Protein-ligand binding affinity prediction exploiting sequence constituent homology.

MOTIVATION: Molecular docking is a commonly used approach for estimating binding conformations and their resultant binding affinities. Machine learning has been successfully deployed to enhance such affinity estimations. Many methods of varying complexity have been developed making use of some or all the spatial and categorical information available in these structures. The evaluation of such methods has mainly been carried out using datasets from PDBbind. Particularly the Comparative Assessment of Scoring Functions (CASF) 2007, 2013, and 2016 datasets with dedicated test sets. This work demonstrates that only a small number of simple descriptors is necessary to efficiently estimate binding affinity for these complexes without the need to know the exact binding conformation of a ligand. RESULTS: The developed approach of using a small number of ligand and protein descriptors in conjunction with gradient boosting trees demonstrates high performance on the CASF datasets. This includes the commonly used benchmark CASF2016 where it appears to perform better than any other approach. This methodology is also useful for datasets where the spatial relationship between the ligand and protein is unknown as demonstrated using a large ChEMBL-derived dataset. AVAILABILITY AND IMPLEMENTATION: Code and data uploaded to https://github.com/abbiAR/PLBAffinity.

Recent molecularly imprinted polymers applications in bioanalysis.

Molecular imprinted polymers (MIPs) as extraordinary compounds with unique features have presented a wide range of applications and benefits to researchers. In particular when used as a sorbent in sample preparation methods for the analysis of biological samples and complex matrices. Its application in the extraction of medicinal species has attracted much attention and a growing interest. This review focus on articles and research that deals with the application of MIPs in the analysis of components such as biomarkers, drugs, hormones, blockers and inhibitors, especially in biological matrices. The studies based on MIP applications in bioanalysis and the deployment of MIPs in high-throughput settings and optimization of extraction methods are presented. A review of more than 200 articles and research works clearly shows that the superiority of MIP techniques lies in high accuracy, reproducibility, sensitivity, speed and cost effectiveness which make them suitable for clinical usage. Furthermore, this review present MIP-based extraction techniques and MIP-biosensors which are categorized on their classes based on common properties of target components. Extraction methods, studied sample matrices, target analytes, analytical techniques and their results for each study are described. Investigations indicate satisfactory results using MIP-based bioanalysis. According to the increasing number of studies on method development over the last decade, the use of MIPs in bioanalysis is growing and will further expand the scope of MIP applications for less studied samples and analytes.

Recent applications of microextraction sample preparation techniques in biological samples analysis.

Analysis of biological samples is affected by interfering substances with chemical properties similar to those of the target analytes, such as drugs. Biological samples such as whole blood, plasma, serum, urine and saliva must be properly processed for separation, purification, enrichment and chemical modification to meet the requirements of the analytical instruments. This causes the sample preparation stage to be of undeniable importance in the analysis of such samples through methods such as microextraction techniques. The scope of this review will cover a comprehensive summary of available literature data on microextraction techniques playing a key role for analytical purposes, methods of their implementation in common biological samples, and finally, the most recent examples of application of microextraction techniques in preconcentration of analytes from urine, blood and saliva samples. The objectives and merits of each microextration technique are carefully described in detail with respect to the nature of the biological samples. This review presents the most recent and innovative work published on microextraction application in common biological samples, mostly focused on original studies reported from 2017 to date. The main sections of this review comprise an introduction to the microextraction techniques supported by recent application studies involving quantitative and qualitative results and summaries of the most significant, recently published applications of microextracion methods in biological samples. This article considers recent applications of several microextraction techniques in the field of sample preparation for biological samples including urine, blood and saliva, with consideration for extraction techniques, sample preparation and instrumental detection systems.

Functionalized graphene oxide tablets for sample preparation of drugs in biological fluids: Extraction of ritonavir, a HIV protease inhibitor, from human saliva and plasma using LC-MS/MS.

