viruses Review Overview of HCV Life Cycle with a Special Focus on Current and Possible Future Antiviral Targets NathalieAlazard-Dany,SolèneDenolly,BertrandBoson andFrançois-LoïcCosset* CIRI—CentreInternationaldeRechercheenInfectiologie,UnivLyon,UniversitéClaudeBernardLyon1,Inserm, U1111,CNRS,UMR5308,ENSLyon,F-69007Lyon,France;[email protected](N.A.-D.); [email protected](S.D.);[email protected](B.B.) * Correspondence:fl[email protected] (cid:1)(cid:2)(cid:3)(cid:1)(cid:4)(cid:5)(cid:6)(cid:7)(cid:8)(cid:1) (cid:1)(cid:2)(cid:3)(cid:4)(cid:5)(cid:6)(cid:7) Received:27November2018;Accepted:2January2019;Published:6January2019 Abstract: HepatitisCinfectionistheleadingcauseofliverdiseasesworldwideandamajorhealth concernthataffectsanestimated3%oftheglobalpopulation. Noveltherapiesavailablesince2014 and 2017 are very efficient and the WHO considers HCV eradication possible by the year 2030. Thesetreatmentsarebasedontheso-calleddirectactingantivirals(DAAs)thathavebeendeveloped throughresearcheffortsbyacademiaandindustrysincethe1990s. AfterabriefoverviewoftheHCV lifecycle,wedescribeherethefunctionsofthedifferenttargetsofcurrentDAAs,themodeofaction oftheseDAAsandpotentialfutureinhibitors. Keywords: HCV;DAA;antiviraltargets 1. Introduction HepatitisCVirus(HCV),theleadingcauseofchronicliverdiseaseworldwide,isapositive-sense single-strandRNAvirusclassifiedintheFlaviviridaefamilyintheHepacivirusgenus[1]. Thefight againstthediseasestartedevenbeforethisagentwasidentifiedin1989,withtheuseofinterferon(IFN) since1986whichwasuntilrecentlythestandardcareofthetreatmentagainstHCVinfection[2,3]. Thetherapeuticalsuccessofthistreatment,aimedatstimulatinghostantiviralresponsestoeliminate thevirus,wasassessedbymonitoringsustainedvirologicalresponses(SVR),asdefinedbyundetectable HCV RNA levels in the blood 12 or 24 weeks after the end of treatment. The IFN treatment was improvedin1998withtheadditionofribavirin,anon-specificantiviralagent,andin2001,byadding polyethylene glycol to interferon molecules (PEG-IFN) [4–7]. The main problem with IFN-based therapies is that SVR rates remain rather modest, especially for the most common HCV genotype worldwide,andareaccompaniedbyconsiderableadverseeffects,makinglongtreatmentduration hardtosupport. Inthe2010s,thehealthauthoritiesapprovedasuccessionofnewmedicinescalleddirect-acting antivirals(DAAs). ThesemoleculesopenedanewerainthetreatmentofHCV,achievinghigherrates ofSVRformostviralgenotypes,withshortertreatmentdurationsandfewersideeffects. Astheir namesuggests,DAAsdirectlytargetviralproteinsthatareessentialforvirusreplication. Afteran outlook of the mains steps of the HCV life cycle, we will review the main targets of the marketed DAAsandthosecurrentlyunderdevelopment. Theresultsofclinicaltrialsarenotaddressedhere, butarereviewedelsewhere[8]. ThetwomainchallengeswhenusingDAAs,asexperiencedinthefightagainstHIV,aretotreat allgenotypesandtofighttheappearanceofresistance.ItisparticularlytrueforHCV,forwhichgenetic variabilityisillustratedbytheexistenceofsevengenotypesandmorethan80differentconfirmed subtypes worldwide [1]. These genotypes and subtypes show different geographical distribution, pathogenesis and response to treatments. Whereas the first DAAs were directed against a single Viruses2019,11,30;doi:10.3390/v11010030 www.mdpi.com/journal/viruses Viruses2019,11,30 2of18 genotype,thenewgenerationofDAAstargetagreatervarietyofgenotypes. PangenotypicDAAswill beparticularlyinterestinginlowandmiddle-incomecountriesastheywillallowtreatmentofHCV patientswithoutpriorgenotypetesting. Extensionoftargetsoutsidethehepacivirusisalsoenvisioned bysomeresearcherstryingtodevelopantiviralsactiveagainstdifferentFlaviviridae[9]. HCVshighgeneticvariabilityisalsoaproblematthelevelofindividuals. Becauseofthehigh replicationrateandthelackofproofreadingactivityoftheHCVRNA-dependentRNA-polymerase (vRdRp),HCVexistswithinitshostasapopulationofslightlydifferentviralvariants,formingthe “quasispecies”[10]. Someofthemutationsinduceaminoacidchangesthatreducethesusceptibility to one or more antiviral drugs and are therefore called resistance-associated substitutions (RASs). VirusesharboringoneormoreRASarecalledresistance-associatedvariants(RAVs)andarefrequently associatedwithDAAstreatmentfailureiftheirfitnessissufficient[11]. RAVscandevelopduring treatment or may pre-exist as naturally occurring variants, albeit at low but sometimes clinically relevantlevels,asreviewedin[12]. Inbothcases,RAVsselectedduringtreatmentandpre-existing RAVscontributetothefailureoftreatments. Thenumberofmutationsnecessaryforavirustobecome resistantandtheprobabilitythatthesemutationsareselectedinthepresenceofthedrugiscalled thegeneticbarrier[13]. Inadditiontobeingpangenotypic,newantiviralsarethereforedeveloped withtheaimofhavinghighgeneticbarrierstoresistance. Theuseofacombinationofantiviralswith differenttargets,eachofthemwithhighpotencyandhighgeneticbarrier,nowallowsahighsuccess ofIFN-freeoralregimensHCVtreatment. 