Competitive Binding Assay Using Fluorescence Resonance Energy Transfer for the Identification of Calmodulin Antagonists

Mobility capillary electrophoresis-native mass spectrometry reveals the dynamic conformational equilibrium of calmodulin and its complexes

Benefitting from the rapid evolution of artificial intelligence and structural biology, an expanding collection of high-resolution protein structures has greatly improved our understanding of protein functions. Yet, proteins are inherently flexible, and these static structures can only offer limited snapshots of their true dynamic nature. The conformational and functional changes of calmodulin (CaM) induced by Ca2+ binding have always been a focus of research. In this study, the conformational dynamics of CaM and its complexes were investigated using a mobility capillary electrophoresis (MCE) and native mass spectrometry (native MS) based method. By analyzing the ellipsoidal geometries of CaM in the solution phase at different Ca2+ concentrations, it is interesting to discover that CaM molecules, whether bound to Ca2+ or not, possess both closed and open conformations. Moreover, each individual CaM molecule actively "jumps" (equilibrium exchange) between these two distinct conformations on a timescale ranging from milli- to micro-seconds. The binding of Ca2+ ions did not affect the structural dynamics of CaM, while the binding of a peptide ligand would stabilize CaM, leading to the observation of a single, compact conformation of the resulting protein complex. A target recognition mechanism was also proposed based on these new findings, suggesting that CaM's interaction with targets may favor a conformational selection model. This enriches our understanding of the binding principles between CaM and its numerous targets.

Unraveling the unexpected aggregation behavior of Pyrazole-Based compounds Targeting Mycobacterium tuberculosis UDP-Galactopyranose mutase

A pyrazole-based compound, MS208, was previously identified as an inhibitor of UDP-Galactopyranose Mutase from Mycobacterium tuberculosis (MtUGM). Targeting this enzyme is a novel therapeutic strategy for the development of new antituberculosis agents because MtUGM is an essential enzyme for the bacterial cell wall synthesis and it is not present in human. It was proposed that MS208 targets an allosteric site in MtUGM as MS208 followed a mixed inhibition model. DA10, an MS208 analogue, showed competitive inhibition rather than mixed inhibition. In this paper, we have used an integrated biophysical approach, including thermal shift assays, dynamic light scattering and nuclear magnetic resonance experiments, to show that MS208 and many analogues displayed unexpected aggregation behavior against MtUGM.

Bisindolylmaleimides New Ligands of CaM Protein

In the present study, we reported the interactions at the molecular level of a series of compounds called Bisindolylmaleimide, as potential inhibitors of the calmodulin protein. Bisindolylmaleimide compounds are drug prototypes derived from Staurosporine, an alkaloid with activity for cancer treatment. Bisindolylmaleimide compounds II, IV, VII, X, and XI, are proposed and reported as possible inhibitors of calmodulin protein for the first time. For the above, a biotechnological device was used (fluorescent biosensor hCaM M124C-mBBr) to directly determine binding parameters experimentally (K_d and stoichiometry) of these compounds, and molecular modeling tools (Docking, Molecular Dynamics, and Chemoinformatic Analysis) to carry out the theoretical studies and complement the experimental data. The results indicate that this compound binds to calmodulin with a K_d between 193–248 nM, an order of magnitude lower than most classic inhibitors. On the other hand, the theoretical studies support the experimental results, obtaining an acceptable correlation between the ΔG_Experimental and ΔG_Theoretical (r² = 0.703) and providing us with complementary molecular details of the interaction between the calmodulin protein and the Bisindolylmaleimide series. Chemoinformatic analyzes bring certainty to Bisindolylmaleimide compounds to address clinical steps in drug development. Thus, these results make these compounds attractive to be considered as possible prototypes of new calmodulin protein inhibitors.

Fluorescence Resonance Energy Transfer Microscopy for Measuring Chromatin Complex Structure and Dynamics

The Polycomb group (PcG) proteins form regulatory complexes that modify the chromatin structure and silence their target genes. Recent works have found that the composition of Polycomb complexes is highly dynamic. Defining the different protein components of each complex is fundamental for better understanding their biological functions. Fluorescent resonance energy transfer (FRET) is a powerful tool to measure protein-protein interactions, in nanometer order and in their native cellular environment. Here we describe the preparation and execution of a typical FRET experiment using CFP-tagged protein as donor and YFP-tagged protein as acceptor. We further show that FRET can be used in a competition assay to measure binding affinities of different components of the same chromatin complex.

Screening calmodulin-binding ligands using intensity-fading matrix-assisted laser desorption/ionization mass spectrometry

RATIONALE

Calmodulin (CaM) plays an important role in the regulation of metabolism, cytoskeleton and cell proliferation. CaM antagonists are a class of drugs that can bind to CaM and modulate the interactions between CaM and their target biological processes. Screening new calmodulin antagonists and developing novel methods for detecting calmodulin ligands are important for developing novel anti-cancer drugs that bind specifically to CaM.

