Anthony O'donoghue

Title(s)Associate Professor, School of Pharmacy and Pharmaceutical Science
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
ORCID ORCID Icon0000-0001-5695-0409 Additional info
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    Collapse Biography 
    Collapse Education and Training
    University of California San FranciscoAssociate Specialist2015Pharmaceutical Chemistry
    University of California San FranciscoPost-Doctoral Training2011Pharmaceutical Chemistry
    National University of Ireland, GalwayPh.D2005Biochemistry
    National University of Ireland, GalwayB.S.2000Biochemistry
    Cork Institute of Technology, IrelandNational Diploma1998Cell & Molecular Biology
    Collapse Awards and Honors
    NIH/NIBIB2019  - 2022Trailblazer Awardee
    International Proteolysis Society2019  - 2023President
    International Proteolysis Society2017  - 2019Member of Council - Treasurer
    Future Science2013  - 2013Bioanalysis Young Investigator Award
    National University of Ireland, Galway2002  - 2003UC Education Abroad Scholarship

    Collapse Overview 
    Collapse Overview
    My laboratory interests lie in the detection and characterization of proteolytic enzymes that are involved in disease. In particular, we are interested in understanding the role of peptidases/proteases at host-pathogen and tumor-stroma interfaces. Our research utilizes a mass spectrometry based platform technology to uncover the global proteolytic activity in complex biological samples such as the secretions of cancer cells and infectious organisms. Our workflow also includes in-depth proteomic analysis to identify the enzymes. Knowledge of which peptidases are functionally active in diseased tissue and not active in healthy tissue allow us to 1) develop peptidase inhibitors to shut down the function, 2) generate peptidase-activated imaging agents to locate the disease or 3) develop peptidase-activated drugs to aid in the delivery of toxic compounds to the site of disease. Using this technology, we have uncovered novel proteolytic activities in gastric juice, pancreatic cyst fluid, serum and neutrophil extracts. In addition our group is highly collaborative and we routinely generate substrate specificity profiles of endo- and exo-peptidases that have been isolated from diverse organisms that includes ticks, crustaceans and parasitic worms.

    Collapse Research 
    Collapse Research Activities and Funding
    Tumor-specific drug activation by pericellular proteases
    NCI R21CA256460Feb 1, 2022 - Jan 31, 2023
    Role: Principal Investigator
    Proteasome inhibitors against mucosal protozoan pathogens
    NIH R01AI158612Sep 22, 2021 - Aug 31, 2026
    Role: Co-Principal Investigator
    Quantification of Proteolytic Activity in Human Milk using Mass Spectrometry
    MOMI Seeds Pilot Grant MOMI 2020Jan 1, 2020 - Jan 1, 2021
    Role: Principal Investigator
    Point-of-Care Quantitation of Sputum Neutrophil Elastase Activity in Chronic Airway Disease
    NIH R21EB028485Jul 1, 2019 - Mar 31, 2022
    Role: Principal Investigator
    Selective proteasome inhibitors for trichomoniasis
    NIH R21AI146387Jul 1, 2019 - Jun 30, 2021
    Role: Co-Principal Investigator
    Global identification of novel protease activity for Coccidioides, the Valley fever pathogen
    NIH/NIAID R21AI140020Jun 22, 2018 - May 31, 2020
    Role: Sub-award PI
    Exploring the proteasome as a new drug target to treat schistosomiasis
    NIH R21AI133393Jun 23, 2017 - May 31, 2019
    Role: Principal Investigator
    Global Profiling of Extracellular Protease Activity from Lung Cancer Cells
    American Cancer Society Institute Research Grant Dec 15, 2016 - Dec 14, 2016
    Role: Principal Investigator
    Global analysis of age-related changes to peptide and protease signaling using patient-derived, age-preserved induced neurons
    UC San Diego Center for Healthy Aging Oct 1, 2016 - Sep 30, 2017
    Role: Principal Investigator
    Rapid Point-of-Care Detection of Candidemia in Serum
    UC San Diego CTRI Apr 1, 2016 - Mar 31, 2017
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications

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    Collapse Twitter

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Structural elucidation of recombinant Trichomonas vaginalis 20S proteasome bound to covalent inhibitors. Nat Commun. 2024 Oct 04; 15(1):8621. Silhan J, Fajtova P, Bartosova J, Hurysz BM, Almaliti J, Miyamoto Y, Eckmann L, Gerwick WH, O'Donoghue AJ, Boura E. PMID: 39366995; PMCID: PMC11452676.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    2. Vaginal Tritrichomonas foetus infection in mice as an in vivo model for drug development against Trichomonas vaginalis. PLoS One. 2024; 19(10):e0308672. Nieskens NM, Miyamoto Y, Hurysz BM, O'Donoghue AJ, Eckmann L. PMID: 39352907; PMCID: PMC11444383.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    3. The proteasome as a drug target for treatment of parasitic diseases. Adv Parasitol. 2024; 126:53-96. Liu LJ, O'Donoghue AJ, Caffrey CR. PMID: 39448194.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    4. Clickable Probes for Pathogen Proteasomes: Synthesis and Applications. ACS Omega. 2024 Aug 13; 9(32):34829-34840. Liu LJ, Lucero B, Manriquez-Rodriguez C, Francisco KR, Teixeira TR, Yohannan DJ, Ballatore C, Myers SA, O'Donoghue AJ, Caffrey CR. PMID: 39157084; PMCID: PMC11325529.
