---

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.

---

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.

---

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.

---

---

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.