- MolScore - Antivirals
- MolScore-Anitibiotics
- Swiss Target Prediction
- SEA
- ChemProt

Target Prediction Softwares (CADD)

A gene, nucleic acid, or protein that may potentially combat a specific disease.

Calvin College

CADD can be used in the following areas of drug design:

- Molecular Modeling 
- Binding Free Energy Estimation Software 
- Binding Site Prediction Software
- Homology Modeling
- QSAR Software
- ADME Toxicity Software
- Ligand Design Software 
- Draw Tools
- Databases
- Docking Software
- Screening Software
- Target Prediction Software

CADD Concepts

The process of determining a drug target. The methods behind this process can draw from disciplines like biology, biochemistry, genetics, or biophysics.

1: Target Identification

The process of certifying a target of a small molecule. In other words, it is looking into the functional role of a target and seeing if a drug works in a clinical setting. 

2: Target Validation

Deore, A., Dhumane, J., Wagh, R., & Sonawane, R. (2019). The Stages of Drug Discovery and Development Process. Asian Journal of Pharmaceutical Research and Development, 7(6), 62-67. https://doi.org/https://doi.org/10.22270/ajprd.v7i6.616

The Stages of Drug Discovery and Development Process

Target


Molecular modeling refers to all the theoretical and computational methods used to model the behavior of molecules. Calculation that are relatively simple can be performed by hand, but inevitably computers are required in the molecular modeling of a reasonably sized system.

  Molecular modeling is used to reduce time and cost in the early stages of drug discovery.


Molecular modeling softwares (CADD)


Softwares that are used to calculate binding affinities of compounds to their primary target. This would allow concentrating efforts in more promising compounds thereby speeding up the drug development process.


Binding Free Energy Estimation Softwares (CADD)


Softwares that use computational methods for the prediction of binding sites. Binding sites are pockets of protein that can be used to bind drugs and this is an important step in the drug design process which can save a lot of resources.


Binding Site Prediction Softwares (CADD)


Homology modeling softwares use computational methods for protein structure prediction from its amino acid sequences.


Homology Modeling  (CADD)


These softwares are used to predict mathematical models which is used to provide insight into the chemical and biological properties of novel compounds.


QSAR softwares (CADD)

Softwares that predict the absorption, distribution, metabolism, excretion, and toxicity (ADMET) of drugs. 


ADME Toxicity Softwares (CADD)


Softwares that aid with the process of ligand-based drug design  which  relies on the knowledge of molecules that bind to the biological target.


Ligand Design Software (CADD)

Draw tools allow researchers to sketch chemical compounds, structures, and reactions.

Draw Tools (CADD)

Chemical databases can speed up the computational methods to build a  hypothesis for the discovery and design of a new drug thereby reducing time and cost. There are large amounts of chemical information available as public chemical databases that researchers can make use of.


Databases (CADD)

Docking is used to predict the preferred orientation of a molecule when it binds to another to form a stable complex. Docking softwares aid drug design by predicting intermolecular frameworks between proteins and proteins or proteins and small molecules.


Docking Softwares (CADD)


These softwares make use of virtual screening tools to predict structures that are most likely to bind to a drug target.


Screening Software (CADD)


- Data mining using bioinformatics 
- Genetic association 
- Expression profile
- Pathway and phenotypic analysis 
- Functional screening

Target Identification Approaches

Steps:
- Checking if a drug target can be reproduced from repeating an experiment
- Introducing a variation to the target environment

Techniques in Testing Reproducibility:
- Affinity chromatography
- Expression-cloning
- Protein microarray
- Reverse transfected cell microarray
- Biochemical suppression
- siRNA
- DNA microarray
- System biology
- Studying existing drugs

Techniques in Target Variation:
- Genetic manipulation of target genes (in vitro) by knocking the gene down (shRNA, siRNA, miRNA), the gene out (CRISPR), or the gene in (viral transfection of mutant genes) 
- Antibodies to block other interactions with the target with high affinity
- Chemical genomics (approaches combatting genome encoding protein)

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