Affinity Capillary Electrophoresis for the Screening of Novel Antimicrobial Targets

Current Trends in SPR Biosensing of SARS-CoV-2 Entry Inhibitors

The emerging risk of viral diseases has triggered the search for preventive and therapeutic agents. Since the beginning of the COVID-19 pandemic, greater efforts have been devoted to investigating virus entry mechanisms into host cells. The feasibility of plasmonic sensing technologies for screening interactions of small molecules in real time, while providing the pharmacokinetic drug profiling of potential antiviral compounds, offers an advantageous approach over other biophysical methods. This review summarizes recent advancements in the drug discovery process of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) inhibitors using Surface Plasmon Resonance (SPR) biosensors. A variety of SPR assay formats are discussed according to the binding kinetics and drug efficacies of both natural products and repurposed drugs. Special attention has been given to the targeting of antiviral agents that block the receptor binding domain of the spike protein (RBD-S) and the main protease (3CLpro) of SARS-CoV-2. The functionality of plasmonic biosensors for high-throughput screening of entry virus inhibitors was also reviewed taking into account experimental parameters (binding affinities, selectivity, stability), potential limitations and future applications.

Fragment Hit Discovery and Binding Site Characterization by Indirect Affinity Capillary Electrophoresis: Application to Factor XIIa

Fragment-based lead discovery is a usual strategy in drug discovery to identify innovative lead compounds. The success of this approach strongly relies on the capacity to detect weak binders and characterize their binding site. NMR and X-ray crystallography are the conventional technologies used to tackle this challenge. However, their large protein consumption and the cost of equipment reduce their accessibility. Here, an affinity capillary electrophoresis methodology was developed that enables the detection of mM binders, the determination of dissociation constants, and the characterization of the fragment binding site. On the basis of multiple equilibrium theory, dissociation constants in the μM-mM range were determined, and a new methodology is proposed to establish graphically if two fragments bind the same protein pocket. The applicability of this methodology was demonstrated experimentally on coagulation factor XIIa by evaluating pairs of fragments with expected behavior. This study reinforces the significance of using affinity capillary electrophoresis to gather valuable information for medicinal chemistry projects.

Systematic Screening of Viral Entry Inhibitors Using Surface Plasmon Resonance

Surface plasmon resonance (SPR) analytical method was initially used as biosensor for analyzing diverse biomolecular interactions and recently gained important place in the drug discovery. Here, I describe the procedures for screening of inhibitors against the viral proteins using the SPR. Using the described procedures, in the past, we were able to identify several antiviral products that interfere viral-host receptor proteins interactions.

Systematic screening of viral entry inhibitors using surface plasmon resonance

Viral binding and entry into host cells for various viruses have been studied extensively, yielding a detailed understanding of the overall viral entry process. As cell entry is an essential and requisite process by which a virus initiates infection, it is an attractive target for therapeutic intervention. The advantages of targeting viral entry are an extracellular target site, relatively easy access for biological interventions, and lower toxicity. Several cell-based strategies and biophysical techniques have been used to screen compounds that block viral entry. These studies led to the discovery of inhibitors against HIV, HCV, influenza, Ebola, and RSV. In recent years, several compounds screened by fragment-based drug discovery have been approved as drugs or are in the final stages of clinical trials. Among fragment screening technologies, surface plasmon resonance has been widely used because it provides accurate information on binding kinetics, allows real-time monitoring of ligand-drug interactions, requires very small sample amounts to perform analyses, and requires no modifications to or labeling of ligands. This review focuses on surface plasmon resonance-based schemes for screening viral entry inhibitors.

