Research ArticleHEALTH AND MEDICINE

How and when does an anticancer drug leave its binding site?

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Science Advances  31 May 2017:
Vol. 3, no. 5, e1700014
DOI: 10.1126/sciadv.1700014
  • Fig. 1 Metastable intermediates, key residues, and interactions relevant to the unbinding of dasatinib from c-Src kinase, along with the associated FES as a function of ligand-binding pocket distance d (in nanometers) and hydration state of binding pocket w.

    Energy is in units of kcal/mol, with contours drawn every 0.5 kcal/mol. Various relevant residues along with water molecules that enter the protein have been marked, and dasatinib is shown using the ball and stick model. State 6 (unbound state) is illustrated separately in Fig. 4. See Results for detailed descriptions of the defining interactions in every state.

  • Fig. 2 The complex network of state-to-state transitions for dasatinib as it moves from bound to unbound state, with rate constants in s−1 and various residence times.

    See Fig. 1 for definition of the various states. The radii of circles for various states are approximately logarithmically proportional to their respective residence times. The full rate constant matrix is provided in the Supplementary Materials.

  • Fig. 3 Various protein structures aligned using the full protein’s heavy atoms, showing the rotation of the αC helix and of the glutamic acid residue (Glu46 in PDB 3G5D).

    Orange represents equilibrated αC helix–in structure, red is the αC helix–out structure (or state 3 in Fig. 1) obtained from our runs, and blue is the αC helix–out structure directly from the PDB database (PDB 4YBK) as reported by Kwarcinski et al. (15). Note how the αC helices in the two out structures overlap fairly well and especially how the glutamic residue is displaced almost identically in a roughly orthogonal direction to what it had in the αC helix–in structure. The stabilizing interaction between residues Arg121 and Glu46 is also illustrated, along with the disordered activation loop in purple. The underlying base structure is a representative αC helix–out structure obtained from our runs. The reported structure (PDB 3G5D) in the protein database has missing residues after the end of the helix, and as such, we do not include them in the comparison here.

  • Fig. 4 An interconnected network of domains through which dasatinib moves once unbound from the primary binding pocket (that is, d > 1.8 nm; see Fig. 1), clearly demonstrating the presence of surface attractive spots.

    Here, various dasatinib snapshots from the unbinding trajectory satisfying d >1.8 nm are marked in purple on the protein (colored by residue name), which for illustrative purposes is kept in the bound pose, and the surface of the protein is represented in gray.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/3/5/e1700014/DC1

    Reliability of time scales

    Master equation

    Effect of force field

    fig. S1. Empirical (dashed line) and fitted cumulative distribution functions (solid line).

    fig. S2. Residence time, eigenvector, and eigenvalue analysis.

    fig. S3. FES as a function of ligand-binding pocket distance d (in nanometers) and hydration state of binding pocket w calculated using the second set of force fields.

    table S1. Residence times and P values for various states

    table S2. Matrix K of state-to-state transition rates.

  • Supplementary Materials

    This PDF file includes:

    • Reliability of time scales
    • Master equation
    • Effect of force field
    • fig. S1. Empirical (dashed line) and fitted cumulative distribution functions (solid line).
    • fig. S2. Residence time, eigenvector, and eigenvalue analysis.
    • fig. S3. FES as a function of ligand-binding pocket distance d (in nanometers) and hydration state of binding pocket w calculated using the second set of force fields.
    • table S1. Residence times and P values for various states
    • table S2. Matrix K of state-to-state transition rates.

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