Antiviral Nucleosides - Chiral Synthesis and Chemotherapy - C. Chu (Elsevier, 2003) WW

263 Pages·2003·11.5 MB·English

PREFACE

Since the discovery of AZT in 1985, soon after the discovery of the human immunode-
ficiency virus (HIV), a number of laboratories of nucleosides and viral pharmacology
intensified their efforts in order to come-up with more safe and potent anti-HIV agents.
From these efforts, scientists further discovered ddl, ddC and d4T as potent and clinically
useful agents, although these agents also possess different profiles of antiviral activity
as well as side-effects. With these agents in hand we opened a new era of combination
chemotherapy of viral diseases. However, retrospectively, the major breakthrough came
when 3TC (lamivudine) was discovered as a potent anti-HIV agent. The discovery of
3TC was almost a shock to conventional nucleoside chemists as 3TC was an oxathiolane
derivative, and furthermore it was an L-nucleoside. L-Nucleosides have previously never
been demonstrated any significant biological activity. Of course, we know now that more
than 70-80 % of AIDS patients are currently taking 3TC as part of combination therapy.
Furthermore, the discovery of 3TC fueled the chemistry of L-nucleosides for the last ten
years. Thanks to 3TC, we are now witnessing at least six L-nucleosides (FTC, L-FMAU,
L-d4FC, L-OddC, L-dT and L-dC) currently undergoing clinical trials. This all happened
in the 90s, thus nucleoside chemists call it the "L-nucleosides decade"
Parts of this book reflect the development of the L-nucleosides chemistry and pharma-
cology, plus other conventional antiviral nucleosides discovered during the last ten years.
This book covers experimental antiviral agents discovered up to the middle of 2002. At
The University of Georgia, I am using the chapters in this book as the text for our gradu-
ate students in medicinal chemistry. It works out well because these chapters not only
cover modem carbohydrate and nucleoside chemistry, but also deal with biology and
chemotherapy of antiviral agents. Thus, these chapters encompass the so called "from
bench to beside." That is what our aspiring graduate students in medicinal chemistry
need to be exposed to due to the interdisciplinary nature of drug discovery and develop-
ment. I hope this book will be useful to those who are already involved in the field for a
quick review as well as graduate students who are entering the field of antiviral chemistry
and chemotherapy.
Finally, I would like to dedicate this book to scientists who have contributed to the
field of nucleoside chemistry and biology. Some of them participated as part of the
Gordon Conference in New Port, Rhode Island in 1997. Keep-up your good work!

C. K. Chu
Athens, Georgia USA
August, 2002

Vll

CHAPTER 1

RECENT ADVANCES IN ANTIVIRAL NUCLEOSIDES

GIUSEPPE GUMINA, YONGSEOK CHOI and CHUNG K. CHU

1.1.
Introduction

During the last two decades, treatment of viral infections has advanced remarkably,
thanks to the heroic efforts of chemists and pharmacologists, the rapid progress of
molecular virology as well as the cumulative knowledge of more detailed mechanism of
action of antiviral agents.^ In recent years, we are facing an outburst of new and emerging
viral diseases, such as new strains of hepatitis and herpes viruses, Ebola virus, West-Nile
virus, plus a number of exotic viruses which, although still isolated in small areas of
the world, have the potential for pandemic outbreak. Besides, the threat that viruses and
other microorganisms could be used as biological weapons in warfare or bioterrorism
has become a reality. Although vaccination is a valuable tool to fight viral diseases and
in some cases is available and successful, the difficulty associated with state- or world-
wide vaccination programs makes antiviral chemotherapy a more practical approach in
the fight to epidemic viral infections.
Among the most successful antiviral agents, nucleoside analogs have been the drugs of
choice in the treatment of a number of deseases caused by herpes simplex virus (HSV),
human cytomegalovirus (HCMV), varicella zoster virus (VZV), human immunodeficiency
virus type 1 (HIV-1) and human hepatitis B (HBV) and C (HCV) vuns. Since 1980, a variety
of biologically interesting and promising nucleosides have been discovered, some of which
are being used clinically or are undergoing preclinical or clinical development. Currently,
eighteen nucleosides are clinically being used for the treatment of HIV-1, herpes virus, HBV,
RSV and HCV infections (Table 1). Despite these achievements, continued discoveries
of novel nucleoside analogs are needed in order to overcome common problems in antiviral
chemotherapy, such as toxicity, metabolic instability and, above all, the emergence of resistant
viral strains as well as of new and emerging viral diseases. So far, a number of reviews have
been published, regarding specific nucleoside classes,^ general aspects of nucleosides^ and
their chemistry^ as well as their antiviral activity spectrum and target of actions.^ In view
of these reviews, the purpose of this chapter is to give a brief overview on the most recent
advances in antiviral nucleosides focusing on the structure-activity relationships with
particular regard to the biochemical mode of action of the most promising nucleosides.

