Computational designing of the ligands of Protein L affinity chromatography based on molecular docking and molecular dynamics simulations.

Protein L is a multidomain protein from Peptostreptococcus magnus with binding affinity to kappa light chain of human immunoglobulin (Ig) which is used for the purification of antibody fragments by affinity chromatography. The advances in protein engineering and computational biology approaches lead to the development of engineered affinity ligands with improved properties including binding affinity. In this study, molecular dynamics simulations (MDs) and Osprey software were used to design single B domains of the Protein L with higher affinity to antibody fragments. The modified B domains were then polymerized to ligand with six B domains by homology modeling methods. The results showed that single B domain mutants of MB1 (Thr865Trp) and MB2 (Thr847Met-Thr865Trp) had higher binding affinity to Fab compared to the wild single B domain. Also, MDs and molecular docking results showed that the polymerized Proteins L including the wild and mutated six B domains (6B0, 6B1, and 6B2) were stable during MDs and the two mutants of 6B1 and 6B2 showed higher binding affinity to Fab relative to the wild type.Communicated by Ramaswamy H. Sarma.

Evaluation of TUBB8 gene alterations in infertile women with oocyte maturation and cleavage arrest referred to Royan Institute.

RESEARCH QUESTION: Are TUBB8 gene variations present in Iranian infertile women with oocyte maturation arrest or embryo cleavage arrest? DESIGN: TUBB8 gene variations were investigated by polymerase chain reaction sequencing on blood samples from 16 women with oocyte maturation arrest and 12 women with cleavage arrest, collectively referred to as the experimental cohort, as well as 56 fertile women as the control group. The Exome Sequencing Project and dbSNP databases and the Genome Aggregation Database were used to search the frequency of corresponding variants. PolyPhen and SIFT were used to conduct in-silico analysis of gene variations and Align-GVGD was used to predict the effect of missense variants on proteins. The homology modelling and structure evaluation of variations was also checked. RESULTS: Two likely pathogenic variants [c.713C>T (p.Thr238Met), c.1054G>T (p.Ala352Ser)] were identified in patients with oocyte maturation arrest and one likely pathogenic variant [c.G763A, (p.Val255Met)] was identified in a patient with cleavage arrest. These changes were absent in controls. CONCLUSIONS: Three deleterious variants in TUBB8 related to oocyte maturation arrest or cleavage arrest and infertility were identified. TUBB8 variant screening for patients with oocyte maturation and cleavage arrest is recommended.

A novel nanocomposite containing zinc ferrite nanoparticles embedded in carboxymethylcellulose hydrogel plus carbon nitride nanosheets with multifunctional bioactivity.

A novel and biologically active nanobiocomposite is synthesized based on carbon nitride nanosheet (g-C3N4) based carboxymethylcellulose hydrogels with embedded zinc ferrite nanoparticles. Physical-chemical aspects, morphological properties, and their multifunctional biological properties have been considered in the process of evaluation of the synthesized structure. The hydrogels' compressive strength and compressive modulus are 1.98 ± 0.03 MPa and 3.46 ± 0.05 MPa, respectively. Regarding the biological response, it is shown that the nanobiocomposite is non-toxic and biocompatible, and hemocompatible (with Hu02 cells). In addition, the developed material offers a suitable antibacterial activity for both Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli).

Determination of antifungal activity and action mechanism of the modified Aurein 1.2 peptide derivatives.

BACKGROUND: With the emergence of drug-resistant fungi and the increased population prone to fungal infections, more effective antifungal drugs are needed. Aurein 1.2 is a potent antimicrobial peptide. Here, we designed a novel derivative of Aurein 1.2, called Aurein N3, which is a modified form of Aurein N2 (another Aurein 1.2 derivative), in which Lys 8 residue was replaced with Leu 13, and was also modified by creating two other mutations. METHODS: Aurein N3 was designed using several algorithms and docking studies. All peptides were synthesized and some of their bio-activity indices such as antifungal properties on 11 fungi, cytotoxicity, hemolysis, and time of the killing were investigated. Electron microscopy, lived/dead staining, and ergosterol binding assay were performed to study their mechanism of action. RESULTS: In comparison to Aurein 1.2 and N2, the docking studies showed that Aurein N3 has reduced binding energy toward ergosterol. The antifungal assessments showed that both Aurein N2 and N3 had strong activity against many fungi. Aurein N3 had lower cytotoxicity and higher binding capability to ergosterol. The hemolytic activity of Aurein N2 and N3 was less than parental Aurein 1.2. All peptides were able to attack the cell wall/membrane and enter the fungi cells. CONCLUSION: Here we introduced a novel derivative of Aurein 1.2 which has lower cytotoxicity, higher ergosterol-binding capability, and comparable antifungal activity compared to the original peptides. It can bind to ergosterol and can also attack the cell wall/membrane of fungi, although more studies are required to find its accurate mechanism of action.

