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1.
Nat Chem Biol ; 20(2): 170-179, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-37919549

RESUMEN

Small molecules that induce protein-protein associations represent powerful tools to modulate cell circuitry. We sought to develop a platform for the direct discovery of compounds able to induce association of any two preselected proteins, using the E3 ligase von Hippel-Lindau (VHL) and bromodomains as test systems. Leveraging the screening power of DNA-encoded libraries (DELs), we synthesized ~1 million DNA-encoded compounds that possess a VHL-targeting ligand, a variety of connectors and a diversity element generated by split-and-pool combinatorial chemistry. By screening our DEL against bromodomains in the presence and absence of VHL, we could identify VHL-bound molecules that simultaneously bind bromodomains. For highly barcode-enriched library members, ternary complex formation leading to bromodomain degradation was confirmed in cells. Furthermore, a ternary complex crystal structure was obtained for our most enriched library member with BRD4BD1 and a VHL complex. Our work provides a foundation for adapting DEL screening to the discovery of proximity-inducing small molecules.


Asunto(s)
Proteínas Nucleares , Proteína Supresora de Tumores del Síndrome de Von Hippel-Lindau , Proteína Supresora de Tumores del Síndrome de Von Hippel-Lindau/química , Proteína Supresora de Tumores del Síndrome de Von Hippel-Lindau/metabolismo , Proteínas Nucleares/metabolismo , Factores de Transcripción , Ubiquitina-Proteína Ligasas/metabolismo , ADN
2.
J Am Chem Soc ; 145(42): 23281-23291, 2023 10 25.
Artículo en Inglés | MEDLINE | ID: mdl-37816014

RESUMEN

The hallmark of a molecular glue is its ability to induce cooperative protein-protein interactions, leading to the formation of a ternary complex, despite weaker binding toward one or both individual proteins. Notably, the extent of cooperativity distinguishes molecular glues from bifunctional compounds, which constitute a second class of inducers of protein-protein interactions. However, apart from serendipitous discovery, there have been limited rational screening strategies for the high cooperativity exhibited by molecular glues. Here, we propose a binding-based screen of DNA-barcoded compounds on a target protein in the presence or absence of a presenter protein, using the "presenter ratio", the ratio of ternary enrichment to binary enrichment, as a predictive measure of cooperativity. Through this approach, we identified a range of cooperative, noncooperative, and uncooperative compounds in a single DNA-encoded library screen with bromodomain containing protein (BRD)9 and the VHL-elongin C-elongin B (VCB) complex. Our most cooperative hit compound, 13-7, exhibits micromolar binding affinity to BRD9 but nanomolar affinity for the ternary complex with BRD9 and VCB, with cooperativity comparable to classical molecular glues. This approach may enable the rational discovery of molecular glues for preselected proteins and thus facilitate the transition to a new paradigm of small-molecule therapeutics.


Asunto(s)
ADN , Proteínas , Sitios de Unión , Dominios Proteicos
3.
Bioorg Med Chem Lett ; 26(17): 4340-4, 2016 09 01.
Artículo en Inglés | MEDLINE | ID: mdl-27476144

RESUMEN

Proline-based trypsin inhibitors occupying the S1-S2-S1' region were identified by an HTS screening campaign. It was discovered that truncation of the P1' moiety and appropriate extension into the S4 region led to highly potent trypsin inhibitors with excellent selectivity against related serine proteases and a favorable hERG profile.


