Perturbation of fluid dynamics properties of water molecules during G protein-coupled receptor-ligand recognition: the human A2A adenosine receptor as a key study

Structure-Based Virtual Screening for Ligands of G Protein-Coupled Receptors: What Can Molecular Docking Do for You?

G protein-coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome and are important therapeutic targets. During the last decade, the number of atomic-resolution structures of GPCRs has increased rapidly, providing insights into drug binding at the molecular level. These breakthroughs have created excitement regarding the potential of using structural information in ligand design and initiated a new era of rational drug discovery for GPCRs. The molecular docking method is now widely applied to model the three-dimensional structures of GPCR-ligand complexes and screen for chemical probes in large compound libraries. In this review article, we first summarize the current structural coverage of the GPCR superfamily and the understanding of receptor-ligand interactions at atomic resolution. We then present the general workflow of structure-based virtual screening and strategies to discover GPCR ligands in chemical libraries. We assess the state of the art of this research field by summarizing prospective applications of virtual screening based on experimental structures. Strategies to identify compounds with specific efficacy and selectivity profiles are discussed, illustrating the opportunities and limitations of the molecular docking method. Our overview shows that structure-based virtual screening can discover novel leads and will be essential in pursuing the next generation of GPCR drugs. SIGNIFICANCE STATEMENT: Extraordinary advances in the structural biology of G protein-coupled receptors have revealed the molecular details of ligand recognition by this large family of therapeutic targets, providing novel avenues for rational drug design. Structure-based docking is an efficient computational approach to identify novel chemical probes from large compound libraries, which has the potential to accelerate the development of drug candidates.

Ligand design by targeting a binding site water

Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood. We investigated how altered interactions with a water network can influence ligand binding to a receptor. A series of ligands of the A_2A adenosine receptor, which either interacted with or displaced an ordered binding site water, were studied experimentally and by molecular dynamics simulations. An analog of the endogenous ligand that was unable to hydrogen bond to the ordered water lost affinity and this activity cliff was captured by molecular dynamics simulations. Two compounds designed to displace the ordered water from the binding site were then synthesized and evaluated experimentally, leading to the discovery of an A_2A agonist with nanomolar activity. Calculation of the thermodynamic profiles resulting from introducing substituents that interacted with or displaced the ordered water showed that the gain of binding affinity was enthalpy driven. Detailed analysis of the energetics and binding site hydration networks revealed that the enthalpy change was governed by contributions that are commonly neglected in structure-based drug optimization. In particular, simulations suggested that displacement of water from a binding site to the bulk solvent can lead to large energy contributions. Our findings provide insights into the molecular driving forces of protein–ligand binding and strategies for rational drug design.

Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood.

In Silico Drug Design for Purinergic GPCRs: Overview on Molecular Dynamics Applied to Adenosine and P2Y Receptors

Molecular modeling has contributed to drug discovery for purinergic GPCRs, including adenosine receptors (ARs) and P2Y receptors (P2YRs). Experimental structures and homology modeling have proven to be useful in understanding and predicting structure activity relationships (SAR) of agonists and antagonists. This review provides an excursus on molecular dynamics (MD) simulations applied to ARs and P2YRs. The binding modes of newly synthesized A1AR- and A3AR-selective nucleoside derivatives, potentially of use against depression and inflammation, respectively, have been predicted to recapitulate their SAR and the species dependence of A3AR affinity. P2Y12R and P2Y1R crystallographic structures, respectively, have provided a detailed understanding of the recognition of anti-inflammatory P2Y14R antagonists and a large group of allosteric and orthosteric antagonists of P2Y1R, an antithrombotic and neuroprotective target. MD of A2AAR (an anticancer and neuroprotective target), A3AR, and P2Y1R has identified microswitches that are putatively involved in receptor activation. The approach pathways of different ligands toward A2AAR and P2Y1R binding sites have also been explored. A1AR, A2AAR, and A3AR were utilizes to study allosteric phenomena, but locating the binding site of structurally diverse allosteric modulators, such as an A3AR enhancer LUF6000, is challenging. Ligand residence time, a predictor of in vivo efficacy, and the structural role of water were investigated through A2AAR MD simulations. Thus, new MD and other modeling algorithms have contributed to purinergic GPCR drug discovery.

