Adenosine A1 receptor antagonists in clinical research and development

DEDTI versus IEDTI: efficient and predictive models of drug-target interactions

Drug repurposing is an active area of research that aims to decrease the cost and time of drug development. Most of those efforts are primarily concerned with the prediction of drug-target interactions. Many evaluation models, from matrix factorization to more cutting-edge deep neural networks, have come to the scene to identify such relations. Some predictive models are devoted to the prediction's quality, and others are devoted to the efficiency of the predictive models, e.g., embedding generation. In this work, we propose new representations of drugs and targets useful for more prediction and analysis. Using these representations, we propose two inductive, deep network models of IEDTI and DEDTI for drug-target interaction prediction. Both of them use the accumulation of new representations. The IEDTI takes advantage of triplet and maps the input accumulated similarity features into meaningful embedding corresponding vectors. Then, it applies a deep predictive model to each drug-target pair to evaluate their interaction. The DEDTI directly uses the accumulated similarity feature vectors of drugs and targets and applies a predictive model on each pair to identify their interactions. We have done a comprehensive simulation on the DTINet dataset as well as gold standard datasets, and the results show that DEDTI outperforms IEDTI and the state-of-the-art models. In addition, we conduct a docking study on new predicted interactions between two drug-target pairs, and the results confirm acceptable drug-target binding affinity between both predicted pairs.

Reversal of Tau-Dependent Cognitive Decay by Blocking Adenosine A1 Receptors: Comparison of Transgenic Mouse Models with Different Levels of Tauopathy

The accumulation of tau is a hallmark of several neurodegenerative diseases and is associated with neuronal hypoactivity and presynaptic dysfunction. Oral administration of the adenosine A₁ receptor antagonist rolofylline (KW-3902) has previously been shown to reverse spatial memory deficits and to normalize the basic synaptic transmission in a mouse line expressing full-length pro-aggregant tau (Tau^ΔK) at low levels, with late onset of disease. However, the efficacy of treatment remained to be explored for cases of more aggressive tauopathy. Using a combination of behavioral assays, imaging with several PET-tracers, and analysis of brain tissue, we compared the curative reversal of tau pathology by blocking adenosine A1 receptors in three mouse models expressing different types and levels of tau and tau mutants. We show through positron emission tomography using the tracer [¹⁸F]CPFPX (a selective A1 receptor ligand) that intravenous injection of rolofylline effectively blocks A₁ receptors in the brain. Moreover, when administered to Tau^ΔK mice, rolofylline can reverse tau pathology and synaptic decay. The beneficial effects are also observed in a line with more aggressive tau pathology, expressing the amyloidogenic repeat domain of tau (TauRD^ΔK) with higher aggregation propensity. Both models develop a progressive tau pathology with missorting, phosphorylation, accumulation of tau, loss of synapses, and cognitive decline. TauRD^ΔK causes pronounced neurofibrillary tangle assembly concomitant with neuronal death, whereas Tau^ΔK accumulates only to tau pretangles without overt neuronal loss. A third model tested, the rTg4510 line, has a high expression of mutant Tau^P301L and hence a very aggressive phenotype starting at ~3 months of age. This line failed to reverse pathology upon rolofylline treatment, consistent with a higher accumulation of tau-specific PET tracers and inflammation. In conclusion, blocking adenosine A1 receptors by rolofylline can reverse pathology if the pathological potential of tau remains below a threshold value that depends on concentration and aggregation propensity.

Structure-based virtual screening discovers potent and selective adenosine A1 receptor antagonists

Development of subtype-selective leads is essential in drug discovery campaigns targeting G protein-coupled receptors (GPCRs). Herein, a structure-based virtual screening approach to rationally design subtype-selective ligands was applied to the A₁ and A_2A adenosine receptors (A₁R and A_2AR). Crystal structures of these closely related subtypes revealed a non-conserved subpocket in the binding sites that could be exploited to identify A₁R selective ligands. A library of 4.6 million compounds was screened computationally against both receptors using molecular docking and 20 A₁R selective ligands were predicted. Of these, seven antagonized the A₁R with micromolar activities and several compounds displayed slight selectivity for this subtype. Twenty-seven analogs of two discovered scaffolds were designed, resulting in antagonists with nanomolar potency and up to 76-fold A₁R-selectivity. Our results show the potential of structure-based virtual screening to guide discovery and optimization of subtype-selective ligands, which could facilitate the development of safer drugs.

The role of adenosine A1 receptor on immune cells

BACKGROUND

Adenosine, acting as a regulator by mediating the activation of G protein-coupled adenosine receptor families (A₁, A₂A, A₂B, and A₃), plays an important role under physiological and pathological conditions. As the receptor with the highest affinity for adenosine, the role of adenosine A₁ receptor (A₁R)-mediated adenosine signaling pathway in the central nervous system has been well addressed. However, functions of A₁R on immune cells are less summarized. Considering that some immune cells express multiple types of adenosine receptors with distinct effects and varied density, exogenous adenosine of different concentrations may induce divergent immune cell functions.

MATERIALS AND METHODS

The literatures about the expression of A₁R and its regulation on immune cells and how it regulates the function of immune cells were searched on PubMed and Google Scholar.

CONCLUSION

In this review, we discussed the effects of A₁R on immune cells, including monocytes, macrophages, neutrophils, dendritic cells, and microglia, and focused on the role of A₁R in regulating immune cells in diseases, which may facilitate our understanding of the mechanisms by which adenosine affects immune cells through A₁R.

