Chemical Probes Review: Choosing the Right Path Towards Pharmacological Targets in Drug Discovery, Challenges and Future Perspectives


Цитировать

Полный текст

Аннотация

:Chemical probes are essential for academic research and target validation for disease identification. They facilitate drug discovery, target function investigation, and translation studies. A chemical probe provides starting material that can accelerate therapeutic values and safety measures for identifying any biological target in drug discovery. Essential read outs depend on their versatility in biochemical testing, proving the hypothesis, selectivity, specificity, affinity towards the target site, and valuable in new therapeutic approaches. Disease management will depend upon chemical probes as a primitive tool to ascertain the physicochemical stability for in vivo and in vitro studies useful for clinical trials and industrial application in the future. For cancer research, bacterial infection, and neurodegenerative disorders, chemical probes are integrated circuits which are on pipeline for the drug discovery process Furthermore, pharmacological modulators incorporate activators, crosslinkers, degraders, and inhibitors. Reports accessed depend on their structural, mechanical, biochemical, and pharmacological characterization in drug discovery research. The perspective for designing any chemical probes concludes with the utilization of drug discovery and identification of the potential target. It focuses mainly on evidence-based studies and produces promising results in successfully delivering novel therapeutics to treat cancers and other disorders at the target site. Moreover, natural product pharmacophores like rapamycin, cephalosporin, and β-lactamase are utilized for drug discovery. Chemical probes revolutionize computational-based study design depending on identifying novel targets within the database framework. Chemical probes are the clinical answers for drug development and goforward tools in solving other riddles for scientists and researchers working in this industries.