Biological investigation of a novel nanocomposite based on functionalized graphene oxide nanosheets with pectin, silk fibroin and zinc chromite nanoparticles.

For biotechnology applications, a novel nanobiocomposite was synthesized based on modification of graphene oxide (GO) by extracted silk fibroin (SF), natural polymer pectin (Pec) and zinc chromite (ZnCr2O4) nanoparticles (NPs). The structure and properties of hybrid nanobiocomposite GO-Pec/SF/ZnCr2O4 such as thermal stability, less toxicity, biocompatibility, antibacterial, and biodegradable were proved by using field emission scanning electron microscope (FE-SEM), Fourier-transformed infrared (FT-IR), Energy dispersive X-ray spectroscopy (EDS), thermal gravimetric analysis (TGA), and X-Ray diffraction (XRD). According to the biological features of substances, the GO-Pec/SF/ZnCr2O4 nanobiocomposite shows perfect results in MTT (83.71 %) and Hemolysis (16.52 %) assays. accordingly, mentioned properties of this nanobiocomposite can be used as a scaffold for medical applications.

Functionalization of chitosan by metformin, nickel metal ions and magnetic nanoparticles as a nanobiocomposite for purification of alkaline phosphatase from hen's egg yolk.

In this study, a novel and green chitosan-metformin/NiCl2/Fe3O4 nanobiocomposite was synthesized and used to purify alkaline phosphatase (ALPs) from hen's egg yolk. For this purpose, after functionalization of the chitosan biopolymer by terephthaloyl chloride-metformin ligand, the coordination with Ni(II) and magnetization process were performed. The structure and properties of the synthesized nanobiocomposite were then evaluated by using analyzes such as FT-IR, EDX, FE-SEM, XRD, TGA and VSM. Purification of ALPs with chitosan-metformin/NiCl2/Fe3O4 nanobiocomposite is a fast, reusable and cost-effective method. By this protocol, 62% purification efficiency was obtained and the synthesized nanobiocomposite was not attached to other proteins in hen's egg yolk. ALPs was obtained approximately in the pure form and the purification process was evaluated using SDS-PAGE. The reusability of nanobiocomposites was evaluated and a slight decrease in adsorption capacity was observed after 4 cycles.

Designing vaccine candidates against dengue virus by in silico studies on structural and nonstructural domains.

One-third of the world's population is at risk of Dengue infection. Envelope domain 3 (EDIII) and nonstructural protein1 (NS1) proteins as the potent antigenicity regions for humoral immunity in addition to the bc loop region as a completely conserved region have been used for designing protective vaccines. We aimed to design vaccine candidates according to the bc loop, EDIII, and NS1 regions of Dengue serotype2 to be used as vaccine candidates for all serotypes of Dengue virus especially serotype 2. Firstly the bc loop region with EDII fragments at both ends as well as EDIII and NS1 regions were used which were linked with the GGGGS linker to the bc loop region. In two other strategies, the bc loop with EDII and NS1 fragments at both ends was used to increase its structural stability. Tertiary structure prediction and validation of vaccine constructs indicated that all vaccine constructs were modeled with high quality and stable structure during molecular dynamics simulation. B cell epitope mapping by Bepipred and ElliPro methods confirmed the existence of high potent epitopes in the bc loop, EDIII, and NS1 regions in both linear and conformational B cell epitopes. Furthermore, molecular docking for the bc loop region demonstrated that all designed vaccines have a higher affinity to interact with 1C19 monoclonal antibody than only the bc loop region or bc loop epitope in the protein EII. Our data of in silico studies indicated that the designed vaccines could effectively induce humoral immunity against four dengue serotypes.

COVID-19: A systematic review and update on prevention, diagnosis, and treatment.

