Mark J. Forster

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

The effect of variation of substitution on the solution conformation of heparin: a spectroscopic and molecular modelling study

The effect of variations in substitution on the conformation of iduronate-containing sequences in heparin and heparan sulphate has been studied using a series of chemically-modified heparins in which substitution with O- and N-sulphate and N-acetyl substituents has been systematically altered. Monosaccharides corresponding to residues in these modified heparins have also been investigated. The conformations of the glycosidic linkages in O- and N-desulphated re-N-acetylated heparin, O-desulphated re-N-sulphated heparin, and 6-O-desulphated re-N-sulphated heparin have been compared with those of N-desulphated re-N-acetylated heparin and of heparin itself, which have been compared with those of N-desulphated re-N-acetylated heparin and of heparin itself, which have previously been reported [B. Mulloy, M.J. Forster, C. Jones, and D.B. Davies, Biochem. J., 293 (1993) 849-858]. The overall conformation of all the polysaccharides is shown to be similar, regardless of substitution pattern. The conformational equilibrium of the pyranose ring of iduronic acid residues in the polysaccharides has been monitored by the use of 13C NMR chemical shift temperature coefficients, and shown to be similar for all the modified heparins with the exception of N-desulphated re-N-acetylated heparin. Circular dichroism spectra of all the polysaccharides are reported, and their variations attributed to differences in the proportions of pyranose ring forms in the iduronate conformational equilibrium.

Minimum information about a bioactive entity (MIABE)

Bioactive molecules such as drugs, pesticides and food additives are produced in large numbers by many commercial and academic groups around the world. Enormous quantities of data are generated on the biological properties and quality of these molecules. Access to such data — both on licensed and commercially available compounds, and also on those that fail during development — is crucial for understanding how improved molecules could be developed. For example, computational analysis of aggregated data on molecules that are investigated in drug discovery programmes has led to a greater understanding of the properties of successful drugs. However, the information required to perform these analyses is rarely published, and when it is made available it is often missing crucial data or is in a format that is inappropriate for efficient data-mining. Here, we propose a solution: the definition of reporting guidelines for bioactive entities — the Minimum Information About a Bioactive Entity (MIABE) — which has been developed by representatives of pharmaceutical companies, data resource providers and academic groups.

Molecular modelling in structural biology.

Molecular modelling is a powerful methodology for analysing the three dimensional structure of biological macromolecules. There are many ways in which molecular modelling methods have been used to address problems in structural biology. It is not widely appreciated that modelling methods are often an integral component of structure determination by NMR spectroscopy and X-ray crystallography. In this review we consider some of the numerous ways in which modelling can be used to interpret and rationalise experimental data and in constructing hypotheses that can be tested by experiment. Genome sequencing projects are producing a vast wealth of data describing the protein coding regions of the genome under study. However, only a minority of the protein sequences thus identified will have a clear sequence homology to a known protein. In such cases valuable three-dimensional models of the protein coding sequence can be constructed by homology modelling methods. Threading methods, which used specialised schemes to relate protein sequences to a library of known structures, have been shown to be able to identify the likely protein fold even in cases where there is no clear sequence homology. The number of protein sequences that cannot be assigned to a structural class by homology or threading methods, simply because they belong to a previously unidentified protein folding class, will decrease in the future as collaborative efforts in systematic structure determination begin to develop. For this reason, modelling methods are likely to become increasingly useful in the near future. The role of the blind prediction contests, such as the Critical Assessment of techniques for protein Structure Prediction (CASP), will be briefly discussed. Methods for modelling protein-ligand and protein-protein complexes are also described and examples of their applications given.

Computational approaches to the identification of heparin-binding sites on the surfaces of proteins.

The identification of heparin-binding sites is important for understanding the physiological function of many secreted proteins. Most of the experimental techniques for mapping these sites do not define them to atomic resolution. The use of automated docking methods can aid this process by facilitating both the design of experiments and visualization of their results. A method designed for a systematic search over the whole protein surface for heparin-binding sites, using heparin oligosaccharide structures as ligands, is described, with its validation and details of several published applications. The scope and limitations of this crude but effective computational chemistry method are discussed.

