Introduction 3. Materials and methods 3.1. In silico studies on CDK2 3.1.1. Molecular docking 3.1.2. Molecular dynamics simulation 3.2. In vitro CDK2 inhibition assay 3.3. In vitro evaluation of antimetastatic potential on B16F10 cell line 3.3.1. Determination of cell viability by MTT assay 3.3.1.1. Preparation of solutions for compounds for MTT assay 3.3.1.2. MTT assay 3.3.2. Preparation of dilutions for colony formation assay, wound scratch assay, and Leighton tube studies 3.3.3. Colony formation assay 3.3.4. Wound healing assay 3.3.5. Determination of cellular morphology by Leighton tube assay 4. Results and Discussion 4.1 In silico studies on CDK2 4.1.1. Molecular docking 4.1.1.1. Validation of docking protocol 4.1.1.2. Docking studies of synthetic flavones 4.1.2. Molecular dynamics simulation 4.2. In vitro CDK2 inhibition assay 4.3. In vitro studies on B16F10 cell line 4.3.1. Synthesized flavones exert cytotoxicity & inhibit the proliferation of B16F10 cells 4.3.2. Synthesized flavones hamper the formation of colonies in B16F10 melanoma 4.3.3. Synthesized flavones inhibit cellular migration in wound scratch assay 4.3.4. Synthesized flavones initiate changes in the morphology of B16F10 cells 5. Conclusion CDK2 Inhibition and antimetastatic effect of flavones 665

Background: EGFR (Epidermal Growth Factor Receptor) and CDK2 (Cyclin Dependent Kinase 2) are important targets in the treatment of many solid tumors and different ligands of these receptors share many common structural features. Objective: The study involved synthesis of benzamide-substituted chalcones and determination of their antiproliferative activity as well as preliminary evaluation of EGFR and CDK2 inhibitory potential using both receptor binding and computational methods. Methods: We synthesized 13 benzamide-substituted chalcone derivatives and tested their antiproliferative activity against MCF-7, HT-29 and U373MG cell-lines using Sulforhodamine B Assay. Four compounds were examined for activity against EGFR and CDK2 kinase. The compounds were docked into both EGFR and CDK2 using Glide software. The stability of the interactions for most active compound was evaluated by Molecular Dynamics Simulation using Desmond software. Molecular Docking studies on mutant EGFR (T790M, T790M/L858R, and T790M/C797S) were also carried out. Results: From the SRB assay, we concluded that compounds 1g, and 1k were effective in inhibiting the growth of MCF-7 cell line whereas the other compounds were moderately active. Most compounds were either moderately active or inactive on U373 MG and HT-29 cell line. Compounds 1g and 1k showed good inhibitory activity against CDK2 kinase while 1d and 1f were moderately active. Compounds 1d, 1f, 1g, and 1k were moderately active against EGFR kinase. Molecular docking reveals involvement of one hydrogen bond with Met793 in binding with EGFR however; it was not stable during simulation and these compounds bind to the receptor mainly via hydrophobic contacts. This fact also points towards a different orientation of the inhibitor within the active site of EGFR kinase. Binding mode analysis for CDK2 inhibition studies indicate that hydrogen bonding interaction with Lys 33 and Leu83 are important for the activity. These interactions were found to be stable throughout the simulation. Considering the results for wild-type EGFR inhibition, the docking studies on mutants were performed and which indicate that the compounds bind to the mutant EGFR but the amino acid residues involved are similar to the wild-type EGFR and therefore, the selectivity seems to be limited. Conclusion: These benzamide-substituted chalcone derivatives will be useful as lead molecules for the further development of newer inhibitors of EGFR and/or CDK2 kinases.

A series of 13 novel cinnamamide-chalcone derivatives (2a-2m) were synthesized and evaluated for their antiproliferative activity against MCF-7, K562, U373MG, and HT-29 cell lines by SRB assay. Considering the activities on MCF-7 cell line, eight compounds were tested for the in-vitro CDK2 inhibition and four (2g, 2h, 2k and 2l) were found to possess good activity (IC 50 <10µM). These four compounds were tested on EGFR kinase to assess the selectivity towards CDK2 and were found be nearly two times more selective.To corroborate the in-vitro enzyme assay data with binding, the compounds were docked into the CDK2 and EGFR using Glide software. The docking studies reveal that all eight compounds form hydrogen bonds with Lys33 (β-3 region) and Leu83 (hinge region) in CDK2 and the docking scores correlate well with the IC 50 values. The most active compounds on CDK2 when docked in EGFR had lower docking scores. Only one compound interacts with Lys721 (β-3 region) and Met769 (hinge region). The stability of interactions with CDK2 was assessed for 2k and 2l by molecular dynamics simulation using Desmond software. In conclusion, three compounds possess excellent activity against MCF-7 cell line and good activity against CDK2.

c-Met kinase and cyclooxygenase 2 (COX-2) enzymes are two significant targets in tumor progression. Chalcone and benzamide moieties were combined using molecular hybridization to assess their potential as c-Met kinase and COX-2 inhibitors. 4-Methylbenzamide and 4-chlorobenzamide chalcone analogs were synthesized, characterized, and evaluated for antiproliferative activity on Michigan Cancer Foundation-7 (MCF-7), HT-29, MDA-MB-231, COLO-205, and A549 cell lines by sulforhodamine-B stain (SRB) assay. Following the SRB assay, compounds were evaluated for their c-Met kinase and COX-2 inhibitory potential. All compounds inhibited COX-2 with half-maximal inhibitory concentration (IC 50 ) <10 µM. Compounds 7h, 7i, 7j, 8f, and 8j inhibited c-Met with IC 50 <10 µM. Compound 7h was evaluated for its long-term antiproliferative and anti-migratory effects by colony formation and wound healing assay. It exerted these effects in a concentration-dependent manner.Compounds 7j and 8j were further evaluated for in vitro antiangiogenic effects.Compound 7j exhibited moderate antiangiogenic effect while compound 8j exhibited strong effect. Compounds 7h, 7i, 7j, 8f, and 8j were evaluated for the serum protein binding, using the in vitro bovine serum albumin binding assay. The results indicated that the tested compounds bind to bovine serum albumin (BSA) and can be further explored by other studies.

We have developed novel series of 5-arylidene-1, 3-thiazolidin-4-one analogues using diethylamine as catalyst. Diethylamine was found suitable in synthesizing variety of title compounds in 62-85% yield. In-vitro anticancer activity of synthesized analogues was evaluated using human breast (MCF7), lung (Hop62) and hepatic (HepG2) cell lines using SRB assay. Amongst the synthesized compounds 9b, 9e, 9f are excellent in inhibiting growth of cancer cell lines with GI50 value <10μg/ml in comparison with Adriamycin standard. We have also performed docking studies using SHP2 in complex with inhibitor (PDB ID: 2Shp) but results were non-supportive, very weak. We found no correlation between anticancer studies and docking studies.