Supplementary materials Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Science, University of Indonesia 1 Designing Cyclopentapeptide Inhibitor of Neuraminidase H5N1 Virus through Molecular and pharmacology Simulation Usman Sumo Friend Tambunan*, Arli Aditya Parikesit, Yossy Carolina Unadi, Djati Kerami Department of Chemistry, Faculty of Mathematics and Sciences, University of Indonesia Depok 16424 (*) Corresponding author: [email protected] Table S1. Contact residue of the ligandd during molecular dynamics at 310 K Ligand steps CLDRC CILRC CIWRC Beginning of Initialization Glu99, Glu99, Arg132, Arg136, Trp159, Ser227, Glu258, Tyr324, Arg348, Arg348, Arg384 Thr128, Arg273, Tyr324, Arg348 Arg98, Glu99, Glu99, Glu99, Thr115, Thr115, Tyr324, Arg348, Arg348 The end of Initialization Glu99, Glu99, Arg132, Arg136, Trp159, Ser227, Glu258, Tyr324, Arg348, Arg348, Arg384 Thr128, Arg273, Tyr324, Arg348, Tyr382 Arg98, Glu99, Glu99, Glu99, Thr115, Thr115, Tyr324, Arg348, Arg348 Production of 5000 picosecond Arg98, Glu99, Glu99, Glu99, Asp131, Asp131, Arg132, Arg132, Arg136, Trp159, Glu208, Ser227, Glu258, Glu258, Arg273, Arg273, Tyr324, Arg348, Arg348, Tyr382 Glu257, Glu258, Glu258, Arg273, Lys412 Arg98, Glu99, Glu99, Glu99, Thr115, Arg136, Ala158, Trp159, Asp179, Arg273, Tyr324, Arg348, Arg348
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Supplementary,materials,,
Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
1,
Designing Cyclopentapeptide Inhibitor of Neuraminidase H5N1 Virus through Molecular and pharmacology Simulation
Usman Sumo Friend Tambunan*, Arli Aditya Parikesit, Yossy Carolina Unadi,
Djati Kerami Department of Chemistry, Faculty of Mathematics and Sciences, University of
Indonesia Depok 16424
(*) Corresponding author: [email protected]
Table S1. Contact residue of the ligandd during molecular dynamics at 310 K
Ligand
steps CLDRC CILRC CIWRC
Beginning of
Initialization
Glu99, Glu99, Arg132,
Arg136, Trp159,
Ser227, Glu258,
Tyr324, Arg348,
Arg348, Arg384
Thr128, Arg273,
Tyr324, Arg348
Arg98, Glu99,
Glu99, Glu99,
Thr115, Thr115,
Tyr324, Arg348,
Arg348
The end of
Initialization
Glu99, Glu99, Arg132,
Arg136, Trp159,
Ser227, Glu258,
Tyr324, Arg348,
Arg348, Arg384
Thr128, Arg273,
Tyr324, Arg348,
Tyr382
Arg98, Glu99,
Glu99, Glu99,
Thr115, Thr115,
Tyr324, Arg348,
Arg348
Production of
5000
picosecond
Arg98, Glu99, Glu99,
Glu99, Asp131,
Asp131, Arg132,
Arg132, Arg136,
Trp159, Glu208,
Ser227, Glu258,
Glu258, Arg273,
Arg273, Tyr324,
Arg348, Arg348,
Tyr382
Glu257, Glu258,
Glu258, Arg273,
Lys412
Arg98, Glu99,
Glu99, Glu99,
Thr115, Arg136,
Ala158, Trp159,
Asp179, Arg273,
Tyr324, Arg348,
Arg348
Supplementary,materials,,
Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
2,
Cooling
Arg98, Glu99, Glu99,
Glu99, Asp131,
Asp131, Arg132,
Arg132, Arg136,
Trp159, Glu208,
Ser227, Glu258,
Glu258, Arg273,
Arg273, Tyr324,
Arg348, Arg348,
Tyr382
Glu257, Glu258,
Glu258, Arg273,
Lys412
Arg98, Glu99,
Glu99, Glu99,
Thr115, Arg136,
Ala158, Trp159,
Asp179, Arg273,
Tyr324, Arg348,
Arg348
Note : Residues in red are the active sites of NA
Table S2. The comparison between contact residue and hydrogen bond
during and after the molecular dynamics simulation at 310 K
Ligand
Simulation
LDR ILR IWR
Molecular
docking
Glu99, Glu99, Glu99,
Arg132, Arg136, Trp159,
Tyr324, Arg348, Tyr382,
Tyr382
Arg98, Thr128,
Arg132, Arg 273,
Asn275, Arg348
Glu99, Glu99,
Glu257, Glu258,
Arg348
Molecular
dynamics 310
K
Arg98, Glu99, Glu99,
Glu99, Asp131, Asp131,
Arg132, Arg132, Arg136,
Trp159, Glu208, Ser227,
Glu258, Glu258, Arg273,
Arg273, Tyr324, Arg348,
Arg348, Tyr382
Glu257, Glu258,
Glu258, Arg273,
Lys412
Arg98, Glu99,
Glu99, Glu99,
Thr115, Arg136,
Ala158, Trp159,
Asp179, Arg273,
Tyr324, Arg348,
Arg348
Note : Residues in red are the active sites of NA
Table S3. Contact residue of molecular dynamics ligand simulation at 312 K
Ligand Steps CLDRC CILRC CIWRC
Beginning of Glu99, Glu99, Glu99, Glu99, Arg98, Glu99,
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Initialization Arg132, Arg136, Trp159, Ser227, Tyr324, Arg348, Tyr382
Arg132, Arg136, Trp159,Ser227 Tyr324, Arg348, Tyr382
Glu99, Glu99, Thr115, Thr115, Tyr324, Arg348, Arg348
The end of Initialization
Glu99, Glu99, Arg132, Arg136, Trp159, Ser227, Tyr324, Arg348, Tyr382
Glu99, Glu99, Arg132, Trp159, Glu208, Tyr324, Arg348, Arg348, Tyr382, Glu405, Glu405
Glu99, Asp131, Glu208, Arg273, Arg273, Asn275, Arg348, Arg410
Production of 5000 ps
Arg98, Glu99, Arg132, Arg136, Glu208, Ser227, Ser227, Glu258, Arg273, Tyr382, Glu405, Arg410
Glu99, Glu99, Arg132, Trp159, Glu208, Tyr324, Arg348, Arg348, Tyr382, Glu405, Glu405
Arg98, Glu99, Asp131, Glu208, Glu208, Tyr382
Cooling
Arg98, Glu99, Glu99, Arg132, Arg136, Ser160, Glu208, Ser227, Glu258, Arg273, Tyr382, Glu405, Glu405, Arg410, Arg410
Glu99, Arg132, Arg132, Ser160, Glu208, Ser227, Arg273, Arg273, Asn275, Arg348, Arg348, Tyr382, Tyr382, Glu405, Glu405, Lys412
Glu99, Asp131, Glu208, Glu208, Trp276, Arg348, Tyr382, Tyr382, Arg410
Note : Residues in red are the active sites of NA
Table S4. Comparison of the formed contact residue and hydrogen bond
