Searching for possible sites of electrophils conjugation with biomolecules using molecular modeling methods
- Авторлар: Belinskaia D.A.1, Savelieva Е.I.2
-
Мекемелер:
- Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences
- Research Institute of Hygiene, Occupational Pathology and Human Ecology
- Шығарылым: Том 51, № 3 (2025)
- Беттер: 496-515
- Бөлім: ОБЗОРНАЯ СТАТЬЯ
- URL: https://ruspoj.com/0132-3423/article/view/687000
- DOI: https://doi.org/10.31857/S0132342325030129
- EDN: https://elibrary.ru/KRHXRF
- ID: 687000
Дәйексөз келтіру
Аннотация
The ability to rapidly form adducts with nucleophilic groups of proteins, nucleic acids and lipids largely determines the toxic effects of electrophiles. Considering that the number of toxic electrophiles is practically unlimited, and they can form adducts with many molecular targets, a purely empirical approach to characterizing the adductome is obviously unproductive. The aim of this study is to develop a method for primary in silico assessment of the probability of conjugation of electrophiles with a particular modification site. For the model group of electrophiles, the quantum-chemical indices were calculated using the density functional theory method, and the molecular docking method was used to search for priority sites of covalent binding of the studied compounds. Based on the obtained results, a scale for assessing the hardness of electrophiles was developed and an algorithm for computer selection of possible conjugation sites of electrophiles with biological macromolecules was compiled.
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Толық мәтін

Авторлар туралы
D. Belinskaia
Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences
Хат алмасуға жауапты Автор.
Email: d_belinskaya@mail.ru
Ресей, prosp. Toreza 44, St. Petersburg, 194223
Е. Savelieva
Research Institute of Hygiene, Occupational Pathology and Human Ecology
Email: d_belinskaya@mail.ru
Ресей, Kuzmolovsky, st. Kapitolovo 93, 188663
Әдебиет тізімі
- Pivotal Role of Mass Spectrometry for the Assessment of Exposure to Reactive Chemical Contaminants: From the Exposome to the Adductome / Debrauwer L., Mervant L., Laprevote,O., Jamin E.L. Eds. / Wiley Periodicals LLC, 2024.
- Knapen M.F., Zusterzeel P.L., Peters W.H., Steegers E.A. // Eur. J. Obstet. Gynecol. Reprod. Biol. 1999. V. 82. P. 171–184. https://doi.org/10.1016/s0301-2115(98)00242-5
- Blum M.M., Schmeißer W., Dentzel M., Thiermann H., John H. // Anal. Bioanal. Chem. 2024. V. 416. P. 5791–5804. https://doi.org/10.1007/s00216-024-05501-8
- Reuter, H., Steinritz, D., Worek, F., John H. // Anal. Bioanal. Chem. 2025. V. 417. P. 1833–1845. https://doi.org/10.1007/s00216-025-05762-x
- Xie Z., Chen J.Y., Gao H., Keith R.J., Bhatnagar A., Lorkiewicz P., Srivastava S. // Environ. Sci. Technol. 2023. V. 57. P. 10563-10573. https://doi.org/10.1021/acs.est.2c09554
- La Barbera G., Shuler M.S., Beck S.H., Ibsen P.H., Lindberg L.J., Karstensen J.G., Dragsted L.O. // Talanta. 2025. V. 282. P. 126985. https://doi.org/10.1016/j.talanta.2024.126985
- Blair I.A. // Biomed. Chromatogr. 2010. V. 1. P. 29–38. https://doi.org/10.1002/bmc.1374
