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1.
Proc Natl Acad Sci U S A ; 121(12): e2313513121, 2024 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-38483989

RESUMO

Cooperative interactions between amino acids are critical for protein function. A genetic reflection of cooperativity is epistasis, which is when a change in the amino acid at one position changes the sequence requirements at another position. To assess epistasis within an enzyme active site, we utilized CTX-M ß-lactamase as a model system. CTX-M hydrolyzes ß-lactam antibiotics to provide antibiotic resistance, allowing a simple functional selection for rapid sorting of modified enzymes. We created all pairwise mutations across 17 active site positions in the ß-lactamase enzyme and quantitated the function of variants against two ß-lactam antibiotics using next-generation sequencing. Context-dependent sequence requirements were determined by comparing the antibiotic resistance function of double mutations across the CTX-M active site to their predicted function based on the constituent single mutations, revealing both positive epistasis (synergistic interactions) and negative epistasis (antagonistic interactions) between amino acid substitutions. The resulting trends demonstrate that positive epistasis is present throughout the active site, that epistasis between residues is mediated through substrate interactions, and that residues more tolerant to substitutions serve as generic compensators which are responsible for many cases of positive epistasis. Additionally, we show that a key catalytic residue (Glu166) is amenable to compensatory mutations, and we characterize one such double mutant (E166Y/N170G) that acts by an altered catalytic mechanism. These findings shed light on the unique biochemical factors that drive epistasis within an enzyme active site and will inform enzyme engineering efforts by bridging the gap between amino acid sequence and catalytic function.


Assuntos
Escherichia coli , beta-Lactamases , Escherichia coli/genética , Domínio Catalítico/genética , Mutação , Substituição de Aminoácidos , beta-Lactamases/química
2.
Proc Natl Acad Sci U S A ; 121(19): e2322934121, 2024 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-38701119

RESUMO

EPH receptors (EPHs), the largest family of tyrosine kinases, phosphorylate downstream substrates upon binding of ephrin cell surface-associated ligands. In a large cohort of endometriotic lesions from individuals with endometriosis, we found that EPHA2 and EPHA4 expressions are increased in endometriotic lesions relative to normal eutopic endometrium. Because signaling through EPHs is associated with increased cell migration and invasion, we hypothesized that chemical inhibition of EPHA2/4 could have therapeutic value. We screened DNA-encoded chemical libraries (DECL) to rapidly identify EPHA2/4 kinase inhibitors. Hit compound, CDD-2693, exhibited picomolar/nanomolar kinase activity against EPHA2 (Ki: 4.0 nM) and EPHA4 (Ki: 0.81 nM). Kinome profiling revealed that CDD-2693 bound to most EPH family and SRC family kinases. Using NanoBRET target engagement assays, CDD-2693 had nanomolar activity versus EPHA2 (IC50: 461 nM) and EPHA4 (IC50: 40 nM) but was a micromolar inhibitor of SRC, YES, and FGR. Chemical optimization produced CDD-3167, having picomolar biochemical activity toward EPHA2 (Ki: 0.13 nM) and EPHA4 (Ki: 0.38 nM) with excellent cell-based potency EPHA2 (IC50: 8.0 nM) and EPHA4 (IC50: 2.3 nM). Moreover, CDD-3167 maintained superior off-target cellular selectivity. In 12Z endometriotic epithelial cells, CDD-2693 and CDD-3167 significantly decreased EFNA5 (ligand) induced phosphorylation of EPHA2/4, decreased 12Z cell viability, and decreased IL-1ß-mediated expression of prostaglandin synthase 2 (PTGS2). CDD-2693 and CDD-3167 decreased expansion of primary endometrial epithelial organoids from patients with endometriosis and decreased Ewing's sarcoma viability. Thus, using DECL, we identified potent pan-EPH inhibitors that show specificity and activity in cellular models of endometriosis and cancer.


