Differential chemoproteomic analysis of RRS-1 candidate molecule and molecules of several nonsteroidal anti-inflammatory drugs

Background. To plan effective and safe pharmacotherapy for inflammation and pain, it is important to evaluate the mechanisms and spectrum of action of nonsteroidal anti-inflammatory drugs (NSAIDs), including their effects on human proteome.

Objective: to identify and evaluate the most significant specific differences of candidate molecule RRS-1 (N-{(Z)-2-(1-methyl-1H-indol-3-yl)1-[(propylamino)carbonyl]vinyl}benzamide) from other NSAIDs through differential chemoreactome analysis.

Material and methods. Chemoproteomic modeling of pharmacological effects of RRS-1 molecule and a number of well-known NSAIDs (diclofenac, nimesulide, ketorolac) on human proteome was carried out on the basis of numerical prediction algorithms over the space of heterogeneous feature descriptions, developed in the topological approach to recognition by Yu.I. Zhuravlev and K.V. Rudakov scientific school.

Results. Significant differences in the effects of the studied molecules were found for 1232 proteins of human proteome. The features of assessing interactions of the studied molecules with 47 target proteins, which most distinguished the effects of RRS-1 molecule from all others were identified. RRS-1 could activate adenosine and dopamine receptors, cannabinoid receptor 2 and GABA_A receptor to a greater extent than other molecules. Activation of these receptors corresponded to anti-inflammatory, anti-nociceptive and neuroprotective effects. RRS-1 could preferably inhibit a number of pro-inflammatory proteins, receptor bradykinin 1, metabotropic glutamate receptor 5, matrix metalloproteinases 8, 9, 12, and blood coagulation factor X. Additionally, RRS-1 molecule showed preferable inhibition of a number of kinases targeted in antitumor and anti-inflammatory therapy. RRS-1, less than other studied molecules, interacted with the receptors of vitamin D3, thyroid hormone, acetylcholine, cannabinoids and opioids, orexin, and various metabolic enzymes, which is important in assessment of the safety of using drugs based on this molecule. RRS-1 characteristically exhibited a moderate profile of antivitamin action: the total score of vitamin and mineral loss (7.4±3.7) was significantly less in comparison to diclofenac (11.7±4.5) and was actually on the same level as nimesulide (6.9±3.7) and ketorolac (6.7±3.6).

Conclusion. Chemoreactomic and chemoproteomic profiling of RRS-1 candidate molecule provided pre-experimental assessments of its efficacy and safety through modeling interactions with the human proteome.

1. Gromova O.A., Torshin I.Iu., Putilina M.V., et al. The chemoreactomic analysis of the central mechanisms of action of non-steroidal anti-inflammatory drugs. S.S. Korsakov Journal of Neurology and Psychiatry. 2020; 120 (1): 70–7 (in Russ.). https://doi.org/10.17116/jnevro202012001170.]

2. Torshin I.Yu., Gromova O.A. Expert data analysis in molecular pharmacology. Мoscow: Moscow Center for Continuous Mathematical Education; 2012: 747 pp. (in Russ.).]

3. Torshin I.Y., Gromova O.A., Fedotova L.E., Gromov A.N. Comparative chemoreactome analysis of dexketoprofen, ketoprofen, and diclofenac. Nevrologiya, neiropsikhiatriya, psikhosomatika / Neurology, Neuro- psychiatry, Psychosomatics. 2018; 10 (1): 47–54 (in Russ.). http://doi.org/10.14412/2074-2711-2018-1-47-54.]

4. Torshin I.Y., Gromova O.A., Stakhovskaya L.V., Semenov V.A. Chemoreactome analysis of tolperisone, tizanidine, and baclofen molecules: anticholinergic, antispasmodic, and analgesic mechanisms of action. Nevrologiya, neiropsikhiatriya, psikhosomatika / Neurology, Neuropsychiatry, Psychosomatics. 2018; 10 (4): 72–80 (in Russ.). http://doi.org/10.14412/2074-2711-2018-4-72-80.]