Since the rapid onset of the COVID-19 or SARS-CoV-2 pandemic in the world in 2019, extensive studies have been conducted to unveil the behavior and emission pattern of the virus in order to determine the best ways to diagnosis of virus and thereof formulate effective drugs or vaccines to combat the disease. The emergence of novel diagnostic and therapeutic techniques considering the multiplicity of reports from one side and contradictions in assessments from the other side necessitates instantaneous updates on the progress of clinical investigations. There is also growing public anxiety from time to time mutation of COVID-19, as reflected in considerable mortality and transmission, respectively, from delta and Omicron variants. We comprehensively review and summarize different aspects of prevention, diagnosis, and treatment of COVID-19. First, biological characteristics of COVID-19 were explained from diagnosis standpoint. Thereafter, the preclinical animal models of COVID-19 were discussed to frame the symptoms and clinical effects of COVID-19 from patient to patient with treatment strategies and in-silico/computational biology. Finally, the opportunities and challenges of nanoscience/nanotechnology in identification, diagnosis, and treatment of COVID-19 were discussed. This review covers almost all SARS-CoV-2-related topics extensively to deepen the understanding of the latest achievements (last updated on January 11, 2022).

Computational Engineering of Protein L to Achieve an Optimal Affinity Chromatography Resin for Purification of Antibody Fragments.

Protein L affinity chromatography is a useful method for the purification of antibody fragments containing kappa light chains. In affinity chromatography, increasing the binding affinity leads to increased product purity, recovery, and dynamic binding capacity (DBC). In this study, molecular docking and molecular dynamics simulation techniques were used to design the engineered Protein L with higher affinity to the kappa light chain. Each engineered ligand was produced as a recombinant protein and coupled to a solid matrix. The purity, recovery, and DBC of the engineered resins were evaluated and then compared to those of a commercially available resin. The results showed important parameters for engineering more efficient Protein L ligands for affinity chromatography.

First report of antifungal activity of CecropinA-Magenin2 (CE-MA) hybrid peptide and its truncated derivatives.

The use of natural antimicrobial peptides (AMPs) is limited. Modifications of peptides by in silico predictions and computational methods can lead to more accurate designs and reducing their high synthesis costs, instability, and cytotoxicity. In this study, the antifungal properties of CecropinA-Magenin2 (CE-MA) hybrid peptide and its truncated derivatives were evaluated. Eleven C-terminal-truncated derivatives were designed and three of them with 10, 8 and 6 residues namely CMt1, CMt2 and CMt3 were selected through an initial screening based on the prediction of antimicrobial and antifungal activities, toxicity and physicochemical properties. These derivatives and the parental CE-MA peptide were synthesized. Then, based on molecular docking studies, antimicrobial tests and cytotoxicity assays, CMt1 peptide was selected for further studies such as time of killing, combinatorial effects with other drugs and the mechanism of action. The results showed that CE-MA is a weak antifungal peptide but its truncated derivative, CMt1 showed a strong antifungal activity with less toxicity. The results of the ergosterol assay, confocal microscopy and FE-SEM studies indicated that invasion to cell wall and membrane components were the main antifungal mechanisms of CMt1 peptide. Altogether, here we introduce a new truncated peptide with a strong antifungal activity with less toxicity which can be a good candidate for further in vivo and clinical studies to be used as an antifungal drug.

Rabies virus matrix protein targets host actin cytoskeleton: a protein-protein interaction analysis.

Multifunctional matrix protein (M) of rabies virus (RABV) plays essential roles in the pathogenesis of rabies infection. Identification of M protein interacting partners in target hosts could help to elucidate the biological pathways and molecular mechanisms involved in the pathogenesis of this virus. In this study, two-dimensional Far-western blotting (2D-Far-WB) technique was applied to find possible matrix protein partners in the rat brainstem. Recombinant RABV M was expressed in Pichia pastoris and was partially purified. Subsequently, 2D-Far-WB-determined six rat brainstem proteins interacted with recombinant M proteins that were identified by mass spectrometry. Functional annotation by gene ontology analysis determined these proteins were involved in the regulation of synaptic transmission processes, metabolic process and cell morphogenesis-cytoskeleton organization. The interaction of viral M protein with selected host proteins in mouse Neuro-2a cells infected with RABV was verified by super-resolution confocal microscopy. Molecular docking simulations also demonstrated the formation of RABV M complexes. However, further confirmation with co-immunoprecipitation was only successful for M-actin cytoplasmic 1 interaction. Our study revealed actin cytoplasmic 1 as a binding partner of M protein, which might have important role(s) in rabies pathogenesis.

