Research laboratory of Michelle Arkin, PhD
Chemical Biology and Biophysics Laboratory

Publications

  1. Hallenbeck KK, Turner DM, Renslo AR, Arkin MR. Targeting Non-Catalytic Cysteine Residues Through Structure-Guided Drug Discovery. Curr Top Med Chem. 2016; 16.
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  2. Liu H, Chen S, Huang K, Kim J, Mo H, Iovine R, Gendre J, Pascal P, Li Q, Sun Y, Dong Z, Arkin M, Guo S, Huang B. A High-Content Larval Zebrafish Brain Imaging Method for Small Molecule Drug Discovery. PLoS One. 2016 October 12; 11(10).
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  3. Bulfer SL, Chou TF, Arkin MR. p97 Disease Mutations Modulate Nucleotide-Induced Conformation to Alter Protein-Protein Interactions. ACS Chem Biol. 2016 August 19; 11(8):2112-6.
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  4. Gallagher CM, Garri C, Cain EL, Ang KK, Wilson CG, Chen S, Hearn BR, Jaishankar P, Aranda-Diaz A, Arkin MR, Renslo AR, Walter P. Ceapins are a new class of unfolded protein response inhibitors, selectively targeting the ATF6α branch. Elife. 2016 July 20; 5.
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  5. Hallenbeck KK, Turner DM, Renslo AR, Arkin MR. Targeting Non-Catalytic Cysteine Residues Through Structure-Guided Drug Discovery. Curr Top Med Chem. 2016 July 19; 16.
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  6. Banerjee S, Bartesaghi A, Merk A, Rao P, Bulfer SL, Yan Y, Green N, Mroczkowski B, Neitz RJ, Wipf P, Falconieri V, Deshaies RJ, Milne JL, Huryn D, Arkin M, Subramaniam S. 2.3 Ã? resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition. Science. 2016 February 19; 351(6275):871-5.
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  7. Arkin M. Interview with Michelle Arkin, PhD. Assay Drug Dev Technol. 2016 February 01; 14(1).
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  8. Visscher M, Arkin MR, Dansen TB. Covalent targeting of acquired cysteines in cancer. Curr Opin Chem Biol. 2016 February 01; 30:61-7.
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  9. Alverez C, Bulfer SL, Chakrasali R, Chimenti MS, Deshaies RJ, Green N, Kelly M, LaPorte MG, Lewis TS, Liang M, Moore WJ, Neitz RJ, Peshkov VA, Walters MA, Zhang F, Arkin MR, Wipf P, Huryn DM. Allosteric Indole Amide Inhibitors of p97: Identification of a Novel Probe of the Ubiquitin Pathway. ACS Med Chem Lett. 2015 December 22; 7(2):182-7.
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  10. Suzawa M, Miranda DA, Ramos KA, Ang KK, Faivre EJ, Wilson CG, Caboni L, Arkin MR, Kim YS, Fletterick RJ, Diaz A, Schneekloth JS, Ingraham HA. A gene-expression screen identifies a non-toxic sumoylation inhibitor that mimics SUMO-less human LRH-1 in liver. eLife Sciences. 2015 December 11; 4.
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  11. Neitz RJ, Bryant C, Chen S, Gut J, Caselli EH, Ponce S, Chowdhury S, Xu H, Arkin MR, Ellman JA, Renslo AR. Tetrafluorophenoxymethyl ketone cruzain inhibitors with improved pharmacokinetic properties as therapeutic leads for Chagas' disease. Bioorg Med Chem Lett. 2015 November 01; 25(21):4834-7.
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  12. Frye SV, Arkin MR, Arrowsmith CH, Conn PJ, Glicksman MA, Hull-Ryde EA, Slusher BS. Tackling reproducibility in academic preclinical drug discovery. Nat Rev Drug Discov. 2015 November 01; 14(11):733-4.
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  13. Alverez C, Arkin MR, Bulfer SL, Colombo R, Kovaliov M, LaPorte MG, Lim C, Liang M, Moore WJ, Neitz RJ, Yan Y, Yue Z, Huryn DM, Wipf P. Structure-Activity Study of Bioisosteric Trifluoromethyl and Pentafluorosulfanyl Indole Inhibitors of the AAA ATPase p97. ACS Med Chem Lett. 2015 October 23; 6(12):1225-30.
