Publications

2025

Combating yellow fever virus with 7-deaza-7-fluoro-2'-C-methyladenosine. LeCher JC, Costa VV, Rust LN, Bassit LC, Patel D, Rezaei S, Moua J, Santos FRdS, Goncalves MR, Queroz-Junior CM, Marim FM, Zhou L, Lee S, McBrayer T, De R, Azadi N, Salman M, Zandi K, Amblard F, Burwitz B, Teixeira MM, Schinazi RF. Antimicrob Agents Chemother. 2025 Apr 14:e0188924. doi: 10.1128/aac.01889-24.

Safety, pharmacokinetics, and biological activity of CD4-mimetic BNM-III-170 in SHIV-infected rhesus macaques. Viox EG, Richard J, Grandea AG 3rd, Nguyen K, Harper J, Auger J, Ding S, Gasser R, Prévost J, Marchitto L, Medjahed H, Bourassa C, Gaudette F, Pagliuzza A, Trifone CA, Gavegnano C, Hurwitz SJ, Park J, Clark NM, Hammad I, Capuano S 3rd, Martin MA, Schinazi RF, Silvestri G, Kulpa DA, Kumar P, Chomont N, Pazgier M, Smith AB 3rd, Sodroski J, Evans DT, Finzi A, Paiardini M. J Virol. 2025 Apr 7:e0006225. doi: 10.1128/jvi.00062-25.

Pathway-instructed therapeutic selection of ruxolitinib reduces neuroinflammation in fungal postinfectious inflammatory syndrome. Hargarten JC, Ssebambulidde K, Anjum SH, Vaughan MJ, Xu J, Ganguly A, Dulek B, Otaizo-Carrasquero F, Song B, Tao S, Park YD, Scott TL, Höltermann TA, Schinazi RF, Chittiboina P, Billioux BJ, Hammoud DA, Olszewski MA, Williamson PR. Sci Adv. 2025 Mar 21;11(12):eadi9885. doi: 10.1126/sciadv.adi9885.

BRAFV600E-PROTAC versus inhibitors in melanoma cells: Deep transcriptomic characterisation. Alhassan SO, Abd Elmageed ZY, Errami Y, Wang G, Abi-Rached JA, Kandil E, Zerfaoui M. Clin Transl Med. 2025 Mar;15(3):e70251. doi: 10.1002/ctm2.70251

Reader comment on: "Comprehensive genotoxicity and carcinogenicity assessment of molnupiravir". Frederick CB, Schinazi RF, Swanstrom R.Toxicol Sci. 2025 Mar 1;204(1):116-117. doi: 10.1093/toxsci/kfae156.

Considerations for capsid-targeting antiretrovirals in pre-exposure prophylaxis. McFadden WM, Faerch M, Kirby KA, Dick RA, Torbett BE, Sarafianos SG. Trends Mol Med. 2025 Feb 27:S1471-4914(25)00013-9. doi: 10.1016/j.molmed.

Adapting a Trapped Ion Mobility Spectrometry-Q-TOF for High m/z Native Mass Spectrometry and Surface-Induced Dissociation. Lin YF, Jones BJ, Ridgeway ME, Panczyk EM, Somogyi A, Kaplan DA, Marathe I, Yun S, Kirby KA, Sarafianos SG, Laganowsky AD, Park MA, Wysocki VH. Anal Chem. 2025 Feb 25;97(7):3827-3835. doi: 10.1021/acs.analchem.4c03557.

The conserved HIV-1 spacer peptide 2 triggers matrix lattice maturation. Stacey JCV, Hrebík D, Nand E, Shetty SD, Qu K, Boicu M, Anders-Össwein M, Uchil PD, Dick RA, Mothes W, Kräusslich HG, Müller B, Briggs JAG. Nature. 2025 Apr;640(8057):258-264. doi: 10.1038/s41586-025-08624-9.

Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley D, Mansky LM, Dick RA, Schur FKM. Nat Struct Mol Biol. 2025 Feb;32(2):268-276. doi: 10.1038/s41594-024-01390-8.

