Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields

Summary A methodology aimed at improving the accuracy of current docking–scoring procedures is proposed, and validated through detailed tests of its performance in predicting the activity of HIV-1 protease inhibitors. This methodology is based on molecular dynamics simulations using a force field whose effective charges are refined by means of a novel procedure that relies on quantum-mechanical calculations and preserves the internal consistency of the parameterization scheme.     

Improved convergence of binding affinities with free energy perturbation: Application to nonpeptide ligands with pp60src SH2 domain

Free Energy Perturbations (FEP) in the context of Monte Carlo (MC) simulations were conducted to predict the relative free energies of binding for a series of human Src SH2 domain ligands. Two procedures for disappearing atoms during a single-topology FEP are investigated and dramatic differences in free energy convergence behavior are seen. Comparison of these two protocols suggests that the coupling of the removal of angular constraints with the disappearance of an atom may significantly slow free energy convergence. The series of ligands under investigation here cover a range of modifications at the 3-position of 4-({[4-(cyclohexyl methoxy)benzyl]amino}carbonyl) phenyl phosphate. Unlike any other compound in this study, the 3-amide analog can form two hydrogen bonds within the region of the perturbation, one to a backbone amide hydrogen and one to a highly coordinated water molecule. Agreement with experimental trends in binding affinity is seen, although the computed relative free energy of binding of the amido compound is underestimated. These results are reconciled by examination of the hydration energies of model systems, which predict primary amides as too hydrophilic.     

Development and validation of a high‐performance liquid chromatography method for the quantification of talazoparib in rat plasma: Application to plasma protein binding studies

A sensitive and selective RP‐HPLC method has been developed and validated for the quantification of a highly potent poly ADP ribose polymerase inhibitor talazoparib (TZP) in rat plasma. Chromatographic separation was performed with isocratic elution method. Absorbance for TZP was measured with a UV detector (SPD‐20A UV–vis) at a λ_max of 227 nm. Protein precipitation was used to extract the drug from plasma samples using methanol–acetonitrile (65:35) as the precipitating solvent. The method proved to be sensitive and reproducible over a 100–2000 ng/mL linearity range with a lower limit of quantification (LLQC) of 100 ng/mL. TZP recovery was found to be >85%. Following analytical method development and validation, it was successfully employed to determine the plasma protein binding of TZP. TZP has a high level of protein binding in rat plasma (95.76 ± 0.38%) as determined by dialysis method.     

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

This paper describes the development of a simple empirical scoringfunction designed to estimate the free energy of binding for aprotein–ligand complex when the 3D structure of the complex is knownor can be approximated. The function uses simple contact terms to estimatelipophilic and metal–ligand binding contributions, a simple explicitform for hydrogen bonds and a term which penalises flexibility. Thecoefficients of each term are obtained using a regression based on 82ligand–receptor complexes for which the binding affinity is known. Thefunction reproduces the binding affinity of the complexes with across-validated error of 8.68 kJ/mol. Tests on internal consistency indicatethat the coefficients obtained are stable to changes in the composition ofthe training set. The function is also tested on two test sets containing afurther 20 and 10 complexes, respectively. The deficiencies of this type offunction are discussed and it is compared to approaches by other workers.     

Protein Alpha Shape Similarity Analysis (PASSA): a new method for mapping protein binding sites. Application in the design of a selective inhibitor of tyrosine kinase 2

We have developed a method that we have called Protein Alpha Shape Similarity Analysis (PASSA), that identifies interaction sites that can be utilised to achieve selectivity towards a protein. We have shown that this method is able to identify residues of tyrosine kinases that interact with known selective inhibitors using the following test cases: Abelson (Abl) kinase in complex with STI-571 and Janus kinase 2 (Jak2) in complex with AG-490. The 3D structures of the tyrosine kinase domains of Tyrosine kinase 2 (Tyk2) and Jak2 have been predicted by homology modelling. Computational docking of AG-490 and a set of tyrphostins known not to inhibit Jak2 indicated that our homology models are able to separate inhibitors from non-inhibitors. PASSA has also been used to identify unique properties of Tyk2. According to our results, interactions with hydrogen acceptors and donors on the following residues can be utilised to achieve selectivity towards Tyk2: Y955, E1053, D1062 and S1063. These residues are placed close to non-conserved hydrophobic pockets. The PASSA results, together with results from Multiple Copy Simultaneous Search (MCSS) were used to suggest functional groups of a selective Tyk2 inhibitor.     

