Publications
2024
6. Oldani EG, Stillman NH, Dohoney RA, Baysah CZ, Kumar S. Inhibition of Phosphorylated Alpha-Synuclein Aggregation by Synthetic Protein Mimetics and Foldamers. ACS Chem. Neuroscience. Under revision.
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5. Stillman NH, Joseph JA, Ahmed J, Baysah CZ, Dohoney RA, Ball TD, Thomas AG, Fitch TC, Donnelly CM, Kumar S. Protein mimetic 2D FAST rescues alpha synuclein aggregation mediated early and post disease Parkinson's phenotypes. Nat Commun. 2024 Apr 30;15(1):3658. doi: 10.1038/s41467-024-47980-4. PMID: 38688913; PMCID: PMC11061149. https://pubmed.ncbi.nlm.nih.gov/38688913/.
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4. Oldani EG, Reynolds Caicedo KM, Spaeth Herda ME, Sachs AH, Chapman EG, Kumar S, Linseman DA, Horowitz S. Manipulating TDP43 Aggregation via RNA G-quadruplexes. bioRxiv 2024.04.30.591873; https://doi.org/10.1101/2024.04.30.591873.
2023
3. Dohoney RA, Joseph JA, Baysah C, Thomas AG, Siwakoti A, Ball TD, Kumar S. "Common-Precursor" Protein Mimetic Approach to Rescue Aβ Aggregation-Mediated Alzheimer's Phenotypes. ACS Chem Biol. 2023 Jul 21;18(7):1510-1522. doi: 10.1021/acschembio.3c00120. Epub 2023 Jun 27. PMID: 37367833. https://pubmed.ncbi.nlm.nih.gov/37367833/
2022
2. Ahmed J, Fitch TC, Donnelly CM, Joseph JA, Ball TD, Bassil MM, Son A, Zhang C, Ledreux A, Horowitz S, Qin Y, Paredes D, Kumar S#. Foldamers Reveal and Validate Novel Therapeutic Targets Associated with Toxic α-Synuclein Self-Assembly. Nature Commun. 2022. April 27;13(1):2273. PubMed PMID: 35477706. #Corresponding Author. https://pubmed.ncbi.nlm.nih.gov/35477706/
2021
1. Palanikumar L, Karpauskaite L, Al-Sayegh M, Chehade I, Alam M, Hassan S, Maity D, Ali L, Kalmouni M, Hunashal Y, Ahmed J, Houhou T, Karapetyan S, Falls Z, Samudrala R, Pasricha R, Esposito G, Afzal AJ, Hamilton AD, Kumar S, Magzoub M. Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function. Nat Commun. 2021 Jun 25;12(1):3962. doi: 10.1038/s41467-021-23985-1. PubMed PMID: 34172723; PubMed Central PMCID: PMC8233319.
Sunil's post doc and graduate work
​1. Maity D, Kumar S, AlHussein R, Gremer L, Howarth M, Karpauskaite L, Hoyer W, Magzoub M, Hamilton AD. Sub-stoichiometric inhibition of IAPP aggregation: a peptidomimetic approach to anti-amyloid agents. RSC Chemical Biology. 2020 August; 1:225-232.
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2. Henning-Knechtel A, Kumar S, Wallin C, Król S, Wärmländer SK, Esposito G, Kirmizialtin S, Gräslund A, Hamilton AD, Magzoub M. Designed Cell-Penetrating Peptide Inhibitors of Amyloid-beta Aggregation and Cytotoxicity. Cell Reports Physical Science. 2020 February; 1(2):100014.
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3. Maity D, Kumar S, Curreli F, Debnath AK, Hamilton AD. α-Helix-Mimetic Foldamers for Targeting HIV-1 TAR RNA. Chemistry. 2019 May 28;25(30):7265-7269. doi: 10.1002/chem.201900139. Epub 2019 Apr 10. PubMed PMID: 30825250.
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4. Kumar S, Henning-Knechtel A, Magzoub M, Hamilton AD. Peptidomimetic-Based Multidomain Targeting Offers Critical Evaluation of Aβ Structure and Toxic Function. J Am Chem Soc. 2018 May 30;140(21):6562-6574. doi: 10.1021/jacs.7b13401. Epub 2018 May 16. PubMed PMID: 29648815.
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5. Lee CH, Yu JR, Kumar S, Jin Y, LeRoy G, Bhanu N, Kaneko S, Garcia BA, Hamilton AD, Reinberg D. Allosteric Activation Dictates PRC2 Activity Independent of Its Recruitment to Chromatin. Mol Cell. 2018 May 3;70(3):422-434.e6. doi: 10.1016/j.molcel.2018.03.020. Epub 2018 Apr 19. PubMed PMID: 29681499; PubMed Central PMCID: PMC5935545.