5. Torshin I.Yu. On optimization problems arising from the application of topological data analysis to the search for forecasting algorithms with fixed correctors. Informatics and Applications. 2023; 17 (2): 2–10 (in Russ.). http://doi.org/10.14357/19922264230201.

6. Trshin I.Yu. Sensing the change: from molecular genetics to personalized medicine. NY: Nova Science Pub Inc; 2012: 366 pp.

7. Torshin I.Y., Rudakov K.V. On the application of the combinatorial theory of solvability to the analysis of chemographs. Part 1: Fundamentals of modern chemical bonding theory and the concept of the chemograph. Pattern Recognit Image Anal. 2014; 24 (1): 11–23. http://doi.org/10.1134/s1054661814010209.

8. Torshin I.Y., Rudakov K.V. On the application of the combinatorial theory of solvability to the analysis of chemographs. Part 2: Local completeness of invariants of chemographs in view of the combinatorial theory of solvability. Pattern Recognit Image Anal. 2014; 24 (2): 196–208. https://doi.org/10.1134/S1054661814020151.

9. Torshin I.Y. The study of the solvability of the genome annotation problem on sets of elementary motifs. Pattern Recognit Image Anal. 2011; 21 (4): 652–62. https://doi.org/10.1134/S1054661811040171.

10. Torshin I.Yu., Rudakov K.V. On the procedures of generation of numerical features over partitions of sets of objects in the problem of predicting numerical target variables. Pattern Recognit Image Anal. 2019; 29 (4): 654–67. https://doi.org/10.1134/S1054661819040175.

11. Schwarz A.M., Keresztes A., Bui T., et al. Terpenes from Cannabis sativa induce antinociception in a mouse model of chronic neuropathic pain via activation of adenosine A2A receptors. Pain. 2024; May 2. https://doi.org/10.1097/j.pain.0000000000003265.

12. Xu J.P., Ouyang Q.W., Shao M.J., et al. Manual acupuncture ameliorates inflammatory pain by upregulating adenosine A(3) receptor in complete Freund's adjuvant-induced arthritis rats. Int Immuno- pharmacol. 2024; 133: 112095. https://doi.org/10.1016/j.intimp.2024.112095.

13. Kishimoto S., Gokoh M., Oka S., et al. 2-arachidonoylglycerol induces the migration of HL-60 cells differentiated into macrophage-like cells and human peripheral blood monocytes through the cannabinoid CB2 receptor-dependent mechanism. J Biol Chem. 2003; 278 (27): 24469–75. https://doi.org/10.1074/jbc.M301359200.

14. Feng W., Song Z.H. Effects of D3.49A, R3.50A, and A6.34E mutations on ligand binding and activation of the cannabinoid-2 (CB2) receptor. Biochem Pharmacol. 2003; 65 (7): 1077–85. https://doi.org/10.1016/s0006-2952(03)00005-4.

15. Liu S., Tang Y., Shu H., et al. Dopamine receptor D2, but not D1, mediates descending dopaminergic pathway-produced analgesic effect in a trigeminal neuropathic pain mouse model. Pain. 2019; 160 (2): 334–44. https://doi.org/10.1097/j.pain.0000000000001414.

16. Garlisi C.G., Xiao H., Tian F., et al. The assignment of chemokine-chemokine receptor pairs: TARC and MIP-1 beta are not ligands for human CC-chemokine receptor 8. Eur J Immunol. 1999; 29 (10): 3210–5. https://doi.org/10.1002/(SICI)1521-4141(199910)29:10<3210::AID-IMMU3210>3.0.CO;2-W.

17. Hayashi T., Takahashi T., Motoya S., et al. MUC1 mucin core protein binds to the domain 1 of ICAM-1. Digestion. 2001; 63 (Suppl. 1): 87–92. https://doi.org/10.1159/000051917.

18. Xiao C., Bator C.M., Bowman V.D., et al. Interaction of coxsackievirus A21 with its cellular receptor, ICAM-1. J Virol. 2001; 75 (5): 2444–51. https://doi.org/10.1128/JVI.75.5.2444-2451.2001.

