Infectious Disorders - Drug Targets 2006, 6. ”-29
`
`I?
`
`Nucleoside Analog Inhibitors of Hepatitis C Virus Replication
`
`S. S. Carroll and D. B. Oisen*
`
`Department ofAntiviml' Research, Merck Research Laboratories. West Point, PA.
`
`1' 9486
`
`infections, 15 are
`Abstract: 0f the 30 compounds currently marketed in the United States for treatment of viral
`nucleoside analogs. demonstrating the utility of this class of compound as a source of antiviral drugs. The success of
`nucleoside analogs in treating other viral
`infections provides a compelling rationale for the significant effort that is
`currently being devoted to the discovery and development of nucleosidc analogs to treat infection by hepatitis C virus
`{HCV) that may lead to improvements in response rates compared to currently available therapies. Several different
`approaches have been adopted to identify promising analogs, including the use of surrogate viruses in cell culture assays,
`screening in the cell-based bicistronic HCV rcplicon assay. and screening nucleoside triphosphates for the ability to
`inhibit the activity of the HCV RNA-dependent RNA polymerase in virro. Several classes of ribonucleoside analogs with
`modifications of the ribose inhibit HCV replication. Nucleoside analogs incorporating a 2‘-C-mcthyl modification are
`potent inhibitors in the rcplicon assay in the absence of cytotoxicity, and appear to exert their inhibition by acting as
`functional chain terminators of RNA synthesis. NM283, a prodrug of 2’-C-methylcytidinc. has entered clinical trials and
`demonstrated viral load reductions in subjects infected with genotype 1 HCV, a genotype known to be difficult to treat
`effectively with currently approved therapies. Overall, results to date offer encouragement that improved therapies to treat
`HCV infection including newly developed nucleoside analogs may become available within the next few years.
`
`Keywords: Nucleoside analog, replicon, structure-activity relationships, RNA polymerase, chain terminator.
`
`HCV BACKGROUND
`
`HCV1 was recognized as the infectious agent responsible
`for community-acquired non-A non-B hepatitis in 1989 [1].
`This discovery made possible the development of diagnostic
`tests for HCV that have reduced the risk of infection through
`blood transfusion. Yet, estimates of the total number of
`infected individuals are currently 17l0~200 million worldwide
`[2]. HCV infection
`is
`the
`leading
`cause of
`liver
`transplantation in the United States, Currently preferred
`therapies to treat HCV infection consist of six to twelve
`month courses of combinations of pegylated interferon o. and
`ribavirin, which result in sustained viral response (SVR. no
`detectable virus six months afier cessation of therapy) in 40—
`60% of treated patients [3, 4]. The SVR rates with patients
`infected with genotype 1 virus, the predominant genotype in
`most western countries, are lower than with genotype 2
`infections [3, 4]. The low SVR coupled with the frequency
`of
`side
`effects
`associated with
`interferon-ribavirin
`
`the development of
`combination therapies necessitates
`improved therapies to treat HCV infection.
`
`HCV is a positive-stranded RNA virus of the family
`Flaviridae, which also includes human pathogens yellow
`fever, West Nile, and dengue viruses. Replication of the
`HCV genome is catalyzed by a complex of virally-encodcd
`and potentially cellular [5] proteins. At
`the heart of the
`replication complex is
`the HCV RNA—dependent RNA
`polymerase (RdRp) which is
`responsible for catalyzing
`ribonucleotidc incorporation leading to the formation of both
`
`‘Addrcss correspondence to this author at
`Research Laboratories, West Point. PA 19486:
`E-mail: david_olsen@merck.com
`
`the WPZéA-SOUO. Merck
`
`the negative strand copy of the viral genome and subsequent
`positive strand copies that serve as the genomes of progeny
`virus. Since it is absolutely required for viral infectivity [6],
`HCV RdRp is a validated and attractive target
`for the
`development of new treatments for HCV infection based on
`administration of compounds
`that directly inhibit viral
`enzyme function.
