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1.
J Mol Biol ; 436(6): 168449, 2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38244767

RESUMO

Inhibition of Insulin-Regulated Aminopeptidase is being actively explored for the treatment of several human diseases and several classes of inhibitors have been developed although no clinical applications have been reported yet. Here, we combine enzymological analysis with x-ray crystallography to investigate the mechanism employed by two of the most studied inhibitors of IRAP, an aryl sulfonamide and a 2-amino-4H-benzopyran named HFI-419. Although both compounds have been hypothesized to target the enzyme's active site by competitive mechanisms, we discovered that they instead target previously unidentified proximal allosteric sites and utilize non-competitive inhibition mechanisms. X-ray crystallographic analysis demonstrated that the aryl sulfonamide stabilizes the closed, more active, conformation of the enzyme whereas HFI-419 locks the enzyme in a semi-open, and likely less active, conformation. HFI-419 potency is substrate-dependent and fails to effectively block the degradation of the physiological substrate cyclic peptide oxytocin. Our findings demonstrate alternative mechanisms for inhibiting IRAP through allosteric sites and conformational restricting and suggest that the pharmacology of HFI-419 may be more complicated than initially considered. Such conformation-specific interactions between IRAP and small molecules can be exploited for the design of more effective second-generation allosteric inhibitors.


Assuntos
Sítio Alostérico , Inibidores Enzimáticos , Insulina , Sulfonamidas , Humanos , Domínio Catalítico/efeitos dos fármacos , Cistinil Aminopeptidase/antagonistas & inibidores , Cistinil Aminopeptidase/química , Inibidores Enzimáticos/farmacologia , Inibidores Enzimáticos/química , Insulina/metabolismo , Sulfonamidas/química , Sulfonamidas/farmacologia , Cristalografia por Raios X , Regulação Alostérica , Sítio Alostérico/efeitos dos fármacos , Células HEK293 , Células CHO , Animais , Cricetulus
2.
Nature ; 626(7999): 643-652, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38109937

RESUMO

Thousands of proteins have been validated genetically as therapeutic targets for human diseases1. However, very few have been successfully targeted, and many are considered 'undruggable'. This is particularly true for proteins that function via protein-protein interactions-direct inhibition of binding interfaces is difficult and requires the identification of allosteric sites. However, most proteins have no known allosteric sites, and a comprehensive allosteric map does not exist for any protein. Here we address this shortcoming by charting multiple global atlases of inhibitory allosteric communication in KRAS. We quantified the effects of more than 26,000 mutations on the folding of KRAS and its binding to six interaction partners. Genetic interactions in double mutants enabled us to perform biophysical measurements at scale, inferring more than 22,000 causal free energy changes. These energy landscapes quantify how mutations tune the binding specificity of a signalling protein and map the inhibitory allosteric sites for an important therapeutic target. Allosteric propagation is particularly effective across the central ß-sheet of KRAS, and multiple surface pockets are genetically validated as allosterically active, including a distal pocket in the C-terminal lobe of the protein. Allosteric mutations typically inhibit binding to all tested effectors, but they can also change the binding specificity, revealing the regulatory, evolutionary and therapeutic potential to tune pathway activation. Using the approach described here, it should be possible to rapidly and comprehensively identify allosteric target sites in many proteins.


Assuntos
Sítio Alostérico , Dobramento de Proteína , Proteínas Proto-Oncogênicas p21(ras) , Humanos , Regulação Alostérica/efeitos dos fármacos , Regulação Alostérica/genética , Sítio Alostérico/efeitos dos fármacos , Sítio Alostérico/genética , Mutação , Ligação Proteica , Proteínas Proto-Oncogênicas p21(ras)/antagonistas & inibidores , Proteínas Proto-Oncogênicas p21(ras)/química , Proteínas Proto-Oncogênicas p21(ras)/genética , Proteínas Proto-Oncogênicas p21(ras)/metabolismo , Reprodutibilidade dos Testes , Especificidade por Substrato/efeitos dos fármacos , Especificidade por Substrato/genética , Termodinâmica
3.
J Biol Chem ; 298(9): 102284, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35868561

RESUMO

cGMP-dependent protein kinase (PKG) represents a compelling drug target for treatment of cardiovascular diseases. PKG1 is the major effector of beneficial cGMP signaling which is involved in smooth muscle relaxation and vascular tone, inhibition of platelet aggregation and signaling that leads to cardioprotection. In this study, a novel piperidine series of activators previously identified from an ultrahigh-throughput screen were validated to directly bind partially activated PKG1α and subsequently enhance its kinase activity in a concentration-dependent manner. Compounds from initial optimization efforts showed an ability to activate PKG1α independent of the endogenous activator, cGMP. We demonstrate these small molecule activators mimic the effect of cGMP on the kinetic parameters of PKG1α by positively modulating the KM of the peptide substrate and negatively modulating the apparent KM for ATP with increase in catalytic efficiency, kcat. In addition, these compounds also allosterically modulate the binding affinity of cGMP for PKG1α by increasing the affinity of cGMP for the high-affinity binding site (CNB-A) and decreasing the affinity of cGMP for the low-affinity binding site (CNB-B). We show the mode of action of these activators involves binding to an allosteric site within the regulatory domain, near the CNB-B binding site. To the best of our knowledge, these are the first reported non-cGMP mimetic small molecules shown to directly activate PKG1α. Insights into the mechanism of action of these compounds will enable future development of cardioprotective compounds that function through novel modes of action for the treatment of cardiovascular diseases.