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  14. Khare S, Roach SL, Barnes SW, Hoepfner D, Walker JR, Chatterjee AK, Neitz RJ, Arkin MR, McNamara CW, Ballard J, Lai Y, Fu Y, Molteni V, Yeh V, McKerrow JH, Glynne RJ, Supek F. Utilizing Chemical Genomics to Identify Cytochrome b as a Novel Drug Target for Chagas Disease. PLoS Pathog. 2015 July 17; 11(7).
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  15. Chimenti MS, Bulfer SL, Neitz RJ, Renslo AR, Jacobson MP, James TL, Arkin MR, Kelly MJ. A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP. J Biomol Screen. 2015 July 01; 20(6):788-800.
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  16. Ekins S, de Siqueira-Neto JL, McCall LI, Sarker M, Yadav M, Ponder EL, Kallel EA, Kellar D, Chen S, Arkin M, Bunin BA, McKerrow JH, Talcott C. Machine Learning Models and Pathway Genome Data Base for Trypanosoma cruzi Drug Discovery. PLoS Negl Trop Dis. 2015 June 26; 9(6).
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  17. Zhang X, Gui L, Zhang X, Bulfer SL, Sanghez V, Wong DE, Lee Y, Lehmann L, Lee JS, Shih PY, Lin HJ, Iacovino M, Weihl CC, Arkin MR, Wang Y, Chou TF. Altered cofactor regulation with disease-associated p97/VCP mutations. Proc Natl Acad Sci U S A. 2015 April 07; 112(14):e1705.
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  18. Tran K, Arkin MR, Beal PA. Tethering in RNA: an RNA-binding fragment discovery tool. Molecules. 2015 March 04; 20(3):4148-61.
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  19. Bulman CA, Bidlow CM, Lustigman S, Cho-Ngwa F, Williams D, Rascón AA Jr, Tricoche N, Samje M, Bell A, Suzuki B, Lim KC, Supakorndej N, Supakorndej P, Wolfe AR, Knudsen GM, Chen S, Wilson C, Ang KH, Arkin M, Gut J, Franklin C, Marcellino C, et al. Repurposing auranofin as a lead candidate for treatment of lymphatic filariasis and onchocerciasis. PLoS Negl Trop Dis. 2015 February 20; 9(2).
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  20. Visperas PR, Winger JA, Horton TM, Shah NH, Aum DJ, Tao A, Barros T, Yan Q, Wilson CG, Arkin MR, Weiss A, Kuriyan J. Modification by covalent reaction or oxidation of cysteine residues in the tandem-SH2 domains of ZAP-70 and Syk can block phosphopeptide binding. Biochem J. 2015 January 01; 465(1):149-161.
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  21. Neitz RJ, Chen S, Supek F, Yeh V, Kellar D, Gut J, Bryant C, Gallardo-Godoy A, Molteni V, Roach SL, Khare S, Stinson M, Chatterjee AK, Robertson S, Renslo AR, Arkin M, Glynne R, McKerrow J, Siqueira-Neto JL. Lead identification to clinical candidate selection: drugs for Chagas disease. J Biomol Screen. 2015 January 01; 20(1):101-111.
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  22. Pfaff SJ, Chimenti MS, Kelly MJ, Arkin MR. Biophysical methods for identifying fragment-based inhibitors of protein-protein interactions. Methods Mol Biol. 2015 January 01; 1278:587-613.
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  23. Rettenmaier TJ, Sadowsky JD, Thomsen ND, Chen SC, Doak AK, Arkin MR, Wells JA. A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1. Proc Natl Acad Sci U S A. 2014 December 30; 111(52):18590-5.
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  24. Arkin MR, Tang Y, Wells JA. Small-molecule inhibitors of protein-protein interactions: progressing toward the reality. Chem Biol. 2014 September 18; 21(9):1102-14.