2. OverviewoftheHCVLifeCycle 2.1. EntryofHCVParticleintoHepatocytes HCV particles are 50–80 nm in diameter and have the particularity of being associated with neutral lipids (cholesterol ester and triglycerides) and apolipoproteins, which confers them their unusuallylowbuoyantdensity(Figure1a)[14,15]. HCVparticlescontainapositivesingle-strand RNAgenomeincloseassociationwiththecoreproteins,envelopedbyalipidmembraneinwhichthe twoviralglycoproteinsE1andE2areanchored. Associationofparticleswithlipidstendstomask theviralglycoproteinsbutarethoughttoplayaroleinvirusentry[16],atleastintheinitialphaseof cellattachment,duringwhichtheinteractionsofapolipoproteinEwithcellsurfaceheparansulfate proteoglycans[16–18]orwithSR-BIhavebeenimplicated[19](Figure1b). HCV E1 and E2 envelope proteins play a major role in virus entry and therefore in virus tropism to hepatocytes. Overcoming the initial difficulty to obtain HCV viral particles, HCV entry was first characterized with the use of HCV pseudo-particles (HCVpp) harboring E1 and E2 glycoproteins [20,21]. E1 and E2 act as complexes of disulfide-bound heterodimers and E2 is clearly identified to be responsible for receptor binding [22,23], whereas E1 seems to be an important component of an atypical fusion machinery, as reviewed recently in [24]. HCV entry is a complex multistep process in which different cellular proteins have been demonstrated to be involved. A cascade of interactions/co-interactions with the Scavenger Receptor class B type I (SR-BI) [23], the human Cluster of Differentiation 81 (CD81) [22] and the tight junction proteins claudin-1(CLDN1)[25]andOccludin(OCLN)[26]hasbeendescribed. Thesefactorsconstitutethe minimalsetofessentialentryreceptorsthatprimetheE1-E2complexforvirusentry[27]. Thisprocess isregulatedbymultiplehostsignalingpathways, inwhich, forexample, epidermalgrowthfactor receptor (EGF-R) is implicated [28]. Additional accessory entry co-factors and/or regulators are constantlydescribed,asrecentlyreviewedin[29]. Followingattachment,HCVparticlesareinternalizedviatheendocyticpathwayandmembrane fusionisdependentonendosomalacidification(Figure1b)[30]. Intheorganism,cell-to-cellspread couldbeanimportantmechanismthatseemstoinvolvesimilaractors[31,32]. Viruses2019,11,30 3of18 Viruses 2019, 11, x FOR PEER REVIEW 3 of 18 Figure1. HCVlipoviroparticlesandtheviruslifecycle. (a)HCVparticlescontainapositivestrand FRigNuAreg 1e.n HomCVe (liinpogvreireonp)aarstiscolecisa atendd wthiteh vCirourse lpifreo cteyicnles,. e(an)v HelCopVe dpabryticalems ecmonbtraainn eai npowsihtiivche sEt1raanndd REN2Agl ygceonpormoete (iinns garreeeenm) basesdodceiadteadn dwaitrhe tCigohretl ypraostseoincisa, teendvweliothpelidp ibdys aa nmdeampborlaipnoep irno tweihnisc.h( bE)1 HanCdV Eli2f eglcyyccolpe.roTtheiends iaffreer eemntbsetdedpesdo fanHdC aVrel itfieghcytlcyl easasroeciinatdeidca wteidthi nlipbildasc ka.ndE RapEonlidpoopplraostmeiincsR. (ebti)c HulCuVm . liMfeW cyMcleem. Tbhrae ndoiuffserWenebt .sLteDpsL oipf idHCDVro plilfeet sc.yTclhee anreeg iantdiviecastterda nidn rbelpalcikc.a tEioRn Einntdeormpleadsmiaitce Rinertiecdu.lum. MW Membranous Web. LD Lipid Droplets. The negative strand replication intermediate in red. 2.2. HCVRNATranslationandReplication 2.2. HCV RNA Translation and Replication TheincomingviralRNA,approximately9.6kbinlength,containsasingleopen-readingframe flankTehde binychoimghinlyg svtriruaclt uRrNedAn, aopnp-trroaxnismlaatteedlyr e9g.6io knbs i(nN lTeRnsg)th(F, icgounrtea2inas) [a2 s].inItglise torpanensl-arteeaddiansga fsrianmglee fplaonlykpedro bteyi nhitghhaltyis sctrou-catnudrepdo nsto-ntr-atnrasnlastliaotneadl lryegpirooncse s(sNedTRbsy) b(Foitghuvrier a2laa)n [d2]h. Iots itsp trroatnesalsaetes,da assi nad siicnagteled pinolyFpigruorteein2 at,hraati siisn gcote- nanpdro tpeoinsts-.trTahneslaCtoiorne,alEly1 apnrdocEes2sesdtr ubcytu braolthp rvoitreainl sa,npdr ehseonstt ipnrothteeasveirsi,o anss , ianrdeicpartoeddu icne dFifgroumre t2hae, Nra-itseirnmg itneanl epnrodtewinhse.r eTahses eCvoerne,n Eo1n satnrudc Etu2r asltr(uNcStu)rparlo pteriontseianrse, epxrperseesnste dinf rtohme vtihreioCn-st,e ramrei npursoodfutcheedp forloympr ottheei nN. -terminal end whereas seven nonstructural (NS) proteins are expreTssheed NfrToRms tchoen Cta-tinermthienmusa oinf tchies- pacotliynpgroetleeimn.e nts that are essential for genome translation and repliTchatei oNnT,Rins ccluondtianign athne inmtaeirnn aclisr-iabcotisnogm eallemenetnrtys sthitaet (aIRreE eSs)seinnttihale f5o(cid:48)r NgeTnRom(Fei gtruarnesl2aat)io[n3 3a,n34d] . rAepnliacbatuionnd,a inntclliuvdeirnsgp aenci fiinctemrniRaNl rAib,omsoimR-a1l2 e2n,tirnyt esriatect i(nIRgEwS)i tihn tthhees e5′s NeqTuRe n(cFeigsuwrea s2ad)e m[33o,n3s4t]r. aAtend atbournedgaunlat telivHeCr VspRecNifAic lemvieRlsNiAn,c melliRcu-1l2tu2r, ei,nstteirmacutliantgin wgittrha ntshleasteio sneaqnudengceens owmaes rdepemlicoantisotrna[te3d5, 3t6o] . rTehguislamtei cHroCRVN RANaAct lsevinelasn inu cneclol ncuvletnutrieo, nsatilmwualyatibnygr tercarnusiltaitnigonA arngdo ngaeuntoem2et roetphlieca5t(cid:48)ioennd [3o5f,3t6h]e. Tvhiriasl mgeicnroomRNe,Ast aacbtisl iizni nagn aunndcopnrvoetnectitoinngali twfaroym