`Extensive structural
`
`information is now available for
`
`HCV RdRp including co-crystals with some non-nuclcoside
`inhibitors [7-11]. As with other polymerases such as the
`Klenow fragment of E. coli DNA polymerase I and HIV
`reverse transcriptasc, the overall structure of HCV RdRp has
`been compared to a right hand with fingers. palm and thumb
`subdomains. Unique to the HCV RdRp, though, are extended
`finger domains that come into contact with the thumb
`leading to a completely encircled active site, which includes
`catalytic aspartic acids 318 and 319. The dynamics of the
`contacts between the fingertips and the thumb have been
`implicated in the mechanism of action of some non—
`nucleoside inhibitors [12]. The C-terminal 21 amino acids
`are highly hydrophobic and likely form a membrane anchor
`[13]. Deletion of the C-tcrrninal
`tail gives rise to a more
`soluble enzyme which is utilized in many in vitro studies
`[14].
`
`NUCLEOSIDES AS THE BASIS FOR ANTIVIRAL
`THERAPIES
`
`Nucleoside analogs are successfully employed to treat
`infections with HIV, hepatitis B virus. and herpes viruses, all
`of which encode a polymerase whose primary activity is
`DNA synthesis. All of the nucleoside drugs used to treat
`these infections can be considered deoxynucleosidc analogs.
`
`18? I -5265l06 $50.00+.00
`
`© 2006 Bentham Science Publishers Ltd.
`
`G|L2001
`l-MAK, INC. V GILEAD PHARMASSET LLC
`|PR201 8-00123
`
`1
`
`GIL2001
`I-MAK, INC. V GILEAD PHARMASSET LLC
`IPR2018-00123
`
`

`

`13
`
`Infectious Disorders - Drug Targets 2006, Vol. 6, No. I
`
`Carroll and (listen
`
`HCV RdRp as an RNA polymerase might be expected to
`exhibit different
`structural
`requirements
`for nuclcoside
`analogs that would function as inhibitors, particularly at the
`2’—position of the ribose where inclusion of a hydroxyl
`would likely be advantageous for recognition by RdRp. The
`presence of a 2‘-hydroxyl group on the nucleoside offers a
`chance for greater selectivity of inhibition of the HCV RdRp
`over cellular DNA polymerases. inhibition of the mitochona
`drial DNA polymerase gamma by deoxynucleoside analog
`triphosphates is thought to be the cause of mitochondrial
`toxicity associated with the administration of some nucleo—
`side analogs,
`for example, ddC‘
`[15, 16]. Mitochondrial
`toxicity is likely the basis for the hyperlactatemia,
`lactic
`acidosis,
`steatosis,
`peripheral
`neuropathy, myopathy,
`cytopenias, pancreatitis, and lipoatrophy that are aSSociated
`with long term use of nucleoside inhibitors of HIV reverse
`transeriptase [[7]. However the use of a ribonucleoside
`analog could also open the door to toxicities assoeiated with
`interfering with one or more of the many other roles that
`ribonucleosldes play in viva — in inter- or
`intracellular
`signaling, energy storage and use, protein modification, or
`cellular RNA synthesis.
`
`chain-
`effective
`an
`for
`requirements
`overall
`The
`terminating nucleoside analog inhibitor for oral treatment of
`HCV infection are numerous. First,
`the analog must be
`absorbed efficiently from the gastrointestinal tract. Nucleo-
`side transporters expressed in the intestinal epithelium that
`are responsible for the uptake of most nucleoside analogs
`
`B
`
`In contrast, passive diffusion
`have been described [18].
`appears to be important for acyclovir. Prodrug approaches to
`improving the oral bioavailability of nucleosides have made
`use of amino acid ester modifications,
`for example
`valacyclovir,
`that
`appear
`to
`allow transport
`by the
`oligopeptide transporter pepTl and others [18, l9].
`
`Additionally, the analog must have acceptable pharmaco-
`kinctic (PK) parameters, have a long half-tife sufficient
`preferably for once or twice a day dosing, and achieve
`significant concentrations in the target organ, liver.
`In this
`sense standard plasma PK analysis,
`though useful
`in
`determining the overall exposure to a compound, can
`actually be misleading. A compound that can achieve
`excellent uptake into the liver may appear to have poor
`exposure in plasma in a short-term analysis, since little
`remains in the circulation. In other words, a high first-pass
`uptake into liver is desirable in this case. Balancing the need
`for high concentrations of the nucleoside in liver is the
`general requirement
`that since drug exposure is typically
`monitored in plasma in the clinical setting, some plasma
`exposure is also required. Optimally, the ratio of compound
`concentration in liver to that
`in plasma will be constant
`across time and species, so that the level of compound in
`plasma will be predictive of liver concentrations when the
`compound is dosed in human subjects.
