New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces

Journal of Chemical Information and Modeling
Knowing how proteins make stable complexes enables the development of inhibitors to preclude protein–protein (P:P) binding. The identification of the specific interfacial residues that mostly contribute to protein binding, denominated as hot spots, is thus critical. Here, we refine an in silico alanine scanning mutagenesis protocol, based on a residue-dependent dielectric constant version of the Molecular Mechanics/Poisson–Boltzmann Surface Area method. We have used a large data set of structurally diverse P:P complexes to redefine the residue-dependent dielectric constants used in the determination of binding free energies. The accuracy of the method was validated through comparison with experimental data, considering the per-residue P:P binding free energy (ΔΔGbinding) differences upon alanine mutation. Different protocols were tested, i.e., a geometry optimization protocol and three molecular dynamics (MD) protocols: (1) one using explicit water...  Read more

Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration

Journal of Chemical Theory and Computation
The accurate prediction of the binding affinities of ligands to proteins is a major goal in drug discovery and personalized medicine. The time taken to make such predictions is of similar importance to their accuracy, precision, and reliability. In the past few years, an ensemble based molecular dynamics approach has been proposed that provides a route to reliable predictions of free energies based on the molecular mechanics Poisson–Boltzmann surface area method which meets the requirements of speed, accuracy, precision, and reliability. Here, we describe an equivalent methodology based on thermodynamic integration to substantially improve the speed, accuracy, precision, and reliability of calculated relative binding free energies. We report the performance of the method when applied to a diverse set of protein targets and ligands. The results are in very good agreement with experimental data (90% of calculations agree to within 1 kcal/mol), while the method is reproducible by...  Read more

Toward Closing the Gap: Quantum Mechanical Calculations and Experimentally Measured Chemical Shifts of a Microcrystalline Lectin

The Journal of Physical Chemistry B
NMR chemical shifts are exquisitely sensitive probes for conformation and dynamics in molecules and supramolecular assemblies. Although isotropic chemical shifts are easily measured with high accuracy and precision in conventional NMR experiments, they remain challenging to calculate quantum mechanically, particularly in inherently dynamic biological systems. Using a model benchmark protein, the 133-residue agglutinin from Oscillatoria agardhii (OAA), which has been extensively characterized by us previously, we have explored the integration of X-ray crystallography, solution NMR, MAS NMR, and quantum mechanics/molecular mechanics (QM/MM) calculations for analysis of 13Cα and 15NH isotropic chemical shifts. The influence of local interactions, quaternary contacts, and dynamics on the accuracy of calculated chemical shifts is analyzed. Our approach is broadly applicable and expected to be beneficial in chemical shift analysis and...  Read more

Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery

Journal of Chemical Theory and Computation
The accurate prediction of protein–ligand binding free energies remains a significant challenge of central importance in computational biophysics and structure-based drug design. Multiple recent advances including the development of greatly improved protein and ligand molecular mechanics force fields, more efficient enhanced sampling methods, and low-cost powerful GPU computing clusters have enabled accurate and reliable predictions of relative protein–ligand binding free energies through the free energy perturbation (FEP) methods. However, the existing FEP methods can only be used to calculate the relative binding free energies for R-group modifications or single-atom modifications and cannot be used to efficiently evaluate scaffold hopping modifications to a lead molecule. Scaffold hopping or core hopping, a very common design strategy in drug discovery projects, is critical not only in the early stages of a discovery campaign where novel active matter must be identified but...  Read more

QM/MM-Based Calculations of Absorption and Emission Spectra of LSSmOrange Variants

The Journal of Physical Chemistry B
The goal of this computational work is to gain new insight into the photochemistry of the fluorescent protein (FP) LSSmOrange. This FP is of interest because besides exhibiting the eponymous large spectral shift (LSS) between the absorption and emission energies, it has been experimentally observed that it can also undergo a photoconversion process, which leads to a change in the absorption wavelength of the chromophore (from 437 to 553 nm). There is strong experimental evidence that this photoconversion is caused by decarboxylation of a glutamate located in the close vicinity of the chromophore. Still, the exact chemical mechanism of the decarboxylation process as well as the precise understanding of structure–property relations in the measured absorption and emission spectra is not yet fully understood. Therefore, hybrid quantum mechanics/molecular mechanics (QM/MM) calculations are performed to model the absorption and emission spectra of the original and photoconverted forms of...  Read more

