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2000
Volume 33, Issue 3
  • ISSN: 0929-8673
  • E-ISSN: 1875-533X

Abstract

Introduction

Cancer remains a leading cause of mortality worldwide. Specific proteins play critical roles in cancer development, and MTH1 is one such protein. MTH1 removes the terminal phosphate groups from oxidized nucleotides like 8-oxo-dGTP and 2-OH-dATP, generated by oxidative stress in tumor cells.

Methods

These oxidized nucleotides can disrupt DNA replication and cell division. By preventing their incorporation into newly synthesized DNA, MTH1 promotes cancer cell proliferation. Developing new anticancer drugs is complex, but interdisciplinary research can significantly contribute to this endeavor. For the first time, we propose a multi-pronged approach utilizing computational chemistry, statistical analysis, machine learning, molecular dynamics simulations, and synthesis to design novel MTH1 inhibitors.

Results

This approach underscores the power of collaboration between diverse scientific disciplines. Our research aims to identify potent MTH1 inhibitors through a synergy of these methodologies.

Conclusion

This comprehensive study demonstrates that computational chemistry, statistical analysis, and MD simulations can be effectively integrated. Our findings from this combined approach illustrate that our newly designed MTH1 inhibitor, Xyl-Trp, can be a promising candidate for MTH1 inhibition.