byd reegcrrauditaitnigo nAbrgyo5n(cid:48)aeuxtoen 2u tcol ethasee 5s′ [e3n7d]. oAf sthiet ivsireasls genentioamlfeo,r sHtaCbiVlizrienpgli caantdio np,roittewcatisnigd eitn ftrifioemd dasegarpadoatetinotnia lbayn 5ti′v eirxaolntuacrgleeats.eTsh [e37v]i.r aAlsR Nit Ais iessaslesnotitahle ftoerm HpClaVte rfeoprlivciartailorne,p itli wcaatsio indethnatitfiperdo adsu ac epsopteonstitiaivl eangteinvoirmale tsaurgseetd. Tfohrea vdirdailt iRoNnaAl pisr oatlesion thpero tdemucptiloatne afnord vviirraall raespsleicmabtiloynt htrhoautg hpraondeugcaetsi vpeo-sseintisvee ingteenrmomedeisa tues(eFdig uforer 1abd).dNitiSo5nBali spthroetveiinra lpRrNodAu-cdteiopne nadnedn tvRiNraAl apsoselymmbelyra tshero(vuRghd Ra pn)e,gtahteivkee-syenesnez iynmteermofedRiNatAe (Fsyignuthree s1ibs).. NWSh5eBn iss uthbeg evniroaml RicNrAep-dliecpoennsdwenetr eRNfirAst peosltyambleisrhaesed ((vFRigduRrpe)2, bth),et hkeeym einnizmymalet roafn RslNatAio nsyanntdherseips.l iWcahtieonn smuabcgheinnoemryicw raespldiceomnos nwsterraet efdirstto ersetqaubliirsehtehde (NFiTgRusrea n2bd),N tSh3e/ m4Ain,iNmSa4l Btr,aNnSsl5aAtioinn aadnddi trieopnlitcoatNioSn5 Bm[a3c8h]i.nAersy dwesacsr idbeemdobneslotrwat,etdh etsoe rreeqpuliicreo ntshew NerTeRinsv aanluda bNleS3to/4oAls, fNorSe4aBr,l yNaSn5tAi- HinC Vadddriutigonsc troe eNniSn5gBa [n3d8]d. iAscso vdeersyc.ribed below, these replicTohnes wfuenrcet iionnvaolfutahbelev tioraollsp froort eeianrslyta arngteit-eHdCbVy dDrAugA sscwreielnlibnegb arniedfl dyidsceosvcreirbye. dhereandinmore detaTilhsei nfutnhcetifoonll oowf tihneg vsieractli ponrost.eiNnsS 2tairsgeatevdir ably pDroAtAeass ewtilhl abtec borniterfilbyu dteessctroibtehde hveirrea lapnodl yinp rmotoerien dmetaatiulsr aitnio tnhea sfowlleolwl ainsgt osetchteioansss.e NmSb2ly iso fa vviirraall pparrotticelaesse. tNhaSt3 ciosnbtroitbhuatesv itroa lthpero vteiraasle pinolvyoplvroetdeiinn mpraotuteroaltyiosnis aosf twheeldl oaws ntos ttrheea maspseamrtbolfyt hoef pvoirlaylp proatretiicnleasn. dNaSh3 eilsic baoseth. NaS v4iArails parcootefaacsteo irnivnotelvraecdt iinng pwroittheoNlySs3is aonfd thaen dchoworninstgreiatmto ptahret omf etmheb praonlyep.rpot7eiwn aasndcl aas hsiefiliecdasaes. NaSv4iAro piso ar icnofaancdtohr ainstemrauclttiinpgle with NS3 and anchoring it to the membrane. p7 was classified as a viroporin and has multiple roles in the assembly and secretion of virions [39]. As illustrated in Figure 2c, most of the viral proteins are Viruses2019,11,30 4of18 Viruses 2019, 11, x FOR PEER REVIEW 4 of 18 roles in the assembly and secretion of virions [39]. As illustrated in Figure 2c, most of the viral mpreomtebirnasnae-raesmsoecmiatberda naen-ads shocaivaet edsevanerdalh afuvencsteiovnesra llifnuknecdt ioton stlhine kreedortgoatnhiezarteioonrg aonf iztahteio nceollfultahre mceelmlublarranmees mrebqruainreesdr efoqru itrheed rfeoprlitchaetiroenp loicfa tthioen HoCftVh egHenCoVmeg eonro lmateero,r dlautreirn,gd uvririnalg avsisreamlabslsye. mTbhley . mThasesmivea srseiavrerarenagrermanegnet mofe cnetloluflcaer lmluelamrbmraenmebs raafnteers HafCteVr iHnfCeVctiionnfe ccotinosnisctso nosf ias t“smoefmab“mraenmoubsr awneobu”s mwaeibn”lym caoinnslytitcuotnedst ietuartelyd iena rilnyfeinctiionnfe cbtyio ndobuybldeo-mubelme-bmraenmeb vraensieclveess i(cDleMsV(D) MorVig)inoaritgininga tfirnogmf rtohme etnhdeoepnldasompliac srmetiiccurelutimcu l(uEmR) ((EFRig)u(Freig 1ubr)e [14b0)]. [4M0o].stM oof stthoe fptrhoetepinrost eoifn sthoef rtehpelirceaptiloicna tcioomnpcolemx palreex naerceensseacreys sfaorry tfhoirs tphrisocpersosc, ebssu,t bNutS4NBS 4aBnda nNdSN5AS5 aArea rteheth memajoarjo arcatoctrosr sini nththe e““mmeemmbbrarannoouus swweebb”” bbiiooggeenneessisis aanndd mmaaiinntteennaannccee tthhaatt ccoonnttaaiinn tthhee rreepplliiccaattiioonn ffaaccttoorriieess ooff tthhee vviirruuss [[4411]].. SSeevveerraall cceelllluullaarr ffaaccttoorrss aarree aallssoo rreeccrruuiitteedd bbyy tthhee vviirraall pprrootteeiinnss ttoo aallllooww tthhiiss pprroocceessss.. Figure2.HCVvirusandrepliconorganizationandmembraneorganizationoftheviralproteins.(a)The Figure 2. HCV virus and replicon organization and membrane organization of the viral proteins. (a) HCVgenomeisapositivestrandRNAcontainingasingleopen-readingframe(fromAUGtostop) The HCV genome is a positive strand RNA containing a single open-reading frame (from AUG to surroundedby5(cid:48)and3(cid:48)highlystructurednon-translatedregions(NTRs).Translationofthepolyprotein stop) surrounded by 5′ and 3′ highly structured non-translated regions (NTRs). Translation of the isenhancedbymiR-122bindinginthe5(cid:48)NTRasindicated. Translationisinitiatedattheinternal polyprotein is enhanced by miR-122 binding in the 5′NTR as indicated. Translation is initiated at the ribosomalentrysite(IRES).Thepolyproteiniscleavedbycellular(whitearrowheads)orviral(black internal ribosomal entry site (IRES). The polyprotein is cleaved by cellular (white arrowheads) or viral arrowhead)proteases.C:Coreprotein.AllNon-Structural(NS)proteins(includingp7)areinblack. (black arrowhead) proteases. C: Core protein. All