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1.
Nature ; 610(7931): 394-401, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-36171293

RESUMO

Filoviruses, including Ebola virus, pose an increasing threat to the public health. Although two therapeutic monoclonal antibodies have been approved to treat the Ebola virus disease1,2, there are no approved broadly reactive drugs to control diverse filovirus infection. Filovirus has a large polymerase (L) protein and the cofactor viral protein 35 (VP35), which constitute the basic functional unit responsible for virus genome RNA synthesis3. Owing to its conservation, the L-VP35 polymerase complex is a promising target for broadly reactive antiviral drugs. Here we determined the structure of Ebola virus L protein in complex with tetrameric VP35 using cryo-electron microscopy (state 1). Structural analysis revealed that Ebola virus L possesses a filovirus-specific insertion element that is essential for RNA synthesis, and that VP35 interacts extensively with the N-terminal region of L by three protomers of the VP35 tetramer. Notably, we captured the complex structure in a second conformation with the unambiguous priming loop and supporting helix away from polymerase active site (state 2). Moreover, we demonstrated that the century-old drug suramin could inhibit the activity of the Ebola virus polymerase in an enzymatic assay. The structure of the L-VP35-suramin complex reveals that suramin can bind at the highly conserved NTP entry channel to prevent substrates from entering the active site. These findings reveal the mechanism of Ebola virus replication and may guide the development of more powerful anti-filovirus drugs.


Assuntos
Microscopia Crioeletrônica , RNA Polimerases Dirigidas por DNA , Ebolavirus , Proteínas Virais Reguladoras e Acessórias , Antivirais/farmacologia , Domínio Catalítico , RNA Polimerases Dirigidas por DNA/química , RNA Polimerases Dirigidas por DNA/metabolismo , RNA Polimerases Dirigidas por DNA/ultraestrutura , Ebolavirus/enzimologia , Doença pelo Vírus Ebola/tratamento farmacológico , Doença pelo Vírus Ebola/virologia , Humanos , Subunidades Proteicas/química , Subunidades Proteicas/metabolismo , RNA Viral/biossíntese , Suramina/química , Suramina/metabolismo , Suramina/farmacologia , Suramina/uso terapêutico , Proteínas Virais Reguladoras e Acessórias/química , Proteínas Virais Reguladoras e Acessórias/metabolismo , Proteínas Virais Reguladoras e Acessórias/ultraestrutura , Replicação Viral
3.
Molecules ; 26(4)2021 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-33670019

RESUMO

Suramin was initially used to treat African sleeping sickness and has been clinically tested to treat human cancers and HIV infection in the recent years. However, the therapeutic index is low with numerous clinical side-effects, attributed to its diverse interactions with multiple biological macromolecules. Here, we report a novel binding target of suramin, human Raf1 kinase inhibitory protein (hRKIP), which is an important regulatory protein involved in the Ras/Raf1/MEK/ERK (MAPK) signal pathway. Biolayer interference technology showed that suramin had an intermediate affinity for binding hRKIP with a dissociation constant of 23.8 µM. Both nuclear magnetic resonance technology and molecular docking analysis revealed that suramin bound to the conserved ligand-binding pocket of hRKIP, and that residues K113, W173, and Y181 play crucial roles in hRKIP binding suramin. Furthermore, suramin treatment at 160 µM could profoundly increase the ERK phosphorylation level by around 3 times. Our results indicate that suramin binds to hRKIP and prevents hRKIP from binding with hRaf1, thus promoting the MAPK pathway. This work is beneficial to both mechanistically understanding the side-effects of suramin and efficiently improving the clinical applications of suramin.


Assuntos
Inibidores de Proteínas Quinases/farmacologia , Proteínas Proto-Oncogênicas c-raf/antagonistas & inibidores , Suramina/farmacologia , Sítios de Ligação/efeitos dos fármacos , Células HEK293 , Humanos , Ligantes , Simulação de Acoplamento Molecular , Inibidores de Proteínas Quinases/química , Proteínas Proto-Oncogênicas c-raf/isolamento & purificação , Proteínas Proto-Oncogênicas c-raf/metabolismo , Suramina/análogos & derivados , Suramina/química
4.
Nat Struct Mol Biol ; 28(3): 319-325, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33674802

RESUMO

The COVID-19 pandemic caused by nonstop infections of SARS-CoV-2 has continued to ravage many countries worldwide. Here we report that suramin, a 100-year-old drug, is a potent inhibitor of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and acts by blocking the binding of RNA to the enzyme. In biochemical assays, suramin and its derivatives are at least 20-fold more potent than remdesivir, the currently approved nucleotide drug for treatment of COVID-19. The 2.6 Å cryo-electron microscopy structure of the viral RdRp bound to suramin reveals two binding sites. One site directly blocks the binding of the RNA template strand and the other site clashes with the RNA primer strand near the RdRp catalytic site, thus inhibiting RdRp activity. Suramin blocks viral replication in Vero E6 cells, although the reasons underlying this effect are likely various. Our results provide a structural mechanism for a nonnucleotide inhibitor of the SARS-CoV-2 RdRp.