Assuntos
Doenças Cardiovasculares , Proteína Quinase Dependente de GMP Cíclico Tipo I , GMP Cíclico , Piperidinas , Trifosfato de Adenosina/metabolismo , Regulação Alostérica/efeitos dos fármacos , Sítio Alostérico/efeitos dos fármacos , Doenças Cardiovasculares/tratamento farmacológico , Doenças Cardiovasculares/enzimologia , GMP Cíclico/metabolismo , Proteína Quinase Dependente de GMP Cíclico Tipo I/metabolismo , Humanos , Piperidinas/farmacologia , Piperidinas/uso terapêutico , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/farmacologia
4.
J Med Chem ; 64(15): 11288-11301, 2021 08 12.
Artigo em Inglês | MEDLINE | ID: mdl-34337952

RESUMO

Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) plays an important role in one-carbon metabolism. The MTHFD2 gene is upregulated in various cancers but very low or undetectable in normal proliferating cells, and therefore a potential target for cancer treatment. In this study, we present the structure of MTHFD2 in complex with xanthine derivative 15, which allosterically binds to MTHFD2 and coexists with the substrate analogue. A kinetic study demonstrated the uncompetitive inhibition of MTHFD2 by 15. Allosteric inhibitors often provide good selectivity and, indeed, xanthine derivatives are highly selective for MTHFD2. Moreover, several conformational changes were observed upon the binding of 15, which impeded the binding of the cofactor and phosphate to MTHFD2. To the best of our knowledge, this is the first study to identify allosteric inhibitors targeting the MTHFD family and our results would provide insights on the inhibition mechanism of MTHFD proteins and the development of novel inhibitors.


Assuntos
Aminoidrolases/antagonistas & inibidores , Inibidores Enzimáticos/farmacologia , Metilenotetra-Hidrofolato Desidrogenase (NADP)/antagonistas & inibidores , Enzimas Multifuncionais/antagonistas & inibidores , Xantina/farmacologia , Sítio Alostérico/efeitos dos fármacos , Aminoidrolases/metabolismo , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Humanos , Metilenotetra-Hidrofolato Desidrogenase (NADP)/metabolismo , Modelos Moleculares , Estrutura Molecular , Enzimas Multifuncionais/metabolismo , Relação Estrutura-Atividade , Xantina/síntese química , Xantina/química
5.
Int J Mol Sci ; 22(14)2021 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-34298987

RESUMO

Limb-girdle muscular dystrophy R1 calpain 3-related (LGMDR1) is an autosomal recessive muscular dystrophy produced by mutations in the CAPN3 gene. It is a rare disease and there is no cure or treatment for the disease while the pathophysiological mechanism by which the absence of calpain 3 provokes the dystrophy in muscles is not clear. However, key proteins implicated in Wnt and mTOR signaling pathways, which regulate muscle homeostasis, showed a considerable reduction in their expression and in their phosphorylation in LGMDR1 patients' muscles. Finally, the administration of tideglusib and VP0.7, ATP non-competitive inhibitors of glycogen synthase kinase 3ß (GSK-3ß), restore the expression and phosphorylation of these proteins in LGMDR1 cells, opening the possibility of their use as therapeutic options.


Assuntos
Glicogênio Sintase Quinase 3 beta/antagonistas & inibidores , Distrofia Muscular do Cíngulo dos Membros/tratamento farmacológico , Proteínas do Tecido Nervoso/antagonistas & inibidores , Transdução de Sinais/efeitos dos fármacos , Trifosfato de Adenosina/metabolismo , Sítio Alostérico/efeitos dos fármacos , Antígeno CD56/análise , Calpaína/deficiência , Calpaína/genética , Fibroblastos/efeitos dos fármacos , Fibroblastos/metabolismo , Regulação da Expressão Gênica/efeitos dos fármacos , Glicogênio Sintase Quinase 3 beta/química , Humanos , Hidrazinas/farmacologia , Hidrazinas/uso terapêutico , Peptídeos e Proteínas de Sinalização Intracelular/genética , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Fibras Musculares Esqueléticas/efeitos dos fármacos , Fibras Musculares Esqueléticas/metabolismo , Proteínas Musculares/deficiência , Proteínas Musculares/genética , Distrofia Muscular do Cíngulo dos Membros/enzimologia , Proteínas do Tecido Nervoso/química , Fosforilação , Processamento de Proteína Pós-Traducional/efeitos dos fármacos , Proteínas Proto-Oncogênicas c-akt/antagonistas & inibidores , Proteínas Proto-Oncogênicas c-akt/fisiologia , Quinolonas/farmacologia , Quinolonas/uso terapêutico , Serina-Treonina Quinases TOR/antagonistas & inibidores , Serina-Treonina Quinases TOR/fisiologia , Tiadiazóis/farmacologia , Tiadiazóis/uso terapêutico , Via de Sinalização Wnt/efeitos dos fármacos
6.
ACS Chem Biol ; 16(6): 991-1002, 2021 06 18.
Artigo em Inglês | MEDLINE | ID: mdl-34048655

