Fig 1.
Evaluation of re-docking accuracy across different docking precision levels.
(A) Superimposition of the LIMKi3 binding conformations obtained from three different accuracy levels with the co-crystal structure. (B) Binding mode of LIMKi3 in the co-crystal state with LIMK1. (C) Binding mode of LIMKi3 with LIMK1 obtained from HTVS accuracy calculation. (D) Binding mode of LIMKi3 with LIMK1 obtained from SP accuracy calculation. (E) Binding mode of LIMKi3 with LIMK1 obtained from XP accuracy calculation.
Table 1.
Evaluation results of screened compounds.
Fig 2.
Pharmacophore features and similarity scores of different compounds.
Base feature spheres for hydrogen bond acceptors (pink), donors (blue), hydrophobes [31], and aromatic rings (orange).
Fig 3.
Medicinal Chemistry Radar Chart.
(A) LIMKi3 (B) HIT100844099 (C) HIT103203505.
Fig 4.
2D Interaction Diagram of Compounds with LIMK1.
(A) LIMKi3 (B) HIT100844099 (C) HIT103203505.
Fig 5.
Binding Stability and Free Energy Calculations of the Three Compounds.
Dynamic changes in RMSD over time: (A) LIMKi3 (B) HIT100844099 (C) HIT103203505. Dynamic changes in MMGBSA over time: (D) LIMKi3 (E) HIT100844099 (F) HIT103203505.
Fig 6.
Interaction Analysis of the Three Compounds with LIMK1.
Dynamic changes in the number of hydrogen bonds over time: (A) LIMKi3 (B) HIT100844099 (C) HIT103203505. Impact on RMSF of LIMK1 before and after binding: (D) LIMKi3 (E) HIT100844099 (F) HIT103203505. Interaction statistics of compounds with different residues: (G) LIMKi3 (H) HIT100844099 (I) HIT103203505. Binding mode of compounds with LIMK1: (J) LIMKi3 (K) HIT100844099 (L) HIT103203505.
Fig 7.
Post-Modifications Evaluation and Interaction Analysis of S11a-0000168202.
(A) Differences before and after scaffold hopping of HIT100844099. (B) Medicinal Chemistry Radar Chart of S11a-0000168202. RMSF differences before and after scaffold hopping for binding with LIMK1: (C) S11a-0000168202 (D) HIT100844099. (E) Dynamic changes in RMSD of S11a-0000168202 over time. (F) Dynamic changes in MMGBSA of S11a-0000168202 over time. (G) Interaction type statistics of S11a-0000168202 with LIMK1.
Fig 8.
Site-Directed Mutagenesis Validation of the Structure-Activity Relationship of S11a-0000168202.
Secondary structure analysis of LIMK1: (A) WT (B) T413A (C) E414A (D) I416A (E) H464A. RMSF of S11a-0000168202 bound to LIMK1 after mutations: (F) T413A (G) E414A (H) I416A (I) H464A.