Isolation and characterization of a novel scFv antibody fragments specific for Hsp70 as a tumor biomarker.

Many studies have shown that more than 50% of tumors express heat shock protein 70 kDa (Hsp70) at the plasma membrane surface while not seen in normal cells, therefore it is a promising therapeutic target in human cancers. Hence, we used phage display technology to produce a single-chain fragment variable (scFv) antibody against human Hsp70. For this, a target peptide from human Hsp70 was designed using bioinformatics studies and was chemically synthesized. Then, the selection was performed using four rounds of biopanning with a stepwise decreased amount of the target peptide. Fourteen positive scFv clones were selected using monoclonal phage enzyme-linked immunosorbent assay screening, which was further characterized by means of the polymerase chain reaction and DNA sequencing. Among them, the G6 clone was selected to express scFv into the Escherichia coli. Expression and purification of the scFv shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and confirmed by Western blot analysis. In silico analysis confirmed specific binding of the scFv to Hsp70 in CDR regions. The specificity of the scFv measured by surface plasmon resonance and immunofluorescence of the A549 human lung carcinoma cell line confirmed the in vitro function of the scFv. Based upon these findings, we propose a novel anti-human Hsp70 scFv as potential immunotherapy agents that may be translated into preclinical/clinical applications.

Effect of acute hypoxia on CXCR4 gene expression in C57BL/6 mouse bone marrow-derived mesenchymal stem cells.

BACKGROUND: One of the most important stimuli in stem cell biology is oxygen. Chemokine receptor 4 (CXCR4) plays a crucial role in the migration and homing of stem cells. In this study, mesenchymal stem cells (MSCs) were exposed to 1% oxygen to investigate the effect of acute hypoxia on CXCR4 gene expression. MATERIALS AND METHODS: MSCs were isolated from C57BL/6 mouse bone marrow and were identified and expanded in normoxic culture. Cells were incubated at 37°C under 1% hypoxic conditions for periods of 4, 8, 16, 24, and 48 h. After hypoxia preconditioning, the cells were placed in normoxic condition for 8 h to achieve cellular hypoxia-reoxygenation. To assess the level of CXCR4 gene expression, real-time quantitative reverse transcription-polymerase chain reaction was carried out for each group. RESULTS: Data from statistical analysis illustrated that exposure of MSCs to acute hypoxic condition down-regulates CXCR4 expression with the maximum under-expression observed in 4 h (0.91 ± 0.107) and 8 h (50 ± 2.98) groups. Moreover, the relative gene expression of CXCR4 was decreased after hypoxia-reoxygenation by more than 80% in 4 h (0.136 ± 0.018) and 24 h (12.77 ± 0.707) groups. CONCLUSION: The results suggest that CXCR4 expression in MSCs decreases upon acute hypoxic stress. Furthermore, hypoxia-reoxygenated MSCs showed decreased expression of CXCR4, compared to cells subjected to acute hypoxia. This difference could have resulted from the cells being compatible with low oxygen metabolism. In summary, before the therapeutic application of MSCs, it should be regarded as a necessity to optimize the oxygen concentration in these cells, as it is a critical factor in modulating CXCR4 expression.

In vitro generation of glucose-responsive insulin producing cells using lentiviral based pdx-1 gene transduction of mouse (C57BL/6) mesenchymal stem cells.

The objective of this study was to evaluate the potential of this type of recombinant lentivirus to generate glucose-responsive insulin producing cells in vitro. All steps of cloning were confirmed using restriction digests. After the transduction, mesenchymal stem cells gradually began to change their morphology and showed differentiation into islet like structures. RT-PCR results confirmed the expression of insulin1, insulin2 and pdx-1 in differentiated cells. Dithizone staining of mouse MSCs showed the concentration of glucose in islet like structures. ELISA analysis validated the insulin secretion of islet like structures which in the high-glucose medium (25mmol/l) was 7.44 fold higher than that secreted in the low-glucose medium (5mmol/l). Our results demonstrated that mouse mesenchymal stem cells can be differentiated into effective glucose-responsive insulin producing cells through our new recombinant lentiviral transduction of pdx-1 gene in vitro. This new lentiviral vector could be suggested as an effective candidate for using in gene therapy of type-1 diabetes.