Molecular Dynamics Simulation of Kynurenine Aminotransferase Type

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Article Cite This: ACS Omega 2019, 4, 710−717

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Molecular Dynamics Simulation of Kynurenine Aminotransferase Type II with Nicotine as a Ligand: A Possible Biochemical Role of Nicotine in Schizophrenia Haruna L. Barazorda-Ccahuana, Christian Zevallos-Delgado, Diego Ernesto Valencia, and Badhin Gómez* Centro de Investigación en Ingeniería MolecularCIIM, Vicerrectorado de Investigación, Universidad Católica de Santa María, Urb. San José s/nUmacollo, Arequipa 04013, Peru

ACS Omega 2019.4:710-717. Downloaded from pubs.acs.org by 95.85.69.36 on 01/09/19. For personal use only.

S Supporting Information *

ABSTRACT: Homodimeric KATII is an enzyme involved in L-kynurenine transamination to kynurenic acid. The increase in kynurenic acid concentration is predominant in schizophrenia and other disorders. Currently, the search for new KATII inhibitors continues to be a challenge. The aim of this work was to analyze the possible role of nicotine in KATII inhibition and compare it with the reversible inhibitor NS1502. We have used computational methods of quantum mechanics, docking, molecular dynamics, and binding energy (molecular mechanics/Poisson−Boltzmann surface area). The results of chemical reactivity showed that the nucleophilic and electrophilic attacks would be more significant in nicotine than in NS1502. The molecular dynamics simulations provided a molecular understanding of the binding interaction of nicotine and NS1502 with KATII. The nicotine binding energy was similar to that of the NS1502 compound; both were placed in the same pocket. Furthermore, the energy distribution analysis of ligands to cofactor lysine pyridoxal-5′-phosphate presented similar values in both cases; consequently, the electrostatic potential of the active site was positive, which leads us to believe that nicotine behaves as the reversible inhibitor NS1502 and could play a neuroprotective role in schizophrenia.

1. INTRODUCTION The increase of kynurenic acid (KYNA) concentration in the brain is related to cognitive dysfunctions in schizophrenia and other psychiatric diseases, causing neurotoxicity.1,2 KYNA was initially found to block all ionotropic glutamate receptors at high micromolar concentrations.3,4 Regardless of its action on glutamatergic receptors, KYNA also has antioxidant properties, which are related to its ability to capture hydroxyl ions, superoxide anions, and other free radicals.5 Astrocytic kynurenine aminotransferases (KATs) mainly catalyze the synthesis of KYNA from its immediate bioprecursor, Lkynurenine (L-KYN), in the brain.6 There have been reported four kynurenine aminotransferase (KAT) isozymes as members of the pyridoxal-5′-phosphate (PLP)-dependent enzymes: KATI, KATII, KATIII, and KATIV.7 KATI and KATII have an essential role in the regulation of the kynurenine pathway. KATII generates high levels of KYNA in the brain, making this process an attractive pharmacological target in the treatment of schizophrenia and other neurological disorders.8,9 KATII has pyridoxal-5′-phosphate (PLP) as a cofactor, which is covalently attached to LYS263 by a Schiff-base linkage, forming a lysine pyridoxal-5′-phosphate (LLP) residue.10 KATII is composed of two identical subunits, forming a homodimeric protein with a molecular weight of 47.6 kDa. The © 2019 American Chemical Society

