# Design, optimization, and ADMET evaluation of S11a-0000168202: A promising LIMK1 inhibitor for gastric cancer treatment

**Authors:** Guojun Li, Jionghuang Chen, Rui Chen, Weihua Yu

PMC · DOI: 10.1371/journal.pone.0323699 · PLOS One · 2025-05-14

## TL;DR

This paper presents a new LIMK1 inhibitor, S11a-0000168202, developed for gastric cancer treatment with promising computational results.

## Contribution

The novel LIMK1 inhibitor S11a-0000168202 was designed and optimized with improved binding and ADMET properties.

## Key findings

- S11a-0000168202 showed enhanced binding stability and interactions with key LIMK1 residues.
- ADMET evaluation indicated favorable properties like moderate lipophilicity and good intestinal absorption.
- The compound remains untested experimentally, highlighting a need for further in vitro and in vivo studies.

## Abstract

This study focuses on the development and optimization of S11a-0000168202, a novel LIMK1 inhibitor with potential therapeutic applications in gastric cancer. Through scaffold hopping and structural modification of HIT100844099, S11a-0000168202 demonstrated enhanced binding stability and stronger interactions with key LIMK1 residues, including GLU-414, ILE-416, and HIS-464. Molecular dynamics simulations and MMGBSA analyses confirmed the compound’s stability, while ADMET evaluation revealed favorable properties such as moderate lipophilicity, good human intestinal absorption, and low P-glycoprotein inhibition. Despite the promising computational results, the lack of experimental validation remains a limitation. Future studies should focus on in vitro and in vivo testing to confirm S11a-0000168202’s efficacy, pharmacokinetics, and safety. This compound holds significant potential as a therapeutic agent for LIMK1-targeted gastric cancer treatment.

## Linked entities

- **Genes:** LIMK1 (LIM domain kinase 1) [NCBI Gene 3984]
- **Proteins:** LIMK1 (LIM domain kinase 1), Mdr65 (Multi drug resistance 65)
- **Diseases:** gastric cancer (MONDO:0001056)

