71. Jones KFM, Demir Ö, Wyllie MK, Grillo MJ, Morris C, Hirakis SP, Kardile RD, Walters MA, Harris RS, Amaro RE, and Harki DA* Development of allosteric small molecule APOBEC3B inhibitors from in silico screening. bioRxiv. [PDF]  

70. Tang J, Moorthy R, Demir Ö, Baker ZD, Naumann JA, Jones KFM, Grillo MJ, Haefner ES, Shi K, Levy MJ, Aihara H, Harris RS, Amaro RE, Levinson NM, and Harki DA* Targeting N-Myc in neuroblastoma with selective Aurora kinase A degraders. bioRxiv. [PDF]  

69. Anderson JJ, Grillo MJ, and Harki DA* Development of allosteric NIK ligands from fragment-based NMR screening. ACS Med. Chem. Lett. 2023, 14, 1815-1820. [PDF][Supporting Information]

68. Passow KT and Harki DA* 4-Isocyanoindole-2ʹ-deoxyribonucleoside (4ICIN): An isomorphic indole nucleoside suitable for inverse electron demand Diels-Alder reactions. Tetrahedron Lett. 2023, 132, 154807. [PDF][Supporting Information]

67. Buchholz CR, Vittengl MS, McPherson JE, Das S, Gee CT, Grillo MJ, Chai SC, Lee RE, Chen T, Harki DA, Shelat AA, and Pomerantz WCK* Fragment-based NMR screening of the BPTF PHD finger methyl lysine reader leads to the first small molecule inhibitors. ACS Med. Chem. Lett. 2023, 14, 1441-1447. [PDF][Supporting Information]

66. Moghadasi SA, Biswas RG, Harki DA, and Harris RS* Rapid resistance profiling of SARS-CoV-2 protease inhibitors. npj Antimicrob. Resist. 2023, 1, 9. [PDF][Supporting Information]

65. Sawyer JM, Passow KT, and Harki DA* Synthesis and photophysical characterization of fluorescent indole nucleoside analogues. RSC Advances 202313, 16369-16376. [PDF][Supporting Information]

64. Faber EB, Sun L, Tang J, Roberts E, Ganeshkumar S, Wang N, Rasmussen D, Majumdar A, Hirsch LE, John K, Yang A, Khalid H, Hawkinson JE, Levinson NM, Chennathukuzhi V, Harki DA, Schönbrunn E, and Georg GI* Development of allosteric, selective cyclin-dependent kinase 2 inhibitors that are negatively cooperative with cyclin binding and show potential as contraceptive agents. Nat. Commun. 2023, 14, 3213[PDF][Supporting Information]

63. Divakaran A, Harki DA, and Pomerantz WCK* Recent progress and structural analyses of domain-selective BET inhibitors. Med. Res. Rev. 2023, 43, 972-1018. [PDF]

62. Jones KFM, Shehata M, Carpenter MA, Amaro RE, and Harki DA* APOBEC3A catalytic inactivity mutation induces tertiary structure destabilization. ACS Med. Chem. Lett. 2023, 14, 338-343. [PDF][Supporting Information]

61. Chinthapatla R, Sotoudegan M, Srivastava P, Anderson TK, Moustafa IM, Passow KT, Kennelly SA, Moorthy R, Dulin D, Feng JY, Harki DA, Kirchdoerfer RN, Cameron CE*, and Arnold JJ* Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease. Nucleic Acids Res. 2023, 51, 315–336. [PDF][Supporting Information]

60. Divakaran A, Scholtz CR, Zahid H, Lin W, Griffith EC, Lee RE, Chen T, Harki DA*, and Pomerantz WCK* Development of an N-terminal BRD4 bromodomain-targeted degrader. ACS Med. Chem. Lett. 2022, 13, 1621-1627. [PDF][Supporting Information]

59. Kennelly SA, Moorthy R, Silva Otero R, and Harki DA* Expanding catch and release DNA decoy (CRDD) technology with pyrimidine mimics. Chem. Eur. J. 2022, e202201355. [PDF][Supporting Information]

