A novel hypothesis for the binding mode of HERG channel blockers

doi:10.1016/j.bbrc.2006.03.146

Biochemical and Biophysical Research Communications

Volume 344, Issue 1, 26 May 2006, Pages 72-78

https://doi.org/10.1016/j.bbrc.2006.03.146 Get rights and content

Abstract

We present a new docking model for HERG channel blockade. Our new model suggests three key interactions such that (1) a protonated nitrogen of the channel blocker forms a hydrogen bond with the carbonyl oxygen of HERG residue T623; (2) an aromatic moiety of the channel blocker makes a π–π interaction with the aromatic ring of HERG residue Y652; and (3) a hydrophobic group of the channel blocker forms a hydrophobic interaction with the benzene ring of HERG residue F656. The previous model assumes two interactions such that (1) a protonated nitrogen of the channel blocker forms a cation-π interaction with the aromatic ring of HERG residue Y652; and (2) a hydrophobic group of the channel blocker forms a hydrophobic interaction with the benzene ring of HERG residue F656. To test these models, we classified 69 known HERG channel blockers into eight binding types based on their plausible binding modes, and further categorized them into two groups based on the number of interactions our model would predict with the HERG channel (two or three). We then compared the pIC₅₀ value distributions between these two groups. If the old hypothesis is correct, the distributions should not differ between the two groups (i.e., both groups show only two binding interactions). If our novel hypothesis is correct, the distributions should differ between Groups 1 and 2. Consistent with our hypothesis, the two groups differed with regard to pIC₅₀, and the group having more predicted interactions with the HERG channel had a higher mean pIC₅₀ value. Although additional work will be required to further validate our hypothesis, this improved understanding of the HERG channel blocker binding mode may help promote the development of in silico predictions methods for identifying potential HERG channel blockers.

Section snippets

Materials and methods

Homology modeling. A homology model of the HERG potassium channel was built on the basis of the 1.7 Å crystal structure (PDB ID code: 1R3J) of the KvAP channel [18], using the homology modeling program, MODELLER v8.0 [19]. A long stretch of amino acids (M579–G603), located at the third extracellular loop of the HERG channel, was not included for the modeling because this region was not present in the template structure and does not appear to be involved in the drug-induced inhibition of the HERG

Results and discussion

To gain new insights into the mechanism(s) by which small molecule inhibitors block HERG channels, we performed a molecular docking simulation. We first built a homology model of the HERG channel based on the KvAP channel structure. We then performed virtual docking of clozapine in the putative binding pocket of the model channel, using the GOLD v2.2 docking program. Our best docking result is shown in Fig. 1. In this prediction, the clozapine made contacts with the S6 transmembrane domain and

Acknowledgment

This work was supported by grants (2003-307 and 2004-307) from the Asan Institute for Life Sciences, Seoul, Korea.