      View in: PubMed   Mentions:
    5. Use of protease substrate specificity screening in the rational design of selective protease inhibitors with unnatural amino acids: Application to HGFA, matriptase, and hepsin. Protein Sci. 2024 Aug; 33(8):e5110. Mahoney MW, Helander J, Kooner AS, Norman M, Damalanka VC, De Bona P, Kasperkiewicz P, Rut W, Poreba M, Kashipathy MM, Battaile KP, Lovell S, O'Donoghue AJ, Craik CS, Drag M, Janetka JW. PMID: 39073183; PMCID: PMC11284329.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    6. Small molecule in situ resin capture provides a compound first approach to natural product discovery. Nat Commun. 2024 Jun 19; 15(1):5230. Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, da Silva EB, O'Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. PMID: 38898025; PMCID: PMC11187115.
      View in: PubMed   Mentions: 1     Fields:    
    7. AI is a viable alternative to high throughput screening: a 318-target study. Sci Rep. 2024 04 02; 14(1):7526. Atomwise AIMS Program. PMID: 38565852; PMCID: PMC10987645.
      View in: PubMed   Mentions: 10     Fields:    
    8. A GMR enzymatic assay for quantifying nuclease and peptidase activity. Front Bioeng Biotechnol. 2024; 12:1363186. Sveiven M, Serrano AK, Rosenberg J, Conrad DJ, Hall DA, O'Donoghue AJ. PMID: 38544982; PMCID: PMC10966768.
      View in: PubMed   Mentions:
    9. Orthogonal Deprotection Strategy of Fmoc Provides Improved Synthesis of Sensitive Peptides: Application to Z-Arg-Lys-AOMK. ACS Omega. 2024 Jan 23; 9(3):3997-4003. Almaliti J, Alhindy M, Yoon MC, Hook V, Molinski TF, O'Donoghue AJ, Gerwick WH. PMID: 38284081; PMCID: PMC10809369.
      View in: PubMed   Mentions:
    10. Valence-driven colorimetric detection of norovirus protease via peptide-AuNP interactions. Chem Commun (Camb). 2023 Oct 17; 59(83):12459-12462. Ling C, Jin Z, Yeung J, da Silva EB, Chang YC, He T, Yim W, O'Donoghue AJ, Jokerst JV. PMID: 37782049.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    11. A Malassezia pseudoprotease dominates the secreted hydrolase landscape and is a potential allergen on skin. Biochimie. 2024 Jan; 216:181-193. Chua W, Marsh CO, Poh SE, Koh WL, Lee MLY, Koh LF, Tang XE, See P, Ser Z, Wang SM, Sobota RM, Dawson TL, Yew YW, Thng S, O'Donoghue AJ, Oon HH, Common JE, Li H. PMID: 37748748.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    12. A dual-binding magnetic immunoassay to predict spontaneous preterm birth. Front Bioeng Biotechnol. 2023; 11:1256267. Sveiven M, Gassman A, Rosenberg J, Chan M, Boniface J, O'Donoghue AJ, Laurent LC, Hall DA. PMID: 37790251; PMCID: PMC10542577.
      View in: PubMed   Mentions:
    13. An approach to zwitterionic peptide design for colorimetric detection of the Southampton norovirus SV3CP protease. Analyst. 2023 Sep 11; 148(18):4504-4512. Yeung J, Jin Z, Ling C, Retout M, Barbosa da Silva E, Damani M, Chang YC, Yim W, O'Donoghue AJ, Jokerst JV. PMID: 37578304; PMCID: PMC10614164.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    14. A Protease-Responsive Polymer/Peptide Conjugate and Reversible Assembly of Silver Clusters for the Detection of Porphyromonas gingivalis Enzymatic Activity. ACS Nano. 2023 09 12; 17(17):17308-17319. Retout M, Amer L, Yim W, Creyer MN, Lam B, Trujillo DF, Potempa J, O'Donoghue AJ, Chen C, Jokerst JV. PMID: 37602819; PMCID: PMC10561899.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    15. Endoproteolysis of Oligopeptide-Based Coacervates for Enzymatic Modeling. ACS Nano. 2023 09 12; 17(17):16980-16992. Jin Z, Ling C, Yim W, Chang YC, He T, Li K, Zhou J, Cheng Y, Li Y, Yeung J, Wang R, Fajtová P, Amer L, Mattoussi H, O'Donoghue AJ, Jokerst JV. PMID: 37579082; PMCID: PMC10614163.
      View in: PubMed   Mentions: 2     Fields:    
    16. Synthesis of indole-based ferulic acid derivatives and in vitro evaluation of antiviral activity against SARS-CoV-2. Medicinal Chemistry Research. 2023; (32):2256-2267. Marina Mol SA Verzola, Daisymara Priscila de Almeida Marques, Elany Barbosa da Silva, Mateus Sá Magalhães Serafim, Rafaela Salgado Ferreira, Pavla Fajtová, Markus Kohlhoff, Anthony John O’Donoghue, Vinícius Gonçalves Maltarollo, Jordana Grazziela Alves Coelho-dos-Reis, Renata Barbosa de Oliveira. View Publication.
