Top-Leads for Swine Influenza A/H1N1 Virus Revealed by Steered Molecular Dynamics Approach Binh Khanh Mai,† Man Hoang Viet,‡ and Mai Suan Li∗,‡ Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam, and Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland E-mail:
[email protected] Supporting Information
Choice of pulling path. As described in the main text, using Caver 2.0, 1 one can show that there are three possible pathways for pulling tamiflu from the active site of wild type A/H5N1 neuraminidase (A/H5N1 NA) . The first path (z-direction) goes through a tunnel surrounded by residues Asp151, Arg152, Ser246, Glu195, Arg292, Asn347 and Arg371 (Fig. S1). This tunnel has the largest average width of 2.51 Å, while the second and third tunnels of second and third paths have average width of 2.16 and 1.88 Å, respectively. Moreover, the first, second and third tunnels have lengths of 5.87 Å, 11.61 Å, and 13.32 Å, respectively. These geometrical parameters imply that moving through the first tunnel would have the smallest rupture force (Fig. S2) as the number of contacts with protein is minimal. One can show that this remains valid for the A/H1N1 ∗ To
whom correspondence should be addressed for Computational Science and Technology ‡ Institute of Physics † Institute
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neuraminidase (A/H1N1 NA) case. Thus the first path along z-direction is chosen for pulling other ligands from the active side of a protein. The number of HBs between tamiflu and A/H1N1 NA is lower than A/H5N1 NA. Time dependencies of the number of HBs between tamiflu and two receptors are shown in Fig. S4. Averaging over time we obtain nHB ≈ 3 and 3.6 for A/H1N1 and A/H5N1, respectively. Thus, the HB network of A/H1N1 NA is weaker than the A/H5N1 NA one. This explains why oseltamivir is better bound to A/H5N1 NA. Existence of hydrogen bonds after rupture. Fig. S7 shows the pattern of the HB network of the relenza complex after the system passed the maximum in the force-time curve (Fig. 4 in the main text). Clearly, three HBs still survive after passing the peak in the force-time curve. Force-time profiles for four top-hit ligands. Fig. S11 shows force-time curves obtained from four independent runs for NSC141562, NSC5069, NSC46080 and NSC117079. Heights of peaks vary from trajectory to trajectory but overall we can rank them as NSC141562 → NSC5069 → NSC46080 → NSC117079. dock . F Correlation between Fmax and Ebind max taken from Table 1 in the main text is plotted as a dock . The later was obtained by the Autodock method 2 (Fig. S13). function of the binding energy Ebind
The correlation between these quantities is rather low (R = 0.49) suggesting that the Autodock may be not adequate enough for predicting the binding affinity.
References (1) Petrek, M.; Otyepka, M.; Banas, P.; Kosinova, P.; Koca1, J.; Damborsky., J. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics 2006, 7, 316. (2) Nguyen, H. T.; Le, L.; Truong, T. N. Top-hits for A/H1N1 identified by virtual screening using ensemble-based docking. PLoS Currents: Influenza. September 3; 1:RRN1030, http: //www.ncbi.nlm.nih.gov/pmc/articles/PMC2762758/. 2009.
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A
B
Fig. S1. Schematic plot of the first tunnel which corresponds to the z-direction. (A) refers to view along this direction while (B) - crosswise view.
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Fig. S2. Force-time profiles for pulling tamiflu from the drug binding pocket of A/H5N1 neuraminidase along three possible paths. Red, orange, and magenta refer to the first (z-direction), second and third paths, respectively. The pulling along the z-direction requires the smallest external force. The pulling speed v = 0.005 nm/s.
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Fig. S3. Force-time profiles for pulling NSC141562, tamiflu, peramivir and relenza from the drug binding pocket of A/H1N1 neuraminidase along the z-direction. Results were obtained from three MD runs.
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Fig. S4. Time dependence of the number of HBs between tamiflu and A/H5N1 NA (black) and A/H1N1 NA (red). The result was obtained from 15 ns equilibrium MD runs.
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Fig. S5. Time dependencies of the number of hydrogen bonds during the unbinding process of tamiflu, relenza, peramivir and NCS141562. Arrows refer to peak positions in Fig. 3a in the main text.
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Fig. S6. The electrostatic potential surface of the binding pocket of the NSC141562 system. E119, D151, E227 and E277 are negatively charged residues. Their carboxyl groups are directed toward the ligand.
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Fig. S7. HB network of relenza after the peak in the force-time profile. Three HBs (dashed lines) still survive after the rupture.
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Fig. S8. The same as in Fig. 4 from the main text but for the second MD run. Similar results have been obtained for remaining 2 runs (not shown).
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Fig. S9. The repulsive interaction between the carbonyl group of peramivir and carboxyl group of Asp151 from the receptor.
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Fig. S10. Electrostatic potential surface of the relenza complex.
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Fig. S11. The force-time profiles obtained in four MD runs for top-hit leads NSC141562, NSC5069, NSC46080 and NSC117079. The maximum forces averaged over four trajectories are equal Fmax = 1769.6 ± 65.3, 1364.9 ± 40.9, 1318.5 ± 48.5 and 1296.6 ± 46.2 pN for NSC141562, NSC5069, NSC46080 and NSC117079, respectively.
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Fig. S12. Chemical structures of four top hits NSC141562, NSC5069, NSC46080 and NSC117079.
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dock obtained by the Autodock Fig. S13. Relationship between Fmax and the binding energy Ebind
method. 2 The straight line is a linear fit y = −141.53 −110.79x with the correlation level R = 0.49.
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Fig. S14. Time dependencies of RMSD for the champion ligand NCS141562, tamiflu, relenza and peramivir. Systems get equilibrated (saturation of curves) after about 7 ns.
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Fig. S15. The force-displacement profiles for tamiflu and sialic acid (SA) in the presence (red) and absence (black) of water. Arrows refer to positions of Fmax in the absence of water. For both tamiflu and SA Fmax (no water)/Fmax (water) ≈ 1.7. This ratio also holds for other ligands (results not shown).
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