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1.
Sci Rep ; 14(1): 12239, 2024 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-38806565

RESUMO

Laser-driven dynamic compression experiments of plastic materials have found surprisingly fast formation of nanodiamonds (ND) via X-ray probing. This mechanism is relevant for planetary models, but could also open efficient synthesis routes for tailored NDs. We investigate the release mechanics of compressed NDs by molecular dynamics simulation of the isotropic expansion of finite size diamond from different P-T states. Analysing the structural integrity along different release paths via molecular dynamic simulations, we found substantial disintegration rates upon shock release, increasing with the on-Hugnoiot shock temperature. We also find that recrystallization can occur after the expansion and hence during the release, depending on subsequent cooling mechanisms. Our study suggests higher ND recovery rates from off-Hugoniot states, e.g., via double-shocks, due to faster cooling. Laser-driven shock compression experiments of polyethylene terephthalate (PET) samples with in situ X-ray probing at the simulated conditions found diamond signal that persists up to 11 ns after breakout. In the diffraction pattern, we observed peak shifts, which we attribute to thermal expansion of the NDs and thus a total release of pressure, which indicates the stability of the released NDs.

2.
Eur J Med Chem ; 269: 116308, 2024 Apr 05.
Artigo em Inglês | MEDLINE | ID: mdl-38503166

RESUMO

Plasmodium multi-resistance, including against artemisinin, seriously threatens malaria treatment and control. Hence, new drugs are urgently needed, ideally targeting different parasitic stages, which are not yet targeted by current drugs. The SUB1 protease is involved in both hepatic and blood stages due to its essential role in the egress of parasites from host cells, and, as potential new target, it would meet the above criteria. We report here the synthesis as well as the biological and structural evaluation of substrate-based α-ketoamide SUB1 pseudopeptidic inhibitors encompassing positions P4-P2'. By individually substituting each position of the reference compound 1 (MAM-117, Ac-Ile-Thr-Ala-AlaCO-Asp-Glu (Oall)-NH2), we better characterized the structural determinants for SUB1 binding. We first identified compound 8 with IC50 values of 50 and 570 nM against Pv- and PfSUB1, respectively (about 3.5-fold higher potency compared to 1). Compound 8 inhibited P. falciparum merozoite egress in culture by 37% at 100 µM. By increasing the overall hydrophobicity of the compounds, we could improve the PfSUB1 inhibition level and antiparasitic activity, as shown with compound 40 (IC50 values of 12 and 10 nM against Pv- and PfSUB1, respectively, IC50 value of 23 µM on P. falciparum merozoite egress). We also found that 8 was highly selective towards SUB1 over three mammalian serine peptidases, supporting the promising value of this compound. Finally, several crystal 3D-structures of SUB1-inhibitor complexes, including with 8, were solved at high resolution to decipher the binding mode of these compounds.


Assuntos
Antimaláricos , Malária Falciparum , Malária , Parasitos , Animais , Subtilisina/metabolismo , Sequência de Aminoácidos , Plasmodium falciparum/metabolismo , Peptídeos , Malária Falciparum/parasitologia , Serina Proteases/metabolismo , Relação Estrutura-Atividade , Antimaláricos/farmacologia , Antimaláricos/química , Proteínas de Protozoários , Mamíferos/metabolismo
3.
Acta Crystallogr D Struct Biol ; 79(Pt 8): 721-734, 2023 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-37428845

RESUMO

The constant selection and propagation of multi-resistant Plasmodium sp. parasites require the identification of new antimalarial candidates involved in as-yet untargeted metabolic pathways. Subtilisin-like protease 1 (SUB1) belongs to a new generation of drug targets because it plays a crucial role during egress of the parasite from infected host cells at different stages of its life cycle. SUB1 is characterized by an unusual pro-region that tightly interacts with its cognate catalytic domain, thus precluding 3D structural analysis of enzyme-inhibitor complexes. In the present study, to overcome this limitation, stringent ionic conditions and controlled proteolysis of recombinant full-length P. vivax SUB1 were used to obtain crystals of an active and stable catalytic domain (PvS1Cat) without a pro-region. High-resolution 3D structures of PvS1Cat, alone and in complex with an α-ketoamide substrate-derived inhibitor (MAM-117), showed that, as expected, the catalytic serine of SUB1 formed a covalent bond with the α-keto group of the inhibitor. A network of hydrogen bonds and hydrophobic interactions stabilized the complex, including at the P1' and P2' positions of the inhibitor, although P' residues are usually less important in defining the substrate specificity of subtilisins. Moreover, when associated with a substrate-derived peptidomimetic inhibitor, the catalytic groove of SUB1 underwent significant structural changes, particularly in its S4 pocket. These findings pave the way for future strategies for the design of optimized SUB1-specific inhibitors that may define a novel class of antimalarial candidates.


