Pharmacophore modelling of vanillin derivatives, favipiravir, chloroquine, hydroxychloroquine, monolaurin and tetrodotoxin as MPro inhibitors of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2).

OBJECTIVES: The aim of this study was to use Ligand-based pharmacophore modelling approach for four established antiviral drugs, namely remdesivir, lopinavir, ritonavir and hydroxychloroquine for COVID-19 inhibitors as training sets. In this study Twenty vanillin derivatives together with monolaurin and tetrodotoxin were used as test sets to evaluate as potential SARS-CoV-2 inhibitors. The Structure-based pharmacophore modelling approach was also performed using 5RE6, 5REX and 5RFZ in order to analyse the binding site and ligand-protein complex interactions. RESULTS: The pharmacophore modelling mode of 5RE6 displayed two Hydrogen Bond Acceptors (HBA) and one Hydrophobic (HY) interaction. Besides, the pharmacophore model of 5REX showed two HBA and two HY interactions. Finally, the pharmacophore model of 5RFZ showed three HBA and one HY interaction. Based on ligand-based approach, 20 Schiff-based vanillin derivatives, showed strong MPro inhibition activity. This was due to their good alignment and common features to PDB-5RE6. Similarly, monolaurin and tetrodotoxin displayed some significant activity against SARS-CoV-2. From structure-based approach, vanillin derivatives (1) to (12) displayed some potent MPro inhibition against SARS-CoV-2. Favipiravir, chloroquine and hydroxychloroquine also showed some significant MPro inhibition.

Synthesis of C12-Keto Saxitoxin Derivatives with Unusual Inhibitory Activity Against Voltage-Gated Sodium Channels.

A novel series of C12-keto-type saxitoxin (STX) derivatives bearing an unusual nonhydrated form of the ketone at C12 has been synthesized, and their NaV -inhibitory activity has been evaluated in a cell-based assay as well as whole-cell patch-clamp recording. Among these compounds, 11-benzylidene STX (3 a) showed potent inhibitory activity against neuroblastoma Neuro 2A in both cell-based and electrophysiological analyses, with EC50 and IC50 values of 8.5 and 30.7 nm, respectively. Interestingly, the compound showed potent inhibitory activity against tetrodotoxin-resistant subtype of NaV 1.5, with an IC50 value of 94.1 nm. Derivatives 3 a-d and 3 f showed low recovery rates from NaV 1.2 subtype (ca 45-79 %) compared to natural dcSTX (2), strongly suggesting an irreversible mode of interaction. We propose an interaction model for the C12-keto derivatives with NaV in which the enone moiety in the STX derivatives 3 works as Michael acceptor for the carboxylate of Asp1717 .

Toxin and toxicity identification of mangrove horseshoe crab Carcinoscorpius rotundicauda collected from South China.

The presence of paralytic shellfish poisoning (PSP), diarrhetic Shellfish Poisoning (DSP), tetrodotoxin (TTX) and its analogues (11-oxoTTX, 4.9-anhydro-11-oxoTTX, 4.9-anhydroTTX, 5-deoxyTTX, 5.11-dideoxyTTX, 5.6.11-trideoxyTTX and 4.9-anhydro-5.6.11-trideoxy TTX) were initially investigated in Carcinoscorpius rotundicauda collected from south China with Liquid chromatography-tandem mass spectrometry (LC-MS-MS) and mouse bioassay. The TTX toxicity was 10.8 ±â€¯3.9 MU/g muscle, 6.3 ±â€¯0.6 MU/g viscera and 6.3 ±â€¯0.6 MU/g eggs in mean value. Merely dcGTX2 and dcSTX were detected in ten Specimens, ranging from 0.01 to 0.77 µg/g. Analyses suggested that these Carcinoscorpius rotundicauda contain TTX and its analogues as the major toxin and PSPs as the minor, respectively. Besides, no DSPs were found.

Structures of human Nav1.7 channel in complex with auxiliary subunits and animal toxins.

Voltage-gated sodium channel Nav1.7 represents a promising target for pain relief. Here we report the cryo-electron microscopy structures of the human Nav1.7-ß1-ß2 complex bound to two combinations of pore blockers and gating modifier toxins (GMTs), tetrodotoxin with protoxin-II and saxitoxin with huwentoxin-IV, both determined at overall resolutions of 3.2 angstroms. The two structures are nearly identical except for minor shifts of voltage-sensing domain II (VSDII), whose S3-S4 linker accommodates the two GMTs in a similar manner. One additional protoxin-II sits on top of the S3-S4 linker in VSDIV The structures may represent an inactivated state with all four VSDs "up" and the intracellular gate closed. The structures illuminate the path toward mechanistic understanding of the function and disease of Nav1.7 and establish the foundation for structure-aided development of analgesics.