Об авторах

Ashima Ahuja

Institute of Pharmaceutical Research, GLA University

Автор, ответственный за переписку.
Email: info@benthamscience.net

Sonia Singh

Institute of Pharmaceutical Research,, GLA University

Email: info@benthamscience.net

Yogesh Murti

Institute of Pharmaceutical Research, GLA University

Email: info@benthamscience.net

Список литературы

  1. Stark, H. The chemical probe – scopes, limitations and challenges. Expert Opin. Drug Discov., 2020, 15(12), 1365-1367. doi: 10.1080/17460441.2020.1781086 PMID: 32551991
  2. Litterman, N.K.; Lipinski, C.A.; Bunin, B.A.; Ekins, S. Computational prediction and validation of an expert’s evaluation of chemical probes. J. Chem. Inf. Model., 2014, 54(10), 2996-3004. doi: 10.1021/ci500445u PMID: 25244007
  3. Advancing Biomedical Research with Quality Chemical Probes. Advancing Biomedical Research with Quality Chemical Probes. Available from: https://www.promega.in/resources/pubhub/features/advancing-biomedical-research-with-quality-chemical-probes/
  4. Bunnage, M.E.; Chekler, E.L.P.; Jones, L.H. Target validation using chemical probes. Nat. Chem. Biol., 2013, 9(4), 195-199. doi: 10.1038/nchembio.1197 PMID: 23508172
  5. Wagner, BK CHAPTER 1: Introduction to chemical probes, in the discovery and utility of chemical probes in target discovery 2020, 1-13.
  6. Cohen, P. Guidelines for the effective use of chemical inhibitors of protein function to understand their roles in cell regulation. Biochem. J., 2010, 425(1), 53-54. doi: 10.1042/BJ20091428 PMID: 20001962
  7. Davies, S.P.; Reddy, H.; Caivano, M.; Cohen, P. Specificity and mechanism of action of some commonly used protein kinase inhibitors. Biochem. J., 2000, 351(1), 95-105. doi: 10.1042/bj3510095 PMID: 10998351
  8. Edwards, A.M.; Bountra, C.; Kerr, D.J.; Willson, T.M. Open access chemical and clinical probes to support drug discovery. Nat. Chem. Biol., 2009, 5(7), 436-440. doi: 10.1038/nchembio0709-436 PMID: 19536100
  9. Boyce, S.; Hill, R.G. Proceedings of the 9th world congress on pain, 2000, pp. 313-324.
  10. Euler, V. U.S. in neurotransmitters in action; Bousfield, D., Ed.; Elsevier Biomedical Press: Amsterdam, 1985, pp. 143-150.
  11. Weigelt, J.; McBroom-Cerajewski, L.D.B.; Schapira, M.; Zhao, Y.; Arrowmsmith, C.H. Structural genomics and drug discovery: All in the family. Curr. Opin. Chem. Biol., 2008, 12(1), 32-39. doi: 10.1016/j.cbpa.2008.01.045 PMID: 18282486
  12. Workman, P.; Collins, I. Probing the probes: Fitness factors for small molecule tools. Chem. Biol., 2010, 17(6), 561-577. doi: 10.1016/j.chembiol.2010.05.013 PMID: 20609406
  13. Albert, A. Objective, quantitative, data-driven assessment of chemical probes. Cell Chem. Biol., 2018, 25, 194-205. doi: 10.1016/j.chembiol.2017.11.004 PMID: 29249694
  14. Dowling, J.E.; Chuaqui, C.; Pontz, T.W.; Lyne, P.D.; Larsen, N.A.; Block, M.H.; Chen, H.; Su, N.; Wu, A.; Russell, D.; Pollard, H.; Lee, J.W.; Peng, B.; Thakur, K.; Ye, Q.; Zhang, T.; Brassil, P.; Racicot, V.; Bao, L.; Denz, C.R.; Cooke, E. Potent and selective inhibitors of CK2 kinase identified through structure-guided hybridization. ACS Med. Chem. Lett., 2012, 3(4), 278-283. doi: 10.1021/ml200257n PMID: 24900464
  15. Zhou, Y.; Zhang, N.; Tang, S.; Qi, X.; Zhao, L.; Zhong, R.; Peng, Y. Exploring the pivotal role of the CK2 hinge region sub-pocket in binding with tricyclic quinolone analogues by computational analysis. Molecules, 2017, 22(5), 840. doi: 10.3390/molecules22050840 PMID: 28534839
