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Molecular docking based virtual screening of carbonic anhydrase IX with coumarin (a cinnamon compund) derived ligands



K. Meenakumari1, G. Bupesh1,2,*, S. Vasanth1, C. Arul Vasu4, K. Pandian3, K. Prabhu6, S. Prasath @ Surendhar5



1Research and Development Wing, Central Research Laboratory, Sree Balaji Medical College and Hospital (SBMCH), BIHER, Chrompet, Chennai - 600044, India; 2Department of Virology, King Institute of Preventive Medicine and Research, Guindy, Chennai - 600032, India; 3Department of Inorganic Chemistry, University of Madras, Guindy Campus, Tamil Nadu, India; 4Department of Zoology, University of Madras, Guindy Campus, Tamil Nadu, India; 5Department of Biomedical Engineering, Bharath Institute of Higher Education & Research, Chennai - 605005, Tamil Nadu, India; 6Department of Anantomy, Sree Balaji Medical College & Hospital, BIHER, Chromepet, Chennai



Dr. G. Bupesh - Phone: +91 8012405965; Email: bupeshgiri55@gmail.com; *Corresponding author


Article Type

Research Article



Received September 27, 2019; Revised October 30, 2019; Accepted October 30, 2019; Published October 31, 2019



It is of interest to design carbonic anhydrase IX (CAIX) inhibitors with improved features using molecular docking based virtual high through put screening of ligands. Coumarin (a cinnamon compound with pharmacological activity) is known as a potent phytal compound blocking tumor growth. Hence, a series of 17 coumarin derivatives were designed using the CHEMSKETCH software for docking analysis with CAIX. The catalytic site analysis of CAIX for binding with ligand molecules were completed using the SCHRODINGER package (2009). Thus, 17 ligands with optimal binding features with CAIX were selected following the calculation of ADME/T properties. We report ligands #41, #42, #19 and #15 showed good docking score, glide energy and hydrogen bond interactions without vdW clash. We further show that N-(3,4,5-trimethoxy-phenyl carbamoylmethyl) designated as compound #41 have the highest binding energy (-61.58) with optimal interactions with the catalytic residues (THR 199, PRO 201, HIS 119, HIS 94) of CAIX.



Carbonic anhydrase IX; coumarin; GLIDE; ADME/T; induced fit docking



Meenakumari et al. Bioinformation 15(10): 744-749 (2019)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.