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1.
FASEB J ; 38(1): e23348, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-38084798

RESUMO

A robust endogenous clock is required for proper function of many physiological processes. The suprachiasmatic nucleus (SCN) constitutes our central circadian clock and allows us to adapt to daily changes in the environment. Aging can cause a decline in the amplitude of circadian rhythms in SCN and peripheral clocks, which contributes to increased risk of several chronic diseases. Strengthening clock function would therefore be an effective strategy to improve health. A high-throughput chemical screening has identified clock-enhancing molecule 3 (CEM3) as small molecule that increases circadian rhythm amplitude in cell lines and SCN explants. It is, however, currently not known whether CEM3 acts by enhancing the amplitude of individual single-cell oscillators or by enhancing synchrony among neurons. In view of CEM3's potential, it is of evident importance to clarify the mode of action of CEM3. Here, we investigated the effects of CEM3 on single-cell PERIOD2::LUCIFERASE rhythms in mouse SCN explants. CEM3 increased the amplitude in approximately 80%-90% of the individual cells in the SCN without disrupting the phase and/or period of their rhythms. Noticeably, CEM3's effect on amplitude is independent of the cell's initial amplitude. These findings make CEM3 a potential therapeutic candidate to restore compromised amplitude in circadian rhythms and will boost the development of other molecular approaches to improve health.


Assuntos
Relógios Circadianos , Ritmo Circadiano , Camundongos , Animais , Ritmo Circadiano/fisiologia , Núcleo Supraquiasmático/fisiologia , Relógios Circadianos/fisiologia , Luciferases/metabolismo , Neurônios/metabolismo
2.
Pharmacol Rev ; 74(2): 340-372, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35302044

RESUMO

Our previous International Union of Basic and Clinical Pharmacology report on the nomenclature and classification of adenosine receptors (2011) contained a number of emerging developments with respect to this G protein-coupled receptor subfamily, including protein structure, protein oligomerization, protein diversity, and allosteric modulation by small molecules. Since then, a wealth of new data and results has been added, allowing us to explore novel concepts such as target binding kinetics and biased signaling of adenosine receptors, to examine a multitude of receptor structures and novel ligands, to gauge new pharmacology, and to evaluate clinical trials with adenosine receptor ligands. This review should therefore be considered a further update of our previous reports from 2001 and 2011. SIGNIFICANCE STATEMENT: Adenosine receptors (ARs) are of continuing interest for future treatment of chronic and acute disease conditions, including inflammatory diseases, neurodegenerative afflictions, and cancer. The design of AR agonists ("biased" or not) and antagonists is largely structure based now, thanks to the tremendous progress in AR structural biology. The A2A- and A2BAR appear to modulate the immune response in tumor biology. Many clinical trials for this indication are ongoing, whereas an A2AAR antagonist (istradefylline) has been approved as an anti-Parkinson agent.


Assuntos
Farmacologia Clínica , Humanos , Ligantes , Receptores Acoplados a Proteínas G , Receptores Purinérgicos P1/fisiologia , Transdução de Sinais
3.
Med Res Rev ; 44(5): 2291-2306, 2024 09.
Artigo em Inglês | MEDLINE | ID: mdl-38634664

RESUMO

Chemokine receptors are relevant targets for a multitude of immunological diseases, but drug attrition for these receptors is remarkably high. While many drug discovery programs have been pursued, most prospective drugs failed in the follow-up studies due to clinical inefficacy, and hence there is a clear need for alternative approaches. Allosteric modulators of receptor function represent an excellent opportunity for novel drugs, as they modulate receptor activation in a controlled manner and display increased selectivity, and their pharmacological profile can be insurmountable. Here, we discuss allosteric ligands and their pharmacological characterization for modulation of chemokine receptors. Ligands are included if (1) they show clear signs of allosteric modulation in vitro and (2) display evidence of binding in a topologically distinct manner compared to endogenous chemokines. We discuss how allosteric ligands affect binding of orthosteric (endogenous) ligands in terms of affinity as well as binding kinetics in radioligand binding assays. Moreover, their effects on signaling events in functional assays and how their binding site can be elucidated are specified. We substantiate this with examples of published allosteric ligands targeting chemokine receptors and hypothetical graphs of pharmacological behavior. This review should serve as an effective starting point for setting up assays for characterizing allosteric ligands to develop safer and more efficacious drugs for chemokine receptors and, ultimately, other G protein-coupled receptors.


