The process of hunt of a lead molecule is a long and a tedious process and one is often demoralized by the endless possibilities one has to search through. Fortunately, computational tools have come to the rescue and have undoubtedly played a pivotal role in rationalizing the path to drug discovery. Of all techniques, molecular docking has played a crucial role in computer aided drug design and has swiftly gained ranks to secure a valuable position in the modern scenario of structure-based drug design. In this chapter, the principle, sampling algorithms, scoring functions and diverse available software’s for molecular docking have been summarized. We demonstrate the interplay of docking, classical techniques of structure-based design and X-ray crystallography in the process of drug discovery. In addition, we dwell upon some of the limitations faced in docking studies. Finally, several success stories of molecular docking approaches in drug discovery have been highlighted, concluding with remarks on molecular docking for the future.

A novel series of imidazo[2,1-b]thiazole-sulfonyl piperazine conjugates (9aa-ee) has been synthesized and evaluated for carbonic anhydrase (CA, EC 4.2.1.1) inhibitory potency against four isoforms: The cytosolic isozyme hCA I, II and trans-membrane tumor-associated isoform hCA IX and hCA XII, taking acetazolamide (AAZ) as standard drug, using a stopped flow CO₂ hydrase assay. The results revealed that most of the compounds showed selective activity against hCA II whereas none of them were active against hCA I, IX, XII (K_i > 100 µM). The physiologically dominant cytosolic isoform hCA II was inhibited by these molecules with inhibition constants in the range of 57.7–98.2 µM. This new derivative, thus, selectively inhibits hCA II over the hCA I, IX, XII isoforms, which may be used for further understanding the physiological roles of some of these isoforms in various pathologies.