QM/MM model study on properties and structure of some antibiotics in gas phase: Comparison of energy and NMR chemical shift

The combination of Quantum Mechanics (QM) and Molecular Mechanics (MM) methods has become an alternative tool for many applications for which pure QM and MM are not suitable. The QM/MM method has been used for different types of problems, for example: structural biology, surface phenomena, and liquid phase. In this paper, we have used these methods for antibiotics and then we compare results. The calculations were done by the full ab initio method (HF/3-21G) and the (HF/STO-3G) and QM/MM (ONIOM) method with HF (3-21G)/AM1/UFF and HF (STO-3G)/AM1/UFF. We found the geometry that has obtained by the QM/MM method to be very accurate, and we can use this rapid method in place of time consuming ab initio methods for large molecules. Comparison of energy values in the QM/MM and QM methods is given. In the present work, we compare chemical shifts and conclude that the QM/MM method is a perturbed full QM method. The work has been done on penicillin, streptomycin, benzyl penicillin, neomycin, kanamycin, gentamicin, and amoxicillin.     

QM/MM model study on properties and structure of some antibiotics in gas phase: Comparison of energy and NMR chemical shift

The combination of Quantum Mechanics (QM) and Molecular Mechanics (MM) methods has become an alternative tool for many applications for which pure QM and MM are not suitable. The QM/MM method has been used for different types of problems, for example: structural biology, surface phenomena, and liquid phase. In this paper, we have used these methods for antibiotics and then we compared results. The calculations were done by the full ab initio method (HF/3-21G) and the (HF/STO-3G) and QM/MM (ONIOM) method with HF (3-21G)/AM1/UFF and HF (STO-3G)/AM1/UFF. We found the geometry obtained by the QM/MM method to be very accurate, and we can use this rapid method in place of time consuming ab initio methods for large molecules. Comparison of energy values in the QM/MM and QM methods is given. In the present work, we compare chemical shifts and conclude that the QM/MM method is a perturbed full QM method. The work has been done on penicillin, streptomycin, benzyl penicillin, neomycin, kanamycin, gentamicin, and amoxicillin.     

Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site

In drug optimization calculations, the molecular mechanics Poisson‐Boltzmann surface area (MM‐PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature. To assess the effect of the force field on the calculation of binding energies, in this article we use large‐scale density functional theory (DFT) calculations as an alternative method to evaluate the energies of the configurations in a “QM‐PBSA” approach. Our DFT calculations are performed with a near‐complete basis set and a minimal parameter implicit solvent model, within the self‐consistent calculation, using the ONETEP program on protein–ligand complexes containing more than 2600 atoms. We apply this approach to the T4‐lysozyme double mutant L99A/M102Q protein, which is a well‐studied model of a polar binding site, using a set of eight small aromatic ligands. We observe that there is very good correlation between the MM and QM binding energies in vacuum but less so in the solvent. The relative binding free energies from DFT are more accurate than the ones from the MM calculations, and give markedly better agreement with experiment for six of the eight ligands. Furthermore, in contrast to MM‐PBSA, QM‐PBSA is able to correctly predict a nonbinder. Proteins 2014; 82:3335–3346. © 2014 Wiley Periodicals, Inc.     

How does the protein environment optimize the thermodynamics of thiol sulfenylation? Insights from model systems to QM/MM calculations on human 2-Cys peroxiredoxin

Protein thiol/sulfenic acid oxidation potentials provide a tool to select specific oxidation agents, but are experimentally difficult to obtain. Here, insights into the thiol sulfenylation thermodynamics are obtained from model calculations on small systems and from a quantum mechanics/molecular mechanics (QM/MM) analysis on human 2-Cys peroxiredoxin thioredoxin peroxidase B (Tpx-B). To study thiol sulfenylation in Tpx-B, our recently developed computational method to determine reduction potentials relatively compared to a reference system and based on reaction energies reduction potential from electronic energies is updated. Tpx-B forms a sulfenic acid (R-SO^?) on one of its active site cysteines during reactive oxygen scavenging. The observed effect of the conserved active site residues is consistent with the observed hydrogen bond interactions in the QM/MM optimized Tpx-B structures and with free energy calculations on small model systems. The ligand effect could be linked to the complexation energies of ligand L with CH₃S^? and CH₃SO^?. Compared to QM only calculations on Tpx-B’s active site, the QM/MM calculations give an improved understanding of sulfenylation thermodynamics by showing that other residues from the protein environment other than the active site residues can play an important role.     

