Homology Modeling Odorant-binding Protein-1 (OBP1) Anopheles Farauti Protein Target for Mosquito Repellent

Abstract

The odorant binding protein (OBP) has a role as a target protein for potential interaction mechanism activity for the development of repellent compounds. The purpose of this study was to analyze the physico-chemical properties of the protein, the stability of the three-dimensional structure of the OBP1 Anopheles farauti protein, and to predict the binding site pocket as the target of the active protein site against inhibitors. Analysis of physico-chemical properties was carried out by the ProtParam Expasy server. The theoretical calculated isoelectric point (pI) was found to be less than 7 indicating the acidic nature of this protein. The aliphatic index of 78 indicates the thermal stability of the protein. The Grand Average of Hydropathicity (GRAVY) is estimated at -0.355; This lower GRAVY value indicates a possible better interaction of this protein with water. Secondary structure analysis was carried out by SOPMA which revealed that Alpha helix (55.86%) predominated among the secondary structural elements followed by Random coil (32.41%), Extended strand (8.97%), and Beta turn (2.76%). Three-dimensional structure modeling of OBP1 Anopheles farauti was performed with the Swiss-Model server and the protein refine Galaxy server. Homology modeling results obtained PDB ID 2ERB template with sequence identity 94.4%. The model was validated for the three-dimensional structure of the protein using the MolProbity, ProSA, ProQ, ERRAT, Verfy3D, and PROCHECK servers. The prediction results of pocket binding sites using DoSiteScore obtained three pocket binding site locations, namely P_0 (Drug score 0.84); P_1 ((0.75); P_2 (Drug score 0.64). Conclusion Homology modeling of the protein OBP1 Anopheles farauti has been carried out and the three-dimensional structure of the Model_OBP1_04 protein has been obtained that meets the criteria for valid structural parameters so that this structure can be used In-silico molecular docking and molecular dynamic studies for the development of mosquitoes repellent.