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1.
Plant J ; 2024 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-38761363

RESUMO

Polyamines are involved in several plant physiological processes. In Arabidopsis thaliana, five FAD-dependent polyamine oxidases (AtPAO1 to AtPAO5) contribute to polyamine homeostasis. AtPAO5 catalyzes the back-conversion of thermospermine (T-Spm) to spermidine and plays a role in plant development, xylem differentiation, and abiotic stress tolerance. In the present study, to verify whether T-Spm metabolism can be exploited as a new route to improve stress tolerance in crops and to investigate the underlying mechanisms, tomato (Solanum lycopersicum) AtPAO5 homologs were identified (SlPAO2, SlPAO3, and SlPAO4) and CRISPR/Cas9-mediated loss-of-function slpao3 mutants were obtained. Morphological, molecular, and physiological analyses showed that slpao3 mutants display increased T-Spm levels and exhibit changes in growth parameters, number and size of xylem elements, and expression levels of auxin- and gibberellin-related genes compared to wild-type plants. The slpao3 mutants are also characterized by improved tolerance to drought stress, which can be attributed to a diminished xylem hydraulic conductivity that limits water loss, as well as to a reduced vulnerability to embolism. Altogether, this study evidences conservation, though with some significant variations, of the T-Spm-mediated regulatory mechanisms controlling plant growth and differentiation across different plant species and highlights the T-Spm role in improving stress tolerance while not constraining growth.

2.
Pharmacol Res ; 203: 107176, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38583687

RESUMO

Cannabidiol (CBD), a non-psychotomimetic constituent of Cannabis sativa, has been recently approved for epileptic syndromes often associated with Autism spectrum disorder (ASD). However, the putative efficacy and mechanism of action of CBD in patients suffering from ASD and related comorbidities remain debated, especially because of the complex pharmacology of CBD. We used pharmacological, immunohistochemical and biochemical approaches to investigate the effects and mechanisms of action of CBD in the recently validated Fmr1-Δexon 8 rat model of ASD, that is also a model of Fragile X Syndrome (FXS), the leading monogenic cause of autism. CBD rescued the cognitive deficits displayed by juvenile Fmr1-Δexon 8 animals, without inducing tolerance after repeated administration. Blockade of CA1 hippocampal GPR55 receptors prevented the beneficial effect of both CBD and the fatty acid amide hydrolase (FAAH) inhibitor URB597 in the short-term recognition memory deficits displayed by Fmr1-Δexon 8 rats. Thus, CBD may exert its beneficial effects through CA1 hippocampal GPR55 receptors. Docking analysis further confirmed that the mechanism of action of CBD might involve competition for brain fatty acid binding proteins (FABPs) that deliver anandamide and related bioactive lipids to their catabolic enzyme FAAH. These findings demonstrate that CBD reduced cognitive deficits in a rat model of FXS and provide initial mechanistic insights into its therapeutic potential in neurodevelopmental disorders.


Assuntos
Canabidiol , Modelos Animais de Doenças , Síndrome do Cromossomo X Frágil , Hipocampo , Receptores de Canabinoides , Reconhecimento Psicológico , Animais , Síndrome do Cromossomo X Frágil/tratamento farmacológico , Síndrome do Cromossomo X Frágil/metabolismo , Canabidiol/farmacologia , Canabidiol/uso terapêutico , Receptores de Canabinoides/metabolismo , Masculino , Reconhecimento Psicológico/efeitos dos fármacos , Hipocampo/efeitos dos fármacos , Hipocampo/metabolismo , Ratos , Proteína do X Frágil da Deficiência Intelectual/metabolismo , Proteína do X Frágil da Deficiência Intelectual/genética , Região CA1 Hipocampal/efeitos dos fármacos , Região CA1 Hipocampal/metabolismo , Memória/efeitos dos fármacos , Receptores Acoplados a Proteínas G/metabolismo , Simulação de Acoplamento Molecular
3.
Int J Mol Sci ; 24(4)2023 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-36835358

