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1.
Crit Rev Clin Lab Sci ; : 1-25, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38850014

ABSTRACT

Transthyretin (TTR), a homotetrameric protein found in plasma, cerebrospinal fluid, and the eye, plays a pivotal role in the onset of several amyloid diseases with high morbidity and mortality. Protein aggregation and fibril formation by wild-type TTR and its natural more amyloidogenic variants are hallmarks of ATTRwt and ATTRv amyloidosis, respectively. The formation of soluble amyloid aggregates and the accumulation of insoluble amyloid fibrils and deposits in multiple tissues can lead to organ dysfunction and cell death. The most frequent manifestations of ATTR are polyneuropathies and cardiomyopathies. However, clinical manifestations such as carpal tunnel syndrome, leptomeningeal, and ocular amyloidosis, among several others may also occur. This review provides an up-to-date listing of all single amino-acid mutations in TTR known to date. Of approximately 220 single-point mutations, 93% are considered pathogenic. Aspartic acid is the residue mutated with the highest frequency, whereas tryptophan is highly conserved. "Hot spot" mutation regions are mainly assigned to ß-strands B, C, and D. This manuscript also reviews the protein aggregation models that have been proposed for TTR amyloid fibril formation and the transient conformational states that convert native TTR into aggregation-prone molecular species. Finally, it compiles the various in vitro TTR aggregation protocols currently in use for research and drug development purposes. In short, this article reviews and discusses TTR mutagenesis and amyloidogenesis, and their implications in disease onset.

2.
J Phys Chem B ; 128(20): 4898-4910, 2024 May 23.
Article in English | MEDLINE | ID: mdl-38733339

ABSTRACT

In-depth characterization of fundamental folding steps of small model peptides is crucial for a better understanding of the folding mechanisms of more complex biomacromolecules. We have previously reported on the folding/unfolding kinetics of a model α-helix. Here, we study folding transitions in chignolin (GYDPETGTWG), a short ß-hairpin peptide previously used as a model to study conformational changes in ß-sheet proteins. Although previously suggested, until now, the role of the Tyr2-Trp9 interaction in the folding mechanism of chignolin was not clear. In the present work, pH-dependent conformational changes of chignolin were characterized by circular dichroism (CD), nuclear magnetic resonance (NMR), ultrafast pH-jump coupled with time-resolved photoacoustic calorimetry (TR-PAC), and molecular dynamics (MD) simulations. Taken together, our results present a comprehensive view of chignolin's folding kinetics upon local pH changes and the role of the Tyr2-Trp9 interaction in the folding process. CD data show that chignolin's ß-hairpin formation displays a pH-dependent skew bell-shaped curve, with a maximum close to pH 6, and a large decrease in ß-sheet content at alkaline pH. The ß-hairpin structure is mainly stabilized by aromatic interactions between Tyr2 and Trp9 and CH-π interactions between Tyr2 and Pro4. Unfolding of chignolin at high pH demonstrates that protonation of Tyr2 is essential for the stability of the ß-hairpin. Refolding studies were triggered by laser-induced pH-jumps and detected by TR-PAC. The refolding of chignolin from high pH, mainly due to the protonation of Tyr2, is characterized by a volume expansion (10.4 mL mol-1), independent of peptide concentration, in the microsecond time range (lifetime of 1.15 µs). At high pH, the presence of the deprotonated hydroxyl (tyrosinate) hinders the formation of the aromatic interaction between Tyr2 and Trp9 resulting in a more disorganized and dynamic tridimensional structure of the peptide. This was also confirmed by comparing MD simulations of chignolin under conditions mimicking neutral and high pH.


