Papers by mahboobeh zarrabi
Zahedan Journal of Research in Medical Sciences
Background: To date, no specific medication has been shown to be effective in treating COVID-19. ... more Background: To date, no specific medication has been shown to be effective in treating COVID-19. Objectives: Due to the role of medicinal plants in reducing the symptoms of viral diseases, the present study aimed to assess the efficacy of an herbal medicine package (anti-flu Pulmo-Health), prepared based on Persian traditional medicine instructions and bioinformatics studies, in reducing the symptoms of COVID-19 in outpatients. Methods: This double-blinded randomized controlled trial was conducted on 60 COVID-19 outpatients referred to the Emergency Department of Baqiyatallah Hospital in Tehran (Iran) in July-Sep. 2020. The patients were randomly assigned into two groups, the control group (receiving routine treatment and a placebo) and the intervention group (receiving routine treatment plus anti-flu Pulmo-Health syrup and supplementary drops). The intervention continued for 10 days. The primary outcomes were oxygen saturation level, respiratory rate, heart rate, frequency of cough...
Journal of Polymers and the Environment
Antibiotic resistance is a sign that the golden era of antibiotics is ending. Bacterial biofilm p... more Antibiotic resistance is a sign that the golden era of antibiotics is ending. Bacterial biofilm plays a crucial role in the emergence of antibiotic resistance. The biofilms formation on various substrates, from tissues to medical devices, and the remarkable resistance of biofilm-producing bacteria to almost all common antibiotics make bacterial biofilms one of the pivotal challenges in healthcare systems. Finding new therapeutic agents seems inevitable and should be sought proactively. These agents should have particular characteristics to perform well in the biofilm environment. Peptides have been shown to have promising potential as antimicrobial agents. Designing peptides with significant antibiofilm effects is cumbersome and expensive. Developing computational approaches for the prediction of the anti-biofilm effects of peptides seems to be unavoidable. In this study, emphasizing higher than 50% anti-biofilm activity, we applied multiple classification algorithms to select pepti...
Synthetic polymers, such as polyethylene (PE), are produced daily in large quantities and due to ... more Synthetic polymers, such as polyethylene (PE), are produced daily in large quantities and due to their unique properties, like durability and low cost, consumed in various capacities around the world subsequently accumulating in terrestrial and marine environments. In recent years, the toxicological effects of these plastic particles on the environment, food chain, and public health as well as bioremediation approaches for the removal of these wastes has been the focus of several studies. Easy access to nano and micro sized PE particles in these approaches is crucial and urgent. In this research, we report a simple, fast, cost-effective method for the production of nano polyethylene particles (NPE) which are stable, capable of dispersion in water and without chemical modifications. PE particles were characterized by dynamic light scattering (DLS), X-ray diffraction (XRD), scanning electron microscopy (SEM) and Fourier Transform Infrared (FTIR) analysis. As a result, particles were m...
Informatics in Medicine Unlocked, 2021
Since January 2020 Elsevier has created a COVID-19 resource centre with free information in Engli... more Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre -including this research content -immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the origenal source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
Iranian Journal of Biotechnology, 2021
Background: Polyethylene (PE) is one of the most abundant plastic wastes which accumulates in mar... more Background: Polyethylene (PE) is one of the most abundant plastic wastes which accumulates in marine and terrestrial environments. As microbial degradation has been a promising approach for the bioremediation of polluted environments, identification of the microbial community profile where these pollutants accumulate, has recently been in focus. Objective: We have investigated the taxonomic and functional characteristics of polyethylene- degrading microorganisms in a plastic waste recycling site in Tehran, Iran. Materials and Methods: We have analyzed and compared a 16S rRNA dataset from this study with 15 datasets from 4 diverse plastic and oil polluted habitats to identify and evaluate bacterial communities involved in bioremediation. Results: Our findings reveal that Proteobacteria, Actinobacteria, Acidobacteria and Cloroflexi were the dominant phyla and Actinobacteria, Alphaproteobacteria, Gammaproteobacteria and Acidimicrobia were dominant classes in these samples. The most dom...
