Benzimidazole and its derivatives are used in organic synthesis and vermicides or fungicides as they inhibit the action of certain microorganisms. The molecules to be analysed were aligned on an appropriate template, which is considered to be common substructure. The protein structure of PDB name along with their inhibitor was retrieved from RCSB Protein Data Bank (PDB entry code: 6T1O). The protein structure were subjected to energy minimization and charge calculation (AMBER7FF99), docking score of compounds on 6T1O PDB describe the ligand interaction. Virtual library of benzimidazoles derivatives to find lead structures to test against C. albicans. Twenty compounds were designed in which heterocyclic ring is substituted at NH group of Substituted ortho-phenylenediamine moiety while some compound also bearing chloro and nitro group on para position of aromatic ring.

Objective: The aim of the present study is to synthesize novel benzimidazole derivatives as potent antifungal agents.Methods: 2-chloromethyl-1H-benzimidazole has been synthesized by refluxing o-phenylenediamine with chloroacetic acid in the presence of 5N HCL. Further, N-substituted benzimidazole derivatives containing various heteroamines and aromatic compounds were synthesized. These, finally, prepared derivatives were kept for in vitro antifungal property.Results: A novel series of antifungal agents, containing benzimidazole nucleus as a basic skeleton, has been synthesized.Conclusion: The synthesized novel benzimidazole derivatives exhibit moderate activity (VMSA 1, 2, 8), some compounds showed significant activity (VMSA 6, 9, and 10), and compound VMSA 4 and 5 exhibits maximum activity.

For the identification of the lead compounds, a molecular docking tool is used. The little structure, namely Ligand, generally holds together the protein places. It describes a similar approach that utilizes to place over another three-dimensional structure of a probable drug on its prospective object sites. Given that, it was worthwhile to build a virtual library of benzimidazole derivatives to find lead structures to test against C. Albicans. The two-dimensional structure of all planned compounds was drawn by using the current version software and pass on to the software window. The energy of all three-dimensional structures was reduced by Molecular Orbital Package up to Root mean square gradient 0.001 and put aside in MDL Molfile (.Mol) format. To assess the likely potential of the Quantitative Structure-Activity Relationship models, the dataset was split into a training set comprising of 32 molecules and a test set of 8 molecules in such a way that the structural variety and an extensive range of biological action in the specific set were added. The IC50 values were transformed to pIC50 to give numerically larger data values.