Assuntos
Antimaláricos , Subtilisina , Plasmodium vivax , Antimaláricos/farmacologia , Antimaláricos/química , Inibidores Enzimáticos/farmacologia , Proteínas de Protozoários/química
4.
Molecules ; 28(13)2023 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-37446746

RESUMO

We previously reported dipeptidomimetic compounds as inhibitors of neuronal and/or inducible NO synthases (n/iNOS) with significant selectivity against endothelial NOS (eNOS). They were composed of an S-ethylisothiocitrullin-like moiety linked to an extension through a peptide bond or a 1,2,4-oxadiazole link. Here, we developed two further series where the extension size was increased to establish more favorable interactions in the NOS substrate access channel. The extension was introduced on the solid phase by the reductive alkylation of an amino-piperidine moiety or an aminoethyl segment in the case of dipeptide-like and 1,2,4-oxadiazole compounds, respectively, with various benzaldehydes. Compared to the previous series, more potent inhibitors were identified with IC50 in the micromolar to the submicromolar range, with significant selectivity toward nNOS. As expected, most compounds did not inhibit eNOS, and molecular modeling was carried out to characterize the reasons for the selectivity toward nNOS over eNOS. Spectral studies showed that compounds were interacting at the heme active site. Finally, selected inhibitors were found to inhibit intra-cellular iNOS and nNOS expressed in RAW264.7 and INS-1 cells, respectively.


Assuntos
Inibidores Enzimáticos , Óxido Nítrico Sintase , Óxido Nítrico Sintase/metabolismo , Inibidores Enzimáticos/química , Dipeptídeos/química , Técnicas de Síntese em Fase Sólida , Óxido Nítrico Sintase Tipo I , Óxido Nítrico Sintase Tipo II , Modelos Moleculares , Óxido Nítrico Sintase Tipo III
5.
Electrophoresis ; 44(7-8): 701-710, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36308033

RESUMO

The use of fluorescently tagged amyloid peptides, implicated in Alzheimer's disease, to study their aggregation at low concentrations is a common method; however, the fluorescent tag should not introduce a bias in the aggregation process. In this work, native amyloid peptides Aß(1-40) and Aß(1-42) and fluorescein-5-isothiocyanate (FITC), tagged ones, were studied using Taylor dispersion analysis coupled with a simultaneous UV and light-emitting diode-induced fluorescence detection, to unravel the effect of FITC on the aggregation process. For that, a total concentration of 100 µM of peptides consisting of a mixture of native and tagged ones (up to 10% in moles) was applied. Results demonstrated that FITC had a strong inhibition effect upon the aggregation behaviour of Aß(1-42), whereas for Aß(1-40), only a retardation in kinetics was observed. It was also shown that when mixed solutions of Aß(1-40) and Aß(1-42) are used, the Aß(1-42) alloform was the leading peptide in the aggregation process, and when the latter was tagged, the aggregation kinetics decreased but the lifetime of potentially toxic oligomers was drastically increased. These results confirmed that the hydrophilicity of the N-terminus part of the peptide plays a major role in the aggregation process.


