Dear Ashish,

Please read the following text which was taken from a review article entitled " Software and resources for computational medicinal chemistry" published in Future Med Chem. 2011 Jun; 3(8): 1057–1085.

The answer is yes, there is a possibility to check bioactivity using one or more of the programs described in this review. If the active site is known, it will be much easier to check the bioactivity of organic compounds on this active site, however, if the active site is not known or not determined by x-ray crystal structure or other techniques such as NMR and etc, it will be difficult to evaluate the bioactivity.

In principle, if the followings two requirements are fulfilled the task for evaluating the bioactivity of an organic compound will be feasible:

(1) A known active site (enzyme or receptor) and (2) availability of an appropriate software that is proved to predict activity with high accuracy (see programs indicated in the review.

After three decades of development, CADD has become a valuable component of drug discovery and development. To describe its typical use, at the beginning of a drug-discovery project, chemoinformatics tools are employed to choose compounds from available sources to be assayed. Some marginally active or better compounds may be found, and then chemical similarity searching techniques are used to find more compounds that should be assayed. If some compounds that are more active are discovered, computationally more expensive techniques are applied, such as docking and pharmacophore modeling, to identify more potent compounds or optimize more ADME/T favorable compounds. Techniques of CADD also provide other options for understanding chemical systems, which yield information that is not easy to obtain in laboratory analysis, and, furthermore, is typically (much) less costly than by experiment. After ups and downs of the perception of CADD in the field of drug development, and perhaps some over-hyping of its promises, especially in the initial phases of new trends in development, one can probably say that the discipline of computational medicinal chemistry has begun to mature and become a realistically assessed and routinely used component of modern drug discovery. The breadth of techniques and tools described in this article imply that, to become a successful computational medicinal chemist, it will be highly beneficial to master different kinds of CADD programs and utilize all computational resources that are valuable for drug design. In addition, having skills in one or more programming languages, such as Python, will help smooth routine drug-design work in a contemporary CADD setup.

While it would be desirable, one cannot bank on the fact that a quantum leap in precision of docking or pharmacophore search will occur in the next few years. Nevertheless, SBVS and LBVS are very likely to become routine in drug-discovery projects if they have not already done so. The use of more accurate methods, such as MD and QM, will continue to grow. Currently, sophisticated CADD tools are typically applied by modeling experts, but are increasingly spreading to the desktops of medicinal chemists as well.

To view the full review article, please use the following text:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413324/

Recent examples of novel inhibitor discovery using molecular docking are listed in the attached files.

Lead discovery using molecular docking

Brian K Shoichet*, Susan L McGovern, Binqing Wei and John J Irwi

Next-generation therapeutics

As the structures of more and more proteins and nucleic acids become available, molecular docking is increasingly considered for lead discovery. Recent studies consider the hit-rate enhancement of docking screens and the accuracy of

docking structure predictions. As more structures are determined experimentally, docking against homology-modeled targets also becomes possible for more proteins. With more docking studies being undertaken, the ‘drug-likeness’ and

specificity of docking hits is also being examined.

Hoping this will be helpful,

Rafik

Hoping this will be helpful,

Rafik

Now a days computer aided drug design (CADD) is very popular technique to optimize a drug candidate. 

Hi

Computer-aided drug design (CADD) plays a vital role in drug discovery and development and has become an indispensable tool in the pharmaceutical industry. Computational medicinal chemists can take advantage of all kinds of software and resources in the computer-aided drug design field for the purposes of discovering and optimizing biologically active compounds. This article reviews software and other resources related to computer-aided drug design approaches, putting particular emphasis on structure-based drug design, ligand-based drug design, chemical databases and chemoinformatics tools.