Bodee Nutho

บดี หนูโท

Assistant Professor
  • B.Sc. (Biochemistry, First-Class Honour) Chulalongkorn University, Thailand
  • M.Sc. (Pharmacology) Mahidol University, Thailand
  • Ph.D. (Biotechnology) Chulalongkorn University, Thailand
Current Research
  • Computer-aided drug design and discovery
  • Molecular dynamics simulation of biomolecules
  • Computational enzymology: modelling biocatalyst
  • Nutho B, Samsri S, Pornsuwan S*. Structural dynamics of the precatalytic state of human cytochrome c upon T28C, G34C, and A50C mutations: A molecular dynamics simulation perspective. ACS Omega 2023 May;8(17):15229-38.
  • Sangkhawasi M, Kerdpol K, Ismail A, Nutho B, Hanpiboon C, Wolschann P, Krusong K, Rungrotmongkol T*, Hannongbua S*. In vitro and In silico study on the molecular encapsulation of α-tocopherol in a large-ring cyclodextrin. Int J Mol Sci 2023 Mar;24(5):4425.
  • Samsri S, Prasertsuk P, Nutho B*, Pornsuwan S*. Molecular insights on the conformational dynamics of a P76C mutant of human cytochrome c and the enhancement on its peroxidase activity. Arch Biochem Biophys 2022 Feb;716:109112.
  • Nutho B*, Yanarojana S, Supavilai P. Structural dynamics and susceptibility of anti-Alzheimer’s drugs donepezil and galantamine against human acetylcholinesterase. Trends Sci 2022 Jun;19(12):4587.
  • Nutho B*, Wilasluck P, Deetanya P, Wangkanont K, Arsakhant P, Saeeng R, Rungrotmongkol T. Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies. Comput Struct Biotechnol J 2022;20:2784-97.
  • Mee-udorn P, Nutho B, Chootrakool R, Maenpuen S, Leartsakulpanich U, Chitnumsub P, Rungrotmongkol T*. Structural dynamics and in silico design of pyrazolopyran-based inhibitors against Plasmodium serine hydroxymethyltransferases. J Mol Liq 2022 Sep;362:119737.
  • Boonma T, Soikudrua N, Nutho B, Rungrotmongkol T, Nunthaboot N*. Insights into binding molecular mechanism of hemagglutinin H3N2 of influenza virus complexed with arbidol and its derivative: A molecular dynamics simulation perspective. Comput Biol Chem 2022 Dec;101:107764.
  • Boonma T, Nutho B, Darai N, Rungrotmongkol T, Nunthaboot N*. Exploring of paritaprevir and glecaprevir resistance due to A156T mutation of HCV NS3/4A protease: molecular dynamics simulation study. J Biomol Struct Dyn 2022;40(12):5283-94.
  • Soonnarong R, Tungsukruthai S, Nutho B, Rungrotmongkol T, Vinayanuwattikun C, Maluangnont T, Chanvorachote P*. Titania nanosheet generates peroxynitrite-dependent S-nitrosylation and enhances p53 function in lung cancer cells. Pharmaceutics 2021 Aug;13(8):1233.
  • Putri HE, Nutho B, Rungrotmongkol T, Sritularak B, Vinayanuwattikun C, Chanvorachote P*. Bibenzyl analogue DS-1 inhibits MDM2-mediated p53 degradation and sensitizes apoptosis in lung cancer cells. Phytomedicine 2021 May;85:153534.
  • Kerdpol K, Nutho B, Krusong K, Poo-arporn RP, Rungrotmongkol T*, Hannongbua S*. Encapsulation of α-tocopherol in large-ring cyclodextrin containing 26 α-D-glucopyranose units: A molecular dynamics study. J Mol Liq 2021 Oct;339:116802.
  • Boonma T, Nutho B, Sungthong B, Sripadung P, Rungrotmongkol T, Nunthaboot N*. Molecular insights into complex formation between scandenin and various types of β-cyclodextrin. J Mol Liq 2021 Dec;344:117774.
  • Bhat N, Nutho B, Vangnai A, Takahashi K, Rungrotmongkol T*. Substrate binding mechanism of glycerophosphodiesterase towards organophosphate pesticides. J Mol Liq 2021 May;329:115526.
