In-silico Evaluation of Hexagamavunon Analogs for Antibacterial Activity Against Helicobacter pylori http://www.doi.org/10.26538/tjnpr/v7i9.8
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Abstract
Helicobacter pylori (H. pylori) infection has been associated with gastric cancer. Antibiotic resistance has reached dangerous levels. Therefore, finding new anti-effective drugs against H. pylori is crucial. This study evaluated the potential of hexagamavunon (HGV) analogs as anti-H. pylori drugs through molecular docking. The AutoDock Vina program was used in the molecular tethering process. The ligands (HGV analogs), were docked to the shikimate kinase enzyme (PDB ID: 3N2E) and urease (PDB ID: 1E9Y) as the targets in inhibiting H. pylori. The parameter observed was the ligands' binding energy (kcal/mol) compared to native ligands. The results of molecular docking of the shikimate kinase enzyme showed that the binding energies of A6 (-10.7), A7 (-9.9), and A11 (-9.9) were lower compared with native ligand binding energy (-9.8). Also, the binding energy of the urease enzyme with A6 (-7.5), A7 (-8.1), and A11 (-7.7) was lower than the binding energy of the urease with native ligand (-3.4). Low binding energy correlated with the strength of the bonds between ligands and receptors. HGV analogs, A6, A7, and A11, have higher anti-H. pylori potential than other analogs because they have the lowest binding energies. Further in vitro research is needed to evaluate the potential of HGV analogs as anti-H. Pylori agents.
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Debraekeleer A, Remaut H. Future perspective for potential Helicobacter pylori eradication therapies. Future Microbiol. 2018;13(6):671–87.
Burkitt MD, Duckworth CA, Williams JM, Pritchard DM. Helicobacter pylori-induced gastric pathology: Insights from in vivo and ex vivo models. DMM Dis Model Mech. 2017;10(2):89–104.
Diaconu S, Predescu A, Moldoveanu A, Pop CS, Fierbințeanu-Braticevici C. Helicobacter pylori infection: old and new. J Med Life [Internet]. 2017;10(2):112–7. Available from: http://www.ncbi.nlm.nih.gov/pubmed/28616085 %0Ahttp://www.pubmedcentral.nih.gov/articlerender.fcgi?a
rtid=PMC5467250
Savoldi A, Carrara E, Graham DY, Conti M, Tacconelli E. Prevalence of Antibiotic Resistance in Helicobacter pylori: A Systematic Review and Meta-analysis in World Health Organization Regions. Gastroenterology [Internet]. 2018;155(5):1372-1382.e17. Available from: https://doi.org/10.1053/j.gastro.2018.07.007
Moss SF. The Clinical Evidence Linking Helicobacter pylori to Gastric Cancer. Cmgh. 2017;3(2):183–91.
Lee YC, Chiang TH, Chou CK, Tu YK, Liao WC, Wu MS, Graham DY. Association between Helicobacter pylori Eradication and Gastric Cancer Incidence: A Systematic Review and Meta-analysis. Gastroenterology. 2016;150(5):1113–24.
Kuo YT, Liou JM, El-Omar EM, Wu JY, Leow AHR, Goh KL, Das R, Lu H, Lin JT, Tu YK, Yamaoka Y, Wu MS. Primary antibiotic resistance in Helicobacter pylori in the Asia-Pacific region: a systematic review and meta-analysis. Lancet Gastroenterol Hepatol. 2017;2(10):707–15.
Bilgilier C, Stadlmann A, Makristathis A, Thannesberger J, Kastner MT, Knoflach P, Steiner, P, Schöniger-Hekele M. Högenauer C, Blesl A, Datz C, Huber-Schönauer U, Schöfl R, Wewalka F, Püspök A, Mitrovits N, Leiner J, Tilg H, Effenberger M, Moser M, Siebert F, Hinterberger I, Wurzer
H, Stupnicki T, Watzinger N, Gombotz G, Hubmann, Klimpel S, Biowski-Frotz S, Schrutka-Kölbl C, Graziadei I, Ludwiczek O, Kundi M, Hirschl AM, Steininger C. Prospective multicentre clinical study on inter- and intrapatient genetic variability for antimicrobial resistance of Helicobacter pylori. Clin Microbiol Infect. 2018;24(3):267–72.
Chey WD, Leontiadis GI, Howden CW, Moss SF. ACG Clinical Guideline: Treatment of Helicobacter pylori Infection. Am J Gastroenterol. 2017;112(2):212–38.
Talebi Bezmin Abadi A, Yamaoka Y. Helicobacter pylori therapy and clinical perspective. J Glob Antimicrob Resist. 2018;14:111–7.
Peng C, Hu Y, Ge Z-M, Zou Q-M, Lyu N-H. Diagnosis and treatment of Helicobacter pylori infections in children and elderly populations. Chronic Dis Transl Med. 2019;5(4):243–51.