RESUMO

The Carnitine-Acylcarnitine Carrier is a member of the mitochondrial Solute Carrier Family 25 (SLC25), known as SLC25A20, involved in the electroneutral exchange of acylcarnitine and carnitine across the inner mitochondrial membrane. It acts as a master regulator of fatty acids ß-oxidation and is known to be involved in neonatal pathologies and cancer. The transport mechanism, also known as "alternating access", involves a conformational transition in which the binding site is accessible from one side of the membrane or the other. In this study, through a combination of state-of-the-art modelling techniques, molecular dynamics, and molecular docking, the structural dynamics of SLC25A20 and the early substrates recognition step have been analyzed. The results obtained demonstrated a significant asymmetry in the conformational changes leading to the transition from the c- to the m-state, confirming previous observations on other homologous transporters. Moreover, analysis of the MD simulations' trajectories of the apo-protein in the two conformational states allowed for a better understanding of the role of SLC25A20 Asp231His and Ala281Val pathogenic mutations, which are at the basis of Carnitine-Acylcarnitine Translocase Deficiency. Finally, molecular docking coupled to molecular dynamics simulations lend support to the multi-step substrates recognition and translocation mechanism already hypothesized for the ADP/ATP carrier.


Assuntos
Carnitina Aciltransferases , Proteínas de Membrana Transportadoras , Proteínas de Transporte da Membrana Mitocondrial , Humanos , Recém-Nascido , Carnitina Aciltransferases/química , Carnitina Aciltransferases/genética , Proteínas de Membrana Transportadoras/química , Proteínas de Membrana Transportadoras/genética , Proteínas de Transporte da Membrana Mitocondrial/química , Proteínas de Transporte da Membrana Mitocondrial/genética , Simulação de Acoplamento Molecular , Simulação por Computador
4.
Int J Mol Sci ; 24(15)2023 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-37569293

RESUMO

Ferroportin (Fpn), a member of the major facilitator superfamily (MFS) of transporters, is the only known iron exporter found in mammals and plays a crucial role in regulating cellular and systemic iron levels. MFSs take on different conformational states during the transport cycle: inward open, occluded, and outward open. However, the precise molecular mechanism of iron translocation by Fpn remains unclear, with conflicting data proposing different models. In this work, amber codon suppression was employed to introduce dansylalanine (DA), an environment-sensitive fluorescent amino acid, into specific positions of human Fpn (V46, Y54, V161, Y331) predicted to undergo major conformational changes during metal translocation. The results obtained indicate that different mutants exhibit distinct fluorescence spectra depending on the position of the fluorophore within the Fpn structure, suggesting that different local environments can be probed. Cobalt titration experiments revealed fluorescence quenching and blue-shifts of λmax in Y54DA, V161DA, and Y331DA, while V46DA exhibited increased fluorescence and blue-shift of λmax. These observations suggest metal-induced conformational transitions, interpreted in terms of shifts from an outward-open to an occluded conformation. Our study highlights the potential of genetically incorporating DA into Fpn, enabling the investigation of conformational changes using fluorescence spectroscopy. This approach holds great promise for the study of the alternating access mechanism of Fpn and advancing our understanding of the molecular basis of iron transport.


Assuntos
Proteínas de Transporte de Cátions , Ferro , Animais , Humanos , Ferro/metabolismo , Proteínas de Transporte de Cátions/metabolismo , Metais/metabolismo , Mamíferos/metabolismo
5.
Molecules ; 28(9)2023 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-37175319

RESUMO

Grape pomaces have a wide and diverse antioxidant phenolics composition. Six Uruguayan red grape pomaces were evaluated in their phenolics composition, antioxidant capacity, and anti-inflammatory properties. Not only radical scavenging methods as DPPH· and ABTS·+ were employed but also ORAC and FRAP analyses were applied to assess the antioxidant potency of the extracts. The antioxidant reactivity of all extracts against hydroxyl radicals was assessed with ESR. The phenol profile of the most bioactive extract was analyzed by HPLC-MS, and a set of 57 structures were determined. To investigate the potential anti-inflammatory activity of the extracts, Nuclear Factor kappa-B (NF-κB) modulation was evaluated in the human colon cancer reporter cell line (HT-29-NF-κB-hrGFP). Our results suggest that Tannat grapes pomaces have higher phenolic content and antioxidant capacity compared to Cabernet Franc. These extracts inhibited TNF-alpha mediated NF-κB activation and IL-8 production when added to reporter cells. A molecular docking study was carried out to rationalize the experimental results allowing us to propose the proactive interaction between the NF-κB, the grape extracts phenols, and their putative anti-inflammatory bioactivity. The present findings show that red grape pomace constitutes a sustainable source of phenolic compounds, which may be valuable for pharmaceutical, cosmetic, and food industry applications.