Assuntos
Inibidores de Proteínas Quinases , Humanos , Feminino , Inibidores de Proteínas Quinases/farmacologia , Inibidores de Proteínas Quinases/química , Endometriose/tratamento farmacológico , Endometriose/metabolismo , Endometriose/patologia , DNA/metabolismo , Receptores da Família Eph/metabolismo , Receptores da Família Eph/antagonistas & inibidores , Receptor EphA2/metabolismo , Receptor EphA2/antagonistas & inibidores , Bibliotecas de Moléculas Pequenas/farmacologia , Bibliotecas de Moléculas Pequenas/química , Movimento Celular/efeitos dos fármacos
3.
Physiol Plant ; 176(4): e14447, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39149796

RESUMO

There is a focus on sustainability when manufacturing materials. Utilizing biobased materials and replacing fossil-based products is the main research focus. Bio-composite materials are applied to packaging, filler coatings, and pharmaceuticals. Here, we used the leaves of the agro-waste plant Albizia lebeck L. to extract cellulose. Chemical treatment causing strong acid hydrolysis successfully extracted the cellulose content from the leaves. The cellulose obtained was then strengthened with polylactic acid to make a biobased film for future applications. Fourier transform spectroscopy, scanning electron microscopy, thermal analysis, particle size analysis, visible UV and elemental analysis were all used to characterize the extracted cellulose. SEM and mechanical property analysis were used to check and describe the quality of the reinforced biofilm. The greatest cellulose yield from this raw material was 50.2%. The crystallinity index and crystallite size (CI 70.3% and CS 11.29 nm) were high in the extracted cellulose. The TG (DTG) curve analysis derivative revealed cellulose particle breakdown was initiated around 305.2°C and can endure temperatures up to 600°C. Biofilms reinforced with polylactic acid cellulose (1, 2, 3, and 5% by weight %) exhibited a smooth and parallel surface. As the filler concentration increased, minor agglomeration occurred. The tensile strength of pure polylactic acid (PLA) (34.72 MPa) was extended up to 38.91 MPa for 5% filler. Similarly, Young's modulus also increased to 5.24 MPa. However, the elongation break decreases with the increase of filler content, and the least value of decrease is 7.5 MPa. Concerning prospective implementations, it is expected that the biobased film and cellulose particles will prove to be more functional.


Assuntos
Biomassa , Celulose , Folhas de Planta , Celulose/química , Celulose/metabolismo , Folhas de Planta/química , Folhas de Planta/metabolismo , Espectroscopia de Infravermelho com Transformada de Fourier , Microscopia Eletrônica de Varredura , Resistência à Tração , Poliésteres/química , Poliésteres/metabolismo , Biofilmes/crescimento & desenvolvimento
4.
Physiol Plant ; 176(2): e14279, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38629121

RESUMO

A number of natural fibers are being proposed for use in composite materials, especially those extracted from local plants, especially those able to grow spontaneously as they are cost-efficient and have unexplored potential. Sansevieria cylindrica, within the Asparagaceae (previously Agavacae) family, has recently been considered for application in polymer and rubber matrix composites. However, its characterization and even the sorting out of technical fiber from the stem remains scarce, with little available data, as is often the case when the fabrication of textiles is not involved. In this study, Sansevieria cylindrica fibers were separated down to the dimensions of a filament at an 8-15 micron diameter from the stem of the plant, then characterized physically and chemically, using Fourier transform infrared spectroscopy (FTIR), morphologically by scanning electron microscopy (SEM), as well as their thermal degradation, by thermogravimetric analysis (TGA). Their crystallinity surface roughness was measured by X-ray diffraction (XRD) and atomic force microscopy (AFM), respectively. The results indicate over 70% cellulose fibers content with a very high crystallinity (92%) and small crystallite size (1.45 nm), which suggests a low water absorption, with thermal degradation peaking at 294°C. Despite this, due to the significant porosity of the cellular structure, the density of 1.06 g cm-3 is quite low for a mainly cellulose fiber. Roughness measurements indicate that the porosities and foamy structure result in a highly negative skewness (-3.953), in the presence of deep valleys, which may contribute to an effective relation with a covering resin.


