P1/P1' modified HIV protease inhibitors as tools in two new sensitive surface plasmon resonance biosensor screening assays

Synthesis, characterization and biological evaluation of a new photoactive hydrogel against Gram-positive and Gram-negative bacteria

Development of a cheap material active against both Gram-positive and Gram-negative bacteria to be used as a novel water-sterilizing device.

Nanobiosensors: Concepts and Variations

Biosensing has been one of the hottest topic attracting scientific minds since long back. It is so as biological entities are very complex and are directly associated with the existence of a healthy environment. The design of biosensors also has witnessed significant changes in the recent past. Biosensors for applications as diverse as food quality estimation, environmental monitoring, and diagnosis of clinical and metabolic complications have come to the fore. Nanotechnology has bestowed some highly exciting ingredients for the improvement of sensing phenomenon. The use of diverse nanomaterials ranging from nanoparticles, nanotubes, nanorods, and nanowires has enabled faster detection and its reproducibility in a much better way. The unique properties of nanomaterials such as high electrical conductivity, better shock bearing ability, and the sensitive responses such as piezoelectric and versatile color based detection mechanisms are only the results of congregation of nanomaterial properties. This paper highlights the different types of biosensors based on different types of nanomaterials and their developmental and implicational aspects.

Development of gadolinium based nanoparticles having an affinity towards melanin

Small Rigid Platforms (SRPs) are sub-5 nanometre gadolinium based nanoparticles that have been developed for multimodal imaging and theranostic applications. They are composed of a polysiloxane network surrounded by gadolinium chelates. A covalent coupling with quinoxaline derivatives has been performed. Such derivatives have proven their affinity for melanin frequently expressed in primary melanoma cases. Three different quinoxaline derivatives have been synthesised and coupled to the nanoparticles. The affinity of the grafted nanoparticles for melanin has then been shown in vitro by surface plasmon resonance on a homemade melanin grafted gold chip.

Protein-Ligand Interactions Using SPR Systems

Surface plasmon resonance (SPR) biosensor technology has become an important tool for drug discovery and basic research. SPR instruments are used for a wide variety of applications including determining the binding kinetics and affinity of an interaction, specificity studies, screening, assay development as well as concentration measurements. The interacting molecules may be proteins, peptides, lipids, viruses, nucleic acids, or small organic molecules such as fragments or drug candidates. The ease with which real time information can be obtained has changed many customer workflows in both antibody and small molecule/fragment interaction analysis, from label based and affinity/IC50 based workflows towards a label free and kinetic based workflow. This chapter focuses on applications for drug discovery, and outlines the experimental design for screening and selection of small molecules from a focused library. Also, determination of kinetics and/or affinity constants of selected ligands, using established SPR methodology is described, together with potential issues during assay development, running of the assay, and results interpretation.

Development of surface plasmon resonance biosensor assays for primary and secondary screening of acetylcholine binding protein ligands

Surface plasmon resonance (SPR) biosensors recently gained an important place in drug discovery. Here we present a primary and secondary SPR biosensor screening methodology. The primary screening method is based on a direct binding assay with covalent immobilized drug target proteins. For the secondary screening method, a sequential competition assay has been developed where the captured protein is first exposed to an unknown test compound, followed directly by an exposure to a high-molecular-weight reporter ligand. Using the high-molecular-weight reporter ligand to probe the remaining free binding site on the sensor, a significant signal enhancement is obtained. Furthermore, this assay format allows the validation of the primary direct binding assay format, efficiently revealing false positive data. As a model system, acetylcholine binding protein (AChBP), which is a soluble model protein for neuronal nicotinic acetylcholine receptors, has been used. The secondary assay is lower in throughput than the primary assay; however, the signal-to-noise ratio is two times higher compared with the direct assay, and it has a z' factor of 0.96. Using both assays, we identified the compound tacrine as a ligand for AChBP.