RESUMO

Allosteric ligands provide new opportunities to modulate G protein-coupled receptor (GPCR) function and present therapeutic benefits over orthosteric molecules. Negative allosteric modulators (NAMs) can inhibit the activation of a receptor and downstream signal transduction. Screening NAMs for a GPCR target is particularly challenging because of the difficulty in distinguishing NAMs from antagonists bound to the orthosteric site as they both show inhibitory effects in receptor signaling assays. Here we report an affinity mass spectrometry (MS)-based approach tailored to screening potential NAMs of a GPCR target especially from fragment libraries. Compared to regular surface plasmon resonance or NMR-based methods for fragment screening, our approach features a reduction of the protein and compound consumption by 2-4 orders of magnitude and an increase in the data acquisition speed by 2-3 orders of magnitude. Our affinity MS-based fragment screening led to the identification of a new NAM of the adenosine A2A receptor (A2AAR) bearing an unprecedented azetidine moiety predicted to occupy the allosteric sodium binding site. Molecular dynamics simulations, ligand structure-activity relationship (SAR) studies, and in-solution NMR analyses further revealed the unique binding mode and antagonistic property of this compound that differs considerably from HMA (5-(N,N-hexamethylene)amiloride), a well-characterized NAM of A2AAR. Taken together, our work would facilitate fragment-based screening of allosteric modulators, as well as guide the design of novel NAMs acting at the sodium ion pocket of class A GPCRs.


Assuntos
Agonistas do Receptor A2 de Adenosina/farmacologia , Antagonistas do Receptor A2 de Adenosina/farmacologia , Regulação Alostérica/efeitos dos fármacos , Receptor A2A de Adenosina/metabolismo , Sódio/metabolismo , Agonistas do Receptor A2 de Adenosina/química , Antagonistas do Receptor A2 de Adenosina/química , Sítio Alostérico/efeitos dos fármacos , Sítios de Ligação/efeitos dos fármacos , Descoberta de Drogas , Humanos , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Receptor A2A de Adenosina/química
7.
Nat Commun ; 12(1): 143, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33420031

RESUMO

Coenzyme A (CoA) is a fundamental co-factor for all life, involved in numerous metabolic pathways and cellular processes, and its biosynthetic pathway has raised substantial interest as a drug target against multiple pathogens including Mycobacterium tuberculosis. The biosynthesis of CoA is performed in five steps, with the second and third steps being catalysed in the vast majority of prokaryotes, including M. tuberculosis, by a single bifunctional protein, CoaBC. Depletion of CoaBC was found to be bactericidal in M. tuberculosis. Here we report the first structure of a full-length CoaBC, from the model organism Mycobacterium smegmatis, describe how it is organised as a dodecamer and regulated by CoA thioesters. A high-throughput biochemical screen focusing on CoaB identified two inhibitors with different chemical scaffolds. Hit expansion led to the discovery of potent and selective inhibitors of M. tuberculosis CoaB, which we show to bind to a cryptic allosteric site within CoaB.


Assuntos
Antituberculosos/farmacologia , Proteínas de Bactérias/antagonistas & inibidores , Carboxiliases/antagonistas & inibidores , Mycobacterium smegmatis/enzimologia , Mycobacterium tuberculosis/efeitos dos fármacos , Peptídeo Sintases/antagonistas & inibidores , Regulação Alostérica/efeitos dos fármacos , Sítio Alostérico/efeitos dos fármacos , Antituberculosos/uso terapêutico , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/ultraestrutura , Carboxiliases/genética , Carboxiliases/metabolismo , Carboxiliases/ultraestrutura , Coenzima A/biossíntese , Cristalografia por Raios X , Ensaios Enzimáticos , Técnicas de Silenciamento de Genes , Ensaios de Triagem em Larga Escala , Humanos , Testes de Sensibilidade Microbiana , Mycobacterium tuberculosis/enzimologia , Mycobacterium tuberculosis/genética , Peptídeo Sintases/genética , Peptídeo Sintases/metabolismo , Peptídeo Sintases/ultraestrutura , Tuberculose/tratamento farmacológico , Tuberculose/microbiologia
8.
Int J Biol Macromol ; 170: 523-531, 2021 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-33387542

RESUMO

Precise monitoring of the enzyme activity by a suitable modulator is one of the very fundamental aspects of drug designing that provides the opportunity to overcome the challenges of several diseases. Herein, inhibition of human Topoisomerase IIα enzyme which serves as a potential target site for several anti-cancer drugs is demonstrated by using ultra-small size gold nanoclusters (Au NCs) with the dimension comparable with size of the active site of the enzyme. Molecular dynamics simulation results demonstrate that the Au NCs strongly interact with the human Topo IIα enzyme at its active site or allosteric site depending on forms of enzyme. Additionally, binding energy and interaction profile provides the molecular basis of understanding of interactions of ultra-small size Au NCs and human Topo IIα enzyme. Enthalpy change (ΔH) and binding constant (K) are measured based on a sequential binding model of the Au NCs with the enzyme as demonstrated by the ITC study. Moreover, the in-vitro inhibition study of the catalytic activity of the enzyme and gel electrophoresis indicates that the ultra-small size Au NCs may be used as a potent inhibitor of human Topo IIα enzyme.


