In silico Identification of Peptide as Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors in Lung Cancer Treatment.

BACKGROUND AND OBJECTIVE: Epidermal growth factor receptor (EGFR) is the biomarker for lung cancer in which the protein has the most active mutated genes in lung cancer patients. Peptides have pharmacological potential as drugs because of their bioactivity and accessibility. The research objective was to obtain peptide compounds drug candidates with good interaction and pharmacological properties that can act as an inhibitor for EGFR for lung cancer treatment by using in silico method. MATERIALS AND METHODS: EGFR protein structure was obtained from Protein Data Bank and the peptide compounds were retrieved from PubChem. Optimization and energy minimization process were done to prepare the peptides for the simulation. Protein-Ligand Interaction Fingerprint (PLIF) was used to determine the pharmacophore features in the EGFR binding site. Both proteins and ligands underwent a virtual screening through rigid and flexible molecular docking simulation and the best ligands were subjected to a computational ADME-Tox properties prediction. RESULTS: After screening through molecular docking simulation, nine best compounds were identified to have a good interaction with EGFR protein according to its binding energy and RMSD value. The compounds were identified to form hydrogen bond interactions with the macromolecule. CONCLUSION: Two peptide compounds (PubChem ID: 20832941 and 9805315) have been predicted as the best ligands with desired pharmacological properties for the inhibition of EGFR tyrosine kinase.

(1)H, (13)C and (15)N backbone assignment of the EC-1 domain of human E-cadherin.

The Extracellular 1 (EC1) domain of E-cadherin has been shown to be important for cadherin-cadherin homophilic interactions. Cadherins are responsible for calcium-mediated cell-cell adhesion located at the adherens junction of the biological barriers (i.e., intestinal mucosa and the blood-brain barrier (BBB)). Cadherin peptides can modulate cadherin interactions to improve drug delivery through the BBB. However, the mechanism of modulating the E-cadherin interactions by cadherin peptides has not been fully elucidated. To provide a basis for subsequent examination of the structure and peptide-binding properties of the EC1 domain of human E-cadherin using solution NMR spectroscopy, the (1)H, (13)C and (15)N backbone resonance of the uniformly labeled-EC1 were assigned and the secondary structure was determined based on the chemical shift values. These resonance assignments are essential for assessing protein-ligand interactions and are reported here.

Enhancement of drug absorption through the blood-brain barrier and inhibition of intercellular tight junction resealing by E-cadherin peptides.

E-cadherin-mediated cell-cell interactions in the zonula adherens play an important role in the formation of the intercellular tight junctions found in the blood-brain barrier. However, it is also responsible for the low permeation of drugs into the brain. In this study, HAV6 peptide derived from the EC1 domain of E-cadherin was found to enhance the permeation of ¹4C-mannitol and [³H(G)]-daunomycin through the blood-brain barrier of the in situ rat brain perfusion model. In addition, HAV6 peptide and verapamil have a synergistic effect in enhancing the BBB permeation of daunomycin. A new intercellular-junction resealing assay was also developed using Caco-2 monolayers to evaluate new peptides (BLG2, BLG3, and BLG4) derived from the bulge regions of the EC2, EC3, and EC4 domains of E-cadherin. BLG2 and BLG4 peptides but not BLG3 peptides were found to be effective in blocking the resealing of the intercellular junctions. The positive control peptides (ADT10, ADT6, and HAV10) block the resealing of the intercellular junctions in a concentration-dependent manner. All these findings suggest that E-cadherin-derived peptides can block E-cadherin-mediated cell-cell interactions. These findings demonstrate that cadherin peptides may offer a useful targeted permeation enhancement of therapeutic agents such as anticancer drugs into the brain.

In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC).