Assuntos
Doença de Alzheimer , Peptídeos beta-Amiloides , Humanos , Fluoresceína-5-Isotiocianato , Fragmentos de Peptídeos , Corantes Fluorescentes
6.
J Med Chem ; 65(24): 16392-16419, 2022 12 22.
Artigo em Inglês | MEDLINE | ID: mdl-36450011

RESUMO

Metallo-ß-lactamases (MBLs) contribute to the resistance of Gram-negative bacteria to carbapenems, last-resort antibiotics at hospital, and MBL inhibitors are urgently needed to preserve these important antibacterial drugs. Here, we describe a series of 1,2,4-triazole-3-thione-based inhibitors displaying an α-amino acid substituent, which amine was mono- or disubstituted by (hetero)aryl groups. Compounds disubstituted by certain nitrogen-containing heterocycles showed submicromolar activities against VIM-type enzymes and strong NDM-1 inhibition (Ki = 10-30 nM). Equilibrium dialysis, native mass spectrometry, isothermal calorimetry (ITC), and X-ray crystallography showed that the compounds inhibited both VIM-2 and NDM-1 at least partially by stripping the catalytic zinc ions. These inhibitors also displayed a very potent synergistic activity with meropenem (16- to 1000-fold minimum inhibitory concentration (MIC) reduction) against VIM-type- and NDM-1-producing ultraresistant clinical isolates, including Enterobacterales and Pseudomonas aeruginosa. Furthermore, selected compounds exhibited no or moderate toxicity toward HeLa cells, favorable absorption, distribution, metabolism, excretion (ADME) properties, and no or modest inhibition of several mammalian metalloenzymes.


Assuntos
Tionas , Inibidores de beta-Lactamases , Humanos , Inibidores de beta-Lactamases/farmacologia , Inibidores de beta-Lactamases/química , Tionas/farmacologia , Células HeLa , Antibacterianos/farmacologia , Antibacterianos/química , beta-Lactamases/metabolismo , Testes de Sensibilidade Microbiana
7.
Sci Adv ; 8(35): eabo0617, 2022 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-36054354

RESUMO

Extreme conditions inside ice giants such as Uranus and Neptune can result in peculiar chemistry and structural transitions, e.g., the precipitation of diamonds or superionic water, as so far experimentally observed only for pure C─H and H2O systems, respectively. Here, we investigate a stoichiometric mixture of C and H2O by shock-compressing polyethylene terephthalate (PET) plastics and performing in situ x-ray probing. We observe diamond formation at pressures between 72 ± 7 and 125 ± 13 GPa at temperatures ranging from ~3500 to ~6000 K. Combining x-ray diffraction and small-angle x-ray scattering, we access the kinetics of this exotic reaction. The observed demixing of C and H2O suggests that diamond precipitation inside the ice giants is enhanced by oxygen, which can lead to isolated water and thus the formation of superionic structures relevant to the planets' magnetic fields. Moreover, our measurements indicate a way of producing nanodiamonds by simple laser-driven shock compression of cheap PET plastics.

8.
Bioorg Med Chem ; 72: 116964, 2022 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-36030663

RESUMO

Metallo-ß-lactamases (MBLs) represent an increasingly serious threat to public health because of their increased prevalence worldwide in relevant opportunistic Gram-negative pathogens. MBLs efficiently inactivate widely used and most valuable ß-lactam antibiotics, such as oxyiminocephalosporins (ceftriaxone, ceftazidime) and the last-resort carbapenems. To date, no MBL inhibitor has been approved for therapeutic applications. We are developing inhibitors characterized by a 1,2,4-triazole-3-thione scaffold as an original zinc ligand and few promising series were already reported. Here, we present the synthesis and evaluation of a new series of compounds characterized by the presence of an arylalkyl substituent at position 4 of the triazole ring. The alkyl link was mainly an ethylene, but a few compounds without alkyl or with an alkyl group of various lengths up to a butyl chain were also synthesized. Some compounds in both sub-series were micromolar to submicromolar inhibitors of tested VIM-type MBLs. A few of them were broad-spectrum inhibitors, as they showed significant inhibitory activity on NDM-1 and, to a lesser extent, IMP-1. Among these, several inhibitors were able to significantly reduce the meropenem MIC on VIM-1- and VIM-4- producing clinical isolates by up to 16-fold. In addition, ACE inhibition was absent or moderate and one promising compound did not show toxicity toward HeLa cells at concentrations up to 250 µM. This series represents a promising basis for further exploration. Finally, molecular modelling of representative compounds in complex with VIM-2 was performed to study their binding mode.