Assuntos
Antivirais/farmacologia , RNA-Polimerase RNA-Dependente de Coronavírus/antagonistas & inibidores , RNA-Polimerase RNA-Dependente de Coronavírus/química , Inibidores Enzimáticos/farmacologia , Suramina/farmacologia , Animais , Antivirais/química , Antivirais/metabolismo , Sítios de Ligação , Domínio Catalítico , Chlorocebus aethiops , RNA-Polimerase RNA-Dependente de Coronavírus/metabolismo , Microscopia Crioeletrônica , Inibidores Enzimáticos/química , Inibidores Enzimáticos/metabolismo , Conformação Proteica , RNA Viral/química , RNA Viral/metabolismo , SARS-CoV-2/efeitos dos fármacos , Suramina/química , Suramina/metabolismo , Células Vero , Replicação Viral/efeitos dos fármacos
5.
Sci Rep ; 10(1): 18850, 2020 11 02.
Artigo em Inglês | MEDLINE | ID: mdl-33139812

RESUMO

The mammalian high mobility group protein AT-hook 2 (HMGA2) is a multi-functional DNA-binding protein that plays important roles in tumorigenesis and adipogenesis. Previous results showed that HMGA2 is a potential therapeutic target of anticancer and anti-obesity drugs by inhibiting its DNA-binding activities. Here we report the development of a miniaturized, automated AlphaScreen ultra-high-throughput screening assay to identify inhibitors targeting HMGA2-DNA interactions. After screening the LOPAC1280 compound library, we identified several compounds that strongly inhibit HMGA2-DNA interactions including suramin, a century-old, negatively charged antiparasitic drug. Our results show that the inhibition is likely through suramin binding to the "AT-hook" DNA-binding motifs and therefore preventing HMGA2 from binding to the minor groove of AT-rich DNA sequences. Since HMGA1 proteins also carry multiple "AT-hook" DNA-binding motifs, suramin is expected to inhibit HMGA1-DNA interactions as well. Biochemical and biophysical studies show that charge-charge interactions and hydrogen bonding between the suramin sulfonated groups and Arg/Lys residues play critical roles in the binding of suramin to the "AT-hook" DNA-binding motifs. Furthermore, our results suggest that HMGA2 may be one of suramin's cellular targets.


Assuntos
Proteínas de Ligação a DNA/antagonistas & inibidores , Proteína HMGA1a/antagonistas & inibidores , Proteína HMGA2/antagonistas & inibidores , Suramina/química , Adipogenia/efeitos dos fármacos , Motivos de Aminoácidos/efeitos dos fármacos , Sequência de Bases/efeitos dos fármacos , Sítios de Ligação/efeitos dos fármacos , Carcinogênese/efeitos dos fármacos , DNA/efeitos dos fármacos , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Proteína HMGA1a/química , Proteína HMGA1a/genética , Proteína HMGA2/química , Proteína HMGA2/genética , Ensaios de Triagem em Larga Escala , Humanos , Suramina/isolamento & purificação , Suramina/farmacologia
6.
Cells ; 9(11)2020 10 29.
Artigo em Inglês | MEDLINE | ID: mdl-33138093

RESUMO

NF-Y is a transcription factor (TF) comprising three subunits (NF-YA, NF-YB, NF-YC) that binds with high specificity to the CCAAT sequence, a widespread regulatory element in gene promoters of prosurvival, cell-cycle-promoting, and metabolic genes. Tumor cells undergo "metabolic rewiring" through overexpression of genes involved in such pathways, many of which are under NF-Y control. In addition, NF-YA appears to be overexpressed in many tumor types. Thus, limiting NF-Y activity may represent a desirable anti-cancer strategy, which is an ongoing field of research. With virtual-screening docking simulations on a library of pharmacologically active compounds, we identified suramin as a potential NF-Y inhibitor. We focused on suramin given its high water-solubility that is an important factor for in vitro testing, since NF-Y is sensitive to DMSO. By electrophoretic mobility shift assays (EMSA), isothermal titration calorimetry (ITC), STD NMR, X-ray crystallography, and molecular dynamics (MD) simulations, we showed that suramin binds to the histone fold domains (HFDs) of NF-Y, preventing DNA-binding. Our analyses, provide atomic-level detail on the interaction between suramin and NF-Y and reveal a region of the protein, nearby the suramin-binding site and poorly conserved in other HFD-containing TFs, that may represent a promising starting point for rational design of more specific and potent inhibitors with potential therapeutic applications.