Assuntos
Vitis , Humanos , Vitis/química , Antioxidantes/química , NF-kappa B , Simulação de Acoplamento Molecular , Extratos Vegetais/farmacologia , Extratos Vegetais/química , Fenóis/química , Anti-Inflamatórios/farmacologia
6.
J Mol Recognit ; 34(3): e2877, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33034105

RESUMO

The anticoagulant therapy is widely used to prevent and treat thromboembolic events. Until the last decade, vitamin K antagonists were the only available oral anticoagulants; recently, direct oral anticoagulants (DOACs) have been developed. Since 55% to 95% of DOACs are bound to plasma proteins, the in silico docking and ligand-binding properties of drugs apixaban, betrixaban, dabigatran, edoxaban, and rivaroxaban and of the prodrug dabigatran etexilate to human serum albumin (HSA), the most abundant plasma protein, have been investigated. DOACs bind to the fatty acid (FA) site 1 (FA1) of ligand-free HSA, whereas they bind to the FA8 and FA9 sites of heme-Fe(III)- and myristic acid-bound HSA. DOACs binding to the FA1 site of ligand-free HSA has been validated by competitive inhibition of heme-Fe(III) recognition. Values of the dissociation equilibrium constant for DOACs binding to the FA1 site (ie, calc KDOAC ) derived from in silico docking simulations (ranging between 1.2 × 10-8 M and 1.4 × 10-6 M) agree with those determined experimentally from competitive inhibition of heme-Fe(III) binding (ie, exp KDOAC ; ranging between 2.5 × 10-7 M and 2.2 × 10-6 M). In addition, this study highlights the inequivalence of rivaroxaban binding to mammalian serum albumin. Given the HSA concentration in vivo (~7.5 × 10-4 M), values of KDOAC here determined indicate that the formation of the HSA:DOACs complexes in the absence and presence of FAs and heme-Fe(III) may occur in vivo. Therefore, HSA appears to be an important determinant for DOACs transport.


Assuntos
Inibidores do Fator Xa/farmacologia , Albumina Sérica Humana/química , Albumina Sérica Humana/metabolismo , Sítios de Ligação , Inibidores do Fator Xa/química , Ácidos Graxos/metabolismo , Humanos , Modelos Moleculares , Simulação de Acoplamento Molecular , Conformação Proteica , Rivaroxabana/química , Rivaroxabana/farmacologia , Equivalência Terapêutica
7.
Int J Mol Sci ; 22(6)2021 Mar 22.
Artigo em Inglês | MEDLINE | ID: mdl-33809947

RESUMO

Huntington's disease is a rare neurodegenerative and autosomal dominant disorder. HD is caused by a mutation in the gene coding for huntingtin (Htt). The result is the production of a mutant Htt with an abnormally long polyglutamine repeat that leads to pathological Htt aggregates. Although the structure of human Htt has been determined, albeit at low resolution, its functions and how they are performed are largely unknown. Moreover, there is little information on the structure and function of Htt in other organisms. The comparison of Htt homologs can help to understand if there is a functional conservation of domains in the evolution of Htt in eukaryotes. In this work, through a computational approach, Htt homologs from lower eukaryotes have been analysed, identifying ordered domains and modelling their structure. Based on the structural models, a putative function for most of the domains has been predicted. A putative C. elegans Htt-like protein has also been analysed following the same approach. The results obtained support the notion that this protein is a orthologue of human Htt.


