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QM/MM Calculations Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is © the Owner Societies 2017 Electronic Supplementary Information for In silico analysis of interaction pattern switching in ligand···receptor binding in Golgi α- mannosidase II induced by inhibitors protonation state V. Sladek,ab J. Kóňa a and H. Tokiwab a) Institute of Chemistry – Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia b) Dept. of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima, Tokyo 171-8501 Japan E-mail: [email protected] ([email protected]); [email protected] Starting geometry and protonation of AA Our models are based on geometries of the crystal structures (PDB ID: 3BLB 1,2 for swainsonine, PDB ID: 2F7O3 for Mannostatin A and PDB ID: 3DX34 for the ligand L5) and docked poses (ligand MAN, L2 and L6) calculated in our previous study.5 The GM enzyme model for docking calculations was based on the crystal structure of the complex swainsonine-GM (PDB ID: 3BLB 1,2) and structurally optimized (side chains of ionisable amino acids, positions and conformations of water molecules and positions of added hydrogen atoms) using Monte Carlo simulations as implemented in the Schrödinger package. -3 6 -3 6 -9 1 The Ki (or IC50) values of the individual inhibitors are: IC50(MAN) > 5 x 10 M , IC50(L2) = 2 x 10 M , Ki(SW) = 3 x 10 M , Ki(MSA) = 3.6 -8 3 -7 4 -5 7 5 x 10 M , Ki(L5) = 3 x 10 , Ki(L6) = 1.3 x 10 . They, along with many more, were comprehensively collected by Bobovska et al. The pKa 8,9 values for the ligands bound in the receptor were estimated by the empirical calculations using the PROPKA 2.0 program considering GM pH optimum of 6, and by DFT calculations (pKa values of ligands in water environment) including empirical corrections from the 10 Jaguar-pKa predictor module of the Schrödinger package. pKa calculations The most potent inhibitors of GM are azasugars. They contain an amino functional group incorporated in a ring moiety of the inhibitor. The pKa values of such ionisable group may range from 5 to 9 depending on the position of the nitrogen atom in the ring as well as on other structural factors (number and position of hydroxyl groups in the ring, the conformation of the ring, chemical external environment 11 of the amino group, etc.). For example, SW, MSA and L6 are of moderate basicity (pKa ≈ 7.5, Table S1) and in physiological pH of Golgi apparatus (pH ≈ 6) or lysosomes (pH ≈ 4.0) the most populated configuration should be expected with the protonated amino group (SW+, + + +2 MSA , L6 ). Yet, the pKa value of the inhibitors in the active site of GM may differ due to the proximity of the Zn ion and other ionisable active-site amino acid residues. Thus, prior to interaction energy calculations of inhibitor···enzyme complexes, pKa calculations of the selected GM inhibitors in water and then in the GM enzyme were performed (Table S1). The main goal was to estimate the population of neutral and protonated configuration in the bound inhibitor···enzyme complexes. According to experimental and the predicted pKa values in water (pH=7), all ligands with the amino group (SW, MSA, L5 and L6) should prefer a protonated state (only for L6 calculated pKa=6.6 differs from experimental pKa=7.4, thus, a neutral form of L6 is incorrectly predicted as the most populated in water). The GM inhibitors 0 0 prefer the protonated form in water (~80-90%). On the other hand, most ligands prefer neutral form [pKa(SW )=5.0, pKa(L5 )=3.3, 0 + pKa(L6 )=4.7] after binding ligands to GM (pH=5.9). Only MSA has the pKa value higher than pH of GM (MSA pKa=6.8; MSA does not have the amino group incorporated in the ring, thus, its pKa value may differ from the values for azasugars). Detailed analysis has shown that +2 +2 Zn , Arg228, His90, His471, Asp92, Asp204 and Asp472 had the most significant influence on the final pKa of the ligand. While Zn , Arg228, His90, and His471 tend to decrease its value, Asp92, Asp204 and Asp472 have the opposite effect. The Zn+2 ion had the major +2 suppressive impact on the pKa values. In conclusion: the shorter the distance of the amino group in the bound inhibitor to the Zn ion, the lower pKa value may be expected. Thus, a position of amino group on the ring of the ligand dictates a preferred protonation state and influences interactions with the receptor. Therefore in general, both forms of the GM inhibitor (in the case of ligands with an ionisable functional group) have to be taken into account when their binding affinities are quantified. 