Modares Journal of Biotechnology

Abstract Epidermal growth factor receptor (EGFR) is one of the most important tyrosine kinase receptors that plays a key role in regulating cellular processes and the progression of many cancers, including lung cancer. In this study, the effects of second-generation EGFR inhibitors, including Afatinib, Dacomitinib, and Neratinib, as well as the candidate drugs Canertinib and Poziotinib, on wild-type EGFR were investigated using molecular dynamics (MD) simulations. For this purpose, structural data were collected and analyzed from reliable databases. Molecular docking studies led to the identification of drug binding sites, and molecular dynamics (MD) simulations under physiological conditions investigated stability and ligand-protein interactions. The parameters such as RMSD, radius of gyration (Rg), SASA, and hydrogen bonds were calculated to evaluate the stability of the protein-ligand complex. The results of the MMPBSA analysis showed that Neratinib, with the lowest free energy of binding (ΔG), has a higher binding affinity to EGFR and demonstrated greater stability during the simulation. Also, the principal component analysis (PCA) showed that the EGFR-Neratinib complex has less dynamics and occupies less phase space, which indicates more stability of this complex.
These results show that of all the compounds studied, Neratinib may be the most potent and promising candidate in advancing combination therapies against EGFR.

Abstract Ferroptosis is a newly identified form of cell death associated with lipid peroxidation. This process is dependent on iron and polyunsaturated fatty acids (PUFAs). Despite the importance of ferroptosis, the molecular details of this process, particularly its impact on cellular membrane properties, remain unknown. In this study, structural and permeability changes in the plasma membrane resulting from lipid peroxidation during ferroptosis were investigated using molecular dynamics simulations. Initially, a model of the human red blood cell membrane was constructed based on experimental data. To simulate ferroptosis, the PUFA lipid chains in the red blood cell membrane were replaced with their hydroperoxide derivatives. Both systems (normal and ferroptotic membranes) were examined in All-Atom molecular dynamics simulations for 300 nanoseconds (with three replicates). The results showed that in the ferroptotic membrane, the thickness decreased, and the surface area increased. Additionally, the hydroperoxide groups in the fatty acid chains moved toward the polar head groups of the phospholipids. Besides these structural changes, the function of the membrane, which typically acts as an impermeable barrier to polar molecules such as water, was disrupted due to lipid peroxidation, while the overall membrane integrity remained intact. In summary, lipid peroxidation in ferroptosis induces significant changes in membrane structure and function, which could be utilized in the development of new treatments for severe diseases such as cancer and neurodegenerative disorders.

Abstract Today, the engineering of bone tissue has created special solutions to restore bone tissue by combining biological materials with a scaffold to provide cells suitable for bone formation and growth factors. In this research, a fusion peptide was designed with bioinformatics methods that can bind to the growth factors involved in bone tissue repair and lead to the trapping of these factors in the lesion site. In this study, heparin-binding domain was placed in the designed peptide and this peptide was complexed with growth factor in monomer and dimer forms with the help of docking. The structures of the complex were selected based on the lowest scores obtained, which included -912.5 and -1117, respectively. According to the results of docking and molecular dynamics simulation, this fusion peptide was able to bind to the growth factor of bone morphogenetic proteins. Based on the results of the simulation, unlike the peptide in the monomer state, the changes in the RMSD diagram of the peptide complex in the dimer state became stable after 10 nanoseconds from the simulation time and remained stable until the end of the simulation. These results show that the resulting complex in the dimer state has a better pattern of stability compared to the monomer state according to the investigation of the RMSD factor.

Abstract PFU DNA polymerse shows the lowest error rate in Polymerase Chain Reaction (PCR) but it seperates from DNA after about 20 nucleotides add to the end of primer strand. The research purpus is processivity improvement of PFU DNA polymerase by means of rational design and point mutation due to lowest enthropy and enthalpy costs. so DNA polymerases in B family with high processivity were selected and their structures and sequences were compared with PFU DNA polymerase then an optimized mutation was induced . Native form and mutant were simulated for 100 ns and the trajectories were analyzed. ΔG_binding was calculated by g_mmpbsa tool and proved that the mutant shows a robust affinity .

