·1990·24.23 MB·English

by  Andrew H.-J. Wang

MOLECULAR BASIS OF SPECIFICITY IN NUCLEIC ACID-DRUG INTERACTIONS
THE JERUSALEM SYMPOSIA ON
QUANTUM CHEMISTRY AND BIOCHEMISTRY
Published by the Israel Academy of Sciences and Humanities,
distributed by Academic Press (N.Y.)
1. The Physicochemical Aspects of Carcinogenesis (October 1968)
2. Quantum Aspects ofH eterocyclic Compounds in Chemistry and Biochemistry (April 1969)
3. Aromaticity, Pseudo-Aromaticity, Antiaromaticity (April 1970)
4. The Purines: Theory and Experiment (April 1971)
5. The Conformation of Biological Molecules and Polymers (April 1972)
Published by the Israel Academy of Sciences and Humanities,
distributed by D. Reidel Publishing Company (Dordrecht, Boston, Lancaster, and Tokyo)
6. Chemical and Biochemical Reactivity (April 1973)
Published and distributed by D. Reidel Publishing Company
(Dordrecht, Boston, Lancaster, and Tokyo)
7. Molecular and Quantum Pharmacology (March/April 1974)
8. Environmental Effects on Molecular Structure and Properties (April 1975)
9. Metal-Ligand Interactions in Organic Chemistry and Biochemistry (April 1976)
10. Excited States in Organic Chemistry and Biochemistry (March 1977)
11. Nuclear Magnetic Resonance Spectroscopy in Molecular Biology (April 1978)
12. Catalysis in Chemistry and Biochemistry Theory and Experiment (April 1979)
13. Carcinogenesis: Fundamental Mechanisms and Environmental Effects (April/May 1980)
14. Intermolecular Forces (ApriI1981)
IS. Intermolecular Dynamics (Maart/ApriII982)
16. Nucleic Acids: The Vectors of Life (May 1983)
17. Dynamics on Surfaces (April/May 1984)
18. Interrelationship Among Aging, Cancer and Differentiation (April/May 1985)
19. Tunneling (May 1986)
20. Large Finite Systems (May 1987)
Published and distributed by Kluwer Academic Publishers
(Dordrecht, Boston, London)
21. Transport through Membranes: Carriers, Channels and Pumps (May 1988)
22. Perspectives in Photosynthesis (May 1989)
VOLUME 23
MOLECULAR BASIS
OF SPECIFICITY
IN NUCLEIC ACID-DRUG
INTERACTIONS
PROCEEDINGS OF THE TwENTY-THIRD JERUSALEM SYMPOSIUM ON
QUANTUM CHEMISTRY ANO BIOCHEMISTRY HELD IN
JERUSALEM, ISRAEL, MAY 14-17, 1990
Edited by
BERNARD PULLMAN
Institut de Biologie Physico-Chimique
(Fondation Edmond de Rothschild), Paris, France
and
JOSHUA JORTNER
Department ofChemistry, University of Tel-Aviv, Israel
"~.
SPRINGER SCIENCE+BUSINESS MEDIA, B.V.
ISBN 978-94-010-5657-1 ISBN 978-94-011-3728-7 (eBook)
DOI 10.1007/978-94-011-3728-7
Printed on acid1ree paper
AlI Rights Reserved
© 1990 Springer Science+Business Media Dordrecht
Originally published by Kluwer Academic Publishers in 1990
Softcover reprint ofthe hardcover 15 t edition
No part of the material protected by this copyright notice may be reproduced or
utilized in any form or by any means, electronic or mechanical,
including photocopying, recording or by any information storage and
retrieval system, without written permission from the copyright owner.
