ander Alex

BLEEP—potential of mean force describing protein–ligand interactions: I. Generating potential

We have developed BLEEP (biomolecular ligand energy evaluation protocol), an atomic level potential of mean force (PMF) describing protein–ligand interactions. The pair potentials for BLEEP have been derived from high‐resolution X‐ray structures of protein–ligand complexes in the Brookhaven Protein Data Bank (PDB), with a careful treatment of homology. The use of a broad variety of protein–ligand structures in the derivation phase gives BLEEP more general applicability than previous potentials, which have been based on limited classes of complexes, and thus represents a significant step forward. We calculate the distance distributions in protein–ligand interactions for all 820 possible pairs that can be chosen from our set of 40 different atom types, including polar hydrogen. We then use a reverse Boltzmann methodology to convert these into energy‐like pair potential functions. Two versions of BLEEP are calculated, one including and one excluding interactions between protein and water. The pair potentials are found to have the expected forms; polar and hydrogen bonding interactions show minima at short range, around 3.0 Å, whereas a typical hydrophobic interaction is repulsive at this distance, with values above 4.0 Å being preferred. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1165–1176, 1999

Intramolecular hydrogen bonding to improve membrane permeability and absorption in beyond rule of five chemical space

Utilising ‘beyond rule of five’ chemical space is becoming increasingly important in drug design, but is usually at odds with good oral absorption. The formation of intramolecular hydrogen bonds in drug molecules is hypothesised to shield polarity facilitating improved membrane permeability and intestinal absorption. NMR based evidence for intramolecular hydrogen bonding in several ‘beyond rule of five’ oral drugs is described. Furthermore, the propensity for these drugs to form intramolecular hydrogen bonds could be predicted for through modelling the lowest energy conformation in the gas phase. The modulation of apparent lipophilicity through intramolecular hydrogen bonding in these molecules is supported by intrinsic cell permeability and intestinal absorption data in rat and human.

BLEEP-POTENTIAL OF MEAN FORCE DESCRIBING PROTEIN-LIGAND INTERACTIONS : II.CALCULATION OF BINDING ENERGIES AND COMPARISON WITH EXPERIMENTAL DATA

We have developed BLEEP (biomolecular ligand energy evaluation protocol), an atomic level potential of mean force (PMF) describing protein–ligand interactions. Here, we present four tests designed to assess different attributes of BLEEP. Calculating the energy of a small hydrogen‐bonded complex allows us to compare BLEEPs description of this system with a quantum‐chemical description. The results suggest that BLEEP gives an adequate description of hydrogen bonding. A study of the relative energies of various heparin binding geometries for human basic fibroblast growth factor (bFGF) demonstrates that BLEEP performs excellently in identifying low‐energy binding modes from decoy conformations for a given protein–ligand complex. We also calculate binding energies for a set of 90 protein–ligand complexes, obtaining a correlation coefficient of 0.74 when compared with experiment. This shows that BLEEP can perform well in the difficult area of ranking the interaction energies of diverse complexes. We also study a set of nine serine proteinase–inhibitor complexes; BLEEPs good performance here illustrates its ability to determine the relative energies of a series of similar complexes. We find that a protocol for incorporating solvation does not improve correlation with experiment. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1177–1185, 1999

Fragment-Based Drug Discovery: What has it Achieved so Far?

Fragment-based drug discovery has proved to be a very useful approach particularly in the hit-to-lead process, providing a complementary tool to traditional high-throughput screening. Although often synonymous with fragment screening, fragment-based drug discovery is a far wider area covering high-throughput screening, fragment screening and virtual screening efforts. The unifying feature of fragment-based drug discovery is the low molecular weight of the hit rather than the approach it originates from. Over the last ten years, fragment-based drug discovery has provided in excess of 50 examples of small molecule hits that have been successfully advanced to leads and therefore resulted in useful substrate for drug discovery programs. To our knowledge, there are currently no marketed drugs that can be attributed to these efforts. However, due to the time scales of drug discovery and development it is likely that over the next few years the number of such examples will increase significantly.

Thermodynamic Optimisation in Drug Discovery: A Case Study Using Carbonic Anhydrase Inhibitors.