Development and validation of a maleimide-based enzyme-linked immunosorbent assay for the detection of tetrodotoxin in oysters and mussels.

The recent detection of tetrodotoxins (TTXs) in puffer fish and shellfish in Europe highlights the necessity to monitor the levels of TTXs in seafood by rapid, specific, sensitive and reliable methods in order to protect human consumers. A previous immunoassay for TTX detection in puffer fish, based on the use of self-assembled monolayers (SAMs) for the immobilization of TTX on maleimide plates (mELISA), has been modified and adapted to the analysis of oyster and mussel samples. Changing dithiol for cysteamine-based SAMs enabled reductions in the assay time and cost, while maintaining the sensitivity of the assay. The mELISA showed high selectivity for TTX since the antibody did not cross-react with co-occurring paralytic shellfish poisoning (PSP) toxins and no interferences were observed from arginine (Arg). Moreover, TTX-coated maleimide plates stored for 3 months at -20°C and 4°C were stable, thus when pre-prepared, the time to perform the assay is reduced. When analyzing shellfish samples, matrix effects and toxin recovery values strongly depended on the shellfish type and the sample treatment. Blank oyster extracts could be directly analyzed without solid-phase extraction (SPE) clean-up, whereas blank mussel extracts showed strong matrix effects and SPE and subsequent solvent evaporation were required for removal. However, the SPE clean-up and evaporation resulted in toxin loss. Toxin recovery values were taken as correction factors (CFs) and were applied to the quantification of TTX contents in the analysis of naturally-contaminated shellfish samples by mELISA. The lowest effective limits of detection (eLODs) were about 20 and 50µg/kg for oyster extracts without and with SPE clean-up, respectively, and about 30µg/kg for mussel extracts with both protocols, all of them substantially below the eLOD attained in the previous mELISA for puffer fish (230µg/kg). Analysis of naturally-contaminated samples by mELISA and comparison with LC-MS/MS quantifications demonstrated the viability of the approach. This mELISA is a selective and sensitive tool for the rapid detection of TTX in oyster and mussel samples showing promise to be implemented in routine monitoring programs to protect human health.

Ultrasensitive Phototriggered Local Anesthesia.

An injectable local anesthetic producing repeatable on-demand nerve block would be desirable for pain management. Here we present a phototriggerable device to achieve repeatable and adjustable on-demand local anesthesia in superficial or deep tissues, consisting of gold nanorods attached to low temperature sensitive liposomes (LTSL). The particles were loaded with tetrodotoxin and dexmedetomidine. Near-infrared light (NIR, 808 nm, continuous wave) could heat gold nanorods at low fluence (short duration and low irradiance), leading to rapid release of payload. In vivo, 1-2 min of irradiation at ≤272 mW/cm2 produced repeatable and adjustable on-demand infiltration anesthesia or sciatic nerve blockade with minimal toxicity. The nerve block intensity and duration correlated with the irradiance and duration of the applied light.

Postnatal development of the dopaminergic signaling involved in the modulation of intestinal motility in mice.

BACKGROUND: Since antidopaminergic drugs are pharmacological agents employed in the management of gastrointestinal motor disorders at all ages, we investigated whether the enteric dopaminergic system may undergo developmental changes after birth. METHODS: Intestinal mechanical activity was examined in vitro as changes in isometric tension. RESULTS: In 2-d-old (P2) mice, dopamine induced a contractile effect, decreasing in intensity with age, replaced, at the weaning (day 20), by a relaxant response. Both responses were tetrodotoxin (TTX)-insensitive. In P2, dopaminergic contraction was inhibited by D1-like receptor antagonist and mimicked by D1-like receptor agonist. In 90-d-old (P90) mice, the relaxation was reduced by both D1- and D2-like receptor antagonists, and mimicked by D1- and D2-like receptor agonists. In P2, contraction was antagonized by phospholipase C inhibitor, while in P90 relaxation was antagonized by adenylyl cyclase inhibitor and potentiated by phospholipase C inhibitor. The presence of dopamine receptors was assessed by immunofluorescence. Quantitative real-time polymerase chain reaction (qRT-PCR) revealed a significant increase in D1, D2, and D3 receptor expression in proximal intestine with the age. CONCLUSION: In mouse small intestine, the response to dopamine undergoes developmental changes shifting from contraction to relaxation at weaning, as the consequence of D2-like receptor recruitment and increased expression of D1 receptors.