58. Moeller NH, Passow KT, Harki DA, and Aihara H* SARS-CoV-2 nsp14 exoribonuclease removes the natural antiviral 3'-deoxy-3',4'-didehydro-cytidine nucleotide from RNA. Viruses 2022, 14, 1790. [PDF][Supporting Information]

57. Moghadasi SA, Esler MA, Otsuka Y, Becker JT, Moraes SN, Anderson CB, Chamakuri S, Belica C, Wick C, Harki DA, Young DW, Scampavia L, Spicer TP, Shi K, Aihara H, Brown WL, and Harris RS* Gain-of-signal assays for probing inhibition of SARS-CoV-2 Mpro/3CLpro in living cells. mBio 2022, 13, e00784-22. [PDF]

56. Grillo MJ, Jones KFM, Carpenter MA, Harris RS, and Harki DA* The current toolbox for APOBEC drug discovery. Trends Pharmacol. Sci. 2022, 43, 362-377. [PDF]

55. Abdel Ghani L, Yusenko MV, Frank D, Moorthy R, Widen JC, Dörner W, Khandanpour C, Harki DA, and Klempnauer K-H* A synthetic covalent ligand of the C/EBPbeta transactivation domain inhibits acute myeloid leukemia cells. Cancer Lett. 2022, 530, 170-180. [PDF][Supporting Information]

54. Cui H, Divakaran A, Hoell ZJ, Ellingson MO, Scholtz CR, Zahid H, Johnson JA, Griffith EC, Gee CT, Lee AL, Khanal S, Shi K, Aihara H, Shah VH, Lee RE, Harki DA, and Pomerantz WCK* A structure-based design approach for generating high affinity BRD4 D1-selective chemical probes. J. Med. Chem. 2022, 65, 2342-2360. [PDF][Supporting Information]

53. Janissen R, Woodman A, Shengjuler D, Vallet T, Lee K-M, Kuijpers L, Moustafa IM, Fitzgerald F, Huang P-N, Perkins AL, Harki DA, Arnold JJ, Solano B, Shih S-R, Vignuzzi M, Cameron CE*, and Dekker NH* Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses. Mol. Cell 2021, 81, 4467-4480. [PDF][Supporting Information]

52. Passow KT, Caldwell HS, Ngo KA, Arnold JJ, Antczak NM, Narayanan A, Jose J, Sturla SJ, Cameron CE, Ciota AT, and Harki DA* A chemical strategy for intracellular arming of an endogenous broad-spectrum antiviral nucleotide. J. Med. Chem. 2021, 64, 15429-15439. [PDF][Supporting Information]

51. Moorthy R, Kennelly SA, Rodriguez DJ, and Harki DA* An efficient synthesis of RNA containing GS-441524: The nucleoside precursor of remdesivir. RSC Advances 2021, 11, 31373-31376. [PDF][Supporting Information]

50. Cui H, Carlson AS, Schleiff MA, Divakaran A, Johnson JA, Buchholz CR, Zahid H, Vail NR, Shi K, Aihara H, Harki DA, Miller GP, Topczewski JJ*, and Pomerantz WCK* 4-Methyl-1,2,3-triazoles as N-acetyl-lysine mimics afford potent BET bromodomain inhibitors with improved selectivity. J. Med. Chem. 2021, 64, 10497-10511. [PDF][Supporting Information]

49. Shi K, Moeller NH, Banerjee S, McCann JL, Carpenter MA, Yin L, Moorthy R, Orellana K, Harki DA, Harris RS, and Aihara H*. Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q. Proc. Natl. Acad. Sci. USA 2021, 118, e2021120118. [PDF][Supporting Information]

48. Emmetiere F, Ratnayake R, Schares HAM, Jones KFM, Bevan-Smith E, Luesch H*, Harki DA*, and Grenning AJ*. Function-oriented and modular (+/-)-cis-pseudoguaianolide synthesis: Discovery of new Nrf2 activators and NF-κB inhibitors. Chem. Eur. J. 2021, 27, 5564-5571. [PDF][Supporting Information]