    17. Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors. Protein Sci. 2023 08; 32(8):e4712. Fink EA, Bardine C, Gahbauer S, Singh I, Detomasi TC, White K, Gu S, Wan X, Chen J, Ary B, Glenn I, O'Connell J, O'Donnell H, Fajtová P, Lyu J, Vigneron S, Young NJ, Kondratov IS, Alisoltani A, Simons LM, Lorenzo-Redondo R, Ozer EA, Hultquist JF, O'Donoghue AJ, Moroz YS, Taunton J, Renslo AR, Irwin JJ, García-Sastre A, Shoichet BK, Craik CS. PMID: 37354015; PMCID: PMC10364469.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCellsPHPublic Health
    18. The importance of good practices and false hits for QSAR-driven virtual screening real application: a SARS-CoV-2 main protease (M pro) case study. Frontiers in Drug Discovery. 2023; 3:1237655. Mateus Sá Magalhães Serafim, Simone Queiroz Pantaleão, Elany Barbosa da Silva, James McKerrow, Anthony J O'Donoghue, Bruno Fernandes Mota, Kathia M Honorio, Vinícius Gonçalves Maltarollo. View Publication.
    19. Distinct Cleavage Properties of Cathepsin B Compared to Cysteine Cathepsins Enable the Design and Validation of a Specific Substrate for Cathepsin B over a Broad pH Range. Biochemistry. 2023 08 01; 62(15):2289-2300. Yoon MC, Phan V, Podvin S, Mosier C, O'Donoghue AJ, Hook V. PMID: 37459182; PMCID: PMC10399199.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    20. Structure-based discovery of thiosemicarbazones as SARS-CoV-2 main protease inhibitors. Future Med Chem. 2023 06; 15(11):959-985. Maltarollo VG, da Silva EB, Kronenberger T, Sena Andrade MM, de Lima Marques GV, Cândido Oliveira NJ, Santos LH, Oliveira Rezende Júnior C, Cassiano Martinho AC, Skinner D, Fajtová P, M Fernandes TH, Silveira Dos Santos ED, Rodrigues Gazolla PA, Martins de Souza AP, da Silva ML, Dos Santos FS, Lavorato SN, Oliveira Bretas AC, Carvalho DT, Franco LL, Luedtke S, Giardini MA, Poso A, Dias LC, Podust LM, Alves RJ, McKerrow J, Andrade SF, Teixeira RR, Siqueira-Neto JL, O'Donoghue A, de Oliveira RB, Ferreira RS. PMID: 37435731.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    21. Chemoproteomic identification of a DPP4 homolog in Bacteroides thetaiotaomicron. Nat Chem Biol. 2023 Dec; 19(12):1469-1479. Keller LJ, Nguyen TH, Liu LJ, Hurysz BM, Lakemeyer M, Guerra M, Gelsinger DJ, Chanin R, Ngo N, Lum KM, Faucher F, Ipock P, Niphakis MJ, Bhatt AS, O'Donoghue AJ, Huang KC, Bogyo M. PMID: 37349583.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    22. Activation mechanism and activity of globupain, a thermostable C11 protease from the Arctic Mid-Ocean Ridge hydrothermal system. Front Microbiol. 2023; 14:1199085. Røyseth V, Hurysz BM, Kaczorowska AK, Dorawa S, Fedøy AE, Arsin H, Serafim MSM, Myers SA, Werbowy O, Kaczorowski T, Stokke R, O'Donoghue AJ, Steen IH. PMID: 37405169; PMCID: PMC10315481.
      View in: PubMed   Mentions:
    23. Empirical Optimization of Peptide Sequence and Nanoparticle Colloidal Stability: The Impact of Surface Ligands and Implications for Colorimetric Sensing. ACS Appl Mater Interfaces. 2023 Apr 26; 15(16):20483-20494. Jin Z, Yeung J, Zhou J, Retout M, Yim W, Fajtová P, Gosselin B, Jabin I, Bruylants G, Mattoussi H, O'Donoghue AJ, Jokerst JV. PMID: 37058597; PMCID: PMC10614165.
      View in: PubMed   Mentions: 4     Fields:    
    24. Mitigating the risk of antimalarial resistance via covalent dual-subunit inhibition of the Plasmodium proteasome. Cell Chem Biol. 2023 05 18; 30(5):470-485.e6. Deni I, Stokes BH, Ward KE, Fairhurst KJ, Pasaje CFA, Yeo T, Akbar S, Park H, Muir R, Bick DS, Zhan W, Zhang H, Liu YJ, Ng CL, Kirkman LA, Almaliti J, Gould AE, Duffey M, O'Donoghue AJ, Uhlemann AC, Niles JC, da Fonseca PCA, Gerwick WH, Lin G, Bogyo M, Fidock DA. PMID: 36963402; PMCID: PMC10198959.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimals
    25. Development of Potent and Highly Selective Epoxyketone-Based Plasmodium Proteasome Inhibitors. Chemistry. 2023 Apr 06; 29(20):e202203958. Almaliti J, Fajtová P, Calla J, LaMonte GM, Feng M, Rocamora F, Ottilie S, Glukhov E, Boura E, Suhandynata RT, Momper JD, Gilson MK, Winzeler EA, Gerwick WH, O'Donoghue AJ. PMID: 36617500; PMCID: PMC10894724.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    26. Peptide valence-induced breaks in plasmonic coupling. Chemical Science. 2023. Yu-Ci Chang, Zhicheng Jin, Ke Li, Jiajing Zhou, Wonjun Yim, Justin Yeung, Yong Cheng, Maurice Retout, Matthew N Creyer, Pavla Fajtová, Tengyu He, Xi Chen, Anthony J. O'Donoghue, Jesse V Jokerst, . View Publication.
    27. Plasma enzymatic activity, proteomics and peptidomics in COVID-19-induced sepsis: A novel approach for the analysis of hemostasis. Front Mol Biosci. 2022; 9:1051471. Dos Santos F, Li JB, Juocys N, Mazor R, Beretta L, Coufal NG, Lam MTY, Odish MF, Irigoyen MC, O'Donoghue AJ, Aletti F, Kistler EB. PMID: 36710882; PMCID: PMC9874325.