Quantum Mechanics/Molecular Mechanics Insights into the Enantioselectivity of the O-Acetylation of (R,S)-Propranolol Catalyzed by Candida antarctica Lipase B

ACS Catalysis
Classical molecular dynamics (MD) simulations and combined quantum mechanics/molecular mechanics (QM/MM) calculations were used to investigate the origin of the enantioselectivity of the Candida antarctica lipase B (CalB) catalyzed O-acetylation of (R,S)-propranolol. The reaction is a two-step process. The initial step is the formation of a reactive acyl enzyme (AcCalB) via a tetrahedral intermediate (TI-1). The stereoselectivity originates from the second step, when AcCalB reacts with the racemic substrate via a second tetrahedral intermediate (TI-2). Reaction barriers for the conversion of (R)- and (S)-propranolol to O-acetylpropranolol were computed for several distinct conformations of TI-2. In QM/MM geometry optimizations and reaction path calculations the QM region was described by density functional theory (B3LYP/TZVP) and the MM region by the CHARMM force field. The QM/MM calculations show that the formation of TI-2 is...  Read more

Plasma Protein Binding of Anisomelic Acid: Spectroscopy and Molecular Dynamic Simulations

Journal of Chemical Information and Modeling
Anisomelic acid (AA) is a macrocyclic cembranolide compound extracted from Anisomeles herbal species. Recently, we have shown that AA possesses both anticancer and antiviral activity. However, to date, the plasma protein binding properties of AA are unknown. Here, we describe the molecular interactions of AA with two serum proteins, human serum albumin (HSA) and bovine serum albumin (BSA), adopting multiple physicochemical methods. Besides, molecular docking and dynamics simulations were performed to predict the interaction mode and the dynamic behavior of AA with HSA and BSA. The experimental results revealed that hydrophobic forces play a significant part in the interaction of AA to HSA and BSA. The outcomes of the principal components analysis (PCA) of the poses based on root-mean-squared distances showed less variation in AA–HSA, opposed to what is seen for BSA–AA. Furthermore, binding free energies estimated for AA–HSA and AA–BSA complexes at different temperatures (298,...  Read more

Hydrogen Abstraction of Camphor Catalyzed by Cytochrome P450cam: A QM/MM Study

The Journal of Physical Chemistry B
A combined quantum mechanics and molecular mechanics (QM/MM, QM = UB3LYP-D3, MM = AMBER) method is used to study the hydrogen abstraction reaction in P450cam catalyzed hydroxylation of camphor in the quartet state. Compared to QM/MM calculations in the literature, this study uses larger basis sets for the most important atoms at the active site and QM/MM Hessian harmonic frequency calculations to determine the standard Gibbs free energy of activation and kinetic isotope effect. The QM/MM covalent boundary is treated with a capping hydrogen atom method, which is simple and robust. An energy barrier of 21.3 kcal/mol and a standard free energy of activation of 16.8 kcal/mol are obtained for this hydrogen abstraction reaction. These values are similar to those reported in the literature, suggesting that when a general protocol is followed, QM/MM results are reproducible. It is found that using a sufficiently large basis set is important to minimize basis set errors.Read more

Multiconformation, Density Functional Theory-Based pKa Prediction in Application to Large, Flexible Organic Molecules with Diverse Functional Groups

Journal of Chemical Theory and Computation
We consider the conformational flexibility of molecules and its implications for micro- and macro-pKa. The corresponding formulas are derived and discussed against the background of a comprehensive scientific and algorithmic description of the latest version of our computer program Jaguar pKa, a density functional theory-based pKa predictor, which is now capable of acting on multiple conformations explicitly. Jaguar pKa is essentially a complex computational workflow incorporating research and technologies from the fields of cheminformatics, molecular mechanics, quantum mechanics, and implicit solvation models. The workflow also makes use of automatically applied empirical corrections which account for the systematic errors resulting from the neglect of explicit solvent interactions in the algorithm’s implicit solvent model. Applications of our program to large, flexible organic molecules representing several...  Read more

Dynamics of Excited States for Fluorescent Emitters with Hybridized Local and Charge-Transfer Excited State in Solid Phase: A QM/MM Study