Assuntos
Tionas , Inibidores de beta-Lactamases , Humanos , Antibacterianos/farmacologia , Inibidores de beta-Lactamases/química , Inibidores de beta-Lactamases/farmacologia , beta-Lactamases/metabolismo , Carbapenêmicos/farmacologia , Ceftazidima , Ceftriaxona , Etilenos , Células HeLa , Ligantes , Meropeném , Testes de Sensibilidade Microbiana , Triazóis/química , Triazóis/farmacologia , Zinco
9.
Nat Commun ; 13(1): 3303, 2022 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-35729158

RESUMO

Electrolytes play an important role in the internal structure and dynamics of water-rich satellites and potentially water-rich exoplanets. However, in planets, the presence of a large high-pressure ice mantle is thought to hinder the exchange and transport of electrolytes between various liquid and solid deep layers. Here we show, using first-principles simulations, that up to 2.5 wt% NaCl can be dissolved in dense water ice at interior conditions of water-rich super-Earths and mini-Neptunes. The salt impurities enhance the diffusion of H atoms, extending the stability field of recently discovered superionic ice, and push towards higher pressures the transition to the stiffer ice X phase. Scaling laws for thermo-compositional convection show that salts entering the high pressure ice layer can be readily transported across. These findings suggest that the high-pressure ice mantle of water-rich exoplanets is permeable to the convective transport of electrolytes between the inner rocky core and the outer liquid layer.

10.
Nat Neurosci ; 25(5): 567-576, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-35501382

RESUMO

Interactions between the immune and central nervous systems strongly influence brain health. Although the blood-brain barrier restricts this crosstalk, we now know that meningeal gateways through brain border tissues facilitate intersystem communication. Cerebrospinal fluid (CSF), which interfaces with the glymphatic system and thereby drains the brain's interstitial and perivascular spaces, facilitates outward signaling beyond the blood-brain barrier. In the present study, we report that CSF can exit into the skull bone marrow. Fluorescent tracers injected into the cisterna magna of mice migrate along perivascular spaces of dural blood vessels and then travel through hundreds of sub-millimeter skull channels into the calvarial marrow. During meningitis, bacteria hijack this route to invade the skull's hematopoietic niches and initiate cranial hematopoiesis ahead of remote tibial sites. As skull channels also directly provide leukocytes to meninges, the privileged sampling of brain-derived danger signals in CSF by regional marrow may have broad implications for inflammatory neurological disorders.


Assuntos
Sistema Glinfático , Meningites Bacterianas , Animais , Medula Óssea , Encéfalo/irrigação sanguínea , Líquido Cefalorraquidiano , Sistema Glinfático/fisiologia , Hematopoese , Camundongos , Crânio
11.
ACS Chem Neurosci ; 13(6): 786-795, 2022 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-35201761

RESUMO

Aggregation of amyloid ß peptides is known to be one of the main processes responsible for Alzheimer's disease. The resulting dementia is believed to be due in part to the formation of potentially toxic oligomers. However, the study of such intermediates and the understanding of how they form are very challenging because they are heterogeneous and transient in nature. Unfortunately, few techniques can quantify, in real time, the proportion and the size of the different soluble species during the aggregation process. In a previous work (Deleanu et al. Anal. Chem. 2021, 93, 6523-6533), we showed the potential of Taylor dispersion analysis (TDA) in amyloid speciation during the aggregation process of Aß (1-40) and Aß (1-42). The current work aims at exploring in detail the aggregation of amyloid Aß (1-40):Aß (1-42) peptide mixtures with different proportions of each peptide (1:0, 3:1, 1:1, 1:3, and 0:1) using TDA and atomic force microscopy (AFM). TDA allowed for monitoring the kinetics of the amyloid assembly and quantifying the transient intermediates. Complementarily, AFM allowed the formation of insoluble fibrils to be visualized. Together, the two techniques enabled us to study the influence of the peptide ratios on the kinetics and the formation of potentially toxic oligomeric species.


