Mehriar Amininasab's research while affiliated with University of Tehran and other places

Background Influenza A virus (IAV) infection remains a serious public health threat. Due to drug resistance and side effects of the conventional antiviral drugs, repurposing the available natural compounds with high tolerability and fewer side effects has attracted researchers’ attention. The aim of this study was to screen in vitro anti-influenza activity of three anionic compounds ascorbate, acetate, and citrate. Methods The non-cytotoxic concentration of the compounds was determined by MTT assay and examined for the activity against IAV in simultaneous, pre-, and post-penetration combination treatments over 1 h incubation on Madin-Darby Canine Kidney (MDCK) cell line. The virus titer and viral load were determined using hemagglutination assay (HA) and qPCR, respectively. Few pro-inflammatory and anti-inflammatory cytokines were evaluated at RNA and protein levels by qPCR and ELISA, respectively. Results The non-cytotoxic concentrations of the ascorbate (200 mg/ml), acetate and citrate (both 3 mg/ml) reduced the viral titer by 6.5, 4.5, and 1.5 logs in the simultaneous combination treatment. The M protein gene copy number decreased significantly in simultaneous treatment ( P < 0.01). The expression of cytokines was also affected by the treatment of these compounds. Conclusions These anionic compounds could affect the influenza virus load, thereby reducing pro-inflammatory cytokines and increasing anti-inflammatory cytokines levels.

Selective induced non-canonical programmed deaths in the lipid raft type 1-enriched MDA-MB-231 is a promising treatment approach. Cationic amphiphilic peptides conjugated to relatively long fatty acyl chains tending to self-aggregate are prone to upregulate necroptotic and paraptotic signaling. We investigated the toxic effects of an N-terminally palmitoylated magainin derivate (P1MK5E) in the MDA-MB-231 cells compared to its structure at molecular level. The modeling showed that the palmitoylation reinforces a turn-like structural motif in the lipopeptide which is likely required for its activity. P1MK5E triggered intracellular generation of reactive oxygen species (ROS), G2-phase arrest, mitochondrial membrane potential (ΔΨmt) disturbance and presumable flopping of phosphatidylserine (PtdSer) to the cancer cell membrane outer surface in comparable manner to doxorubicin (DOX) inducing apoptotic signaling. Despite forming extensive congregates of different sizes at the cell surface, P1MK5E had little impacts on the MDA-MB-231 membrane integrity. The cell death upon exposure to the lipopeptide was, however, caspase 3 independent and characterized by cytoplasmic vacuolation and no distinct nuclear fragmentation that is to be privileged in the treatment of apoptotic resistance pathways in triple-negative breast cancers (TNBCs).

Generation of an herbicide-tolerant cultivar could be an important goal in rice breeding program. Therefore, a direct mutagenesis approach (megaprimer technique) was employed to generate the EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) mutant version called epsps in which glycine 96 was replaced by alanine. Then both EPSPS and epsps genes were separately cloned into pET22b system following transformation of E. coli BL21. The transformed bacteria showed a higher expression level of EPSPS and epsps extending their survival in presence of high levels of glyphosate. Interestingly, the bacteria harboring pET22b:epsps could grow in the medium containing 18 mM glyphosate. Subsequently, Hashemi rice cultivar was used to generate two types of transgenic rice including plants harboring either EPSPS (35S:EPSPS) or epsps (35S:epsps). Molecular analysis was performed on T3 putative transgenic plants so as to confirm the presence and expression of transgenes. The results demonstrated that 35S:epsps is actively and stably transcribed in T3 transgenic plants and developed a considerable tolerance towards glyphosate in comparison with the 35S:EPSPS plants. When compared to non-transgenic plants, the epsps mutant plants accumulated higher levels of chlorophyll and carotenoid in association with less shikimic acid, which are considered as some indicators of glyphosate side effects. Moreover, flavonoid accumulation was accompanied by enhanced levels of alkaloids and lower levels of proline in 35S:epsps plants; indicating that shikimic acid pathway is well functioning and transgenic plants especially 35S:epsps experienced less stress. Therefore, for the first time, rice was successfully transformed by 35S:epsps resulting in generation of transgenic plants with a considerable level of glyphosate tolerance.

Cucurbit[n]urils (CB[n], n = 5, 6, 7, 8, 10, 14) and their derivatives due to the hydrophobic cavities and polar carbonyl portals have been considerably explored for their potential uses as drug delivery systems. It is important to understand how these macrocyclic compounds interact with guests. Camptothecin (CPT), as a natural alkaloid, is a topoisomerase inhibitor with antitumor activity against breast, pancreas and lung cancers. The application of this drug in cancer therapy is restricted due to its low aqueous solubility and high toxicity. Recently, the complex formation between the cucurbit[7]uril (CB[7]) / acyclic cucurbit[4]uril (aCB[4]) nanocontainers and CPT have been evaluated to overcome the potential drawbacks of the related drug. Herein, using computational methods, we identified the interaction mechanism of CPT with CB[7]/aCB[4]s consist of benzene and naphthalene sidewalls (aCB[4]benzene and aCB[4]naphthalene, respectively), since the experimental approaches have not completely provided information at the molecular level. Our molecular docking and molecular dynamics (MD) simulations show that CB[7] and its two acyclic derivatives form stable inclusion complexes with CPT especially through hydrophobic interactions. We also found that aCB[4]s with the aromatic sidewalls can attach to CPT through π-π interactions. This investigation highlights aCB[4]s due to the structural properties and flexible nature as a better nanocontainers for controlled release delivery of pharmaceutical agents in comparison with CB[7] nanocontainer.