Phototriggered Local Anesthesia.

We report a phototriggerable formulation enabling in vivo repeated and on-demand anesthesia with minimal toxicity. Gold nanorods (GNRs) that can convert near-infrared (NIR) light into heat were attached to liposomes (Lip-GNRs), enabling light-triggered phase transition of their lipid bilayers with a consequent release of payload. Lip-GNRs containing the site 1 sodium channel blocker tetrodotoxin and the α2-adrenergic agonist dexmedetomidine (Lip-GNR-TD) were injected subcutaneously in the rat footpad. Irradiation with an 808 nm continuous wave NIR laser produced on-demand and repeated infiltration anesthesia in the rat footpad in proportion to the irradiance, with minimal toxicity. The ability to achieve on-demand and repeated local anesthesia could be very beneficial in the management of pain.

Isolation of 6-deoxytetrodotoxin from the pufferfish, Takifugu pardalis, and a comparison of the effects of the C-6 and C-11 hydroxy groups of tetrodotoxin on its activity.

Identification of new tetrodotoxin (TTX, 1) analogues would be significant in the elucidation of its biosynthetic pathway and a study of its structure-activity relationships. In this study, a new TTX analogue, 6-deoxyTTX (2), was isolated from the ovary of the pufferfish, Takifugu pardalis, and the structure was determined using spectroscopic methods. Compound 2 was also identified in other marine animals, Nassarius snail and blue-ringed octopuses, using LC-MS. Furthermore, we investigated the voltage-gated sodium channel blocking activity of 2 by examination of the inhibitory activities to cytotoxicity induced by ouabain and veratridine in mouse neuroblastoma cells (Neuro-2a). The activities were then compared with those of 1, 11-deoxyTTX (3), and 6,11-dideoxyTTX (4). The EC50 value for 2 was estimated to be 6.5±2.2 nM, approximately 3-fold larger than that of 1 (2.1±0.6 nM) and approximately 20-fold smaller than that of 3. These results suggested that contribution of the C-6 hydroxy group to the activity is less than that of the C-11 hydroxy group.

Decomposition of tetrodotoxin using multi-gas plasma jet.

In this study, non-thermal multi-gas plasma treatments were performed for Tetrodotoxin (TTX) solution, and TTX decomposition was analyzed by liquid chromatography coupled with electrospray time-of-flight mass spectrometry. The TTX mass spectrum signal was reduced by plasma irradiations to different levels by using various gas species. Nitrogen plasma exhibited the optimal capability for TTX decomposition, followed by oxygen, argon, and carbon dioxide plasmas. The TTX concentration decreased 100-fold by nitrogen plasma treatment for 10 min.

Up-regulation of NaV1.7 sodium channels expression by tumor necrosis factor-α in cultured bovine adrenal chromaffin cells and rat dorsal root ganglion neurons.

BACKGROUND: Tumor necrosis factor-α (TNF-α) is not only a key regulator of inflammatory response but also an important pain modulator. TNF-α enhances both tetrodotoxin-sensitive (TTX-S) and tetrodotoxin-resistant Na channel currents in dorsal root ganglion (DRG) neurons. However, it remains unknown whether TNF-α affects the function and expression of the TTX-S NaV1.7 Na channel, which plays crucial roles in pain generation. METHODS: We used cultured bovine adrenal chromaffin cells expressing the NaV1.7 Na channel isoform and compared them with cultured rat DRG neurons. The expression of TNF receptor 1 and 2 (TNFR1 and TNFR2) in adrenal chromaffin cells was studied by Semiquantitative reverse transcription-polymerase chain reaction. The effects of TNF-α on the expression of NaV1.7 were examined with reverse transcription-polymerase chain reaction and Western blot analysis. Results were expressed as mean ± SEM. RESULTS: TNFR1 and TNFR2 were expressed in adrenal chromaffin cells, as well as reported in DRG neurons. TNF-α up-regulated NaV1.7 mRNA by 132% ± 9% (N = 5, P = 0.004) in adrenal chromaffin cells, as well as 117% ± 2% (N = 5, P < 0.0001) in DRG neurons. Western blot analysis showed that TNF-α increased NaV1.7 protein up to 166% ± 24% (N = 5, corrected P < 0.0001) in adrenal chromaffin cells, concentration- and time-dependently. CONCLUSIONS: TNF-α up-regulated NaV1.7 mRNA in both adrenal chromaffin cells and DRG neurons. In addition, TNF-α up-regulated the protein expression of the TTX-S NaV1.7 channel in adrenal chromaffin cells. Our findings may contribute to understanding the peripheral nociceptive mechanism of TNF-α.

