Irene Nobeli

Protein promiscuity and its implications for biotechnology

Molecular recognition between proteins and their interacting partners underlies the biochemistry of living organisms. Specificity in this recognition is thought to be essential, whereas promiscuity is often associated with unwanted side effects, poor catalytic properties and errors in biological function. Recent experimental evidence suggests that promiscuity, not only in interactions but also in the actual function of proteins, is not as rare as was previously thought. This has implications not only for our fundamental understanding of molecular recognition and how protein function has evolved over time but also in the realm of biotechnology. Understanding protein promiscuity is becoming increasingly important not only to optimize protein engineering applications in areas as diverse as synthetic biology and metagenomics but also to lower attrition rates in drug discovery programs, identify drug interaction surfaces less susceptible to escape mutations and potentiate the power of polypharmacology.

Hydrogen bonding properties of oxygen and nitrogen acceptors in aromatic heterocycles

The directionality and relative strengths of hydrogen bonds to monocyclic aromatic heterocycles were investigated using crystal structure data and theoretical calculations. Surveys of the Cambridge Structural Database for hydrogen bonds between C(sp3)(SINGLE BOND)O(SINGLE BOND)H and aromatic fragments containing one or more nitrogen and/or oxygen heteroatoms showed that hydrogen bonds to nitrogen atoms are much more abundant than to oxygen. Distinct preferred orientations were also revealed in these surveys. Theoretical calculations were performed on the interaction of methanol with pyridine, pyrimidine, pyrazine, pyridazine, oxazole, isoxazole, 1,2,4‐oxadiazole, and furan as models for the heterocyclic fragments. The intermolecular potential surface was thoroughly scanned using a model potential that accurately described the electrostatic forces (derived from distributed multipole analysis) with empirical parameters for the repulsion and dispersion terms. Minima on this surface agreed well with the observed orientations in the data base and they were typically deeper for nitrogen than for oxygen acceptors, although the hydrogen bond strength and geometry was influenced by other heteroatoms in the ring. These results were confirmed by highly accurate intermolecular perturbation theory calculations, which also estimated the deviations from hydrogen bonding in the traditional nitrogen lone pair direction that could occur with negligible reduction in the interaction energy. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 2060–2074, 1997

Prokaryotic Navms Channel as a Structural and Functional Model for Eukaryotic Sodium Channel Antagonism.

Significance Many drugs used to treat pain, epilepsy, and cardiac arrhythmias target human voltage-gated sodium-selective channels. Surprisingly, we found that a bacterial voltage-gated sodium channel is also inhibited by many eukaryotic sodium channel antagonists. This bacterial channel was crystallized with several brominated blocker compounds, and the high-resolution structures reveal a common antagonist binding site in the cavity of the pore. Electrophysiology studies of channels with mutations at adjacent residues validate the site. These results suggest that despite millions of years of evolution separating human and bacterial sodium channels, these simple bacterial channels can be a valuable tool for screening and rational design of human drugs. Voltage-gated sodium channels are important targets for the development of pharmaceutical drugs, because mutations in different human sodium channel isoforms have causal relationships with a range of neurological and cardiovascular diseases. In this study, functional electrophysiological studies show that the prokaryotic sodium channel from Magnetococcus marinus (NavMs) binds and is inhibited by eukaryotic sodium channel blockers in a manner similar to the human Nav1.1 channel, despite millions of years of divergent evolution between the two types of channels. Crystal complexes of the NavMs pore with several brominated blocker compounds depict a common antagonist binding site in the cavity, adjacent to lipid-facing fenestrations proposed to be the portals for drug entry. In silico docking studies indicate the full extent of the blocker binding site, and electrophysiology studies of NavMs channels with mutations at adjacent residues validate the location. These results suggest that the NavMs channel can be a valuable tool for screening and rational design of human drugs.

Ligand selectivity and competition between enzymes in silico.

In a cell, there are many possibilities for cross interactions between enzymes and small molecules, arising from the similarities in the structures of the metabolites and the flexibility in binding of protein active sites. Despite this promiscuity, the cognate partners must be able to recognize each other in vivo, for the cell to function efficiently. This study examines the basis of this selectivity in recognition using standard docking calculations and finds significant improvement when proteins and ligands are cross-docked. We find that cognate molecules rarely form the most stable complexes and that specificity may be driven either by recognition of the substrate by the enzyme or the recognition of the enzyme by the substrate. Despite limitations of the in silico methods, especially the scoring functions, these calculations highlight the need to consider cross reactions in the cell and suggest that localization and compartmentalization must be important factors in the evolution of complex cells. However, the inherent promiscuity of these interactions can also benefit an organism, by facilitating the evolution of new functions from old ones. The results also suggest that high-throughput screening should involve not just a panel of small molecules, but also a panel of proteins to test for cross-reactivity.