Assuntos
Doença de Alzheimer , Amiloidose , Amiloide , Peptídeos beta-Amiloides , Humanos , Cinética , Microscopia de Força Atômica , Fragmentos de Peptídeos
12.
ChemMedChem ; 17(7): e202100699, 2022 04 05.
Artigo em Inglês | MEDLINE | ID: mdl-35050549

RESUMO

Metallo-ß-lactamases (MBLs) are increasingly involved as a major mechanism of resistance to carbapenems in relevant opportunistic Gram-negative pathogens. Unfortunately, clinically efficient MBL inhibitors still represent an unmet medical need. We previously reported several series of compounds based on the 1,2,4-triazole-3-thione scaffold. In particular, Schiff bases formed between diversely 5-substituted-4-amino compounds and 2-carboxybenzaldehyde were broad-spectrum inhibitors of VIM-type, NDM-1 and IMP-1 MBLs. Unfortunately, these compounds were unable to restore antibiotic susceptibility of MBL-producing bacteria, probably because of poor penetration and/or susceptibility to hydrolysis. To improve their microbiological activity, we synthesized and characterized compounds where the hydrazone-like bond of the Schiff base analogues was replaced by a stable ethyl link. This small change resulted in a narrower inhibition spectrum, as all compounds were poorly or not inhibiting NDM-1 and IMP-1, but showed a significantly better activity on VIM-type enzymes, with Ki values in the µM to sub-µM range. The resolution of the crystallographic structure of VIM-2 in complex with one of the best inhibitors yielded valuable information about their binding mode. Interestingly, several compounds were shown to restore the ß-lactam susceptibility of VIM-type-producing E. coli laboratory strains and also of K. pneumoniae clinical isolates. In addition, selected compounds were found to be devoid of toxicity toward human cancer cells at high concentration, thus showing promising safety.


Assuntos
Tionas , Inibidores de beta-Lactamases , Antibacterianos/química , Antibacterianos/farmacologia , Escherichia coli , Humanos , Testes de Sensibilidade Microbiana , Tionas/farmacologia , Triazóis/química , Inibidores de beta-Lactamases/química , beta-Lactamases/metabolismo
13.
Bioorg Chem ; 119: 105539, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34894575

RESUMO

It is urgent to develop less toxic and more efficient treatments for leishmaniases and trypanosomiases. We explore the possibility to target the parasite mitochondrial HslVU protease, which is essential for growth and has no analogue in the human host. For this, we develop compounds potentially inhibiting the complex assembly by mimicking the C-terminal (C-ter) segment of the ATPase HslU. We previously showed that a dodecapeptide derived from Leishmania major HslU C-ter segment (LmC12-U2, Cpd 1) was able to bind to and activate the digestion of a fluorogenic substrate by LmHslV. Here, we present the study of its structure-activity relationships. By replacing each essential residue with related non-proteinogenic residues, we obtained more potent analogues. In particular, a cyclohexylglycine residue at position 11 (cpd 24) allowed a more than three-fold gain in potency while reducing the size of compound 24 from twelve to six residues (cpd 50) without significant loss of potency, opening the way toward short HslU C-ter peptidomimetics as potential inhibitors of HslV proteolytic function. Finally, conjugates constituted of LmC6-U2 analogues and a mitochondrial penetrating peptide were found to penetrate into the promastigote form of L. infantum and to inhibit the parasite growth without showing toxicity toward human THP-1 cells at the same concentration (i.e. 30 µM).


Assuntos
Adenosina Trifosfatases/antagonistas & inibidores , Inibidores Enzimáticos/farmacologia , Adenosina Trifosfatases/metabolismo , Sobrevivência Celular/efeitos dos fármacos , Células Cultivadas , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/química , Humanos , Leishmania major/enzimologia , Estrutura Molecular , Relação Estrutura-Atividade , Células THP-1
14.
Molecules ; 26(24)2021 Dec 17.
Artigo em Inglês | MEDLINE | ID: mdl-34946739

