Protein-fragment Complexes Research Articles

A Benchmark Study of Protein-Fragment Complex Structure Calculations with NMR2.

Protein-fragment complex structures are particularly sought after in medicinal chemistry to rationally design lead molecules. These structures are usually derived using X-ray crystallography, but the failure rate is non-neglectable. NMR is a possible alternative for the calculation of weakly interacting complexes. Nevertheless, the time-consuming protein signal assignment step remains a barrier to its routine application. NMR Molecular Replacement (NMR2) is a versatile and rapid method that enables the elucidation of a protein-ligand complex structure. It has been successfully applied to peptides, drug-like molecules, and more recently to fragments. Due to the small size of the fragments, ca < 300 Da, solving the structures of the protein-fragment complexes is particularly challenging. Here, we present the expected performances of NMR2 when applied to protein-fragment complexes. The NMR2 approach has been benchmarked with the SERAPhic fragment library to identify the technical challenges in protein-fragment NMR structure calculation. A straightforward strategy is proposed to increase the method's success rate further. The presented work confirms that NMR2 is an alternative method to X-ray crystallography for solving protein-fragment complex structures.

LEADS-FRAG: A Benchmark Data Set for Assessment of Fragment Docking Performance.

Fragment-based drug design is a popular approach in drug discovery, which makes use of computational methods such as molecular docking. To assess fragment placement performance of molecular docking programs, we constructed LEADS-FRAG, a benchmark data set containing 93 high-quality protein-fragment complexes that were selected from the Protein Data Bank using a rational and unbiased process. The data set contains fully prepared protein and fragment structures and is publicly available. Moreover, we used LEADS-FRAG for evaluating the small-molecule docking programs AutoDock, AutoDock Vina, FlexX, and GOLD for their fragment docking performance. GOLD in combination with the scoring function ChemPLP and AutoDock Vina performed best and generated near-native conformations (root mean square deviation <1.5 Å) for more than 50% of the data set considering the top-ranked docking pose. Taking into account all docking poses, the tested programs generated near-native conformations for up to 86% of the fragments in LEADS-FRAG. By rescoring all docking poses with the GOLD scoring functions and the Protein-Ligand Informatics force field, the number of near-native conformations increased up to 40% with respect to the top-rescored poses. Our results show that conventional small-molecule docking programs achieve a satisfactory fragment docking performance when utilizing rescoring.

Fragment Hits: What do They Look Like and How do They Bind?

A “fragment hit”, a molecule of low molecular weight that has been validated to bind to a target protein, can be an effective chemical starting point for a drug discovery project. Our ability to find and progress fragment hits could potentially be improved by enhancing our understanding of their binding properties, which to date has largely been based on tacit knowledge and reports from individual projects. In the work reported here, we systematically analyzed the molecular and binding properties of fragment hits using 489 published protein–fragment complexes. We identified a number of notable features that these hits tend to have in common, including preferences in buried surface area upon binding, hydrogen bonding and other directional interactions with the protein targets, structural topology, functional-group occurrence, and degree of carbon saturation. In the future, taking account of these preferences in designing and selecting fragments to screen against protein targets may increase the chances of success in fragment screening campaigns.

Protein-ligand structure guided by backbone and side-chain proton chemical shift perturbations.

The fragment-based drug design approach consists of screening libraries of fragment-like ligands, to identify hits that typically bind the protein target with weak affinity (100 μM-5 mM). The determination of the protein-fragment complex 3D structure constitutes a crucial step for uncovering the key interactions responsible for the protein-ligand recognition, and for growing the initial fragment into potent active compounds. The vast majority of fragments are aromatic compounds that induce chemical shift perturbations (CSP) on protein NMR spectra. These experimental CSPs can be quantitatively used to guide the ligand docking, through the comparison between experimental CSPs and CSP back-calculation based on the ring current effect. Here we implemented the CSP back-calculation into the scoring function of the program PLANTS. We compare the results obtained with CSPs measured either on amide or aliphatic protons of the human peroxiredoxin 5. We show that the different kinds of protons lead to different results for resolving the 3D structures of protein-fragment complexes, with the best results obtained with the Hα protons.

Fragment-screening at the BESSY II MX-beamlines of the Helmholtz-Zentrum Berlin

"Within the last decade, the fragment-based screening approach has been matured to a reliable and powerful instrument of pharmaceutical drug discovery. The success of fragment screening strongly depends on the quality of the chosen fragment library (100-200 Da), the quality of the target protein diffraction as well as the possibility to use high throughput methods for the screen application. A thorough crystallographic analysis of many protein-fragment complex structures and their binding modes has the perspective to result in the development of new potential lead structures and to map the interaction landscape of protein surfaces. Recently we started the development of a dedicated experimental facility for high throughput fragment screening at the BESSY II storage ring. The in house data processing pipeline ""XDSAPP"" [1] has been developed to speed up the data evaluation of large amounts of diffraction data. We have assembled a fragment library of 96 compounds and have validated this library against two target proteins. These first results suggest that our library is capable of identifying binding partners at a hit rate of close to 10%. This library together with a fully automated beam line [2] will be made accessible to users, thus enabling fragment-screening experiments on a much broader basis. "

Virtual Fragment Docking by Glide: a Validation Study on 190 Protein−Fragment Complexes

The docking accuracy of Glide was evaluated using 16 different docking protocols on 190 protein-fragment complexes representing 78 targets. Standard precision docking (Glide SP) based protocols showed the best performance. The average root-mean-square deviation (rmsd) between the docked and cocrystallized poses achieved by Glide SP with pre- and postprocessing was 1.17 A, and an acceptable binding mode with rmsd < 2 A could be found in 80% of the cases. Comparison of the docking results produced by different protocols suggests that the sampling efficacy of Glide is adequate for fragment docking. The docking accuracy seems to be limited by the performance of scoring schemes, which is supported by the weak correlation between experimental binding affinities and GlideScores. Cross-docking experiments performed on 8 targets represented by 63 complexes revealed that Glide SP gave similar results to that of the computationally more intensive Glide XP. The average rmsd achieved by Glide SP with pre- and postprocessing was 2.06 A, and an acceptable binding mode with rmsd < 2 A could be found in 63% of the cases. These cross-docking results were improved significantly selecting the optimal X-ray structure for each target (average rmsd = 1.3 A, success rate = 77%), indicating the importance of enrichment studies and the use of multiple X-ray structures in virtual fragment screening.

Computational fragment-based drug design to explore the hydrophobic subpocket of the mitotic kinesin Eg5 allosteric binding site

Eg5, a mitotic kinesin exclusively involved in the formation and function of the mitotic spindle has attracted interest as an anticancer drug target. Eg5 is co-crystallized with several inhibitors bound to its allosteric binding pocket. Each of these occupies a pocket formed by loop5/helix α2. Recently designed inhibitors additionally occupy a hydrophobic pocket of this site. The goal of the present study was to identify new fragments which fill this hydrophobic pocket and might be interesting chemical moieties to design new inhibitors. We've used the fragment based protocol of MED-SuMo which exploits the whole PDB on the basis that similar protein surfaces might bind the same fragment. The MED-SuMo software is able to compare and superimpose similar protein-ligand interaction surfaces at PDB scale. Protein-fragment complexes are encoded as MED-Portions by cross-mining 3D PDB ligand structures with fragment-like PubChem molecules. Inhibitors are designed by hybridising MED-Portions with MED-Hybridise. Without using the known Eg5 PDB ligands that occupy the hydrophobic pocket, we've predicted new potential ligands that would fill simultaneously both pockets. Some of the latter are identified in libraries of synthetically accessible molecules by the MED-Search software.