Baltas N, Karaoglu SA, Tarakci C, Kolayli S. Effect of propolis in gastric disorders: inhibition studies on the growth of Helicobacter pylori and production of its urease. J Enzyme Inhib Med Chem. 2016;31:46–50.
Savoldl A, Carrara E, Graham D, Conti M, Tacconelli E. Prevalence of Antibiotic Resistance in Helicobcater pylori: Revisón sistemática y Metaanálisis en las Regiones de laOMS. Gastroenterology. 2018;155(5):1372–82.
Zhou JT, Li CL, Tan LH, Xu YF, Liu YH, Mo ZZ, Dou YX, Su R, Su ZR, Hunag P, Xie JH. Inhibition of Helicobacter pylori and its associated urease by Palmatine: Investigation on the potential mechanism. PLoS One. 2017;12(1):1–15.
Prado V, Lence E, Maneiro M, Vázquez-Ucha JC, Beceiro A, Thompson P, Hawkins AR, González-Bello C. Targeting the Motion of Shikimate Kinase: Development of Competitive Inhibitors that Stabilize an Inactive Open Conformation of the Enzyme. J Med Chem. 2016;59(11):5471–87.
Tarsia C, Danielli A, Florini F, Cinelli P, Ciurli S, Zambelli B. Targeting Helicobacter pylori urease activity and maturation: In-cell high-throughput approach for drug discovery. Biochim Biophys Acta - Gen Subj. 2018;1862(10):2245–53.
Francenia Santos-Sánchez N, Salas-Coronado R, Hernández-Carlos B, Villanueva-Cañongo C. Shikimic Acid Pathway in Biosynthesis of Phenolic Compounds. Plant Physiol Asp Phenolic Compd. 2019;1–15.
Ansari S, Yamaoka Y. Survival of Helicobacter pylori in gastric acidic territory. Helicobacter. 2017;22(4):1–13.
Golonko A, Lewandowska H, Świsłocka R, Jasińska UT, Priebe W, Lewandowski W. Curcumin as tyrosine kinase inhibitor in cancer treatment. Eur J Med Chem. 2019;181.
Meiyanto E, Septisetyani EP, Larasati YA, Kawaichi M. Curcumin analog pentagamavunon-1 (PGV-1) sensitizes widr cells to 5-fluorouracil through inhibition of NF-κB activation. Asian Pacific J Cancer Prev. 2018;19(1):49–56.
Kaladhar D, Banjara T, Kant S, Tiwari Mishra S, Kumari Dupplala S. In Silico Screening of Compounds From Turmeric (Curcuma Longa L.) Against Cancer Causing Proteins. Int J Curr Trends Eng Technol www.ijctet.org [Internet]. 2018;01:2395–3152. Available from: www.ijctet.org,
Wijianto B, Purnomo H, Nurrochmad A. Qsar And Synthesis Of Curcumin Analogues As Antibacterial. 2018;17(8):72–82.
Vetvicka V, Vetvickova J, Fernandez-Botran R. Effects of curcumin on Helicobacter pylori infection. Ann Transl Med. 2016;4(24):1–7.
Ranjbar R, Mohammadi A. Synergistic effects of combined curcumin and antibiotic in ameliorating an animal model of Helicobacter pylori infection. Biomed Res. 2018;29(8):1702–7.
Banuppriya G, Sribalan R, Padmini V. Evaluation of Antioxidant, Anti-Inflammatory, Antibacterial Activity and In Silico Molecular Docking Study of Pyrazole Curcumin Bisacetamide Analogs. ChemistrySelect. 2017;2(28):9168– 73.
Shrivash MK, Mishra S, UpmaNarain, Pandey J, Misra K. In-silico designing, chemical synthesis, characterization and in-vitro assessment of antibacterial properties of some analogues of curcumin. Microb Pathog [Internet]. 2018;123(May):89–97. Available from: https://doi.org/10.1016/j.micpath.2018.06.030
Zorofchian Moghadamtousi S, Abdul Kadir H,Hassandarvish P, Tajik H, Abubakar S, Zandi K. A review on antibacterial, antiviral, and antifungal activity of curcumin. Biomed Res Int. 2014;2014.
Khor PY, Aluwi MFFM, Rullah K, Lam KW. Insights on the synthesis of asymmetric curcumin derivatives and their biological activities. Eur J Med Chem. 2019;183.
Noureddin, Sawsan A., El-Shishtawy RM, Al-Footy KO. Curcumin analogues and their hybrid molecules as multifunctional drugs. Eur J Med Chem. 2019;182.
Wijianto B, Ritmaleni, Purnomo H, Nurrochmad A. in Silico and in Vitro Assay of Hgv Analogue As Antibacterial. Int J Pharm Pharm Sci. 2019;11(3):78–85.
Safitri CINH, Ritmaleni, Rintiswati N, Sardjiman, Kaneko T. Evaluation of benzylidene-acetone analogues of curcumin as antituberculosis. Asian J Pharm Clin Res. 2018;11(4):226–30.