Insights of Worsening Renal Function in Type 1 Cardiorenal Syndrome: From the Pathogenesis, Biomarkers to Treatment

Type-1 cardiorenal syndrome refers to acute kidney injury induced by acute worsening cardiac function. Worsening renal function is a strong and independent predictive factor for poor prognosis. Currently, several problems of the type-1 cardiorenal syndrome have not been fully elucidated. The pathogenesis mechanism of renal dysfunction is unclear. Besides, the diagnostic efficiency, sensitivity, and specificity of the existing biomarkers are doubtful. Furthermore, the renal safety of the therapeutic strategies for acute heart failure (AHF) is still ambiguous. Based on these issues, we systematically summarized and depicted the research actualities and predicaments of the pathogenesis, diagnostic markers, and therapeutic strategies of worsening renal function in type-1 cardiorenal syndrome.

In silico investigation of the selectivity mechanism of A1AR and A2AAR antagonism

Adenosine A1 receptor (A1AR) and adenosine A2A receptor (A2AAR) are AR isoforms that share high homology but play many different roles in terms of regulating arteriolar pressure and urine flow as well as relieving neurodegenerative disorders.

Adenosine receptor antagonists: Recent advances and therapeutic perspective

Adenosine is an endogenous purine-based nucleoside expressed nearly in all body tissues. It regulates various body functions by activating four G-protein coupled receptors, A₁, A_2A, A_2B, and A₃. These receptors are widely acknowledged as drug targets for treating different neurological, metabolic, and inflammatory diseases. Although numerous adenosine receptor inhibitors have been developed worldwide, achieving target selectivity is still a big hurdle in drug development. However, the identification of specific radioligands-based affinity assay, fluorescent ligands, and MS-based ligand assay have contributed to the development of selective and potent adenosine ligands. In recent years various small heterocyclic-based molecules have shown some promising results. Istradefylline has been approved for treating Parkinson's in Japan, while preladenant, tozadenant, CVT-6883, MRS-1523, and many more are under different phases of clinical development. The present review is focused on the quest to develop potent and selective adenosine inhibitors from 2013 to early 2021 by various research groups. The review also highlights their biological activity, selectivity, structure-activity relationship, molecular docking, and mechanistic studies. A special emphsesis on drug designing strategies has been also given the manuscript. The comprehensive compilation of research work carried out in the field will provide inevitable scope for designing and developing novel adenosine inhibitors with improved selectivity and efficacy.

CD26 expression and adenosine deaminase activity in regulatory T cells (Treg) and CD4(+) T effector cells in patients with head and neck squamous cell carcinoma

Adenosine deaminase (ADA) is responsible for the deamination of immunosuppressive adenosine to inosine. In human T lymphocytes, ADA is associated with dipeptidyl peptidase IV (CD26). ADA expression and activity were evaluated in regulatory T cells (Treg) and CD4(+) T effector cells (Teff) of patients with head and neck squamous cell cancer (HNSCC). CD4(+)CD39(+) and CD4(+)CD39(neg) T cells were isolated by single-cell sorting from the peripheral blood of 15 HNSCC patients and 15 healthy donors (NC). CD26/ADA expression in these cells was studied by multicolor flow cytometry, confocal microscopy, RT-PCR and immunohistochemistry in tumor tissues. ADA activity was evaluated by mass spectrometry, suppression of Teff proliferation in CFSE assays and cytokine production by Luminex. CD4(+)CD39(+) Treg had low and CD4(+)CD39(neg) Teff high CD26/ADA expression and ADA activity in NC or HNSCC. The frequency and suppressor activity of CD39(+)CD26(neg) Treg were elevated in patients relative to NC (p < 0.01). However, ADA activity in patients' CD4(+)CD39(neg) Teff was decreased (p < 0.05), resulting in extracellular adenosine accumulation. Also, patients' Teff were more sensitive to inhibitory signals delivered via adenosine receptors. IL-2, IL12 and INFγ upregulated ADA expression and activity in CD4(+)CD39(neg) Teff, whereas IL-10, PGE(2) and CADO downregulated it. The differentially expressed CD26/ADA can serve as surface markers for functionally-active CD39(+)CD26(neg) Treg.

Modern trends in diuretics development

Diuretics are the first-line therapy for widespread cardiovascular and non-cardiovascular diseases. Traditional diuretics are commonly prescribed for treatment in patients with hypertension, edema and heart failure, as well as with a number of kidney problems. They are diseases with high mortality, and the number of patients suffering from heart and kidney diseases is increasing year by year. The use of several classes of diuretics currently available for clinical use exhibits an overall favorable risk/benefit balance. However, they are not devoid of side effects. Hence, pharmaceutical researchers have been making efforts to develop new drugs with a better pharmacological profile. High-throughput screening, progress in protein structure analysis and modern methods of chemical modification have opened good possibilities for identification of new promising agents for preclinical and clinical testing. In this review, we provide an overview of the medicinal chemistry approaches toward the development of small molecule compounds showing diuretic activity that have been discovered over the past decade and are interesting drug candidates. We have discussed promising natriuretics/aquaretics/osmotic diuretics from such classes as: vasopressin receptor antagonists, SGLT2 inhibitors, urea transporters inhibitors, aquaporin antagonists, adenosine receptor antagonists, natriuretic peptide receptor agonists, ROMK inhibitors, WNK-SPAK inhibitors, and pendrin inhibitors.

