Page 103 - GPD-3-2

Gene & Protein in Disease Inhibition of SOD1 in diseases

1. Introduction (www.ligq.qb.fcen.uba.ar), utilizing the full pipeline
setting. LIGQ constructs a compound set with documented
The copper-dependent enzyme superoxide dismutase binding evidence to the input protein or similar ones,
1 (SOD1) belongs to the SOD enzyme family, which is leveraging prior biological assays.
1
distributed across various cell organelles. SOD1 facilitates
the conversion of superoxide anions into hydrogen 2.3. Clustering analysis
peroxide and oxygen, thus maintaining low levels of
superoxide. This function is crucial due to the toxicity and The obtained sets of ligands in SMILES format underwent
1,2
poor membrane permeability of superoxide. SOD1, a scrutiny to eliminate any non-drug-like molecules.
copper/zinc-containing enzyme, is found in the cytosol, Subsequently, clustering analysis with multidimensional
nucleus, and intermembrane space of mitochondria. In scaling was conducted on the ChemMine server (http://
15
contrast, SOD2, a manganese-containing enzyme, resides chemmine.ucr.edu/) utilizing the ligands’ SMILES
in the mitochondrial matrix, and extracellular SOD representations.
(ecSOD or SOD3), a secreted copper-containing protein, 2.4. In silico absorption, distribution, metabolism,
is located in the extracellular matrix. 1,2 and excretion (ADME) prediction
Mutations in SOD1 are found in approximately 20% of The compounds underwent in silico ADME screening using
amyotrophic lateral sclerosis (ALS)-affected families and can the SwissADME server (www.swissadme.ch), employing
16
3,4
be inherited in autosomal dominant or recessive patterns. default parameters and utilizing the SMILES format.
Over 160 mutations in SOD1 have been linked to ALS, Duplicated ligands and those with low gastrointestinal
primarily comprising missense mutations along with a absorption (GIA) were subsequently excluded from
minority of small deletions and truncations. Notably, mis- further analyses.
5
folding and aggregation of mutant SOD1, rather than loss of
enzymatic function, are central to ALS pathology. Mutant 2.5. Molecular docking
6
SOD1 interacts with the dynein-dynactin complex in motor
neurons, leading to impaired axonal transport and correlating Molecular docking studies followed the protocol outlined
17
with disease progression in SOD1 transgenic mice. 7,8 by Fatoki et al. Initially, the ligands’ SMILES underwent
3D structure optimization using ACDLab/Chemsketch
In addition, SOD1 plays a crucial role in growth software and were saved in.mol format. Subsequently,
factor signaling in endothelial and tumor cells. SOD1- PyMol software facilitated the conversion of ligand files
deficient mice have been demonstrated to exhibit increased from. mol to. pdb format. The 3D structure of human
susceptibility to liver tumors due to elevated DNA mutation SOD1 was retrieved in AlphFold pdb format from the
9,10
rates. Knockdown of SOD1 induces senescence in Uni Prot data base. Before docking, both the ligands and
fibroblasts and decreases fertility in female mice. 11,12 target protein structures in pdb format were converted to
Conversely, overexpression of SOD1 in lung cancer cells pdbqt format using AutoDock Tools v1.5.6. Following
18
promotes growth by enhancing survival mechanisms, this, ligand-protein molecular docking was performed
suggesting modulation of cellular redox status, including utilizing AutoDock Vina v1.2.3. 19,20 Post-docking, binding
SOD1 inhibition, as a potential therapeutic strategy for affinity was determined, and close interactions between
13
cancer treatment. In light of these considerations, this study the ligands and targets were analyzed and visualized using
aimed to identify potential SOD1 modulators using in silico ezLigPlot on the ezCADD web server available at http://
rational virtual enrichment screening, pharmacokinetics, dxulab.org/software. 21
docking, and molecular dynamic simulations (MDSs).
2.6. Molecular dynamics simulation
2. Materials and methods
Molecular dynamics simulations were conducted for
2.1. Protein-protein interaction (PPI) analysis 100 ns using Desmond, a package of Schrödinger LLC. 22-24

The 3D structure of the human SOD1 protein (UniProt The initial configurations of the protein and ligand
ID: P00441, gene ID: SOD1), retrieved from the UniProt complexes for molecular dynamics simulations were
database (www.uniprot.org), served as the basis for this obtained from docking studies. Preprocessing of the
study. Its UniProt ID was subjected to PPI analysis using protein-ligand complexes was performed using Maestro’s
the STRING webserver (https://string-db.org/). 14 protein preparation wizard, which included optimization
and minimization of the complexes. All systems were
2.2. Rational virtual screening prepared using the System Builder tool with the solvent
The UniProt ID of the protein was employed for rational model employing an orthorhombic box with TIP3P
enrichment virtual screening using the LIGQ webserver water molecules. The Optimized Potential for Liquid

Volume 3 Issue 2 (2024) 2 doi: 10.36922/gpd.3042