Table Of ContentStuart LeGrice · Matthias Gotte Editors
Human
Immunodefi ciency
Virus Reverse
Transcriptase
A Bench-to-Bedside Success
Human Immunodefi ciency Virus
Reverse Transcriptase
Stuart LeGrice • Matthias Gotte
Editors
Human Immunodefi ciency
Virus Reverse Transcriptase
A Bench-to-Bedside Success
Editors
Stuart LeGrice Matthias Gotte
HIV Drug Resistance Program McGill University
National Cancer Institute Montreal, QC, Canada
Frederick, MD, USA
ISBN 978-1-4614-7290-2 ISBN 978-1-4614-7291-9 (eBook)
DOI 10.1007/978-1-4614-7291-9
Springer New York Heidelberg Dordrecht London
Library of Congress Control Number: 2013940181
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Preface
The Reverse Transcriptase (RT) of Human Immunodefi ciency Virus Type 1 (HIV-
1) arguably ranks among one of the most extensively studied retroviral enzymes.
Heterologous expression and purifi cation of HIV-1 RT in the early 1980s, approval
of the fi rst nucleoside analogue RT inhibitor (NRTI) in 1987, discovery of resis-
tance to RT inhibitors, and approval of the fi rst nonnucleoside analogue RT inhibi-
tor (NNRTI) in 1996 and the various crystal structures of RT with or without bound
substrate(s) and/or inhibitors represent only a few of the important milestones that
describe a bench-to-bedside success in the continuing effort to combat HIV-1
infection and its consequences. Nucleoside and nonnucleoside RT inhibitors
remain important components in frequently used drug regimens to treat the infection.
RT inhibitors also play important roles in recently validated strategies to prevent
transmission of the virus.
The relevance of HIV-1 RT as a drug target has simultaneously triggered
interest in basic research studies aimed at providing a more detailed under-
standing of interactions between proteins, nucleic acids, and small-molecule
ligands in general terms. In light of the ever-growing knowledge on the struc-
ture and function of HIV-1 RT, this enzyme serves as a valuable “model sys-
tem” in efforts to develop novel experimental tools and to explain biochemical
processes.
This book is designed to provide an overview of important aspects in past and
current HIV-1 RT research, with a focus on mechanistic aspects and translation of
knowledge into drug discovery and development. The fi rst section includes chapters
with emphasis placed on the coordination of the RT-associated DNA polymerase
and ribonuclease H (RNase H) activities. The second covers mechanisms of action
and future perspectives associated with NRTIs and NNRTIs, while the third section
includes chapters focusing on novel strategies to target the RT enzyme. Chapters of
the fi nal part are intended to discuss mechanisms involved in HIV variability and the
development of drug resistance. We hope that these contributions will stimulate
v
vi Preface
interest and encourage research aimed at the development of novel RT inhibitors.
The lack of bona fi de RNase H inhibitors with potent antiviral activity provides an
example for challenges and opportunities in the fi eld.
Frederick, MD, USA Stuart LeGrice
Montreal, QC, Canada Matthias Gotte
In Memoriam: Walter A. Scott
February 1, 1943–January 28, 2013
As the publication of this book was nearing completion, the HIV research commu-
nity was saddened to learn of the sudden passing of one of its contributors, Walter
Scott, professor of biochemistry and molecular biology, University of Miami Miller
School of Medicine. For those who did not know Walter personally, he will be
remembered for his seminal research that unveiled the mechanism through which
HIV-1 RT confers resistance to the nucleoside inhibitor AZT. These fi ndings invigo-
rated the fi eld and propelled the careers of many of us. As colleagues who interacted
with him personally, we are left with memories of Walter as a quiet and unassuming
individual who coupled a passion for his science with a sense of wisdom and humor,
and someone who dedicated his life to providing guidance to the many students that
passed through his laboratory. The impish smile was rarely absent from Walter’s
face, regardless of whether he was discussing important research or conjuring up his
next joke. Steve Hughes of the National Cancer Institute and a colleague who
closely followed Walter’s research described him as “in every sense, one of the best
people in the fi eld.”
vii
viii In Memoriam: Walter A. Scott
Born in Los Angeles and raised in Oregon, Walter received his Ph.D. in
physiological chemistry in 1970 from the University of Wisconsin, and following
post-doctoral research at the University of California at San Francisco and Johns
Hopkins University School of Medicine, he joined the faculty of the University of
Miami in 1975. After several years studying gene regulation in SV40, he turned his
attention to HIV in 1989, combining his own research program with directing the
Pediatric Retrovirology Laboratory of the university’s Pediatric AIDS Clinical
Trials Unit. During this time, he also coauthored several papers with his wife, Gwen,
a faculty member of the Division of Infectious Diseases.
The personal nature of Walter’s interaction with colleagues is perhaps best
summarized by Peter Meyer, lead author on the 1998 PNAS publication describing
the mechanism of AZT resistance, who recalled that he was “like a hand on your
shoulder, not someone looking over your shoulder.” At times when we feel the pres-
sure of teaching, conducting research and applying for funding, Walter reminded us
that there is a lighter, and equally important, side to life, which he most certainly
enjoyed to the fullest. His namesake and Scottish novelist once commented that “a
sound head, an honest heart, and a humble spirit are the three best guides through
time and to eternity.” Walter was endowed with each of these attributes, and will be
dearly missed.
Contents
1 Development of the First AIDS Drugs: AZT and Other
Dideoxynueosides ................................................................................... 1
Robert Yarchoan and Hiroaki Mitsuya
Part I Structure and Function of HIV RT
2 Proviral DNA Synthesis in HIV: Background ..................................... 23
Dorota Piekna-Przybylska and Robert A. Bambara
3 The RNase H Domain: Structure, Function and Mechanism ............ 53
Marcin Nowotny and Małgorzata Figiel
4 Conformational Dynamics of Reverse Transcription ......................... 77
Stuart F.J. LeGrice
Part II Mechanism of Action of Approved RT Inhibitors
5 Nucleoside RT Inhibitors: Structural and Molecular Biology ........... 99
Gaofei Lu, Antonio J. Acosta-Hoyos, and Walter A. Scott
6 Nonnucleoside Reverse Transcriptase Inhibitors (NNRTIs) .............. 123
Kalyan Das, Eddy Arnold, and Stephen H. Hughes
Part III Alternative Strategies to Interfere with the Function of HIV RT
7 Ribonuclease H Inhibitors: Structural and Molecular Biology ......... 143
Jason W. Rausch
8 Targeting Small Molecules and Peptides to the
p66-p51 Reverse Transcriptase Interface ............................................ 173
Daouda Abba Moussa, Audrey Agopian, and Gilles Divita
ix