Assuntos
Sansevieria , Celulose/química , Flores , Espectroscopia de Infravermelho com Transformada de Fourier , Água
5.
J Proteome Res ; 22(6): 2092-2108, 2023 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-37220064

RESUMO

Ovarian cancer (OC) is one of the deadliest cancers affecting the female reproductive system. It may present little or no symptoms at the early stages and typically unspecific symptoms at later stages. High-grade serous ovarian cancer (HGSC) is the subtype responsible for most ovarian cancer deaths. However, very little is known about the metabolic course of this disease, particularly in its early stages. In this longitudinal study, we examined the temporal course of serum lipidome changes using a robust HGSC mouse model and machine learning data analysis. Early progression of HGSC was marked by increased levels of phosphatidylcholines and phosphatidylethanolamines. In contrast, later stages featured more diverse lipid alterations, including fatty acids and their derivatives, triglycerides, ceramides, hexosylceramides, sphingomyelins, lysophosphatidylcholines, and phosphatidylinositols. These alterations underscored unique perturbations in cell membrane stability, proliferation, and survival during cancer development and progression, offering potential targets for early detection and prognosis of human ovarian cancer.


Assuntos
Cistadenocarcinoma Seroso , Neoplasias Ovarianas , Camundongos , Animais , Feminino , Humanos , Lipidômica , Estudos Longitudinais , Neoplasias Ovarianas/metabolismo , Esfingomielinas/metabolismo , Cistadenocarcinoma Seroso/metabolismo
6.
Molecules ; 25(23)2020 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-33261104

RESUMO

In the present study, a model is presented to optimize the fabrication parameters of natural fiber reinforced polyester matrix composites with dual fillers. In particular, jute fiber mat was chosen as reinforcement and eggshell powder (ESP) and montmorillonite nanoclay (NC) were selected as fillers. The weight per square meter (GSM) of the fiber, the weight percentage of ESP and NC have been chosen as independent variables and the influence of these variables on tensile, flexural and impact strength of the composite has been inspected. The permutations of the different combinations of factors are intended to accomplish higher interfacial strength with the lowest possible number of tested specimens. The experiments were designed by the Taguchi strategy and a novel multi-objective optimization technique named COPRAS (COmplex PRoportional ASsessment of alternatives) was used to determine the optimal parameter combinations. Affirmation tests were performed with the optimal parameter settings and the mechanical properties were evaluated and compared. Experimental results show that fiber GSM and eggshell powder content are significant variables that improve mechanical strength, while the nanoclay appears less important.


Assuntos
Argila/química , Resinas Compostas/normas , Corchorus/química , Casca de Ovo/química , Vidro/química , Nanoestruturas/química , Poliésteres/química , Animais , Resinas Compostas/química , Elasticidade , Filtração/instrumentação , Teste de Materiais , Metacrilatos/química , Nanotecnologia , Pós/química , Propriedades de Superfície , Resistência à Tração
7.
Bioconjug Chem ; 30(8): 2209-2215, 2019 08 21.
Artigo em Inglês | MEDLINE | ID: mdl-31329429

RESUMO

A strategy for DNA-compatible, palladium-catalyzed hydroxycarbonylation of (hetero)aryl halides on DNA-chemical conjugates has been developed. This method generally provided the corresponding carboxylic acids in moderate to very good conversions for (hetero)aryl iodides and bromides, and in poor to moderate conversions for (hetero)aryl chlorides. These conditions were further validated by application within a DNA-encoded chemical library synthesis and subsequent discovery of enriched features from the library in selection experiments against two protein targets.


Assuntos
DNA/química , Hidrocarbonetos Halogenados/química , Bibliotecas de Moléculas Pequenas/síntese química , Catálise , Paládio , Proteínas/antagonistas & inibidores
8.
J Med Chem ; 67(1): 620-642, 2024 01 11.
Artigo em Inglês | MEDLINE | ID: mdl-38117688

