Publications

Xu W, Langhans SA, Johnson DK, Stauff E, Kandula VVR, Kecskemethy HH, Averill LW, Yue X. Radiotracers for Molecular Imaging of Angiotensin-Converting Enzyme 2. Int J Mol Sci. 2024 Aug 30;25(17). doi: 10.3390/ijms25179419. Review. PubMed PMID: 39273366; PubMed Central PMCID: PMC11395405
Hall KT, Kenedy MR, Johnson DK, Hefty PS, Akins DR. A conserved C-terminal domain of TamB interacts with multiple BamA POTRA domains in Borreliella burgdorferi. PLoS One. 2024;19(8):e0304839. doi: 10.1371/journal.pone.0304839. eCollection 2024. PubMed PMID: 39208212; PubMed Central PMCID: PMC11361582.
Murphy BT, Wiepen JJ, Graham DE, Swanson SK, Kashipathy MM, Cooper A, Battaile KP, Johnson DK, Florens L, Blevins JS, Lovell S, Zückert WR. Borrelia burgdorferi BB0346 is an Essential, Structurally Variant LolA Homolog that is Primarily Required for Homeostatic Localization of Periplasmic Lipoproteins. bioRxiv. 2024 Aug 6;. doi: 10.1101/2024.08.06.606844. PubMed PMID: 39149330; PubMed Central PMCID:
Kerr CM, Pfannenstiel JJ, Alhammad YM, O'Connor JJ, Ghimire R, Shrestha R, Khattabi R, Saenjamsai P, Parthasarathy S, McDonald PR, Gao P, Johnson DK, More S, Roy A, Channappanavar R, Fehr AR. Mutation of a highly conserved isoleucine residue in loop 2 of several β-coronavirus macrodomains indicates that enhanced ADP-ribose binding is detrimental to infection. bioRxiv. 2024 Jul 12;. doi: 10.1101/2024.01.03.574082. PubMed PMID: 38260573; PubMed Central PMCID: PMC10802294.
McCloskey E, Kashipathy M, Cooper A, Gao P, Johnson DK, Battaile KP, Lovell S, Davido DJ. HSV-1 ICP0 dimer domain adopts a novel β-barrel fold. Proteins. 2024 Jul;92(7):830-841. doi: 10.1002/prot.26673. Epub 2024 Feb 19. PubMed PMID: 38372168; PubMed Central PMCID: PMC11147711.
Flint Z, Grannemann H, Baffour K, Koti N, Taylor E, Grier E, Sutton C, Johnson D, Dandawate P, Patel R, Santra S, Banerjee T. Mechanistic Insights Behind the Self-Assembly of Human Insulin under the Influence of Surface-Engineered Gold Nanoparticles. ACS Chem Neurosci. 2024 Jun 5;15(11):2359-2371. doi: 10.1021/acschemneuro.4c00226. Epub 2024 May 10. PubMed PMID: 38728258; PubMed Central PMCID: PMC11157486.
Kim Y, Pool E, Kim E, Dampalla CS, Nguyen HN, Johnson DK, Lovell S, Groutas WC, Chang K-O. Potent small molecule inhibitors against the 3C protease of foot-and-mouth disease virus. Microbiol Spectr. 2024 Apr 2;12(4):e0337223. doi: 10.1128/spectrum.03372-23. Epub 2024 Mar 11. PubMed PMID: 38466127; PubMed Central PMCID: PMC10986521.
Myers MJ, Xu Z, Ryan BJ, DeMars ZR, Ridder MJ, Johnson DK, Krute CN, Flynn TS, Kashipathy MM, Battaile KP, Schnicker N, Lovell S, Freudenthal BD, Bose JL. Molecular basis for the activation of the Fatty Acid Kinase complex of Staphylococcus aureus. bioRxiv. 2024 Mar 19;. doi: 10.1101/2024.03.19.585040. PubMed PMID: 38562735; PubMed Central PMCID: PMC10983944
Li P, Kim Y, Dampalla CS, Nhat Nguyen H, Meyerholz DK, Johnson DK, Lovell S, Groutas WC, Perlman S, Chang K-O. Potent 3CLpro inhibitors effective against SARS-CoV-2 and MERS-CoV in animal models by therapeutic treatment. mBio. 2024 Feb 14;15(2):e0287823. doi: 10.1128/mbio.02878-23. Epub 2023 Dec 21. PMID: 38126789; PMCID: PMC10865860.
Bowen HG, Kenedy MR, Johnson DK, MacKerell AD, Akins DR, Identification of a novel transport system in Borrelia burgdorferi that links the inner and outer membranes, Pathogens and Disease, Volume 81, 2023, ftad014, https://doi.org/10.1093/femspd/ftad014
He, H., Pramanik, A. S., Swanson, S. K., Johnson, D. K., Florens, L. & Zückert, W. R. (2023). A Borrelia burgdorferi LptD homolog is required for flipping of surface lipoproteins through the spirochetal outer membrane. Molecular Microbiology, 00, 1– 16. doi:10.1111/mmi.15072
Thapa P, Upadhyay SP, Singh V, Boinpelly VP, Zhou J, Johnson DK, Gurung P, Lee ES, Sharma R, Sharma M. Chalcone: A potential scaffold for NLRP3 inflammasome inhibitors. Eur J Med Chem Rep,Volume 7, 2023, 100100, doi:10.1016/j.ejmcr.2022.100100.