Antiviral Nucleosides: Chiral Synthesis and Chemotherapy, Ed. by C.K. Chu. 1 — 76
© 2003 Elsevier B.V. All rights reserved.

G. Gumina, Y. Choi and C. K. Chu

Table 1.
Antiviral nucleosides used in clinics

Generic name

Anti-HIV agents

Zidovudine

Didanosine

Zalcitabine

Stavudine

Lamivudine

Abacavir

Tenofovir disoproxil

Anti-HBV agent

Lamivudine

Anti-Herpetic agents

Idoxuridine

Trifluridine

Acedurid

Vidarabine

Acyclovir

Valaciclovir

Penciclovir

Famciclovir

Ganciclovir

Cidofovir

Virazole

Acronyms

AZT

ddl

ddC

d4T

3TC

1596U89

PMPA

3TC

IdU

TFT

EdU

araA

ACV

val-ACV

PCV

FCV

DHPG

(S)-HPMPC

Ribavirin

Target viruses

HIV-1

HIV-1

HIV-1

HIV-1

HIV-1

HIV-1

HIV-1

HBV

HSV-1/2

HSV-1/2

HSV-1/2

HSV-1/2

HSV-1/2,

HSV-1/2,

HSV-1/2,

HSV-1/2,

HCMV

HCMV

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J

>-

"

,

\

>

)

vzv

vzv

vzv

vzv

}

RSV, HCV

Mode of action

Reverse transcriptase inhibitor/
chain terminator

Reverse transcriptase inhibitor/
chain terminator

DNA polymerase inhibitor;
topical use

Selective viral DNA
polymerase inhibitor

Valine ester prodrug of acyclovir

Selective viral DNA
polymerase inhibitor; topical use

Oral prodrug of PCV

Selective viral DNA
polymerase inhibitor

Viral RNA polymerase inhibitor

Recent Advances in Antiviral Nucleosides

1.2.
Structural features of nucleosides as antiviral agents

Nucleoside analogs as inhibitors of viral replications usually act by interaction of their
triphosphates with viral polymerases. As structural units of nucleic acids, the nucleoside
triphosphates (NTPs) are the substrates for polymerase enzymes, which catalyze the
polymerization of the NTPs. The biosynthesis of the NTPs is controlled by nucleoside
kinases. The structural requirements of nucleosides to interact with kinases and poly-
merases have important implications in the design of potential antiviral nucleosides
(Figure 1). The 5'-hydroxymethyl group and the base moiety of nucleosides interact
with kinases and their complementary nucleotides on the DNA template. The sugar
moiety of the nucleoside can be considered as a spacer to connect the hydroxymethyl
group and the base moiety.^ Therefore, modification of the sugar moiety has provided
opportunities in the design of biologically active nucleosides.

Some viruses, such as herpes viruses, encode their own nucleoside-phosphorylat-
ing enzymes, which offers the potential for a therapeutic target.^ Nucleosides, which
are preferably phosphorylated by viral enzymes rather than by the cellular homologue,
are only activated in infected cells and can have high selectivity against these viruses.
This is, for example, the main factor in the success of acyclovir (ACV). However, other
viruses, such as HIV and HBV, do not encode nucleoside kinases. In order to be active
against these viruses, nucleoside analogs have to be phosphorylated by cellular kinases.
Thus, the selectivity between antiviral activity and cellular toxicity depends on the sub-
strate specificity of the NTPs for viral and host polymerases, and often the therapeutic
exploitation of active nucleosides is compromised by the toxicity resulting from inhibi-
tion of the host enzymes or incorporation in the host nucleic acids.

In general, enzymes act on one enantiomer of a chiral substrate, the specificity of which
is related to the unique structure of the enzymes.^ However, recent findings have indicated
that there are some exceptions to this rule among enzymes involved in the phosphory-
lation of nucleosides.^'^'^'^° For instance, herpes virus thymidine kinases (TKs) phos-
phorylate both D- and L-enantiomeric forms of several uracil analogs as well as acyclic
nucleosides, cellular deoxycytidine (dCyd) kinase phosphorylates both enantiomeric
forms of several dCyd analogs, and some viral DNA polymerases, such as herpes viruses,
HIV-1 RT and HBV DNA polymerase, are inhibited by the triphosphates of a number
of L-nucleosides. These findings offer new opportunities for antiviral chemotherapy,
although, at the molecular level, it is not completely understood how kinases phosphory-
late both D- and L-nucleosides.

In recent years, a growing number of nucleoside analogs have been discovered
which exert their antiviral activity by inhibiting enzymes different from polymerases,
such as inosine monophosphate dehydrogenase, 5'-adenosylhomocysteine hydrolase,
orotidine 5'-monophosphate decarboxylase and CTP synthetase.^^ Such compounds may
prove useful because, by targeting different enzymes, they may offer synergistic action
with classic polymerase inhibitors.