PREFACE
One of the central problems in the study of the
mechanism of DNA-ligand interactions is the existence and
nature of sequence specificity with respect to the base
pairs of DNA. The presence of such a specificity could be
of particular significance because it might possibly mean
the involvement of specific genes in the effectiveness of
the different drugs. The elucidation of the factors
responsible for the specificity could then be important for
the development of compounds susceptible to contribute to
the control of gene expression and also to the development
of rationally conceived, improved new generations of
effective and specific chemotherapeutic agents. Important
recent achievements, experimental and theoretical, in the
analysis of such sequence specificities open prospects for
possible rapid progress in this field.
The 23rd Jerusalem symposium was devoted to the
exploration of these recent achievements in relation to
many types of ligand, with special emphasis on antitumor
drugs.
All major types of interaction, intercalation, groove
binding, covalent linking, coordination, have been
considered. So was also the effect of the interaction on
the structure and properties of the nucleic acids and the
relationship between the interaction and biological or
pharmacological activities.
We feel that this Volume presents a relatively
complete up-to-date account of the state of the art in this
important field of research.
As the twenty two preceding ones this Symposium was
held under the auspices of the Israel Academy of Sciences
and Humanities and the Hebrew University of Jerusalem. It
was sponsored by the Institut de Biologie Physico-Chimique,
Fondation Edmond de Rothschild of Paris. We wish to express
once again our gratitude to the Baron Edmond de Rothschild
for his constant and generous support which makes this
continuous endeavour possible.
We wish also to present our grateful appreciation to
the Administrative staff of the Israel Academy, and in
particular to Mrs Avaigail Hyam, for the efficiency and
excellency of the local arrangements.
Bernard PULLMAN
Joshua JORTNER.
v
TABLE OF CONTENTS
PREFACE V
A.H.J. WANG, Y.-C. LIAW, H. ROBINSON and Y.-G. GAO /
Mutual Conformational Adaptation of Both
Ligand and Receptor in Antitumor Drug-DNA
Complexes
B. NORDEN, S. ERIKSSON, S.K. KIM, M. KUBISTA, R. LYNG
and B. AKERMAN / DNA Drug Interactions studied
with Polarized Light Spectroscopy : the DAPI
Case 23
S. NEIDLE, D.G. BROWN, T.C. JENKINS, C.A. LAUGHTON,
M.R. SANDERSON and J.V. SKELLY / Drug-DNA
Recognition : Sequence Specificity of the DNA
Minor Groove Binder Berenil 43
R. H. SHAFER, M. YOSHIDA, D. L. BANVILLE and S. HU /
Binding of Minor Groove Ligands to Short DNA
Segments: Berenil Complexed with d(GCAATTGC)2
and d(GCTTAAGC)2 59
V. MURRAY / The Sequence Specificity of Damage Caused
by [125I ]-Labelled Hoechst 33258 and UV/
IodoHoechst 33258 in Intact Cells and in
Cloned Sequences of Purified DNA which differ
by a Small Number of Base Substitutions 67
R.H. SARMA, M.H. SARMA, K. UMEMOTO, G. GUPTA and A.E.
GARCIA / Structure and Dynamics of a [ 1 : 1]