Recent advances in affinity capillary electrophoresis for binding studies

The present review covers recent advances and important applications of affinity capillary electrophoresis (ACE). It provides an overview about various ACE types, including ACE-MS, the multiple injection mode, the use of microchips and field-amplified sample injection-ACE. The most common scenarios of the studied affinity interactions are protein-drug, protein-metal ion, protein-protein, protein-DNA, protein-carbohydrate, carbohydrate-drug, peptide-peptide, DNA-drug and antigen-antibody. Approaches for the improvements of ACE in term of precision, rinsing protocols and sensitivity are discussed. The combined use of computer simulation programs to support data evaluation is presented. In conclusion, the performance of ACE is compared with other techniques such as equilibrium dialysis, parallel artificial membrane permeability assay, high-performance affinity chromatography as well as surface plasmon resonance, ultraviolet, circular dichroism, nuclear magnetic resonance, Fourier transform infrared, fluorescence, MS and isothermal titration calorimetry.

Fragment screening by SPR and advanced application to GPCRs

Surface plasmon resonance (SPR) is one of the primary biophysical methods for the screening of low molecular weight 'fragment' libraries, due to its low protein consumption and 'label-free' methodology. SPR biosensor interaction analysis is employed to both screen and confirm the binding of compounds in fragment screening experiments, as it provides accurate information on the affinity and kinetics of molecular interactions. The most advanced application of the use of SPR for fragment screening is against membrane protein drug targets, such G-protein coupled receptors (GPCRs). Biophysical GPCR assays using SPR have been validated with pharmacological measurements approximate to cell-based methods, yet provide the advantage of biophysical methods in their ability to measure the weak affinities of low molecular weight fragments. A number of SPR fragment screens against GPCRs have now been disclosed in the literature. SPR fragment screening is proving versatile to screen both thermostabilised GPCRs and solubilised wild type receptors. In this chapter, we discuss the state-of-the-art in GPCR fragment screening by SPR and the technical considerations in performing such experiments.

Affinity assays for decrypting protein targets of unknown function

The application of label-independent biophysical assays (affinity assays) to carefully selected libraries of biochemicals, natural products and known bioactive molecules generates a powerful tool to identify ligands indicative of protein function. Detection of ligand binding does not require the measurement of enzyme activity, thus every cofactor, ion, reactant or product might be identified separately. One such assay, ThermoFluor(®), monitors ligand perturbation of protein thermostability. In conjunction with a functional probe library (FPL), this assay has been used to decrypt the function of orphan proteins.:

Fragment screening using capillary electrophoresis (CEfrag) for hit identification of heat shock protein 90 ATPase inhibitors

CEfrag is a new fragment screening technology based on affinity capillary electrophoresis (ACE). Here we report on the development of a mobility shift competition assay using full-length human heat shock protein 90α (Hsp90α), radicicol as the competitor probe ligand, and successful screening of the Selcia fragment library. The CEfrag assay was able to detect weaker affinity (IC(50) >500 µM) fragments than were detected by a fluorescence polarization competition assay using FITC-labeled geldanamycin. The binding site of selected fragments was determined by co-crystallization with recombinant Hsp90α N-terminal domain and X-ray analysis. The results of this study confirm that CEfrag is a sensitive microscale technique enabling detection of fragments binding to the biological target in near-physiological solution.

Emerging role of surface plasmon resonance in fragment-based drug discovery

Surface plasmon resonance (SPR) offers a method of biophysical fragment screening that is fast, efficient, cost effective and accurate. SPR is increasingly being adopted as a secondary assay to validate fragment hits. Recently, technical advances have resulted in the emergence of SPR as a primary screening methodology for fragment-based drug discovery. Moreover, SPR biosensor assays can be developed for a wide range of proteins, including membrane proteins, such as G-protein-coupled receptors. In this review, we discuss the advantages and limitations of SPR fragment screening including experimental consideration of reducing false positive and false negative rates to a minimum. We discuss how ligand efficiency can be used both as a method to eliminate false positives and to understand which fragments in a library may be a source of false negatives.

