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In Silico Analysis Determining the Binding Interactions of NAD(P)H: Quinone Oxidoreductase 1 and Resveratrol via Docking and Molecular Dynamic Simulations

Year 2023, Volume: 82 Issue: 2, 280 - 288, 21.12.2023
https://doi.org/10.26650/EurJBiol.2023.1352396

Abstract

Objective: NAD(P)H: Quinone oxidoreductase1 (NQO1) plays a crucial role in cellular defense against oxidative stress. Overexpression of NQO1 is linked to various cancer pathways. Despite its potential, the actual mechanisms to inhibit NQO1 and increase the efficacy of standard therapeutic options are not yet established. Resveratrol is an anti-cancer polyphenol found in dietary products and red wine. The objective of this investigation is to employ in silico methods to explore how resveratrol interacts with NQO1.

Materials and Methods: Docking analysis of resveratrol against NQO1 was performed using Glide. The most efficiently docked complex was characterized and analyzed by measuring intermolecular (IM) hydrogen (H)-bonds and binding energy values, additional hydrophobic, and electrostatic interactions. IM interaction between complexed protein and compound was demonstrated using LigPlot+ and the Schrödinger ligand interaction module. Molecular dynamics tools were employed to examine the physical movement of molecules to evaluate how macromolecular structures relate to their functions.

Results: The results of this investigation depicted a strong affinity of resveratrol againstNQO1followed byMDsimulations (NQO1- resveratrol complex-binding energy: -2.847kcal/mol). Resveratrol’s robust binding affinity through docking and molecular dynamic simulations highlights a significant change around 90 ns. The H-bonds number was inversely linked with the resveratrol-NQO1 complex stability. The NQO1-Resveratrol complex displayed dynamic motion, as revealed by porcupine projections, indicating alterations in its movement and flexibility.

Conclusion: The present in silico analysis suggests a possible alteration in resveratrol’s orientation in the protein binding pocket. The findings encourage further investigation, including validation using in vitro and in vivo assays.