Assuntos
Eucariotos , Proteína Huntingtina/química , Modelos Moleculares , Conformação Proteica , Animais , Humanos , Domínios e Motivos de Interação entre Proteínas , Homologia de Sequência de Aminoácidos , Especificidade da Espécie , Relação Estrutura-Atividade
8.
Int J Mol Sci ; 22(24)2021 Dec 19.
Artigo em Inglês | MEDLINE | ID: mdl-34948418

RESUMO

Coloring is one of the most important characteristics in commercial flowers and fruits, generally due to the accumulation of carotenoid pigments. Enzymes of the CCD4 family in citrus intervene in the generation of ß-citraurin, an apocarotenoid responsible for the reddish-orange color of mandarins. Citrus CCD4s enzymes could be capable of interacting with the thylakoid membrane inside chloroplasts. However, to date, this interaction has not been studied in detail. In this work, we present three new complete models of the CCD4 family members (CCD4a, CCD4b, and CCD4c), modeled with a lipid membrane. To identify the preference for substrates, typical carotenoids were inserted in the active site of the receptors and the protein-ligand interaction energy was evaluated. The results show a clear preference of CCD4s for xanthophylls over aliphatic carotenes. Our findings indicate the ability to penetrate the membrane and maintain a stable interaction through the N-terminal α-helical domain, spanning a contact surface of 2250 to 3250 Å2. The orientation and depth of penetration at the membrane surface suggest that CCD4s have the ability to extract carotenoids directly from the membrane through a tunnel consisting mainly of hydrophobic residues that extends up to the catalytic center of the enzyme.


Assuntos
Carotenoides/metabolismo , Citrus/metabolismo , Dioxigenases/metabolismo , Proteínas de Plantas/metabolismo , Carotenoides/química , Citrus/química , Dioxigenases/química , Modelos Moleculares , Proteínas de Plantas/química , Ligação Proteica , Domínios Proteicos , Especificidade por Substrato , Xantofilas/química , Xantofilas/metabolismo
9.
IUBMB Life ; 72(4): 716-723, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31614076

RESUMO

Neonicotinoids are a widely used class of insecticides that target the acetylcholine recognition site of the nicotinic acetylcholine receptors in the central nervous system of insects. Although neonicotinoids display a high specificity for insects, their use has been recently debated since several studies led to the hypothesis that they may have adverse ecological effects and potential risks to mammals and even humans. Due to their hydrophobic nature, neonicotinoids need specific carriers to allow their distribution in body fluids. Human serum albumin (HSA), the most abundant plasma protein, is a key carrier of endogenous and exogenous compounds. The in silico docking and ligand binding properties of acetamiprid, clothianidin, dinotefuran, imidacloprid, nitenpyram, thiacloprid, and thiamethoxam to HSA are here reported. Neonicotinoids bind to multiple fatty acid (FA) binding sites, preferentially to the FA1 pocket, with high affinity. Values of the dissociation equilibrium constant for neonicotinoid binding FA1 of HSA (i.e., calc Kn ) derived from in silico docking simulations (ranging between 3.9 × 10-5 and 6.3 × 10-4 M) agree with those determined experimentally from competitive inhibition of heme-Fe(III) binding (i.e., exp Kn ; ranging between 2.1 × 10-5 and 6.9 × 10-5 M). Accounting for the HSA concentration in vivo (~7.5 10-4 M), values of Kn here determined suggest that the formation of the HSA:neonicotinoid complexes may occur in vivo. Therefore, HSA appears to be an important determinant for neonicotinoid transport and distribution to tissues and organs, particularly to the liver where they are metabolized.


Assuntos
Neonicotinoides/metabolismo , Albumina Sérica Humana/metabolismo , Humanos , Inseticidas/química , Inseticidas/metabolismo , Inseticidas/farmacocinética , Simulação de Acoplamento Molecular , Neonicotinoides/química , Neonicotinoides/farmacocinética , Albumina Sérica Humana/química , Termodinâmica
10.
IUBMB Life ; 72(4): 698-705, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31869003

RESUMO

In recent years, the high throughput and the low cost of next-generation sequencing (NGS) technologies have led to an increase of the amount of (meta)genomic data, revolutionizing genomic research studies. However, the quality of sequencing data could be affected by experimental errors derived from defective methods and protocols. This represents a serious problem for the scientific community with a negative impact on the correctness of studies that involve genomic sequence analysis. As a countermeasure, several alignment and taxonomic classification tools have been developed to uncover and correct errors. In this critical review some of these integrated software tools and pipelines used to detect contaminations in reference genome databases and sequenced samples are reported. In particular, case studies of bacterial contaminations, contaminations of human origin, mitochondrial contaminations of ancient DNA, and cross contaminations are examined.