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References

  1. D’AutréauxB. ToledanoM.B. ROS as signalling molecules: Mechanisms that generate specificity in ROS homeostasis.Nat. Rev. Mol. Cell Biol.200781081382410.1038/nrm2256 17848967
    [Google Scholar]
  2. YangH. VillaniR.M. WangH. SimpsonM.J. RobertsM.S. TangM. LiangX. The role of cellular reactive oxygen species in cancer chemotherapy.J. Exp. Clin. Cancer Res.201837126610.1186/s13046‑018‑0909‑x 30382874
    [Google Scholar]
  3. CommonerB. TownsendJ. PakeG. Free radicals in biological materials.Nature1954174443268969110.1038/174689a0 13213980
    [Google Scholar]
  4. ChioI.I.C. TuvesonD.A. ROS in cancer: The burning question.Trends Mol. Med.201723541142910.1016/j.molmed.2017.03.004 28427863
    [Google Scholar]
  5. DahlgrenC. KarlssonA. Respiratory burst in human neutrophils.J. Immunol. Methods19992321-231410.1016/S0022‑1759(99)00146‑5 10618505
    [Google Scholar]
  6. SrinivasU.S. TanB.W.Q. VellayappanB.A. JeyasekharanA.D. ROS and the DNA damage response in cancer.Redox Biol.20192510108410.1016/j.redox.2018.101084 30612957
    [Google Scholar]
  7. ApelK. HirtH. Reactive oxygen species: Metabolism, oxidative stress, and signal transduction.Annu. Rev. Plant Biol.200455137339910.1146/annurev.arplant.55.031903.141701 15377225
    [Google Scholar]
  8. SteenkenS. JovanovicS.V. How easily oxidizable is DNA? One-electron reduction potentials of adenosine and guanosine radicals in aqueous solution.J. Am. Chem. Soc.1997119361761810.1021/ja962255b
    [Google Scholar]
  9. SeidelC.A.M. SchulzA. SauerM.H.M. Nucleobase-specific quenching of fluorescent dyes. 1. Nucleobase one-electron redox potentials and their correlation with static and dynamic quenching efficiencies.J. Phys. Chem.1996100135541555310.1021/jp951507c
    [Google Scholar]
  10. HildenbrandK. Schulte-FrohlindeD. ESR spectra of radicals of single-stranded and double-stranded DNA in aqueous solution. Implications for. OH-induced strand breakage.Free Radic. Res. Commun.1990114-519520610.3109/10715769009088916 1965722
    [Google Scholar]
  11. DaviesM.J. The oxidative environment and protein damage.Biochim. Biophys. Acta. Proteins Proteomics2005170329310910.1016/j.bbapap.2004.08.007 15680218
    [Google Scholar]
  12. FabriniR. BocediA. PallottiniV. CanutiL. De CanioM. UrbaniA. MarzanoV. CornettaT. StanoP. GiovanettiA. StellaL. CaniniA. FedericiG. RicciG. Nuclear shield: A multi-enzyme task-force for nucleus protection.PLoS One2010512e1412510.1371/journal.pone.0014125 21170318
    [Google Scholar]
  13. MimuraY. ImamotoN. Nuclear organization.Encyclopedia of Cell Biology. BradshawR.A. StahlP.D. Academic Press201631131810.1016/B978‑0‑12‑394447‑4.20027‑8
    [Google Scholar]
  14. SalvadorA. SousaJ. PintoR.E. Hydroperoxyl, superoxide and pH gradients in the mitochondrial matrix: A theoretical assessment.Free Radic. Biol. Med.200131101208121510.1016/S0891‑5849(01)00707‑9 11705699
    [Google Scholar]
  15. KumariS. BadanaA.K. GM.M. GS. MallaR. Reactive oxygen species: A key constituent in cancer survival.Biomark. Insights201813117727191875539110.1177/1177271918755391 29449774
    [Google Scholar]
  16. SchieberM. ChandelN.S. ROS function in redox signaling and oxidative stress.Curr. Biol.20142410R453R46210.1016/j.cub.2014.03.034 24845678
    [Google Scholar]
  17. ShahM.A. RogoffH.A. Implications of reactive oxygen species on cancer formation and its treatment.Semin. Oncol.202148323824510.1053/j.seminoncol.2021.05.002 34548190
    [Google Scholar]
  18. KumarR. PrasadH.K. KumarM. The double-edged sword role of ROS in cancer.Handbook of Oxidative Stress in Cancer: Mechanistic AspectsSpringer Nature SingaporeSingapore20221103111910.1007/978‑981‑15‑9411‑3_71
    [Google Scholar]
  19. MartindaleJ.L. HolbrookN.J. Cellular response to oxidative stress: Signaling for suicide and survival.J. Cell. Physiol.2002192111510.1002/jcp.10119 12115731
    [Google Scholar]
  20. YinY. ChenF. Targeting human MutT homolog 1 (MTH1) for cancer eradication: Current progress and perspectives.Acta Pharm. Sin. B202010122259227110.1016/j.apsb.2020.02.012 33354500
