Protein interaction predictions from diverse sources

Protein-protein interactions play an important role in many cellular processes. The availability of a comprehensive and accurate list of protein interactions can facilitate drug target discovery. Recent advances in high-throughput experimental technologies have generated enormous amounts of data and provided valuable resources for studying protein interactions. However, these technologies suffer from high error rates because of their inherent limitations. Therefore, computational approaches capable of incorporating multiple data sources are needed to fully take advantage of the rapid accumulation of data. In this review, we focus on the computational methods that integrate multiple data sources by combining direct measurements on protein interactions from diverse organisms, and by integrating different types of indirect information from various genomic and proteomic approaches.     

An evaluation of Bayesian microcomputer predictions of theophylline concentrations in newborn infants

Determination of appropriate theophylline maintenance doses in preterm infants is confounded by interpatient variability. This study evaluated the performance of an IBM PC computer program applying Bayesian regression before and during steady state in 37 preterm infants. Prior population estimates of clearance and distribution volume in preterm infants and Bayesian estimates of clearance and distribution volume based on one to three theophylline plasma concentrations were used to predict subsequent concentrations (drawn 1-17 days later). We assessed the accuracy and precision of the predictive performance of the Bayesian program with the mean prediction error and the mean absolute prediction error. The absolute prediction error (mean absolute error +/- SEM) significantly decreased with increasing feedback concentrations from 3.54 +/- 0.45 micrograms/ml (population estimates) to 2.74 +/- 0.42 (one feedback) and 2.02 +/- 0.35 micrograms/ml (two feedback concentrations). Mean prediction errors (+/- SEM) based on one to three feedbacks (-1.5 +/- 0.40 micrograms/ml) were significant improvements over population predictions (-2.63 +/- 0.72 micrograms/ml, p less than 0.05), although a small but significant average overprediction remained. Absolute prediction error was correlated with postconceptional and postnatal age when zero or one but not two feedback concentrations were available. Computer program predictions based on one measured feedback concentration were more accurate and precise than population-based predictions. Refinement of population parameters or two feedback concentrations further improved performance.     

Protein binding of nifedipine

The protein binding of nifedipine in concentrations up to 1200 ng ml-1 has been measured in serum, pure human albumin solution and pure human alpha 1-acid glycoprotein (AAG) solutions by ultrafiltration. The drug was extensively bound in serum from four healthy volunteers with a mean (+/- s.d.) fraction bound of 0.992 +/- 0.008. In albumin solution (40 g litre-1) the mean (+/- s.d.) fraction bound 0.970 +/- 0.012, was not significantly different (P greater than 0.05) from that in serum, suggesting that albumin is the major, but not necessarily the only, binding protein for nifedipine in serum. The binding of nifedipine in solutions of AAG was proportional to the AAG concentration and ranged from 0.514 +/- 0.059 to 0.755 +/- 0.035 in solutions containing 50 and 150 mg % AAG, respectively. Binding of nifedipine in all protein solutions was linear.     

Protein binding of propisomide

This paper describes the protein binding of propisomide to human serum and isolated proteins using equilibrium dialysis. The drug is exclusively bound to alpha1-acid glycoprotein with high affinity. The binding is saturable even at low concentrations of the drug. Thus, the fraction unbound varied from 0.05 to 0.60 with decreasing serum concentration. The major metabolite of the drug or other drugs with affinity for alpha1-acid glycoprotein can displace propisomide from its binding site only when present in serum at high levels. Two ultrafiltration techniques are compared to equilibrium dialysis for the determination of serum protein binding of propisomide. Ultrafiltration does not give reliable results. Equilibrium dialysis is retained as an accurate method for the determination of the fraction unbound of propisomide.     