47. Cui H, Divakaran A, Pandey AK, Johnson JA, Zahid H, Hoell ZJ, Ellingson MO, Shi K, Aihara H, Harki DA, and Pomerantz WCK*. Selective N-terminal BET bromodomain inhibitors by targeting non-conserved residues and structured water displacement. Angew. Chem. Intl. Ed. 2021, 60, 1220-1226. [PDF][Supporting Information]

46. Jackson PA, Schares HAM, Jones KFM, Widen JC, Dempe DP, Grillet F, Cuellar ME, Walters MA, Harki DA*, and Brummond KM*. Synthesis of guaianolide analogues with a tunable alpha-methylene-gamma-lactam electrophile and correlating bioactivity with thiol reactivity. J. Med. Chem. 2020, 63, 14951-14978. [PDF][Supporting Information]

45. Passow KT, Antczak NM, Sturla SJ and Harki DA*. Synthesis of 4-cyanoindole nucleosides, 4-cyanoindole-2'-deoxyribonucleoside-5'-triphosphate (4CIN-TP) and enzymatic incorporation of 4CIN-TP into DNA. Curr. Protoc. Nucleic Acid Chem. 2020, 80, e101. [PDF]

44. Kvach MV, Barzak FM, Harjes S, Schares HAM, Kurup HM, Jones KF, Sutton L, Donahue J, D'Aquila RT, Jameson GB, Harki DA, Krause KL, Harjes E* and Filichev VV*. Differential inhibition of APOBEC3 DNA-mutator isozymes by fluoro- versus non-fluoro-substituted 2'-deoxyzebularine embedded in single-stranded DNA. ChemBioChem 2020, 21, 1028-1035. [PDF][Supporting Information]

43. Shi K, Demir Ö, Carpenter MA, Banerjee S, Harki DA, Amaro RE, Harris RS and Aihara H*. Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B. FASEB BioAdvances 2020, 2, 49-58. [PDF][Supporting Information]

42. Kvach MV, Barzak FM, Harjes S, Schares HAM, Jameson GB, Ayoub AM, Moorthy R, Aihara H, Harris RS, Filichev V*, Harki DA* and Harjes E*. Inhibiting APOBEC3 activity with single-stranded DNA containing 2'-deoxyzebularine analogs. Biochemistry 2019, 58, 391-400. [PDF][Supporting Information]

41. Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS and Amaro RE*. Determinants of oligonucleotide selectivity of APOBEC3B. J. Chem. Inf. Model. 2019, 59, 2264-2273. [PDF]

40. Divakaran A, Talluri SK, Ayoub AM, Mishra NK, Cui H, Widen JC, Berndt N, Zhu J-Y, Carlson AS, Topczewski JJ, Schonbrunn EK, Harki DA* and Pomerantz WCK*. Molecular basis for the N-terminal bromodomain and extra terminal (BET) family selectivity of a dual kinase-bromodomain inhibitor. J. Med. Chem. 2018, 61, 9316-9334. [PDF][Supporting Information]

39. Passow KT and Harki DA*. 4-Cyanoindole-2'-deoxyribonucleoside (4CIN): A universal fluorescent nucleoside analogue. Org. Lett. 2018, 20, 4310-4313. [PDF] [Supporting Information]

38. Naumann JA, Widen JC, Jonart LA, Ebadi M, Tang J, Gordon DJ, Harki DA  and Gordon PM*. SN-38 conjugated gold nanoparticles activated by Ewing sarcoma specific mRNAs exhibit in vitro and in vivo efficacy. Bioconjug. Chem. 2018, 29, 1111-1118. [PDF] [Supporting Information]