"Adenosine an old player with new possibilities in kidney diseases": Preclinical evidences and clinical perspectives

Renal injury might originate from multiple factors like ischemia reperfusion (I/R), drug toxicity, cystic fibrosis, radio contrast agent etc. The four adenosine receptor subtypes have been identified and found to show diverse physiological and pathological roles in kidney diseases. The activation of A₁ adenosine receptor (A₁) protects against acute kidney injury by improving renal hemodynamic alterations, decreasing tubular necrosis and its inhibition might facilitate removal of toxin or drug metabolite in chronic kidney disease models. Furthermore, recent findings revealed that A_2A receptor subtype activation regulates macrophage phenotype in experimental models of nephritis. Interestingly the emerging role of adenosine kinase inhibitors in kidney diseases has been discussed which act by increasing adenosine availability at target sites and thereby promote A_2A receptor stimulation. In addition, the least explored adenosine receptor subtype A₃ inhibition was observed to exert anti- oxidant, immunosuppressive and anti-fibrotic effects, but more studies are required to confirm its benefits in other renal injury models. The clinical studies targeting A₁ receptor in patients with pre-existing kidney disease have yielded disappointing results, perhaps owing to the origin of unexpected neurological complications during the course of trial. Importantly, conducting well designed clinical trials and testing adenosine modulators with lesser brain penetrability could clear the way for clinical approval of these agents for patients with renal functional impairments.

Diabetes Affects the A1 Adenosine Receptor-Dependent Action of Diadenosine Tetraphosphate (Ap4A) on Cortical and Medullary Renal Blood Flow

Diabetes through adenosine A1 receptor (A1R) and P2 receptors (P2Rs) may lead to disturbances in renal microvasculature. We investigated the renal microvascular response to Ap4A, an agonist of P2Rs, in streptozotocin-induced diabetic rats. Using laser Doppler flowmetry, renal blood perfusion (RBP) was measured during infusion of Ap4A alone or in the presence of A1R antagonist, either DPCPX (8-cyclopentyl-1,3-dipropylxanthine) or 8-cyclopentyltheophylline (CPT). Ap4A induced a biphasic response in RBP: a phase of rapid decrease was followed by a rapid increase, which was transient in diabetic rats but extended for 30 min in nondiabetic rats. Phase of decreased RBP was not affected by DPCPX or CPT in either group. Early and extended increases in RBP were prevented by DPCPX and CPT in nondiabetic rats, while in diabetic rats, the early increase in RBP was not affected by these antagonists. A1R mRNA and protein levels were increased in isolated glomeruli of diabetic rats, but no changes were detected in P2Y1R and P2Y2R mRNA. Presence of unblocked A1R is a prerequisite for the P2R-mediated relaxing effect of Ap4A in nondiabetic conditions, but influence of A1R on P2R-mediated renal vasorelaxation is abolished under diabetic conditions.

Differential expression, function and prognostic value of miR-17-92 cluster in ER-positive and triple-negative breast cancer

Recent evidence has shown that the miR-17-92 cluster can function either as oncogene or tumor suppressor in human cancers. The function of miR-17-92 in subtypes of breast cancer remains largely unknown. The expression of miR-17-92 is elevated in triple negative breast cancer (TNBC) but reduced in estrogen receptor (ER)-positive breast cancer (ERPBC). We show that increased expression of miRNAs belonging to the miR-17-92 cluster is associated with poor outcome in TNBC, whereas the expression of miR-17-92 miRNAs is with good outcome in ERPBC. We show that ectopic expression of miR-17-92 inhibited cell growth and invasion of ER-positive and HER2-enriched cells. On the contrary, miR-17-92 expression enhanced cell growth and invasion of TNBC cells. Further, we found that miR-17-92 expression sensitized MCF7 cells to chemotherapeutic compounds, whereas it rendered SKBR3 cells resistant to them. We found that expression of ADORA1 was reduced by miR-17-92-expressing breast cancer cells, specifically in ERPBC. We observed an inverse correlation between the expression of ADORA1 and miR-17-92 in human breast cancer. Treatment with DPCPX, a selective ADORA1 antagonist, abolished the difference in the growth of control and miR-17-92 overexpressing MCF7 cells and identified ADORA1 as a key functional target of miR-17-92 in ERPBC. Furthermore, increased expression of ADORA1 in ERPBC is associated with a poor outcome. Our observations underscore the context-dependent role of miR-17-92 in breast cancer subtypes and suggest that miR-17-92 could serve as novel prognostic markers in breast cancer.

Medicinal Chemistry and Therapeutic Potential of Agonists, Antagonists and Allosteric Modulators of A1 Adenosine Receptor: Current Status and Perspectives

Adenosine is a purine nucleoside, responsible for the regulation of a wide range of physiological and pathophysiological conditions by binding with four G-protein-coupled receptors (GPCRs), namely A1, A2A, A2B and A3 adenosine receptors (ARs). In particular, A1 AR is ubiquitously present, mediating a variety of physiological processes throughout the body, thus represents a promising drug target for the management of various pathological conditions. Agonists of A1 AR are found to be useful for the treatment of atrial arrhythmia, angina, type-2 diabetes, glaucoma, neuropathic pain, epilepsy, depression and Huntington's disease, whereas antagonists are being investigated for the treatment of diuresis, congestive heart failure, asthma, COPD, anxiety and dementia. However, treatment with full A1 AR agonists has been associated with numerous challenges like cardiovascular side effects, off-target activation as well as desensitization of A1 AR leading to tachyphylaxis. In this regard, partial agonists of A1 AR have been found to be beneficial in enhancing insulin sensitivity and subsequently reducing blood glucose level, while avoiding severe CVS side effects and tachyphylaxis. Allosteric enhancer of A1 AR is found to be potent for the treatment of neuropathic pain, culminating the side effects related to off-target tissue activation of A1 AR. This review provides an overview of the medicinal chemistry and therapeutic potential of various agonists/partial agonists, antagonists and allosteric modulators of A1 AR, with a particular emphasis on their current status and future perspectives in clinical settings.

