Pharmacophore-based virtual screening, biological evaluation and binding mode analysis of a novel protease-activated receptor 2 antagonist.
Protease-activated receptor 2 (PAR2) is a G protein-coupled receptor, mediating inflammation and pain signaling in neurons, thus it is considered to be a potential therapeutic target for inflammatory diseases. In this study, we performed a ligand-based virtual screening of 1.6 million compounds by employing a common-feature pharmacophore model and two-dimensional similarity search to identify a new PAR2 antagonist. The common-feature pharmacophore model was established based on the biological screening results of our in-house library. The initial virtual screening yielded a total number of 47 hits, and additional biological activity tests including PAR2 antagonism and anti-inflammatory effects resulted in a promising candidate, compound 43, which demonstrated an IC50 value of 8.22 µM against PAR2. In next step, a PAR2 homology model was constructed using the crystal structure of the PAR1 as a template to explore the binding mode of the identified ligands. A molecular docking method was optimized by comparing the binding modes of a known PAR2 agonist GB110 and antagonist GB83, and applied to predict the binding mode of our hit compound 43. In-depth docking analyses revealed that the hydrophobic interaction with Phe243(5.39) is crucial for PAR2 ligands to exert antagonistic activity. MD simulation results supported the predicted docking poses that PAR2 antagonist blocked a conformational rearrangement of Na(+) allosteric site in contrast to PAR2 agonist that showed Na(+) relocation upon GPCR activation. In conclusion, we identified new a PAR2 antagonist together with its binding mode, which provides useful insights for the design and development of PAR2 ligands.
Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 136-791, Republic of Korea.|Department of Biotechnology, Yonsei University, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
Nam-Chul
NC
Cho
Department of Pharmaceutical Biochemistry, College of Pharmacy, Kyung Hee University, Dongdaemun-gu, Seoul, 130-701, Republic of Korea.
Seoung-Hwan
SH
Seo
Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 136-791, Republic of Korea.|Department of Biotechnology, Yonsei University, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
Dohee
D
Kim
Department of Pharmaceutical Biochemistry, College of Pharmacy, Kyung Hee University, Dongdaemun-gu, Seoul, 130-701, Republic of Korea.
Ji-Sun
JS
Shin
Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 136-791, Republic of Korea.
Jeongmin
J
Ju
Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 136-791, Republic of Korea.
Jihye
J
Seong
Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 136-791, Republic of Korea.
Seon Hee
SH
Seo
Department of Global Medical Science, Sungshin University, Seoul, 142-732, Republic of Korea.
Iiyoun
I
Lee
Department of Pharmaceutical Biochemistry, College of Pharmacy, Kyung Hee University, Dongdaemun-gu, Seoul, 130-701, Republic of Korea.
Kyung-Tae
KT
Lee
Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 136-791, Republic of Korea.|Department of Biological Science, Korea University of Science and Technology, 52 Eoeun dong, Yuseong-gu, Daejeon, 305-333, Republic of Korea.
Yun Kyung
YK
Kim
Department of Biotechnology, Yonsei University, Seodaemun-gu, Seoul, 120-749, Republic of Korea. ktno@bmdrc.org.
Kyoung Tai
KT
No
Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 136-791, Republic of Korea. anpae@kist.re.kr.|Department of Biological Science, Korea University of Science and Technology, 52 Eoeun dong, Yuseong-gu, Daejeon, 305-333, Republic of Korea. anpae@kist.re.kr.
Ae Nim
AN
Pae
D000595:Amino Acid Sequence; D000818:Animals; D016466:CHO Cells; D003412:Cricetulus; D055808:Drug Discovery; D006801:Humans; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D044464:Receptor, PAR-2 / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism*; D016415:Sequence Alignment; D054852:Small Molecule Libraries / Q000737:chemistry* / Q000494:pharmacology*
D044464:Receptor, PAR-2; D054852:Small Molecule Libraries
G protein-coupled receptor; Molecular docking; Molecular dynamics simulation; Na+ allosteric site; Protease-activated receptor 2; Virtual screening