Advances in Computational Techniques to Study GPCR-Ligand Recognition

G-protein-coupled receptors (GPCRs) are among the most intensely investigated drug targets. The recent revolutions in protein engineering and molecular modeling algorithms have overturned the research paradigm in the GPCR field. While the numerous ligand-bound X-ray structures determined have provided invaluable insights into GPCR structure and function, the development of algorithms exploiting graphics processing units (GPUs) has made the simulation of GPCRs in explicit lipid-water environments feasible within reasonable computation times. In this review we present a survey of the recent advances in structure-based drug design approaches with a particular emphasis on the elucidation of the ligand recognition process in class A GPCRs by means of membrane molecular dynamics (MD) simulations

5,7-Disubstituted-[1,2,4]triazolo[1,5-a][1,3,5]triazines as pharmacological tools to explore the antagonist selectivity profiles toward adenosine receptors

The structureeactivity relationship of new 5,7-disubstituted-[1,2,4]triazolo[1,5-a][1,3,5]triazines as adenosine receptors (ARs) antagonists has been explored. The introduction of a benzylamino group at C5 with a free amino group at C7 increases the affinity toward all the ARs subtypes (10: KihA1 \ubc 94.6 nM; KihA2A \ubc 1.11 nM; IC50hA2B \ubc 2214 nM; KihA3 \ubc 30.8 nM). Replacing the free amino group at C7 with a phenylureido moiety yields a potent and quite selective hA2A AR antagonist (14: hA2A AR Ki \ubc 1.44 nM; hA1/hA2A \ubc 216.0; hA3/hA2A \ubc 20.6). This trend diverges from the analysis on the pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidine series previously reported. With the help of an in silico receptor-driven approach, we have rationalized these observations and elucidated from a molecular point of view the role of the benzylamino group at C5 in determining affinity toward the hA2A AR

Conjugates between minor groove binders and Zn(II)-tach complexes: Synthesis, characterization, and interaction with plasmid DNA

A new family of conjugates between a Zn(II)-tach complex and (indole)(2) or benzofuran-indole amide minor groove binders connected through alkyl or oxyethyl linkers of different lengths has been prepared. The conjugates bind strongly to DNA. However, the complexation to DNA to promote the Zn(II) catalyzed hydrolytic cleavage of the DNA results instead in its inhibition. This inhibition effect has been confirmed also using Cu(II). Modeling studies suggest that in the most stable complex conformation, the minor groove binder and the linker lie in the minor groove hampering the interaction between the metal complex and the phosphate backbone of DNA. Therefore, the linear arrangement of minor groove binder-linker-metal complex appears to be effective to ensure tight binding but unproductive from a hydrolytic point of view. (C) 2017 Elsevier Ltd. All rights reserved

Structural Probing and Molecular Modeling of the A3 Adenosine Receptor: A Focus on Agonist Binding

Adenosine is an endogenous modulator exerting its functions through the activation of four adenosine receptor (AR) subtypes, termed A1, A2A, A2B and A3, which belong to the G protein-coupled receptor (GPCR) superfamily. The human A3AR (hA3AR) subtype is implicated in several cytoprotective functions. Therefore, hA3AR modulators, and in particular agonists, are sought for their potential application as anti-inflammatory, anticancer, and cardioprotective agents. Structure-based molecular modeling techniques have been applied over the years to rationalize the structure–activity relationships (SARs) of newly emerged A3AR ligands, guide the subsequent lead optimization, and interpret site-directed mutagenesis (SDM) data from a molecular perspective. In this review, we showcase selected modeling-based and guided strategies that were applied to elucidate the binding of agonists to the A3AR and discuss the challenges associated with an accurate prediction of the receptor extracellular vestibule through homology modeling from the available X-ray templates