Drug-DNA Complex Analysis of 2D NMR Data
Using Molecular Mechanics and Molecular
Dynamics Calculations 75
D.E. WEMMER, P. FAGAN and J.G. PELTON / Determination
of Distamycin-A Binding Modes by NMR 95
J.W. LOWN / Molecular Mechanisms of DNA Sequence
Recogni tion by Groove Binding Ligands
Biochemical and Biological Consequences 103
viii TABLE OF CONTENTS
J. B. CHAIRES I Daunomycin Binding to DNA : from the
Macroscopic to the Microscopic 123
D.R. PHILLIPS, C. CULLINANE, H. TRIST and R.J. WHITE /
In vitro Transcription Analysis of the
Sequence Specificity of Reversible and
Irreversible Complexes of Adriamycin with DNA 137
R. REHFUSS, J. GOODISMAN and J.C. DABROWIAK /
Quantitative Footprinting Analysis of the
Actiomycin D-DNA Interaction 157
G. CAPRANICO and F. ZUNINO I Structural Requirements
for DNA Topoisomerase II Inhibition by
Anthracyclines 167
D.E. GRAVES and R.M. WADKINS / Thermodynamic Studies
of Amsacrine Antitumor Agents with Nucleic
Acids 117
L.P.G. WAKELIN and W. A. DENNY I Kinetic and
Equilibrium Binding studies of a Series of
Intercalating Agents that Bind by Threading a
Sidechain Through the DNA Helix 191
M. PALUMBO and B. GATTO I Aminoacyl-Anthraquinones
DNA-Binding and Sequence Specificity 207
M.J. WARING / The Molecular Basis of Specific
Recognition Between Echinomycin and DNA 225
C. AUCLAIR, F. SUBRA, D. MRANI , G. GOSSELIN, J . L.
IMBACH and C. PAOLETTI I Bis
Pyrrolecarboxamides Linked to Intercalating
Chromophore Oxazolopyridocarbazole (OPC)
