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PUBLICATIONS

  • Bhandari S, Ongwae GM, Dash R, Liu Z, Chordia MD, He Y, Pires MM. “A generalizable assay for intracellular accumulation to profile cytosolic drug delivery in mammalian cells.” Commun Chem. 2026;9:94. https://doi.org/10.1038/s42004-026-01898-8

  • Wittle L, Ocius KL, Chordia MD, van Wagoner C, Bullock TNJ, Pires MM. “Identification and Evaluation of Benzimidazole-Agonists of Innate Immune Receptor NOD2.” ACS Infect Dis. 2026. https://doi.org/10.1021/acsinfecdis.5c00737

  • He Y, Ongwae GM, Mondal A, Moses JA, Mittal J, Pires MM. “A high-throughput, flow cytometry approach to measure phase behavior and exchange in biomolecular condensates.” Nat Commun. 2026. https://doi.org/10.1038/s41467-025-68093-6

  • Ongwae GM, et al. “Click-based determination of accumulation of molecules in Escherichia coli.” Nat Commun. 2026. https://doi.org/10.1038/s41467-026-68717-5

  • Lepori I, et al. “Defining the Molecular Language of Accumulation in Mycobacteria.” Nat Microbiol. 2026 (accepted). Preprint: https://doi.org/10.1101/2025.02.27.640664

  • Newkirk SE, Kelly JJ, Chordia MD, Dou Y, Zhang T, Pires MM. “Small Molecule Modulation of MHC-I Surface Expression.” J Med Chem. 2025;68(21):22301-22311. https://doi.org/10.1021/acs.jmedchem.5c01149

  • Dash R, et al. “Systematic Determination of the Impact of Structural Edits on Peptide Accumulation into Mycobacteria.” ACS Chem Biol. 2025;20(8):1962-1979. https://doi.org/10.1021/acschembio.5c00330

  • Lepori I, et al. “The Mycomembrane Differentially and Heterogeneously Restricts Antibiotic Permeation.” ACS Infect Dis. 2025;11(7):1893-1906. https://doi.org/10.1021/acsinfecdis.4c01062

  • Sharifian Gh M, et al. “Lacritin cleavage-potentiated targeting of iron-respiratory reciprocity promotes bacterial death.” J Biol Chem. 2025;301(5):108455. https://doi.org/10.1016/j.jbc.2025.108455

  • Kelly JJ, Dalesandro BE, Liu Z, Chordia MD, Ongwae GM, Pires MM. “Measurement of Accumulation of Antibiotics to Staphylococcus aureus in Phagosomes of Live Macrophages.” Angew Chem Int Ed Engl. 2024;63(3):e202313870. https://doi.org/10.1002/anie.202313870

  • Ocius KL, Kolli SH, Ahmad SS, Dressler JM, Chordia MD, Jutras BL, Rutkowski MR, Pires MM. “Noninvasive Analysis of Peptidoglycan from Living Animals.” Bioconjug Chem. 2024;35(4):489-498. https://doi.org/10.1021/acs.bioconjchem.4c00007

  • Kelly JJ, Ankrom ET, Newkirk SE, Thevenin D, Pires MM. “Targeted acidosis mediated delivery of antigenic MHC-binding peptides.” Front Immunol. 2024;15:1337973. https://doi.org/10.3389/fimmu.2024.1337973

  • Shaku MT, Um PK, Ocius KL, Apostolos AJ, Pires MM, Bishai WR, Kana BD. “A modified BCG with depletion of enzymes associated with peptidoglycan amidation induces enhanced protection against tuberculosis in mice.” Elife. 2024;13:e89157. https://doi.org/10.7554/eLife.89157

  • Cardenas AJ, Thomas KS, Broden MW, Ferraro NJ, Pires MM, John CM, Jarvis GA, Criss AK. “Neisseria gonorrhoeae scavenges host sialic acid for Siglec-mediated, complement-independent suppression of neutrophil activation.” mBio. 2024;15(5):e0011924. https://doi.org/10.1128/mbio.00119-24

  • Dash R, Holsinger KA, Chordia MD, Gh MS, Pires MM. “Bioluminescence-Based Determination of Cytosolic Accumulation of Antibiotics in Escherichia coli.” ACS Infect Dis. 2024;10(5):1602-1611. https://doi.org/10.1021/acsinfecdis.3c00684

