Letters in Drug Design & Discovery - Volume 16, Issue 8, 2019

Background: None small cell cancer (NSCLC) is one of the most common cancer around the globe. First generation EGFR-TKI such as gefitinib and erlotinib are now documentated a prolonged PFS in NSCLC patients with EGFR activating mutation. However, upon continuous treatment, patients become resistant due toCEE T790M mutation in most cases.Second generation covalent EGFR inhibitors like afatinib have a moderate inhibition to EGFRT790M in preclinical models,but it is lacking efficacy in the clinical use for patients with T790M mutation due to the dose-limiting EGFRWT-driven toxicities.Third generation EGFR inhibitors have the potential to overcome EGFRT790M resistance mutations while reducing EGFRWT-driven toxicities and are now under active research. Methods: We took compound 6 as our lead compound. We focused on structural modifications around the hydrophile side chain, the linker, and the Micheal addition receptor moiety of AMG. A novel series of Oxopyrido[2,3-d]pyrimidine-7-ones derivatives have been designed and synthesized. Their kinase inhibition activity against EGFRWT and EGFRL858R/T790M were tested by ELISA assays. SRB test was used for cellular anti-proliferation evaluation. Results: A total of 21 novel Oxopyrido[2,3-d]pyrimidine-7-ones derivatives have been designed and synthesized. The compounds were characterized with 1H-NMR and HRMS. Their structureactivity relationships have been preliminaryly investigated. As a result, compound 7k showed comparable activity in kinase inhibition assay and cell growth inhibition assay with our lead compound 6. Higher activity and selectivity over EGFRWT were observed in the in vitro antitumour assay comparing compound 7k to AZD-9291. Compound 7a exhibited higher selectivity over EGFRWT in kinase inhibition assay, but poor cell inhibition to NCI-1975 cell line. The in vivo pharmacokinetic studies in rats showed that compound 9a exhibited improved pharmacokinetic profiles comparing to 6. Compound 9a was also efficacious in an NCI-H1975 murine xenograft model 30 mg/kg QD. Conclusion: Compound 9a has a potent kinase inhibition to EGFRT790M and has a high selectivity over EGFRWT. It’s also efficacious in an in vivo pharmacodynamic evaluation assay. Significant advantages were observed in pharmacokinetic evaluation comparing 9a to 6, which provide us a reference to further drug design and research.

Background: Diabetes mellitus is the third-largest non-communicable chronic disease worldwide. There are many effective drugs, but the long-term use of these clinical drugs may cause various side effects. Therefore, it is urgent to develop new antidiabetic molecules with higher efficacy and lower toxicity. Methods: Fifteen new 3-aryl-1-(5-methylisoxazol-3-ylamino)-1-(4-nitrophenyl)propan-1-one were synthesized directly through the Mannich reaction of 4-nitroacetophenone, 3-amino-5- methylisoxazole and aromatic aldehydes catalyzed by concentrated hydrochloric acid. The molecular structures of the products were fully characterized by 1H NMR, 13C NMR, ESI MS and HRMS. The peroxisome proliferator-activated receptor (PPAR) response element and α-glucosidase inhibitory activity of these compounds were evaluated in vitro. Molecular docking, molecular physical parameters calculation, and molecular toxicity prediction were performed to analyze the structure- activity relationship and evaluate the druggability of these compounds theoretically. Results: All compounds exhibited weak antidiabetic activities, but compound 15 showed promising as a high performance, dual-target antidiabetic lead compound with peroxisome proliferatoractivated receptor (PPAR) response element relative agonist activity of 99.55% at 27.2 nmol·mL−1 and α-glucosidase inhibitory activity of 35.21% at 13.6 nmol·mL−1. All compounds obtained may have no cardiotoxicity, no acute toxicity, no carcinogenic, and within safe range of mutagenic risk. Conclusion: This study identified a potential PPAR lead molecule and presented an unusual strategy for antidiabetic drug development.

