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1.
Bioorg Med Chem ; 103: 117577, 2024 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-38518735

RESUMO

Small-molecule antivirals that prevent the replication of the SARS-CoV-2 virus by blocking the enzymatic activity of its main protease (Mpro) are and will be a tenet of pandemic preparedness. However, the peptidic nature of such compounds often precludes the design of compounds within favorable physical property ranges, limiting cellular activity. Here we describe the discovery of peptide aldehyde Mpro inhibitors with potent enzymatic and cellular antiviral activity. This structure-activity relationship (SAR) exploration was guided by the use of calculated hydration site thermodynamic maps (WaterMap) to drive potency via displacement of waters from high-energy sites. Thousands of diverse compounds were designed to target these high-energy hydration sites and then prioritized for synthesis by physics- and structure-based Free-Energy Perturbation (FEP+) simulations, which accurately predicted biochemical potencies. This approach ultimately led to the rapid discovery of lead compounds with unique SAR that exhibited potent enzymatic and cellular activity with excellent pan-coronavirus coverage.


Assuntos
COVID-19 , Proteases 3C de Coronavírus , SARS-CoV-2 , Humanos , Peptídeos/farmacologia , Antivirais/farmacologia , Antivirais/química , Inibidores de Proteases/farmacologia , Inibidores de Proteases/química , Simulação de Acoplamento Molecular
2.
Int J Mol Sci ; 22(2)2021 Jan 08.
Artigo em Inglês | MEDLINE | ID: mdl-33429995

RESUMO

We describe the assembly and annotation of a chemogenomic set of protein kinase inhibitors as an open science resource for studying kinase biology. The set only includes inhibitors that show potent kinase inhibition and a narrow spectrum of activity when screened across a large panel of kinase biochemical assays. Currently, the set contains 187 inhibitors that cover 215 human kinases. The kinase chemogenomic set (KCGS), current Version 1.0, is the most highly annotated set of selective kinase inhibitors available to researchers for use in cell-based screens.


Assuntos
Descoberta de Drogas , Inibidores de Proteínas Quinases/química , Proteínas Serina-Treonina Quinases/química , Bibliotecas de Moléculas Pequenas/química , Humanos , Inibidores de Proteínas Quinases/uso terapêutico , Proteínas Serina-Treonina Quinases/antagonistas & inibidores , Bibliotecas de Moléculas Pequenas/uso terapêutico , Relação Estrutura-Atividade
3.
J Virol ; 82(11): 5279-94, 2008 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-18367524

RESUMO

Severe acute respiratory syndrome (SARS) coronavirus infection and growth are dependent on initiating signaling and enzyme actions upon viral entry into the host cell. Proteins packaged during virus assembly may subsequently form the first line of attack and host manipulation upon infection. A complete characterization of virion components is therefore important to understanding the dynamics of early stages of infection. Mass spectrometry and kinase profiling techniques identified nearly 200 incorporated host and viral proteins. We used published interaction data to identify hubs of connectivity with potential significance for virion formation. Surprisingly, the hub with the most potential connections was not the viral M protein but the nonstructural protein 3 (nsp3), which is one of the novel virion components identified by mass spectrometry. Based on new experimental data and a bioinformatics analysis across the Coronaviridae, we propose a higher-resolution functional domain architecture for nsp3 that determines the interaction capacity of this protein. Using recombinant protein domains expressed in Escherichia coli, we identified two additional RNA-binding domains of nsp3. One of these domains is located within the previously described SARS-unique domain, and there is a nucleic acid chaperone-like domain located immediately downstream of the papain-like proteinase domain. We also identified a novel cysteine-coordinated metal ion-binding domain. Analyses of interdomain interactions and provisional functional annotation of the remaining, so-far-uncharacterized domains are presented. Overall, the ensemble of data surveyed here paint a more complete picture of nsp3 as a conserved component of the viral protein processing machinery, which is intimately associated with viral RNA in its role as a virion component.


Assuntos
Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/metabolismo , Animais , Chlorocebus aethiops , Cobalto/metabolismo , Ácidos Nucleicos/metabolismo , Filogenia , Ligação Proteica , Proteínas Quinases/metabolismo , Proteômica , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Sensibilidade e Especificidade , Células Vero , Proteínas não Estruturais Virais/genética , Proteínas não Estruturais Virais/isolamento & purificação , Vírion/genética , Vírion/metabolismo
4.
Biochemistry ; 47(51): 13514-23, 2008 Dec 23.
Artigo em Inglês | MEDLINE | ID: mdl-19053248

RESUMO

Nitrilases are a large and diverse family of nonpeptidic C-N hydrolases. The mammalian genome encodes eight nitrilase enzymes, several of which remain poorly characterized. Prominent among these are nitrilase-1 (Nit1) and nitrilase-2 (Nit2), which, despite having been shown to exert effects on cell growth and possibly serving as tumor suppressor genes, are without known substrates or selective inhibitors. In previous studies, we identified several nitrilases, including Nit1 and Nit2, as targets for dipeptide-chloroacetamide activity-based proteomics probes. Here, we have used these probes, in combination with high-resolution crystallography and molecular modeling, to systematically map the active site of Nit2 and identify residues involved in molecular recognition. We report the 1.4 A crystal structure of mouse Nit2 and use this structure to identify residues that discriminate probe labeling between the Nit1 and Nit2 enzymes. Interestingly, some of these residues are conserved across all vertebrate Nit2 enzymes and, conversely, not found in any vertebrate Nit1 enzymes, suggesting that they are key discriminators of molecular recognition between these otherwise highly homologous enzymes. Our findings thus point to a limited set of active site residues that establish distinct patterns of molecular recognition among nitrilases and provide chemical probes to selectively perturb the function of these enzymes in biological systems.


