Comparison of radii sets,entropy, QM methods,and sampling on MM‐PBSA,MM‐GBSA,and QM/MM‐GBSA ligand binding energies of F. tularensis enoyl‐ACP reductase (FabI)

To validate a method for predicting the binding affinities of FabI inhibitors, three implicit solvent methods, MM‐PBSA, MM‐GBSA, and QM/MM‐GBSA were carefully compared using 16 benzimidazole inhibitors in complex with Francisella tularensis FabI. The data suggests that the prediction results are sensitive to radii sets, GB methods, QM Hamiltonians, sampling protocols, and simulation length, if only one simulation trajectory is used for each ligand. In this case, QM/MM‐GBSA using 6 ns MD simulation trajectories together with GB^neck2, PM3, and the mbondi2 radii set, generate the closest agreement with experimental values (r² = 0.88). However, if the three implicit solvent methods are averaged from six 1 ns MD simulations for each ligand (called “multiple independent sampling”), the prediction results are relatively insensitive to all the tested parameters. Moreover, MM/GBSA together with GB^HCT and mbondi, using 600 frames extracted evenly from six 0.25 ns MD simulations, can also provide accurate prediction to experimental values (r² = 0.84). Therefore, the multiple independent sampling method can be more efficient than a single, long simulation method. Since future scaffold expansions may significantly change the benzimidazole's physiochemical properties (charges, etc.) and possibly binding modes, which may affect the sensitivities of various parameters, the relatively insensitive “multiple independent sampling method” may avoid the need of an entirely new validation study. Moreover, due to large fluctuating entropy values, (QM/)MM‐P(G)BSA were limited to inhibitors’ relative affinity prediction, but not the absolute affinity. The developed protocol will support an ongoing benzimidazole lead optimization program. © 2015 Wiley Periodicals, Inc.     

Cooperativity between the Halogen Bond and the Hydrogen Bond in H3N⋅⋅⋅XY⋅⋅⋅HF Complexes (X,Y=F,Cl, Br)

Ab initio calculations are used to provide information on H₃N???XY???HF triads (X, Y=F, Cl, Br) each having a halogen bond and a hydrogen bond. The investigated triads include H₃N???Br₂‐HF, H₃N???Cl₂???HF, H₃N???BrCI???HF, H₃N???BrF???HF, and H₃N???ClF???HF. To understand the properties of the systems better, the corresponding dyads are also investigated. Molecular geometries, binding energies, and infrared spectra of monomers, dyads, and triads are studied at the MP2 level of theory with the 6‐311++G(d,p) basis set. Because the primary aim of this study is to examine cooperative effects, particular attention is given to parameters such as cooperative energies, many‐body interaction energies, and cooperativity factors. The cooperative energy ranges from ?1.45 to ?4.64 kcal mol^?1, the three‐body interaction energy from ?2.17 to ?6.71 kcal mol^?1, and the cooperativity factor from 1.27 to 4.35. These results indicate significant cooperativity between the halogen and hydrogen bonds in these complexes. This cooperativity is much greater than that between hydrogen bonds. The effect of a halogen bond on a hydrogen bond is more pronounced than that of a hydrogen bond on a halogen bond.     

Comparative assessment of computational methods for the determination of solvation free energies in alcohol‐based molecules

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson–Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane‐alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM‐based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane‐alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane‐alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug‐binding in computer‐aided drug design. © 2013 Wiley Periodicals, Inc.     

Halogen Bonding： An AIM Analysis of the Weak Interactions

A series of complexes formed between halogen-containing molecules and ammonia have been investigated by means of the atoms in molecules （AIM） approach to gain a deeper insight into halogen bonding. The existence of the halogen bond critical points （XBCP） and the values of the electron density （Pb） and Laplacian of electron density （V2pb） at the XBCP reveal the closed-shell interactions in these complexes. Integrated atomic properties such as charge, energy, polarization moment, volume of the halogen bond donor atoms, and the corresponding changes （△） upon complexation have been calculated. The present calculations have demonstrated that the halogen bond represents different AIM properties as compared to the well-documented hydrogen bond. Both the electron density and the Laplacian of electron density at the XBCP have been shown to correlate well with the interaction energy, which indicates that the topological parameters at the XBCP can be treated as a good measure of the halogen bond strength In addition, an excellent linear relationship between the interatomic distance d（X…N） and the logarithm of Pb has been established.     