Assuntos
Receptores de Quimiocinas , Humanos , Receptores de Quimiocinas/metabolismo , Regulação Alostérica/efeitos dos fármacos , Animais , Ligantes
4.
Purinergic Signal ; 20(2): 193-205, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-37423967

RESUMO

Evaluation of kinetic parameters of drug-target binding, kon, koff, and residence time (RT), in addition to the traditional in vitro parameter of affinity is receiving increasing attention in the early stages of drug discovery. Target binding kinetics emerges as a meaningful concept for the evaluation of a ligand's duration of action and more generally drug efficacy and safety. We report the biological evaluation of a novel series of spirobenzo-oxazinepiperidinone derivatives as inhibitors of the human equilibrative nucleoside transporter 1 (hENT1, SLC29A1). The compounds were evaluated in radioligand binding experiments, i.e., displacement, competition association, and washout assays, to evaluate their affinity and binding kinetic parameters. We also linked these pharmacological parameters to the compounds' chemical characteristics, and learned that separate moieties of the molecules governed target affinity and binding kinetics. Among the 29 compounds tested, 28 stood out with high affinity and a long residence time of 87 min. These findings reveal the importance of supplementing affinity data with binding kinetics at transport proteins such as hENT1.


Assuntos
Transportador Equilibrativo 1 de Nucleosídeo , Tioinosina , Humanos , Transporte Biológico , Tioinosina/metabolismo , Tioinosina/farmacologia , Transportador Equilibrativo 1 de Nucleosídeo/química , Transportador Equilibrativo 1 de Nucleosídeo/metabolismo
5.
Purinergic Signal ; 2024 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-38879664

RESUMO

The human equilibrative nucleoside transporter 1 (SLC29A1, hENT1) is a solute carrier that modulates the passive transport of nucleosides and nucleobases, such as adenosine. This nucleoside regulates various physiological processes, such as vasodilation and -constriction, neurotransmission and immune defense. Marketed drugs such as dilazep and dipyridamole have proven useful in cardiovascular afflictions, but the application of hENT1 inhibitors can be beneficial in a number of other diseases. In this study, 39 derivatives of dilazep's close analogue ST7092 were designed, synthesized and subsequently assessed using [3H]NBTI displacement assays and molecular docking. Different substitution patterns of the trimethoxy benzoates of ST7092 reduced interactions within the binding pocket, resulting in diminished hENT1 affinity. Conversely, [3H]NBTI displacement by potentially covalent compounds 14b, 14c, and 14d resulted in high affinities (Ki values between 1.1 and 17.5 nM) for the transporter, primarily by the ability of accommodating the inhibitors in various ways in the binding pocket. However, any indication of covalent binding with amino acid residue C439 remained absent, conceivably as a result of decreased nucleophilic residue reactivity. In conclusion, this research introduces novel dilazep derivatives that are active as hENT1 inhibitors, along with the first high affinity dilazep derivatives equipped with an electrophilic warhead. These findings will aid the rational and structure-based development of novel hENT1 inhibitors and pharmacological tools to study hENT1's function, binding mechanisms, and its relevance in (patho)physiological conditions.

6.
Int J Mol Sci ; 25(7)2024 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-38612509

RESUMO

Cancer remains a leading cause of mortality worldwide and calls for novel therapeutic targets. Membrane proteins are key players in various cancer types but present unique challenges compared to soluble proteins. The advent of computational drug discovery tools offers a promising approach to address these challenges, allowing for the prioritization of "wet-lab" experiments. In this review, we explore the applications of computational approaches in membrane protein oncological characterization, particularly focusing on three prominent membrane protein families: receptor tyrosine kinases (RTKs), G protein-coupled receptors (GPCRs), and solute carrier proteins (SLCs). We chose these families due to their varying levels of understanding and research data availability, which leads to distinct challenges and opportunities for computational analysis. We discuss the utilization of multi-omics data, machine learning, and structure-based methods to investigate aberrant protein functionalities associated with cancer progression within each family. Moreover, we highlight the importance of considering the broader cellular context and, in particular, cross-talk between proteins. Despite existing challenges, computational tools hold promise in dissecting membrane protein dysregulation in cancer. With advancing computational capabilities and data resources, these tools are poised to play a pivotal role in identifying and prioritizing membrane proteins as personalized anticancer targets.