Molecular Dynamics Simulations of Adenosine Receptors: Advances, Applications and Trends

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Adenosine receptors (ARs) are transmembrane proteins that belong to the G protein-coupled receptors (GPCRs) superfamily and mediate the biological functions of adenosine. To date, four AR subtypes are known, namely A1, A2A, A2B and A3 that exhibit different signaling pathways, tissue localization, and mechanisms of activation. Moreover, the widespread ARs and their implication in numerous physiological and pathophysiological conditions had made them pivotal therapeutic targets for developing clinically effective agents.

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The crystallographic success in identifying the 3D crystal structures of A2A and A1 ARs has dramatically enriched our understanding of their structural and functional properties such as ligand binding and signal transduction. This, in turn, has provided a structural basis for a larger contribution of computational methods, particularly molecular dynamics (MD) simulations, toward further investigation of their molecular properties and designing bioactive ligands with therapeutic potential. MD simulation has been proved to be an invaluable tool in investigating ARs and providing answers to some critical questions. For example, MD has been applied in studying ARs in terms of ligand-receptor interactions, molecular recognition, allosteric modulations, dimerization, and mechanisms of activation, collectively aiding in the design of subtype selective ligands.

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In this review, we focused on the advances and different applications of MD simulations utilized to study the structural and functional aspects of ARs that can foster the structure-based design of drug candidates. In addition, relevant literature was briefly discussed which establishes a starting point for future advances in the field of drug discovery to this pivotal group of drug targets.

Supervised Molecular Dynamics (SuMD) Approaches in Drug Design

Supervised MD (SuMD) is a computational method that enables the exploration of ligand-receptor recognition pathway in a reduced timescale. The performance speedup is due to the incorporation of a tabu-like supervision algorithm on the ligand-receptor approaching distance into a classic molecular dynamics (MD) simulation. SuMD enables the investigation of ligand-receptor binding events independently from the starting position, chemical structure of the ligand (small molecules or peptides), and also from its receptor-binding affinity. The application of SuMD highlights an appreciable capability of the technique to reproduce the crystallographic structures of several ligand-protein complexes and can provide high-quality protein-ligand models of for which yet experimental confirmation of binding mode is not available.

Current and Future Challenges in GPCR Drug Discovery

GPCRs play a pervasive physiological role and, in turn, are the leading target class for pharmaceuticals. Beginning with the determination of the structure of rhodopsin, and dramatically accelerating since the reporting of the first ligand-mediated GPCR X-ray structures, our understanding of the structural and functional characteristics of these proteins has grown dramatically. Deploying this now rapidly emerging information for drug discovery has already been extensively demonstrated through a watershed of studies appearing in numerous scientific reports. Included in these expositions are areas such as sites and characteristics of ligand to GPCR binding, protein activation, effector bias, allosteric mechanisms, dimerization, polypharmacology and others. Computational chemistry studies are demonstrating an increasing role in capitalizing on the structural studies to further advance our understanding of these proteins as well as to drive drug discovery. Such drug discovery activities range from the design of orthosteric site inhibitors through, for example, allosteric modulators, biased ligands, partial agonists and bitopic ligands. Herein, these topics are outlined through specific examples in the hopes of providing a glimpse of the state of the field.

Design, synthesis and evaluation of 2-aryl benzoxazoles as promising hit for the A2A receptor

The development of adenosine A2A receptor antagonists has received much interest in recent years for the treatment of neurodegenerative diseases. Based on docking studies, a new series of 2-arylbenzoxazoles has been identified as potential A2AR antagonists. Structure-affinity relationship was investigated in position 2, 5 and 6 of the benzoxazole heterocycle leading to compounds with a micromolar affinity towards the A2A receptor. Compound F1, with an affinity of 1 μm, presented good absorption, distribution, metabolism and excretion properties with an excellent aqueous solubility (184 μm) without being cytotoxic at 100 μm. This compound, along with low-molecular weight compound D1 (Ki = 10 μm), can be easily modulated and thus considered as relevant starting points for further hit-to-lead optimisation.

Ultraslow Water-Mediated Transmembrane Interactions Regulate the Activation of A2A Adenosine Receptor

Water molecules inside a G-protein coupled receptor (GPCR) have recently been spotlighted in a series of crystal structures. To decipher the dynamics and functional roles of internal water molecules in GPCR activity, we studied the A2A adenosine receptor using microsecond molecular-dynamics simulations. Our study finds that the amount of water flux across the transmembrane (TM) domain varies depending on the receptor state, and that the water molecules of the TM channel in the active state flow three times more slowly than those in the inactive state. Depending on the location in solvent-protein interface as well as the receptor state, the average residence time of water in each residue varies from ∼O(10(2)) ps to ∼O(10(2)) ns. Especially, water molecules, exhibiting ultraslow relaxation (∼O(10(2)) ns) in the active state, are found around the microswitch residues that are considered activity hotspots for GPCR function. A continuous allosteric network spanning the TM domain, arising from water-mediated contacts, is unique in the active state, underscoring the importance of slow water molecules in the activation of GPCRs.