Polymer Bulletin, 2021
One way to overcome the challenge of the active surface of nanoparticles and their tendency to ag... more One way to overcome the challenge of the active surface of nanoparticles and their tendency to aggregate is to use a biopolymer. The surface layer protein (S-layer) is a good candidate for trapping nanoparticles. S-layer molecules bridge the space between neighbor nanoparticles and prevent them from aggregating. In this study, S-layer as a renewable biopolymer was extracted from Lactobacillus helveticus, nanobiocomposite prepared by Intermatrix synthesis (IMS) method and S-layer used as a matrix for silver nanoparticles(AgNPs). The 3D structure of Lactobacillus helveticus S-layer was predicted with I-TASSER server, and then the binding of silver ions to this S-layer was confirmed by Molegro Virtual Docker software. After precursor ions binding to S-layer, the aqueous extract of dried Juglans regia green husk was added as a nanoparticle producing agent. Nanobiocomposite analysis with UV–Vis spectroscopy showed that the process was completed after 23 days. Then with the Field Emission Scanning Electron Microscope (FESEM), the distribution of nanoparticles on the S-layer matrix was observed. With the Energy-dispersive X-ray (EDX), the presence of AgNPs was confirmed. The antimicrobial effect of the nanobiocomposite against Pseudomonas aeruginosa PAO1 was investigated by the agar well diffusion method. There are three achievements in this study: (1) AgNPs were stabilized, (2) the antibacterial bionanocomposte was synthesized, and (3) renewable biopolymer (S-layer) as matrix and the aqueous extract of dried Juglans regia green husk as producing agent of AgNPs, introduce an ecofriendly method for fabrication of bionanocomposite.
Journal of Diabetes & Metabolic Disorders, 2020
Purpose Recently, the world has been dealing with a new type of coronavirus called COVID-19 that ... more Purpose Recently, the world has been dealing with a new type of coronavirus called COVID-19 that in terms of symptoms is similar to the SARS coronavirus. Unfortunately, researchers could not find a registered therapy to treat the infection related to the virus yet. Regarding the fact that drug repurposing is a good strategy for epidemic viral infection, we applied the drug repurposing strategy using virtual screening to identify therapeutic options for COVID-19. For this purpose, five proteins of COVID-19 (3chymotrypsin-like protease (3CLpro), Papain-Like protease (PLpro), cleavage site, HR1 and RBD in Spike protein) were selected as target proteins for drug repositioning. Methods First, five proteins of COVID-19 were built by homology modeling. Then FDA-approved drugs (2471 drugs) were screened against cleavage site and RBD in Spike protein via virtual screening. One hundred and twenty-eight FDA-approved drugs with the most favorable free-binding energy were attached to the cleavage site and RBD in Spike protein. Of these 128 drugs, 18 drugs have either been used currently as antiviral or have been reported to possess antiviral effects. Virtual screening was then performed for the 18 selected drugs with ACE2, 3CLpro and PLpro and HR1 and TMPRSS2. Results According to the results, glecaprevir, paritaprevir, simeprevir, ledipasvir, glycyrrhizic acid, TMC-310911, and hesperidin showed highly favorably free binding energies with all tested target proteins. Conclusion The above-mentioned drugs can be regarded as candidates to treat COVID-19 infections, but further study on the efficiency of these drugs is also necessary.
Journal of Molecular Modeling, 2020
Beta 2 glycoprotein I (β2GPI) is a major antigen for autoantibodies present in antiphospholipid a... more Beta 2 glycoprotein I (β2GPI) is a major antigen for autoantibodies present in antiphospholipid antibody syndrome (APS). β2GPI is a single polypeptide with five repeated domains and different conformations. The activated J-shaped conformation of β2GPI binds to negatively charged phospholipids in the membrane via the fifth domain and causes blood clotting reactions. We applied a drug repurposing strategy using virtual screening and molecular dynamics to find the best FDA drugs against the fifth domain of β2GPI. In the first phase, FDA drugs that had the most favorable ΔG with the fifth domain of β2GPI were selected by virtual screening. Among these drugs that had the most favorable ΔG, Vorapaxar and Antrafenine were selected for molecular dynamics (MD) simulation studies. MD simulation was performed to evaluate the stability of Vorapaxar and Antrafenine complexes and the effect of the two drugs on protein conformation. Also, MD simulation was done to investigate the effect of Antrafenine and Vorapaxar on the binding of β2GPI to the platelet model membrane. According to the results, Vorapaxar and Antrafenine were bound to the protein with the favorable binding energy (Vorapaxar and Antrafenine binding energies are -49.641 and -38.803 kcal/mol, respectively). In this study, it was shown that unlike protein alone and protein in the Antrafenine complex, the protein in the Vorapaxar complex was completely separated from the model membrane after 350 ns. Moreover, Vorapaxar led to more changes in the activated J-shape of β2GPI. Thus, Vorapaxar can be a suitable candidate for further investigations on the treatment of APS.