References

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  • Starcher CL, Pay SL, Singh N, et al. Targeting base ex-cision repair in cancer: NQO1-bioactivatable drugs improve tumor selectivity and reduce treatment toxicity through ra-diosensitization of human cancer. Front Oncol. 2020;10:1575. doi:10.3389/fonc.2020.01575 google scholar
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  • Soleas GJ, Diamandis EP, Goldberg DM. Resveratrol: A molecule whose time has come? And gone? Clin Biochem. 1997;30(2):91-113. google scholar
  • Wright JS, Johnson ER, DiLabio GA. Predicting the activity of phenolic antioxidants: Theoretical method, analysis of substituent effects, and application to major families of antioxidants. J Am Chem Soc. 2001;123(6):1173-1183. google scholar
  • Ji Q, Liu X, Han Z, et al. Resveratrol suppresses epithelial-to-mesenchymal transition in colorectal cancer through TGF-beta1/Smads signaling pathway mediated Snail/E-cadherin ex-pression. BMC Cancer. 2015;15:97. doi:10.1186/s12885-015-1119-y google scholar
  • Bian P, Hu W, Liu C, Li L. Resveratrol potentiates the anti-tumor effects of rapamycin in papillary thyroid cancer: PI3K/AKT/mTOR pathway involved. Arch Biochem Biophys. 2020;689:108461. doi:10.1016/j.abb.2020.108461 google scholar
  • Hope C, Planutis K, Planutiene M, et al. Low concentrations of resveratrol inhibit Wnt signal throughput in colon-derived cells:Implications for colon cancer prevention. Mol Nutr Food Res. 2008;52 Suppl 1(Suppl 1):S52-61. google scholar
  • Ren B, Kwah MX, Liu C, et al. Resveratrol for cancer therapy: Challenges and future perspectives. Cancer Lett. 2021;515:63-72. google scholar
  • Morris GM, Huey R, Lindstrom W, et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785-2791. google scholar
  • Kim S, Chen J, Cheng T, et al. PubChem in 2021: New data content and improved web interfaces. Nucleic Acids Res. 2021;49(D1):388-395. google scholar
  • Behera SK, Vhora N, Contractor D, et al. Computational drug repurposing study elucidating simultaneous inhibition of entry and replication of novel corona virus by Grazoprevir. Sci Rep. 2021;11(1):7307. doi:10.1038/s41598-021-86712-2 google scholar
  • Durrant JD, McCammon JA. Molecular dynamics simulations and drug discovery. BMC Biol. 2011;9:71. doi:10.1186/1741-7007-9-71 google scholar
  • Raghu R, Devaraji V, Leena K, et al. Virtual screening and dis-covery of novel aurora kinase inhibitors. Curr Top Med Chem.2014;14(17):2006-2019. google scholar
  • Shivakumar D, Williams J, Wu Y, Damm W, Shelley J, Sherman W. Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J Chem Theory Comput. 2010;6(5):1509-1519. google scholar
  • Aier I, Varadwaj PK, Raj U. Structural insights into conforma-tional stability of both wild-type and mutant EZH2 receptor. Sci Rep. 2016;6:34984. doi:10.1038/srep34984 google scholar
  • Deniz U, Ozkirimli E, Ulgen KO. A systematic methodology for large scale compound screening: A case study on the discovery of novel S1PL inhibitors. JMol Graph Model. 2016;63:110-124. google scholar
  • Behera SK, Mahapatra N, Tripathy CS, Pati S. Drug repurpos-ing for identification of potential inhibitors against SARS-CoV-2 spike receptor-binding domain: An in silico approach. Indian J Med Res. 2021;153(1 & 2):132-143. google scholar
  • Pace CN, Fu H, Lee Fryar K, et al. Contribution of hydrogen bonds to protein stability. Protein Sci. 2014;23(5):652-661. google scholar
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  • Dariya B, Behera SK, Srivani G, Farran B, Alam A, Nagaraju GP. Computational analysis of nuclear factor-kappaB and resveratrol in colorectal cancer. J Biomol Struct Dyn. 2021;39(8):2914-2922. google scholar
  • Al-Karmalawy AA, Dahab MA, Metwaly AM, et al. Molec-ular docking and dynamics simulation revealed the poten-tial inhibitory activity of ACEIs against SARS-CoV-2 tar-geting the hACE2 receptor. Front Chem. 2021;9:661230. doi:10.3389/fchem.2021.661230 google scholar
  • Morris JH, Meng EC, Ferrin TE. Computational tools for the interactive exploration of proteomic and structural data. Mol Cell Proteomics. 2010;9(8):1703-1715. google scholar
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  • Nagaraju GP, Farran B, Farren M, et al. Napabucasin (BBI 608), a potent chemoradiosensitizer in rectal cancer. Cancer. 2020;126(14):3360-3371. google scholar
Year 2023, Volume: 82 Issue: 2, 280 - 288, 21.12.2023
https://doi.org/10.26650/EurJBiol.2023.1352396

