Ruyun Ji

Brownian Dynamics Simulations of the Recognition of the Scorpion Toxin Maurotoxin with the Voltage-Gated Potassium Ion Channels

The recognition of the scorpion toxin maurotoxin (MTX) by the voltage-gated potassium (Kv1) channels, Kv1.1, Kv1.2, and Kv1.3, has been studied by means of Brownian dynamics (BD) simulations. All of the 35 available structures of MTX in the Protein Data Bank (http://www.rcsb.org/pdb) determined by nuclear magnetic resonance were considered during the simulations, which indicated that the conformation of MTX significantly affected both the recognition and the binding between MTX and the Kv1 channels. Comparing the top five highest-frequency structures of MTX binding to the Kv1 channels, we found that the Kv1.2 channel, with the highest docking frequencies and the lowest electrostatic interaction energies, was the most favorable for MTX binding, whereas Kv1.1 was intermediate, and Kv1.3 was the least favorable one. Among the 35 structures of MTX, the 10th structure docked into the binding site of the Kv1.2 channel with the highest probability and the most favorable electrostatic interactions. From the MTX-Kv1.2 binding model, we identified the critical residues for the recognition of these two proteins through triplet contact analyses. MTX locates around the extracellular mouth of the Kv1 channels, making contacts with its beta-sheets. Lys23, a conserved amino acid in the scorpion toxins, protrudes into the pore of the Kv1.2 channel and forms two hydrogen bonds with the conserved residues Gly401(D) and Tyr400(C) and one hydrophobic contact with Gly401(C) of the Kv1.2 channel. The critical triplet contacts for recognition between MTX and the Kv1.2 channel are Lys23(MTX)-Asp402(C)(Kv1), Lys27(MTX)-Asp378(D)(Kv1), and Lys30(MTX)-Asp402(A)(Kv1). In addition, six hydrogen-bonding interactions are formed between residues Lys23, Lys27, Lys30, and Tyr32 of MTX and residues Gly401, Tyr400, Asp402, Asp378, and Thr406 of Kv1.2. Many of them are formed by side chains of residues of MTX and backbone atoms of the Kv1.2 channel. Five hydrophobic contacts exist between residues Pro20, Lys23, Lys30 and Tyr32 of MTX and residues Asp402, Val404, Gly401, and Arg377 of the Kv1.2 channel. The simulation results are in agreement with the previous molecular biology experiments and explain the binding phenomena between MTX and Kv1 channels at the molecular level. The consistency between the results of the BD simulations and the experimental data indicated that our three-dimensional model of the MTX-Kv1.2 channel complex is reasonable and can be used in additional biological studies, such as rational design of novel therapeutic agents blocking the voltage-gated channels and in mutagenesis studies in both the toxins and the Kv1 channels. In particular, both the BD simulations and the molecular mechanics refinements indicate that residue Asp378 of the Kv1.2 channel is critical for its recognition and binding functionality toward MTX. This phenomenon has not been appreciated in the previous mutagenesis experiments, indicating this might be a new clue for additional functional study of Kv1 channels.

Brownian Dynamics Simulations of the Recognition of the Scorpion Toxin P05 with the Small-conductance Calcium-activated Potassium Channels

