Applied Bioinformatics Assignment 5docx

1. Submitted to: Dr. Pramod Katara
Submitted by: Sarita Maurya
M.Sc (3rd semester), Centre of Bioinformatics, University of Allahabad.
CONTENT:-
1) Protein-Protein Interaction
2) Protein-ligand Interaction
3) Docking
4) Pharmacophore
5) Virtual Screening
Assignment-5
Topic-
Discuss BioinformaticsApproacheIn molecular interaction Analysis:Protein-Protein interaction,
Protein-ligand interaction(Docking,Pharmacophore,Virtual Screening.
Bioinformatics:-
Bioinformatics is the application of computational technology to handle
the rapidly growing repository of information related to molecular
biology. Bioinformatics combines different fields of study, including
computer sciences, molecular biology, biotechnology, statistics and
engineering. It is particularly useful for managing and analyzing large
sets of data, such as those generated by the fields of genomics and
proteomics.
Protein-Protein Interaction:-

2. •Protein–protein interactions occur when two or more proteins bind together.
•Proteins control and mediate many of the biological activities of cells by these
interactions.
•Information about PPIs -
the basis for new therapeutic approaches.
•The structure of a protein influences its function by determining the other molecules
with which it can interact and the consequences of those interactions.
•Multi subunit protein –hemoglobin, core RNA polymerase, small nuclear
ribonucleoproteins and the ribosome etc.
Transient protein interaction: strong and irreversible, it readily undergoes changes in
the oligomeric state.
•Interactions of protein kinases, protein phosphatases, glycosyl transferases, acyl
transferases, proteases, etc., with their substrate proteins.–Proteins for Cell growth, cell
cycle, metabolic pathways, and signal transduction
•These interactions are very important in our lives as any disorder in them can lead to
fatal diseases such as Alzheimer’s and Creutzfeld- Jacob Disease.
•Perhaps the most well known example of Protein-Protein Interaction is between Actin
and Myosin while regulating Muscular contraction in our body.
Types of Protein-Protein InteractionsOn the basis of their
CompositionHomo-Oligomers: These are macromolecule complexes having one type
-Oligomers: These are
macromolecule complexes having multiple types protein subunits. e.g. : PPI between
Cytochrome Oxidase and TRPC3 (Transient receptor potential cation channelsOn the
basis of duration.
•Stable Interactions: These comprise of interactions that last for a long duration. These
Interactions carry out Functional or Structural roles.e.g.: Haemoglobin structure.
•Transient Interactions : Interactions that last a short period of time.e.g.: Muscle
Contraction.
Effects of protein interaction
•They can alter the kinetic properties of proteins
•Protein interactions are one common mechanism to allow for substrate channeling.
•Can result in the formation of a new binding site.
•Can inactivate a protein
•Can change the specificity of a protein for its substrate
•Identify the different interactions, understand the extent to which they take place in the
cell, and determine the consequences of the interaction.

3. Another way of classification for methods for identification of PPIs-
•The first is ‘atomic observation’ in which the protein interaction detected using, for
example, X-ray crystallography. These experiments can yield specific information on
the atoms or residues involved in the interaction.•The second is a ‘direct interaction
observation’ where protein interaction between two partners can be detected as in a
two-hybrid experiment.•At a third levelof observation, multi-protein complexes can be
detected using methods such as immuno-precipitation or mass-specific analysis. This
type of experiment does not reveal the chemical detail of the interactions or even reveal
whichproteins are in direct contact but gives information as to whichproteins are found
in a complex at a given time.
YEAST TWO HYBRID SYSTEM-
•This is method that uses transcriptional activity as a measure of protein-protein
interaction.
•It relies on the modular nature of many site-specific transcriptional activators, which
consist of a DNA-binding domain and a transcriptional activation domain.
•DNA-binding domain serves to target the activator to the specific genes that will be
expressed.
•Activation domain contacts other proteins of the transcriptional machinery to enable
transcription to occur.
•yeast two-hybrid (Y2H) system has variations involving different reagents and has
been adapted to high-throughput screening.
•The strategy interrogates two proteins, called bait and prey, coupled to two halves of a
transcription factor and expressed in yeast.
•If the proteins make contact, they reconstitute a transcription factor that activates a
reporter gene.
Protein-ligand Interaction-
●A protein ligand is an atom, a molecule or an ion which can bind to a specific site (the
binding site) on a protein.
●AKA affinity reagents or protein binders.
●To date, antibodies are the most widely used protein ligands in life-science
investigations.
●Other molecules such as, nucleic acids, peptides are also being used.

4. ●Main methods to study protein–ligand interactions are principal hydrodynamic and
calorimetric techniques, and principal spectroscopic and structural methods such as
1. Fourier transform spectroscopy
2. Raman spectroscopy
3. Fluorescence spectroscopy
4. Circular dichroism
5. Nuclear magnetic resonance
6. Mass spectrometry
7. Atomic force microscope
8. Paramagnetic probes
9. Dual Polarisation Interferometry.
●Molecular recognition via protein–ligand interactions is of fundamental importance to
most processes occurring within living organisms.
●Transmission of signals via molecular complementarity is essential to all life
processes.
●The evolution ofprotein function includes the development of highly specific sites for
the binding of ligands with affinities tailored to meet the needs of biological function.
●Cooperativity in ligand binding plays an important role in the regulation of biological
function.
●Cooperativity in ligand binding is linked to conformational change in the protein.
●Well‐ defined mathematical expressions based on the stoichiometry of the binding
equilibrium provide a means for quantifying ligand‐ binding interactions.
●The equilibrium constants of ligand–macromolecule interactions provide a
thermodynamic measure of the strength of the interaction.
●The atomic resolution structures of ligand complexes provide a chemical basis for
understanding protein–ligand interactions and these structures are often used as the
basis for the design of small‐ molecule drugs for the treatment of disease.
●The equilibrium constants of ligand–macromolecule interactions provide a
thermodynamic measure of the strength of the interaction.
●The atomic resolution structures of ligand complexes provide a chemical basis for
understanding protein–ligand interactions and these structures are often used as the
basis for the design of small‐ molecule drugs for the treatment of disease.