Subject(s)
Molecular Dynamics Simulation , Oligopeptides , Protein Folding , Hydrogen-Ion Concentration , Kinetics , Oligopeptides/chemistry , Protein Structure, Secondary
3.
J Sci Food Agric ; 104(11): 6541-6552, 2024 Aug 30.
Article in English | MEDLINE | ID: mdl-38520251

ABSTRACT

BACKGROUND: Aquaponic systems are sustainable processes of managing water and nutrients for food production. An innovate nutrient-efficient catfish-based (Clarias gariepinus) aquaponics system was implemented for producing two cultivars of two leafy vegetables largely consumed worldwide: lamb's lettuce (Valerianella locusta var. Favor and Valerianella locusta var. de Hollande) and arugula (Eruca vesicaria var. sativa and Eruca sativa). Different growing treatments (4 × 2 factorial design) were applied to plants of each cultivar, grown at two light intensities (120 and 400 µmol m-2 s-1). During growth, several morphological characteristics (root length, plant height, leaf number, foliage diameter and biggest leaf length) were measured. At harvest, plants were weighed and examined qualitatively in terms of greenness and health status. Additionally, leaf extracts were obtained and used to determine total phenolic contents, antioxidant capacities, and levels of cytotoxicity to Caco-2 intestinal model cells. RESULTS: After a 5-week growth period, both lamb's lettuce cultivars presented high levels of greenness and health status, at both light intensities, particularly the var. de Hollande that also showed higher average performance in terms of plant morphology. In turn, arugula cultivars showed lower levels of greenness and health status, especially the cultivar E. vesicaria var. sativa submitted to direct sunlight during growth. In addition, plant specimens submitted to higher levels of light intensity showed higher contents in antioxidants/polyphenols. Cultivars with a higher content in antioxidants/polyphenols led to higher Caco-2 cell viability. CONCLUSION: For successful industrial implementation of the aquaponics technology, different and optimized acclimatizing conditions must be applied to different plant species and cultivars. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.


Subject(s)
Catfishes , Lactuca , Light , Plant Leaves , Animals , Humans , Catfishes/growth & development , Catfishes/metabolism , Lactuca/growth & development , Lactuca/chemistry , Lactuca/radiation effects , Lactuca/metabolism , Plant Leaves/chemistry , Plant Leaves/growth & development , Plant Leaves/metabolism , Plant Leaves/radiation effects , Caco-2 Cells , Antioxidants/metabolism , Antioxidants/analysis , Phenols/metabolism , Phenols/analysis
4.
Plants (Basel) ; 13(3)2024 Jan 31.
Article in English | MEDLINE | ID: mdl-38337960

ABSTRACT

Crithmum maritimum L. (sea fennel), an edible xerophyte of coastal habitats, is considered an emerging cash crop for biosaline agriculture due to its salt-tolerance ability and potential applications in the agri-food sector. Here, the nutritional value and bioactive properties of sea fennel are described. Sea fennel leaves, flowers, and schizocarps are composed of carbohydrates (>65%) followed by ash, proteins, and lipids. Sea fennel's salty, succulent leaves are a source of omega-6 and omega-3 polyunsaturated fatty acids, especially linoleic acid. Extracts obtained from flowers and fruits/schizocarps are rich in antioxidants and polyphenols and show antimicrobial activity against Staphylococcus aureus, Staphylococcus epidermis, Candida albicans, and Candida parapsilosis. Plant material is particularly rich in sodium (Na) but also in other nutritionally relevant minerals, such as calcium (Ca), chlorine (Cl), potassium (K), phosphorus (P), and sulfur (S), beyond presenting a potential prebiotic effect on Lactobacillus bulgaricus and being nontoxic to human intestinal epithelial Caco-2 model cells, up to 1.0% (w/v). Hence, the rational use of sea fennel can bring nutrients, aroma, and flavor to culinary dishes while balancing microbiomes and contributing to expanding the shelf life of food products.