37. Widen JC, Kempema AM, Baur JW, Skopec HM, Edwards JT, Brown TJ, Brown DA, Meece FA and Harki DA*. Helenalin analogues targeting NF-κB p65: Thiol reactivity and cellular potency studies of varied electrophilies. ChemMedChem 2018, 13, 303-311. [PDF] [Supporting Information]

Widen ChemMedChem 2018 Cover

Article featured on the ChemMedChem cover [PDF]

Featured in the virtual issue "MedChem in the USA"



36. Olson ME, Harris RS and Harki DA*. APOBEC enzymes as targets for virus and cancer therapy. Cell Chem. Biol. 201825, 36-49. [PDF]

35. Dulin D, Arnold JJ, van Laar T, Oh H-S, Lee C, Perkins AL, Harki DA, Depken M*, Cameron CE*, and Dekker NH*. Incorporation of nucleotide analogues by an RNA-dependent RNA polymerase leaves fingerprints in the pausing kinetics. Cell Rep. 2017, 21, 1063-1076. [PDF] [Supporting Information]

34. Shi K, Carpenter MA, Banerjee S, Shaban NM, Kurahashi K, Salamango DJ, McCann JL, Starrett GJ, Duffy JV, Demir Ö, Amaro RE, Harki DA, Harris RS* and Aihara H*. Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat. Struct. Mol. Biol. 2017, 24, 131-139. [PDF] [Supporting Information]

Journal Cover

 Article featured on the Nat. Struct. Mol. Biol. cover (PDF)




33. Jackson PA, Widen JC, Harki DA* and Brummond KM*. Covalent modifiers: A chemical perspective on the reactivity of α,β-unsaturated carbonyls with thiols via hetero-Michael addition reactions. J. Med. Chem. 2017, 60, 839-885. [PDF]

Featured as a Most Read article on the J. Med. Chem. website.

32. Richards CM, Li M, Perkins AL, Rathore A, Harki DA, and Harris RS*. Reassessing APOBEC3G inhibition by HIV-1 Vif-derived peptides. J. Mol. Biol. 2017, 429, 88-96. [PDF]

31. Widen JC, Kempema, AM, Villalta, PW and Harki DA*. Targeting NF-κB p65 with a helenalin inspired bis-electrophile. ACS Chem. Biol. 2017, 12, 102-113. [PDF] [Supporting Information]

Highlight on John Widen: Introducing Our Authors - ACS Chemical Biology.

30. Wells SM, Widen JC, Harki DA* and Brummond KM*. Alkyne ligation handles: Propargylation of hydroxyl, sulfhydryl, amino, and carboxyl groups via the Nicholas reaction. Org. Lett. 2016, 18, 4566-4569. [PDF] - [Supporting Information]

29. Breunig SL, Olson ME, and Harki DA*. Rapid, microwave accelerated synthesis of [1,2,4]triazolo[3,4-b][1,3,4]oxadiazoles from 4-acylamino-1,2,4-triazoles. Tetrahedron Lett. 2016, 57, 4056-4060. [PDF] Supporting information

28.  Perkins AL, Peterson KL, Beito TG, Flatten KS, Kaufmann SH and Harki DA*. Synthesis of a peptide-universal nucleotide antigen: Towards next-generation antibodies to detect topoisomerase I-DNA covalent complexes. Org. Biomol. Chem. 2016, 14, 4103-4109. [PDF] - [Supporting Information]

27.  Struntz NB and Harki DA*. Catch & release DNA decoys: Capture and photochemical dissociation of NF-kappaB transcription factors. ACS Chem. Biol. 2016, 11, 1631-1638. [PDF] - [Supporting Information]

Highlight on Nick Struntz: Introducing Our Authors - ACS Chemical Biology.

