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1.
RSC Med Chem ; 2024 Aug 26.
Article in English | MEDLINE | ID: mdl-39290380

ABSTRACT

Neurodegenerative disorders comprise a series of heterogeneous conditions that affect millions of people worldwide, representing a significant health burden in both developed and developing countries. Without disease-modifying treatments currently available, the development of effective neurotherapeutics is a health priority. In this work, a new series of peptide-conjugates of the Glypromate neuropeptide is reported to determine the interplay of annular constriction and neuroprotective activity. To this end, (1R,3S,4S)-2-azanorbornane-3-carboxylic acid was used as an l-proline and l-pipecolic acid surrogate in addition to functionalization of the glutamate residue with relevant active pharmaceutical ingredients (APIs), namely amantadine, memantine, and (R)-1-aminoindane. Using non-differentiated SH-SY5Y cells, conjugates 14a and 15a, functionalized with amantadine, significantly reduced protein aggregation, with 15a outperforming both Glypromate (2-fold enhancement, p < 0.05) and an equimolar mixture of Glypromate and amantadine (p < 0.0001). On the other hand, in SH-SY5Y differentiated cells, conjugate 18c functionalized with (R)-1-aminoindane counteracted the toxicity elicited by paraquat (p < 0.0001), while Glypromate was found to exacerbate the neurotoxicity. Altogether, this work adds new insights into Glypromate research by demonstrating that chemical conjugation and annular constriction are effective strategies to tune neuroprotective responses against different neurotoxic stimuli, paving the way for the development of new neurotherapeutics.

2.
Biomed Pharmacother ; 173: 116345, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38442670

ABSTRACT

Antagonists of the A2B adenosine receptor have recently emerged as targeted anticancer agents and immune checkpoint inhibitors within the realm of cancer immunotherapy. This study presents a comprehensive evaluation of novel Biginelli-assembled pyrimidine chemotypes, including mono-, bi-, and tricyclic derivatives, as A2BAR antagonists. We conducted a comprehensive examination of the adenosinergic profile (both binding and functional) of a large compound library consisting of 168 compounds. This approach unveiled original lead compounds and enabled the identification of novel structure-activity relationship (SAR) trends, which were supported by extensive computational studies, including quantum mechanical calculations and free energy perturbation (FEP) analysis. In total, 25 molecules showed attractive affinity (Ki < 100 nM) and outstanding selectivity for A2BAR. From these, five molecules corresponding to the new benzothiazole scaffold were below the Ki < 10 nM threshold, in addition to a novel dual A2A/A2B antagonist. The most potent compounds, and the dual antagonist, showed enantiospecific recognition in the A2BAR. Two A2BAR selective antagonists and the dual A2AAR/A2BAR antagonist reported in this study were assessed for their impact on colorectal cancer cell lines. The results revealed a significant and dose-dependent reduction in cell proliferation. Notably, the A2BAR antagonists exhibited remarkable specificity, as they did not impede the proliferation of non-tumoral cell lines. These findings support the efficacy and potential that A2BAR antagonists as valuable candidates for cancer therapy, but also that they can effectively complement strategies involving A2AAR antagonism in the context of immune checkpoint inhibition.


Subject(s)
Antineoplastic Agents , Colorectal Neoplasms , Humans , Purinergic P1 Receptor Antagonists , Receptor, Adenosine A2B/metabolism , Adenosine A2 Receptor Antagonists/pharmacology , Structure-Activity Relationship , Antineoplastic Agents/pharmacology , Colorectal Neoplasms/drug therapy
3.
Eur J Med Chem ; 267: 116174, 2024 Mar 05.
Article in English | MEDLINE | ID: mdl-38306884

