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.     

Alpha7 nicotinic acetylcholine receptor agonists: prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach

A group of agonists for the alpha7 neuronal nicotinic acetylcholine receptors (nAChRs) was investigated, and their free energies of binding DeltaG(bind) were calculated by applying the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach. This method, based on molecular dynamics simulations of fully solvated protein-ligand complexes, allowed us to estimate the contribution of both polar and nonpolar terms as well as the entropy to the overall free energy of binding. The calculated results were in a good agreement with the experimentally determined DeltaG(bind) values, thereby pointing to the MM-PBSA protocol as a valuable computational tool for the rational design of specific agents targeting the neuronal alpha7 nAChR subtypes.     

Computational analysis of the cathepsin B inhibitors activities through LR‐MMPBSA binding affinity calculation based on docked complex

Cathepsin B, a ubiquitous lysosomal cysteine protease, is involved in many biological processes related to several human diseases. Inhibitors targeting the enzyme have been investigated as possible diseases treatments. A set of 37 compounds were recently found active in a high throughput screening assay to inhibit the catalytic activity of Cathepsin B, with chemical structures and biological test results available to the public in the PubChem BioAssay Database (AID 820). In this study, we compare these experimental activities to the results of theoretical predictions from binding affinity calculation with a LR‐MM‐PNSA approach based on docked complexes. Strong correlations (r² = 0.919 and q² = 0.887 for the best) are observed between the theoretical predictions and experimental biological activity. The models are cross‐validated by four independent predictive experiments with randomly split compounds into training and test sets. Our results also show that the results based on protein dimer show better correlations with experimental activity when compared to results based on monomer in the in silico calculations. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Retention of structurally diverse drugs in human serum albumin chromatography and its potential to simulate plasma protein binding

The retention behavior of 39 structurally diverse neutral, basic and acidic drugs was investigated on an HSA stationary phase using PBS buffer (pH 7.0) and acetonitrile or 2-propanol as organic modifiers. Extrapolated or directly measured log k_w values as well as isocratic retention factors were correlated with plasma protein binding data taken from the literature. Retention factors determined in the presence of 10% acetonitrile led to high quality 1:1 correlation with apparent log K_HSA values. The derived reference equation was successfully validated using a secondary set of 24 drugs. Further analysis of HSA retention into more fundamental properties revealed the involvement of anionic species in solute-stationary phase interactions, expressed by the negatively charged fraction, besides the partitioning mechanism which was reflected by lipophilicity. Protonation of basic drugs, although less important, may also influence retention, leading to reduced partitioning into the HSA surface as a net effect, while it seems to have no effect on HSA binding. The above results were further confirmed by linear solvation energy relationships (LSER).     

The estimation of the hydrophobic and electrostatic contributions to the free energy change upon cationic surfactants binding to Jack bean urease

The binding of a homologous series of n-alkyltrimethyl ammonium bromides with Jack bean urease (JBU) have been studied previously. It has been suggested that both electrostatic and hydrophobic interactions are involved in the formation of surfactant-protein complexes, but there is not any quantities analyzing method for resolution of their contributions in the process. In the present study, at first, the intrinsic Gibbs free energy of binding, ΔG_b,ν, has been calculated for these systems and the trend of variation for both binding sets have been interpreted on basis of cooperativity and hydrophobicity of surfactants. Subsequently, a novel approach has been introduced for estimation of electrostatic and hydrophobic interactions in ΔG_b,ν, by considering of this fact that ΔG_b,ν is the summation of electrostatic, ΔG_b,ν(ele), and hydrophobic, ΔG_b,ν(hyd), parts and considering this fact that just ΔG_b,ν(hyd) is a function of hydrocarbon tail length of surfactant (C_n). The results represents the higher positive rule of electrostatic interactions in binding affinity of first set and inhibiting rule of this interaction in the second binding set. The predominate driving force in the second binding set is entropy statistical effect, which arises from numerous number of binding sites in this set. A binding mechanism on basis of structural changes in JBU due to its interaction with cationic surfactants has also been proposed.     

Molecular dynamics simulations reveal the allosteric effect of F1174C resistance mutation to ceritinib in ALK-associated lung cancer

Anaplastic lymphoma kinase (ALK) has become as an important target for the treatment of various human cancers, especially non-small-cell lung cancer. A mutation, F1174C, suited in the C-terminal helix αC of ALK and distal from the small-molecule inhibitor ceritinib bound to the ATP-binding site, causes the emergence of drug resistance to ceritinib. However, the detailed mechanism for the allosteric effect of F1174C resistance mutation to ceritinib remains unclear. Here, molecular dynamics (MD) simulations and binding free energy calculations [Molecular Mechanics/Generalized Born Surface Area (MM/GBSA)] were carried out to explore the advent of drug resistance mutation in ALK. MD simulations observed that the exquisite aromatic-aromatic network formed by residues F1098, F1174, F1245, and F1271 in the wild-type ALK-ceritinib complex was disrupted by the F1174C mutation. The resulting mutation allosterically affected the conformational dynamic of P-loop and caused the upward movement of the P-loop from the ATP-binding site, thereby weakening the interaction between ceritinib and the P-loop. The subsequent MM/GBSA binding free energy calculations and decomposition analysis of binding free energy validated this prediction. This study provides mechanistic insight into the allosteric effect of F1174C resistance mutation to ceritinib in ALK and is expected to contribute to design the next-generation of ALK inhibitors.     

Minimum MD simulation length required to achieve reliable results in free energy perturbation calculations: Case study of relative binding free energies of fructose‐1,6‐bisphosphatase inhibitors

In an attempt to establish the criteria for the length of simulation to achieve the desired convergence of free energy calculations, two studies were carried out on chosen complexes of FBPase‐AMP mimics. Calculations were performed for varied length of simulations and for different starting configurations using both conventional‐ and QM/MM‐FEP methods. The results demonstrate that for small perturbations, 1248 ps simulation time could be regarded a reasonable yardstick to achieve convergence of the results. As the simulation time is extended, the errors associated with free energy calculations also gradually tapers off. Moreover, when starting the simulation from different initial configurations of the systems, the results are not changed significantly, when performed for 1248 ps. This study carried on FBPase‐AMP mimics corroborates well with our previous successful demonstration of requirement of simulation time for solvation studies, both by conventional and ab initio FEP. The establishment of aforementioned criteria of simulation length serves a useful benchmark in drug design efforts using FEP methodologies, to draw a meaningful and unequivocal conclusion. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011