NoTox: Toxicity Analysis of Molecules and their derivatives Primary Advisor : Professor David J. Wild Bioinformatics Advisor: Professor Sun Kim.

NoTox: Toxicity Analysis of NoTox: Toxicity Analysis of Molecules and their Molecules and their derivativesderivatives

Primary Advisor : Professor David J. Wild Bioinformatics Advisor: Professor Sun Kim.

What is Computational What is Computational ToxicologyToxicologyComputational toxicology is an emerging

field that constitutes methodical approaches to analyze the harmful effects on the environment and public health due to exposure to chemicals.

Computational toxicology may be defined as the application of the tools developed using computational biology concepts to analyze the risk that some chemicals pose to human health and the environment.

Types of toxicologyTypes of toxicologyThe different types of toxicology includeToxicogenomicsAquatic ToxicologyChemical toxicologyEcotoxicologyEnvironment toxicologyMedical ToxicologyForensic ToxicologyRef: Wikipedia

How is computational How is computational toxicology studies important toxicology studies important to biologyto biologyComputational toxicity is an

increasingly important field with implications throughout biomedical science and drug discovery. To name a few applications

Providing molecular profiling approaches to toxicology

Drug toxicityGene- Drug interaction studiesToxicological analysis of Biological

molecules and their derivatives

Shortcomings Shortcomings The shortcomings of most

computational toxicology methods areMost toxicity methods concentrate on

determining whether a particular compound has toxic properties or not. The methods do not necessarily help in understanding whether modifying a particular molecule synthetically to reduce toxic effects is possible.

It also does not concentrate on identifying and analysing the reason for toxicity of most molecules.

Problems analyzedProblems analyzedIf we have a toxic molecule, can we

find a synthetic alternative that might be non toxic

If we have a non-toxic molecule, might it be metabolized or changed in the body to something toxic?

We use some cheminformatics representations called SMILES and SMIRKS to deal with these problems

Terminologies - Terminologies - SMILES/SMIRKSSMILES/SMIRKSSMILES is the acronym for Simplified Molecular

Input Line Entry Specification. Each molecule has a unique canonicalized

SMILES representation (Eg c1ccccc1 represents benzene).

SMIRKS is a reaction transform language. In general two different kinds of SMIRKS are in

use to show transformations. Functional group transformations and molecular framework modifications. An example for SMIRKS would be

[O:1]=[C:2][Cl:3].[N:4][H:5]>>[O:1]=[C:2][N:4]

this is an example of a simple displacement reaction representation

Drug Guru - Literature Drug Guru - Literature ReviewReviewDrug Guru is a web based computer

software program that applies medicinal chemistry transformation reactions to an input structure.

The transformation reactions are medicinal chemistry design rules of thumb taken from other drug discovery programs.

The output of this program is a list of analogs that can be used for further synthesis.

Ref: [1]

Screen shot of drug guruScreen shot of drug guru

Drug Guru to NoToxDrug Guru to NoTox

Drug Guru uses smirks to develop alternative compounds based on medicinal chemistry reactions.

NoTox combines the concept of Drug Guru with a different field – Toxicity.

NoToxNoToxTool to predict alternatives for a

given molecule based on reaction transformations

Tool to test the toxicity of any given molecule

Helps in comparing the toxicity of the original and the derived molecule

NoTox - Input NoTox - Input RequirementsRequirementsThe input query (Original

molecule) should be in the form of SMILES.

The reaction transformations should be in the form of SMIRKS

The SMIRKS used are a more specific form of the reaction.

Flowchart of NOTOXFlowchart of NOTOX

SmirksgenSmirksgenThe program generates

derivatives for a given molecule based on the specified reaction transformation rules.

Openeye software for library generation

The smirksgen program is developed in Python and it takes in input from a GUI developed using HTML

Toxicity prediction using Toxicity prediction using ToxtreeToxtreeToxtree is an open source application

that uses the decision tree approach to identify the toxicity of a molecule represented as SMILES.

It provides 5 plugins. In NoTox, we make use of the Cramer's rule decision tree approach to determine toxicity.

The input molecules are classified in the increasing levels of toxicity as Class 1, Class II and Class III

NoTox - Features availableNoTox - Features available

Apart from Smirksgen and Toxtree,NoTox Provides access to

another tool WENDI that helps in the profiling of any particular molecule.

NoTox also has a feature that helps in the validation of the input SMILES

Screen shot of NoToxScreen shot of NoTox

ATP Example ATP Example

OBJECTIVEOBJECTIVEIdentifying a molecule with

desirable properties and activity towards the human body.