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6. Birol M, Kumar S, Rhoades E, Miranker AD. Conformational switching within dynamic oligomers underpins toxic gain-of-function by diabetes-associated amyloid. Nat Commun. 2018 Apr 3;9(1):1312. doi: 10.1038/s41467-018-03651-9. PubMed PMID: 29615609; PubMed Central PMCID: PMC5882805.
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7. Kumar S, Vogel MC, Hamilton AD. Teaching an old scaffold new recognition tricks: oligopyrrolamide antagonists of IAPP aggregation. Org Biomol Chem. 2018 Jan 31;16(5):733-741. doi: 10.1039/c7ob02910a. PubMed PMID: 29303519.
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8. Kumar S, Henning-Knechtel A, Chehade I, Magzoub M, Hamilton AD. Foldamer-Mediated Structural Rearrangement Attenuates Aβ Oligomerization and Cytotoxicity. J Am Chem Soc. 2017 Nov 29;139(47):17098-17108. doi: 10.1021/jacs.7b08259. Epub 2017 Nov 10. PubMed PMID: 29058422.
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9. Kumar S, Hamilton AD. α-Helix Mimetics as Modulators of Aβ Self-Assembly. J Am Chem Soc. 2017 Apr 26;139(16):5744-5755. doi: 10.1021/jacs.6b09734. Epub 2017 Apr 12. PubMed PMID: 28273416.
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10. Kumar S, Birol M, Miranker AD. Foldamer scaffolds suggest distinct structures are associated with alternative gains-of-function in a preamyloid toxin. Chem Commun (Camb). 2016 May 11;52(38):6391-4. doi: 10.1039/c6cc01248e. Epub 2016 Apr 15. PubMed PMID: 27079937; PubMed Central PMCID: PMC4871714.
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11. Kumar S, Birol M, Schlamadinger DE, Wojcik SP, Rhoades E, Miranker AD. Foldamer-mediated manipulation of a pre-amyloid toxin. Nat Commun. 2016 Apr 25;7:11412. doi: 10.1038/ncomms11412. PubMed PMID: 27108700; PubMed Central PMCID: PMC4848510.
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12. Kumar S, Ranjan N, Kellish P, Gong C, Watkins D, Arya DP. Multivalency in the recognition and antagonism of a HIV TAR RNA-TAT assembly using an aminoglycoside benzimidazole scaffold. Org Biomol Chem. 2016 Feb 14;14(6):2052-6. doi: 10.1039/c5ob02016f. PubMed PMID: 26765486; PubMed Central PMCID: PMC4837457.
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13. Kumar S, Spano MN, Arya DP. Influence of linker length in shape recognition of B* DNA by dimeric aminoglycosides. Bioorg Med Chem. 2015 Jul 1;23(13):3105-9. doi: 10.1016/j.bmc.2015.04.082. Epub 2015 May 8. PubMed PMID: 26025072; PubMed Central PMCID: PMC4837466.
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14. Watkins D, Kumar S, Green KD, Arya DP, Garneau-Tsodikova S. Influence of linker length and composition on enzymatic activity and ribosomal binding of neomycin dimers. Antimicrob Agents Chemother. 2015 Jul;59(7):3899-905. doi: 10.1128/AAC.00861-15. Epub 2015 Apr 20. PubMed PMID: 25896697; PubMed Central PMCID: PMC4468663.
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15. Kumar S, Schlamadinger DE, Brown MA, Dunn JM, Mercado B, Hebda JA, Saraogi I, Rhoades E, Hamilton AD, Miranker AD. Islet amyloid-induced cell death and bilayer integrity loss share a molecular origin targetable with oligopyridylamide-based α-helical mimetics. Chem Biol. 2015 Mar 19;22(3):369-78. doi: 10.1016/j.chembiol.2015.01.006. Epub 2015 Mar 5. PubMed PMID: 25754474; PubMed Central PMCID: PMC4384466.
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16. Kellish PC, Kumar S, Mack TS, Spano MN, Hennig M, Arya DP. Multivalent Amino Sugars to Recognize Different TAR RNA Conformations. Medchemcomm. 2014 Aug 1;5(8):1235-1246. doi: 10.1039/C4MD00165F. Epub 2014 May 30. PubMed PMID: 27076899; PubMed Central PMCID: PMC4828046.
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17. Kumar S, Newby Spano M, Arya DP. Shape readout of AT-rich DNA by carbohydrates. Biopolymers. 2014 Jul;101(7):720-32. doi: 10.1002/bip.22448. PubMed PMID: 24281844; PubMed Central PMCID: PMC4112085.