Influence of insertion of a noble gas atom on halogen bonding in H2O···XCCNgF and H3N···XCCNgF (X = Cl and Br; Ng = Ar, Kr, and Xe) complexes

The H₂O···XCCNgF and H₃N···XCCNgF (X = Cl and Br; Ng = Ar, Kr, and Xe) complexes have been studied with quantum chemical calculations at the MP2/aug-cc-pVTZ level. The results show that the inserted noble gas atom has an enhancing effect on the strength of halogen bond, and this enhancement is weakened with the increase of noble gas atomic number. The methyl and Li substituents in the electron donor strengthen the halogen bond. The interaction energy increases from ?3.75 kcal/mol in H₃N–BrCCF complex to ?9.66 kcal/mol in H₂LiN–BrCCArF complex. These complexes have been analyzed with atoms in molecules, natural bond orbital, molecular electrostatic potentials, and energy decomposition calculations.     

A Halogen‐Bonded Dimeric Resorcinarene Capsule

Iodine (I₂) acts as a bifunctional halogen‐bond donor connecting two macrocyclic molecules of the bowl‐shaped halogen‐bond acceptor, N‐cyclohexyl ammonium resorcinarene chloride 1 , to form the dimeric capsule [(1,4‐dioxane)₃@ 1 ₂(I₂)₂]. The dimeric capsule is constructed solely through halogen bonds and has a single cavity (V=511 ų) large enough to encapsulate three 1,4‐dioxane guest molecules.     

Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility

We present a series of molecular‐mechanics‐based protein refinement methods, including two novel ones, applied as part of an induced fit docking procedure. The methods used include minimization; protein and ligand sidechain prediction; a hierarchical ligand placement procedure similar to a‐priori protein loop predictions; and a minimized Monte Carlo approach using normal mode analysis as a move step. The results clearly indicate the importance of a proper opening of the active site backbone, which might not be accomplished when the ligand degrees of freedom are prioritized. The most accurate method consisted of the minimized Monte Carlo procedure designed to open the active site followed by a hierarchical optimization of the sidechain packing around a mobile flexible ligand. The methods have been used on a series of 88 protein‐ligand complexes including both cross‐docking and apo‐docking members resulting in complex conformations determined to within 2.0 Å heavy‐atom RMSD in 75% of cases where the protein backbone rearrangement upon binding is less than 1.0 Å α‐carbon RMSD. We also demonstrate that physics‐based all‐atom potentials can be more accurate than docking‐style potentials when complexes are sufficiently refined. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Microwave‐Assisted One‐Pot Synthesis of 2‐(Substituted phenyl)‐1H‐benzimidazole Derivatives

A series of 2‐(substituted phenyl)‐1H‐benzimidazole derivatives with various 5‐and 6‐position substituents (‐H, ‐CH₃, ‐CF₃) were synthesized via microwave irradiation using a short synthetic route and Na₂S₂O₅ as oxidant. This simple, fast, and efficient preparation of benzimidazole derivatives has been developed using readily available and inexpensive reagents (aldehydes and 1,2‐phenylenediamines) under solvent‐free conditions.     

Assessing the quality of absolute hydration free energies among CHARMM‐compatible ligand parameterization schemes

Multipurpose atom‐typer for CHARMM (MATCH), an atom‐typing toolset for molecular mechanics force fields, was recently developed in our laboratory. Here, we assess the ability of MATCH‐generated parameters and partial atomic charges to reproduce experimental absolute hydration free energies for a series of 457 small neutral molecules in GBMV2, Generalized Born with a smooth SWitching (GBSW), and fast analytical continuum treatment of solvation (FACTS) implicit solvent models. The quality of hydration free energies associated with small molecule parameters obtained from ParamChem, SwissParam, and Antechamber are compared. Given optimized surface tension coefficients for scaling the surface area term in the nonpolar contribution, these automated parameterization schemes with GBMV2 and GBSW demonstrate reasonable agreement with experimental hydration free energies (average unsigned errors of 0.9–1.5 kcal/mol and R² of 0.63–0.87). GBMV2 and GBSW consistently provide slightly more accurate estimates than FACTS, whereas Antechamber parameters yield marginally more accurate estimates than the current generation of MATCH, ParamChem, and SwissParam parameterization strategies. Modeling with MATCH libraries that are derived from different CHARMM topology and parameter files highlights the importance of having sufficient coverage of chemical space within the underlying databases of these automated schemes and the benefit of targeting specific functional groups for parameterization efforts to maximize both the breadth and the depth of the parameterized space. © 2013 Wiley Periodicals, Inc.     