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  25. Chou TF, Bulfer SL, Weihl CC, Li K, Lis LG, Walters MA, Schoenen FJ, Lin HJ, Deshaies RJ, Arkin MR. Specific inhibition of p97/VCP ATPase and kinetic analysis demonstrate interaction between D1 and D2 ATPase domains. J Mol Biol. 2014 July 29; 426(15):2886-99.
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  26. Dar RD, Hosmane NN, Arkin MR, Siliciano RF, Weinberger LS. Screening for noise in gene expression identifies drug synergies. Science. 2014 Jun 20; 344(6190):1392-6.
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  27. Arkin MR, Ang KK, Chen S, Davies J, Merron C, Tang Y, Wilson CG, Renslo AR. UCSF Small Molecule Discovery Center: Innovation, Collaboration and Chemical Biology in the Bay Area. Comb Chem High Throughput Screen. 2014 May; 17(4):333-42.
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  28. Flygare JA, Arkin MR. Inhibiting caspase-6 activation and catalytic activity for neurodegenerative diseases. Curr Top Med Chem. 2014; 14(3):319-25.
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  29. Murray J, Giannetti AM, Steffek M, Gibbons P, Hearn BR, Cohen F, Tam C, Pozniak C, Bravo B, Lewcock J, Jaishankar P, Ly CQ, Zhao X, Tang Y, Chugha P, Arkin MR, Flygare J, Renslo AR. Tailoring small molecules for an allosteric site on procaspase-6. ChemMedChem. 2014 Jan; 9(1):73-7.
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  30. Wilson CG M, Arkin MR. Probing structural adaptivity at PPI interfaces with small molecules. Drug Discov. Today: Technol. 2013 December 01; 10(4):501-508.
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  31. Slusher BS, Conn PJ, Frye S, Glicksman M, Arkin M. Bringing together the academic drug discovery community. Nat Rev Drug Discov. 2013 Oct 31; 12(11):811-2.
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  32. Sun Y, Dong Z, Jin T, Ang KH, Huang M, Haston KM, Peng J, Zhong TP, Finkbeiner S, Weiss WA, Arkin MR, Jan LY, Guo S. Imaging-based chemical screening reveals activity-dependent neural differentiation of pluripotent stem cells. Elife. 2013; 2:e00508.
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  33. Bagriantsev SN, Ang KH, Gallardo-Godoy A, Clark KA, Arkin MR, Renslo AR, Minor DL. A High-Throughput Functional Screen Identifies Small Molecule Regulators of Temperature- and Mechano-Sensitive K2P Channels. ACS Chem Biol. 2013 Jun 17.
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  34. Sidrauski C, Acosta-Alvear D, Khoutorsky A, Vedantham P, Hearn BR, Li H, Gamache K, Gallagher CM, Ang KK, Wilson C, Okreglak V, Ashkenazi A, Hann B, Nader K, Arkin MR, Renslo AR, Sonenberg N, Walter P. Pharmacological brake-release of mRNA translation enhances cognitive memory. Elife. 2013; 2:e00498.
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  35. Choy JW, Bryant C, Calvet CM, Doyle PS, Gunatilleke SS, Leung SS, Ang KK, Chen S, Gut J, Oses-Prieto JA, Johnston JB, Arkin MR, Burlingame AL, Taunton J, Jacobson MP, McKerrow JM, Podust LM, Renslo AR. Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target. Beilstein J Org Chem. 2013; 9:15-25.
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  36. Heise CE, Murray J, Augustyn KE, Bravo B, Chugha P, Cohen F, Giannetti AM, Gibbons P, Hannoush RN, Hearn BR, Jaishankar P, Ly CQ, Shah K, Stanger K, Steffek M, Tang Y, Zhao X, Lewcock JW, Renslo AR, Flygare J, Arkin MR. Mechanistic and structural understanding of uncompetitive inhibitors of caspase-6. PLoS One. 2012; 7(12):e50864.
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  37. Gunatilleke SS, Calvet CM, Johnston JB, Chen CK, Erenburg G, Gut J, Engel JC, Ang KK, Mulvaney J, Chen S, Arkin MR, McKerrow JH, Podust LM. Diverse inhibitor chemotypes targeting Trypanosoma cruzi CYP51. PLoS Negl Trop Dis. 2012; 6(7):e1736.
