CEMCE publications 2017

1.  Mutso, M., Saul, S., Rausalu, K., Susova, O., Žusinaite, E., Mahalingam, S. and Merits, A. (2017). Reverse genetic system, genetically stable reporter viruses and packaged subgenomic replicon based on Brazilian Zika virus isolate. Journal of General Virology, 98, 2712-2724. doi: 10.1099/jgv.0.000938
2. Teo, T.H., Chan, Y.H., Lee, W.W., Lum, F.M., Amrun, S.N., Her, Z., Rajarethinam, R., Merits, A., Rötzschke, O., Rénia, L. and Ng, L.F. (2017). Fingolimod treatment abrogates chikungunya virus-induced arthralgia. Sci Transl Med., 9, pii: eaal1333. doi: 10.1126/scitranslmed.aal1333. 
3. Ehteshami, M., Tao, S., Zandi, K., Hsiao, H.M., Jiang, Y., Hammond, E., Amblard, F., Russell, O.O., Merits, A. and Schinazi, R.F. (2017). Characterization of β-D-N4-hydroxycytidine as a novel inhibitor of Chikungunya virus. Antimicrob Agents Chemother. 61(4). pii: e02395-16. doi: 10.1128/AAC.02395-16. 
4. Wichit, S., Hamel, R., Bernard, E., Talignani, L., Diop, F., Ferraris, P., Liegeois, F., Ekchariyawat, P., Luplertlop, N., Surasombatpattana, P., Thomas, F., Merits, A., Choumet, V., Roques, P., Yssel, H., Briant, L. and Misse, D. (2017). Imipramine inhibits chikungunya virus replication in human skin fibroblasts through interference with intracellular cholesterol trafficking. Scientific Reports, 7(1):3145. doi: 10.1038/s41598-017-03316-5. 
5. Oo, A., Rausalu, K., Merits, A., Higgs, S., Vanlandingham, D., Abu Bakar, S. and Zandi, K. (2017). Deciphering the potential of baicalin as an antiviral agent for Chikungunya virus infection. Antiviral Research, 150:101-111. doi: 10.1016/j.antiviral.2017.12.012. 
6. Lum, F.-M., Lin, C., Susova, O.Y, Teo, T.-H., Fong, S.-W., Mak, T.-M., Lee, L.K., Chong, C.-Y., Lye, D.C.B., Lin, R.T.P., Merits, A., Leo, Y.-S. and Ng, L.F.P. (2017). Sensitive detection of Zika virus antigen in patients’ whole blood as an alternative diagnostic approach. The Journal of Infectious Diseases, 216, 182-190. doi: 10.1093/infdis/jix276.
7. Hellström, K., Kallio, K., Utt, A., Quirin, T., Jokitalo, E., Merits, A. and Ahola, T. (2017). Partially uncleaved alphavirus replicase forms spherule structures in the presence and absence of RNA template. Journal of Virology, 91, pii: e00787-17. doi: 10.1128/JVI.00787-17. Print 2017 Sep 15. 
8. Sankovski, E.; Abroi, A.; Ustav, M. Jr; Ustav, M.; (2017). Nuclear myosin 1 associates with papillomavirus E2 regulatory protein and influences viral replication. Virology, 514, 142−155.j.virol.2017.11.013. 
9. Toots, M.; Ustav, M. Jr.; Männik, A.; Mumm, K.; Tämm, K.; Tamm, T.; Ustav, E.; Ustav, M. (2017). Identification of several high-risk HPV inhibitors and drug targets with a novel high-throughput screening assay. PLoS Pathogens, 13 (2), e1006168.10.1371/journal.ppat.1006168. 
10. Todorova B, Adam L, Culina S, Boisgard R, Martinon F, Cosma A, Ustav M, Kortulewski T, Le Grand R, Chapon C. Electroporation as a vaccine delivery system and a natural adjuvant to intradermal administration of plasmid DNA in macaques. Sci Rep. 2017 Jun 23;7(1):4122. doi: 10.1038/s41598-017-04547-2. 
11. Henno L, Tombak EM, Geimanen J, Orav M, Ustav E, Ustav M.Analysis of Human Papillomavirus Genome Replication Using Two- and Three-Dimensional Agarose Gel Electrophoresis.  Curr Protoc Microbiol. 2017 May 16;45:14B.10.1-14B.10.37. doi: 10.1002/cpmc.28. 