Historically the early stages of drug discovery have been based on finding the highest affinity compounds that bind to the target of interest, with little consideration for the forces driving the binding event. The association constant (Ka) can be defined by the equation DG = RTln Ka, with DG =DH TDS. To fully describe Ka it would therefore be beneficial to characterize both of the thermodynamic terms (DH and DS) that drive this affinity for binding. The importance of separating affinity into its thermodynamic components is emphasized by the ubiquitous “enthalpy/entropy compensation effect”, where large changes in DH and DS tend to be of similar but opposite signs and there is no net change in affinity, despite potentially very different binding mode. It has been proposed by Freire, and Ward & Holdgate that it is advantageous, in terms of both potency and selectivity, to start from an enthalpically-driven lead. It can also be argued that choosing compounds with different binding modes increases the variety of chemical substrate for optimization, therefore reducing the risk of all the compounds encountering the same side effects. These points emphasize the need to measure thermodynamic signatures of lead compounds as early in the drug discovery process as possible. The only method that directly measures the thermodynamics of a binding event in solution is isothermal titration calorimetry (ITC). Even though ITC can give a full thermodynamic signature (DGobs, DHobs, DSobs and KB, obs) from a single experiment, the full utilization of the technique for lead optimization has been hampered by technical limitations requiring substantial quantities of reagents. In addition, data have frequently been collected from optimized, but varied, experimental conditions for a particular system, and without appropriate controls the interpretation of results between studies is difficult. Here, we demonstrate that with recent advances in ITC technology and comparing subtly modified ligands against the same target, under identical conditions, and with X-ray data support, thermodynamic measurements can provide medicinal chemists with another differentiator in their quest to discover the best lead compounds. Moreover, these data are informative to medicinal chemists as they are applicable to situations where a less complete biophysical analysis is possible. We chose human carbonic anhydrase (hCA II) as a favorable system for this investigation as there is already a wealth of both 3D structures and calorimetric data available, which has established this protein as the leading model system. Additionally, the protein binds benzene sulfonamides (BSAs) with a 1:1 stoichiometry and does not undergo gross conformational changes upon binding, providing an essentially thermodynamically closed system that will therefore not complicate interpretation of the binding thermodynamics. The binding of BSA to hCA II is driven mainly through four H bonds from the sulfonamide, two H bonds to the Zn co-factor (which is itself coordinated by three histidine residues: His 94, His 96 and His 119) and two H bonds to Thr 199. The dominance of this sulfonamide interaction means that any changes in the thermodynamics of binding caused by additions to the benzene ring may be small and therefore requires careful experimental design. In addition, the effect that aryl substituents may have in terms of electron-withdrawing effects etc. on the sulfonamide binding must also be considered. ITC analysis was performed on seventeen benzene sulfonamide derivatives (1–17) and three benzylamide para-substituted benzene sulfonamides (18–20) by titration into hCA II. In

Using density functional theory to rationalise the mass spectral fragmentation of maraviroc and its metabolites

Tandem mass spectrometry (MS/MS) is widely used for the identification of metabolites at all stages of the pharmaceutical discovery and development process. The assignment of ions in the product ion spectra can be time-consuming and hence delay feedback of results that may influence the direction of a project. A deeper understanding of the processes involved in generation of the product ions formed via collision-induced dissociation may allow development of chemically intelligent software to aid spectral interpretation. Current commercially available spectral interpretation software takes a mainly arithmetical approach resulting in extensive lists of numerically plausible ions, many of which may not be chemically feasible. In this study, high-resolution MS/MS spectra were obtained for maraviroc and two of its synthetic metabolites, and structures for the product ions proposed. Density functional theory (DFT) based on in silico modelling was undertaken to investigate whether the fragmentation observed was potentially a result of bond lengthening (and hence weakening) as a consequence of protonation of the molecule at the most thermodynamically stable site(s). It was determined that for all three compounds, where the product ions resulted from simple bond cleavages (not rearrangements), the bonds that cleaved had been calculated to elongate after protonation. It was also noted that the protonated molecule may represent a mixture of singly charged protonated species and that the most basic sites in the molecule may not necessarily be the most thermodynamically stable for protonation.

Evaluation of a knowledge-based potential of mean force for scoring docked protein-ligand complexes.