Assuntos
DNA Topoisomerases Tipo II/metabolismo , Corantes Fluorescentes/química , Ouro/química , Nanopartículas Metálicas/química , Sítio Alostérico/efeitos dos fármacos , Catálise/efeitos dos fármacos , Domínio Catalítico/efeitos dos fármacos , DNA Topoisomerases Tipo II/química , Humanos , Simulação de Dinâmica Molecular , Neoplasias/metabolismo
9.
J Recept Signal Transduct Res ; 41(2): 153-158, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32752909

RESUMO

MAP kinase is one of the important targets in the treatment of osteoarthritis, inflammation and cancer. Many p38 inhibitors with diverse chemical structures and modes of protein interaction have been designed on the basis of their ability to compete with ATP site or allosteric site for binding to MAP Kinase. This study involves the molecular docking of benzimidazoles containing 4H-chrome-4-one derivatives as potent inhibitors of the MAP kinase enzyme. The compounds were computationally designed and optimized with the molecular docking to investigate the interactions between the target compounds and the amino acid residues of the MAP Kinase. The inhibitory activities against human MAP kinase enzyme were investigated by molecular docking using the Autodock and discovery studio software. All the designed compounds were shown good binding energy when compared with the binging energies of standard drug Imatinib (anti-cancer). Among all the designed compounds, compound D1 and D6 have higher binding energy values when compared to standard drug. Here we also studied the molecular properties of designed compound using Molinspiration software. Further, we planned to synthesis these benzimidazole derivatives and screen for in-vitro and in-vivo of anti-cancer activity.


Assuntos
Benzimidazóis/química , Desenho de Fármacos , Inibidores de Proteínas Quinases/química , Proteínas Quinases p38 Ativadas por Mitógeno/química , Trifosfato de Adenosina/química , Sítio Alostérico/efeitos dos fármacos , Benzimidazóis/uso terapêutico , Simulação por Computador , Ensaios de Seleção de Medicamentos Antitumorais , Humanos , Mesilato de Imatinib , Simulação de Acoplamento Molecular , Estrutura Molecular , Neoplasias/tratamento farmacológico , Inibidores de Proteínas Quinases/uso terapêutico , Relação Estrutura-Atividade , Proteínas Quinases p38 Ativadas por Mitógeno/antagonistas & inibidores , Proteínas Quinases p38 Ativadas por Mitógeno/uso terapêutico , Proteínas Quinases p38 Ativadas por Mitógeno/ultraestrutura
10.
Cancer Cell ; 39(2): 225-239.e8, 2021 02 08.
Artigo em Inglês | MEDLINE | ID: mdl-33357454

RESUMO

TP53 is the most frequently mutated gene in cancer, yet these mutations remain therapeutically non-actionable. Major challenges in drugging p53 mutations include heterogeneous mechanisms of inactivation and the absence of broadly applicable allosteric sites. Here we report the identification of small molecules, including arsenic trioxide (ATO), an established agent in treating acute promyelocytic leukemia, as cysteine-reactive compounds that rescue structural p53 mutations. Crystal structures of arsenic-bound p53 mutants reveal a cryptic allosteric site involving three arsenic-coordinating cysteines within the DNA-binding domain, distal to the zinc-binding site. Arsenic binding stabilizes the DNA-binding loop-sheet-helix motif alongside the overall ß-sandwich fold, endowing p53 mutants with thermostability and transcriptional activity. In cellular and mouse xenograft models, ATO reactivates mutant p53 for tumor suppression. Investigation of the 25 most frequent p53 mutations informs patient stratification for clinical exploration. Our results provide a mechanistic basis for repurposing ATO to target p53 mutations for widely applicable yet personalized cancer therapies.


Assuntos
Sítio Alostérico/efeitos dos fármacos , Antineoplásicos/farmacologia , Trióxido de Arsênio/farmacologia , Leucemia Promielocítica Aguda/tratamento farmacológico , Mutação/efeitos dos fármacos , Proteína Supressora de Tumor p53/genética , Células A549 , Animais , Apoptose/efeitos dos fármacos , Linhagem Celular , Linhagem Celular Tumoral , Feminino , Células HCT116 , Células HEK293 , Humanos , Células MCF-7 , Camundongos , Camundongos Endogâmicos NOD , Camundongos Nus , Camundongos SCID , Células PC-3
11.
Nat Commun ; 11(1): 6387, 2020 12 14.
Artigo em Inglês | MEDLINE | ID: mdl-33318494

RESUMO

Inositol-Requiring Enzyme 1 (IRE1) is an essential component of the Unfolded Protein Response. IRE1 spans the endoplasmic reticulum membrane, comprising a sensory lumenal domain, and tandem kinase and endoribonuclease (RNase) cytoplasmic domains. Excess unfolded proteins in the ER lumen induce dimerization and oligomerization of IRE1, triggering kinase trans-autophosphorylation and RNase activation. Known ATP-competitive small-molecule IRE1 kinase inhibitors either allosterically disrupt or stabilize the active dimeric unit, accordingly inhibiting or stimulating RNase activity. Previous allosteric RNase activators display poor selectivity and/or weak cellular activity. In this study, we describe a class of ATP-competitive RNase activators possessing high selectivity and strong cellular activity. This class of activators binds IRE1 in the kinase front pocket, leading to a distinct conformation of the activation loop. Our findings reveal exquisitely precise interdomain regulation within IRE1, advancing the mechanistic understanding of this important enzyme and its investigation as a potential small-molecule therapeutic target.