Assuntos
Fator de Ligação a CCAAT/antagonistas & inibidores , Fator de Ligação a CCAAT/química , Suramina/química , Suramina/farmacologia , Fatores de Transcrição/antagonistas & inibidores , Fatores de Transcrição/química , Sequência de Aminoácidos , Fenômenos Biofísicos , DNA/metabolismo , Humanos , Espectroscopia de Ressonância Magnética , Simulação de Dinâmica Molecular , Multimerização Proteica , Relação Estrutura-Atividade
7.
Eur J Med Chem ; 206: 112656, 2020 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-32827875

RESUMO

The inhibition of protein function by small compounds plays a critical role in controlling cell proliferation. We report on a new class of small molecule (NCTU-Alan-2026) inhibitors for cell proliferation. NCTU-Alan-2026 blocks the interaction between FGF1 and its receptor FGF1R2D2. Extensive NMR studies combined with fluorescence experiments provided the specific mechanism of how NCTU-Alan-2026 could inhibit cell proliferation. We describe an innovative therapeutic approach for anti-proliferation and demonstrate an example of inhibition of small molecules by blocking the protein-protein interaction. We found that the compound NCTU-Alan-2026 blocked the interaction between the two proteins FGF1 and FGF1R2D2 and inhibited cell proliferation. The toxicity of NCTU-Alan-2026 is lower than that of suramin. Thus, NCTU-Alan-2026 could be a better drug than suramin in the treatment of cancer.


Assuntos
Antineoplásicos/química , Antineoplásicos/farmacologia , Fator 1 de Crescimento de Fibroblastos/metabolismo , Receptor Tipo 2 de Fator de Crescimento de Fibroblastos/metabolismo , Suramina/química , Suramina/farmacologia , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Humanos , Ligação Proteica/efeitos dos fármacos
8.
PLoS One ; 15(5): e0233089, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32459810

RESUMO

Many drugs are promiscuous and bind to multiple targets. On the one hand, these targets may be linked to unwanted side effects, but on the other, they may achieve a combined desired effect (polypharmacology) or represent multiple diseases (drug repositioning). With the growth of 3D structures of drug-target complexes, it is today possible to study drug promiscuity at the structural level and to screen vast amounts of drug-target interactions to predict side effects, polypharmacological potential, and repositioning opportunities. Here, we pursue such an approach to identify drugs inactivating B-cells, whose dysregulation can function as a driver of autoimmune diseases. Screening over 500 kinases, we identified 22 candidate targets, whose knock out impeded the activation of B-cells. Among these 22 is the gene KDR, whose gene product VEGFR2 is a prominent cancer target with anti-VEGFR2 drugs on the market for over a decade. The main result of this paper is that structure-based drug repositioning for the identified kinase targets identified the cancer drug ibrutinib as micromolar VEGFR2 inhibitor with a very high therapeutic index in B-cell inactivation. These findings prove that ibrutinib is not only acting on the Bruton's tyrosine kinase BTK, against which it was designed. Instead, it may be a polypharmacological drug, which additionally targets angiogenesis via inhibition of VEGFR2. Therefore ibrutinib carries potential to treat other VEGFR2 associated disease. Structure-based drug repositioning explains ibrutinib's anti VEGFR2 action through the conservation of a specific pattern of interactions of the drug with BTK and VEGFR2. Overall, structure-based drug repositioning was able to predict these findings at a fraction of the time and cost of a conventional screen.


Assuntos
Reposicionamento de Medicamentos/métodos , Pirazóis/química , Pirazóis/farmacologia , Pirimidinas/química , Pirimidinas/farmacologia , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/antagonistas & inibidores , Adenina/análogos & derivados , Tirosina Quinase da Agamaglobulinemia/antagonistas & inibidores , Tirosina Quinase da Agamaglobulinemia/metabolismo , Linfócitos B/metabolismo , Humanos , Células Jurkat , Piperidinas , Interferência de RNA , Transdução de Sinais/efeitos dos fármacos , Suramina/química , Suramina/farmacologia , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/metabolismo
9.
Sci Rep ; 10(1): 3490, 2020 02 26.
Artigo em Inglês | MEDLINE | ID: mdl-32103057