Assuntos
Proteínas de Membrana , Neoplasias , Humanos , Reações Cruzadas , Descoberta de Drogas , Aprendizado de Máquina , Neoplasias/tratamento farmacológico
7.
Trends Biochem Sci ; 44(10): 861-871, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31101454

RESUMO

The important role of ligand-receptor binding kinetics in drug design and discovery is increasingly recognized by the drug research community. Over the past decade, accumulating evidence has shown that optimizing the ligand's dissociation rate constant can lead to desirable duration of in vivo target occupancy and, hence, improved pharmacodynamic properties. However, the association rate constant as a pharmacological principle remains less investigated, whereas it can play an equally important role in the selection of drug candidates. This review provides a compilation and discussion of otherwise scarce and dispersed information on this topic, bringing to light the importance of drug-target association in kinetics-directed drug design and discovery.


Assuntos
Sistemas de Liberação de Medicamentos , Descoberta de Drogas , Humanos , Cinética , Ligantes
8.
FASEB J ; 36(6): e22358, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35604751

RESUMO

G protein-coupled receptors (GPCRs) are known to be involved in tumor progression and metastasis. The adenosine A1 receptor (A1 AR) has been detected to be over-expressed in various cancer cell lines. However, the role of A1 AR in tumor development is not yet well characterized. A series of A1 AR mutations were identified in the Cancer Genome Atlas from cancer patient samples. In this study, we have investigated the pharmacology of mutations located outside of the 7-transmembrane domain by using a "single-GPCR-one-G protein" yeast system. Concentration-growth curves were obtained with the full agonist CPA for 12 mutant receptors and compared to the wild-type hA1 AR. Most mutations located at the extracellular loops (EL) reduced the levels of constitutive activity of the receptor and agonist potency. For mutants at the intracellular loops (ILs) of the receptor, an increased constitutive activity was found for mutant receptor L211R5.69 , while a decreased constitutive activity and agonist response were found for mutant receptor L113F34.51 . Lastly, mutations identified on the C-terminus did not significantly influence the pharmacological function of the receptor. A selection of mutations was also investigated in a mammalian system. Overall, similar effects on receptor activation compared to the yeast system were found with mutations located at the EL, but some contradictory effects were observed for mutations located at the IL. Taken together, this study will enrich the insight of A1 AR structure and function, enlightening the consequences of these mutations in cancer. Ultimately, this may provide potential precision medicine in cancer treatment.


Assuntos
Neoplasias , Adenosina/farmacologia , Animais , Linhagem Celular , Humanos , Mamíferos/metabolismo , Mutação , Neoplasias/tratamento farmacológico , Neoplasias/genética , Receptor A1 de Adenosina/genética , Receptor A1 de Adenosina/metabolismo , Saccharomyces cerevisiae/genética
9.
J Chem Inf Model ; 63(6): 1745-1755, 2023 03 27.
Artigo em Inglês | MEDLINE | ID: mdl-36926886