Magnitude and origin of the attraction and directionality of the halogen bonds of the complexes of C6F5X and C6H5X (X = I, Br, Cl and F) with pyridine

The geometries and interaction energies of complexes of pyridine with C₆F₅X, C₆H₅X (X=I, Br, Cl, F and H) and R_FI (R_F=CF₃, C₂F₅ and C₃F₇) have been studied by ab initio molecular orbital calculations. The CCSD(T) interaction energies (E_int) for the C₆F₅X–pyridine (X=I, Br, Cl, F and H) complexes at the basis set limit were estimated to be ?5.59, ?4.06, ?2.78, ?0.19 and ?4.37 kcal mol^?1, respectively, whereas the E_int values for the C₆H₅X–pyridine (X=I, Br, Cl and H) complexes were estimated to be ?3.27, ?2.17, ?1.23 and ?1.78 kcal mol^?1, respectively. Electrostatic interactions are the cause of the halogen dependence of the interaction energies and the enhancement of the attraction by the fluorine atoms in C₆F₅X. The values of E_int estimated for the R_FI–pyridine (R_F=CF₃, C₂F₅ and C₃F₇) complexes (?5.14, ?5.38 and ?5.44 kcal mol^?1, respectively) are close to that for the C₆F₅I–pyridine complex. Electrostatic interactions are the major source of the attraction in the strong halogen bond although induction and dispersion interactions also contribute to the attraction. Short‐range (charge‐transfer) interactions do not contribute significantly to the attraction. The magnitude of the directionality of the halogen bond correlates with the magnitude of the attraction. Electrostatic interactions are mainly responsible for the directionality of the halogen bond. The directionality of halogen bonds involving iodine and bromine is high, whereas that of chlorine is low and that of fluorine is negligible. The directionality of the halogen bonds in the C₆F₅I– and C₂F₅I–pyridine complexes is higher than that in the hydrogen bonds in the water dimer and water–formaldehyde complex. The calculations suggest that the C? I and C? Br halogen bonds play an important role in controlling the structures of molecular assemblies, that the C? Cl bonds play a less important role and that C? F bonds have a negligible impact.     

A short synthesis of the parp inhibitor 2‐(4‐trifluoro‐methylphenyl)benzimidazole‐4‐carboxamide (NU1077)

A four‐step synthesis of the PARP inhibitor 2‐(4‐trifluoromethylphenyl)benzimidazole‐4‐carboxamide (1, NU1077) is presented. Condensation of 2,3‐diaminotoluene and 4‐trifluoromethylbenzaldehyde afforded 4‐methyl‐2‐(4‐trifluoromethylphenyl)benzimidazole. Oxidation of the methyl group with potassium permanganate in warm t‐butanol afforded the carboxylic acid that was converted to the corresponding carboxamide via,/ the acid chloride.     

The Kalimantacin Polyketide Antibiotics Inhibit Fatty Acid Biosynthesis in Staphylococcus aureus by Targeting the Enoyl‐Acyl Carrier Protein Binding Site of FabI

The enoyl‐acyl carrier protein reductase enzyme FabI is essential for fatty acid biosynthesis in Staphylococcus aureus and represents a promising target for the development of novel, urgently needed anti‐staphylococcal agents. Here, we elucidate the mode of action of the kalimantacin antibiotics, a novel class of FabI inhibitors with clinically‐relevant activity against multidrug‐resistant S. aureus. By combining X‐ray crystallography with molecular dynamics simulations, in vitro kinetic studies and chemical derivatization experiments, we characterize the interaction between the antibiotics and their target, and we demonstrate that the kalimantacins bind in a unique conformation that differs significantly from the binding mode of other known FabI inhibitors. We also investigate mechanisms of acquired resistance in S. aureus and identify key residues in FabI that stabilize the binding of the antibiotics. Our findings provide intriguing insights into the mode of action of a novel class of FabI inhibitors that will inspire future anti‐staphylococcal drug development.     