Bai N, Adeshina Y, Bychkov I, Xia Y, Gowthaman R, Miller SA, Gupta AK, Johnson DK, Lan L, Golemis EA, Makhov PB, Xu L, Pillai MM, Boumber Y, Karanicolas J. Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry. bioRxiv [Preprint]. 2023 Jan 10:2023.01.09.523326. doi: 10.1101/2023.01.09.523326. PMID: 36711508; PMCID: PMC9882015.
Nishikawa S, Kaida A., Parrales A, Ranjan A, Alalem M, Ren H, Schoenen FJ, Johnson DK, Iwakuma T. DNAJA1- and conformational mutant p53-dependent inhibition of cancer cell migration by a novel compound identified through a virtual screen. Cell Death Discov. 8, 437 (2022). doi:10.1038/s41420-022-01229-5
Perera KD, Johnson DK, Lovell S, Groutas WC, Chang KO, Kim Y. Potent Protease Inhibitors of Highly Pathogenic Lagoviruses: Rabbit Hemorrhagic Disease Virus and European Brown Hare Syndrome Virus. Microbiol Spectr . 2022 Aug 31;10(4):e0014222. doi: 10.1128/spectrum.00142-22. Epub 2022 Jun 29.
Sherrill LM, Joya EE, Walker A, Roy A, Alhammad YM, Atobatele M, Wazir S, Abbas G, Keane P, Zhuo J, Leung AKL, Johnson DK, Lehtiö L, Fehr AR, Ferraris D. Design, synthesis and evaluation of inhibitors of the SARS-CoV-2 nsp3 macrodomain. Bioorg Med Chem. 2022 Aug 1;67:116788. doi: 10.1016/j.bmc.2022.116788. Epub 2022 May 11. PubMed PMID: 35597097; PubMed Central PMCID: PMC9093066.
Roy A, Alhammad YM, McDonald P, Johnson DK, Zhuo J, Wazir S, Ferraris D, Lehtiö L, Leung AKL, Fehr AR. Discovery of compounds that inhibit SARS-CoV-2 Mac1-ADP-ribose binding by high-throughput screening. Antiviral Research, Volume 203, 2022, 105344, ISSN 0166-3542. doi:10.1016/j.antiviral.2022.105344.
Henderson IM, Marez C, Dokladny K, Smoake J, Martinez M, Johnson DK, Uhl GR. Substrate-selective positive allosteric modulation of PTPRD’s phosphatase by flavonols. Biochemical Pharmacology, Volume 202, 2022, 115109, ISSN 0006-2952. doi: 10.1016/j.bcp.2022.115109.
Henderson IM, Zeng F, Bhuiyan NH, Luo D, Martinez M, Smoake J, Bi F, Perera C, Johnson D, Prisinzano TE, Wang W, Uhl GR. Structure-activity studies of PTPRD phosphatase inhibitors identify a 7-cyclopentymethoxy illudalic acid analog candidate for development. Biochem Pharmacol. 2022 Jan;195:114868. doi: 10.1016/j.bcp.2021.114868. Epub 2021 Dec 2.
Kazmierski WM, Miriyala N, Johnson DK, and Baskaran S. The Discovery of Conformationally Constrained Bicyclic Peptidomimetics as Potent Hepatitis C NS5A Inhibitors. ACS Med. Chem. Lett. 2021, 12, 11, 1649–1655. DOI: 10.1021/acsmedchemlett.1c00391.
Upadhyay SP, Singh V, Sharma R, Zhou Z, Thapa P, Johnson DK, Keightley A, Chen M, Suo W, Sharma M. Influence of ligand geometry on cholinesterase enzyme - A comparison of 1-isoindolinone based structural analog with Donepezil. Journal of Molecular Structure. 2022, Jan 9; 1247:131385. doi: 10.1016/j.molstruc.2021.131385.
Ly CY, Yu C, McDonald PR, Roy A, Johnson DK, Davido DJ. Simple and rapid high-throughput assay to identify HSV-1 ICP0 transactivation inhibitors. Antiviral Res. 2021 Aug 9;194:105160. doi: 10.1016/j.antiviral.2021.105160.
Voth LS, O'Connor JJ, Kerr CM, Doerger E, Schwarting N, Sperstad P, Johnson DK, Fehr AR. Unique Mutations in the Murine Hepatitis Virus Macrodomain Differentially Attenuate Virus Replication, Indicating Multiple Roles for the Macrodomain in Coronavirus Replication. J Virol. 2021 Jul 12;95(15):e0076621. doi: 10.1128/JVI.00766-21. Epub 2021 Jul 12. PMID: 34011547; PMCID: PMC8274620.