ABSTRACT

Neurodegenerative disorders of the central nervous system (CNS) such as Alzheimer's and Parkinson's diseases, afflict millions globally, posing a significant public health challenge. Despite extensive research, a critical hurdle in effectively treating neurodegenerative diseases is the lack of neuroprotective drugs that can halt or reverse the underlying disease processes. In this work, we took advantage of the neuroprotective properties of the neuropeptide glycyl-l-prolyl-l-glutamic acid (Glypromate) for the development of new peptidomimetics using l-pipecolic acid as a proline surrogate and exploring their chemical conjugation with relevant active pharmaceutical ingredients (API) via a peptide bond. Together with prolyl-based Glypromate conjugates, a total of 36 conjugates were toxicologically and biologically evaluated. In this series, the results obtained showed that a constrained ring (l-proline) at the central position of the peptide motif accounts for enhanced toxicological profiles and biological effects using undifferentiated and differentiated human neuroblastoma SH-SY5Y cells. Additionally, it was shown that biased biological responses are API-dependent. Conjugation with (R)-1-aminoindane led to a 38-43% reduction of protein aggregation induced by Aß25-35 (10 µM), denoting a 3.2-3.6-fold improvement in comparison with the parent neuropeptide, with no significative difference between functionalization at α and γ-carboxyl ends. On the other hand, the best-performing neuroprotective conjugate against the toxicity elicited by 6-hydroxydopamine (6-OHDA, 125 µM) was obtained by conjugation with memantine at the α-carboxyl end, resulting in a 2.3-fold improvement of the neuroprotection capacity in comparison with Glypromate neuropeptide. Altogether, the chemical strategy explored in this work shows that the neuroprotective capacity of Glypromate can be modified and fine-tuned, opening a new avenue for the development of biased neurotherapeutics for CNS-related disorders.


Subject(s)
Neuroblastoma , Neurodegenerative Diseases , Neuropeptides , Neuroprotective Agents , Humans , Neuroprotection , Cell Line, Tumor , Neuroblastoma/drug therapy , Neuroprotective Agents/pharmacology , Neuroprotective Agents/therapeutic use , Oxidopamine/toxicity , Oligopeptides/pharmacology , Oligopeptides/therapeutic use , Neuropeptides/pharmacology , Apoptosis
4.
ACS Med Chem Lett ; 14(12): 1656-1663, 2023 Dec 14.
Article in English | MEDLINE | ID: mdl-38116429

ABSTRACT

This work describes the synthesis and pharmacological and toxicological evaluation of melanostatin (MIF-1) bioconjugates with amantadine (Am) via a peptide linkage. The data from the functional assays at human dopamine D2 receptors (hD2R) showed that bioconjugates 1 (EC50 = 26.39 ± 3.37 nM) and 2 (EC50 = 17.82 ± 4.24 nM) promote a 3.3- and 4.9-fold increase of dopamine potency, respectively, at 0.01 nM, with no effect on the efficacy (Emax = 100%). In this assay, MIF-1 was only active at the highest concentration tested (EC50 = 23.64 ± 6.73 nM, at 1 nM). Cytotoxicity assays in differentiated SH-SY5Y cells showed that both MIF-1 (94.09 ± 5.75%, p < 0.05) and carbamate derivative 2 (89.73 ± 4.95%, p < 0.0001) exhibited mild but statistical significant toxicity (assessed through the MTT reduction assay) at 200 µM, while conjugate 1 was found nontoxic at this concentration.

5.
Biomed Pharmacother ; 164: 114934, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37236027

ABSTRACT

Synthetic cannabinoid receptor agonists (SCRAs) constitute the largest and most defiant group of abuse designer drugs. These new psychoactive substances (NPS), developed as unregulated alternatives to cannabis, have potent cannabimimetic effects and their use is usually associated with episodes of psychosis, seizures, dependence, organ toxicity and death. Due to their ever-changing structure, very limited or nil structural, pharmacological, and toxicological information is available to the scientific community and the law enforcement offices. Here we report the synthesis and pharmacological evaluation (binding and functional) of the largest and most diverse collection of enantiopure SCRAs published to date. Our results revealed novel SCRAs that could be (or may currently be) used as illegal psychoactive substances. We also report, for the first time, the cannabimimetic data of 32 novel SCRAs containing an (R) configuration at the stereogenic center. The systematic pharmacological profiling of the library enabled the identification of emerging Structure-Activity Relationship (SAR) and Structure-Selectivity Relationship (SSR) trends, the detection of ligands exhibiting incipient cannabinoid receptor type 2 (CB2R) subtype selectivity and highlights the significant neurotoxicity of representative SCRAs on mouse primary neuronal cells. Several of the new emerging SCRAs are currently expected to have a rather limited potential for harm, as the evaluation of their pharmacological profiles revealed lower potencies and/or efficacies. Conceived as a resource to foster collaborative investigation of the physiological effects of SCRAs, the library obtained can contribute to addressing the challenge posed by recreational designer drugs.


