DNA Topoisomerases: Biochemistry and Molecular Biology

308 Pages·1994·6.082 MB·English

by  Leroy F. Liu (Eds.)

Serial Editors
J. Thomas August Ferid Murad
Department of Pharmacology Molecular Geriatrics Corporation
Johns Hopkins University Lake Bluff, Illinois
Baltimore, Maryland
M. W. Anders Joseph T. Coyle
Department of Pharmacology McLean Hospital
University of Rochester Harvard Medical School
Rochester. New York Belmont, Massachusetts
Advisory Board
R. Wayne Alexander Leroy Liu
Harvard Medical School Department of Pharmacology
Rrigham and Women's Hospital Rutgers University
Department of Medicine UMDNJ-Robert Wood Johnson
Cardiovascular Division Medical School
Boston, Massachusetts Piscataway, New Jersey
Jay A. Berzofsky Anthony Y. H. Lu
National Institutes of Health Department of Animal Drug Metabolism
Bethesda. Maryland Merck, Sharp and Dohme Laboratories
Rahway. New Jersey
Floyd E. Bloom
Division of Preclinical Neuroscience Lawrence 1. Marnett
Department of Basic and heclinicat Research Department of Chemistry
Scripps Clinic and Research Institute Wayne State University
La Jolla. California Detroit. Michigan
Thomas F. Burks Thomas A. Raffin
Office of Research and Academic Affairs Division of Pulmonary and Critical Care
University of Texas Health Sciences Center Medicine
Houston, Texas Stanford University Medical Center
Stanford, California
Anthony Cerami
Laboratory of Medical Biochemistry David Scheinberg
The Rockefeller University Memorial Sloan Kettering Cancer
New York, New York Center
New York, New York
Morley Hollenberg
Faculty of Medicine Stephen Waxman
Department of Pharmacology and Therapeutics Division of Neurology
Health Sciences Center Yale University School of Medicine
The University of Calgary New Haven. Connecticut
Calgary. Alberta, Canada
Thomas C. Westfall
Joseph Larner Department of Pharmacological and
Department of Pharmacology Physiological Sciences
University of Virginia School of Medicine St. Louis University Medical Center
Charlottesville, Virginia St. Louis, Missouri
Advances in
Pharmacology
Volume 29A
DNA Topoisomerases:
Biochemistry and Molecular Biology
Edited by
Leroy F. Liu
University of Medicine and Dentistry of New Jersey
Robert Wood Johnson Medical School
Piscataway, New Jersey
Academic Press
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Copyright 0 1994 by ACADEMIC PRESS, INC.
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Contributors
Numbers in porenfheses indicate the pages on which the authors' confribufions begin.
Anni H. Andersen (83), Department of MoIecular Biology, University of
Aarhus, 8000 Aarhus C, Denmark
Sheryl D. Brown (191), Department of Biochemistry, Duke University
Medical Center, Durham, North Carolina 27710
James J. Champoux (71), Department of Microbiology, School of Medi-
cine, University of Washington, Seattle, Washington 98 195
Yuk-Ching Tse-Dinh (21), Department of Biochemistry and Molecular
Biology, New York Medical College, Valhalla, New York 10595
Karl Drlica (263),P ublic Health Research Institute, Department of Micro-
biology, New York University School of Medicine, New York, New
York 10016
Marc Drolet (13 5), Department of Microbiology and Immunology, Univer-
sity of Montreal, Montreal, Quebec, Canada H3C 357
Martin Gellert (39), Laboratory of Molecular Biology, National Institute
of Diabetes, Digestive and Kidney Diseases, National Institutes of Health,
Bethesda, Maryland 20892
Tao-shih Hsieh (19 1), Department of Biochemistry, Duke University Med-
ical Center, Durham, North Carolina 27710
Wai Mun Huang (201), Department of Cellular Viral and Molecular Biol-
ogy, University of Utah Medical Center, Salt Lake City, Utah 84132
Jaulang Hwang (16 7), Institute of Molecular Biology, Academia Sinica,
and Institute of Biochemistry, Yang Ming Medical College, Taipei, Taiwan
11529, Republic of China
Ching-Long Hwong (16 71, Institute of Molecular Biology, Academia Sin-
ica, and Institute of Biochemistry, Yang Ming Medical College, Taipei,
Taiwan 11529, Republic of China
Hideo lkeda (147), Department of Molecular Biology, The Institute of
Medical Science, The University of Tokyo, Tokyo 108, Japan
Barry Kreiswirth (263), Department of Health, City of New York, New
York, New York 10016
xiii
xiv Confributors
Maxwell P. Lee (191),D epartment of Biochemistry, Duke University Med-
ical Center, Durham, North Carolina 27710
Leroy F. Liu (135))D epartment of Pharmacology, University of Medicine
and Dentistry of New Jersey, Robert Wood Johnson Medical School,
Piscataway, New Jersey 08854
Rolf Menzel (39), Bristol-Myers Squibb, Pharmaceutical Institute,
Princeton, New Jersey 08540
Harold C. Neu (227), Departments of Medicine and Pharmacology, Col-
lege of Physicians 8z Surgeons, Columbia University, New York, New
York 10032
John L. Nitiss (10 3), Developmental Therapeutics Section, Division of
Hematology/Oncology, Childrens Hospital, and Departments of Pediat-
rics and Biochemistry, University of Southern California Medical School,
Los Angeles, California 90089
Linus 1. Shen (285), Anti-infective Research Division, Abbott Labora-
tories, Abbott Park, Illinois 60064
Jesper Q. Svejstrup (83),D epartment of Molecular Biology, University
of Aarhus, SO00 Aarhus C, Denmark
James C. Wang (1)) Department of Cellular and Molecular Biology, Har-
vard University, Cambridge, Massachusetts 02138
Ole Westergaard (83)) Department of Molecular Biology, University of
Aarhus, 8000 Aarhus C, Denmark
Hai-Young Wu (13 5), Department of Pharmacology, Wayne State Univer-
sity School of Medicine, Detroit, Michigan 48201
Preface
Over the past half century, many chemicals of either synthetic or natural
origin have been successfully used in the treatment of cancer. Most if not
all of these drugs were developed empirically based on their antitumor
activities in uitro and in uiuo. The elucidation of their mechanisms of action
has invariably come much later. Topoisomerase drugs are no exception to
this rule.