`
`Once it has been absorbed into blood the analog must
`enter hepatocytes,
`either
`through nucleoside or other
`transporters or by passive diffusion, as shown in Fig {I}. The
`
`3215!: Modifications
`
`HO
`
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`
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`i
`
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`
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`x
`
`Fig. (I). Intracellular metabolism of nucleoside analogs. A ribonucteoside analog with a modified ribose enters a cell via nucleoside
`transponers, passive diffilsion, or peptide tranSporters. 1n the intracellular environment, the nucleoside can either undergo S’-phospho_tylation
`to the monophosphate by the action of' a nucleoside kinase, conversion to a base modified form {8’} via nucleoside metabolizing enzymes
`such as adenosine deaminase. or “base-swapping” via purine nucleoside phosphorylase which reversibly catatyzcs the cleavage of the
`glycosidic bond. The monophosphatc is converted to the diphosphate via nucleotidyt kinase. The diphoSphate may be converted to a
`deoxyribose diphosphate by ribonucleotide reductase, which may then be incorporated into cellular DNA. Altemately the disphosphate may
`be converted to the triphosphate by nucleoside diphosphate kinase.
`
`2
`
`

`

`Nutteoside Arming Inhibitors offleporr‘ris C Virus Replication
`
`Infectious Disorders - Drug Targets 2006, V0}. 6, No. I
`
`19
`
`roles of equilibrative and concentrative transporters in the
`uptake and efflux of nucleoside analogs from cells have been
`recently reviewed [20]. The analog must
`then serve as a
`substrate for three intracellular kinases to be converted to the
`active S‘-triphosphate,
`in general without undergoing
`unwanted metabolism through
`the
`activity of other
`nucleos(t)ide metabolizing enzymes. Modification of an
`adenine base by adenosine deaminase, for example, would
`form the inosine analog, which may not be inhibitory to
`polymerase activity. Cleavage of
`the glycosidic bond
`through the activity of purine nucleoside phosphorylase
`(PNP) can result in scrambling of a modified ribose with
`other nucleobases. In particular, conversion of the diphos—
`phate to a deoxynucleoside diphosphate via ribonucleotide
`reductase is undesirable for nucleobase—modified analogs,
`since that would allow for possible incorporation into
`cellular nuclear DNA which may lead to mutagenesis and
`carcinogenesis. For nucleoside analogs intended to treat
`hepatitis, an important consideration is the expression pattern
`of transporters and the nucleoside metabolizing enzymes
`specific to hepatic tissue which is characterized by high
`catabolic rates [21].
`
`it
`Once the 5‘-triphosphate of the analog is generated,
`must serve specifically as a substrate for the HCV RdRp and
`not as a substrate for cellular RNA polymerases and be
`incorporated into HCV genomic RNA. Incorporation of the
`nucleotide analog must take place against a background of
`competing natural nucleoside triphosphates that are present
`at concentrations that range from hundreds of micromolar for
`CTP, UT? and GTP to millimolar concentrations for
`intracellular ATP [22].
`In contrast
`the concentrations of
`deoxynucleoside triphosphates are generally 10-fold lower.
`Thus, effective inhibition through incorporation of a chain
`terminator may be more difficult
`to
`achieve
`in
`the
`intracellular environment with an RdRp than with a DNA
`polymerase. Once incorporated, the analog should no longer
`support further RNA synthesis by prevcnting the addition of
`more nucleotides.
`In the absence of a mechanism for
`
`excision of the incorporated chain terminator. the truncated
`viral genome would be unable to support further rounds of
`RNA synthesis. Although
`it
`has
`not
`been
`directly
`demonstrated, since HCV RdRp catalyzes the incorporation
`of ribonucleotides with concomitant release of pyrophos~
`phate,
`it must
`also
`catalyze
`the
`reverse
`reaction,
`pyrophosphorolysis. It remains to be seen whether such an
`excision mechanism operates
`in cells and under what
`conditions. These multiple
`requirements
`for
`effective
`nucleoside analog inhibitors present a real challenge to drug
`development.