Spectroscopic Measurement of a Halogen Bond Energy

Halogen bonding (XB) has emerged as an important bonding motif in supramolecules and biological systems. Although regarded as a strong noncovalent interaction, benchmark measurements of the halogen bond energy are scarce. Here, a combined anion photoelectron spectroscopy and density functional theory (DFT) study of XB in solvated Br^? anions is reported. The XB strength between the positively‐charged σ‐hole on the Br atom of the bromotrichloromethane (CCl₃Br) molecule and the Br^? anion was found to be 0.63 eV (14.5 kcal mol^?1). In the neutral complexes, Br(CCl₃Br)_1,2, the attraction between the free Br atom and the negatively charged equatorial belt on the Br atom of CCl₃Br, which is a second type of halogen bonding, was estimated to have interaction strengths of 0.15 eV (3.5 kcal mol^?1) and 0.12 eV (2.8 kcal mol^?1).     

The Kalimantacin Polyketide Antibiotics Inhibit Fatty Acid Biosynthesis in Staphylococcus aureus by Targeting the Enoyl-Acyl Carrier Protein Binding Site of FabI

The enoyl-acyl carrier protein reductase enzyme FabI is essential for fatty acid biosynthesis in Staphylococcus aureus and represents a promising target for the development of novel, urgently needed anti-staphylococcal agents. Here, we elucidate the mode of action of the kalimantacin antibiotics, a novel class of FabI inhibitors with clinically-relevant activity against multidrug-resistant S. aureus. By combining X-ray crystallography with molecular dynamics simulations, in vitro kinetic studies and chemical derivatization experiments, we characterize the interaction between the antibiotics and their target, and we demonstrate that the kalimantacins bind in a unique conformation that differs significantly from the binding mode of other known FabI inhibitors. We also investigate mechanisms of acquired resistance in S. aureus and identify key residues in FabI that stabilize the binding of the antibiotics. Our findings provide intriguing insights into the mode of action of a novel class of FabI inhibitors that will inspire future anti-staphylococcal drug development.     

An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions

Presented here is a method, the hierarchical charge partitioning (HCP) approximation, for speeding up computation of pairwise electrostatic interactions in biomolecular systems. The approximation is based on multiple levels of natural partitioning of biomolecular structures into a hierarchical set of its constituent structural components. The charge distribution in each component is systematically approximated by a small number of point charges, which, for the highest level component, are much fewer than the number of atoms in the component. For short distances from the point of interest, the HCP uses the full set of atomic charges available. For long‐distance interactions, the approximate charge distributions with smaller sets of charges are used instead. For a structure consisting of N charges, the computational cost of computing the pairwise interactions via the HCP scales as O(N log N), under assumptions about the structural organization of biomolecular structures generally consistent with reality. A proof‐of‐concept implementation of the HCP shows that for large structures it can lead to speed‐up factors of up to several orders of magnitude relative to the exact pairwise O(N²) all‐atom computation used as a reference. For structures with more than 2000–3000 atoms the relative accuracy of the HCP (relative root‐mean‐square force error per atom), approaches the accuracy of the particle mesh Ewald (PME) method with parameter settings typical for biomolecular simulations. When averaged over a set of 600 representative biomolecular structures, the relative accuracies of the two methods are roughly equal. The HCP is also significantly more accurate than the spherical cutoff method. The HCP has been implemented in the freely available nucleic acids builder (NAB) molecular dynamics (MD) package in Amber tools. A 10 ns simulation of a small protein indicates that the HCP based MD simulation is stable, and that it can be faster than the spherical cutoff method. A critical benefit of the HCP approximation is that it is algorithmically very simple, and unlike the PME, the HCP is straightforward to use with implicit solvent models. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Parameterization of the Hamiltonian Dielectric Solvent (HADES) Reaction‐Field Method for the Solvation Free Energies of Amino Acid Side‐Chain Analogs

Optimization of the Hamiltonian dielectric solvent (HADES) method for biomolecular simulations in a dielectric continuum is presented with the goal of calculating accurate absolute solvation free energies while retaining the model’s accuracy in predicting conformational free‐energy differences. The solvation free energies of neutral and polar amino acid side‐chain analogs calculated by using HADES, which may optionally include nonpolar contributions, were optimized against experimental data to reach a chemical accuracy of about 0.5 kcal mol^?1. The new parameters were evaluated for charged side‐chain analogs. The HADES results were compared with explicit‐solvent, generalized Born, Poisson–Boltzmann, and QM‐based methods. The potentials of mean force (PMFs) between pairs of side‐chain analogs obtained by using HADES and explicit‐solvent simulations were used to evaluate the effects of the improved parameters optimized for solvation free energies on intermolecular potentials.     

