European Journal of Chemistry 2020, 11(2), 168-178 | doi: | Get rights and content


In silico screening for the interaction of small molecules with their targets and evaluation of therapeutic efficacy by free online tools

Praveen Kumar (1,*) orcid , Nayak Devappa Satyanarayan (2) orcid , Subba Rao Venkata Madhunapantula (3) orcid , Hulikal Shivashankara Santhosh Kumar (4) orcid , Rajeshwara Achur (5) orcid

(1) Department of Biochemistry, Kuvempu University, Jnana Sahyadri 577451, Shimoga, Karnataka, India
(2) Department of Pharmaceutical Chemistry, Kuvempu University, Post Graduate Centre, Kadur 577458, Chikkamagaluru Dist., Karnataka, India
(3) Center of Excellence in Molecular Biology and Regenerative Medicine Laboratory, Department of Biochemistry, Jagadguru Sri Shivarathreeshwara Medical College, Academy of Higher Education and Research, Mysuru, Karnataka, 570015, India
(4) Department of Biotechnology, Kuvempu University, Jnana Sahyadri 577451, Shimoga, Karnataka, India
(5) Department of Biochemistry, Kuvempu University, Jnana Sahyadri 577451, Shimoga, Karnataka, India
(*) Corresponding Author

Received: 24 Jan 2020 | Revised: 17 Apr 2020 | Accepted: 21 Apr 2020 | Published: 30 Jun 2020 | Issue Date: June 2020


Pharmaceutical chemistry deals with the process of isolating organic compounds from natural sources or chemically synthesizing them in order to explore potential drugs. Drugs are small molecules, used to prevent or treat various diseases. Of several lead molecules, only few of them reach clinical trial phases and emerge as effective drugs, whereas the majority will be eliminated at different stages. On the other hand, due to the lack of proper identification of their pharmacokinetic properties and biological potential, many small molecules fail to reach this stage. This could be because of the fact that it is either time consuming and costly or there is full of uncertainty due to lack of analyses that are necessary for the confirmation. In the post-genomic era, computational methods have been implemented in almost all stages of drug research and development owing to the drastic increase in the available knowledge about small molecules and the target biomacromolecule. This includes identifying the suitable and specific targets for drug candidates, lead discovery, lead optimization and ultimately preclinical phases. In this context, numerous websites have become highly valuable and influence the drug development and discovery process. Here, we have attempted to bring together some of the online computational approaches and tools that are available to facilitate research efforts in the field of drug discovery and drug design. The output information from these tools is extremely helpful in selecting and deciding about the future direction or specific path needed to be followed by the researchers. These computational methods are indeed help to focus the intended research in the right direction. As detailed in this review, the information provided about the servers and methods should be useful throughout the process of screening of synthesized or chemical database originated small molecules to find the appropriate targets along with the active sites without depending on any commercial tools or time-consuming and costly assays. It should however be remembered that the bioinformatics-based prediction cannot completely replace the wet lab data of chemical compounds or specific assays.


CASTp; ADMET; STRING; ChemAxon; Doxorubicin; MTiAutoDock

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DOI: 10.5155/eurjchem.11.2.168-178.1962

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How to cite

Kumar, P.; Satyanarayan, N.; Madhunapantula, S.; Kumar, H.; Achur, R. Eur. J. Chem. 2020, 11(2), 168-178. doi:10.5155/eurjchem.11.2.168-178.1962
Kumar, P.; Satyanarayan, N.; Madhunapantula, S.; Kumar, H.; Achur, R. In silico screening for the interaction of small molecules with their targets and evaluation of therapeutic efficacy by free online tools. Eur. J. Chem. 2020, 11(2), 168-178. doi:10.5155/eurjchem.11.2.168-178.1962
Kumar, P., Satyanarayan, N., Madhunapantula, S., Kumar, H., & Achur, R. (2020). In silico screening for the interaction of small molecules with their targets and evaluation of therapeutic efficacy by free online tools. European Journal of Chemistry, 11(2), 168-178. doi:10.5155/eurjchem.11.2.168-178.1962
Kumar, Praveen, Nayak Devappa Satyanarayan, Subba Rao Venkata Madhunapantula, Hulikal Shivashankara Santhosh Kumar, & Rajeshwara Achur. "In silico screening for the interaction of small molecules with their targets and evaluation of therapeutic efficacy by free online tools." European Journal of Chemistry [Online], 11.2 (2020): 168-178. Web. 8 Jul. 2020
Kumar, Praveen, Satyanarayan, Nayak, Madhunapantula, Subba, Kumar, Hulikal, AND Achur, Rajeshwara. "In silico screening for the interaction of small molecules with their targets and evaluation of therapeutic efficacy by free online tools" European Journal of Chemistry [Online], Volume 11 Number 2 (30 June 2020)

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