  16. Knapp, S.; Arruda, P.; Blagg, J.; Burley, S.; David, H. Drewry; Edwards, Aled.; Fabbro, Doriano.; Gillespie, Paul.; Gray, Nathanael S.; Kuster, Bernhard.; Lackey, Karen E; Mazzafera, Paulo.; Tomkinson, Nicholas C O.; Willson, Timothy M.; Gray, Paul; J Zuercher, William. A public-private partnership to unlock the untargeted kinome. Nat. Chem. Biol., 2013, 9, 1-7.
  17. Patricelli, M.P.; Nomanbhoy, T.K.; Wu, J.; Brown, H.; Zhou, D.; Zhang, J.; Jagannathan, S.; Aban, A.; Okerberg, E.; Herring, C.; Nordin, B.; Weissig, H.; Yang, Q.; Lee, J.D.; Gray, N.S.; Kozarich, J.W. In situ kinase profiling reveals functionally relevant properties of native kinases. Chem. Biol., 2011, 18(6), 699-710. doi: 10.1016/j.chembiol.2011.04.011 PMID: 21700206
  18. Deepa, P.; Thirumeignanam, D. Understanding the impact of anticancer halogenated inhibitors and various functional groups (X = Cl, F, CF3, CH3, NH2, OH, H) of casein kinase 2 (CK2). J. Biomol. Struct. Dyn., 2022, 40(11), 5036-5052. doi: 10.1080/07391102.2020.1866075 PMID: 33375908
  19. Atkinson, E.L.; Iegre, J.; Brear, P.D.; Zhabina, E.A.; Hyvönen, M.; Spring, D.R. Downfalls of chemical probes acting at the kinase ATP-Site: CK2 as a case study. Molecules, 2021, 26(7), 1977. doi: 10.3390/molecules26071977 PMID: 33807474
  20. Pardhi, T.; Vasu, K. Identification of dual kinase inhibitors of CK2 and GSK3β: Combined qualitative and quantitative pharmacophore modeling approach. J. Biomol. Struct. Dyn., 2018, 36(1), 177-194. doi: 10.1080/07391102.2016.1270856 PMID: 27960601
  21. Stone, Samantha; J, David.;, Newman; Colletti, Steven L.; S. Tan, Derek Cheminformatic analysis of natural product-based drugs and chemical probes. Natural products as chemical probes. Nat. Prod. Rep., 2022, 39, 20-32.
  22. Carlson, E.E. Natural products as chemical probes. ACS Chem. Biol., 2010, 5(7), 639-653. doi: 10.1021/cb100105c PMID: 20509672
  23. Sehgal, S.N.; Baker, H.; Vézina, C. Rapamycin (AY-22,989), a new antifungal antibiotic. II. Fermentation, isolation and characterization. J. Antibiot. (Tokyo), 1975, 28(10), 727-732. doi: 10.7164/antibiotics.28.727 PMID: 1102509
  24. Abraham, R.T. Mammalian target of rapamycin: Immunosuppressive drugs uncover a novel pathway of cytokine receptor signaling. Curr. Opin. Immunol., 1998, 10(3), 330-336. doi: 10.1016/S0952-7915(98)80172-6 PMID: 9638370
  25. Fingar, D.C.; Blenis, J. Target of rapamycin (TOR): An integrator of nutrient and growth factor signals and coordinator of cell growth and cell cycle progression. Oncogene, 2004, 23(18), 3151-3171. doi: 10.1038/sj.onc.1207542 PMID: 15094765
  26. Heitman, J.; Movva, N.R.; Hall, M.N. Targets for cell cycle arrest by the immunosuppressant rapamycin in yeast. Science, 1991, 253(5022), 905-909. doi: 10.1126/science.1715094 PMID: 1715094
  27. Crespo, J.L.; Hall, M.N. Elucidating TOR signaling and rapamycin action: Lessons from Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev., 2002, 66(4), 579-591. doi: 10.1128/MMBR.66.4.579-591.2002 PMID: 12456783
  28. Vézina, C.; Kudelski, A.; Sehgal, S.N. Rapamycin (AY-22,989), a new antifungal antibiotic. I. Taxonomy of the producing streptomycete and isolation of the active principle. J. Antibiot. (Tokyo), 1975, 28(10), 721-726. doi: 10.7164/antibiotics.28.721 PMID: 1102508
  29. Harding, M.W.; Galat, A.; Uehling, D.E.; Schreiber, S.L. A receptor for the immuno-suppressant FK506 is a cis–trans peptidyl-prolyl isomerase. Nature, 1989, 341(6244), 758-760. doi: 10.1038/341758a0 PMID: 2477715
