Table 1.
Structural details of Mitapivat and its top-performing derivatives, including similarity score, SMILES notation, and 2D representation. This table presents only the highest-ranked derivatives based on docking performance and interaction similarity to native Mitapivat. The complete list of derivatives is provided in Supplementary Table 1.
Fig 1.
Structural alignment and similarity analysis of Mitapivat and its derivatives.
(a) 2D alignment of Mitapivat and representative derivatives, showing conservation of the central structure with variable substituents localized to peripheral regions. (b) 3D conformational superposition of Mitapivat and its derivatives, highlighting consistent alignment of the aromatic and sulfonyl cores with subtle deviations in side-chain orientations. (c) Pairwise similarity heatmap of 190 derivatives (similarity score ≥0.90), where deep blue indicates high structural conservation and red/orange regions correspond to lower similarity clusters. (d) Principal component analysis (PCA) of molecular descriptors, illustrating clustering of most derivatives around the Mitapivat scaffold, with select analogues dispersed along principal components, reflecting chemical diversity introduced by substituent modifications.
Table 2.
Comparative docking results of Mitapivat, phenylalanine (allosteric inhibitor), and top-performing derivatives with PKLR, including binding affinities and interaction energy components. The complete molecular docking results are presented in Supplementary Table 2.
Fig 2.
2D interaction maps of Mitapivat and its best-performing derivatives with the PKLR binding site.
(a) PKLR_Mitapivat complex. (b) PKLR_CHEMBL3729403 complex. (c) PKLR_CHEMBL3728962 complex. (d) PKLR_CHEMBL3729860 complex. (e) PKLR_CHEMBL4297223 complex. (f) PKLR_CHEMBL4299940 complex. The interaction types are color-coded as follows: hydrogen bonds (bright green), carbon-hydrogen bonds (light green), van der Waals interactions (pale green), Pi-Alkyl (pink), and Pi-Sigma (purple).
Fig 3.
Comparative 3D binding poses of Mitapivat and its best-performing derivatives in the PKLR allosteric binding site.
(a) PKLR_Mitapivat complex. (b) PKLR_CHEMBL3729403 complex. (c) PKLR_CHEMBL3728962 complex. (d) PKLR_CHEMBL3729860 complex. (e) PKLR_CHEMBL4297223 complex. (f) PKLR_CHEMBL4299940 complex.
Table 3.
Molecular interaction profiles of PKLR with Mitapivat, Phenylalanine, and top-performing derivatives.
Fig 4.
HOMO–LUMO profiles of Mitapivat and its best-performing derivatives.
(a) Mitapivat. (b) CHEMBL3729403. (c) CHEMBL3728962. (d) CHEMBL3729860. (e) CHEMBL4297223. (f) CHEMBL4299940. Blue regions represent HOMO orbital localization, while red regions denote LUMO orbital distribution.
Table 4.
Frontier molecular orbital energies, HOMO–LUMO gap, and dipole moments of Mitapivat and its best-performing derivatives.
Fig 5.
(a) PKLR_Mitapivat complex. (b) PKLR_CHEMBL3729403 complex. (c) PKLR_CHEMBL3728962 complex. (d) PKLR_CHEMBL3729860 complex. (e) PKLR_CHEMBL4297223 complex. (f) PKLR_CHEMBL4299940 complex. Yellow spheres indicate hydrophobic interactions, green arrows represent hydrogen bond donors, and red arrows signify hydrogen bond acceptors.
Table 5.
MD simulation parameters of PKLR complexes with Mitapivat, phenylalanine, and top-performing derivatives over 200 ns of simulations, including RMSD, RMSF, RoG, SASA, ligand–protein center-of-mass distance, and hydrogen bond interactions.
Fig 6.
MD simulation results for PKLR in complex with Mitapivat, phenylalanine, and top-performing derivatives over 200 ns of simulation.
(a) Root mean square deviation (RMSD), reflecting the overall conformational stability of the protein–ligand complexes. (b) Root mean square fluctuation (RMSF), providing residue-level insights into backbone flexibility, particularly in the active-site regions. (c) Radius of gyration (RoG), indicating the degree of compactness and folding stability of the protein throughout the trajectory. (d) Solvent accessible surface area (SASA), showing changes in surface exposure and solvation upon ligand binding. (e) Ligand–protein center-of-mass distance, illustrating the persistence and dynamic retention of ligands within the binding cavity. (f) Number of hydrogen bonds, representing the occupancy and stability of polar contacts sustaining protein–ligand interactions.
Table 6.
MM/PBSA binding free energies (ΔG_binding) of Mitapivat, phenylalanine, and selected derivatives in complex with PKLR.
Fig 7.
Heatmap of per-residue energy contributions (kcal/mol) in the PKLR allosteric binding site.
(a) PKLR_Mitapivat complex. (b) PKLR_Phenylalanine complex. (c) PKLR_CHEMBL3729403 complex. (d) PKLR_CHEMBL3729860 complex.
Table 7.
In silico pharmacokinetics and ADMET properties of top-performing Mitapivat derivatives.
Fig 8.
Retrosynthetic routes toward prioritized Mitapivat derivatives.
(a) Retrosynthetic pathway leading to CHEMBL3729403, a sulfonamide-modified Mitapivat analogue, obtained via coupling of a chlorophenyl-substituted hydroxy-pyrrolidine amide with a heteroaryl sulfonyl chloride derivative. (b) Retrosynthetic pathway leading to CHEMBL3729860, a hybrid Mitapivat–sulfonamide analogue, synthesized through the combination of a sulfonamide–benzoic acid derivative bearing a fused fluoropyridyl-naphthyl sulfone with a hydroxy-pyrrolidine benzylamine fragment carrying a chlorophenyl substitution.