Yeast as a tool to select inhibitors of the cullin deneddylating enzyme Csn5

References

• Yu Z, Kleifeld O, Lande-Atir A, et al. Dual function of Rpn5 in two PCI complexes, the 26S proteasome and COP9 signalosome. Mol Biol Cell 2011;22:911–20
   PubMed Web of Science ®Google Scholar
• Pick E, Golan A, Zimbler JZ, et al. The minimal deneddylase core of the COP9 signalosome excludes the Csn6 MPN-domain. PLoS One 2012;7:e43980
   PubMed Web of Science ®Google Scholar
• Pick E, Hofmann K, Glickman MH. PCI complexes: beyond the proteasome, CSN, and eIF3 Troika. Mol Cell 2009;35:260–4
   PubMed Web of Science ®Google Scholar
• Cope GA, Suh GS, Aravind L, et al. Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science 2002;298:608–11
   PubMed Web of Science ®Google Scholar
• Wee S, Hetfeld B, Dubiel W, Wolf DA. Conservation of the COP9/signalosome in budding yeast. BMC Genet 2002;3:15
   PubMed Web of Science ®Google Scholar
• Rabut G, Le Dez G, Verma R, et al. The TFIIH subunit Tfb3 regulates cullin neddylation. Mol Cell 2011;43:488–95
   PubMed Web of Science ®Google Scholar
• Maytal‐Kivity V, Piran R, et al. COP9 signalosome components play a role in the mating pheromone response of S. cerevisiae. EMBO Reports 2002;3:1215–21
   PubMed Web of Science ®Google Scholar
• Zemla A, Thomas Y, Kedziora S, et al. CSN- and CAND1-dependent remodelling of the budding yeast SCF complex. Nat Commun 2013;4:1641
   PubMed Web of Science ®Google Scholar
• Richardson KS, Zundel W. The emerging role of the COP9 signalosome in cancer. Mol Cancer Res 2005;3:645–53
   PubMed Web of Science ®Google Scholar
• Shackleford TJ, Claret FX. JAB1/CSN5: a new player in cell cycle control and cancer. Cell Division 2010;5:26
   PubMed Web of Science ®Google Scholar
• Adler AS, Littlepage LE, Lin M, et al. CSN5 isopeptidase activity links COP9 signalosome activation to breast cancer progression. Cancer Res 2008;68:506–15
   PubMed Web of Science ®Google Scholar
• Adler AS, Lin M, Horlings H, et al. Genetic regulators of large-scale transcriptional signatures in cancer. Nat Genet 2006;38:421–30
   PubMed Web of Science ®Google Scholar
• Tomoda K, Kubota Y, Kato JY. Degradation of the cyclin-dependent-kinase inhibitor p27Kip1 is instigated by Jab1. Nature 1999;398:160–5
   PubMed Web of Science ®Google Scholar
• Pan Y, Zhang Q, Tian L, et al. Jab1/CSN5 negatively regulates p27 and plays a role in the pathogenesis of nasopharyngeal carcinoma. Cancer Res 2012;72:1890–900
   PubMed Web of Science ®Google Scholar
• Pick E, Bramasole L. Moonlighting and pleiotropy within two regulators of the degradation machinery: the proteasome lid and the CSN. Biochem Soc Trans 2014;42:1786–91
   PubMed Web of Science ®Google Scholar
• Bae MK, Ahn MY, Jeong JW, et al. Jab1 interacts directly with HIF-1alpha and regulates its stability. J Biol Chem 2002;277:9–12
   PubMed Web of Science ®Google Scholar
• Luo Z, Yu G, Lee HW, et al. The Nedd8-activating enzyme inhibitor MLN4924 induces autophagy and apoptosis to suppress liver cancer cell growth. Cancer Res 2012;72:3360–71
   PubMed Web of Science ®Google Scholar
• Abidi N, Xirodimas DP. Regulation of cancer-related pathways by protein NEDDylation and strategies for the use of NEDD8 inhibitors in the clinic. Endocr-Relat Cancer 2015;22:T55–70
   PubMed Web of Science ®Google Scholar
• Mori M, Yoneda-Kato N, Yoshida A, Kato JY. Stable form of JAB1 enhances proliferation and maintenance of hematopoietic progenitors. J Biol Chem 2008;283:29011–21
   PubMed Web of Science ®Google Scholar
• Pulvino M, Chen L, Oleksyn D, et al. Inhibition of COP9-signalosome (CSN) deneddylating activity and tumor growth of diffuse large B-cell lymphomas by doxycycline. Oncotarget 2015;6:14796
   PubMed Web of Science ®Google Scholar
• Cope GA, Deshaies RJ. COP9 signalosome: a multifunctional regulator of SCF and other cullin-based ubiquitin ligases. Cell 2003;114:663–71
   PubMed Web of Science ®Google Scholar
• Lyapina S, Cope G, Shevchenko A, et al. Promotion of NEDD-CUL1 conjugate cleavage by COP9 signalosome. Science 2001;292:1382–5
   PubMed Web of Science ®Google Scholar
• Ambroggio XL, Rees DC, Deshaies R. J. JAMM: a metalloprotease-like zinc site in the proteasome and signalosome. PLoS Biol 2004;2:E2
   PubMed Web of Science ®Google Scholar
• Echalier A, Pan Y, Birol M, et al. Insights into the regulation of the human COP9 signalosome catalytic subunit, CSN5/Jab1. Proc Natl Acad Sci USA 2013;110:1273–8
   PubMed Web of Science ®Google Scholar