Subject(s)
Cannabis , Designer Drugs , Animals , Mice , Cannabinoid Receptor Agonists/pharmacology , Designer Drugs/toxicity , Structure-Activity Relationship , Ligands
6.
ACS Chem Neurosci ; 14(4): 554-572, 2023 02 15.
Article in English | MEDLINE | ID: mdl-36735764

ABSTRACT

Neurodegenerative diseases of the central nervous system (CNS) pose a serious health concern worldwide, with a particular incidence in developed countries as a result of life expectancy increase and the absence of restorative treatments. Presently, treatments for these neurological conditions are focused on managing the symptoms and/or slowing down their progression. As so, the research on novel neuroprotective drugs is of high interest. Glypromate (glycyl-l-prolyl-l-glutamic acid, also known as GPE), an endogenous small peptide widespread in the brain, holds great promise to tackle neurodegenerative diseases such as Parkinson's, Alzheimer's, and Huntington's, s well as other CNS-related disorders like Rett and Down's syndromes. However, the limited pharmacokinetic properties of Glypromate hinder its clinical application. As such, intense research has been devoted to leveraging the pharmacokinetic profile of this neuropeptide. This review aims to offer an updated perspective on Glypromate research by exploring the vast array of chemical derivatizations of more than 100 analogs described in the literature over the past two decades. The collection and discussion of the most relevant structure-activity relationships will hopefully guide the discovery of new Glypromate-based neuroprotective drugs.


Subject(s)
Central Nervous System Diseases , Neurodegenerative Diseases , Neuropeptides , Neuroprotective Agents , Neurosciences , Humans , Neuroprotective Agents/therapeutic use , Neuroprotective Agents/pharmacokinetics , Neurodegenerative Diseases/drug therapy
7.
J Med Chem ; 66(1): 890-912, 2023 01 12.
Article in English | MEDLINE | ID: mdl-36517209

ABSTRACT

The modulation of the A2B adenosine receptor is a promising strategy in cancer (immuno) therapy, with A2BAR antagonists emerging as immune checkpoint inhibitors. Herein, we report a systematic assessment of the impact of (di- and mono-)halogenation at positions 7 and/or 8 on both A2BAR affinity and pharmacokinetic properties of a collection of A2BAR antagonists and its study with structure-based free energy perturbation simulations. Monohalogenation at position 8 produced potent A2BAR ligands irrespective of the nature of the halogen. In contrast, halogenation at position 7 and dihalogenation produced a halogen-size-dependent decay in affinity. Eight novel A2BAR ligands exhibited remarkable affinity (Ki < 10 nM), exquisite subtype selectivity, and enantioselective recognition, with some eutomers eliciting sub-nanomolar affinity. The pharmacokinetic profile of representative derivatives showed enhanced solubility and microsomal stability. Finally, two compounds showed the capacity of reversing the antiproliferative effect of adenosine in activated primary human peripheral blood mononuclear cells.


Subject(s)
Halogenation , Purinergic P1 Receptor Antagonists , Cricetinae , Animals , Humans , CHO Cells , Leukocytes, Mononuclear/metabolism , Adenosine A2 Receptor Antagonists/pharmacology , Receptor, Adenosine A2B/metabolism , Ligands , Halogens
8.
J Immunother Cancer ; 10(5)2022 05.
Article in English | MEDLINE | ID: mdl-35580926

ABSTRACT

BACKGROUND: Adenosine is a metabolite that suppresses antitumor immune response of T and NK cells via extracellular binding to the two subtypes of adenosine-2 receptors, A2ARs. While blockade of the A2AARs subtype effectively rescues lymphocyte activity, with four A2AAR antagonists currently in anticancer clinical trials, less is known for the therapeutic potential of the other A2BAR blockade within cancer immunotherapy. Recent studies suggest the formation of A2AAR/A2BAR dimers in tissues that coexpress the two receptor subtypes, where the A2BAR plays a dominant role, suggesting it as a promising target for cancer immunotherapy. METHODS: We report the synthesis and functional evaluation of five potent A2BAR antagonists and a dual A2AAR/A2BAR antagonist. The compounds were designed using previous pharmacological data assisted by modeling studies. Synthesis was developed using multicomponent approaches. Flow cytometry was used to evaluate the phenotype of T and NK cells on A2BAR antagonist treatment. Functional activity of T and NK cells was tested in patient-derived tumor spheroid models. RESULTS: We provide data for six novel small molecules: five A2BAR selective antagonists and a dual A2AAR/A2BAR antagonist. The growth of patient-derived breast cancer spheroids is prevented when treated with A2BAR antagonists. To elucidate if this depends on increased lymphocyte activity, immune cells proliferation, and cytokine production, lymphocyte infiltration was evaluated and compared with the potent A2AAR antagonist AZD-4635. We find that A2BAR antagonists rescue T and NK cell proliferation, IFNγ and perforin production, and increase tumor infiltrating lymphocytes infiltration into tumor spheroids without altering the expression of adhesion molecules. CONCLUSIONS: Our results demonstrate that A2BAR is a promising target in immunotherapy, identifying ISAM-R56A as the most potent candidate for A2BAR blockade. Inhibition of A2BAR signaling restores T cell function and proliferation. Furthermore, A2BAR and dual A2AAR/A2BAR antagonists showed similar or better results than A2AAR antagonist AZD-4635 reinforcing the idea of dominant role of the A2BAR in the regulation of the immune system.