Modeling intrinsic electrophysiology of AII amacrine cells: preliminary results.

In patients who have lost their photoreceptors due to retinal degenerative diseases, it is possible to restore rudimentary vision by electrically stimulating surviving neurons. AII amacrine cells, which reside in the inner plexiform layer, split the signal from rod bipolar cells into ON and OFF cone pathways. As a result, it is of interest to develop a computational model to aid in the understanding of how these cells respond to the electrical stimulation delivered by a prosthetic implant. The aim of this work is to develop and constrain parameters in a single-compartment model of an AII amacrine cell using data from whole-cell patch clamp recordings. This model will be used to explore responses of AII amacrine cells to electrical stimulation. Single-compartment Hodgkin-Huxley-type neural models are simulated in the NEURON environment. Simulations showed successful reproduction of the potassium currentvoltage relationship and some of the spiking properties observed in vitro.

Synthesis and biological characterization of synthetic analogs of Huwentoxin-IV (Mu-theraphotoxin-Hh2a), a neuronal tetrodotoxin-sensitive sodium channel inhibitor.

Huwentoxin-IV (HWTX-IV, also named Mu-theraphotoxin-Hh2a) is a typical inhibitor cystine knot peptide isolated from the venom of Chinese tarantula Ornithoctonus huwena and is found to inhibit tetrodotoxin-sensitive (TTX-S) sodium channels from mammalian sensory neurons. This peptide binds to neurotoxin receptor site 4 located at the extracellular S3-S4 linker of domain II in neuronal sodium channels. However, the molecular surface of HWTX-IV interaction with sodium channels remains unknown. In this study, we synthesized HWTX-IV and three mutants (T28D, R29A and Q34D) and characterized their functions on TTX-S sodium channels from adult rat dorsal root ganglion (DRG) neurons. Analysis of liquid chromatography, mass spectrometry and circular dichroism spectrum indicated that all four synthetic peptides are properly folded. Synthetic HWTX-IV exhibited the same activity as native HWTX-IV, while three mutations reduced toxin binding affinities by 10-200 fold, indicating that the basic or vicinal polar residues Thr²8, Arg²9, and Gln³4 in C-terminus might play critical roles in the interaction of HWTX-IV with TTX-S sodium channels.

Examination of transformation among tetrodotoxin and its analogs in the living cultured juvenile puffer fish, kusafugu, Fugu niphobles by intramuscular administration.

In puffer fish, tetrodotoxin (TTX) exists as the major toxin with chemically equilibrium analogs (4-epiTTX, 4,9-anhydroTTX) and chemically non-equilibrium analogs (deoxy analogs, 11-oxoTTX, 4-S-cysteinylTTX). There are two purposes to this study: 1) to search for the reason why TTX is the most major analog in puffer fish, even 4,9-anhydroTTX is chemically more stable, 2) to investigate whether or not chemically non-equilibrium analogs are transformed in puffer fish, because these were predicted to be biosynthetic intermediates. Pure TTX, 4-epiTTX, 4,9-anhydroTTX, and 11-oxoTTX were separately administrated to the cultured non-toxic juvenile puffer fish kusafugu, Fugu niphobles by intramuscular injection. Sixteen days after administration, TTX analogs in the whole fish were analyzed by LC-fluorescent detection and LC/MS. By the administration of TTX, 4-epiTTX, and 4,9-anhydroTTX, 34-40% of the administrated doses of the toxins were accumulated, and 4,9-anhydroTTX has become the major toxin after inter-conversion. This result indicates discrepancy from the previous ones wherein TTX was predominantly accumulated when TTXs were administrated through diets; this suggests that dietary administration might be necessary to accumulate TTX as the major toxin, and not 4,9-anhydroTTX. Transformations from TTX to deoxy analogs or 11-oxoTTX, or from 11-oxoTTX to TTX were not detected in this study.

6,11-Dideoxytetrodotoxin from the puffer fish, Fugu pardalis.