- Koivisto P., Peltonen K. // Anal. Bioanal. Chem. 2010. V. 398. P. 2563–2572. https://doi.org/10.1007/s00216-010-4217-3
- Pearson R.G. // J. Am. Chem. Soc. 1963. V. 85. P. 3533–3539. https://doi.org/10.1021/ja00905a001
- LoPachin R.M., Geohagen B.C., Nordstroem L.U. // Toxicology. 2019. V. 418. P. 62–69. https://doi.org/10.1016/j.tox.2019.02.005
- Tong G.C., Cornwell W.K., Means G.E. // Toxicol. Lett. 2004. V. 147. P. 127-131. https://doi.org/10.1016/j.toxlet.2003.10.021
- Hashimoto K., Aldridge W.N. // Biochem. Pharmacol. 1970. V. 19. P. 2591–2604. https://doi.org/10.1016/0006-2952(70)90009-2
- Springer D.L., Bull R.J., Goheen S.C., Sylvester D.M., Edmonds C.G. // J. Toxicol. Environ. Health. 1993. V. 40. P. 161–176. https://doi.org/10.1080/15287399309531785
- Basile A., Ferranti P., Moccaldi R., Spagnoli G., Sannolo N. // J Chromatogr A. 2008. V. 1215. P. 74-81. https://doi.org/10.1016/j.chroma.2008.10.093
- Luo Y.S., Long T.Y., Shen L.C., Huang S.L., Chiang S.Y., Wu K.Y. // Chem. Biol. Interact. 2015. V. 237. P. 38–46. https://doi.org/10.1016/j.cbi.2015.05.002
- Doerge D.R., Gamboa da Costa G., McDaniel L.P., Churchwell M.I., Twaddle N.C., Beland F.A. // Mutat. Res. 2005. V. 580. P. 131–141. https://doi.org/10.1016/j.mrgentox.2004.10.013
- Gan J.C., Oandasan A., Ansari G.A.S. // Chemosphere. 1991. V. 23. P. 939–947. https://doi.org/10.1016/0045-6535(91)90098-X
- Lassé M., Stampfli A.R., Orban T., Bothara R.K., Gerrard J.A., Fairbanks A.J., Pattinson N.R., Dobson R.C.J. // Biochim. Biophys. Acta Gen. Subj. 2021. V. 1865. е130013. https://doi.org/10.1016/j.bbagen.2021.130013
- Moghe A., Ghare S., Lamoreau B., Mohammad M., Barve S., McClain C., Joshi-Barve S. // Toxicol. Sci. 2015. V. 143. P. 242–255. https://doi.org/10.1093/toxsci/kfu233
- Wang H.T., Zhang S., Hu Y., Tang M.S. // Chem. Res. Toxicol. 2009. V. 22. P. 511–517. https://doi.org/10.1021/tx800369y
- LeBlanc A., Shiao T.C., Roy R., Sleno L. // Chem. Res. Toxicol. 2014. V. 27. P. 1632–1639. https://doi.org/10.1021/tx500284g
- Hoos J.S., Damsten M.C., de Vlieger J.S., Commandeur J.N., Vermeulen N.P., Niessen W.M., Lingeman H., Irth H. // J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2007. V. 859. P. 147–156. https://doi.org/10.1016/j.jchromb.2007.09.015
- Switzar L., Kwast L.M., Lingeman H., Giera M., Pieters R.H., Niessen W.M. // J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2013. V. 917–918. P. 53–61. https://doi.org/10.1016/j.jchromb.2012.12.033
- Axworthy D.B., Hoffmann K.J., Streeter A.J., Calleman C.J., Pascoe G.A., Baillie T.A. // Chem. Biol. Interact. 1988. V. 68. P. 99–116. https://doi.org/10.1016/0009-2797(88)90009-9
- Bischoff K. // Veterinary Toxicology (Third Edition) Basic and Clinical Principles / Ed. Gupta R.C. Academic Press, 2018. P. 357–384. https://doi.org/10.1016/B978-0-12-811410-0.00021-0
- Ozawa M., Kubo T., Lee S.H., Oe T. // J. Toxicol. Sci. 2019. V. 44. P. 559–563. https://doi.org/10.2131/jts.44.559
- Yin H., Guo Y., Zeng T., Zhao X., Xie K. // PLoS One. 2013. V. 8. e76011. https://doi.org/10.1371/journal.pone.0076011
- DeCaprio A.P., O’Neill E.A. // Toxicol. Appl. Pharmacol. 1985. V. 78. P. 235–247. https://doi.org/10.1016/0041-008x(85)90287-x