## Full-text entities

- **Genes:** LIMK2 (LIM domain kinase 2) [NCBI Gene 3985], LIMK1 (LIM domain kinase 1) [NCBI Gene 3984] {aka LIMK, LIMK-1}, PDCD1 (programmed cell death 1) [NCBI Gene 5133] {aka ADMIO4, AIMTBS, CD279, PD-1, PD1, SLEB2}, CYP1A1 (cytochrome P450 family 1 subfamily A member 1) [NCBI Gene 1543] {aka AHH, CP11, CYP1, CYPIA1, P1-450, P450-C}, ABL2 (ABL proto-oncogene 2, non-receptor tyrosine kinase) [NCBI Gene 27] {aka ABLL, ARG}, Limk1 (LIM domain kinase 1) [NCBI Gene 16885] {aka KIZ-1, LIMK-1, Limk}, ROCK1 (Rho associated coiled-coil containing protein kinase 1) [NCBI Gene 6093] {aka P160ROCK, ROCK-I}, CYP2D6 (cytochrome P450 family 2 subfamily D member 6 (gene/pseudogene)) [NCBI Gene 1565] {aka CPD6, CYP2D, CYP2D7AP, CYP2D7BP, CYP2D7P2, CYP2D8P2}, CYP1A2 (cytochrome P450 family 1 subfamily A member 2) [NCBI Gene 1544] {aka CP12, CYPIA2, P3-450, P450(PA)}, ABCB1 (ATP binding cassette subfamily B member 1) [NCBI Gene 5243] {aka ABC20, CD243, CLCS, ENPAT, GP170, MDR1}, ASPM (assembly factor for spindle microtubules) [NCBI Gene 259266] {aka ASP, Calmbp1, MCPH5}, CYP2C19 (cytochrome P450 family 2 subfamily C member 19) [NCBI Gene 1557] {aka CPCJ, CYP2C, CYPIIC17, CYPIIC19, P450C2C, P450IIC19}, PAK1 (p21 (RAC1) activated kinase 1) [NCBI Gene 5058] {aka IDDMSSD, PAKalpha, alpha-PAK, p65-PAK}, ERBB2 (erb-b2 receptor tyrosine kinase 2) [NCBI Gene 2064] {aka CD340, HER-2, HER-2/neu, HER2, MLN 19, MLN-19}, SLTM (SAFB like transcription modulator) [NCBI Gene 79811] {aka Met}, UBE2K (ubiquitin conjugating enzyme E2 K) [NCBI Gene 3093] {aka E2-25K, HIP2, HYPG, LIG, UBC1}, PRKAA2 (protein kinase AMP-activated catalytic subunit alpha 2) [NCBI Gene 5563] {aka AMPK, AMPK2, AMPKa2, PRKAA}, CFL1 (cofilin 1) [NCBI Gene 1072] {aka CFL, HEL-S-15, cofilin}, CD274 (CD274 molecule) [NCBI Gene 29126] {aka ADMIO5, B7-H, B7H1, PD-L1, PDCD1L1, PDCD1LG1}, ROCK2 (Rho associated coiled-coil containing protein kinase 2) [NCBI Gene 9475] {aka ROCK-II}, CYP3A4 (cytochrome P450 family 3 subfamily A member 4) [NCBI Gene 1576] {aka CP33, CP34, CYP3A, CYP3A3, CYPIIIA3, CYPIIIA4}, CYP2C9 (cytochrome P450 family 2 subfamily C member 9) [NCBI Gene 1559] {aka CPC9, CYP2C, CYP2C10, CYPIIC9, P450-2C9, P450IIC9}, KCNH2 (potassium voltage-gated channel subfamily H member 2) [NCBI Gene 3757] {aka ERG-1, ERG1, H-ERG, HERG, HERG1, Kv11.1}, LNPEP (leucyl and cystinyl aminopeptidase) [NCBI Gene 4012] {aka CAP, IRAP, P-LAP, PLAP}
- **Diseases:** HIV-1 infection (MESH:D015658), metastasis (MESH:D009362), glaucoma (MESH:D005901), cancer (MESH:D009369), Gastric cancer (MESH:D013274), MSI-H (MESH:D000848), respiratory toxicity (MESH:D012140), carcinogenic (MESH:D011230), oral toxicity (MESH:D064420), Helicobacter pylori infection (MESH:D016481), DILI (MESH:D056486), neurological disorders (MESH:D009461), cardiotoxicity (MESH:D066126)
- **Chemicals:** carbon (MESH:D002244), HIS (MESH:D006639), sulfur (MESH:D013455), trastuzumab (MESH:D000068878), SP (MESH:C000604007), THR- (MESH:D013912), VAL (MESH:D014633), CYS (MESH:D003545), AMES (MESH:C017501), ALA (MESH:D000409), hydrogen (MESH:D006859), salt (MESH:D012492), amino acids (MESH:D000596), GLU-414 (-), ATP (MESH:D000255), pyrrolopyrimidine (MESH:C527741), NaCl (MESH:D012965), LEU (MESH:D007930), Fu (MESH:D005472), ASN (MESH:D001216), LYS (MESH:D008239), ILE (MESH:D007532), COF (MESH:C043212), water (MESH:D014867), GLU (MESH:D018698), LIMKi3 (MESH:C000632957), LX-7101 (MESH:C000607841), PHE (MESH:D010649), MOF (MESH:C037042), pembrolizumab (MESH:C582435)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Rattus norvegicus (brown rat, species) [taxon 10116], Actinopterygii (fishes, superclass) [taxon 7898], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** T413A, H464A, E414A, serine/threonine, I416A
- **Cell lines:** Caco-2 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0025), CCK-8 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_2873), AGS — Homo sapiens (Human), Gastric adenocarcinoma, Cancer cell line (CVCL_0139), LIMKi3 — Mus musculus (Mouse), Hybridoma (CVCL_C6V6), MKN-45 — Homo sapiens (Human), Gastric adenocarcinoma, Cancer cell line (CVCL_0434)

## Full text

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## Figures

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## References

49 references — full list in the complete paper: https://tomesphere.com/paper/PMC12077675/full.md

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Source: https://tomesphere.com/paper/PMC12077675