5. Docking
What Is Docking....?
•Docking attempts to find the “best” matching between two molecules.
•Docking is a method which predicts the preferred orientation of one molecule to a
second when bound to form a stable complex with overall minimum energy.
Docking can be between:-
•Protein - Ligand
•Protein – Protein
•Protein – Nucleotide
A Typical Docking Workflow

6. Key Stages In Docking
Types of docking:-
1. Rigid Docking (Lock and Key)
• In rigid docking, the internal geometry of both the receptor and ligand are treated
as rigid.
2. Flexible Docking (Induced fit)
• An enumeration on the rotations of one of the molecules (usually smaller one) is
performed. Every rotation the energy is calculated; later the most optimum pose is
selected.
3. Manual docking

7. MANUAL DOCKING Dock or fit a molecule in the binding site Binding group
on the ligand and binding site are known, defined by the operator. Ideal
bonding distance for potential interaction is defined.
Software's
SANJEEVINI – IIT Delhi
(www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp)
• GOLD – University of Cambridge ,UK
(www.ccdc.cam.ac.uk/Solutions/GoldSuite/Pages/GOLD.aspx)
• AUTODOCK - Scripps Research Institute,USA
(autodock.scripps.edu/),other.
Applications:-
• Virtual screening (hit identification) docking with a scoring function
can be
used to quickly screen large databases of potential drugs in silico to
identify
molecules that are likely to bind to protein target of interest.
• Drug Discovery (lead optimization) docking can be used to predict in
where
and in which relative orientation a ligand binds to a protein (binding
mode or
pose). This information may in turn be used to design more potent and
selective
analogs.
• Bioremediation Protein ligand docking can also be used to predict
pollutants
that can be degraded by enzymes.
Docking based screening:-
1) Virtual based screening
2) Molecular based screening
Molecular based screening:-
• Docking- the process by which molecular modeling software fits a
molecule

8. into target binding sites.
• Used for finding binding modes of protein with ligands/inhibitors
• In molecular docking, attempt to predict the structure of the
intermolecular
complex formed between two or more molecules.
Molecular docking tries to predict the structure of the intermolecular
complex
formed between two or more constituent molecules.
Molecular docking has become an increasingly important tool for drug
discovery.
Steps involve in Molecular Docking

9. Pharmacophore
Defination:-
●A pharmacophore is a specific 3D arrangement of functional groups within a
molecular framework that are necessory to bind to a macromolecule and/or an enzyme
active site.
●The identification of pharmacophore is important step in understanding the
interactions between a receptor and a ligand.
●Many possible iterations between ligand and receptor.
●Depending on size of active, various steric-electrostatic and hydrophobic contacts.
●Some contacts or sites are more important than others.
●The specific interactions that are crucial for ligand recognition and binding by the
receptor are thermal pharmacophore.
●These interactions are directly involved in the structural integrity of receptor or in the
mechanism of its action.
●Pharmacophore model is derived from a set of known ligands for a target.
●Aslo using the set of features common to a series of active molecules.
●Features may include – acceptors, donors, ring centroids, hydrophobes etc.
●A 3D pharmacophore is used to define relationships between groups or features.
●Pharmacophore hypothisis are generated by the multiple conformations of the set of
molecules.
●When protein is unknown, it is more efficient.
●With the generated hypothysis, it is possible to search the database for new hit
compounds.
●Searching the possible low energy conformations of known inhibitors can identify
pharmacophores.
Different methods:-
●The conformation search can be quite large and can be approaches using folowing
methods
–Systematic search method
–Distance geometry method

10. –Clique detection algorithm.
Systematic search method:-
●Generates sterically allowed molecular conformations by systematically varying sets
of specified torsion angles.
Distance geometry method:-
●Randomly samples conformations and are particularly powerful for problems dealing
with molecular matching and flexibility.
●Used by rubicon.
●Clique detection algorithm:-
s common sets of inter feature distances within the group of active molecules.
●Tolerences on the distances matches aaccount for the use ofdiscret conformations and
uncertenties in pharmacophore.
●Used by DiscoTech.
Virtual Screening
• The process of drug discovery has been reorganize with the development of
genomics, proteomics, bioinformatics and efficient technologies like
combinatorial chemistry, high throughput screening, virtual screening, de novo
design, in vitro, in silico screening and structure-based drug design.
• Virtual screening has emerged as a reliable, cost-effective and time-saving
technique for the discovery of lead compounds.
• The virtual screening approach for docking small molecules into a known
protein structure is a powerful tool for drug design that has become an integral
part of the drug discovery process in recent years.
• Based on molecule modeling and computational analysis of chemical data
those compounds should be identified that are relevant for certain biological
receptor.
Any virtual screening method faces two critical issues:

11. The main steps are:
(1) Identify and determine the structure of the receptor.
(2) Suggest a set of potential ligands that bound the receptor based on
theoretical principles and experimental data.
(3) Determine the structure of the receptor-ligand that leads to successful
bound with a minimum energy levels.
(4) Repeat steps (2) and (3) in order to improve the receptor-ligand interaction.