Background: In an effort to establish new drug candidates with improved antiproliferative activity, we report here a novel class of compounds designed rationally by the replacement of an ethyl group in tamoxifen with a methylene (1H-1,2,4-triazole) and the introduction of 1,4- substituted 1,2,3-triazoles in the basic side chain. Methods: Magnetically separable iron oxide nanoparticles have been found to effectively catalyze the one-pot multicomponent click synthesis of 1,4-disubstituted 1,2,3-triazole conjugates in water. IR, 1HNMR, 13CNMR and HRMS experiments have been implemented for the unmistakable determination of the regiochemistry of the process. The novel compounds were evaluated for their antiproliferative activity against four human tumor cell lines, namely, MCF-7, MDA-MB-231, HeLa, and A549. Cell growth inhibition was assessed according to the standard Sulforhodamine B (SRB) cell proliferation method. Results: The most active compounds 4h, 4n and 5a have been identified with superior GI50 values in the range of 0.13–0.31 μM as compared with the reference drug, tamoxifen (0.25-0.72 μM). Conclusion: Additionally, taking the stereochemistry into consideration, E isomers seem slightly more active towards the tested cancer cell lines with respect to Z isomers.

Background: Isocitrate dehydrogenase 2 (IDH2) is an enzyme catalyzing the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG) in the tricarboxylic acid (TCA). Evidences suggest that the specific mutations in IDH2 are critical to the growth and reproduction of severe tumors especially leukemia and glioblastoma. It is found that the inhibitors of mutant IDH2 are promising anti-tumor therapeutics. Methods: A virtual screening strategy combining molecular similarity search and molecular docking was performed in the binding site of AGI-6780. YL-16, YL-17 and YL-18 were identified as novel mutant IDH2 inhibitors for the reduction of (D)-2-hydroxyglutarate in cellular evaluation. In addition, all the three compounds showed inhibition against IDH2-R172K mutated HEK-293T cells, while weak inhibition against wide-type IDH2 (WT-IDH2) HEK-293T cells. Results: Significantly, YL-17 showed 84.55% inhibitory activity against IDH2-R172K at 1 μM and weak cytotoxicity to wide-type IDH2 at 50 μM. Conclusion: YL-17 was highlighted as a new mutant IDH2 inhibitor that could be further developed for therapeutic applications.

Background: S-dihydro-alkyloxy-benzyl-oxopyrimidines (S-DABOs) as non-nucleoside reverse transcriptase inhibitors have received considerable attention during the last decade due to their high potency against HIV-1. Methods: In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR) of a series of 38 S-DABO analogues developed in our lab was studied using Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA). The Docking/MMFF94s computational protocol based on the co-crystallized complex (PDB ID: 1RT2) was used to determine the most probable binding mode and to obtain reliable conformations for molecular alignment. Statistically significant CoMFA (q2=0.766 and r2=0.949) and CoMSIA (q2=0.827 and r2=0.974) models were generated using the training set of 30 compounds on the basis of hybrid docking-based and ligand-based alignment. Results: The predictive ability of CoMFA and CoMSIA models was further validated using a test set of eight compounds with predictive r2 pred values of 0.843 and 0.723, respectively. Conclusion: The information obtained from the 3D contour maps can be used in designing new SDABO derivatives with improved HIV-1 inhibitory activity.

Background: The drug-drug self-assembly was considered as a simple and efficient approach to prepare high drug loading nano-drug carriers and present new opportunities for cancer therapeutics. The strategy of PTX amphiphiles preparation would be a possible way to solve the poor water solubility of PTX. Methods: The PTX-YSL conjugate were synthesized and characterized. The PTX-YSL nanocarriers was prepared by a simple self-assembly method. In vitro cell studies and pharmacokinetic studies were evaluated for their in vitro anti-tumor activities and blood retention time. Results: The structures of PTX-YSL conjugate were confirmed by LC-MS, 1H NMR and FTIR. The size and morphology of the PTX-YSL self-assembled nanocarriers were observed with TEM and DLS. PTX-YSL nanocarriers could facilitate cellular uptake and had low cytotoxicity. PTX-YSL nanocarriers have longer blood retention for enhancing accumulation in the tumor tissues via EPR effect. Conclusion: This drug delivery system formed by PTX-YSL conjugates constitutes a promising and effective drug carrier in cancer therapy.

