Page 116 - ITPS-7-2

INNOSC Theranostics and
Pharmacological Sciences PI3K-α inhibitors for cancer immunotherapy

in identifying the interactions of ionizable residues in the evaluated to determine the optimal site for binding.
protein together with their structural determinants along The mathematical correlations depicted in Equations I
with significantly perturbed pKa values that contributed and II were used by Maestro to compute the druggability
to the stability of the protein. The last step of protein and site scores, respectively. These procedures culminated
refinement was energy minimization and the deletion of in detecting deep binding sites/pockets for potential
water molecules around the ligand. In this step, the root receptors, specific to a protein-ligand complex.
mean square deviation (RMSD) for heavy atom coverage Druggability (D) score = 0.094√n + 0.60δ − 0.34ω (I)
was set to 0.30 Å. This was carried out while pushing the
minimization using the OPLS3 (optimized potentials for Site score = 0.0733√n + 0.6688δ − 0.20ω (II)
liquid simulations-3) force field and concurrently deleting Where, n is the number of site points (capped at 100); δ
water molecules within 3 Å from the ligand (HETs). is the enclosure score; and ω is the hydrophilic score.
The primary objective of protein minimization was to
remove steric clashes, reorganize structural features 2.5. Ligand refinement
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such as bond angles, bond lengths, and torsional angles, The idea behind ligand refinement is to transform two-
and remove strained conformations arising from crystal dimensional (2D) or three-dimensional (3D) structures
packing artifacts, experimental errors, or inaccuracies in into corresponding low-energy 3D structures in the
computational modeling. 40 structure-data file (.sdf) format, with the option to expand
2.4. Binding site/pocket identification each input structure by creating variations on ionization
state, tautomers, stereochemistry, and ring confirmations,
With a large amount of protein data available in the thereby generating broad chemical and structural diversity
UniProt database, only a fraction of it is functionally from a single input structure. In this study, the LigPrep
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annotated. Consequently, understanding the biological or package in Schrödinger Maestro (Schrödinger Release
biochemical role of protein with an interacting partner in 2020-3: LigPrep, Schrödinger, LLC, United States, 2023)
a binding relationship remains a fundamental challenge in was employed to prepare the ligands.
the fields of medicinal chemistry, genomic bioinformatics, The 6PYS is a co-crystallized protein with a ligand,
and pharmacology. This underscores the importance of P5J (Figure 2). The ligand P5J was isolated from the
automated sequencing tools. Protein function is closely protein complex and refined using LigPrep in Maestro.
correlated with the small molecules that attach to them. The ligand states were generated at pH 7 ± 2.0 using
These small molecules may function as substrates or the Hamette and Taft methodology encoded in the
products of an enzyme reaction, cofactors that are crucial
for catalysis, 41,42 or they may provide crucial structural or
regulatory functions. Hence, protein-ligand interaction in
43
the context of binding sites is critical for drug discovery,
44
and understanding responses to drugs. 45
Binding site identification was conducted following a
predictive approach using the SiteMap wizard in Maestro.
To conduct binding site prediction, the ligand in the 6PYS
protein-ligand complex was masked. To find, visualize, and
evaluate protein binding sites, the identification of top-
ranked potential receptor binding sites was prioritized.
This necessitated the search of at least 15 site points per
reported site, from which up to five site-point groupings
were to be reported. The strategy for identifying binding
pockets involved employing a more restrictive definition
of hydrophobicity and having a standard grid and crop
site maps at 4 Å from the nearest site point. Furthermore,
the binding site attributes such as druggable sites, docking
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space (site score), and desirable ligand size, as well as
other parameters including pocket volume, exposure
score, contact score, and hydrophobic interaction score, Figure 2. 2D representation of ligand P5J in 6PYS human protein complex.
P5J refers to (3S)-3-benzyl-3-methyl-5-[5-(2-methyl pyrimidine-5-yl)
were computed using the SiteMap algorithm. Furthermore, pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-dihydro-2H-indol-2-one; chemical
the respective values of these binding site attributes were structural formula: C H N O; molecular weight: 446.503 g/mol.
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Volume 7 Issue 2 (2024) 6 doi: 10.36922/itps.2340