Abstract

References

  • Nishida-Tamehiro K, Kimura A, Tsubata T, Takahashi S, Suzuki H. Antioxidative enzyme NAD(P)H quinone oxidore-ductase 1 (NQO1) modulates the differentiation of Th17 cells by regulating ROS levels. PLoS One. 2022;17(7):e0272090. doi:10.1371/journal.pone.0272090 google scholar
  • Preethi S, Arthiga K, Patil AB, Spandana A, Jain V. Review on NAD(P)H dehydrogenase quinone 1 (NQO1) pathway. Mol Biol Rep. 2022;49(9):8907-8924 google scholar
  • Ross D, Siegel D. The diverse functionality of NQO1 and its roles in redox control. Redox Biol. 2021;41:101950. doi:10.1016/j.redox.2021.101950 google scholar
  • Beaver SK, Mesa-Torres N, Pey AL, Timson DJ. NQO1: A target for treating cancer and neurological diseases, and a model to understand loss of function disease mechanisms. Biochim Biophys Acta Proteins Proteom. 2019;1867(7-8):663-676. google scholar
  • Li X, Liu Z, Zhang A, et al. NQO1 targeting prodrug triggers innate sensing to overcome checkpoint blockade resistance. Nat Commun. 2019;10(1):3251. doi:10.1038/s41467-019-11238-1 google scholar
  • Parkinson EI, Hergenrother PJ. Deoxynyboquinones as NQO1-activated cancer therapeutics. Acc Chem Res. 2015;48(10):2715-2723. google scholar
  • Lundberg AP, Francis JM, Pajak M, et al. Pharmacokinetics and derivation of an anticancer dosing regimen for the novel anti-cancer agent isobutyl-deoxynyboquinone (IB-DNQ), a NQO1 bioactivatable molecule, in the domestic felid species. Invest New Drugs. 2017;35(2):134-144. google scholar
  • Oh ET, Park HJ. Implications of NQO1 in cancer therapy. BMB Rep. 2015;48(11):609-617. google scholar
  • Liu Y, Jiang M, Zhao Z, Wang N, Wang K, Yuan Y. Cyclic amplification of intracellular ROS boosts enzymatic prodrug activation for enhanced chemo-immunotherapy. Acta Biomater. 2023;166:567-580. google scholar
  • Yang PW, Xu PL, Cheng CS, et al. Integrating network pharmacol-ogy and experimental models to investigate the efficacy of QYHJ on pancreatic cancer. J Ethnopharmacol. 2022;297:115516. doi:10.1016/j.jep.2022.115516 google scholar
  • Xia MH, Yan XY, Zhou L, et al. p62 suppressed VK3-induced oxidative damage through Keap1/Nrf2 pathway in human ovarian cancercells. J Cancer. 2020;11(6):1299-1307. google scholar
  • Li J, Zhang J, Zhu Y, Afolabi LO, Chen L, Feng X. Natural compounds, optimal combination of brusatol and polydatin pro-mote anti-tumor effect in breast cancer by targeting nrf2 signaling pathway. Int JMol Sci. 2023;24(9). doi:10.3390/îjms24098265 google scholar
  • Tsai HY, Bronner MP, March JK, et al. Metabolic targeting of NRF2 potentiates the efficacy of the TRAP1 inhibitor G-TPP through reduction of ROS detoxification in colorectal cancer. Can-cer Lett. 2022;549:215915. doi:10.1016/j.canlet.2022.215915 google scholar
  • Ramesh PS, Raja S, Udayakumar SH, Chandrashekar S, Nataraj SM, Devegowda D. Role of NRF2 cascade in determining the differential response of cervical cancer cells to anticancer drugs: An in vitro study. Mol Biol Rep. 2022;49(1):109-119. google scholar
  • Bovilla VR, Kuruburu MG, Bettada VG, et al. Targeted inhibi-tion of anti-inflammatory regulator nrf2 results in breast can-cer retardation in vitro and in vivo. Biomedicines. 2021;9(9). doi:10.3390/biomedicines9091119 google scholar
  • Ross D, Siegel D. Functions of NQO1 in cellular protec-tion and CoQ(10) metabolism and its potential role as a re-dox sensitive molecular switch. Front Physiol. 2017;8:595. doi:10.3389/fphys.2017.00595 google scholar
