Stability Analysis of the Asiatic Acid-COX-2 Complex Using 100 ns Molecular Dynamic Simulations and Its Selectivity against COX-2 as a Potential Anti-Inflammatory Candidate.

Asiatic acid, a triterpenoid compound, has been shown to have anti-inflammatory activity through the inhibition of the formation of cyclooxygenase-2 (COX-2) in vitro and in vivo. This study was conducted to determine the binding stability and the inhibitory potential of asiatic acid as an anti-inflammatory candidate. The study involved in vitro testing utilizing a colorimetric kit as well as in silico testing for the pharmacophore modeling and molecular dynamic (MD) simulation of asiatic acid against COX-2 (PDB ID: 3NT1). The MD simulations showed a stable binding of asiatic acid to COX-2 and an RMSD range of 1-1.5 Å with fluctuations at the residues of Phe41, Leu42, Ile45, Arg44, Asp367, Val550, Glu366, His246, and Gly227. The total binding energy of the asiatic acid-COX-2 complex is -7.371 kcal/mol. The anti-inflammatory activity of the asiatic acid inhibition of COX-2 was detected at IC50 values of 120.17 µM. Based on pharmacophore modeling, we discovered that carboxylate and hydroxyl are the two main functional groups that act as hydrogen bond donors and acceptors interacting with the COX-2 enzyme. From the results, it is evident that asiatic acid is a potential anti-inflammatory candidate with high inhibitory activity in relation to the COX-2 enzyme.

In-silico Molecular Interaction of Short Synthetic Lipopeptide/Importin-alpha and In-vitro Evaluation of Transgene Expression Mediated by Liposome- Based Gene Carrier.

BACKGROUND: Lipopeptide-based gene carriers have shown low cytotoxicity, are capable of cell membrane penetration, are easy to manufacture and therefore are great potential candidates for gene delivery applications. OBJECTIVES: This study aims to explore a range of short synthetic lipopeptides, (Lau: Lauryl; Pal: Palmitoyl) consisting of an alkyl chain, one cysteine (C), 1 to 2 histidine (H), and lysine (K) residues by performing in-silico molecular interaction and in-vitro evaluation. METHODS: The molecular interactions between the lipopeptides and Importin-α receptor were performed using AutoDock Vina and Amber14. The lipopeptide/DNA complexes were evaluated in- -vitro for their interactions, particle size, zeta potential and transgene expression. Transfection efficiency of the lipopeptides and Pal-CKKHH-derived liposome was carried out based on luciferase transgene expression. RESULTS: The in-silico interaction showed that Lau-CKKH and Pal-CKKHH hypothetically expedited nuclear uptake. Both lipopeptides had lower binding energy (-6.3 kcal/mol and -6.2 kcal/mol, respectively), compared to the native ligand, viz, nuclear localization sequence (-5.4 kcal/mol). The short lipopeptides were able to condense DNA molecules and efficiently form compacted nanoparticles. Based on the in-vitro evaluation on COS-7, Pal-CKKHH was found to be the best transfection agent amongst the lipopeptides. Its transfection efficiency (ng Luc/mg total protein) increased up to ~3-fold higher (1163 + 55) as it was formulated with helper lipid DOPE (1:2). The lipopeptide- based liposome (Pal-CKKHH: DOPE=1:2) also facilitated luciferase transgene expression on human embryonic kidney cells (293T) and human cervical adenocarcinoma cells (HeLa) with transfection efficiency 1779 +52 and 260 + 22, respectively. CONCLUSION: Our study for the first time has shown that the fully synthesized short lipopeptide Pal- CKKHH is able to interact firmly with the Importin-α. The lipopeptide is able to condense DNA molecules efficiently, facilitate transgene expression, expedite the nuclear uptake process, and hence has the characteristics of a potential transfection agent.

Determination of Anthraquinone in Some Indonesian Black Tea and Its Predicted Risk Characterization.

Anthraquinone (AQ) levels in some Indonesian dried tea leaves samples from different plantation areas and their brewed tea samples were determined by gas chromatography-tandem mass spectrometry methods. The mean lower bound, middle bound, and upper bound of AQ levels in 59 dried tea leaves samples were 82.2, 82.8, and 83.4 µg/kg, respectively, while their 95%th percentile values were identical at 190.3 µg/kg (0.1903 mg/kg). In a transfer rate study, the mean and 95%th AQ levels in 30 dried tea leaves samples with AQ level ≥ LOQ (limit of quantification) were 128.6 and 194.5 µg/kg (0.1945 mg/kg), while those of their corresponding brewed tea samples were 2.1 and 3.4 µg/kg, respectively. The mean and 95%th transfer rates of AQ into brewed tea samples were 51.99 and 88.17%. Using these data and taking into account daily tea consumption, calculated cancer potency slope factor, benchmark dose of 10% effect at lower bound 95% confidence interval of AQ, and average body weight, the risk characterization due to exposure to this compound from tea consumption was calculated and stated as incremental lifetime cancer risk (ILCR) and margin of exposure (MOE). The overall results revealed that AQ levels in dried tea leaves up to the highest level found in the samples lead to an ILCR of not more than 10-6 and an MOE of not less than 104 and hence was predicted to give sufficient consumer protection.

Computational Study of Imidazolylporphyrin Derivatives as a Radiopharmaceutical Ligand for Melanoma.