ARG399, TYR142, SER143, and ASN202 residues from one subunit and GLY39, LEU40, ILE19, ARG20, and TYR74 from the opposite subunit define the substrate-binding site and contact the L-KYN molecule.11 ARG20 is a notable residue in the active site, whose side chain has π−cation interactions with the aromatic ring of L-KYN.12 KATII N-terminal residues allow the entry of L-KYN into the active site by undergoing a conformational change, helping anchor the substrate with the cavity inner residues. L-KYN forms hydrogen bonds with ASN202 and GLY39 in the amine group and a salt bridge with ARG399 in the carboxyl group.13,14 The development of new inhibitors of KATII continues to be a challenge. Actually, there are a reduced number of reversible inhibitors15−18 such as a chemical compound 2-(5,6-dichloro1,3-dioxo-1,3-dihydro-2H-isoindole-2-yl)-3-phenylpropanoic acid (NS1502) with a molecular structure derived from previous irreversible inhibitors. NS1502 interacts strategically with the active site of the enzyme, forming hydrogen bonds with the TYR142 and ASN202 residues and directly interacting with LLP263 through its phenyl aromatic ring.19 This type of Received: September 5, 2018 Accepted: December 26, 2018 Published: January 9, 2019 710

DOI: 10.1021/acsomega.8b02287 ACS Omega 2019, 4, 710−717

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Figure 1. Geometric optimization of ligands.

Figure 2. Frontier molecular orbital isosurfaces.

2. RESULTS AND DISCUSSION 2.1. Molecular Geometry and Chemical Reactivity Properties. The molecular structure of nicotine shows pyridine and pyrrole rings, and the structure of NS1502 shows a dichlorophthalimide and the amino acid phenylalanine. Analysis of the electrostatic potential map has shown that in NS1502 the negative charge is located on the nitrogen atom, whereas in nicotine the negative charge is located on the oxygen atoms and the rest of the atoms remain almost positive (see Figure 1). Frontier molecular orbitals provide relevant information about reactivity. Figure 2 shows the highest-occupied molecular orbital (HOMO) and the lowest-unoccupied molecular orbital (LUMO). The HOMO energy is situated on the nitrogen atom in the aromatic ring of the nicotine pyrrole and the benzyl ring in NS1502. In contrast, the LUMO energy is situated on the

inhibitor is a good model to compare with other new inhibitors that could have some effect on KATII. There is evidence of a correlation between mental disorders and smoking and nicotine addiction.20 However, in some studies, the use of nicotine has improved the cognitive performance of patients with neurodegenerative diseases and psychiatric disorders,21,22 so they suggest the neuroprotective role of nicotine.23,24 This effect seems to have a relationship with the mitochondrial respiratory chain, independent of its receptor.25,26 The aim of the present investigation was to explore the effect of nicotine on KATII using quantum mechanics and molecular dynamics (MD). 711


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Table 1. Global Reactivity Indices of Nicotine and NS1502 in Electronvolts molecule

EHOMO

ELUMO

μa

χb

ηc

Sd

ωe

nicotine NS1502

−7.8116 −8.4252

0.3826 −1.6795

3.7145 5.0523

−3.7145 −5.0523

4.0971 3.3729

0.2441 0.2960

1.6838 3.7841

a

Chemical potential. bElectronegativity. cHardness. dSoftness. eElectrophilicity.

Figure 3. Fukui function isosurfaces.

two identical subunits and an active site with LLP (the PLP cofactor linked to LYS263). 2.2. Docking Analysis. Molecular docking studies using PatchDock were carried out to determine the molecular complex formed by interaction of two ligands (nicotine and NS1502). We considered the top energetic scored solution, PatchDock server, followed by refinement in FireDock; this was the first approximation of coupling. The atomic contact energies (ACEs) of NS1502 and nicotine were −12.24 and −7.13 kcal/ mol, respectively, showing high-probability interaction values and an energetically favorable model of coupling with homodimeric KATII. We also analyzed the ACE of crystal structures PDB ID: 5TF5 KATII−NS1502 and PDB ID: 2RNR KATII−L-kynurenine (L-KYN), to compare these results with the first predictions. 5TF5 and 2RNR complexes showed ACEs of −15.93 and −9.15 kcal/mol, respectively. In this case, we found that nicotine and L-KYN presented approximate ACE value of −7.13 and −9.15 kcal/mol, respectively; these values are shown in Table 2. The comparison of the attraction energy suggests a spontaneous affinity for nicotine as seen in other compounds; likewise, the investigations by Jayawickrama et al. described that the ARG20, ARG399, and ASN202 residues are necessary for the coupling between estrogen and its derivatives in the active site of KATII.27 2.3. Molecular Dynamics Trajectory Analysis. The equilibrium simulations were carried out for temperature T ≈ 309.65 K and mass density ρ ≈ 1025 kg/m3. After equilibrium simulations, the MD production simulations at 50 ns were analyzed. The root-mean-square deviation (RMSD) of homodimeric KATII without the ligand has a value of 0.32 ± 0.04 nm. The RMSDs of homodimeric KATII with nicotine and NS1502 have values of 0.25 ± 0.04 and 0.24 ± 0.04 nm, respectively; these results are shown in Figure 5.