  • Gong Q, Yang F, Hu J, et al. Rational designed highly sensi-tive NQO1-activated near-infrared fluorescent probe combined with NQO1 substrates in vivo: An innovative strategy for NQO1-overexpressing cancer theranostics. Eur J Med Chem. 2021;224:113707. doi:10.1016/j.ejmech.2021.113707 google scholar
  • Zhao W, Jiang L, Fang T, et al. Beta-Lapachone selectively kills hepatocellular carcinoma cells by targeting NQO1 to induce ex-tensive dna damage and PARP1 hyperactivation. Front Oncol. 2021;11:747282. doi:10.3389/fonc.2021.747282 google scholar
  • Starcher CL, Pay SL, Singh N, et al. Targeting base ex-cision repair in cancer: NQO1-bioactivatable drugs improve tumor selectivity and reduce treatment toxicity through ra-diosensitization of human cancer. Front Oncol. 2020;10:1575. doi:10.3389/fonc.2020.01575 google scholar
  • Pervaiz S. Resveratrol-from the bottle to the bedside? Leuk Lymphoma. 2001;40(5-6):491-498.10428190109097648 google scholar
  • Soleas GJ, Diamandis EP, Goldberg DM. Resveratrol: A molecule whose time has come? And gone? Clin Biochem. 1997;30(2):91-113. google scholar
  • Wright JS, Johnson ER, DiLabio GA. Predicting the activity of phenolic antioxidants: Theoretical method, analysis of substituent effects, and application to major families of antioxidants. J Am Chem Soc. 2001;123(6):1173-1183. google scholar
  • Ji Q, Liu X, Han Z, et al. Resveratrol suppresses epithelial-to-mesenchymal transition in colorectal cancer through TGF-beta1/Smads signaling pathway mediated Snail/E-cadherin ex-pression. BMC Cancer. 2015;15:97. doi:10.1186/s12885-015-1119-y google scholar
  • Bian P, Hu W, Liu C, Li L. Resveratrol potentiates the anti-tumor effects of rapamycin in papillary thyroid cancer: PI3K/AKT/mTOR pathway involved. Arch Biochem Biophys. 2020;689:108461. doi:10.1016/j.abb.2020.108461 google scholar
  • Hope C, Planutis K, Planutiene M, et al. Low concentrations of resveratrol inhibit Wnt signal throughput in colon-derived cells:Implications for colon cancer prevention. Mol Nutr Food Res. 2008;52 Suppl 1(Suppl 1):S52-61. google scholar
  • Ren B, Kwah MX, Liu C, et al. Resveratrol for cancer therapy: Challenges and future perspectives. Cancer Lett. 2021;515:63-72. google scholar
  • Morris GM, Huey R, Lindstrom W, et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785-2791. google scholar
  • Kim S, Chen J, Cheng T, et al. PubChem in 2021: New data content and improved web interfaces. Nucleic Acids Res. 2021;49(D1):388-395. google scholar
  • Behera SK, Vhora N, Contractor D, et al. Computational drug repurposing study elucidating simultaneous inhibition of entry and replication of novel corona virus by Grazoprevir. Sci Rep. 2021;11(1):7307. doi:10.1038/s41598-021-86712-2 google scholar
  • Durrant JD, McCammon JA. Molecular dynamics simulations and drug discovery. BMC Biol. 2011;9:71. doi:10.1186/1741-7007-9-71 google scholar
  • Raghu R, Devaraji V, Leena K, et al. Virtual screening and dis-covery of novel aurora kinase inhibitors. Curr Top Med Chem.2014;14(17):2006-2019. google scholar
  • Shivakumar D, Williams J, Wu Y, Damm W, Shelley J, Sherman W. Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J Chem Theory Comput. 2010;6(5):1509-1519. google scholar
  • Aier I, Varadwaj PK, Raj U. Structural insights into conforma-tional stability of both wild-type and mutant EZH2 receptor. Sci Rep. 2016;6:34984. doi:10.1038/srep34984 google scholar