Subject(s)
Neoplasms , Purinergic P1 Receptor Antagonists , Adenosine/pharmacology , Humans , Lymphocytes/metabolism , Neoplasms/drug therapy , Receptor, Adenosine A2B/genetics , Receptor, Adenosine A2B/metabolism
9.
ACS Med Chem Lett ; 13(2): 243-249, 2022 Feb 10.
Article in English | MEDLINE | ID: mdl-35178181

ABSTRACT

A library of potent and highly A3AR selective pyrimidine-based compounds was designed to explore non-orthosteric interactions within this receptor. Starting from a prototypical orthosteric A3AR antagonist (ISVY130), the structure-based design explored functionalized residues at the exocyclic amide L1 region and aimed to provide additional interactions outside the A3AR orthosteric site. The novel ligands were assembled through an efficient and succinct synthetic approach, resulting in compounds that retain the A3AR potent and selective profile while improving the solubility of the original scaffold. The experimentally demonstrated tolerability of the L1 region to structural functionalization was further assessed by molecular dynamics simulations, giving hints of the non-orthosteric interactions explored by these series. The results pave the way to explore newly functionalized A3AR ligands, including covalent drugs and molecular probes for diagnostic and delivery purposes.

10.
J Med Chem ; 65(3): 2091-2106, 2022 02 10.
Article in English | MEDLINE | ID: mdl-35068155

ABSTRACT

We herein document a large collection of 108 2-amino-4,6-disubstituted-pyrimidine derivatives as potent, structurally simple, and highly selective A1AR ligands. The most attractive ligands were confirmed as antagonists of the canonical cyclic adenosine monophosphate pathway, and some pharmacokinetic parameters were preliminarilly evaluated. The library, built through a reliable and efficient three-component reaction, comprehensively explored the chemical space allowing the identification of the most prominent features of the structure-activity and structure-selectivity relationships around this scaffold. These included the influence on the selectivity profile of the aromatic residues at positions R4 and R6 of the pyrimidine core but most importantly the prominent role to the unprecedented A1AR selectivity profile exerted by the methyl group introduced at the exocyclic amino group. The structure-activity relationship trends on both A1 and A2AARs were conveniently interpreted with rigorous free energy perturbation simulations, which started from the receptor-driven docking model that guided the design of these series.


Subject(s)
Adenosine A1 Receptor Antagonists/chemistry , Pyrimidines/chemistry , Adenosine A1 Receptor Antagonists/metabolism , Adenosine A1 Receptor Antagonists/pharmacokinetics , Binding Sites , Cell Line , Drug Design , Drug Stability , Humans , Kinetics , Molecular Docking Simulation , Pyrimidines/metabolism , Pyrimidines/pharmacokinetics , Receptor, Adenosine A1/chemistry , Receptor, Adenosine A1/metabolism , Receptor, Adenosine A2A/chemistry , Receptor, Adenosine A2A/metabolism , Structure-Activity Relationship
11.
ACS Chem Neurosci ; 12(19): 3615-3624, 2021 10 06.
Article in English | MEDLINE | ID: mdl-34515466

ABSTRACT

Neurodegenerative disorders of the central nervous system are a class of heterogeneous pathologies affecting millions of people worldwide and represent a global health burden in developed and developing countries. Without restorative treatments currently available, research on neuroprotective drugs is considered a health priority. In this study, new analogues of the glycyl-l-prolyl-l-glutamic acid (Glypromate) neuropeptide were designed, synthesized, and biologically evaluated using (1R,3S,4S)-2-azanorbornane-3-carboxylic acid as a hybrid construct of l-proline and l-pipecolic acid. Neuroprotection assays carried out in human neuroblastoma SH-SY5Y cells using 6-hydroxydopamine as a stress inducer showed great percentage of recovery (29.7-40.0%) at 100 µM. Among this series, [(1R,3S,4S)-2-glycyl-2-azanorbornane-3-carbonyl]-l-aspartic acid (2a) stands out with a remarkable percentage of recovery (40.0%, at 100 µM) and safe toxicological profile in SH-SY5Y and human adipose mesenchymal stem cells.