What is unusual about topoisomerases is their covalent interaction with
DNA. Topoisomerase drugs apparently work by converting these essential
DNA enzymes into DNA-cleaving nucleases that destroy the genetic mate-
rial of the cell. This kind of mechanism is expected to be intrinsically
highly effective in killing cells. It is perhaps not surprising that topoisomer-
ases have turned out to be highly effective targets for therapeutics ranging
from antibiotics to antitumor drugs.
Over the past ten years, studies of topoisomerases as antitumor drug
targets have been particularly intensive. This is in part due to the rather
recent identification of topoisomerases as the molecular targets for many
antitumor drugs. One hopes that through studies of these antitumor drugs,
new and improved therapies for cancer can be developed.
This book is designed to be a long-lasting reference book for students
and researchers of pharmacology, toxicology, molecular biology, oncol-
ogy, and infectious diseases. I am particularly indebted to Patti Vendula.
Without her help the book would have never been published.
Leroy F. Liu
xv
DNA Topoisomerases as Targets of
Therapeutics: An Overview
~
James C. Wang
Department of Cellular and Molecular Biology
Harvard University
Cambridge, Massachusetts 02138
1. History and Classification of DNA Topoisomerases
The genesis of DNA topoisomerases as drug targets illustrates the potential
benefit of research motivated by curiosity and curiosity alone. The discov-
ery of the double-helix structure of DNA led immediately to the realization
that the separation of two intertwined chains in a long duplex DNA, during
replication, for example, might be problematic. Watson and Crick (1953)
wrote in one of their epic papers on DNA:
Since the two chains in our model are intertwined, it is essential for them to
untwist if they are to separate. As they make one complete turn around each
other in 34 A, there will be about 150 turns per million molecular weight, so
that whatever the precise structure of the chromosome a considerable amount
of uncoiling would be necessary. It is well known from microscopic observation
that much coiling and uncoiling occurs during mitosis, and though this is on
a much larger scale it probably reflects similar processes on a molecular level.
Although it is difficult at the moment to see how these processes occur without
everything getting tangled, we do not feel that this objection will be insuperable.
The mechanical problem of separating two intertwined chains became
a topological one a decade later with the discovery of covalently closed
circular DNA: duplex DNA rings each made of two intertwined single-
stranded rings of complementary nucleotide sequences (Weil and Vino-
grad, 1963; Dulbecco and Vogt, 1963). In such a molecule, the two single-
Advances in Pharmacology, Volume 29A
Copyright 0 1994 by Academic Press, Inc. AII rights of reproduction in any form reserved 1
2 James C. Wang
stranded rings are topologically linked, and therefore cannot come apart
without at least one transient break in one of the two strands.
A fundamental parameter describing the order or extent of topological
linkage of two intertwined rings is the linking number. Imagine that a
duplex DNA ring n base pairs (bp) in contour length is placed flat on a
planar surface. The linking number Lk is then the number of times the
two single strands revolve around each other (see Appendix I in Volume
29B for a more precise definition and discussions). If the DNA is in its
most stable structure, under physiological conditions the right-handed
double-helix makes one full turn every 10.5 bp, and therefore its linking
number Lk" is expected to be n110.5; the superscript in the symbol Lk"
specifies the most stable or relaxed state of the molecule.
When Lk of a DNA ring is greater or smaller than Lk" for the same
molecule, the molecule is strained. Similar to a torsionally unbalanced
rope, DNA rings with values of Lk that deviate significantly from the
corresponding values of Lk" would often assume contorted forms; because
a duplex DNA is made of two coiled chains to begin with, such contorted
double-helical molecules are referred to as being supercoiled, superhelical,
or supertwisted (Vinograd et al., 1965). Figure 1 depicts electron micro-
graphs of a supercoiled and a relaxed DNA ring.