Non-Structural (NS) proteins (including p7) are in (b)ExampleoforganizationofaHCVsubgenomicrepliconthatwereextensivelyusedforantiviraldrug black. (b) Example of organization of a HCV subgenomic replicon that were extensively used for screenings,theycontainalltheproteinsnecessaryandsufficientforHCVRNAreplication.Neomycin: antiviral drug screenings, they contain all the proteins necessary and sufficient for HCV RNA Neomycinresistancegene. ECMV:EncephalomyocarditisVirus. (c)MembraneassociationofHCV replication. Neomycin: Neomycin resistance gene. ECMV: Encephalomyocarditis Virus. (c) proteins.Hatchedbarsrepresentamphipathicalphahelixortransmembranedomainsanchoringthe Membrane association of HCV proteins. Hatched bars represent amphipathic alpha helix or proteinstothemembrane.TwoexamplesofessentialcellularproteinsinteractingwithNS5Aareshown. transmembrane domains anchoring the proteins to the membrane. Two examples of essential cellular Thethreemaintypesofinhibitorsusedintheclinic(indicatedinredbytheirsuffix)areindicatednext proteins interacting with NS5A are shown. The three main types of inhibitors used in the clinic totheirtarget. (indicated in red by their suffix) are indicated next to their target. Describing the huge number of host factors that have been implicated in HCV replication is Describing the huge number of host factors that have been implicated in HCV replication is beyond the scope of this review but can be found elsewhere [42]. However, we will mention beyond the scope of this review but can be found elsewhere [42]. However, we will mention a few a few targets of particular importance in the context of antiviral research. Cyclophilins, cellular targets of particular importance in the context of antiviral research. Cyclophilins, cellular peptidyl- propyl cis-trans isomerase, were, for example, described as important co-factors for HCV and other viruses replication, as shown using cyclophilin inhibitors developed against HIV [43]. Cyclophilin A Viruses2019,11,30 5of18 peptidyl-propylcis-transisomerase,were,forexample,describedasimportantco-factorsforHCV and other viruses replication, as shown using cyclophilin inhibitors developed against HIV [43]. Cyclophilin A interacts with NS5A and is essential for the “membranous web” formation [44,45]. Phosphatidyinositol-4-phosphate-kinase-IIIalphaisanothercentralhostfactorinteractingwithNS5A, inducingaccumulationofPI4Pwithinthemembranousweb[46], andprovidesanexampleofthe compleximbricationbetweentheHCVlifecycleandlipidmetabolism[17]. 2.3. HCVAssembly,BuddingandSecretion Since2005,thedevelopmentofHCVmolecularclonesthatrecapitulateallthestepsoftheviruslife cycleallowedmuchprogressintheunderstandingofHCVassembly,buddingandsecretion[47–49]. Viralassemblyis,however,stillnotfullydescribed,asthemodelsdonotreflectalltheinteractions withliverlipidmetabolismandgenerateparticlesthatpoorlyresemblethoseproducedininfected individuals[16,47,50]. Viral assembly occurs near replication complexes at assembly sites associated to ER-derived membranes,incloseproximitytolipiddropletswherecoreproteinscanaccumulate(Figure1b)[51,52]. NS5Ahasbeenidentifiedasakeyplayerinthetransitionbetweenviralreplicationandassembly,in additiontoitsroleinreplication,andwasdemonstratedtobeinvolvedinRNAgenomedeliveryto theCoreproteins[53,54]. NS2andp7alsoplayacentralroleinvirusassemblythroughtheirdifferent interactionswithstructuralandnon-structuralproteins. Mostnotably,theycoordinatetherecruitment ofCoreandtheenvelopeglycoproteinsE1E2aswellasNS3andNS5Atotheassemblysites,allowing thegatheringofallviralactorsforassemblycorrectlyinthesameplace[55–60]. Thesmallp7viroporin wasdemonstratedtoactinconcertwithNS2inthisprocessaswellasbeingimportantatthelaterstage ofviralenvelopment[58,59,61]. NS4BwasalsodemonstratedtoplayaroleinHCVassembly[62]. Besidesviralproteins,severalcellularproteinshavebeendescribedasmainfactorsforHCVassembly, suchasDGAT1[63,64]andESCRTproteins[65–68]. ViralparticlesacquiretheirenvelopebybuddingattheER.Asmentionedabove,lipidcomposition oftheviralparticlesresemblesthatofVLDLsandHCVvirionformation,andreleasemayhighjack theirassemblypathway[69]. Maturationofthelipoviroparticlesmayalsorequireanunconventional passagethroughtheGolgiapparatusandatrans-endosomalsecretoryroute(reviewedin[52]),butalso occursatapost-egressstep[16,70]. p7,ApoEandnumeroushostproteinsknowntobeinvolvedin thesespathwaysarenecessaryforthisprocess. TheshortoverviewofHCVlifecyclepresentedhereprovidesastrikingexampleofthefactthat viralproteinsaremulti-purposeandexertseveralfunctionsintheviralreplicationcycle,thusreflecting genetic economy. In an attempt to fight HCV infection, most of these proteins therefore stand as potentialantiviraltargets,astheyareindispensableforoneormorestepsoftheviralcycle. Before discussingthepossibilitytotargetviralentryorassembly,wewillreviewthethreemaintargetsof DAAtreatments,whicharemainlyinvolvedinvirusreplication: NS3/4A,NS5BandNS5A. 3. CurrentAntiviralTargets 3.1. NS3/4AInhibitors TheexperienceofantiproteasedevelopmentintheHIVfieldfacilitatedtheearlydevelopment