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Eureka with G P S Raghava, Interview on Rajya Sabha TV (YouTube Link)

Lead Optimization

Lead identification/optimization is the one of the most important steps in drug development. The chemical structure of the lead compound is used as a starting point for chemical modifications in order to improve potency, selectivity, or pharmacokinetic parameters. Once a molecule is identified, the next step is to check its ADMET (Adsorption, Distribution, Metabolism, Excretion and Toxicity) properties. If the molecule has no toxicity and no mutagenicity either, it has potential for use as lead molecule. Further optimization gives better quality of lead molecules. These may subsequently be developed as drug(s).

Links to databases of drug molecules and small chemical molecules are given below:

Web Servers/Databases/Mirror Sites Link:

Drug Molecules DatabaseDescription
CMC (Comprehensive Medicinal Chemistry) MDLdatabase provides 3D models and important biochemical properties including drug class, logP, and pKa values for over 8,400 pharmaceutical compounds
Dictionary of Drugstructured database holding information on chemical substances
DrugBank combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
Drug@FDAInformation about FDA approved drug products
MDDR (MDL Drug Data Report)database covering the patent literature, journals, meetings and congresses
FDA Druglist of drugs approved by the FDA
MedChemdatabase contains more than 55,000 compounds with 75,000 names and 32,000 CAS numbers. In addition, there are 61,000 measured logP values, 13,900 pKa values, 26,000 activities, and Rubicon 3D coordinates for almost 49,000 structures.
WDI (World Drug Index)drug database of almost 80,000 drugs and pharmacologically active compounds, including all marketed drugs
NCI Drug Dictionarycontains technical definitions and synonyms for drugs/agents used to treat patients with cancer or conditions related to cancer
PharmaGKBIntegrated resource about how variation in human genetics leads to variation in response to drugs.
Rx ListThe internet drug list
SDD (Super Drug Database)contains 2.396 compounds with 108.198 conformers

Chemical Compounds DatabaseDescription
ACD (Available Chemicals Directory) chemical sourcing database
ASINEXlead generation and lead optimization
Bionet DatabaseScreening compounds database
CAP (Chemicals Available for Purchase) database provides the contents of many commercial suppliers' catalogs from a single database that is easy to use, consistently formatted, and frequently updated.
ChEBireely available dictionary of molecular entities focused on 'small' chemical compounds.
ChemBankfreely available data derived from small molecules and small-molecule screens, and resources for studying the data so that biological and medical insights can be gained.
ChemDBChemical dataset
ChemStarprovides Synthetic Organic Compounds for HTS, Building Blocks for Combinatorial Chemistry, Custom Synthesis, Pre-plated Library, Virtual Database
CSD (Cambridge Structural Database)world repository of small molecule crystal structures
HIC-Up (Hetero-compound Information Centre - Uppsala)freely accessible resource for structural biologists who are dealing dealing with hetero-compounds ("small molecules")
IBS (Inter Biosceen) DatabaseChemical library for screening
Maybridge Databasedesigns and produces innovative chemical Building Blocks and Screening Compounds, and provides Medicinal Chemistry for the drug discovery industry
MDPI (Molecular Diversity Preservation International)Compounds Database
MSDchemConsistent and enriched library of ligands, small molecules and monomers that are referred as residues and hetgroups in any PDB entry
NCI Database
PDBsumprovides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.
PubChemprovides information on the biological activities of small molecules
Relibaseligand overlays and binding mode comparisons
SPRESIdatabase containing over 6.1 million molecules, 3.85 million reactions, 636,000 references, 164,000 patents
Zinccontains over 8 million purchasable compounds in ready- to-dock, 3D formats

Virtual ScreeningDescription
ChemDBChemical dataset
ChemID Plusallows users to search compound identifiers such as chemical name or CAS Registry Number on the NLM ChemIDplus database of over 370,000 chemicals.
ChemBankallows users to search small compounds, assays and proteins
ZINCcontains over 8 million purchasable compounds in ready- to-dock, 3D formats
IB Screen databaseChemical library for screening
Maybridge Databasedesigns and produces innovative chemical Building Blocks and Screening Compounds, and provides Medicinal Chemistry for the drug discovery industry
MDL SCDConsolidated Supplier Catalogs for High-Throughput Screening
BioscreeningOnline searchable database of available compounds
TimTecsynthetic organic compound library
RPBS ADME ToxADME-Tox (poor absorption, distribution, metabolism, elimination (ADME) or toxicity) filtering for small compounds
PDB Chemical SearchSubstructure search against 8458 chemical compounds from PDB