The recognition of the scorpion toxin P05 and the small-conductance, calcium-activated potassium (SK) channels, rsk1, rsk2, and rsk3, has been studied by means of the Brownian dynamics (BD) method. All of the 25 available structures of P05 in the RCSB Protein Data Bank determined by NMR were considered during the simulation, which indicated that the conformation of P05 affects both the recognition and binding between the two proteins significantly. Comparing the top four high-frequency structures of P05 binding to the SK channels, we found that the rsk2 channel, with high frequencies and lowest electrostatic interaction energies (E (int)(ES)), is the most favorable for P05 binding, while rsk3 is intermediate, and rsk1 is the least favorable. Among the 25 structures of P05, the 13th structure docks into the binding site of the rsk2 channel with the highest probability and most favorable electrostatic interactions. From the P05-rsk2 channel binding model, we identified the residues critical for the recognition of these two proteins through triplet contact analyses. P05 locates around the extracellular mouth of the SK channels and contacts the SK channels using its alpha-helix rather than beta-sheets. The critical triplet contacts for recognition between P05 and the rsk2 channel are Arg6 (P05)-Asp364 (SK), Arg7 (P05)-Asn368 (SK), and Arg13 (P05)-Asp341 (SK). The structure of the P05-rsk2 complex with the most favorable electrostatic interaction energy was further refined by molecular mechanics, showing that six hydrogen bonding interactions exist between P05 and the rsk2 channel: one hydrogen bond is formed between Arg6 (P05) and Asp364(D) (rsk2); Arg7 (P05) forms three hydrogen bonds with Asp341(B) (rsk2)) and Asp364(C) (rsk2); two hydrogen bonds are formed by Arg13 (P05) with Asp341(A) (rsk2) and Asp364(B) (rsk2). The simulation results are in good agreement with the previous molecular biological experiments and can explain the binding phenomena between P05 and SK channels at the level of molecular structure. The consistency between the results of the BD simulations and the experimental data indicated that our 3D model of the P05-rsk2 channel complex is reasonable and can be employed in further biological studies, such as rational design of the novel therapeutic agents blocking the small-conductance, calcium-activated and apamin-sensitive potassium channels, and for mutagenesis studies in both toxins and SK channels. In particular, both the BD simulations and the molecular mechanics refinements indicate that residue Asp364 of the rsk2 channel is critical for its recognition and binding functionality towards P05. This phenomenon has not been appreciated in the previous mutagenesis experiments, indicating that this might be a new clue for further functional study of SK channels.

Brownian dynamics simulations of interaction between scorpion toxin Lq2 and potassium ion channel.

The association of the scorpion toxin Lq2 and a potassium ion (K(+)) channel has been studied using the Brownian dynamics (BD) simulation method. All of the 22 available structures of Lq2 in the Brookhaven Protein Data Bank (PDB) determined by NMR were considered during the simulation, which indicated that the conformation of Lq2 affects the binding between the two proteins significantly. Among the 22 structures of Lq2, only 4 structures dock in the binding site of the K(+) channel with a high probability and favorable electrostatic interactions. From the 4 candidates of the Lq2-K(+) channel binding models, we identified a good three-dimensional model of Lq2-K(+) channel complex through triplet contact analysis, electrostatic interaction energy estimation by BD simulation and structural refinement by molecular mechanics. Lq2 locates around the extracellular mouth of the K(+) channel and contacts the K(+) channel using its beta-sheet rather than its alpha-helix. Lys27, a conserved amino acid in the scorpion toxins, plugs the pore of the K(+) channel and forms three hydrogen bonds with the conserved residues Tyr78(A-C) and two hydrophobic contacts with Gly79 of the K(+) channel. In addition, eight hydrogen-bonds are formed between residues Arg25, Cys28, Lys31, Arg34 and Tyr36 of Lq2 and residues Pro55, Tyr78, Gly79, Asp80, and Tyr82 of K(+) channel. Many of them are formed by side chains of residues of Lq2 and backbone atoms of the K(+) channel. Thirteen hydrophobic contacts exist between residues Met29, Asn30, Lys31 and Tyr36 of Lq2 and residues Pro55, Ala58, Gly79, Asp80 and Tyr82 of the K(+) channel. These favorable interactions stabilize the association between the two proteins. These observations are in good agreement with the experimental results and can explain the binding phenomena between scorpion toxins and K(+) channels at the level of molecular structure. The consistency between the BD simulation and the experimental data indicates that our three-dimensional model of Lq2-K(+) channel complex is reasonable and can be used in further biological studies such as rational design of blocking agents of K(+) channels and mutagenesis in both toxins and K(+) channels.