pyridine ring of nicotine and on the phthalimide group and dichloro groups in NS1502, which being a sigma-donor and πacceptor promote the increase of LUMO energy. The global reactivity indices such as chemical potential (μ), electronegativity (χ), hardness (η), softness (S), and electrophilicity (ω) are shown in Table 1. The chemical hardness value of NS1502 is lower than that of nicotine, showing a hardly deformable electron cloud. The low reactivity of nicotine indicates the possible formation of hydrogen bonds and nonbonded interactions. The softness value of NS1502 is higher than that of nicotine, representing an increased capability to donate and accept electrons. The Fukui function represents local reactivity indices; the nucleophilic attack (f+) occurred on the pyridine nitrogen atom of nicotine (Figure 3a); meanwhile, in NS1502, it occurred on two carbonyl groups bound to the nitrogen atom of the phthalimide group, with a lower capacity than that of the nicotine molecule, according to Figure 3b. The electrophilic attack occurred on the N-methyl group of the pyrrole ring of nicotine (Figure 3c) and on carbon atoms of the benzyl ring in NS1502 (Figure 3d). We found that nicotine would react with similar magnitudes for nucleophilic and electrophilic attacks and that the attacks in both cases occurred on the nitrogen atoms, which have two unpaired electrons with the capability to form hydrogen bonds. The nucleophilic and electrophilic attacks were weak in NS1502 and were linked to steric effects. We obtained the Hirshfeld charges for LLP, nicotine, and NS1502 by quantum mechanics. The Hirshfeld charges define the relative deformation electronic density and allow the calculation of the external electrostatic potential between atoms in the same molecule. These parameters are given in the Supporting Information (Figures S1−S3). In Figure 4, we describe the structure of homodimeric KATII, constituted by 712


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binding with nicotine and NS1502. The energy contribution of van der Waals (VdW) interaction was more significant than that of the electrostatic energy. The energy contribution per residue is reported in Table S1 and Figure S4 of the Supporting Information. According to this, the energy contribution of LLP was similar in both cases. The attraction of nicotine to the active site seems to be spontaneous and this attraction energy is placed in a position similar to that for L-KYN because of its affinity to residues present in the active site (see Figure 7). 2.5. Electrostatic Potential. The electrostatic potential maps of the last frame of the 50 ns trajectory from KATII−LLP, KATII−NS1502, and KATII−nicotine in the range of −5kT/e (negative) to 5kT/e (positive) showed us a positively charged catalytic site (see Figure 8). The electrostatic potential surfaces at different times (0, 10, 20, 30, 40, and 50 ns) of the MD simulation were analyzed. The electrostatic potential change occurred in the surroundings of the structure when KATII is attached to the ligands, being most noticeable in the KATII− nicotine complex; (for details, see Figure S5 in the Supporting Information). On the other hand, the catalytic site, despite showing changes in potential, usually has a similar shape in the KATII−NS1502 and KATII−nicotine complexes (see Figure S6). The positive electrostatic potential areas are probably induced by the amino acids interacting with the ligands in both cases, such as LLP263, ARG399, ARG20, and polar amino acids. These positive areas play an essential role in the process of binding to the catalytic site of KATII, promoting the hydrophobic interaction.