Integration of fragment screening and library design

With more than 10 years of practical experience and theoretical analysis, fragment-based drug discovery (FBDD) has entered the mainstream of the pharmaceutical and biotech industries. An array of biophysical techniques has been used to detect the weak interaction between a fragment and the target. Each technique presents its own requirements regarding the fragment collection and the target; therefore, in order to optimize the potential of FBDD, the nature of the target should be a driving factor for simultaneous development of both the library and the screening technology. A roadmap is now available to guide fragment-to-lead evolution when structural information is available. The next challenge is to apply FBDD to targets for which high-resolution structural information is not available.

Implementation of chemometric methodology in ACE: Predictive investigation of protein–ligand binding

An ACE predictive investigation of protein-ligand binding using a highly effective chemometric response surface design technique is presented. Here, K(d) was estimated using one noninteracting standard which relates to changes in the electrophoretic mobility of carbonic anhydrase B (CAB, EC 4.2.1.1) on complexation with the ligand 4-carboxybenzenesulfonamide (CBSA) present in the electrophoresis buffer. Experimental factors including injection time, capillary length, and applied voltage were selected and tested at three levels in a Box-Behnken design. Statistical analysis results were used to create a mathematical model for response surface prediction via contour and surface plots at a given target response (K(d) = 1.19x10(-6) M). As expected, there were a number of predicted solutions that reached our target response based on the significance of each factor at appropriate levels. The adequacy of the model was validated by experimental runs with the predicted model solution (capillary length = 47 cm, voltage = 11 kV, injection time = 0.01 min) presented in detail as an example.

Crystal structure of S. aureus YlaN, an essential leucine rich protein involved in the control of cell shape

The crystal structure of a conserved leucine rich protein, YlaN, from Staphylococcus aureus has been determined by X-ray crystallography to 2.3 A resolution. Whilst the precise function of S. aureus YlaN is unknown its homologue in B. subtilis has been shown to be essential for cell survival and is thought to be involved in controlling cell shape. The structure of S. aureus YlaN provides the first view of its protein family, which reveals that it is a novel homodimer whose subunit architecture is comprised of an antiparallel 3 helix bundle reminiscent of the helical arrangements seen in leucine zipper proteins. Analysis of the pattern of sequence conservation on the structure has led to the identification of two connected solvent exposed patches of conserved residues in each subunit located at one end of but on opposite faces of the molecule. We suggest that YlaN has a binding role in the cell rather than a catalytic function and a search for its ligand is underway to accelerate its exploitation as a target for antibiotic discovery.

Chemical genetics: an evolving toolbox for target identification and lead optimization

Chemical genetics combines chemistry with biology as a means of exploring the function of unknown proteins or identifying the proteins responsible for a particular phenotype. Chemical genetics is thus a valuable tool in the identification of novel drug targets. This chapter describes the application of chemical genetics in traditional and systems-based approaches to drug target discovery and the tools/approaches that appear most promising for guiding future pharmaceutical development.

Universal screening methods and applications of ThermoFluor

The genomics revolution has unveiled a wealth of poorly characterized proteins. Scientists are often able to produce milligram quantities of proteins for which function is unknown or hypothetical, based only on very distant sequence homology. Broadly applicable tools for functional characterization are essential to the illumination of these orphan proteins. An additional challenge is the direct detection of inhibitors of protein-protein interactions (and allosteric effectors). Both of these research problems are relevant to, among other things, the challenge of finding and validating new protein targets for drug action. Screening collections of small molecules has long been used in the pharmaceutical industry as 1 method of discovering drug leads. Screening in this context typically involves a function-based assay. Given a sufficient quantity of a protein of interest, significant effort may still be required for functional characterization, assay development, and assay configuration for screening. Increasingly, techniques are being reported that facilitate screening for specific ligands for a protein of unknown function. Such techniques also allow for function-independent screening with better characterized proteins. ThermoFluor, a screening instrument based on monitoring ligand effects on temperature-dependent protein unfolding, can be applied when protein function is unknown. This technology has proven useful in the decryption of an essential bacterial enzyme and in the discovery of a series of inhibitors of a cancer-related, protein-protein interaction. The authors review some of the tools relevant to these research problems in drug discovery, and describe our experiences with 2 different proteins.