RESUMO

Solute carriers (SLCs) are relatively underexplored compared to other prominent protein families such as kinases and G protein-coupled receptors. However, proteins from the SLC family play an essential role in various diseases. One such SLC is the high-affinity norepinephrine transporter (NET/SLC6A2). In contrast to most other SLCs, the NET has been relatively well studied. However, the chemical space of known ligands has a low chemical diversity, making it challenging to identify chemically novel ligands. Here, a computational screening pipeline was developed to find new NET inhibitors. The approach increases the chemical space to model for NETs using the chemical space of related proteins that were selected utilizing similarity networks. Prior proteochemometric models added data from related proteins, but here we use a data-driven approach to select the optimal proteins to add to the modeled data set. After optimizing the data set, the proteochemometric model was optimized using stepwise feature selection. The final model was created using a two-step approach combining several proteochemometric machine learning models through stacking. This model was applied to the extensive virtual compound database of Enamine, from which the top predicted 22,000 of the 600 million virtual compounds were clustered to end up with 46 chemically diverse candidates. A subselection of 32 candidates was synthesized and subsequently tested using an impedance-based assay. There were five hit compounds identified (hit rate 16%) with sub-micromolar inhibitory potencies toward NET, which are promising for follow-up experimental research. This study demonstrates a data-driven approach to diversify known chemical space to identify novel ligands and is to our knowledge the first to select this set based on the sequence similarity of related targets.


Assuntos
Proteínas da Membrana Plasmática de Transporte de Norepinefrina , Proteínas da Membrana Plasmática de Transporte de Norepinefrina/antagonistas & inibidores , Proteínas da Membrana Plasmática de Transporte de Norepinefrina/genética , Ligantes , Filogenia , Humanos , Linhagem Celular , Conjuntos de Dados como Assunto , Ligação Proteica , Modelos Biológicos
10.
PLoS Comput Biol ; 17(11): e1009152, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34818333

RESUMO

Transmembranal G Protein-Coupled Receptors (GPCRs) transduce extracellular chemical signals to the cell, via conformational change from a resting (inactive) to an active (canonically bound to a G-protein) conformation. Receptor activation is normally modulated by extracellular ligand binding, but mutations in the receptor can also shift this equilibrium by stabilizing different conformational states. In this work, we built structure-energetic relationships of receptor activation based on original thermodynamic cycles that represent the conformational equilibrium of the prototypical A2A adenosine receptor (AR). These cycles were solved with efficient free energy perturbation (FEP) protocols, allowing to distinguish the pharmacological profile of different series of A2AAR agonists with different efficacies. The modulatory effects of point mutations on the basal activity of the receptor or on ligand efficacies could also be detected. This methodology can guide GPCR ligand design with tailored pharmacological properties, or allow the identification of mutations that modulate receptor activation with potential clinical implications.


Assuntos
Receptor A2A de Adenosina/química , Agonistas do Receptor A2 de Adenosina/química , Agonistas do Receptor A2 de Adenosina/farmacologia , Antagonistas do Receptor A2 de Adenosina/química , Antagonistas do Receptor A2 de Adenosina/farmacologia , Substituição de Aminoácidos , Biologia Computacional , Humanos , Ligantes , Modelos Moleculares , Simulação de Dinâmica Molecular , Mutação Puntual , Conformação Proteica/efeitos dos fármacos , Receptor A2A de Adenosina/genética , Receptor A2A de Adenosina/metabolismo , Termodinâmica
11.
Nature ; 540(7633): 458-461, 2016 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-27926736

RESUMO

CC chemokine receptor 2 (CCR2) is one of 19 members of the chemokine receptor subfamily of human class A G-protein-coupled receptors. CCR2 is expressed on monocytes, immature dendritic cells, and T-cell subpopulations, and mediates their migration towards endogenous CC chemokine ligands such as CCL2 (ref. 1). CCR2 and its ligands are implicated in numerous inflammatory and neurodegenerative diseases including atherosclerosis, multiple sclerosis, asthma, neuropathic pain, and diabetic nephropathy, as well as cancer. These disease associations have motivated numerous preclinical studies and clinical trials (see http://www.clinicaltrials.gov) in search of therapies that target the CCR2-chemokine axis. To aid drug discovery efforts, here we solve a structure of CCR2 in a ternary complex with an orthosteric (BMS-681 (ref. 6)) and allosteric (CCR2-RA-[R]) antagonist. BMS-681 inhibits chemokine binding by occupying the orthosteric pocket of the receptor in a previously unseen binding mode. CCR2-RA-[R] binds in a novel, highly druggable pocket that is the most intracellular allosteric site observed in class A G-protein-coupled receptors so far; this site spatially overlaps the G-protein-binding site in homologous receptors. CCR2-RA-[R] inhibits CCR2 non-competitively by blocking activation-associated conformational changes and formation of the G-protein-binding interface. The conformational signature of the conserved microswitch residues observed in double-antagonist-bound CCR2 resembles the most inactive G-protein-coupled receptor structures solved so far. Like other protein-protein interactions, receptor-chemokine complexes are considered challenging therapeutic targets for small molecules, and the present structure suggests diverse pocket epitopes that can be exploited to overcome obstacles in drug design.