2024

The conserved HIV-1 spacer peptide 2 triggers matrix lattice maturation. Stacey JCV, Hrebík D, Nand E, Shetty SD, Qu K, Boicu M, Anders-Össwein M, Dick RA, Mothes W, Kräusslich HG, Müller B, Briggs JAG. bioRxiv [Preprint]. 2024 Nov 6:2024.11.06.622200. doi: 10.1101/2024.11.06.622200.

Discovery of Hepatitis B Virus Surface Antigen Suppressor GS-8873. Kato D, Choy RW, Canales E, Dick RA, Lake AD, Shapiro ND, Chin E, Li J, Zhang JR, Wu Q, Saito RD, Metobo S, Aktoudianakis E, Schroeder SD, Yang ZY, Glatt DM, Balsitis S, Gamelin L, Yu M, Cheng G, Delaney WE 4th, Link JO. ACS Med Chem Lett. 2024 Mar 22;15(4):546-554. doi: 10.1021/acsmedchemlett.4c00037. eCollection 2024 Apr 11.

Unconventional stabilization of the human T-cell leukemia virus type 1 immature Gag lattice. Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley D, Mansky LM, Dick RA, Schur FK. Nat Struct Mol Biol. 2024 Sep 6. doi: 10.1038/s41594-024-01390-8.

Long-term 3D cell culture models for hepatitis B virus studies. Jones CE, Dangas G, Norris AC, Koenig M, Li DY, Shue TM, Athanasiadis A, Barbosa L, Zhou Y, Levenson KC, Zou C, de Jong YP, Michailidis E. Virology. 2024 Dec; 600:110265. doi: 10.1016/j.virol.2024.110265.

Myrtus communis L. Essential Oil Exhibits Antiviral Activity against Coronaviruses. Li DY, Donadu MG, Shue T, Dangas G, Athanasiadis A, Lan S, Wen X, Battah B, Zanetti S, Mazzarello V, Sarafianos SG, Ferrari M, Michailidis E. Pharmaceuticals (Basel). 2024 Sep 10;17(9):1189. doi: 10.3390/ph17091189.

A genome-wide arrayed CRISPR screen identifies PLSCR1 as an intrinsic barrier to SARS-CoV-2 entry that recent virus variants have evolved to resist. Le Pen J, Paniccia G, Kinast V, Moncada-Velez M, Ashbrook AW, Bauer M, Hoffmann HH, Pinharanda A, Ricardo-Lax I, Stenzel AF, Rosado-Olivieri EA, Dinnon KH 3rd, Doyle WC, Freije CA, Hong SH, Lee D, Lewy T, Luna JM, Peace A, Schmidt C, Schneider WM, Winkler R, Yip EZ, Larson C, McGinn T, Menezes MR, Ramos-Espiritu L, Banerjee P, Poirier JT, Sànchez-Rivera FJ, Cobat A, Zhang Q, Casanova JL, Carroll TS, Glickman JF, Michailidis E, Razooky B, MacDonald MR, Rice CM. PLoS Biol. 2024;22(9):e3002767. doi: 10.1371/journal.pbio.3002767. eCollection 2024 Sep.

The structural and mechanistic bases for the viral resistance to allosteric HIV-1 integrase inhibitor pirmitegravir. Dinh T, Tber Z, Rey JS, Mengshetti S, Annamalai AS, Haney R, Briganti L, Amblard F, Fuchs JR, Cherepanov P, Kim K, Schinazi RF, Perilla JR, Kim B, Mamuka Kvaratskhelia. ASM Journals / mBio Oct 15, 2024.

Biochemical Simulation of Mutation Synthesis and Repair during SARS-CoV-2 RNA Polymerization. Oo A, Chen Z, Cao D, Cho YJ, Liang B, Schinazi RF, Kim B. Virology Oct 01, 2024.

Acetylation of SAMHD1 at lysine 580 is crucial for blocking HIV-1 infection. Bulnes-Ramos A, Schott K, Rabinowitz J, Luchsinger C, Bertelli C, Miyagi E, Yu CH, Persaud M, Shepard C, König R, Kim B, Ivanov DN, Strebel K, Diaz-Griffero F. mBio 2024 Sep 11 / ASM Journals, Vol. 15, No. 9. Aug 20, 2024.