ofdrugsinhibitingNS3,aswellasthefactthatinvitromodelswerealreadyavailableandcomplete replicationsystemswerenotnecessaryforpreliminaryscreenings. Theproteasedomainoftheprotein was targeted by the first HCV antivirals that were introduced on the market and by the currently recommendednewDAAs. Thesemoleculesaresuffixed-previrandareoftencollectivelyreferredtoas proteasesinhibitors(PIs). NS3proteaseactivityplaysacentralroleintheviralpolyproteinmaturation, as it cleaves four peptide junctions between the non-structural proteins, in complex with NS4A (Figure2)[71–73]. Theproteaseactivityisalsoimplicatedinthemodulationoftheantiviralinnate immuneresponse[74]. Thestructureoftheproteasedomainrevealedatypicalchymotrypsin-like Viruses2019,11,30 6of18 fold,trypsin-likeproteinasewithtwoβ-barrelsandahighlyconservedcatalytictriad(His-57,Asp-81, Ser-139),andabindingsiteforthepeptidicNS4Acofactorthatisdistantfromthecatalyticsite[75,76]. NS4AisanessentialcofactorforNS3enzymaticactivitiesthathelpstolocalizeNS3tothemembrane andanchorstheHCVreplicationcomplexatthecellularmembrane[77–79]. Inadditiontoitstypicalserineproteasedomain,NS3containsashortN-terminalamphipathic α helix (designated Helix α ) and a C-terminal helicase/NTPase domain, which is implicated in 0 several critical steps of the virus life cycle [75,80]. Helix α plays an important role in membrane 0 association,subcellularlocalizationandstabilityoftheNS3/NS4Acomplex,andparticipatesinHCV virionmorphogenesis[77,81,82].Thehelicase/NTPAsedomainwasdemonstratedtobindandunwind RNAduplexesduringviralgenomereplication,makingNS3/4Acomplexanimportantcomponentof theviralreplicationcomplex,alsoimplicatedinvirusparticleassembly[78,82,83]. Drugstargeting functionsotherthantheprotease,forexamplehelicaseactivity,havealreadybeenenvisionedand couldbedevelopedinthefuture[84]. AsNS3andNS4A,butalsothedifferentNS3domains,donot actindependently,theinhibitorscanaffectseveralfunctionsofthecomplex,allowinginhibitionof multiplestepsbytargetingasinglemolecule[85–87]. PioneerworksoninhibitionofNS3/4aproteaseactivityidentifiedcleavagesubstrateproductsas potentialPIs[88,89]. BoceprevirandTelaprevir,thefirsttwoDAAsthatbenefitedfromamarketing approvalin2011,werebothpeptidomimeticlinearketoamidesthatbindtheactivesiteoftheprotease domainofNS3[90,91]. BothDAAswereusedincombinationwithPEG-IFNandribavirin,andwere soon discontinued in most countries due to their low genetic barriers to resistance, restriction to genotype 1 virus and severe adverse side effects [92]. Further development of PIs resulted in improvedantiviralpotencyandapprovalofthemainPIsrecommendedtodateindifferentcountries, thePIsbeing: Glecaprevir,Paritaprevir,GrazoprevirandVoxilaprevir[93,94]. Theavailablecrystal structuresofNS3incomplexwithcandidatecompoundsfacilitatedstructure-baseddesignthathas beenextensivelyusedtoconfronttheissuesofpotency,resistanceandpharmacokinetics,leadingto thedevelopmentofmanynewmolecules,asreviewedin[8]. Intermsofresistance,preferentiallociof RASswereidentifiedwiththefirstgenerationofPIsandweretakenintoaccountfortheoptimization ofthenextDAAgeneration[95,96]. Theefficiencyofthesemolecules,especiallyincombinationwith DAAstargetingotherviralproteins,allowedthedevelopmentandapprovaloflongawaitedIFN-free regimentreatmentswithparticularlyhighSVRandlowsideeffects[97]. 3.2. NS5BInhibitors The function of the NS5B protein at the 3(cid:48)-end of the genome was evident as soon as the sequence of the HCV genome became available, on the basis of sequence comparison with other viruses[98]. ThebiochemicalactivityoftheNS5Bproteinasareplicasewasconfirmedsoonafter[99] as well as the secondary structure of its catalytic site, which was found to be typical of a vRdRp: aright-handlikestructure,withfingers,palmandthumbsubdomains[100–102]. TheNS5Bprotein, however,showssomeparticularities: abeta-hairpinloopinsertioninthethumbdomainthoughtto modulate the polymerase activity and an hydrophobic C-terminal domain, anchoring the protein tomembranes[103]. ThevRdRpwasefficientlyproducedindifferentsystemswithoutthisanchor, allowingfurthercharacterizationoftheproteinproperties[104,105]. Playingsuchanimportantrole in the viral life cycle and given the wealth of information available for related proteins, the NS5B polymerasewasidentifiedveryearlyasatargetofchoiceforantiviraldevelopmentandiscertainly oneofthebestcharacterizedHCVenzyme,asreviewedin[106]. Twotypesofinhibitorsthattarget thecatalyticornon-catalyticsitesofthisproteinhavebeendeveloped. Basedonknowledgeaboutcellularandviralpolymerases,thefirstinhibitorsdevelopedagainst NS5B were nucleo(s)tides inhibitors (NIs). These inhibitors mimic the natural substrate of the enzyme—theyaretypicallyincorporatedintothenascentRNAchainsandterminateRNAsynthesis. Theirdevelopmentis,however,complicatedbytheirinstabilityandtendencytobeinactivatedby thecellularmetabolism. Sofosbuvirisanuridineanalogue,thefirstNItobeapprovedbytheFDA Viruses2019,11,30 7of18 in2013,andstillpartofmostoftherecommendedtreatmentcombinations[107]. Therealchallenge