`
`Despite these challenges, several different nucleoside
`analogs that
`inhibit HCV replication as measured in the
`replicon assay have been discovered. The majority of the
`published infomiation is available for the class of nucleoside
`analogs
`containing a
`2’-C~methyl
`substituent. Recent
`reviews of progress in the discovery and development of
`other classes of inhibitors of HCV replication are available
`[23-26]. The proposed mechanism of ribavirin notwith~
`standing, this review will focus on novel nucleoside analogs
`that inhibit HCV RdRp.
`
`2’-C-METHYL
`OF
`DISCOVERY
`ADENOSINE ANALOGS
`
`MODIFIED
`
`In the past, the inability to propagate HCV robustly in
`cell culture necessitated the use of surrogate assays to screen
`for inhibitors of viral replication. Bovine viral diarrhea virus
`(BVDV) is a pestivirus within the family Flavivirr‘dae, with
`homology to HCV that has been used as a surrogate, since it
`is easily propagated in cultures of MDBK cells, and does not
`infect humans. The use of BVDV antiviral assays for
`investigating inhibitors has primarily been replaced with
`assays based on the HCV replicon [27]. Recently, cell
`culture systems capable of propagating HCV have been
`developed [28-30]
`that will
`likely replace the replicon
`system for routine compound screening.
`
`level of homology between the RNA
`The overall
`polymerases ofHCV and BVDV, even when ignoring an N-
`terminal domain of BVDV RdRp that is not found in the
`HCV enzyme, is quite low. However, within the active sites
`of the polymerases,
`the homology is much stronger,
`suggesting that BVDV might be a useful surrogate for HCV
`for discovery of activevsite directed inhibitors, such as
`nucleoside analogs. Confounding this approach,
`though,
`would be the use of MDBK cells to propagate BVDV which
`might have different capabilities for converting nucleoside
`analogs to the active S’rtriphosphates than human hepatic or
`hepatoma cells [31]. The low overall homology between
`HCV and BVDV RdRp suggests that searches for non-active
`site directed compounds analogous to the non-nucleoside
`reverse
`transcriptase inhibitors of HIV might not be
`successful. This lack of correspondence has been borne out
`experimentally by the
`identification of non—nucleoside
`inhibitors (Nle} that are BVDV- or HCV-specific [10. 32-
`37].
`
`identified as potent
`2’—C—Methyl nucleosides were
`inhibitors of BVDV replication in cell culture by screening
`libraries of nucleoside analogs
`(R. LaFemina, personal
`communication; [38]). Subsequently it was shown that the
`5’-triphosphates of 2’-C-Me~nucleosides can inhibit
`the
`catalytic activity of both BVDV and HCV RdRp in vitro. In
`parallel
`to screening nucleosides in BVDV antiviral cell
`culture assays, chemically synthesized nucleoside triphos-
`phates were screened for inhibition of purified HCV RdRp.
`The in virro screens for HCV RdRp inhibitors aided in the
`understanding of some aspects of the structure-activity
`relationships for inhibition of the target enzyme.
`
`STRUCTURE-ACTIVITY RELATIONSHIPS OF 2’-
`MODIFIED NUCLEOSIDE ANALOGS
`
`Structural modifications to the ribose and nucleobase
`
`for
`have delineated some aspects of the requirements
`efficient inhibition in both the RdRp and cell—based replicori
`assay. In general the results indicate that a very narrow range
`of substituents gives rise to potent inhibition, particularly in
`the replicon assay, owing in large part
`to the multiple
`structural requirements for efficient uptake of the nucleoside
`into the cell, conversion to the 5’-triphosphate, and the
`absence of unwanted metabolic conversion to inactive
`
`that are necessary in order to inhibit viral RNA
`analogs,
`replication in the cellular environment.
`
`3
`
`

`

`20
`
`Infectious Disorders - Drug Targets 2006, V0}. 6. No. I
`
`Modifications to the ribose have investigated the size,
`hydrophobicity,
`electronics,
`and
`regiospecificity
`of
`substituents‘ with the focus on modifications at the 2’ and 3’
`positions, as shown in Fig, (2), Conversion of the TC-
`methyl substituent of the adenosine analog (I) to 2’-C-ethyl
`(2} completely abolishes inhibition by the nucieoside in the
`replicon assay, and by the corresponding 5‘—triphosphate in
`the enzyme assay [39]. Modeling of the ethyl substituted
`analog into the enzyme active site in the position that
`corresponds to the substrate nucleoside triphosphate suggests
`that where
`the
`2’—C-methyl modification
`can
`be
`accommodated into the enzyme active site, the larger ethyl
`modification would clash stericaliy with the side chain of
`Scr282. analogously to the steric clash between the 2’—C-
`methyl substituent with the methyl group of the resistance
`mutation Ser282Thr, as discussed below.
