Effect of atomic charge,solvation, entropy,and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease

The molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and MM-generalized-Born surface area (MM-GBSA) approaches are commonly used in molecular modeling and drug design. Four critical aspects of these approaches have been investigated for their effect on calculated binding energies: (1) the atomic partial charge method used to parameterize the ligand force field, (2) the method used to calculate the solvation free energy, (3) inclusion of entropy estimates, and (4) the protonation state of the ligand. HIV protease has been used as a test case with six structurally different inhibitors covering a broad range of binding strength to assess the effect of these four parameters. Atomic charge methods are demonstrated to effect both the molecular dynamics (MD) simulation and MM-PB(GB)SA binding energy calculation, with a greater effect on the MD simulation. Coefficients of determination and Spearman rank coefficients were used to quantify the performance of the MM-PB(GB)SA methods relative to the experimental data. In general, better performance was achieved using (i) atomic charge models that produced smaller mean absolute atomic charges (Gasteiger, HF/STO-3G and B3LYP/cc-pVTZ), (ii) the MM-GBSA approach over MM-PBSA, while (iii) inclusion of entropy had a slightly positive effect on correlations with experiment. Accurate representation of the ligand protonation state was found to be important. It is demonstrated that these approaches can distinguish ligands according to binding strength, underlining the usefulness of these approaches in computer-aided drug design. © 2012 Wiley Periodicals, Inc.     

Molecular dynamic and free energy studies of primary resistance mutations in HIV-1 protease-ritonavir complexes

To understand the basis of drug resistance of the HIV-1 protease, molecular dynamic (MD) and free energy calculations of the wild-type and three primary resistance mutants, V82F, I84V, and V82F/I84V, of HIV-1 protease complexed with ritonavir were carried out. Analysis of the MD trajectories revealed overall structures of the protein and the hydrogen bonding of the catalytic residues to ritonavir were similar in all four complexes. Substantial differences were also found near the catalytic binding domain, of which the double mutant complex has the greatest impact on conformational changes of the protein and the inhibitor. The tip of the HIV-1 protease flap of the double mutant has the greater degree of opening with respect to that of the others. Additionally, the phenyl ring of Phe82 moves away from the binding pocket S1', and the conformational change of ritonavir subsite P1' consequently affects the cavity size of the protein and the conformational energy of the inhibitor. Calculations of binding free energy using the solvent continuum model were able to reproduce the same trend of the experimental inhibition constant. The results show that the resistance mutants require hydrophobic residues to maintain the interactions in the binding pocket. Changes of the cavity volume correlate well with free energy penalties due to the mutation and are responsible for the loss of drug susceptibility.     

Ab initio calculation of the interaction energy in the P2 binding pocket of HIV‐1 protease

Interactions at the P2 binding pocket of human immunodeficiency virus type 1 (HIV‐1) protease have been studied using calculated interaction energies for model systems that mimic this binding pocket. Models were built for the P2 pocket of HIV‐1 protease in complex with TMC114, nelfinavir, and amprenavir. A two‐step procedure was applied. In the first step, the size of the model system was confined to ～40 atoms, and the interaction energy was calculated at different computational levels. In the second step, the size of the system was increased to 138 atoms, and the calculations were only performed at the HF/6‐31G** level. The interaction energy of the HIV‐1 protease/TMC114 complex was found to be more favorable than the interaction energies of the other complexes because of the additional hydrogen bond interaction this inhibitor is able to make with the HIV‐1 protease backbone. The results of the calculations are supported by stockholder charges and electrostatic potential maps. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Accessing the applicability of polarized protein‐specific charge in linear interaction energy analysis

The reliability of the linear interaction energy (LIE) depends on the atomic charge model used to delineate the Coulomb interaction between the ligand and its environment. In this work, the polarized protein‐specific charge (PPC) implementing a recently proposed fitting scheme has been examined in the LIE calculations of the binding affinities for avidin and β‐secretase binding complexes. This charge fitting scheme, termed delta restrained electrostatic potential, bypasses the prevalent numerical difficulty of rank deficiency in electrostatic‐potential‐based charge fitting methods via a dual‐step fitting strategy. A remarkable consistency between the predicted binding affinities and the experimental measurement has been observed. This work serves as a direct evidence of PPC's applicability in rational drug design. © 2014 Wiley Periodicals, Inc.     