Properties Related to the Selective Binding to
DNA at Rich Sequences 247
J.H. Van de SANDE, B. W. KALISCH and M. W. GERMANN I
Parallel-Stranded Nucleic Acids and their
Interaction with Intercalating and Groove
Binding Drugs 261
T. MONTENAY-GARESTIER, J.S. SUN, J. CHOMILIER, J.L.
MERGNY, M. TAKASUGI, U. ASSELINE, N.T. THUONG,
M. ROUGEE and C. HELENE I Design of
Bifunctional Nucleic Acid Ligands 275
C. HELENE, J.C. FRANCOIS, C. GIOVANNANGELI, T. SAISON
BEHMOARAS, U. ASSELINE and N.T. THUONG I
TABLE OF CONTENTS ix
Sequence-Specific Recognition and CLeavage of
Duplex DNA by Derivatized Oligonucleotides 291
J.D. HOESCHELE, A.J. KRAKER, Y. QU.B. Van HOUTEN and
N. FARRELL / Bis(Platinum) Complexes.
Chemistry, Antitumor Activity and DNA-Binding 301
N. ZEIN, W-D. DING, G.A. ELLESTAD / Interaction of
Calicheamicin with DNA 323
W. D. WILSON, F.A. TANIOUS, H. BUCZAK, M.K.
VENKATRAMANAN, B.P. DAS and D.W. BOYKIN / The
Effects of Ligand Structure on Binding Mode
and Specificity in the Interaction of Un fused
Aromatic Cations with DNA 331
B.C. BAGULEY, K.M. HOLDAWAY and G.J. FINLAY /
Modulation of Protein-DNA Interactions by
Intercalating and Nonintercalating Agents 355
F. ARCAMONE / Antitumor Antibiotics Endowed with DNA
Sequence Specificity 369
R.J. FIEL, B.G. JENKINS and J.L. ALDERFER / cationic
Porphyrin-DNA Complexes Specificity of
Binding Modes 385
B. PULLMAN / Complementary Studies on Sequence
Specificity in DNA-Antitumor Drugs
Interactions 401
P.E. NIELSEN, B.M.G. CONS, K.R. FOX and V.B. SOMMER /
Uranyl Photofootprinting. DNA Structural
Changes upon Binding of Mithramycin 423
N.E. GEACINTOV, M. COSMAN, V. IBANEZ, S.S. BIRKE and
C.E. SWENBERG / Characteristics of Noncovalent
and Covalent Interactions of (+) and (-) Anti
Benzo[a]pyrene Diol Epoxide stereoisomers of
Different Biological Activities with DNA 433
M.P. STONE, S. GOPALAKRISHNAN, K.D. RANEY, V.M. RANEY,
S. BYRD and T.M. HARRIS / Aflatoxin-DNA
Binding and the Characterization of Aflatoxin
B1-Oligodeoxynucleotide Adducts by IH NMR
Spectroscopy 451
J. W. KOZARICH / Sequence Specific Isotope Effects on
the Cleavage of DNA by Radical-Generating
Drugs 481
x TABLE OF CONTENTS
L.L. SHEN, M.G. BURES, D.T.W. CHU and J.J. PLATTNER /
Quinolone-DNA Interaction : How a Small Drug
Molecule Acquires High DNA Binding Affinity
and Specificity 495
J . A. HARTLEY / Mechanisms of DNA Sequence Selective
Modifications by Alkylating Agents 513
M. A. WARPEHOSKI, P. McGOVREN, M. A. MITCHELL and L. H .
HURLEY / Contrasting Mechanisms for the
Sequence Recognition of DNA by(+)- and (-)-CC-
1065 531
M. TOMASZ, H. BOROWY-BOROWSKI B.F., McGUINNESS/ Course
of Recognition and Covalent Reactions Between
Mitomycin C and DNA : Sequence Selectivity of
a Cross-Linking Drug 551
R.H. DURLAND, D.J. KESSLER, M. DUVIC and M. HOGAN /
Triplex Forming Oligonucleotide Reagents
Rationalization of DNA site Selectivity and
Application in a Pharmaceutical context 565
w.
LEUPIN / Experimental Proofs of a Drug's DNA
Specificity 579
Mutual Conformational Adaptation of Both Ligand and Receptor in
Antitumor Drug-DNA Complexes.
Andrew H.-J. Wang*, Yen-Chywan Liaw, Howard Robinson and Yi-Gui Gao
Department of Physiology and Biophysics
University of Illinois at Urbana-Champaign
Urbana, IL 61801
ABSTRACT. Many antitumor/anticancer drugs bind and interact with DNA double helix to
exert their biological activities. The consequence of the binding process is that both the drug
and the DNA molecule change their conformations to accommodate each other to optimize the
binding interactions. Two series of drug-DNA complexes associated with intercalator and
minor-groove binder, with their structures derived from the high resolution x-ray diffraction
analysis, are used to illustrate this concept of mutual conformational adaptation between
ligand and receptor. Anthracylcine drugs, including daunomycin, adriamycin and
nogalamycin, intercalate between CpG base pairs using the aglycone chromophore with its
elongated direction almost perpendicular to the Cl'-Cl' vector of the neighboring base pairs.
Around the anthracycline intercalator, DNA stretches the two complementary backbones in a
different manner to move the base pairs 6.8 A apart. On the one side, the dC changes the e/'
combinatory torsion angles to -[-1000/1800], while keeping the glycosyl X angle near high anti
range [-900]. On the other side, all torsion angles are maintained close to those of B-DNA with
the exception of the glycosyl X angle changing to normal anti range [ca. -1500]. All sugar
puckers are in the C2'-endo family. Daunomycin and adriamycin adjust the glycosyl ether
linkage (between ring A and amino sugar) torsion angle such that the amino sugar fits better in
the minor groove. In contrast, nogalamycin has a gentle bend in the long direction of the
aglycone chromophore, bringing the aminoglucose and nogalose closer to each other. In the
minor groove binding drug-DNA dodecamer complexes, there is a wide range of backbone
torsion angles in the DNA molecules despite the uniform narrow minor groove width
associated with the central AT sequences. Drug molecules (netropsin, distamycin and Hoechst
33258) exhibit sufficient flexibility and adjust their conformations to follow the contour
surface of the right-handed B-DNA minor groove.
INTRODUCTION
DNA plays central roles in the biological activities of all living cells. The intricate and
precise regulation of the expression of various genes encoded in the DNA nucleotide sequences
by many regulatory proteins and enzymes have become an extremely critical issue to be
unraveled in modern biology. Gene regulation is presumably determined by the DNA itself and
its interactions with proteins. Therefore it is not surprising that many small molecular ligands
*
To whom correspondence should be addressed.
B. Pullman and f. fortner (eds.). Molecular Basis ofS pecificity in Nucleic Acid-Drug Interactions. 1-21.
© 1990 Kluwer Academic Publishers.