Modulating biomolecular condensates: a novel approach to drug discovery

Nature Reviews Drug Discovery, Год журнала: 2022, Номер 21(11), С. 841 - 862

Опубликована: Авг. 16, 2022

In the past decade, membraneless assemblies known as biomolecular condensates have been reported to play key roles in many cellular functions by compartmentalizing specific proteins and nucleic acids subcellular environments with distinct properties. Furthermore, growing evidence supports view that often form phase separation, which a single-phase system demixes into two-phase consisting of condensed dilute particular biomolecules. Emerging understanding condensate function normal aberrant states, mechanisms formation, is providing new insights human disease revealing novel therapeutic opportunities. this Perspective, we propose such could enable previously unexplored drug discovery approach based on identifying condensate-modifying therapeutics (c-mods), discuss strategies, techniques challenges involved.

Язык: Английский

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Phase separation by the SARS-CoV-2 nucleocapsid protein: Consensus and open questions

Journal of Biological Chemistry, Год журнала: 2022, Номер 298(3), С. 101677 - 101677

Опубликована: Фев. 4, 2022

In response to the recent SARS-CoV-2 pandemic, a number of labs across world have reallocated their time and resources better our understanding virus. For some viruses, including SARS-CoV-2, viral proteins can undergo phase separation: biophysical process often related partitioning protein RNA into membraneless organelles in vivo. this review, we discuss emerging observations separation by nucleocapsid (N) protein—an essential required for replication—and possible vivo functions that been proposed N-protein separation, replication, genomic packaging, modulation host-cell infection. Additionally, since relatively large studies examining published short span time, take advantage situation compare results from similar experiments studies. Our evaluation highlights potential strengths pitfalls drawing conclusions single set experiments, as well value publishing overlapping scientific performed simultaneously multiple labs. virus responsible COVID-19 ongoing has exacted an enormous toll on human health, with >5.6 million deaths >350 infections currently attributed (according World Health Organization data, https://covid19.who.int/, accessed 1/26/22). The pandemic had already led estimated $16 trillion global economic costs October 2020 (1Cutler D.M. Summers L.H. virus.JAMA. 2020; 324: 1495-1496Google Scholar) disrupted nearly every sector, science. Over past year half, extraordinary progress made improving novel Emerging experimental implicate critical factor mediating (gRNA) Intriguingly, N ability (PS), which is now considered pervasive phenomenon organizing broad diversity biological processes cells. models, results, PS protein. given remarkable publications topic within ∼ 1 year, leverage unusual evaluate how work, parallel independent groups, may shape resulting conclusions. practice, science sequentially: one discovery typically precedes, informs, directs subsequent experimentation. incentive structure science, rewards novelty, promotes sequential model, disincentivizes focused replication validation. One limitation model subtle differences design sometimes significant impact thus influence direction experiments. However, publication was punctuated pandemic. Many historically little or no prior experience virology applied respective areas expertise questions SARS-CoV-2. This abrupt reallocation same study many organically created question its own: what happens when perform publish closely parallel? Here, reporting examine question. prototypical function coronaviral condense organize gRNA nascent virions (2Chang C. Hou M.-H. Chang C.-F. Hsiao C.-D. Huang T.-H. SARS coronavirus - forms functions.Antiviral Res. 2014; 103: 39-50Google Scholar). Virion formation occurs via accumulation structural [the spike (S), envelope (E), membrane (M), proteins] at ER-Golgi intermediate compartment (ERGIC) membrane. Multiple suggest strand dense, locally ordered ribonucleoprotein (RNP) regions consisting predominantly associated (3Klein S. Cortese M. Winter S.L. Wachsmuth-Melm Neufeldt C.J. Cerikan B. Stanifer M.L. Boulant Bartenschlager R. Chlanda P. characterized situ cryo-electron tomography.Nat. Commun. 