duringthedevelopmentofSofosbuvirwastounderstandthemetabolismofthecandidateinhibitors byliverenzymestofindtheoptimalformulationforaprodrug[108]. Shorttreatmentdurationsof HCVtreatmentsshouldpreventtheside-effects,duetotheknowntendencyofNIstohavecumulative toxicity[109]. Amajorconcernduringantiviraldrugdevelopmentistheappearanceofresistance, particularlyinviruseslikeHCV,whosevRdRpwasdemonstratedtobeerror-prone. Thecatalytic siteofthevRdRpis,however,highlyconservedbetweengenotypes,suggestingthepangenotypic potentialofsuchadrugandaminimalriskoftheemergenceofviralresistance.Thesehypotheseswere confirmedbytheanalysisofclinicaldatademonstratingtheextremelyrareappearanceofresistance mutationsagainstNIs,whichusuallyinduceanimportantreductioninviralfitness[110,111]. Withits favorablesafetyandtolerabilityprofile,itshighgeneticbarriertoresistanceanditsactivityagainst mostgenotypes,SofosbuvirisanantiviralofchoiceinmostcurrentHCVtreatmentcombinations. The second class of inhibitors, referred to as non-nucleoside inhibitors (NNIs), do not bind to the catalytic site of the enzyme [106]. They were discovered as inhibitors of the polymerase activityinscreensusingtherepliconsystem,whenresistancemutationswerediscoveredinNS5B outside the catalytic site. These inhibitors exert their effect by inhibiting conformational changes requiredforpolymeraseactivity. Withthedrugstestedtodate,fivedifferentbindingsiteshavebeen discovered—twointhepalm,twointhethumbandoneinthebeta-hairpinchainofNS5B.Dasabuvir, theonlyNNIapprovedtodatebytheFDA,targetsthepalmofNS5Bandisrecommendedforgenotype 1treatmentonly[112]. NextgenerationNNIsarecurrentlybeingtestedandcharacterized. Themode ofactionofTegobuvir, apromisingmemberoftheimidazopyridineclassidentifiedinphenotypic screens,was,forexample,showntocovalentlybindtheNS5Bbeta-hairpinafteractivationbycellular enzymes[113]. NNIstargetpoorlyconservedsequencesandthereforeshowlowerbarriertoresistance thanNIsandpoorpangenotypicactivity,evenifthesedefaultsareattenuatedintheupcomingnext generationNNIs. Theyare,however,alreadyusefulwhenusedincombinationwithothermorepotent drugsinsomeclinicalpresentations,toreinforcetheefficacyofthetreatmentandcontributetoreduce treatmentduration. 3.3. NS5AInhibitors NS5Ahaslongbeenconsideredasapotentialantiviraltarget, sinceitwasknownearlytobe essential for viral RNA replication [114] and later also for viral assembly. The protein comprises threedomainsseparatedbyshortlow-complexitysequences[115]. TheN-terminaldomainIisthe bestorganizedandcharacterized. ItwasdemonstratedtobindZinc, tobewell-structured, witha shortamphipathichelixintheveryNterminusnecessaryformembranetargetingandtobeessential for genome replication [76,114,115]. The two C-terminal domains are, in contrast, predicted to be intrinsicallydisordered. NS5Aisknowntoexistindifferentlyphosphorylatedformsandtointeract withahugenumberofviralandcellularproteins,includingitselftoformdimersandmaybeoligomers. Incontrasttotheabove-mentionedinhibitors,NS5Ainhibitorscouldnotbedevelopedusing biochemicalassays,astheproteinhasnoknownintrinsicenzymaticactivity. Interestingmolecules wereidentifiedduringthescreeningoflibrariesofcompoundsbydifferentcompanies. Daclatasvir (DCV)was,forexample,identifiedbyscreeningoveramillionofcompoundsagainstHCVreplicons, eliminatingfromthesortingboththecompoundsactiveagainstotherviruses—astheywouldnotbe specificenough—andthoseinhibitingtheenzymaticactivityofNS3orNS5B[116]. Thedevelopment ofresistancetothebestcandidatewasdemonstratedtobeassociatedwithspecificmutationsinthe domainIofNS5A,therebyidentifyingNS5Aasthetargetoftheinhibitor. Inapreliminaryclinical trial,asingledoseofDCVresultedinarapidvirologicalresponse,demonstratingthatNS5Awasa promisingtargetforanti-HCVtherapy[116]. DCVwasshowntobindNS5AclosetotheN-terminus ofdomain1,atthejunctionwiththeamphipathichelixthatanchorsNS5Aatthemembranes,without perturbing the dimerization nor the stability of the protein [117–120]. It was further shown that DCVandDCV-relatedmoleculesinhibittheformationofnewDMVsthatcontainsthereplication Viruses2019,11,30 8of18 complexes[45,118]. OthercompoundssuchasLedipasvirandOmbitasvirhavesimilarpropertiesand thesamebindingsitetoNS5A[121,122]. Secondgenerationinhibitorsweretestedand/oroptimized tobepangenotypic,activeagainstpreviouslyidentifiedNS5ARAVsandcommonNS5Apolymorphs, andhavereducedtoxicity,asexemplifiedbyElbasvirandVelpatasvir[123,124]. Better understanding of NS5A functions is now coming from studies using the inhibitors, asreviewedin[125,126]. Asscreeningofthecompoundshasbeenmadeonreplicons, thestudies initially focused on their impact on virus replication and cellular partners. As mentioned earlier, NS5Awasshowntoplayanimportantroleinthemembranouswebformationnecessaryforviral replication[41]. Testsoncell-infectiousclonesdemonstratedthatNS5Ahasmultiplecomplementary activitiesintheviruslifecycle,suchasviralassembly[127]andmoreparticularlyonthetransferofthe genometotheassemblysites[54]. DirectbindingofNS5AinhibitorstoNS5Ahasbeenreported,anda RASwasshowedtoactbydecreasingthebindingofDCV[120]andLedipasvir[121]toNS5A.DCVwas firstdescribedasinhibitingHCVreplicationbyprobablyinhibitingtheformationofdouble-membrane vesicles required for the replication of the viral genome [118]. In addition, some studies reported an action on assembly [127,128] by preventing the delivery of RNA to the core protein, the main componentoftheHCVnucleocapsid[54]. Descriptionoftheexactmechanismsoftheinhibitorsare stillongoing,butinhibitionofNS5Aseemstoactonmultiplestepsofthevirallifecycle,augmenting itseffects. 