Subject(s)
Neuroblastoma , Neurodegenerative Diseases , Neuroprotective Agents , Humans , Neuroprotective Agents/pharmacology , Oligopeptides
12.
J Med Chem ; 64(12): 8710-8726, 2021 06 24.
Article in English | MEDLINE | ID: mdl-34110150

ABSTRACT

Using a previously unexplored, efficient, and versatile multicomponent method, we herein report the rapid generation of novel potent and subtype-selective DRD2 biased partial agonists. This strategy exemplifies the search for diverse and previously unexplored moieties for the secondary/allosteric pharmacophore of the common phenyl-piperazine scaffold. The pharmacological characterization of the new compound series led to the identification of several ligands with excellent DRD2 affinity and subtype selectivity and remarkable functional selectivity for either the cAMP (22a and 24d) or the ß-arrestin (27a and 29c) signaling pathways. These results were further interpreted on the basis of molecular models of these ligands in complex with the recent DRD2 crystal structures, highlighting the critical role of the secondary/allosteric pharmacophore in modulating the functional selectivity profile.


Subject(s)
Piperazines/pharmacology , Receptors, Dopamine D2/agonists , Cyclic AMP/metabolism , Drug Design , Drug Partial Agonism , HEK293 Cells , Humans , Molecular Docking Simulation , Molecular Structure , Piperazines/chemical synthesis , Piperazines/metabolism , Receptors, Dopamine D2/metabolism , Signal Transduction/drug effects , Structure-Activity Relationship , beta-Arrestins/metabolism
13.
J Med Chem ; 64(9): 6209-6220, 2021 05 13.
Article in English | MEDLINE | ID: mdl-33861612

ABSTRACT

The control of Parkinson's disease (PD) is challenged by the motor and non-motor fluctuations as well as dyskinesias associated with levodopa long-term therapy. As such, pharmacological alternatives to reduce the reliance on this drug are needed. Melanostatin (MIF-1), a positive allosteric modulator (PAM) of D2 receptors (D2R), is being explored as a novel pharmacological approach focused on D2R potentiation. In this work, 3-furoic acid (3-Fu) was successfully employed as an l-proline (Pro) surrogate, affording two potent MIF-1 analogues, methyl 3-furoyl-l-leucylglycinate (4a) and 3-furoyl-l-leucylglycinamide (6a). In this series, the C-terminal carboxamide moiety was found crucial to enhancing the potency and toxicological profile, yet it is not considered a requisite for the PAM activity. Conformational analysis excludes 4a from adopting the claimed type II ß-turn. The discovery and validation of 6a as a lead compound open a new avenue for the development of a novel class of anti-Parkinson therapeutics targeting the D2R.


Subject(s)
Drug Design , Furans/chemistry , MSH Release-Inhibiting Hormone/chemistry , MSH Release-Inhibiting Hormone/pharmacology , Proline/chemistry , Receptors, Dopamine D2/metabolism , Allosteric Regulation/drug effects , Cell Line , Humans , Structure-Activity Relationship
14.
ACS Chem Neurosci ; 12(1): 203-215, 2021 01 06.
Article in English | MEDLINE | ID: mdl-33347281