Assuntos
Trifosfato de Adenosina/metabolismo , Endorribonucleases/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Ribonucleases/metabolismo , Trifosfato de Adenosina/química , Sítio Alostérico/efeitos dos fármacos , Cristalografia por Raios X , Retículo Endoplasmático/metabolismo , Endorribonucleases/química , Técnicas de Inativação de Genes , Humanos , Ligantes , Modelos Moleculares , Fosforilação , Conformação Proteica , Dobramento de Proteína , Inibidores de Proteínas Quinases/química , Inibidores de Proteínas Quinases/metabolismo , Inibidores de Proteínas Quinases/farmacologia , Multimerização Proteica , Proteínas Serina-Treonina Quinases/química , Ribonucleases/química , Resposta a Proteínas não Dobradas
12.
Nat Commun ; 11(1): 4370, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32873792

RESUMO

BRAF kinase, a critical effector of the ERK signaling pathway, is hyperactivated in many cancers. Oncogenic BRAFV600E signals as an active monomer in the absence of active RAS, however, in many tumors BRAF dimers mediate ERK signaling. FDA-approved RAF inhibitors poorly inhibit BRAF dimers, which leads to tumor resistance. We found that Ponatinib, an FDA-approved drug, is an effective inhibitor of BRAF monomers and dimers. Ponatinib binds the BRAF dimer and stabilizes a distinct αC-helix conformation through interaction with a previously unrevealed allosteric site. Using these structural insights, we developed PHI1, a BRAF inhibitor that fully uncovers the allosteric site. PHI1 exhibits discrete cellular selectivity for BRAF dimers, with enhanced inhibition of the second protomer when the first protomer is occupied, comprising a novel class of dimer selective inhibitors. This work shows that Ponatinib and BRAF dimer selective inhibitors will be useful in treating BRAF-dependent tumors.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/farmacologia , Sistema de Sinalização das MAP Quinases/efeitos dos fármacos , Neoplasias/tratamento farmacológico , Inibidores de Proteínas Quinases/farmacologia , Proteínas Proto-Oncogênicas B-raf/antagonistas & inibidores , Sítio Alostérico/efeitos dos fármacos , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Linhagem Celular Tumoral , Cristalografia por Raios X , Desenho de Fármacos , Ensaios de Seleção de Medicamentos Antitumorais , Humanos , Imidazóis/farmacologia , Imidazóis/uso terapêutico , Sistema de Sinalização das MAP Quinases/genética , Simulação de Acoplamento Molecular , Mutação , Neoplasias/genética , Neoplasias/patologia , Inibidores de Proteínas Quinases/química , Inibidores de Proteínas Quinases/uso terapêutico , Multimerização Proteica/efeitos dos fármacos , Subunidades Proteicas/antagonistas & inibidores , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Proteínas Proto-Oncogênicas B-raf/genética , Proteínas Proto-Oncogênicas B-raf/metabolismo , Proteínas Proto-Oncogênicas B-raf/ultraestrutura , Piridazinas/farmacologia , Piridazinas/uso terapêutico , Bibliotecas de Moléculas Pequenas , Relação Estrutura-Atividade
13.
J Virol ; 94(21)2020 10 14.
Artigo em Inglês | MEDLINE | ID: mdl-32796069

RESUMO

Zika virus (ZIKV) remains a potentially significant public health concern because it can cause teratogenic effects, such as microcephaly in newborns and neurological disease, like Guillain-Barré syndrome. Together with efforts to develop a vaccine, the discovery of antiviral molecules is important to control ZIKV infections and to prevent its most severe symptoms. Here, we report the development of small nonnucleoside inhibitors (NNIs) of ZIKV RNA-dependent RNA polymerase (RdRp) activity. These NNIs target an allosteric pocket (N pocket) located next to a putative hinge region between the thumb and the palm subdomains that was originally described for dengue virus (DENV) RdRp. We first tested the activity of DENV RdRp N-pocket inhibitors against ZIKV RdRp, introduced chemical modifications into these molecules, and assessed their potency using both enzymatic and cell-based assays. The most potent compound had a 50% inhibitory concentration value of 7.3 µM and inhibited ZIKV replication in a cell-based assay with a 50% effective concentration value of 24.3 µM. Importantly, we report four high-resolution crystal structures detailing how these NNIs insert into the N pocket of ZIKV RdRp. Our observations point to subtle differences in the size, shape, chemical environment, and hydration of the N pocket from ZIKV RdRp from those of the N pocket from DENV RdRp that are crucial for the design of improved antiviral inhibitors with activity against ZIKV.IMPORTANCE Zika virus belongs to the Flavivirus genus, which comprises several important human pathogens. There is currently neither an approved vaccine nor antiviral drugs available to prevent infection by ZIKV. The nonstructural protein 5 (NS5) polymerase, which is responsible for replicating the viral RNA genome, represents one of the most promising targets for antiviral drug development. Starting from compounds recently developed against dengue virus NS5, we designed and synthesized inhibitors targeting Zika virus NS5. We show that these novel compounds inhibit viral replication by targeting the polymerase activity. High-resolution X-ray crystallographic structures of protein-inhibitor complexes demonstrated specific binding to an allosteric site within the polymerase, called the N pocket. This work paves the way for the future structure-based design of potent compounds specifically targeting ZIKV RNA polymerase activity.