Asunto(s)
Pancreatitis/tratamiento farmacológico , Inhibidores de Tripsina/síntesis química , Inhibidores de Tripsina/uso terapéutico , Cristalografía por Rayos X , Activación Enzimática/efectos de los fármacos , Humanos , Concentración 50 Inhibidora , Estructura Molecular , Relación Estructura-Actividad , Inhibidores de Tripsina/química , Inhibidores de Tripsina/farmacología
4.
bioRxiv ; 2023 May 24.
Artículo en Inglés | MEDLINE | ID: mdl-37292909

RESUMEN

The hallmark of a molecular glue is its ability to induce cooperative protein-protein interactions, leading to the formation of a ternary complex, despite weaker binding towards one or both individual proteins. Notably, the extent of cooperativity distinguishes molecular glues from bifunctional compounds, a second class of inducers of protein-protein interactions. However, apart from serendipitous discovery, there have been limited rational screening strategies for the high cooperativity exhibited by molecular glues. Here, we propose a binding-based screen of DNA-barcoded compounds on a target protein in the presence and absence of a presenter protein, using the "presenter ratio", the ratio of ternary enrichment to binary enrichment, as a predictive measure of cooperativity. Through this approach, we identified a range of cooperative, noncooperative, and uncooperative compounds in a single DNA-encoded library screen with bromodomain (BRD)9 and the VHL-elongin C-elongin B (VCB) complex. Our most cooperative hit compound, 13-7 , exhibits micromolar binding affinity to BRD9 but nanomolar affinity for the ternary complex with BRD9 and VCB, with cooperativity comparable to classical molecular glues. This approach may enable the discovery of molecular glues for pre-selected proteins and thus facilitate the transition to a new paradigm of molecular therapeutics.

5.
Nat Commun ; 14(1): 4930, 2023 08 15.
Artículo en Inglés | MEDLINE | ID: mdl-37582753

RESUMEN

Diversity-oriented synthesis (DOS) is a powerful strategy to prepare molecules with underrepresented features in commercial screening collections, resulting in the elucidation of novel biological mechanisms. In parallel to the development of DOS, DNA-encoded libraries (DELs) have emerged as an effective, efficient screening strategy to identify protein binders. Despite recent advancements in this field, most DEL syntheses are limited by the presence of sensitive DNA-based constructs. Here, we describe the design, synthesis, and validation experiments performed for a 3.7 million-member DEL, generated using diverse skeleton architectures with varying exit vectors and derived from DOS, to achieve structural diversity beyond what is possible by varying appendages alone. We also show screening results for three diverse protein targets. We will make this DEL available to the academic scientific community to increase access to novel structural features and accelerate early-phase drug discovery.


Asunto(s)
Descubrimiento de Drogas , Bibliotecas de Moléculas Pequeñas , Bibliotecas de Moléculas Pequeñas/química , Descubrimiento de Drogas/métodos , Biblioteca de Genes , ADN/genética , ADN/química
6.
Biochim Biophys Acta ; 1804(3): 454-62, 2010 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-20152788

RESUMEN

The ATP-competitive inhibitors dasatinib and nilotinib, which bind to catalytically different conformations of the Abl kinase domain, have recently been approved for the treatment of imatinib-resistant CML. These two new drugs, albeit very efficient against most of the imatinib-resistant mutants of Bcr-Abl, fail to effectively suppress the Bcr-Abl activity of the T315I (or gatekeeper) mutation. Generating new ATP site-binding drugs that target the T315I in Abl has been hampered, amongst others, by target selectivity, which is frequently an issue when developing ATP-competitive inhibitors. Recently, using an unbiased cellular screening approach, GNF-2, a non-ATP-competitive inhibitor, has been identified that demonstrates cellular activity against Bcr-Abl transformed cells. The exquisite selectivity of GNF-2 is due to the finding that it targets the myristate binding site located near the C-terminus of the Abl kinase domain, as demonstrated by genetic approaches, solution NMR and X-ray crystallography. GNF-2, like myristate, is able to induce and/or stabilize the clamped inactive conformation of Abl analogous to the SH2-Y527 interaction of Src. The molecular mechanism for allosteric inhibition by the GNF-2 inhibitor class, and the combined effects with ATP-competitive inhibitors such as nilotinib and imatinib on wild-type Abl and imatinib-resistant mutants, in particular the T315I gatekeeper mutant, are reviewed.