4. PotentialFutureTargets 4.1. TargetingOtherViralProteins Asmentionedintheintroduction,allviralproteinsessentialforviralreplicationareconsideredas potentialantiviraltargets. Themainstrategytocombatresistanceemergenceistocombineinhibitors thattargetdifferentproteinsinordertolimitthepossibilitiesofappearanceofcross-resistantmutations. Thishasledtoresearchonalternativeantiviraltargetsinadditiontotheabove-describedprotease, polymeraseandNS5A. Thesmallp7non-structuralproteinisperhapsthemostattractiveofthepotentialalternative antiviral targets. In early studies using HCV replicons, p7 was found to be dispensable for viral replication [38]. But it soon became evident that p7 was essential for other steps of the virus-life cycle [129]. Studies of the functions of p7 became possible when the HCV cellular clones became available[130,131]andtheproteinwasdemonstratedtoplayamajorroleintheassemblyandrelease ofinfectiousHCVparticles[44]. Indeed, p7isamultifunctionalproteinthatregulatesthecellular secretorypathwayaswellastheinteractionsbetweenviralproteins,andthelocalizationofNS2and coreproteinstowardscapsidenvelopment[55,56,58–61,132]. p7isalsoabletoformhomo-oligomersthatassembletoformionchannelstructuresandwas therefore classified as a viroporin [44]. The precise role of this function, however, remains poorly definedbutmaybeimportantfortheregulationofthesecretionofviralparticles[131,133]. Viroporins areconsideredasanattractiveclassofantiviraltargets,withanincreasingnumberofsuchproteins describedandcharacterized,andthesuccessofusinghostionchannelinhibitorsinothermedical domains[134]. Inaddition,thesameinhibitorscanactonviroporinsofdifferentvirusesandmaylead tothefindingofabroad-spectrumantiviral. TheM2viroporinofinfluenzaAvirusisthebeststudied exampleofthisclassofmolecule[135]. M2wasalsothetargetoftheadamantaneclassofinhibitors thathavebeenextensivelyusedagainstInfluenzaAinfectionsincethe1960s,eventhoughtheircurrent useisnowlimitedduetotheappearanceofwidespreadresistance. Althoughp7isquitedifferent fromM2,itwasshowntobeinhibitedbythissameclassofinhibitors[136],eventhoughclinicaltrials incombinationwithIFNtreatmentshowednobeneficialeffects[137]. Otherp7inhibitorshavebeen describedordesignedlike,forexample,GSK-2,hexamethylamiloride(HMA)orBIT225[138–141]. BIT225wasofparticularinterestsinceitisabletoblockbothp7andVpufromHIV,whichmightbea Viruses2019,11,30 9of18 waytotreatHCV/HIVco-infectedpatients. Alltheseinhibitorshavedifferentefficienciesdepending onthegenotypeofHCV[136]andapangenotypicp7inhibitorisstillnotavailable. The last two nonstructural proteins, NS2 and NS4B, have also been targeted in preliminary studies[142–144]. Despitetheirpotentialutilityandcomplementaritytothecurrenttreatments,these moleculesmaybenotdevelopedfurtherforthemomentasthecurrentlyexistingtreatmentsarejudged bymanyassufficient. 4.2. Host-TargetingAgentsagainstViralReplicationandEntry The appearance of resistance to antivirals in HCV, a highly mutable genome, could limit the futuresuccessofalltheabove-mentionedDAAs. Increasingthenumberofviraltargetstofightthe appearanceofresistancesisthemainoptiontodate,buttargetingofsomehostfactorsthathavebeen describedascrucialforviralreplicationorentryhaslongbeenenvisioned. Themainadvantagesof theseso-calledhost-targetingantivirals(HTA)overDAAsareahighergeneticbarriertoresistance andtheirpangenotypicantiviralactivity. Theimprovedknowledgeofvirus–hostinteractionhasledto theidentificationofpotentialtargetssuchascyclophilinandmiR-122inhibitors[145,146]. Interferon,thefirsthistoricaltreatmentagainstHCV,wasinfactamemberofaspecialclassof HTAsometimesreferredtoasimmunomodulatingproteins. CyclophilinAinhibitors,derivedornot fromcyclosporins,immunosuppressivemoleculesthatwereisolatedfromfungus,weredemonstrated earlytohavepotentanti-HCVactivities[43]. Oncedevoidoftheirimmunosuppressiveproperties, theseinhibitorswerethefirstHTAstogototheclinicandweredemonstratedtohavesomepotential. Cyclophilinsareagroupofmultifunctionalcellularproteinsinvolvedinproteinfolding,trafficking andcellsignaling.ThemodeofactionofcyclophilinAinhibitorsistodisruptitsinteractionwithNS5A andpreventMVBbiogenesis[44,45]. BecausesomeCyclophilinAinhibitorswerealsodemonstrated to restrict HIV replication, they could potentially be of interest to treat patients with HIV/HCV co-infection[147]. Hostproteinsarenottheonlypossibletargets—clinicalproof-of-conceptstudies havedemonstratedthatmiR-122inhibitorsefficientlyreduceviralloadinchronicallyinfectedHCV patients[148,149]. However,theseinhibitors,whichrequireparenteraladministration,areunlikely to be developed