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DEVELOPMENT OF METHODS OF SIMULATION OF THE INTERACTION OF BIOLOGICALLY ACTIVE SUBSTANCES WITH THE ACTIVE CENTER OF ANGIOTENSIN-CONVERTING ENZYME

https://doi.org/10.19163/2307-9266-2017-5-5-487-503

Abstract

Nowadays cardiovascular diseases are the main cause of death among the population around the word. The development of new drugs, giving a possibility to normalize blood pressure, is a promising direction in the field of pharmacy and medicine. Now inhibitors of angiotensinconverting enzyme (ACE) are widely adopted for the treatment of hypertension and chronic heart failure. The principle of action of ACE inhibitors is based on blocking the conversion of angiotensin I into angiotensin II, which mediates vasodilation.

The aim of the work is a selection of methods of lisinopril interaction with the active center of angiotensin-converting enzyme by molecular dynamics methods.

Materials and methods. Lisinopril molecule was used as a ligand; the charges of that ligand were calculated with the density functional theory (DFT) and ub3lyp method with the basis sets 6-31G* and 6-311G**. Simulation of 75 ns of molecular dynamics of lisinopril interaction with the active center of ACE was carried out in the Bioevrica program. As a result of molecular dynamics simulation, the trajectory of the “lisinopril-ACE” system was obtained. After that a comparison of ligand conformations at different points in simulation time with the experimental conformation of the value of standard deviation of coordinates of atoms was made.

Results and discussion.The results of simulation have showed that lisinopril with the charges corresponding to basis set 6-311G** behaves consistent with the x-ray data in the active center of the ACE, in contrast to lisinopril with the charges calculated by basis set 6-31G*.

Conclusion. The methods of lisinopril interaction modeling with the active center of angiotensin-converting enzyme has been selected. The obtained technique can be used for studying the interaction of substances, similar in structure to lisinopril with the active center of the enzyme (ACE).

About the Authors

A. A. Glushko
Рyatigorsk Medical Pharmaceutical Institute of Volgograd Medical State University
Russian Federation

Glushko Alexander Alekseevich – Candidate of Sciences (Pharmacy), Lecturer of the Department of Inorganic, Physical and Colloid Chemistry.

11, Kalinin Ave., Pyatigorsk, 357532



A. S. Chiriapkin
Рyatigorsk Medical Pharmaceutical Institute of Volgograd Medical State University
Russian Federation

Chiriapkin Alexey Sergeevich – student.

11, Kalinin Ave., Pyatigorsk, 357532



V. S. Chiriapkin
Рyatigorsk Medical Pharmaceutical Institute of Volgograd Medical State University
Russian Federation

Chiriapkin Vitaly Sergeevich – student.

11, Kalinin Ave., Pyatigorsk, 357532



A. M. Murtuzalieva
Рyatigorsk Medical Pharmaceutical Institute of Volgograd Medical State University
Russian Federation

Murtuzalieva Asyat Muradovna – student.

11, Kalinin Ave., Pyatigorsk, 357532



Yu. A. Polkovnikova
Federal State Budget Educational Institution of Higher Education “Voronezh State University”
Russian Federation

Polkovnikova Yulia Alexandrovna – Candidate of Sciences (Pharmacy), docent.

3, Student Street, Voronezh, 394036



References

1. Hilal-Dandan R. Renin and Angiotensin. Chapter 26. In Laurence L. Brunton, John S. Lazo, Keith L. Parker, editors. “Goodman & Gilman’s”. The pharmacological basis of therapeutics (12th ed.). New York: McGraw-Hill; 2006:721–44.

2. Bangalore S, Fakheri R, Wandel S, Toklu B, Wandel J, Messerli FH. Renin angiotensin system inhibitors for patients with stable coronary artery disease without heart failure: systematic review and meta-analysis of randomized trials. BMJ (Clinical research ed.) [Internet]. 2017;356. [cited 2017 Nov 03]. Available from: http://www. bmj.com/content/356/bmj.j4. DOI:10.1136/bmj.j4

3. Shafi S. Role of ace inhibitors in atherosclerosis. International journal of biomedical and advance research. 2013;12:849–54.

4. Jandeleit-Dahm K, Cooper ME. Hypertension and diabetes: role of the renin-angiotensin system. Endocrinol. Metab. Clin. North Am. 2006;35(3):469–90. DOI:10.1016/j.ecl.2006.06.007

5. Preobrazhenskii DV, Nekrasova NI, Talyzina IV, Pataraia SA, Bugrimova MA. Lizinopril gidrofilnyj ingibitor angiotenzinprevrashchayushchego fermenta dlitelnogo dejstviya osobennosti klinicheskoj farmakologii i diapazon klinicheskogo primeneniya [Lisinopril is hydrophilic angiotensinconverting enzyme inhibitor long-acting: features of clinical pharmacology and the range of clinical applications]. RMJ. 2010;10:684. Russian.

6. Mollica L, Theret I, Antoine M, Perron-Sierra F, Charton Y, Fourquez J-M, Wierzbicki M, Boutin JA, Ferry G, Decherchi S, Bottegoni G, Ducrot P, Cavalli A. Molecular dynamics simulations and kinetic measurements to estimate and predict protein−ligand residence times. J. Med. Chem. 2016;59(15):7167–76. DOI: 10.1021/acs.jmedchem.6b00632

7. Sharma R, Dhingra N, Patil S. CoMFA, CoMSIA, HQSAR and molecular docking analysis of ionone-based chalcone derivatives as antiprostate cancer activity. Indian J Pharm Sci. 2016 Jan-Feb;78(1):54–64.