ABSTRACT

This work describes the synthesis and pharmacological evaluation of 2-furoyl-based Melanostatin (MIF-1) peptidomimetics as dopamine D2 modulating agents. Eight novel peptidomimetics were tested for their ability to enhance the maximal effect of tritiated N-propylapomorphine ([3H]-NPA) at D2 receptors (D2R). In this series, 2-furoyl-l-leucylglycinamide (6a) produced a statistically significant increase in the maximal [3H]-NPA response at 10 pM (11 ± 1%), comparable to the effect of MIF-1 (18 ± 9%) at the same concentration. This result supports previous evidence that the replacement of proline residue by heteroaromatic scaffolds are tolerated at the allosteric binding site of MIF-1. Biological assays performed for peptidomimetic 6a using cortex neurons from 19-day-old Wistar-Kyoto rat embryos suggest that 6a displays no neurotoxicity up to 100 µM. Overall, the pharmacological and toxicological profile and the structural simplicity of 6a makes this peptidomimetic a potential lead compound for further development and optimization, paving the way for the development of novel modulating agents of D2R suitable for the treatment of CNS-related diseases. Additionally, the pharmacological and biological data herein reported, along with >20 000 outcomes of preclinical assays, was used to seek a general model to predict the allosteric modulatory potential of molecular candidates for a myriad of target receptors, organisms, cell lines, and biological activity parameters based on perturbation theory (PT) ideas and machine learning (ML) techniques, abbreviated as ALLOPTML. By doing so, ALLOPTML shows high specificity Sp = 89.2/89.4%, sensitivity Sn = 71.3/72.2%, and accuracy Ac = 86.1%/86.4% in training/validation series, respectively. To the best of our knowledge, ALLOPTML is the first general-purpose chemoinformatic tool using a PTML-based model for the multioutput and multicondition prediction of allosteric compounds, which is expected to save both time and resources during the early drug discovery of allosteric modulators.


Subject(s)
MSH Release-Inhibiting Hormone , Macrophage Migration-Inhibitory Factors , Peptidomimetics , Allosteric Regulation , Animals , Dopamine , Intramolecular Oxidoreductases , MSH Release-Inhibiting Hormone/pharmacology , Machine Learning , Peptidomimetics/pharmacology , Rats , Rats, Inbred WKY
15.
J Med Chem ; 64(1): 458-480, 2021 01 14.
Article in English | MEDLINE | ID: mdl-33372800

ABSTRACT

We present and thoroughly characterize a large collection of 3,4-dihydropyrimidin-2(1H)-ones as A2BAR antagonists, an emerging strategy in cancer (immuno) therapy. Most compounds selectively bind A2BAR, with a number of potent and selective antagonists further confirmed by functional cyclic adenosine monophosphate experiments. The series was analyzed with one of the most exhaustive free energy perturbation studies on a GPCR, obtaining an accurate model of the structure-activity relationship of this chemotype. The stereospecific binding modeled for this scaffold was confirmed by resolving the two most potent ligands [(±)-47, and (±)-38 Ki = 10.20 and 23.6 nM, respectively] into their two enantiomers, isolating the affinity on the corresponding (S)-eutomers (Ki = 6.30 and 11.10 nM, respectively). The assessment of the effect in representative cytochromes (CYP3A4 and CYP2D6) demonstrated insignificant inhibitory activity, while in vitro experiments in three prostate cancer cells demonstrated that this pair of compounds exhibits a pronounced antimetastatic effect.


Subject(s)
Adenosine A2 Receptor Antagonists/pharmacology , Pyrimidines/pharmacology , Receptor, Adenosine A2B/drug effects , Adenosine A2 Receptor Antagonists/metabolism , Animals , CHO Cells , Cricetulus , Cyclic AMP/metabolism , HEK293 Cells , HeLa Cells , Humans , Models, Molecular , Neoplasm Metastasis/prevention & control , Pyrimidines/chemistry , Pyrimidines/metabolism , Radioligand Assay , Receptor, Adenosine A2B/metabolism , Stereoisomerism , Structure-Activity Relationship
16.
Angew Chem Int Ed Engl ; 59(38): 16536-16543, 2020 09 14.
Article in English | MEDLINE | ID: mdl-32542862

ABSTRACT

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X-ray crystallography to reveal the binding mode of an antagonist series to the A2A adenosine receptor (AR). Eight A2A AR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A2A AR were experimentally determined and investigated through a cycle of ligand-FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X-ray crystallography of the A2A AR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A2A AR, an emerging target in immuno-oncology.