5.
Proteins ; 92(2): 219-235, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37814578

ABSTRACT

Interleukin-4 (IL-4) is a hematopoietic cytokine composed by a four-helix bundle stabilized by an antiparallel beta-sheet and three disulfide bonds: Cys3-Cys127, Cys24-Cys65, and Cys46-Cys99. IL-4 is involved in several immune responses associated to infection, allergy, autoimmunity, and cancer. Besides its physiological relevance, IL-4 is often used as a "model" for protein design and engineering. Hence, to understand the role of each disulfide in the structure and dynamics of IL-4, we carried out several spectroscopic analyses (circular dichroism [CD], fluorescence, nuclear magnetic resonance [NMR]), and molecular dynamics (MD) simulations on wild-type IL-4 and four IL-4 disulfide mutants. All disulfide mutants showed loss of structure, altered interhelical angles, and looser core packings, showing that all disulfides are relevant for maintaining the overall fold and stability of the four-helix bundle motif, even at very low pH. In the absence of the disulfide connecting both protein termini Cys3-Cys127, C3T-IL4 showed a less packed protein core, loss of secondary structure (~9%) and fast motions on the sub-nanosecond time scale (lower S2 order parameters and larger τc correlation time), especially at the two protein termini, loops, beginning of helix A and end of helix D. In the absence of Cys24-Cys65, C24T-IL4 presented shorter alpha-helices (14% loss in helical content), altered interhelical angles, less propensity to form the small anti-parallel beta-sheet and increased dynamics. Simultaneously deprived of two disulfides (Cys3-Cys127 and Cys24-Cys65), IL-4 formed a partially folded "molten globule" with high 8-anilino-1-naphtalenesulphonic acid-binding affinity and considerable loss of secondary structure (~50%decrease), as shown by the far UV-CD, NMR, and MD data.


Subject(s)
Disulfides , Interleukin-4 , Protein Conformation , Interleukin-4/chemistry , Disulfides/chemistry , Protein Structure, Secondary , Magnetic Resonance Spectroscopy , Circular Dichroism
6.
Bioorg Med Chem ; 93: 117443, 2023 10 01.
Article in English | MEDLINE | ID: mdl-37634417

ABSTRACT

Photodynamic therapy (PDT) is an established anticancer treatment that combines the use of a photosensitiser (PS) and a light source of a specific wavelength for the generation of reactive oxygen species (ROS) that are toxic to the tumour cells. Foscan® (mTHPC) is a clinically-approved chlorin used for the PDT treatment of advanced head and neck, prostate and pancreatic cancers but is characterized by being photochemically unstable and associated with prolonged skin photosensitivity. Herein, we report the synthesis of new 4,5,6,7-tetrahydropyrazolo[1,5-a]pyridine-fused chlorins, having the meso-tetra(3-hydroxyphenyl)macrocycle core of mTHPC, by exploring the [8π + 2π] cycloaddition of a meso-tetra(3-hydroxyphenyl)porphyrin derivative with diazafulvenium methides. These chlorins have photochemical properties similar to Foscan® but are much more photostable. Among the novel compounds, two chlorins with a hydroxymethyl group and its azide derivative present in the 4,5,6,7-tetrahydropyrazolo[1,5-a]pyridine-fused system, are promising photodynamic agents with activity in the 100 nM range against triple-negative breast cancer cells and, in the case of azidomethyl chlorin, a safer phototherapeutic index compared to Foscan®.


Subject(s)
Pancreatic Neoplasms , Photochemotherapy , Porphyrins , Male , Humans , Porphyrins/pharmacology , Pyridines
7.
Cureus ; 15(6): e40149, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37425562