The impact of genomics on discovering drugs against infectious diseases

Genomics is accelerating the progress in data generation and interpretation in the global analyses of components of cells, including the spectrum of lipids, RNA, metabolites, proteins, mutational phenotypes or DNA methylation sites. Integration of the knowledge generated by these diverse strategies is predicted to have a tremendous impact on approaches to rational drug discovery against infectious diseases.

Conserved P-loop GTPases of unknown function in bacteria: an emerging and vital ensemble in bacterial physiology

Establishing the roles of conserved gene products in bacteria is of fundamental importance to our understanding of the core protein complement necessary to sustain cellular life. P-loop GTPases and related ATPases represent an abundant and remarkable group of proteins in bacteria that, in many cases, have evaded characterization. Here, efforts aimed at understanding the cellular function of a group of 8 conserved, poorly characterized genes encoding P-loop GTPases, era, obg, trmE, yjeQ, engA, yihA, hflX, ychF, and a related ATPase, yjeE, are reviewed in considerable detail. While concrete cellular roles remain elusive for all of these genes and considerable pleiotropy has plagued their study, experiments to date have frequently implicated the ribosome. In the case of era, obg, yjeQ, and engA, the evidence is most consistent with roles in ribosome biogenesis, though the prediction is necessarily putative. While the protein encoded in trmE clearly has a catalytic function in tRNA modification, the participation of its GTPase domain remains obscure, as do the functions of the remaining proteins. A full understanding of the cellular functions of all of these important proteins remains the goal of ongoing studies of cellular phenotype and protein biochemistry.

Recent applications of affinity interactions in capillary electrophoresis

Systems biology depends on a comprehensive assignment and characterization of the interactions of proteins and polypeptides (functional proteomics) and of other classes of biomolecules in a given organism. High‐capacity screening methods are in place for ligand capture and interaction screening, but a detailed dynamic characterization of molecular interactions under physiological conditions in efficiently separated mixtures with minimal sample consumption is presently provided only by electrophoretic interaction analysis in capillaries, affinity CE (ACE). This has been realized in different fields of biology and analytical chemistry, and the resulting advances and uses of ACE during the last 2.5 years are covered in this review. Dealing with anything from small divalent metal ions to large supramolecular assemblies, the applications of ACE span from low‐affinity binding of broad specificity being exploited in optimizing selectivity, e.g., in enantiomer analysis to miniaturized affinity technologies, e.g., for fast processing immunoassay. Also, approaches that provide detailed quantitative characterization of analyte–ligand interaction for drug, immunoassay, and aptamer development are increasingly important, but various approaches to ACE are more and more generally applied in biological research. In addition, the present overview emphasizes that distinct challenges regarding sensitivity, parallel processing, information‐rich detection, interfacing with MS, analyte recovery, and preparative capabilities remain. This will be addressed by future technological improvements that will ensure continuing new applications of ACE in the years to come.

Multiple-injection affinity capillary electrophoresis to examine binding constants between glycopeptide antibiotics and peptides

Multiple-injection affinity capillary electrophoresis (MIACE) was used to determine binding constants (K(b)) between vancomycin, ristocetin, and teicoplanin from Streptomyces orientalis, Nocardia lurida, and Actinoplanes teichomyceticus, respectively, and fluorenylmethoxycarbonyl (Fmoc)-(Gly, Ala, Val, and Phe)-D-Ala-D-Ala peptides. In this technique, separate plugs of sample containing non-interacting standards, peptide one, buffer, and peptide two, were injected into the capillary column and electrophoresed. Peptides migrate through the column at similar electrophoretic mobilities but remain as distinct zones due to the buffer plug between peptides. The electrophoresis is then carried out in an increasing concentration of antibiotic in the running buffer. Continued electrophoresis results in a shift in the migration time of the peptides upon binding to the antibiotic. Analysis of the change in the relative migration time ratio (RMTR) of the resultant complexes relative to the non-interacting standards, as a function of the concentration of antibiotic yields a value for K(b). MIACE is a versatile technique that can be used to measure affinity constants between ligands of similar relative molecular mass and charge without the need of separate binding experiments. The findings described, herein, demonstrate the advantages of using MIACE to estimate binding parameters between ligands and receptors.