  30. Bierer, B.E.; Mattila, P.S.; Standaert, R.F.; Herzenberg, L.A.; Burakoff, S.J.; Crabtree, G.; Schreiber, S.L. Two distinct signal transmission pathways in T lymphocytes are inhibited by complexes formed between an immunophilin and either FK506 or rapamycin. Proc. Natl. Acad. Sci. USA, 1990, 87(23), 9231-9235. doi: 10.1073/pnas.87.23.9231 PMID: 2123553
  31. Dancey, J. mTOR signaling and drug development in cancer. Nat. Rev. Clin. Oncol., 2010, 7(4), 209-219. doi: 10.1038/nrclinonc.2010.21 PMID: 20234352
  32. Roberts, B.E.; Duennwald, M.L.; Wang, H.; Chung, C.; Lopreiato, N.P.; Sweeny, E.A.; Knight, M.N.; Shorter, J. A synergistic small-molecule combination directly eradicates diverse prion strain structures. Nat. Chem. Biol., 2009, 5(12), 936-946. doi: 10.1038/nchembio.246 PMID: 19915541
  33. Patury, S.; Miyata, Y.; Gestwicki, J. Pharmacological targeting of the Hsp70 chaperone. Curr. Top. Med. Chem., 2009, 9(15), 1337-1351. doi: 10.2174/156802609789895674 PMID: 19860737
  34. Evans, CG; Chang, L; Gestwicki, JE Heat shock protein 70 (Hsp70) as an emerging drug target. J Med Chem, 2010. Epub Mar 24
  35. Butt, M.S.; Sultan, M.T. Green tea: Nature’s defense against malignancies. Crit. Rev. Food Sci. Nutr., 2009, 49(5), 463-473. doi: 10.1080/10408390802145310 PMID: 19399671
  36. Jinwal, U.K.; Miyata, Y.; Koren, J., III; Jones, J.R.; Trotter, J.H.; Chang, L.; O’Leary, J.; Morgan, D.; Lee, D.C.; Shults, C.L.; Rousaki, A.; Weeber, E.J.; Zuiderweg, E.R.P.; Gestwicki, J.E.; Dickey, C.A. Chemical manipulation of hsp70 ATPase activity regulates tau stability. J. Neurosci., 2009, 29(39), 12079-12088. doi: 10.1523/JNEUROSCI.3345-09.2009 PMID: 19793966
  37. Oddo, S.; Caccamo, A.; Shepherd, J.D.; Murphy, M.P.; Golde, T.E.; Kayed, R.; Metherate, R.; Mattson, M.P.; Akbari, Y.; LaFerla, F.M. Triple-transgenic model of Alzheimer’s disease with plaques and tangles: intracellular Abeta and synaptic dysfunction. Neuron, 2003, 39(3), 409-421. doi: 10.1016/S0896-6273(03)00434-3 PMID: 12895417
  38. Castellanos-Ortega, M.R.; Cruz-Aguado, R.; Martínez-Martí, L. Nerve growth factor: Possibilities and limitations of its clinical application. Rev. Neurol., 1999, 29(5), 439-447. PMID: 10584248
  39. Skovronsky, D.M.; Lee, V.M.Y.; Trojanowski, J.Q. Neurodegenerative diseases: New concepts of pathogenesis and their therapeutic implications. Annu. Rev. Pathol., 2006, 1(1), 151-170. doi: 10.1146/annurev.pathol.1.110304.100113 PMID: 18039111
  40. Shigemori, H.; Wakuri, S.; Yazawa, K.; Nakamura, T.; Sasaki, T.; Kobayashi, J. Fellutamides A and B, cytotoxic peptides from a marine fish-possessing fungus Penicillium fellutanum. Tetrahedron, 1991, 47(40), 8529-8534. doi: 10.1016/S0040-4020(01)82396-6
  41. Hines, J.; Groll, M.; Fahnestock, M.; Crews, C.M. Proteasome inhibition by fellutamide B induces nerve growth factor synthesis. Chem. Biol., 2008, 15(5), 501-512. doi: 10.1016/j.chembiol.2008.03.020 PMID: 18482702
  42. Yamaguchi, K.; Tsuji, T.; Wakuri, S.; Yazawa, K.; Kondo, K.; Shigemori, H.; Kobayashi, J. Stimulation of nerve growth factor synthesis and secretion by fellutamide A in vitro. Biosci. Biotechnol. Biochem., 1993, 57(2), 195-199. doi: 10.1271/bbb.57.195 PMID: 7763492
  43. Brody, L.C.; Mitchell, G.A.; Obie, C.; Michaud, J.; Steel, G.; Fontaine, G.; Robert, M.F.; Sipila, I.; Kaiser-Kupfer, M.; Valle, D. Ornithine delta-aminotransferase mutations in gyrate atrophy. Allelic heterogeneity and functional consequences. J. Biol. Chem., 1992, 267(5), 3302-3307. doi: 10.1016/S0021-9258(19)50731-1 PMID: 1737786