Safitri CINH, Rintiswati N, Kaneko T. Antimycobacterial Activity of Benzylidene Acetone Analogues on Curcumin Against Resistant And Sensitive Mycobacterium Tuberculosis. IOSR J Dent Med Sci. 2017;16(12):21–6.
Rahmania TA, Ritmaleni R, Setyowati EP. In silico and in vitro assay of Hexagamavunon-6 analogs, Dibenzilyden-NMethyl-4-piperidone as antibacterial agents. J Appl Pharm Sci. 2020;10(3):39–43.
Wardani AK, Ritmaleni, Setyowati EP. Molecular Docking Studies Of HGV-6 Analogue As A Potential PBP-1A Inhibitor. Int J Pharm Pharm Sci. 2020;12(4):8–12.
Du B-X, Qin Y, Jiang Y-F, Xu Y, Yiu S-M, Yu H, Shin JY. Compound–protein interaction prediction by deep learning: Databases, descriptors and models. Drug Discov Today. 2022;27(5):1350–66.
Wang M, Liu Y, Liu Y, Xia Z. MOFs and PDA-supported immobilization of BSA in open tubular affinity capillary electrochromatography: Prediction and study on drugprotein interactions. Talanta. 2022;237.
Vieira TF, Sousa SF. Comparing AutoDock and Vina in ligand/decoy discrimination for virtual screening. Appl Sci (S. 2019;9(21):1-18.
Yasman S, Yanuar A, Tamimi Z, Riadhi SR. In Silico Analysis of Sea Cucumber Bioactive Compounds as AntiBreast Cancer Mechanism Using AutoDock Vina. Iran J Pharm Sci. 2020;16(1):1–8.
Sokalingam S, Munussami G, Kim JR, Lee SG. Validation on the molecular docking efficiency of lipocalin family of proteins. J Ind Eng Chem. 2018;67:293–300.
Chagas CM, Moss S, Alisaraie L. Drug metabolites and their effects on the development of adverse reactions: Revisiting Lipinski's Rule of Five. Int J Pharm. 2018;549(1–2):133–49.
Huang H, Chu CL, Chen L, Shui D. Evaluation of potential inhibitors of squalene synthase based on virtual screening and in vitro studies. Comput Biol Chem. 2019;80:390–7.
Benet LZ, Hosey CM, Ursu O, Oprea TuI. BDDCS, the Rule of 5 and Drugability. Adv Drug Deliv Rev. 2016;101:89–98.
Goyal M, Chauhan S, Goyal P, Prabha J. Structural modeling of shikimate pathway enzymes for herbicide and drug development : A review. J Entomol Zool Stud. 2018;6(2):785–90.
Graham DY, Miftahussurur M. Helicobacter pylori urease for diagnosis of Helicobacter pylori infection: A mini review. J Adv Res. 2018;13:51–7.
de Souza AS, Pacheco BDC, Pinheiro S, Muri EMF, Dias LRS, Lima CHS, Garrett R, de Moraes MBM, de Souza BEG, Puzer L. 3-Acyltetramic acids as a novel class of inhibitors for human kallikreins 5 and 7. Bioorganic Med Chem Lett [Internet]. 2019;29(9):1094–8. Available from:
https://doi.org/10.1016/j.bmcl.2019.02.031
Al-Karmalawy AA, Dahab MA, Metwaly AM, Elhady SS, Elkaeed EB, Eissa IH, Darwish KM. Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of ACEIs Against SARS-CoV-2 Targeting the hACE2 Receptor. Front Chem. 2021;9(May).
Rahayu S, Prasetyawan S, Suprihatin T, Ciptadi G. In-silico study of Marselia crenata compounds as activator Keap1/Nrf2 pathway in ovarian function. IOP Conf Ser Earth Environ Sci. 2021;743(1).
Kanagavalli U, Deboral E, Lakshmipriya MD, Sadiq AM, Priya AM. In silico Molecular Docking of Anthraquinone Identified from Boerhavia diffusa Linn against Bax and Bcl-2 Gene. J Pharm Res Int. 2021;33:352–9.
Singh R, Bhardwaj VK, Sharma J, Purohit R, Kumar S. Insilico evaluation of bioactive compounds from tea as potential SARS-CoV-2 nonstructural protein 16 inhibitors. J Tradit Complement Med [Internet]. 2022;12(1):35–43. Available from: https://doi.org/10.1016/j.jtcme.2021.05.005
Martiz RM, Patil SM, Abdulaziz M, Babalghith A, AlAreefi M, Al-Ghorbani M, Kumar JM, Prasad A, Nagalingaswamy NPM, Ramu R. Defining the Role of Isoeugenol from Ocimum tenuiflorum against Diabetes Mellitus-Linked Alzheimer's Disease through Network Pharmacology and Computational Methods. Molecules. 2022;27(8):1-21.
Sundari S, Mas’ud A, Sari DRT. Molecular Docking Discovered Potential of Cyclooxygenase – 2 InhibitorActivity of Oily Compounds of Walnuts. Trop J Nat Prod Res. 2022;6(12):1947–52.