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Regarding the importance of inhibiting VEGF and unique features of VHHs as a new generation of antibody-based therapeutics, the present study aimed to generate VHHs against the receptor binding domain of VEGF, thereby blocking of VEGF binding to its receptor. After preparing the gene repertoire of VHH fragments from an immunized camel, a VHH phage display library was constructed. We adopted a stringent successive biopanning to isolate the phages displaying VHH with high affinity to VEGF-RBD.A significant enrichment of phages that specifically bound to the target protein was obtained after six rounds of panning. Of the specific clones with high binding affinity screened by monoclonal phage ELISA, 52% shared the same VHH sequence, showing its high enrichment. Using molecular simulation of antigen-antibody interaction based on the crystallographic information of VEGF/VEGFR2, molecular dynamics simulations and MM/PBSA free energy calculations, we provide a reliable picture of the binding site of antibody on antigen. The key residues in the VEvhh1-VEGF interface were dissected and the energetics was analyzed by MM/PBSA. The results of studies revealed that VEvhh1 binds to the receptor binding site of VEGF with high binding energy and showed the highest affinity to the residues of VEGF which are responsible for VEGF binding to VEGFR2. Also the antibody potently covers these key functional residues of VEGF, thereby inhibiting VEGF binding to its receptor and probably abrogating its biological activity. This study may represent VEvhh1 as an anti-VEGF and anti-angiogenic candidate.

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Endostatin suppresses growth and progression of many tumors through binding to endothelial cell surface and extracellular matrix proteins like integrin, heparin, matrix metalloproteinase-2 and transglutaminase-2. There is an arginine rich motif on the surface of endostatin that is essential for binding to some of aforementioned proteins. It has been shown that a 27 amino acid peptide derived from amino terminal of endostatin responsible for its anti-angiogenic and anti-tumor activities and mutation of histidines bound to Zn significantly reduce its activity. In the present study, as regards the importance of Zn-binding loop in amino terminal and arginine 27 in carboxyl terminal, peptides corresponding to this region and a mutated variant including isoleusin 26 to arginine mutation synthesized and their structure and interaction with matrix metalloproteinase-2 and transglutaminase-2 analyzed using fluorescence spectroscopy, molecular dynamic and docking simulation techniques. This study aimed to analyze effect of placing two positively charged arginines on the structure and interaction of this fragment of endostatin. Results showed that placing two arginines close together in the carboxyl terminal of peptide increases fluctuations in total structure of peptide, alters Zn-binding loop in the amino terminal and makes binding energy of peptide to matrix metalloproteinase-2 and transglutaminase-2 more negative. It can be inferred that repulsion of two positively charged arginines in carboxyl terminal induces conformational changes in the whole structure and in the amino terminal loop region.

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Marine organisms are one of the valuable resource of pharmaceutical. In the last decade, the commercial value of these organisms and the use of compounds derived from them in biological research and drug development, have made them as an important new source for anti-cancer drugs. Microtubules are one of important drug targets in cancer cells therapy and their related inhibitors are being developed widely. In this study the structure of more than 3,000 compounds that contributed marine organism were constructed and optimized by ChemAxon. The affinity of compounds into colchicine/epothilone binding sites in αβ-tubulin structure, was examined using structure-based virtual screening (docking). Results of docking studies were shown that some compounds have high and better binding affinity than colchicine and epothilone inhibitors. MNP14107 and MNP0565 compounds have high affinity for the colchicine and epothilone binding sites respectively. We propose the MNP14107 and MNP0565 compounds as new and the best candidates for the inhibition of tubulin.

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Backgrounds: A short sequence of viral protein or peptide, can be used as a potential vaccine for the treatment of that virus. Considering all variants of concern (VOC), vaccine design with peptide for Severe Acute Respiratory Syndrome coronavirus 2 (SARS CoV2) is a challenging job for scientists.
Materials & Methods: In this current study, an epitope containing peptide vaccine for nonstructural protein 4 (nsp 4) of SARS CoV2 coronavirus has been predicted. With the help of a modified method for both B and T call epitope prediction, verified by molecular docking studies, linear B cell and T cell epitopes for nsp4 protein, are predicted here. Predicted epitopes are analyzed further with population coverage calculation and epitope conservancy analysis.
Findings: A short peptide sequence   ⁷⁴QRGGSYTNDKA⁸⁴  has been selected as B cell epitope considering the scores for surface accessibility, hydrophilicity, beta turn prediction for each amino acid residues.
Similarly, the peptide sequences ³⁵⁹ FLAHIQWMV³⁶⁷ and   ³⁵⁹ FLAHIQWVMFTPLV³⁷³ are predicted as T cell epitopes for MHC-I and MHC-II molecules. These two potential epitopes can interest with HLA-A*02:01 and HLA-DRB*01:01, MHC allelic proteins respectively with lowest IC₅₀ values.
Furthermore, no amino acid mutations are observed in GISAD Global initiate on sharing all influenza data) database for alpha, beta, gamma and delta variance of concerns (VOC). Among seven amino acid point mutation of nsp 4 protein in Omicron variant, none of them is present in the peptide sequences of predicted epitope-based vaccines.
Conclusion: The short peptide sequences can be predicted as vaccines to prevent coronavirus infections for all variants of concerns.
 