Background: Matrix metalloproteinase-9 (MMP-9) plays a crucial role in the development and progression of cancer. Therefore, identifying its inhibitors has enjoyed numerous attentions. In this report, a hybrid approach, including pharmacophore-based virtual screening, docking studies, and density functional theory (DFT) binding energy calculations followed by molecular dynamics simulations, was used to identify potential MMP-9 inhibitors. Methods: Pharmacophore modeling based on ARP101, as a known MMP-9 inhibitor, was performed and followed by virtual screening of ZINC database and docking studies to introduce a set of new ligands as candidates for potent inhibitors of MMP-9. The binding energies of MMP-9 and the selected ligands as well as ARP101, were estimated via the DFT energy calculations. Subsequently, molecular dynamics simulations were applied to evaluate and compare the behavior of ARP101 and the selected ligand in a dynamic environment. Results: (S,Z)-6-(((2,3-dihydro-1H-benzo[d]imidazol-2-yl)thio)methylene)-2-((4,6,7-trimethylquinazolin- 2-yl)amino)-1,4,5,6-tetrahydropyrimidin-4-ol, ZINC63611396, with the largest DFT binding energy, was selected as a proper potent MMP-9 inhibitor. Molecular dynamics simulations indicated that the new ligand was stable in the active site. Conclusion: The results of this study revealed that compared to the binding energies achieved from the docking studies, the binding energies obtained from the DFT calculations were more consistent with the intermolecular interactions. Also, the interaction between the Zinc ion and ligand, in particular the Zn2+-ligand distance, played a profound role in the quantity of DFT binding energies.

Background: An extensive study of 19 pyrazole derivatives were carried out based on the evaluation of DNA cleavage properties, antimicrobial and cytotoxic activities and 4D-QSAR analysis including pharmacophore modelling and bioactivity prediction by the Electron Conformational-Genetic Algorithm (EC-GA) method. Methods: The pyrazole derivatives were tested for their antimicrobial activity against certain human pathogenic organisms using the agar diffusion procedure. Binding of compounds with DNA was studied by gel electrophoresis using plasmid pBR322 DNA. The compounds were investigated for their properties as cytotoxic agents by brine shrimp lethality bioassay. To identify the pharmacophoric elements and find out the most important molecular properties which govern cytotoxic activity, multiple conformations of the compounds were used. Results: The urea derivatives of pyrazole had higher antibacterial activities against Gram-negative bacteria than against Gram-positive bacteria. Many of the compounds were found to cleave plasmid pBR322 DNA from the supercoiled form to the nicked circular. The cytotoxicity values of the compounds ranged from 13.87 to 84.1 μg/mL. The generated QSAR model was evaluated through the use of the Leave-One-Out Cross Validation (LOO-CV) method. A statistically significant and considerably predictive QSAR model was obtained with 4- descriptors resulting in R2 training =0.8223, R2 test =0.9346, q2=0.6201, q2 ext1=0.8672, q2 ext2= 0.8662 and q2 ext3=0.9511. Discussion: The generated model demonstrates that geometrical parameters are more correlated with cytotoxic activity. The resulting EC-GA model would provide benefits to design novel bioactive pyrazole derivatives which are more potent and have less side effects. Conclusion: It is believed that the generated QSAR model gives insight into developing new more potent pyrazole derivative drugs.

Background: Hypertension is one of the key risk factors for cardiovascular disease, it is regulated through Renin Angiotensin Aldosterone System (RAAS) cascade. Renin catalyzes the initial rate-limiting step in RAAS system, that influences the synthesis of angiotensin I from precursor angiotensin. Renin inhibition could be a potential step for the blood pressure lowering mechanism as well as for organ protection. Methods: In order to understand the structure-activity association of direct renin inhibitors (DRIs), we have carried out three-dimensional quantitative structure activity relationship (3D-QSAR), molecular docking studies and Density Functional Theory (DFT) analysis to identify the attractive compounds. Five-point pharmacophore model of one acceptor, three hydrophobic groups and one aromatic ring was chosen for the dataset of 40 compounds. Results: The generated 3D-QSAR model shows that the alignment has a good correlation coefficient for the training set compounds, which comprise the value of R2 = 0.96, SD = 0.1, and F = 131.3. The test compounds had Q2 = 0.91, RMSE = 0.25, and Pearson-R = 0.97, which describes the predicted model was reliable. Discussion: External validations were carried out to validate the predicted QSAR model. Further, the significant compounds were studied using different in silico approaches in order to explore the difference in the atomic configuration and binding mechanism of the identified compounds. Conclusion: The molecular dynamics simulation of the complex was analyzed and confirmed the stability of the compounds in the protein. The outcome of the result could be useful to improve the safety and efficacy of DRIs that can be projected to clinical trials.