QM/MM free energy simulations: recent progress and challenges

Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computational cost and accuracy. Here, we review several recent developments in free energy methods most relevant to QM/MM simulations and discuss several topics motivated by these developments using simple but informative examples that involve processes in water. For chemical reactions, we highlight the value of invoking enhanced sampling technique (e.g. replica-exchange) in umbrella sampling calculations and the value of including collective environmental variables (e.g. hydration level) in metadynamics simulations; we also illustrate the sensitivity of string calculations, especially free energy along the path, to various parameters in the computation. Alchemical free energy simulations with a specific thermodynamic cycle are used to probe the effect of including the first solvation shell into the QM region when computing solvation free energies. For cases where high-level QM/MM potential functions are needed, we analyse two different approaches: the QM/MM–MFEP method of Yang and co-workers and perturbative correction to low-level QM/MM free energy results. For the examples analysed here, both approaches seem productive although care needs to be exercised when analysing the perturbative corrections.     

Modelling flavin and substrate substituent effects on the activation barrier and rate of oxygen transfer by p-hydroxybenzoate hydroxylase

The simulation of enzymatic reactions, using computer models, is becoming a powerful tool in the most fundamental challenge in biochemistry: to relate the catalytic activity of enzymes to their structure. In the present study, various computed parameters were correlated with the natural logarithm of experimental rate constants for the hydroxylation of various substrate derivatives catalysed by wild-type para-hydroxybenzoate hydroxylase (PHBH) as well as for the hydroxylation of the native substrate (p-hydroxybenzoate) by PHBH reconstituted with a series of 8-substituted flavins. The following relative parameters have been calculated and tested: (a) energy barriers from combined quantum mechanical/molecular mechanical (QM/MM) (AM1/CHARMM) reaction pathway calculations, (b) gas-phase reaction enthalpies (AM1) and (c) differences between the HOMO and LUMO energies of the isolated substrate and cofactor molecules (AM1 and B3LYP/6-31+G(d)). The gas-phase approaches yielded good correlations, as long as similarly charged species are involved. The QM/MM approach resulted in a good correlation, even including differently charged species. This indicates that the QM/MM model accounts quite well for the solvation effects of the active site surroundings, which vary for differently charged species. The correlations obtained demonstrate quantitative structure activity relationships for an enzyme-catalysed reaction including, for the first time, substitutions on both substrate and cofactor.     

Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods

The [NiFe] hydrogenases catalyse the reversible conversion of H₂ to protons and electrons. The active site consists of a Fe ion with one carbon monoxide, two cyanide, and two cysteine (Cys) ligands. The latter two bridge to a Ni ion, which has two additional terminal Cys ligands. It has been suggested that one of the Cys residues is protonated during the reaction mechanism. We have used combined quantum mechanical and molecular mechanics (QM/MM) geometry optimisations, large QM calculations with 817 atoms, and QM/MM free energy simulations, using the TPSS and B3LYP methods with basis sets extrapolated to the quadruple zeta level to determine which of the four Cys residues is more favourable to protonate for four putative states in the reaction mechanism, Ni-SI_a, Ni-R, Ni-C, and Ni-L. The calculations show that for all states, the terminal Cys-546 residue is most easily protonated by 14–51 kJ/mol, owing to a more favourable hydrogen-bond pattern around this residue in the protein.     

