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SUPPLEMENTARY MATERIAL
Molecular modelling studies on the interactions of 7-methoxytacrine-4-
pyridinealdoxime with VX-inhibited HssAChE. A near attach approach to
assess different spacer-lengths.
Jorge Alberto Valle da Silva, [email protected] a,1, Eugenie Nepovimova,
[email protected] b, Teodorico Castro Ramalho, [email protected] c, Kamil Kuca,
[email protected] d, Tanos Celmar Costa França, [email protected] a, d.
aLaboratory of Molecular Modelling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro/RJ, Brazil;
bBiomedical Research Centre, University Hospital Hradec Kralove, Czech Republic;
cLaboratory of Molecular Modelling, Chemistry Department, Federal University of Lavras, Lavras, MG, Brazil;
dCenter for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Hradec Kralove, Czech Republic.
1 Present address: Chemical, Biological, Radiological and Nuclear Institute, Avenida das
Americas, 28705, Barra de Guaratiba Rio de Janeiro, RJ, Brazil.
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Figure S1. Protonation states of hybrids nC. Molecular structures of ligands predicted
through protonation analysis as the highest percentage of micro species. Result of the original
hybrid 5C [11] is highlighted in blue.
Figure S2. Re-docking results. Re-docking evaluation of HI-6 by overlapping of pose over
conformation within HssAChE/VX/HI-6 complex (modeled from MmAChE/GB/HI-6
crystallographic complex).
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Table S1. Docking results for hybrids from 1C to 10C. Results of the best pose selected for
each compound as NAC approach (Figure 2) [6,14-16].
Hybrid
s nC
The best pose selected regarding the highest ratio θOPO/dOP
dOP
(nm)θOPO
Einter
(kJ/mol)
EH−bond
(kJ/mol)
H-bond
interaction
residues a
Hydrophobic interactions
( π-π ) a, b
1C 0.57 154° - 520.11 - 30.00Tyr124,
Ser125
Tyr72, Trp86, Phe123,
Tyr124, Trp286,
Phe295, Phe297, Tyr337,
Phe338, Tyr341, His447
2C 0.50 151° - 517.15 - 31.38 Tyr124
Tyr72, Tyr124, Trp286,
His287, Phe295, Phe297,
Tyr337, Phe338, Tyr341
3C 0.67 148° - 671.84 - 34.79
Tyr124,
Ser125,
Ser298
Tyr72, Trp86, Tyr124,
Trp286, His287, Phe295,
Phe297, Phe299, Tyr337,
Phe338, Tyr341
4C 0.48 158° - 560.68 - 19.95 Tyr124
Tyr72, Tyr124, Trp286,
His287, Phe295, Phe297,
Tyr337, Phe338, Tyr341
5C 0.51 159° - 514.65 - 24.86 Tyr124
Tyr72, Tyr124, Trp286,
His287, Phe295, Phe297,
Tyr337, Phe338, Tyr341
6C 0.53 148° - 551.36 - 14.07VX-
Ser203
Tyr72, Tyr124, Trp286,
His287, Phe295, Phe297,
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Hybrid
s nC
The best pose selected regarding the highest ratio θOPO/dOP
dOP
(nm)θOPO
Einter
(kJ/mol)
EH−bond
(kJ/mol)
H-bond
interaction
residues a
Hydrophobic interactions
( π-π ) a, b
Tyr337, Phe338, Tyr341
7C 0.40 149° - 594.30 - 5.17
Tyr72,
Tyr124,
His287
Tyr72, Tyr124, Trp286,
His287, Phe295, Phe297,
Tyr337, Phe338, Tyr341
8C 0.42 163° - 530.91 - 13.41
Tyr124,
VX-
Ser203
Tyr72, Phe123, Tyr124,
Trp286, Phe295,
Phe297, Phe299, Tyr337,
Phe338, Tyr341, His447
9C 0.38 174° - 473.14 - 13.89Tyr124,
Ser125
Tyr72, Trp86, Tyr124,
Trp286, His287, Phe295,
Phe297, Tyr337, Phe338,
Tyr341, His447
10C 0.59 158° - 615.71 - 15.49Tyr124,
Ser125
Tyr72, Trp86, Phe123,
Tyr124, Trp286,
Phe295, Phe297, Tyr337,
Phe338, Tyr341, His447
a Residues in bold highlight the interactions with PAS (Tyr72, Tyr124, Trp286 and Ser298) and CAS (VX-
Ser203 adduct and His447).
b Hydrophobic interactions amongst aromatic rings roughly in parallel.
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Figure S3. Dynamic behaviour of hybrids 4C and 5C. Plots of dOP throughout 50 ns of MD
simulation and the last frame of each ligand.