further in the context of efficient oral regimen. Another problem could be that targetingsuchanimportantmoleculeinliverfunctionmayhavesomeimpactonliverphysiologyand deleterioussideeffects. HTAsarelessspecificthanhighlyefficientDAAsthatwerefasterintotheclinic,butthisisalsoone oftheiradvantages. InadditiontotheirpangenotypicpotentialintheHCVfield,theycouldalsolead tothediscoveryofbroad-spectrumantivirals,sincethehosttargetedproteincanbeimplicatedinthe replicationofotherviruses. Targetinghostlipidsynthesisandmetabolismtoinhibitviralreplication (andlimitliverdiseaseprogressioninthecaseofHCV)is,forexample,envisionedagainstbothHCV andDenguevirus[150]. Someofthesedrugsemergefromrepurposingstrategiesandthereforealso havetheadvantageoverDAAstobeobtainedatlowcost. Oneimportantlimitation,however,isthe riskthattheyalterimportantfunctions,andtheirsideeffectsneedthereforetobecarefullyaddressed, evenifshorttreatmentdurationintheHCVfieldcouldlimittheseeffects. Nomatterhoweffectivemoleculesinhibitingviralreplicationbytargetingviralorhostfactors are,theydonotprotectnon-infectedhepatocytesfrominfection. Preventingvirusentryis,however, an important goal, especially in the context of graft reinfection after liver transplant, but also in preventive treatments or to fight persistent infection [151]. The understanding of the complex mechanisms of HCV entry in cells has increased a lot in the past few years, with the description ofanumberofreceptororco-factorswhichmakesallofthempotentiallysuitabletargets[152]. Theuse ofneutralizingantibodiesagainstviralorhostproteinsdemonstratedthefeasibilitytofightHCVin chronicallyinfectedanimalmodelsbytargetingvirusentry[153,154]. ITX5061,anantagonistofSR-BI, waseventestedinaphaseItrialtopreventlivergraftreinfection,withencouragingeffects[155].Given thenumerousessentialcellularpartnersidentifiedtodate,alltheentrysteps(attachment,binding, fusion)couldinprinciplebetargetedbyantiviralstargetingvirusentry[151]. Viruses2019,11,30 10of18 5. ConcludingRemarks Considerable research efforts on HCV biology by academics and industrials has led to the discoveryofhighlyefficientDAAslessthan25yearsaftertheidentificationofthevirus. Thisgreat achievementmayleadtoaprogressivelossofinterestinthedevelopmentoffurtherresearchinthe field. Manypotentiallyinterestingmoleculeshavealreadybeenhaltedatearlystagesofdevelopment andwillcertainlynotbetestedfurther. Sustainedeffortsareneeded,however,ifwearetoreachthe 2030eradicationobjectivesetbytheWHO. Inaneradicationstrategycontext,DAAscannotbetheonlyarmoftheplan. Theyarestillhigh costandthereforepoorlyavailableinlowincomecountrieswhereHCVincidenceishigh. Thisisnot theironlylimitation. TreatmentwithDAAsmayleadtotheemergenceofresistantstrains,doesnot protectfromreinfectionand,asinfectionisasymptomatic,peopleunawareoftheirstatuscontinueto transmitthevirus. Inaddition,thehighefficiencyratesstillleavesomepatientswithouttherapeutic options. Thesearenowaminorityofpatientsandoftenreferredtoas“hard-to-treatpatients”;they are those who are co-infected with HBV, those who present liver or renal dysfunction and those whounderwentlivertransplantationorprevioustreatmentfailure[97,156]. Potentiallydeleterious drug–druginteractionswithothertreatments,againstHIVforexample,isalsoamajorconcernwith thedevelopmentanduseofthesenewtreatments[157]. Lastbutnotleast,theinhibitorsonthemarket havenotbeenusedforalongtimeandtheappearanceofresistantstrainsisnotunexpected,possibly leadingtoincreasingthenumberorpatientswithouttreatmentoptionsinthefuture. HistoryandmodelingsuggestthatHCVeradicationwillnecessitateavaccine. Progressinthe understanding of the immune response to HCV has led to different vaccinal strategies, including DNA,peptidesorrecombinantproteins,vector-basedvaccines,andvirus-likeparticlesordendritic cell-basedvaccinationstrategies;theseareatvariouslevelsofdevelopment(recentlyreviewedin[158]). ThechallengeistodevelopavaccineelicitingbothabroadT-cellresponseandneutralizingantibodies againstahighlyvariablevirushiddeninlipoviroparticles. Theobjectiveseemsachievableinthenext fewyears,ifresearchinthisdirectionremainsstillsupportedagainstthisnow“curable”disease. Funding: This work was supported by the French “Agence Nationale de la Recherche sur le SIDA et les HépatitesVirales”(ANRS),theEuropeanResearchCouncil(ERC-2008-AdG-233130-HEPCENT)andtheLabEx Ecofect (ANR-11-LABX-0048) of the “Université de Lyon”, within the program “Investissements d’Avenir” (ANR-11-IDEX-0007)operatedbytheFrenchNationalResearchAgency(ANR). ConflictsofInterest:Theauthorsdeclarenoconflictofinterest. References 1. 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InternationalHepatitisInterventionalTherapyGroup(IHIT).Lancet1998,352,1426–1432.[CrossRef] 5. Manns,M.P.;McHutchison,J.G.;Gordon,S.C.;Rustgi,V.K.;Shiffman,M.;Reindollar,R.;Goodman,Z.D.; Koury,K.;Ling,M.;Albrecht,J.K.Peginterferonalfa-2bplusribavirincomparedwithinterferonalfa-2bplus ribavirinforinitialtreatmentofchronichepatitisC:Arandomisedtrial.Lancet2001,358,958–965.[CrossRef]
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