Assuntos
Pirrolidinonas/química , Pirrolidinonas/farmacologia , Quinazolinas/química , Quinazolinas/farmacologia , Receptores CCR2/antagonistas & inibidores , Receptores CCR2/química , Sítio Alostérico/efeitos dos fármacos , Sítios de Ligação , Quimiocinas CC/metabolismo , Cristalografia por Raios X , Desenho de Fármacos , Proteínas Heterotriméricas de Ligação ao GTP/metabolismo , Humanos , Ligantes , Modelos Moleculares
12.
Int J Mol Sci ; 23(3)2022 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-35163125

RESUMO

The organic cation transporters OCT1-3 (SLC22A1-3) facilitate the transport of cationic endo- and xenobiotics and are important mediators of drug distribution and elimination. Their polyspecific nature makes OCTs highly susceptible to drug-drug interactions (DDIs). Currently, screening of OCT inhibitors depends on uptake assays that require labeled substrates to detect transport activity. However, these uptake assays have several limitations. Hence, there is a need to develop novel assays to study OCT activity in a physiological relevant environment without the need to label the substrate. Here, a label-free impedance-based transport assay is established that detects OCT-mediated transport activity and inhibition utilizing the neurotoxin MPP+. Uptake of MPP+ by OCTs induced concentration-dependent changes in cellular impedance that were inhibited by decynium-22, corticosterone, and Tyrosine Kinase inhibitors. OCT-mediated MPP+ transport activity and inhibition were quantified on both OCT1-3 overexpressing cells and HeLa cells endogenously expressing OCT3. Moreover, the method presented here is a valuable tool to identify novel inhibitors and potential DDI partners for MPP+ transporting solute carrier proteins (SLCs) in general.


Assuntos
Impedância Elétrica , Regulação da Expressão Gênica/efeitos dos fármacos , Proteínas de Transporte de Cátions Orgânicos/metabolismo , Transportador 1 de Cátions Orgânicos/metabolismo , Transportador 2 de Cátion Orgânico/metabolismo , 1-Metil-4-fenilpiridínio/efeitos adversos , Transporte Biológico , Transporte Biológico Ativo , Células HEK293 , Herbicidas/efeitos adversos , Humanos , Proteínas de Transporte de Cátions Orgânicos/antagonistas & inibidores , Proteínas de Transporte de Cátions Orgânicos/genética , Transportador 1 de Cátions Orgânicos/antagonistas & inibidores , Transportador 1 de Cátions Orgânicos/genética , Transportador 2 de Cátion Orgânico/antagonistas & inibidores , Transportador 2 de Cátion Orgânico/genética
13.
Molecules ; 27(12)2022 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-35744872

RESUMO

Overexpression of the adenosine A1 receptor (A1AR) has been detected in various cancer cell lines. However, the role of A1AR in tumor development is still unclear. Thirteen A1AR mutations were identified in the Cancer Genome Atlas from cancer patient samples. We have investigated the pharmacology of the mutations located at the 7-transmembrane domain using a yeast system. Concentration-growth curves were obtained with the full agonist CPA and compared to the wild type hA1AR. H78L3.23 and S246T6.47 showed increased constitutive activity, while only the constitutive activity of S246T6.47 could be reduced to wild type levels by the inverse agonist DPCPX. Decreased constitutive activity was observed on five mutant receptors, among which A52V2.47 and W188C5.46 showed a diminished potency for CPA. Lastly, a complete loss of activation was observed in five mutant receptors. A selection of mutations was also investigated in a mammalian system, showing comparable effects on receptor activation as in the yeast system, except for residues pointing toward the membrane. Taken together, this study will enrich the view of the receptor structure and function of A1AR, enlightening the consequences of these mutations in cancer. Ultimately, this may provide an opportunity for precision medicine for cancer patients with pathological phenotypes involving these mutations.


