In vitro study of the expression of autophagy genes ATG101, mTOR and AMPK in breast cancer with treatment of lactoferrin and in silico study of their communication networks and protein interactions.

Autophagy is a new window of science that has been noticed due to the importance of specific therapies in cancer. In this study, the effect of lactoferrin (Lf) on the expression level of ATG101, mTOR and AMPK genes in breast cancer cell line MCF7, as well as the interaction between lactoferrin protein and their protein were investigated. The expression level of the genes was measured using a real-time PCR method. PDB, UniProt, KEGG, and STRING databases and ClusPro webserver and PyMol software were used in silico study. The results showed that the expression level of the ATG101 gene in treatment with concentrations of 100, 400, 600, and 800 µg/ml Lf decreased by 0.05, 0.13, 0.54 and 0.77, respectively. The expression level of the mTOR gene in treatment with concentrations of 100, 400, 600, and 800 µg/ml Lf decreased by 0.07, 0.05, 0.13, and 0.49 times respectively. The level of the AMPK gene expression in treatment with concentrations of 100, 400, 600, and 800 µg/ml Lf decreased by 0.05, 0.01, 0.06, and 0.03, respectively. Virtualization of the interaction of Lf protein with ATG101, mTOR and AMPK proteins by Pymol software showed that the N lobe region of Lf interacted with the HORMA domain of ATG101 protein, the fat domain of mTOR protein, and the CTD domain of AMPK protein. Although Lf was not able to increase the expression of autophagy-inducing genes, it may be able to induce autophagy through protein interaction by activating or inhibiting proteins related to autophagy regulation.

Potential suppression of multidrug-resistance-associated protein 1 by coumarin derivatives: an insight from molecular docking and MD simulation studies.

Human MRP1 protein plays a vital role in cancer multidrug resistance. Coumarins show promising pharmacological properties. Virtual screening, ADMET, molecular docking and molecular dynamics (MD) simulations were utilized as pharmacoinformatic tools to identify potential MRP1 inhibitors among coumarin derivatives. Using in silico ADMET, 50 hits were further investigated for their selectivity toward the nucleotide-binding domains (NBDs) of MRP1 using molecular docking. Accordingly, coumarin, its symmetrical ketone derivative Lig. No. 4, and Reversan were candidates for focused docking study with the NBDs domains compared with ATP. The result indicates that Lig. No. 4, with the best binding score, interacts with NBDs via hydrogen bonds with residues: GLN713, LYS684, GLY683, CYS682 in NBD1, and GLY1432, GLY771, SER769 and GLN1374 in NBD2, which mostly overlap with ATP binding residues. Moreover, doxorubicin (Doxo) was docked to the transmembrane domains (TMDs) active site of MRP1. Doxo interaction with TMDs was subjected to MD simulation in the NBDs free and occupied with Lig. No. 4 states. The results showed that Doxo interacts more strongly with TMD residues in inward facing feature of TMDs helices. However, when Lig. No. 4 exists in NBDs, Doxo interactions are different, and TMD helices show more outward-facing conformation. This result may suggest a partial competitive inhibition mechanism for the Lig. No. 4 on MRP1 compared with ATP. So, it may inhibit active complex formation by interfering with ATP entrance to NBDs and locking MRP1 conformation in outward-facing mode. This study suggests a valuable coumarin derivative that can be further investigated for potent MRP1 inhibitors.Communicated by Ramaswamy H. Sarma.

HIGHLIGHTSVirtual screening scored a symmetrical ketone derivative IUPAC ([2-[(1E, 4E)-5-(2-acetyloxyphenyl)-3-oxopenta-1, 4-dienyl] phenyl] acetate); PubChem CID 5468558 (Lig. No. 4 in this study) as the best candidate among coumarins to inhibit MRP1.This compound binds to NBD1 and NBD2 of ABC transporters via hydrogen bonds shared with residues that are also involved in the ATP binding.This result, if not at all, suggest a partial competitive inhibition mechanism for Lig. No. 4 on the MRP1 protein.Molecular dynamics simulation study reveals different doxorubicin binding modes in interaction with MRP1 transmembrane domain in free and occupied NBDs with Lig. No. 4.Lig. No. 4 is a valuable candidate for further drug development studies to suppress drug resistance.

Abiraterone and D4, 3-keto Abiraterone binding to CYP17A1, a structural comparison study by molecular dynamic simulation.

The importance of computer-aided drug design and development is clear nowadays. These approaches smooth the way of designing some efficient candidates based on drugs in use. At this place, we studied the mechanism of D4-abiraterone (D4A), the active metabolite of Abiraterone (Abi), binding to CYP17A1 compared with Abi. The molecular dynamics simulation results reveal that the metabolite, which lacks the key 3ß-OH group, has a varied H-bond forming pattern. The critical H-bond between 3ß-OH of Abi with Asn_202 turns to 3 Keto-O of D4A with Arg_239 in the substrate-binding site. This interaction causes a remarkable distance of 0.63 nm between D4A nitrogen and Fe in heme, which reduces its 17,20 lyase selectivity. The D4A keto moiety presents an immense number of H-bond with surrounding solvent molecules compared with the Abi hydroxyl group. As a result, D4A develops a weaker H-bond network with the enzyme. Otherwise, the heterocyclic nature of inhibitors helps for noticeable van der Waals interaction formation with CYP17A1. However, Abi stabilized position in the binding site helps more van der Waals interactions deposition than D4A. These results convinced the importance of the conserved H-bond for acquiring the proper position by the substrate or inhibitor in the binding site.

A combination of bioactive and nonbioactive alkyl-peptides form a more stable nanofiber structure for differentiating neural stem cells: a molecular dynamics simulation survey.

Self-assembling alkyl-peptides are important molecules due to their ability to construct nano-level structures such as nanofibers to be utilized as tissue engineering scaffolds. The bioactive epitope of FAQRVPP which acts as neural stem cells (NSCs) outgrowth inducing factor is used in nanofiber structures. Based on previous experimental studies the density and distribution pattern of the epitopes on the surface of the nanofibers plays an important role in the differentiation function efficiency. We decided to survey and compare the stability of two pre-constructed fiber structures in the forms of all-functionalized nanofiber (containing only bioactive alkyl-peptides) and distributed functionalized nanofiber (a combination of nonbioactive and bioactive alkyl-peptides with ratio 2:1). Our findings reveal that the all-functionalized fiber shows an unstable structure and is split into intermediate micelle-like structures to reduce compactness and steric hindrance of functional epitopes whereas the distributed functionalized fiber shows an integrated stable nanofiber with a more amount of beta sheets that are well-organized and oriented around the hydrophobic core. The hydrogen bonds and energy profiles of the structures indicate the role of hydrophobic interactions during the alkyl-chain core formation and the important role of electrostatic interactions and hydrogen bond network in the stability of the final structures. Finally, it seems that the possibility of the presence of intermediate structure is increased in the all-functionalized nanofiber environment, and it can reduce functional efficiency of the scaffolds. These findings can help to design more efficient nanofiber structures with different goals in scaffolds for tissue engineering. Abbreviations MD Molecular Dynamics NSCs Neural Stem Cells PME Particle mesh Ewald RDF Radial Distribution Function RG Radius of gyration RASA Relative Accessible Surface Area RMSD Root Mean Square Deviations SASA Solvent Accessible Surface Area. Communicated by Ramaswamy H. Sarma.