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1.
Sci Rep ; 12(1): 15828, 2022 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-36138056

RESUMO

The cobalt (II) complexes have been synthesized from the reaction of the cationic entities (3,4-dimethylaniline (1) and histamine (2)) with metallic salt CoCl2⋅6H2O and thiocyanate ion (SCN-) as a ligand in H2O/ethanolic solution and processing by the evaporation crystal growth method at room temperature to get crystals. The synthesized complex has been fully characterized by single-crystal X-ray diffraction. UV-Visible, FTIR spectroscopy, TGA analysis, and DFT circulations were also performed. The crystal structural analysis reveals that the solid (1) {[Co(SCN)4] (C8H12N)3}·Cl crystallizes in the monoclinic system with the space group P21/n and the solid (2) {[Co(SCN)4](C5H11N3)2}·2Cl crystallizes in the monoclinic space group P21/m. Metal cations are joined into corrugated chains parallel to the b-axis direction in (1) and (2) by four thiocyanate anions. The crystal structures of (1) and (2) were calculated using XRPD data, indicating that they are closely connected to the DRX mono-crystal results. Different interactions pack the system into a ring formed by N-H⋯Cl and N-H⋯S hydrogen bonds. C-H⋯π and the π⋯π stacking of anilinuim ring for (1) and N-H⋯S intermolecular interactions for (1) and (2) increase the crystals' robustness. Hirshfeld surface analysis cum 2D fingerprint plots visualize the main intermolecular interactions with their contributions in the solid-state phase. The molecular geometries of both complexes obtained from the crystal structure were used for quantum chemical calculation. Here, frontier orbital analysis and electrostatic potential illustrate the chemical reactivities of metal-organic complexes. QTAIM and NCI analysis reveal the strength of interactions at the electronic level.


Assuntos
Cobalto , Complexos de Coordenação , Antioxidantes , Cátions , Cobalto/química , Histamina , Ligantes , Modelos Moleculares , Teoria Quântica , Tiocianatos/química
2.
J Phys Chem B ; 126(37): 7126-7134, 2022 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-36069763

RESUMO

Dihydrofolate reductase (DHFR) is a well-studied, clinically relevant enzyme known for being highly dynamic over the course of its catalytic cycle. However, the role dynamic motions play in the explicit hydride transfer from the nicotinamide cofactor to the dihydrofolate substrate remains unclear because reaction initiation and direct spectroscopic examination on the appropriate time scale for such femtosecond to picosecond motions is challenging. Here, we employ pre-steady-state kinetics to observe the hydride transfer as directly as possible in two different species of DHFR: Escherichia coli and Homo sapiens. While the hydride transfer has been well-characterized in DHFR from E. coli, improvements in time resolution now allow for sub-millisecond dead times for stopped-flow spectroscopy, which reveals that the maximum rate is indeed faster than previously recorded. The rate in the human enzyme, previously only estimated, is also able to be directly observed using cutting-edge stopped-flow instrumentation. In addition to the pH dependence of the hydride transfer rates for both enzymes, we examine the primary H/D kinetic isotope effect to reveal a temperature dependence in the human enzyme that is absent from the E. coli counterpart. This dependence, which appears above a temperature of 15 °C is a shared feature among other hydride transfer enzymes and is also consistent with computational work suggesting the presence of a fast promoting-vibration that provides donor-acceptor compression on the time scale of catalysis to facilitate the chemistry step.


Assuntos
Escherichia coli , Tetra-Hidrofolato Desidrogenase , Catálise , Escherichia coli/metabolismo , Humanos , Cinética , Modelos Moleculares , Niacinamida , Conformação Proteica , Tetra-Hidrofolato Desidrogenase/química
3.
4.
J Phys Chem B ; 126(38): 7373-7384, 2022 Sep 29.
Artigo em Inglês | MEDLINE | ID: mdl-36103309