11: 5885Google Scholar, 4Yao H. Song Y. Chen Wu N. Xu J. Sun Zhang Weng T. Z. Cheng L. Shi D. Lu X. Lei Crispin et al.Molecular architecture virus.Cell. 183: 730-738.e13Google 5Cao Cai Xiao Rao Hu Yang Xing Wang Li Zhou Xue genome inside virion.Nat. 2021; 12: 3917Google Locally RNPs be further organized more complex arrangements clustering particular stoichiometries geometries Scholar), although other evidence models SARS-CoV linear, helical RNP arrangement 6Filho H.V.R. Jara G.E. Batista F.A.H. Schleder G.R. Tonoli C.C. Soprano A.S. Guimarães Borges A.C. Cassago A. Bajgelman M.C. Marques R.E. Trivella D.B.B. Franchini K.G. Figueira A.C.M. Benedetti C.E. al.Structural dynamics induced binding.bioRxiv. ([preprint])https://doi.org/10.1101/2021.08.27.457964Google These preferentially accumulate curved membranes indicating either association aids curvature during virion formation, are preferred recruitment surface RNPs. also interacts luminal domain (i.e., interior virions) M protein, mechanism N-containing ERGIC (7Lu Ye Q. Singh Cao Diedrich J.K. Yates J.R. Villa E. Cleveland D.W. Corbett K.D. phosphoprotein mutually exclusive condensates membrane-associated protein.Nat. 502Google Some suggests both interact E (8Tseng Y.-T. S.-M. K.-J. C.-T. palmitoylation nucleocapid not promoting virus-like particle production.J. Biomed. Sci. 21: 34Google 9Li Guo Tian Liu Qu Yin Zhu Peng al.Virus-host interactome proteomic survey reveal virulence factors influencing pathogenesis.Med. (N. Y.). 2: 99-112.e7Google While precise detail regarding interactions individual molecules intact still forthcoming, clearly plays central role compaction organization virions. involves two distinct yet coexisting phases well-mixed solution: dense high concentration dilute low (10Banani S.F. Lee H.O. Hyman A.A. Rosen M.K. Biomolecular condensates: Organizers cellular biochemistry.Nat. Rev. Mol. Cell Biol. 2017; 18: 285-298Google Subsequent initial PS, additional transitions change material properties (11Patel Jawerth Maharana Jahnel Hein M.Y. Stoynov Mahamid Saha Franzmann T.M. Pozniakovski Poser I. Maghelli Royer L.A. Weigert al.A liquid-to-solid transition ALS FUS accelerated disease mutation.Cell. 2015; 162: 1066-1077Google 12Molliex Temirov Coughlin Kanagaraj A.P. Kim H.J. Mittag Taylor J.P. Phase complexity domains stress granule assembly drives pathological fibrillization.Cell. 163: 123-133Google Consequently, exhibit consistent liquids, gels, solids (13Boeynaems Alberti Fawzi N.L. Polymenidou Rousseau F. Schymkowitz Shorter Wolozin Van Den Bosch Tompa Fuxreiter Protein A new cell biology.Trends 2018; 28: 420-435Google these influenced sequence, concentration, presence concentrations molecules, physical chemical environment. key features “multivalency,” describes binding sites partner molecules. occur single-component multicomponent systems (14Dignon G.L. Best R.B. Mittal From molecular driving forces macroscopic properties.Annu. Phys. Chem. 71: 53-75Google 15Ruff K.M. Dar Pappu R.V. Polyphasic linkage ligand regulation biomolecular condensates.Biophys. 2021302Google system, driven homotypic between identical biopolymers), whereas co-PS system heterotypic different biopolymers) combination interactions. type multivalent observe certain appear common among known separate. example, separating contain RNA-binding domains, intrinsically disordered (IDRs), oligomerization low-complexity domains. gained attention biology due connection “biomolecular condensates” 13Boeynaems 16Hyman Weber C.A. Jülicher Liquid-liquid biology.Annu. Dev. 30: 39-58Google enriched nucleic acids. Much like observed vitro, consist network (often acids, proteins, biopolymers). types described, (but limited to) granules, P-bodies, nucleoli, nuclear speckles, germ Cajal bodies Each condensate sets constituent properties, functions, stability, regulation. Regardless differences, condensation represents elegant solution concentrating groups regulatable sensitive fashion. Given prevalence, diversity, importance eukaryotes, it perhaps surprise viruses able manipulate endogenous trigger entirely host cells (17Gaete-Argel Márquez C.L. Barriga G.P. Soto-Rifo Valiente-Echeverría Strategies success. Viral organelles.Front. Cell. Infect. Microbiol. 