3. CONCLUSIONS In this study, we have explored the possible role of nicotine in KATII and compared it with the reversible inhibitor NS1502. The results of chemical reactivity showed that the nicotine structure presented a low deformable electronic density in comparison to that of NS1502. Additionally, the Fukui function analysis indicated that nicotine suffers nucleophilic and electrophilic attacks of similar magnitudes, whereas in the NS1502 inhibitor, the nucleophilic and electrophilic attacks are relatively weak and linked to steric effects. We estimate the first approximation of coupling energy by considering the highest score, where the amino acids related to coupling were PRO18, ILE19, MET22, SER143, TYR142, TYR74, and ARG399. The MD analysis showed that KATII without the ligand is slow to reach the equilibrium, whereas systems with ligands manage to stabilize the protein. It should be noted that the residues involved in coupling with nicotine were those that had greater fluctuations, unlike the inhibitor NS1502. The binding free energy obtained by MM/PBSA showed that the KATII− NS1502 complex presented the highest energy. Moreover, the energy contribution between the ligands and the LLP cofactor favored the positive charge of the active site. The electrostatic potential surfaces of the active sites in both systems were positively charged, which leads us to believe that nicotine behaves similarly to the reversible inhibitor. Finally, these results give us an idea of what might happen if kynurenine aminotransferase type II is used against nicotine because some studies have reported the presence of nicotine in the mitochondrial system and indicate that the presence of unknown receptors with nicotine seems to be related. At this point, we believe that nicotine may act to modulate the production of kynurenic acid and thus may act as a neuroprotector in schizophrenia.

Figure 4. Structural features of KATII.

Table 2. First Approximation of Dockinga docking

global energy

aVdW

rVdW

ACE

KATII/NS1502 KATII/nicotine 2RNR

−45.69 −25.86 −46.48

−20.23 −11.32 −22.65

5.11 2.90 2.54

−12.24 −7.13 −9.15

a

All values are in kcal/mol.

The analysis of the root-mean-square fluctuation (RMSF) plot for each residue revealed that the active site of the homodimeric KATII with nicotine was altered because of high fluctuations in this site. The highest fluctuations occurred in the N-terminal region residues of one subunit and C-terminal region residues of the other subunit (Figure 6), in accordance with Han et al.10 and Nematollahi et al.,28 who identified essential residues from the N-terminal region of KATII for binding with Lkynurenine. 2.4. Free-Energy Calculations. The molecular mechanics/ Poisson−Boltzmann surface area (MM/PBSA) free energies of the complexes are listed in Table 3. The results showed that NS1502 and nicotine showed affinity with values of −127.78 and −77.97 kJ/mol, respectively. The positive value of the polar solvation energy indicated a little contribution of the ligand 713


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Figure 5. RMSD plot of three systems at 50 ns in an isobaric−isothermic ensemble.

Figure 6. RMSF diagram of homodimeric KATII revealing the important residues of the active site.

Table 3. Average MM/PBSA Free Energies of KATII Complexesa ligand

van der Waals energy

electrostatic energy

polar solvation energy

SASA energy

binding energy

NS1502 nicotine

−176.778 ± 2.058 −92.601 ± 2.906

−0.726 ± 0.685 −2.033 ± 0.392

68.663 ± 2.478 28.553 ± 1.485

−19.01 ± 0.244 −11.982 ± 0.206

−127.783 ± 3.012 −77.974 ± 2.090

a

All values are in kJ/mol.

Figure 7. Energy contribution and hydrophobic affinity.

