In Silico Modeling and Structural Analysis of Soluble Epoxide Hydrolase Inhibitors for Enhanced Therapeutic Design

Human soluble epoxide hydrolase (sEH), a dual-functioning homodimeric enzyme with hydrolase and phosphatase activities, is known for its pivotal role in the hydrolysis of epoxyeicosatrienoic acids. Inhibitors targeting sEH have shown promising potential in the treatment of various life-threatening diseases. In this study, we employed a range of in silico modeling approaches to investigate a diverse dataset of structurally distinct sEH inhibitors. Our primary aim was to develop predictive and validated models while gaining insights into the structural requirements necessary for achieving higher inhibitory potential. To accomplish this, we initially calculated molecular descriptors using nine different descriptor-calculating tools, coupled with stochastic and non-stochastic feature selection strategies, to identify the most statistically significant linear 2D-QSAR model. The resulting model highlighted the critical roles played by topological characteristics, 2D pharmacophore features, and specific physicochemical properties in enhancing inhibitory potential. In addition to conventional 2D-QSAR modeling, we implemented the Transformer-CNN methodology to develop QSAR models, enabling us to obtain structural interpretations based on the Layer-wise Relevance Propagation (LRP) algorithm. Moreover, a comprehensive 3D-QSAR analysis provided additional insights into the structural requirements of these compounds as potent sEH inhibitors. To validate the findings from the QSAR modeling studies, we performed molecular dynamics (MD) simulations using selected compounds from the dataset. The simulation results offered crucial insights into receptor-ligand interactions, supporting the predictions obtained from the QSAR models. Collectively, our work serves as an essential guideline for the rational design of novel sEH inhibitors with enhanced therapeutic potential. Importantly, all the in silico studies were performed using open-access tools to ensure reproducibility and accessibility.

Hyponatremic dehydration: an analysis of 78 cases

Our purpose was to determine the frequency of convulsion in children with hyponatremic dehydration (HD). We also investigated whether or not there was a relationship between the severity of hyponatremia and the degrees of malnutrition in our region (Eastern Anatolia of Turkey) in where malnutrition is frequently observed. In this study, the clinical and laboratory findings of 78 patients with diarrhoea (acute, persistent or chronic diarrhoea) and HD were studied. When diarrhoea lasts longer than 2 and 4 weeks they were accepted as persistent and chronic diarrhoea, respectively. Patients were said to have HD if they had the clinical findings of dehydration associated with hyponatremia [Serum sodium (SNa) <130 mmol/L)]. Nutritional status of the children was assessed by the Gomez classification using weight for age; it was accepted as normal those were between 90%-110%, mild malnutrition 75%-89%, moderate malnutrition 60%-74% and severe malnutrition <60%. Of 78 patients, 40 were boys, 38 were girls. The age and weight of the patients ranged from 40 days to 36 months (8.94 +/- 5.49 months) and from 2000 to 10,300 g (5535.25 +/- 1702.10 g) respectively. All patients except four had malnutrition; 15 (20.3%) had mild malnutrition, 30 (40.5%) had moderate malnutrition and 29 (39.2%) had severe malnutrition. Forty-seven patients had acute, 16 patients had persistent, and 15 patients had chronic diarrhoea. SNa levels were between 104 and 129 mmol/L (121.21 +/- 6.12 mmol/L). There was not statistically a significant difference between SNa level and the degree of malnutrition, and SNa level and the types (acute, persistent or chronic) of diarrhoea (p > 0.05). Of 78 patients, 12 (15.3%) patients had convulsion, of whom eight had convulsion associated with fever. Convulsion was noted in nine (19.1%) and three (18.7%) patients with acute and persistent diarrhoea, respectively (p > 0.05). Also, we observed that when hyponatremia was severer, convulsions tended to be more occuring (p < 0.05). Five (6.4%) children died and all of them had severe malnutrition and septicemia. We determined that the frequency of convulsion in HD was 15.3% (12/78), and there was not a difference between the cases of acute, persistent and chronic diarrhoea for the frequency of convulsion. We also found a significant difference was not present between SNa level and the degree of malnutrition, and between SNa level and the types (acute, persistent or chronic) diarrhoea. However, we observed that when hyponatremia was severer, convulsions tended to be more occuring.