  44. Wood, K.; Cornwell, W.D.; Jackson, J.R. Past and future of the mitotic spindle as an oncology target. Curr. Opin. Pharmacol., 2001, 1(4), 370-377. doi: 10.1016/S1471-4892(01)00064-9 PMID: 11710735
  45. Cruz-Monserrate, Z.; Vervoort, H.C.; Bai, R.; Newman, D.J.; Howell, S.B.; Los, G.; Mullaney, J.T.; Williams, M.D.; Pettit, G.R.; Fenical, W.; Hamel, E. Diazonamide A and a synthetic structural analog: Disruptive effects on mitosis and cellular microtubules and analysis of their interactions with tubulin. Mol. Pharmacol., 2003, 63(6), 1273-1280. doi: 10.1124/mol.63.6.1273 PMID: 12761336
  46. Williams, N.S.; Burgett, A.W.G.; Atkins, A.S.; Wang, X.; Harran, P.G.; McKnight, S.L. Therapeutic anticancer efficacy of a synthetic diazonamide analog in the absence of overt toxicity. Proc. Natl. Acad. Sci. USA, 2007, 104(7), 2074-2079. doi: 10.1073/pnas.0611340104 PMID: 17287337
  47. Wang, G.; Shang, L.; Burgett, A.W.G.; Harran, P.G.; Wang, X. Diazonamide toxins reveal an unexpected function for ornithine δ-amino transferase in mitotic cell division. Proc. Natl. Acad. Sci. USA, 2007, 104(7), 2068-2073. doi: 10.1073/pnas.0610832104 PMID: 17287350
  48. Wang, T.; Lawler, A.M.; Steel, G.; Sipila, I.; Milam, A.H.; Valle, D. Mice lacking ornithine–δ–amino–transferase have paradoxical neonatal hypoornithinaemia and retinal degeneration. Nat. Genet., 1995, 11(2), 185-190. doi: 10.1038/ng1095-185 PMID: 7550347
  49. Lindquist, N.; Fenical, W.; Van Duyne, G.D.; Clardy, J. Isolation and structure determination of diazonamides A and B, unusual cytotoxic metabolites from the marine ascidian Diazona chinensis. J. Am. Chem. Soc., 1991, 113(6), 2303-2304. doi: 10.1021/ja00006a060
  50. Seiler, N. Ornithine aminotransferase, a potential target for the treatment of hyperammonemias. Curr. Drug Targets, 2000, 1(2), 119-154. doi: 10.2174/1389450003349254 PMID: 11465067
  51. Frye, S.V. The art of the chemical probe. Nat. Chem. Biol., 2010, 6(3), 159-161. doi: 10.1038/nchembio.296 PMID: 20154659
  52. Kolbe, K.; Veleti, S.K.; Johnson, E.E.; Cho, Y.W.; Oh, S.; Barry, C.E. III; Cho, Young-Woo; S, Oh; CE, Barry Role of chemical biology in tuberculosis drug discovery and diagnosis. ACS Infect. Dis., 2018, 4(4), 458-466. doi: 10.1021/acsinfecdis.7b00242 PMID: 29364647
  53. Lee, J.; Schapira, M. The promise and peril of chemical probe negative controls. ACS Chem. Biol., 2021, 16(4), 579-585. doi: 10.1021/acschembio.1c00036 PMID: 33745272
  54. Castaldi, M.P.; Hendricks, J.A.; Zhang, A.X. ‘Design, synthesis, and strategic use of small chemical probes toward identification of novel targets for drug development’. Curr. Opin. Chem. Biol., 2020, 56, 91-97. doi: 10.1016/j.cbpa.2020.03.003 PMID: 32375076
  55. Zhu, H.; Hamachi, I. Fluorescence imaging of drug target proteins using chemical probes. J. Pharm. Anal., 2020, 10(5), 426-433. doi: 10.1016/j.jpha.2020.05.013 PMID: 33133726
  56. Ortega, C.; Anderson, L.N.; Frando, A.; Sadler, N.C.; Brown, R.W.; Smith, R.D.; Wright, A.T.; Grundner, C. Systematic survey of serine hydrolase activity in mycobacterium tuberculosis defines changes associated with persistence. Cell Chem. Biol., 2016, 23(2), 290-298. doi: 10.1016/j.chembiol.2016.01.003 PMID: 26853625
  57. Tallman, K.R.; Levine, S.R.; Beatty, K.E. Profiling esterases in mycobacterium tuberculosis using far-red fluorogenic substrates. ACS Chem. Biol., 2016, 11(7), 1810-1815. doi: 10.1021/acschembio.6b00233 PMID: 27177211