Assuntos
Antivirais/síntese química , RNA Polimerase Dependente de RNA/antagonistas & inibidores , Sulfonas/síntese química , Tiofenos/síntese química , Proteínas Virais/antagonistas & inibidores , Regulação Alostérica , Sítio Alostérico/efeitos dos fármacos , Sequência de Aminoácidos , Animais , Antivirais/farmacologia , Sítios de Ligação , Linhagem Celular Tumoral , Cricetulus , Desenho de Fármacos , Expressão Gênica , Hepatócitos , Humanos , Cinética , Modelos Moleculares , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , RNA Polimerase Dependente de RNA/química , RNA Polimerase Dependente de RNA/genética , RNA Polimerase Dependente de RNA/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Relação Estrutura-Atividade , Especificidade por Substrato , Sulfonas/farmacologia , Tiofenos/farmacologia , Proteínas Virais/química , Proteínas Virais/genética , Proteínas Virais/metabolismo , Replicação Viral/efeitos dos fármacos , Zika virus/efeitos dos fármacos , Zika virus/enzimologia , Zika virus/genética , Zika virus/isolamento & purificação , Infecção por Zika virus/virologia
14.
Bioorg Med Chem Lett ; 30(20): 127471, 2020 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-32781219

RESUMO

Ubiquitin specific protease-7 (USP7) is considered an attractive target for cancer therapy by promoting degradation of the tumor suppressor p53 and negatively affecting the immune response to tumors. However, the development of selective non-covalent USP7 inhibitors has proven challenging. In this work we report the NMR characterization of a weak binder from SPR screening of an in-house fragment library which reveals that it binds to the allosteric palm site of the catalytic domain. Molecular modeling combined with 1HNMR saturation transfer difference and NOESY experiments enabled structure-based design of additional compounds showing IC50 values in the low-micromolar range with good selectivity over the closest homolog USP47. The most potent analogue represents a promising starting point for the development of novel, selective USP7 inhibitors.


Assuntos
Amidas/farmacologia , Descoberta de Drogas , Bibliotecas de Moléculas Pequenas/farmacologia , Peptidase 7 Específica de Ubiquitina/antagonistas & inibidores , Sítio Alostérico/efeitos dos fármacos , Amidas/síntese química , Amidas/química , Relação Dose-Resposta a Droga , Humanos , Modelos Moleculares , Estrutura Molecular , Bibliotecas de Moléculas Pequenas/síntese química , Bibliotecas de Moléculas Pequenas/química , Relação Estrutura-Atividade , Peptidase 7 Específica de Ubiquitina/metabolismo
15.
Pharmacol Rep ; 72(4): 799-813, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32666476

RESUMO

BACKGROUND: The epidermal growth factor receptor (EGFR) inhibitors represent the first-line therapy regimen for non-small cell lung cancer (NSCLC). Most of these inhibitors target the ATP-site to stop the aggressive development of NSCLC. Stabilization of the ATP-binding on EGFR is difficult due to autophosphorylation of the EGFR domain. This leads to activation of nonintrinsic influence of the tumor microenvironment and expression of anti-apoptotic pathways and drug resistance. METHODS: The NSCLC related literature search was carried out using online databases such as Scopus, Web of Sciences, PubMed, Protein Data Bank and UniPort for the last ten years and selected articles are referred for discussion in this review. RESULTS: To overcome the problem of mutations in NSCLC, the allosteric site of EGFR was targeted, which shows significant therapeutic outcome without causing resistance. Compounds like EAI001, EAI045 JBJ-04-125-02, DDC4002 and a series of small molecules with an affinity towards the EGFR allosteric site are reported and are under the investigational stage. These compounds are categorized under fourth-generation anti-NSCLC agents. CONCLUSION: Composition of this review highlights the advantage of inhibiting allosteric site in the EGFRTK receptor domains and presents a comparative analysis of the new fourth-generation anti-NSCLC agents to overcome the drug resistance.