12. Viira, B.; García-Sosa, A. T.; Maran, U. Chemical Structure and Correlation Analysis of HIV-1 NNRT and NRT Inhibitors and Database-Curated, Published Inhibition Constants with Chemical Structure in Diverse Datasets. J. Mol. Graph. Model. 2017, 76, 205-223. 
13. Dowaidar, M.; Regberg, J.; Dobchev, D.A.; Lehto, T.; Hallbrink, M.; Karelson, M.; Langel, U., Refinement of a Quantitative Structure-Activity Relationship Model for Prediction of Cell-Penetrating Peptide Based Transfection Systems, Int. J. Peptide Res. Ther., 2017, 23, 91-100.
14. Sidorova, Y.A.; Bespalov, M.M., Wong, A.W.; Kambur, O.; Jokinen, V.; Lilius, T.O.; Suleymanova, I.; Karelson, G.; Rauhala, P.V.; Karelson, M., Osborne, P.B.; Keast, J.R.; Kalso, E.A.; Saarma M. A novel small molecule GDNF receptor RET agonist, BT13, promotes neurite growth from sensory neurons in vitro and attenuates experimental neuropathy in the rat, Frontiers in Pharmacology, 2017, 8, 365. 
15. Sidorov, P.; Viira, B.; Davioud-Charvet, E.; Maran, U.; Marcou, G.; Horvath, D.; Varnek, A. QSAR modeling and chemical space analysis of antimalarial compounds. J. Comp. Aided. Mol. 2017, 31, 441-451. DOI: 10.1007/s10822-017-0019-4. 
16. Tetko, I. V.; Maran, U.; Tropsha A. Public (Q)SAR services, integrated modeling environments, and molecular repositories on the web: state of the art and perspectives for future development. Mol. Inf. 2017, 35, 1600082. DOI: 10.1002/minf.201600082 
17. Olsson, M.A.; Garcia-Sosa, A.T.; Ryde, U., Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking. J. Comput-Aided Mol. Design, DOI:10.1007/s10822-017-0056-z (Epub 2017 Sep 06)   
18. Linke C, Chasapi A, González-Novo A, Al Sawad I, Tognetti S, Klipp E, Loog M, Krobitsch S, Posas F, Xenarios I, Barberis M. A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle. NPJ Syst Biol Appl. 2017 Mar 6;3:7. doi: 10.1038/s41540-017-0008-1. 
19. Goldstein A, Siegler N, Goldman D, Judah H, Valk E, Kõivomägi M, Loog M, Gheber L.Three Cdk1 sites in the kinesin-5 Cin8 catalytic domain coordinate motor localization and activity during anaphase. Cell Mol Life Sci. 2017 Sep;74(18):3395-3412. doi: 10.1007/s00018-017-2523-z. 
20. Huter P, Arenz S, Bock LV, Graf M, Frister JO, Heuer A, Peil L, Starosta AL, Wohlgemuth I, Peske F, Nováček J, Berninghausen O, Grubmüller H, Tenson T, Beckmann R, Rodnina MV, Vaiana AC, Wilson DN. (2017). Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P. Mol Cell; 68(3):515-527.e6. doi: 10.1016/j.molcel.2017.10.014. 
21. Varik V, Oliveira SRA, Hauryliuk V, Tenson T. (2017). HPLC-based quantification of bacterial housekeeping nucleotides and alarmone messengers ppGpp and pppGpp.Sci Rep.; 7(1):11022. doi: 10.1038/s41598-017-10988-6. 
22. Pärnaste L, Arukuusk P, Langel K, Tenson T, Langel Ü. (2017). The Formation of Nanoparticles between Small Interfering RNA and Amphipathic Cell-Penetrating Peptides. Mol Ther Nucleic Acids.; 7:1-10. doi: 10.1016/j.omtn.2017.02.003. 
23. Beljantseva J, Kudrin P, Andresen L, Shingler V, Atkinson GC, Tenson T, Hauryliuk V. (2017). Negative allosteric regulation of Enterococcus faecalis small alarmone synthetase RelQ by single-stranded RNA. Proc Natl Acad Sci U S A.; 114(14):3726-3731. doi: 10.1073/pnas.1617868114. 
24. Beljantseva J, Kudrin P, Jimmy S, Ehn M, Pohl R, Varik V, Tozawa Y, Shingler V, Tenson T, Rejman D, Hauryliuk V. (2017). Molecular mutagenesis of ppGpp: turning a RelA activator into an inhibitor. Sci Rep.; 7:41839. doi: 10.1038/srep41839. 