RESUMO

The search for new prominent chemosensors is significantly related to the rationalization of possible multiple pathways of excited-state deactivation. We have prepared and studied compound α-(2-hydroxyphenyl)-N-phenylnitrone (Nit-OH), observing that Nit-OH is stable in acetonitrile solution under UV-vis light. The experimentally observed 540 nm fluorescence for Nit-OH was shown to be related to excitation at 360 nm from the highest occupied molecular orbital to the lowest unoccupied molecular orbital (HOMO-LUMO transition). Potential energy curves (PECs) for the S1 state of Nit-OH did show that there are structures associated with excited-state intramolecular proton transfer (ESIPT), and the existence of an intramolecular H-bonding was confirmed using X-ray powder diffraction (XRD). Twisted intramolecular charge transfer (TICT) took place following ESIPT, and a nonradiative deactivation at the S1/S0 conical intersection occurred; aggregation-induced emission was observed at 540 nm associated with the formation of a stacked dimer. Anti-Kasha emission from the S2 was proposed based on the dependence of the fluorescence excitation wavelength on Nit-OH concentration. From the calculation of the PEC for the S2 state, we obtained radiative transitions at 379 and 432 nm, similar to the obtained experimental values of 383 and 453 nm. We proposed a Jablonski-like diagram that depicts all experimental and theoretical electronic transitions for Nit-OH, summarizing the unique intricate photophysical behavior of this nitrone derivative.


Assuntos
Eletrônica , Prótons , Acetonitrilas , Modelos Moleculares , Espectrometria de Fluorescência
5.
J Phys Chem A ; 126(38): 6686-6694, 2022 Sep 29.
Artigo em Inglês | MEDLINE | ID: mdl-36112415

RESUMO

Organic acids are released during wildfire combustion and can influence aerosol formation and growth. Conformational flexibility is thought to be advantageous in stabilizing the precritical nucleus in the process of aerosol particle formation and allowing for further complexation with other atmospheric constituents. We describe here a study of the conformational flexibility of vanillic acid and its monohydrate using electronic structure calculations and Fourier transform microwave spectroscopy. Computationally, 12 and 28 conformers were found for the monomer and monohydrate, respectively. The two lowest energy conformers of both the vanillic acid monomer and the vanillic acid-water complex could be experimentally identified. The deviation between experimental and theoretical rotational constants determined at the MP2/aug-cc-pVTZ and DFT B3LYP-D3(BJ)/def2-TZVP levels of theory is less than 1%. No tunneling splittings were observed, which suggests a relatively high barrier to methyl internal rotation, in agreement with other, previously studied vanillin derivatives. Furthermore, no c-type transitions could be observed for the vanillic acid monomer, in agreement with the computed zero c-dipole moment component of the two lowest energy structures. For the monohydrate the absence of c-type transitions is rationalized by averaging over a large amplitude motion involving the free H atom of the water unit. From the theoretical structures, it is apparent that intramolecular hydrogen bonds play a significant role in stabilizing the lowest energy conformers. To further characterize the intramolecular interactions in the monomer and intra- and intermolecular interactions in the monohydrate, quantum theory of atoms-in-molecules (QTAIM), noncovalent interactions (NCI), and intrinsic bond strength index (IBSI) analyses were performed. The atmospheric abundance of the vanillic acid monohydrate relative to the monomer was evaluated to assess its atmospheric significance.


Assuntos
Ácido Vanílico , Água , Modelos Moleculares , Conformação Molecular , Análise Espectral
6.
PLoS Comput Biol ; 18(9): e1010539, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-36112717

RESUMO

Despite the immense progress recently witnessed in protein structure prediction, the modeling accuracy for proteins that lack sequence and/or structure homologs remains to be improved. We developed an open-source program, DeepFold, which integrates spatial restraints predicted by multi-task deep residual neural-networks along with a knowledge-based energy function to guide its gradient-descent folding simulations. The results on large-scale benchmark tests showed that DeepFold creates full-length models with accuracy significantly beyond classical folding approaches and other leading deep learning methods. Of particular interest is the modeling performance on the most difficult targets with very few homologous sequences, where DeepFold achieved an average TM-score that was 40.3% higher than trRosetta and 44.9% higher than DMPfold. Furthermore, the folding simulations for DeepFold were 262 times faster than traditional fragment assembly simulations. These results demonstrate the power of accurately predicted deep learning potentials to improve both the accuracy and speed of ab initio protein structure prediction.


