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

Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method

Proteins are vital components of living systems, serving as building blocks, molecular machines, enzymes, receptors, ion channels, sensors, and transporters. Protein-protein interactions (PPIs) are a key part of their function. There are more than 645,000 reported disease-relevant PPIs in the human interactome, but drugs have been developed for only 2% of these targets. The advances in PPI-focused drug discovery are highly dependent on the availability of structural data and accurate computational tools for analysis of this data. Quantum mechanical approaches are often too expensive computationally, 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. FMO provides essential information for PPI drug discovery, namely, identification of key interactions formed between residues of two proteins, including their strength (in kcal/mol) and their chemical nature (electrostatic or hydrophobic). In this chapter, we have demonstrated how three different FMO-based approaches (pair interaction energy analysis (PIE analysis), subsystem analysis (SA) and analysis of protein residue networks (PRNs)) have been applied to study PPI in three protein-protein complexes

Structural and Conformational Dependence of Optical Rotation Angles

The ability to compute and to interpret optical rotation angles of chiral molecules is of great value in assigning relative and absolute stereochemistry. The molar rotations for an indoline and an azetidine, as well as for menthol and menthone, were calculated using ab inito methods and compared to the experimental values. In one case the calculated rotation angle allowed the assignment of the absolute configuration of a heterocycle of unknown stereochemistry. The critical importance of Boltzmann averaging of conformers for reliable prediction of the optical rotation angle was established. Comparisons between static-field and time-dependent methods were made pointing to the limits and validity of the methods as electronic resonance is approached. A protocol analogous to population analysis was used to analyze atomic contributions to the rotation angle in specific conformers. The combination of atomic contribution maps and conformational analysis may provide an indirect tool to assist in three-dimensional structure determination

Exploring the optical activity tensor by anisotropic Rayleigh optical activity scattering

Rayleigh optical activity (RayOA) spectroscopy promises to provide an elegant and robust analytical method to probe molecular stereochemistry. A careful selection of RayOA variants such as right-angle depolarized ICP (incident circular polarization) or backscattering DCP1 (in-phase dual circular polarization) allows analysis of the anisotropic component of the scattered light. In this study, we show that calculated anisotropic Rayleigh optical activity quantities provide key advantages over isotropic chiroptical quantities (such as optical rotation and RayOA variants domi nated by isotropic invariants): 1) higher sensitivity for probing the chiroptical tensor G′, 2) reduced dependence on small geometry changes, and 3) much less stringent computational demand for predicting an accurate sign than for optical rotation. Moreover, the stereochemical information provided by anisotropic RayOA and its invariants can be used to develop chirality descriptors because of the apparent correlation between structure/stereochemistry and the sign and magnitude of the anisotropic Rayleigh optical activity quantities. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA

Tunneling energy effects on GC oxidation in DNA

Hole-mediated electronic couplings, reorganization energies, and electron transfer (ET) rates are examined theoretically for hole-transfer reactions in DNA. Electron transfer rates are found to depend critically on the energy gap between the donor/acceptor states and the intervening bases-the tunneling energy gap. The calculated distance decay exponent for the square of the electronic coupling, β, for hole transfer between GC base pairs (and pi-electron D/A pairs) ranges from 0.95 to 1.5 Å -1 in the model structures as the tunneling energy gap varies from 0.3 to 0.8 eV (which we argue is the range of energy gaps for GC oxidation probed in recent experiments). We show that the tunneling energy gap depends on the ET reorganization energy, which itself grows rapidly with distance for ET over 1-5 base pairs. Inclusion of the distance dependence of reorganization energies for these hole transfer reactions gives the tunneling rates an apparent decay exponent of ∼1.5-2.5 Å -1. We show that ET rates observed in DNA across one and two base pairs are reasonably well described with single-step ET theories, using our calculated couplings and reorganization energies. However, the computed single-step tunneling (superexchange) ET rates for donor and acceptor species separated by three or more base pairs are much smaller than observed. We conclude that longer-distance ET probably proceeds through thermal population of intermediate hole states of the bridging bases. Switching between mechanisms as distance grows beyond a few base pairs is likely to be a general characteristic of ET in small tunneling energy gap systems.link_to_subscribed_fulltex