Various atomic charge calculation schemes of CoMFA on HIF‐1 inhibitors of moracin analogs

Selection of appropriate partial charges in a molecule is crucial to derive good quantitative structure–activity relationship models. In this work, several partial atomic charges were assigned and tested in a comparative molecular field analysis (CoMFA) models. Many CoMFA models were generated for a series of hypoxia inducible factor 1 (HIF‐1) inhibitors using various partial atomic charges including charge equalization, Mülliken population analysis (MPA), natural population analysis, and electrostatic potential (ESP)‐derived charges. These atomic charges were investigated at various theoretical levels such as empirical, semiempirical, Hartree–Fock (HF), and density functional theory (DFT). Among them, Merz‐Singh‐Kollman (MK) ESP‐derived charges at the level of HF/6‐31G* gave the highest predictive q² with experimental pIC₅₀ values. With this charge scheme, a detailed analysis of CoMFA model was performed to understand the electrostatic interactions between ligand and receptor. More elaborate charge calculation schemes such as HF and DFT correlated more strongly with activity than empirical or semiempirical schemes. The choice of optimization methods was important. As geometries were fully optimized at the given levels of theory, the aligned structures were different. They differed considerably, especially for the flexible parts. This was likely the source of the substantial variation of q² values, even when the same steric factor was considered without electrostatic parameters. ESP‐derived charges were most appropriate to describe CoMFA electrostatic interactions among MPA, NBA, and ESP charges. Overall q² values vary considerably (0.8–0.5) depending on the charge schemes applied. The results demonstrate the need to consider more appropriate atomic charges rather than default CoMFA charges. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Effect of interprotein polarization on protein–protein binding energy

Molecular dynamics simulation in explicit water for the binding of the benchmark barnase‐barstar complex was carried out to investigate the effect polarization of interprotein hydrogen bonds on its binding free energy. Our study is based on the AMBER force field but with polarized atomic charges derived from fragment quantum mechanical calculation for the protein complex. The quantum‐derived atomic charges include the effect of polarization of interprotein hydrogen bonds, which was absent in the standard force fields that were used in previous theoretical calculations of barnase‐barstar binding energy. This study shows that this polarization effect impacts both the static (electronic) and dynamic interprotein electrostatic interactions and significantly lowers the free energy of the barnase‐barstar complex. © 2012 Wiley Periodicals, Inc.     

Synthesis and properties of organosoluble polyimides based on 4,4′‐bis(4‐amino‐2‐trifluoromethylphenoxy)benzophenone

A novel, fluorinated diamine monomer with the ether–ketone group, 4,4′‐bis(4‐amino‐2‐trifluoromethylphenoxy)benzophenone ( 2 ), was prepared through the nucleophilic substitution reaction of 2‐chloro‐5‐nitrobenzotrifluoride and 4,4′‐dihydroxybenzophenone in the presence of potassium carbonate, followed by catalytic reduction with hydrazine and Pd/C. Flourinated polyimides (PIs) 5a – f and copolyimides (co‐PIs) 5c / a – f were synthesized from 2 and various commercial aromatic dianhydrides via thermal or chemical imidization. PIs 5a – f had inherent viscosities ranging from 0.72 to 1.22 dL/g. Besides the chemical imidization of 5c ( C ), the 5 ( C ) series were soluble in amide‐type solvents and even in less polar solvents, but PIs 5a – f prepared via thermal imidization were insoluble. PI films 5a – f exhibited tensile strengths ranging from 92 to 112 MPa, elongations at break from 8 to 15%, and initial moduli from 2.0 to 2.1 GPa. The glass‐transition temperatures of the 5 series were in the range of 232–278 °C, and the 10% weight‐loss temperatures were above 535 °C, with more than a 50% char yield at 800 °C in nitrogen. In comparison of the PI 5 series with the analogous non‐fluorinated PIs 6 series based on 4,4′‐bis(4‐aminophenoxy)benzophenone, the 5 series revealed better solubility, lower color intensity, dielectric constant, and moisture absorption. Their PI films had cutoff wavelengths between 370 and 410 nm, b* values ranging from 9.6 to 58.3, dielectric constants of 3.05–3.64 (1 MHz), with moisture absorption in the range of 0.08–0.38 wt %. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 222–236, 2004     

Electrostatic polarization is critical for the strong binding in streptavidin‐biotin system

The origin of strong affinity of biotin and its analogs binding to (strept)avidin is still the subject of an ongoing controversy. In this work, thermodynamic integration is carried out to study of the difference of binding free energies between biotin and iminobiotin to streptavidin. Three atomic charge schemes are implemented and compared. One is the traditional AMBER charge, and the other two, termed the polarized protein‐specific charge, are based on a linear scaling quantum mechanical method and a continuous solvation model and have polarization effect partially or fully included. The result indicates that when nonpolarized AMBER force field is applied, the result is much underestimated. When electronic polarization is gradually included, the difference of binding affinity increases along with it. Using the linear‐response approximation to eliminate the error in self‐charging process, the corrected binding affinity agrees well with the experimental observation. This study is direct evidence indicating that polarization effect is critical for the strong binding in streptavidin‐biotin system. © 2012 Wiley Periodicals, Inc.     