RESUMO

Alzheimer's disease (AD) is a devastating neurodegenerative disorder, one of the main characteristics of which is the abnormal accumulation of amyloid peptide (Aß) in the brain. Whereas ß-secretase supports Aß formation along the amyloidogenic processing of the ß-amyloid precursor protein (ßAPP), α-secretase counterbalances this pathway by both preventing Aß production and triggering the release of the neuroprotective sAPPα metabolite. Therefore, stimulating α-secretase and/or inhibiting ß-secretase can be considered a promising anti-AD therapeutic track. In this context, we tested andrographolide, a labdane diterpene derived from the plant Andrographis paniculata, as well as 24 synthesized derivatives, for their ability to induce sAPPα production in cultured SH-SY5Y human neuroblastoma cells. Following several rounds of screening, we identified three hits that were subjected to full characterization. Interestingly, andrographolide (8,17-olefinic) and its close derivative 14α-(5',7'-dichloro-8'-quinolyloxy)-3,19-acetonylidene (compound 9) behave as moderate α-secretase activators, while 14α-(2'-methyl-5',7'-dichloro-8'-quinolyloxy)-8,9-olefinic compounds 31 (3,19-acetonylidene) and 37 (3,19-diol), whose two structures are quite similar although distant from that of andrographolide and 9, stand as ß-secretase inhibitors. Importantly, these results were confirmed in human HEK293 cells and these compounds do not trigger toxicity in either cell line. Altogether, these findings may represent an encouraging starting point for the future development of andrographolide-based compounds aimed at both activating α-secretase and inhibiting ß-secretase that could prove useful in our quest for the therapeutic treatment of AD.


Assuntos
Doença de Alzheimer/metabolismo , Secretases da Proteína Precursora do Amiloide/metabolismo , Precursor de Proteína beta-Amiloide/metabolismo , Diterpenos , Ativadores de Enzimas , Diterpenos/síntese química , Diterpenos/química , Diterpenos/farmacologia , Ativadores de Enzimas/síntese química , Ativadores de Enzimas/química , Ativadores de Enzimas/farmacologia , Células HEK293 , Humanos
15.
Philos Trans A Math Phys Eng Sci ; 379(2211): 20200430, 2021 Nov 29.
Artigo em Inglês | MEDLINE | ID: mdl-34628944

RESUMO

The energy landscape of the fast-ion conductor Bi4V2O11 is studied using density functional theory. There are a large number of energy minima, dominated by low-lying thermally accessible configurations in which there are equal numbers of oxygen vacancies in each vanadium-oxygen layer, a range of vanadium coordinations and a large variation in Bi-O and V-O distances. By dividing local minima in the energy landscape into sets of configurations, we then examine diffusion in each different layer using ab initio molecular dynamics. These simulations show that the diffusion mechanism mainly takes place in the 〈110〉 directions in the vanadium layers, involving the cooperative motion of the oxide ions between the O(2) and O(3) sites in these layers, but not O(1) in the Bi-O layers, in agreement with experiment. O(1) vacancies in the Bi-O layers are readily filled by the migration of oxygens from the V-O layers. The calculated ionic conductivity is in reasonable agreement with the experiment. We compare ion conduction in δ-Bi4V2O11 with that in δ-Bi2O3. This article is part of the Theo Murphy meeting issue 'Understanding fast-ion conduction in solid electrolytes'.

16.
Eur J Med Chem ; 226: 113873, 2021 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-34626878

RESUMO

Metallo-ß-lactamases (MBLs) are important contributors of Gram-negative bacteria resistance to ß-lactam antibiotics. MBLs are highly worrying because of their carbapenemase activity, their rapid spread in major human opportunistic pathogens while no clinically useful inhibitor is available yet. In this context, we are exploring the potential of compounds based on the 1,2,4-triazole-3-thione scaffold as an original ligand of the di-zinc active sites of MBLs, and diversely substituted at its positions 4 and 5. Here, we present a new series of compounds substituted at the 4-position by a thioether-containing alkyl chain with a carboxylic and/or an aryl group at its extremity. Several compounds showed broad-spectrum inhibition with Ki values in the µM to sub-µM range against VIM-type enzymes, NDM-1 and IMP-1. The presence of the sulfur and of the aryl group was important for the inhibitory activity and the binding mode of a few compounds in VIM-2 was revealed by X-ray crystallography. Importantly, in vitro antibacterial susceptibility assays showed that several inhibitors were able to potentiate the activity of meropenem on Klebsiella pneumoniae clinical isolates producing VIM-1 or VIM-4, with a potentiation effect of up to 16-fold. Finally, a selected compound was found to only moderately inhibit the di-zinc human glyoxalase II, and several showed no or only moderate toxicity toward several human cells, thus favourably completing a promising behaviour.