Background: Benzimidazoles and its derivatives have been attracting interest for many years because of their biological activities. Benzimidazoles containing different heterocyclic moieties have wide range of biological activities such as antimicrobial, antioxidant, anticancer, antiviral, etc. Methods: In this study, some benzimidazole derivatives containing furan, oxadiazole, triazole and thiadiazole moieties have been synthesized and then evaluated for their antioxidant and antiurease activities. Results: The results showed that all the tested benzimidazoles indicated remarkable urease inhibitory potentials with IC50 values ranging between 0.303±0.03 to 0.591±0.08 μM. Conclusion: In conclusion, synthesized benzimidazole derivatives showed good antioxidant and antiurease activities. Heterocyclic groups on benzimidazole nucleus enhance the activities.

Background: Alternatives routes of delivery for Insulin have been evaluated to improve treatment for Diabetes Mellitus. The oral route is the most convenient physiologically; it releases in a similar way to endogenous secretion. Flexible liposomes have deformable abilities to pass through membranes with adequate therapeutic effects, but they have been tested only dermally. Objective: Our aim was to develop an oral nanocarrier based on flexible liposomes for insulin with polymer addition to reduce gastrointestinal degradation. Methods: Different percentages of polyethylene glycol were added to a conventional formulation of flexible liposomes. The manufacturing procedure was the heating method. Z potential, size particle, polydispersity index and encapsulation percentage were evaluated. A release profile was performed in the stomach and intestinal pH mediums by two-stage reverse dialysis method. The in-vivo test was performed in experimental diabetic rats by oral, transdermal and subcutaneous routes. Results: All the formulations showed polydispersity but adequate Z potential. The 10% PEG formulation obtained the best insulin enclosure with 81.9%. The insulin integrity after preparation was confirmed by polyacrylamide gel electrophoresis. PEG and non-PEG formulations showed similar behavior in acid release profile but the release and stability of lipid structures were better and longer in intestinal pH conditions. In vivo tests showed a reduction to normal glucose levels only in subcutaneous route. Conclusion: The polymer inclusion in flexible liposomes generates an adequate nanocarrier for proteins in terms of stability and composition; although its in-vivo use reduces glucose levels in subcutaneous route, the effect was not adequate in oral route.

Background: There is a great unmet medical need for new anticancer small molecule therapeutics. Exhaustive literature review suggests that benzothiazole derivatives have good potential to exhibit anticancer activity. Compounds that inhibit the kinase activity of EGFR are of potential interest as new antitumor agent. Objective: To design, synthesize and carry out in silico along with biological evaluation of 2- substituted benzothiazole compounds with EGFR inhibitory activity. Methods: Benzothiazole derivatives designed from molecular docking method for potential EGFR tyrosine kinase inhibition have been synthesized based on the docking results and characterized. Insilico studies were carried out to understand the mode of EGFR enzyme inhibition by our molecules. As a preliminary study, these compounds were first screened for antioxidant activity and then for anticancer activity against MCF-7 cell lines and A549 cell line. Results: Compound B5 showed potent anticancer activity on MCF-7 cell line with IC50 value of 9.7μM and compound B8 showed significant anticancer activity on A549 cell line with IC50 value of 49.7μM in comparison with the standard drug Doxorubicin (IC50 = 1.4μM on MCF-7 and 1.0μM on A549 cell lines). In EGFR inhibitory activity B8 showed maximum activity on A549 cell line by inactivating 69.10% of EGFR phosphorylation and B7 showed maximum activity on MCF-7 cell line by inactivating 41.90% of EGFR phosphorylation in comparison with the reference drug Gefitinib. Molecular dynamics simulation studies suggest that benzothiazole derivative could also bind to allosteric site and inhibit the EGFR enzyme activity. Conclusion: Reported compounds have shown potent anticancer activity through EGFR inhibition by possibly binding at allosteric site.