The Journal of Physical Chemistry A
The highly efficient organic light-emitting diodes (OLEDS) based on fluorescent emitters with hybridized local and charge-transfer (HLCT) excited state have attracted great attention recently. The excited-state dynamics of the fluorescent molecule with consideration of molecular interaction are studied using the hybrid quantum mechanics/molecular mechanics method. The results show that, in solid state, the internal conversion rate (KIC) between the first singlet excited state (S1) and the ground state (S0) is smaller than the fluorescent rate (Kr), while in gas phase KIC is much larger than Kr. By analyzing the Huang–Rhys (HR) factor and reorganization energy (λ), we find that these two parameters in solid state are much smaller than those in gas phase due to the suppression of the vibration modes in low-frequency regions (<200 cm–1) related with dihedral angles between donor and acceptor...  Read more

A Nonadiabatic Excited State Molecular Mechanics/Extended Hückel Ehrenfest Method

The Journal of Physical Chemistry C
In this work we study intramolecular vibronic relaxation effects and photoisomerization dynamics in atomistic molecular systems by means of a mixed self-consistent quantum–classical Ehrenfest formalism for nonadiabatic molecular dynamics (NA-MD) in the excited state. The quantum mechanical part of the method is based on the extended Hückel formalism, whereas the nuclei are treated with the molecular mechanics method. The self-consistent coupling between quantum and classical degrees of freedom is achieved by nonadiabatic Hellmann–Feynman–Pulay forces that conserve the total (quantum–classical) energy. Moreover, this work demonstrates the capabilities of a method that combines two simple though efficient computational schemes to describe complex excited state effects such as photoisomerization dynamics of stilbene and azobenzene molecules. In particular, for stilbene we point out the key importance of hydrogen out-of-plane (HOOP) modes to trigger the isomerization of the...  Read more

Human Ferrochelatase: Insights for the Mechanism of Ferrous Iron Approaching Protoporphyrin IX by QM/MM and QTCP Free Energy Studies

Journal of Chemical Information and Modeling
Ferrochelatase catalyzes the insertion of ferrous iron into protoporphyrin IX, the terminal step in heme biosynthesis. Some disputes in its mechanism remain unsolved, especially for human ferrochelatase. In this paper, high-level quantum mechanical/molecular mechanics (QM/MM) and free-energy studies were performed to address these controversial issues including the iron-binding site, the optimal reaction path, the substrate porphyrin distortion, and the presence of the sitting-atop (SAT) complex. Our results reveal that the ferrous iron is probably at the binding site coordinating with Met76, and His263 plays the role of proton acceptor. The rate-determining step is either the first proton removed by His263 or the proton transition within the porphyrin with an energy barrier of 14.99 or 14.87 kcal/mol by the quantum mechanical thermodynamic cycle perturbation (QTCP) calculations, respectively. The fast deprotonation step with the conservative residues rather than porphyrin deformation...  Read more

A new, double-inversion mechanism of the F− + CH3Cl SN2 reaction in aqueous solution

Physical Chemistry Chemical Physics
Atomic-level, bimolecular nucleophilic substitution reaction mechanisms have been studied mostly in the gas phase, but the gas-phase results cannot be expected to reliably describe condensed-phase chemistry. As a novel, double-inversion mechanism has just been found for the F + CH3Cl SN2 reaction in the gas phase [Nat. Commun., 2015, 6, 5972], here, using multi-level quantum mechanics methods combined with the molecular mechanics method, we discovered a new, double-inversion mechanism for this reaction in aqueous solution. However, the structures of the stationary points along the reaction path show significant differences from those in the gas phase due to the strong influence of solvent and solute interactions, especially due to the hydrogen bonds formed between the solute and the solvent. More importantly, the relationship between the two double-inversion transition states is...  Read more

Solvation free energies for periodic surfaces: comparison of implicit and explicit solvation models

Physical Chemistry Chemical Physics
The evaluation of solvation energies is a great challenge. We focus here on an organic molecule chemisorbed at a metal–liquid interface, as a prototypical system, essential in tribology, electrochemistry and heterogeneous catalysis. We compare an established implicit solvation scheme with a strategy based on molecular mechanics (MM) free energy perturbation (FEP) seeded by QM computations. First, we benchmark the approaches against experimental hydration energies of standard (organic) molecules and find acceptable errors in the order of 0.06 eV (1.3 kcal mol−1). Then, the impact of various parameters on the solvation energy of an adsorbate have been assessed on a typical system of interest, levulinic acid adsorbed at a Ru(0001)/water interface. We identify the need for dipole corrections or symmetric slabs when including solvation effects on metallic surfaces. The MM-FEP scheme is revealed to be as reliable as the implicit solvent for water. In the case...  Read more