PROCOGNATE: a cognate ligand domain mapping for enzymes

PROCOGNATE is a database of protein cognate ligands for the domains in enzyme structures as described by CATH, SCOP and Pfam, and is available as an interactive website or a flat file. This article gives an overview of the database and its generation and presents a new website front end, as well as recent increased coverage in our dataset via inclusion of Pfam domains. We also describe navigation of the website and its features. The current version (1.3) of PROCOGNATE covers 4123, 4536, 5876 structures and 377, 326, 695 superfamilies/families in CATH, SCOP and Pfam, respectively. PROCOGNATE can be accessed at: http://www.ebi.ac.uk/thornton-srv/databases/procognate/

Crystallographic and Cellular Characterisation of Two Mechanisms Stabilising the Native Fold of α1-Antitrypsin: Implications for Disease and Drug Design

The common Z mutant (Glu342Lys) of α1-antitrypsin results in the formation of polymers that are retained within hepatocytes. This causes liver disease whilst the plasma deficiency of an important proteinase inhibitor predisposes to emphysema. The Thr114Phe and Gly117Phe mutations border a surface cavity identified as a target for rational drug design. These mutations preserve inhibitory activity but reduce the polymerisation of wild-type native α1-antitrypsin in vitro and increase secretion in a Xenopus oocyte model of disease. To understand these effects, we have crystallised both mutants and solved their structures. The 2.2 Å structure of Thr114Phe α1-antitrypsin demonstrates that the effects of the mutation are mediated entirely by well-defined partial cavity blockade and allows in silico screening of fragments capable of mimicking the effects of the mutation. The Gly117Phe mutation operates differently, repacking aromatic side chains in the helix F–β-sheet A interface to induce a half-turn downward shift of the adjacent F helix. We have further characterised the effects of these two mutations in combination with the Z mutation in a eukaryotic cell model of disease. Both mutations increase the secretion of Z α1-antitrypsin in the native conformation, but the double mutants remain more polymerogenic than the wild-type (M) protein. Taken together, these data support different mechanisms by which the Thr114Phe and Gly117Phe mutations stabilise the native fold of α1-antitrypsin and increase secretion of monomeric protein in cell models of disease.

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.

Therapeutic target-site variability in α1-antitrypsin characterized at high resolution

A new 1.8 Å resolution structure of α1-antitrypsin demonstrates structural variability within an allosteric site in the molecule.

Interaction of N-methyl-2-alkenyl-4-quinolones with ATP-dependent MurE ligase of Mycobacterium tuberculosis: antibacterial activity, molecular docking and inhibition kinetics

Objectives The aim of this study was to comprehensively evaluate the antibacterial activity and MurE inhibition of a set of N-methyl-2-alkenyl-4-quinolones found to inhibit the growth of fast-growing mycobacteria. Methods Using the spot culture growth inhibition assay, MICs were determined for Mycobacterium tuberculosis H37Rv, Mycobacterium bovis BCG and Mycobacterium smegmatis mc2155. MICs were determined for Mycobacterium fortuitum, Mycobacterium phlei, methicillin-resistant Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa using microplate dilution assays. Inhibition of M. tuberculosis MurE ligase activity was determined both by colorimetric and HPLC methods. Computational modelling and binding prediction of the quinolones in the MurE structure was performed using Glide. Kinetic experiments were conducted for understanding possible competitive relations of the quinolones with the endogenous substrates of MurE ligase. Results The novel synthetic N-methyl-2-alkenyl-4-quinolones were found to be growth inhibitors of M. tuberculosis and rapid-growing mycobacteria as well as methicillin-resistant S. aureus, while showing no inhibition for E. coli and P. aeruginosa. The quinolones were found to be inhibitory to MurE ligase of M. tuberculosis in the micromolar range (IC50 ∼40–200 μM) when assayed either spectroscopically or by HPLC. Computational docking of the quinolones on the published M. tuberculosis MurE crystal structure suggested that the uracil recognition site is a probable binding site for the quinolones. Conclusions N-methyl-2-alkenyl-4-quinolones are inhibitors of mycobacterial and staphylococcal growth, and show MurE ligase inhibition. Therefore, they are considered as a starting point for the development of increased affinity MurE activity disruptors.

Targeting serpins in high-throughput and structure-based drug design

Native, metastable serpins inherently tend to undergo stabilizing conformational transitions in mechanisms of health (e.g., enzyme inhibition) and disease (serpinopathies). This intrinsic tendency is modifiable by ligand binding, thus structure-based drug design is an attractive strategy in the serpinopathies. This can be viewed as a labor-intensive approach, and historically, its intellectual attractiveness has been tempered by relatively limited success in development of drugs reaching clinical practice. However, the increasing availability of a range of powerful experimental systems and higher-throughput techniques is causing academic and early-stage industrial pharmaceutical approaches to converge. In this review, we outline the different systems and techniques that are bridging the gap between what have traditionally been considered distinct disciplines. The individual methods are not serpin-specific. Indeed, many have only recently been applied to serpins, and thus investigators in other fields may have greater experience of their use to date. However, by presenting examples from our work and that of other investigators in the serpin field, we highlight how techniques with potential for automation and scaling can be combined to address a range of context-specific challenges in targeting the serpinopathies.