Three New Scorpion Chloride Channel Toxins as Potential Anti-Cancer Drugs: Computational Prediction of The Interactions With Hmmp-2 by Docking and Steered Molecular Dynamics Simulations.

Scorpion venom is a rich source of toxins which have great potential to develop new therapeutic agents. Scorpion chloride channel toxins (ClTxs), such as Chlorotoxin selectively inhibit human Matrix Methaloproteinase-2 (hMMP-2). The inhibitors of hMMP-2 have potential use in cancer therapy. Three new ClTxs, meuCl14, meuCl15 and meuCl16, derived from the venom transcriptome of Iranian scorpion, M. eupeus (Buthidea family), show high sequence identity (71.4%) with Chlorotoxin. Here, 3-D homology model of new ClTxs were constructed. The models were optimized by Molecular Dynamics simulation based on MDFF (molecular dynamics flexible fitting) method. New ClTxs indicate the presence of CSαß folding of other scorpion toxins. A docking followed by steered molecular dynamics (SMD) simulations to investigate the interactions of meuCl14, meuCl15, and meuCl16 with hMMP-2 was applied. The current study creates a correlation between the unbinding force and the inhibition activities of meuCl14, meuCl15 and meuCl16 to shed some insights as to which toxin may be used as a drug deliverer. To this aim, SMD simulations using Constant Force Pulling method were carried out. The SMD provided useful details related to the changes of electrostatic, van de Waals (vdW), and hydrogen-bonding (H-bonding) interactions between ligands and receptor during the pathway of unbinding. According to SMD results, the interaction of hMMP-2 with meuCl14 is more stable. In addition, Arginine residue was found to contribute significantly in interaction of ClTxs with hMMP-2. All in all, the present study is a dynamical approach whose results are capable of being implemented in structure-based drug design.

First Transcriptome Analysis of Iranian Scorpion, Mesobuthus Eupeus Venom Gland.

Scorpions are generally an important source of bioactive components, including toxins and other small peptides as attractive molecules for new drug development. Mesobuthus eupeus, from medically important and widely distributed Buthidae family, is the most abundant species in Iran. Researchers are interesting on the gland of this scorpion due to the complexity of its venom. Here, we have analyzed the transcriptome based on expressed sequence tag (EST) database from the venom tissue of Iranian M. eupeus by constructing a cDNA library and subsequent Sanger sequencing of obtained inserts. Sixty-three unique transcripts were identified, which were grouped in different categories, including Toxins (44 transcripts), Cell Proteins (9 transcripts), Antimicrobial Peptides (4 transcripts) and Unknown Peptides (3 transcripts). The analysis of the ESTs revealed several new components categorized among various toxin families with effect on ion channels. Sequence analysis of a new precursor provides evidence to validate the first CaTxs from M. eupeus. The results are exploration of the diversity of precursors expressed of Iranian M. eupeus venom gland. We further described comparative analysis of venom components of Iranian M. eupeus with other sibling species.

Molecular dynamic of curcumin/chitosan interaction using a computational molecular approach: Emphasis on biofilm reduction.

Nanotechnology-based drug delivery systems have been used to enhance bioavailability and biological activities. Chitosan incorporating curcumin can serve as a biocompatible substitute for metallic nanoparticles in preventing biofilm formation of Streptococcus mutans and plaque on teeth. The interactions between chitosan nanoparticle as a carrier and curcumin, a natural antibacterial agent, were simulated. The binding conformation between curcumin-chitosan was obtained using the Lamarckian Genetic Algorithm in Autodock™ software in chitosan nanoparticle. The interaction stability was examined in the molecular dynamic stages, with isothermal-isobaric ensemble in the CHARMM Force Field. The results showed the root mean square deviation (RMSD) and the root mean square fluctuations (RMSF) for all complex's atoms were relaxed after 4ns (RMSD for the all-atoms was 26.81±0.1 (Å); RMSF 1.13±0.02Å). For each section, the estimation of RMSD, RMSF, radius of gyration, inter-H bond and other analysis confirmed that, during the first interval;10ns, there was a stable binding between the two sections. Although all bindings disappeared from 10 to 20ns, the curcumin was trapped inside the chitosan nanoparticles, and no release took place until 20ns, after which the curcumin began to release. This trend suggests that chitosan nanoparticle has ability to carry the curcumin.

Apta-nanosensor preparation and in vitro assay for rapid Diazinon detection using a computational molecular approach.

Aptamers (ss-DNA or ss-RNA), also known as artificial antibodies, have been selected in vitro median to bind target molecules with high affinity and selectivity. Diazinon is one of the most widely used organophosphorus insecticides in developing and underdeveloped countries as insecticide and acaricide. Diazinon is readily absorbed from the gastrointestinal system and rapidly distributed throughout the body. Thus, the design of clinical and laboratory diagnostics using nanobiosensors is necessary. A computational approach allows us to screen or rank receptor structure and predict interaction outcomes with a deeper understanding, and it is much more cost effective than laboratory attempts. In this research, the best sequence (high affinity bind Diazinon-ssDNA) was ranked among 12 aptamers isolated from SELEX experimentation. Docking results, as the first virtual screening stage and static technique, selected frequent conformation of each aptamer. Then, the quantity and quality of aptamer-Diazinon interaction were simulated using molecular dynamics as a mobility technique. RMSD, RMSF, radius of gyration, and the number of hydrogen bonds formed between Diazinon-aptamer were monitored to assess the quantity and quality of interactions. G-quadruplex DNA aptamer (DF20) showed to be a reliable candidate for Diazinon biosensing. The apta-nanosensor designed using simulation results allowed with linearity detection in the range of .141-.65 nM and a LOD of 17.903 nM, and it was validated using a computational molecular approach.

Design and evaluation of an apta-nano-sensor to detect Acetamiprid in vitro and in silico.

Pesticide detection is a main concern of food safety experts. Therefore, it is urgent to design an accurate, rapid, and cheap test. Biosensors that detect pesticide residues could replace current methods, such as HPLC or GC-MC. This research designs a biosensor based on aptamer (Oligonucleotide ss-DNA) in the receptor role, silver nanoparticles (AgNPs) as optical sensors and salt (NaCl) as the aggregative inducer of AgNPs to detect the presence of Acetamiprid. After optimization, .6 µM aptamer and 100 mM salt were employed. The selectivity and sensitivity of the complex were examined by different pesticides and different Acetamiprid concentrations. To simulate in vitro experimental conditions, bioinformatics software was used as in silico analysis. The results showed the detection of Acetamiprid at the .02 ppm (89.8 nM) level in addition to selectivity. Docking outputs introduced two loops as active sites in aptamer and confirmed aptamer-Acetamiprid bonding. Circular dichroism spectroscopy (CD) confirmed upon Acetamiprid binding, aptamer was folded due to stem-loop formation. Stability of the Apt-Acetamiprid complex in a simulated aqueous media was examined by molecular dynamic studies.