RESUMO

ß-Lactamase enzymes hydrolyze and thereby provide bacterial resistance to the important ß-lactam class of antibiotics. The OXA-48 and NDM-1 ß-lactamases cause resistance to the last-resort ß-lactams, carbapenems, leading to a serious public health threat. Here, we utilized DNA-encoded chemical library (DECL) technology to discover novel ß-lactamase inhibitors. We exploited the ß-lactamase enzyme-substrate binding interactions and created a DECL targeting the carboxylate-binding pocket present in all ß-lactamases. A library of 106 compounds, each containing a carboxylic acid or a tetrazole as an enzyme recognition element, was designed, constructed, and used to identify OXA-48 and NDM-1 inhibitors with micromolar to nanomolar potency. Further optimization led to NDM-1 inhibitors with increased potencies and biological activities. This work demonstrates that the carboxylate-binding pocket-targeting DECL, designed based on substrate binding information, aids in inhibitor identification and led to the discovery of novel non-ß-lactam pharmacophores for the development of ß-lactamase inhibitors for enzymes of different structural and mechanistic classes.


Assuntos
Antibacterianos , Inibidores de beta-Lactamases , Inibidores de beta-Lactamases/farmacologia , Inibidores de beta-Lactamases/química , Antibacterianos/farmacologia , Antibacterianos/química , beta-Lactamases/metabolismo , beta-Lactamas/farmacologia , Penicilinas , DNA , Testes de Sensibilidade Microbiana
9.
Science ; 384(6698): 885-890, 2024 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-38781365

RESUMO

Men or mice with homozygous serine/threonine kinase 33 (STK33) mutations are sterile owing to defective sperm morphology and motility. To chemically evaluate STK33 for male contraception with STK33-specific inhibitors, we screened our multibillion-compound collection of DNA-encoded chemical libraries, uncovered potent STK33-specific inhibitors, determined the STK33 kinase domain structure bound with a truncated hit CDD-2211, and generated an optimized hit CDD-2807 that demonstrates nanomolar cellular potency (half-maximal inhibitory concentration = 9.2 nanomolar) and favorable metabolic stability. In mice, CDD-2807 exhibited no toxicity, efficiently crossed the blood-testis barrier, did not accumulate in brain, and induced a reversible contraceptive effect that phenocopied genetic STK33 perturbations without altering testis size. Thus, STK33 is a chemically validated, nonhormonal contraceptive target, and CDD-2807 is an effective tool compound.


Assuntos
Anticoncepção , Anticoncepcionais Masculinos , Inibidores de Proteínas Quinases , Proteínas Serina-Treonina Quinases , Bibliotecas de Moléculas Pequenas , Animais , Humanos , Masculino , Camundongos , Barreira Hematotesticular/metabolismo , Anticoncepcionais Masculinos/química , Anticoncepcionais Masculinos/farmacologia , Inibidores de Proteínas Quinases/farmacologia , Inibidores de Proteínas Quinases/química , Proteínas Serina-Treonina Quinases/antagonistas & inibidores , Proteínas Serina-Treonina Quinases/química , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/farmacologia , Testículo/efeitos dos fármacos , Anticoncepção/métodos , Relação Estrutura-Atividade
10.
Environ Sci Pollut Res Int ; 30(49): 107498-107516, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37126160

RESUMO

The near-dry electrical discharge machining processes have been conducted using air-mist or gas mist as a dielectric fluid to minimize the environmental impacts. In this article, near-dry electrical discharge machining (NDEDM) experiments have been performed to improve machining performance using an oxygen-mist dielectric fluid, a copper composite electrode, and Cu-Al-Be polycrystalline shape memory alloy (SMA) work materials. The copper composite electrode is made up of 12 wt% silicon carbide and 9 wt% graphite particles. The oxygen-mist pressure (Op), pulse on time (Ton), spark current (Ip), gap voltage (Gv), and flow rate of mixed water (Fr) were used as process parameters, and the material removal rate (MRR), tool wear rate (TWR), and surface roughness (SR) were used as performance characteristics. The global optimal alternative solution has been predicted by the PROMETHEE-II (Preference Ranking Organization METhod for Enrichment Evaluations-II) optimization technique. The best combinations of process parameters have been used to examine the microstructure of composite tools and SMA-machined surfaces by scanning electron microscopy (SEM) analysis. The best global optimum settings (oP: 9 bar, Ip: 60 µs, Ip: 12 A, Gv: 40 V, and Fr: 12 ml/min) are predicted to attain optimum machining performance (MRR: 39.049 g/min, TWR: 1.586 g/min, and SR: 1.78 µm). The tool wear rate of the NDEDM process has been significantly reduced by the copper composite electrode due to increasing microhardness, wear resistance, and melting point. When compared to the pure copper electrode tool, the MRR of NDEDM is improved to 21.91%, while the TWR and SR are reduced to 46.66% and 35.02%, respectively.