Abstract Matrix metalloproteinases (MMPs) are a zinc endopeptidase family that increases the metastatic behavior of human malignant tumors. Epigallocatechin gallate (EGCG) is a major component of green tea polyphenols and is used as an MMP inhibitor in cancer treatment. This study aims to develop and optimize the loading of EGCG in the liposomal delivery system in an experimental/ computational way. In this study, nanoliposomes were prepared by passive loading and thin-film hydration method. Size, zeta potential, stability, encapsulation efficiency, and nanoliposome drug release profile were investigated. Cytotoxicity of nanoliposomes was evaluated on three breast cancer cell lines using an MTT viability assay. To investigate the EGCG-Liposome interaction, coarse-grained Molecular Dynamic simulations were carried out. The mean diameter of liposome was 73.6±6.9 nm, the surface charge was -14.6 mV and the encapsulation efficiency was 78.5±7.3%. The encapsulation of EGCG into the liposome caused a continuous release of the drug after 72 h, which also increased the potency of the drug. Due to the EGCG hydrophobic properties, the major distribution is located at the hydrophobic part of the membrane. The energy and radial distribution function results indicate the stability of liposomes. Simulation results demonstrate that the majority of the drug is surrounded by liposomes, which indicates high encapsulation efficiency and confirms the developed synthesis method. Due to the low solubility of the drug, it seems that the use of liposomal carriers to deliver and release EGCG is a suitable solution to increase the efficiency of the drug.

Abstract The COVID-19 pandemic has created a global health crisis, and developing effective treatments is essential to prevent the spread of the disease and save millions of lives. One of the key proteins involved in the replication cycle of SARS-CoV-2, the virus that causes COVID-19, is the main protease enzyme, 3CL^pro. Due to its high importance, this enzyme is the subject of molecular, structural, and clinical investigations, and efforts have been made to develop drugs that can inhibit its activity. One such drug is the chemical compound N3, which has been found to have a high inhibitory effect against 3CL^pro. However, traditional medicine perspectives on this issue have been less explored. In this research, molecular docking interaction simulation and all-atom molecular dynamics (MD) simulation were conducted to study the potential inhibitory capability of generally available 21 plant-extracted compounds against the 3CL^pro enzyme. Three compounds with the highest inhibition probability were selected from the molecular docking results and subjected to 100 ns of MD simulation to investigate their stability and structural-dynamic-energetic features. Beside the complexes stability, the results from the simulation demonstrated that, all our selected three compounds induce N3 comparable structural-dynamics characteristics to 3CL^pro and, therefore, are expected to have a similar inhibitory ability against this enzyme. Compound number 5 was found to have the most favorable binding energy and was proposed as the best plant substitute for N3. The results from this research can be directly used to design experimental research for 3CLpro enzyme inhibition, saving the time-financial cost.

Abstract Aim: Follistatin-like protein 1 (FSTL1) is a secreted glycoprotein that plays an important role in regulating cell survival, proliferation, differentiation, migration, inflammation, and modulating the immune system. The FK domain in FSTL1 has 10 conserved cysteine residues that form 5 disulfide bonds. Despite extensive studies on the function of FSTL1, limited structural information is available about this biologically important molecule.
Materials and Methods:Using the SWISS-MODEL server and using the crystal structure of the FK domain of the mouse FSTL1 protein with the code (PDB: 6jzw) as a template, structural models of the FK domain of the human FSTL1 protein were prepared. In the next step, the resulting structures were checked using Swiss-PDB Viewer 4.10, Chimera 1.12 software, Ramachandaran diagram and PDBSUM server, in terms of the distance between two cysteine residues, the modeling error range, and the formation of disulfide bonds. Molecular dynamics simulations were performed using the AMBER software package with the ff14SB force field.
Results: The results showed that the FK domain without disulfide bond has root mean square deviations (RMSD) and root mean square fluctuations (RMSF), higher than the native FK domain. In addition, the radius of gyration in domain without disulfide bonds is significantly lower than that of native FK domain. The results show that the disulfide bonds of the FK domain play a role in the stability of the structural folding of the FK domain and the removal of these bonds increases the structural flexibility of this domain.

Abstract Vitamins D and E are two common medicines for diabetes treatment. Among the main issues in this field is the release of insulin into the circulatory system. Increasing the stability of insulin hexamer is an evolving strategy in improving insulin secretion efficiency. Insulin protein is commonly found in three forms: monomer, dimer, and hexamer. In this study, for the first time, computational approaches were used to investigate the effect of vitamins D3 and E on the stability of insulin hexamer. The molecular docking results indicate six specific binding sites for these vitamins. These bind to the hydrophobic sites of insulin subunits due to their structural rings and hydrophobic properties. The G-mmpbsa analysis indicates the stabilizing role of both vitamins. The binding of these vitamins to the hexamer has significantly increased the binding energy between insulin subunits. Also, the number of hydrogen bonds between monomeric subunits of each insulin homodimer increased in the presence of the vitamins. It also significantly increases the number of internal hydrogen bonds of hexamer protein. Accordingly, vitamins D3 and E bind to and stabilize the insulin hexamer, resulting in a slower and more balanced insulin release as well as a longer half-life for the dimer in the bloodstream. These findings will pave the way to design a new strategy to regulate insulin release and increase its half-life in the blood for type II diabetes treatment. Besides, hexamer stabilization can be an effective treatment strategy for type I diabetes through slow release from an implanted biosensor system.