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Aims: The Mesd is a universal inhibitor and has therapeutic effect against triple negative breast cancer. The peptide derived from carboxyl terminal, similar to protein, acts as an inhibitor of the pathway. The aim of this study was to investigate the probable binding sites of Mesd and its peptide derived from carboxyl terminal on LRP6 first and second beta-propeller domains from a structural point of view in drug design.
Materials & Methods: This experimental study was conducted, using blind and site-directed molecular docking simulation with ClusPro and Haddock and molecular dynamic simulation. The binding sites of Mesd and the peptide on the first and second beta-propeller domains of receptor LRP6 were investigated and the selected complexes were structurally analyzed.
Findings: Extensive levels of Mesd protein were found to interact with LRP6 and the levels involved in the peptide were much lower. The binding region of Mesd to LRP6 was from the carboxyl terminal. The binding region of the peptide and the protein on LRP6 was a similar region between First and Second Beta-Propeller Domains of LRP6. The RMSD and RMSF chart of the Mesd complex and its peptide was approximately the same with the first functional domain of the LRP6 co-receptor.
Conclusion: The binding region of the peptide and the protein on LRP6 is not completely similar, but according to molecular simulation of selected complexes, the pattern of the inhibition mechanism is common and emphasizes on inter domain motion control from a structural point of view. Interactive region of each ligand is similar to a region of the co-receptor, which has maximum flexibility. Molecular docking simulation of Mesd and co-receptor shows important role of carboxyl terminal of the protein to bind to LRP6.

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The CD80 protein, a member of the super-family of immunoglobulin, is a transmembrane protein expressed on the surface of the antigen-presenting cells (APC). This protein has two receptors on the surface of T cells (CTLA-4 and CD28), due to the binding of this protein to these receptors, the inhibitory and stimulatory pathway in the T cells begin, respectively. Naturally, CD80 proteins tend to have more binding affinity to CTLA-4 than CD28, and this is a factor in the extinction of T cells in the immune system in order to prevent autoimmunity. The aim of the present study is to create a variant of the CD80 protein that has an increased binding affinity to CD28 to bind to this receptor more strongly and induce more simulate pathways than the wild type of this protein (primary CD80 protein) in T cells. To identify this variant, first, the ancestral sequence was mutated by R software at positions 31 and 92 with amino acids that play an important role in the formation of hydrogen bonds. The R software output sequences were modeled with the SWISS-MODEL server. Then, each output model was docked with the HADDOCK server, and finally, the electrostatic and van der Waals energies between the receptors and the ligands were calculated. Among all the built-in models, the mutated K31Y, R92F has the best electrostatic and van der Waals energies and has the ability to have a much better connection to its CD28 receptor compared to the ancestral type of CD80.

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 Beet curly top Iran virus (BCTIV) and Beet curly top virus (BCTV) are responsible for the curly top disease in sugar beet Beta vulgaris L. and many other plants. Mixed infection by BCTIV and BCTV in sugar beet plants results in a synergistic interaction, with more severe symptoms than plants infected by either virus, accompanied by an increase in BCTIV and a decrease in BCTV titers. Interaction of the Replication associated protein (Rep) with the nonanucleotide motif within the origin of replication is crucial for the replication of the geminivirus genome. Using an in silico approach, we investigated the possible contribution of the interaction between Rep and the nonanucleotide motifs in the interference between BCTIV and BCTV in mixed infections. The physicochemical characterization of both Reps was performed, and their secondary and tertiary structures were predicted by SOMPA tool and I-TASSER server, respectively. Then, the binding affinity of each Rep towards cognate and non-cognate viral nonanucleotide motifs was assessed using Docking simulations. Cluster analysis of HADDOCK revealed that the total binding energy of BCTV Rep toward its cognate nonanucleotide motif was lower than for the BCTIV complex, confirming a higher affinity of BCTV encoded Rep for its nonanucleotide motif. Interestingly, the BCTIV Rep showed the highest affinity for the nonanucleotide motif of the non-cognate BCTV nonanucleotide motif. Since the replication of geminiviruses relies on species-specific Rep interactions and activities, this result could be considered responsible for the competitive interference of BCTIV towards BCTV.