Search of ligands for the amyloidogenic protein beta2-microglobulin by capillary electrophoresis and other techniques

Beta2-microglobulin (beta2-m) is a small amyloidogenic protein normally present on the surface of most nucleated cells and responsible for dialysis-related amyloidosis, which represents a severe complication of long-term hemodialysis. A therapeutic approach for this amyloidosis could be based on the stabilization of beta2-m through the binding to a small molecule, and consequent inhibition of protein misfolding and amyloid fibril formation. A few compounds have been described to weakly bind beta2-m, including the drug suramin. The lack of a binding site for nonpolypeptidic ligands on the beta2-m structure makes it difficult for both the identification of functional groups responsible for the binding and the search of hits to be optimized. The characterization of the binding properties of suramin for beta2-m by using three different techniques (surface plasmon resonance, affinity CE (ACE), ultrafiltration) is here described and the results obtained are compared. The common features of the chemical structures of the compounds known to bind the protein led us to select 200 sulfonated/suramin-like molecules from a wider chemical library on the basis of similarity rules, so as to possibly single out some interesting hits and to gain more information on the functional groups involved in the binding. The development of screening methods to test the compounds by using ultrafiltration and ACE is described.

An expression vector containing a rhamnose-inducible promoter provides tightly regulated gene expression in Burkholderia cenocepacia

Infection of the respiratory tract caused by Burkholderia cepacia complex poses a serious risk for cystic fibrosis (CF) patients due to the high morbidity and mortality associated with the chronic infection and the lack of efficacious antimicrobial treatments. A detailed understanding of the pathogenicity of B. cepacia complex infections is hampered in part by the limited availability of genetic tools and the inherent resistance of these isolates to the most common antibiotics used for genetic selection. In this study, we report the construction of an expression vector which uses the rhamnose-regulated P(rhaB) promoter of Escherichia coli. The functionality of the vector was assessed by expressing the enhanced green fluorescent protein (eGFP) gene (e-gfp) and determining the levels of fluorescence emission. These experiments demonstrated that P(rhaB) is responsive to low concentrations of rhamnose and it can be effectively repressed with 0.2% glucose. We also demonstrate that the tight regulation of gene expression by P(rhaB) promoter allows us to extend the capabilities of this vector to the identification of essential genes.

Capillary electrophoresis technologies for screening in drug discovery

The high separation efficiency of capillary electrophoresis (CE), combined with the high selectivity and sensitivity of mass spectrometry (MS) detection offers the potential of unique resolving power and high-throughput capacity to the analysis and structural identification of complex mixtures. Recent advances in CE-MS interfaces and commercially available 96-capillary instruments have made the implementation of routine CE methods for drug screening feasible.:

A phthalide with in vitro growth inhibitory activity from an oidiodendron strain

A screening campaign was implemented utilizing capillary electrophoresis as a primary assay to discover binders to the cancer target Akt1 from a crude natural extract library. Fungal extracts with binding activities were characterized for biochemical inhibition of Akt1 to phosphorylate the downstream substrate protein Bad. One of the crude extracts with bioactivity selected for isolation and structure elucidation from fermentation of the fungal culture Oidiodendron sp. F01895 yielded a new trihydroxy phthalide (1). The structure of 1 was determined by a combination of 1D and 2D NMR spectroscopic data along with high-resolution mass spectrometric data. Compound 1 displays inhibition of Akt1 biochemical activity in vitro and confers growth inhibition on some cancer-derived cell lines in culture.