Cheminformatics!! The Digital Sciences'

The use of computational and informational techniques to understand the development as well as the challenges related to chemical sciences is termed Cheminformatics. It can also be mentioned, as the division of chemistry that has evolved through the progressive development of approaches along with computer and information science techniques. It is a field of science where computational methods are applied to solve various problems and challenges. The invention of epigenetic chemical probes, archiving and retrieving data on molecular structures, reaction pathways, molecular interactions, drug designing-delivering strategies, large combinatorial databases, etc., are the significant areas that involve Cheminformatics. Some of the Cheminformatic techniques that display an innovative role in the field of medicine and research are-

• Virtual screening automatically evaluates very large libraries of compounds with the help of computer programs.
• Quantitative structure-activity relationship (QSAR), which summarizes the Physico-chemical properties of chemicals or novel drugs.
• Molecular mechanics, in which force field is used for the optimization and minimization of energy of a molecule.
• Semi-empirical methods, use simplified versions of empirical corrections to improve the performance of any drug.
• Density functional methods, which verifies the electronic structure of an atom or a molecule.
• Molecular dynamics, explore the conformational space of large molecules like proteins.
• Monte Carlo analyzes the physical movement of atoms and molecules.

Computational chemistry software packages viz., molecular graphics, Quantum Chemistry, Protein dynamics, molecular design software, etc., are made available free and licensed to enhance the developments in the field of research. Besides, some of the publicly available databases representing a molecule are PubChem (the world’s largest free Chemistry database), ChemSpider (a free online chemical database that offers access to every detail of chemical specie required for discovering and designing drug molecules), chEMBL(a manually curated database of bioactive molecules)., etc which contain plenty of information about physical and chemical properties along with a structural representation of more than a hundred million compounds. To have a better insight, we can have an example of how to represent the molecular structure in the form of text, this can be done with the help of SMILES (Simplified Molecular Input Line Entry System). SMILES represents the structure of chemical species in the form of line- notation i.e., as ASCII strings. This system has significance as many computers software are more familiar with the ASCII format instead of 3D notation. For example, Cephalostatin-1 can be represented in SMILES format as-

Technique	Virtual image	Application	Example
Virtual Screening		Machine learning algorithms that use training and test datasets composed of known active and known inactive compounds.	Acceptor and donor Pharmacophores
QSAR		Prediction of chemical toxicity, designing of drugs, investigation of mechanism.	Monoaminoxidase inhibitors, Quinolines, Pyridines, etc.
Molecular mechanics		Calculation of geometries, energies, and structural-based designing of the drug.	Most of the organic chemical species.
Semi-empirical methods		Treats large molecules, fast method and cost-effective.	Unsaturated chemical compounds and radicals.
Density Functional Theory/ methods		Determines the probability of finding the electrons. Also, verifies the mechanism pathways.	Most of the ionic and organic compounds.
Molecular         Dynamics		Drug designing and structural determination, Protein folding, and used in molecular recognition.	Biomedicines, Pharmaceutical sciences.
Monte Carlo		Used widely in statistical physics, designing, and comparing experimental data with theory.	Oil reserve estimation, Disease infection estimation, etc.

About the author

Shweta Potdar is a faculty of Chemistry at Acropolis Institute of Management Studies and Research (AIMSR) in the Department of BIOSCIENCES. She is pursuing her PhD from the School of Chemical Sciences, DAVV University, Indore. She is MPSET qualified and has received two Gold Medals in MSc Chemistry. She has a consolidated research experience of 4 years. Her research area comprises Synthetic Chemistry, Medicinal Chemistry, Computational Chemistry, Heterogeneous catalysis, and Nanotechnology. She has publications in various reputed international and national journals. Also, she has participated in many international and national conferences, seminars, and workshops and presented her research work.  

Note: The views expressed in this article are solely author’s own and do not reflect/represent those of Shiksha