 

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In the present study, the structure of three common anticancer drugs including 6-thioguanine (6-TG), hydroxyurea (NH) and busulfan were optimized using quantum computational and obtained minimum energy for them. Also, optimization structure of gold nanoparticle was investigated by density functional theory (DFT). Finally, the binding energy of Au nanoparticle was calculated with the optimized structures of drugs. All different sites of drugs that can be interacted with nanoparticle were considered and the most stable structure was chosen for further study. These calculations were performed using FHI-aims which is a software package based on DFT. The bond length and the best interaction energy were reported in this work. To better investigation of the location of the interaction, the type of orbitals involved in the interaction and their shapes are shown. Gap energy analysis showed that the lowest energy was related to the complex of gold nanoparticle with 6-thioguanine, which confirms the chemical stability of this drug with nanoparticle. Investigations showed that the binding energy of gold nanoparticle with drugs is busulfan > hydroxyurea> 6-thioguanine so busulfan has more affinity to bind with gold nanoparticle.
Au nanoparticle as an anticancer drug deliver was studied with the molecular docking calculations. The human albumin serum (HSA) binding with three anticancer drugs was docked individually with Hex 8 software and their active sites of interaction were shown as well as.  Finally, the binding energies and types of interactions such as electrostatic, van der Waals and hydrogen bonds between HSA and Au@ drugs were presented, clearly.

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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.

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Nowadays, the peptides and proteins possessing anti-cancer, anti-allergic and anti-inflammatory properties are used for disease treatment. Brazzein is a sweet protein containing 54 amino acids and according to reports, it has anti-cancer properties based on sequence and structurehas sequence. In this study, the role of position 40 aspartate in the structure and function of wild brazzein protein and mutants as well as the anti-cancer properties of the peptides obtained on the TLR5 receptor were investigated. For this, several models of mutated forms were designed and constructed using Modeller.v.9.20 software. Then, the accuracy of the models and the physico-chemical properties of wild type (WT) and mutants of D40N, D40R and D40Deletion were evaluated using various bioinformatics servers and softwares including ProtParam, ProtScale, SAVES, PIC, ModEval, and PredyFlexy. For predicting anticancer properties, the sequence of WT protein and mutants was examined and compared using ACPred and iACP servers. The quality and analysis of WT protein and mutants binding as a ligand with TLR5 receptor, triggering an anti-cancer signaling pathway, were investigated through molecular docking using HADDOCK software.The results of bioinformatics parameters analysis indicated the possibility of improving the stability of brazzein structure and function, and the probability of increasing the available surface to bind to the receptor. Moreover, based on the results of molecular docking analyses, the ability binding TLR5 receptor was higher in D40R than the other proteins indicating an increased probability in anti-cancer properties of the mutant.

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Alzheimer’s disease (AD) is the most common type of dementia in the elderly. The neuropathology and treatment of AD is not precisely determined yet, but according to the pathological studies, AD is associated with presence of toxic soluble oligomers and insoluble senile plaques formed by amyloidosis of Amyloid Beta (Aβ) in neocortical region of brain. The V10HHQKLVFFAE22 is a critical region of Aβ42 which facilitates aggregation process. An attractive therapeutic approach to treat AD is to identify small ligands that are capable of binding to critical residues in order to inhibit or reverse Aβ amyloidosis process as source of neurotoxicity. In this area, therapeutic efforts designed various organic agents and most of them focused on the N-terminal sequence of Aβ. Here, a peptide inhibitor derived from the C-terminal of Aβ (G33LMVG37) is utilized as inhibitor and combined Docking and Molecular dynamics simulation used to find the binding sights in the critical region (V10HHQKLVFFAE22). The simulation identified tree stable binding sites for Aβ42 inhibition by penta peptide. This result indicate that this penta-peptide is capable to inhibit aggregation process and can be consider as an drug for AD preclinical studies.

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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.

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The orbital rendezvous and docking with Position and attitude nonlinear dynamics is one of the most challenging problems in the Aerospace engineering. The attitude and position of a chaser spacecraft, desired to rendezvous with a target spacecraft, have to be determined with respect to the target, as a result relative equations have to be considered. The chaser is controlled by actuators to rendezvous safely and stably under the conditions and requirements. In this paper rendezvous dynamics for target in a circular orbit is assumed as nonlinear second-order clohessy-wiltshire relative motion equations. Shauner and hempel relative equations are considered for target in elliptical orbit. Cost function has been chosen in a manner to minimize the control effort and to give smooth states. Nonlinear optimal control for rendezvous with a target in circular orbit using state dependent riccati equation by means of eigen vectors of the Hamiltonian matric is compared with linear quadratic regulator method for both linear and nonlinear systems and then stability and robustness of the results are analysed. Optimal control of a elliptical rendezvous is discussed independently. For navigational porpose it is important to express relative motion in inertial frame, this is accomplished by introducing an appropriate transformation.