Assuntos
Cobre , Ligas de Memória da Forma , Ligas , Eletrodos , Oxigênio
11.
bioRxiv ; 2023 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-36711577

RESUMO

Ovarian cancer (OC) is one of the deadliest cancers affecting the female reproductive system. It may present little or no symptoms at the early stages, and typically unspecific symptoms at later stages. High-grade serous ovarian cancer (HGSC) is the subtype responsible for most ovarian cancer deaths. However, very little is known about the metabolic course of this disease, particularly in its early stages. In this longitudinal study, we examined the temporal course of serum lipidome changes using a robust HGSC mouse model and machine learning data analysis. Early progression of HGSC was marked by increased levels of phosphatidylcholines and phosphatidylethanolamines. In contrast, later stages featured more diverse lipids alterations, including fatty acids and their derivatives, triglycerides, ceramides, hexosylceramides, sphingomyelins, lysophosphatidylcholines, and phosphatidylinositols. These alterations underscored unique perturbations in cell membrane stability, proliferation, and survival during cancer development and progression, offering potential targets for early detection and prognosis of human ovarian cancer. Teaser: Time-resolved lipidome remodeling in an ovarian cancer model is studied through lipidomics and machine learning.

12.
bioRxiv ; 2023 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-37961688

RESUMO

No effective screening tools for ovarian cancer (OC) exist, making it one of the deadliest cancers among women. Considering little is known about the detailed progression and metastasis mechanism of OC at a molecular level, it is crucial to gain more insights on how metabolic and signaling alterations accompany its development. Herein, we present a comprehensive study using ultra-high-resolution Fourier transform ion cyclotron resonance matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to investigate the spatial distribution and alterations of lipids in ovarian tissues collected from double knockout (n = 4) and a triple mutant mouse models (n = 4) of high-grade serous ovarian cancer (HGSC). Lipids belonging to a total of 15 different classes were annotated and their abundance changes compared to those in healthy mouse reproductive tissue (n = 4), mapping onto major lipid pathways involved in OC progression. From intermediate-stage OC to advanced HGSC, we provide a direct visualization of lipid distributions and their biological links to inflammatory response, cellular stress, cell proliferation, and other processes. We also show the ability to distinguish tumors at different stages from healthy tissues via a number of highly specific lipid biomarkers, providing targets for future panels that could be useful in diagnosis.

13.
J Med Chem ; 66(3): 2143-2160, 2023 02 09.
Artigo em Inglês | MEDLINE | ID: mdl-36719862

RESUMO

The discovery of monokinase-selective inhibitors for patients is challenging because the 500+ kinases encoded by the human genome share highly conserved catalytic domains. Until now, no selective inhibitors unique for a single transforming growth factor ß (TGFß) family transmembrane receptor kinase, including bone morphogenetic protein receptor type 2 (BMPR2), have been reported. This dearth of receptor-specific kinase inhibitors hinders therapeutic options for skeletal defects and cancer as a result of an overactivated BMP signaling pathway. By screening 4.17 billion "unbiased" and "kinase-biased" DNA-encoded chemical library molecules, we identified hits CDD-1115 and CDD-1431, respectively, that were low-nanomolar selective kinase inhibitors of BMPR2. Structure-activity relationship studies addressed metabolic lability and high-molecular-weight issues, resulting in potent and BMPR2-selective inhibitor analogs CDD-1281 (IC50 = 1.2 nM) and CDD-1653 (IC50 = 2.8 nM), respectively. Our work demonstrates that DNA-encoded chemistry technology (DEC-Tec) is reliable for identifying novel first-in-class, highly potent, and selective kinase inhibitors.