RESUMO

Spatial heterogeneity is a fundamental feature of the tumor microenvironment (TME), and tackling spatial heterogeneity in neoplastic metabolic aberrations is critical for tumor treatment. Genome-scale metabolic network models have been used successfully to simulate cancer metabolic networks. However, most models use bulk gene expression data of entire tumor biopsies, ignoring spatial heterogeneity in the TME. To account for spatial heterogeneity, we performed spatially-resolved metabolic network modeling of the prostate cancer microenvironment. We discovered novel malignant-cell-specific metabolic vulnerabilities targetable by small molecule compounds. We predicted that inhibiting the fatty acid desaturase SCD1 may selectively kill cancer cells based on our discovery of spatial separation of fatty acid synthesis and desaturation. We also uncovered higher prostaglandin metabolic gene expression in the tumor, relative to the surrounding tissue. Therefore, we predicted that inhibiting the prostaglandin transporter SLCO2A1 may selectively kill cancer cells. Importantly, SCD1 and SLCO2A1 have been previously shown to be potently and selectively inhibited by compounds such as CAY10566 and suramin, respectively. We also uncovered cancer-selective metabolic liabilities in central carbon, amino acid, and lipid metabolism. Our novel cancer-specific predictions provide new opportunities to develop selective drug targets for prostate cancer and other cancers where spatial transcriptomics datasets are available.


Assuntos
Redes e Vias Metabólicas/genética , Neoplasias da Próstata/patologia , Ácido Araquidônico/metabolismo , Cisteína/metabolismo , Bases de Dados Factuais , Humanos , Masculino , Transportadores de Ânions Orgânicos/antagonistas & inibidores , Transportadores de Ânions Orgânicos/metabolismo , Neoplasias da Próstata/metabolismo , Estearoil-CoA Dessaturase/antagonistas & inibidores , Estearoil-CoA Dessaturase/metabolismo , Ácido Succínico/metabolismo , Suramina/química , Suramina/metabolismo , Microambiente Tumoral
10.
Cell Biochem Biophys ; 78(1): 15-22, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31893350

RESUMO

Anions enter from the cytoplasm into the channel pore of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channel not via a central pathway but via a single lateral portal or fenestration. High Cl- conductance is dependent on electrostatic attraction of cytoplasmic Cl- ions by four positively charged amino acid side-chains located within this portal. Here we use a mutagenic approach to investigate the functional effects of transplanting or supplementing these positive charges at nearby portal-lining sites. Using patch clamp recording, we find that the functionally important positive charges at K190 and R303 can be transplanted to four nearby sites (N186, L197, W356, and A367) with little loss of Cl- conductance. Introduction of additional positive charge at these sites had almost no effect on Cl- conductance, but did increase the sensitivity to channel block by intracellular suramin and Pt(NO2)42- anions. We suggest that it is the number of positive charges within the portal, rather than their exact location, that is the most important factor influencing Cl- conductance. The portal appears well optimized in terms of charge distribution to maximize Cl- conductance.


Assuntos
Regulador de Condutância Transmembrana em Fibrose Cística/metabolismo , Citoplasma/metabolismo , Animais , Ânions/química , Ânions/metabolismo , Linhagem Celular , Complexos de Coordenação/química , Complexos de Coordenação/metabolismo , Cricetinae , Regulador de Condutância Transmembrana em Fibrose Cística/antagonistas & inibidores , Regulador de Condutância Transmembrana em Fibrose Cística/genética , Humanos , Mutagênese Sítio-Dirigida , Técnicas de Patch-Clamp , Platina/química , Eletricidade Estática , Suramina/química , Suramina/metabolismo
11.
FEBS Lett ; 594(1): 94-103, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31359422

RESUMO

Extracellular levels of soluble TIMP-3 are low, reflecting its binding by extracellular matrix (ECM) components including sulfated glycosaminoglycans (SGAGs) and endocytosis via low density lipoprotein receptor-related protein 1. Since TIMP-3 inhibits ECM degradation, the ability of SGAGs to elevate extracellular TIMP-3 is significant for osteoarthritis treatment. Previous studies of such interactions have utilized immobilized TIMP-3 or ligands. Here, we report the thermodynamics of the interactions of the sGAG-binding N-domain of TIMP-3 with chondroitin sulfate, pentosan polysulfate, and suramin in solution using isothermal titration calorimetry. All three interactions are driven by a favorable negative enthalpy change combined with an unfavorable decrease in entropy. The heat capacity changes (ΔCp ) for all of the interactions are zero, indicating an insignificant contribution from hydrophobic interactions.