      View in: PubMed   Mentions:
    28. Multiplex substrate profiling by mass spectrometry for proteases. Methods Enzymol. 2023; 682:375-411. Rohweder PJ, Jiang Z, Hurysz BM, O'Donoghue AJ, Craik CS. PMID: 36948708; PMCID: PMC10201391.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    29. Characterization of glutamate carboxypeptidase 2 orthologs in trematodes. Parasit Vectors. 2022 Dec 20; 15(1):480. Jedlickova L, Peterkova K, Boateng EM, Ulrychova L, Vacek V, Kutil Z, Jiang Z, Novakova Z, Snajdr I, Kim J, O'Donoghue AJ, Barinka C, Dvorak J. PMID: 36539882; PMCID: PMC9768917.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    30. Identification of a Papain-Like Protease Inhibitor with Potential for Repurposing in Combination with an Mpro Protease Inhibitor for Treatment of SARS-CoV-2. Archives of Clinical and Biomedical Research. 2022; (6):993-1002. Jesus Campagna, Barbara Jagodzinska, Pablo Alvarez, Constance Yeun, Kathryn M Enquist, Whitaker Cohn, Pavla Fajtová, Anthony J O’Donoghue, Vaithilingaraja Arumugaswami, Melody MH Li, Robert Damoiseaux and Varghese John. View Publication.
    31. Peptide Amphiphile Mediated Co-assembly for Nanoplasmonic Sensing. Angew Chem Int Ed Engl. 2023 01 23; 62(4):e202214394. Jin Z, Li Y, Li K, Zhou J, Yeung J, Ling C, Yim W, He T, Cheng Y, Xu M, Creyer MN, Chang YC, Fajtová P, Retout M, Qi B, Li S, O'Donoghue AJ, Jokerst JV. PMID: 36409652; PMCID: PMC9852014.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    32. The human pathobiont Malassezia furfur secreted protease Mfsap1 regulates cell dispersal and exacerbates skin inflammation. Proc Natl Acad Sci U S A. 2022 12 06; 119(49):e2212533119. Goh JPZ, Ruchti F, Poh SE, Koh WLC, Tan KY, Lim YT, Thng STG, Sobota RM, Hoon SS, Liu C, O'Donoghue AJ, LeibundGut-Landmann S, Oon HH, Li H, Dawson TL. PMID: 36442106; PMCID: PMC9894114.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimals
    33. Spacer Matters: All-Peptide-Based Ligand for Promoting Interfacial Proteolysis and Plasmonic Coupling. Nano Lett. 2022 11 23; 22(22):8932-8940. Jin Z, Ling C, Li Y, Zhou J, Li K, Yim W, Yeung J, Chang YC, He T, Cheng Y, Fajtová P, Retout M, O'Donoghue AJ, Jokerst JV. PMID: 36346642.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    34. Allergen Content and Protease Activity in Milk Feeds from Mothers of Preterm Infants. Breastfeed Med. 2022 Nov; 17(11):947-957. Luskin K, Mortazavi D, Bai-Tong S, Bertrand K, Chambers C, Schulkers-Escalante K, Ahmad A, Luedtke S, O'Donoghue AJ, Ghassemian M, Geng B, Leibel SL, Leibel SA. PMID: 36251466; PMCID: PMC10081709.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCTClinical Trials
    35. Cathepsin B Dipeptidyl Carboxypeptidase and Endopeptidase Activities Demonstrated across a Broad pH Range. Biochemistry. 2022 09 06; 61(17):1904-1914. Yoon MC, Hook V, O'Donoghue AJ. PMID: 35981509; PMCID: PMC9454093.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    36. A Self-Immolative Fluorescent Probe for Selective Detection of SARS-CoV-2 Main Protease. Anal Chem. 2022 08 30; 94(34):11728-11733. Xu M, Zhou J, Cheng Y, Jin Z, Clark AE, He T, Yim W, Li Y, Chang YC, Wu Z, Fajtová P, O'Donoghue AJ, Carlin AF, Todd MD, Jokerst JV. PMID: 35973073; PMCID: PMC9396966.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    37. Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease Mpro and Papain-like Protease PLpro of SARS-CoV-2. J Chem Inf Model. 2022 12 26; 62(24):6553-6573. Santos LH, Kronenberger T, Almeida RG, Silva EB, Rocha REO, Oliveira JC, Barreto LV, Skinner D, Fajtová P, Giardini MA, Woodworth B, Bardine C, Lourenço AL, Craik CS, Poso A, Podust LM, McKerrow JH, Siqueira-Neto JL, O'Donoghue AJ, da Silva Júnior EN, Ferreira RS. PMID: 35960688.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    38. Native metabolomics identifies the rivulariapeptolide family of protease inhibitors. Nat Commun. 2022 08 08; 13(1):4619. Reher R, Aron AT, Fajtová P, Stincone P, Wagner B, Pérez-Lorente AI, Liu C, Shalom IYB, Bittremieux W, Wang M, Jeong K, Matos-Hernandez ML, Alexander KL, Caro-Diaz EJ, Naman CB, Scanlan JHW, Hochban PMM, Diederich WE, Molina-Santiago C, Romero D, Selim KA, Sass P, Brötz-Oesterhelt H, Hughes CC, Dorrestein PC, O'Donoghue AJ, Gerwick WH, Petras D. PMID: 35941113; PMCID: PMC9358669.