Binding free energies for nicotine analogs inhibiting cytochrome P450 2A6 by a combined use of molecular dynamics simulations and QM/MM-PBSA calculations

Molecular dynamics (MD) simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have been performed to explore the dynamic behaviors of cytochrome P450 2A6 (CYP2A6) binding with nicotine analogs (that are typical inhibitors) and to calculate their binding free energies in combination with Poisson–Boltzmann surface area (PBSA) calculations. The combined MD simulations and QM/MM-PBSA calculations reveal that the most important structural parameters affecting the CYP2A6-inhibitor binding affinity are two crucial internuclear distances, that is, the distance between the heme iron atom of CYP2A6 and the coordinating atom of the inhibitor, and the hydrogen-bonding distance between the N297 side chain of CYP2A6 and the pyridine nitrogen of the inhibitor. The combined MD simulations and QM/MM-PBSA calculations have led to dynamic CYP2A6-inhibitor binding structures that are consistent with the observed dynamic behaviors and structural features of CYP2A6-inhibitor binding, and led to the binding free energies that are in good agreement with the experimentally-derived binding free energies. The agreement between the calculated binding free energies and the experimentally-derived binding free energies suggests that the combined MD and QM/MM-PBSA approach may be used as a valuable tool to accurately predict the CYP2A6-inhibitor binding affinities in future computational design of new, potent and selective CYP2A6 inhibitors.     

Molecular modeling of green fluorescent protein: structural effects of chromophore deprotonation

Molecular dynamics (MD) simulations were carried out to study the conformational rearrangement induced by deprotonation of the fluorescent chromophore in GFP, as well as the associated changes in the hydrogen-bonding network. For both the structures with either a neutral or an anionic chromophore, it was found that the beta-barrel was stable and rigid, and the conformation of the chromophore was consistent with the available x-ray structure. The conformational change in Thr203 due to deprotonation was also found to be consistent with the three-state isomerization model. Although GFP is highly fluorescent, denatured-GFP is nonfluorescent, indicating that the environment of the protein plays an important role in its fluorescence behavior. Our MD simulations, which explore the effect of the protein shell on the conformation of the chromophore, find the flexibility of the central chromophore to be significantly restricted due to the rigid nature of the protein shell. The hydrogen-bonding between the chromophore and neighboring residues was also shown to contribute to the chromophore rigidity. In addition to the MD studies, quantum mechanics/molecular mechanics (QM/MM) ONIOM calculations were carried out to investigate the effect of the beta-barrel on the internal rotation in the chromophore. Along with providing quantitative values for torsional rotation barriers about the bridging bond in the chromophore, the ONIOM calculations also validate our MD force field parameters.     

Calculation of chromophore excited state energy shifts in response to molecular dynamics of pigment-protein complexes

The absorption and energy transfer properties of photosynthetic pigments are strongly influenced by their local environment or “site.” Local electrostatic fields vary in time with protein and chromophore molecular movement and thus transiently influence the excited state transition properties of individual chromophores. Site-specific information is experimentally inaccessible in many light-harvesting pigment–proteins due to multiple chromophores with overlapping spectra. Full quantum mechanical calculations of each chromophores excited state properties are too computationally demanding to efficiently calculate the changing excitation energies along a molecular dynamics trajectory in a pigment–protein complex. A simplified calculation of electrostatic interactions with each chromophores ground to excited state transition, the so-called charge density coupling (CDC) for site energy, CDC, has previously been developed to address this problem. We compared CDC to more rigorous quantum chemical calculations to determine its accuracy in computing excited state energy shifts and their fluctuations within a molecular dynamics simulation of the bacteriochlorophyll containing light-harvesting Fenna–Mathews–Olson (FMO) protein. In most cases CDC calculations differed from quantum mechanical (QM) calculations in predicting both excited state energy and its fluctuations. The discrepancies arose from the inability of CDC to account for the differing effects of charge on ground and excited state electron orbitals. Results of our study show that QM calculations are indispensible for site energy computations and the quantification of contributions from different parts of the system to the overall site energy shift. We suggest an extension of QM/MM methodology of site energy shift calculations capable of accounting for long-range electrostatic potential contributions from the whole system, including solvent and ions.     

Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods

Mechanistic studies on the hydrolytic dehalogenation catalyzed by haloalkane dehalogenases are of importance for environmental and industrial applications. Here, Car-Parrinello (CP) and ONIOM hybrid quantum-mechanical/molecular mechanics (QM/MM) are used investigate the second reaction step of the catalytic cycle, which comprises a general base-catalyzed hydrolysis of an ester intermediate (EI) to alcohol and free enzyme. We focus on the enzyme LinB from Sphingomonas paucimobilis UT26, for which the X-ray structure at atomic resolution is available. In agreement with previous proposals, our calculations suggest that a histidine residue (His272), polarized by glutamate (Glu132), acts as a base, accepting a proton from the catalytic water molecule and transferring it to an alcoholate ion. The reaction proceeds through a metastable tetrahedral intermediate, which shows an easily reversed reaction to the EI. In the formation of the products, the protonated aspartic acid (Asp108) can easily adopt conformation of the relaxed state found in the free enzyme. The overall free energy barrier of the reaction calculated by potential of the mean force integration using CP-QM/MM calculations is equal to 19.5 +/- 2 kcal . mol(-1). The lowering of the energy barrier of catalyzed reaction with respect to the water reaction is caused by strong stabilization of the reaction intermediate and transition state and their preorganization by electrostatic field of the enzyme.     

QM/MM investigation of structure and spectroscopic properties of a vanadium-containing peroxidase

We present a comprehensive analysis of the most likely ground state configuration of the resting state of vanadium dependent chloroperoxidase (VCPO) based on quantum mechanics/molecular mechanics (QM/MM) evaluations of ground state properties, UV-vis spectra and NMR chemical shifts. Within the QM/MM framework, density functional theory (DFT) calculations are used to characterize the resting state of VCPO via time-dependent density functional theory (TD-DFT) calculations of electronic excitation energies and NMR chemical shifts. Comparison with available experimental data allows us to determine the most likely protonation state of VCPO, a state which results in a doubly protonated axial oxygen, a site largely stabilized by hydrogen bonds. We found that the bulk of the protein that is beyond the immediate layer surrounding the cofactor, has an important electrostatic effect on the absorption maximum. Through examination of frontier orbitals, we analyze the nature of two bound water molecules and the extent to which relevant residues in the active site influence the spectroscopy calculations.     

Lysine carboxylation in proteins: OXA-10 beta-lactamase

An increasing number of proteins are being shown to have an N(zeta)-carboxylated lysine in their structures, a posttranslational modification of proteins that proceeds without the intervention of a specific enzyme. The role of the carboxylated lysine in these proteins is typically structural (hydrogen bonding or metal coordination). However, carboxylated lysines in the active sites of OXA-10 and OXA-1 beta-lactamases and the sensor domain of BlaR signal-transducer protein serve in proton transfer events required for the functions of these proteins. These examples demonstrate the utility of this unusual amino acid in acid-base chemistry, in expansion of function beyond those of the 20 standard amino acids. In this study, the ONIOM quantum-mechanical/molecular-mechanical (QM/MM) method is used to study the carboxylation of lysine in the OXA-10 beta-lactamase. Lys-70 and the active site of the OXA-10 beta-lactamase were treated with B3LYP/6-31G(d,p) density functional calculations and the remainder of the enzyme with the AMBER molecular mechanics force field. The barriers for unassisted carboxylation of neutral lysine by carbon dioxide or bicarbonate are high. However, when the reaction with CO2 is catalyzed by a molecule of water in the active site, it is exothermic by about 13 kcal/mol, with a barrier of approximately 14 kcal/mol. The calculations show that the carboxylation and decarboxylation of Lys-70 are likely to be accompanied by deprotonation and protonation of the carbamate, respectively. The analysis may also be relevant for other proteins with carboxylated lysines, a feature that may be more common in nature than previously appreciated.     