Assuntos
DNA , Transdução de Sinais , Humanos , Biblioteca Gênica , Receptores de Proteínas Morfogenéticas Ósseas Tipo II/química , Receptores de Proteínas Morfogenéticas Ósseas Tipo II/genética , Receptores de Proteínas Morfogenéticas Ósseas Tipo II/metabolismo
14.
Andrology ; 11(5): 808-815, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-36209044

RESUMO

BACKGROUND: A safe, effective, and reversible nonhormonal male contraceptive drug is greatly needed for male contraception as well as for circumventing the side effects of female hormonal contraceptives. Phosducin-like 2 (PDCL2) is a testis-specific phosphoprotein in mice and humans. We recently found that male PDCL2 knockout mice are sterile due to globozoospermia caused by impaired sperm head formation, indicating that PDCL2 is a potential target for male contraception. Herein, our study for the first time developed a biophysical assay for PDCL2 allowing us to screen a series of small molecules, to study structure-activity relationships, and to discover two PDCL2 binders with novel chemical structure. OBJECTIVE: To identify a PDCL2 ligand for therapeutic male contraception, we performed DNA-encoded chemical library (DECL) screening and off-DNA hit validation using a unique affinity selection mass spectrometry (ASMS) biophysical profiling strategy. MATERIALS AND METHODS: We employed the screening process of DECL, which contains billions of chemically unique DNA-barcoded compounds generated through individual sequences of reactions and different combinations of functionalized building blocks. The structures of the PDCL2 binders are proposed based on the sequencing analysis of the DNA barcode attached to each individual DECL compound. The proposed structure is synthesized through multistep reactions. To confirm and determine binding affinity between the DECL identified molecules and PDCL2, we developed an ASMS assay that incorporates liquid chromatography with tandem mass spectrometry (LC-MS/MS). RESULTS: After a screening process of PDCL2 with DECLs containing >440 billion compounds, we identified a series of hits. The selected compounds were synthesized as off-DNA small molecules, characterized by spectroscopy data, and subjected to our ASMS/LC-MS/MS binding assay. By this assay, we discovered two novel compounds, which showed good binding affinity for PDCL2 in comparison to other molecules generated in our laboratory and which were further confirmed by a thermal shift assay. DISCUSSION AND CONCLUSION AND RELEVANCE: With the ASMS/LC-MS/MS assay developed in this paper, we successfully discovered a PDCL2 ligand that warrants further development as a male contraceptive.


Assuntos
DNA , Bibliotecas de Moléculas Pequenas , Humanos , Masculino , Feminino , Animais , Camundongos , DNA/metabolismo , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/metabolismo , Bibliotecas de Moléculas Pequenas/farmacologia , Descoberta de Drogas , Ligantes , Cromatografia Líquida , Espectrometria de Massas em Tandem , Sêmen/metabolismo
15.
Front Chem ; 11: 1332816, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-38260043

RESUMO

No effective screening tools for ovarian cancer (OC) exist, making it one of the deadliest cancers among women. Considering that little is known about the detailed progression and metastasis mechanism of OC at a molecular level, it is crucial to gain more insights into how metabolic and signaling alterations accompany its development. Herein, we present a comprehensive study using ultra-high-resolution Fourier transform ion cyclotron resonance matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to investigate the spatial distribution and alterations of lipids in ovarian tissues collected from double knockout (n = 4) and triple mutant mouse models (n = 4) of high-grade serous ovarian cancer (HGSOC). Lipids belonging to a total of 15 different classes were annotated and their abundance changes were compared to those in healthy mouse reproductive tissue (n = 4), mapping onto major lipid pathways involved in OC progression. From intermediate-stage OC to advanced HGSC, we provide direct visualization of lipid distributions and their biological links to inflammatory response, cellular stress, cell proliferation, and other processes. We also show the ability to distinguish tumors at different stages from healthy tissues via a number of highly specific lipid biomarkers, providing targets for future panels that could be useful in diagnosis.

