Protein　kinase　casein　kinase　2　(CK2)　is　involved　in　a　variety　of　important　cellular　physiological　processes,　and　aberrant　CK2　activity　is　associated　with　a　wide　variety　of　human　diseases.　5-(3-Chlorophenylamino)benzo[c][2,6]naphthyridine-8-carboxylic　acid　(CX-4945)　represents　the　first　orally　bioavailable　and　highly　selective　small　molecule　inhibitor　of　CK2.　In　the　present　work,　a　series　of　tricyclic　quinolone　analogs　were　studied　by　utilizing　a　combination　of　three-dimensional　quantitative　structure　activity　relationship,　molecular　docking,　and　molecular　dynamics　(MD)　simulation　methods.　CoMFA　and　CoMSIA　analyses　were　done　using　ligand-based　and　receptor-based　(RB)　alignment　schemes,　and　the　RB　CoMSIA　model　(q　(2)　=　0.647,　r　(2)　=　0.934,　r　(pred)　(2)　=　0.74)　including　the　steric,　electronic,　and　hydrogen　bond　donor　fields　shows　good　correlative　and　predictive　ability.　By　combining　the　contour　maps　of　RB　CoMSIA　model　with　the　binding　pocket　of　human　CK2　alpha,　the　crucial　structural　elements　responsible　for　inhibitory　activity　are　investigated.　Also,　the　mechanism　of　how　different　isomers　influence　the　binding　affinity　is　elucidated　from　the　MD　simulation.　All　these　results　are　in　good　accordance　and　complementary　to　each　other,　and　may　provide　the　rational　clues　to　design　more　potent　CK2　inhibitors.