Assuntos
Biologia Computacional , Aprendizado Profundo , Algoritmos , Biologia Computacional/métodos , Bases de Dados de Proteínas , Modelos Moleculares , Conformação Proteica , Dobramento de Proteína , Proteínas/química , Software
7.
J Phys Chem A ; 126(38): 6657-6667, 2022 Sep 29.
Artigo em Inglês | MEDLINE | ID: mdl-36122186

RESUMO

In this work we tackle the problem of the substituent effects in the Diels-Alder cycloadditions between triazolinediones (TADs) and anthracene. Experiments showed that aryl TADs substituted with electron-withdrawing groups (EWG) are more reactive than those substituted with electron-donating (EDG) or alkyl groups. However, the molecular origin of this preference is not yet understood. By a combination of methods including the activation strain model (ASM), energy decomposition analysis (EDA), molecular orbital (MO) theory, and conceptual density functional theory (CDFT), we disclosed the substituent effects of TADs. First, ASM/EDA analysis revealed that the reactivity of alkyl and aryl-substituted TADs is controlled by interaction energies, ΔEint, which are ultimately defined by orbital interactions between frontier molecular orbitals. Moreover, alkyl-TADs are also controlled by the extent of strain at the transition state. The MO analysis suggested that the rate acceleration for EWG-substituted TADs is due to a more favorable orbital interaction between the HOMO of anthracene and the LUMO of the TADs, which is corroborated by calculations of charge transfer at the transition states. From CDFT, the chemical potential of anthracene is higher than those of TADs, indicating a flow of electron density from anthracene to TADs, in agreement with the results from the electrophilicity index.


Assuntos
Antracenos , Elétrons , Reação de Cicloadição , Modelos Moleculares
8.
PLoS One ; 17(9): e0275108, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36170645

RESUMO

Coal is the largest non-renewable energy as well as an important basic energy and industrial raw material. Thus, correctly understanding the molecular structure characteristics of coal has important theoretical value for realizing carbon neutralization. In this work, we clarified the molecular structure characteristics of anthracite, where the organic matter in anthracite was characterized and analyzed by industrial/elemental analysis, FTIR, XPS, XRD and solid 13C NMR. The ratio of bridge carbon to the perimeter carbon of anthracite was 0.38, and the degree of condensation in the aromatic structure was high. Nitrogen in coal primarily exists in the form of pyridine and pyrrole. Based on the information on functional group composition, the carbon skeleton structure, and surface element composition, a molecular structure model of Yangquan anthracite could be constructed, where the molecular formula was C208H162O12N4. This study may serve as a reference for researchers in this field to consult and refer to the construction ideas and methods of molecular structure models of different coal samples.


Assuntos
Carvão Mineral , Nitrogênio , Carbono , Carvão Mineral/análise , Modelos Moleculares , Estrutura Molecular , Nitrogênio/análise , Piridinas , Pirróis
9.
Cell Rep ; 40(13): 111408, 2022 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-36170828

RESUMO

The AAA+ protein, Skd3 (human CLPB), solubilizes proteins in the mitochondrial intermembrane space, which is critical for human health. Skd3 variants with defective protein-disaggregase activity cause severe congenital neutropenia (SCN) and 3-methylglutaconic aciduria type 7 (MGCA7). How Skd3 disaggregates proteins remains poorly understood. Here, we report a high-resolution structure of a Skd3-substrate complex. Skd3 adopts a spiral hexameric arrangement that engages substrate via pore-loop interactions in the nucleotide-binding domain (NBD). Substrate-bound Skd3 hexamers stack head-to-head via unique, adaptable ankyrin-repeat domain (ANK)-mediated interactions to form dodecamers. Deleting the ANK linker region reduces dodecamerization and disaggregase activity. We elucidate apomorphic features of the Skd3 NBD and C-terminal domain that regulate disaggregase activity. We also define how Skd3 subunits collaborate to disaggregate proteins. Importantly, SCN-linked subunits sharply inhibit disaggregase activity, whereas MGCA7-linked subunits do not. These advances illuminate Skd3 structure and mechanism, explain SCN and MGCA7 inheritance patterns, and suggest therapeutic strategies.