Sensitive and simultaneous determination of HIV protease inhibitors in rat biological samples by liquid chromatography-mass spectrometry

A sensitive and simultaneous liquid chromatographic-mass spectrometric (LC/MS) method for the determination of current four HIV protease inhibitors (PIs), indinavir (IDV), saquinavir (SQV), nelfinavir (NFV) and amprenavir (APV) in rat plasma and liver dialysate by a microdialysis method was described. An isocratic LC/MS method in combination with atmospheric pressure chemical ionization was developed for the determination of these four PIs in biological samples in the same run. The analytes including an internal standard were extracted from 100 microL of plasma or 150 microL of liver dialysate samples by salting-out with 100 microL of ice-cold 2 M K(3)PO(4) followed by ether extraction. The separation of analytes was carried out on a reversed-phase semi-micro column using 50% of acetonitrile containing 1% acetic acid as mobile phase at a flow rate of 0.2mL/min(-1). The separation was completed within 5 min. Precision, recovery and limits of detection indicated that the method was suitable for the quantitative determination of these PIs in rat plasma or liver dialysate. This simple, sensitive and highly specific LC/MS method is suitable for pharmacokinetic studies and therapeutic drug monitoring in AIDS patients who receive double protease therapy.     

Molecular modeling studies of human immunodeficiency virus type 1 protease inhibitors using three‐dimensional quantitative structure‐activity relationship,virtual screening,and docking simulations

In this paper, two 3‐dimensional quantitative structure‐activity relationship models for 60 human immunodeficiency virus (HIV)‐1 protease inhibitors were established using random sampling analysis on molecular surface and translocation comparative molecular field vector analysis (Topomer CoMFA). The non–cross‐validation (r²), cross‐validation (q²), correlation coefficient of external validation (Q²_ext), and F of 2 models were 0.94, 0.80, 0.79, and 198.84 and 0.94, 0.72, 0.75, and 208.53, respectively. The results indicated that 2 models were reasonable and had good prediction ability. Topomer Search was used to search R groups in the ZINC database, 20 new compounds were designed, and the Topomer CoMFA model was used to predicate the biological activity. The results showed that 18 new compounds were more active than the template molecule. So the Topomer Search is effective in screening and can guide the design of new HIV/AIDS drugs. The mechanism of action was studied by molecular docking, and it showed that the protease inhibitors and Ile50, Asp25, and Arg8 sites of HIV‐1 protease have interactions. These results have provided an insight for the design of new potent inhibitors of HIV‐1 protease.     

Protein‐specific force field derived from the fragment molecular orbital method can improve protein–ligand binding interactions

Accurate computational estimate of the protein–ligand binding affinity is of central importance in rational drug design. To improve accuracy of the molecular mechanics (MM) force field (FF) for protein–ligand simulations, we use a protein‐specific FF derived by the fragment molecular orbital (FMO) method and by the restrained electrostatic potential (RESP) method. Applying this FMO‐RESP method to two proteins, dodecin, and lysozyme, we found that protein‐specific partial charges tend to differ more significantly from the standard AMBER charges for isolated charged atoms. We did not see the dependence of partial charges on the secondary structure. Computing the binding affinities of dodecin with five ligands by MM PBSA protocol with the FMO‐RESP charge set as well as with the standard AMBER charges, we found that the former gives better correlation with experimental affinities than the latter. While, for lysozyme with five ligands, both charge sets gave similar and relatively accurate estimates of binding affinities. © 2013 Wiley Periodicals, Inc.     

Long‐Range Electrostatics‐Induced Two‐Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site

Neutron crystallography was used to directly locate two protons before and after a pH‐induced two‐proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV‐1 protease. The two‐proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low‐pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.     