    [Google Scholar]
  21. FarandJ. KropfJ.E. BlomgrenP. XuJ. SchmittA.C. NewbyZ.E. WangT. MurakamiE. BarauskasO. SudhamsuJ. FengJ.Y. Niedziela-MajkaA. SchultzB.E. SchwartzK. Viatchenko-KarpinskiS. KornyeyevD. KashishianA. FanP. ChenX. LansdonE.B. PortsM.O. CurrieK.S. WatkinsW.J. NotteG.T. Discovery of potent and selective MTH1 inhibitors for oncology: Enabling rapid target (In) validation.ACS Med. Chem. Lett.202011335836410.1021/acsmedchemlett.9b00420 32184970
    [Google Scholar]
  22. LibertiM.V. LocasaleJ.W. The Warburg effect: How does it benefit cancer cells?Trends Biochem. Sci.201641321121810.1016/j.tibs.2015.12.001 26778478
    [Google Scholar]
  23. ZambranoA. MoltM. UribeE. SalasM. GLUT1 in cancer cells and the inhibitory action of resveratrol as a potential therapeutic strategy.Int. J. Mol. Sci.20192013337410.3390/ijms20133374 31324056
    [Google Scholar]
  24. BukkuriA. GatenbyR.A. BrownJ.S. GLUT1 production in cancer cells: A tragedy of the commons.NPJ Syst. Biol. Appl.202282210.1038/s41540‑022‑00229‑6
    [Google Scholar]
  25. CaoX. DuX. JiaoH. AnQ. ChenR. FangP. WangJ. YuB. Carbohydrate-based drugs launched during 2000-2021.Acta Pharm. Sin. B202212103783382110.1016/j.apsb.2022.05.020 36213536
    [Google Scholar]
  26. DiezD.M. BarrC.D. Cetinkaya-RundelM. OpenIntro Statistics.Boston, MA, USAOpenIntro2012
    [Google Scholar]
  27. ChandaD. HarohallyN.V. Revisiting Amadori and Heyns synthesis: Critical percentage of acyclic form play the trick in addition to catalyst.Tetrahedron Lett.201859312983298810.1016/j.tetlet.2018.06.050
    [Google Scholar]
  28. ZhanD. ZhangX. LiJ. DingX. CuiY. JiaJ. MTH1 inhibitor TH287 suppresses gastric cancer development through the regulation of PI3K/AKT signaling.Cancer Biother. Radiopharm.202035322323210.1089/cbr.2019.3031 32077746
    [Google Scholar]
  29. ShiX.L. LiY. ZhaoL.M. SuL.W. DingG. Delivery of MTH1 inhibitor (TH287) and MDR1 siRNA via hyaluronic acid-based mesoporous silica nanoparticles for oral cancers treatment.Colloids Surf. B Biointerfaces201917359960610.1016/j.colsurfb.2018.09.076 30352381
    [Google Scholar]
  30. ShaoY. MolnarL.F. JungY. KussmannJ. OchsenfeldC. BrownS.T. GilbertA.T. SlipchenkoL.V. LevchenkoS.V. O’NeillD.P. DiStasio JrR.A. Advances in methods and algorithms in a modern quantum chemistry program package.Phys. Chem. Chem. Phys.20068273172319110.1039/B517914A
    [Google Scholar]
  31. TrottO. OlsonA.J. Software news and update AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function.J. Comput. Chem.200931455461
    [Google Scholar]
  32. SeeligerD. de GrootB.L. Ligand docking and binding site analysis with PyMOL and Autodock/Vina.J. Comput. Aided Mol. Des.201024541742210.1007/s10822‑010‑9352‑6 20401516
    [Google Scholar]
  33. YokoyamaT. KitakamiR. MizuguchiM. Discovery of a new class of MTH1 inhibitor by X-ray crystallographic screening.Eur. J. Med. Chem.201916715316010.1016/j.ejmech.2019.02.011 30771603
    [Google Scholar]
  34. KettleJ.G. AlwanH. BistaM. BreedJ. DaviesN.L. EckersleyK. FilleryS. FooteK.M. GoodwinL. JonesD.R. KäckH. LauA. NissinkJ.W.M. ReadJ. ScottJ.S. TaylorB. WalkerG. WisslerL. WylotM. Potent and selective inhibitors of MTH1 probe its role in cancer cell survival.J. Med. Chem.20165962346236110.1021/acs.jmedchem.5b01760 26878898
    [Google Scholar]
  35. RahmF. ViklundJ. TrésauguesL. EllermannM. GieseA. EricssonU. ForsblomR. GinmanT. GüntherJ. HallbergK. LindströmJ. PerssonL.B. SilvanderC. TalagasA. Díaz-SáezL. FedorovO. HuberK.V.M. PanagakouI. SiejkaP. GorjánáczM. BauserM. AnderssonM. Creation of a novel class of potent and selective MutT homologue 1 (MTH1) inhibitors using fragment-based screening and structure-based drug design.J. Med. Chem.20186162533255110.1021/acs.jmedchem.7b01884 29485874
    [Google Scholar]
  36. PetrocchiA. LeoE. ReynaN.J. HamiltonM.M. ShiX. ParkerC.A. MseehF. BardenhagenJ.P. LeonardP. CrossJ.B. HuangS. JiangY. CardozoM. DraettaG. MarszalekJ.R. ToniattiC. JonesP. LewisR.T. Identification of potent and selective MTH1 inhibitors.Bioorg. Med. Chem. Lett.20162661503150710.1016/j.bmcl.2016.02.026 26898335