Asunto(s)
Adenosina Trifosfato/química , Ácido Mirístico/química , Inhibidores de Proteínas Quinasas/química , Proteínas Proto-Oncogénicas c-abl/antagonistas & inhibidores , Proteínas Proto-Oncogénicas c-abl/química , Adenosina Trifosfato/metabolismo , Regulación Alostérica/efectos de los fármacos , Regulación Alostérica/genética , Benzamidas , Cristalografía por Rayos X , Resistencia a Antineoplásicos/efectos de los fármacos , Resistencia a Antineoplásicos/genética , Humanos , Mesilato de Imatinib , Mutación Missense , Ácido Mirístico/metabolismo , Neoplasias/tratamiento farmacológico , Neoplasias/enzimología , Neoplasias/genética , Resonancia Magnética Nuclear Biomolecular , Piperazinas/química , Piperazinas/uso terapéutico , Inhibidores de Proteínas Quinasas/uso terapéutico , Estructura Terciaria de Proteína/genética , Proteínas Proto-Oncogénicas c-abl/genética , Proteínas Proto-Oncogénicas c-abl/metabolismo , Pirimidinas/química , Pirimidinas/uso terapéutico
7.
Bioorg Med Chem Lett ; 21(23): 7030-3, 2011 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-22004721

RESUMEN

Protein kinases are widely recognized as important therapeutic targets due to their involvement in signal transduction pathways. These pathways are tightly controlled and regulated, notably by the ability of kinases to selectively phosphorylate a defined set of substrates. As part of a study on the substrate requirements of Insulin-like Growth Factor 1 Receptor (IGF-1R) and Insulin Receptor (InsR), we evaluated and applied a universal assay system able to monitor the phosphorylation of unlabelled peptides of any length in real time. In contrast to already reported profiling methodologies, we were able to assess the k(cat)/K(M) ratio of peptides as short as tetramers. Notably, we were able to identify an efficient pentamer substrate that exhibited kinetic properties close to those of a 250-amino acid protein derived from IRS-1, a natural substrate of IGF-1R and InsR.


Asunto(s)
Sondas Moleculares/química , Péptidos/química , Receptor IGF Tipo 1/química , Secuencia de Aminoácidos , Cristalografía por Rayos X , Modelos Moleculares , Sondas Moleculares/genética , Datos de Secuencia Molecular , Péptidos/genética , Fosforilación , Unión Proteica , Receptor de Insulina/química , Receptor de Insulina/genética , Especificidad por Sustrato
8.
ACS Comb Sci ; 22(3): 120-128, 2020 03 09.
Artículo en Inglés | MEDLINE | ID: mdl-32040908

RESUMEN

The use of DNA-encoded libraries has emerged as a powerful hit generation technology. Combining the power of combinatorial chemistry to enumerate large compound collections with the efficiency of affinity selection in pools, the methodology makes it possible to interrogate vast chemical space against biological targets of pharmaceutical relevance. Thus, the chemical transformations employed for the synthesis of encoded libraries play a crucial role in the identification of diverse and drug-like starting points. Currently established transformations have mostly been limited to water-compatible reactions to accommodate the growing oligonucleotide tag. Herein, we describe the development of a practical catch-and-release methodology utilizing a cationic, amphiphilic PEG-based polymer to perform chemical transformations on immobilized DNA conjugates under anhydrous conditions. We demonstrate the usefulness of our APTAC (amphiphilic polymer-facilitated transformations under anhydrous conditions) approach by performing several challenging transformations on DNA-conjugated small molecules in pure organic solvents: the addition of a carbanion equivalent to a DNA-conjugated ketone in tetrahydrofuran, the synthesis of saturated heterocycles using the tin (Sn) amine protocol (SnAP) in dichloromethane, and the dual-catalytic (Ir/Ni) metallaphotoredox decarboxylative cross-coupling of carboxylic acids to DNA-conjugated aryl halides in DMSO. In addition, we demonstrate the feasibility of the latter in multititer-plate format.


