Computer aided identification of sodium channel blockers in the clinical treatment of epilepsy using molecular docking tools



Uzma Shaheen1, Jyothy Akka1, Jitendra Singh Hinore3, Amandeep Girdhar3, Srinivas Bandaru1, 2, Tharaparambil Gangadharan Sumithnath4, Anuraj Nayarisseri3* & Anjana Munshi5



1Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad – 500 016, Telangana, India; 2National Institute of Pharmaceutical Education and Research, Hyderabad – 500 037, Telangana, India; 3In silico Research Laboratory, Eminent Biosciences, Indore – 452 010, Madhya Pradesh, India; 4St. Martin’s Engineering College, Jawaharlal Nehru Technological University, Hyderabad -500 014, Telangana, India; 5Centre for Human Genetics, Central University of Punjab, Bathinda- 151 001, Punjab, India


Email; *Corresponding author


Article Type




Received February 22, 2015; Accepted March 14, 2015; Published March 31, 2015



Phenytoin (PHT) and Carbamazepine (CBZ) are excellent sodium channel blockers administered in clinical treatment of epileptic seizures. However, the narrow therapeutic range and limited pharmacokinetics of these drugs have raised serious concerns in the proper management of epilepsy. To overcome this, the present study attempts to identify a candidate molecule with superior pharmacological profile than PHT and CBZ through In silico approaches. PHT and CBZ served as query small molecules for Tanimoto based similarity search with a threshold of 95% against PubChem database. Aided by MolDock algorithm, high affinity similar compound against each query was retrieved. PHT and CBZ and their respective similar were further tested for toxicity profiles, LC 50 values and biological activity. Compounds, NSC403438 and AGN-PC-0BPCBP respectively similar to PHT and CBZ demonstrated higher affinity to sodium channel protein than their respective leads. Of particular relevance, NSC403438 demonstrated highest binding affinity bestowed with least toxicity, better LC 50 values and optimal bioactivity. NSC403438 was further mapped for its structure based pharmacophoric features. In the study, we report NSC403438 as potential sodium channel blocker as a better candidate than PHT and CBZ which can be put forth for pharmacodynamic and pharmacokinetic studies.



Sodium channel blockers, Virtual Screening, Phenytoin, Carbamazepine, NSC403438 and AGN-PC-0BPCBP



AEDs: Antiepileptic drugs, BLAST: Basic Local Alignment Search Tool, CBZ: Carbamazepine, GEFS+: Generalized Epilepsy with Febrile Seizures Plus, GPCR: G Protein Coupled Receptor, Nav: Sodium channel with specific voltage conduction, PDB: Protein Data Bank, PHT: Phenytoin, PIR: Protein Information resources, SAVES: Structural Analysis and Verification Server, VGSC: Voltage-gated Sodium channels



Shaheen et al. Bioinformation 11(3): 131-137 (2015)

Edited by

P Kangueane






Biomedical Informatics



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