Other DatabaseDescription
ADME DBdatabase containing information on Human Cytochrome P450 metabolism, kinetics, transporter and structure
DTP AIDS Antiviral ScreenAIDS antiviral screeninf library
GLIDA:GPCR Ligand DatabaseA complex information system covering biological information of GPCRs as well as chemical information of their known ligands.
NCI Anti Cancer AgentDTP Human Tumor Cell Line Screen
Pharmeksdiverse, predominantly heterocyclic, organic library
RPSB Collectiondatabases of small chemical compounds to identify potential hits that could block the active site or exosite of a target protein
Anti HIV/OI Chemical Compounds DatabaseAnti-HIV/OI chemical compound database
FDA Databasesdifferent FDA drug and drug related information databases
Pesticide DatabasePesticide database

Ligand Binding AffinitiesDescription
AffinDBAffinity database for protein-ligand
BindingDBweb-accessible database of experimentally determined protein–ligand binding affinities
DLRPdatabase of protein ligand and protein receptor pairs that are known to interact with each other
DrugBank detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information
Ligand dissociation constants for GPCRsprovide information on ligand dissociation constants for GPCRs
KiBankdatabase contains binding affinity, structures of chemicals and target proteins, and many useful links and information.
PDBbind collection of experimentally measured binding affinity data
PDSP Drug KiDBprovides screening of novel psychoactive compounds for pharmacological and functional activity at cloned human or rodent CNS receptors, channels, and transporters
Relibaseeasy searching of protein-ligand complexes
SCORPIO(structure-calorimetry)FREE online
WOMBATWOrld of Molecular BioAcTivity

Standalone Softwares

Software for ScreeningDescription
Calalyst (Discovery studio)collection of pharmacophore modeling tools
SybylComputational Informatics Software for Molecular Modelers
Vlife Sciencescollection of various applications related to drug and molecular discovery
Schrordingerchemical simulation software

Software for Molecular Descriptor CalculationDescription
ADAPTa computational model platform developed for pharmacokinetic and pharmacodynamic applications
Dragonan application for the calculation of molecular descriptors
MolconZstandard program for generation of Molecular Connectivity, Shape, and Information Indices for Quantitative Structure Activity Relationship (QSAR) Analyses
MOEintegrates tools for computer-assisted drug discovery
OpenMolGriddrug-design using Grid technology
VLife MDSworkbench for computer aided drug design (CADD) and molecule discovery
Codessaadvanced, fully featured Quantitative Structure/Activity Relationship (QSAR) program that ties information from AMPAC™ and other Quantum Mechanics programs with experimental data
JoeLibCheminformatics algorithm library, which was designed for prototyping, data mining, graph mining, and of course algorithm development
CDKOpen source Java computational chemistry package which supports chemical structure drawing and the graphical layout of 2D chemical structures.
PreADMETDescriptor Calculation, Druglikeness Prediction: Rule-based Druglike Screening, ADME Prediction: Examination of various ADME properties of drug candidates, Chemical Library Design: Powerful Workspace, Molecular Set and Molecular Table
ADMETWorks ModelBuildera tool for building mathematical models that can later be used for predicting various chemical and biological properties of compounds
CAChecomputer-aided chemistry modelling package designed for experimental chemists conducting research in life science, materials and chemistry
VolSurfa computational procedure aimed to produce and to explore the physicochemical property space of a molecule (or library of molecules) starting from 3D maps of interaction energies between the molecule and chemical probes
TSARa fully integrated quantitative structure-activity relationship (QSAR) package for library design and lead optimization
Almondprogram specifically developed for generating and handling alignment independent descriptors called GRIND (GRid INdependent Descriptors).
JKlustora Java software for diversity calculations and clustering

Online Tool for Molecular Descriptor Calculation

PreADMETa web-based application for predicting ADME data and building drug-like library using in silico method
MolinspiratonCalculation of Molecular Properties and Drug-likeness
EDragonapplication for the calculation of molecular descriptors
MODEL - Molecular Descriptor LabComputing structural and physichemical properties of molecules from their 3D structures.

Software for file Conversion

Open Babelan open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
EBabelInteractive Molecular Structure Formats Interconversion Program
VEGA ZZ 2.2.0convert several molecular file formats
GalaxyInput molecule SMILES to generate the 3D Structure

Software for Quantum Mechanics

AMPAC 4.0 with GUIset of tools to study molecular structure and chemical reactions
GAMESSa general ab initio quantum chemistry package
Gaussianpredicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types
HuckelCalculates electronic properties of molecules
hmo10 Huckel molecular orbital calculator
JaguarRapid ab initio electronic structure package
MOPACa semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation

Web Interface on Libraries

There are number of libraries (e.g. RCDK 0.3.0, RCDK 2.8.1, rpubchem) which provides tools for the serching of molecules from databases. Though these libraries are powerful but one need expertise in computer. Development of web interfaces over these libraries are going on in order to provide service to users who have little or no knowledge of computer.


Cheminformatics This website contains links to cheminformatics programs and QSAR datasets.