  58. Tallman, K.R.; Levine, S.R.; Beatty, K.E. Small-molecule probes reveal esterases with persistent activity in dormant and reactivating mycobacterium tuberculosis. ACS Infect. Dis., 2016, 2(12), 936-944. doi: 10.1021/acsinfecdis.6b00135 PMID: 27690385
  59. Lentz, C.S.; Ordonez, A.A.; Kasperkiewicz, P.; La Greca, F.; O’Donoghue, A.J.; Schulze, C.J.; Powers, J.C.; Craik, C.S.; Drag, M.; Jain, S.K.; Bogyo, M. Design of selective substrates and activity-based probes for hydrolase important for pathogenesis 1 (HIP1) from Mycobacterium tuberculosis. ACS Infect. Dis., 2016, 2(11), 807-815. doi: 10.1021/acsinfecdis.6b00092 PMID: 27739665
  60. Ansong, C.; Ortega, C.; Payne, S.H.; Haft, D.H.; Chauvignè-Hines, L.M.; Lewis, M.P.; Ollodart, A.R.; Purvine, S.O.; Shukla, A.K.; Fortuin, S.; Smith, R.D.; Adkins, J.N.; Grundner, C.; Wright, A.T. Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. Chem. Biol., 2013, 20(1), 123-133. doi: 10.1016/j.chembiol.2012.11.008 PMID: 23352146
  61. Wolfe, L.M.; Veeraraghavan, U.; Idicula-Thomas, S.; Schürer, S.; Wennerberg, K.; Reynolds, R.; Besra, G.S.; Dobos, K.M. A chemical proteomics approach to profiling the ATP-binding proteome of Mycobacterium tuberculosis. Mol. Cell. Proteomics, 2013, 12(6), 1644-1660. doi: 10.1074/mcp.M112.025635 PMID: 23462205
  62. Benjamin, P. Duckworth; Wilson, Daniel J.; M. Nelson, Kathryn; Boshoff, Helena I.; Barry, Clifton E., III; Aldrich, Courtney C. Development of a selective activity-based probe for adenylating enzymes: Profiling mbta involved in siderophore biosynthesis from mycobacterium tuberculosis. ACS Chem. Biol., 2012, 7(10), 1653-1658. doi: 10.1021/cb300112x PMID: 22796950
  63. Carlson, E.E.; May, J.F.; Kiessling, L.L. Chemical probes of UDP-galactopyranose mutase. Chem. Biol., 2006, 13(8), 825-837. doi: 10.1016/j.chembiol.2006.06.007 PMID: 16931332
  64. Kastrinsky, D.B.; Barry, C.E., III Synthesis of labeled meropenem for the analysis of M. tuberculosis transpeptidases. Tetrahedron Lett., 2010, 51(1), 197-200. doi: 10.1016/j.tetlet.2009.10.124 PMID: 20161438
  65. Kong, Y.; Yao, H.; Ren, H.; Subbian, S.; Cirillo, S.L.G.; Sacchettini, J.C.; Rao, J.; Cirillo, J.D. Imaging tuberculosis with endogenous β-lactamase reporter enzyme fluorescence in live mice. Proc. Natl. Acad. Sci. USA, 2010, 107(27), 12239-12244. doi: 10.1073/pnas.1000643107 PMID: 20566877
  66. Xie, H.; Mire, J.; Kong, Y.; Chang, M.; Hassounah, H.A.; Thornton, C.N.; Sacchettini, J.C.; Cirillo, J.D.; Rao, J. Rapid point-of-care detection of the tuberculosis pathogen using a BlaC-specific fluorogenic probe. Nat. Chem., 2012, 4(10), 802-809. doi: 10.1038/nchem.1435 PMID: 23000993
  67. Cheng, Y.; Xie, H.; Sule, P.; Hassounah, H.; Graviss, E.A.; Kong, Y.; Cirillo, J.D.; Rao, J. Fluorogenic probes with substitutions at the 2 and 7 positions of cephalosporin are highly BlaC-specific for rapid Mycobacterium tuberculosis detection. Angew. Chem. Int. Ed., 2014, 53(35), 9360-9364. doi: 10.1002/anie.201405243 PMID: 24989449
  68. Carlson, E.E.; Cravatt, B.F. Chemoselective probes for metabolite enrichment and profiling. Nat. Methods, 2007, 4(5), 429-435. doi: 10.1038/nmeth1038 PMID: 17417646
  69. Blum, G.; von Degenfeld, G.; Merchant, M.J.; Blau, H.M.; Bogyo, M. Noninvasive optical imaging of cysteine protease activity using fluorescently quenched activity-based probes. Nat. Chem. Biol., 2007, 3(10), 668-677. doi: 10.1038/nchembio.2007.26 PMID: 17828252