    [Google Scholar]
  37. RudlingA. GustafssonR. AlmlöfI. HomanE. ScobieM. Warpman BerglundU. HelledayT. StenmarkP. CarlssonJ. Fragment-based discovery and optimization of enzyme inhibitors by docking of commercial chemical space.J. Med. Chem.201760198160816910.1021/acs.jmedchem.7b01006 28929756
    [Google Scholar]
  38. PengC. LiY.H. YuC.W. ChengZ.H. LiuJ.R. HsuJ.L. HsinL.W. HuangC.T. JuanH.F. ChernJ.W. ChengY.S. Inhibitor development of MTH1 via high-throughput screening with fragment based library and MTH1 substrate binding cavity.Bioorg. Chem.202111010481310.1016/j.bioorg.2021.104813 33774493
    [Google Scholar]
  39. YinY. SasakiS. TaniguchiY. Effects of 8-halo-7-deaza-2-deoxyguanosine triphosphate on DNA synthesis by DNA polymerases and cell proliferation.Bioorg. Med. Chem.201624163856386110.1016/j.bmc.2016.06.030 27372838
    [Google Scholar]
  40. PállS. AbrahamM.J. KutznerC. HessB. LindahlE. Tackling exascale software challenges in molecular dynamics simulations with GROMACS.EASC201432710.1007/978‑3‑319‑15976‑8_1
    [Google Scholar]
  41. SchnupfU. WillettJ.L. BosmaW.B. MomanyF.A. DFT conformational studies of α-maltotriose.J. Comput. Chem.20082971103111210.1002/jcc.20872 18069685
    [Google Scholar]
  42. HumphreyW. DalkeA. SchultenK. VMD: Visual molecular dynamics.J. Mol. Graph.19961413338, 27-2810.1016/0263‑7855(96)00018‑58744570
    [Google Scholar]
  43. SvenssonL.M. JemthA.S. DesrosesM. LosevaO. HelledayT. HögbomM. StenmarkP. Crystal structure of human MTH1 and the 8-oxo-dGMP product complex.FEBS Lett.2011585162617262110.1016/j.febslet.2011.07.017 21787772
    [Google Scholar]
  44. GadH. KoolmeisterT. JemthA.S. MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool.Nature201450821522110.1038/nature13181
    [Google Scholar]
  45. ZhaoY. TruhlarD.G. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other functionals.Theor. Chem. Acc.20081201-321524110.1007/s00214‑007‑0310‑x
    [Google Scholar]
  46. MarenichA.V. CramerC.J. TruhlarD.G. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.J. Phys. Chem. B2009113186378639610.1021/jp810292n 19366259
    [Google Scholar]
  47. LemkulJ.A. BevanD.R. Destabilizing Alzheimer’s Abeta (42) protofibrils with morin: Mechanistic insights from molecular dynamics simulations.Biochemistry201049183935394610.1021/bi1000855 20369844
    [Google Scholar]
  48. NedyalkovaM.A. MadurgaS. TobiszewskiM. SimeonovV. Calculating the partition coefficients of organic solvents in octanol/water and octanol/air.J. Chem. Inf. Model.20195952257226310.1021/acs.jcim.9b00212 31042037
    [Google Scholar]
  49. KalhorS. FattahiA. Design of amino acid- and carbohydrate-based anticancer drugs to inhibit polymerase η.Sci. Rep.20221211846110.1038/s41598‑022‑22810‑z 36323739
    [Google Scholar]
  50. MansourianM. MahnamK. Madadkar-SobhaniA. FassihiA. SaghaieL. Insights into the human A1 adenosine receptor from molecular dynamics simulation: Structural study in the presence of lipid membrane.Med. Chem. Res.201524103645365910.1007/s00044‑015‑1409‑6
    [Google Scholar]
  51. MorrisG.M. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function.J. Comput. Chem.19981916391662
    [Google Scholar]
  52. Santos-MartinsD. Solis-VasquezL. TillackA.F. SannerM.F. KochA. ForliS. Accelerating AutoDock4 with GPUs and gradient-based local search.J. Chem. Theory Comput.20211721060107310.1021/acs.jctc.0c01006 33403848
    [Google Scholar]
  53. MaoK.Z. Orthogonal forward selection and backward elimination algorithms for feature subset selection.IEEE Trans. Syst. Man Cybern. B Cybern.200434162963410.1109/TSMCB.2002.804363 15369099
    [Google Scholar]
  54. GhuleS. DashS.R. BagchiS. JoshiK. VankaK. Predicting the redox potentials of phenazine derivatives using DFT-assisted machine learning.ACS Omega2022714117421175510.1021/acsomega.1c06856 35449912
    [Google Scholar]
  55. NakhwanM. DuangsoithongR. Comparison analysis of data augmentation using bootstrap, GANs and autoencoder.2022 14th Int. Conf. Knowl. Smart Technol. (KST)2022182310.1109/KST53302.2022.9729065