16.
Nat Commun ; 13(1): 6726, 2022 11 07.
Artigo em Inglês | MEDLINE | ID: mdl-36344533

RESUMO

ß-lactamases inactivate ß-lactam antibiotics leading to drug resistance. Consequently, inhibitors of ß-lactamases can combat this resistance, and the ß-lactamase inhibitory protein (BLIP) is a naturally occurring inhibitor. The widespread CTX-M-14 and CTX-M-15 ß-lactamases have an 83% sequence identity. In this study, we show that BLIP weakly inhibits CTX-M-14 but potently inhibits CTX-M-15. The structure of the BLIP/CTX-M-15 complex reveals that binding is associated with a conformational change of an active site loop of ß-lactamase. Surprisingly, the loop structure in the complex is similar to that in a drug-resistant variant (N106S) of CTX-M-14. We hypothesized that the pre-established favorable loop conformation of the N106S mutant would facilitate binding. The N106S substitution results in a ~100- and 10-fold increase in BLIP inhibition potency for CTX-M-14 and CTX-M-15, respectively. Thus, this indicates that an active site loop in ß-lactamase toggles between conformations that control antibiotic hydrolysis and inhibitor susceptibility. These findings highlight the role of accessible active site conformations in controlling enzyme activity and inhibitor susceptibility as well as the influence of mutations in selectively stabilizing discrete conformations.


Assuntos
Antibacterianos , Escherichia coli , Antibacterianos/farmacologia , Antibacterianos/química , Domínio Catalítico , Hidrólise , Escherichia coli/metabolismo , beta-Lactamases/metabolismo
17.
ACS Comb Sci ; 22(2): 80-88, 2020 02 10.
Artigo em Inglês | MEDLINE | ID: mdl-31913011

RESUMO

Reaction heterogeneity, poor pH control, and catalyst decomposition in the ring-closing metathesis (RCM) of DNA-chemical conjugates lead to poor yields of the cyclized products. Herein we address these issues with a RCM reaction system that includes a novel aqueous solvent combination to enable reaction homogeneity, an acidic buffer system which masks traditionally problematic functional groups, and a decomposition-resistant catalyst which maximizes conversion to the cyclized product. Additionally, we provide a systematic study of the substrate scope of the on-DNA RCM reaction, a demonstration of its applicability to a single-substrate DNA-encoded chemical library that includes sequencing analysis, and the first successful stapling of an unprotected on-DNA [i, i+4] peptide.


Assuntos
DNA/química , Peptídeos/química , Bibliotecas de Moléculas Pequenas/química , Soluções Tampão , Catálise , Ciclização , DNA/síntese química , Biblioteca Gênica , Peptídeos/síntese química , Bibliotecas de Moléculas Pequenas/síntese química
18.
ACS Infect Dis ; 6(5): 1214-1227, 2020 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-32182432

RESUMO

Bacterial resistance to ß-lactam antibiotics is largely mediated by ß-lactamases, which catalyze the hydrolysis of these drugs and continue to emerge in response to antibiotic use. ß-Lactamases that hydrolyze the last resort carbapenem class of ß-lactam antibiotics (carbapenemases) are a growing global health threat. Inhibitors have been developed to prevent ß-lactamase-mediated hydrolysis and restore the efficacy of these antibiotics. However, there are few inhibitors available for problematic carbapenemases such as oxacillinase-48 (OXA-48). A DNA-encoded chemical library approach was used to rapidly screen for compounds that bind and potentially inhibit OXA-48. Using this approach, a hit compound, CDD-97, was identified with submicromolar potency (Ki = 0.53 ± 0.08 µM) against OXA-48. X-ray crystallography showed that CDD-97 binds noncovalently in the active site of OXA-48. Synthesis and testing of derivatives of CDD-97 revealed structure-activity relationships and informed the design of a compound with a 2-fold increase in potency. CDD-97, however, synergizes poorly with ß-lactam antibiotics to inhibit the growth of bacteria expressing OXA-48 due to poor accumulation into E. coli. Despite the low in vivo activity, CDD-97 provides new insights into OXA-48 inhibition and demonstrates the potential of using DNA-encoded chemistry technology to rapidly identify ß-lactamase binders and to study ß-lactamase inhibition, leading to clinically useful inhibitors.