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Citation Excerpt :
The binding site reports published showed that the residues such as T623 (tryptophan), Y652 (tyrosine) and F656 (phenylalanine) are predominantly present in the active site. These aromatic amino acids interact with the aromatic ring in the molecules through π-π and hydrophobic interactions and the polar groups in the molecules interact with the carbonyl groups in the residue T623 [20–24,41,69]. These studies concluded that the quantitative and qualitative models provided valuable information on the structural pattern and properties required for the hERG ion channel blocking activity.
The development of novel bioactive molecules without hERG ion channel blocking activities is one of the important tasks for the drug discovery scientists. Both experimental and in silico techniques are applied for screening/assaying of novel molecules and existing molecules against hERG ion channel to study its cardiotoxicity. Hence, in the present investigation, QSAR and multialgorithm based classification analysis such as Random Forest (RF), Decision Tree (DT), Support Vector Machine (SVM) and Naive Bayesian (BN) were performed on the data set possessed hERG ion channel blocking activity using different variable (MOE-descriptors and MACCS Fingerprints). The models developed with the MLR and the machine learning techniques provided significant results which were confirmed by their acceptable statistical parameter values. Further, the sum of ranking differences (SRDs) calculated for the models showed that the Model 6-MOE, Model 7-MOE, Model 4-SVM, Model 7-SVM and Model 9-SVM are having smaller SRD values and are placed as top ranked models. The MOE-descriptors and the MACCS Fingerprints contributed in these models revealed that the volume-surface area properties, negative charge on the vdW surface area, number of fluorine atom, number of aromatic ring/atoms, less number of oxygen and hydrogen bonding and donor atoms are contributed for the activity. Furthermore the MACCS Fingerprints such as MACCSFP42, MACCSFP85, MACCSFP122 and MACCSFP139 also explain the polarity of the compounds. The structural pattern analysis with the MACCS Fingerprint revealed that the aromatic rings responsible for hydrophobicity, halogen and heteroatoms provide polarity to the compounds and the asymmetric carbon make the compounds are highly flexible. These studies concluded that the derived results can be used for prediction of hERG ion channel blocking activity of novel molecules.
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Jingzhaotoxin-I, -III, -IV, -XIII, and −35 (JZTX-I, -III, -IV, -XIII, and −35), gating modifier toxins isolated from the venom of the Chinese tarantula Chilobrachys Jingzhao, were reported to act on cardiac sodium channels and Kv channels. JZTX-I and JZTX-XIII inhibited the hERG channel with the IC₅₀ value of 626.9 nM and 612.6 nM, respectively. JZTX-III, -IV, and −35 share high sequence similarity with JZTX-I and JZTX–XIII, but they showed much lower affinity on the hERG channel compared with JZTX-I and JZTX-XIII. The inhibitory potency of the above five toxins on the hERG channel was not in accordance with their affinity on the Nav1.5 and Kv2.1 channels, indicating that the bioactive surfaces of the five toxins interacting with hERG, Nav1.5 and Kv2.1 are at least in part different. Structure-function analysis of the gating modifier toxins suggested that the functional bioactive surface binding to the hERG channel consists of a conserved hydrophobic patch, surrounding acidic residues (Glu10 in JZTX-XIII, Glu11 in JZTX-I), and basic residues which may be different from residues binding to the Kv2.1 channel.
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All along the drug development process, one of the most frequent adverse side effects, leading to the failure of drugs, is the cardiac arrhythmias. Such failure is mostly related to the capacity of the drug to inhibit the human ether-à-go-go-related gene (hERG) cardiac potassium channel. The early identification of hERG inhibition properties of biological active compounds has focused most of attention over the years. In order to prevent the cardiac side effects, a great number of in silico, in vitro and in vivo assays have been performed. The main goal of these studies is to understand the reasons of these effects, and then to give information or instructions to scientists involved in drug development to avoid the cardiac side effects. To evaluate anticipated cardiovascular effects, early evaluation of hERG toxicity has been strongly recommended for instance by the regulatory agencies such as U.S. Food and Drug Administration (FDA) and European Medicines Agency (EMA). Thus, following an initial screening of a collection of compounds to find hits, a great number of pharmacomodulation studies on the novel identified chemical series need to be performed including activity evaluation towards hERG. We provide in this concise review clear guidelines, based on described examples, illustrating successful optimization process to avoid hERG interactions as cases studies and to spur scientists to develop safe drugs.
Removal of hERG potassium channel affinity through introduction of an oxygen atom: Molecular insights from structure-activity relationships of strychnine and its analogs
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hERG blockers which have a basic nitrogen prefer to form a cation–π interaction with the aromatic ring of hERG residue Y652. Some blockers which have powerful hydrophobic groups may preferentially form a hydrophobic interaction with the benzene ring of hERG residue F656 (Choe et al., 2006; Fernandez et al., 2004). In our study, we constructed six alanine mutants (T623A, S624A, V625A, G648A, Y652A, F656A) and tested the inhibitory potency of strychnine and brucine on the above six mutants.
Nux vomica has been effectively used in Traditional Chinese Medicine. The processing of Nux vomica is necessary to reduce toxicity before it can be used in clinical practice. However, the mechanism for processing detoxification is unclear. hERG channels have been subjected to a routine test for compound cardiac toxicity in the drug development process. Therefore, we examined the effects and mechanisms of strychnine and brucine, two main ingredients of Nux vomica, and their N-oxides on hERG channels. Strychnine and brucine exhibited concentration-dependent inhibition of hERG channels with IC₅₀ values of 25.9 μM and 44.18 μM, respectively. However, their nitrogen oxidative derivatives produced by processing of Nux vomica, strychnine N-oxide and brucine N-oxide, lost their activity on hERG channels. Compared to their parent compounds, only an oxygen atom was introduced in the nitrogen oxidative isoforms to compensate for the N⁺ − charge, suggesting that the protonated nitrogen is the key group for strychnine and brucine binding to hERG channel. Alanine-mutagenesis identified Y652 is the most important residue for strychnine and brucine binding to hERG channel. Y652A mutation increased the IC₅₀ for strychnine and brucine by 21.64-fold and 29.78-fold that of WT I_hERG, respectively. Docking simulations suggested that the protonated nitrogen of strychnine and brucine formed a cation–π interaction with the aromatic ring of Y652. This study suggests that introduction of an oxygen to compensate for the N⁺ − charge could be a useful strategy for reducing hERG potency and increasing the safety margin of alkaloid-type compounds in drug development.
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2017, European Journal of Pharmaceutical Sciences
Coumarins have received a considerable attention in the last three decades as the lead structures for the discovery of orally administrated chemotherapeutics. Despite of the large amounts of in vitro activity information, relatively a little is known about their bioavailability in vivo. This paper presents an evaluation of drug-likeness of 31 coumarin derivatives on the basis of Lipinski's rule of five, and computed ADMET parameters (adsorption, distribution, metabolism, elimination and toxicity). Nine compounds which were predicted as showing the cardiotoxicity, were examined as hERG K⁺ channel blockers using in silico approach. Additionally, an impact of the acetyl group at benzene ring on pharmacokinetic profile was scrutinized for the tested coumarin derivatives. None of the analyzed coumarins violated the Lipinski's rule of five for orally administered drugs, and all tested compounds will remain in the qualitative likelihood of crossing the blood-brain barrier. 7-O-Alkilaminocoumarins showed no hepatotoxicity, but introduction of the nitrile or the amidine groups increased the levels of the hepatoxicity markers. Computed parameters of toxicity revealed cardiotoxic potency of twenty-five tested compounds. The proposed hERG K⁺ channel binding simulations helped in the understanding the molecular basis of coumarins cardiotoxicity. The presented theoretical studies explained some aspects of coumarin pharmacokinetics and identified the positive effect of the acetoxy substituent on the tested parameters.

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A novel hypothesis for the binding mode of HERG channel blockers

Abstract

Section snippets

Materials and methods

Results and discussion

Acknowledgment

Cell

FEBS Lett.

Cell Calcium

Eur. J. Pharmacol.

J. Biomol. Screen

Bioorg. Med. Chem. Lett.

Drug Discov. Today

J. Biol. Chem.

Trends Pharmacol. Sci.

J. Mol. Biol.

J. Mol. Biol.

J. Biol. Chem.

Tissue and species distribution of mRNA for the IKr-like K+ channel, erg

Circ. Res.

Tissue and species distribution of mRNA for the IKr-like K⁺ channel, erg