2019; 9: 336Google 18Etibor T.A. Yamauchi Amorim M.J. Liquid lifecycles: Review perspectives.Viruses. 13: 366Google Shortly after emergence would behavior might mediate RNA–protein packaging virions, modulate (namely, granules) direct interaction (19Cascarina S.M. Ross E.D. condensates.FASEB 34: 9832-9842Google ensuing months, various aspects modulation, innate immune pathways, kinases, were formally 20Zhao Yu L.-M. J.-Q. W. Xia Han Q.-Y. W.-H. A.-L. al.GCG inhibits disrupting liquid 2114Google 21Iserman Roden Boerneke M.A. Sealfon R.S.G. McLaughlin G.A. Jungreis Fritch E.J. Y.J. Ekena Weidmann Theesfeld Kellis Troyanskaya O.G. Baric R.S. 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Stanley Schaletzky Yildiz RNA.PLoS 19e3001425Google 29Savastano Ibáñez de Opakua Rankovic Zweckstetter Nucleocapsid RNA-rich polymerase-containing condensates.Nat. 6041Google 30Carlson C.R. Asfaha J.B. Ghent C.M. Howard Hartooni Safari Frankel A.D. Morgan D.O. Phosphoregulation basis dual functions.Mol. 1092-1103.e4Google 31Luo Zhao Ma Jin He Zou Liang Chi al.SARS-CoV-2 G3BPs disassemble facilitate production.Sci. Bull. 66: 1194-1204Google 32Perdikari Murthy Ryan V.H. Watters Naik M.T. phase-separates hnRNPs.EMBO 39e106478Google 33Wang undergoes through N-terminal region.Cell 5Google 34Wu Zhuang Xie Cui RNA-induced facilitates NF-κB hyper-activation inflammation.Signal Transduct. Target. Ther. 6: 167Google 35Chen P.H. Liquid–liquid RNA.Cell 1143-1145Google 36Zhao Ge Yuan Xiong Feng Shu Lang al.Understanding characteristics provides therapeutic opportunity against SARS-CoV-2.Protein 734-740Google Figure affecting vitro vivo, each discussed sections. purported and, broadly, learned “consensus” view timeframe. We note while done best faithfully interpret available all present rigorous quantification methods differed studies; therefore, based least degree subjective interpretation. containing prion-like (37Fomicheva prions granules: Defining compositional promote assemblies.Int. 22: 1251Google 38March Z.M. King O.D. Prion-like epigenetic regulators, scaffolds subcellular organization, drivers neurodegenerative disease.Brain 2016; 1647: 9-18Google 39Harrison A.F. health disease.Biochem. 474: 1417-1438Google itself capable undergoing (40Van Treeck Protter D.S.W. Matheny Khong Link C.D. Parker self-assembly contributes defining transcriptome.Proc. Natl. Acad. U. 115: 2734-2739Google induce specific lower (41Lin maturation phase-separated droplets proteins.Mol. 60: 208-219Google regulate variety ways [reviewed (42Roden Gladfelter contributions 183-195Google Scholar)]. contains structured (43Zhou Zeng von Brunn Structural characterization C-terminal protein.Mol. 1: 2Google 44Yang Kang insight reveals recognition transcriptional regulatory sequences.Front. 8: 624765Google 45Peng Du Dorje Qi Luo Gao G.F. Structures perspectives drug design.EMBO 39e105938Google 46Kang Hong Yan Shan Crystal unique targeting sites.Acta Pharm. Sin. 10: 1228-1238Google 47Wu Qavi A.J. Hachim Kavian Cole A.R. Moyle A.B. Wagner N.D. Sweeney-Gibbons Rohrs H.W. Gross Peiris J.S.M. Basler C.F. Farnsworth C.W. Valkenburg S.A. Amarasinghe G.K. al.Characterization functional consequences domain.iScience. 102681Google flanking IDRs enhance (44Yang alone exhibited weak undetectable majority almost universally evaluated depth (Fig. 1Ai). RNAs varying lengths sequences degrees, suggesting somewhat nonspecific (though N+RNA greater sequence specificity, later section). tested wide range concentrations, exceedingly amounts tended inhibit re-entrant imbalance Electrostatic consistently implicated regulating RNA-dependent 1Aii). salt salts used (48Alberti Considerations challenges studying liquid-liquid condensates.Cell. 176: 419-434Google generally presumed reflect electrostatic PS. Lower enhanced (20Zhao throu