ABSTRACT

Groin pain is a common problem in athletes, leading to significant distress and long periods of absence from sports. Nonsurgical interventions are usually the first line of treatment. However, the most effective intervention for groin pain is unknown and recommendations are scarce. The primary objective of this systematic review was to assess the effectiveness of nonsurgical interventions in the treatment of long-standing groin pain in athletes and to provide some guidance for clinical practice and further research. A search strategy was performed in March 2020 in Pubmed, Google Scholar, PEDro, and Cochrane Central Register of Controlled Trials databases, without any time restrictions. Only randomized controlled trials (RCT) were included for full-text analysis. Data on the patient's characteristics, duration of pain, study groups, outcome measures results, follow-up time, and return to play time were extracted. The risk of bias in each study was assessed using the Cochrane risk-of-bias assessment tool. Data for analysis could not be pooled for meta-analysis and, as such, a narrative summary of the outcomes was instead performed. The certainty of the evidence was assessed using a variation of the GRADE approach for when a meta-analysis is not possible to perform. Seven RCTs were included for analysis. Most studies were classified as uncertain risk of bias. All studies provided evidence that nonsurgical interventions have significant positive effects and may lead to good outcomes concerning pain, function, and return to sports at previous levels. The certainty of the evidence was assessed to be low using the modified GRADE approach. Despite the low quality of the available evidence, nonsurgical treatments demonstrated efficacy in the management of groin pain and should probably be the initial approach to treatment. More RCTs of high quality are necessary to provide clear recommendations on the most efficient nonsurgical treatment strategy for groin pain.

8.
Cureus ; 15(5): e39781, 2023 May.
Article in English | MEDLINE | ID: mdl-37398834

ABSTRACT

CrossFit (CrossFit Inc, Washington, DC) is a recent, high-intensity strength and conditioning sport that is growing in popularity worldwide. Potential risks and injuries have been described in previous reports. Distal humeral fractures without direct trauma were related to sports like baseball or wrestling. However, they have never been reported in a CrossFit athlete. We present the first case of distal humeral fracture associated with a CrossFit workout, during a gymnastic movement. Our patient had no relevant medical history but the investigation revealed reduced vitamin D levels and low bone density. The patient was surgically treated and he completed the rehabilitation program. He returned to sports practice 12 weeks after the surgery.

9.
Cureus ; 15(6): e40192, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37431333

ABSTRACT

Over the years, chondroitin sulfate (CS) has been used as a slow-acting drug for the treatment of osteoarthritis, for the reduction of pain and improvement of function, and for its disease-modifying properties by limiting cartilage volume loss and joint space narrowing progression. However, there have been inconsistencies in published trials regarding clinical efficacy, with reports of a lack of significant effects compared to placebo. The therapeutic effects of chondroitin sulfate may depend on many variables, such as the source of origin, purity, and contamination with by-products. Another source of confusion may be related to the fact that CS is commonly combined with glucosamine, which makes it challenging to isolate the specific contribution of chondroitin to the therapeutic outcome. This is aggravated by the fact that CS supplements, used in many countries, are not regulated, and labels wrongly claim high levels of purity. Many of these inferior CS products may have been used in clinical trials, which may have had limited but significant results. This has led to recent recommendations to opt for higher-purity pharmacologic-grade CS for the treatment of OA. This article aims to provide an up-to-date view of the current literature regarding the biological effects and efficacy of CS and discusses the quality of available chondroitin sulfate supplements and the current direction in CS investigation. This review concludes that pharmacologic-grade CS supplements may have clinically significant benefits when properly standardized; however, high-quality evidence from properly designed clinical trials is still needed to draw definitive conclusions about clinical efficacy in osteoarthritis.

10.
Cureus ; 15(5): e38527, 2023 May.
Article in English | MEDLINE | ID: mdl-37273344

ABSTRACT

Acute rupture of the plantar fascia is a rare but potentially debilitating injury in athletes, particularly those involved in running and jumping sports. Early recognition and prompt treatment are crucial for a successful recovery and return to play. Conservative treatment, including rest, immobilization, and physical therapy, may be effective in most cases, while surgical intervention may be required in those that are nonresponsive to conservative treatment. We report a case of plantar fascia rupture in a 22-year-old male semi-professional football player who presented with sudden severe pain in the sole of his right foot during a match, followed by a popping sensation and inability to weight bear. The athlete was healthy and had no history of previous injury in the right foot. MRI confirmed a complete rupture of the plantar fascia. The player was treated conservatively and underwent a rehabilitation program. The player returned to full competition after nine weeks, with no limitations.

