Organization, Function, and Therapeutic Targeting of the Morbillivirus RNA-Dependent RNA Polymerase Complex

viruses Review Organization, Function, and Therapeutic Targeting of the Morbillivirus RNA-Dependent RNA Polymerase Complex Julien Sourimant and Richard K. Plemper * Institute for Biomedical Sciences, Georgia State University, 100 Piedmont Av, Atlanta, GA 30303, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-404-413-3579 Academic Editor: Eric Freed Received: 3 August 2016; Accepted: 5 September 2016; Published: 10 September 2016 Abstract: The morbillivirus genus comprises major human and animal pathogens, including the highly contagious measles virus. Morbilliviruses feature single stranded negative sense RNA genomes that are wrapped by a plasma membrane-derived lipid envelope. Genomes are encapsidated by the viral nucleocapsid protein forming ribonucleoprotein complexes, and only the encapsidated RNA is transcribed and replicated by the viral RNA-dependent RNA polymerase (RdRp). In this review, we discuss recent breakthroughs towards the structural and functional understanding of the morbillivirus polymerase complex. Considering the clinical burden imposed by members of the morbillivirus genus, the development of novel antiviral therapeutics is urgently needed. The viral polymerase complex presents unique structural and enzymatic properties that can serve as attractive candidates for druggable targets. We evaluate distinct strategies for therapeutic intervention and examine how high-resolution insight into the organization of the polymerase complex may pave the path towards the structure-based design and optimization of next-generation RdRp inhibitors. Keywords: measles virus; morbillivirus; viral polymerase; antiviral drug; polymerase inhibitor 1. Introduction The paramyxovirus family encompasses a broad and diverse range of human and animal pathogens. In addition to the morbillivirus genus, the family includes the aquaparamyxo-, avula-, ferla-, henipa-, respiro-, and rubulaviruses. All spread through the respiratory route, but the morbilliviruses are characterized by extremely high infection rates. The genus includes the exclusively human-tropic measles virus (MeV) as well as pathogens infecting terrestrial carnivores (canine distemper virus, CDV), felines (feline morbillivirus, FeMV), livestock (Peste-des-petits-ruminants virus, PPRV, and Rinderpest virus, RPV), or marine mammals (cetacean morbillivirus, CeMV, and phocine distemper virus, PDV) [1] (Figure1A). Viruses 2016, 8, 251; doi:10.3390/v8090251 www.mdpi.com/journal/viruses Viruses 2016, 8, 251 2 of 21 Viruses 2016, 8, 251 2 of 21 FigureFigure 1. Overview 1. Overview of the of themorbillivirus morbillivirus genus. genus. (A) (PhylogeneticA) Phylogenetic analysis analysis of amino of amino acid acidsequences sequences of nucleocapsidof nucleocapsid genes genesof different of different morbillivirus morbillivirus reference reference strains. strains. The unrooted The unrooted tree was tree constructed was constructed using the usingneighbor the‐joining neighbor-joining method. Branch method. lengths Branch are relative lengths and are proportional relative and to proportional the number of to substitutions. the number of Thesubstitutions. unit of branch The length unit of is branch the number length of is thesubstitutions number of (excluding substitutions gaps) (excluding at each gaps)given at nucleotide each given position.nucleotide Alignments position. were Alignments made with were ClustalW2 made with [2–4] ClustalW2 and trees [2– 4rendered] and trees with rendered Drawtree with from Drawtree the PHYLIPfrom package the PHYLIP 3.67 package[5,6]. Genbank 3.67 [5 accession,6]. Genbank IDs: accessionFeMV JQ411014; IDs: FeMV MeV JQ411014; NC_001498; MeV PDV NC_001498; P35944; PPRV PDV NC_006383;P35944; PPRV CeMV NC_006383; NC_005283; CeMVCDV NC_001921; NC_005283; RPV CDV YP_087120.2); NC_001921; (B) RPV Cartoon YP_087120.2); of morbillivirus (B) Cartoon genome of organization.morbillivirus genome organization. MeV is responsible for major pediatric morbidity and mortality, and is considered to belong to the MeV is responsible for major pediatric morbidity and mortality, and is considered to belong to the most infectious viral pathogens identified to date [7–9]. A safe and effective live‐attenuated vaccine is most infectious viral pathogens identiﬁed to date [7–9]. A safe and effective live-attenuated vaccine available, but the high transmissibility of the virus requires approximately 95% herd immunity to is available, but the high transmissibility of the virus requires approximately 95% herd immunity to suppress sporadic outbreaks [10], a level that has not yet been reached in many geographic areas [11]. Severalsuppress factors sporadic are hindering outbreaks the [required10], a level 100% that vaccination has not