Chemical Informatics Cheminformatics

Bioinformatics Infrastructure Facility North-East Institute of Science & Technology

Salam Pradeep

What is Chemical Informatics

Chemoinformatics or chemical informatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. It is the mixing of those information resources to transform data into information and information into knowledge for the intended purpose of making better decisions faster in the area of drug lead identification and optimization. In silico techniques are used in pharmaceutical companies in the process of drug discovery. These methods can also be used in chemical & allied industries in various other forms.

What is Computational Chemistry

branch of chemistry that uses computers to assist in solving chemical problems.  Uses the results of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules & solids.  Its results normally complement the information obtained by chemical experiments & in some cases predict unobserved chemical phenomena.  Widely used in the design of new drugs and materials.

Chemical & Ligand Databases
 Beilstein

Database (Commercial)  NCBI – PubChem  ChemBank  DrugBank  ChemSpider  LOLI database  RX List  HIC Up – Hetero Compound Info Center

Chemical Similarity Search
 ChemBank

(Web based)  ACD (Advanced Chemistry Development) Free Software  Molsoft (Web based)

Chem Bank

It is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program & funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG).

ACD Chemsketch Structure Search

Molsoft Chemical Search
Molsoft is a La Jolla, California based company that is a primary source of new breakthrough technologies in modeling, docking, computational chemistry and biology. Online Tools: 1. PDB Viewer 2. 2D to 3D Converter 3. Chemical Search Drug Likeness 4. ODA – Optimal Docking Areas

Drug Bank

Chemical File Formats
File Ext alc cdx cer c3d cif mol smiles, smi sdf Format Name Alchemy Format ChemDraw, Cambridge Soft Accelrys MSI Cerius II Chem3D, Cambridge Soft Crystallographic Information File, CCDC MDL Molfile Simplified molecular input line entry specification Structure-Data File

Chem Office

molecule editor developed by the cheminformatics company CambridgeSoft.  ChemOffice comprises ChemDraw, Chem3D and ChemFinder.  Available for Apple Macintosh and Microsoft Windows.  Designed for Chemist and Biologists

Chem Draw
 Chemical

structure to name conversion  Chemical name to structure conversion  NMR spectrum simulation  Mass spectrum simulation  Structure cleanup  Extensive collection of templates  Anti-aliased graphics

Powerful Features
 Convert

Name to Structure

Calculate Properties

1H NMR Prediction

Chem Finder
 ChemFinder®

is a database management system for working with chemical information.  It provides a place to store chemical structures, physical properties, notes, tables of data, and charts based on that data.  With ChemFinder, we can search through data efficiently and quickly, and we can organize the data instantly.

Compound Library

PASS (Demo 51 Activities)

Professional (Prediction of Activity Spectra for Substances) predicts the biological activity spectra for substances on the basis of their structural formulae, includes SAR Base (Structure-Activity Relationships data and knowledge Base) and provides its creating, updating and training.  Predicts 51 Biological Activities

Pharmacological Effects

  

Antihypertensive: Substance used for hypertonia treatment. Substance reduces the increased arterial blood pressure. Vasodilator: Substance that causes relaxation of blood vessels. Diuretic: Substance that promotes the excretion of urine by direct action on kidney function. Uric acid excretion stimulant: Substance that increases the urinary excretion of uric acid, thereby reducing the concentration of uric acid in the blood. Angiotensin AT2 receptor antagonist: Substance that binds to the angiotensin AT2 receptor and prevents its stimulation. Saluretic: Substance that promotes excretion of sodium and chloride ions in the urine.

Molecular Mechanisms
Calcium channel antagonist Renin inhibitor Neuropeptide Y antagonist Dopamine D1 agonist Phosphodiesterase I inhibitor Vasopressin 2 antagonist Dopamine D2 agonist Vasopressin 1 antagonist

Endothelin receptor antagonist

Nitric oxide agonist

Adenosine receptor agonist

Metalloproteinase inhibitor

Endothelin A receptor antagonis

Potassium channel activator

Nitric oxide donor

Adrenaline antagonist

Beta adrenoreceptor antagonist

Calcium antagonist

Carbonic anhydrase inhibitor

Angiotensin antagonist

Beta 1 adrenoreceptor antagonist

Kinesin antagonist

Guanylate cyclase stimulant

Dopamine agonist

Angiotensin II receptor antagonist Adenosine A2 receptor agonist

5 Hydroxytryptamine 2 antagonist Endothelin B receptor antagonist

Neutral endopeptidase inhibitor Adenosine A1 receptor antagonist 5 Hydroxytryptamine 1A agonist

Antidiuretic hormone antagonist Phosphodiesterase IV inhibitor Alpha 2 adrenoreceptor antagonist

Angiotensin AT1 receptor antagonist

Side Effects and Toxicity
 Carcinogenic:

Substance that produces cancer.  Embryotoxic: Substance damaging to the embryo, which may result in death or in abnormal development.  Teratogen: Substance that causes the production of physical defects in the developing embryo.


Abraham Solvent

H-Bonding acidity parameter H-Bonding basicity parameter Partition Coefficient between gaseous phase and hexadecane Polarity / polarizability parameter Excessive molar refraction Mcgowan volume

Chem 3D
 Chem3D

enables to create color models of chemical and biochemical compounds.  Once we sketch a model, we can calculate a variety of molecular properties - electrostatic potentials, bond energies, and spectrum prediction.  It combines powerful building, analysis, and computational tools with intuitive menus and a powerful scripting interface.

Force Field Calculations
 MM2:

Most commonly used for calculating properties of organic molecular models. - Correlates the potential energy surface to the conformations of our model  MMFF94: Used to perform energy minimization calculations on proteins & biological structure.

MM2 & MMFF94
 Energy

Minimization: The atoms location for a build model is not accurate compared to the actual one. Hence EM  Molecular Dynamics: Uses Newtonian mechanics to simulate motion of atoms, adding or subtracting kinetic energy as the model’s temperature increases or decreases.

The General Atomic and Molecular Electronic Structure System (GAMESS)  A general ab initio quantum chemistry package maintained by the Gordon research group at Iowa State University.  Minimize Energy  Optimize to Transition State  Compute Properties  Run Frequency  Predict IR/Raman Spectra  Predict NMR Spectra

Lipinski Rule of Five

  

Lipinski's Rule of Five states that, in general, an orally active drug has no more than one violation of the following criteria: Not more than 5 hydrogen bond donors (nitrogen or oxygen atoms with one or more hydrogen atoms) Not more than 10 hydrogen bond acceptors (nitrogen or oxygen atoms) A molecular weight under 500 g/mol A partition coefficient log P less than 5 Note that all numbers are multiples of five, which is the origin of the rule's name.

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