11.
Int J Mol Sci ; 24(3)2023 Feb 03.
Article in English | MEDLINE | ID: mdl-36769298

ABSTRACT

Influenza viruses are responsible for significant morbidity and mortality worldwide in winter seasonal outbreaks and in flu pandemics. Influenza viruses have a high rate of evolution, requiring annual vaccine updates and severely diminishing the effectiveness of the available antivirals. Identifying novel viral targets and developing new effective antivirals is an urgent need. One of the most promising new targets for influenza antiviral therapy is non-structural protein 1 (NS1), a highly conserved protein exclusively expressed in virus-infected cells that mediates essential functions in virus replication and pathogenesis. Interaction of NS1 with the host proteins PI3K and TRIM25 is paramount for NS1's role in infection and pathogenesis by promoting viral replication through the inhibition of apoptosis and suppressing interferon production, respectively. We, therefore, conducted an analysis of the druggability of this viral protein by performing molecular dynamics simulations on full-length NS1 coupled with ligand pocket detection. We identified several druggable pockets that are partially conserved throughout most of the simulation time. Moreover, we found out that some of these druggable pockets co-localize with the most stable binding regions of the protein-protein interaction (PPI) sites of NS1 with PI3K and TRIM25, which suggests that these NS1 druggable pockets are promising new targets for antiviral development.


Subject(s)
Influenza A virus , Influenza, Human , Humans , Antiviral Agents/pharmacology , Antiviral Agents/metabolism , Influenza, Human/metabolism , Influenza A virus/metabolism , Viral Nonstructural Proteins/metabolism , Phosphatidylinositol 3-Kinases/metabolism
12.
Biomedicines ; 10(12)2022 Dec 17.
Article in English | MEDLINE | ID: mdl-36552032

ABSTRACT

Protein aggregation and subsequent accumulation of insoluble amyloid fibrils with cross-ß structure is an intrinsic characteristic of amyloid diseases, i.e., amyloidoses. Amyloid formation involves a series of on-pathway and off-pathway protein aggregation events, leading to mature insoluble fibrils that eventually accumulate in multiple tissues. In this cascade of events, soluble oligomeric species are formed, which are among the most cytotoxic molecular entities along the amyloid cascade. The direct or indirect action of these amyloid soluble oligomers and amyloid protofibrils and fibrils in several tissues and organs lead to cell death in some cases and organ disfunction in general. There are dozens of different proteins and peptides causing multiple amyloid pathologies, chief among them Alzheimer's, Parkinson's, Huntington's, and several other neurodegenerative diseases. Amyloid fibril disassembly is among the disease-modifying therapeutic strategies being pursued to overcome amyloid pathologies. The clearance of preformed amyloids and consequently the arresting of the progression of organ deterioration may increase patient survival and quality of life. In this review, we compiled from the literature many examples of chemical and biochemical agents able to disaggregate preformed amyloids, which have been classified as molecular chaperones, chemical chaperones, and pharmacological chaperones. We focused on their mode of action, chemical structure, interactions with the fibrillar structures, morphology and toxicity of the disaggregation products, and the potential use of disaggregation agents as a treatment option in amyloidosis.