19. Wei S., Nandi S., Chitu V., et al. Functional overlap but differential expression of CSF-1 and IL-34 in their CSF-1 receptor-mediated regulation of myeloid cells. J Leukoc Biol. 2010; 88 (3): 495–505. https://doi.org/10.1189/jlb.1209822.

20. Han J., Chitu V., Stanley E.R., et al. Inhibition of colony stimulating factor-1 receptor (CSF-1R) as a potential therapeutic strategy for neurodegenerative diseases: opportunities and challenges. Cell Mol Life Sci. 2022; 79 (4): 219. https://doi.org/10.1007/s00018-022-04225-1.

21. Hoarau C., Gérard B., Lescanne E., et al. TLR9 activation induces normal neutrophil responses in a child with IRAK-4 deficiency: involvement of the direct PI3K pathway. J Immunol. 2007; 179 (7): 4754–65. https://doi.org/10.4049/jimmunol.179.7.4754.

22. Tralau T., Meyer-Hoffert U., Schröder J.M., Wiedow O. Human leukocyte elastase and cathepsin G are specific inhibitors of C5a-dependent neutrophil enzyme release and chemotaxis. Exp Dermatol. 2004; 13 (5): 316–25. https://doi.org/10.1111/j.0906-6705.2004.00145.x.

23. Minakami R., Katsuki F., Yamamoto T., et al. Molecular cloning and the functional expression of two isoforms of human metabotropic glutamate receptor subtype 5. Biochem Biophys Res Commun. 1994; 199 (3): 1136–43. https://doi.org/10.1006/bbrc.1994.1349.

24. Marumoto T., Hirota T., Morisaki T., et al. Roles of aurora-A kinase in mitotic entry and G2 checkpoint in mammalian cells. Genes Cells. 2002; 7 (11): 1173–82. https://doi.org/10.1046/j.1365-2443.2002.00592.x.

25. Walter A.O., Seghezzi W., Korver W., et al. The mitotic serine/threonine kinase Aurora2/AIK is regulated by phosphorylation and degradation. Oncogene. 2000; 19 (42): 4906–16. https://doi.org/10.1038/sj.onc.1203847.

26. Borah N.A., Reddy M.M. Aurora kinase B inhibition: a potential therapeutic strategy for cancer. Molecules. 2021; 26 (7): 1981. https://doi.org/10.3390/molecules26071981.

27. Matsuura I., Denissova N.G., Wang G., et al. Cyclin-dependent kinases regulate the antiproliferative function of Smads. Nature. 2004; 430 (6996): 226–31. https://doi.org/10.1038/nature02650.

28. Simone C., Stiegler P., Bagella L., et al. Activation of MyoD-dependent transcription by cdk9/cyclin T2. Oncogene. 2002; 21 (26): 4137–48. https://doi.org/10.1038/sj.onc.1205493.

29. Li J., Shi J., Pan Y., et al. Transcription modulation by CDK9 regulates inflammatory genes and RIPK3-MLKL-mediated necroptosis in periodontitis progression. Sci Rep. 2019; 9 (1): 17369. https://doi.org/10.1038/s41598-019-53910-y.

30. Kwak Y.T., Ivanov D., Guo J., et al. Role of the human and murine cyclin T proteins in regulating HIV-1 tat-activation. J Mol Biol. 1999; 288 (1): 57–69. https://doi.org/10.1006/jmbi.1999.2664.

31. Oshimori N., Ohsugi M., Yamamoto T. The Plk1 target Kizuna stabilizes mitotic centrosomes to ensure spindle bipolarity. Nat Cell Biol. 2006; 8 (10): 1095–101. https://doi.org/10.1038/ncb1474.

32. Daub H., Blencke S., Habenberger P., et al. Identification of SRPK1 and SRPK2 as the major cellular protein kinases phosphorylating hepatitis B virus core protein. J Virol. 2002; 76 (16): 8124–37. https://doi.org/10.1128/jvi.76.16.8124-8137.2002.

33. Frame S., Cohen P., Biondi R.M. A common phosphate binding site explains the unique substrate specificity of GSK3 and its inactivation by phosphorylation. Mol Cell. 2001; 7 (6): 1321–7. https://doi.org/10.1016/s1097-2765(01)00253-2.