New Trends in Inspecting GPCR-ligand Recognition Process: the Contribution of the Molecular Modeling Section (MMS) at the University of Padova

In this review, we present a survey of the recent advances carried out by our research groups in the field of ligand-GPCRs recognition process simulations recently implemented at the Molecular Modeling Section (MMS) of the University of Padova. We briefly describe a platform of tools we have tuned to aid the identification of novel GPCRs binders and the better understanding of their binding mechanisms, based on two extensively used computational techniques such as molecular docking and MD simulations. The developed methodologies encompass: (i) the selection of suitable protocols for docking studies, (ii) the exploration of the dynamical evolution of ligand-protein interaction networks, (iii) the detailed investigation of the role of water molecules upon ligand binding, and (iv) a glance at the way the ligand might go through prior reaching the binding site.

Modeling ligand recognition at the P2Y12 receptor in light of X-ray structural information

The G protein-coupled P2Y12 receptor (P2Y12R) is an important antithrombotic target and of great interest for pharmaceutical discovery. Its recently solved, highly divergent crystallographic structures in complex either with nucleotides (full or partial agonist) or with a nonnucleotide antagonist raise the question of which structure is more useful to understand ligand recognition. Therefore, we performed extensive molecular modeling studies based on these structures and mutagenesis, to predict the binding modes of major classes of P2Y12R ligands previously reported. Various nucleotide derivatives docked readily to the agonist-bound P2Y12R, but uncharged nucleotide-like antagonist ticagrelor required a hybrid receptor resembling the agonist-bound P2Y12R except for the top portion of TM6. Supervised molecular dynamics (SuMD) of ticagrelor binding indicated interactions with the extracellular regions of P2Y12R, defining possible meta-binding sites. Ureas, sulfonylureas, sulfonamides, anthraquinones and glutamic acid piperazines docked readily to the antagonist-bound P2Y12R. Docking dinucleotides at both agonist- and antagonist-bound structures suggested interactions with two P2Y12R pockets. Thus, our structure-based approach consistently rationalized the main structure-activity relationships within each ligand class, giving useful information for designing improved ligands.

Molecular docking screening using agonist-bound GPCR structures: probing the A2A adenosine receptor

Crystal structures of G protein-coupled receptors (GPCRs) have recently revealed the molecular basis of ligand binding and activation, which has provided exciting opportunities for structure-based drug design. The A2A adenosine receptor (A2AAR) is a promising therapeutic target for cardiovascular diseases, but progress in this area is limited by the lack of novel agonist scaffolds. We carried out docking screens of 6.7 million commercially available molecules against active-like conformations of the A2AAR to investigate whether these structures could guide the discovery of agonists. Nine out of the 20 predicted agonists were confirmed to be A2AAR ligands, but none of these activated the ARs. The difficulties in discovering AR agonists using structure-based methods originated from limited atomic-level understanding of the activation mechanism and a chemical bias toward antagonists in the screened library. In particular, the composition of the screened library was found to strongly reduce the likelihood of identifying AR agonists, which reflected the high ligand complexity required for receptor activation. Extension of this analysis to other pharmaceutically relevant GPCRs suggested that library screening may not be suitable for targets requiring a complex receptor-ligand interaction network. Our results provide specific directions for the future development of novel A2AAR agonists and general strategies for structure-based drug discovery.

Alternative quality assessment strategy to compare performances of GPCR-ligand docking protocols: the human adenosine A(2A) receptor as a case study

The progress made in the field of G protein-coupled receptors (GPCRs) structural determination has increased the adoption of docking-driven approaches for the identification or optimization of novel potent and selective ligands. In this work, we compared the performances of the 16 different docking/scoring combinations using the recently released crystal structures of the human A2A AR (hA2A AR) in complex with both agonists and antagonists. The proposed evaluation strategy encompasses the use of three complementary "quality descriptors": (a) the number of conformations generated by a docking algorithm having a RMSD value lower than the crystal structure resolution (R); (b) a novel consensus-based function defined as "protocol score"; and (c) the interaction energy maps (IEMs) analysis, based on the identification of key ligand-receptor interactions observed in the crystal structures.