13.
Eur J Phys Rehabil Med ; 58(5): 767-773, 2022 Oct.
Article in English | MEDLINE | ID: mdl-36052891

ABSTRACT

BACKGROUND: Point-of-care ultrasound can be used to assess muscle thickness. However, its reliability has not been fully evaluated. AIM: This study aimed to assess the intrarater and inter-rater reliability of point-of-care ultrasound for the estimation of quadriceps and rectus femoris thickness in patients from a rehabilitation setting. DESIGN: This is a cross-sectional study. SETTING: This study was conducted at the Department of Physical Medicine and Rehabilitation of a tertiary care hospital. POPULATION: Twenty-nine inpatients consecutively selected after admission. METHODS: Four observers, two trained and two untrained, used point-of-care ultrasound to measure quadriceps femoris and rectus femoris thickness. Each observer performed two measurements followed by a second set of two measurements three hours later. Intraclass correlation coefficients (ICC) were then calculated. RESULTS: Both intrarater and inter-rater ICC were higher than 0.888 for both quadriceps and rectus femoris measurements. Reliability was highest when ICC were calculated based on the average of two measurements, with the intrarater ICC being of 0.956 (95% CI: 0.937-0.970) for rectus femoris and of 0.966 (95% CI: 0.951-0.976) for quadriceps femoris; and with the inter-rater ICC being of 0.919 (95% CI: 0.863-0.957) for rectus femoris and 0.945 (95% CI: 0.907- 0.971) for quadriceps femoris. Trained and untrained observers did not have significantly different ICC values. CONCLUSIONS: These results suggest that point-of-care ultrasound is a reliable option to measure muscle thickness of knee extensors by the same or different observers. CLINICAL REHABILITATION IMPACT: Measuring knee extensors thickness may aid to adequately modulate treatment choices in patients with disability. This study suggests that quadriceps and rectus femoris muscle thickness measured after a short training course, by either an experienced or inexperienced clinician, presents high reliability. Reliability can be increased if the average of two measurements is used. Besides being inexpensive and portable, point-of-care ultrasound is a reliable tool for measuring knee extensors' thickness, rendering it potentially adequate to be used in clinical practice.


Subject(s)
Point-of-Care Systems , Quadriceps Muscle , Cross-Sectional Studies , Humans , Quadriceps Muscle/diagnostic imaging , Quadriceps Muscle/physiology , Reproducibility of Results , Ultrasonography/methods
15.
J Cheminform ; 14(1): 40, 2022 Jun 26.
Article in English | MEDLINE | ID: mdl-35754029

ABSTRACT

Drug design is an important area of study for pharmaceutical businesses. However, low efficacy, off-target delivery, time consumption, and high cost are challenges and can create barriers that impact this process. Deep Learning models are emerging as a promising solution to perform de novo drug design, i.e., to generate drug-like molecules tailored to specific needs. However, stereochemistry was not explicitly considered in the generated molecules, which is inevitable in targeted-oriented molecules. This paper proposes a framework based on Feedback Generative Adversarial Network (GAN) that includes optimization strategy by incorporating Encoder-Decoder, GAN, and Predictor deep models interconnected with a feedback loop. The Encoder-Decoder converts the string notations of molecules into latent space vectors, effectively creating a new type of molecular representation. At the same time, the GAN can learn and replicate the training data distribution and, therefore, generate new compounds. The feedback loop is designed to incorporate and evaluate the generated molecules according to the multiobjective desired property at every epoch of training to ensure a steady shift of the generated distribution towards the space of the targeted properties. Moreover, to develop a more precise set of molecules, we also incorporate a multiobjective optimization selection technique based on a non-dominated sorting genetic algorithm. The results demonstrate that the proposed framework can generate realistic, novel molecules that span the chemical space. The proposed Encoder-Decoder model correctly reconstructs 99% of the datasets, including stereochemical information. The model's ability to find uncharted regions of the chemical space was successfully shown by optimizing the unbiased GAN to generate molecules with a high binding affinity to the Kappa Opioid and Adenosine [Formula: see text] receptor. Furthermore, the generated compounds exhibit high internal and external diversity levels 0.88 and 0.94, respectively, and uniqueness.