QM/MM studies of enzymes

Combined quantum-mechanics/molecular-mechanics (QM/MM) methods are making rapid progress both methodologically and with respect to their range of application. Mechanistic studies on enzymes, including contributions towards the understanding of enzyme catalysis, continue to be a major target. They are joined by calculations of pK(a) values, redox properties, ground- and excited-state spectroscopic parameters, and excited-state dynamics. Methodological advances include improved QM/MM schemes, in particular new approaches for an effective treatment of the QM-MM electrostatic interactions, and the incorporation of new efficient and accurate QM methods in QM/MM schemes.     

Sequence selectivity of azinomycin B in DNA alkylation and cross-linking: a QM/MM study

Azinomycin B—a well-known antitumor drug—forms cross-links with DNA through alkylation of purine bases and blocks tumor cell growth. This reaction has been modeled using the ONIOM (B3LYP/6-31?+?g(d):UFF) method to understand the mechanism and sequence selectivity. ONIOM results have been checked for reliability by comparing them with full quantum mechanics calculations for selected paths. Calculations reveal that, among the purine bases, guanine is more reactive and is alkylated by aziridine ring through the C10 position, followed by alkylation of the epoxide ring through the C21 position of Azinomycin B. While the mono alkylation is controlled kinetically, bis-alkylation is controlled thermodynamically. Solvent effects were included using polarized-continuum-model calculations and no significant change from gas phase results was observed.

Refined models of New Delhi metallo-beta-lactamase-1 with inhibitors: an QM/MM modeling study

New Delhi metallo-beta-lactamase 1 (NDM-1) has been identified as a potential target for the treatment of multi-drug resistance bacterial infections. We used molecular docking, normal MD, SIE, QM/MM MD simulations, QM/MM GBSA binding free energy, and QM/MM GBSA alanine-scanning mutagenesis techniques to investigate interactions of the NDM-1 with 11 inhibitors (Tigecycline, BAL30072, D-captopril, Penicillin G, Ampicillin, Carbenicillin, Cephalexin, Cefaclor, Nitrocefin, Meropenem, and Imipenem). From our normal MD and QM/MM simulations, the correlation coefficients between the predicted binding free energies and experimental values are .88 and .93, respectively. Then simulations, which combined QM/MM/GBSA and alanine-scanning mutagenesis techniques, were performed and our results show that two residues (Lys211 and His250) have the strongest impact on the binding affinities of the 11 NDM-1/inhibitors. Therefore, our approach theoretically suggests that the two residues (Lys211 and His250) are responsible for the selectivity of NDM-1 associated inhibitors.     

A QM/MM analysis of the conformations of crystalline sucrose moieties

Both ab initio quantum mechanics (QM) and molecular mechanics (MM) were used to produce a hybrid energy surface for sucrose that simultaneously provides low energies for conformations that are observed in crystal structures and high energies for most unobserved structures. HF/6-31G* QM energies were calculated for an analogue based on tetrahydropyran (THP) and tetrahydrofuran (THF). Remaining contributions to the potential energy of sucrose were calculated with MM. To do this, the MM surface for the analogue was subtracted from the MM surface for the disaccharide, and the QM surface for the analogue was added. Prediction of the distribution of observable geometries was enhanced by reducing the strength of the hydrogen bonding. Reduced hydrogen-bonding strength is probably useful because many crystalline sucrose moieties do not have intramolecular hydrogen bonds between the fructose and glucose residues. Therefore, hydrogen bonding does not play a large role in determining the molecular conformation. On the hybrid energy surface that was constructed with a dielectric constant of 3.5, the average potential energy of 23 sucrose moieties from crystal structures is 1.16 kcal/mol, and the population of observed structures drops off exponentially as the energy increases.