during molecular docking and dynamics at 312 K
Ligand
Simulation
CLDRC CILRC CIWRC
Molecular Docking Arg98, Glu99,
Arg132, Arg136,
Glu208, Ser227,
Ser227, Glu258,
Arg273, Tyr382,
Glu405, Arg410
Glu99, Glu99,
Arg132, Trp159,
Glu208, Tyr324,
Arg348, Arg348,
Tyr382, Glu405,
Glu405
Arg98, Glu99,
Asp131, Glu208,
Glu208, Tyr382
Molecular
Dynamics 312 K
Arg98, Glu99,
Arg132, Arg136,
Glu99, Glu99,
Arg132, Trp159,
Arg98, Glu99,
Asp131, Glu208,
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Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
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Glu208, Ser227,
Glu258, Arg273,
Tyr382, Glu405,
Arg410
Glu208, Tyr324,
Arg348, Arg348,
Tyr382, Glu405,
Glu405
Glu208, Tyr382
Note : Residues in red are the active sites of NA
a)
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Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
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b)
Figure S1. The visualization of active side residue interactions of Ligand CLDRC during the beginning pf initialisation stage (a) Temperature of 310K and (b) Temperature of 312K
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a)
b)
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Figure S2. The visualisation of active side residue interactions of CLDRC ligand during the end of initialisation stage(a) Temperature of 310K and (b) Temperature of 312K
a)
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Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
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b)
Figure S3. Visualisation of active side residue interactions of CLDRC ligand during production stage (a) Temperature of 310K and (b) Temperature of 312K
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Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
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a)
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b)
Figure S4. The visualisation of active site residue interactions of CLDRC ligand during cooling stage. (a) Temperature of 310K and (b) Temperature of 312K
.
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Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
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a)
b)
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Figure S5. The visualisation of active site resiude interactions of CILRC ligand during the beginning of initialisation stage (a) Temperature of 310K and (b) Temperature of 312K
a)
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b)
Figure S6. The visualisation of active side interactions of CILRC ligand during the end of initialisation stage (a) Temperature of 310K and (b)Temperature of 312K
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Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
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a)
b)
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Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
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Figure S7. The visualisation of active site residue interactions of CILRC
ligand during production stage (a) Temperature of 310K and (b) Temperature of 312K
a)
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Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
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b)
Figure S8. The visualisation of active site residue interactions of CILRC ligand during cooling stage (a) Temperature of 310K dan (b) Temperature of 312K
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Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
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a)
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b)
Figure S9. The visualisation of active site residue interactions of CIWRC
ligand during the beginning of initialisation stage. (a)
Temperature of 310K and (b) Temperature of 312K
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a)
b)
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Figure S10. The visualisation of active site residue interactions of CIWRC
ligand during the end of the initialisation stage (a)
Temperature of 310K and (b) Temperature of 312K
a)
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Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
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b)
Figure S11. The visualisation of active site residue interactions of CIWRC
ligand during the production stage (a) Temperature of 310K and (b)
Temperature of 312K
Supplementary,materials,,
Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
22,
a)
b)
Supplementary,materials,,
Bioinformatics,Research,Group,,Department,of,Chemistry,,Faculty,of,Mathematics,and,Science,,University,of,Indonesia,
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Figure S12. The visualisation of active site residue interactions of CIWRC
ligand during the cooling stage (a) Temperature of 310K and (b)
Temperature of 312K
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