In this work, graphene oxide-based tablets (GO-Tabs) were prepared by applying a thin layer of functionalized GO on a polyethylene substrate. The GO was functionalized with amine groups (-NH2 ) by poly(ethylene glycol)bis(3-aminopropyl) terminated (GO-NH2 -PEG-NH2 ). The functionalized GO-Tabs were used for the extraction of ritonavir (RTV) in human saliva samples. RTV in plasma and saliva samples was analyzed using LC-MS/MS. Gradient LC system with MS/MS in the positive-ion mode [electrospray ionization (ESI+)] was used. The transitions m/z 721 → 269.0 and m/z 614 → 421 were used for RTV and the internal standard indinavir, respectively. This study determined the human immunodeficiency virus protease inhibitor RTV in human saliva samples using functionalized GO-Tab and LC-MS/MS, and the method was validated. The standard calibration curve for plasma and saliva samples was constructed from 5.0 to 2000 nmol L-1 . The limit of detection was 0.1 nmol L-1 , and the limit of quantification was 5.0 nmol L-1 in both plasma and saliva matrices. The intra- and inter-assay precision values were found to be between 1.5 and 5.8%, and the accuracy values ranged from 88.0 to 108% utilizing saliva and plasma samples. The extraction recovery was more than 80%, and the presented functionalized GO-Tabs could be reused for more than 10 extractions without deterioration in recovery.

Recent Applications of Molecularly Imprinted Sol-Gel Methodology in Sample Preparation.

Due to their selectivity and chemical stability, molecularly imprinted polymers have attracted great interest in sample preparation. Imprinted polymers have been applied for the extraction and the enrichment of different sorts of trace analytes in biological and environmental samples before their analysis. Additionally, MIPs are utilized in various sample preparation techniques such as SPE, SPME, SBSE and MEPS. Nevertheless, molecularly imprinted polymers suffer from thermal (stable only up to 150 °C) and mechanical stability issues, improper porosity and poor capacity. The sol-gel methodology as a promising alternative to address these limitations allowing the production of sorbents with controlled porosity and higher surface area. Thus the combination of molecularly imprinted technology and sol-gel technology can create influential materials with high selectivity, high capacity and high thermal stability. This work aims to present an overview of molecularly imprinted sol-gel polymerization methods and their applications in analytical and bioanalytical fields.

On-line determination of sarcosine in biological fluids utilizing dummy molecularly imprinted polymers in microextraction by packed sorbent.

Several years ago, sarcosine received attention as a prostate-cancer marker. Prostate cancer is one of the most widespread types of tumor diseases in men. The prostate-specific antigen is normally used as a marker, and it can only be detected in blood with a sensitivity of approximately 80%. In the present study, dummy molecularly imprinted polymers in microextraction by packed sorbent with on-line liquid chromatography coupled to tandem mass spectrometry was used for the determination of sarcosine in human plasma and urine samples. The polymer network glycine was used for the dummy molecularly imprinted polymers. The selectivity of the method was evaluated using similar prostate-cancer biomarkers. In addition, various parameters affecting the extraction performance were investigated. The method limits of detection and quantification in the plasma and urine were 1.0 and 3.0 ng/mL, respectively. The values of the coefficient of determination were over 0.99 for all runs in the studied concentration range (3.0-10 000 ng/mL). The method recovery was 87 and 89% in plasma and urine, respectively. The intraday and interday precisions of sarcosine in the plasma and urine samples were in the ranges of 4.0-7.1, 3.0-6.3, 2.9-4.7, and 5.0-6.7, respectively.

PconsC: combination of direct information methods and alignments improves contact prediction.