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  38. Pu M, Hayashi T, Cottam H, Mulvaney J, Arkin M, Corr M, Carson D, Messer K. Analysis of high-throughput screening assays using cluster enrichment. Stat Med. 2012 Dec 30; 31(30):4175-89.
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  39. Rogers KE, Keränen H, Durrant JD, Ratnam J, Doak A, Arkin MR, McCammon JA. Novel cruzain inhibitors for the treatment of Chagas' disease. Chem Biol Drug Des. 2012 Sep; 80(3):398-405.
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  40. Wu VM, Chen SC, Arkin MR, Reiter JF. Small molecule inhibitors of Smoothened ciliary localization and ciliogenesis. Proc Natl Acad Sci U S A. 2012 Aug 21; 109(34):13644-9.
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  41. Debnath A, Parsonage D, Andrade RM, He C, Cobo ER, Hirata K, Chen S, García-Rivera G, Orozco E, Martínez MB, Gunatilleke SS, Barrios AM, Arkin MR, Poole LB, McKerrow JH, Reed SL. A high-throughput drug screen for Entamoeba histolytica identifies a new lead and target. Nat Med. 2012 Jun; 18(6):956-60.
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  42. Arkin MR, Connor PR, Emkey R, Garbison KE, Heinz BA, Wiernicki TR, Johnston PA, Kandasamy RA, Rankl NB, Sittampalam S. FLIPR Assays for GPCR and Ion Channel Targets. Assay Guidance Manual. 2012 May 01; 0.
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  43. Arkin MR, Glicksman MA, Fu H, Havel JJ, Du Y. Inhibition of Protein-Protein Interactions: Non-Cellular Assay Formats. Assay Guidance Manual. 2012 March 18; 0.
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  44. Zhong M, Gadek TR, Bui M, Shen W, Burnier J, Barr KJ, Hanan EJ, Oslob JD, Yu CH, Zhu J, Arkin MR, Evanchik MJ, Flanagan WM, Hoch U, Hyde J, Prabhu S, Silverman JA, Wright J. Discovery and Development of Potent LFA-1/ICAM-1 Antagonist SAR 1118 as an Ophthalmic Solution for Treating Dry Eye. ACS Med Chem Lett. 2012 January 31; 3(3):203-206.
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  45. Lee H, Moody-Davis A, Saha U, Suzuki BM, Asarnow D, Chen S, Arkin M, Caffrey CR, Singh R. Quantification and clustering of phenotypic screening data using time-series analysis for chemotherapy of schistosomiasis. BMC Genomics. 2012; 13 Suppl 1:S4.
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  46. Tang Y, Wells JA, Arkin MR. Structural and enzymatic insights into caspase-2 protein substrate recognition and catalysis. J Biol Chem. 2011 Sep 30; 286(39):34147-54.
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  47. De Muylder G, Ang KK, Chen S, Arkin MR, Engel JC, McKerrow JH. A screen against Leishmania intracellular amastigotes: comparison to a promastigote screen and identification of a host cell-specific hit. PLoS Negl Trop Dis. 2011 Jul; 5(7):e1253.
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  48. Ang KK, Ratnam J, Gut J, Legac J, Hansell E, Mackey ZB, Skrzypczynska KM, Debnath A, Engel JC, Rosenthal PJ, McKerrow JH, Arkin MR, Renslo AR. Mining a cathepsin inhibitor library for new antiparasitic drug leads. PLoS Negl Trop Dis. 2011; 5(5):e1023.
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  49. Ben Khalaf N, De Muylder G, Ratnam J, Kean-Hooi Ang K, Arkin M, McKerrow J, Chenik M. A high-throughput turbidometric assay for screening inhibitors of Leishmania major protein disulfide isomerase. J Biomol Screen. 2011 Jun; 16(5):545-51.
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  50. Gut J, Ang KK, Legac J, Arkin MR, Rosenthal PJ, McKerrow JH. An image-based assay for high throughput screening of Giardia lamblia. J Microbiol Methods. 2011 Mar; 84(3):398-405.