  70. Blum, G.; Mullins, S.R.; Keren, K.; Fonovič, M.; Jedeszko, C.; Rice, M.J.; Sloane, B.F.; Bogyo, M. Dynamic imaging of protease activity with fluorescently quenched activity-based probes. Nat. Chem. Biol., 2005, 1(4), 203-209. doi: 10.1038/nchembio728 PMID: 16408036
  71. Alexandra, J. Lukasiewicza; Contrerasa, Lydia M. Antisense probing of dynamic RNA structures. Methods, 2020, 1-8.
  72. Russell, R.; Herschlag, D. Probing the folding landscape of the Tetrahymena ribozyme: Commitment to form the native conformation is late in the folding pathway. J. Mol. Biol., 2001, 308(5), 839-851. doi: 10.1006/jmbi.2001.4751 PMID: 11352576
  73. Hefti, A.F. Periodontal probing. Crit. Rev. Oral Biol. Med., 1997, 8(3), 336-356. doi: 10.1177/10454411970080030601 PMID: 9260047
  74. Ding, Y.; Li, Z.; Xu, C.; Qin, W.; Wu, Q.; Wang, X.; Cheng, X.; Li, L.; Huang, W. Fluorogenic probes/inhibitors of β‐lactamase and their applications in drug‐resistant bacteria. Angew. Chem. Int. Ed., 2021, 60(1), 24-40. doi: 10.1002/anie.202006635 PMID: 32592283
  75. New noninvasive chemical probe detects common species of staph bacteria in the body. Available from: https://www.news-medical.net/news/20140203/New-noninvasive-chemical-probe-detects-common-species-of-staph-bacteria-in-the-body.aspx
  76. Yoon, S.A.; Park, S.Y.; Cha, Y.; Gopala, L.; Lee, M.H. Strategies of detecting bacteria using fluorescence-based dyes. Front Chem., 2021, 9, 743923. doi: 10.3389/fchem.2021.743923
  77. Available from: https://www.pnnl.gov/science/highlights/highlight.asp?id=1266
  78. Zhang, C.; Stockwell, S.R.; Elbanna, M.; Ketteler, R.; Freeman, J.; Al-Lazikani, B.; Eccles, S.; De Haven Brandon, A.; Raynaud, F.; Hayes, A.; Clarke, P.A.; Workman, P.; Mittnacht, S. Signalling involving MET and FAK supports cell division independent of the activity of the cell cycle-regulating CDK4/6 kinases. Oncogene, 2019, 38(30), 5905-5920. doi: 10.1038/s41388-019-0850-2 PMID: 31296956
  79. Antolin, A.A.; Workman, P.; Al-Lazikani, B. Public resources for chemical probes: the journey so far and the road ahead. Future Med. Chem., 2021, 13(8), 731-747.
  80. Paiva, S.L.; Crews, C.M. Targeted protein degradation: Elements of PROTAC design. Curr. Opin. Chem. Biol., 2019, 50, 111-119. doi: 10.1016/j.cbpa.2019.02.022 PMID: 31004963
  81. Workman, P.; Antolin, A.A.; Al-Lazikani, B. Transforming cancer drug discovery with Big Data and AI. Expert Opin. Drug Discov., 2019, 14(11), 1089-1095. doi: 10.1080/17460441.2019.1637414 PMID: 31284790
  82. Mullard, A. A probe for every protein. Nat. Rev. Drug Discov., 2019, 18(10), 733-736. doi: 10.1038/d41573-019-00159-9 PMID: 31570852
  83. Jones, L.H. Cell permeable affinity- and activity-based probes. Future Med. Chem., 2015, 7(16), 2131-2141. doi: 10.4155/fmc.15.100 PMID: 26511518
  84. Available from: https://patents.google.com/patent/WO2010114599A1
  85. Available from: https://patents.google.com/patent/US8962853B2/en
  86. Available from: https://patents.google.com/patent/US8697357
  87. Available from: https://pubchem.ncbi.nlm.nih.gov/patent/US-10704087-B2
  88. Available from: https://patents.google.com/patent/US7375198
  89. Lai, H.M.; Ng, W.L.; Gentleman, S.M.; Wu, W. Chemical probes for visualizing intact animal and human brain tissue. Cell Chem. Biol., 2017, 24(6), 659-672. doi: 10.1016/j.chembiol.2017.05.015 PMID: 28644957