4. COMPUTATIONAL DETAILS 4.1. Geometry Optimization. We calculated the density functional theory (DFT) ground state of three molecules: the reversible KATII inhibitor NS1502 ((2R)-2-(5,6-dichloro-1,3-

dioxo-1,3-dihydro-2H-isoindol-2-yl)-3-phenylpropanoic, PDB ID: 7AR); nicotine (3-[(2S)-1-methylpyrrolidin-2-yl]pyridine, PubChem CID: 942); and pyridoxal-5′-phosphate (PLP) cofactor, which is linked to the LYS263 residue of KATII 714


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philicity (ω) were based on the finite approximation,33 given by the following relation μ= =

I+A I+A I−A 1 ; χ=− ; η= ; S= ; ω 2 2 2 η μ2 2η

The Fukui function was studied as local reactivity indices following the Parr and Yang equations,34 where nucleophilic attacks, electrophilic attacks, and radical attacks were deduced by eqs 34−5, respectively

(PDB ID: 2QLR), using the CAM-B3LYP29 functional and TZVP basis set on Gaussian 09.30 Visual representations were done using Avogadro.31 Molecular electronic properties were analyzed from geometry optimization. The highest-occupied molecular orbital (HOMO) and the lowest-unoccupied molecular orbital (LUMO) energies were obtained from simple-point energy calculations using CAM-B3LYP/TZVP. The potential ionization value (I) and the electron affinity (A) were obtained from eqs 1 and 2, both from the DFT Koopmans mathematical relation.32 (1)

A = −E LUMO (gN)

(2)

(3)

f − (r ) ≈ ρHOMO (r )

(4)

f 0 (r ) ≈ ρHOMO (r ) + ρLUMO (r )

(5)

The analysis of electronic isosurfaces has been considered to be an important tool in the determination of correlation between molecular physicochemical properties and their biological activities. A quantitative description of the molecular charge distribution was provided using the Hirshfeld population method35 and frequency calculation. Topological information for each model was obtained from the automatic OPLS-AA topology generator web program, TPPMKTOP, developed by the ERG research group (http://erg.biophys.msu.ru/tpp/). 4.2. System Preparation. Three systems were prepared. The first corresponded to homodimeric KATII with PDB ID: 2QLR, obtained from the Protein Data Bank (PDB; https:// www.rcsb.org/); water molecules and other compounds were removed using UCSF Chimera.36 The second and third systems resulted from the docking of homodimeric KATII with nicotine and NS1502, respectively, previously optimized by quantum mechanics. The docking study was carried out on the PatchDock online server,37 which performs couplings based on the geometry and finds coupling transformations, producing an excellent molecular complementarity form. We used an RMSD of 1.5 Å, suggested for an enzyme−inhibitor type of complex; for docking refinement, we used the FireDock online server.38 4.3. Molecular Dynamics Simulation. The following calculations were performed in GROMACS 2016.439 using the OPLS-AA40,41 force field. We used a cubic box with a distance of 1.2 nm between the outside of the protein and the edge of the box, centering the protein in the box and adding water molecules (water model TIP4P), 42 which provides a reasonable description of liquid water and aqueous solutions,43 and add ions (Na or Cl) to neutralize the systems. Energy minimization was done with a steep descent algorithm for a 1 fs step during a trajectory of 200 ps. It was realized to relax the molecular geometry, avoiding any atomic clash that may exist. Periodic boundary conditions in xyz directions, 1.0 nm cutoff for short-range van der Waals (VdW) electrostatic interactions, and 1.0 nm cutoff for long-range particle-mesh Ewald electrostatic interactions were established.44 Equilibrium MD simulations were performed in two steps with the leap-frog integrator. The first step was in the canonical ensemble (NVT) of 0.5 ns, and the second step was in the isothermal−isobaric ensemble (NPT) of 0.5 ns, relaxing the systems to a constant pressure ensemble. The temperature was 309.65 K, regulated by a V-rescale thermostat, a modification of the Berendsen

Figure 8. Electrostatic potential isosurfaces mapped onto KATII; potentials range from −5kT/e (red) to +5kT/e (blue).