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  51. Wilson CG, Arkin MR. Small-molecule inhibitors of IL-2/IL-2R: lessons learned and applied. Curr Top Microbiol Immunol. 2011; 348:25-59.
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  52. Zhong M, Hanan EJ, Shen W, Bui M, Arkin MR, Barr KJ, Evanchik MJ, Hoch U, Hyde J, Martell JR, Oslob JD, Paulvannan K, Prabhu S, Silverman JA, Wright J, Yu CH, Zhu J, Flanagan WM. Structure-activity relationship (SAR) of the a-amino acid residue of potent tetrahydroisoquinoline (THIQ)-derived LFA-1/ICAM-1 antagonists. Bioorg Med Chem Lett. 2011 Jan 1; 21(1):307-10.
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  53. Zhong M, Shen W, Barr KJ, Arbitrario JP, Arkin MR, Bui M, Chen T, Cunningham BC, Evanchik MJ, Hanan EJ, Hoch U, Huen K, Hyde J, Kumer JL, Lac T, Lawrence CE, Martell JR, Oslob JD, Paulvannan K, Prabhu S, Silverman JA, Wright J, Yu CH, Zhu J, Flanagan WM. Discovery of tetrahydroisoquinoline (THIQ) derivatives as potent and orally bioavailable LFA-1/ICAM-1 antagonists. Bioorg Med Chem Lett. 2010 Sep 1; 20(17):5269-73.
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  54. Engel JC, Ang KK, Chen S, Arkin MR, McKerrow JH, Doyle PS. Image-based high-throughput drug screening targeting the intracellular stage of Trypanosoma cruzi, the agent of Chagas' disease. Antimicrob Agents Chemother. 2010 Aug; 54(8):3326-34.
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  55. Hawtin RE, Stockett DE, Byl JA, McDowell RS, Nguyen T, Arkin MR, Conroy A, Yang W, Osheroff N, Fox JA. Voreloxin is an anticancer quinolone derivative that intercalates DNA and poisons topoisomerase II. PLoS One. 2010; 5(4):e10186.
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  56. Mott BT, Ferreira RS, Simeonov A, Jadhav A, Ang KK, Leister W, Shen M, Silveira JT, Doyle PS, Arkin MR, McKerrow JH, Inglese J, Austin CP, Thomas CJ, Shoichet BK, Maloney DJ. Identification and optimization of inhibitors of Trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB. J Med Chem. 2010 Jan 14; 53(1):52-60.
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  57. Bryant C, Kerr ID, Debnath M, Ang KK, Ratnam J, Ferreira RS, Jaishankar P, Zhao D, Arkin MR, McKerrow JH, Brinen LS, Renslo AR. Novel non-peptidic vinylsulfones targeting the S2 and S3 subsites of parasite cysteine proteases. Bioorg Med Chem Lett. 2009 Nov 1; 19(21):6218-21.
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  58. McKerrow JH, Doyle PS, Engel JC, Podust LM, Robertson SA, Ferreira R, Saxton T, Arkin M, Kerr ID, Brinen LS, Craik CS. Two approaches to discovering and developing new drugs for Chagas disease. Mem Inst Oswaldo Cruz. 2009 Jul; 104 Suppl 1:263-9.
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  59. Arkin MR, Whitty A. The road less traveled: modulating signal transduction enzymes by inhibiting their protein-protein interactions. Curr Opin Chem Biol. 2009 Jun; 13(3):284-90.
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  60. Rubio BK, Tenney K, Ang KH, Abdulla M, Arkin M, McKerrow JH, Crews P. The marine sponge Diacarnus bismarckensis as a source of peroxiterpene inhibitors of Trypanosoma brucei, the causative agent of sleeping sickness. J Nat Prod. 2009 Feb 27; 72(2):218-22.
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  61. Conroy A, Stockett DE, Walker D, Arkin MR, Hoch U, Fox JA, Hawtin RE. SNS-032 is a potent and selective CDK 2, 7 and 9 inhibitor that drives target modulation in patient samples. Cancer Chemother Pharmacol. 2009 Sep; 64(4):723-32.