Theoretical Investigations on the Mechanism of Hetero‐Diels–Alder Reactions of Brassard’s Diene and 1, 3‐Butadiene Catalyzed by a Tridentate Schiff Base Titanium(IV) Complex

The mechanism of the hetero‐Diels–Alder reactions of Brassard’s diene and 1,3‐butadiene catalyzed by a titanium(IV) complex of a tridentate Schiff base was investigated by DFT and ONIOM methods. The calculations indicate that the mechanism of the reaction is closely related to the nucleophilicity–electrophilicity between diene and carbonyl substrates. A stepwise pathway is adopted for Brassard’s diene, and the step corresponding to the formation of the C? C bond is predicted to be the rate‐determining step with a free‐energy barrier of 8.4 kcal mol^?1. For 1,3‐butadiene, the reaction takes place along a one‐step, two‐stage pathway with a free‐energy barrier of 14.9 kcal mol^?1. For Brassard’s diene as substrate, the OCH₃ and OSi(CH₃)₃ substituents may play a key role in the formation of the transition state and zwitterionic intermediate by participating in charge transfer from Brassard’s diene to formaldehyde. The combination of the phenyl groups at the amino alcohol moiety and the ortho‐tert‐butyl group of the salicylaldehyde moiety in the chiral tridentate Schiff base ligand plays an important role in the control of the stereoselectivity, which is in agreement with experimental observations.     

Comments on Empirical Correlations between Reduction Potential of Carbon-Halogen Bonds and NQR. Frequencies of Halogen Atoms in Organic Molecules

An empirical linear correlation exists between nuclear quadrupole resonance frequencies of halogen nuclei (³⁵Cl, ⁷⁹Br, ¹²⁷I) and the polarographic reduction potentials in series of organic halides. In terms of electronic structure this is interpreted as a significant relationship between the average p-electron population at halogen atoms and the first vacant molecular orbital of halogenated molecules. On the basis of the present correlations conclusions are drawn about some controversial mechanistic aspects of the electroreduction of the carbon-halogen bond.     

A Crystallographic Charge Density Study of the Partial Covalent Nature of Strong N⋅⋅⋅Br Halogen Bonds

The covalent nature of strong N?Br???N halogen bonds in a cocrystal ( 2 ) of N‐bromosuccinimide ( NBS ) with 3,5‐dimethylpyridine ( lut ) was determined from X‐ray charge density studies and compared to a weak N?Br???O halogen bond in pure crystalline NBS ( 1 ) and a covalent bond in bis(3‐methylpyridine)bromonium cation (in its perchlorate salt ( 3 ). In 2 , the donor N?Br bond is elongated by 0.0954 Å, while the Br???acceptor distance of 2.3194(4) is 1.08 Å shorter than the sum of the van der Waals radii. A maximum electron density of 0.38 e Å^?3 along the Br???N halogen bond indicates a considerable covalent contribution to the total interaction. This value is intermediate to 0.067 e Å^?3 for the Br???O contact in 1 , and approximately 0.7 e Å^?3 in both N?Br bonds of the bromonium cation in 3 . A calculation of the natural bond order charges of the contact atoms, and the σ*(N1?Br) population of NBS as a function of distance between NBS and lut , have shown that charge transfer becomes significant at a Br???N distance below about 3 Å.     

The Synthesis and Biological Evaluation of N‐Substituted 1H‐Benzimidazol‐2‐yl‐1H‐pyrazole‐3,5‐diamines

The synthesis of 1H‐benzimidazol‐2‐yl‐1H‐pyrazole‐3,5‐diamines has been developed. Synthesized bisheteroaryls contain two privileged medicinal scaffolds, aminopyrazole and benzimidazole, with two diversity positions at N1 of benzimidazole and C3 of pyrazole, respectively. The three‐step synthesis includes the Mitsunobu N‐alkylation of benzimidazole and subsequent one‐pot formation of aminopyrazole involving substitution of methylthio groups with amine and hydrazine followed with final ring closure. Inhibitory activity toward cyclin‐dependent kinase 2/cyclin E and cytotoxicity against two cancer cell lines were evaluated for all novel pyrazoles. Two compounds showed modest cyclin‐dependent kinase inhibition activity and cytotoxicity against cancer cell lines K562 and MCF7.