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The application of carriers is a proper means of improving the transfer and increasing the bioavailability of bioactive compounds. α-lactalbumin is the second major component of whey protein nutritionally consisted of Trp, Lys and Cys residues which can be employed as nutraceutical carriers. Oleuropein is a bioactive compound with pharmaceutical and antioxidant properties which is found abundantly in olive leaves and at lower levels in olive oil. The current study was undertaken to explore the interaction of α-lactalbumin-oleuropein complex at 25, 50 and 72 ˚C at pH 7 by using fluorescent, UV and circular dichroism spectroscopy techniques together with molecular docking. The results from UV and fluorescent studies demonstrate that site and binding constant are increased as the temperature increased due to the change in conformation and rearrangement of protein structure. Moreover, circular dichroism results depicted that α-helix and β-sheet structures are decreased and increased respectively as a result of temperature increase up to 72 ˚C. Ultimately, the molecular docking findings revealed that the best binding energy for complex formation was about -6.3 kCal/mol and the best binding site was between the α-helix and β-sheet cleft. The findings give us useful information regarding the interaction of oleuropein and α-lactalbumin which can be further used to produce functional foods.
Key words: α-lactalbumin; oleuropein; spectroscopy; molecular docking, functional products

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The presence of methicillin-resistant (MRSA) and vancomycin-resistant (VRSA) Staphylococcus aureus in food raises a public health concern. This study aimed to investigate the antibacterial and anti-biofilm activity of some Lamiaceae essential oils including Melissa Officinalis, Salvia officinalis, and Mentha piperita against MRSA and for the first time on VRSA strains. For this purpose, the disk diffusion test, minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), minimum biofilm inhibitory concentration (MBIC), and minimum biofilm eradication concentration (MBEC) were determined. Then, M. Officinalis essential oil compounds were investigated against PBP2a, agrA, and Bap proteins using AutoDocK Vina. Finally, pharmacokinetic properties were investigated using ADMETsar and SwissADME servers. Based on the obtained results, the MIC and MBC values of M. Officinalis essential oil against MRSA strain were equal to 0.05 and 0.112 mg/ml, and against VRSA strain were equal to 1.8 and 2.5 mg/ml, respectively. The MBIC and MBEC of M. Officinalis essential oil against MRSA strain were equal to 0.03 mg/ml and 0.112 mg/ml, and against VRSA strain were equal to 0.9 mg/ml and 3.2 mg/ml, respectively. The results of molecular docking showed that β-Caryophyllene had a greater binding affinity to PBP2a protein either in the active site or in the allosteric site (-6.6kcal/mol). On the other hand, the effective compounds of this essential oil, especially citronellol, thymol, and citral, were acceptable in terms of pharmacokinetic properties. Since natural antibiotics can be an alternative to conventional antibiotics in the treatment of Staphylococcus aureus food-borne diseases, the results of this study showed that Melissa Officinalis essential oil is effective on the growth and biofilm of MRSA and VRSA strains, and it can be used as a drug candidate in the prevention and treatment of infections caused by antibiotic-resistant strains of this bacterium.

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Trying to treat COVID-19 patients has caused serious problems for the scientists. There are many routinely used drugs in clinical settings without definite effects, and more studies should be done so as to reach a successful treatment for COVID-19. Our aim is to evaluate four suggested chemicals using virtual analysis tools based on the drug-screening approach and application of cheminformatics, pharmacotoxicology and docking.
Four repurposed drugs: rizatriptan, dasabuvir, pravastatin, and empagliflozin are used in the study. The 3D structure of COVID-19 Main Protease (M Pro) was obtained from protein data bank (PDB) with PDB code: 6LU7, as the target of binding site screening. Besides, cheminformatics, pharmacotoxicology and human proteins targets for each drug was evaluated using SwissADME interface, SwissTarget Prediction web server, toxicity estimation software tool (T.E.S.T) and Toxtree-v3.1.0.1851 offline software.
The docking scores (DOS) were -139.399, -125.707, -102.183 and -99.6642 for dasabuvir, rizatriptan, empagliflozin and pravastatin, respectively. In addition, the quantitative structure-activity relationship (QSAR) and pharmacotoxicologic evaluations show dasabuvir has more acceptable results than the others. Human protein target-exploration show that rizatriptan interacts with G protein-coupled receptor and kinase enzymes, pravastatin targets the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, while empagliflozin interacts with sodium/glucose cotransporters (SLC). But, dasabuvir targets human protein with too low scores.
Virtual screening applied to four potential anti-COVID-19 drugs shows that dasabuvir may be a safer and efficient agent, regarding pharmacotoxicology and therapeutic purposes. However, virtually screened agent/s should be evaluated by experimental models for ultimate confirmation.