yet coverage been reached that is in necessary many geographic to compensate areas for [11 ]. a lowSeveral rate of factors primary are vaccination hindering the failure required and induce 100% vaccination this degree of coverage herd immunity. that is necessary Predominantly, to compensate these includefor a limited low rate access of primary to the vaccine vaccination in parts failure of the and developing induce this world degree and of a growing herd immunity. refusal of Predominantly, vaccination duethese to parental include concerns limited access and/or to religious the vaccine beliefs in parts [12,13]. of the As developinga consequence, world MeV and remains a growing endemic refusal in of largevaccination geographical due areas to parental and is concernsresponsible and/or for substantial religious beliefsmorbidity [12, 13worldwide]. As a consequence, [11]. MeV remains endemicWhereas in increasing large geographical vaccination areas coverage and is will responsible be vital fortowards substantial stopping morbidity endemic worldwide transmission [11 and]. suppressingWhereas measles, increasing complementing vaccination vaccination coverage will with be vital an effective towards stoppingantiviral endemicdrug for transmission post‐exposure and prophylaxissuppressing may measles, allow for complementing the rapid suppression vaccination of local with anMeV effective outbreaks antiviral in areas drug with for post-exposureoverall good vaccinationprophylaxis coverage, may allow such as for North the rapid America suppression [14], and cut of local short MeV a potential outbreaks prolonged in areas endgame with overall for global good MeVvaccination eradication coverage, that tests such political as North will and America public [ 14resolve], and [15,16]. cut short a potential prolonged endgame for globalThe paramyxovirus MeV eradication RNA that dependent tests political RNA will polymerase and public (RdRp) resolve complex [15,16]. is increasingly recognized as an attractiveThe paramyxovirus target for therapeutic RNA dependent intervention RNA polymerase [17,18]. In (RdRp) addition complex to evaluating is increasingly recent recognizedprogress towardsas an the attractive fundamental target understanding for therapeutic of the intervention spatial organization [17,18]. Inand addition function toof the evaluating morbillivirus recent polymerase,progress towardswe will the assess fundamental in this understandingreview candidate of thedruggable spatial organizationtarget sites andand function discuss ofthe the characterizationmorbillivirus and polymerase, developmental we will status assess of inselected this review morbillivirus candidate RdRp druggable inhibitors. target sites and discuss the characterization and developmental status of selected morbillivirus RdRp inhibitors. 2. The Morbillivirus RNA Dependent RNA Polymerase (RdRp) Complex 2. The Morbillivirus RNA Dependent RNA Polymerase (RdRp) Complex Morbilliviruses possess 15 to 16 kilobase RNA genomes of negative polarity that contain six open reading Morbillivirusesframes, leading to possess the expression 15 to 16 of kilobase eight proteins: RNA genomes the structural of negative nucleocapsid polarity‐ (N), that phospho contain‐ (P),six matrix open (M), reading fusion frames, (F), hemagglutinin leading to the (H) expression and large of (L) eight proteins, proteins: as well the as structural the non‐ nucleocapsid-structural V and (N), C proteinsphospho- (Figure (P), matrix1B). (M), fusion (F), hemagglutinin (H) and large (L) proteins, as well as the non-structural V and C proteins (Figure1B). Viruses 2016, 8, 251 3 of 21 The coding regions of the RNA genome are ﬂanked by 30 leader and 50 trailer sequences that are necessary for the initiation of transcription and replication [19,20]. Furthermore, the six open reading frames are separated by intergenic junctions containing signal elements for the initiation and termination of transcription [21]. Coding and non-coding regions are implicated in virulence [22]. Additionally, like many other members of the paramyxovirus family, morbilliviruses strictly adhere to a “rule of six”, meaning that the total genome length represents a multiple of six [21,23,24]. Upon viral entry into a cell, the RdRp complex is responsible for all polymerase activity involving the viral genome, thus functioning as a transcriptase synthesizing viral mRNAs and a replicase generating positive polarity antigenomes and progeny genomes [25]. In addition to host cell cofactors, the RdRp complex is comprised of the viral L protein, which mediates all enzymatic activities, and the P protein as its mandatory cofactor. The RNA genomes and antigenomes are encapsidated by the viral N protein during synthesis, and only these N:RNA ribonucleoprotein complexes

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