`
`The importance of the stereoelectronic character of the
`2’-C-rnethyl to inhibition was investigated by conversion of
`the methyl group to either CHEF {3) or to CF; (4) [39]. [n the
`case of CHEF, a 16-fold reduction in inhibitory potency in
`the
`replicon assay was observed. whereas
`the CF;
`substitution led to abolishment of cell—based activity. The
`stereospecificity for inhibition was examined by inverting
`
`Carrot! and 0km
`
`the configuration at the 2’-position. The inverted analog (5)
`was not inhibitory either as the triphosphate in the enzyme
`assay or as the nucleoside in the replicon assay. suggesting
`the importance of maintaining the ribo configuration at the
`2’-carbon [39]. The critical
`importance of retaining the 3’-
`hydroxyl to inhibitory potency is demonstrated by the lack of
`activity of the 3‘—deoxy-2’—C-mcthyladenosine analog (6) in
`both the enzyme and replicon assays. Though HCV RdRp
`does not make use of the 3‘-hydroxyl of 2’-C-methyl
`nucleotides as a nucleophile during extension as discussed
`below, the 3’~hydroxyl likely serves as an important binding
`determinant for the initial incorporation event that leads to
`formation of the analog-terminated primer. Moving the
`methyl substituent from the 2‘-carbon to the 3’-carbon {7}
`also leads to complete loss of inhibitory potency [39].
`
`Exploration of the structure-activity relationships of the
`nucleobasc reveals modifications that enhance inhibitory
`potency. 2’-C-Methyicytidine (8) and 2’-C-methylguanosine
`(9) were both active in the rcplicon assay though with
`reduced
`potency
`relative
`to
`2’-C-methyladenosine,
`suggesting that
`the identity of the base is not critical
`to
`inhibition [40]. The reduced inhibitory potency relative to
`the adenosine analog is a consequence of deleterious
`
`H2
`
`/=”
`WW.'
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`H6
`1.replit:on E050 = 0.25 W
`enzyme IC50 = 1.9 “M
`
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`
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`
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`enzyme K350 3‘ 5i] iJM
`
`3. replicon ECSO = 4 uM
`enzyme ICSO = 4.5uM
`
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`erevme I050 > 50 W
`
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`enzyme ICW > 50 14M
`
`0
`
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`
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`enzymelCMJ = 0.2 pM
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`
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`
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`
`9.
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`replioon E650 = 2.7ul'vt
`enzyme I050 = 0.15 pM
`
`
`
`10.
`
`replicon E050 = 0.25 an
`enzyme It?“ =0.12 nM
`
`repicon E055 =29 1.1M
`11. R1 = Me
`12. R1 = (3(0le cytotoxic
`13. R1 = CN cytotoxic
`
`14. R2 = Cl cytotoxic
`15. R2 = Br
`cytotoxic
`16. R2 = F
`replicon E050 = 0.07;.LM
`
`Fig. (2). Structure activity relationships for inhibition of ] lCV" RdRp by nucleoside analogs.
`
`4
`
`

`

`Nucleosr'o‘e Analog Inhibitors of Hepatitis C Virus Repficarion
`
`Infectious Disorders - Drug Targets 2906, Vol. 6, No.
`
`i'
`
`2]
`
`metabolism to the inactive uridine analog in the case of 2’—C—
`merhylcytidine, and a reduction in cellular uptake andfor
`efficiency of kinasing in the case of the guanosine analog.