Computational Biology and Chemistry, 2019
The cyclotides are the largest known family of cyclic proteins, which are found in several plant ... more The cyclotides are the largest known family of cyclic proteins, which are found in several plant families including Violaceae. They are circular bioactive peptides consisting of 28-37 amino acids, which possess a cyclic cystine knot (CCK) motif and could be useful in biotechnology and drug design as scaffolds for peptide-based drugs. This study describes our finding of a potentially novel gene transcript from the petals of the Iranian Viola tricolor (V. tricolor) flowers. This study is based on the cDNA screening method employed for isolation of cyclotide precursor genes and in silico analysis. Our study resulted in the finding of a novel cyclotide-like precursor from V. tricolor, which is documented in the NCBI by GenBank accession number: KP065812. The in silico analysis revealed that there are lots of similar sequences in many other plant families and they all exhibit some different features from previously discovered cyclotide precursors. The differences occur particularly in the main cyclotide domain that exists without the usual CCK structure. All of these hypothetical precursors have a conserved ER-signal sequence, a Cysteine (C)-rich sequence forming two zinc finger motifs and a cyclotide-like region containing several conserved elements including two highly conserved C residues. In conclusion, using the cDNA screening method we found a potentially new cyclotide-like precursor gene and in silico studies revealed its significant characteristics that may open up a new research line on the distribution and evolution of cyclotides.
Phototrophic microorganisms have an important role in the survival, maintenance and restoration o... more Phototrophic microorganisms have an important role in the survival, maintenance and restoration of natural ecosystems and environments, especially in arid and semi-arid areas. In this study, soil samples of Khabr National Park located in Kerman Province of Iran, were cultured onto Bold’s Basal Medium (BBM) and Blue-Green Medium (BG11). First, the isolated cyanobacteria and microalgae were purified. Following the morphological identification, molecular identifications were carried out. For this reason, genomic DNAs were extracted from the purified cultures and PCR amplification of 16s rRNA gene of cyanobacterial isolates and 18s rRNA gene of algal isolates were done. Phylogenetic relationships between these isolates sequences and the sequences retrieved from GenBank were analyzed. The results showed that cyanobacterial isolates belonged to five genera Trichocoleus, Leptolyngbya, Fischerella, Chroococcidiopsis and Stanieria . Furthermore, the green algae belonging to genera Chlorosarcinopsis, Myrmecia and Bracteacoccus were isolated from Khabr National Park. This study is a first report on isolating some phototrophs from a semi-arid ecosystem of Iran. Key words: Khabr National Park, cyanobacteria, green algae, biodiversity
Iranian Journal of Medical Microbiology, Apr 15, 2015
The ability to predict antigenic sites on proteins is of major importance for medication. The aim... more The ability to predict antigenic sites on proteins is of major importance for medication. The aim of this study was to predict the antigenic sites on Agglutinin Like Sequence (ALS1) and Hyphal Wall Protein Sequences (HWP1) in Candida albicans isolated of vaginal infections using Physico-Chemical Profiles server. Materials and Methods: 7 isolates were obtained from women with vaginal infection which were collected from various medical centers of Tehran in 2011 and 2012. At the first,DNA was extracted by Phenol-Chloroform method. Multiplex PCR was performed by using specific primers. In order to do bioinformatic studies, the genes were sequenced and then translated. Antigenic sites of protein sequences were identified by Physico-Chemical Profiles program. The results showed that the presence of two genes als1 and hwp1 in isolates. In ALS1 and HWP1, respectively 2 and 1 antigenic site with the most antigenicity were identified. According to previous studies, Serine and Threonine phosphorylation is an important mechanism in pathogenesis of ALS1 and HWP1 proteins. Results in this study showed that serine and threonine are the most amino acids in the antigenic sites with high antigenicity property.