Fast and accurate determination of the relative binding affinities of small compounds to HIV‐1 protease using non‐equilibrium work

The fast pulling ligand (FPL) out of binding cavity using non‐equilibrium molecular dynamics (MD) simulations was demonstrated to be a rapid, accurate and low CPU demand method for the determination of the relative binding affinities of a large number of HIV‐1 protease (PR) inhibitors. In this approach, the ligand is pulled out of the binding cavity of the protein using external harmonic forces, and the work of pulling force corresponds to the relative binding affinity of HIV‐1 PR inhibitor. The correlation coefficient between the pulling work and the experimental binding free energy of shows that FPL results are in good agreement with experiment. It is thus easier to rank the binding affinities of HIV‐1 PR inhibitors, that have similar binding affinities because the mean error bar of pulling work amounts to . The nature of binding is discovered using the FPL approach. © 2016 Wiley Periodicals, Inc.     

Partially bio‐based aromatic polyimides derived from 2,5‐furandicarboxylic acid with high thermal and mechanical properties

Two novel bio‐based diamines are synthesized through introduction of renewable 2,5‐furandicarboxylic acid (2,5‐FDCA), and the corresponding aromatic polyimides (PIs) are then prepared by these diamines with commercially available aromatic dianhydrides via two‐step polycondensation. The partially bio‐based PIs possess high glass transition temperatures (T_gs) in the range from 266 to 364 °C, high thermal stability of 5% weight loss temperatures (T_5%s) over 420 °C in nitrogen and outstanding mechanical properties with tensile strengths of 79–138 MPa, tensile moduli of 2.5–5.4 GPa, and elongations at break of 3.0–12.3%. Some colorless PI films (PI‐1‐b and PI‐1‐c) with the transmittances at 450 nm over 85% are prepared. The overall properties of 2,5‐FDCA‐based PIs are comparable with petroleum‐based PI derived from isophthalic acid, displaying the potential for development of innovative bio‐based materials. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2018 , 56, 1058–1066     

Sputtering properties for polyimide by vacuum electrospray droplet impact (V‐EDI) using size‐selected cluster ions

Recently, the vacuum electrospray droplet impact (V‐EDI) was developed as a cluster ion beam source in our laboratory. To attain the ion beam stability and compact design of the ion source, a silica nano‐capillary with 15 µm i.d. was used as the emitter of the beam. It was found that stable electrospray was generated from the capillary tip without the use of laser heating when aqueous solution of 20% ethanol was used. The m/z distribution of electrospray droplets was measured by pulsing the primary beam. By assuming that the charged droplets contain 50% of the excess charges defined by the Rayleigh limit equation, the average mass, and charge of the droplets generated by the present V‐EDI are estimated as 2.5 × 10⁸ u and + 625 charges, respectively, i.e. [(H₂O)_14,000,000 + 625H]⁶²⁵⁺. By chopping the primary cluster beam, clusters composed of smaller m/z clusters (group 1: G1, [(H₂O)_46,000 + 36H]³⁶⁺) and those of larger m/z clusters (group 2: G2, [(H₂O)_560,000 + 125H]¹²⁵⁺) were generated. Surface analysis for polyimide (PI) film by X‐ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) was made using G1, G2, and non‐selected cluster beams. No selective etching was observed when G1, G2, and non‐selected beams were used. However, larger surface roughening was observed when smaller size cluster beams were used. This suggests that larger size clusters cure the surface damage caused by the smaller ones. Copyright © 2016 John Wiley & Sons, Ltd.     

Binding structures of tri‐N‐acetyl‐β‐glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field

Lysozyme is a well‐studied enzyme that hydrolyzes the β‐(1,4)‐glycosidic linkage of N‐acetyl‐β‐glucosamine (NAG)_n oligomers. The active site of hen egg‐white lysozyme (HEWL) is believed to consist of six subsites, A‐F that can accommodate six sugar residues. We present studies exploring the use of polarizable force fields in conjunction with all‐atom molecular dynamics (MD) simulations to analyze binding structures of complexes of lysozyme and NAG trisaccharide, (NAG)₃. MD trajectories are applied to analyze structures and conformation of the complex as well as protein–ligand interactions, including the hydrogen‐bonding network in the binding pocket. Two binding modes (ABC and BCD) of (NAG)₃ are investigated independently based on a fixed‐charge model and a polarizable model. We also apply molecular mechanics with generalized born and surface area (MM‐GBSA) methods based on MD using both nonpolarizable and polarizable force fields to compute binding free energies. We also study the correlation between root‐mean‐squared deviation and binding free energies of the wildtype and W62Y mutant; we find that for this prototypical system, approaches using the MD trajectories coupled with implicit solvent models are equivalent for polarizable and fixed‐charge models. © 2012 Wiley Periodicals, Inc.