16.
Food Res Int ; 157: 111399, 2022 07.
Article in English | MEDLINE | ID: mdl-35761653

ABSTRACT

Helichrysum italicum (H. italicum) is a halophyte shrub with bright yellow flowers with a strong curry-like aroma. The essential oils of H. italicum have been used in the production of cosmetics and pharmaceuticals, due to their antiallergic and anti-inflammatory properties. In the agri-food sector, H. italicum flowers can be used for seasoning and flavoring food, and as natural food preservatives. Here, we report on the composition, bioactive compounds, and nutritive value of H. italicum flowers. Flowers were mainly composed of carbohydrates (>80 % dry weight), followed by minerals (6.31 ± 0.95 % dw), protein (5.44 ± 0.35 % dw), and lipids (3.59 % ± 0.53 % dw). High percentages of Fe, Zn, Ca, and K were found in the flower material, along with a high content in antioxidants, polyphenols, and carotenoids, as corroborated by the nuclear magnetic resonance (NMR) data. Flowers were mainly composed of saturated fatty acids (SFAs) (54.50 ± 0.95 % of total FA), followed by polyunsaturated fatty acids (PUFAs) (37.73 ± 1.25 % of total FA) and monounsaturated fatty acids (MUFAs) (7.77 ± 0.34 %), as detected by gas chromatography mass spectrometry (GC-MS). The omega-6 PUFA linoleic acid (22.55 ± 0.76 % of total FA) was the most abundant fatty acid found. Flower extracts showed antimicrobial activity against Saccharomyces cerevisiae and Komagataella phaffii, as well as against Gram-negative (Klebsiella pneumoniae) and Gram-positive (Staphylococcus aureus) bacteria. H. italicum flower material was nontoxic to human intestinal Caco-2 model cells at concentrations up to 1.0 % w/v.


Subject(s)
Helichrysum , Oils, Volatile , Caco-2 Cells , Flowers/chemistry , Helichrysum/chemistry , Humans , Nutritive Value , Oils, Volatile/chemistry
17.
Int J Mol Sci ; 23(9)2022 Apr 19.
Article in English | MEDLINE | ID: mdl-35562892

ABSTRACT

Phenylketonuria (PKU) is a rare metabolic disease caused by variations in a human gene, PAH, encoding phenylalanine hydroxylase (PAH), and the enzyme converting the essential amino acid phenylalanine into tyrosine. Many PKU-causing variations compromise the conformational stability of the encoded enzyme, decreasing or abolishing its catalytic activity, and leading to an elevated concentration of phenylalanine in the blood, which is neurotoxic. Several therapeutic approaches have been developed to treat the more severe manifestations of the disorder, but they are either not entirely effective or difficult to adhere to throughout life. In a search for novel pharmacological chaperones to treat PKU, a lead compound was discovered (compound IV) that exhibited promising in vitro and in vivo chaperoning activity on PAH. The structure of the PAH-IV complex has been reported. Here, using alchemical free energy calculations (AFEC) on the structure of the PAH-IV complex, we design a new generation of compound IV-analogues with a higher affinity for the enzyme. Seventeen novel analogues were synthesized, and thermal shift and isothermal titration calorimetry (ITC) assays were performed to experimentally evaluate their stabilizing effect and their affinity for the enzyme. Most of the new derivatives bind to PAH tighter than lead compound IV and induce a greater thermostabilization of the enzyme upon binding. Importantly, the correspondence between the calculated alchemical binding free energies and the experimentally determined ΔΔGb values is excellent, which supports the use of AFEC to design pharmacological chaperones to treat PKU using the X-ray structure of their complexes with the target PAH enzyme.


Subject(s)
Phenylalanine Hydroxylase , Phenylketonurias , Calorimetry , Humans , Phenylalanine/metabolism , Phenylalanine Hydroxylase/chemistry , Phenylketonurias/metabolism , Protein Folding
18.
Int J Mol Sci ; 23(5)2022 Feb 26.
Article in English | MEDLINE | ID: mdl-35269739