Assuntos
Sulfatos de Condroitina/farmacologia , Simulação de Acoplamento Molecular , Poliéster Sulfúrico de Pentosana/farmacologia , Suramina/farmacologia , Inibidor Tecidual de Metaloproteinase-3/química , Sítios de Ligação , Sulfatos de Condroitina/química , Humanos , Poliéster Sulfúrico de Pentosana/química , Ligação Proteica , Suramina/química , Inibidor Tecidual de Metaloproteinase-3/metabolismo
12.
Eur J Med Chem ; 186: 111789, 2020 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-31727469

RESUMO

Dual- or multi-target drugs are particularly promising for the treatment of complex diseases such as (neuro)inflammatory disorders. In the present study, we identified dual antagonists for two related pro-inflammatory G protein-coupled receptors (GPCRs), the purinergic receptor P2Y2 receptor, and the orphan receptor GPR17. Based on the lead compound suramin small molecules were designed, synthesized, and modified, including benzenesulfonate, benzenesulfonamide, dibenzamide and diphenylurea derivatives. Structure-activity relationship studies identified 3-nitrophenyl 4-benzamidobenzenesulfonic acid derivatives as dual P2Y2R/GPR17 antagonists. In particular, 3-nitrophenyl 4-(4-chlorobenzamido)benzenesulfonate (14l, IC50 3.01 µM at P2Y2R, and 3.37  µM at GPR17) and 3-nitrophenyl-4-(2-chlorobenzamido)benzenesulfonate (14m, IC50 3.17 µM at P2Y2R, and 1.67 µM at GPR17) exhibited dual antagonistic activity. Compound 14l was shown to act as an allosteric antagonist at both receptors. In addition, GPR17-selective antagonists were identified including 3-nitrophenyl 4-benzamidobenzenesulfonate (14a, IC50 3.20 µM) and 3-nitrophenyl 4-(3-(trifluoromethyl)benzamido)benzenesulfonate (14f, IC50 3.88 µM). The developed antagonists were selective versus other closely related P2Y receptors. They were found to possess high chemical and metabolic stability in human liver microsomes and therefore present good starting points for developing potent multi-target drugs with potential applications in inflammatory diseases.


Assuntos
Desenho de Fármacos , Receptores Acoplados a Proteínas G/antagonistas & inibidores , Receptores Purinérgicos P2Y2/metabolismo , Suramina/farmacologia , Animais , Células CHO , Cricetulus , Relação Dose-Resposta a Droga , Humanos , Microssomos Hepáticos/química , Microssomos Hepáticos/metabolismo , Estrutura Molecular , Receptores Acoplados a Proteínas G/metabolismo , Relação Estrutura-Atividade , Suramina/síntese química , Suramina/química
13.
Biomolecules ; 11(1)2020 Dec 31.
Artigo em Inglês | MEDLINE | ID: mdl-33396366

RESUMO

Molecular targeting of growth factors has shown great therapeutic potential in pharmaceutical research due to their roles in pathological conditions. In the present study, we developed a novel suramin fragment and deoxycholic acid conjugate (SFD) that exhibited the potential to bind to the heparin-binding site (HBD) of vascular endothelial growth factor (VEGF) and to inhibit its pathogenic action for the first time. Notably, SFD was optimally designed for binding to the HBD of VEGF using the naphthalenetrisulfonate group, allowing to observe its excellent binding efficacy in a surface plasmon resonance (SPR) study, showing remarkable binding affinity (KD = 3.8 nM) as a small molecule inhibitor. In the tubular formation assay, it was observed that SFD could bind to HBD and exhibit antiangiogenic efficacy by inhibiting VEGF, such as heparins. The cellular treatment of SFD resulted in VEGF-inhibitory effects in human umbilical vein endothelial cells (HUVECs). Therefore, we propose that SFD can be employed as a novel drug candidate to inhibit the pathophysiological action of VEGF in diseases. Consequently, SFD, which has a molecular structure optimized for binding to HBD, is put forward as a new chemical VEGF inhibitor.


Assuntos
Heparina/química , Suramina/química , Fator A de Crescimento do Endotélio Vascular/genética , Sítios de Ligação/efeitos dos fármacos , Acetato de Desoxicorticosterona/química , Acetato de Desoxicorticosterona/farmacologia , Heparina/farmacologia , Células Endoteliais da Veia Umbilical Humana , Humanos , Suramina/farmacologia , Ressonância de Plasmônio de Superfície , Fator A de Crescimento do Endotélio Vascular/antagonistas & inibidores
14.
Open Biol ; 9(8): 190117, 2019 08 30.
Artigo em Inglês | MEDLINE | ID: mdl-31409229