Paclitaxel (PTX) is a natural terpenoid compound that has been broadly studied for its antitumor activities and widely used as a chemotherapy medication. The treatment efficacy of PTX is affected by its low aqueous solubility, thus causing a subject of extensive research. In recent years, synthetic molecular containers such as cucurbit[n]urils (CB[n]s) and their derivatives have been significantly developing because of their remarkable ability to bind hydrophobic and cationic drugs. Recent experimental studies have shown that acyclic CB[n]-type containers (aCB[n]s), as new derivatives of the family of CB[n]s, increase the solubility of insoluble pharmaceuticals. However, the nature by which the drug interacts with carriers remains largely unknown. In this study, molecular docking and molecular dynamics (MD) simulation were performed to understand how CB[7] and aCB[4] nanocontainers interact with PTX which affect its aqueous solubility. The results clarify how the flexibility of containers is influenced by their structure and how this affects their interactions with PTX. Our results reveal that although both CB[7] and aCB[4] are capable of binding to PTX, the affinity to aCB[4] is higher than that of CB[7]. It has also been shown that the binding to both CB[7] and aCB[4] is probably an entropy-driven process. This research supports the potential use of the cucurbit[n]urils and their acyclic derivatives as drug delivery systems.

Structural characterization of intrinsically disordered proteins (IDPs) is paramount and challenging in structural biology. In this regard, a de novo computational protocol is introduced to build heterogeneous structural libraries for amyloid-β (Aβ) as a critical IDP. This method combines the strength of the simulated annealing – in jumping over energy barriers and escaping from traps – with short conventional molecular dynamics simulations to quickly explore local regions of the conformational space. The protocol efficiency and reliability in building Aβ conformational library is compared with two widely used simulation methods, replica exchange molecular dynamics and multiple trajectory sampling. The probability distribution functions of various structural and energetic features are constructed for each library, and also the diversity and convergence rates in these protocols were compared. Our results show that the suggested protocol is a successful computational method in the generation of a diverse conformational library of the Aβ monomer in agreement with experimental data. This method focuses on visiting more conformations in less computational time without paying attention to the statistical weight of each state in the library. We believe that the suggested computational technique can be used for generating a reasonable starting pool for subsequent reweighting with experimental data to obtain a statistical ensemble.

A new member of kunitz-type protein family, PPTI (Pseudocerastes Persicus Trypsin Inhibitor), was isolated from the venom of Persian false horned viper Pseudocerastes persicus and characterized. Mass spectrometry and amino acid sequencing revealed that PPTI is a 68 amino acid protein with molecular weight of about 7.6 kDa. The first amino acid residue of PPTI is N-terminally blocked via a post translational modification to pyroglutamyl. Sequence comparison against UniProtKB shows a high sequence similarity of PPTI with kunitz-type proteins, especially serine protease inhibitors and dendrotoxins (DTXs). The number of cysteines and disulfide bonding pattern of PPTI are the same as kunitz-type proteins. Based on sequence derive information, anti-protease activity of PPTI against trypsin was experimentally examined. The constructed homology models of PPTI confirmed the ability of PPTI to fold similarly to kunitz domain. The presence of characteristic basic-hydrophobic functional dyad of DTXs in PPTI supports its inhibitory potential against potassium channels. In summary, this study hypothesized the dual functionality of PPTI according to its inhibitory effect on trypsin and its potential ability in blocking potassium channel.

The bacterial selectivity of an amphiphilic library of small Arg/Trp‐rich cyclic α/β‐tetra‐, α/β‐penta‐, and α/β‐hexapeptides, which contained asymmetric backbone configurations and differed in hydrophobicity and content of alternating D,L‐amino acids, was investigated against Bacillus subtilis and Escherichia coli. The structural analyses showed that the peptides tend to form assemblies of different shapes. All‐L‐peptides, especially the most hydrophobic pentamers, were stronger anti‐B. subtilis. With the exception to cyclo(Phe‐DTrp‐β3hArg‐Arg‐DTrp), the peptides had no effects on E. coli inner membrane but lyzed the lipopolysaccharide layer according to their activity pattern. The activities adversely changed with decreasing the number of amide intramolecular hydrogen bonds in assemblies of diastereomeric peptides and the ratio of hydrophobic/hydrophilic solvent accessible surface area. The remarkable enhanced entropic contribution for the partitioning of the least conformationally constrained cyclo(Trp‐DPhe‐β3hTrp‐Arg‐DArg) into the membranes supported the strong self‐assembly behavior, which therefore, makes the peptide less penetrable through E. coli outer layer.

3D representation of constructed homology model of free firefly luciferase (PDB codes of templates: 1BA3, 1LCI and 3IEP; target model is in yellow color). (TIF)

The motion along eigenvector 2 for f298L simulation. (MPG)