High‐throughput LC–MS/MS method with 96‐well plate precipitation for the determination of arotinolol and amlodipine in a small volume of rat plasma: Application to a pharmacokinetic interaction study

A rapid, sensitive, and selective liquid chromatography with tandem mass spectrometry method was developed and fully validated for the simultaneous quantification of arotinolol and amlodipine in rat plasma. Two internal standards were introduced with metoprolol as the internal standard of arotinolol and (S)‐amlodipine‐d4 as the internal standard of amlodipine. The analytes were isolated from 50.0 μL plasma samples by a simple protein precipitation using acetonitrile. The chromatographic separation was achieved in 5 min on a C18 column. The mobile phase consisted of phase A 5% methanol and phase B 95% methanol (both containing 0.5% formic acid and 5 mM ammonium acetate) and was delivered in gradient elution at 0.300 mL/min. Quantification was performed in multiple reaction monitoring mode with the transition m/z 372.1 → 316.1 for arotinolol, m/z 268.2 → 116.2 for metoprolol, m/z 409.1 → 238.1 for amlodipine and m/z 413.1 → 238.1 for (S)‐amlodipine‐d4. Linearity was obtained over the range of 0.200–40.0 ng/mL for arotinolol (r² = 0.9988) and 0.500–100 ng/mL for amlodipine (r² = 0.9985) in rat plasma. The validated data have met the acceptance criteria in FDA guideline. This method was successfully applied to a pharmacokinetic interaction study in rats, and the results indicated that there was no significant drug–drug interaction between arotinolol and amlodipine.     

Evaluation of the limit of performance of an analytical method based on a statistical calculation of its critical concentrations according to ISO standard 11843: Application to routine control of banned veterinary drug residues in food according to European Decision 657/2002/EC

Traceability of the measurement of analytical parameters capable of evaluating the performance of methods is an important concept for the assessment of quality for the routine control, especially for residue monitoring of non-authorized medicinal substances in food from animal origin. The European Decision no. 657/2002/EC recommends to calculate two statistical limits, CCα and CCβ, which allow to evaluate the critical concentrations above which the method reliably distinguish and quantify a substance taking into account the variability of the method and the statistical risk to take a wrong decision. The calculation, which can be derived from the ISO standard no. 11843 is applied on a routine basis. An example displays a very simple way for evaluating the performance of an LC-MSMS method which has been validated a few years ago and is qualified onto a Micromass Quattro LCZ tandem mass spectrometer to monitor and confirm the nitrofuran metabolite residues in food from animal origin. Community Reference Laboratory for Antimicrobial Veterinary Drug Residue Control in Food from Animal Origin     

Simultaneous quantitative analysis of phosphocreatine,creatine and creatinine in plasma of children by HPLC–MS/MS method: Application to a pharmacokinetic study in children with viral myocarditis

A simple and rapid HPLC–MS/MS method was developed and validated for simultaneous measurement of phosphocreatine and its metabolites creatine and creatinine in children's plasma. A 50 μL aliquot of plasma was prepared by protein precipitation with acetonitrile–water (1000 μL, 1:1, v/v) followed by separation on a Hypersil Gold C₁₈ column (35°C) with gradient mobile phase consisting of 2 mm ammonium acetate aqueous solution (pH 10) and methanol at a flow rate of 0.3 mL/min and analyzed by mass spectrometry in both positive (phosphocreatine) and negative (creatine and creatinine) ion multiple reaction monitoring mode. Good linearity (r > 0.99) was obtained for the three analytes. The intra‐day and inter‐day values of CV were <5.46% (?13.09% ≤ RE ≤ 2.57%). The average recoveries of the three analytes were 70.9–97.5%. No obvious impact was found for the quantitation of three analytes in normal, hemolyzed and hyperlipemic plasma. In the end, this method was successfully applied to a pharmacokinetic study of phosphocreatine in children (six cases) with viral myocarditis of children after intravenous infusion of 2 g of the test drug. The pharmacokinetc parameters of phosphocreatine/creatine were as follows: t_1/2 0.24/0.83 h, T_max 0.49/0.55 h, C_max 47.34/59.29 μg/mL, AUC_last 17.07/59.63 h μg/mL, AUC_inf 17.16/79.01 h μg/mL and MRT 0.29/0.67 h.