How Sure Can We Be about ML Methods-Based Evaluation of Compound Activity: Incorporation of Information about Prediction Uncertainty Using Deep Learning Techniques

A great variety of computational approaches support drug design processes, helping in selection of new potentially active compounds, and optimization of their physicochemical and ADMET properties. Machine learning is a group of methods that are able to evaluate in relatively short time enormous amounts of data. However, the quality of machine-learning-based prediction depends on the data supplied for model training. In this study, we used deep neural networks for the task of compound activity prediction and developed dropout-based approaches for estimating prediction uncertainty. Several types of analyses were performed: the relationships between the prediction error, similarity to the training set, prediction uncertainty, number and standard deviation of activity values were examined. It was tested whether incorporation of information about prediction uncertainty influences compounds ranking based on predicted activity and prediction uncertainty was used to search for the potential errors in the ChEMBL database. The obtained outcome indicates that incorporation of information about uncertainty of compound activity prediction can be of great help during virtual screening experiments.

Identification of new potent A1 adenosine receptor antagonists using a multistage virtual screening approach

The use of antagonists for each adenosine receptor (AR) subtype as potent clinical candidates is of growing interest due to their involvement in the treatment of various diseases. The recent resolution of several A₁ and A_2A ARs X-ray structures provides opportunities for structure-based drug design. In this study, we describe the discovery of novel A₁AR antagonists by applying a multistage virtual screening approach, which is based on random forest (RF), e-pharmacophore modeling and docking methods. A multistage virtual screening approach was applied to screen the ChemDiv library (1,492,362 compounds). Among the final hits, 22 compounds were selected for further radioligand binding assay analysis against human A₁AR, and 18 compounds (81.82% success) exhibited nanomolar or low micromolar binding potency (K_i). Then, we selected six compounds (pK_i > 6) to further evaluate their antagonist profile in a cAMP functional assay, and we found that they had low micromolar antagonistic activity (pIC₅₀ = 5.51-6.38) for the A₁AR. Particularly, four of six compounds (pK_i > 6) showed very good affinity (pK_i = 6.11-7.13) and selectively (>100-fold) for A₁AR over A_2AAR. Moreover, the novelty analysis suggested that four of six compounds (pK_i > 6) were dissimilar to existing A₁AR antagonists and hence represented novel A₁AR antagonists. Further molecular docking and molecular dynamics (MD) studies showed that the three selective compounds 15, 20 and 22 were stabilized (RMS_lig value ≤ 2 Å) inside the binding pocket of A₁AR with similar orientations to the docking pose in 100-ns MD simulations, whereas they escaped from the binding area of A_2AAR with larger values of RMS_lig (RMS_lig ≥ 2 Å). We hope that these findings provide new insights into the discovery of drugs targeting A₁AR and facilitate research on new drugs and treatments for A₁AR-related human pathologies.

Development of New Methods Needs Proper Evaluation-Benchmarking Sets for Machine Learning Experiments for Class A GPCRs

New computational approaches for virtual screening applications are constantly being developed. However, before a particular tool is used to search for new active compounds, its effectiveness in the type of task must be examined. In this study, we conducted a detailed analysis of various aspects of preparation of respective data sets for such an evaluation. We propose a protocol for fetching data from the ChEMBL database, examine various compound representations in terms of the possible bias resulting from the way they are generated, and define a new metric for comparing the structural similarity of compounds, which is in line with chemical intuition. The newly developed method is also used for the evaluation of various approaches for division of the data set into training and test set parts, which are also examined in detail in terms of being the source of possible results bias. Finally, machine learning methods are applied in cross-validation studies of data sets constructed within the paper, constituting benchmarks for the assessment of computational methods developed for virtual screening tasks. Additionally, analogous data sets for class A G protein-coupled receptors (100 targets with the highest number of records) were prepared. They are available at http://gmum.net/benchmarks/ , together with script enabling reproduction of all results available at https://github.com/lesniak43/ananas .

Conjugable A3 adenosine receptor antagonists for the development of functionalized ligands and their use in fluorescent probes

Compounds able to simultaneously bind a biological target and be conjugated to a second specific moiety are attractive tools for the development of multi-purpose ligands useful as multi-target ligands, receptor probes or drug delivery systems, with both therapeutic and diagnostic applications. The human A₃ adenosine receptor is a G protein-coupled receptor involved in many physio-pathological conditions, e.g. cancer and inflammation, thus representing a promising research target. In this work, two series of conjugable hA₃AR antagonists, based on the pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidine nucleus, were developed. The introduction of an aromatic ring at the 5 position of the scaffold, before (phenylacetamido moiety) or after (1,2,3-triazole obtained by click chemistry) the conjugation is aimed to increase affinity and selectivity towards the hA₃AR receptor. As expected, conjugable compounds showed good affinity towards the hA₃AR. In order to prove their potential in the development of hA₃AR ligands for different purposes, compounds were also functionalized with fluorescent probes. Unfortunately, conjugation decreased affinity and selectivity for the target as compared to the hA_2AAR. Computational studies identified specific non-conserved residues of the extracellular loops which constitute a structural barrier able to discriminate between ligands, giving insights into the rational development of new highly selective ligands.

Pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidines to develop functionalized ligands to target adenosine receptors: fluorescent ligands as an example

A series of adenosine receptor antagonists bearing a reactive linker was developed. Functionalization of these derivatives is useful to easily obtain multi-target ligands, receptor probes, drug delivery systems, and diagnostic or theranostic systems. The pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidine scaffold was chosen as a pharmacophore for the adenosine receptors. It was substituted at the 5 position with reactive linkers of different lengths. Then, these compounds were used to synthesise probes for the adenosine receptors by functionalization with a fluorescent moiety. Both series of compounds were evaluated for their binding at the four adenosine receptor subtypes. Different affinity and selectivity profiles were observed towards hA1, hA2A and hA3 adenosine receptors. In particular, fluorescent compounds behave as dual hA2A/hA3 ligands. Computational studies suggested different binding modes for developed compounds at the three receptors. Both molecular docking and supervised molecular dynamics (SuMD) simulations confirmed that the preferred binding mode at the single receptor was driven by the substitution present at the 5 position. Obtained results rationalized the compounds' binding profile at the adenosine receptors and pave the way for the development of more potent conjugable and conjugated ligands targeting these membrane receptors.

Ability of γδ T cells to modulate the Foxp3 T cell response is dependent on adenosine

Whether γδ T cells inhibit or enhance the Foxp3 T cell response depends upon their activation status. The critical enhancing effector in the supernatant is adenosine. Activated γδ T cells express adenosine receptors at high levels, which enables them to deprive Foxp3⁺ T cells of adenosine, and to inhibit their expansion. Meanwhile, cell-free supernatants of γδ T cell cultures enhance Foxp3 T cell expansion. Thus, inhibition and enhancement by γδ T cells of Foxp3 T cell response are a reflection of the balance between adenosine production and absorption by γδ T cells. Non-activated γδ T cells produce adenosine but bind little, and thus enhance the Foxp3 T cell response. Activated γδ T cells express high density of adenosine receptors and have a greatly increased ability to bind adenosine. Extracellular adenosine metabolism and expression of adenosine receptor A2ARs by γδ T cells played a major role in the outcome of γδ and Foxp3 T cell interactions. A better understanding of the functional conversion of γδ T cells could lead to γδ T cell-targeted immunotherapies for related diseases.

New potent and selective A1 adenosine receptor antagonists as potential tools for the treatment of gastrointestinal diseases

The synthesis of 9-alkyl substituted adenine derivatives presenting aromatic groups and cycloalkyl rings in 8- and N⁶-position, respectively, is reported. The compounds were tested with radioligand binding studies showing, in some cases, a low nanomolar A₁ adenosine receptor affinity and a very good selectivity versus the other adenosine receptor subtypes. Functional assays at human adenosine receptors and at a mouse ileum tissue preparation clearly demonstrate the antagonist profile of these molecules, with inhibitory potency at nanomolar level. A molecular modeling study, consisting in docking analysis at the recently reported A₁ adenosine receptor crystal structure, was performed for the interpretation of the obtained pharmacological results. The N⁶-cyclopentyl-9-methyl-8-phenyladenine (17), resulting the most active derivative of the series (K_i = 2.8 nM and IC₅₀ = 14 nM), was also very efficacious in counteracting the effect of the agonist CCPA on mouse ileum contractility. This new compound represents a tool for the development of new agents for the treatment of intestinal diseases as constipation and postoperative ileus.

Safety issues of compounds acting on adenosinergic signalling

OBJECTIVES

Much research has been performed on the field of identifying the roles of adenosine and adenosinergic signalling, but a relatively low number of marketing authorizations have been granted for adenosine receptor (AdR) ligands. In part, this could be related to their safety issues; therefore, our aim was to examine the toxicological and adverse effects data of different compounds acting on adenosinergic signalling, including different AdR ligands and compounds resembling the structure of adenosine. We also wanted to present recent pharmaceutical developments of experimental compounds that showed promising results in clinical trial setting.

KEY FINDINGS

Safety issues of compounds modulating adenosinergic signalling were investigated, and different mechanisms were presented. Structurally different classes of compounds act on AdRs, the most important being adenosine, adenosine derivatives and other non-nucleoside compounds. Many of them are either not selective enough or are targeting other targets of adenosinergic signalling such as metabolizing enzymes that regulate adenosine levels. Many other targets are also involved that are not part of adenosinergic signalling system such as GABA receptors, different channels, enzymes and others. Some synthetic AdR ligands even showed to be genotoxic.

SUMMARY

Current review presents safety data of adenosine, adenosine derivatives and other non-nucleoside compounds that modulate adenosinergic signalling. We have presented different mechanisms that participate to an adverse effect or toxic outcome. A separate section also deals with possible organ-specific toxic effects on different in-vitro and in-vivo models.

Pharmacological reasons that may explain why randomized clinical trials have failed in acute heart failure syndromes

Acute heart failure (AHF) represents a clinical challenge as it encloses a heterogeneous group of syndromes (AHFS) with different pathophysiology, clinical presentations, prognosis and response to therapy. In the last 25years multiple therapeutic targets have been identified and numerous new drugs were evaluated but, up to now, all failed to demonstrate a consistent benefit on clinical outcomes. Moreover, a repeated finding has been the poor correlation between the encouraging results of preclinical and early clinical trials and the lack of effect on outcomes observed in phase III trials. We review several possible pharmacological reasons that may explain the lack of success to develop new drugs and the pharmacological challenges to overcome in the future to develop new more effective and safer drugs for the treatment of AHFS.