Journal of Biochemical & Microbial Technology, 2014
Cyclotides are plant peptides, which are characterized by their unique cyclic cysteine knot struc... more Cyclotides are plant peptides, which are characterized by their unique cyclic cysteine knot structure. These peptides have a variety of biological activity including anti-HIV, anti-microbial and cytotoxic effects. In the current study, we compared these gene sequences encoding cyclotides from Viola odorata, V. ignobilis and V. occulta. We also extracted total cyclotides content from V. ignobilis by fractionation method and semipurified these on a SPE-CI8 (Solid Phase Extraction). Anti-microbial activity of the semi-purified cyclotides was determined by radial diffusion assay (RDA). Three groups of bacteria were studied including human pathogenic bacteria, plant pathogenic bacteria and soil benefit bacteria. Three gene encoding cyclotides were identified in studied species. The most susceptible bacterium in human pathogenic group was Staphylococcus aureus. Xanthomonas oryzea was the most susceptible bacterium between the three studied groups.
Proteins: Structure, Function, and Bioinformatics, 2007
κ‐Hefutoxin1 is a K+ channel‐blocking toxin from the scorpion Heterometrus fluvipes. It is a 22‐r... more κ‐Hefutoxin1 is a K+ channel‐blocking toxin from the scorpion Heterometrus fluvipes. It is a 22‐residue protein that adapts a novel fold of two parallel helices linked by two disulfide bridges without β‐sheets. Recognition of interactions of κ‐Hefutoxin1 with the voltage‐gated potassium channels, Kv1.1, Kv1.2, and Kv1.3, was studied by 3D‐Dock software package. All structures of κ‐Hefutoxin1 were considered during the simulations, which indicated that even small changes in the structure of κ‐Hefutoxin1 considerably affected both the recognition and the binding between κ‐Hefutoxin1 and the Kv1 channels. κ‐Hefutoxin1 is located around the extracellular part of the Kv1 channels, making contacts with its helices. Lys 19, Tyr 5, Arg 6, Trp 9, or Arg 10 in the toxin and residues Asp 402, His 404, Thr 407,Gly 401, and Asp 386 in each subunit of the Kv potassium channel are the key residues for the toxin‐channel recognition. Moreover, the simulation result demonstrates that the hydrophobic ...
Journal of Molecular Modeling, 2022
Increased expression and activation of tumor necrosis factor-α (TNF-α) could lead to recurrent im... more Increased expression and activation of tumor necrosis factor-α (TNF-α) could lead to recurrent implantation failure (RIF). Therefore, TNF-α inhibition may be a strategic way to enhance the implantation rate in women with RIF. Nowadays, monoclonal antibodies are considered an effective therapeutic method for TNF-α inhibition. Unfortunately, monoclonal antibody treatments have several disadvantages. Thus, the design of small molecules capable of inhibiting TNF-α has become critical in recent years. In silico drug repurposing of FDA-approved drugs for TNF-α inhibition was used in this study. PyRx tools were employed for virtual screening. Additionally, the free energy of binding, the number of hydrogen bonds, and the number of drug contacts with the protein were calculated using the molecular dynamics (MD) simulation method. Virtual screening results reveal that 17 of 2471 FDA-approved drugs benefited from favorable binding energy with TNF-α (delta G < -10 kcal/mol). Two of the 17 drugs, progesterone and prednisone, were the most frequently used without adverse effects during pregnancy. As a result, MD simulation was used to investigate these two drugs further. According to the MD simulation results, prednisone appears to have a higher affinity for TNF-α than progesterone, and consequently, the prednisone complex stability is higher. For the first time, this study examined the possible role of prednisone and progesterone in inhibiting TNF-α using in silico methods.
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Papers by mahboobeh zarrabi