Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method

G-protein-coupled receptors (GPCRs) have enormous physiological and biomedical importance, and therefore it is not surprising that they are the targets of many prescribed drugs. Further progress in GPCR drug discovery is highly dependent on the availability of protein structural information. However, the ability of X-ray crystallography to guide the drug discovery process for GPCR targets is limited by the availability of accurate tools to explore receptor-ligand interactions. Visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum mechanics (QM) approaches are often too computationally expensive to be of practical use in time-sensitive situations, but the fragment molecular orbital (FMO) method offers an excellent solution that combines accuracy, speed, and the ability to reveal key interactions that would otherwise be hard to detect. Integration of GPCR crystallography or homology modelling with FMO reveals atomistic details of the individual contributions of each residue and water molecule toward ligand binding, including an analysis of their chemical nature. Such information is essential for an efficient structure-based drug design (SBDD) process. In this chapter, we describe how to use FMO in the characterization of GPCR-ligand interactions

First principles-based calculations of free energy of binding: application to ligand binding in a self-assembling superstructure

The accurate prediction of ligand binding affinities to a protein remains a desirable goal of computational biochemistry. Many available methods use molecular mechanics (MM) to describe the system, however, MM force fields cannot fully describe the complex interactions involved in binding, specifically electron transfer and polarization. First principles approaches can fully account for these interactions, and with the development of linear-scaling first principles programs, it is now viable to apply first principles calculations to systems containing tens of thousands of atoms. In this paper, a quantum mechanical Poisson?Boltzmann surface area approach is applied to a model of a protein?ligand binding cavity, the “tennis ball” dimer. Results obtained from this approach demonstrate considerable improvement over conventional molecular mechanics Poisson?Boltzmann surface area due to the more accurate description of the interactions in the system. For the first principles calculations in this study, the linear-scaling density functional theory program ONETEP is used, allowing the approach to be applied to receptor?ligand complexes of pharmaceutical interest that typically include thousands of atoms.<br/

GPCR structure, function, drug discovery and crystallography: report from Academia-Industry International Conference (UK Royal Society) Chicheley Hall, 1-2 September 2014

G-protein coupled receptors (GPCRs) are the targets of over half of all prescribed drugs today. The UniProt database has records for about 800 proteins classified as GPCRs, but drugs have only been developed against 50 of these. Thus, there is huge potential in terms of the number of targets for new therapies to be designed. Several breakthroughs in GPCRs biased pharmacology, structural biology, modelling and scoring have resulted in a resurgence of interest in GPCRs as drug targets. Therefore, an international conference, sponsored by the Royal Society, with world-renowned researchers from industry and academia was recently held to discuss recent progress and highlight key areas of future research needed to accelerate GPCR drug discovery. Several key points emerged. Firstly, structures for all three major classes of GPCRs have now been solved and there is increasing coverage across the GPCR phylogenetic tree. This is likely to be substantially enhanced with data from x-ray free electron sources as they move beyond proof of concept. Secondly, the concept of biased signalling or functional selectivity is likely to be prevalent in many GPCRs, and this presents exciting new opportunities for selectivity and the control of side effects, especially when combined with increasing data regarding allosteric modulation. Thirdly, there will almost certainly be some GPCRs that will remain difficult targets because they exhibit complex ligand dependencies and have many metastable states rendering them difficult to resolve by crystallographic methods. Subtle effects within the packing of the transmembrane helices are likely to mask and contribute to this aspect, which may play a role in species dependent behaviour. This is particularly important because it has ramifications for how we interpret pre-clinical data. In summary, collaborative efforts between industry and academia have delivered significant progress in terms of structure and understanding of GPCRs and will be essential for resolving problems associated with the more difficult targets in the future.ISSN:0028-1298ISSN:1432-191

Efficient quantum computation of molecular forces and other energy gradients

While most work on the quantum simulation of chemistry has focused on computing energy surfaces, a similarly important application requiring subtly different algorithms is the computation of energy derivatives. Almost all molecular properties can be expressed an energy derivative, including molecular forces, which are essential for applications such as molecular dynamics simulations. Here, we introduce new quantum algorithms for computing molecular energy derivatives with significantly lower complexity than prior methods. Under cost models appropriate for noisy-intermediate scale quantum devices we demonstrate how low rank factorizations and other tomography schemes can be optimized for energy derivative calculations. We perform numerics revealing that our techniques reduce the number of circuit repetitions required by many orders of magnitude for even modest systems. In the context of fault-tolerant algorithms, we develop new methods of estimating energy derivatives with Heisenberg limited scaling incorporating state-of-the-art techniques for block encoding fermionic operators. Our results suggest that the calculation of forces on a single nucleus may be of similar cost to estimating energies of chemical systems, but that further developments are needed for quantum computers to meaningfully assist with molecular dynamics simulations.Comment: 48 pages, 14 page appendix, 10 figures. v2 contains updated lambdas (rescaling factors) for sparse FT encodings and some NISQ methods, obtained by localizing orbital

Zero-point tunneling splittings in compounds with multiple hydrogen bonds calculated by the rainbow instanton method

Zero-point tunneling splittings are calculated, and the values are compared with the experimentally observed values for four compounds in which the splittings are due to multiple-proton transfer along hydrogen bonds. These compounds are three binary complexes, namely, the formic acid and benzoic acid dimer and the 2-pyridone-2-hydroxypyridine complex, in which the protons move in pairs, and the calix[4]arene molecule, in which they move as a quartet. The calculations make use of and provide a test for the newly developed rainbow approximation for the zero-temperature instanton action which governs the tunneling splitting (as well as the transfer rate). This approximation proved to be much less drastic than the conventional adiabatic and sudden approximations, leading to a new general approach to approximate the instanton action directly. As input parameters the method requires standard electronic-structure data and the Hessians of the molecule or complex at the stationary configurations only; the same parameters also yield isotope effects. Compared to our earlier approximate instanton method, the rainbow approximation offers an improved treatment of the coupling of the tunneling mode to the other vibrations. Contrary to the conventional instanton approach based on explicit evaluation of the instanton trajectory, both methods bypass this laborious procedure, which renders them very efficient and capable of handling systems that thus far have not been handled by other theoretical methods. Past results for model systems have shown that the method should be valid for a wide range of couplings. The present results for real compounds show that it gives a satisfactory account of tunneling splittings and isotope effects in systems with strong coupling that enhances tunneling, thus demonstrating its applicability to low-temperature proton dynamics in systems with multiple hydrogen bonds.Peer reviewed: YesNRC publication: Ye