SUMMARY: Recently, several new contact prediction methods have been published. They use (i) large sets of multiple aligned sequences and (ii) assume that correlations between columns in these alignments can be the results of indirect interaction. These methods are clearly superior to earlier methods when it comes to predicting contacts in proteins. Here, we demonstrate that combining predictions from two prediction methods, PSICOV and plmDCA, and two alignment methods, HHblits and jackhmmer at four different e-value cut-offs, provides a relative improvement of 20% in comparison with the best single method, exceeding 70% correct predictions for one contact prediction per residue. AVAILABILITY: The source code for PconsC along with supplementary data is freely available at http://c.pcons.net/ CONTACT: arne@bioinfo.se SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Dried saliva spot as a sampling technique for saliva samples.

For the first time, dried saliva spot (DSS) was used as a sampling technique for saliva samples. In the DSS technique 50 µL of saliva was collected on filter paper and the saliva was then extracted with an organic solvent. The local anesthetic lidocaine was used as a model compound, which was determined in the DSS using liquid chromatography and mass spectrometry. The results obtained for the determination of lidocaine in saliva using DSS were compared with those from a previous study using a microextraction by packed sorbent syringe as the sampling method for saliva. This study shows that DSS can be used for the analysis of saliva samples. The method is promising and very easy in terms of sampling and extraction procedures. The results from this study are in good agreement with those from our previous work on the determination of lidocaine in saliva. DSS can open a new dimension in the saliva handling process in terms of sampling, storing and transport.

Evaluation of microextraction by packed sorbent and micro-liquid chromatography-tandem mass spectrometry as a green approach in bioanalysis.

In this study the use of micro-liquid chromatography coupled to tandem mass spectrometry (µLC-MS/MS) was investigated in routine bioanalysis application for separation and quantification of pro-drug AZD6319 (developed for aldezheimer treatment). Microextraction by packed sorbent (MEPS) was used as sample clean-up method. The focus of this study was put on the evaluation of the usability of smaller column diameters such as 1.0 and 0.3 mm instead of 2.1 mm in bioanalysis application to reduce solvent consumption and sample volumes. Solvent consumption was reduced by 80% when a 1.0 mm column was used compared with 2.1 mm column. Robustness of the micro-columns in terms of accuracy and precision was investigated. The application of µLC-MS/MS for the quantitative analysis of AZD6319 in plasma samples showed good selectivity, accuracy and precision. The coefficients of determination (R(2) ) were >0.998 for all runs using plasma samples on the studied micro-columns. The inter-day accuracy values for quality control samples ranged from 99 to 103% and from 96 to 105% for 0.3 × 50 mm and 1.0 × 50 mm columns, respectively. The inter-day precision values ranged from 4.0 to 9.0% and from 4.0 to 8.0% for 0.3 × 50 and 1.0 × 50 mm columns, respectively. In addition the sensitivity was increased by three times using a 1.0 mm column compared with 2.1 mm. Furthermore, robustness of the micro-columns from different manufacturers was investigated.

Screening and determination of drugs in human saliva utilizing microextraction by packed sorbent and liquid chromatography-tandem mass spectrometry.

This study presents a new method for collecting and handling saliva samples using an automated analytical microsyringe and microextraction by packed syringe (MEPS). The screening and determination of lidocaine in human saliva samples utilizing MEPS and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were carried out. An exact volume of saliva could be collected. The MEPS C8 -cartridge could be used for 50 extractions before it was discarded. The extraction recovery was about 60%. The pharmacokinetic curve of lidocaine in saliva using MEPS-LC-MS/MS is reported.

Microextraction approaches for bioanalytical applications: An overview.

Biological samples are usually complex matrices due to the presence of proteins, salts and a variety of organic compounds with chemical properties similar to those of the target analytes. Therefore, sample preparation is often mandatory in order to isolate the analytes from troublesome matrices before instrumental analysis. Because the number of samples in drug development, doping analysis, forensic science, toxicological analysis, and preclinical and clinical assays is steadily increasing, novel high throughput sample preparation approaches are calling for. The key factors in this development are the miniaturization and the automation of the sample preparation approaches so as to cope with most of the twelve principles of green chemistry. In this review, recent trends in sample preparation and novel strategies will be discussed in detail with particular focus on sorptive and liquid-phase microextraction in bioanalysis. The actual applicability of selective sorbents is also considered. Additionally, the role of 3D printing in microextraction for bioanalytical methods will be pinpointed.