Assuntos
Sítio Alostérico/efeitos dos fármacos , Protocolos de Quimioterapia Combinada Antineoplásica/administração & dosagem , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Resistencia a Medicamentos Antineoplásicos/efeitos dos fármacos , Neoplasias Pulmonares/tratamento farmacológico , Sítio Alostérico/fisiologia , Animais , Antineoplásicos/administração & dosagem , Carcinoma Pulmonar de Células não Pequenas/diagnóstico , Carcinoma Pulmonar de Células não Pequenas/metabolismo , Sistemas de Liberação de Medicamentos/métodos , Sistemas de Liberação de Medicamentos/tendências , Resistencia a Medicamentos Antineoplásicos/fisiologia , Receptores ErbB/antagonistas & inibidores , Receptores ErbB/química , Receptores ErbB/metabolismo , Humanos , Neoplasias Pulmonares/diagnóstico , Neoplasias Pulmonares/metabolismo , Estrutura Secundária de Proteína
16.
Molecules ; 25(4)2020 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-32079098

RESUMO

Protein kinase (CK2) has emerged as an attractive cancer therapeutic target and recent efforts have been made to develop its inhibitors. However, the development of selective inhibitors remains challenging because of the highly conserved ATP-binding pocket (orthosteric site) of kinase family. As an alternative strategy, allosteric inhibitors, by targeting the much more diversified allosteric site relative to the conserved ATP-binding site, achieve better pharmacological advantages than orthosteric inhibitors. Traditional serendipitous screening and structure-based design are robust tools for the discovery of CK2 allosteric inhibitors. In this review, we summarize the recent advances in the identification of CK2 allosteric inhibitors. Firstly, we briefly present the CK2 allosteric sites. Then, the allosteric inhibitors targeting the well-elucidated allosteric sites (α/ß interface, αD pocket and interface between the Glycine-rich loop and αC-helix) are highlighted in the discovery process and possible binding modes with the allosteric sites are described. This study is expected to provide valuable clues for the design of CK2 allosteric inhibitors.


Assuntos
Antineoplásicos/química , Compostos de Bifenilo/química , Inibidores de Proteínas Quinases/química , Regulação Alostérica , Sítio Alostérico/efeitos dos fármacos , Sequência de Aminoácidos , Antineoplásicos/farmacologia , Compostos de Bifenilo/farmacologia , Caseína Quinase II/antagonistas & inibidores , Caseína Quinase II/química , Descoberta de Drogas , Humanos , Interações Hidrofóbicas e Hidrofílicas , Cinética , Simulação de Acoplamento Molecular , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Inibidores de Proteínas Quinases/farmacologia , Relação Estrutura-Atividade , Especificidade por Substrato , Termodinâmica
17.
J Med Chem ; 63(6): 2930-2940, 2020 03 26.
Artigo em Inglês | MEDLINE | ID: mdl-32068404

RESUMO

The molecular chaperone TRAP1 is the mitochondrial paralog of Hsp90 and is overexpressed in many cancer cells. The orthosteric ATP-binding site of TRAP1 has been considered the primary inhibitor binding location, but TRAP1 allosteric modulators have not yet been investigated. Here, we generated and characterized the Hsp90 inhibitor PU-H71, conjugated to the mitochondrial delivery vehicle triphenylphosphonium (TPP) with a C10 carbon spacer, named SMTIN-C10, to enable dual binding to orthosteric and allosteric sites. In addition to tight binding with the ATP-binding site through the PU-H71 moiety, SMTIN-C10 interacts with the E115 residue in the N-terminal domain through the TPP moiety and subsequently induces structural transition of TRAP1 to a tightly packed closed form. The data indicate the existence of a druggable allosteric site neighboring the orthosteric ATP pocket that can be exploited to develop potent TRAP1 modulators.


Assuntos
Sítio Alostérico/efeitos dos fármacos , Antineoplásicos/química , Antineoplásicos/farmacologia , Benzodioxóis/química , Benzodioxóis/farmacologia , Proteínas de Choque Térmico HSP90/antagonistas & inibidores , Purinas/química , Purinas/farmacologia , Linhagem Celular Tumoral , Proteínas de Choque Térmico HSP90/química , Proteínas de Choque Térmico HSP90/metabolismo , Humanos , Simulação de Acoplamento Molecular , Neoplasias/tratamento farmacológico , Neoplasias/metabolismo , Conformação Proteica/efeitos dos fármacos
18.
ACS Chem Neurosci ; 11(4): 628-637, 2020 02 19.
Artigo em Inglês | MEDLINE | ID: mdl-31968162

RESUMO

CC chemokine receptor 2 (CCR2) and its endogenous CC chemokine ligands are associated with numerous inflammatory, neurodegenerative diseases, and cancer. CCR2 is becoming an attractive target in the treatment of autoimmune disease and neurodegenerative diseases. The orthosteric antagonist BMS-681 and allosteric antagonist CCR2-RA-[R] of CCR2 show positive binding cooperativity. We performed well-tempered metadynamics simulations and Gaussian accelerated MD simulations to reveal the influence of the orthosteric antagonist on the unbinding of allosteric antagonist of CCR2. We revealed different unbinding pathways of CCR2-RA-[R] in binary complex CCR2-VT5 and ternary complex CCR2-73R-VT5. The different unbinding pathways of CCR2-RA-[R] are due to the conformational dynamics of TM6. We obtained the significant conformational differences of the intracellular side of TM6 upon CCR2 binding to different ligands by GaMD simulation. The conformational dynamics of TM6 are consistent with the unbinding pathway analysis. GaMD simulations indicate that BMS-681 binding restricts the bend of intracellular side of TM6 by stabilizing the extracellular sides of TM6 and TM7. The charged residues Arg2065.43 of TM5 and Glu2917.39 of TM7 play key roles in stabling TM7 and TM6. TM6 and TM7 are crucial components in the orthosteric and allosteric binding sites. Our results illustrate the conformational details about the effect of the orthosteric antagonist on the allosteric antagonist of CCR2. The conformational dynamics of CCR2 upon binding to different ligands can provide a rational basis for development of allosteric ligands of CCR2.