- Yan B., DeCaprio A.P., Zhu M., Bank S. // Chem. Biol. Interact. 1996. V. 102. P. 101–116. https://doi.org/10.1016/s0009-2797(96)03738-6
- DeCaprio A.P., Strominger N.L., Weber P. // Toxicol. Appl. Pharmacol. 1983. V. 68. P. 297–307. https://doi.org/10.1016/0041-008x(83)90014-5
- Ichihara G., Amarnath V., Valentine H.L., Takeshita T., Morimoto K., Sobue T., Kawai T., Valentine W.M. // Int. Arch. Occup. Environ. Health. 2019. V. 92. P. 873– 881. https://doi.org/10.1007/s00420-019-01430-7
- Wang Y., Yu H., Shi X., Luo Z., Lin D., Huang M. // J. Biol. Chem. 2013. V. 288. P. 15980-15987. https://doi.org/10.1074/jbc.M113.467027
- Ding A., Ojingwa J.C., McDonagh A.F., Burlingame A.L., Benet L.Z. // Proc. Natl. Acad. Sci. USA. 1993. V. 90. P. 3797–3801. https://doi.org/10.1073/pnas.90.9.3797
- Wu Y., Chen L., Chen J., Xue H., He Q., Zhong D., Diao X. // Drug Metab. Dispos. 2023. V. 51. P. 8–16. https://doi.org/10.1124/dmd.122.001019
- Scaloni A., Ferranti P., De Simone G., Mamone G., Sannolo N., Malorni A. // FEBS Lett. 1999. V. 452. P. 190–194. https://doi.org/10.1016/S0014-5793(99)00601-8
- Ferraro G., Massai L., Messori L., Merlino A. // Chem. Commun. (Camb). 2015. V. 51. P. 9436–9439. https://doi.org/10.1039/C5CC01751C
- Minet E., Cheung F., Errington G., Sterz K., Scherer G. // Biomarkers. 2011. V. 16. P. 89–96. https://doi.org/10.3109/1354750x.2010.533287
- Lin C.Y., Lee H.L., Sung F.C., Su T.C. // Environ. Pollut. 2018. V. 239. P. 493–498. https://doi.org/10.1016/j.envpol.2018.04.010
- Benz F.W., Nerland D.E., Li J., Corbett D. // Fundam. Appl. Toxicol. 1997. V. 36. P. 149–156. https://doi.org/10.1006/faat.1997.2295
- Walker V.E., Fennell T.R., Walker D.M., Bauer M.J., Upton P.B., Douglas G.R., Swenberg J.A. // Chem. Res. Toxicol. V. 2020. V. 33. P. 1609–1622. https://doi.org/10.1021/acs.chemrestox.0c00153
- Kaur S., Hollander D., Haas R., Burlingame A.L. // J. Biol. Chеm. 1989. V. 264. P. 16981–16984.
- Basile A., Ferranti P., Mamone G., Manco I., Pocsfalvi G., Malorni A., Acampora A., Sannolo N. // Rapid Commun Mass Spectrom. 2002. V. 16. P. 871– 878. https://doi.org/10.1002/rcm.655
- Greim H. // Toxicol Lett. 2003. V. 138. P. 1–8. https://doi.org/10.1016/s0378-4274(02)00408-3
- Rappaport S.M., Yeowell-O'Connell K., Bodell W., Yager J.W., Symanski E. // Cancer Res. 1996. V. 56. P. 5410–5416.
- Dai J., Zhang F., Zheng J. // Anal. Biochem. 2010. V. 405. P. 73–81. https://doi.org/10.1016/j.ab.2010.05.001
- Jаgr M., Mrаz J., Linhart I., Strаnskу V., Pospísil M. // Chem. Res. Toxicol. 2007. V. 20. P. 1442–1452. https://doi.org/10.1021/tx700057t
- Koskinen M., Plnа K. // Chem. Biol. Interact. 2000. V. 129. P. 209–229. https://doi.org/10.1016/s0009-2797(00)00206-4
- Yeowell-O'Connell K., Rothman N., Smith M.T., Hayes R.B., Li G., Waidyanatha S., Dosemeci M., Zhang L., Yin S., Titenko-Holland N., Rappaport S.M. // Carcinogenesis. 1998. V. 19. P. 1565–1571. https://doi.org/10.1093/carcin/19.9.1565
- Rappaport S.M., Yeowell-O'Connell K., Smith M.T., Dosemeci M., Hayes R.B., Zhang L., Li G., Yin S., Rothman N. // J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2002. V. 778. P. 367–374. https://doi.org/10.1016/s0378-4347(01)00457-1