Assuntos
Anquirinas , Proteínas de Choque Térmico , Trifosfato de Adenosina/metabolismo , Anquirinas/metabolismo , Proteínas de Choque Térmico/metabolismo , Humanos , Modelos Moleculares , Nucleotídeos/metabolismo , Transporte Proteico
10.
BMC Bioinformatics ; 23(Suppl 3): 397, 2022 Sep 28.
Artigo em Inglês | MEDLINE | ID: mdl-36171544

RESUMO

BACKGROUND: Advances in imagery at atomic and near-atomic resolution, such as cryogenic electron microscopy (cryo-EM), have led to an influx of high resolution images of proteins and other macromolecular structures to data banks worldwide. Producing a protein structure from the discrete voxel grid data of cryo-EM maps involves interpolation into the continuous spatial domain. We present a novel data format called the neural cryo-EM map, which is formed from a set of neural networks that accurately parameterize cryo-EM maps and provide native, spatially continuous data for density and gradient. As a case study of this data format, we create graph-based interpretations of high resolution experimental cryo-EM maps. RESULTS: Normalized cryo-EM map values interpolated using the non-linear neural cryo-EM format are more accurate, consistently scoring less than 0.01 mean absolute error, than a conventional tri-linear interpolation, which scores up to 0.12 mean absolute error. Our graph-based interpretations of 115 experimental cryo-EM maps from 1.15 to 4.0 Å resolution provide high coverage of the underlying amino acid residue locations, while accuracy of nodes is correlated with resolution. The nodes of graphs created from atomic resolution maps (higher than 1.6 Å) provide greater than 99% residue coverage as well as 85% full atomic coverage with a mean of 0.19 Å root mean squared deviation. Other graphs have a mean 84% residue coverage with less specificity of the nodes due to experimental noise and differences of density context at lower resolutions. CONCLUSIONS: The fully continuous and differentiable nature of the neural cryo-EM map enables the adaptation of the voxel data to alternative data formats, such as a graph that characterizes the atomic locations of the underlying protein or macromolecular structure. Graphs created from atomic resolution maps are superior in finding atom locations and may serve as input to predictive residue classification and structure segmentation methods. This work may be generalized to transform any 3D grid-based data format into non-linear, continuous, and differentiable format for downstream geometric deep learning applications.


Assuntos
Aminoácidos , Proteínas , Microscopia Crioeletrônica/métodos , Modelos Moleculares , Conformação Proteica , Proteínas/química
11.
Protein Sci ; 31(10): e4428, 2022 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-36173174

RESUMO

Many proteins have low thermodynamic stability, which can lead to low expression yields and limit functionality in research, industrial and clinical settings. This article introduces two, web-based tools that use the high-resolution structure of a protein along with the Rosetta molecular modeling program to predict stabilizing mutations. The protocols were recently applied to three genetically and structurally distinct proteins and successfully predicted mutations that improved thermal stability and/or protein yield. In all three cases, combining the stabilizing mutations raised the protein unfolding temperatures by more than 20°C. The first protocol evaluates point mutations and can generate a site saturation mutagenesis heatmap. The second identifies mutation clusters around user-defined positions. Both applications only require a protein structure and are particularly valuable when a deep multiple sequence alignment is not available. These tools were created to simplify protein engineering and enable research that would otherwise be infeasible due to poor expression and stability of the native molecule.


Assuntos
Engenharia de Proteínas , Proteínas , Modelos Moleculares , Mutação , Engenharia de Proteínas/métodos , Proteínas/química , Proteínas/genética , Termodinâmica
12.
Acta Crystallogr D Struct Biol ; 78(Pt 9): 1090-1098, 2022 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-36048149

RESUMO

Interactive model building can be a difficult and time-consuming step in the structure-solution process. Automated model-building programs such as Buccaneer often make it quicker and easier by completing most of the model in advance. However, they may fail to do so with low-resolution data or a poor initial model or map. The Buccaneer pipeline is a relatively simple program that iterates Buccaneer with REFMAC to refine the model and update the map. A new pipeline called ModelCraft has been developed that expands on this to include shift-field refinement, machine-learned pruning of incorrect residues, classical density modification, addition of water and dummy atoms, building of nucleic acids and final rebuilding of side chains. Testing was performed on 1180 structures solved by experimental phasing, 1338 structures solved by molecular replacement using homologues and 2030 structures solved by molecular replacement using predicted AlphaFold models. Compared with the previous Buccaneer pipeline, ModelCraft increased the mean completeness of the protein models in the experimental phasing cases from 91% to 95%, the molecular-replacement cases from 50% to 78% and the AlphaFold cases from 82% to 91%.