Assuntos
Neoplasias , Receptor A1 de Adenosina , Adenosina/metabolismo , Adenosina/farmacologia , Animais , Humanos , Mamíferos , Mutação , Neoplasias/tratamento farmacológico , Neoplasias/genética , Estrutura Secundária de Proteína , Receptor A1 de Adenosina/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo
14.
Purinergic Signal ; 17(1): 85-108, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33313997

RESUMO

Adenosine receptors, G protein-coupled receptors (GPCRs) that are activated by the endogenous ligand adenosine, have been considered potential therapeutic targets in several disorders. To date however, only very few adenosine receptor modulators have made it to the market. Increased understanding of these receptors is required to improve the success rate of adenosine receptor drug discovery. To improve our understanding of receptor structure and function, over the past decades, a diverse array of molecular probes has been developed and applied. These probes, including radioactive or fluorescent moieties, have proven invaluable in GPCR research in general. Specifically for adenosine receptors, the development and application of covalent or reversible probes, whether radiolabeled or fluorescent, have been instrumental in the discovery of new chemical entities, the characterization and interrogation of adenosine receptor subtypes, and the study of adenosine receptor behavior in physiological and pathophysiological conditions. This review summarizes these applications, and also serves as an invitation to walk another mile to further improve probe characteristics and develop additional tags that allow the investigation of adenosine receptors and other GPCRs in even finer detail.


Assuntos
Trifosfato de Adenosina/metabolismo , Sondas Moleculares , Receptores Purinérgicos P1/metabolismo , Animais , Descoberta de Drogas , Corantes Fluorescentes , Humanos
15.
Med Res Rev ; 40(2): 683-708, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31495942

RESUMO

The function of G protein-coupled receptors (GPCRs) can be modulated by compounds that bind to other sites than the endogenous orthosteric binding site, so-called allosteric sites. Structure elucidation of a number of GPCRs has revealed the presence of a sodium ion bound in a conserved allosteric site. The small molecule amiloride and analogs thereof have been proposed to bind in this same sodium ion site. Hence, this review seeks to summarize and reflect on the current knowledge of allosteric effects by amiloride and its analogs on GPCRs. Amiloride is known to modulate adenosine, adrenergic, dopamine, chemokine, muscarinic, serotonin, gonadotropin-releasing hormone, GABAB , and taste receptors. Amiloride analogs with lipophilic substituents tend to be more potent modulators than amiloride itself. Adenosine, α-adrenergic and dopamine receptors are most strongly modulated by amiloride analogs. In addition, for a few GPCRs, more than one binding site for amiloride has been postulated. Interestingly, the nature of the allosteric effect of amiloride and derivatives varies considerably between GPCRs, with both negative and positive allosteric modulation occurring. Since the sodium ion binding site is strongly conserved among class A GPCRs it is to be expected that amiloride also binds to class A GPCRs not evaluated yet. Investigating this typical amiloride-GPCR interaction further may yield general insight in the allosteric mechanisms of GPCR ligand binding and function, and possibly provide new opportunities for drug discovery.


Assuntos
Amilorida/análogos & derivados , Amilorida/farmacologia , Descoberta de Drogas , Receptores Acoplados a Proteínas G/metabolismo , Regulação Alostérica , Amilorida/química , Animais , Humanos
16.
Brief Bioinform ; 19(2): 277-285, 2018 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-27789427

RESUMO

High-throughput screening (HTS) campaigns are routinely performed in pharmaceutical companies to explore activity profiles of chemical libraries for the identification of promising candidates for further investigation. With the aim of improving hit rates in these campaigns, data-driven approaches have been used to design relevant compound screening collections, enable effective hit triage and perform activity modeling for compound prioritization. Remarkable progress has been made in the activity modeling area since the recent introduction of large-scale bioactivity-based compound similarity metrics. This is evidenced by increased hit rates in iterative screening strategies and novel insights into compound mode of action obtained through activity modeling. Here, we provide an overview of the developments in data-driven approaches, elaborate on novel activity modeling techniques and screening paradigms explored and outline their significance in HTS.