Asunto(s)
Técnicas Químicas Combinatorias , ADN/química , Polímeros/química , Bibliotecas de Moléculas Pequeñas/síntesis química , Tensoactivos/química , Estructura Molecular , Bibliotecas de Moléculas Pequeñas/química
9.
Medchemcomm ; 9(7): 1188-1193, 2018 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-30109007

RESUMEN

Herein, we describe the development of copper-catalyzed cross-coupling of DNA-conjugated aryl iodides with aliphatic amines. This protocol leverages a novel ligand, 2-((2,6-dimethoxyphenyl)amino)-2-oxoacetic acid, to effect the transformation in aqueous DMSO, under mild conditions and in air, making it an ideal candidate for the synthesis of DNA-encoded libraries.

11.
Chem Commun (Camb) ; (5): 508-9, 2002 Mar 07.
Artículo en Inglés | MEDLINE | ID: mdl-12120564

RESUMEN

The solid-phase synthesis of the antiprotozoal cyclic tetrapeptide apicidin A is reported and its synthetic accessibility is contrasted with that of a structurally similar reduced cyclic tetrapeptoid analogue.


Asunto(s)
Péptidos Cíclicos/síntesis química , Antiprotozoarios/síntesis química , Inhibidores Enzimáticos/síntesis química , Inhibidores de Histona Desacetilasas
12.
Eur J Med Chem ; 57: 1-9, 2012 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-23041456

RESUMEN

Protein kinases are widely recognized as important therapeutic targets due to their involvement in signal transduction pathways. These pathways are tightly controlled and regulated, notably by the ability of kinases to selectively phosphorylate a defined set of substrates. A wide variety of disorders can arise as a consequence of abnormal kinase-mediated phosphorylation and numerous kinase inhibitors have earned their place as key components of the modern pharmacopeia. Although "traditional" kinase inhibitors typically act by preventing the interaction between the kinase and ATP, thus stopping substrate phosphorylation, an alternative approach consists in disrupting the protein-protein interaction between the kinase and its downstream partners. In order to facilitate the identification of potential chemical starting points for substrate-site inhibition approaches, we desired to investigate the application of Substrate Activity Screening to kinases. We herein report a proof-of-concept study demonstrating, on a model tyrosine kinase, that the key requirements of this methodology can be met. Namely, using peptides as model substrates, we show that a simple ADP-accumulation assay can be used to monitor substrate efficiency and that efficiency can be optimized in a modular manner. More importantly, we demonstrate that structure-efficiency relationships translate into structure-activity relationships upon conversion of the substrates into inhibitors.


Asunto(s)
Péptidos/química , Inhibidores de Proteínas Quinasas/química , Proteínas Tirosina Quinasas Receptoras/química , Adenosina Trifosfato/química , Ensayos Analíticos de Alto Rendimiento , Humanos , Cinética , Péptidos/antagonistas & inhibidores , Unión Proteica , Inhibidores de Proteínas Quinasas/síntesis química , Proteínas Tirosina Quinasas Receptoras/antagonistas & inhibidores , Proteínas Recombinantes de Fusión/antagonistas & inhibidores , Proteínas Recombinantes de Fusión/química , Relación Estructura-Actividad , Especificidad por Sustrato
13.
J Med Chem ; 55(22): 9722-34, 2012 Nov 26.
Artículo en Inglés | MEDLINE | ID: mdl-23067318

RESUMEN

A prodrug approach to optimize the oral exposure of a series of sphingosine 1-phosphate receptor 1 (S1P(1)) antagonists for chronic efficacy studies led to the discovery of (S)-2-{[3'-(4-chloro-2,5-dimethylphenylsulfonylamino)-3,5-dimethylbiphenyl-4-carbonyl]methylamino}-4-dimethylaminobutyric acid methyl ester 14. Methyl ester prodrug 14 is hydrolyzed in vivo to the corresponding carboxylic acid 15, a potent and selective S1P(1) antagonist. Oral administration of the prodrug 14 induces sustained peripheral blood lymphocyte reduction in rats. In a rat cardiac transplantation model coadministration of a nonefficacious dose of prodrug 14 with a nonefficacious dose of sotrastaurin (19), a protein kinase C inhibitor, or everolimus (20), an mTOR inhibitor, effectively prolonged the survival time of rat cardiac allografts. This demonstrates that clinically useful immunomodulation mediated by the S1P(1) receptor can be achieved with an S1P(1) antagonist generated in vivo after oral administration of its prodrug.