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18. Kumar S, Brown MA, Nath A, Miranker AD. Folded small molecule manipulation of islet amyloid polypeptide. Chem Biol. 2014 Jun 19;21(6):775-81. doi: 10.1016/j.chembiol.2014.05.007. Epub 2014 Jun 12. PubMed PMID: 24930968; PubMed Central PMCID: PMC4139143.
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19. Watkins D, Ranjan N, Kumar S, Gong C, Arya DP. An assay for human telomeric G-quadruplex DNA binding drugs. Bioorg Med Chem Lett. 2013 Dec 15;23(24):6695-9. doi: 10.1016/j.bmcl.2013.10.030. Epub 2013 Nov 1. PubMed PMID: 24246738; PubMed Central PMCID: PMC4112084.
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20. Ranjan N, Kumar S, Watkins D, Wang D, Appella DH, Arya DP. Recognition of HIV-TAR RNA using neomycin-benzimidazole conjugates. Bioorg Med Chem Lett. 2013 Oct 15;23(20):5689-93. doi: 10.1016/j.bmcl.2013.08.014. Epub 2013 Aug 14. PubMed PMID: 24012122; PubMed Central PMCID: PMC4048829.
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21. King A, Watkins D, Kumar S, Ranjan N, Gong C, Whitlock J, Arya DP. Characterization of ribosomal binding and antibacterial activities using two orthogonal high-throughput screens. Antimicrob Agents Chemother. 2013 Oct;57(10):4717-26. doi: 10.1128/AAC.00671-13. Epub 2013 Jul 15. PubMed PMID: 23856777; PubMed Central PMCID: PMC3811423.
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22. Kumar S, Miranker AD. A foldamer approach to targeting membrane bound helical states of islet amyloid polypeptide. Chem Commun (Camb). 2013 May 25;49(42):4749-51. doi: 10.1039/c3cc41452c. PubMed PMID: 23579860; PubMed Central PMCID: PMC3968531.
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23. Watkins D, Norris FA, Kumar S, Arya DP. A fluorescence-based screen for ribosome binding antibiotics. Anal Biochem. 2013 Mar 15;434(2):300-7. doi: 10.1016/j.ab.2012.12.003. Epub 2012 Dec 19. PubMed PMID: 23262284; PubMed Central PMCID: PMC4048832.
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24. Kumar S, Kellish P, Robinson WE Jr, Wang D, Appella DH, Arya DP. Click dimers to target HIV TAR RNA conformation. Biochemistry. 2012 Mar 20;51(11):2331-47. doi: 10.1021/bi201657k. Epub 2012 Mar 9. PubMed PMID: 22339203; PubMed Central PMCID: PMC3673543.
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25. Kumar S, Arya DP. Recognition of HIV TAR RNA by triazole linked neomycin dimers. Bioorg Med Chem Lett. 2011 Aug 15;21(16):4788-92. doi: 10.1016/j.bmcl.2011.06.058. Epub 2011 Jun 21. PubMed PMID: 21757341; PubMed Central PMCID: PMC3673547.
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26. Kumar S, Xue L, Arya DP. Neomycin-neomycin dimer: an all-carbohydrate scaffold with high affinity for AT-rich DNA duplexes. J Am Chem Soc. 2011 May 18;133(19):7361-75. doi: 10.1021/ja108118v. Epub 2011 Apr 27. PubMed PMID: 21524066; PubMed Central PMCID: PMC3641821.
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27. Ranjan N, Andreasen KF, Kumar S, Hyde-Volpe D, Arya DP. Aminoglycoside binding to Oxytricha nova telomeric DNA. Biochemistry. 2010 Nov 16;49(45):9891-903. doi: 10.1021/bi101517e. Epub 2010 Oct 22. PubMed PMID: 20886815; PubMed Central PMCID: PMC3641841.
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28. Xue L, Xi H, Kumar S, Gray D, Davis E, Hamilton P, Skriba M, Arya DP. Probing the recognition surface of a DNA triplex: binding studies with intercalator-neomycin conjugates. Biochemistry. 2010 Jul 6;49(26):5540-52. doi: 10.1021/bi100071j. PubMed PMID: 20499878; PubMed Central PMCID: PMC3641831.
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29. Xi H, Kumar S, Dosen-Micovic L, Arya DP. Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices. Biochimie. 2010 May;92(5):514-29. doi: 10.1016/j.biochi.2010.02.004. Epub 2010 Feb 16. PubMed PMID: 20167243; PubMed Central PMCID: PMC3977217.
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30. Xi H, Gray D, Kumar S, Arya DP. Molecular recognition of single-stranded RNA: neomycin binding to poly(A). FEBS Lett. 2009 Jul 7;583(13):2269-75. doi: 10.1016/j.febslet.2009.06.007. Epub 2009 Jun 9. PubMed PMID: 19520078; NIHMSID:NIHMS129384.
