**3.1 Pharmacophore modeling**

Pharmacophore is one of the most promising *in silico* concepts, which is utilized to screen large compound libraries. The process includes combining medicinal chemistry and computational chemistry that can screen and optimize lead compounds for the development of the final drug candidate [50]. The pharmacophore model can function in two ways such as ligand-based modeling and structure-based modeling (**Figure 2**). The ligand-based model is fully based on computerized for simplifying drug discovery in the macromolecular target structure [51]. It generates three-dimensional (3D) structures for interacting ligand and macromolecules. Software such as Schrödinger (https://www.schrodinger.com/) and so on are used for pharmacophore drug design. Furthermore, the direct interaction of 3D structure with macromolecule ligand complex is arranged by structure-based pharmacophore modeling. The investigation of the complementary chemical feature of the active site and their spatial relationships and assembly with the selected feature will be generated using the structure-based pharmacophore modeling [52]. Discovery studio is usually practiced for the implementation of the structure-based pharmacophore method. The catalyst feature of pharmacophoric is H-bond acceptor, H-bond donor, and hydrophobic. Virtual-based pharmacophore screening has been reducing the possibility of arising problems about inadequate consideration of protein selectivity with the optimizing

#### **Figure 2.**

*Pharmacophore model-based virtual screening process for identification of small molecular candidates against a specific disease.*

*Immunoinformatics and Computer-Aided Drug Design as New Approaches against Emerging… DOI: http://dx.doi.org/10.5772/intechopen.101367*

score and insufficient design by leading a tolerance radius for each feature [53]. The main purpose of pharmacophore model-based virtual screening is to count the highest molecules hit, which has similar or nearest the target.