Assuntos
Aminoidrolases/química , Proteômica/métodos , Sequência de Aminoácidos , Animais , Cristalografia por Raios X/métodos , Fígado/metabolismo , Camundongos , Modelos Moleculares , Conformação Molecular , Dados de Sequência Molecular , Conformação Proteica , Estrutura Terciária de Proteína , Homologia de Sequência de Aminoácidos
5.
J Med Chem ; 61(6): 2384-2409, 2018 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-29485864

RESUMO

We report the discovery of 7-oxo-2,4,5,7-tetrahydro-6 H-pyrazolo[3,4- c]pyridine derivatives as a novel class of receptor interacting protein 1 (RIP1) kinase inhibitors. On the basis of the overlay study between HTS hit 10 and GSK2982772 (6) in RIP1 kinase, we designed and synthesized a novel class of RIP1 kinase inhibitor 11 possessing moderate RIP1 kinase inhibitory activity and P-gp mediated efflux. The optimization of the core structure and the exploration of appropriate substituents utilizing SBDD approach led to the discovery of 22, a highly potent, orally available, and brain-penetrating RIP1 kinase inhibitor with excellent PK profiles. Compound 22 significantly suppressed necroptotic cell death both in mouse and human cells. Oral administration of 22 (10 mg/kg, bid) attenuated disease progression in the mouse experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis (MS). Moreover, analysis of structure-kinetic relationship (SKR) for our novel chemical series was also discussed.


Assuntos
Encéfalo/metabolismo , Complexo de Proteínas Formadoras de Poros Nucleares/antagonistas & inibidores , Inibidores de Proteínas Quinases/síntese química , Inibidores de Proteínas Quinases/farmacologia , Piridinas/síntese química , Piridinas/farmacologia , Proteínas de Ligação a RNA/antagonistas & inibidores , Animais , Morte Celular/efeitos dos fármacos , Linhagem Celular , Encefalomielite Autoimune Experimental/tratamento farmacológico , Ensaios de Triagem em Larga Escala , Humanos , Camundongos , Modelos Moleculares , Simulação de Acoplamento Molecular , Necrose , Inibidores de Proteínas Quinases/farmacocinética , Piridinas/farmacocinética , Relação Estrutura-Atividade
6.
PLoS One ; 12(8): e0181585, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28767711

RESUMO

Protein kinases are highly tractable targets for drug discovery. However, the biological function and therapeutic potential of the majority of the 500+ human protein kinases remains unknown. We have developed physical and virtual collections of small molecule inhibitors, which we call chemogenomic sets, that are designed to inhibit the catalytic function of almost half the human protein kinases. In this manuscript we share our progress towards generation of a comprehensive kinase chemogenomic set (KCGS), release kinome profiling data of a large inhibitor set (Published Kinase Inhibitor Set 2 (PKIS2)), and outline a process through which the community can openly collaborate to create a KCGS that probes the full complement of human protein kinases.


Assuntos
Bases de Dados de Produtos Farmacêuticos , Inibidores de Proteínas Quinases/farmacologia , Bibliotecas de Moléculas Pequenas/farmacologia , Descoberta de Drogas/métodos , Genômica/métodos , Humanos , Inibidores de Proteínas Quinases/química , Bibliotecas de Moléculas Pequenas/química , Relação Estrutura-Atividade
7.
J Virol ; 81(21): 12049-60, 2007 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-17728234

RESUMO

This paper describes the structure determination of nsp3a, the N-terminal domain of the severe acute respiratory syndrome coronavirus (SARS-CoV) nonstructural protein 3. nsp3a exhibits a ubiquitin-like globular fold of residues 1 to 112 and a flexibly extended glutamic acid-rich domain of residues 113 to 183. In addition to the four beta-strands and two alpha-helices that are common to ubiquitin-like folds, the globular domain of nsp3a contains two short helices representing a feature that has not previously been observed in these proteins. Nuclear magnetic resonance chemical shift perturbations showed that these unique structural elements are involved in interactions with single-stranded RNA. Structural similarities with proteins involved in various cell-signaling pathways indicate possible roles of nsp3a in viral infection and persistence.


Assuntos
Espectroscopia de Ressonância Magnética/métodos , RNA Polimerase Dependente de RNA/química , Coronavírus Relacionado à Síndrome Respiratória Aguda Grave/metabolismo , Proteínas não Estruturais Virais/química , Sequência de Aminoácidos , Relação Dose-Resposta a Droga , Espectrometria de Massas , Modelos Moleculares , Conformação Molecular , Dados de Sequência Molecular , Conformação Proteica , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , RNA Viral/química , RNA Polimerase Dependente de RNA/metabolismo , Homologia de Sequência de Aminoácidos , Proteínas não Estruturais Virais/metabolismo , Proteínas Virais/química
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