Figure S4. Temporal RMSD. Plots of RMSD throughout 50 ns of MD simulation.
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Figure S5. Behaviour of dOP. Plots of dOP per ligand throughout 50 ns of MD simulation.
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Figure S6. Last frames after 50 ns of MD simulation. Comparisons amongst last frames.
Ligands are shown in green, residues of CAS in yellow and others in blue. H-bonds and dOP
are shown in blue and brown dashed lines respectively.
Figure S7. H-bond interactions of hybrid 4C (PAS). (a) and (c) plots of H-bond
interactions with the atoms of Glu202, Tyr124 and Glu285 throughout 50 ns of MD
simulation. (b) and (d) variation of distances d of the H-bonds formed. “⟨ ⟩” represents the
mean of d values.
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Figure S8. H-bond interactions of hybrid 5C (PAS) with PAS. (a) plot of H-bond
interactions with the atoms of Tyr124 throughout 50 ns of MD simulation. (b) variation of
distances d of the H-bond formed. “⟨ ⟩” represents the mean of d values.
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Figure S9. H-bond interactions of hybrid 5C (PAS). (a) and (b) plots of H-bond
interactions with amongst the ligand, Asp74, Thr83, and Tyr341 throughout 50 ns of MD
simulation. (c) and (d) variation of distances d of the H-bonds formed. “⟨ ⟩” represents the
average d values.
Figure S10. H-bond interactions of hybrid 4C (PAS) deprotonated. (a) and (b) plots of H-
bond interactions with the atoms of Tyr72, Tyr124 and His447 throughout 50 ns of MD
simulation. (c) and (d) variation of distances d of the H-bonds formed. “⟨ ⟩” represents the
mean of d values.
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Figure S11. H-bond interactions of hybrid 4C (PAS) deprotonated within PAS. (a) plots
of H-bond interactions formed between Glu285 and Ser298 throughout 50 ns of MD
simulation of hybrid 4C (PAS) deprotonated. (b) variation of distances d of the H-bonds
formed. “⟨ ⟩” represents the average d values.
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Figure S12. H-bond interactions of hybrid 5C deprotonated. (a) and (c) plots of H-bond
interactions with Tyr124 and Glu292 throughout 50 ns of MD simulation. (b) and (d)
variation of distances d of the H-bonds formed. “⟨ ⟩” represents the average d values.
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Table S2. Relative binding free energies per key residues. The most significant
contributions ⟨ ∆ GResidue⟩ of key amino acid residues to ⟨ ∆ GBinding ⟩.
Contributions
per residue a, b, c
Hybrid 4C
(PAS)
Hybrid 5C
(PAS)
Hybrid 4C
(PAS)
deprotonated
Hybrid 5C
deprotonated
Asp74:
⟨ ∆ EMM ⟩ d -62.02 ± 8.48 -101.99 ± 5.99 -45.30 ± 7.70 -29.04 ± 5.91
⟨ ∆ GPolar ⟩ d 17.58 ± 5.17 64.59 ± 13.13 14.96 ± 8.25 6.67 ± 8.23
⟨ ∆ GNonpolar ⟩ d -0.19 ± 0.20 -0.64 ± 0.22 -0.40 ± 0.34 -0.06 ± 0.13
⟨ ∆ GResidue⟩ e -44.63 ± 5.29 -38.04 ±9.72 -30.74 ± 3.74 -22.44 ± 5.06
% of ⟨ ∆ GBinding ⟩ f 5.88% 5.29% 6.77% 5.16%
Glu84:
⟨ ∆ EMM ⟩ d - -52.45 ± 4.72 - -
⟨ ∆ GPolar ⟩ d - 13.31 ± 4.30 - -
⟨ ∆ GNonpolar ⟩ d - -0.02 ± 0.04 - -
⟨ ∆ GResidue⟩ e - -39.16 ± 1.73 - -
% of ⟨ ∆ GBinding ⟩ f - 5.44% - -
Tyr124 (PAS g):
⟨ ∆ EMM ⟩ d - - - -1.41 ± 1.00
⟨ ∆ GPolar ⟩ d - - - 1.35 ± 1.36
⟨ ∆ GNonpolar ⟩ d - - - -0.19 ±0.20
⟨ ∆ GResidue⟩ e - - - -0.25 ±0.59
% of ⟨ ∆ GBinding ⟩ f - - - 0.06%
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Contributions
per residue a, b, c
Hybrid 4C
(PAS)
Hybrid 5C
(PAS)
Hybrid 4C
(PAS)
deprotonated
Hybrid 5C
deprotonated
Glu202 (PAS g):
⟨ ∆ EMM ⟩ d -88.60 ± 10.14 -55.06 ± 1.71 -17.15 ± 1.41 -
⟨ ∆ GPolar ⟩ d 39.07 ± 7.52 13.89 ± 3.12 -4.70 ± 4.56 -
⟨ ∆ GNonpolar ⟩ d - 0.06 ± 0.08 - - -
⟨ ∆ GResidue⟩ e -49.59 ± 8.64 -41.18 ± 3.20 -12.46 ± 4.95 -
% of ⟨ ∆ GBinding ⟩ f 6.54% 5.72% 2.74% -
a Some key amino acid residues.