  • Ankrom ET, Dalesandro B, Pires MM, Thevenin D. “Selective Recruitment of Antibodies to Cancer Cells and Immune Cell-mediated Killing via In Situ Click Chemistry.” ChemMedChem. 2024;19:e202400356. https://doi.org/10.1002/cmdc.202400356

  • Kelly JJ, Bloodworth N, Shao Q, Shabanowitz J, Hunt D, Meiler J, Pires MM. “A Chemical Approach to Assess the Impact of Post-translational Modification on MHC Peptide Binding and Effector Cell Engagement.” ACS Chem Biol. 2024;19(9):1991-2001. https://doi.org/10.1021/acschembio.4c00312

  • Bollinger KW, Muh U, Ocius KL, Apostolos AJ, Pires MM, Helm RF, Popham DL, Weiss DS, Ellermeier CD. “Identification of a family of peptidoglycan transpeptidases reveals that Clostridioides difficile requires noncanonical cross-links for viability.” Proc Natl Acad Sci U S A. 2024;121(34):e2408540121. https://doi.org/10.1073/pnas.2408540121

  • Dalesandro BE, Pires MM. “Immunotargeting of Gram-Positive Pathogens via a Cell Wall Binding Tick Antifreeze Protein.” J Med Chem. 2023;66(1):503-515. https://doi.org/10.1021/acs.jmedchem.2c01464

  • Liu Z, Lepori I, Chordia MD, Dalesandro BE, Guo T, Dong J, Siegrist MS, Pires MM. “A Metabolic-Tag-Based Method for Assessing the Permeation of Small Molecules Across the Mycomembrane in Live Mycobacteria.” Angew Chem Int Ed Engl. 2023;62(20):e202217777. https://doi.org/10.1002/anie.202217777

  • Ongwae GM, Lepori I, Chordia MD, Dalesandro BE, Apostolos AJ, Siegrist MS, Pires MM. “Measurement of Small Molecule Accumulation into Diderm Bacteria.” ACS Infect Dis. 2023;9(1):97-110. https://doi.org/10.1021/acsinfecdis.2c00435

  • Shaku MT, Ocius KL, Apostolos AJ, Pires MM, VanNieuwenhze MS, Dhar N, Kana BD. “Amidation of glutamate residues in mycobacterial peptidoglycan is essential for cell wall cross-linking.” Front Cell Infect Microbiol. 2023;13:1205829. https://doi.org/10.3389/fcimb.2023.1205829

  • Apostolos AJ, Chordia MD, Kolli SH, Dalesandro BE, Rutkowski MR, Pires MM. “Real-time non-invasive fluorescence imaging of gut commensal bacteria to detect dynamic changes in the microbiome of live mice.” Cell Chem Biol. 2022;29(12):1721-1728. https://doi.org/10.1016/j.chembiol.2022.11.010

  • Apostolos AJ, Kelly JJ, Ongwae GM, Pires MM. “Structure Activity Relationship of the Stem Peptide in Sortase A Mediated Ligation from Staphylococcus aureus.” ChemBioChem. 2022;23(20):e202200412. https://doi.org/10.1002/cbic.202200412

  • Apostolos AJ, Ocius KL, Koyasseril-Yehiya TM, Santamaria C, Silva JRA, Lameira J, Alves CN, Siegrist MS, Pires MM. “Metabolic Processing of Selenium-Based Bioisosteres of meso-Diaminopimelic Acid in Live Bacteria.” Biochemistry. 2022;61(13):1404-1414. https://doi.org/10.1021/acs.biochem.2c00120

  • Ferraro NJ, Pires MM. “Genetic Determinants of Surface Accessibility in Staphylococcus aureus.” Bioconjug Chem. 2022;33(5):767-772. DOI lookup pending (PMC9297832); preprint: https://doi.org/10.1101/2021.09.03.458708

  • Apostolos AJ, Pires MM. “Impact of crossbridge structure on peptidoglycan crosslinking: A synthetic stem peptide approach.” Methods Enzymol. 2022;665:259-279. https://doi.org/10.1016/bs.mie.2021.11.019