Subject(s)
Purinergic P1 Receptor Antagonists/chemistry , Receptor, Adenosine A2A/chemistry , Thermodynamics , Binding Sites/drug effects , Crystallography, X-Ray , Humans , Models, Molecular , Molecular Structure , Purinergic P1 Receptor Antagonists/pharmacology , Receptor, Adenosine A2A/metabolism
17.
J Med Chem ; 63(14): 7721-7739, 2020 07 23.
Article in English | MEDLINE | ID: mdl-32573250

ABSTRACT

A systematic exploration of bioisosteric replacements for furan and thiophene cores in a series of potent A2BAR antagonists has been carried out using the nitrogen-walk approach. A collection of 42 novel alkyl 4-substituted-2-methyl-1,4-dihydrobenzo[4,5]imidazo[1,2-a]pyrimidine-3-carboxylates, which contain 18 different pentagonal heterocyclic frameworks at position 4, was synthesized and evaluated. This study enabled the identification of new ligands that combine remarkable affinity (Ki < 30 nM) and exquisite selectivity. The structure-activity relationship (SAR) trends identified were substantiated by a molecular modeling study, based on a receptor-driven docking model and including a systematic free energy perturbation (FEP) study. Preliminary evaluation of the CYP3A4 and CYP2D6 inhibitory activity in optimized ligands evidenced weak and negligible activity, respectively. The stereospecific interaction between hA2BAR and the eutomer of the most attractive novel antagonist (S)-18g (Ki = 3.66 nM) was validated.


Subject(s)
Adenosine A2 Receptor Antagonists/pharmacology , Imidazoles/pharmacology , Pyrimidines/pharmacology , Receptor, Adenosine A2B/metabolism , Adenosine A2 Receptor Antagonists/chemical synthesis , Adenosine A2 Receptor Antagonists/metabolism , Animals , CHO Cells , Cell Line, Tumor , Cricetulus , Cytochrome P-450 CYP2D6 Inhibitors/chemical synthesis , Cytochrome P-450 CYP2D6 Inhibitors/metabolism , Cytochrome P-450 CYP2D6 Inhibitors/pharmacology , Cytochrome P-450 CYP3A Inhibitors/chemical synthesis , Cytochrome P-450 CYP3A Inhibitors/metabolism , Cytochrome P-450 CYP3A Inhibitors/pharmacology , Humans , Imidazoles/chemical synthesis , Imidazoles/metabolism , Molecular Docking Simulation , Molecular Structure , Pyrimidines/chemical synthesis , Pyrimidines/metabolism , Stereoisomerism , Structure-Activity Relationship
18.
J Med Chem ; 62(20): 9315-9330, 2019 10 24.
Article in English | MEDLINE | ID: mdl-31557025

ABSTRACT

We report the identification of two subsets of fluorinated nonxanthine A2B adenosine receptor antagonists. The novel derivatives explore the effect of fluorination at different positions of two pyrimidine-based scaffolds. The most interesting ligands combine excellent hA2B affinity (Ki < 15 nM) and remarkable subtype selectivity. The results of functional cAMP experiments confirmed the antagonistic behavior of representative ligands. The compounds were designed on the basis of previous molecular models of the stereoselective binding of the parent scaffolds to the hA2B receptor, and we herein provide refinement of such models with the fluorinated compounds, which allows the explanation of the spurious effects of the fluorination at the different positions explored. These models are importantly confirmed by a synergistic study combining chiral HPLC, circular dichroism, diastereoselective synthesis, molecular modeling, and X-ray crystallography, providing experimental evidence toward the stereospecific interaction between optimized trifluorinated stereoisomers and the hA2B receptor.


Subject(s)
Adenosine A2 Receptor Antagonists/chemistry , Pyrimidines/chemistry , Receptor, Adenosine A2B/chemistry , Adenosine A2 Receptor Antagonists/metabolism , Binding Sites , Crystallography, X-Ray , Drug Design , Humans , Hydrogen Bonding , Ligands , Molecular Conformation , Molecular Dynamics Simulation , Protein Isoforms/antagonists & inhibitors , Protein Isoforms/genetics , Protein Isoforms/metabolism , Pyrimidines/metabolism , Receptor, Adenosine A2B/genetics , Receptor, Adenosine A2B/metabolism , Stereoisomerism , Structure-Activity Relationship
19.
Chem Res Toxicol ; 32(9): 1811-1823, 2019 09 16.
Article in English | MEDLINE | ID: mdl-31327231