Assuntos
Algoritmos , Software , Cristalografia por Raios X , Modelos Moleculares , Proteínas/química
13.
Molecules ; 27(17)2022 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-36080425

RESUMO

A concept of piezo-responsive hydrogen-bonded π-π-stacked organic frameworks made from Knoevenagel-condensed vanillin-barbiturate conjugates was proposed. Replacement of the substituent at the ether oxygen atom of the vanillin moiety from methyl (compound 3a) to ethyl (compound 3b) changed the appearance of the products from rigid rods to porous structures according to optical microscopy and scanning electron microscopy (SEM), and led to a decrease in the degree of crystallinity of corresponding powders according to X-ray diffractometry (XRD). Quantum chemical calculations of possible dimer models of vanillin-barbiturate conjugates using density functional theory (DFT) revealed that π-π stacking between aryl rings of the vanillin moiety stabilized the dimer to a greater extent than hydrogen bonding between carbonyl oxygen atoms and amide hydrogen atoms. According to piezoresponse force microscopy (PFM), there was a notable decrease in the vertical piezo-coefficient upon transition from rigid rods of compound 3a to irregular-shaped aggregates of compound 3b (average values of d33 coefficient corresponded to 2.74 ± 0.54 pm/V and 0.57 ± 0.11 pm/V), which is comparable to that of lithium niobate (d33 coefficient was 7 pm/V).


Assuntos
Barbitúricos , Oxigênio , Barbitúricos/química , Benzaldeídos , Hidrogênio , Ligação de Hidrogênio , Modelos Moleculares
14.
Acta Crystallogr C Struct Chem ; 78(Pt 9): 462-469, 2022 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-36063373

RESUMO

Two new 1,2,4-triazine-containing sulfonamide derivatives, namely, 4-bromo-N-(5,6-diphenyl-2H-1,2,4-triazin-3-ylidene)benzenesulfonamide, C21H15BrN4O4S, 3a, and methyl 2-{[(5,6-diphenyl-1,2,4-triazin-3-yl)sulfamoyl]methyl}benzoate, C24H20N4O4S, 3b, which crystallize in the different sulfonimide and sulfonamide tautomeric forms, respectively, were synthesized and characterized by spectroscopic, X-ray diffraction and theoretical calculation methods. Both molecules adopt a very similar conformation of the common part of the structure and the differences occur within the substituents on the sulfonamide group. The amino groups characteristic for the existing tautomeric forms are involved in strong intermolecular N-H...N and N-H...O hydrogen bonds in 3a and 3b, respectively. The Hirshfeld surface analysis showed that H...H contacts constitute a high percentage of the intermolecular interactions. Theoretical calculations at the ab initio DFT/B3LYP/6-311++G(d,p) level showed that the two tautomeric forms observed for 3a and 3b can co-exist in chloroform, ethanol and water solutions, with a distinct predominance of the sulfonamide form; the participation of the sulfonimide form increases with increasing solvent polarity.


Assuntos
Sulfonamidas , Triazinas , Cristalografia por Raios X , Ligação de Hidrogênio , Modelos Moleculares
15.
Sci Rep ; 12(1): 15100, 2022 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-36068257

RESUMO

We report for the first time the use of experimental electron density (ED) as training data for the generation of drug-like three-dimensional molecules based on the structure of a target protein pocket. Similar to a structural biologist building molecules based on their ED, our model functions with two main components: a generative adversarial network (GAN) to generate the ligand ED in the input pocket and an ED interpretation module for molecule generation. The model was tested on three targets: a kinase (hematopoietic progenitor kinase 1), protease (SARS-CoV-2 main protease), and nuclear receptor (vitamin D receptor), and evaluated with a reference dataset composed of over 8000 compounds that have their activities reported in the literature. The evaluation considered the chemical validity, chemical space distribution-based diversity, and similarity with reference active compounds concerning the molecular structure and pocket-binding mode. Our model can generate molecules with similar structures to classical active compounds and novel compounds sharing similar binding modes with active compounds, making it a promising tool for library generation supporting high-throughput virtual screening. The ligand ED generated can also be used to support fragment-based drug design. Our model is available as an online service to academic users via https://edmg.stonewise.cn/#/create .