  • Sikorski EL, Wehr J, Ferraro NJ, Rizzo SM, Pires MM, Thevenin D. “Selective Display of a Chemoattractant Agonist on Cancer Cells Activates the Formyl Peptide Receptor 1 on Immune Cells.” ChemBioChem. 2022;23(8):e202100521. https://doi.org/10.1002/cbic.202100521

  • Ongwae GM, Chordia MD, Cawley JL, Dalesandro BE, Wittenberg NJ, Pires MM. “Targeting of Pseudomonas aeruginosa cell surface via GP12, an Escherichia coli specific bacteriophage protein.” Sci Rep. 2022;12:721. https://doi.org/10.1038/s41598-021-04627-4

  • Apostolos AJ, Ferraro NJ, Dalesandro BE, Pires MM. “SaccuFlow: A High-Throughput Analysis Platform to Investigate Bacterial Cell Wall Interactions.” ACS Infect Dis. 2021;7(8):2483-2491. https://doi.org/10.1021/acsinfecdis.1c00255

  • Ferraro NJ, Kim S, Im W, Pires MM. “Systematic Assessment of Accessibility to the Surface of Staphylococcus aureus.” ACS Chem Biol. 2021;16(11):2527-2536. https://doi.org/10.1021/acschembio.1c00604

  • Dalesandro BE, Pires MM. “Induction of Endogenous Antibody Recruitment to the Surface of the Pathogen Enterococcus faecium.” ACS Infect Dis. 2021;7(5):1116-1125. https://doi.org/10.1021/acsinfecdis.0c00547

  • Apostolos AJ, Nelson JM, Silva JRA, Lameira J, Achimovich AM, Gahlmann A, Alves CN, Pires MM. “Facile Synthesis and Metabolic Incorporation of m-DAP Bioisosteres Into Cell Walls of Live Bacteria.” ACS Chem Biol. 2020;15(11):2966-2975. https://doi.org/10.1021/acschembio.0c00618

  • Apostolos AJ, Pidgeon SE, Pires MM. “Remodeling of Cross-bridges Controls Peptidoglycan Cross-linking Levels in Bacterial Cell Walls.” ACS Chem Biol. 2020;15(5):1261-1267. https://doi.org/10.1021/acschembio.0c00002

  • Ongwae GM, Morrison KR, Allen RA, Kim S, Im W, Wuest WM, Pires MM. “Broadening Activity of Polymyxin by Quaternary Ammonium Grafting.” ACS Infect Dis. 2020;6(6):1427-1435. https://doi.org/10.1021/acsinfecdis.0c00037

  • Wehr J, Sikorski EL, Bloch E, Feigman MS, Ferraro NJ, Baybutt TR, Snook AE, Pires MM, Thevenin D. “pH-Dependent Grafting of Cancer Cells with Antigenic Epitopes Promotes Selective Antibody-Mediated Cytotoxicity.” J Med Chem. 2020;63(7):3713-3722. https://doi.org/10.1021/acs.jmedchem.0c00016

  • Wang L, Jakob DS, Wang H, Apostolos A, Pires MM, Xu XG. “Generalized Heterodyne Configurations for Photoinduced Force Microscopy.” Anal Chem. 2019;91(20):13251-13259. https://doi.org/10.1021/acs.analchem.9b03712

  • Pidgeon SE, Apostolos AJ, Nelson JM, Shaku M, Rimal B, Islam MN, Crick DC, Kim SJ, Pavelka MS, Kana BD, Pires MM. “L,D-Transpeptidase Specific Probe Reveals Spatial Activity of Peptidoglycan Cross-Linking.” ACS Chem Biol. 2019;14(10):2185-2196. https://doi.org/10.1021/acschembio.9b00427

  • Kim S, Pires MM, Im W. “Insight into Elongation Stages of Peptidoglycan Processing in Bacterial Cytoplasmic Membranes.” Sci Rep. 2018;8:17704. https://doi.org/10.1038/s41598-018-36075-y

  • Feigman MS, Kim S, Pidgeon SE, Yu Y, Ongwae GM, Patel DS, Regen S, Im W, Pires MM. “Synthetic Immunotherapeutics Against Gram-negative Pathogens.” Cell Chem Biol. 2018;25(10):1185-1194. https://doi.org/10.1016/j.chembiol.2018.05.019