Quantitative structure-activity relationship studies on 1-aryl-tetrahydroisoquinoline analogs as active anti-HIV agents

Predictive quantitative structure-activity relationship analysis was developed for a diverse series of recently synthesized 1-aryl-tetrahydroisoquinoline analogs with anti-HIV activities in this study. The conventional 2D-QSAR models were developed by genetic function approximation (GFA) and stepwise multiple linear regression (MLR) with acceptable explanation of 94.9% and 95.5% and good predicted power of 91.7% and 91.7%, respectively. The results of the 2D-QSAR models were further compared with 3D-QSAR model generated by molecular field analysis (MFA), investigating the substitutional requirements for the favorable receptor-drug interaction and quantitatively indicating the important regions of molecules for their activities. The results obtained by combining these methodologies give insights into the key features for designing more potent analogs against HIV.

A new strategy for improved secondary screening and lead optimization using high-resolution SPR characterization of compound-target interactions

Biophysical label-free assays such as those based on SPR are essential tools in generating high-quality data on affinity, kinetic, mechanistic and thermodynamic aspects of interactions between target proteins and potential drug candidates. Here we show examples of the integration of SPR with bioinformatic approaches and mutation studies in the early drug discovery process. We call this combination 'structure-based biophysical analysis'. Binding sites are identified on target proteins using information that is either extracted from three-dimensional structural analysis (X-ray crystallography or NMR), or derived from a pharmacore model based on known binders. The binding site information is used for in silico screening of a large substance library (e.g. available chemical directory), providing virtual hits. The three-dimensional structure is also used for the design of mutants where the binding site has been impaired. The wild-type target and the impaired mutant are then immobilized on different spots of the sensor chip and the interactions of compounds with the wild-type and mutant are compared in order to identify selective binders for the binding site of the target protein. This method can be used as a cost-effective alternative to high-throughput screening methods in cases when detailed binding site information is available. Here, we present three examples of how this technique can be applied to provide invaluable data during different phases of the drug discovery process.

Technological Advances in High-Throughput Screening

High-throughput screening (HTS) is the process of testing a large number of diverse chemical structures against disease targets to identify 'hits'. Compared to traditional drug screening methods, HTS is characterized by its simplicity, rapidness, low cost, and high efficiency, taking the ligand-target interactions as the principle, as well as leading to a higher information harvest. As a multidisciplinary field, HTS involves an automated operation-platform, highly sensitive testing system, specific screening model (in vitro), an abundant components library, and a data acquisition and processing system. Various technologies, especially the novel technologies such as fluorescence, nuclear-magnetic resonance, affinity chromatography, surface plasmon resonance, and DNA microarray, are now available, and the screening of more than 100,000 samples per day is already possible. Fluorescence-based assays include the scintillation proximity assay, time-resolved energy transfer, fluorescence anisotropy, fluorescence correlation spectroscopy, and fluorescence fluctuation spectroscopy. Fluorescence-based techniques are likely to be among the most important detection approaches used for HTS due to their high sensitivity and amenability to automation, giving the industry-wide drive to simplify, miniaturize, and speed up assays. The application of NMR technology to HTS is another recent trend in drug research. One advantage afforded by NMR technology is that it can provide direct information on the affinity of the screening compounds and the binding location of protein. The structure-activity relationship acquired from NMR analysis can sharpen the library design, which will be very important in furnishing HTS with well-defined drug candidates. Affinity chromatography used for library screening will provide the information on the fundamental processes of drug action, such as absorption, distribution, excretion, and receptor activation; also the eluting curve can give directly the possibility of candidate drug. SPR can measure the quantity of a complex formed between two molecules in real-time without the need for fluorescent or radioisotopic labels. SPR is capable of characterizing unmodified biopharmaceuticals, studying the interaction of drug candidates with macromolecular targets, and identifying binding partners during ligand fishing experiments. DNA microarrays can be used in HTS be used to further investigate the expression of biological targets associated with human disease, which then opens new and exciting opportunities for drug discovery. Without doubt, the addition of new technologies will further increase the application of HTS in drug screening and its related fields.