Assuntos
Sulfetos/farmacologia , Tionas/farmacologia , Triazóis/farmacologia , Inibidores de beta-Lactamases/farmacologia , beta-Lactamases/metabolismo , Relação Dose-Resposta a Droga , Humanos , Estrutura Molecular , Relação Estrutura-Atividade , Sulfetos/química , Tionas/síntese química , Tionas/química , Triazóis/síntese química , Triazóis/química , Inibidores de beta-Lactamases/síntese química , Inibidores de beta-Lactamases/química
17.
J Vis Exp ; (175)2021 09 17.
Artigo em Inglês | MEDLINE | ID: mdl-34605802

RESUMO

We have developed a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts, water-based fluids, and various supercritical fluids. The package is a collection of Python scripts that include two major libraries dealing with file formats and with crystallography. All the scripts are run at the command line. We propose a simplified format to store the atomic trajectories and relevant thermodynamic information of the simulations, which is saved in UMD files, standing for Universal Molecular Dynamics. The UMD package allows the computation of a series of structural, transport and thermodynamic properties. Starting with the pair-distribution function it defines bond lengths, builds an interatomic connectivity matrix, and eventually determines the chemical speciation. Determining the lifetime of the chemical species allows running a full statistical analysis. Then dedicated scripts compute the mean-square displacements for the atoms as well as for the chemical species. The implemented self-correlation analysis of the atomic velocities yields the diffusion coefficients and the vibrational spectrum. The same analysis applied on the stresses yields the viscosity. The package is available via the GitHub website and via its own dedicated page of the ERC IMPACT project as open-access package.


Assuntos
Simulação de Dinâmica Molecular , Software
18.
Bioorg Chem ; 113: 105024, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34116340

RESUMO

In Gram-negative bacteria, the major mechanism of resistance to ß-lactam antibiotics is the production of one or several ß-lactamases (BLs), including the highly worrying carbapenemases. Whereas inhibitors of these enzymes were recently marketed, they only target serine-carbapenemases (e.g. KPC-type), and no clinically useful inhibitor is available yet to neutralize the class of metallo-ß-lactamases (MBLs). We are developing compounds based on the 1,2,4-triazole-3-thione scaffold, which binds to the di-zinc catalytic site of MBLs in an original fashion, and we previously reported its promising potential to yield broad-spectrum inhibitors. However, up to now only moderate antibiotic potentiation could be observed in microbiological assays and further exploration was needed to improve outer membrane penetration. Here, we synthesized and characterized a series of compounds possessing a diversely functionalized alkyl chain at the 4-position of the heterocycle. We found that the presence of a carboxylic group at the extremity of an alkyl chain yielded potent inhibitors of VIM-type enzymes with Ki values in the µM to sub-µM range, and that this alkyl chain had to be longer or equal to a propyl chain. This result confirmed the importance of a carboxylic function on the 4-substituent of 1,2,4-triazole-3-thione heterocycle. As observed in previous series, active compounds also preferentially contained phenyl, 2-hydroxy-5-methoxyphenyl, naphth-2-yl or m-biphenyl at position 5. However, none efficiently inhibited NDM-1 or IMP-1. Microbiological study on VIM-2-producing E. coli strains and on VIM-1/VIM-4-producing multidrug-resistant K. pneumoniae clinical isolates gave promising results, suggesting that the 1,2,4-triazole-3-thione scaffold worth continuing exploration to further improve penetration. Finally, docking experiments were performed to study the binding mode of alkanoic analogues in the active site of VIM-2.