RESUMO

Minichromosome maintenance protein 10 (Mcm10) is essential for DNA unwinding by the replisome during S phase. It is emerging as a promising anti-cancer target as MCM10 expression correlates with tumour progression and poor clinical outcomes. Here we used a competition-based fluorescence polarization (FP) high-throughput screening (HTS) strategy to identify compounds that inhibit Mcm10 from binding to DNA. Of the five active compounds identified, only the anti-parasitic agent suramin exhibited a dose-dependent decrease in replication products in an in vitro replication assay. Structure-activity relationship evaluation identified several suramin analogues that inhibited ssDNA binding by the human Mcm10 internal domain and full-length Xenopus Mcm10, including analogues that are selective for Mcm10 over human RPA. Binding of suramin analogues to Mcm10 was confirmed by surface plasmon resonance (SPR). SPR and FP affinity determinations were highly correlated, with a similar rank between affinity and potency for killing colon cancer cells. Suramin analogue NF157 had the highest human Mcm10 binding affinity (FP Ki 170 nM, SPR KD 460 nM) and cell activity (IC50 38 µM). Suramin and its analogues are the first identified inhibitors of Mcm10 and probably block DNA binding by mimicking the DNA sugar phosphate backbone due to their extended, polysulfated anionic structures.


Assuntos
Inibidores Enzimáticos/farmacologia , Proteínas de Manutenção de Minicromossomo/antagonistas & inibidores , Suramina/farmacologia , Animais , Sobrevivência Celular/efeitos dos fármacos , Sobrevivência Celular/genética , Replicação do DNA/efeitos dos fármacos , Proteínas de Ligação a DNA/antagonistas & inibidores , Descoberta de Drogas/métodos , Inibidores Enzimáticos/química , Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Cinética , Proteínas de Manutenção de Minicromossomo/genética , Estrutura Molecular , Ligação Proteica , Suramina/análogos & derivados , Suramina/química , Xenopus
15.
Phys Chem Chem Phys ; 21(20): 10644-10659, 2019 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-31080973

RESUMO

Dynamic increase of resistant bacterial infectious diseases continuously requires development of novel compounds against them. The molecular level understanding of the mechanism and interactions of natural host-defense peptides or antimicrobial peptides (AMPs) is an important step towards rational design and development of compounds inspired by their function. A particular set of these peptides have disordered structure, the ordering of which may modify their antimicrobial properties. Recent experiments demonstrate that such conformational transitions of AMPs could be mediated by the presence of small organic compounds, such as approved drug molecules. However, the molecular mechanisms underlying these structural changes are unclear. In this study, we apply molecular docking and molecular dynamics-based approaches to rigorously analyze the interactions between the drug suramin and the AMP CM15, a synthetic unstructured hybrid peptide. We characterize the energetic properties of putative CM15-suramin complexes revealing particular impacts of CM15 residues as well as the parts of suramin on these interactions. We find that α-helical content of the peptide is increased in the presence of suramin, which is in agreement with the experimental data. Kinetics analysis from canonical molecular dynamics and metadynamics simulations suggest that the effect of suramin does not promote the formation of α-helix but rather results from its ability to stabilize the α-helical population in the conformational pool of the peptide. Potentially, understanding the physico-chemical basis underlying the interactions between drug molecules and disordered AMPs will prove useful in strategies for antimicrobial compound development. Further on, the given computational protocol for the analysis of such flexible systems provide a basis for future theoretical investigation of similar biomolecular complexes.


Assuntos
Peptídeos Catiônicos Antimicrobianos/química , Simulação por Computador , Modelos Químicos , Suramina/química , Anti-Infecciosos/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular
16.
Sci Rep ; 9(1): 6350, 2019 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-31015525

RESUMO

Vitamin B12 acts as a cofactor for various metabolic reactions important in living organisms. The Vitamin B12 biosynthesis is restricted to prokaryotes, which means, all eukaryotic organisms must acquire this molecule through diet. This study presents the investigation of Vitamin B12 metabolism and the characterization of precorrin-4 C(11)-methyltransferase (CobM), an enzyme involved in the biosynthesis of Vitamin B12 in Corynebacterium pseudotuberculosis. The analysis of the C. pseudotuberculosis genome identified two Vitamin B12-dependent pathways, which can be strongly affected by a disrupted vitamin metabolism. Molecular dynamics, circular dichroism, and NMR-STD experiments identified regions in CobM that undergo conformational changes after s-adenosyl-L-methionine binding to promote the interaction of precorrin-4, a Vitamin B12 precursor. The binding of s-adenosyl-L-methionine was examined along with the competitive binding of adenine, dATP, and suramin. Based on fluorescence spectroscopy experiments the dissociation constant for the four ligands and the target protein could be determined; SAM (1.4 ± 0.7 µM), adenine (17.8 ± 1.5 µM), dATP (15.8 ± 2.0 µM), and Suramin (6.3 ± 1.1 µM). The results provide rich information for future investigations of potential drug targets within the C. pseudotuberculosis's Vitamin B12 metabolism and related pathways to reduce the pathogen's virulence in its hosts.