I = −E HOMO (gN)

f + (r ) ≈ ρLUMO (r )

Global reactivity indices such as chemical potential (μ), electronegativity (χ), hardness (η), softness (S), and electro715


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(2) Jayawickrama, G. S.; Sadig, R. R.; Sun, G.; Nematollahi, A.; Nadvi, N. A.; Hanrahan, J. R.; Gorrell, M. D.; Church, W. B. Kynurenine aminotransferases and the prospects of inhibitors for the treatment of schizophrenia. Curr. Med. Chem. 2015, 22, 2902−2918. (3) Perkins, M.; Stone, T. An iontophoretic investigation of the actions of convulsant kynurenines and their interaction with the endogenous excitant quinolinic acid. Brain Res. 1982, 247, 184−187. (4) Erhardt, S.; Schwieler, L.; Nilsson, L.; Linderholm, K.; Engberg, G. The kynurenic acid hypothesis of schizophrenia. Physiol. Behav. 2007, 92, 203−209. (5) Lugo-Huitrón, R.; Blanco-Ayala, T.; Ugalde-Muniz, P.; CarrilloMora, P.; Pedraza-Chaverri, J.; Silva-Adaya, D.; Maldonado, P.; Torres, I.; Pinzon, E.; Ortiz-Islas, E.; et al. On the antioxidant properties of kynurenic acid: free radical scavenging activity and inhibition of oxidative stress. Neurotoxicol. Teratol. 2011, 33, 538−547. (6) Mehta, P. K.; Hale, T. I.; Christen, P. Aminotransferases: demonstration of homology and division into evolutionary subgroups. FEBS J. 1993, 214, 549−561. (7) Yu, P.; Li, Z.; Zhang, L.; Tagle, D. A.; Cai, T. Characterization of kynurenine aminotransferase III, a novel member of a phylogenetically conserved KAT family. Gene 2006, 365, 111−118. (8) Pellicciari, R.; Rizzo, R. C.; Costantino, G.; Marinozzi, M.; Amori, L.; Guidetti, P.; Wu, H.-Q.; Schwarcz, R. Modulators of the Kynurenine Pathway of Tryptophan Metabolism: Synthesis and Preliminary Biological Evaluation of (S)-4-(Ethylsulfonyl) benzoylalanine, a Potent and Selective Kynurenine Aminotransferase II (KAT II) Inhibitor. ChemMedChem 2006, 1, 528−531. (9) Rossi, F.; Schwarcz, R.; Rizzi, M. Curiosity to kill the KAT (kynurenine aminotransferase): structural insights into brain kynurenic acid synthesis. Curr. Opin. Struct. Biol. 2008, 18, 748−755. (10) Han, Q.; Robinson, H.; Li, J. Crystal structure of human kynurenine aminotransferase II. J. Biol. Chem. 2008, 283, 3567−3573. (11) Rossi, F.; Garavaglia, S.; Montalbano, V.; Walsh, M. A.; Rizzi, M. Crystal structure of human kynurenine aminotransferase II, a drug target for the treatment of schizophrenia. J. Biol. Chem. 2008, 283, 3559−3566. (12) Bellocchi, D.; Macchiarulo, A.; Carotti, A.; Pellicciari, R. Quantum mechanics/molecular mechanics (QM/MM) modeling of the irreversible transamination of L-kynurenine to kynurenic acid: the round dance of kynurenine aminotransferase II. Biochim. Biophys. Acta 2009, 1794, 1802−1812. (13) Zakrocka, I.; Targowska-Duda, K. M.; Wnorowski, A.; Kocki, T.; ́ iak, K.; Turski, W. A. Angiotensin II Type 1 Receptor Blockers Józw Inhibit KAT II Activity in the Brain−Its Possible Clinical Applications. Neurotoxic. Res. 2017, 32, 639−648. (14) Nematollahi, A.; Sun, G.; Harrop, S. J.; Hanrahan, J. R.; Church, W. B. Structure of the PLP-form of the human kynurenine aminotransferase II in a novel spacegroup at 1.83 Å resolution. Int. J. Mol. Sci. 2016, 17, No. 446. (15) Linderholm, K. R.; Alm, M. T.; Larsson, M. K.; Olsson, S. K.; Goiny, M.; Hajos, M.; Erhardt, S.; Engberg, G. Inhibition of kynurenine aminotransferase II reduces activity of midbrain dopamine neurons. Neuropharmacology 2016, 102, 42−47. (16) Tuttle, J. B.; Anderson, M.; Bechle, B. M.; Campbell, B. M.; Chang, C.; Dounay, A. B.; Evrard, E.; Fonseca, K. R.; Gan, X.; Ghosh, S.; et al. Structure-based design of irreversible human KAT II inhibitors: Discovery of new potency-enhancing interactions. ACS Med. Chem. Lett. 2012, 4, 37−40. (17) Nematollahi, A.; Sun, G.; Jayawickrama, G. S.; Church, W. B. Kynurenine aminotransferase Isozyme inhibitors: a review. Int. J. Mol. Sci. 2016, 17, No. 946. (18) Nematollahi, A.; Aminimoghadamfarouj, N.; Bret Church, W. Essential structural features of novel antischizophrenic drugs: A review. Med. Chem. 2014, 10, 541−549. (19) Nematollahi, A.; Sun, G.; Jayawickrama, G. S.; Hanrahan, J. R.; Church, W. B. Crystal structure and mechanistic analysis of a novel human kynurenine aminotransferase-2 reversible inhibitor. Med. Chem. Res. 2017, 26, 2514−2519.