DNA rings that differ only in their linking numbers are topological
isomers, or topoisomers. The linking number of a covalently closed circu-
lar DNA cannot be altered without at least transiently breaking one of
the two DNA strands; the same holds for interconversion between any
pair of topoisomers. In other words, Lk is a topological invariant. Lk",
however, is not. By specifying Lk" as the linking number of the DNA in
its most stable structure, the quantity becomes dependent on the experi-
mental conditions, as "the most stable structure" is dependent on the
experimental conditions.
The above description sets the stage for the unexpected entrance of the
first DNA topoisomerase. It is now widely known that covalently closed
DNAs from natural sources are often negatively supercoiled, meaning
that Lk is lower than Lk" for such a DNA (Vinograd et al., 1965; Bauer,
1978). When the extent of supercoiling of intracellular coliphage A DNA
was examined, it was found that cell extracts of Escherichia coli contained
an activity capable of converting the negatively supercoiled form of A
DNA rings to the relaxed form (Wang, 1969). Initially, it was thought that
the activity might be an endonuclease, which, in the presence of excess
DNA ligase, would convert the supercoiled form to the relaxed form.
Upon purification of the activity, then termed the "w protein," it became
clear that it represented a new class of enzyme that does both the breakage
and rejoining of DNA strands (Wang, 1971). Eight years later, the term
DNA Topoisomerases as Targets of Therapeutics 3
Fig. 1 Electron micrographs illustrating a relaxed (left) and a supercoiled (right) DNA
molecule. The size of the DNA is about 10,OOO bp. (From Wang, 1980.)
“DNA topoisomerase” was coined for an enzyme that catalyzes the inter-
conversion of DNA topoisomers (Wang and Liu, 1979), and the E. coli
w protein became E. coil DNA topoisomerase I.
Shortly after the discovery of the E. coli enzyme, an activity capable
of relaxing supercoiled DNA was found in mouse cell extracts (Champoux
and Dulbecco, 1972); this activity has subsequently been termed mouse
DNA topoisomerase I. It turns out that E. coli and mouse DNA topoisom-
erase I represent two ubiquitous subgroups of DNA topoisomerases. Both
4 JarnesC. Wang
are classified as type I DNA topoisomerases, enzymes that break tran-
siently one strand at a time to form a gate for the passage of another
strand through it; in terms of their amino acid sequences and reaction
mechanisms, however, these two subgroups are rather distinct (see Chap-
ters 2 and 4).
The discovery of type I1 DNA topoisomerases started with the seminal
finding of an ATP-dependent DNA supercoiling activity in E. coli cell
extracts (Gellert et al., 1976). During the course of studying site-specific
recombination catalyzed by phage X Int protein, it was observed that the
negatively supercoiled DNA substrate could be replaced by the covalently
closed relaxed form only if the latter was incubated with a fraction from
E. coli cells in the presence of ATP. Purification of the essential activity
from this fraction Ied to the identification of E. coli DNA gyrase, a ubiqui-
tous enzyme subsequently found in all eubacteria. Bacterial gyrase is a
member of a family of evolutionarily and structural related DNA topoisom-
erases; other members of the family include phage T4 DNA topoisomerase
(Liu et al., 1979; Stetler et al., 1979) and eukaryotic DNA topoisomerase
I1 (Baldi et al., 1980; Hsieh and Brutlag, 1980).
Several key observations contributed to the realization that the type I1
enzymes, in addition to their ATP requirement, possess mechanistic fea-
tures that are distinct from those of their type I cousins. First, it was
observed in 1977 that in the presence of nalidixic or oxolinic acid, a
quinolone drug that targets bacterial gyrase, the addition of a protein
denaturant to the gyrase-DNA complex resulted in the formation of
double-stranded breaks in the DNA, with protein molecules covalently
linked to the 5' ends (Sugino et al., 1977; Gellert et ai., 1977). Second,
several of the type I1 enzymes were found to catalyze knottinghnknotting
and catenatioddecatenation of covalently closed double-stranded DNA
rings (Kreuzer and Cozzarelli, 1980; Liu et al., 1980; Baldi el al., 1980;
Hsieh and Brutlag, 1980). The type I enzymes were known to catalyze
knottinghnknotting and catenation/decatenation of single-stranded DNA
rings (Liu et nl., 1976; Champoux, 1977; Kirkegaard and Wang, 1978), or
double-stranded DNA rings with single-stranded nicks or gaps, but not
covalently closed duplex rings (Tse and Wang, 1980; Brown and Coz-
zarelli, 1981). Third, when linking number changes catalyzed by the
type I1 enzymes where quantitated, it was found that they occur in steps
of two (Brown and Cozzarelli, 1979; Liu et al., 1980; Hsieh and Brutlag,
1980). All of these results can be explained by the catalysis of the pas-
sage of one double-stranded DNA segment through a transient double-
stranded DNA break in another, and this feature distinguishes the type I1
enzymes from the type I enzymes. Within the type 11 DNA topoisomerase
subgroup, only bacterial gyrase can catalyze negative supercoiling, and