8. Garsia-Dzhakas SR, Avdeenko TV. Multiservernyj podhod k vysokoproizvoditelnomu vychisleniyu molekulyarnyh deskriptorov [Multi-server approach to high-performance calculating of the molecular descriptors]. Science bulletin NSTU. 2015;58:148–60. DOI: 10.17212/1814-1196-2015-1-148-160. Russian.

9. Gloushko AA., Voronkov AV., Kodonidi IP., Bicherov AB., Chernikov MB. Molekulyarnyj doking N-zameshchennogo proizvodnogo izohinolonas kataliticheskim domenom C [Molecular docking od N-substituted derivative of isoquinolone with catalyc domain of protein kinase C]. Pharmacy & Pharmacology. 2014;1(2):3–7. DOI: 10.19163/2307-9266-2014-2-1(2)-3-7. Russian.

10. Norman GJe., Stegailov VV. Stohasticheskaya teoriya metoda klassicheskoj molekulyarnoj dinamiki [Stochastic theory of the classical molecular dynamics]. Matematical models and computer simulation. Modelirovanie. 2012;6(24):3–44. Russian.

11. Soubrier F, Alhenc-Gelas F, Hubert C, Allegrini J, John M, Tregear G, Corvol P. Two putative active centers in human angiotensin I-converting enzyme revealed by molecular cloning. Proc. Natl. Acad. Sci. U.S.A. 1988;85:9386–90.

12. Corradi HR, Schwager SLU, Nchinda AT, Sturrock ED, Acharya KR. Crystal structure of the N domain of human somatic angiotensin I-converting enzyme provides a structural basis for domain-specific inhibitor design. J. Mol. Biol. 2006;357:964–74. DOI: 10.1016/j.jmb.2006.01.048

13. Natesh R, Schwager SLU, Sturrock ED, Acharya KR. Crystal structure of the human angiotensin-converting enzyme-lisinopril complex. Nature. 2003;421:551–4. DOI: 10.1038/nature01370

14. Akif M, Georgiadis D, Mahajan A, Dive V, Sturrock ED, Isaac RE, Acharya KR. High resolution crystal structures of drosophila melanogaster angiotensin converting enzyme in complex with novel inhibitors and anti-hypertensive drugs. J. Mol. Biol. 2010;400:502–17. DOI: 10.1016/j.jmb.2010.05.024

15. Teppen BJ. HyperChem, release 2: molecular modeling for the personal computer. J. Chem. Inf. Comput. Sci. 1992;6(32):757–9.

16. Stephens PJ, Devlin FJ, Chabalowski CF, Frisch MJ. Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J. Phys. 1994;98(45):11623–7. DOI: 10.1021/j100096a001

17. Minkin VI, Simkin BI, Miniaev RM. Stroenie molekul [The structure of the molecules]. Rostov-on-don: Phoenix; 1997. 560 p. Russian.

18. Gendugov TA, Shcherbakova LI, Glushko AA, Kоdonidi IP, Sochnev VS. Izuchenie vzaimodejstviya proizvodnyh 4-oksopirimidina s aktivnym centrom ciklooksigenazy-2 metodom molekulyarnoj dinamiki [Study of 4-oxopirimidine derivatives interaction with the active site of cyclooxygenase-2 using molecular dynamics]. Modern problems of science and education. [Internet] 2015;2. [cited 2017 Iun 10]. Available from: https://science-education.ru/ru/article/view?id=22796. Russian.

19. Khalilova SV. Modelirovanie processa zhidkostnoj ekstrakcii biologicheski aktivnyh veshchestv metodom molekulyarnoj dinamiki v programme Bioevrika [Modeling of solvent extraction process of biologically active substances by the method of molecular dynamics in the program of Bioafrica]. The collection of materials of VI all-Russian scientific conference of students and postgraduates with international participation “Young pharmacy is a potential future”; 2016 April 25–26; St. Petersburg: Publishing house of SPCPA; 2016:118–20. Russian.

20. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995;117(19):5179–97. DOI: 10.1021/ja00124a002

21. Leontyev IV, Stuchebrukhov AA. Polarizable mean-field model of water for biological simulations with amber and charmm force fields. J. Chem. Theory Comput. 2012;8(9):3207–16. DOI: 10.1021/ct300011h

22. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983;2(79):926–35. DOI: 10.1063/1.445869

23. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984;81:3684–90. DOI: 10.1063/1.448118

24. Forli S, Huey R, Pique ME, Sanner MF, Goodsell DS, Olson AJ. Computational protein–ligand docking and virtual drug screening with the AutoDock suite. Nature Protocols. 2016;5(11):905–19. DOI: 10.1038/nprot.2016.051

25. Hildebrandt AK, Diezen M, Lengauer T, Lenhof HP, Althaus E, Hildebrandt A. Efficient computation of root mean square deviations under rigid transformations. J Comput Chem. 2014. Apr 15;35(10):765–71. DOI: 10.1002/jcc.23513


Review

For citations:


Glushko A.A., Chiriapkin A.S., Chiriapkin V.S., Murtuzalieva A.M., Polkovnikova Yu.A. DEVELOPMENT OF METHODS OF SIMULATION OF THE INTERACTION OF BIOLOGICALLY ACTIVE SUBSTANCES WITH THE ACTIVE CENTER OF ANGIOTENSIN-CONVERTING ENZYME. Pharmacy & Pharmacology. 2017;5(5):487-503. (In Russ.) https://doi.org/10.19163/2307-9266-2017-5-5-487-503

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