Assuntos
COVID-19 , Elétrons , Humanos , Ligantes , Modelos Moleculares , SARS-CoV-2
16.
J Comput Chem ; 43(26): 1814-1824, 2022 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-36054659

RESUMO

Atoms in molecules, noncovalent index, and natural bond orbital methods are commonly invoked to identify the presence of various noncovalent bonds and to measure their strength. However, there are numerous instances in the literature where these methods provide contradictory or apparently erroneous interpretations of the bonding. The range of reliability of these methods is assessed by calculations of a variety of systems, which include an H-bond, halogen bond, π-tetrel bond, CH··HC interaction, and a pairing of two anions. While the results appear to be meaningful for the equilibrium geometries, and those where the two subunits are progressively pulled apart, these techniques erroneously predict a progressively stronger bonding interaction as the two units are compressed and the interaction becomes clearly repulsive. The methods falsely indicate a bonding interaction in the CH··HC arrangement, and incorrectly mimic the behavior of the energy when two anions approach. These approaches are also unreliable for understanding angular deformations.


Assuntos
Halogênios , Teoria Quântica , Halogênios/química , Ligação de Hidrogênio , Modelos Moleculares , Reprodutibilidade dos Testes
17.
SAR QSAR Environ Res ; 33(9): 677-700, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-36093620

RESUMO

The application of QSAR along with other in silico tools like molecular docking, and molecular dynamics provide a lot of promise for finding new treatments for life-threatening diseases like Type 2 diabetes mellitus (T2DM). The present study is an attempt to develop Monte Carlo algorithm-based QSAR models using freely available CORAL software. The experimental data on the α-amylase inhibition by a series of benzothiazole-linked hydrazone/2,5-disubstituted-1,3,4-oxadiazole hybrids were selected as endpoint for the model generation. Initially, a total of eight QSAR models were built using correlation intensity index (CII) as a criterion of predictive potential. The model developed from split 6 using CII was the most reliable because of the highest numerical value of the determination coefficient of the validation set (r2VAL = 0.8739). The important structural fragments responsible for altering the endpoint were also extracted from the best-built model. With the goal of improved prediction quality and lower prediction errors, the validated models were used to build consensus models. Molecular docking was used to know the binding mode and pose of the selected derivatives. Further, to get insight into their metabolism by living beings, ADME studies were investigated using internet freeware, SwissADME.


Assuntos
Diabetes Mellitus Tipo 2 , Relação Quantitativa Estrutura-Atividade , Benzotiazóis , Consenso , Humanos , Hidrazonas , Modelos Moleculares , Simulação de Acoplamento Molecular , Oxidiazóis , alfa-Amilases
18.
SAR QSAR Environ Res ; 33(9): 701-728, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-36106834

RESUMO

In this work we have collected a set of 30 trypanosomicidal naphthoquinones and developed pharmacophoric and 3D-QSAR models as tools for the design of new potential anti-Chagasic compounds. Firstly, qualitative information was obtained from SAR and pharmacophoric models identifying some fragments around the 2-aryloxynaphthoquinone scaffold important for the antiparasitic activity. Then, 3D-QSAR CoMFA and CoMSIA models were developed. The models showed adequate statistical parameters where the steric, electrostatic, and hydrophobic features explain the trypanosomicidal effect. Therefore, to validate our models, we carried out the design, synthesis, and biological evaluation on T. cruzi epimastigotes of five new compounds (33a-e). According to CoMFA model, three out of five compounds showed pIC50 values within one logarithmic unit of deviation. The two compounds that did not fit the predictions were those with high lipophilicity, which agreed with the SAR and pharmacophore models. Docking and molecular dynamic studies were performed on T. cruzi trypanothione reductase, in a proposed binding site for this type of naphthoquinone. Interestingly, 33a-e showed the same interaction pattern as a naphthoquinone inhibitor (2). Finally, predicted drug-likeness properties indicated that 33a-e have optimal oral bioavailability. Thus, this study provides new in silico models for obtaining novel trypanosomicidal compounds.