25. Kudrin P, Varik V, Oliveira SR, Beljantseva J, Del Peso Santos T, Dzhygyr I, Rejman D, Cava F, Tenson T, Hauryliuk V. (2017). Subinhibitory Concentrations of Bacteriostatic Antibiotics Induce relA-Dependent and relA-Independent Tolerance to β-Lactams. Antimicrob Agents Chemother.; 61(4). pii: e02173-16. doi: 10.1128/AAC.02173-16. 
26. Mets T, Lippus M, Schryer D, Liiv A, Kasari V, Paier A, Maiväli Ü, Remme J, Tenson T, Kaldalu N. (2017). Toxins MazF and MqsR cleave Escherichia coli rRNA precursors at multiple sites. RNA Biol.; 14(1):124-135. doi: 10.1080/15476286.2016.1259784. 
27. Preem L, Mahmoudzadeh M, Putrinš M, Meos A, Laidmäe I, Romann T, Aruväli J, Härmas R, Koivuniemi A, Bunker A, Tenson T, Kogermann K. (2017). Interactions between Chloramphenicol, Carrier Polymers, and Bacteria-Implications for Designing Electrospun Drug Delivery Systems Countering Wound Infection. Mol Pharm.; 14(12):4417-4430. doi: 10.1021/acs.molpharmaceut.7b00524. 
28. Shim JM, Kim J, Tenson T, Min JY, Kainov DE. (2017). Influenza Virus Infection, Interferon Response, Viral Counter-Response, and Apoptosis.Viruses.; 9(8). pii: E223. doi: 10.3390/v9080223. Review. 
29. Konik, Y.; Elek, G. Z.; Kaabel, S.; Järving, I.; Lopp, M.; Kananovich, D. Synthesis of gamma-keto sulfones by copper-catalyzed oxidative sulfonylation of tertiary cyclopropanols Organic & Biomolecular Chemistry, 2017, v. 15, p. 8334-8340.
30. Elek, G. Z.; Borovkov, V.; Lopp, M.; Kananovich, D. G. Enantioselective One-Pot Synthesis of alpha,beta-Epoxy Ketones via Aerobic Oxidation of Cyclopropanols. Organic Lett., 2017, v. 19, p. 3544-3547. 
31. Preegel, G.; Silm, E.; Kaabel, S.; Järving, I.; Rissanen, K.; Lopp, M.. Asymmetric Organocatalytic Michael Addition-Cyclization Cascade of Cyclopentane-1,2-dione with Substituted alpha,beta-Unsaturated Aldehydes. Synthesis, 2017, v.49, p. 3118-3125. 
32. Konik, Y.; Kudrjashova, M.; Konrad, N.; Kaabel, S.; Järving, I.; Lopp, M.; Kananovich, D.. Two-step conversion of carboxylic esters into distally fluorinated ketones via ring cleavage of cyclopropanol intermediates: application of sulfinate salts as fluoroalkylating reagents. Organic and Biomolecular Chem., 2017, v. 15, p. 4635-4643. 
33. Metsala, A.; Žari, S.; Kanger, T.. Reaction path scans: Aza-Michael reactions of isatin Imines. Computational and Theoretical Chemistry, 2017, 1117, 30–40.
34. Kaasik, M.; Kaabel, S.; Kriis, K.; Järving, I.; Aav, R.; Rissanen, K.; Kanger, T.. Synthesis and Characterisation of Chiral Triazole-Based Halogen-Bond Donors: Halogen Bonds in the Solid State and in Solution. Chem. Eur. J. 2017, 23, 7337 – 7344. 
35. Ošeka, M.; Kimm, M.; Järving, I.; Lippur, K.; Kanger, T.. Two Catalytic Methods of an Asymmetric Wittig [2,3]-Rearrangement. J. Org. Chem., 2017, 82, 2889−2897.
36. Kriis, K.; Melnik, T.; Lips, K.; Juhanson, I.; Kaabel, S.; Järving, I.; Kanger, T. Asymmetric Synthesis of 2,3,4-Trisubstituted Piperidines. Synthesis, 2017, 49, 604-614. 
37. Fomitsenko, M.; Peterson, A.; Reile, I.; Cong, H.; Kaabel, S.; Prigorchenko, E.; Järving, I.; Aav, R.. A quantitative method for analysis of mixtures of homologues and stereoisomers of hemicucurbiturils that allows us to follow their formation and stability. New J. Chem., 2017,v. 41, p. 2490-2497. 