      View in: PubMed   Mentions: 10     Fields:    
    39. Protease-Responsive Peptide-Conjugated Mitochondrial-Targeting AIEgens for Selective Imaging and Inhibition of SARS-CoV-2-Infected Cells. ACS Nano. 2022 08 23; 16(8):12305-12317. Cheng Y, Clark AE, Zhou J, He T, Li Y, Borum RM, Creyer MN, Xu M, Jin Z, Zhou J, Yim W, Wu Z, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. PMID: 35878004; PMCID: PMC9344892.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    40. Discovery of pH-Selective Marine and Plant Natural Product Inhibitors of Cathepsin B Revealed by Screening at Acidic and Neutral pH Conditions. ACS Omega. 2022 Jul 26; 7(29):25346-25352. Phan VV, Mosier C, Yoon MC, Glukhov E, Caffrey CR, O'Donoghue AJ, Gerwick WH, Hook V. PMID: 35910167; PMCID: PMC9330179.
      View in: PubMed   Mentions: 3  
    41. Dysregulation of Neuropeptide and Tau Peptide Signatures in Human Alzheimer's Disease Brain. ACS Chem Neurosci. 2022 07 06; 13(13):1992-2005. Podvin S, Jiang Z, Boyarko B, Rossitto LA, O'Donoghue A, Rissman RA, Hook V. PMID: 35758417; PMCID: PMC9264367.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    42. Small-Molecule Thioesters as SARS-CoV-2 Main Protease Inhibitors: Enzyme Inhibition, Structure-Activity Relationships, Antiviral Activity, and X-ray Structure Determination. J Med Chem. 2022 07 14; 65(13):9376-9395. Pillaiyar T, Flury P, Krüger N, Su H, Schäkel L, Barbosa Da Silva E, Eppler O, Kronenberger T, Nie T, Luedtke S, Rocha C, Sylvester K, Petry MRI, McKerrow JH, Poso A, Pöhlmann S, Gütschow M, O'Donoghue AJ, Xu Y, Müller CE, Laufer SA. PMID: 35709506.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    43. Discovery of Triple Inhibitors of Both SARS-CoV-2 Proteases and Human Cathepsin L. Pharmaceuticals (Basel). 2022 Jun 13; 15(6). Meewan I, Kattoula J, Kattoula JY, Skinner D, Fajtová P, Giardini MA, Woodworth B, McKerrow JH, Lage de Siqueira-Neto J, O'Donoghue AJ, Abagyan R. PMID: 35745663; PMCID: PMC9230533.
      View in: PubMed   Mentions: 6  
    44. Antiviral cyclic peptides targeting the main protease of SARS-CoV-2. Chem Sci. 2022 Mar 30; 13(13):3826-3836. Johansen-Leete J, Ullrich S, Fry SE, Frkic R, Bedding MJ, Aggarwal A, Ashhurst AS, Ekanayake KB, Mahawaththa MC, Sasi VM, Luedtke S, Ford DJ, O'Donoghue AJ, Passioura T, Larance M, Otting G, Turville S, Jackson CJ, Nitsche C, Payne RJ. PMID: 35432913; PMCID: PMC8966731.
      View in: PubMed   Mentions: 22  
    45. Intramolecular Interactions Enhance the Potency of Gallinamide A Analogues against Trypanosoma cruzi. J Med Chem. 2022 03 10; 65(5):4255-4269. Barbosa Da Silva E, Sharma V, Hernandez-Alvarez L, Tang AH, Stoye A, O'Donoghue AJ, Gerwick WH, Payne RJ, McKerrow JH, Podust LM. PMID: 35188371.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    46. Molecular Features of CA-074 pH-Dependent Inhibition of Cathepsin B. Biochemistry. 2022 02 15; 61(4):228-238. Yoon MC, Christy MP, Phan VV, Gerwick WH, Hook G, O'Donoghue AJ, Hook V. PMID: 35119840; PMCID: PMC9096814.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    47. Peptidic Sulfhydryl for Interfacing Nanocrystals and Subsequent Sensing of SARS-CoV-2 Protease. Chemistry of Materials. 2022; 34(3):1259-1268. Jin, Zhicheng Yeung, Justin Zhou, Jiajing Cheng, Yong Li, Yi Mantri, Yash He, Tengyu Yim, Wonjun Xu, Ming Wu, Zhuohong Fajtova, Pavla Creyer, Matthew N. Moore, Colman Fu, Lei Penny, William F. O’Donoghue, Anthony J. Jokerst, Jesse V. View Publication.
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    49. A Charge-Switchable Zwitterionic Peptide for Rapid Detection of SARS-CoV-2 Main Protease. Angew Chem Int Ed Engl. 2022 02 21; 61(9):e202112995. Jin Z, Mantri Y, Retout M, Cheng Y, Zhou J, Jorns A, Fajtova P, Yim W, Moore C, Xu M, Creyer MN, Borum RM, Zhou J, Wu Z, He T, Penny WF, O'Donoghue AJ, Jokerst JV. PMID: 34936725; PMCID: PMC8854333.
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    50. Distinct Dibasic Cleavage Specificities of Neuropeptide-Producing Cathepsin L and Cathepsin V Cysteine Proteases Compared to PC1/3 and PC2 Serine Proteases. ACS Chem Neurosci. 2022 01 19; 13(2):245-256. Yoon MC, Ames J, Mosier C, Jiang Z, Podvin S, O'Donoghue AJ, Hook V. PMID: 34986304; PMCID: PMC9070308.