Abstract Transforming growth factor beta (TGF-β), is a small homodimeric signaling protein. The TGF-β isoforms (TGFβ1, β2 and β3) are involved in many cellular processes including growth inhibition, extracellular matrix remodeling, tissue development, cell migration, invasion and immune regulation. For research aims, TGFβs are overexpressed using recombinant eukaryotic cell or bacterial expression systems. For achieving an efficient purification of TGF-β by immobilized metal ion affinity chromatography (IMAC), a histidine tag was placed either at the C-terminal (C-TGFβ) or N-terminal (N-TGFβ) region of the sequence and the effect of His-tag on TGF-β structure has been studied by computational tools. Proteins 3D structures were modeled using MODELLER software and molecular dynamics simulation of native TGF-β and modelled proteins, N-TGFβ and C-TGFβ were studied in water by GROMACS package. Protein dynamics modeling indicated that the His-tag attached at the C-terminus but not at the N-terminus of the TGF-β can affect the fluctuations of amino acids and protein structure. It is concluded that the C-terminal tagging may cause distortion and misfolding in the structure.

Abstract Glucoamylase, is an important economic enzyme due to its ability to hydrolyze starch and β-D-glucose polymers. Understanding of factors affecting the thermal stability of the glucoamylase enzyme is critical in the production of isoenzymes with high heat or cold stability. In this study, the effect of temperature on the structure and properties of each of the isoenzymes of the mesophilic, thermophilic and psychrophilic glucoamylase were studied. For this purpose, molecular dynamics simulation was used to assess these factors and structural differences. 240 nanosecond of MD simulation was done for three isoenzymes of glucoamylase in four temperatures at 300, 350, 400 and 450 K. The variations of each of these parameters were compared for three isoenzymes, and it was found that among the computable factors in molecular dynamics simulation, electrostatic energy of protein with water, van der Waals energy between proteins and water, free energy solubility (∆G_solvation), instability parameter, nonpolar solvent accessible surface, and total solvent accessible surface can be used to predict thermal stability of a protein during increase of temperature.

Abstract The interactions between carbon nanotubes (CNTs) and proteins were considered much attention. Advanced CNT applied biomolecules require mutual understanding of their interactions with biological molecules. Enhanced biomedical applications of CNTs have necessitated the need for the understanding their interaction with biomolecules. Non-covalent interactions of blood peptides, such as hepcidin, with carbon nanotubes, have important effects in a wide range of biological applications that are detected by analyzing the thermodynamic parameters of the interaction between CNTs and peptides. In addition, the effects of different parameters in order to evaluate how the interaction of CNTs with peptide affects and structural changes and stability of peptides were studied. In this study, based on molecular dynamics (MD) simulation, the structural changes of hepcidin 20 in interaction with multi walled carbon nanotubes (MWCNTs-COOH ) were investigated. The simulation results revealed that carbon nanotubes cause to loose the hepcidin structure and make structural changes in this peptide. On the other hand, the loose of the hepcidin structure may lead to a change in its activity. The results indicated that significant changes were made in the structure of hepcidin 20 in the presence of carbon nanotubes. The difference of parameter amounts calculated in heptidine 20 is related to their N-terminal, and loop regions.

Abstract Liposomes or biological vesicles are formed from cholesterol, phospholipids, and water. Also, sometimes other biological and non-biological molecules imported in the structure of liposome. The stability of the liposomes in the treatment of diseases and drug delivery, it is vitally important and can be influenced by the composition of phospholipid. In addition, the presence or absence of cholesterol may also affect the stability of liposome. Also, the formation of liposomes is affected by the presence or absence of cholesterol. In this study, we are seeking to affect the presence or absence of cholesterol on the stability and the formation of the liposome. For this purpose, the molecular dynamics simulation method is used. Liposomes that they are simulated was of two types of liposomes type I and liposome type II. The formation analyzes including radial distribution function and solvent accessible surface area showed that each of liposomes created. The type I liposome created one nanodisc structure and type II liposome created two nanodisc structures. Also, energy analysis including total energy, van der Waals interaction energy, and electrostatic interaction energy showed that type I liposome is more stable. Because the cholesterol molecules are the presence of in this liposome structure, that ability to gives hydrogen bonding with side lipids and an increase of stability. In addition, hydrophobic interactions between cholesterol and phospholipids as well as distribution and proper orientation of these parts play a major stake in the stability of the structure.