Optical rotation computation, total synthesis, and stereochemistry assignment of the marine natural product pitiamide A

We report the joint application of ab initio computations and total synthesis to assign the absolute configuration of a new natural product. The expected specific rotations of the (7S,10R)- and (7R,10R)-isomers of pitiamide A in a CHCl3 solvent continuum model were determined as +8 and - 39, respectively, by CADPAC calculations of the electric-dipole-magnetic- dipole polarizability tensor. Total syntheses of these two stereoisomers of the marine metabolite were achieved by a convergent strategy that utilized Evans' oxazolidinone alkylation, a novel water-accelerated modification of Negishi's zirconocene-catalyzed asymmetric carbometalation as well as an unusual segment condensation via Mitsunobu alkylation of a nosyl-activated amide. The experimental optical rotation measurements confirmed the results of the computational optical rotation predictions. On the basis of NMR comparisons, the configuration of pitiamide A was assigned as (7R,10R). These studies highlight the considerable structural significance of [α](D) data, but, because the optical rotation of the natural product was different from either synthetic diastereomer, our work serves also as an illustration of potential problems with obtaining accurate experimental [α](D) data for natural samples

Synthetic and model computational studies of molar rotation additivity for interacting chiral centers: a reinvestigation of van't Hoff's principle.

When plane-polarized light impinges on a solution of optically active molecules, the polarization of the light that emerges is rotated. This simple phenomenon arises from the interaction of light with matter and is well understood, in principle, van't Hoff's rule of optical superposition correlates the molar rotation with the individual contributions to optical activity of isolated centers of asymmetry. This straightforward empirical additivity rule is rarely used for structure elucidation nowadays because of its limitations in the assessment of conformationally restricted or interacting chiral centers. However, additivity can be used successfully to assign the configuration of complex natural products such as hennoxazole A if appropriate synthetic partial structures are available. Therefore, van't Hoff's principle is a powerful stereochemical complement to natural products' total synthesis. The quest for reliable quantitative methods to calculate the angle of rotation a priori has been underway for a long time. Both classical and quantum methods for calculating molar rotation have been developed. Of particular practical importance for determining the absolute structure of molecules by calculation is the manner in which interactions between multiple chiral centers in a single molecule are included, leading to additive or non-additive optical rotation angles. This problem is addressed here using semi-empirical electronic structure models and the Rosenfeld equation

A gradient-directed Monte Carlo approach for protein design

We develop a new global optimization strategy, gradient-directed Monte Carlo (GDMC) sampling, to optimize protein sequence for a target structure using RosettaDesign. GDMC significantly improves the sampling of sequence space, compared to the classical Monte Carlo search protocol, for a fixed backbone conformation as well as for the simultaneous optimization of sequence and structure. As such, GDMC sampling enhances the efficiency of protein design. © 2010 Wiley Periodicals, Inc.link_to_subscribed_fulltex

Hole size and energetics in double helical DNA: Competition between quantum delocalization and solvation localization

The transition between single step long-range tunneling and multistep hopping transport in DNA electron transfer depends on a myriad of factors including sequence, distance, conformation, solvation and, consequently, hole state energetics. We show that the solvation energetics of hole (radical cation) states in DNA is comparable to the quantum delocalization energetics of the hole. That is, the solvation forces that tend to localize the hole compete with the quantum effects that give rise to hole delocalization. The net result is that the hole states are predicted to be relatively compact (one to three base pairs in length) and that the "trap depth" of these holes is expected to be much shallower than anticipated by gas-phase quantum chemical analysis of base stacks. This analysis predicts guanine oxidation potential dependence on the length of GC runs to be modest (differences <0.1 V for holes from one to three base pairs). The lowering of the trapped hole binding energy has significant implications for the structure and mobility of hole states in DNA.link_to_subscribed_fulltex