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    51. Improved Scalable Synthesis of Clinical Candidate KZR-616, a Selective Immunoproteasome Inhibitor. ChemistrySelect. 2021; 6(44):12461-12465. Almaliti, Jehad Fajtová, Pavla O'Donoghue, Anthony J. AlHindy, Momen Gerwick, William H. View Publication.
    52. Potent Anti-SARS-CoV-2 Activity by the Natural Product Gallinamide A and Analogues via Inhibition of Cathepsin L. J Med Chem. 2022 02 24; 65(4):2956-2970. Ashhurst AS, Tang AH, Fajtová P, Yoon MC, Aggarwal A, Bedding MJ, Stoye A, Beretta L, Pwee D, Drelich A, Skinner D, Li L, Meek TD, McKerrow JH, Hook V, Tseng CT, Larance M, Turville S, Gerwick WH, O'Donoghue AJ, Payne RJ. PMID: 34730959; PMCID: PMC8577376.
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    53. A novel class of TMPRSS2 inhibitors potently block SARS-CoV-2 and MERS-CoV viral entry and protect human epithelial lung cells. Proc Natl Acad Sci U S A. 2021 10 26; 118(43). Mahoney M, Damalanka VC, Tartell MA, Chung DH, Lourenço AL, Pwee D, Mayer Bridwell AE, Hoffmann M, Voss J, Karmakar P, Azouz NP, Klingler AM, Rothlauf PW, Thompson CE, Lee M, Klampfer L, Stallings CL, Rothenberg ME, Pöhlmann S, Whelan SPJ, O'Donoghue AJ, Craik CS, Janetka JW. PMID: 34635581; PMCID: PMC8694051.
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    55. Differential Neuropeptidomes of Dense Core Secretory Vesicles (DCSV) Produced at Intravesicular and Extracellular pH Conditions by Proteolytic Processing. ACS Chem Neurosci. 2021 07 07; 12(13):2385-2398. Jiang Z, Lietz CB, Podvin S, Yoon MC, Toneff T, Hook V, O'Donoghue AJ. PMID: 34153188; PMCID: PMC8267839.
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    56. Activatable Carbocyanine Dimers for Photoacoustic and Fluorescent Detection of Protease Activity. ACS Sens. 2021 06 25; 6(6):2356-2365. Moore C, Borum RM, Mantri Y, Xu M, Fajtová P, O'Donoghue AJ, Jokerst JV. PMID: 34038103; PMCID: PMC8375416.
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    57. Mutant Presenilin 1 Dysregulates Exosomal Proteome Cargo Produced by Human-Induced Pluripotent Stem Cell Neurons. ACS Omega. 2021 May 25; 6(20):13033-13056. Podvin S, Jones A, Liu Q, Aulston B, Mosier C, Ames J, Winston C, Lietz CB, Jiang Z, O'Donoghue AJ, Ikezu T, Rissman RA, Yuan SH, Hook V. PMID: 34056454; PMCID: PMC8158845.
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    59. Insights into the catalytic properties of the mitochondrial rhomboid protease PARL. J Biol Chem. 2021 Jan-Jun; 296:100383. Lysyk L, Brassard R, Arutyunova E, Siebert V, Jiang Z, Takyi E, Morrison M, Young HS, Lemberg MK, O'Donoghue AJ, Lemieux MJ. PMID: 33556373; PMCID: PMC7966987.
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    62. The Pseudomonas aeruginosa protease LasB directly activates IL-1β. EBioMedicine. 2020 Oct; 60:102984. Sun J, LaRock DL, Skowronski EA, Kimmey JM, Olson J, Jiang Z, O'Donoghue AJ, Nizet V, LaRock CN. PMID: 32979835; PMCID: PMC7511813.
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    63. High-Resolution Mass Spectrometry-Based Approaches for the Detection and Quantification of Peptidase Activity in Plasma. Molecules. 2020 Sep 06; 25(18). Maffioli E, Jiang Z, Nonnis S, Negri A, Romeo V, Lietz CB, Hook V, Ristagno G, Baselli G, Kistler EB, Aletti F, O'Donoghue AJ, Tedeschi G. PMID: 32899982; PMCID: PMC7571063.
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    64. Engineering of multiple trypsin/chymotrypsin sites in Cry3A to enhance its activity against Monochamus alternatus Hope larvae. Pest Manag Sci. 2020 Sep; 76(9):3117-3126. Guo Y, Wang Y, O'Donoghue AJ, Jiang Z, Carballar-Lejarazú R, Liang G, Hu X, Wang R, Xu L, Guan X, Zhang F, Wu S. PMID: 32323409.
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    66. Cathepsin B in neurodegeneration of Alzheimer's disease, traumatic brain injury, and related brain disorders. Biochim Biophys Acta Proteins Proteom. 2020 08; 1868(8):140428. Hook V, Yoon M, Mosier C, Ito G, Podvin S, Head BP, Rissman R, O'Donoghue AJ, Hook G. PMID: 32305689; PMCID: PMC7261628.
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    71. 20S Proteasome as a Drug Target in Trichomonas vaginalis. Antimicrob Agents Chemother. 2019 11; 63(11). O'Donoghue AJ, Bibo-Verdugo B, Miyamoto Y, Wang SC, Yang JZ, Zuill DE, Matsuka S, Jiang Z, Almaliti J, Caffrey CR, Gerwick WH, Eckmann L. PMID: 31451503; PMCID: PMC6811414.
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    77. Discovery of Selective Matriptase and Hepsin Serine Protease Inhibitors: Useful Chemical Tools for Cancer Cell Biology. J Med Chem. 2019 01 24; 62(2):480-490. Damalanka VC, Han Z, Karmakar P, O'Donoghue AJ, La Greca F, Kim T, Pant SM, Helander J, Klefström J, Craik CS, Janetka JW. PMID: 30571119.