Asunto(s)
Aminobutiratos/síntesis química , Trasplante de Corazón , Linfocitos/efectos de los fármacos , Profármacos/síntesis química , Receptores de Lisoesfingolípidos/antagonistas & inhibidores , Sulfonamidas/síntesis química , Administración Oral , Aminobutiratos/administración & dosificación , Aminobutiratos/farmacología , Animales , Linfocitos/metabolismo , Espectroscopía de Resonancia Magnética , Masculino , Estructura Molecular , Profármacos/administración & dosificación , Profármacos/farmacología , Ratas , Ratas Endogámicas Lew , Sulfonamidas/administración & dosificación , Sulfonamidas/farmacología
14.
Chem Biol ; 19(9): 1142-51, 2012 Sep 21.
Artículo en Inglés | MEDLINE | ID: mdl-22999882

RESUMEN

Lymphocyte trafficking is critically regulated by the Sphingosine 1-phosphate receptor-1 (S1P(1)), a G protein-coupled receptor that has been highlighted as a promising therapeutic target in autoimmunity. Fingolimod (FTY720, Gilenya) is a S1P(1) receptor agonist that has recently been approved for the treatment of multiple sclerosis (MS). Here, we report the discovery of NIBR-0213, a potent and selective S1P(1) antagonist that induces long-lasting reduction of peripheral blood lymphocyte counts after oral dosing. NIBR-0213 showed comparable therapeutic efficacy to fingolimod in experimental autoimmune encephalomyelitis (EAE), a model of human MS. These data provide convincing evidence that S1P(1) antagonists are effective in EAE. In addition, the profile of NIBR-0213 makes it an attractive candidate to further study the consequences of S1P(1) receptor antagonism and to differentiate the effects from those of S1P(1) agonists.


Asunto(s)
Compuestos de Anilina/farmacología , Compuestos de Anilina/uso terapéutico , Dipéptidos/farmacología , Dipéptidos/uso terapéutico , Encefalomielitis Autoinmune Experimental/tratamiento farmacológico , Receptores de Lisoesfingolípidos/antagonistas & inhibidores , Administración Oral , Compuestos de Anilina/administración & dosificación , Compuestos de Anilina/química , Animales , Células CHO , Cricetinae , Cricetulus , Dipéptidos/administración & dosificación , Dipéptidos/química , Modelos Animales de Enfermedad , Relación Dosis-Respuesta a Droga , Encefalomielitis Autoinmune Experimental/patología , Femenino , Humanos , Leucocitos Mononucleares/efectos de los fármacos , Recuento de Linfocitos , Ratones , Ratones Endogámicos BALB C , Ratones Endogámicos C57BL , Estructura Molecular , Ratas , Ratas Endogámicas Lew , Ratas Wistar , Receptores de Esfingosina-1-Fosfato , Relación Estructura-Actividad , Especificidad por Sustrato
15.
Org Biomol Chem ; 1(10): 1711-9, 2003 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-12926359

RESUMEN

The development and preparation of the 2,4-dimethoxybenzyl arylhydrazine (DMBAH) linker 3, a new class of "latent" safety-catch linker which is stable under Mitsunobu alkylation conditions and in the presence of amines and hydrazine, is reported. The utility of the new linker is exemplified by the synthesis of ketopiperazines (MKPs) 24 bearing up to four points of diversity using a cyclitive cleavage approach.


Asunto(s)
Reactivos de Enlaces Cruzados/química , Hidrazinas/química , Piperazinas/síntesis química , Técnicas Químicas Combinatorias/métodos , Reactivos de Enlaces Cruzados/síntesis química , Hidrazinas/síntesis química , Piperazinas/química , Resinas Sintéticas/química
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