Robust optimization of SVM hyperparameters in the classification of bioactive compounds

Background

Support Vector Machine has become one of the most popular machine learning tools used in virtual screening campaigns aimed at finding new drug candidates. Although it can be extremely effective in finding new potentially active compounds, its application requires the optimization of the hyperparameters with which the assessment is being run, particularly the C and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\gamma$$\end{document}γ values. The optimization requirement in turn, establishes the need to develop fast and effective approaches to the optimization procedure, providing the best predictive power of the constructed model.

Results

In this study, we investigated the Bayesian and random search optimization of Support Vector Machine hyperparameters for classifying bioactive compounds. The effectiveness of these strategies was compared with the most popular optimization procedures—grid search and heuristic choice. We demonstrated that Bayesian optimization not only provides better, more efficient classification but is also much faster—the number of iterations it required for reaching optimal predictive performance was the lowest out of the all tested optimization methods. Moreover, for the Bayesian approach, the choice of parameters in subsequent iterations is directed and justified; therefore, the results obtained by using it are constantly improved and the range of hyperparameters tested provides the best overall performance of Support Vector Machine. Additionally, we showed that a random search optimization of hyperparameters leads to significantly better performance than grid search and heuristic-based approaches.

Conclusions

The Bayesian approach to the optimization of Support Vector Machine parameters was demonstrated to outperform other optimization methods for tasks concerned with the bioactivity assessment of chemical compounds. This strategy not only provides a higher accuracy of classification, but is also much faster and more directed than other approaches for optimization. It appears that, despite its simplicity, random search optimization strategy should be used as a second choice if Bayesian approach application is not feasible.Graphical abstract

Exploiting uncertainty measures in compounds activity prediction using support vector machines

The great majority of molecular modeling tasks require the construction of a model that is then used to evaluate new compounds. Although various types of these models exist, at some stage, they all use knowledge about the activity of a given group of compounds, and the performance of the models is dependent on the quality of these data. Biological experiments verifying the activity of chemical compounds are often not reproducible; hence, databases containing these results often possess various activity records for a given molecule. In this study, we developed a method that incorporates the uncertainty of biological tests in machine-learning-based experiments using the Support Vector Machine as a classification model. We show that the developed methodology improves the classification effectiveness in the tested conditions.

Adenosine A1 modulators: a patent update (2008 to present)

INTRODUCTION

In 2008, we published our review titled 'Therapeutic potential of A1 adenosine receptor ligands - a survey of recent patent literature' that reported the compounds active on A1 adenosine receptors (ARs) and the applications of A1 AR ligands patented in the period 2005 - 2008.

AREAS COVERED

This article is a discussion of the patents about the same subjects, issued in the period 2008 to present. It is organized similarly to the first one, with a section about new compounds, subdivided on the basis of their functional activity (agonists, antagonists and allosteric modulators) and a section regarding new therapeutic applications.

EXPERT OPINION

The main novelty is represented by the patenting of A1 AR ligands with dual selectivity which may show, in some conditions, better efficacy and fewer side effects. Moreover, while the way to arrive into the market appears full of obstacles for selective A1 ligands that need systemic administration for long-term therapy, better chances are foreseen in applications requiring topical administration.

Adenosine receptors as drug targets--what are the challenges?

Adenosine signalling has long been a target for drug development, with adenosine itself or its derivatives being used clinically since the 1940s. In addition, methylxanthines such as caffeine have profound biological effects as antagonists at adenosine receptors. Moreover, drugs such as dipyridamole and methotrexate act by enhancing the activation of adenosine receptors. There is strong evidence that adenosine has a functional role in many diseases, and several pharmacological compounds specifically targeting individual adenosine receptors--either directly or indirectly--have now entered the clinic. However, only one adenosine receptor-specific agent--the adenosine A2A receptor agonist regadenoson (Lexiscan; Astellas Pharma)--has so far gained approval from the US Food and Drug Administration (FDA). Here, we focus on the biology of adenosine signalling to identify hurdles in the development of additional pharmacological compounds targeting adenosine receptors and discuss strategies to overcome these challenges.

Loss of A(1) adenosine receptor attenuates alpha-naphthylisothiocyanate-induced cholestatic liver injury in mice

Cholestasis has limited therapeutic options and is associated with high morbidity and mortality. The A(1) adenosine receptor (A(1)AR) was postulated to participate in the pathogenesis of hepatic fibrosis induced by experimental extrahepatic cholestasis; however, the contribution of A(1)AR to intrahepatic cholestatic liver injury remains unknown. Here, we found that mice lacking A(1)AR were resistant to alpha-naphthyl isothiocyanate (ANIT)-induced liver injury, as evidenced by lower serum liver enzyme levels and reduced extent of histological necrosis. Bile acid accumulation in liver and serum was markedly diminished in A(1)AR(-/-) mice compared with wild-type (WT) mice. However, biliary and urinary outputs of bile acids were significantly enhanced in A(1)AR(-/-) mice. In the liver, mRNA expression of genes related to bile acid transport (Bsep and Mdr2) and hydroxylation (Cyp3a11) was increased in A(1)AR(-/-) mice. In the kidney, A(1)AR deficiency prevented the decrease of glomerular filtration rate caused by ANIT. Treatment of WT mice with A(1)AR antagonist DPCPX also protected against ANIT hepatotoxicity. Our results indicated that lack of A(1)AR gene protects mice from ANIT-induced cholestasis by enhancing toxic biliary constituents efflux through biliary excretory route and renal elimination system and suggested a potential role of A(1)AR as therapeutic target for the treatment of intrahepatic cholestasis.