34. Hourai S., Fujishima T., Kittaka A., et al. Probing a water channel near the A-ring of receptor-bound 1 alpha,25-dihydroxyvitamin D3 with selected 2 alpha-substituted analogues. J Med Chem. 2006; 49 (17): 5199–205. https://doi.org/10.1021/jm0604070.

35. Borngraeber S., Budny M.J., Chiellini G., et al. Ligand selectivity by seeking hydrophobicity in thyroid hormone receptor. Proc Natl Acad Sci USA. 2003; 100 (26): 15358–63. https://doi.org/10.1073/pnas.2136689100.

36. Shen X.M., Okuno T., Milone M., et al. Mutations causing slow-channel myasthenia reveal that a valine ring in the channel pore of muscle AChR is optimized for stabilizing channel gating. Hum Mutat. 2016; 37 (10): 1051–9. https://doi.org/10.1002/humu.23043.

37. Hua T., Vemuri K., Pu M., et al. Crystal structure of the human cannabinoid receptor CB(1). Cell. 2016; 167 (3): 750–62.e14. https://doi.org/10.1016/j.cell.2016.10.004.

38. Leskelä T.T., Lackman J.J., Vierimaa M.M., et al. Cys-27 variant of human δ-opioid receptor modulates maturation and cell surface delivery of Phe-27 variant via heteromerization. J Biol Chem. 2012; 287 (7): 5008–20. https://doi.org/10.1074/jbc.M111.305656.

39. Yin J., Babaoglu K., Brautigam C.A., et al. Structure and ligand-binding mechanism of the human OX1 and OX2 orexin receptors. Nat Struct Mol Biol. 2016; 23 (4): 293–9. https://doi.org/10.1038/nsmb.3183.

40. Park S.H., Choi H.J., Yang H., et al. Endoplasmic reticulum stress-activated C/EBP homologous protein enhances nuclear factor-kappaB signals via repression of peroxisome proliferator-activated receptor gamma. J Biol Chem. 2010; 285 (46): 35330–9. https://doi.org/10.1074/jbc.M110.136259.

41. Engeli R.T., Rhouma B.B., Sager C.P., et al. Biochemical analyses and molecular modeling explain the functional loss of 17β-hydro-xysteroid dehydrogenase 3 mutant G133R in three Tunisian patients with 46, XY Disorders of Sex Development. J Steroid Biochem Mol Biol. 2016; 155 (Pt A): 147–54. https://doi.org/10.1016/j.jsbmb.2015.10.023.

42. Mao S.S., Cooper C.M., Wood T., et al. Characterization of plasmin-mediated activation of plasma procarboxypeptidase B. Modulation by glycosaminoglycans. J Biol Chem. 1999; 274 (49): 35046–52. https://doi.org/10.1074/jbc.274.49.35046.

43. Ghersi G., Zhao Q., Salamone M., et al. The protease complex consisting of dipeptidyl peptidase IV and seprase plays a role in the migration and invasion of human endothelial cells in collagenous matrices. Cancer Res. 2006; 66 (9): 4652–61. https://doi.org/10.1158/0008-5472.CAN-05-1245.

44. Dobrikov M., Dobrikova E., Shveygert M., Gromeier M. Phos- phorylation of eukaryotic translation initiation factor 4G1 (eIF4G1) by protein kinase C{alpha} regulates eIF4G1 binding to Mnk1. Mol Cell Biol. 2011; 31 (14): 2947–59. https://doi.org/10.1128/MCB.05589-11.

45. Lau E., Kluger H., Varsano T., et al. PKCε promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria. Cell. 2012; 148 (3): 543–55. https://doi.org/10.1016/j.cell.2012.01.016.

46. Yoshida K., Liu H., Miki Y. Protein kinase C delta regulates Ser46 phosphorylation of p53 tumor suppressor in the apoptotic response to DNA damage. J Biol Chem. 2006; 281 (9): 5734–40. https://doi.org/10.1074/jbc.M512074200.