Assuntos
Genômica/métodos , Metagenoma/genética , Software , Bactérias/genética , DNA Antigo , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Mitocôndrias/genética
11.
Int J Mol Sci ; 21(24)2020 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-33333976

RESUMO

MOTIVATION: Bringing a new drug to the market is expensive and time-consuming. To cut the costs and time, computer-aided drug design (CADD) approaches have been increasingly included in the drug discovery pipeline. However, despite traditional docking tools show a good conformational space sampling ability, they are still unable to produce accurate binding affinity predictions. This work presents a novel scoring function for molecular docking seamlessly integrated into DockingApp, a user-friendly graphical interface for AutoDock Vina. The proposed function is based on a random forest model and a selection of specific features to overcome the existing limits of Vina's original scoring mechanism. A novel version of DockingApp, named DockingApp RF, has been developed to host the proposed scoring function and to automatize the rescoring procedure of the output of AutoDock Vina, even to nonexpert users. RESULTS: By coupling intermolecular interaction, solvent accessible surface area features and Vina's energy terms, DockingApp RF's new scoring function is able to improve the binding affinity prediction of AutoDock Vina. Furthermore, comparison tests carried out on the CASF-2013 and CASF-2016 datasets demonstrate that DockingApp RF's performance is comparable to other state-of-the-art machine-learning- and deep-learning-based scoring functions. The new scoring function thus represents a significant advancement in terms of the reliability and effectiveness of docking compared to AutoDock Vina's scoring function. At the same time, the characteristics that made DockingApp appealing to a wide range of users are retained in this new version and have been complemented with additional features.


Assuntos
Simulação de Acoplamento Molecular/métodos , Software , Bases de Dados de Proteínas , Desenho de Fármacos , Descoberta de Drogas/métodos , Ligantes , Modelos Teóricos , Reprodutibilidade dos Testes , Interface Usuário-Computador
12.
Int J Mol Sci ; 21(18)2020 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-32947891

RESUMO

Members of the major facilitator superfamily of transporters (MFS) play an essential role in many physiological processes such as development, neurotransmission, and signaling. Aberrant functions of MFS proteins are associated with several diseases, including cancer, schizophrenia, epilepsy, amyotrophic lateral sclerosis and Alzheimer's disease. MFS transporters are also involved in multidrug resistance in bacteria and fungi. The structures of most MFS members, especially those of members with significant physiological relevance, are yet to be solved. The lack of structural and functional information impedes our detailed understanding, and thus the pharmacological targeting, of these transporters. To improve our knowledge on the mechanistic principles governing the function of MSF members, molecular dynamics (MD) simulations were performed on the inward-facing and outward-facing crystal structures of the human ferroportin homologue from the Gram-negative bacterium Bdellovibrio bacteriovorus (BdFpn). Several simulations with an excess of iron ions were also performed to explore the relationship between the protein's dynamics and the ligand recognition mechanism. The results reinforce the existence of the alternating-access mechanism already described for other MFS members. In addition, the reorganization of salt bridges, some of which are conserved in several MFS members, appears to be a key molecular event facilitating the conformational change of the transporter.