NSD2 drives T(4;14) myeloma cell dependence on adenylate kinase 2 by diverting one-carbon metabolism to the epigenome. Sobh, A, Encinas E, Patel A, Surapaneni G, Bonilla E, Kaestner C, Poullard J, Clerio M, Vasan K, Freeman T, Lv D, Dupere-Richer D, Riva A, Barwick B.G., Zhou D, Boise L.H., Mitsiades C.S., Kim B, Bennett R.L., Chandel N.S, Licht J.D. Blood, vol. 144, no. 3, 18 July 2024, pp. 283–295.

The thioredoxin system determines CHK1 inhibitor sensitivity via redox-mediated regulation of ribonucleotide reductase activity. Prasad C.B., Oo A., Liu Y, Qiu Z, Zhong Y, Li N, Singh D, Xin X, Cho Y.J., Li Z, Zhang X, Yan C, Zheng Q, Wang Q.E., Guo D, Kim B, Zhang J. Nat Commun. 2024 May 31.

SAMHD1 expression contributes to doxorubicin resistance and predicts survival outcomes in diffuse large B-cell lymphoma patients. Daddacha W, Monroe D, Schlafstein AJ, Withers AE, Thompson EB, Danelia D, Luong NC, Sesay F, Rath SK, Usoro ER, Essien ME, Jung AT, Jiang JG, Hu J, Mahboubi B, Williams A, Steinbeck JE, Yang X, Buchwald ZS, Dynan WS, Switchenko JM, Kim B, Khan MK, Jaye DL, Yu DS. NAR Cancer. 2024 Feb 2024.

SOX11 is a novel binding partner and endogenous inhibitor of SAMHD1 ara-CTPase activity in mantle cell lymphoma. Morsy MHA, Lilienthal I, Lord M, Merrien M, Wasik AM, Amador V, Sureda-Gómez M, Johansson HJ, Lehtiö J, García-Torre B, Martin-Subero JI, Tsesmetzis N, Tao S, Schinazi RF, Kim B, Sorteberg AL, Wickström M, Sheppard D, Rassidakis GZ, Taylor IA, Christensson B, Campo E, Herold N, Sander B. Blood. Jan 18, 2024.

Dimming the corona: studying SARS-coronavirus-2 at reduced biocontainment level using replicons and virus-like particles. Neilsen G, Mathew AM, Castro JM, McFadden WM, Wen X, Ong YT, Tedbury PR, Lan S, Sarafianos SG. mBio. 2024 Nov 12: e0336823. doi: 10.1128/mbio.03368-23. Online ahead of print. PMID: 39530689

HIV-1 usurps mixed-charge domain-dependent CPSF6 phase separation for higher-order capsid binding, nuclear entry and viral DNA integration. Jang S, Bedwell GJ, Singh SP, Yu HJ, Arnarson B, Singh PK, Radhakrishnan R, Douglas AW, Ingram ZM, Freniere C, Akkermans O, Sarafianos SG, Ambrose Z, Xiong Y, Anekal PV, Montero Llopis P, KewalRamani VN, Francis AC, Engelman AN. Nucleic Acids Res. 2024 Oct 14;52(18):11060-11082. doi: 10.1093/nar/gkae769.PMID: 39258548 Free PMC article.

Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries. Akaberi D, Pourghasemi Lati M, Krambrich J, Berger J, Neilsen G, Strandback E, Turunen SP, Wannberg J, Gullberg H, Moche M, Chinthakindi PK, Nyman T, Sarafianos SG, Sandström A, Järhult JD, Sandberg K, Lundkvist Å, Verho O, Lennerstrand. J. Antimicrob Agents Chemother. 2024 Oct 8;68(10): e0090924. doi: 10.1128/aac.00909-24.

Mpox Virus is Inhibited by Nucleoside Analogues Including the Acyclic Phosphonates Tenofovir and Adefovir. Lee J, Boggs EA, Zhang H, Tedbury PR, Sarafianos SG. bioRxiv; doi: https://doi.org/10.1101/2023.06.30.547277

Design and Synthesis of New GS-6207 Subtypes for Targeting HIV-1 Capsid Protein. Akther T, McFadden WM, Zhang H, Kirby KA, Sarafianos SG, Wang Z. Int J Mol Sci. 2024 Mar 27;25(7):3734. doi: 10.3390/ijms25073734.PMID: 38612545.