Protein binding of flucloxacillin in neonates

The isoxazolyl penicillins, including flucloxacillin, have the highest levels of plasma protein binding among the semisynthetic penicillins. Because only the free fraction of the penicillin is pharmacologically active, it would be useful to measure both protein-bound and free flucloxacillin to determine its protein binding. Until now, flucloxacillin protein binding in newborn infants has been investigated in only two studies with relatively small populations. In the present study, flucloxacillin protein binding was investigated in 56 (preterm) infants aged 3 to 87 days (gestational age, 25-41 weeks). Surplus plasma samples from routine gentamicin assays of each infant were collected and combined to obtain a sufficiently large sample for analysis. Free flucloxacillin was separated from protein-bound flucloxacillin using ultrafiltration. Reversed-phase high-performance liquid chromatography with ultraviolet detection was used to measure free flucloxacillin concentrations in ultrafiltrate and total flucloxacillin concentrations in pooled plasma. Flucloxacillin protein binding was 74.5% +/- 13.1% (mean +/- standard deviation) with a high variability among the infants (34.3% to 89.7%). High Pearson correlations were found between protein binding and the covariates-plasma albumin concentration (r = 0.804, P < 0.001, n = 18) and plasma creatinine concentration (r = -0.601, P < 0.001, n = 45). Statistically significant but less striking correlations were found between protein binding and gestational age, postconceptional age, body weight, and triglyceride concentration. Because of the high variability of protein binding among infants, it is difficult to devise a flucloxacillin dosage regimen effective for all infants. Individualized dosing, based on free flucloxacillin concentrations, might help to optimize treatment of late-onset neonatal sepsis, but practical obstacles will probably prevent analysis of free flucloxacillin concentrations in newborn infants on a routine basis.     

Protein binding of ceftriaxone in extravascular fluids

Ceftriaxone binding in extravascular fluids and diluted plasma was characterized by equilibrium dialysis techniques and the data was subjected to Scatchard analysis. The extent of ceftriaxone binding in extravascular fluids (synovial, lymph, ascites, and pleural exudate) was less than plasma due primarily to lower albumin concentrations. Ceftriaxone capacity constants were highly correlated (r2 = 0.900, p less than 0.001) with measured albumin concentrations (range of 43 g/L for albumin to 4.7 g/L for one of the pleural exudate samples). The binding affinity constant (M-1 x 10(-4] was comparable for plasma (3.67), synovial fluid (4.14), and lymph (3.40), but was lower for ascites (2.37) and pleural fluid (range of 2.77 to 0.31). Plasma samples diluted with plasma water (range of 100 to 3%) exhibited a common affinity constant (mean value 4.03 x 10(4) M-1) and capacity constants which correlated directly with albumin concentration (r2 = 0.998, p less than 0.001). Analysis of these observations suggests that extravascular binding of ceftriaxone can readily be predicted if extravascular albumin concentration and corresponding disease-state plasma protein binding are known.     

Protein binding of digoxin in human serum

Summary The protein binding of digoxin in human serum was investigated using equilibrium dialysis and tritium-labelled digoxin. A constant protein bound fraction of about 30% was found over a wide range of concentrations of digoxin including therapeutic levels. Interpretation of the findings according to the law of mass-action showed an association constantK = 0.68·10^–5l/mol; and, the number of binding sites,n , indicating an almost infinite apparent maximum binding capacity and a very small affinity of human serum proteins for digoxin.Supported by the Schweizer Nationalfond zur Förderung der wissenschaftlichen Forschung.     

Hit identification and binding mode predictions by rigorous free energy simulations

The identification of lead molecules using computational modeling often relies on approximate, high-throughput approaches, of limited accuracy. We show here that, with a methodology we recently developed, it is possible to predict the relative binding free energies of structurally diverse ligands of the estrogen receptor-alpha using a rigorous statistical thermodynamics approach. Predictions obtained from the simulations with an explicit solvation model are in good qualitative agreement with experimental data, while simulations with implicit solvent models or rank ordering by empirical scoring functions yield predictions of lower quality. In addition, it is shown that free energy techniques can be used to select the most likely binding mode from a set of possible orientations generated by a docking program. It is suggested that the free energy techniques outlined in this study can be used to rank-order, by potency, structurally diverse compounds identified by virtual screening, de novo design or scaffold hopping programs.     