Nagamalla, S., Johnson, D.K. & Sathyamoorthi, S. Sulfamate-tethered aza-Wacker approach towards analogs of Bactobolin A. Med Chem Res 30, 1348–1357 (2021). https://doi.org/10.1007/s00044-021-02724-7
Sharma KK, Cassell RJ, Meqbil YJ, Su H, Blaine A, Cummins BR, Mores K, Johnson DK, van Rijn R, Altman, RA. Modulating β-Arrestin-2 Recruitment at the δ- and μ-Opioid Receptors Using Peptidomimetic Ligands. RSC Med. Chem., 2021, DOI: 10.1039/D1MD00025J
Bawa S, Gameros S, Baumann K, Brooks DS, Kollhoff JA, Zolkiewski M, Re Cecconi AD, Panini N, Russo M, Piccirillo R, Johnson DK, Kashipathy MM, Battaile KP, Lovell S, Bouyain SEA, Kawakami J, Geisbrecht ER. Costameric integrin and sarcoglycan protein levels are altered in a Drosophila model for Limb-girdle muscular dystrophy type 2H. Mol Biol Cell. 2021 Feb 1;32(3):260-273. doi: 10.1091/mbc.E20-07-0453. Epub 2020 Dec 9. PubMed PMID: 33296226; PubMed Central PMCID: PMC8098830.
Alhammad YMO, Kashipathy MM, Roy A, Gagné JP, McDonald P, Gao P, Nonfoux L, Battaile KP, Johnson DK, Holmstrom ED, Poirier GG, Lovell S, Fehr AR. The SARS-CoV-2 Conserved Macrodomain Is a Mono-ADP-Ribosylhydrolase. J Virol. 2021 Jan 13;95(3):e01969-20. doi: 10.1128/JVI.01969-20. PMID: 33158944; PMCID: PMC7925111.
Yang Y, Borel T, de Azambuja F, Johnson D, Sorrentino JP, Udokwu C, Davis I, Liu A, Altman RA. Diflunisal Derivatives as Modulators of ACMS Decarboxylase Targeting the Tryptophan-Kynurenine Pathway. J Med Chem. 2021 Jan 14;64(1):797-811. doi: 10.1021/acs.jmedchem.0c01762. Epub 2020 Dec 28. PubMed PMID: 33369426; PubMed Central PMCID: PMC7856275.
Jain A, Hu G, Kumar Ratnakaram SS, Johnson DK, Picking WD, Picking WL, Middaugh CR. Preformulation Characterization and the Effect of Ionic Excipients on the Stability of a Novel DB Fusion Protein. J Pharm Sci. 2021 Jan;110(1):108-123. doi: 10.1016/j.xphs.2020.09.008. Epub 2020 Sep 8. PubMed PMID: 32916136; PubMed Central PMCID: PMC7750262.
Tamura P, Fruehan C, Johnson DK, Hinkes P, Williams TD, Welti R. Fatty Acid Composition by Total Acyl Lipid Collision-Induced Dissociation Time-of-Flight (TAL-CID-TOF) Mass Spectrometry. Methods Mol Biol. 2021;2295:117-133. doi: 10.1007/978-1-0716-1362-7_8. PubMed PMID: 34047975.
Muthuramalingam M, Whittier SK, Lovell S, Battaile KP, Tachiyama S, Johnson DK, Picking WL, Picking WD. The Structures of SctK and SctD from Pseudomonas aeruginosa Reveal the Interface of the Type III Secretion System Basal Body and Sorting Platform. J Mol Biol. 2020 Dec 4;432(24):166693. doi: 10.1016/j.jmb.2020.10.027. Epub 2020 Oct 27. PubMed PMID: 33122003.
Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods. 2020 Jul;17(7):665-680. doi: 10.1038/s41592-020-0848-2. Epub 2020 Jun 1. Review. PubMed PMID: 32483333; PubMed Central PMCID: PMC7603796.
Joseph AM, Pohl AE, Ball TJ, Abram TG, Johnson DK, Geisbrecht BV, Shames SR. The Legionella pneumophila Metaeffector Lpg2505 (MesI) Regulates SidI-Mediated Translation Inhibition and Novel Glycosyl Hydrolase Activity. Infect Immun. 2020 Apr 20;88(5). doi: 10.1128/IAI.00853-19. Print 2020 Apr 20. PubMed PMID: 32122942; PubMed Central PMCID: PMC7171249.
Soules KR, Dmitriev A, LaBrie SD, Dimond ZE, May BH, Johnson DK, Zhang Y, Battaile KP, Lovell S, Hefty PS. Structural and ligand binding analyses of the periplasmic sensor domain of RsbU in Chlamydia trachomatis support a role in TCA cycle regulation. Mol Microbiol. 2020 Jan;113(1):68-88. doi: 10.1111/mmi.14401. Epub 2019 Nov 7. PubMed PMID: 31637787; PubMed Central PMCID: PMC7007330.
Fruehan C, Johnson D, Welti R. LipidomeDB Data Calculation Environment Has Been Updated to Process Direct-Infusion Multiple Reaction Monitoring Data. Lipids. 2018 Nov;53(11-12):1019-1020. doi: 10.1002/lipd.12111. Epub 2018 Dec 21. PubMed PMID: 30575037; PubMed Central PMCID: PMC6375751.