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    79. Characterization of PdCP1, a serine carboxypeptidase from Pseudogymnoascus destructans, the causal agent of White-nose Syndrome. Biol Chem. 2018 11 27; 399(12):1375-1388. Beekman C, Jiang Z, Suzuki BM, Palmer JM, Lindner DL, O'Donoghue AJ, Knudsen GM, Bennett RJ. PMID: 30367778.
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    80. Activity profiling of peptidases in Angiostrongylus costaricensis first-stage larvae and adult worms. PLoS Negl Trop Dis. 2018 10; 12(10):e0006923. Rebello KM, McKerrow JH, Mota EM, O'Donoghue AJ, Neves-Ferreira AGC. PMID: 30379807; PMCID: PMC6231675.
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    81. A Commensal Dipeptidyl Aminopeptidase with Specificity for N-Terminal Glycine Degrades Human-Produced Antimicrobial Peptides in Vitro. ACS Chem Biol. 2018 09 21; 13(9):2513-2521. Xu JH, Jiang Z, Solania A, Chatterjee S, Suzuki B, Lietz CB, Hook VYH, O'Donoghue AJ, Wolan DW. PMID: 30085657; PMCID: PMC7293822.
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    82. Validation of Babesia proteasome as a drug target. Int J Parasitol Drugs Drug Resist. 2018 12; 8(3):394-402. Jalovecka M, Hartmann D, Miyamoto Y, Eckmann L, Hajdusek O, O'Donoghue AJ, Sojka D. PMID: 30103207; PMCID: PMC6092455.
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    83. SmSP2: A serine protease secreted by the blood fluke pathogen Schistosoma mansoni with anti-hemostatic properties. PLoS Negl Trop Dis. 2018 04; 12(4):e0006446. Leontovyc A, Ulrychová L, O'Donoghue AJ, Vondrášek J, Marešová L, Hubálek M, Fajtová P, Chanová M, Jiang Z, Craik CS, Caffrey CR, Mareš M, Dvorák J, Horn M. PMID: 29677188; PMCID: PMC5931690.
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    84. Substrate Specificity of Cysteine Proteases Beyond the S2 Pocket: Mutagenesis and Molecular Dynamics Investigation of Fasciola hepatica Cathepsins L. Front Mol Biosci. 2018; 5:40. Corvo I, Ferraro F, Merlino A, Zuberbühler K, O'Donoghue AJ, Pastro L, Pi-Denis N, Basika T, Roche L, McKerrow JH, Craik CS, Caffrey CR, Tort JF. PMID: 29725596; PMCID: PMC5917446.
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    86. Skin Commensal Malassezia globosa Secreted Protease Attenuates Staphylococcus aureus Biofilm Formation. J Invest Dermatol. 2018 05; 138(5):1137-1145. Li H, Goh BN, Teh WK, Jiang Z, Goh JPZ, Goh A, Wu G, Hoon SS, Raida M, Camattari A, Yang L, O'Donoghue AJ, Dawson TL. PMID: 29246799.
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    88. Immunoproteasome functions explained by divergence in cleavage specificity and regulation. Elife. 2017 11 28; 6. Winter MB, La Greca F, Arastu-Kapur S, Caiazza F, Cimermancic P, Buchholz TJ, Anderl JL, Ravalin M, Bohn MF, Sali A, O'Donoghue AJ, Craik CS. PMID: 29182146; PMCID: PMC5705213.
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    89. Development of a Potent Inhibitor of the Plasmodium Proteasome with Reduced Mammalian Toxicity. J Med Chem. 2017 08 10; 60(15):6721-6732. LaMonte GM, Almaliti J, Bibo-Verdugo B, Keller L, Zou BY, Yang J, Antonova-Koch Y, Orjuela-Sanchez P, Boyle CA, Vigil E, Wang L, Goldgof GM, Gerwick L, O'Donoghue AJ, Winzeler EA, Gerwick WH, Ottilie S. PMID: 28696697; PMCID: PMC5554889.
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    92. Multiplex Substrate Profiling by Mass Spectrometry for Kinases as a Method for Revealing Quantitative Substrate Motifs. Anal Chem. 2017 04 18; 89(8):4550-4558. Meyer NO, O'Donoghue AJ, Schulze-Gahmen U, Ravalin M, Moss SM, Winter MB, Knudsen GM, Craik CS. PMID: 28322550; PMCID: PMC5500290.
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    93. Targeting proteasomes in infectious organisms to combat disease. FEBS J. 2017 05; 284(10):1503-1517. Bibo-Verdugo B, Jiang Z, Caffrey CR, O'Donoghue AJ. PMID: 28122162.
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    94. Integrated Activity and Genetic Profiling of Secreted Peptidases in Cryptococcus neoformans Reveals an Aspartyl Peptidase Required for Low pH Survival and Virulence. PLoS Pathog. 2016 Dec; 12(12):e1006051. Clarke SC, Dumesic PA, Homer CM, O'Donoghue AJ, La Greca F, Pallova L, Majer P, Madhani HD, Craik CS. PMID: 27977806; PMCID: PMC5158083.
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    95. Procathepsin E is highly abundant but minimally active in pancreatic ductal adenocarcinoma tumors. Biol Chem. 2016 09 01; 397(9):871-81. O'Donoghue AJ, Ivry SL, Chaudhury C, Hostetter DR, Hanahan D, Craik CS. PMID: 27149201; PMCID: PMC5712230.