  • Feigman MS, Pires MM. “Synthetic Immunobiotics: A Future Success Story in Small Molecule-Based Immunotherapy?” ACS Infect Dis. 2018;4(5):664-672. https://doi.org/10.1021/acsinfecdis.7b00261

  • Sabulski MJ, Pidgeon SE, Pires MM. “Immuno-Targeting of Staphylococcus aureus via Surface Remodeling Complexes.” Chem Sci. 2017;8(10):6804-6809. https://doi.org/10.1039/c7sc02721d

  • Pidgeon SE, Pires MM. “Cell Wall Remodeling of Staphylococcus aureus in Live Caenorhabditis elegans.” Bioconjug Chem. 2017;28(9):2310-2315. https://doi.org/10.1021/acs.bioconjchem.7b00363

  • Pidgeon SE, Pires MM. “Vancomycin-Dependent Response in Live Drug-Resistant Bacteria via Metabolic Labeling.” Angew Chem Int Ed Engl. 2017;56(30):8839-8843. https://doi.org/10.1002/anie.201704851

  • Pidgeon SE, Pires MM. “Cell Wall Remodeling by a Synthetic Analog Reveals Metabolic Adaptation in Vancomycin Resistant Enterococci.” ACS Chem Biol. 2017;12(7):1913-1918. https://doi.org/10.1021/acschembio.7b00412

  • Fura JM, Sarkar S, Pidgeon SE, Pires MM. “Combatting Bacterial Pathogens with Immunomodulation and Infection Tolerance Strategies.” Curr Top Med Chem. 2017;17(3):290-304. https://doi.org/10.2174/1568026616666160829160707

  • Yu Y, Sabulski MJ, Schell WA, Pires MM, Perfect JR, Regen SL. “Simple Strategy for Taming Membrane-Disrupting Antibiotics.” Bioconjug Chem. 2016;27(12):2850-2853. https://doi.org/10.1021/acs.bioconjchem.6b00629

  • Sarkar S, Libby EA, Pidgeon SE, Dworkin J, Pires MM. “In Vivo Probe of Lipid II-Interacting Proteins.” Angew Chem Int Ed Engl. 2016;55(29):8401-8404. https://doi.org/10.1002/anie.201603441

  • Fura JM, Pidgeon SE, Birabaharan M, Pires MM. “Dipeptide-Based Metabolic Labeling of Bacterial Cells for Endogenous Antibody Recruitment.” ACS Infect Dis. 2016;2(4):302-309. https://doi.org/10.1021/acsinfecdis.6b00007

  • Fura JM, Kearns D, Pires MM. “D-Amino Acid Probes for Penicillin Binding Protein-based Bacterial Surface Labeling.” J Biol Chem. 2015;290(51):30540-30550. https://doi.org/10.1074/jbc.M115.683342

  • Pidgeon SE, Pires MM. “Metabolic remodeling of bacterial surfaces via tetrazine ligations.” Chem Commun. 2015;51(51):10330-10333. https://doi.org/10.1039/C5CC01693B

  • Fura JM, Pires MM. “D-amino carboxamide-based recruitment of dinitrophenol antibodies to bacterial surfaces via peptidoglycan remodeling.” Biopolymers. 2015;104(4):351-359. https://doi.org/10.1002/bip.22618

  • Pidgeon SE, Fura JM, Leon W, Birabaharan M, Vezenov D, Pires MM. “Metabolic Profiling of Bacteria by Unnatural C-terminated D-Amino Acids.” Angew Chem Int Ed Engl. 2015;54(21):6158-6162. https://doi.org/10.1002/anie.201409927

  • Sabulski MJ, Wang Y, Pires MM. “PAD2 Activity Monitored via a Fluorescent Substrate Analog.” Chem Biol Drug Des. 2015;86(4):599-605. https://doi.org/10.1111/cbdd.12526

  • Sarkar S, Pires MM. “D-Amino Acids Do Not Inhibit Biofilm Formation in Staphylococcus aureus.” PLoS One. 2015;10(2):e0117613. https://doi.org/10.1371/journal.pone.0117613

  • Fura JM, Sabulski MJ, Pires MM. “D-Amino Acid Mediated Recruitment of Endogenous Antibodies to Bacterial Surfaces.” ACS Chem Biol. 2014;9(7):1480-1489. https://doi.org/10.1021/cb5002685

