Binding Mode And Design Of The Inhibitors Targeting Protein Tyrosine Phosphatase 1B

Protein tyrosine phosphatase 1B（PTP1B）negatively regulates the signaling pathways of insulin and leptin,and it has become a drug target for the treatment of type 2 diabetes.PTP1B inhibitors effectively improve the sensitivity of insulin receptors and are of great significance for the treatment of insulin resistance-related diseases.However,no drugs targeting the PTP1B have been approved for marketing.Two main challenges are facing the development of effective PTP1B inhibitors.On one hand,because the PTP family has highly conserved catalytic sites,many PTP1B inhibitors have poor selectivity.On the other hand,the positively charged residues in PTP1B active site tend to attract highly charged inhibitors,but compounds with highly charged anions are difficult to penetrate the cell membrane,which affects the oral bioavailability of the drug.Using traditional methods such as high-throughput screening and live animal experiments to study novel PTP1B inhibitors is faced with dilemmas such as time-consuming,labor-intensive,low hit rate,and adverse side effects.Moreover,there is also randomness in the further optimization and design of known active inhibitors.Therefore,it can effectively increase the hit rate of PTP1B inhibitors and reduce the incidence of adverse reactions by using computer-aided drug design methods to explore the binding mode of inhibitors and PTP1B and to rationally design and screen small molecular structures.In this work,various computational simulation methods were used to study the mechanism of Varic acid inhibitors and PTP1B and to design and screen novel PTP1B inhibitors.The main research contents of this study are as follows:（1）Research on the binding mode of PTP1B and Varic acid inhibitors.Using molecular docking,molecular dynamics simulation,MM/GBSA binding free energy calculation to study the binding modes of Varic acid inhibitors on PTP1B.The most likely binding modes（pose A）were determined according to the binding conformations and interactions.The predicted binding free energy of each inhibitor-PTP1B complex is highly consistent with the experimental inhibitory activity log(IC₅₀).The interaction mechanisms of the 2,4-dihydroxy-6-propyl-benzoic acid moiety shared by the compounds 1,4,and 6 are similar.By hydrogen bond analysis,the number of hydrogen-bonding residues is shown in ascending order for compounds1,4,and 6.Compared with other inhibitors,compound 3 has the fewest stable hydrogen bonds.Although compounds 4 and 5 differ only in the carboxyl group,their binding modes are not the same.Tyr46,Ser216,Ala217,Ile219,Arg221,and Gln262 have significant contributions to the binding from the per-residue energy.Finally,the influence of different residues around the catalytic site,the shape of the binding site,and the interaction between the compound and protein on the inhibitor selectivity were discussed.（2）Design of novel PTP1B inhibitors based on Trivaric acid.Through statistical analysis of the binding mode of 35 PTP1B complex crystal structures,we found that the main interactions of PTP1B-inhibitor are hydrogen bonds and hydrophobic interaction,followed by salt bridges.The key residues forming hydrogen bonds are Ser216–Arg221 on the P loop and the surrounding residues Asp48,Asp181,Phe182,Gln262,and Gln266.The residues that contribute the most to the hydrophobic interaction are Tyr46 and Phe182,which can formπ-πstacking with the aromatic ring of the ligand.In addition,Arg24,Lys120 and Arg254 can form salt bridges with ligands.Therefore,by analysing the interactions of PTP1B crystals and the binding modes of PTP1B-Varic acid inhibitors,we designed 17 Varic acid derivatives based on the structure of compound 6.After ADMET evaluation,ten structures were excluded,and the retained seven derivatives have more favourable binding free energy than the known inhibitor（compound 6）.Moreover,four of the derivatives may be selective.Finally,according to the differences in structure and binding free energy of 17 molecules,the influence of each structural unit on the binding affinity was analyzed.（3）Exploring novel PTP1B inhibitors using combined virtual screening methods.We performed a combined approach including multicomplex pharmacophore,molecular docking-based screening,van der Waals energy normalization,pose scaling factor,ADMET evaluation and molecular dynamics simulation to select PTP1B inhibitors from three databases（Pub Chem,Ch EMBL and ZINC）.We identified three potential PTP1B inhibitors,compounds 1,4 and 5,with favorable binding energy and good oral bioavailability.The energetic and geometrical analyses show that the three compounds are stably bound to PTP1B,via occupying both the catalytic site（site A）and the proximal noncatalytic site（site B or C）,which may have the selectivity.This combined screening strategy provided a feasible protocol that can identify inhibitors that can be satisfied with the selectivity of certain multiple-site binding region and suggested three potential PTP1B inhibitors to treat of type 2 diabetes.Using various computational biology methods such as molecular docking,molecular dynamics simulation,binding free energy calculation,virtual screening,ADMET evaluation,etc.,this study revealed the binding mode of Varic acid inhibitors and PTP1B,designed a series of novel Varic acids derivatives,predicted their binding affinity and ADMET properties and screened the candidates with selectivity and oral bioavailability.The conclusions provide theoretical guidance for the developing and designing of effective PTP1B inhibitors,and offer a screening protocol to identify selective inhibitors targeting multiple-sites.