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Conformation and Permeability: Cyclic Hexapeptide Diastereomers

  • Satoshi Ono*
    Satoshi Ono
    Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
    *E-mail: [email protected] (S. Ono).
    More by Satoshi Ono
    Orcidhttp://orcid.org/0000-0001-5631-5923
  • , 
  • Matthew R. Naylor
    Matthew R. Naylor
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
    More by Matthew R. Naylor
    Orcidhttp://orcid.org/0000-0001-7043-5972
  • , 
  • Chad E. Townsend
    Chad E. Townsend
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
    More by Chad E. Townsend
  • , 
  • Chieko Okumura
    Chieko Okumura
    Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
    More by Chieko Okumura
  • , 
  • Okimasa Okada
    Okimasa Okada
    Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
    More by Okimasa Okada
  • , and 
  • R. Scott Lokey*
    R. Scott Lokey
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
    *E-mail: [email protected] (R. S. Lokey).
    More by R. Scott Lokey
    Orcidhttp://orcid.org/0000-0001-9891-1248
Cite this: J. Chem. Inf. Model. 2019, 59, 6, 2952–2963
Publication Date (Web):May 1, 2019
https://doi.org/10.1021/acs.jcim.9b00217
Copyright © 2019 American Chemical Society
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    Abstract

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    Conformational ensembles of eight cyclic hexapeptide diastereomers in explicit cyclohexane, chloroform, and water were analyzed by multicanonical molecular dynamics (McMD) simulations. Free-energy landscapes (FELs) for each compound and solvent were obtained from the molecular shapes and principal component analysis at T = 300 K; detailed analysis of the conformational ensembles and flexibility of the FELs revealed that permeable compounds have different structural profiles even for a single stereoisomeric change. The average solvent-accessible surface area (SASA) in cyclohexane showed excellent correlation with the cell permeability, whereas this correlation was weaker in chloroform. The average SASA in water correlated with the aqueous solubility. The average polar surface area did not correlate with cell permeability in these solvents. A possible strategy for designing permeable cyclic peptides from FELs obtained from McMD simulations is proposed.

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jcim.9b00217.

    • Free-energy landscapes of (ϕ,ψ) for each solvent (Figures S1–S3); backbone hydrogen-bond patterns of each compound and solvent (Figures S4–S11); free-energy landscapes for PC-1 and PC-3 (Figure S12); log Dcyc/w vs average SASA and PSA for each solvent (Figure S13); representative structures of β-turn pattern F and G (Figure S14); overlaps between the FELs from the PC plane (Figure S15); free-energy landscapes of (ϕ,ψ) for known cyclic peptides (Figure S16); zones for virtual states and real potential energy for each solvent (Tables S1–S3); backbone (ϕ,ψ) values for representative structures shown in Figure 4 (Table S4) (PDF)

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