银杏内酯B在血浆中的蛋白结合率研究

目的测定银杏内酯B(ginkgolide B,GB)与大鼠和人的血浆蛋白结合率。方法将血浆样品加入内标23-羟基白桦酸,乙醚液液萃取后,高效液相色谱-质谱联用仪分析,采用平衡透析法测定GB在大鼠及人血浆中的血浆蛋白结合率。结果人和大鼠血浆中GB药物浓度在0.05～5.00 mg.L-1范围内血浆蛋白结合呈线性关系;GB与大鼠血浆蛋白结合率约为25%,与人血浆蛋白结合率约为20%。结论 GB的血浆蛋白结合率较低,在人血浆的蛋白结合率略低于大鼠,但不存在显著性差异;约80%的药物以游离态形式存在。     

Protein binding of salicylate in cutaneous hepatic porphyria

Summary (1) Plasma protein binding of salicylate was studied in 14 patients with cutaneous hepatic porphyria (CHP) and 11 normal subjects using ultrafiltration with centrifugation (membrane cones) and continuous ultrafiltration. (2) Albumin and haemoglobin levels were significantly reduced in patients with CHP, and salicylate binding by ultrafiltration/centrifugation was 65% compared with 84% in normal subjects. (3) Plasma porphyrin levels were raised, but did not correlate with salicylate binding, and protoporphyrin or uroporphyrin added to plasma did not alter the amount of drug bound. (4) Palmitate added to plasma reduced salicylate binding by 9 to 20% but a crossover of patient and normal plasma proteins and ultrafiltrates confirmed that no other ultrafiltrable metabolites present in patient plasma appeared to cause decreased binding. (5) Scatchard plots obtained by continuous ultrafiltration for normal and patient plasma showed a reduction in the number of primary and secondary binding sites and an increase in the intrinsic association constants for both these sites. (6) It was concluded that the decreased salicylate binding in CHP was due to a reduced albumin concentration and altered salicylate albumin interaction.     

Protein binding of indomethacin in human cerebrospinal fluid

The binding of the non-steroidal anti-inflammatory drug indomethacin to proteins in human cerebrospinal fluid (CSF), drawn during lumbar puncture from 10 patients affected by lumbosciatica, was measured by equilibrium dialysis and spectrofluorimetry. Similar binding studies on human serum albumin solutions (0.5 and 1 g/L) were performed using the same techniques. The mean binding percentage of indomethacin determined by equilibrium dialysis was 40%. The results obtained by both techniques allowed us to conclude that the binding of indomethacin in CSF was essentially due to albumin.     

Protein binding and disposition of lignocaine in the elderly

Summary Single dose studies were performed in six young and six elderly nonsmokers using lignocaine as a model drug with high intrinsic clearance. Subjects received lignocaine 250 mg orally and 50 mg intravenously in random order and drug concentrations in blood and plasma were measured for up to 8 h after dose. Protein binding was estimated at 37 °C by equilibrium dialysis. Indocyanine green kinetics were also calculated in each individual following 0.15 mg/kg intravenously.Bioavailability of lignocaine was greater in the elderly but there was no apparent difference in the rate of absorption. Intrinsic clearance of lignocaine was lower in the aged. Elimination half-life was longer in the elderly but there was no significant difference in apparent volume of distribution or systemic clearance of lignocaine. Plasma clearance of indocyanine green showed no correlation with systemic lignocaine clearance and was lower in the aged subjects. Blood/plasma lignocaine ratio was less than unity in both groups. Binding of lignocaine to plasma proteins showed concentration-dependence and was higher in the geriatric group. Maximum binding capacity of lignocaine was greater in the elderly but the binding affinity did not significantly change with age.Greater oral bioavailability of drugs like lignocaine may produce higher plasma concentrations in the elderly. Unlike indocyanine green, the systemic clearance of lignocaine was unaltered by age in this group of non-smokers. The protein-binding of lignocaine, like many other basic drugs, is increased in elderly subjects.