Assuntos
Tionas/química , Inibidores de beta-Lactamases/química , beta-Lactamases/química , Antibacterianos/síntese química , Antibacterianos/química , Antibacterianos/metabolismo , Antibacterianos/farmacologia , Sítios de Ligação , Sobrevivência Celular/efeitos dos fármacos , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Escherichia coli/enzimologia , Células HeLa , Humanos , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/isolamento & purificação , Testes de Sensibilidade Microbiana , Simulação de Acoplamento Molecular , Ligação Proteica , Relação Estrutura-Atividade , Tionas/metabolismo , Triazóis/química , Inibidores de beta-Lactamases/metabolismo , beta-Lactamases/metabolismo
19.
Anal Chem ; 93(16): 6523-6533, 2021 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-33852281

RESUMO

Aggregation mechanisms of amyloid ß peptides depend on multiple intrinsic and extrinsic physicochemical factors (e.g., peptide chain length, truncation, peptide concentration, pH, ionic strength, temperature, metal concentration, etc.). Due to this high number of parameters, the formation of oligomers and their propensity to aggregate make the elucidation of this physiopathological mechanism a challenging task. From the analytical point of view, up to our knowledge, few techniques are able to quantify, in real time, the proportion and the size of the different soluble species during the aggregation process. This work aims at demonstrating the efficacy of the modern Taylor dispersion analysis (TDA) performed in capillaries (50 µm i.d.) to unravel the speciation of ß-amyloid peptides in low-volume peptide samples (∼100 µL) with an analysis time of ∼3 min per run. TDA was applied to study the aggregation process of Aß(1-40) and Aß(1-42) peptides at physiological pH and temperature, where more than 140 data points were generated with a total volume of ∼1 µL over the whole aggregation study (about 0.5 µg of peptides). TDA was able to give a complete and quantitative picture of the Aß speciation during the aggregation process, including the sizing of the oligomers and protofibrils, the consumption of the monomer, and the quantification of different early- and late-formed aggregated species.


Assuntos
Peptídeos beta-Amiloides , Fragmentos de Peptídeos , Peptídeos beta-Amiloides/análise , Peptídeos beta-Amiloides/química , Metais
20.
Metallomics ; 13(6)2021 06 08.
Artigo em Inglês | MEDLINE | ID: mdl-33881548

RESUMO

Lactation and gestation are among the physiological events that trigger the most intense changes in body calcium (Ca) fluxes. Along with the composition of the animal 2021 diet, these events are suspected to impact the Ca isotopic composition of Ca body reservoirs but their dynamics are poorly understood. In this study, we monitored a group of domestic sows across a full reproduction cycle. We collected tissues and fluids (blood, urine, milk, colostrum, umbilical blood, adult and piglet bones) at different steps of gestation and lactation, and analyzed their Ca isotopic compositions (i.e. δ44/42Ca) by means of multi-collector inductively coupled plasma mass spectrometry. Among other results, we report the first observations of Ca isotopic fractionation between maternal and umbilical blood (Δ44/42Caumbilical blood-sow blood = -0.18 ± 0.11‰, n = 3). Our data also highlight that gestation and lactation periods are characterized by small diet-bone Ca isotopic offsets (Δ44/42Cabone-diet = -0.28 ± 0.11‰, n = 3), with 44Ca-enriched blood compositions during nursing (Δ44/42Canursing blood-gestation blood = $+ 0.42{\rm{\,\,}}_{ - 0.12}^{ + 0.11}$‰, n = 3). Under the light of an up-to-date mammalian box model, we explored different scenarios of gestation and lactation Ca fluxes experienced by a sow-like animal. These simulations suggest that gestation changes on body δ44/42Ca values may result from the intensification of Ca absorption by the animal, whereas the production of 44Ca-depleted milk is the main driver for the 44Ca enrichment in blood during lactation. In addition, our results also support that bone mineralization could be associated with a more restricted Ca isotopic fractionation than previously envisioned. Together, these results refine the framework of Ca isotope applications, notably regarding the monitoring of human bone balance and the study of species and ecosystems from the present and the past.


Assuntos
Ração Animal/análise , Líquidos Corporais/metabolismo , Osso e Ossos/química , Isótopos de Cálcio/análise , Cálcio/metabolismo , Lactação , Modelos Biológicos , Animais , Animais Recém-Nascidos , Líquidos Corporais/química , Feminino , Gravidez , Suínos
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