26.  Patel AG, Flatten KS, Peterson KL, Beito TG, Schneider PA, Perkins AL, Harki DA, Kaufmann SH*. Immunodetection of human topoisomerase I-DNA covalent complexes. Nucleic Acids Res. 2016, 44, 2816-2826. [PDF] - [Supporting Information]

25.  Richards C, Albin JS, Demir Ö, Shaban NM, Luengas EM, Land AM, Anderson BD, Holten JR, Anderson JS, Harki DA, Amaro RE, and Harris RS*. The binding interface between human APOBEC3F and HIV-1 Vif elucidated by genetic and computational approaches. Cell Rep. 2015, 13, 1781-1788. [PDF] - [Supporting Information]

24.  Kerr JP, Robinson P, Shi G, Bogush AI, Kempema AM, Hexum JK, Becerra N, Harki DA, Martin SS, Ratieri R, Prosser BLand Ward CW*. Detyrosinated microtubules modulate mechanotransduction in heart and skeletal muscle. Nat. Commun. 2015, 6, 8526. [PDF] - [Supporting Information

23.  Olson ME, Abate-Pella D, Perkins AL, Li M, Carpenter MA, Rathore A, Harris RS and Harki DA*. Oxidative reactivities of 2-furylquinolines: Ubiquitous scaffolds in common high-throughput screening libraries. J. Med. Chem. 2015, 58, 7419-7430. [PDF] - [Supporting Information]

Commentary: False Positives Are Always Waiting - In the Pipeline (Derek Lowe).

22.  Kempema AM, Widen JC, Hexum JK, Andrews TW, Wang D, Rathe SK, Meece FA, Noble K, Sachs Z, Largaespada DA and Harki DA*. Synthesis and antileukemic activities of C1-C10 modified parthenolide analogues. Bioorg. Med. Chem. 2015, 23, 4737-4745. [PDF] Supporting information

21.  Hexum JK, Becker CM, Kempema AM, Ohlfest JR, Largaespada DA and Harki DA*. Parthenolide prodrug LC-1 slows growth of intracranial glioma. Bioorg. Med. Chem. Lett. 2015, 25, 2493-2495. [PDF]

20.  Brand LJ, Olson ME, Ravindranathan P, Guo H, Kempema AM, Andrews TE, Chen X, Raj GV, Harki DA and Dehm SM*. EPI-001 is a selective peroxisome proliferator-activated receptor-gamma modulator with inhibitory effects on androgen receptor expression and activity in prostate cancer. Oncotarget 2015, 6, 3811-3824. [PDF]

19.  Wen B, Hexum JK, Widen JC, Harki DA* and Brummond KM*. A redox economical synthesis of bioactive 6,12-guaianolides. Org. Lett. 2013, 15, 2644-2647. [PDF] - [Supporting Information]

18.  Andrews TE, Wang D, and Harki DA*. Cell surface markers of cancer stem cells: diagnostic macromolecules and targets for drug delivery. Drug Deliv. Transl. Res. 2013, 3, 121-142. [PDF]

17.  Olson ME, Li M, Harris RS and Harki DA*. Small molecule APOBEC3G DNA cytosine deaminase inhibitors based on a 4-amino-1,2,4-triazole-3-thiol scaffold. ChemMedChem 2013, 8, 112-117. [PDF] - [Supporting Information]

book cover

 Article featured on the ChemMedChem cover [PDF]




16.  Struntz NB, Hu T, White BR, Olson ME, and Harki DA*. Inhibition of guanosine monophosphate synthetase by the substrate enantiomer L-XMP. ChemBioChem 2012, 13, 2517-2520. [PDF] - [Supporting Information]

15.  Hexum JK, Tello-Aburto R, Struntz NB, Harned AM*, and Harki DA*. Bicyclic cyclohexenones as inhibitors of NF-kappaB signaling. ACS Med. Chem. Lett. 2012, 3, 459-464. [PDF] - [Supporting Information]

14.  Li M, Shandilya SMD, Carpenter MA, Rathore A, Brown WL, Perkins AL, Harki DA, Solberg J, Hook DJ, Johnson JR, Krogan NJ, Somasundaran M, Ali A, Schiffer CA, and Harris RS*. First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G. ACS Chem. Biol. 2012, 7, 506-517. [PDF] - [Supporting Information]

For manuscripts listed above: † = co-first authors; * = corresponding author.