A Tag-Free Platform for Synthesis and Screening of Cyclic Peptide Libraries. Bruce A, Adebomi V, Czabala P, Palmer J, McFadden WM, Lorson ZC, Slack RL, Bhardwaj G, Sarafianos SG, Raj M. Angew. Chem Int Ed Engl. 2024 May 21;63(21):e202320045. doi: 10.1002/anie.202320045. PMID:38529717

Identification of clickable HIV-1 capsid-targeting probes for viral replication inhibition. McFadden WM, Casey-Moore MC, Bare GAL, Kirby KA, Wen X, Li G, Wang H, Slack RL, Snyder AA, Lorson ZC, Kaufman IL, Cilento ME, Tedbury PR, Gembicky M, Olson AJ, Torbett BE, Sharpless KB, Sarafianos SG. Cell Chem Biol. 2024 Mar 21;31(3):477-486.e7. doi: 10.1016/j.chembiol.2024.02.012. PMID: 38518746

Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization. Gres AT, Kirby KA, McFadden WM, Du H, Liu D, Xu C, Bryer AJ, Perilla JR, Shi J, Aiken C, Fu X, Zhang P, Francis AC, Melikyan GB, Sarafianos SG. Nat Commun. 2023 Sep 12;14(1):5614. doi: 10.1038/s41467-023-41197-7.

Best Scientific Publication of the Year Pediatrics Award-2024.

State of the ART (antiretroviral therapy): Long-acting HIV-1 therapeutics. Ravichandran SM, McFadden WM, Snyder AA, Sarafianos SG. Global Health and Medicine, GHM-24-01049-RV, in press.

The Discovery and Development of Islatravir (4’-Ethynyl-2-fluoro-2’-deoxyadenosine; EFdA, MK-8591) Snyder AA, Wen X, Michailidis E, Kirby KA, Mitsuya H, Sarafianos, SG. Trends in Antiviral Drug Development, in press.

Synthesis and biological evaluation of novel peptidomimetic inhibitors of the coronavirus 3C-like protease. Amblard F, LeCher JC, De R, Zhou S, Liu P, Goh SL, Tao S, Patel D, Downs-Bowen J, Zandi K, Zhang H, Chaudhry G, McBrayer T, Muczynski M, Al-Homoudi A, Engel J, Lan S, Sarafianos SG, Kovari LC, Schinazi RF. Eur J Med Chem. 2024 Mar 15;268:116263. doi: 10.1016/j.ejmech.2024.116263. Epub 2024 Feb 24.

The Discovery and Preclinical Profile of ALG-000184, a Prodrug of the Potent Hepatitis B Virus Capsid Assembly Modulator ALG-001075. Vendeville S, Amblard F, Bassit L, Beigelman LN, Blatt LM, Chen X, Chou L, Kum DB, Chanda S, Deval J, Geng X, Gupta K, Jekle A, Hu H, Hu X, Kang H, Liu C, Liu J, McGowan DC, Misner DL, Raboisson P, Sanchez AA, Serebryany V, Stoycheva AD, Symons JA, Tan H, Vanrusselt H, Williams C, Welch M, Zhang L, Zhang Q, Zhang Y, Schinazi RF, Smith DB, Debing Y. J Med Chem. 2024 Nov 22. doi: 10.1021/acs.jmedchem.4c01814.

Cannabinoid-Inspired Inhibitors of the SARS-CoV-2 Coronavirus 2'-O-Methyltransferase (2'-O-MTase) Non-Structural Protein (Nsp10-16). Benjamin MM, Hanna GS, Dickinson CF, Choo YM, Wang X, Downs-Bowen JA, De R, McBrayer TR, Schinazi RF, Nielson SE, Hevel JM, Pandey P, Doerksen RJ, Townsend DM, Zhang J, Ye Z, Wyer S, Bialousow L, Hamann MT. Molecules. 2024 Oct 28;29(21):5081. doi: 10.3390/molecules29215081.