  • Hrycyna CA, Summers RL, Lehane AM, Pires MM, Namanja H, Bohn K, Kuriakose J, Ferdig M, Henrich PP, Fidock DA, Kirk K, Chmielewski J, Martin RE. “Quinine Dimers Are Potent Inhibitors of the Plasmodium falciparum Chloroquine Resistance Transporter and Are Active against Quinoline-Resistant P. falciparum.” ACS Chem Biol. 2014;9(3):722-730. https://doi.org/10.1021/cb4008953

  • Sabulski MJ, Fura JM, Pires MM. “Fluorescence-based Monitoring of PAD4 Activity via a Pro-fluorescence Substrate Analog.” J Vis Exp. 2014;(93):e52114. https://doi.org/10.3791/52114

  • Wildeman E, Pires MM. “Facile Fluorescence-Based Detection of PAD4-Mediated Citrullination.” ChemBioChem. 2013;14(8):963-967. https://doi.org/10.1002/cbic.201300173

  • Reig AJ, Pires MM, Snyder RA, Wu Y, Jo H, Kulp DW, Butch SE, Calhoun JR, Szyperski T, Solomon EI, DeGrado WF. “Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins.” Nat Chem. 2012;4(11):900-906. https://doi.org/10.1038/nchem.1454 (erratum: https://doi.org/10.1038/nchem.1519)

  • Pires MM, Lee J, Ernenwein D, Chmielewski J. “Controlling the Morphology of Metal-Promoted Higher Ordered Assemblies of Collagen Peptides with Varied Core Lengths.” Langmuir. 2012;28(4):1993-1997. https://doi.org/10.1021/la203848r

  • Pires MM, Przybyla DE, Rubert Perez CM, Chmielewski J. “Metal-Mediated Tandem Coassembly of Collagen Peptides into Banded Microstructures.” J Am Chem Soc. 2011;133(37):14469-14471. https://doi.org/10.1021/ja2042645

  • Pires MM, Ernenwein D, Chmielewski J. “Selective Decoration and Release of His-tagged Proteins from Metal-Assembled Collagen Peptide Microflorettes.” Biomacromolecules. 2011;12(7):2429-2433. https://doi.org/10.1021/bm2004934

  • Pires MM, Przybyla DE, Chmielewski J. “A Metal-Collagen Peptide Framework for Three-Dimensional Cell Culture.” Angew Chem Int Ed Engl. 2009;48(42):7813-7817. https://doi.org/10.1002/anie.200902375

  • Namanja HA, Emmert D, Pires MM, Hrycyna CA, Chmielewski J. “Inhibition of Human P-glycoprotein Transport and Substrate Binding Using a Galantamine Dimer.” Biochem Biophys Res Commun. 2009;388(4):672-676. https://doi.org/10.1016/j.bbrc.2009.08.056

  • Pires MM, Chmielewski J. “Self-Assembly of Collagen Peptides into Microflorettes via Metal Coordination.” J Am Chem Soc. 2009;131(7):2706-2712. https://doi.org/10.1021/ja8088845

  • Pires MM, Emmert D, Hrycyna CA, Chmielewski J. “Inhibition of P-Glycoprotein-Mediated Paclitaxel Resistance by Reversibly Linked Quinine Homodimers.” Mol Pharmacol. 2009;75(1):92-100. https://doi.org/10.1124/mol.108.050492

  • Pires MM, Chmielewski J. “Fluorescence Imaging of Cellular Glutathione Using a Latent Rhodamine.” Org Lett. 2008;10(5):837-840. https://doi.org/10.1021/ol702769n

  • Pires MM, DeTuri VF. “Structural, Energetic, and Infrared Spectra Insights into Methanol Clusters (CH3OH)n, for n = 2 to 12, 16, 20. ONIOM as an Efficient Method of Modeling Large Methanol Clusters.” J Chem Theory Comput. 2007;3(3):1073-1082. https://doi.org/10.1021/ct600348x

  • Pires MM, Hrycyna CA, Chmielewski J. “Bivalent Probes of the Human Multidrug Transporter P-Glycoprotein.” Biochemistry. 2006;45(39):11695-11702. https://doi.org/10.1021/bi0608109

©2020 by Pires Laboratory.

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