  90. Chang, W.M.; Dakanali, M.; Capule, C.C.; Sigurdson, C.J.; Yang, J.; Theodorakis, E.A. ANCA: A family of fluorescent probes that bind and stain amyloid plaques in human tissue. ACS Chem. Neurosci., 2011, 2(5), 249-255. doi: 10.1021/cn200018v PMID: 21743829
  91. McMurray, L.; Macdonald, J.A.; Ramakrishnan, N.K.; Zhao, Y.; Williamson, D.W.; Tietz, O.; Zhou, X.; Kealey, S.; Fagan, S.G.; Smolek, T.; Cubinkova, V.; Žilka, N.; Spillantini, M.G.; Tolkovsky, A.M.; Goedert, M.; Aigbirhio, F.I. Synthesis and assessment of novel probes for imaging tau pathology in transgenic mouse and rat models. ACS Chem. Neurosci., 2021, 12(11), 1885-1893. doi: 10.1021/acschemneuro.0c00790 PMID: 33689290
  92. Watanabe, H. Development of SPECT probes for in vivo imaging of β-amyloid and tau aggregates in the alzheimer’s disease brain. Pharmacy Magazine, 2017, 137(11), 1361-1365. doi: 10.1248/yakushi.17-00156 PMID: 29093372
  93. Ono, M.; Watanabe, H.; Kitada, A.; Matsumura, K.; Ihara, M.; Saji, H. Highly selective Tau-SPECT imaging probes for detection of neurofibrillary tangles in alzheimer’s disease. Sci. Rep., 2016, 6(1), 34197. doi: 10.1038/srep34197 PMID: 27687137
  94. Cui, M. Past and recent progress of molecular imaging probes for β-amyloid plaques in the brain. Curr. Med. Chem., 2013, 21(1), 82-112. doi: 10.2174/09298673113209990216 PMID: 23992340
  95. Brelstaff, J.; Ossola, B.; Neher, J.J.; Klingstedt, T.; Nilsson, K.P.R.; Goedert, M.; Spillantini, M.G.; Tolkovsky, A.M. The fluorescent pentameric oligothiophene pFTAA identifies filamentous tau in live neurons cultured from adult P301S tau mice. Front. Neurosci., 2015, 9, 184. doi: 10.3389/fnins.2015.00184 PMID: 26074756
  96. Blau, R.; Shelef, O.; Shabat, D.; Satchi-Fainaro, R. Chemiluminescent probes in cancer biology. Nat. Rev. Bioeng., 2023, 1(9), 648-664. doi: 10.1038/s44222-023-00074-0
  97. Benezra, M.; Penate-Medina, O.; Zanzonico, P.B.; Schaer, D.; Ow, H.; Burns, A.; DeStanchina, E.; Longo, V.; Herz, E.; Iyer, S.; Wolchok, J.; Larson, S.M.; Wiesner, U.; Bradbury, M.S. Multimodal silica nanoparticles are effective cancer-targeted probes in a model of human melanoma. J. Clin. Invest., 2011, 121(7), 2768-2780. doi: 10.1172/JCI45600 PMID: 21670497
  98. van Dam, G.M.; Themelis, G.; Crane, L.M.A.; Harlaar, N.J.; Pleijhuis, R.G.; Kelder, W.; Sarantopoulos, A.; de Jong, J.S.; Arts, H.J.G.; van der Zee, A.G.J.; Bart, J.; Low, P.S.; Ntziachristos, V. Intraoperative tumor-specific fluorescence imaging in ovarian cancer by folate receptor-α targeting: first in-human results. Nat. Med., 2011, 17(10), 1315-1319. doi: 10.1038/nm.2472 PMID: 21926976
  99. Lamberts, L.E.; Koch, M.; de Jong, J.S.; Adams, A.L.L.; Glatz, J.; Kranendonk, M.E.G.; Terwisscha van Scheltinga, A.G.T.; Jansen, L.; de Vries, J.; Lub-de Hooge, M.N.; Schröder, C.P.; Jorritsma-Smit, A.; Linssen, M.D.; de Boer, E.; van der Vegt, B.; Nagengast, W.B.; Elias, S.G.; Oliveira, S.; Witkamp, A.J.; Mali, W.P.T.M.; Van der Wall, E.; van Diest, P.J.; de Vries, E.G.E.; Ntziachristos, V.; van Dam, G.M. Tumor-specific uptake of fluorescent bevacizumab-IRDye800CW microdosing in patients with primary breast cancer: A phase I feasibility study. Clin. Cancer Res., 2017, 23(11), 2730-2741. doi: 10.1158/1078-0432.CCR-16-0437 PMID: 28119364
  100. Seah, D.; Cheng, Z.; Vendrell, M. Fluorescent probes for imaging in humans: Where are we now? ACS Nano, 2023, 17(20), 19478-19490. doi: 10.1021/acsnano.3c03564 PMID: 37787658

Дополнительные файлы

Доп. файлы
Действие
1. JATS XML
Скачать

© Bentham Science Publishers, 2024