G. Gumina, Y. Choi and C K. Chu

HO-i
B

1 ^

O
II
•Q-P-O
B

-Q-P-O-P-O-P-O
B

0
O
"O-P-O-P-O

6' 6'

Interaction with viral DNA polymerases

O ^

and/or

Interaction with cellular DNA polynnerases a, p, y, e

[ Antiviral activity J

cytotoxicity,
mitochondrial toxicity,
antitumor activity

A: virus-encoded TK, cellular TK, dCyd kinase, dPyr kinase, dGua kinase,
5'-nucleotidase, adenosine phosphotransferase, or UL97 gene product, etc.

B: Nucleotide kinases or 5-phosphoribosyl-1-pyrophosphate synthetase, etc.
C: NDP kinase, phosphoenolpyruvate carboxykinase, phosphoglycerate kinase
or creatine kinase, etc.

Figure 1. General mode of action of nucleoside analogs.

1.3.
2'-Deoxy nucleosides and related analogs

2'-Deoxy nucleoside analogs have proved effective against DNA viruses, such as HSV,
VZV, EBV and HBV. Some nucleosides of this class show poor selectivity between
the viral polymerases and the host polymerases due to their structural resemblance to
natural substrates. However, modification of the base moiety or the sugar portion as well
as the use of the unnatural L-enantiomer have been shown to reduce cellular toxicity,
as in the case of 2'-fluoro-5-methyl-p-L-arabinofuranosyluracil (L-FMAU).^^

Recent Advances in Antiviral
Nucleosides

Since the discovery of the first antiherpes compound, 5-iodo-2'-deoxyuridine (1, IdU)/^^
a modifications of the 5-position of the pyrimidine moiety have produced a number of
active antiviral compounds (Figure 2)P Several 5-substituted 2'-deoxy-uridines, such as
5-trifluoromethyl-2'-deoxyuridine (2, TFT)!^^ and 5-ethyl-2'-deoxyuridine (3, EdU)/^^
have been approved for the treatment of herpetic keratitis. IdU and TFT are phosphory-
lated to their triphosphates by the virus-encoded TK. The triphosphates inhibit HSV
DNA polymerase as well as, even though to a lesser extent, cellular polymerases. EdU
has higher affinity for the herpesvirus-induced TK than for the cellular TK, and its tri-
phosphate is incorporated to a large extent into the viral DNA.^^'^^"^

BVdU (4, brivudin) was originally synthesized by Walker and co-workers and shown
to be a potent and selective anti-herpes agent. ^"^ It is specifically phosphorylated by virus-
encoded TK and nucleoside diphosphate (NDP) kinase to give BVdUTP, which may act
as either an inhibitor of or a substrate for viral DNA polymerase. However, BVdU is
cleaved by pyrimidine nucleoside phosphorylases to (£)-5-(2-bromovinyl)uracil (BVU),
which is cytotoxic.^^ The marked loss of activity of BVdU in thymidine kinase-deficient
(TK) HSV-1 or VZV strains has been bypassed by its incorporation into phosphorami-
date prodrugs {vide infra)}^ The inhibitory effects of several 5-alkynyl-2'-deoxyuridine
analogs on virus replication, host cell metabolism and tumor cell proliferation have been
investigated, among which 5-ethynyl-2'-deoxyuridine (5) is the most cytotoxic against
L1210 cells.^^ 5-Heteroaryl-substituted 2'-deoxyuridines,^^'^^ i.e. 5-(3-Bromoisoxazol-
5-yl)-2'-deoxyuridine (6), 5-(5-bromothien-2-yl)-2'-deoxyuridine (7) and 5-(5-chloro-
thien-2-yl)-2'-deoxyuridine (8) also share with BVdU a common antiviral spectrum
against various strains of HSV-1 and VZV, but not HSV-2, HCMV or TK" HSV-l.^'^

0
o

HO—1
' ^ N ^ O
O ' ^ N "
|—OH

HO
OH

1 (IdU, X = l)
2 (TFT,X = CF3)
3 (EdU, X = Et)
4 (BVdU, X = (E)-bromovinyl)
5 (X = CsCH)
6 (X = 3-Br-isoxazol-5-yl)
7 (X = 5-Br-thien-2-yl)
8 (X = 5-Cl-thien-2-yl)

9
(L-ldU, X = 1)

10 (L-BVdU, X = (E)-bromovinyl)
11 (L-dT,X = CH3)

Figure 2. 2'-Deoxyuridine analogs.

Focher et al. have demonstrated that L-IdU (9), L-BVDU (10) and L-thymidine (11, L-dT)
(Figure 2) are not recognized by human cytosolic TK in vitro, but function as a substrate
for HSV-1 TK and inhibit HSV-1 proliferation in infected cells.^ L-dT is selectively
phosphorylated in vivo to L-dTMP by HSV-1 TK. L-dTMP is further phosphorylated
to the di- and triphosphate forms by non-stereospecific cellular kinases. L-dTTP not