Nicolas Moitessier

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go

Accelerating the drug discovery process requires predictive computational protocols capable of reducing or simplifying the synthetic and/or combinatorial challenge. Docking‐based virtual screening methods have been developed and successfully applied to a number of pharmaceutical targets. In this review, we first present the current status of docking and scoring methods, with exhaustive lists of these. We next discuss reported comparative studies, outlining criteria for their interpretation. In the final section, we describe some of the remaining developments that would potentially lead to a universally applicable docking/scoring method.

Docking Ligands into Flexible and Solvated Macromolecules. 1. Development and Validation of FITTED 1.0

We report the development and validation of a novel suite of programs, FITTED 1.0, for the docking of flexible ligands into flexible proteins. This docking tool is unique in that it can deal with both the flexibility of macromolecules (side chains and main chains) and the presence of bridging water molecules while treating protein/ligand complexes as realistically dynamic systems. This software relies on a genetic algorithm to account for the flexibility of the two molecules as well as the location of bridging water molecules. In addition, FITTED 1.0 features a novel application of a switching function to retain or displace key water molecules from the protein-ligand complexes. Two independent modules, ProCESS and SMART, were developed to set up the proteins and the ligands prior to the docking stage. Validation of the accuracy of the software was achieved via the application of FITTED 1.0 to the docking of inhibitors of HIV-1 protease, thymidine kinase, trypsin, factor Xa, and MMP to their respective proteins.

Docking ligands into flexible and solvated macromolecules. 3. Impact of input ligand conformation, protein flexibility, and water molecules on the accuracy of docking programs.

Several modifications and additions to Fitted1.5 led to the development of Fitted2.6. Among the novel implementations are a matching algorithm-enhanced genetic algorithm and a ring conformational search algorithm. With these various optimizations, we also hoped to remove the biases and to develop a docking program that would provide results (i.e., poses) as independent as possible to the input ligand and protein conformations and used parameters, although keeping the options to provide additional experimental information. These biases were investigated within Fitted2.6 along with FlexX, GOLD, Glide, and Surflex. The input ligand conformation was found to have a major impact on the program accuracy as drops as large as 10-50% were observed with all the programs but Fitted. This comparative study also demonstrates that the accuracy of Fitted is similar to that of other widely used programs. We have also demonstrated that protein flexibility, displaceable water molecules, and ring conformational search algorithms, three of the main Fitted features, significantly increased its accuracy. Finally, we also proposed potential modifications to the available programs to further improve their accuracy in binding mode prediction.

Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins

In our previous report, we investigated the impact of protein flexibility and the presence of water molecules on the pose-prediction accuracy of major docking programs. To complete these investigations, we report herein a study of the impact of these two aspects on the accuracy of scoring functions. To this effect, we developed two sets of protein/ligand complexes made up of ligands cross-docked or cocrystallized with a large variety of proteins, featuring bridging water molecules and demonstrating protein flexibility. Efforts were made to reduce the correlation between the molecular weights of the selected ligands and their binding affinities, a major bias in some previously reported benchmark sets. Using these sets, 18 available scoring functions have been assessed for their accuracy to predict binding affinities and to rank-order compounds by their affinity to cocrystallized proteins. This study confirmed the good and similar accuracy of Xscore, GlideScore, DrugScore(CSD), GoldScore, PLP1, ChemScore, RankScore, and the eHiTS scoring function. Our next investigations demonstrated that most of the assessed scoring functions were much less accurate when the correct protein conformation was not provided. This study also revealed that considering the water molecules for scoring does not greatly affect the accuracy. Finally, this work sheds light on the high correlation between scoring functions and the poor increase in accuracy one can expect from consensus scoring.

