Design, Synthesis, Activity And Molecular Dynamics Studies Of Selective Src Homology 2 (SH2) Domain-Containing Phosphatase 2 (SHP-2) Inhibitors

Objective: leukemia is a high case fatality rate and a poor prognosis malignant tumor. In 2012 leukemia developed in 352,000 people globally and caused 265,000 deaths. At present, bone marrow transplant is still the best treatment, but because the HLA match the same probability is very small and it could not meet the clinical needs, thus, molecular targeted therapy became a wonderful method to treat leukemia. In recent years, protein tyrosine phosphatase SHP-2 became a perfect anti-leukemia target, which plays significant roles in the regulation of signal transduction in leukemia cell growth.The active site of protein tyrosine phosphatase(PTP) with different functions is most highly conservative, so it is difficult to selective SHP-2 inhibitors without side effects. In this study, three-dimensional pharmacophore model for SHP-2 and its highly homologous PTP1 B and TCPTP were built and then based on the constructed the theory of function model modify # 324, a lead compound, after that molecular docking technology was used to predict the capability of candidates to inhibit SHP-2, PTP1 B, and TCPTP. Hopefully, this may help us to discover selective SHP-2 inhibitors.Methods: 1. The experiment uses the synthetic compounds with active data to generate three-dimensional pharmacophore model of the SHP-2, PTP1 B, and TCPTP using the Hiphop programme, and based on it, a known active compound # 324 was further modified to design a series of SHP-2 small molecule inhibitors.2. The ADME predictions of these compounds were done by using Qikprop. 3. The designed compounds were docked into the receptors downloaded from PDB bank to further clarify the interaction between the antagonists and the receptor by using CADD technology. 4. By searching Sci Finder databases, a series of candidates were synthesized and were approved by 1H-NMR and MS. In the synthesis section, we modified the synthesis process, thus, the yield is improved by comparing the litereature. 5. The inhibitory of these synthetic candidates were tested by using the in vitro biological activity assay. 6. Molecular dynamics simulations of the representative compounds were performed to study the stability of compound-target complex. It may provide a theoretical foundation for the discovery of the selectiveSHP-2 inhibitors.Results: 1. The best SHP-2 inhibitors including six pharmacophore model elements(one aromatic ring center, two hydrogen bonds receptors and three hydrophobic groups);PTP1B inhibitors of the best model includes seven pharmacophore elements(three aromatic ring center, one hydrophobic groups and three hydrogen bond receptor);TCPTP inhibitors of the best model includes six pharmacophore elements(two aromatic ring center, two hydrophobic groups and one hydrogen bond receptor).According to the generated pharmacophore model, the active compound # 324 was modified, which has devised a series of potential selective SHP2 receptor inhibitor.2. Based on the rule of Lipinski five, 36 compounds could be drug candidates. 3. On the fundamental of the docking score and docking model, one compound which inhibited SHP-2(-14.1 k J/mol) over PTP1 B and TCPTP(less than-2 k J/mol) were obtained, suggesting that the designed compound would become as selective SHP2 inhibitors in theory.4. In the synthetic section, the synthetic routes were designed and obtained through the reactions of nucleophilic substitution and Gewald reaction. These candidates were approved by 1H-NMR and MS. 5. The inhibitory activity of SHP-2, PTP1 B and TCPTP were determination. Bioactive data shows that some of these compounds could become selective SHP-2 inhibitors. 6. In the molecular dynamic section, we simulated how the compounds bind to SHP-2, PTP1 B and TCPTP, and the interactions of compounds with enzymes were interpreted in a dynamic manner.Conclutions: This paper use Discovery Studio software(Hip Hop algorithjns) to construct pharmacophore models of multiple PTPs related targets of the family of protein tyrosine phosphatase SHP-2, PTP1 B and TCPTP. According to the construct the corresponding pharmacophore model, a series of SHP-2 inhibitors was designed. In theory, the interaction mechanism of the designed compounds and SHP-2 receptor was studied. The enzyme experiment showed that part of the design of compounds could selectively inhibit SHP-2 enzyme activity having the potential research value. The candidate binding to SHP-2, PTP1 B and TCPTP were carried out by using Gromacs, and the interactions of compounds with the three enzymes were interpreted in a dynamic manner, which lay the foundation for the discovery of novelantileukemia drugs.