Assuntos
Corynebacterium pseudotuberculosis/metabolismo , Vitamina B 12/metabolismo , Adenina/química , Adenina/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Cinética , Ligantes , Simulação de Dinâmica Molecular , Ligação Proteica , Estrutura Secundária de Proteína , S-Adenosilmetionina/química , S-Adenosilmetionina/metabolismo , Espectrometria de Fluorescência , Homologia Estrutural de Proteína , Suramina/química , Suramina/metabolismo , Vitamina B 12/biossíntese , Vitamina B 12/química
17.
Bioorg Med Chem Lett ; 29(9): 1106-1112, 2019 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-30852084

RESUMO

All living organisms contain a unique class of molecular chaperones called 60 kDa heat shock proteins (HSP60 - also known as GroEL in bacteria). While some organisms contain more than one HSP60 or GroEL isoform, at least one isoform has always proven to be essential. Because of this, we have been investigating targeting HSP60 and GroEL chaperonin systems as an antibiotic strategy. Our initial studies focused on applying this antibiotic strategy for treating African sleeping sickness (caused by Trypanosoma brucei parasites) and drug-resistant bacterial infections (in particular Methicillin-resistant Staphylococcus aureus - MRSA). Intriguingly, during our studies we found that three known antibiotics - suramin, closantel, and rafoxanide - were potent inhibitors of bacterial GroEL and human HSP60 chaperonin systems. These findings prompted us to explore what other approved drugs, natural products, and known bioactive molecules might also inhibit HSP60 and GroEL chaperonin systems. Initial high-throughput screening of 3680 approved drugs, natural products, and known bioactives identified 161 hit inhibitors of the Escherichia coli GroEL chaperonin system (4.3% hit rate). From a purchased subset of 60 hits, 29 compounds (48%) re-confirmed as selective GroEL inhibitors in our assays, all of which were nearly equipotent against human HSP60. These findings illuminate the notion that targeting chaperonin systems might be a more common occurrence than we previously appreciated. Future studies are needed to determine if the in vivo modes of action of these approved drugs, natural products, and known bioactive molecules are related to GroEL and HSP60 inhibition.


Assuntos
Produtos Biológicos/química , Chaperonina 10/metabolismo , Chaperonina 60/metabolismo , Rafoxanida/química , Salicilanilidas/química , Suramina/química , Produtos Biológicos/metabolismo , Chaperonina 10/antagonistas & inibidores , Chaperonina 60/antagonistas & inibidores , Escherichia coli/metabolismo , Humanos , Concentração Inibidora 50 , Dobramento de Proteína , Rafoxanida/metabolismo , Salicilanilidas/metabolismo , Suramina/metabolismo
18.
J Med Chem ; 62(8): 4110-4119, 2019 04 25.
Artigo em Inglês | MEDLINE | ID: mdl-30925051

RESUMO

Zika virus (ZIKV), a mosquito-borne flavivirus, is a global health concern because of its association with severe neurological disorders. Currently, there are no antiviral therapies that have been specifically approved to treat ZIKV, and there is an urgent need to develop effective anti-ZIKV agents. Here, we report anti-ZIKV activity of 16 synthetic carbohydrate receptors (SCRs) that inhibit ZIKV infection in Vero and HeLa cells. Using a ZIKV reporter virus particle-based infection assay, our data demonstrates these SCRs are highly potent with IC50s as low as 0.16 µM and negligible toxicity at several-fold higher concentrations. Time-of-addition studies showed that these SCRs inhibit the early stages of the virus infection, which is consistent with the proposed mode of action, where the SCRs likely inhibit binding between the virus and cell-surface glycans, thereby preventing viral entry into the cells and, as such, this study demonstrates a potential new strategy against ZIKV.


Assuntos
Antivirais/química , Carboidratos/química , Receptores Artificiais/química , Zika virus/fisiologia , Animais , Antivirais/farmacologia , Antivirais/uso terapêutico , Sobrevivência Celular/efeitos dos fármacos , Chlorocebus aethiops , Células HeLa , Humanos , Receptores Artificiais/síntese química , Receptores Artificiais/metabolismo , Relação Estrutura-Atividade , Suramina/química , Suramina/farmacologia , Células Vero , Internalização do Vírus/efeitos dos fármacos , Infecção por Zika virus/tratamento farmacológico , Infecção por Zika virus/patologia
19.
Chembiochem ; 20(12): 1578-1590, 2019 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-30720915