ABSTRACT

ChEMBL biological activities prediction for 1-5-bromofur-2-il-2-bromo-2-nitroethene (G1) is a difficult task for cytokine immunotoxicity. The current study presents experimental results for G1 interaction with mouse Th1/Th2 and pro-inflammatory cytokines using a cytometry bead array (CBA). In the in vitro test of CBA, the results show no significant differences between the mean values of the Th1/Th2 cytokines for the samples treated with G1 with respect to the negative control, but there are moderate differences for cytokine values between different periods (24/48 h). The experiments show no significant differences between the mean values of the pro-inflammatory cytokines for the samples treated with G1, regarding the negative control, except for the values of tumor necrosis factor (TNF) and Interleukin (IL6) between the group treated with G1 and the negative control at 48 h. Differences occur for these cytokines in the periods (24/48 h). The study confirmed that the antimicrobial G1 did not alter the Th1/Th2 cytokines concentration in vitro in different periods, but it can alter TNF and IL6. G1 promotes free radicals production and activates damage processes in macrophages culture. In order to predict all ChEMBL activities for drugs in other experimental conditions, a ChEMBL data set was constructed using 25 biological activities, 1366 assays, 2 assay types, 4 assay organisms, 2 organisms, and 12 cytokine targets. Molecular descriptors calculated with Rcpi and 15 machine learning methods were used to find the best model able to predict if a drug could be active or not against a specific cytokine, in specific experimental conditions. The best model is based on 120 selected molecular descriptors and a deep neural network with area under the curve of the receiver operating characteristic of 0.904 and accuracy of 0.832. This model predicted 1384 G1 biological activities against cytokines in all ChEMBL data set experimental conditions.


Subject(s)
Anti-Bacterial Agents/pharmacology , Antifungal Agents/pharmacology , Cytokines/metabolism , Furans/pharmacology , Th1-Th2 Balance/drug effects , Animals , Decision Trees , Deep Learning , Discriminant Analysis , Female , Mice, Inbred BALB C , Th1 Cells/drug effects , Th2 Cells/drug effects
20.
ACS Chem Neurosci ; 10(8): 3690-3702, 2019 08 21.
Article in English | MEDLINE | ID: mdl-31347842

ABSTRACT

This work describes the synthesis and pharmacological evaluation of picolinoyl-based peptidomimetics of melanocyte stimulating hormone release inhibiting factor 1 (MIF-1) as dopamine modulating agents. Eight novel peptidomimetics were tested for their ability to enhance the maximal effect of tritiated N-propylapomorphine ([3H]-NPA) at dopamine D2 receptors (D2R). Methyl picolinoyl-l-valyl-l-alaninate (compound 6b) produced a statistically significant increase in the maximal [3H]-NPA response at 0.01 nM (11.9 ± 3.7%), which is close to the effect of MIF-1 in this assay at same concentration (18.3 ± 9.1%). Functional assays measuring cAMP mobilization in the presence of dopamine corroborate the activity of peptidomimetic 6b as a positive allosteric modulator (PAM) of D2R. In this assay, 6b produced a typical bell-shaped dose-response curve similar to that of the parent neuropeptide (18.3 ± 7.1% for 6b vs 15.4 ± 5.5% for MIF-1, both at 0.1 nM). Dose-response curves for dopamine in the presence of 6b show EC50 (0.33 ± 0.21 µM for 6b vs 0.17 ± 0.07 µM for MIF-1) and Emax (86.0 ± 5.4% for 6b vs 93.6 ± 4.4% for MIF-1) comparable to those of MIF-1, both at 0.01 nM. Furthermore, peptidomimetic 6b was tested for agonist activity at the human D2R and the results show that it displays no intrinsic agonism effect, endorsing its activity as a PAM of D2R. Cytotoxic and neurotoxic assays were performed for peptidomimetic 6b using HEK 293T cells and cortex neurons from 19 day old Wistar-Kyoto rat embryos, respectively, suggesting this analogue displays no toxicity effect in these assays up to 100 µM. Conformational energy minimization for 6b shows that this peptidomimetic cannot adopt the postulated type-II ß-turn bioactive conformation, endorsing the possibility of an extended bioactive conformation as claimed by other researchers as a second bioactive conformation of MIF-1. Overall, the pharmacological and toxicological profile of peptidomimetic 6b together with its favorable druglike properties and structural simplicity makes it a potential lead compound for further development and optimization.


Subject(s)
Dopamine Agents/pharmacology , MSH Release-Inhibiting Hormone/pharmacology , Neurons/drug effects , Peptidomimetics/pharmacology , Receptors, Dopamine D2/metabolism , Allosteric Regulation/drug effects , Animals , Cerebral Cortex/drug effects , Cerebral Cortex/metabolism , Cyclic AMP/metabolism , Dopamine/metabolism , Dopamine Agents/chemistry , HEK293 Cells , Humans , Neurons/metabolism , Peptidomimetics/chemistry , Rats , Rats, Wistar
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