METHODS

An intensity-fading matrix-assisted laser desorption/ionization mass spectrometry (IF-MALDI-MS) method for screening calmodulin ligands was established, with the non-binding drug propranolol as the internal control. The experimental sample was prepared by mixing the positive ligand trifluoperazine (or chlorpromazine), propranolol and Ca(2+)-CaM. The control sample was treated in the same way without the addition of CaM. The experimental and control samples were both analyzed by MALDI-MS. Based on the relative intensity fading (IF) of the ligand to propranolol, the MS conditions were optimized and then used to study the binding of eight alkaloids and calmodulin. Competitive experiments were performed in a similar way by adding two drugs to compare their binding affinities with calmodulin.

RESULTS

The matrix 2,6-dihydroxyacetophenone (DHAP) was suitable for detecting calmodulin ligands. Compared with propranolol, the relative intensities of six free drugs (berbamine, tetrandrine, papaverine, reserpine, brucine and tetrahydropalmatine) clearly faded after the addition of calmodulin, indicating that they can bind with CaM. The other two alkaloids (strychnine and piperine) had no or weak interaction with the target protein. Based on the data from the competitive binding experiments, the binding affinities of five drugs to calmodulin were obtained in the order: tetrandrine > trifluoperazine > berbamine > chlorpromazine > imipramine.

CONCLUSIONS

The IF-MALDI-MS method was successfully applied to screen novel calmodulin agents at both qualitative and semiquantitative levels. The new ligands may be novel leads for CaM antagonists.

Atomic force microscopy study of the conformational change in immobilized calmodulin

Maintaining the biological functionality of immobilized proteins is the key to the success of numerous protein-based biomedical devices. To that end, we studied the conformational change in calmodulin (CaM) immobilized on chemical patterns. 1-Cysteine-mutated calmodulin was immobilized on a mercapto-terminated surface through cysteine-Hg-mercapto coupling. Utilizing atomic force microscopy (AFM), the average height of immobilized calmodulin was determined to be 1.87 ± 0.19 nm. After incubation in EGTA solution, the average height of the protein changed to 2.26 ± 0.21 nm, indicating the conformational change of CaM to Apo-CaM. Immobilized CaM also demonstrated a conformational change upon the reaction with known calmodulin antagonist chlorpromazine (CPZ). After incubation in CPZ solution, the average height of CPZ-bound CaM increased to 2.32 ± 0.20 nm, demonstrating that immobilized CaM has a similar response to that in bulk solution. These results show that the immobilization of calmodulin on a solid support does not interfere with the ability of the protein to bind calcium and calmodulin antagonists. Our results demonstrate the feasibility of employing AFM to probe and understand protein conformational changes.

Photophysical characterization of a FRET system using tailor-made DNA oligonucleotide sequences

We have carried out a detailed photophysical study of the FRET D/A pair consisting of a carbostyril donor and a Ru(II)bathophenanthroline complex acceptor in double-stranded synthetic DNA. Altogether 13 different double-stranded 30 base pair DNAs showing small incremental differences in the distances between donor and acceptor were synthesized. Using the fluorescence of the donor as well as of the acceptor, D/A separations were determined and compared to those derived from a well-established model for DNA distance calculations. The model calculations and anisotropy studies revealed that the donor can nearly be seen as a free rotator allowing the application of the established FRET data evaluation.

A whole-cell assay for the high throughput screening of calmodulin antagonists

Cell-based screening systems for pharmaceuticals are desired over molecular biosensing systems because of the information they provide on toxicity and bioavailability. However, the majority of sensing systems developed are molecular biosensing type screening systems and cannot be easily adapted to cell-based screening. In this study, we demonstrate that protein-based molecular sensing systems that employ a fluorescent protein as a signal transducer are amenable to cell-based sensing by expressing the protein molecular sensing system in the cell and employing these cells for screening of desired molecules. To achieve this, we expressed a molecular sensing system based on the fusion protein of calmodulin (CaM) and enhanced green fluorescent protein (EGFP) in bacterial cells, and utilized these cells for the screening of CaM antagonists. In the presence of Ca(2+), CaM undergoes a conformational change exposing a hydrophobic pocket that interacts with CaM-binding proteins, peptides, and drugs. This conformational change induced in CaM leads to a change in the microenvironment of EGFP, resulting in a change in its fluorescence intensity. The observed change in fluorescence intensity of EGFP can be correlated to the concentration of the analyte present in the sample. Dose-response curves for various tricyclic antidepressants were generated using cells containing CaM-EGFP fusion protein. Additionally, we demonstrate the versatility of our system for studying protein-protein interactions by using cells to study the binding of a peptide to CaM. The study showed that the CaM-EGFP fusion protein within the intact cells responds similarly to that of the isolated fusion protein, hence eliminating the need for any isolation and purification steps. We have demonstrated that this system can be used for the rapid screening of various CaM antagonists that are potential antipsychotic drugs.

Use of a fluorescent polarization based high throughput assay to identify new Calmodulin ligands

In order to develop a fluorescence polarization (FP) assay for calcium binding proteins, a fluorescent peptides based library of 1328 compounds has been synthesized. The use of this library has been validated by setting up a FP-high-throughput screening (FP-HTS) assay for calmodulin using the synthetic gene product (synCaM). With this assay, a set of 880 FDA approved compounds was screened. Besides the promazine class, we discovered two new classes of compounds that interact with calmodulin in a calcium dependent manner. One class has compounds with anti-histaminic/spasmolytic activities, and the other one are detergents with antibacterial activities.