RESUMO

Antimicrobial peptides (AMPs) kill bacteria by targeting their membranes through various mechanisms involving peptide assembly, often coupled with disorder-to-order structural transition. However, for several AMPs, similar conformational changes in cases in which small organic compounds of both endogenous and exogenous origin have induced folded peptide conformations have recently been reported. Thus, the function of AMPs and of natural host defence peptides can be significantly affected by the local complex molecular environment in vivo; nonetheless, this area is hardly explored. To address the relevance of such interactions with regard to structure and function, we have tested the effects of the therapeutic drug suramin on the membrane activity and antibacterial efficiency of CM15, a potent hybrid AMP. The results provided insight into a dynamic system in which peptide interaction with lipid bilayers is interfered with by the competitive binding of CM15 to suramin, resulting in an equilibrium dependent on peptide-to-drug ratio and vesicle surface charge. In vitro bacterial tests showed that when CM15⋅suramin complex formation dominates over membrane binding, antimicrobial activity is abolished. On the basis of this case study, it is proposed that small-molecule secondary structure regulators can modify AMP function and that this should be considered and could potentially be exploited in future development of AMP-based antimicrobial agents.


Assuntos
Anti-Infecciosos , Peptídeos Catiônicos Antimicrobianos , Suramina , Anti-Infecciosos/química , Anti-Infecciosos/farmacologia , Peptídeos Catiônicos Antimicrobianos/química , Peptídeos Catiônicos Antimicrobianos/farmacologia , Células Cultivadas , Dicroísmo Circular/métodos , Escherichia coli , Humanos , Bicamadas Lipídicas/química , Estrutura Secundária de Proteína , Suramina/química , Suramina/farmacologia
20.
Acta Biomater ; 84: 378-390, 2019 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-30528604

RESUMO

Suramin (SM), a drug for African sleeping sickness and river blindness therapy, has been investigated in various clinical trials for cancer therapy. However, SM was eventually withdrawn from the market because of its narrow therapeutic window and the side effects associated with multiple targets. In this work, we developed a simple but effective system based on a nontoxic dose of SM combined with a chemotherapeutic agent for the treatment of metastatic triple-negative breast cancer (TNBC). SM and glycol chitosan (GCS) formed nanogels because of the electrostatic effect, whereas doxorubicin (DOX) was incorporated into the system through the hydrophilic and hydrophobic interactions between DOX and GCS as well as the ionic interactions between DOX and SM to yield GCS-SM/DOX nanoparticles (NPs). GCS-SM/DOX NPs have a size of approximately 186 nm and a spherical morphology. In vitro experiments showed that GCS-SM NPs could effectively inhibit cancer cell migration and invasion, as well as angiogenesis. Furthermore, in a TNBC lung metastasis animal model, GCS-SM/DOX NPs significantly reduced tumor burden and extended the lifespan of animals, while not inducing cardio and renal toxicities associated with the DOX and SM, respectively. As all the components used in this system are biocompatible and easy for large-scale fabrication, the GCS-SM/DOX system is highly translatable for the metastatic breast cancer treatment. STATEMENT OF SIGNIFICANCE: The doxorubicin-loaded glycol chitosan-suramin nanoparticle (GCS-SM/DOX) is novel in the following aspects: SM acts as not only a gelator for the first time in the preparation of the nanoparticle but also an active pharmaceutical agent in the dosage form. GCS-SM/DOX NP significantly reduced tumor burden and extended the lifespan of animals with triple-negative breast cancer lung metastasis. GCS-SM/DOX NPs attenuate cardio and renal toxicities associated with the DOX and SM. The GCS-SM/DOX system is highly translatable because of its simple, one-pot, and easy-to-scale-up preparation protocol.


Assuntos
Quitosana , Doxorrubicina , Neoplasias Pulmonares , Nanopartículas , Suramina , Neoplasias de Mama Triplo Negativas , Animais , Linhagem Celular Tumoral , Quitosana/química , Quitosana/farmacocinética , Quitosana/farmacologia , Doxorrubicina/química , Doxorrubicina/farmacocinética , Doxorrubicina/farmacologia , Feminino , Células Endoteliais da Veia Umbilical Humana , Humanos , Interações Hidrofóbicas e Hidrofílicas , Neoplasias Pulmonares/tratamento farmacológico , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/patologia , Neoplasias Pulmonares/secundário , Camundongos , Camundongos Nus , Nanopartículas/química , Nanopartículas/uso terapêutico , Metástase Neoplásica , Suramina/química , Suramina/farmacocinética , Suramina/farmacologia , Neoplasias de Mama Triplo Negativas/tratamento farmacológico , Neoplasias de Mama Triplo Negativas/metabolismo , Neoplasias de Mama Triplo Negativas/patologia , Ensaios Antitumorais Modelo de Xenoenxerto
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