  • Deniz U, Ozkirimli E, Ulgen KO. A systematic methodology for large scale compound screening: A case study on the discovery of novel S1PL inhibitors. JMol Graph Model. 2016;63:110-124. google scholar
  • Behera SK, Mahapatra N, Tripathy CS, Pati S. Drug repurpos-ing for identification of potential inhibitors against SARS-CoV-2 spike receptor-binding domain: An in silico approach. Indian J Med Res. 2021;153(1 & 2):132-143. google scholar
  • Pace CN, Fu H, Lee Fryar K, et al. Contribution of hydrogen bonds to protein stability. Protein Sci. 2014;23(5):652-661. google scholar
  • Vladilo G, Hassanali A. Hydrogen bonds and life in the universe. Life (Basel). 2018;8(1). doi:10.3390/life8010001 google scholar
  • Bissantz C, Kuhn B, Stahl M. A medicinal chemist’s guide to molecular interactions. JMed Chem. 2010;53(14):5061-5084. google scholar
  • Chen D, Oezguen N, Urvil P, Ferguson C, Dann SM, Savidge TC. Regulation of protein-ligand binding affinity by hydrogen bond pairing. Sci Adv. 2016;2(3):e1501240. doi:10.1126/sciadv.1501240 google scholar
  • Hamelberg D, Mongan J, McCammon JA. Accelerated molec-ular dynamics: Apromising and efficient simulation method for biomolecules. J Chem Phys. 2004;120(24):11919-11929. google scholar
  • Ferenczy GG, Kellermayer M. Contribution of hydrophobic inter-actions to protein mechanical stability. Comput Struct Biotechnol J. 2022;20:1946-1956. google scholar
  • Dariya B, Behera SK, Srivani G, Farran B, Alam A, Nagaraju GP. Computational analysis of nuclear factor-kappaB and resveratrol in colorectal cancer. J Biomol Struct Dyn. 2021;39(8):2914-2922. google scholar
  • Al-Karmalawy AA, Dahab MA, Metwaly AM, et al. Molec-ular docking and dynamics simulation revealed the poten-tial inhibitory activity of ACEIs against SARS-CoV-2 tar-geting the hACE2 receptor. Front Chem. 2021;9:661230. doi:10.3389/fchem.2021.661230 google scholar
  • Morris JH, Meng EC, Ferrin TE. Computational tools for the interactive exploration of proteomic and structural data. Mol Cell Proteomics. 2010;9(8):1703-1715. google scholar
  • Sliwoski G, Kothiwale S, Meiler J, Lowe EW, Jr. Computational methods in drug discovery. Pharmacol Rev. 2014;66(1):334-395. google scholar
  • Sadybekov AV, Katritch V. Computational approaches streamlin-ing drug discovery. Nature. 2023;616(7958):673-685. google scholar
  • Du X, Li Y, Xia YL, et al. Insights into protein-ligand interactions: Mechanisms, models, and methods. Int J Mol Sci. 2016;17(2). doi:10.3390/ijms17020144 google scholar
  • Nagaraju GP, Farran B, Farren M, et al. Napabucasin (BBI 608), a potent chemoradiosensitizer in rectal cancer. Cancer. 2020;126(14):3360-3371. google scholar
There are 48 citations in total.

Details

Primary Language English
Subjects Structural Biology
Journal Section Themed Articles - Research Articles
Authors

Santosh Kumar Behera 0000-0001-7915-187X

Christoffer Lambring 0009-0003-2921-5021

Albina Hashmi 0009-0006-9467-0196

Sriharika Gottipolu 0009-0000-9325-4998

Riyaz Basha 0000-0002-4071-0993

Publication Date December 21, 2023
Submission Date August 31, 2023
Published in Issue Year 2023 Volume: 82 Issue: 2

Cite

AMA Behera SK, Lambring C, Hashmi A, Gottipolu S, Basha R. In Silico Analysis Determining the Binding Interactions of NAD(P)H: Quinone Oxidoreductase 1 and Resveratrol via Docking and Molecular Dynamic Simulations. Eur J Biol. December 2023;82(2):280-288. doi:10.26650/EurJBiol.2023.1352396