Assuntos
Proteínas de Bactérias/metabolismo , Bdellovibrio bacteriovorus/metabolismo , Proteínas de Transporte de Cátions/metabolismo , Motivos de Aminoácidos , Apoproteínas/química , Apoproteínas/metabolismo , Proteínas de Bactérias/química , Proteínas de Transporte de Cátions/química , Cristalografia por Raios X , Ferro/metabolismo , Ligantes , Modelos Moleculares , Simulação de Dinâmica Molecular , Ligação Proteica , Conformação Proteica
13.
Molecules ; 25(9)2020 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-32397407

RESUMO

Butylated hydroxytoluene (BHT) is one of the most commonly used synthetic antioxidants in food, cosmetic, pharmaceutical and petrochemical products. BHT is considered safe for human health; however, its widespread use together with the potential toxicological effects have increased consumers concern about the use of this synthetic food additive. In addition, the estimated daily intake of BHT has been demonstrated to exceed the recommended acceptable threshold. In the present work, using BHT as a case study, the usefulness of computational techniques, such as reverse screening and molecular docking, in identifying protein-ligand interactions of food additives at the bases of their toxicological effects has been probed. The computational methods here employed have been useful for the identification of several potential unknown targets of BHT, suggesting a possible explanation for its toxic effects. In silico analyses can be employed to identify new macromolecular targets of synthetic food additives and to explore their functional mechanisms or side effects. Noteworthy, this could be important for the cases in which there is an evident lack of experimental studies, as is the case for BHT.


Assuntos
Hidroxitolueno Butilado/toxicidade , Aditivos Alimentares/toxicidade , Proteínas/análise , Hidroxitolueno Butilado/química , Simulação por Computador , Aditivos Alimentares/química , Humanos , Ligantes , Modelos Moleculares , Conformação Molecular , Simulação de Acoplamento Molecular , Proteínas/química
14.
Crit Rev Biochem Mol Biol ; 52(5): 554-582, 2017 10.
Artigo em Inglês | MEDLINE | ID: mdl-28635330

RESUMO

Insulin-degrading enzyme (IDE) is a ubiquitous zinc peptidase of the inverzincin family, which has been initially discovered as the enzyme responsible for insulin catabolism; therefore, its involvement in the onset of diabetes has been largely investigated. However, further studies on IDE unraveled its ability to degrade several other polypeptides, such as ß-amyloid, amylin, and glucagon, envisaging the possible implication of IDE dys-regulation in the "aggregopathies" and, in particular, in neurodegenerative diseases. Over the last decade, a novel scenario on IDE biology has emerged, pointing out a multi-functional role of this enzyme in several basic cellular processes. In particular, latest advances indicate that IDE behaves as a heat shock protein and modulates the ubiquitin-proteasome system, suggesting a major implication in proteins turnover and cell homeostasis. In addition, recent observations have highlighted that the regulation of glucose metabolism by IDE is not merely based on its largely proposed role in the degradation of insulin in vivo. There is increasing evidence that improper IDE function, regulation, or trafficking might contribute to the etiology of metabolic diseases. In addition, the enzymatic activity of IDE is affected by metals levels, thus suggesting a role also in the metal homeostasis (metallostasis), which is thought to be tightly linked to the malfunction of the "quality control" machinery of the cell. Focusing on the physiological role of IDE, we will address a comprehensive vision of the very complex scenario in which IDE takes part, outlining its crucial role in interconnecting several relevant cellular processes.


Assuntos
Insulisina/metabolismo , Doença de Alzheimer/enzimologia , Doença de Alzheimer/patologia , Animais , Diabetes Mellitus Tipo 2/enzimologia , Diabetes Mellitus Tipo 2/patologia , Humanos , Insulisina/fisiologia , Agregação Patológica de Proteínas/enzimologia , Agregação Patológica de Proteínas/patologia , Conformação Proteica
15.
Bioinformatics ; 34(5): 878-880, 2018 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-29126218

RESUMO

Summary: Recently, LIBRA, a tool for active/ligand binding site prediction, was described. LIBRA's effectiveness was comparable to similar state-of-the-art tools; however, its scoring scheme, output presentation, dependence on local resources and overall convenience were amenable to improvements. To solve these issues, LIBRA-WA, a web application based on an improved LIBRA engine, has been developed, featuring a novel scoring scheme consistently improving LIBRA's performance, and a refined algorithm that can identify binding sites hosted at the interface between different subunits. LIBRA-WA also sports additional functionalities like ligand clustering and a completely redesigned interface for an easier analysis of the output. Extensive tests on 373 apoprotein structures indicate that LIBRA-WA is able to identify the biologically relevant ligand/ligand binding site in 357 cases (∼96%), with the correct prediction ranking first in 349 cases (∼98% of the latter, ∼94% of the total). The earlier stand-alone tool has also been updated and dubbed LIBRA+, by integrating LIBRA-WA's improved engine for cross-compatibility purposes. Availability and implementation: LIBRA-WA and LIBRA+ are available at: http://www.computationalbiology.it/software.html. Contact: polticel@uniroma3.it. Supplementary information: Supplementary data are available at Bioinformatics online.