Role of A1 receptors in renal sympathetic neurotransmission in the mouse kidney

A(1) receptors may participate in renal sympathetic neurotransmission by enhancing the postjunctional effects of norepinephrine. The purpose of this study was to test this concept using A(1) receptor knockout (A(1)AR-/-) mice. In isolated kidneys from nontransgenic mice perfused with Tyrode's solution at a constant rate, renal sympathetic nerve stimulation (RSNS) increased (P < 0.0001) renal venous perfusate levels of inosine (adenosine metabolite) from 23.9 ± 3.7 to 32.7 ± 5.1, 68.2 ± 12.4, and 94.0 ± 14.3 ng/ml at 3, 5, and 7 Hz, respectively (n = 28), suggesting frequency-dependent production of adenosine. Conversely, RSNS decreased (P < 0.0001) renal venous perfusate levels of 5'-AMP (adenosine precursor) from 1.4 ± 0.3 to 1.1 ± 0.3, 0.80 ± 0.2, and 0.6 ± 0.2 ng/ml at 3, 5, and 7 Hz, respectively (n = 28), suggesting frequency-dependent increased metabolism of 5'-AMP. In kidneys from nontransgenic mice, blockade of adenosine receptors with 1,3-dipropyl-8-p-sulfophenylxanthine attenuated (P = 0.0130) vasoconstrictor responses to RSNS at 3, 5, and 7 Hz [control (n = 29): 22 ± 4, 34 ± 6, 42 ± 6 mmHg, respectively; 1,3-dipropyl-8-p-sulfophenylxanthine-treated (n = 11): 6 ± 1, 12 ± 3, 15 ± 3 mmHg, respectively]. In A(1)AR-/- kidneys (n = 10), vasoconstrictor responses to RSNS at 3, 5, and 7 Hz were 7 ± 3, 20 ± 5, and 36 ± 9 mmHg, respectively. In kidneys from wild-type littermates (n = 9), responses were 27 ± 9, 58 ± 14, and 59 ± 11 mmHg, respectively (effect of genotype: P = 0.0363). In kidneys from nontransgenic mice, 2-chloro-N(6)-cyclopentyladenosine (CCPA; highly selective A(1) receptor agonist) increased renal vasoconstriction induced by norepinephrine (P = 0.0008; n = 28). In kidneys from A(1)AR-/- the response to norepinephrine was attenuated and the ability of CCPA to enhance responses to norepinephrine was abolished. In conclusion, adenosine formed during RSNS enhances the postjunctional effects of released norepinephrine by activating A(1) receptors.

Endogenous adenosine contributes to renal sympathetic neurotransmission via postjunctional A1 receptor-mediated coincident signaling

Adenosine A(1) receptor antagonists have diuretic/natriuretic activity and may be useful for treating sodium-retaining diseases, many of which are associated with increased renal sympathetic tone. Therefore, it is important to determine whether A(1) receptor antagonists alter renal sympathetic neurotransmission. In isolated, perfused rat kidneys, renal vasoconstriction induced by renal sympathetic nerve simulation was attenuated by 1) 1,3-dipropyl-8-p-sulfophenylxanthine (xanthine analog that is a nonselective adenosine receptor antagonist, but is cell membrane impermeable and thus does not block intracellular phosphodiesterases), 2) xanthine amine congener (xanthine analog that is a selective A(1) receptor antagonist), 3) 1,3-dipropyl-8-cyclopentylxanthine (xanthine analog that is a highly selective A(1) receptor antagonist), and 4) FK453 (nonxanthine analog that is a highly selective A(1) receptor antagonist). In contrast, FR113452 (enantiomer of FK453 that does not block A(1) receptors), MRS-1754 (selective A(2B) receptor antagonist), and VUF-5574 (selective A(3) receptor antagonist) did not alter responses to renal sympathetic nerve stimulation, and ZM-241385 (selective A(2A) receptor antagonist) enhanced responses. Antagonism of A(1) receptors did not alter renal spillover of norepinephrine. 2-Chloro-N(6)-cyclopentyladenosine (highly selective A(1) receptor agonist) increased renal vasoconstriction induced by exogenous norepinephrine, an effect that was blocked by 1,3-dipropyl-8-cyclopentylxanthine, U73122 (phospholipase C inhibitor), GF109203X (protein kinase C inhibitor), PP1 (c-src inhibitor), wortmannin (phosphatidylinositol 3-kinase inhibitor), and OSU-03012 (3-phosphoinositide-dependent protein kinase-1 inhibitor). These results indicate that adenosine formed during renal sympathetic nerve stimulation enhances the postjunctional effects of released norepinephrine via coincident signaling and contributes to renal sympathetic neurotransmission. Likely, the coincident signaling pathway is: phospholipase C → protein kinase C → c-src → phosphatidylinositol 3-kinase → 3-phosphoinositide-dependent protein kinase-1.