`One of the most useful modifications of the base that has
`been identified is the 7—deaza—purine substitution. The 7-
`deaza modification was
`first
`identified as
`a potencyw
`enhancing substitution within the context of the enzyme
`assay, By comparison of [C59 values for inhibition in the
`enzyme assay for pairs of nucleoside triphosphates with
`either nitrogen or carbon at the 7-position of either adenine
`or guanine-containing analogs and with several different
`ribose modifications, a consistent 10-20-fold increase in
`inhibitory potency was observed for the 7-deaza version,
`demonstrating that the 7—deaza modification is beneficial to
`inhibitory potency independent of the nature of the ribose
`modification [4]},
`in fact, the substrate efficiency of ATP
`compared to that of T—deaza—ATP (tubercidin iriphosphate)
`also demonstrated a 10-fold improvement for the 7-deaza—
`modified
`triphosphate,
`suggesting
`that
`the
`improved
`recognition by the enzyme for the 7-deaza substitution does
`not require any ribose modification (Carroll, 8., unpublished
`observation).
`
`The physical basis for the improved recognition of the 7—
`deaza substitution by HCV RdRp is not clear but could be a
`result of changes in glycosidic bond angle or length. or
`changes in the electronic character of the purine base, or
`possibly suggestive of a direct
`interaction between a
`hydrophobic region of the RdRp active site and the 7-
`position of the purine base. A number of substituents at the
`7-deaza position are tolerated by HCV RdRp, including 7—
`methyl (ll), T-carboxamidc (sangivamycin analog, 12},
`7—
`cyano {toyocamycin analog, 13) with little change in
`inhibitory potency in the enzyme assay. However. in general,
`substitutions at the 7-position give rise to cytotoxicity in the
`cell-based assay and are therefore not useful [40, 42]. A
`trend towards decreasing cytotoxicity was noted for the 7—
`halogen substituted series, ”ii-Br > ”ii-Cl > 7-1: (compounds
`14—16). The i-F-Tdeaza—Z’-C—methyladenosine analog was
`found to be essentially non—cytotoxic by MTS assay in the
`replicon cells at 100 paid, but
`to have the most potent
`repiicon EC50 measured for a nucleoside analog (EC 50 = 0.0?
`pM) [40]. Further investigations of 16 are underway.
`
`The 7—deaza-adenosine modification is beneficial not just
`in terms of target enzyme potency but also in terms of
`stabilization of the analog to unwanted modification by
`adenosine-metabolizing enzymes. Most notably, the 7—deaza—
`modification essentially eliminates the ability of adenosine
`deaminase (ADA) to convert the 2’—C-methyladenosine to
`the corresponding inosine analog which is inactive in the
`either the replicon or enzyme assays. Under conditions
`where 2’—C-methyl adenosine is quantitatively converted to
`2’—C-rnethylinosine in in virro ADA-catalyzed reactions. 2’-
`C—methyl-7—deazaadenosine is left
`intact [40]. The lack of
`conversion of the 7~dcaza—adenosine analog is related to the
`mechanism of catalysis by ADA, wherein the 7—nitrogen is
`protonated to aid in the delocalization of charge that occurs
`during formation of a tetrahedral intermediate that results in
`disptacement of the 67amino group by hydroxyl anion [43].
`
`purine
`the
`phosphorolysis of
`the
`PNP catalyzes
`giycosidic bond, resulting in removal of the modified ribose,
`
`and allowing for subsequent metabolism of the ribose. The
`2'~C-methyl substitution itself reduces the ability of PNP to
`catalyze glycosidic bond breaking [39]. However,
`the F’-
`deaza modification further stabilizes the glycosidic bond to
`PNP-cataiyzed breakdown, further increasing the metabolic
`stabiiity of 7~deazaesubstituted nucleoside analogs
`[40].
`These results demonstrating increased stability to adenosine-
`metabolizing enzymes in vin'o correlate well with increased
`pharmacokinetic stability in vivo as discussed below.
`
`MECHANISM OF CHAIN TERMINATION BY 2'-C-
`METHYL NUCLEOTIDES
`
`The physical mechanism of the inhibition of RdRp
`activity by 2’—C—methyl—modified nucleotides appears to
`involve disruption of the growth of the RNA strand after
`incorporation of
`the modified
`nucleotide. Typically
`nucleoside analogs used as antiviral therapeutics act as chain
`terminators due to the absence of the 3‘-hydroxyl group that
`functions as the nucleophile during extension of the DNA
`chain by incorporation of a nucleotide. Thus. analogs such as
`AZT, 3TC, ddC, d4T and the active forms of didanosine, and
`abacavir are incorporated onto the 3'-end of a growing
`primer strand but are unable to support further elongation of
`the growing strand. The family of 2’-C-methyl modified
`nucieotides appears to act via a similar mechanism despite
`the fact
`that
`the 3’—hydroxyl
`is still present
`in the 2‘—C-
`methyl
`nucleotides. The 2‘-C-methyl nucleotides
`are
`therefore non-obligate chain ten-ninators.