Optimization of P1-P3 groups in symmetric and asymmetric HIV-1 protease inhibitors

HIV-1 protease is an important target for treatment of AIDS, and efficient drugs have been developed. However, the resistance and negative side effects of the current drugs has necessitated the development of new compounds with different binding patterns. In this study, nine C-terminally duplicated HIV-1 protease inhibitors were cocrystallised with the enzyme, the crystal structures analysed at 1.8-2.3 A resolution, and the inhibitory activity of the compounds characterized in order to evaluate the effects of the individual modifications. These compounds comprise two central hydroxy groups that mimic the geminal hydroxy groups of a cleavage-reaction intermediate. One of the hydroxy groups is located between the delta-oxygen atoms of the two catalytic aspartic acid residues, and the other in the gauche position relative to the first. The asymmetric binding of the two central inhibitory hydroxyls induced a small deviation from exact C2 symmetry in the whole enzyme-inhibitor complex. The study shows that the protease molecule could accommodate its structure to different sizes of the P2/P2' groups. The structural alterations were, however, relatively conservative and limited. The binding capacity of the S3/S3' sites was exploited by elongation of the compounds with groups in the P3/P3' positions or by extension of the P1/P1' groups. Furthermore, water molecules were shown to be important binding links between the protease and the inhibitors. This study produced a number of inhibitors with Ki values in the 100 picomolar range.

Synthesis and HSA binding characterisation of the water soluble 7-succinylpaclitaxel

A water soluble paclitaxel analogue, the 7-hemisuccinylpaclitaxel, was synthesised and its binding to human serum albumin (HSA) was characterised by difference circular dichroism and optical biosensor methodologies. The carboxylate group was introduced at paclitaxel C-7 position to improve the drug water solubility without significantly changing the biological activity. The paclitaxel analogue showed a relatively low affinity to HSA (3.5x10(4) M(-1)), while no significant interactions were evidenced with selective markers for the most characterised binding sites on the carrier, suggesting a non-selective binding to low affinity binding sites.

Kinetic and mechanistic analysis of the association and dissociation of inhibitors interacting with secreted aspartic acid proteases 1 and 2 from Candida albicans

In order to elucidate the characteristics of different aspartic proteases (Sap) secreted by Candida albicans, the kinetics of the interaction (k(on), k(off)) between Sap1 and Sap2 with acetyl-pepstatin and pepstatin A was determined at different pH by biosensor technology. The enzymes were biotinylated and coupled to a streptavidin-coated sensor chip, whereupon acetyl-pepstatin or pepstatin A was injected and the interaction was measured in real time. Sap2 showed a faster k(on) and a higher affinity for acetyl-pepstatin than Sap1, regardless of pH. The values for both k(on) and k(off) decreased with increased pH from 3.8 to 5.0, except for the k(off) for Sap1, which was only influenced by the pH change from 3.8 to 4.4. Binding of acetyl-pepstatin to Sap1 or Sap2 obviously proceeds by a different mechanism than dissociation of the inhibitor. Association appears to be coupled to protonation of a catalytic aspartic acid residue, consistent with reduced k(on) values at higher pH. In contrast, the stability of the complex is reduced at lower pH due to reduced hydrogen bonding capacity of aspartic acid residues acting as hydrogen bond acceptors. Differences in the number and distribution of charged nonactive site residues in Sap1 and Sap2 evidently result in different electrostatic properties of the binding sites, primarily influencing the association step.

Spying on HIV with SPR

The application of surface plasmon resonance (SPR)-based optical biosensors has contributed extensively to our understanding of functional aspects of HIV. SPR biosensors allow the analysis of real-time interactions of any biomolecule, be it protein, nucleic acid, lipid, carbohydrate or small molecule, without the need for intrinsic or extrinsic probes. As such, the technology has been used to analyze molecular interactions associated with every aspect of the viral life cycle, from basic studies of binding events occurring during docking, replication, budding and maturation to applied research related to vaccine and inhibitory drug development. Along the way, SPR biosensors have provided a unique and detailed view into the inner workings of HIV.

Survey of the year 2001 commercial optical biosensor literature

We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.