Assuntos
Domínio Catalítico , Biologia Computacional/métodos , Ligantes , Proteínas/metabolismo , Software , Algoritmos , Sítios de Ligação , Humanos , Cinesinas/metabolismo , Ligação Proteica , Conformação Proteica
16.
IUBMB Life ; 71(3): 398-399, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30548956

RESUMO

In the "Hypothesis" paper entitled "Lanthanides-Based Catalysis in Eukaryotes" (IUBMB Life 2018 Nov;70(11):1067-1075), we analyzed the possibility that Ce3+ -dependent methanol dehydrogenases (MDHs) could be found not only in archaea and bacteria but also in eukaryotic organisms. This hypothesis was based on the observation that MDHs protein sequences carrying the signature of Ce3+ -based active sites could be found in genome-derived proteomes of the eukaryotes Plasmodium yoelii yoelii, Nephila clavipes, Hyalella azteca, Pantholops hodgsonii, and Homo sapiens. Data were analyzed following standard procedures employed in the study of phylogenetic relationships among members of protein families and their occurrence in diverse organisms. Furthermore, the study relied on current annotations of protein sequences in the nonredundant protein sequences database, which we did not have any element to doubt about. After the publication of this hypothesis, following analyses carried out by Prof. Huub Op den Camp (Department of Microbiology, Faculty of Science, Radboud University, 6500 GL Nijmegen, The Netherlands), evidence has emerged that the sequences of the putative eukaryotic homologs of bacterial lanthanide-dependent MDHs, identified in our work, either derive from wrong annotation in GenBank or from undetected and pervasive bacterial contamination of the corresponding genomes. Thus, even though our study was technically correct, we were induced to support the initial hypothesis due to annotation errors and undetected bacterial contamination of the relevant genomes in the nucleotide sequences database. Therefore, at present, the hypothesis put forward in our article is not backed up by the currently available data. On a different note, this issue calls for a much higher attention on the integrity/correctness of the data deposited in the sequence databases, a need already highlighted in the literature also for the opposite problem, that is, human contamination of genomic data of other organisms. © 2018 IUBMB Life, 71(3):398-399, 2019.


Assuntos
Eucariotos , Elementos da Série dos Lantanídeos , Sequência de Aminoácidos , Catálise , Humanos , Filogenia
17.
J Comput Aided Mol Des ; 33(10): 887-903, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31628659

RESUMO

In the current "genomic era" the number of identified genes is growing exponentially. However, the biological function of a large number of the corresponding proteins is still unknown. Recognition of small molecule ligands (e.g., substrates, inhibitors, allosteric regulators, etc.) is pivotal for protein functions in the vast majority of the cases and knowledge of the region where these processes take place is essential for protein function prediction and drug design. In this regard, computational methods represent essential tools to tackle this problem. A significant number of software tools have been developed in the last few years which exploit either protein sequence information, structure information or both. This review describes the most recent developments in protein function recognition and binding site prediction, in terms of both freely-available and commercial solutions and tools, detailing the main characteristics of the considered tools and providing a comparative analysis of their performance.