Inhibitors of Prolyl Oligopeptidases for the Therapy of Human Diseases: Defining Diseases and Inhibitors

Keywords: Prolyl oligopeptidase inhibitors ; neurological disorders ; peptidomimetics Reference EPFL-ARTICLE-148691doi:10.1021/jm901104gView record in Web of Science Record created on 2010-05-06, modified on 2017-05-12

Docking Ligands into Flexible and Solvated Macromolecules. 2. Development and Application of Fitted 1.5 to the Virtual Screening of Potential HCV Polymerase Inhibitors

HCV NS5B polymerase is a validated target for the treatment of hepatitis C, known to be one of the most challenging enzymes for docking programs. In order to improve the low accuracy of existing docking methods observed with this challenging enzyme, we have significantly modified and updated F itted 1.0, a recently reported docking program, into F itted 1.5. This enhanced version is now applicable to the virtual screening of compound libraries and includes new features such as filters and pharmacophore- or interaction-site-oriented docking. As a first validation, F itted 1.5 was applied to the testing set previously developed for F itted 1.0 and extended to include hepatitis C virus (HCV) polymerase inhibitors. This first validation showed an increased accuracy as well as an increase in speed. It also shows that the accuracy toward HCV polymerase is better than previously observed with other programs. Next, application of F itted 1.5 to the virtual screening of the Maybridge library seeded with known HCV polymerase inhibitors revealed its ability to recover most of these actives in the top 5% of the hit list. As a third validation, further biological assays uncovered HCV polymerase inhibition for selected Maybridge compounds ranked in the top of the hit list.

Design, synthesis and preliminary biological evaluation of a focused combinatorial library of stereodiverse carbohydrate-scaffold-based peptidomimetics.

A focused combinatorial library of 126 mimetics of the RGD sequence based on sugar scaffolds have been rationally constructed using molecular modeling, with a particular emphasis on the stereodiversity of the library. A liquid phase, mix and divide synthesis was used, active compounds being identified by using orthogonal libraries and recursive deconvolution strategies.

Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography

Golgi α‐mannosidase II (GMII), a zinc‐dependent glycosyl hydrolase, is a promising target for drug development in anti‐tumor therapies. Using X‐ray crystallography, we have determined the structure of Drosophila melanogaster GMII (dGMII) complexed with three different inhibitors exhibiting IC50s ranging from 80 to 1000 μM. These structures, along with those of seven other available dGMII/inhibitor complexes, were then used as a basis for the evaluation of seven docking programs (GOLD, Glide, FlexX, AutoDock, eHiTS, LigandFit, and FITTED). We found that small inhibitors could be accurately docked by most of the software, while docking of larger compounds (i.e., those with extended aromatic cycles or long aliphatic chains) was more problematic. Overall, Glide provided the best docking results, with the most accurately predicted binding around the active site zinc atom. Further evaluation of Glides performance revealed its ability to extract active compounds from a benchmark library of decoys. Proteins 2007.

Design, modeling and synthesis of functionalized paromamine analogs

Abstract Based on the published NMR structure of the antibiotic paromomycin complexed with the A-site of Escherichia coli 16S ribosomal RNA, a set of C-5 functionalized analogs of paromamine was designed and synthesized, incorporating cyclic and acyclic appendages and terminating with one or more ammonium groups.

Platinum(II) phenanthroimidazoles for targeting telomeric G-quadruplexes.

A rationally designed progression of phenanthroimidazole platinum(II) complexes were examined for their ability to target telomere‐derived intramolecular G‐quadruplex DNA. Through the use of circular dichroism, fluorescence displacement assays, and molecular modeling we show that these complexes template and stabilize G‐quadruplexes from sequences based on the human telomeric repeat (TTAGGG)n. The greatest stabilization was observed for the p‐chlorophenyl derivative 6 (G4DC50=0.31 μM). We also show that the G‐quadruplex binding complexes are able to inhibit telomerase activity through a modified telomerase repeat amplification protocol (TRAP‐LIG assay). Preliminary cell studies show that complex 6 is preferentially cytotoxic toward cancer over normal cell lines, indicating its potential use in cancer therapy.