BACKGROUND: The cervical cancer is the second most prevalent cancer for the woman in the world. It is caused by the oncogenic human papilloma virus (HPV). The inhibition activity of histone deacetylase (HDAC) is a potential strategy for cancer therapy. Suberoylanilide hydroxamic acid (SAHA) is widely known as a low toxicity HDAC inhibitor. This research presents in silico SAHA modification by utilizing triazole, in order to obtain a better inhibitor. We conducted docking of the SAHA inhibitor and 12 modified versions to six class II HDAC enzymes, and then proceeded with drug scanning of each one of them. RESULTS: The docking results show that the 12 modified inhibitors have much better binding affinity and inhibition potential than SAHA. Based on drug scan analysis, six of the modified inhibitors have robust pharmacological attributes, as revealed by drug likeness, drug score, oral bioavailability, and toxicity levels. CONCLUSIONS: The binding affinity, free energy and drug scan screening of the best inhibitors have shown that 1c and 2c modified inhibitors are the best ones to inhibit class II HDAC.

Structural modifications of ICAM-1 cyclic peptides to improve the activity to inhibit heterotypic adhesion of T cells.

Lymphocyte function-associated antigen-1 (LFA-1)/intercellular adhesion molecule-1 (ICAM-1) interaction plays an important role in the formation of the immunological synapse between T cells and antigen-presenting cells. Blocking of LFA-1/ICAM-1 interactions has been shown to suppress the progression of autoimmune diseases. cIBR peptide (cyclo(1,12)PenPRGGSVLVTGC) inhibits ICAM-1/LFA-1 interaction by binding to the I-domain of LFA-1. To increase the bioactivity of cIBR peptide, we systemically modified the structure of the peptide by (i) replacing the Pen residue at the N-terminus with Cys, (ii) cyclization using amide bond formation between Lys-Glu side chains, and (iii) reducing the peptide size by eliminating the C-terminal residue. We found that the activity of cIBR peptide was not affected by replacing Phe with Cys. Peptide cyclization by forming the Lys-Glu amide bond also increased the activity of cIBR peptide, presumably due to the resistance of the amide bond to the reducing nature of glutathione in plasma. We also found that a reduced derivative of cIBR with eight residues (cyclo(1,8)CPRGGSVC) has a bioactivity similar to that of the larger cIBR peptides. Our findings suggest that, by systemically modifying the structure of cIBR peptide, the biological activity of these derivatives can be optimized for future use to inhibit T-cell adhesion in in vivo models of autoimmune diseases.

Increasing paracellular porosity by E-cadherin peptides: discovery of bulge and groove regions in the EC1-domain of E-cadherin.

PURPOSE: The objective of this work is to evaluate the ability of peptides derived from the bulge (HAV-peptides) and groove (ADT-peptides) regions of E-cadherin EC1-domain to increase the paracellular porosity of the intercellular junctions of Madin-Darby canine kidney (MDCK) cell monolayers. METHODS: Peptides were synthesized using a solid-phase method and were purified using semi-preparative HPLC. MDCK monolayers were used to evaluate the ability of cadherin peptides to modulate cadherin-cadherin interactions in the intercellular junctions. The increase in intercellular junction porosity was determined by the change in transepithelial electrical resistance (TEER) values and the paracellular transport of 14C-mannitol. RESULTS: HAV- and ADT-peptides can lower the TEER value of MDCK cell monolayers and enhance the paracellular permeation of 14C-mannitol. HAV- and ADT-decapeptides can modulate the intercellular junctions when they are added from the basolateral side but not from the apical side; on the other hand. HAV- and ADT-hexapeptides increase the paracellular porosity of the monolayers when added from either side. Conjugation of HAV- and ADT-peptides using omega-aminocaproic acid can only work to modulate the paracellular porosity when ADT-peptide is at the N-terminus and HAV-peptide is at the C-terminus; because of its size, the conjugate can only modulate the intercellular junction when added from the basolateral side. CONCLUSIONS: Peptides from the bulge and groove regions of the EC1 domain of E-cadherin can inhibit cadherin-cadherin interactions, resulting in the opening of the paracellular junctions. These peptides may be used to improve paracellular permeation of peptides and proteins. Furthermore, this work suggests that both groove and bulge regions of EC-domain are important for cadherin-cadherin interactions.