Interaction of antagonists with calmodulin: insights from molecular dynamics simulations

Experiment and Simulation Reveal Residue Details for How Target Binding Tunes Calmodulin's Calcium-Binding Properties

We aim to elucidate the molecular mechanism of the reciprocal relation of calmodulin's (CaM) target binding and its affinity for calcium ions (Ca²⁺), which is central to decoding CaM-dependent Ca²⁺ signaling in a cell. We employed stopped-flow experiments and coarse-grained molecular simulations that learn the coordination chemistry of Ca²⁺ in CaM from first-principle calculations. The associative memories as part of the coarse-grained force fields built on known protein structures further influence CaM's selection of its polymorphic target peptides in the simulations. We modeled the peptides from the Ca²⁺/CaM-binding domain of Ca²⁺/CaM-dependent kinase II (CaMKII), CaMKIIp (293-310) and selected distinctive mutations at the N-terminus. Our stopped-flow experiments have shown that the CaM's affinity for Ca²⁺ in the bound complex of Ca²⁺/CaM/CaMKIIp decreased significantly when Ca²⁺/CaM bound to the mutant peptide (296-AAA-298) compared to that bound to the wild-type peptide (296-RRK-298). The coarse-grained molecular simulations revealed that the 296-AAA-298 mutant peptide destabilized the structures of Ca²⁺-binding loops at the C-domain of CaM (c-CaM) due to both loss of electrostatic interactions and differences in polymorphic structures. We have leveraged a powerful coarse-grained approach to advance a residue-level understanding of the reciprocal relation in CaM, that could not be possibly achieved by other computational approaches.

High-affinity tamoxifen analogues retain extensive positional disorder when bound to calmodulin

Using a combination of NMR and fluorescence measurements, we have investigated the structure and dynamics of the complexes formed between calcium-loaded calmodulin (CaM) and the potent breast cancer inhibitor idoxifene, a derivative of tamoxifen. High-affinity binding (K d ∼ 300  nM) saturates with a 2 : 1 idoxifene : CaM complex. The complex is an ensemble where each idoxifene molecule is predominantly in the vicinity of one of the two hydrophobic patches of CaM but, in contrast with the lower-affinity antagonists TFP, J-8, and W-7, does not substantially occupy the hydrophobic pocket. At least four idoxifene orientations per domain of CaM are necessary to satisfy the intermolecular nuclear Overhauser effect (NOE) restraints, and this requires that the idoxifene molecules switch rapidly between positions. The CaM molecule is predominantly in the form where the N and C-terminal domains are in close proximity, allowing for the idoxifene molecules to contact both domains simultaneously. Hence, the 2 : 1 idoxifene : CaM complex illustrates how high-affinity binding occurs without the loss of extensive positional dynamics.

The chemosensitizing agent lubeluzole binds calmodulin and inhibits Ca(2+)/calmodulin-dependent kinase II

An affinity capillary electrophoresis (ACE) method to estimate apparent dissociation constants between bovine brain calmodulin (CaM) and non-peptidic ligands was developed. The method was validated reproducing the dissociation constants of a number of well-known CaM ligands. In particular, the potent antagonist 125-C9 was ad hoc synthesized through an improved synthetic procedure. The ACE method was successfully applied to verify CaM affinity for lubeluzole, a well-known neuroprotective agent recently proved useful to potentiate the activity of anti-cancer drugs. Lubeluzole was slightly less potent than 125-C9 (Kd = 2.9 ± 0.7 and 0.47 ± 0.06 μM, respectively) and displayed Ca(2+)/calmodulin-dependent kinase II (CaMKII) inhibition (IC50 = 40 ± 1 μM). Possible binding modes of lubeluzole to CaM were explored by docking studies based on the X-ray crystal structures of several trifluoperazine-CaM complexes. An estimated dissociation constant in good agreement with the experimental one was found and the main aminoacidic residues and interactions contributing to complex formation were highlighted. The possibility that interference with Ca(2+) pathways may contribute to the previously observed chemosensitizing effects of lubeluzole on human ovarian adenocarcinoma and lung carcinoma cells are discussed.

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.

Allosteric effects of the antipsychotic drug trifluoperazine on the energetics of calcium binding by calmodulin

Trifluoperazine (TFP; Stelazine) is an antagonist of calmodulin (CaM), an essential regulator of calcium-dependent signal transduction. Reports differ regarding whether, or where, TFP binds to apo CaM. Three crystallographic structures (1CTR, 1A29, and 1LIN) show TFP bound to (Ca(2+))(4)-CaM in ratios of 1, 2, or 4 TFP per CaM. In all of these, CaM domains adopt the "open" conformation seen in CaM-kinase complexes having increased calcium affinity. Most reports suggest TFP also increases calcium affinity of CaM. To compare TFP binding to apo CaM and (Ca(2+))(4)-CaM and explore differential effects on the N- and C-domains of CaM, stoichiometric TFP titrations of CaM were monitored by (15)N-HSQC NMR. Two TFP bound to apo CaM, whereas four bound to (Ca(2+))(4)-CaM. In both cases, the preferred site was in the C-domain. During the titrations, biphasic responses for some resonances suggested intersite interactions. TFP-binding sites in apo CaM appeared distinct from those in (Ca(2+))(4)-CaM. In equilibrium calcium titrations at defined ratios of TFP:CaM, TFP reduced calcium affinity at most levels tested; this is similar to the effect of many IQ-motifs on CaM. However, at the highest level tested, TFP raised the calcium affinity of the N-domain of CaM. A model of conformational switching is proposed to explain how TFP can exert opposing allosteric effects on calcium affinity by binding to different sites in the "closed," "semi-open," and "open" domains of CaM. In physiological processes, apo CaM, as well as (Ca(2+))(4)-CaM, needs to be considered a potential target of drug action.