    [Google Scholar]
  56. PedregosaF. VaroquauxG. GramfortA. MichelV. ThirionB. GriselO. BlondelM. PrettenhoferP. WeissR. DubourgV. VanderplasJ. Scikit-learn: Machine learning in Python.J. Mach. Learn. Res.20111228252830
    [Google Scholar]
  57. Random Forest Classifier https://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestClassifier.html
  58. WipfD. NagarajanS. A new view of automatic relevance determination.2007Available from: https://proceedings. neurips.cc/paper_files/paper/2007/file/9c01802ddb981e6bcfbec0f0516b8e35-Paper.pdf
    [Google Scholar]
  59. DavydovA.S. Solitons in Molecular Systems 113.DordrechtReidel198510.1007/978‑94‑017‑3025‑9
    [Google Scholar]
  60. BerendsenH.J.C. PostmaJ.P.M. van GunsterenW.F. DiNolaA. HaakJ.R. Molecular dynamics with coupling to an external bath.J. Chem. Phys.19848183684369010.1063/1.448118
    [Google Scholar]
  61. YadavR.K. YadavaU. Molecular dynamics simulation of DNA duplex, analog of PPT (polypurine tract), its conformation and hydration: A theoretical study.Med. Chem. Res.201423128028610.1007/s00044‑013‑0631‑3
    [Google Scholar]
  62. DardenT. YorkD. PedersenL. Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems.J. Chem. Phys.19939812100891009210.1063/1.464397
    [Google Scholar]
  63. KumariR. KumarR. LynnA. g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.J. Chem. Inf. Model.20145471951196210.1021/ci500020m 24850022
    [Google Scholar]
  64. AzémaL. BringaudF. BlonskiC. PériéJ. Chemical and enzymatic synthesis of fructose analogues as probes for import studies by the hexose transporter in parasites.Bioorg. Med. Chem.20008471772210.1016/S0968‑0896(00)00018‑3 10819160
    [Google Scholar]
  65. Brittain, H.G., Ed.; Profiles of drug substances, excipients, and related methodology.Academic Press2020
    [Google Scholar]
  66. MoldoveanuS.C. DavidV. Modern sample preparation for chromatography.Elsevier202144745310.1016/C2011‑0‑00093‑5
    [Google Scholar]
  67. MartinT. User’s guide for test (toxicity estimation software tool) a program to estimate toxicity from molecular structure.2016Available from: https://www.epa.gov/sites/default/files/2016-05/documents/600r16058.pdf
    [Google Scholar]
  68. ChemIDplusAvailable from: http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp
  69. SchultzT.W. BryantS.E. LinD.T. Structure-toxicity relationships for Tetrahymena: Aliphatic aldehydes.Bull. Environ. Contam. Toxicol.199452227928510.1007/BF00198500 8123990
    [Google Scholar]
  70. RomesburgH.C. Cluster Analysis for Researchers;Lifelong Learning Publishers1984334
    [Google Scholar]
  71. ZhuJ. WarrenJ.D. DanishefskyS.J. Synthetic carbohydrate-based anticancer vaccines: The Memorial Sloan-Kettering experience.Expert Rev. Vaccines20098101399141310.1586/erv.09.95
    [Google Scholar]
  72. AkiyamaS. SaekiH. NakashimaY. IimoriM. KitaoH. OkiE. OdaY. NakabeppuY. KakejiY. MaeharaY. Prognostic impact of MutT homolog-1 expression on esophageal squamous cell carcinoma.Cancer Med.20176125826610.1002/cam4.979 27917618
    [Google Scholar]
  73. LiJ. YangC.C. TianX.Y. LiY.X. CuiJ. ChenZ. DengZ.L. ChenF.J. HayakawaH. SekiguchiM. CaiJ.P. MutT-related proteins are novel progression and prognostic markers for colorectal cancer.Oncotarget201786210571410572610.18632/oncotarget.22393 29285286
    [Google Scholar]
  74. WangJ.Y. LiuG.Z. WilmottJ.S. LaT. FengY.C. YariH. YanX.G. ThorneR.F. ScolyerR.A. ZhangX.D. JinL. Skp2-mediated stabilization of MTH1 promotes survival of melanoma cells upon oxidative stress.Cancer Res.201777226226623910.1158/0008‑5472.CAN‑17‑1965 28947420
    [Google Scholar]
  75. LiD.N. YangC.C. LiJ. YangQ.G.O. ZengL.T. FanG.Q. LiuT.H. TianX.Y. WangJ.J. ZhangH. DaiD.P. The high expression of MTH1 and NUDT5 promotes tumor metastasis and indicates a poor prognosis in patients with non-small-cell lung cancer.Biochim. Biophys. Acta Mol. Cell Res.2021186811889510.1016/j.bbamcr.2020.118895
    [Google Scholar]
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