  • Nutho B, Pengthaisong S, Tankrathok A, Lee VS, Cairns JRK, Rungrotmongkol T, et al. Structural basis of specific glucoimidazole and mannoimidazole binding by Os3BGlu7. Biomolecules. 2020;10(6):1-19.
  • Nutho B, Mahalapbutr P, Hengphasatporn K, Pattaranggoon NC, Simanon N, Shigeta Y, et al. Why are lopinavir and ritonavir effective against the newly emerged coronavirus 2019? Atomistic insights into the inhibitory mechanisms. Biochemistry. 2020;59(18):1769-79.
  • Petsri K, Yokoya M, Tungsukruthai S, Rungrotmongkol T, Nutho B, Vinayanuwattikun C, et al. Structure–activity relationships and molecular docking analysis of Mcl-1 targeting renieramycin T analogues in patient-derived lung cancer cells. Cancers. 2020;12(4).
  • Hotarat W, Nutho B, Wolschann P, Wolschann P, Rungrotmongkol T, Rungrotmongkol T, et al. Delivery of alpha-mangostin using cyclodextrins through a biological membrane: Molecular dynamics simulation. Molecules. 2020;25(11).
  • Nutho B, Rungrotmongkol T. Binding recognition of substrates in NS2B/NS3 serine protease of Zika virus revealed by molecular dynamics simulations. J Mol Graph Model. 2019;92:227-35.
  • Nutho B, Mulholland AJ, Rungrotmongkol T. The reaction mechanism of Zika virus NS2B/NS3 serine protease inhibition by dipeptidyl aldehyde: A QM/MM study. Phys Chem Chem Phys. 2019;21(27):14945-56.
  • Nutho B, Mulholland AJ, Rungrotmongkol T. Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Support a Concerted Reaction Mechanism for the Zika Virus NS2B/NS3 Serine Protease with Its Substrate. J Phys Chem B. 2019;123(13):2889-903.
  • Kammarabutr J, Mahalapbutr P, Nutho B, Kungwan N, Rungrotmongkol T. Low susceptibility of asunaprevir towards R155K and D168A point mutations in HCV NS3/4A protease: A molecular dynamics simulation. J Mol Graph Model. 2019;89:122-30.
  • Boonma T, Nutho B, Rungrotmongkol T, Nunthaboot N. Understanding of the drug resistance mechanism of hepatitis C virus NS3/4A to paritaprevir due to D168N/Y mutations: A molecular dynamics simulation perspective. Comput Biol Chem. 2019;83.
  • Panman W, Nutho B, Chamni S, Dokmaisrijan S, Kungwan N, Rungrotmongkol T. Computational screening of fatty acid synthase inhibitors against thioesterase domain. J Biomol Struct Dyn. 2018;36(15):4114-25.
  • Mahalapbutr P, Nutho B, Wolschann P, Chavasiri W, Kungwan N, Rungrotmongkol T. Molecular insights into inclusion complexes of mansonone E and H enantiomers with various β-cyclodextrins. J Mol Graph Model. 2018;79:72-80.
  • Wongpituk P, Nutho B, Panman W, Kungwan N, Wolschann P, Rungrotmongkol T, et al. Structural dynamics and binding free energy of neral-cyclodextrins inclusion complexes: Molecular dynamics simulation. Mol Simul. 2017;43(13-16):1356-63.
  • Nutho B, Nunthaboot N, Wolschann P, Kungwan N, Rungrotmongkol T. Metadynamics supports molecular dynamics simulation-based binding affinities of eucalyptol and beta-cyclodextrin inclusion complexes. RSC Adv. 2017;7(80):50899-911.
  • Nutho B, Meeprasert A, Chulapa M, Kungwan N, Rungrotmongkol T. Screening of hepatitis C NS5B polymerase inhibitors containing benzothiadiazine core: a steered molecular dynamics. J Biomol Struct Dyn. 2017;35(8):1743-57.
  • Jetsadawisut W, Nutho B, Meeprasert A, Rungrotmongkol T, Kungwan N, Wolschann P, et al. Susceptibility of inhibitors against 3C protease of coxsackievirus A16 and enterovirus A71 causing hand, foot and mouth disease: A molecular dynamics study. Biophys Chem. 2016;219:9-16.
  • Nutho B, Khuntawee W, Rungnim C, Pongsawasdi P, Wolschann P, Karpfen A, et al. Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes. Beilstein J Org Chem. 2014;10:2789-99.