Assuntos
Desenho de Fármacos , Descoberta de Drogas/métodos , Ensaios de Triagem em Larga Escala/métodos , Modelos Moleculares , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/metabolismo , Animais , Coleta de Dados , Humanos , Relação Estrutura-Atividade
17.
J Chem Inf Model ; 60(10): 4664-4672, 2020 10 26.
Artigo em Inglês | MEDLINE | ID: mdl-32931270

RESUMO

Proteins often have both orthosteric and allosteric binding sites. Endogenous ligands, such as hormones and neurotransmitters, bind to the orthosteric site, while synthetic ligands may bind to orthosteric or allosteric sites, which has become a focal point in drug discovery. Usually, such allosteric modulators bind to a protein noncompetitively with its endogenous ligand or substrate. The growing interest in allosteric modulators has resulted in a substantial increase of these entities and their features such as binding data in chemical libraries and databases. Although this data surge fuels research focused on allosteric modulators, binding data is unfortunately not always clearly indicated as being allosteric or orthosteric. Therefore, allosteric binding data is difficult to retrieve from databases that contain a mixture of allosteric and orthosteric compounds. This decreases model performance when statistical methods, such as machine learning models, are applied. In previous work we generated an allosteric data subset of ChEMBL release 14. In the current study an improved text mining approach is used to retrieve the allosteric and orthosteric binding types from the literature in ChEMBL release 22. Moreover, convolutional deep neural networks were constructed to predict the binding types of compounds for class A G protein-coupled receptors (GPCRs). Temporal split validation showed the model predictiveness with Matthews correlation coefficient (MCC) = 0.54, sensitivity allosteric = 0.54, and sensitivity orthosteric = 0.94. Finally, this study shows that the inclusion of accurate binding types increases binding predictions by including them as descriptor (MCC = 0.27 improved to MCC = 0.34; validated for class A GPCRs, trained on all GPCRs). Although the focus of this study is mainly on class A GPCRs, binding types for all protein classes in ChEMBL were obtained and explored. The data set is included as a supplement to this study, allowing the reader to select the compounds and binding types of interest.


Assuntos
Descoberta de Drogas , Receptores Acoplados a Proteínas G , Regulação Alostérica , Sítio Alostérico , Ligantes
18.
J Chem Inf Model ; 60(9): 4283-4295, 2020 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-32343143

RESUMO

Kinases are frequently studied in the context of anticancer drugs. Their involvement in cell responses, such as proliferation, differentiation, and apoptosis, makes them interesting subjects in multitarget drug design. In this study, a workflow is presented that models the bioactivity spectra for two panels of kinases: (1) inhibition of RET, BRAF, SRC, and S6K, while avoiding inhibition of MKNK1, TTK, ERK8, PDK1, and PAK3, and (2) inhibition of AURKA, PAK1, FGFR1, and LKB1, while avoiding inhibition of PAK3, TAK1, and PIK3CA. Both statistical and structure-based models were included, which were thoroughly benchmarked and optimized. A virtual screening was performed to test the workflow for one of the main targets, RET kinase. This resulted in 5 novel and chemically dissimilar RET inhibitors with remaining RET activity of <60% (at a concentration of 10 µM) and similarities with known RET inhibitors from 0.18 to 0.29 (Tanimoto, ECFP6). The four more potent inhibitors were assessed in a concentration range and proved to be modestly active with a pIC50 value of 5.1 for the most active compound. The experimental validation of inhibitors for RET strongly indicates that the multitarget workflow is able to detect novel inhibitors for kinases, and hence, this workflow can potentially be applied in polypharmacology modeling. We conclude that this approach can identify new chemical matter for existing targets. Moreover, this workflow can easily be applied to other targets as well.


