**5. Conclusion**

*Homology Molecular Modeling - Perspectives and Applications*

elucidated in 2016 (PDB ID: 5T1A [45]).

copied from the corresponding template (PDB: 1F88) and the N-terminal domain and the remaining loops were built de novo using MODELER 6.2. Confirmations of the models were done using PROCHECK and were selected as the input structure for MD Loop Refinement. The resulting model consisting of the TMHs and all ECLs and ICLs, was validated by MD conformational analysis, which showed it to be consistent with the then currently available SDM data and was used to gain insights into the molecular basis of the initiation and development of HIV-1 infection. This

information could be useful in the rational design of HIV-1 entry blockers.

Chronologically, the time when the structural information about chemokine receptors was unavailable Gugan et al. in 2012 carried out the investigations on the binding site of CCR2 [43]. A comparative model was generated using the template structure of CXCR4 (PDB ID: 3ODU [44]). The structure of CXCR4 (PDB ID: 3ODU) was elucidated in 2010. One of the key findings along with the binding site residues is that the disulfide bridge was produced between Cys113-Cys190 of the selected CCR2 model and was also later observed in the crystal structure which was

In the similar manner, Changdev et al. in 2013 developed the 3-D model for CCR5 using the template CXCR4 (PDB ID: 3ODU; resolution 2.5 Å) modeled by MODELER 9.2 [46] to explore the biding site of the receptor [47]. Significantly, the modeled structure coincides with the crystal structure of the CCR5 (PDB ID:4MBS [20]) whose structural information was determined by Tan et al. in 2013 [48]. The research by Anand et al. in 2011 on the accuracy of homology modeling revealed the comparison study between the reported models along with the crystal structure of CCR5 (PDB ID:4MBS)[49]. The findings have identified the importance of multi-template model in determining the insights of structural information of the receptor possessing its own merits and demerits. The inhibitor Maraviroc was docked to the single template and multi-template models of bovine rhodopsin (PDB ID: 1F88), β2 adrenergic receptor (PDB ID: 2RH1 [50]) and CXCR4 (PDB ID: 3ODU). The critical salt-bridge interaction established by Maraviroc with Glu283 of the receptor was genuinely observed in modeled structure and crystal structure. In the process of building model of a particular GPCR usually many models are constructed with varying side chains and almost identical backbone. This is done to check which model among all the constructed models shows maximum affinity towards various ligands. So the model showing consisting binding mode is selected for further analysis. An example of this is the study done by Mateusz N et al. where 400 homology models of serotonin 5-HT1A receptor, one of the most documented monoamine GPCR, was modeled using Modeler 7v7 [51] with the crystal structure of bovine rhodopsin (PDB:1F88) as template [52]. These models varied considerably in their side chain but the polypeptide backbone varied only marginally from the template. Arylpiperazines test ligands were docked to all the 400 models with default parameters without any constraints. A detailed analysis of the docking poses revealed intrinsic information about crucial ionic bonds that were formed d almost exclusively in the case of receptors with the gauche(−) conformation of the Asp3.32 ø1 angle. Such insights led to the development of 200 new homology models with all the changes incorporated. Molecular docking was once again done on all the 200 new models and the complexes were scored using various scoring functions to

The past few years have seen remarkable advances in the structural biology of G-protein coupled receptors (GPCRs) and separate databases exist to study GPCRs. The applications of structural studies of GPCRs have various goals and these goals trigger myriad scientific investigations. For the GPCRs whose structures have now been solved, the homology models developed earlier based on rhodopsin, have been the first step in discovering the versatility of their structural studies. Due to the

**62**

choose the best models.

The research in GPCRs is a global phenomenon and this is possible only if we have structural insights based on structural studies of GPCRs. Owing to the difficulty in crystallizing the GPCRs, it was once construed that structural studies of GPCRs were impossible. But with the technological advancements in the computational techniques, building a model structure based on the homology of a particular receptor with a template structure became possible. Thus homology modeling and models generated via tools like MODELER unraveled the unexplored arenas in the research of GPCRs. These models served a greater purpose to the pharmaceutical industries wherein GPCRs became famous drug discovery targets. The many experimental structures constructed using previously solved structures as templates were further scrutinized based on their efficiency in showing a consisting binding mode with various ligands. Recent times have seen use of Cryo EM techniques in solving structures of GPCRs. But still contribution made by techniques like homology modeling in the structural studies of GPCRs will always remain as a mile stone.