Assuntos
Doença de Chagas , Naftoquinonas , Trypanosoma cruzi , Antiparasitários , Doença de Chagas/tratamento farmacológico , Humanos , Modelos Moleculares , Naftoquinonas/farmacologia , Relação Quantitativa Estrutura-Atividade
19.
J Phys Chem A ; 126(36): 6171-6184, 2022 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-36053120

RESUMO

Spectroscopic and thermodynamics properties including bond dissociation energies (BDEs), adiabatic electron affinities (AEAs), and ionization energies (IEs) have been predicted for AcH and PaH using the Feller-Peterson-Dixon composite approach. Comparisons with previous studies on ThH and UH were performed to identify possible trends in the actinide series. Multireference CASPT2 calculations were used to predict the spin-orbit effects and obtain potential energy curves for the low-lying Ω states around the equilibrium distance as well as the vertical detachment energies (VDEs) from AcH- and PaH- to excited states of the neutral species. The calculated AEA for AnH (An = Ac, Th, Pa, U) showed that the AEA increases from AcH (0.425 eV) to ThH (0.820 eV) and decreases to PaH (0.781 eV) and to UH (0.457 eV), whereas the IE values are 5.887 eV (AcH), 6.181 eV (ThH), 6.204 eV (PaH), and 6.182 eV (UH). The ground state of AcH, AcH-, PaH, and PaH- are predicted to be1Σ+0,2Π3/2, 3H4, and 4I9/2, respectively. The BDEs for AcH and PaH are 276.4 and 237.2 kJ/mol, and those for AcH- and PaH- are 242.8 and 239.8 kJ/mol, respectively. The natural bond analysis shows a significant ionic character, An+H-, in the bonding of the neutral hydrides.


Assuntos
Actínio , Protoactínio , Elétrons , Modelos Moleculares , Termodinâmica
20.
Proc Natl Acad Sci U S A ; 119(37): e2206905119, 2022 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-36067318

RESUMO

The protein mediator of ERBB2-driven cell motility 1 (Memo1) is connected to many signaling pathways that play key roles in cancer. Memo1 was recently postulated to bind copper (Cu) ions and thereby promote the generation of reactive oxygen species (ROS) in cancer cells. Since the concentration of Cu as well as ROS are increased in cancer cells, both can be toxic if not well regulated. Here, we investigated the Cu-binding capacity of Memo1 using an array of biophysical methods at reducing as well as oxidizing conditions in vitro. We find that Memo1 coordinates two reduced Cu (Cu(I)) ions per protein, and, by doing so, the metal ions are shielded from ROS generation. In support of biological relevance, we show that the cytoplasmic Cu chaperone Atox1, which delivers Cu(I) in the secretory pathway, can interact with and exchange Cu(I) with Memo1 in vitro and that the two proteins exhibit spatial proximity in breast cancer cells. Thus, Memo1 appears to act as a Cu(I) chelator (perhaps shuttling the metal ion to Atox1 and the secretory path) that protects cells from Cu-mediated toxicity, such as uncontrolled formation of ROS. This Memo1 functionality may be a safety mechanism to cope with the increased demand of Cu ions in cancer cells.


Assuntos
Proteínas de Transporte de Cobre , Cobre , Peptídeos e Proteínas de Sinalização Intracelular , Metalochaperonas , Chaperonas Moleculares , Linhagem Celular Tumoral , Cobre/metabolismo , Proteínas de Transporte de Cobre/genética , Proteínas de Transporte de Cobre/metabolismo , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Íons/metabolismo , Metalochaperonas/genética , Metalochaperonas/metabolismo , Modelos Moleculares , Chaperonas Moleculares/genética , Chaperonas Moleculares/metabolismo , Oxirredução , Ligação Proteica , Espécies Reativas de Oxigênio/metabolismo
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