ABSTRACT

Interleukin-1 receptor type 1 (IL-1R1) is a key player in inflammation and immune responses. This receptor regulates IL-1 activity in two forms: as a membrane-bound form and as a soluble ectodomain. The details and differences between the conformational dynamics of the membrane-bound and the soluble IL-1R1 ectodomains (ECDs) remain largely elusive. Here, we study and compare the structural dynamics of the soluble and membrane-bound IL-1R1-ECDs using molecular dynamics (MD) simulations, focusing on the flexible interdomain linker of the ECD, as well as the spatial rearrangements between the Ig-like domains of the ECD. To explore the membrane-bound conformations, a full-length IL-1R1 structural model was developed and subjected to classical equilibrium MD. Comparative analysis of multiple MD trajectories of the soluble and the membrane-bound IL-1R1-ECDs reveals that (i) as somewhat expected, the extent of the visited "open-to-closed" transitional states differs significantly between the soluble and membrane-bound forms; (ii) the soluble form presents open-closed transitions, sampling a wider rotational motion between the Ig-like domains of the ECD, visiting closed and "twisted" conformations in higher extent, whereas the membrane-bound form is characterized by more conformationally restricted states; (iii) interestingly, the backbone dihedral angles of residues Glu202, Glu203 and Asn204, located in the flexible linker, display the highest variations during the transition between discrete conformational states detected in IL-1R1, thus appearing to work as the "central wheel of a clock's movement". The simulations and analyses presented in this contribution offer a deeper insight into the structure and dynamics of IL-1R1, which may be explored in a drug discovery setting.


Subject(s)
Molecular Dynamics Simulation , Protein Conformation
19.
Int J Mol Sci ; 23(3)2022 Feb 02.
Article in English | MEDLINE | ID: mdl-35163653

ABSTRACT

The interleukin-1 receptor type 1 (IL-1R1) holds pivotal roles in the immune system, as it is positioned at the "epicenter" of the inflammatory signaling networks. Increased levels of the cytokine IL-1 are a recognized feature of the immune response in the central nervous system (CNS) during injury and disease, i.e., neuroinflammation. Despite IL-1/IL-1R1 signaling within the CNS having been the subject of several studies, the roles of IL-1R1 in the CNS cellular milieu still cause controversy. Without much doubt, however, the persistent activation of the IL-1/IL-1R1 signaling pathway is intimately linked with the pathogenesis of a plethora of CNS disease states, ranging from Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and multiple sclerosis (MS), all the way to schizophrenia and prion diseases. Importantly, a growing body of evidence is showing that blocking IL-1R1 signaling via pharmacological or genetic means in different experimental models of said CNS diseases leads to reduced neuroinflammation and delayed disease progression. The aim of this paper is to review the recent progress in the study of the biological roles of IL-1R1, as well as to highlight key aspects that render IL-1R1 a promising target for the development of novel disease-modifying treatments for multiple CNS indications.


Subject(s)
Central Nervous System Diseases/immunology , Neuroinflammatory Diseases/immunology , Receptors, Interleukin-1 Type I/immunology , Animals , Humans
20.
Virology ; 565: 106-116, 2022 01 02.
Article in English | MEDLINE | ID: mdl-34773868

ABSTRACT

Influenza NS1 is a promising anti-influenza target, considering its conserved and druggable structure, and key function in influenza replication and pathogenesis. Notwithstanding, target identification and validation, strengthened by experimental data, are lacking. Here, we further explored our previously designed structure-based antiviral rationale directed to highly conserved druggable NS1 regions across a broad spectrum of influenza A viruses. We aimed to identify NS1-mutated viruses exhibiting a reduced growth phenotype and/or an altered cell apoptosis profile. We found that NS1 mutations Y171A, K175A (consensus druggable pocket 1), W102A (consensus druggable pocket 3), Q121A and G184P (multiple consensus druggable pockets) - located at hot spots amenable for pharmacological modulation - significantly impaired A(H1N1)pdm09 virus replication, in vitro. This is the first time that NS1-K175A, -W102A, and -Q121A mutations are characterized. Our map-and-mutate strategy provides the basis to establish the NS1 as a promising target using a rationale with a higher resilience to resistance development.


Subject(s)
Influenza A virus/genetics , Influenza A virus/pathogenicity , Influenza, Human/virology , Orthomyxoviridae Infections/virology , Viral Nonstructural Proteins/genetics , Virus Replication , Amino Acid Substitution , Animals , Apoptosis , Cell Line , Dogs , Drug Discovery , HEK293 Cells , Host Microbial Interactions , Humans , Influenza, Human/metabolism , Madin Darby Canine Kidney Cells , Mutation , Orthomyxoviridae Infections/metabolism
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