1 Table S1. Calculated pKa values of ligands at the quantum mechanics level (in water) and at the empirical level (in the GM enzyme) as well as estimated ratios of neutral and protonated forms in water [LIG0/LIG+(aq)] and in GM 0 + [LIG /LIG (GM)] based on pKa calculations. pK pK a pK a a a LIG0/LIG+ LIG0/LIG+(GM) HN+-R (exp) (aq) (GM) 3 (aq)b (%) (%) pH=7 pH=5.9 + SW HN -R3 7.5 7.8 5.0 8/92 94/6 + MSA H3N -R 7.6 7.6 6.8 12/88 6/94 7.7 10/90 8.0 5/95 + L5 H3N -R 7.7 3.3 10/90 99.9/0.1 7.8 8/92 7.9 7/93 + L6 H2N - 7.4 6.6 4.7 80/20 97/3 R2 6.7 75/25 20/80c a pKa values for the secondary (in L6) and primary amino groups (in MSA and L5) for all two (or three) hydrogens were calculated. b a ratio calculated from predicted pKa(aq) in water c a ratio calculated from experimental pKa of 7.4 in water QM/MM calculations Complexes (enzyme-inhibitor) were optimized at the hybrid QM/MM level using the QSite12 program which couples the Jaguar13 and Impact14 programs of the Schrödinger package10. The QM/MM methodology (an additive scheme) with hydrogen caps on boundary QM atoms and electrostatic treatment at the interface between the QM and MM regions using Gaussian charge distributions represented on a grid (keyword HCAPESCHG=3) was employed. The QM part of the model consisted of 156 atoms from enzyme: side chains of Trp95, His90, Asp92, Asp204, Phe206, Arg228, Asp341, Trp415, His471, Asp472, Tyr727, Arg876 and Zn+2 ion, and of atoms of the bound inhibitor. For the QM part, the DFT methodology was used, applying the meta hybrid Minnesota functional with double the amount of nonlocal exchange (M06-2X) with the Los Alamos national laboratory effective core potential (LACVP**) basis set.15–17 In the LACVP** basis set the valence electrons are described by the Pople’s split valence double-ξ basis set [6-31G(d,p)]18 augmented by polarization on all atoms. The M06-2X functional was chosen based on previous benchmark studies on sugars19,20 and sugar phosphates21 in which Minnesota functionals with double the amount of nonlocal exchange together with functionals parametrized for kinetics gave the best prediction for reactivity of the O-glycosidic bond. The MM part of the system was treated with the OPLS2005 force fields with no cut-offs introduced for nonbonding interactions.22 All stationary points were characterized as minima or transition states by vibrational frequency calculations calculated from Hessian from the end of the optimization (keyword IFREQ= −1). Convergence thresholds for the energy and gradient change were set to be 5×10−5Hartree and 4.5×10−4Hartree Bohr−1, respectively. The ultrafine integration grid (the Mura-Knowles radial shell distribution scheme),23 which has 125 radial shells and uses an angular offset of 30 (434 angular points per shell) with no pruning as defined in the Qsite program (keywords GDFTFINE= −14, GDFTGRAD= −14, GDFTMED= −14), was set for all calculations because of the systematic grid errors found for the Minnesota functional family with a standard integration grid.17,24 In mapping the potential energy surface (PES) of the catalytic reaction, one-dimensional scan procedures were performed along the O1–C1 and C1–OAsp204 reaction coordinates stepped by 0.1 Å with remaining coordinates optimized. A transition state was refined from the maxima found on the scanned PES and optimized without any geometry constraints. Transition state searches (keywords IQST = 0, IGEOPT = 2) were performed by using a quasi-Newton method.25–27 The transition state was verified as having one large imaginary frequency by a vibrational frequency calculation. In addition, intrinsic reaction coordinate (IRC) calculations were performed to prove that TS connects the right reactant and product minima. The IRC calculations allowed sliding downhill from the TS along the TS eigenvector, calculating the gradient and taking a small step in the negative gradient direction to reach energy minima corresponding to the TS. 2 Fragment definition and geometries After the QM/MM optimization the whole receptor site was formally separated into four domains; D1, D2, D3 and D4. This separation was necessary in order to reduce the calculation requirements in the SAPT analysis. However, this separation enables one to analyse the contributions to the total binding mode in a more detailed and localized manner. The fragment composition is the following: D1: His90, Asp92-1, Asp204-1, Asp3410, His471, Asp472-1, Zn+2 D2: Phe206, Trp415, Tyr727 D3: Trp95, Arg876+1, Gly877 D4: Arg228+1, Tyr269 The fragments were not re-optimized after separation.
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