STRUCTURE MODELLING

Function of sec y protein

The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 15 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2
and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed
of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which
forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may
move independently. SecY is required to insert newly synthesized SecY into the inner membrane.
Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting
in cell death; while this may be true, overexpression also results in FtsH-mediated degradation of SecY.

Structural modelling using SWISS MODEL

Steps involved are1. Insert FASTA format sequence of the protein in SWISS MODEL, the sequence can be
obtained from NCBI.
2. Paste the sequence and press build model option.
3. SWISS MODEL will provide three models. The first model is selected and the structure is
analysed.

DRUG IDENTIFICATION AND STRUCTURE INFORMATION

Drug bank is used for obtaining the appropriate drug that acts on the tuberculosis.

Ethionamide is a second-line antitubercular agent that inhibits mycolic acid synthesis, for use in
the treatment of pulmonary and extrapulmonary tuberculosis when other antitubercular drugs have
failed.

Mechanism of action
Ethinamate is bacteriostatic against M. tuberculosis. In a study examining ethionamide resistance,
ethionamide administered orally initially decreased the number of culturable Mycobacterium
tuberculosis organisms from the lungs of H37Rv infected mice. Drug resistance developed with
continued ethionamide monotherapy, but did not occur when mice received ethionamide in
combination with streptomycin or isoniazid. Ethionamide may be bacteriostatic or bactericidal in
action, depending on the concentration of the drug attained at the site of infection and the
susceptibility of the infecting organism. Ethionamide, like prothionamide and pyrazinamide, is a
nicotinic acid derivative related to isoniazid. It is thought that ethionamide undergoes intracellular
modification and acts in a similar fashion to isoniazid. Isoniazid inhibits the synthesis of mycoloic
acids, an essential component of the bacterial cell wall. Specifically isoniazid inhibits InhA, the
enoyl reductase from Mycobacterium tuberculosis, by forming a covalent adduct with the NAD
cofactor. It is the INH-NAD adduct that acts as a slow, tight-binding competitive inhibitor of InhA.

DOCKING
Proteinligand docking is a molecular modelling technique. The goal of proteinligand docking is
to predict the position and orientation of a ligand (a small molecule) when it is bound to a protein
receptor or enzyme.

Various docking softwares are used for this purpose1.

2.
3.
4.

AutoDock
DOCK
LigandFit
SwissDock

And many more. We used SwissDock for protein ligand docking.

SwissDock is a docking web server. The structure of the target protein, as well as that of the ligand,
can be automatically prepared for docking. In addition, the cumbersome syntax of the docking
engine is hidden behind a clean web interface providing reasonable alternative sets of parameters
as well as sample input files. All calculations are performed on the server side, so that docking runs
do not require any computational power from the user. The interpretation of docking results and
their integration into existing research pipelines is greatly facilitated by the seamless visualization
of docking predictions in the UCSF Chimera molecular viewer, which can be launched directly
from the web browser.
INPUT
Only three steps are required to start a docking assay through the web interface of SwissDock:
users must define a protein structure, one or several putative ligands and docking parameters.

Target selection

A target protein structure can be determined either by specifying its identifier from the Protein
Data Bank or by uploading structure files.

The first option allows users who are not familiar with 3D structure files to start a docking assay
with only a PDB code.
The second option allows the uploading of user-defined or edited target structures. Since the
calculations are performed in the CHARMM force field, SwissDock supports the uploading of
CHARMM formatted files in addition to the commonly used PDB format: protein structures can be
uploaded as a set of protein structure file (PSF), coordinate file (CRD) and extra topology (RTF)
and parameter files (PAR).
Ligand selection

A ligand can be selected either by specifying its identifier from the ZINC database (23) or by
uploading structure files. The former possibility allows users who are not familiar with 3D
structure files to start a docking assay with only a ZINC accession code (AC). The latter allows
uploading several ligands at once or uploading ligands that are not present in the ZINC database.
Docking parameters
Docking type

Three docking parameter presets can be selected: very fast, fast and accurate.
Definition of the region of interest

When using default parameters, the whole target protein structure is considered during the docking.
However, if the target protein is particularly large and/or if the putative binding pocket is already
known, the docking can be restricted to an rectangular region of space to perform a local docking
assay.
Outputs

After a docking assay has been submitted, it can be tracked thanks to a dedicated URL provided on
the submission confirmation page. If an (optional) email address has been specified in the
submission form, this URL is also sent to the user by email, as well as a link to the docking result
web page once the docking is completed.