Adenosine receptor targeting in health and disease

INTRODUCTION

The adenosine receptors A(1), A(2A), A(2B) and A(3) are important and ubiquitous mediators of cellular signaling that play vital roles in protecting tissues and organs from damage. In particular, adenosine triggers tissue protection and repair by different receptor-mediated mechanisms, including increasing the oxygen supply:demand ratio, pre-conditioning, anti-inflammatory effects and the stimulation of angiogenesis.

AREAS COVERED

The state of the art of the role of adenosine receptors which have been proposed as targets for drug design and discovery, in health and disease, and an overview of the ligands for these receptors in clinical development.

EXPERT OPINION

Selective ligands of A(1), A(2A), A(2B) and A(3) adenosine receptors are likely to find applications in the treatment of pain, ischemic conditions, glaucoma, asthma, arthritis, cancer and other disorders in which inflammation is a feature. The aim of this review is to provide an overview of the present knowledge regarding the role of these adenosine receptors in health and disease.

Adenosine receptors in health and disease

The adenosine receptors A(1), A(2A), A(2B), and A(3) are important and ubiquitous mediators of cellular signaling, which play vital roles in protecting tissues and organs from damage. In particular, adenosine triggers tissue protection and repair by different receptor-mediated mechanisms, including an increase of oxygen supply/demand ratio, preconditioning, anti-inflammatory effects, and stimulation of angiogenesis. Considerable advances have been recently achieved in the pharmacological and molecular characterization of adenosine receptors, which have been proposed as targets for drug design and discovery. At the present time, it can be speculated that adenosine A(1), A(2A), A(2B), and A(3) receptor-selective ligands may show utility in the treatment of pain, ischemic conditions, glaucoma, asthma, arthritis, cancer, and other disorders in which inflammation is a feature. This chapter documents the present state of knowledge of adenosine receptors' role in health and disease.

Recent developments in adenosine receptor ligands and their potential as novel drugs

Medicinal chemical approaches have been applied to all four of the adenosine receptor (AR) subtypes (A(1), A(2A), A(2B), and A(3)) to create selective agonists and antagonists for each. The most recent class of selective AR ligands to be reported is the class of A(2B)AR agonists. The availability of these selective ligands has facilitated research on therapeutic applications of modulating the ARs and in some cases has provided clinical candidates. Prodrug approaches have been developed which improve the bioavailability of the drugs, reduce side-effects, and/or may lead to site-selective effects. The A(2A) agonist regadenoson (Lexiscan®), a diagnostic drug for myocardial perfusion imaging, is the first selective AR agonist to be approved. Other selective agonists and antagonists are or were undergoing clinical trials for a broad range of indications, including capadenoson and tecadenoson (A(1) agonists) for atrial fibrillation, or paroxysmal supraventricular tachycardia, respectively, apadenoson and binodenoson (A(2A) agonists) for myocardial perfusion imaging, preladenant (A(2A) antagonist) for the treatment of Parkinson's disease, and CF101 and CF102 (A(3) agonists) for inflammatory diseases and cancer, respectively.

Targeting iNKT cells for the treatment of sickle cell disease

Sickle cell disease (SCD) causes widely disseminated vaso-occlusive episodes. Building on evidence implicating invariant NKT (iNKT) cells in the pathogenesis of ischemia/reperfusion injury, recent studies demonstrate that blockade of iNKT cell activation in mice with SCD reduces pulmonary inflammation and injury. In patients with SCD, iNKT cells in blood are increased in absolute number and activated in comparison to healthy controls. iNKT cell activation is reduced by agonists of adenosine 2A receptors (A(2A)Rs) such as the clinically approved coronary vasodilator, regadenoson. An ongoing multi-center, dose-finding and safety trial of infused regadenoson, has been initiated and is providing preliminary data about its safety and efficacy to treat SCD. Very high accumulation of adenosine may have deleterious effects in SCD through activation of adenosine 2B receptors that are insensitive to regadenoson. Future possible therapeutic approaches for treating SCD include selective A(2B)R antagonists and antibodies that deplete iNKT cells.

Renal effects of the novel selective adenosine A1 receptor blocker SLV329 in experimental liver cirrhosis in rats

Liver cirrhosis is often complicated by an impaired renal excretion of water and sodium. Diuretics tend to further deteriorate renal function. It is unknown whether chronic selective adenosine A(1) receptor blockade, via inhibition of the hepatorenal reflex and the tubuloglomerular feedback, might exert diuretic and natriuretic effects without a reduction of the glomerular filtration rate. In healthy animals intravenous treatment with the novel A(1) receptor antagonist SLV329 resulted in a strong dose-dependent diuretic (up to 3.4-fold) and natriuretic (up to 13.5-fold) effect without affecting creatinine clearance. Male Wistar rats with thioacetamide-induced liver cirrhosis received SLV329, vehicle or furosemide for 12 weeks. The creatinine clearance of cirrhotic animals decreased significantly (-36.5%, p<0.05), especially in those receiving furosemide (-41.9%, p<0.01). SLV329 was able to prevent this decline of creatinine clearance. Mortality was significantly lower in cirrhotic animals treated with SLV329 in comparison to animals treated with furosemide (17% vs. 54%, p<0.05). SLV329 did not relevantly influence the degree of liver fibrosis, kidney histology or expression of hepatic or renal adenosine receptors. In conclusion, chronic treatment with SLV329 prevented the decrease of creatinine clearance in a rat model of liver cirrhosis. Further studies will have to establish whether adenosine A(1) receptor antagonists are clinically beneficial at different stages of liver cirrhosis.