38. Kaabel, S.; Adamson, J.; Topic, F.; Kiesila, A.; Kalenius, E.; Oeren, M.; Reimund, M.; Prigorchenko, E.; Lõokene, A.; Reich, H.; Rissanen, K.; Aav, R.. Chiral hemicucurbit[8]uril as an anion receptor: selectivity to size, shape and charge distribution. Chemical Science, 2017, v. 8, p. 2184-2190.
39. Jalakas, P.; Huang, Y-C.; Yeh, Y-H.; Zimmerli, L.; Merilo, E.; Kollist, H.; Brosche, M. (2017). The role of ENHANCED RESPONSES TO ABA1 (ERA1) in Arabidopsis stomatal responses is beyond ABA signaling. Plant Physiology, 174 (2), 665−671.10.1104/pp.17.00220.
40. Vaidya, A.S.; Peterson, F.C.; Yarmolinsky, D.; Merilo, E.; Verstraeten, I.; Park, S.Y.; Elzinga, D.; Kaundal, A.; Helander, J.; Lozano-Juste, J.; Otani, M.; Wu, K.; Jensen, D.R.; Kollist, H.; Volkman, B.F.; Cutler, S.R. (2017). A Rationally Designed Agonist Defines Subfamily IIIA Abscisic Acid Receptors As Critical Targets for Manipulating Transpiration. ACS Chemical Biology, 12: 2842-2848; DOI: 10.1021/acschembio.7b00650. 
41. Horak, H.; Kollist, H.; Merilo, E. (2017). Fern Stomatal Responses to ABA and CO2 Depend on Species and Growth Conditions. Plant Physiology, 174: 672-679. DOI: 10.1104/pp.17.00120. 
42. Jalakas, P., Yarmolinsky, D., Kollist, H. and Brosche, M. (2017). Isolation of Guard-cell Enriched Tissue for RNA Extraction. Bio-protocol 7(15): e2447. DOI: 10.21769/BioProtoc.2447. 
43. Kurrikoff K, Veiman KL, Künnapuu K, Peets EM, Lehto T, Pärnaste L, Arukuusk P, Langel Ü. Effective in vivo gene delivery with reduced toxicity, achieved by charge and fatty acid -modified cell penetrating peptide. Sci Rep. 2017 Dec 6;7(1):17056. doi: 10.1038/s41598-017-17316-y. PMID: 29213085
44. Krõlov K, Uusna J, Grellier T, Andresen L, Jevtuševskaja J, Tulp I, Langel Ü. Implementation of antimicrobial peptides for sample preparation prior to nucleic acid amplification in point-of-care settings. Expert Rev Mol Diagn. 2017 Dec;17(12):1117-1125. doi:   10.1080/14737159.2017.1386557. Epub 2017 Oct 9. PMID: 28965426
45. Dowaidar M, Gestin M, Cerrato CP, Jafferali MH, Margus H, Kivistik PA, Ezzat K, Hallberg E, Pooga M, Hällbrink M, Langel Ü. Role of autophagy in cell-penetrating peptide transfection model. Sci Rep. 2017 Oct 3;7(1):12635. doi: 10.1038/s41598-017-12747-z. PMID: 28974718 
46. Urgard E, Brjalin A, Langel Ü, Pooga M, Rebane A, Annilo T. Comparison of Peptide- and Lipid-Based Delivery of miR-34a-5p Mimic into PPC-1 Cells. Nucleic Acid Ther. 2017 Oct;27(5):295-302. doi: 10.1089/nat.2017.0670. Epub 2017 Jun 28. PMID: 28657476 
47. Vasconcelos L, Lehto T, Madani F, Radoi V, Hällbrink M, Vukojević V, Langel Ü.  Simultaneous membrane interaction of amphipathic peptide monomers, self-aggregates and cargo complexes detected by fluorescence correlation spectroscopy. Biochim Biophys Acta. 2017 Sep 28;1860(2):491-504. doi: 10.1016/j.bbamem.2017.09.024. [Epub ahead of print] PMID: 28962904 
48. Dowaidar M, Abdelhamid HN, Hällbrink M, Freimann K, Kurrikoff K, Zou X, Langel Ü. Magnetic Nanoparticle Assisted Self-assembly of Cell Penetrating Peptides-Oligonucleotides Complexes for Gene Delivery. Sci Rep. 2017 Aug 22;7(1):9159. doi: 10.1038/s41598-017-09803-z. PMID: 28831162 
49. Ly Pärnaste, Piret Arukuusk, Kent Langel, Tanel Tenson, Ülo Langel The formation of nanoparticles between small interfering RNA and amphipathic cell-penetrating peptiides Molecular Therapy – Nucleic Acids 