The presence of an unknown dideoxy analog of tetrodotoxin was suggested on the liquid chromatography/electrospray ionization-mass spectrometry mass chromatogram of the ovaries of the puffer fish, Fugu pardalis, in single ion monitoring mode to detect at m/z 288. We succeeded to isolate this analog (approximately 0.4 mg) from 200 g of the ovaries and the structure was determined as 6,11-dideoxytetrodotoxin by spectroscopic methods (high resolution-fast atom bombardment-MS and NMR spectroscopy). The discovery of the new analog is highly significant with respect to the biosynthesis or metabolism of tetrodotoxin. We also roughly determined the value of IC(50) (mice, intraperitoneal) for 6,11-dideoxytetrodotoxin as 420 microg/kg and thus it is 42 times less toxic than tetrodotoxin.

Distribution of tetrodotoxin, saxitoxin, and their analogs among tissues of the puffer fish Fugu pardalis.

The anatomical distribution of tetrodotoxin (TTX), saxitoxin (STX) and their analogs (TTXs, STXs) in three female and three male specimens of the marine puffer fish Fugu pardalis from Miyagi Prefecture, 2005, Japan, were studied. 5-DeoxyTTX, 11-deoxyTTX, and 5,6,11-trideoxyTTX were quantified by liquid chromatography/mass spectrometry (LC/MS) for the first time, and other TTXs and STXs were determined by liquid chromatography-fluorescent detection (LC-FLD). As a result, 5,6,11-trideoxyTTX was found to be the major TTX analog in all tissues tested, whereas 5-deoxyTTX and 11-deoxyTTX were minor components. Especially, in female (n=3), the ratios of 5,6,11-trideoxyTTX to total of all TTX analogs (mole/mole) in ovaries (mean+/-SD, 0.42+/-0.055) were significantly larger than those in livers (0.17+/-0.025) (P<0.05). In contrary, the ratios of 4,9-anhydroTTX to total of all TTX analogs in livers (0.27+/-0.047) were significantly larger than those in ovaries (0.073+/-0.040) (P<0.01). The ratios of TTX to total of all TTX analogs were not significantly different between ovaries (0.47+/-0.078) and livers (0.55+/-0.067). In male (n=3), all these ratios were not significantly different between livers and testis. 4-S-CysteinylTTX was detected in liver, spleen, gall, and intestine in 1-6mole% of total of all TTX analogs, supporting our previous hypothesis that 4-S-cysteinylTTX is a metabolite of TTX.

Structure-activity relationship of an alpha-toxin Bs-Tx28 from scorpion (Buthus sindicus) venom suggests a new alpha-toxin subfamily.

Scorpion venoms are among the most widely known source of peptidyl neurotoxins used for callipering different ion channels, e.g., for Na(+), K(+), Ca(+) or Cl(-). An alpha-toxin (Bs-Tx28) has been purified from the venom of scorpion Buthus sindicus, a common yellow scorpion of Sindh, Pakistan. The primary structure of Bs-Tx28 was established using a combination of MALDI-TOF-MS, LC-ESI-MS, and automated Edman degradation analysis. Bs-Tx28 consists of 65 amino acid residues (7274.3+/-2Da), including eight cysteine residues, and shows very high sequence identity (82-94%) with other long-chain alpha-neurotoxins, active against receptor site-3 of mammalian (e.g., Lqq-IV and Lqh-IV from scorpions Leiurus sp.) and insect (e.g., BJalpha-IT and Od-1 from Buthotus judaicus and Odonthobuthus doriae, respectively) voltage-gated Na(+) channels. Multiple sequence alignment and phylogenetic analysis of Bs-Tx28 with other known alpha- and alpha-like toxins suggests the presence of a new and separate subfamily of scorpion alpha-toxins. Bs-Tx28 which is weakly active in both, mammals and insects (LD(50) 0.088 and 14.3microg/g, respectively), shows strong induction of the rat afferent nerve discharge in a dose-dependent fashion (EC(50)=0.01microg/mL) which was completely abolished in the presence of tetrodotoxin suggesting the binding of Bs-Tx28 to the TTX-sensitive Na(+)-channel. Three-dimensional structural features of Bs-Tx28, established by homology modeling, were compared with other known classical alpha-mammal (AaH-II), alpha-insect (Lqh-alphaIT), and alpha-like (BmK-M4) toxins and revealed subtle variations in the Nt-, Core-, and RT-CT-domains (functional domains) which constitute a "necklace-like" structure differing significantly in all alpha-toxin subfamilies. On the other hand, a high level of conservation has been observed in the conserved hydrophobic surface with the only substitution of W43 (Y43/42) and an additional hydrophobic character at position F40 (L40/A/V/G39), as compared to the other mentioned alpha-toxins. Despite major differences within the primary structure and activities of Bs-Tx28, it shares a common structural and functional motif (e.g., transRT-farCT) within the RT-CT domain which is characteristic of scorpion alpha-mammal toxins.