b Calculated in kJ/mol.
c Values in bold for key contributions discussed in the text.
d Calculated through MM-PBSA methodology [53].
e Calculated as shown in equation 5.
f Calculated as shown in equation 4.
g Interactions within PAS or CAS as indicated in Figure 2.
Table S2. Relative binding free energies per key residues. The most significant
contributions ⟨ ∆ GResidue⟩ of key amino acid residues to ⟨ ∆ GBinding ⟩ (Cont.).
Contributions
per residue a, b, c
Hybrid 4C
(PAS)
Hybrid 5C
(PAS)
Hybrid 4C
(PAS)
deprotonated
Hybrid 5C
deprotonated
Glu285 (PAS g):
⟨ ∆ EMM ⟩ d -112.94 ± 14.04 - -86.79 ± 15.31 -48.41 ± 12.27
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Contributions
per residue a, b, c
Hybrid 4C
(PAS)
Hybrid 5C
(PAS)
Hybrid 4C
(PAS)
deprotonated
Hybrid 5C
deprotonated
⟨ ∆ GPolar ⟩ d 68.98 ± 11.93 - 71.21 ± 11.50 26.32 ± 19.49
⟨ ∆ GNonpolar ⟩ d -0.29 ± 0.12 - -0.23 ± 0.10 -0.33 ± 0.30
⟨ ∆ GResidue⟩ e -44.26 ± 9.98 - -15.81 ± 9.70 -22.41 ± 9.72
% of ⟨ ∆ GBinding ⟩ f 5.83% - 3.48% 5.16%
Trp286 (PAS g):
⟨ ∆ EMM ⟩ d - - - -19.27 ± 3.84
⟨ ∆ GPolar ⟩ d - - - 6.96 ± 1.36
⟨ ∆ GNonpolar ⟩ d - - - -2.29 ±0.49
⟨ ∆ GResidue⟩ e - - - -14.59 ± 3.77
% of ⟨ ∆ GBinding ⟩ f - - - 3.36%
Glu292:
⟨ ∆ EMM ⟩ d -59.41 ± 7.43 -57..39 ± 5.88 -36.68 ± 3.43 -46.34 ± 18.60
⟨ ∆ GPolar ⟩ d 12.64 ± 7.81 10.88 ± 5.87 5.31 ± 3.97 16.93 ± 22.06
⟨ ∆ GNonpolar ⟩ d -0.02 ± 0.06 - 0.03 ± 0.08 - 0.01 ± 0.02 -0.66 ± 0.50
⟨ ∆ GResidue⟩ e -46.78 ± 4.42 -46.54 ± 2.72 -31.38 ± 1.94 -30.07 ± 5.07
% of ⟨ ∆ GBinding ⟩ f 6.17% 6.47% 6.91% 6.92%
a Some key amino acid residues.
b Calculated in kJ/mol.
c Values in bold for key contributions discussed in the text.
d Calculated through MM-PBSA methodology [53].
e Calculated as shown in equation 5.
f Calculated as shown in equation 4.
g Interactions within PAS and CAS as indicated in Figure 2.
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Figure S13. Relative binding free energies per key residues. Comparisons amongst the
most significant contributions ⟨ ∆ GResidue⟩ of key amino acid residues to ⟨ ∆ GBinding ⟩.
Table S3. Relative binding free energies through NAC approach. Relative binding
energies computed for the NAC frames selected.
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LIGAND Figure Frame a t(ns)∆ GNAC frame
(kJ/mol) b
∆ G1st frame
(kJ/mol) b
∆ ∆ GBinding
(kJ/mol) c
Hybrid 4C (PAS)
deprotonated7 (a) 162 3.24 - 443.367 - 442.177 - 1.190
Hybrid 5C
deprotonated7 (b) 140 2.80 - 481.755 - 381.415 - 100.340
a Selected with the highest ratio θOPO /dOP.b Calculated as equation 3 just for the respective frame.c Calculated as equation 6.
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