• Tran HJ, Allen MD, Löwe J, Bycroft M. Structure of the Jab1/MPN domain and its implications for proteasome function. Biochemistry 2003;42:11460–5
   PubMed Web of Science ®Google Scholar
• Lingaraju GM, Bunker RD, Cavadini S, et al. Crystal structure of the human COP9 signalosome. Nature 2014;512:161–5
   PubMed Web of Science ®Google Scholar
• Infante P, Mori M, Alfonsi R, et al. Gli1/DNA interaction is a druggable target for Hedgehog-dependent tumors. EMBO J 2015;34:200–17
   PubMed Web of Science ®Google Scholar
• Mascarello A, Mori M, Chiaradia-Delatorre LD, et al. Discovery of Mycobacterium tuberculosis protein tyrosine phosphatase B (PtpB) inhibitors from natural products. PLoS One 2013;8:e77081
   PubMed Web of Science ®Google Scholar
• Congreve M, Carr R, Murray C, Jhoti H. A ‘rule of three’ for fragment-based lead discovery? Drug Discov Today 2003;8:876–7
   PubMed Web of Science ®Google Scholar
• Day JA, Cohen SM. Investigating the selectivity of metalloenzyme inhibitors. J Med Chem 2013;56:7997–8007
   PubMed Web of Science ®Google Scholar
• FRED, version 3.0.1. OpenEye scientific coftware, Santa Fe, NM. Available from: http://www.eyesopen.com [last accessed 25 Feb 2016]
   Google Scholar
• McGann M. FRED pose prediction and virtual screening accuracy. J Chem Inf Model 2011;51:578–96
   PubMed Web of Science ®Google Scholar
• McGann M. FRED and HYBRID docking performance on standardized datasets. J Comput Aided Mol Des 2012;26:897–906
   PubMed Web of Science ®Google Scholar
• Licursi V, Salvi C, De Cesare V, et al. The COP9 signalosome is involved in the regulation of lipid metabolism and of transition metals uptake in Saccharomyces cerevisiae. FEBS J 2014;281:175–90
   PubMed Web of Science ®Google Scholar
• Nielsen TK, Hildmann C, Dickmanns A, et al. Crystal structure of a bacterial class 2 histone deacetylase homologue. J Mol Biol 2005;354:107–20
   PubMed Web of Science ®Google Scholar
• Holmes IP, Gaines S, Watson SP, et al. The identification of β-hydroxy carboxylic acids as selective MMP-12 inhibitors. Bioorg Med Chem Lett 2009;19:5760–3
   PubMed Web of Science ®Google Scholar
• Bertini I, Calderone V, Fragai M, et al. X‐ray structures of binary and ternary enzyme‐product‐inhibitor complexes of matrix metalloproteinases. Angew Chem 2003;115:2777–80
   Google Scholar
• Mori M, Massaro A, Calderone V, et al. Discovery of a new class of potent MMP inhibitors by structure-based optimization of the arylsulfonamide scaffold. ACS Med Chem Lett 2013;4:565–9
   PubMed Web of Science ®Google Scholar
• Panina NS, Belyaev AN, Simanova SA. Carboxylic acids and their anions. Acid and ligand properties. Russ J Gen Chem 2002;72:91–4
   Web of Science ®Google Scholar
• Rinaldi T, Ricci C, Porro D, et al. A mutation in a novel yeast proteasomal gene, RPN11/MPR1, produces a cell cycle arrest, overreplication of nuclear and mitochondrial DNA, and an altered mitochondrial morphology. MBC 1998;9:2917–31
   PubMed Web of Science ®Google Scholar
• Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970;227:680–5
   PubMed Web of Science ®Google Scholar
• Shivakumar D, Williams J, Wu Y, et al. Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J Chem Theory Comput 2010;6:1509–19
   PubMed Web of Science ®Google Scholar
• Bowers KJ, Chow E, Xu H, et al. Scalable algorithms for molecular dynamics simulations on commodity clusters. Conference, Proceedings of the ACM/IEEE on Supercomputing, 2006, p. 43
   Google Scholar
• OEDocking 3.0.1: OpenEye Scientific Software, Santa Fe, NM. Available from: http://www.eyesopen.com [last accessed 25 Feb 2016]
   Google Scholar
• FILTER 2.5.1.4: OpenEye Scientific Software, Santa Fe, NM. Available from: http://www.eyesopen.com [last accessed 25 Feb 2016].
   Google Scholar
• QUACPAC 1.5.0: OpenEye Scientific Software, Santa Fe, NM. Available from: http://www.eyesopen.com [last accessed 25 Feb 2016]
   Google Scholar
• OMEGA2 2.4.6: OpenEye Scientific Software, Santa Fe, NM. Available from: http://www.eyesopen.com [last accessed 25 Feb 2016]
   Google Scholar
• Hawkins PC, Skillman AG, Warren GL, et al. Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database. J Chem Inf Model 2010;50:572–84
   PubMed Web of Science ®Google Scholar
• MarvinSketch 6.1.4: ChemAxon. Available from: http://www.chemaxon.com [last accessed 25 Feb 2016]
   Google Scholar
• Case DA, Darden TA, Cheatham TE, et al. AMBER 12; University of California, San Francisco, 2012
   Google Scholar