Docking and biological activity of pteridine analogs: search for inhibitors of pteridine reductase enzymes from Trypanosoma cruzi

Therapeutic potential of pteridine derivatives: A comprehensive review

Pteridines are aromatic compounds formed by fused pyrazine and pyrimidine rings. Many living organisms synthesize pteridines, where they act as pigments, enzymatic cofactors, or immune system activation molecules. This variety of biological functions has motivated the synthesis of a huge number of pteridine derivatives with the aim of studying their therapeutic potential. This review gathers the state-of-the-art of pteridine derivatives, describing their biological activities and molecular targets. The antitumor activity of pteridine-based compounds is one of the most studied and advanced therapeutic potentials, for which several molecular targets have been identified. Nevertheless, pteridines are also considered as very promising therapeutics for the treatment of chronic inflammation-related diseases. On the other hand, many pteridine derivatives have been tested for antimicrobial activities but, although some of them resulted to be active in preliminary assays, a deeper research is needed in this area. Moreover, pteridines may be of use in the treatment of many other diseases, such as diabetes, osteoporosis, ischemia, or neurodegeneration, among others. Thus, the diversity of the biological activities shown by these compounds highlights the promising therapeutic use of pteridine derivatives. Indeed, methotrexate, pralatrexate, and triamterene are Food and Drug Administration approved pteridines, while many others are currently under study in clinical trials.

PSI-DOCK: towards highly efficient and accurate flexible ligand docking

We have developed a new docking method, Pose-Sensitive Inclined (PSI)-DOCK, for flexible ligand docking. An improved SCORE function has been developed and used in PSI-DOCK for binding free energy evaluation. The improved SCORE function was able to reproduce the absolute binding free energies of a training set of 200 protein-ligand complexes with a correlation coefficient of 0.788 and a standard error of 8.13 kJ/mol. For ligand binding pose exploration, a unique searching strategy was designed in PSI-DOCK. In the first step, a tabu-enhanced genetic algorithm with a rapid shape-complementary scoring function is used to roughly explore and store potential binding poses of the ligand. Then, these predicted binding poses are optimized and compete against each other by using a genetic algorithm with the accurate SCORE function to determine the binding pose with the lowest docking energy. The PSI-DOCK 1.0 program is highly efficient in identifying the experimental binding pose. For a test dataset of 194 complexes, PSI-DOCK 1.0 achieved a 67% success rate (RMSD < 2.0 A) for only one run and a 74% success rate for 10 runs. PSI-DOCK can also predict the docking binding free energy with high accuracy. For a test set of 64 complexes, the correlation between the experimentally observed binding free energies and the docking binding free energies for 64 complexes is r = 0.777 with a standard deviation of 7.96 kJ/mol. Moreover, compared with other docking methods, PSI-DOCK 1.0 is extremely easy to use and requires minimum docking preparations. There is no requirement for the users to add hydrogen atoms to proteins because all protein hydrogen atoms and the flexibility of the terminal protein atoms are intrinsically taken into account in PSI-DOCK. There is also no requirement for the users to calculate partial atomic charges because PSI-DOCK does not calculate an electrostatic energy term. These features are not only convenient for the users but also help to avoid the influence of different preparation methods.

Crystal structure of Trypanosoma cruzi pteridine reductase 2 in complex with a substrate and an inhibitor

Reduced pteridines are required for a number of important cellular functions. Trypanosomatid parasites, unlike their mammalian hosts, are pteridine auxotrophs and salvage the precursor pteridines from the host and reduce them to the respective biologically active tetrahydro forms using parasite-encoded enzymes. These enzymes may offer selective drug targets. In Leishmania, pteridine reductase 1 (PTR1), the primary enzyme for reducing pterins, is also responsible for resistance to antifolate drugs. Typically, PTR1 is more active with fully oxidized biopterin and folate than with their reduced counterparts. We have identified an enzyme, TcPTR2 of Trypanosoma cruzi, which though very similar to PTR1 in its primary sequence, can reduce only dihydrobiopterin and dihydrofolate and not oxidized pteridines. The structures of an inhibitor (methotrexate) and a substrate (dihydrofolate) complex of this enzyme demonstrate that the orientation of the substrate and the inhibitor in the active site of TcPTR2 are different from each other. However, the orientation of each ligand is similar to that of the corresponding ligand in Leishmania major PTR1 complexes.