N4-Hydroxycytidine/molnupiravir inhibits RNA virus-induced encephalitis by producing mutated viruses with Reduced Fitness. Ojha D, Hill CS, Zhou S, Evans A, Leung JM, Schneider CA, Amblard F, Woods TA, Schinazi RF, Baric RS, Peterson KE, Swanstrom R. PLoS Pathog. 2024 Sep 30;20(9):e1012574. doi: 10.1371/journal.ppat.1012574.

Protocol for the creation and characterization of SARS-CoV-2 variant testing panels using remnant clinical samples for diagnostic assay testing. Bassit L, Bowers HB, Greenleaf M, Sabino C, Lai E, Yu G, Piantadosi A, Wang E, O'Sick W, McLendon K, Sullivan JA, Schinazi RF, Damhorst GL, Lam W, Rao A. STAR Protoc. 2024 Sep 20;5(3):103146. doi: 10.1016/j.xpro.2024.103146. Epub 2024 Jun 20.

Why Certain Repurposed Drugs Are Unlikely to Be Effective Antivirals to Treat SARS-CoV-2 Infections. Hurwitz SJ, De R, LeCher JC, Downs-Bowen JA, Goh SL, Zandi K, McBrayer T, Amblard F, Patel D, Kohler JJ, Bhasin M, Dobosh BS, Sukhatme V, Tirouvanziam RM, Schinazi RF. Viruses. 2024 Apr 22;16(4):651. doi: 10.3390/v16040651.

Biophysics-Guided Lead Discovery of HBV Capsid Assembly Modifiers. Fan Z, Pavlova A, Jenkins MC, Bassit L, Salman M, Lynch DL, Patel D, Korablyov M, Finn MG, Schinazi RF, Gumbart JC. ACS Infect Dis. 2024 Apr 12;10(4):1162-1173. doi: 10.1021/acsinfecdis.3c00479. Epub 2024 Apr 2.

Direct Synthesis of Aryloxy Phosphonamidate Nucleotide Prodrugs Using the Cross Metathesis Assisted by Ultrasonic Irradiation. Choi SM, Nam YE, An YJ, Choi ER, Park H, Schinazi RF, Cho JH. Org Lett. 2024 Jun 14;26(23):4841-4846. doi: 10.1021/acs.orglett.4c00094. Epub 2024 Feb 21.

Development of robust antiviral assays using relevant apical-out human airway organoids. Lee JH, LeCher JC, Parigoris E, Shinagawa N, Sentosa J, Manfredi C, Goh SL, De R, Tao S, Zandi K, Amblard F, Sorscher EJ, Spence JR, Tirouvanziam R, Schinazi RF, Takayama S. bioRxiv [Preprint]. 2024 Jul 12:2024.01.02.573939. doi: 10.1101/2024.01.02.573939.

Informatics and Computational Approaches for the Discovery and Optimization of Natural Product-Inspired Inhibitors of the SARS-CoV-2 2'-O-Methyltransferase. Hanna GS, Benjamin MM, Choo YM, De R, Schinazi RF, Nielson SE, Hevel JM, Hamann MT. J Nat Prod. 2024 Feb 23;87(2):217-227. doi: 10.1021/acs.jnatprod.3c00875.

Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome. Xu P, Yang T, Kundnani DL, Sun M, Marsili S, Gombolay AL, Jeon Y, Newnam G, Balachander S, Bazzani V, Baccarani U, Park VS, Tao S, Lori A, Schinazi RF, Kim B, Pursell ZF, Tell G, Vascotto C, Storici F. Nucleic Acids Res. 2024 Feb 9;52(3):1207-1225. doi: 10.1093/nar/gkad1204.

2023

Risener, C. J., Woo, S., Samarakoon, T., Caputo, M., Edwards, E., Klepzig, K., Applequest, W., Zandi, K., Goh, S. L., Downs-Bowen, J. A., Schinazi, R. F., Quave, C. L.: Botanical inhibitors of SARS-CoV-2 viral entry: a phylogenetic perspective. Sci Rep 2023; 13(1):1244. PMCID: PMC9868516.

Biteau NG, Amichai SA, Azadi N, De R, Downs-Bowen J, Lecher JC, MacBrayer T, Schinazi RF, Amblard F. Synthesis of 4'-Substituted Carbocyclic Uracil Derivatives and Their Monophosphate Prodrugs as Potential Antiviral Agents. Viruses. 2023 Feb 16;15(2):544. doi: 10.3390/v15020544. PMID: 36851758; PMCID: PMC9962574.