From Professor Harki's postdoctoral, graduate, and undergraduate research:

13.  Zhang Y, Sicot G, Cui X, Vogel M, Wuertzer CA, Lezon-Geyda K, Wheeler J, Harki DA, Muzikar KA, Stolper DA, Dervan PB, and Perkins AS. Targeting a DNA binding motif of the EVI1 protein by a pyrrole-imidazole polyamide. Biochemistry 2011, 50, 10431-10441.

12.  Chenoweth DM, Harki DA, and Dervan PB. Oligomerization route to Py-Im polyamide macrocycles. Org. Lett. 2009, 11, 3590-3593.

11.  Chenoweth DM, Harki DA, Phillips JW, Dose C, and Dervan PB. Cyclic pyrrole-imidazole polyamides targeted to the androgen response element. J. Am. Chem. Soc. 2009, 131, 7182-7188.

10.  Chenoweth DM, Harki DA, and Dervan PB. Solution-phase synthesis of pyrrole-imidazole polyamides. J. Am. Chem. Soc. 2009, 131, 7175-7181.

9.  Harki DA, Satyamurthy N, Stout DB, Phelps ME, and Dervan PB. In vivo imaging of pyrrole-imidazole polyamides with positron emission tomography. Proc. Natl. Acad. Sci. USA 2008, 105, 13039-13044.

8.  Zamyatkin DF, Parra F, Martín Alonso JM, Harki DA, Peterson BR, Grochulski P, and Ng KKS. Structural insights into mechanisms of catalysis and inhibition in Norwalk virus polymerase. J. Biol. Chem. 2008, 283, 7705-7712.

7.  Graci JD, Too K, Smidansky ED, Edathil JP, Barr EW, Harki DA, Galarraga JE, Bollinger Jr. JM, Peterson BR, Loakes D, Brown DM, and Cameron CE. Lethal mutagenesis of picornaviruses with N6-modified purine nucleoside analogues. Antimicrob. Agents Chemother. 2008, 52, 971-979.

6.  Graci JD, Harki DA, Korneeva VS, Edathil JP, Too K, Franco D, Smidansky ED, Paul AV, Peterson BR, Brown DM, Loakes D, and Cameron CE. Lethal mutagenesis of poliovirus mediated by a mutagenic pyrimidine analogue. J. Virol. 2007, 81, 11256-11266.

5.  Harki DA, Graci JD, Edathil JP, Castro C, Cameron CE, and Peterson BR. Synthesis of a universal 5-nitroindole ribonucleotide and incorporation into RNA by a viral RNA-dependent RNA polymerase. ChemBioChem 2007, 8, 1359-1362.

4.  Harki DA, Graci JD, Galarraga JE, Chain WJ, Cameron CE, and Peterson BR. Synthesis and antiviral activity of 5-substituted cytidine analogues: identification of a potent inhibitor of viral RNA-dependent RNA polymerases. J. Med. Chem. 2006, 49, 6166-6169.

3.  Simeonova PP, Hulderman T, Harki D, Luster MI. Arsenic exposure accelerates atherogenesis in apolipoprotein E-/- mice. Environ. Health Perspect. 2003, 111, 1744-1748.

2.  Harki DA, Graci JD, Korneeva VS, Ghosh SKB, Hong Z, Cameron CE, and Peterson BR. Synthesis and antiviral evaluation of a mutagenic and non-hydrogen bonding ribonucleoside analogue: 1-β-D-ribofuranosyl-3-nitropyrrole. Biochemistry 2002, 41, 9026-9033.

1.  Simeonova PP, Wang S, Toriuma W, Kommineni V, Matheson J, Unimye N, Kayama F, Harki D, Ding M, Vallyathan V, Luster MI. Arsenic mediates cell proliferation and gene expression in the bladder epithelium: association with activating protein-1 transactivation. Cancer Res. 2000, 60, 3445-3453.