`
`the
`supporting chain termination as
`evidence
`The
`mechanism of inhibition by 2’-C-methy| nucleotides comes
`from analysis of polyacrylamide gel electrophoresis — based
`nucleotide incorporation experiments. Hairpin RNAs formed
`from synthetic oligoribonucleosides have been found to
`serve as efficient templates for RNA synthesis catalyzed by
`HCV RdRp [44]. An example of the designed structure of an
`RNA hairpin template is shown in Fig. (3). which has been
`labeled with ”P at its 5’—end via polynucleotide kinase. The
`RNA template and products resulting from the incorporation
`of nucleotides or nucleotide analogs are then separated via
`gel electrophoresis and visualized via Phosphorlmaging. In
`the case of this RNA template sequence, the first nucleotide
`to be incorporated would be an adenosine or adenosine
`analog, which would be followed by incorporation of a
`uridine or uridine analog, as shown in the control reactions
`on the left side of the gel. HCV RdRp is capable of
`incorporating 3’-deoxy-adenosine monophosphate, but
`is
`incapable of extending the 3‘—deoxy-adenosine monophos-
`phate once it has been incorporated, as expected for this
`obligate chain terminating analog. as shown in lanes 6 and 7.
`HCV RdRp is aiso capable of incorporating 7—deaza—
`adenosine monophosphate (tubercidin monophosphate) into
`this RNA hairpin, and is also capable of extending the
`incorporated T—deaza—adenosinc by addition of the next
`nucleotide, as shown in lanes 8 and 9. However even though
`HCV RdRp can incorporate either 2’-C-methyladencsine or
`2’-C-methyl-‘i—deaza-adenosine into the RNA template, the
`enzyme is incapable of adding the next nucleotide onto the
`end of the analog-tenninated template. Thus the 2’~C—methyl
`nucleoside analogs act as chain terminators.
`
`5
`
`

`

`22
`
`Infectious Disorders - Drug Targets 2006. Vol 6. No. I
`
`Carrot! and Olsen
`
`U
`
`u
`
`00 CCC GGU AGA 5’
`
`U CC GGG CC 3‘
`
`E
`
`++++
`
`ATP (pM)
`UTP (HM)
`3‘dATl’ (HM)
`T-deaz.a~ATP (HM)
`2"-('- lVie-ATP (HM)
`7-dcaza—2'-C Mc-ATP (pM)
`Fig. (3). Gel based incorporationfextension assays. The hairpin RNA oligoribonucleotide with the sequence shown was radiolabeled at the
`5‘~end with 32P-phosphate via polynucleotide kinase. Reactions were catalyzed by purified HCV RdRp in the presence of the indicated
`concentrations of nucleoside triphosphates. Reactions were quenched by addition of loading buffer and reaction products were separated on
`20% polyacrylamide-S M urea sequencing gels. Radiolabeled products were visualized with Phosphorlmaging. The sequence was chosen so
`that the first nucleotide to be incorporated onto the 3‘-end of the hairpin is AMP (third lane of the gel from the left}, followed by
`incorporation of UMP (4"' lane). 3’-deoxy~AMP is incorporated in place of AMP [5‘h lane), but the product of incorporation of 3‘»dAMP
`cannot be extended by addition of UTP. Tubercidin triphosphate serves as a substrate for HCV RdRp, and can be incorporated in place of
`AMP and the product of the incorporation can be extended by addition of UMP (lanes 7 and 8). Both 2’-C-Me-ATP and 2‘-C-Me-7-deaza~
`ATP can be incorporated onto the end of the RNA, but neither is efficiently extended by addition of UTP. A trace of extended product is
`evident with 2’-C~Me—ATP that is absent with the T-deaza analog.
`
`ll) 10
`
`l0 [0
`
`IO 10
`
`2 0
`
`10!