The Biomolecular Ligand Energy Evaluation Protocol (BLEEP) is a knowledge‐based potential derived from high‐resolution X‐ray structures of protein–ligand complexes. The performance of this potential in ranking the hypothetical structures resulting from a docking study has been evaluated using fifteen protein–ligand complexes from the Protein Data Bank. In the majority of complexes BLEEP was successful in identifying the native (experimental) binding mode or an alternative of low rms deviation (from the native) as the lowest in energy. Overall BLEEP is slightly better than the DOCK energy function in discriminating native‐like modes. Even when alternative binding modes rank lower than the native structure, a reasonable energy is assigned to the latter. Breaking down the BLEEP scores into the atom–atom contributions reveals that this type of potential is grossly dominated by longer range interactions (>5 Å), which makes it relatively insensitive to small local variations in the binding site. However, despite this limitation, the lack, at present, of accurate protein–ligand potentials means that BLEEP is a promising approach to improve the filtering of structures resulting from docking programs. Moreover, BLEEP should improve with the continuously increasing number of complexes available in the PDB.

Fast and accurate predictions of relative binding energies

Abstract We report on the development of a fast, empirical method for estimating the binding affinity of protein-ligand complexes. The method is of comparable accuracy to existing empirical methods, but uses fewer parameters. We also report on experiments, using a combined quantum mechanical/molecular mechanical (QM/MM) approach, applied to a dataset of thermolysin inhibitors, with improved performance.

Predicting collision‐induced dissociation mass spectra: understanding the role of the mobile proton in small molecule fragmentation

RATIONALE Intramolecular proton migration has been reported to be required for fragmentation by collision-induced dissociation (CID). If the collision energy is required to provide energy for proton movement to a ‘dissociative’ site, it may be possible to predict the optimal collision energy for fragmentation using quantum computational chemistry software. A greater understanding of the mechanism(s) of proton migration is necessary. METHODS The product ion spectra of seven compounds were obtained at collision energies stepped in the range from 5 to 50 eV, with precursor ions being generated in positive ion mode by both atmospheric pressure chemical ionization (APCI) and electrospray ionisation (ESI) (using an ESCi ionisation source with or without corona discharge, respectively). The products ions observed at each collision energy were assessed in terms of structure to ascertain if they were formed as a result of protonation at the initial ionisation site or if the proton had migrated to a dissociative site. RESULTS Proton migration was shown to be independent of collision energy, stability of the protonated molecule and the distance that the proton moved. Therefore, proton migration is not a barrier to fragmentation as the proton appears to be fully mobile at 5 eV. As proton migration is independent of collision energy for these compounds, whereas fragmentation is energy dependent, protonation at the dissociative site alone is not sufficient to cause bond cleavage. CONCLUSIONS The role of collision energy in bond cleavage may be to increase the vibrational energy of the bond and/or increase the rate of bond cleavage such that it occurs within the residence time of the ion within the collision cell rather than to supply the energy for proton migration. Therefore, quantum chemistry alone cannot predict the collision energies appropriate for fragmentation on the basis of modelling proton movements.

Chapter 5:Contribution of Structure-Based Drug Design to the Discovery of Marketed drugs

Structure-based drug design has played a role in the discovery of many drugs from many different disease areas, and it is now arguably an essential contributor to addressing the need to improve research and development productivity faced by the pharmaceutical industry. The purpose of this review is to highlight the impact of protein structures solved by X-ray and NMR techniques, as well as other techniques such as isothermal titration calorimetry, on structure-based discovery. The importance of these methods in drug discovery will be underscored by examples of drugs approved up until the end of 2009, which were discovered utilising structural information. These examples will highlight that structure-based drug design has moved on from just using structural knowledge to optimise potency to using it also with selectivity, pharmacokinetic and pharmaceutical properties in mind. Following on from this, a medicinal chemists perspective aims to highlight the benefits and advantages of structure-based drug design but also to provide an opinion on the pitfalls and hype surrounding this technology. In particular, this section will draw on examples to highlight its impact and limitations on assessing druggability, as well as factors to consider when using structure-based drug design in lead generation and the optimisation of leads for potency, selectivity and pharmacokinetic properties. Finally, some forward looking thoughts will be proposed with regard to the future of structure-based drug design and where emphasis could be placed to increase the impact of this approach on drug discovery productivity.