Distinct Requirements for Tail-Anchored Membrane Protein Biogenesis in Escherichia coli.

Tail-anchored membrane proteins (TAMPs) are a distinct subset of inner membrane proteins (IMPs) characterized by a single C-terminal transmembrane domain (TMD) that is responsible for both targeting and anchoring. Little is known about the routing of TAMPs in bacteria. Here, we have investigated the role of TMD hydrophobicity in tail-anchor function in Escherichia coli and its influence on the choice of targeting/insertion pathway. We created a set of synthetic, fluorescent TAMPs that vary in the hydrophobicity of their TMDs and corresponding control polypeptides that are extended at their C terminus to create regular type II IMPs. Surprisingly, we observed that TAMPs have a much lower TMD hydrophobicity threshold for efficient targeting and membrane insertion than their type II counterparts. Using strains conditional for the expression of known membrane-targeting and insertion factors, we show that TAMPs with strongly hydrophobic TMDs require the signal recognition particle (SRP) for targeting. Neither the SecYEG translocon nor YidC appears to be essential for the membrane insertion of any of the TAMPs studied. In contrast, corresponding type II IMPs with a TMD of sufficient hydrophobicity to promote membrane insertion followed an SRP- and SecYEG translocon-dependent pathway. Together, these data indicate that the capacity of a TMD to promote the biogenesis of E. coli IMPs is strongly dependent upon the polypeptide context in which it is presented.IMPORTANCE A subset of membrane proteins is targeted to and inserted into the membrane via a hydrophobic transmembrane domain (TMD) that is positioned at the very C terminus of the protein. The biogenesis of these so-called tail-anchored proteins (TAMPs) has been studied in detail in eukaryotic cells. Various partly redundant pathways were identified, the choice for which depends in part on the hydrophobicity of the TMD. Much less is known about bacterial TAMPs. The significance of our research is in identifying the role of TMD hydrophobicity in the routing of E. coli TAMPs. Our data suggest that both the nature of the TMD and its role in routing can be very different for TAMPs versus "regular" membrane proteins. Elucidating these position-specific effects of TMDs will increase our understanding of how prokaryotic cells face the challenge of producing a wide variety of membrane proteins.

Preparation of monolithic molecularly imprinted polymer sol-gel packed tips for high-throughput bioanalysis: extraction and quantification of L-tyrosine in human plasma and urine samples utilizing liquid chromatography and tandem mass spectrometry.

In situ monolithic molecularly imprinted polymer sol-gel packed tips (MMSTs) were prepared and evaluated for the extraction of lung cancer biomarker L-tyrosine (Tyr) from human plasma and urine samples. Several extraction parameters such as the conditioning, washing and elution solutions, pH and time were investigated. The enrichment factor (EF) and extraction recovery (ER) were studied. MMST showed good selectivity and a high extraction recovery, and MMST as a sorbent showed good stability and repeatability. The method validation showed good regression correlation coefficients for plasma and urine samples (R(2)≥0.996) within the concentration range of 5-1000 and 1-1000 nmol L(-1) in plasma and urine samples, respectively. The lower limits of quantification (LLOQ) in the plasma and urine samples were 5 and 1 nmol L(-1), respectively. The between-batch precision for Tyr in plasma ranged from 1.0 to 6.0%, and in urine it was from 1.0 to 7.0%. The results show that the developed method has more facility, stability, durability and repeatability compared with previous similar methods. To the best of our knowledge, this is the first study aimed at the selective separation of Tyr as a lung cancer biomarker by MMSTs from biological matrixes and detection by LC/MS/MS.