BACKGROUND: Melanoma is the most aggressive type of skin cancer. Metastatic melanoma is extremely difficult to treat with current therapy methods such as surgery. On the other hand, it is a good opportunity to develop a radiopharmaceutical using a radionuclide such as Technetium (Tc) for diagnostic and Rhenium (Re) for therapeutic purposes. T3,4BCPP has been be used as a radioimaging agent for melanoma cancers experimentally. The aim of the present research was to design new imidazolylporphyrin derivatives with better selectivity and higher affinity than those of T3,4BCPP by molecular modeling. METHODS: Eight types of Re- and Tc-labeled imidazolylporphyrins were docked to Fibroblast Growth Factor Receptor 1 (FGFR1, PDB ID: 5AM6) using AutoDock 4.2. FGFR1 was simulated by Molecular Dynamic (MD) simulation for 30 ns using NAMD 2.10 at 37 °C. The obtained conformations were then applied in a molecular docking simulation. Dovitinib (natural ligand of FGFR1), Re- and Tc-T3, 4BCPP were used as references. RESULTS: The MD simulation resulted in an RMSD of 3.8 Å. From all the studied imidazolylporphyrin derivatives, Tc-cD3, 4BCPMIP and Re-cD3, 4BCPIP had the best docking parameter. Tc-cD3, 4BCPMIP had a free binding energy of -4.06 kcal/mol, while that of Re-cD3, 4BCPIP was -4.35 kcal/mol. CONCLUSION: It is concluded that cD3,4BCPMIP and cD3,4BCPIP are two potential candidate ligands for a melanoma radiopharmaceutical kit.

Molecular docking and dynamics simulations on the interaction of cationic porphyrin-anthraquinone hybrids with DNA G-quadruplexes.

A series of cationic porphyrin-anthraquinone hybrids bearing either pyridine, imidazole, or pyrazole rings at the meso-positions have been investigated for their interaction with DNA G-quadruplexes by employing molecular docking and molecular dynamics simulations. Three types of DNA G-quadruplexes were utilized, which comprise parallel, antiparallel, and mixed hybrid topologies. The porphyrin hybrids have a preference to bind with parallel and mixed hybrid structures compared to the antiparallel structure. This preference arises from the end stacking of porphyrin moiety following G-stem and loop binding of anthraquinone tail, which is not found in the antiparallel due to the presence of diagonal and lateral loops that crowd the G-quartet. The binding to the antiparallel, instead, occurred with poorer affinity through both the loop and wide groove. All sites of porphyrin binding were confirmed by 6 ns molecular dynamics simulation, as well as by the negative value of the total binding free energies that were calculated using the MMPBSA method. Free energy analysis shows that the favorable contribution came from the electrostatic term, which supposedly originated from the interaction of either cationic pyridinium, pyrazole, or imidazole groups and the anionic phosphate backbone, and also from the van der Waals energy, which primarily contributed through end stacking interaction.

Binding of tetrakis(pyrazoliumyl)porphyrin and its copper(II) and zinc(II) complexes to poly(dG-dC)2 and poly(dA-dT)2.

Interactions of cationic porphyrins bearing five-membered rings at the meso position, meso-tetrakis(1,2-dimethylpyrazolium-4-yl)porphyrin (MPzP; M is H2, Cu(II) or Zn(II)), with synthetic polynucleotides poly(dG-dC)2 and poly(dA-dT)2 have been characterized by viscometric, visible absorption, circular dichroisim and magnetic circular dichroism spectroscopic and melting temperature measurements. Both H2PzP and CuPzP are intercalated into poly(dG-dC)2 and are outside-bound to the major groove of poly(dA-dT)2, while ZnPzP is outside-bound to the minor groove of poly(dA-dT)2 and surprisingly is intercalated into poly(dG-dC)2. The binding constants of the porphyrin and poly(dG-dC)2 and poly(dA-dT)2 are on the order of 10(6) M(-1) and are comparable to those of other cationic porphyrins so far reported. The process of the binding of the porphyrin to poly(dG-dC)2 and poly(dA-dT)2 is exothermic and enthalpically driven for H2PzP, whereas it is endothermic and entropically driven for CuPzP and ZnPzP. These results have revealed that the kind of the central metal ion of metalloporphyrins influences the characteristics of the binding of the porphyrins to DNA.

NO-donors (VII [1]): synthesis and cyclooxygenase inhibitory properties of N-and S-nitrooxypivaloyl-cysteine derivatives of naproxen -- a novel type of NO-NSAID.

Nitric oxide (NO)has been reported to subserve many of the same mucosal protection mechanisms as prostaglandins and is sufficient for acute gastroprotection and ulcer healing. In fact, NO-donating NSAID hybrid compounds such as the nitrooxybutyl ester of naproxen show reduced ulcerogenic activity while maintaining anti-inflammatory activity. We introduce two prototypes of novel triple-hybrid compounds consisting of cysteine which is known to enhance the activity of organic nitrates and to reduce nitrate tolerance, an NSAID (naproxen), and an organic nitrate (nitrooxypivaloic acid). L-Cysteine ethyl ester first was N-acylated in a CH(2)Cl(2)/H(2)O twophase system using the acid chlorides of naproxen or nitrooxypivaloic acid, respectively, and sodium acetate, or alternatively using the DCC-activated nitrooxy acid in absolute CH(2)Cl(2). The N-acylated intermediates were subsequently S-acylated using the acid chlorides or alternatively the carbonyldiimidazole (CDI)-activated acids again. The two naproxen-cysteine-nitrate hybrid prodrugs were screened in vitro for their cyclooxygenase inhibitory properties relative to naproxen. In this screening the N-nitrooxyacylcysteine derivative was found to be inactive in the concentration range of 0.1-10 micromol/L against both COX-1 and COX-2, while the S-nitrooxyacylcysteine derivative had only weak activity against COX-1.