A QM/MM study of the binding of RAPTA ligands to cathepsin B

We have carried out quantum mechanical (QM) and QM/MM (combined QM and molecular mechanics) calculations, as well as molecular dynamics (MD) simulations to study the binding of a series of six RAPTA (Ru(II)-arene-1,3,5-triaza-7-phosphatricyclo-[3.3.1.1] decane) complexes with different arene substituents to cathepsin B. The recently developed QM/MM-PBSA approach (QM/MM combined with Poisson-Boltzmann solvent-accessible surface area solvation) has been used to estimate binding affinities. The QM calculations reproduce the antitumour activities of the complexes with a correlation coefficient (r(2)) of 0.35-0.86 after a conformational search. The QM/MM-PBSA method gave a better correlation (r(2) = 0.59) when the protein was fixed to the crystal structure, but more reasonable ligand structures and absolute binding energies were obtained if the protein was allowed to relax, indicating that the ligands are strained when the protein is kept fixed. In addition, the best correlation (r(2) = 0.80) was obtained when only the QM energies were used, which suggests that the MM and continuum solvation energies are not accurate enough to predict the binding of a charged metal complex to a charged protein. Taking into account the protein flexibility by means of MD simulations slightly improves the correlation (r(2) = 0.91), but the absolute energies are still too large and the results are sensitive to the details in the calculations, illustrating that it is hard to obtain stable predictions when full flexible protein is included in the calculations

Activation of carboplatin by chloride ions: a theoretical investigation

We carried out a theoretical study to investigate the thermodynamics and the kinetics of the reaction of the anticancer drug carboplatin with chloride ions, of potential interest to clarify the in vivo mechanism of action of this compound. The reaction consists of two consecutive substitution steps that lead to the removal of the malonate moiety and the formation of cisplatin. Because the acidity of the solution seems to play an important role on the actual outcome and rate of the reaction, different pH conditions (corresponding to neutral, weakly acidic, and strongly acidic environments) have been investigated, by considering differently protonated species. Our results are in good agreement with the few experimental evidences, indicating that the process is very unlikely to occur in neutral or weak acidic media, whereas a concentrated acidic environment leads to the fast and irreversible conversion of carboplatin to cisplatin

In silico 3D modeling of binding activities

In silico three-dimensional (3D) molecular modeling tools based upon the receptor/enzyme-ligand docking simulation in protein crystal structures and/or homology modeling of receptors have been reliably used in pharmacological research and development for decades. Molecular docking methodologies are helpful for revealing facets of activation and inactivation, thus improving mechanistic understanding and predicting molecular ligand binding activity, and they can have a high level of accuracy, and have also been explored and applied in chemical risk assessment. This computational approach is, however, only applicable for chemical hazard identification situations where the specific target receptor for a given chemical is known and the crystal structure/homology model of the receptor is available

Pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidines and Structurally Simplified Analogs. Chemistry and SAR Profile as Adenosine Receptor Antagonists

A review.  Adenosine was defined as a neuromodulator which exerts its action by interaction with specific G-protein coupled receptor termed adenosine receptors.  Adenosine receptors are expressed in several tissues and cells of our body and exist as four different subtypes of these receptors: A1, A2A, A2B and A3.  In the last years significant efforts were made to obtain highly potent and selective ligands for the four adenosine receptors subtypes.  Both agonists and antagonists were used as pharmacol. tools to study therapeutic implications of enhancing or blocking the adenosine receptors activity, and some of these compds. have reached clin. phases.  The pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidines (PTPs) represent one of the several templates designed as adenosine receptor antagonists.  A lot of synthetic work was made on this scaffold in order to obtain potent A2A and A3 antagonists.  Here were reviewed the synthetic approaches followed by both academia and industry to introduce different substituents at different positions of the PTP nucleus, in particular at the 2, 5, 7, 8 and 9 positions.  Nevertheless PTP derivs. are tricyclic compds. with a high mol. wt. which exhibit limitations such as poor aq. soly. and difficult synthetic prepn.  With the aim to obtain derivs. with the same potency and selectivity of PTP but with better drug-like properties, researchers made structural simplification of this scaffold.  Replacement of the pyrazole or triazole rings of PTP led to the [1,2,4]triazolo[1,5-c]pyrimidine and pyrazolo[3,4- d]pyrimidine derivs., resp.  Synthetic strategies for these compds. were reported, combined with the SAR profile on the adenosine receptors