Abstract Aims: Targeting DNA lies at the heart of anti-cancer therapies. Hence, DNA-binding drugs and their interaction with DNA have recently drawn the attention of researchers. Since DNA minor groove binders (MGBs) act as potent anti-tumor agents, there is a need to have detailed insights on how they interact with DNA. The mechanism of action of the majority of MGBs is not well studied at the molecular level.
Materials and Methods: Herein, molecular docking and dynamics simulations were performed, using AutoDock Vina and NAMD softwares, respectively, to evaluate the binding of A derivatives (Tallimustine, PNU 151807, and ) to , and to compare their interaction energy and binding patterns.
Findings: All three drugs were stably bound throughout the simulation, causing only minor modifications to the structure of DNA. Results of interaction energy analyses together with LigPlot outcomes showed that A/T residues are responsible for making the majority of non-bonding interactions in the case of all three drugs, showing a good agreement with previously reported findings on MGBs.
Conclusion: A/T residues are responsible for making the majority of non-bonding interactions in the case of all three drugs, showing a good agreement with previously reported findings on MGBs. Furthermore, our studies have shown that to the other members of the Distamycin A family, makes stronger interactions with , making it a better candidate for cancer therapy goals.

Abstract Aims: Molecular insights into the analyte-bioreceptor interactions play a vital role in the efficacy of designing biosensors. Biosensors that utilize aptamers as bioreceptors are highly efficient with high specificity and reusability. Aptasensors can be used in a variety of conditions of in vivo or in vitro. The aim of this study was to study the changes in the solvent conditions of the binding of MUC1-G peptide and the anti-MUC1 aptamer.
Materials and Methods: The molecular dynamics simulation method has been used to investigate the change of molecular interactions due to selective variations in solvent conditions. The results can be used to reflect a variety of environments, in which the aptasensor utilizes anti-MUC1 S2.2 aptamer as a bioreceptor and MUC1–G peptide as a biomarker.
Findings: Based on the calculated binding energies, the medium containing 0.10M NaCl and anti-MUC1 S2.2 aptamer demonstrates the highest affinity toward the MUC1-G peptide among the studied concentrations of NaCl, and the arginine amino acid has a key role in the aptamer–peptide binding. Conclusion: The results of MD simulation indicated that the increase in the concentration of NaCl in the interaction environment leads to a decrease in binding energies; therefore, the binding affinity of the anti-MUC1 aptamer to MUC1-G peptide decreases. Insights from present modeling demonstrate the selectiveness and sensitivity to solvent conditions, which should be considered in the development of biosensors.

Abstract Aims: Today, due to the advent of drug resistance in cancer cells against conventional drugs, attention has been paid to the development of anti-cancer drugs with new mechanisms. Pardaxin is an amphipathic polypeptide neurotoxin.The aim of this study was to investigate the interaction of antimicrobial peptide pardaxin with DPPC (composed of 1, 2-dipalmitoyl-sn-glycero-3-phosphocholine) bilayers by molecular dynamics simulation.
Materials & Methods: In the present study, simulations for different membrane environments were designed under neutral pH conditions. At first, the Linux system was used to install the VMD 1.8.6 (Visual Molecular Dynamics) software; then, Gromacs 4.5.5 software was used to perform all the simulations. The pdb peptide structure (1XC0) was prepared from the Protein Data Bank and DPPC lipid bilayer was used for lipid-peptide simulation.
Findings: During the 500 nanoseconds of simulation, the peptide was infiltrated into the membrane. In the DPPC system, at first, the number of hydrogen bonds between the peptide and the lipid bilayer were increased and, then, remained almost constant until the end of the simulation and decreased over time with the number of hydrogen bonds between peptides and water. Pardaxin contacted with the membrane surface and entered into the membrane. In the presence of the peptide, the thickness of the membrane and the range of each lipid decreased and the membrane penetration increased.
Conclusion: The mechanism of Pardaxin is dependent on the bilayer composition, so that the pardaxin peptide contacts with DPPC lipid membrane surface and enters into it.

Abstract Bacteriorhodopsin (bR) is a membrane protein that acts as a light-driven proton pump in Halobacterium salinarum. This protein contains seven transmembrane α-helical subunits, helices A–G, one beta-sheet and a retinal chromophore. Studies show that bR have the property of absorbing the microwave. Among several methods molecular dynamics simulation (MD) is the most systemic approach. With this method we can study structural changes and dynamic of macromolecules. In this project, we use modeling and molecular dynamic simulation. To obtain more accurate structures after the equilibration a 15 ns MD simulation was done. After that, in order to find the effective sites of microwave absorption on bR a production run was performed with applying electric field in the time intervals of 786 ps that is equal to one sinusoidal frequency at microwave spectrum. At last, conformational changes under effect of sinusoidal wave has been assigned the effective sites of microwave absorption in the protein. Our study shows that microwave in the frequency of 8 GHZ and the time interval that mentioned above, cannot make significant changes on the protein. In the other hand, we have seen some reversible changes in Beta-sheet and D, C, B helices.