- Grigoryan H., Edmands W.M.B., Lan Q., Carlsson H., Vermeulen R., Zhang L., Yin S.N., Li G.L., Smith M.T., Rothman N., Rappaport S.M. // Carcinogenesis. 2018. V. 39. P. 661–668. https://doi.org/10.1093/carcin/bgy042
- Yeowell-O’Connell K., McDonald T.A., Rappaport S.M. // Anal. Biochem. 1996. V. 237. P. 49–55. https://doi.org/10.1006/abio.1996.0199
- Zarth A.T., Murphy S.E., Hecht S.S. // Chem. Biol. Interact. 2015. V. 242. P. 390–395. https://doi.org/10.1016/j.cbi.2015.11.005
- Zheng L., Li Y., Wu D., Xiao H., Zheng S., Wang G., Sun Q. // MedComm-Oncology. 2023. V. 2. e56. https://doi.org/10.1002/mog2.56
- Carlsson H., Törnqvist M. // Basic Clin. Pharmacol. Toxicol. 2017. V. 121. Suppl. 3. P. 44–54. https://doi.org/10.1111/bcpt.12715
- van Vugt-Lussenburg B.M.A., Capinha L., Reinen J., Rooseboom M., Kranendonk M., Onderwater R.C.A., Jennings P. // Chem. Res. Toxicol. 2022. V. 35. P. 1184– 1201. https://doi.org/10.1021/acs.chemrestox.2c00067
- Chao M.-R., Chang Y.-J., Cooke M.S., Hu C.-W. // Trends Analyt. Chem. 2024. V. 180. е117900. https://doi.org/10.1016/j.trac.2024.117900
- Walmsley S.J., Guo J., Tarifa A., DeCaprio A.P., Cooke M.S., Turesky R.J., Villalta P.W. // Chem. Res. Toxicol. 2024. V. 37. P. 302–310. https://doi.org/10.1021/acs.chemrestox.3c00302
- Chen H.J.C. // Chem. Res. Toxicol. 2023. V. 36. P. 132– 140. https://doi.org/10.1021/acs.chemrestox.2c00354
- Behl T., Rachamalla M., Najda A., Sehgal A., Singh S., Sharma N., Bhatia S., Al-Harrasi A., Chigurupati S., Vargas-De-La-Cruz C., Hobani Y.H., Mohan S., Goyal A., Katyal T., Solarska E., Bungau S. // Int. J. Mol. Sci. 2021. V. 22. е10141. https://doi.org/10.3390/ijms221810141
- Hanwell M.D., Curtis D.E., Lonie D.C., Vandermeersch T., Zurek E., Hutchison G.R. // J. Cheminform. 2012. V. 4. P. 17. https://doi.org/10.1186/1758-2946-4-17
- Hein K.L., Kragh-Hansen U., Morth J.P., Jeppesen M.D., Otzen D., Møller J.V., Nissen P. // J. Struct. Biol. V. 2010. V. 171. P. 353–360. https://doi.org/10.1016/j.jsb.2010.03.014
- Bucci E., Razynska A., Kwansa H., Gryczynski Z., Collins J.H., Fronticelli C., Unger R., Braxenthaler M., Moult J., Ji X., Gilliland G. // Biochemistry. 1996. V. 35. P. 3418–3425. https://doi.org/10.1021/bi952446b
- Sinning I., Kleywegt G.J., Cowan S.W., Reinemer P., Dirr H.W., Huber R., Gilliland G.L., Armstrong R.N., Ji X., Board P.G, Olin B., Mannervik B., Jones T.A. // J. Mol. Biol. 1993. V. 232. P. 192-212. https://doi.org/10.1006/jmbi.1993.1376.
- Humphrey W., Dalke A., Schulten K. // J. Mol. Graph. 1996. V. 14. P. 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
- Neese F. // Wiley Interdiscip. Rev. Comput. Mol. Sci. 2022. V. 12. e1606. https://doi.org/10.1002/wcms.1606
- Melnikov F., Geohagen B.C., Gavin T., LoPachin R.M., Anastas P.T., Coish P., Herr D.W. // Neurotoxicology. 2020. V. 79. P. 95–103. https://doi.org/10.1016/j.neuro.2020.04.009
- Eberhardt J., Santos-Martins D., Tillack A.F., Forli S. // J. Chem. Inf. Model. 2021. V. 61. P. 3891–3898. https://doi.org/10.1021/acs.jcim.1c00203
- Belinskaia D.A., Savelieva E.I., Karakashev G.V., Orlova O.I., Leninskii M.A., Khlebnikova N.S., Shestakova N.N., Kiskina A.R. // Int. J. Mol. Sci. 2021. V. 22. e9021. https://doi.org/10.3390/ijms22169021
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