Urinary tract infection and antibiotic susceptibility in malnourished children

In this study, 31 (30%) cases of urinary tract infection (UTI) of 103 patients with malnutrition, who were admitted to our hospital, were investigated prospectively. Our purpose was to determine the frequency of UTI, species of bacteria caused to infection and their antibiotic susceptibility in infants with malnutrition. The mean age of the patients with UTI was 11.5+/-7.6 months (ranging 50 days-30 months). The main symptoms were fever, vomiting, diarrhea, cough, and seizures. The mean body weight was 5.8+/-1.9 kg (2-10 kg), and height was 67.5+/-7.8 cm (53-85 cm). Seven of them had mild, 11 had moderate, and 13 had severe malnutrition. The most common isolated microorganism from urine cultures was Escherichia coli (54.8%). Most strains of Escherichia coli were resistant to co-trimoxazole (82.3%), ceftriaxone (17.6%), cefotaxime (17.6%), and ciprofloxacine (17.6%), but none of them were resistant to gentamicin. In conclusion, we would like to emphasize that UTI predominantly by gram negative microorganisms are frequent in the infants with malnutrition, and these microorganisms are mostly resistant to co-trimoxazole which is used commonly in practical medicine and prophylaxis.

Shedding of human thyrotropin receptor ectodomain. Involvement of a matrix metalloprotease

The thyrotropin (TSH) receptor in human thyroid glands has been shown to be cleaved into an extracellular alpha subunit and a transmembrane beta subunit held together by disulfide bridges. An excess of the latter component relative to the former suggested the shedding of the ectodomain. Indeed we observed such a shedding in cultures of human thyrocytes and permanently transfected L or Chinese hamster ovary cells. The shedding was increased by inhibitors of endocytosis, recycling, and lysosomal degradation, suggesting that it was dependent on receptor residency at the cell surface. It was slightly increased by TSH and phorbol esters, whereas forskolin and 8-bromo-cyclic AMP were without effect. Decreasing the serum concentration in cell culture medium enhanced the shedding by an unknown mechanism. The shedding of the TSH receptor alpha domain is the consequence of two events: cleavage of the receptor into alpha and beta subunits and reduction of the disulfide bridge(s). The complete inhibition of soluble TSH receptor shedding by the specific inhibitor BB-2116 indicated that the cleavage reaction is catalyzed probably at the cell surface by a matrix metalloprotease. This shedding mechanism may be responsible for the presence of soluble TSH receptor alpha subunit in human circulation.

Structure of the human luteinizing hormone-choriogonadotropin receptor gene: unusual promoter and 5' non-coding regions

The complete organization of the human luteinizing hormone-choriogonadotropin (LH/CG) receptor (LH/CGR) gene and the structure of 1591 bp of its 5' flanking region have been determined. This gene spans over 70 kbp and contains 11 exons. The first ten exons and part of the last exon encode the extracellular domain of the receptor while the transmembrane and intracellular domains are encoded by the remaining part of the last exon. The gene encodes a 701 amino acids long preprotein, contrary to a previous report of 699 amino acids. Primer extension experiments and polymerase chain reaction (PCR) mapping allowed definition of the transcription initiation site, which is located 1085 bp upstream from the initiation codon. The 5' non-coding region is thus unusually long. The promoter region which is different from the murine LH/CG receptor promoter, contains two putative TATA boxes at positions -34 and -47 and a CAAT box consensus sequence at position -89. A consensus sequence corresponding to a cAMP responsive element is found at position -697. Seven API consensus sequences are also found in the 5' flanking region of the gene. Southern blot experiments demonstrated an informative biallelic polymorphism within the human LH/CG receptor gene locus using BglII endonuclease. The cloning of the human LH/CGR gene and the determination of the organization and structure of its 5' flanking region allow the study of its hormonal, developmental and tissue-specific regulation. Primers and PCR conditions are described for the direct genomic sequencing of all the exons of the gene. This information should facilitate the study of pathological mutations of the receptor.