Cation–π interactions in CREBBP bromodomain inhibition: an electrostatic model for small-molecule binding affinity and selectivity

Organic & Biomolecular Chemistry
CREBBP bromodomains, epigenetic “reader” proteins that recognize acetylated histone lysine residues, are a current target for cancer therapy. We show that experimental CREBBP binding affinities of small-molecules with aromatic or heteroaromatic functional groups are strongly influenced by a cation–π interaction with a positively charged arginine residue. For a series of fifteen 5-isoxazolylbenzimidazole derivatives, the strength of this non-covalent interaction is directly related to improvements in binding to CREBBP. The aromatic substituents’ inductive and resonance effects are not obviously correlated with observed structure and affinity relationships. In contrast, a coulombic electrostatic model can quantitatively predict the interaction strength. We have assessed different Molecular Mechanics (MM) and Quantum Mechanics (QM) descriptions of the protein–ligand interaction. Quantitative models for binding affinity were generated from: (1) Poisson Boltzmann Surface Area...  Read more

Microstructural Analysis of Perfluoropentacene Films on Graphene and Graphite: Interface-Mediated Alignment and Island Formation

Crystal Growth & Design
The epitaxial growth of the n-type organic semiconductor perfluoropentacene (C22F14, PFP) on graphite and graphene substrates is analyzed by combining X-ray diffraction, scanning tunneling microscopy (STM), atomic force microscopy, and transmission electron microscopy. On both graphite and graphene substrates, PFP forms islands where molecules adopt the π-stacked polymorph with lying molecular orientation relative to the substrate. By performing azimuthal analyses, we identify the epitaxial relation between the PFP islands and the graphite substrate and gain insights into the crystal habitus of the PFP islands. Combining low-temperature STM measurements with molecular mechanics calculations, we provide a consistent mechanism for the azimuthal alignment at the PFP/graphene interface and the lateral positioning of the organic adsorbate on the graphene substrate.Read more

Experimental and Computational Analysis of Protein Stabilization by Gly-to-d-Ala Substitution: A Convolution of Native State and Unfolded State Effects

Journal of the American Chemical Society
The rational and predictable enhancement of protein stability is an important goal in protein design. Most efforts target the folded state, however stability is the free energy difference between the folded and unfolded states thus both are suitable targets. Strategies directed at the unfolded state usually seek to decrease chain entropy by introducing cross-links or by replacing glycines. Cross-linking has led to mixed results. Replacement of glycine with an l-amino acid, while reducing the entropy of the unfolded state, can introduce unfavorable steric interactions in the folded state, since glycine is often found in conformations that require a positive φ angle such as helical C-capping motifs or type I′ and II″ β-turns. l-Amino acids are strongly disfavored in these conformations, but d-amino acids are not. However, there are few reported examples and conflicting results have been...  Read more

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

Journal of Chemical Theory and Computation
Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking have been parametrized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data. The energy function improves performance in a wide range of protein structure prediction challenges, including monomeric...  Read more

Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer

The Journal of Physical Chemistry Letters
The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.Read more

Constructing an Interpolated Potential Energy Surface of a Large Molecule: A Case Study with Bacteriochlorophyll a Model in the Fenna–Matthews–Olson Complex

Journal of Chemical Theory and Computation
Constructing a reliable potential energy surface (PES) is a key step toward computationally studying the chemical dynamics of any molecular system. The interpolation scheme is a useful tool that can closely follow the accuracy of quantum chemical means at a dramatically reduced computational cost. However, applying interpolation to building a PES of a large molecule is not a straightforward black-box approach, as it frequently encounters practical difficulties associated with its large dimensionality. Here, we present detailed courses of applying interpolation toward building a PES of a large chromophore molecule. We take the example of S0 and S1 electronic states of bacteriochlorophyll a (BChla) molecules in the Fenna–Matthews–Olson light harvesting complex. With a reduced model molecule that bears BChla’s main π-conjugated ring, various practical approaches are designed for improving the PES quality in a stable manner and for...  Read more