thermostat, and the pressure was 1.0 bar, regulated using a Parrinello−Rahman barostat. A position restraint was applied to the protein backbone using the linear constraint solver (LINCS)45 algorithm. Production molecular dynamics (MD) simulation was carried out in the NPT ensemble for 50 ns and 2 fs steps, without any position restraint. Periodic boundary conditions were applied for a continuous system, with temperature (309.65 K) and pressure (1.0 bar) being constant and the isothermal compressibility of water being 4.5 × 10−5 bar−1. Trajectory analysis was carried out using in-built tools in GROMACS, and data plotting was performed with Gnuplot 5.246 software. Temperature and density plots were analyzed for equilibrium calculations. Moreover, the root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) from the MD production simulation were analyzed. The binding free energy of the last 100 ps from the MD trajectory was analyzed using the molecular mechanics Poisson−Boltzmann surface area (MM/PBSA) method implemented in GROMACS software.47 We calculated the electrostatic potential of the last 50 ns frame using the Poisson−Boltzmann equation. To do this, we added atomic charges in PDB 2PQR,48 using the AMBER49 force field. Besides, electrostatic potential isosurfaces were analyzed using APBS software.50 Finally, UCSF Chimera and VMD51 were used as structure visualization software packages.

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ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acsomega.8b02287.

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Figure S1, OPLS-AA force field of LLP; Figure S2, OPLSAA force field of NS1502; Figure S3, OPLS-AA force field of nicotine; Figure S4, binding free energy of the last 100 ps of MD simulations; Figure S5, side view of the electrostatic potential surface of KATII; Figure S6, electrostatic potential surface of the active site of KATII; and Table S1, energy contribution per residue of the active site (PDF)

AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Phone: +51 982895967. ORCID

Haruna L. Barazorda-Ccahuana: 0000-0001-8791-0506 Diego Ernesto Valencia: 0000-0002-5533-2753 Badhin Gómez: 0000-0001-6539-1207 Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS The authors thank the financial support by CONCYTEC under Project 140-2015 FONDECYT. Badhin Gómez is grateful for UAM Iztapalapa for the use of licensed Gaussian 09 software in the Yoltla supercomputer.

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REFERENCES

(1) Pershing, M. L.; Bortz, D. M.; Pocivavsek, A.; Fredericks, P. J.; Jørgensen, C. V.; Vunck, S. A.; Leuner, B.; Schwarcz, R.; Bruno, J. P. Elevated levels of kynurenic acid during gestation produce neurochemical, morphological, and cognitive deficits in adulthood: implications for schizophrenia. Neuropharmacology 2015, 90, 33−41. 716


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Molecular Dynamics Simulation of Kynurenine Aminotransferase Type

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