Observing the Toxicological effects due to the activity of the identified molecule .

WHY ATP?? WHY ATP?? ATP acts as a coenzyme in most

intracellular energy transfer reactions.

ATP acts as a substrate for kinases in signal transduction pathways.

It is a major component of the Krebs cycle.

Mechanism of action of ATP Mechanism of action of ATP and Its Usesand Its UsesThe main action of ATP is

phosphorylation.A double displacement reaction

takes place between the phosphate molecule in ATP and the hydroxyl hydrogen of the reacting molecule.

The reaction is depicted as follows. R-OH . ATP >> R-O-phosphate .

ADP

Testing effect of ATP on Testing effect of ATP on human bodyhuman body

Our objective is to study the toxicological effects of ATP on the human body.

We use our tool NoTox to study the toxicological effects due to the reaction of ATP with other molecules.

Input data Using SmilesInput data Using SmilesThe test molecules were

obtained by doing a substructure search in pubchem and the test set was a list of 100 molecules that contained a substructure that can react with ATP.

The smiles format was obtained for these molecules using the molinspiration software.

The reaction The reaction transformationstransformations500 reactions from Kegg

involving ATP were studied and the mechanism of each reaction was observed and generalized to 2 SMIRKS rules one each for aromatic and aliphatic compounds

The resultThe resultThe toxicity of the input molecule

was usually Class 1 or Class 2The toxicity of the derivative was

always found to be Class 3.It was observed that the reaction

of a molecule with ATP increases the toxicity of the derivative.

This suggests that ATP increases the toxicity in the body when it reacts with the biological molecules.

Evidence for the resultEvidence for the result Journal articles substantiate the observed result that

ATP increases the toxicity of the molecule it reacts with. Some of the examples of the journal articles are

Mallick.N, Rai .LC. Metal induced inhibition of photosynthesis, photosynthetic electron transport chain and ATP content of Anabaena doliolum and Chlorella vulgaris: interaction with exogenous ATP, Biomed Environ Sci. 1992 Sep;5(3):241-50

Lundy, Paul ; Frew, R. ; Vair, C. ; Nelson, P. ; Gong, W ,Mediation of Sulfur Mustard Cellular Toxicity by ATP: A Possible Mechanism of Action of Sulfur Mustard Toxicity, ADA412934

KOBAYASHI K. ; RATAIN M. J. ; Pharmacodynamics and long-term toxicity of etoposide, Cancer chemotherapy and pharmacology   ISSN 0344-5704   CODEN CCPHDZ 

SummarySummary

NoTox can be used to search for non-toxic alternatives to toxic compounds,and to find possible toxic metabolites

Initial experiments indicate the method is useful

Further work should be carried out to evaluate NoTox for both of theseapplications

Future WorkFuture Work

An evaluation study that looks at the following can be performed

Known toxic compounds and their derivatives

Use information from metabolic database to evaluate the toxic effects due to any particular metabolic pathway.

ReferencesReferences Kent D.Stewart, Melisa Shiroda, Craig A. James , Drug Guru: A computer

Software Program for drug design using medicinal chemistry rules, doi: 10.1016/j. bmc. 2006.06.024

Robert J.Kavlock et.al , Computational Toxicology- A state of the Science mini review , doi: 10.1093/toxsci/kfm297

Mallick.N, Rai .LC. Metal induced inhibition of photosynthesis, photosynthetic electron transport chain and ATP content of Anabaena doliolum and Chlorella vulgaris: interaction with exogenous ATP, Biomed Environ Sci. 1992 Sep;5(3):241-50

Lundy, Paul ; Frew, R. ; Vair, C. ; Nelson, P. ; Gong, W ,Mediation of Sulfur Mustard Cellular Toxicity by ATP: A Possible Mechanism of Action of Sulfur Mustard Toxicity, ADA412934

KOBAYASHI K. ; RATAIN M. J. ; Pharmacodynamics and long-term toxicity of etoposide, Cancer chemotherapy and pharmacology   ISSN 0344-5704   CODEN CCPHDZ 

www.daylight.com www.eyesopen.com http://ambit.acad.bg/toxTree/ Wikipedia

AcknowledgementsAcknowledgementsProfessor David WildProfessor Sun KimThe faculty of the Bioinformatics

and the Cheminformatics department.

Linda Hostetter and Rachel Lawmaster.

THANK UTHANK U