N18 : A COMPUTATIONAL INVESTIGATION

Abstract Ab initio quantum mechanics methods have been applied to study the cage-like polynitrogen cluster N 18 . The previously reported cage-like structure of the N 18 molecule with symmetry C 2v has been optimized at the RHF/4-31G ∗ , RHF/6-31G ∗ , DFT(B3LYP, B3P86, BHLYP)/6-31G ∗ and MP2(full)/6-31G ∗ levels of theory. The harmonic vibration frequencies and their infrared (IR) and Raman intensities have also been reported at RHF/4-31G ∗ , RHF/6-31G ∗ , as well as the B3P86/6-31G ∗ level. The results show that the investigated cage-like structure is stable on the potential energy hypersurface, lying above separated nitrogen molecules by about 50 kcal mol −1 of nitrogen atoms, with a stability comparable with the dodecahedral N 20 molecule. The resultant structure also suggests the aromaticity of conjugated pentagons which stabilizes the cage-like polynitrogen clusters.

Synthesis and insulin-sensitizing activity of a novel kind of benzopyran derivative.

A series of benzopyran derivatives was synthesized and their insulin-sensitizing activities were evaluated in 3T3-L1 cells. Compounds 6 and 11 exhibited more potent insulin-sensitizing activity than rosiglitazone.

Synthesis and acetylcholinesterase inhibitory activity of huperzine A-E2020 combined compound.

The synthesis of huperzine-E2020 combined compound (3) has been accomplished and the activities of 3 and the intermediates 12 and 13 to inhibit the activity of acetylcholinesterase have been measured. Conformation analyses and molecular docking studies of E2020 and the eight isomers of 12 were carried out. The results indicated that binding energies of all isomers of 12 with AChE was much lower than E2020 except for isomer RRZ, which might be the reason that the activity of 12 was lower than that of E2020. Interaction pattern of RRZ in AChE was also studied. Both binding energy and interaction pattern shows that the biological activity of RRZ might be higher than that of E2020.

Synthesis and antibacterial activity of oxazolidinone containing sulphonyl group

A series of oxazolidinone derivatives carrying sulphonyl group was synthesized and their antibacterial activity was evaluated in vitro. Many of such compounds demonstrated potent antibacterial activity. The activity of a novel compound (YC-20) was 2-4-fold more potent than that of linezolid.

A 3d-qsar study on ginkgolides and their analogues with comparative molecular field analysis

Comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) paradigm was used to study the correlation between the physicochemical properties and the in vitro bioactivities of ginkgolide analogues. The correlation derived from CoMFA analysis has a good predictive capability. Based on the result of CoMFA analysis, we designed some compounds. Pharmacological assay indicated that three of these new designed compounds are 2 and 4 times more potent than that of ginkgolides.

Synthesis and evaluation of a series of benzopyran derivatives as PPAR α/γ agonists

A series of benzopyran derivatives were synthesized and evaluated for PPAR alpha/gamma agonist activities. Most of the compounds exhibit reasonable PPAR alpha and PPAR gamma agonist activities. In particular, compounds 7b, 8b, 8e and 8h with remarkable PPARg EC(50) values of 0.001microM are excellent full PPAR gamma agonists with the functional potency about 130, 20 times stronger than that of leading compound 5 and rosiglitazone, respectively. Compounds 7a, 7c, 7d and 8a are dual PPAR alpha/gamma agonists, and all of them gave comparable or stronger PPAR alpha/gamma agonist efficacy than that of the corresponding positive control.

Design, synthesis and evaluation of novel oxazaphosphorine prodrugs of 9-(2-phosphonomethoxyethyl)adenine (PMEA, adefovir) as potent HBV inhibitors.

A series of novel oxazaphosphorine prodrugs of 9-(2-phosphonomethoxyethyl)adenine (PMEA, adefovir) were synthesized and their anti-hepatitis B virus (HBV) activity was evaluated in HepG2 2.2.15 cells, with adefovir dipivoxil as a reference drug. In the cell assays, compounds 7b and 7d exhibited anti-HBV activity comparable to that of adefovir dipivoxil, while compound 7c, with an IC(50) value of 0.12 microM, was found to be three times more potent than the reference compound. In vitro stability studies showed that (S(P),S)-7c, the diastereomer of compound 7c, was stable in human blood plasma but underwent rapid metabolism to release the parent drug PMEA in liver microsomes. The possible metabolic pathway of (S(P),S)-7c in human liver microsomes was described. These findings suggest that compound (S(P),S)-7c is a promising anti-HBV drug candidate for further development.