Assuntos
Proteínas de Bactérias/antagonistas & inibidores , Bibliotecas de Moléculas Pequenas , Inibidores de beta-Lactamases , DNA , Escherichia coli/efeitos dos fármacos , Inibidores de beta-Lactamases/farmacologia , beta-Lactamases
19.
Biol Reprod ; 81(2): 284-92, 2009 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-19299314

RESUMO

Theca-interstitial (T-I) cells of the ovary synthesize androgens in response to luteinizing hormone (LH). In pathological conditions such as polycystic ovarian syndrome, T-I cells are hyperactive in androgen production in response to LH and insulin. Because cholesterol is an essential substrate for androgen production, we examined the effect of human chorionic gonadotropin (hCG) and insulin on signaling pathways that are known to increase cholesterol accumulation in steroidogenic cells. Specifically, the effect of hCG and insulin on sterol regulatory element-binding transcription factor 1a (SREBF1a) required for cholesterol biosynthesis and uptake was examined. Primary cultures of T-I cells isolated from 25-day-old rat ovaries responded to hCG and insulin to increase the active/processed form of SREBF1a. The hCG and insulin significantly reduced insulin-induced gene 1 (INSIG1) protein, a negative regulator of SREBF processing. Furthermore, an increase in the expression of selected SREBF target genes, 3-hydroxy-3-methylglutaryl-coenzyme A reductase (Hmgcr) and mevalonate kinase (Mvk), was also observed. Protein kinase A (PRKA) inhibitor completely abolished the hCG-induced increase in SREBF1a, while increasing INSIG1. Although the hCG-induced depletion of total and free cholesterol was abolished by aminoglutethimide, the stimulatory effect on SREBF1a was not totally suppressed. Treatment with 25-hydroxycholesterol abrogated the effect of hCG on SREBF1a. Inhibition of the phosphatidylinositol 3-kinase pathway did not block the insulin-induced increase in SREBF1a, whereas mitogen-activated protein kinase inhibition reduced the insulin response. These results suggest that the increased androgen biosynthesis by T-I cells in response to hCG and insulin is regulated, at least in part, by increasing the expression of sterol response element-responsive genes by increasing SREBF1a.


Assuntos
Gonadotropina Coriônica/fisiologia , Insulina/fisiologia , Proteína de Ligação a Elemento Regulador de Esterol 1/genética , Células Tecais/metabolismo , Proteínas Quinases Ativadas por AMP/antagonistas & inibidores , Aminoglutetimida/metabolismo , Análise de Variância , Androgênios/biossíntese , Androstenodiona/biossíntese , Animais , Células Cultivadas , Colesterol/metabolismo , Gonadotropina Coriônica/metabolismo , Feminino , Regulação da Expressão Gênica , Hidroxicolesteróis/metabolismo , Hidroximetilglutaril-CoA Redutases/genética , Hidroximetilglutaril-CoA Redutases/metabolismo , Insulina/metabolismo , Peptídeos e Proteínas de Sinalização Intracelular , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Proteína Quinase 1 Ativada por Mitógeno/antagonistas & inibidores , Inibidores de Fosfoinositídeo-3 Quinase , Fosfotransferases (Aceptor do Grupo Álcool)/genética , Fosfotransferases (Aceptor do Grupo Álcool)/metabolismo , Ratos , Ratos Sprague-Dawley , Esteroide 17-alfa-Hidroxilase/metabolismo , Proteína de Ligação a Elemento Regulador de Esterol 1/metabolismo , Células Tecais/química
20.
Org Lett ; 21(7): 2194-2199, 2019 04 05.
Artigo em Inglês | MEDLINE | ID: mdl-30860855

RESUMO

A hypodiboric acid system for the reduction of nitro groups on DNA-chemical conjugates has been developed. This transformation provided good to excellent yields of the reduced amine product for a variety of functionalized aromatic, heterocyclic, and aliphatic nitro compounds. DNA tolerance to reaction conditions, extension to decigram scale reductions, successful use in a DNA-encoded chemical library synthesis, and subsequent target selection are also described.


Assuntos
Aminas/química , Compostos de Boro/química , DNA/metabolismo , Nitrocompostos/química , Catálise , DNA/química , Estrutura Molecular
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