Язык: Английский

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TRIM28-mediated nucleocapsid protein SUMOylation enhances SARS-CoV-2 virulence

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Янв. 4, 2024

Abstract Viruses, as opportunistic intracellular parasites, hijack the cellular machinery of host cells to support their survival and propagation. Numerous viral proteins are subjected host-mediated post-translational modifications. Here, we demonstrate that SARS-CoV-2 nucleocapsid protein (SARS2-NP) is SUMOylated on lysine 65 residue, which efficiently mediates SARS2-NP’s ability in homo-oligomerization, RNA association, liquid-liquid phase separation (LLPS). Thereby innate antiviral immune response suppressed robustly. These roles can be achieved through intermolecular association between SUMO conjugation a newly identified SUMO-interacting motif SARS2-NP. Importantly, widespread SARS2-NP R203K mutation gains novel site SUMOylation further increases LLPS immunosuppression. Notably, E3 ligase TRIM28 responsible for catalyzing SUMOylation. An interfering peptide targeting interaction was screened out block LLPS, consequently inhibit replication rescue immunity. Collectively, these data critical virulence, therefore provide strategy antagonize SARS-CoV-2.

Язык: Английский

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Viroplasms: Assembly and Functions of Rotavirus Replication Factories

Viruses, Год журнала: 2021, Номер 13(7), С. 1349 - 1349

Опубликована: Июль 12, 2021

Viroplasms are cytoplasmic, membraneless structures assembled in rotavirus (RV)-infected cells, which intricately involved viral replication. Two virus-encoded, non-structural proteins, NSP2 and NSP5, the main drivers of viroplasm formation. The (as far as is known) functions these proteins described. Recent studies using plasmid-only-based reverse genetics have significantly contributed to elucidation crucial roles RV Thus, it has been recognized that viroplasms resemble liquid-like protein–RNA condensates may be formed via liquid–liquid phase separation (LLPS) NSP5 at early stages infection. Interactions between RNA chaperone multivalent, intrinsically disordered protein result their condensation (protein droplet formation), plays a central role assembly. These droplets provide unique molecular environment for establishment inter-molecular contacts (+)ssRNA transcripts, followed by assortment equimolar packaging. Future efforts improve our understanding replication genome should focus on complex composition, changes dynamically throughout cycle, support distinct virion

Язык: Английский

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Phase separation in viral infections

Trends in Microbiology, Год журнала: 2022, Номер 30(12), С. 1217 - 1231

Опубликована: Июль 25, 2022

Язык: Английский

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Liquid Phase Partitioning in Virus Replication: Observations and Opportunities

Annual Review of Virology, Год журнала: 2022, Номер 9(1), С. 285 - 306

Опубликована: Июнь 16, 2022

Viruses frequently carry out replication in specialized compartments within cells. The effect of these structures on virus is poorly understood. Recent research supports phase separation as a foundational principle for organization cellular components with the potential to influence viral replication. In this review, described context formation centers, an emphasis nonsegmented negative-strand RNA viruses. Consideration given interplay between and critical processes transcription genome replication, role regions pathogen-host interactions discussed. Finally, questions that must be addressed fully understand how influences life cycle are presented, along information about new approaches could used make important breakthroughs emerging field.

Язык: Английский

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Molecular mechanisms of stress-induced reactivation in mumps virus condensates

Cell, Год журнала: 2023, Номер 186(9), С. 1877 - 1894.e27

Опубликована: Апрель 1, 2023

Negative-stranded RNA viruses can establish long-term persistent infection in the form of large intracellular inclusions human host and cause chronic diseases. Here, we uncover how cellular stress disrupts metastable host-virus equilibrium induces viral replication a culture model mumps virus. Using combination cell biology, whole-cell proteomics, cryo-electron tomography, show that factories are dynamic condensates identify largely disordered phosphoprotein as driver their assembly. Upon stress, increased phosphorylation at its interaction interface with polymerase coincides formation stable complex. By obtaining atomic models for authentic virus nucleocapsid, elucidate concomitant conformational change exposes genome to machinery. These events constitute stress-mediated switch within provide an environment support upregulation replication.

Язык: Английский

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A viral biomolecular condensate coordinates assembly of progeny particles

Nature, Год журнала: 2023, Номер 616(7956), С. 332 - 338

Опубликована: Апрель 5, 2023

Язык: Английский

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Understanding Influenza

Methods in molecular biology, Год журнала: 2025, Номер unknown, С. 1 - 26

Опубликована: Янв. 1, 2025

Язык: Английский

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New Perspectives on the Biogenesis of Viral Inclusion Bodies in Negative-Sense RNA Virus Infections

Cells, Год журнала: 2021, Номер 10(6), С. 1460 - 1460

Опубликована: Июнь 10, 2021

Infections by negative strand RNA viruses (NSVs) induce the formation of viral inclusion bodies (IBs) in host cell that segregate as well cellular proteins to enable efficient replication. The induction those membrane-less compartments leads inevitably structural remodeling architecture. Recent studies suggested IBs have properties biomolecular condensates (or liquid organelles), previously been shown for other like stress granules or P-bodies. Biomolecular are highly dynamic structures formed liquid-liquid phase separation (LLPS). Key drivers LLPS cells multivalent protein:protein and protein:RNA interactions leading specialized areas recruit molecules with similar properties, while non-similar excluded. These typical features also a common characteristic biogenesis bodies. Viral predominantly induced expression nucleoprotein (N, NP) phosphoprotein (P); both characterized special protein architecture containing multiple disordered regions RNA-binding domains contribute different functions. P keeps N soluble after allow concerted binding RNA. This results encapsidation genome N, acts additionally cofactor polymerase, enabling transcription Here, we will review function upon infection NSVs respect their nature condensates.

Язык: Английский

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