Assuntos
Antineoplásicos , Proteínas Proto-Oncogênicas c-ret , Antineoplásicos/farmacologia , Desenho de Fármacos , Polifarmacologia , Inibidores de Proteínas Quinases/farmacologia
19.
J Pharmacol Exp Ther ; 369(1): 144-151, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30670479

RESUMO

Adenosine receptors (ARs) represent key drug targets in many human pathologies, including cardiovascular, neurologic, and inflammatory diseases. To overcome the very rapid metabolization of adenosine, metabolically stable AR agonists and antagonists were developed. However, few of these molecules have reached the market due to efficacy and safety issues. Conjugation of adenosine to squalene to form squalene-adenosine (SQAd) nanoparticles (NPs) dramatically improved the pharmacological efficacy of adenosine, especially for neuroprotection in stroke and spinal cord injury. However, the mechanism by which SQAd NPs displayed therapeutic activity remained totally unknown. In the present study, two hypotheses were discussed: 1) SQAd bioconjugates, which constitute the NP building blocks, act directly as AR ligands; or 2) adenosine, once released from intracellularly processed SQAd NPs, interacts with these receptors. The first hypothesis was rejected, using radioligand displacement assays, as no binding to human ARs was detected, up to 100 µM SQAd, in the presence of plasma. Hence, the second hypothesis was examined. SQAd NPs uptake by HepG2 cells, which was followed using radioactive and fluorescence tagging, was found to be independent of equilibrative nucleoside transporters but rather mediated by low-density lipoprotein receptors. Interestingly, it was observed that after cell internalization, SQAd NPs operated as an intracellular reservoir of adenosine, followed by a sustained release of the nucleoside in the extracellular medium. This resulted in a final paracrine-like activation of the AR pathway, evidenced by fluctuations of the second messenger cAMP. This deeper understanding of the SQAd NPs mechanism of action provides a strong rational for extending the pharmaceutical use of this nanoformulation.


Assuntos
Adenosina/química , Adenosina/metabolismo , Nanopartículas/química , Pró-Fármacos/metabolismo , Receptores Purinérgicos P1/metabolismo , Esqualeno/química , Esqualeno/metabolismo , Animais , Transporte Biológico , Células CHO , Cricetulus , Espaço Extracelular/metabolismo , Células HEK293 , Células Hep G2 , Humanos , Concentração de Íons de Hidrogênio , Ligantes
20.
Purinergic Signal ; 15(2): 139-153, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30919204

RESUMO

There is a growing interest in understanding the binding kinetics of compounds that bind to G protein-coupled receptors prior to progressing a lead compound into clinical trials. The widely expressed adenosine A3 receptor (A3AR) has been implicated in a range of diseases including immune conditions, and compounds that aim to selectively target this receptor are currently under development for arthritis. Kinetic studies at the A3AR have been performed using a radiolabelled antagonist, but due to the kinetics of this probe, they have been carried out at 10 °C in membrane preparations. In this study, we have developed a live cell NanoBRET ligand binding assay using fluorescent A3AR antagonists to measure kinetic parameters of labelled and unlabelled compounds at the A3AR at physiological temperatures. The kinetic profiles of four fluorescent antagonists were determined in kinetic association assays, and it was found that XAC-ser-tyr-X-BY630 had the longest residence time (RT = 288 ± 62 min) at the A3AR. The association and dissociation rate constants of three antagonists PSB-11, compound 5, and LUF7565 were also determined using two fluorescent ligands (XAC-ser-tyr-X-BY630 or AV039, RT = 6.8 ± 0.8 min) as the labelled probe and compared to those obtained using a radiolabelled antagonist ([3H]PSB-11, RT = 44.6 ± 3.9 min). There was close agreement in the kinetic parameters measured with AV039 and [3H]PSB-11 but significant differences to those obtained using XAC-S-ser-S-tyr-X-BY630. These data indicate that selecting a probe with the appropriate kinetics is important to accurately determine the kinetics of unlabelled ligands with markedly different kinetic profiles.


Assuntos
Antagonistas do Receptor A3 de Adenosina/farmacocinética , Transferência Ressonante de Energia de Fluorescência/métodos , Medições Luminescentes , Receptor A3 de Adenosina/metabolismo , Células HEK293 , Humanos , Cinética
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