Assuntos
Biologia Computacional/métodos , Desenho de Fármacos , Aprendizado de Máquina , Proteínas/química , Proteínas/metabolismo , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/metabolismo , Sequência de Aminoácidos , Inteligência Artificial , Humanos , Ligantes , Modelos Moleculares , Ligação Proteica , Conformação Proteica , Homologia de Sequência , Software
18.
J Enzyme Inhib Med Chem ; 34(1): 740-752, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30829081

RESUMO

Fourteen polyamine analogues, asymmetric or symmetric substituted spermine (1-9) or methoctramine (10-14) analogues, were evaluated as potential inhibitors or substrates of two enzymes of the polyamine catabolic pathway, spermine oxidase (SMOX) and acetylpolyamine oxidase (PAOX). Compound 2 turned out to be the best substrate for PAOX, having the highest affinity and catalytic efficiency with respect to its physiological substrates. Methoctramine (10), a well-known muscarinic M2 receptor antagonist, emerged as the most potent competitive PAOX inhibitor known so far (Ki = 10 nM), endowed with very good selectivity compared with SMOX (Ki=1.2 µM vs SMOX). The efficacy of methoctramine in inhibiting PAOX activity was confirmed in the HT22 cell line. Methoctramine is a very promising tool in the design of drugs targeting the polyamine catabolism pathway, both to understand the physio-pathological role of PAOX vs SMOX and for pharmacological applications, being the polyamine pathway involved in various pathologies.


Assuntos
Diaminas/farmacologia , Inibidores Enzimáticos/farmacologia , Oxirredutases atuantes sobre Doadores de Grupo CH-NH/antagonistas & inibidores , Poliaminas/farmacologia , Diaminas/síntese química , Diaminas/química , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Humanos , Estrutura Molecular , Oxirredutases atuantes sobre Doadores de Grupo CH-NH/metabolismo , Poliaminas/síntese química , Poliaminas/química , Relação Estrutura-Atividade , Poliamina Oxidase
19.
Int J Mol Sci ; 20(10)2019 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-31117183

RESUMO

In this work, the information contained in the contacts between fragments of small-molecule ligands and protein residues has been collected and its exploitability has been verified by using the scoring of docking simulations as a test case for bringing about a proof of concept. Contact statistics between small-molecule fragments and binding site residues were collected and analyzed using a dataset composed of 200,000+ binding sites and associated ligands, derived from the database of the LIBRA ligand binding site recognition software, as a starting point. The fragments were generated by applying the decomposition algorithm implemented in BRICS. A simple "potential" based on the contact frequencies was tested against the CASF-2013 benchmark; its performance was then evaluated through the rescoring of docking poses generated for the DUD-E dataset. The results obtained indicate that this approach, its simplicity notwithstanding, yields promising results that are comparable, and in some cases, superior, to those obtained with other, more complex scoring functions.


Assuntos
Ligantes , Simulação de Acoplamento Molecular , Proteínas/metabolismo , Sítios de Ligação , Ligação Proteica
20.
J Infect Dis ; 218(9): 1424-1435, 2018 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-29868851

RESUMO

Background: The pathogenic effects of Clostridium difficile are primarily attributable to the production of the large protein toxins (C difficile toxins [Tcd]) A (TcdA) and B (TcdB). These toxins monoglucosylate Rho GTPases in the cytosol of host cells, causing destruction of the actin cytoskeleton with cytotoxic effects. Low human serum albumin (HSA) levels indicate a higher risk of acquiring and developing a severe C difficile infection (CDI) and are associated with recurrent and fatal disease. Methods: We used a combined approach based on docking simulation and biochemical analyses that were performed in vitro on purified proteins and in human epithelial colorectal adenocarcinoma cells (Caco-2), and in vivo on stem cell-derived human intestinal organoids and zebrafish embryos. Results: Our results show that HSA specifically binds via its domain II to TcdA and TcdB and thereby induces their autoproteolytic cleavage at physiological concentrations. This process impairs toxin internalization into the host cells and reduces the toxin-dependent glucosylation of Rho proteins. Conclusions: Our data provide evidence for a specific HSA-dependent self-defense mechanism against C difficile toxins and provide an explanation for the clinical correlation between CDI severity and hypoalbuminemia.


Assuntos
Proteínas de Bactérias/metabolismo , Toxinas Bacterianas/metabolismo , Clostridioides difficile/metabolismo , Enterotoxinas/metabolismo , Albumina Sérica Humana/metabolismo , Animais , Células CACO-2 , Linhagem Celular Tumoral , Humanos , Peixe-Zebra/metabolismo
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