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  62. Arkin M, Moasser MM. HER-2-directed, small-molecule antagonists. Curr Opin Investig Drugs. 2008 Dec; 9(12):1264-76.
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  63. Choong IC, Serafimova I, Fan J, Stockett D, Chan E, Cheeti S, Lu Y, Fahr B, Pham P, Arkin MR, Walker DH, Hoch U. A diaminocyclohexyl analog of SNS-032 with improved permeability and bioavailability properties. Bioorg Med Chem Lett. 2008 Nov 1; 18(21):5763-5.
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  64. Arkin M. Protein-protein interactions and cancer: small molecules going in for the kill. Curr Opin Chem Biol. 2005 Jun; 9(3):317-24.
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  65. Waal ND, Yang W, Oslob JD, Arkin MR, Hyde J, Lu W, McDowell RS, Yu CH, Raimundo BC. Identification of nonpeptidic small-molecule inhibitors of interleukin-2. Bioorg Med Chem Lett. 2005 Feb 15; 15(4):983-7.
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  66. Raimundo BC, Oslob JD, Braisted AC, Hyde J, McDowell RS, Randal M, Waal ND, Wilkinson J, Yu CH, Arkin MR. Integrating fragment assembly and biophysical methods in the chemical advancement of small-molecule antagonists of IL-2: an approach for inhibiting protein-protein interactions. J Med Chem. 2004 Jun 3; 47(12):3111-30.
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  67. Arkin MR, Wells JA. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat Rev Drug Discov. 2004 Apr; 3(4):301-17.
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  68. Hyde J, Braisted AC, Randal M, Arkin MR. Discovery and characterization of cooperative ligand binding in the adaptive region of interleukin-2. Biochemistry. 2003 Jun 3; 42(21):6475-83.
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  69. Braisted AC, Oslob JD, Delano WL, Hyde J, McDowell RS, Waal N, Yu C, Arkin MR, Raimundo BC. Discovery of a potent small molecule IL-2 inhibitor through fragment assembly. J Am Chem Soc. 2003 Apr 2; 125(13):3714-5.
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  70. Arkin MR, Randal M, DeLano WL, Hyde J, Luong TN, Oslob JD, Raphael DR, Taylor L, Wang J, McDowell RS, Wells JA, Braisted AC. Binding of small molecules to an adaptive protein-protein interface. Proc Natl Acad Sci U S A. 2003 Feb 18; 100(4):1603-8.
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  71. Wells J, Arkin M, Braisted A, DeLano W, McDowell B, Oslob J, Raimundo B, Randal M. Drug discovery at signaling interfaces. Ernst Schering Res Found Workshop. 2003; (42):19-27.
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  72. Arkin M, Lear JD. A new data analysis method to determine binding constants of small molecules to proteins using equilibrium analytical ultracentrifugation with absorption optics. Anal Biochem. 2001 Dec 1; 299(1):98-107.
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  73. Arkin MR, Wells JA. Probing the importance of second sphere residues in an esterolytic antibody by phage display. J Mol Biol. 1998 Dec 11; 284(4):1083-94.
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  74. Arkin MR, Stemp ED, Pulver SC, Barton JK. Long-range oxidation of guanine by Ru(III) in duplex DNA. Chem Biol. 1997 May; 4(5):389-400.
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  75. Arkin MR, Stemp ED, Holmlin RE, Barton JK, Hörmann A, Olson EJ, Barbara PF. Rates of DNA-mediated electron transfer between metallointercalators. Science. 1996 Jul 26; 273(5274):475-80.
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  76. Murphy CJ, Arkin MR, Ghatlia ND, Bossmann S, Turro NJ, Barton JK. Fast photoinduced electron transfer through DNA intercalation. Proc Natl Acad Sci U S A. 1994 Jun 7; 91(12):5315-9.
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  77. Murphy CJ, Arkin MR, Jenkins Y, Ghatlia ND, Bossmann SH, Turro NJ, Barton JK. Long-range photoinduced electron transfer through a DNA helix. Science. 1993 Nov 12; 262(5136):1025-9.
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