Identification of 4-S-Cysteinyltetrodotoxin from the liver of the puffer fish, Fugu pardalis, and formation of thiol adducts of tetrodotoxin from 4,9-anhydrotetrodotoxin.

The metabolic pathway of tetrodotoxin (TTX), a powerful and specific voltage-gated sodium channel blocker, has not been well-clarified either in TTX-poisoned patients or in puffer fish. 4-S-CysteinylTTX (4-CysTTX) was isolated from the liver of the puffer fish, Fugu pardalis, as the first adduct of TTX with thiol. The structure was fully characterized by electrospray ionization-MS and two-dimensional NMR spectroscopy. The configuration of Cys in this compound was confirmed to be S (L-Cys) by application of the Marfey's method to cystine obtained from 4-CysTTX by iodine oxidation. We also found that 4-CysTTX was derived from 4,9-anhydroTTX by incubation with a large excess of Cys in aqueous buffer (pH 8.0) for 90 min at 40 degrees C in 33% yield by HPLC. GSH also reacted with 4,9-anhydroTTX to form 4-S-glutathionylTTX (4-GSTTX) in 39% yield under the same conditions, whereas TTX scarcely reacted with Cys and GSH. These reactions were strictly pH-dependent, giving the highest yield at pH 8.0. 4-GSTTX was converted to 4,9-anhydroTTX in 0.8 M sodium phosphate buffer (pH 8.0) at 25 degrees C. Its half-life was approximately 4 h. The minimum lethal doses of 4-CysTTX and 4-GSTTX to mice by ip injection were more than 140 and 860 microg/kg (n = 2), which were 14- and 86-fold larger than the LD(50) of TTX, respectively. 4-GSTTX was hydrolyzed to 4-CysTTX by gamma-glutamyltranspeptidase (Sigma, catalog no. G9270), which was supposed to contain cysteinylglycine dipeptidase. We also examined the effect of Cys or GSH coinjection (ip) with TTX to mice for detoxification of TTX and concluded that these coinjections did not reduce the toxicity of TTX.

Selective detection of saxitoxin over tetrodotoxin using acridinylmethyl crown ether chemosensor.

At pH 7.1, saxitoxin decomposes to produce a trace impurity that can interfere with fluorescence sensing when using irradiation wavelengths near 325 nm. The fluorophore acridine is found to be a suitable component of arylmethyl crown ether chemosensors for the fluorescent detection of saxitoxin. These sensors are selective for the detection of saxitoxin over tetrodotoxin.

Modeling P-loops domain of sodium channel: homology with potassium channels and interaction with ligands.

A large body of experimental data on Na+ channels is available, but the interpretation of these data in structural terms is difficult in the absence of a high-resolution structure. Essentially different electrophysiological and pharmacological properties of Na+ and K+ channels and poor identity of their sequences obstruct homology modeling of Na+ channels. In this work, we built the P-loops model of the Na+ channel, in which the pore helices are arranged exactly as in the MthK bacterial K+ channel. The conformation of the selectivity-filter region, which includes residues in positions -2 through +4 from the DEKA locus, was shaped around rigid molecules of saxitoxin and tetrodotoxin that are known to form multiple contacts with this region. Intensive Monte Carlo minimization that started from the MthK-like conformation produced practically identical saxitoxin- and tetrodotoxin-based models. The latter was tested to explain a wide range of experimental data that were not used at the model building stage. The docking of tetrodotoxin analogs unambiguously predicted their optimal orientation and the interaction energy that correlates with the experimental activity. The docking of mu-conotoxin produced a binding model consistent with experimentally known toxin-channel contacts. Monte Carlo-minimized energy profiles of tetramethylammonium pulled through the selectivity-filter region explain the paradoxical experimental data that this organic cation permeates via the DEAA but not the AAAA mutant of the DEKA locus. The model is also consistent with earlier proposed concepts on the Na+ channel selectivity as well as Ca2+ selectivity of the EEEE mutant of the DEKA locus. Thus, the model integrates available experimental data on the Na+ channel P-loops domain, and suggests that it is more similar to K+ channels than was believed before.