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    98. Design of Selective Substrates and Activity-Based Probes for Hydrolase Important for Pathogenesis 1 (HIP1) from Mycobacterium tuberculosis. ACS Infect Dis. 2016 11 11; 2(11):807-815. Lentz CS, Ordonez AA, Kasperkiewicz P, La Greca F, O'Donoghue AJ, Schulze CJ, Powers JC, Craik CS, Drag M, Jain SK, Bogyo M. PMID: 27739665; PMCID: PMC5109297.
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    99. Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles. Proc Natl Acad Sci U S A. 2016 Apr 05; 113(14):E2001-10. Julien O, Zhuang M, Wiita AP, O'Donoghue AJ, Knudsen GM, Craik CS, Wells JA. PMID: 27006500; PMCID: PMC4833263.
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    103. Destructin-1 is a collagen-degrading endopeptidase secreted by Pseudogymnoascus destructans, the causative agent of white-nose syndrome. Proc Natl Acad Sci U S A. 2015 Jun 16; 112(24):7478-83. O'Donoghue AJ, Knudsen GM, Beekman C, Perry JA, Johnson AD, DeRisi JL, Craik CS, Bennett RJ. PMID: 25944934; PMCID: PMC4475985.
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    105. Global substrate profiling of proteases in human neutrophil extracellular traps reveals consensus motif predominantly contributed by elastase. PLoS One. 2013; 8(9):e75141. O'Donoghue AJ, Jin Y, Knudsen GM, Perera NC, Jenne DE, Murphy JE, Craik CS, Hermiston TW. PMID: 24073241; PMCID: PMC3779220.
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    106. Dissecting the active site of the collagenolytic cathepsin L3 protease of the invasive stage of Fasciola hepatica. PLoS Negl Trop Dis. 2013; 7(7):e2269. Corvo I, O'Donoghue AJ, Pastro L, Pi-Denis N, Eroy-Reveles A, Roche L, McKerrow JH, Dalton JP, Craik CS, Caffrey CR, Tort JF. PMID: 23875031; PMCID: PMC3708847.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    107. Substrate specificity of MarP, a periplasmic protease required for resistance to acid and oxidative stress in Mycobacterium tuberculosis. J Biol Chem. 2013 May 03; 288(18):12489-99. Small JL, O'Donoghue AJ, Boritsch EC, Tsodikov OV, Knudsen GM, Vandal O, Craik CS, Ehrt S. PMID: 23504313; PMCID: PMC3642297.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    108. Detection and Quantification of Endoprotease Activity Using a Coomassie Dye-Binding Assay. Laboratory Protocols in Fungal Biology. 2012; 309-313. Anthony J. O'Donoghue, Cathal Mahon. View Publication.
    109. Global identification of peptidase specificity by multiplex substrate profiling. Nat Methods. 2012 Nov; 9(11):1095-100. O'Donoghue AJ, Eroy-Reveles AA, Knudsen GM, Ingram J, Zhou M, Statnekov JB, Greninger AL, Hostetter DR, Qu G, Maltby DA, Anderson MO, Derisi JL, McKerrow JH, Burlingame AL, Craik CS. PMID: 23023596; PMCID: PMC3707110.
      View in: PubMed   Mentions: 88     Fields:    Translation:HumansAnimalsCells
    110. Characterization of gut-associated cathepsin D hemoglobinase from tick Ixodes ricinus (IrCD1). J Biol Chem. 2012 Jun 15; 287(25):21152-63. Sojka D, Franta Z, Frantová H, Bartosová P, Horn M, Váchová J, O'Donoghue AJ, Eroy-Reveles AA, Craik CS, Knudsen GM, Caffrey CR, McKerrow JH, Mares M, Kopácek P. PMID: 22539347; PMCID: PMC3375538.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    111. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21; 481(7381):365-70. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. PMID: 22190034; PMCID: PMC3310911.
      View in: PubMed   Mentions: 423     Fields:    Translation:HumansCells
    112. Characterization of a multimeric, eukaryotic prolyl aminopeptidase: an inducible and highly specific intracellular peptidase from the non-pathogenic fungus Talaromyces emersonii. Microbiology (Reading). 2009 Nov; 155(Pt 11):3673-3682. Mahon CS, O'Donoghue AJ, Goetz DH, Murray PG, Craik CS, Tuohy MG. PMID: 19556294; PMCID: PMC2888130.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    113. A parasite cysteine protease is key to host protein degradation and iron acquisition. J Biol Chem. 2008 Oct 24; 283(43):28934-43. O'Brien TC, Mackey ZB, Fetter RD, Choe Y, O'Donoghue AJ, Zhou M, Craik CS, Caffrey CR, McKerrow JH. PMID: 18701454; PMCID: PMC2570886.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    114. Inhibition of a secreted glutamic peptidase prevents growth of the fungus Talaromyces emersonii. J Biol Chem. 2008 Oct 24; 283(43):29186-95. O'Donoghue AJ, Mahon CS, Goetz DH, O'Malley JM, Gallagher DM, Zhou M, Murray PG, Craik CS, Tuohy MG. PMID: 18687686; PMCID: PMC2570871.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    115. Cloning and characterization of osteoclast precursors from the RAW264.7 cell line. In Vitro Cell Dev Biol Anim. 2006 Jul-Aug; 42(7):182-8. Cuetara BL, Crotti TN, O'Donoghue AJ, McHugh KP. PMID: 16948499; PMCID: PMC2883882.
      View in: PubMed   Mentions: 39     Fields:    Translation:AnimalsCells
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