50. Cerrato CP, Langel Ü.  Effect of a Fusion Peptide by Covalent Conjugation of a Mitochondrial Cell-Penetrating Peptide and a Glutathione Analog Peptide. Mol Ther Methods Clin Dev. 2017 May 4;5:221-231. doi: 10.1016/j.omtm.2017.04.010. eCollection 2017 Jun 16. PMID: 28567432 
51. Jevtuševskaja J, Krõlov K, Tulp I, Langel Ü. The effect of main urine inhibitors on the activity of different DNA polymerases in loop-mediated isothermal amplification Expert Rev Mol Diagn. 2017 Jan 29:1-8. doi: 10.1080/14737159.2017.1283218. [Epub ahead of print] PMID: 28092481 
52. Lehto T, Vasconcelos L, Margus H, Figueroa R, Pooga M, Hällbrink M, Langel Ü. Saturated Fatty Acid Analogues of Cell-Penetrating Peptide PepFect14: Role of Fatty Acid Modification in Complexation and Delivery of Splice-Correcting Oligonucleotides. Bioconjug Chem. 2017 Mar 15;28(3):782-792. doi: 10.1021/acs.bioconjchem.6b00680. Epub 2017 Mar 2. PMID: 28209057 
53. Cerrato CP, Künnapuu K, Langel Ü. Cell-penetrating peptides with intracellular organelle targeting. Expert Opin Drug Deliv. 2017 Feb;14(2):245-255. doi: 10.1080/17425247.2016.1213237. PMID: 27426871 (11) (viide eelmisele tippkeskusele)
54. Gestin M, Dowaidar M, Langel Ü. Uptake Mechanism of Cell-Penetrating Peptides. Adv Exp Med Biol. 2017;1030:255-264. doi: 10.1007/978-3-319-66095-0_11. PMID: 29081057
55. DowaidarM, Regberg J, Dobchev DA, Lehto T, Hällbrink M, Karelson M, Langel Ü  Refinement of a Quantitative Structure–Activity Relationship Model for Prediction of Cell-Penetrating Peptide Based Transfection Systems International Journal of Peptide Research and Therapeutics March 2017, Volume 23, Issue 1, pp 91–100 
56. Lee, D.J.; Kessel, E.; Lehto, T.; Liu, X.; Yoshinaga, N.; Padari, K.; Chen, Y.C.; Kempter, S.; Uchida, S.; Rädler, J.; Pooga, M.; Sheu, M.T.; Kataoka, K.; Wagner, E. (2017) Systemic delivery of Folate-PEG siRNA Lipopolyplexes with Enhanced Intracellular Stability for in vivo Gene Silencing in Leukemia. Bioconjugate Chemistry 28(9), 2393-2409.
57. Ruisu, K.; Meier, R.; Kask, K.; Tõnissoo, T., Velling, T.; Pooga, M. (2017) RIC8A is essential for the organisation of actin cytoskeleton and cell-matrix interaction, Experimental Cell Research, 357(2), 181-191.
58. Lulla, V., Karo-Astover, L., Rausalu, K., Saul, S., Merits, A. and Lulla, A. (2018) Timeliness of proteolytic events is prerequisite for efficient functioning of the alphaviral replicase. Journal of Virology, pii: JVI.00151-18. doi: 10.1128/JVI.00151-18.
59. Bartholomeeusen, K., Utt, A., Coppens, S., Rausalu, K., Vereecken, K., Ariën, K.K. and Merits, A. (2018). A Chikungunya virus trans-replicase system reveals the importance of delayed non-structural polyprotein processing for efficient replication complex formation in mosquito cells. Journal of Virology, pii: JVI.00152-18. doi: 10.1128/JVI.00152-18.
60. Mutso, M., Morro, A.M., Smedberg, C., Kasvandik, S., Aquilimeba, M., Teppor, M., Tarve, L., Lulla, A., Lulla, V., Saul, S., Thaa, B., McInerney, G.M., Merits, A. and Varjak, M. (2018). Mutation of CD2AP and SH3KBP1 binding motif in alphavirus nsP3 hypervariable domain results in attenuated virus. Viruses. 10(5). pii: E226. doi: 10.3390/v10050226.