Cicka D, Niu Q, Qui M, Qian K, Miller E, Fan D, Mo X, Ivanov AA, Sarafianos SG, Du Y, Fu H. TMPRSS2 and SARS-CoV-2 SPIKE interaction assay for uHTS. J Mol Cell Biol. 2023 Mar 15:mjad017. doi: 10.1093/jmcb/mjad017. Epub ahead of print. PMID: 36921991.

Lan S, Neilsen G, Slack RL, Cantara WA, Castaner AE, Lorson ZC, Lulkin N, Zhang H, Lee J, Cilento ME, Tedbury PR, Sarafianos SG. Nirmatrelvir Resistance in SARS-CoV-2 Omicron_BA.1 and WA1 Replicons and Escape Strategies. bioRxiv [Preprint]. 2023 Jan 3:2022.12.31.522389. doi: 10.1101/2022.12.31.522389. PMID: 36656782; PMCID: PMC9844013.

Balasubramaniam A, Tedbury PR, Mwangi SM, Liu Y, Li G, Merlin D, Gracz AD, He P, Sarafianos SG, Srinivasan S. SARS-CoV-2 Induces Epithelial-Enteric Neuronal Crosstalk Stimulating VIP Release. Biomolecules. 2023 Jan 20;13(2):207. doi: 10.3390/biom13020207. PMID: 36830577; PMCID: PMC9953368.

Singer MR, Dinh T, Levintov L, Annamalai AS, Rey JS, Briganti L, Cook NJ, Pye VE, Taylor IA, Kim K, Engelman AN, Kim B, Perilla JR, Kvaratskhelia M, Cherepanov P. The Drug-Induced Interface That Drives HIV-1 Integrase Hypermultimerization and Loss of Function. mBio. 2023 Feb 28;14(1):e0356022. doi: 10.1128/mbio.03560-22. Epub 2023 Feb 6. PMID: 36744954; PMCID: PMC9973045.

Lee D, Le Pen J, Yatim A, Dong B, Aquino Y, Ogishi M, Pescarmona R, Talouarn E, Rinchai D, Zhang P, Perret M, Liu Z, Jordan I, Elmas Bozdemir S, Bayhan GI, Beaufils C, Bizien L, Bisiaux A, Lei W, Hasan M, Chen J, Gaughan C, Asthana A, Libri V, Luna JM, Jaffré F, Hoffmann HH, Michailidis E, Moreews M, Seeleuthner Y, Bilguvar K, Mane S, Flores C, Zhang Y, Arias AA, Bailey R, Schlüter A, Milisavljevic B, Bigio B, Le Voyer T, Materna M, Gervais A, Moncada-Velez M, Pala F, Lazarov T, Levy R, Neehus AL, Rosain J, Peel J, Chan YH, Morin MP, Pino-Ramirez RM, Belkaya S, Lorenzo L, Anton J, Delafontaine S, Toubiana J, Bajolle F, Fumadó V, DeDiego ML, Fidouh N, Rozenberg F, Pérez-Tur J, Chen S, Evans T, Geissmann F, Lebon P, Weiss SR, Bonnet D, Duval X; CoV-Contact Cohort§; COVID Human Genetic Effort¶; Pan-Hammarström Q, Planas AM, Meyts I, Haerynck F, Pujol A, Sancho-Shimizu V, Dalgard CL, Bustamante J, Puel A, Boisson-Dupuis S, Boisson B, Maniatis T, Zhang Q, Bastard P, Notarangelo L, Béziat V, Perez de Diego R, Rodriguez-Gallego C, Su HC, Lifton RP, Jouanguy E, Cobat A, Alsina L, Keles S, Haddad E, Abel L, Belot A, Quintana-Murci L, Rice CM, Silverman RH, Zhang SY, Casanova JL. Inborn errors of OAS-RNase L in SARS-CoV-2-related multisystem inflammatory syndrome in children. Science. 2023 Feb 10;379(6632):eabo3627. doi: 10.1126/science.abo3627. Epub 2023 Feb 10. PMID: 36538032