Assuntos
Sítios de Ligação/fisiologia , Fenômenos Biofísicos/fisiologia , Simulação de Dinâmica Molecular , Receptores CCR2/metabolismo , Regulação Alostérica/efeitos dos fármacos , Sítio Alostérico/efeitos dos fármacos , Humanos , Conformação Proteica
19.
Eur J Med Chem ; 184: 111749, 2019 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-31589992

RESUMO

Fructose-1,6-bisphosphatase (FBPase) is an essential enzyme of GNG pathway. Significant advances demonstrate the FBPase plays a critical role in treatment of diabetes. Numerous FBPase inhibitors were developed by targeting AMP site, nevertheless, none of these inhibitors has exhibited suitable potency and druggability. Herein, a new allosteric site (C128) on FBPase was discovered, and several nitrostyrene compounds exhibiting potent FBPase inhibitions were found covalently bind to C128 site on FBPase. Mutagenesis suggest that C128 is the only cysteine that can influence FBPase inhibition, the N125-S124-S123 pathway was most likely involved in allosteric signaling transmission between C128 and active site. However, these nitrostyrenes may bind with multiple cysteine besides C128 in FBPase. To improve pocket selectivity, a series of novel compounds (14a-14n) were re-designed rationally by integrating fragment-based covalent virtual screening and machine-learning-based synthetic complexity evaluation. As expected, the mass spectrometry validated that the proportion of title compounds binding to the C128 in FBPase was significantly higher than that of nitrostyrenes. Notably, under physiological and pathological conditions, the treatment of compounds 14b, 14c, 14i or 14n led to potent inhibition of glucose production, as well as decreased triglyceride and total cholesterol levels in mouse primary hepatocytes. We highlight a novel paradigm that molecular targeting C128 site on FBPase can have potent hypoglycemic effect.


Assuntos
Descoberta de Drogas , Inibidores Enzimáticos/farmacologia , Frutose-Bifosfatase/antagonistas & inibidores , Hipoglicemiantes/farmacologia , Sítio Alostérico/efeitos dos fármacos , Animais , Sobrevivência Celular/efeitos dos fármacos , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Frutose-Bifosfatase/metabolismo , Glucose/antagonistas & inibidores , Glucose/biossíntese , Hepatócitos/efeitos dos fármacos , Hepatócitos/metabolismo , Hipoglicemiantes/síntese química , Hipoglicemiantes/química , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Simulação de Dinâmica Molecular , Estrutura Molecular , Ratos , Relação Estrutura-Atividade
20.
Biomolecules ; 9(10)2019 10 12.
Artigo em Inglês | MEDLINE | ID: mdl-31614784

RESUMO

Approximately 80% of adults are infected with a member of the herpesviridae family. Herpesviruses establish life-long latent infections within neurons, which may reactivate into lytic infections due to stress or immune suppression. There are nine human herpesviruses (HHV) posing health concerns from benign conditions to life threatening encephalitis, including cancers associated with viral infections. The current treatment options for most HHV conditions mainly include several nucleoside and nucleotide analogs targeting viral DNA polymerase. Although these drugs help manage infections, their common mechanism of action may lead to the development of drug resistance, which is particularly devastating in immunocompromised patients. Therefore, new classes of drugs directed against novel targets in HHVs are necessary to alleviate this issue. We analyzed the conservation rates of all proteins in herpes simplex virus 1 (HHV-1), a representative of the HHV family and one of the most common viruses infecting the human population. Furthermore, we generated a full-length structure model of the most conserved HHV-1 protein, the DNA packaging terminase pUL15. A series of computational analyses were performed on the model to identify ATP and DNA binding sites and characterize the dynamics of the protein. Our study indicates that proteins involved in HHV-1 DNA packaging and cleavage are amongst the most conserved gene products of HHVs. Since the packaging protein pUL15 is the most conserved among all HHV-1 gene products, the virus will have a lower chance of developing resistance to small molecules targeting pUL15. A subsequent analysis of the structure of pUL15 revealed distinct ATP and DNA binding domains and the elastic network model identifies a functionally important hinge region between the two domains of pUL15. The atomic information on the active and allosteric sites in the ATP- and DNA-bound model of pUL15 presented in this study can inform the structure-based drug discovery of a new class of drugs to treat a wide range of HHVs.


Assuntos
Antivirais/farmacologia , Empacotamento do DNA/efeitos dos fármacos , Endodesoxirribonucleases/antagonistas & inibidores , Simplexvirus/efeitos dos fármacos , Simplexvirus/enzimologia , Proteínas Virais/antagonistas & inibidores , Proteínas Virais/química , Sítio Alostérico/efeitos dos fármacos , DNA Viral/metabolismo , Endodesoxirribonucleases/metabolismo , Testes de Sensibilidade Microbiana , Simplexvirus/genética , Proteínas Virais/metabolismo
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