`
`The physical basis for the chain termination mechanism
`is unknown but a potential explanation is illustrated in the
`model shown in Fig. (4). This model was constructed using
`the initiation complex from a co-crystal of the bacteriophage
`phi-6 RdRp [45], consisting of two nucleoside triphosphates
`hydrogen bonded to the 3’-end of a single stranded RNA
`template bound to the phi-6 RdRp. One of the nucleoside
`triphosPhates corresponds to the nucleophile or primer 3’~
`terminal nucleotide {the one on the left in Figure (4)), and
`the
`other
`corresponds
`to
`a
`“substrate"
`nucleoside
`triphosphate, the pyrophosphate of which is displaced during
`catalysis. The initiation complex was copied into the HCV
`RdRp active site [8]. For
`illustrative purposes both the
`nucleophilic nucleoside triphosphate and the
`substrate
`nucleoside triphosphate are shown as 2’-C-rnethyl-adenosine
`triphosphatcs in the Figure. In the case of chain termination
`the RdRp is capable of incorporating the 2‘-C-n1ethyl
`nucleotide analog. We suppose that the enzyme can then
`translocate forward on the template strand such that
`the
`nucleotide
`analog now occupies
`the primer-terminus
`position, corresponding to the nucleophile during catalysis.
`When the substrate nucleoside triphosphate then binds (as
`shown in Fig.
`(4)
`the substrate is another 2‘-C-methyl
`adenosine triphosphate, but
`it could be any nucleoside
`triphosphatc)
`the 2’-C-mcthyl group of the incorporated
`analog is now in proximity to both the ribose ring oxygen,
`and the 8-position of the nucleobase of the incoming
`
`nucleoside triphosphatc, as represented by the yellow and
`red crosshatching. Thus the methyl group may provide a
`stel‘ic clash that either prevents binding or prevents optima]
`alignment of the substrate nucleoside triphosphate to inhibit
`efficient nucleophilic attack of the 3’-hydroxyl on the alpha-
`phosphorous, thus preventing chain extension of the 2‘-C-
`methyl analog-terminated primer.
`
`RESISTANCE T0 INHIBITION BY 2’-C-METHYL
`NUCLEOSIDES
`
`One of the most convincing lines of evidence to establish
`the intracellular target of inhibition by a given antiviral
`compound is the generation of resistance to inhibition in a
`cell culture setting. Mapping the mutation that creates
`resistance to a target gene, and correlating changes in the
`inhibitory potency of the compound in biochemical assays of
`the mutated enzyme demonstrates the validity of the target.
`Additionally,
`in vitro resistance
`studies
`can provide
`infotmation regarding the likelihood of the appearance of
`resiStance
`during
`clinical
`use of
`an
`investigational
`compound,
`as well
`as
`information on
`the potential
`deleterious effects of the mutation on the replicative capacity
`of the mutated virus.
`
`Resistance to 2’-C-methyl nucleosides in the bicistronic
`replicon assay is engendered by a single amino acid change,
`Ser282Thr, within the active site ofthe RdRp [46]. A 38-fold
`
`U i
`
`f}
`10
`
`it)
`
`if]
`ja.
`
`6
`
`

`

`Nrreteoi'ide Analog Inhibitors afHeparr‘riis C Virus Replication
`
`Infectious Disorders - Drug Targets 2006. Vol. 6, No. i'
`
`23
`
`
`
`Fig. (4). A model of the active site of HCV RdRp. The model was constructed using the structure of a de novo initiation complex structure of
`the phi~6 bacteriophage RdRp [45] containing a bound template RNA coordinated to two nucleoside triphosphates. The protein structure was
`replaced with the crystal structure of the HCVr RdRp [8]. In place of the nuclcosidc triphosphatcs were modeled two molecules of 2‘~C~
`methyl—T—dcazaadenosine triphosphate. The crosshatching represents a van der Waals radius of the Z'methyl group of one nucleoside analog
`and the ribosc ring oxygen and 8-position of the other. The blue numbers represent distances in Angstroms from the methyl carbon to the
`ring oxygen and 8-positions of the other nucleoside analog. The purple spheres represent Mg++ ions required for catalysis.
`
`loss of inhibitory potency was determined for 2‘—C—mcthyl
`adenosine in the resistant replicon. The mutation is quite
`specific for
`the 2’-C—methyl modification as shown by
`essentially no change in inhibitory potency for 2’-O-
`methylcytidine. where the methyl group is now present as an
`ether
`linkage. Likewise a 10-fold loss of potency was
`observed for inhibition by 2'-Cwmethyl~guanosine wit