N.m.r. and conformational analysis of the capsular polysaccharide from Streptococcus pneumoniae type 4

The 1H- and 13C-n.m.r. data on the capsular polysaccharide (1) produced by Streptococcus pneumoniae type 4, the depyruvated polysaccharide (2), and a tetrasaccharide (3a) derived by Smith degradation of 2 were used as constraints on a computer-generated model of the conformation of 1 and to assess the effects of the pyruvic acetal substituent on the conformation. The dynamics of the polysaccharide systems and the influence of the pyruvic acetal were investigated using 13C-n.m.r. relaxation measurements.

NOEMOL: integrated molecular graphics and the simulation of nuclear overhauser effects in NMR spectroscopy

Nuclear Overhauser effects (NOEs) are a widely used method of determining the spatial proximity of spins in Nuclear Magnetic Resonance (NMR) spectroscopy. This paper describes a C program developed for the Sun-3 workstation family that allows the computation of multispin NOE effects for a given molecular structure and given NMR parameters (i.e., resonance frequency and correlation time for molecular reorientation). The integration of these facilities with simple molecular graphics display routines allows modifications to the molecular conformation (such as bond rotations) to be performed, and the effect of these modifications on the NOE effects can then be rapidly calculated and easily visualized. Using the Sun windowing system, the NOE effects can be calculated for two (or more) candidate structures and compared to experimental NMR results. The overall molecular reorientation can be modeled by either isotropic or symmetric top diffusion models, and the internal motions of methyl groups are modeled using an algorithm reported by Tropp.

Application of drug discovery software to the identification of heparin-binding sites on protein surfaces: a computational survey of the 4-helix cytokines

Heparin, best known as a potent anticoagulant, also interacts with many other proteins for which the natural ligand is heparan sulfate (HS). The hope that HS would display specific sequences which would bind selectively to each of these proteins has not been fulfilled, but this may be at least in part due to the relationship between HS sequence and 3D structure. The example of FGF-1 is used to demonstrate that many different sequences can give rise to the 3D patterns of charge, which form binding motifs for proteins. Partly because of this redundancy in sequence-to-structure relationship, the application of conventional high-throughput drug discovery methods for the development of heparin or heparan based therapeutic agents is not yet practicable. However, it is possible to adapt systematic docking calculations to work in a moderately high throughput manner to screen protein structures from the Protein Data Bank (PDB) for predicted heparin-binding sites. A survey of protein structures in the Structural Classification of Protiens (SCOP) superfamily of 4-helical cytokines is presented.

Empowering industrial research with shared biomedical vocabularies.

The life science industries (including pharmaceuticals, agrochemicals and consumer goods) are exploring new business models for research and development that focus on external partnerships. In parallel, there is a desire to make better use of data obtained from sources such as human clinical samples to inform and support early research programmes. Success in both areas depends upon the successful integration of heterogeneous data from multiple providers and scientific domains, something that is already a major challenge within the industry. This issue is exacerbated by the absence of agreed standards that unambiguously identify the entities, processes and observations within experimental results. In this article we highlight the risks to future productivity that are associated with incomplete biological and chemical vocabularies and suggest a new model to address this long-standing issue.

Rationalizing nuclear Overhauser effect data for compounds adopting multiple-solution conformations

An algorithm is described for refining the populations of a set of multiple‐solution conformers using experimental nuclear Overhauser effects (nOes). The method is based upon representing the effective relaxation matrix for the set of interconverting proposed conformers as a linear combination of relaxation matrices (LCORMs) due to each conformer. The conformer population derivative of the nOe is derived from a Taylor series expression for the calculated nOe. This derivative may then be used in a standard nonlinear least‐squares refinement procedure. The LCORM nOe procedure is tested using a monosaccharide system, 1‐O‐methyl‐α‐L‐iduronate, that is known to exhibit conformational variability. The measured nOes for this system are used to refine the populations of a set of three static conformers, namely, the 1C4, 4C1, and 2S0 ring conformers. The populations thus derived are compared to those previously obtained using nuclear magnetic resonance proton‐proton coupling constant information. Two possible extensions to the method are discussed: The first uses combined nOe and coupling constant data while the second removes the restrictions that the conformers used for fitting be rigid entities.