Interplay between estrogens, progestins, retinoic acid and AP-1 on a single regulatory site in the progesterone receptor gene

Transcriptional regulation of the progesterone receptor gene involves induction by estrogens and down-regulation by progestins, retinoic acid, and AP-1 proteins. We have previously identified an intragenic (+698/+723) estrogen-responsive element present in the progesterone receptor gene, which binds the estradiol receptor and mediates estrogen and 4-OH tamoxifen induction. Progesterone receptor gene expression was equally stimulated by estradiol and 4-OH tamoxifen in the presence of a NH2 terminally deleted estrogen receptor mutant lacking activation function 1, suggesting that activation function 2 was the predominant activation domain. This was confirmed by the lack of activity of an estrogen receptor mutant deleted of activation function 2. Repression by progestins, retinoic acid, and AP-1 was mediated by the same estrogen responsive element although retinoic and progesterone receptors as well as AP-1 proteins did not bind to this element. Repression by these proteins appears to involve different transactivating regions of the estrogen receptor. Repression by retinoic receptors involved only activation function 2 whereas repression by progesterone receptor and AP-1 necessitated both functional domains. Since these proteins act without directly contacting the DNA, it seems likely that repression may be achieved by protein-protein interactions among different domains of the estrogen receptor and/or the transcriptional machinery.

Processing of the precursors of the human thyroid-stimulating hormone receptor in various eukaryotic cells (human thyrocytes, transfected L cells and baculovirus-infected insect cells)

The complementary DNA for human thyroid-stimulating hormone (TSH) receptor encodes a single protein with a deduced molecular mass of 84.5 kDa. This protein is cleaved during its maturation in the human thyroid since the receptor protein has been shown to be composed of two subunits (alpha subunit of approximately 53 kDa and beta subunit of approximately 38 kDa) held together by disulfide bridges [Loosfelt, H., Pichon, C., Jolivet, A., Misrahi, M., Caillou, B., Jamous, M., Vannier, B. & Miligrom, E. (1992) Proc. Natl Acad. Sci. USA 89, 3765-3769]. A similar processing occurs in an L cell line permanently expressing the human TSH receptor. The processing is however incomplete, resulting in a permanent accumulation of a 95-kDa high-mannose precursor which is present only in trace amounts in the thyroid. Pulse-chase experiments show the successive appearance in the L cells of two precursors: initially the approximately 95-kDa high-mannose glycoprotein followed by a approximately 120-kDa species containing mature oligosaccharides. This latter precursor is then processed into the alpha and beta subunits. In primary cultures of human thyrocytes precursors of similar size are detected. Spodoptera frugiperda insect cells (Sf9 and Sf21) infected with a recombinant baculovirus encoding the human TSH receptor synthesize a monomeric protein of about 90 kDa soluble only in denaturing conditions. Comparison with the product of in vitro transcription-translation experiments (approximately 80 kDa), suggests that it may be incompletely or improperly glycosylated. The TSH receptor expressed in these cells is unable to bind the hormone. Immunoelectron microscopy studies show that in human thyrocytes most of the receptor is present on the cell surface; in L cells the receptor is detected on the cell surface, as well as in the endoplasmic reticulum and in the Golgi apparatus (this intracellular pool of receptor molecules probably corresponding to the high-mannose precursor); in insect cells nearly all the receptor molecules are trapped in the endoplasmic reticulum. These differences in receptor distribution are concordant with the differences observed for receptor processing.

Structure of the human progesterone receptor gene

The complete organization of the human progesterone receptor (hPR) gene has been determined. It spans over 90 kbp and contains eight exons. The first exon encodes the N-terminal part of the receptor. The DNA binding domain is encoded by two exons, each exon corresponding to one zinc finger. The steroid binding domain is encoded by five exons. The nucleotide sequence of 1144 bp of the 5' flanking region has been determined.

Composite structure of the human thyrotropin receptor gene

The exon/intron organization and the structure of the 5' flanking region of the human thyrotropin receptor gene (hTSH-R) were determined. The hTSH-R gene spans more than 60 kb and is split into ten exons. The extracellular domain is encoded by the first nine exons and part of the last exon, whereas the transmembrane and intracellular domains are encoded in totality by the last exon. The leucine-rich repeats of the extracellular domain are encoded as monomers or multimers by separate exons. The TSH receptor gene seems to have arisen by insertion of a DNA sequence encoding repeated leucine-rich elements between the regions encoding the extracellular and the transmembrane domains of a proto-receptor gene ressembling the intronless beta adrenergic receptor genes. Primer extension and S1 mapping experiments identified three transcription start sites. In the hTSH-R gene, the main site was located 157 bp upstream from the start of translation. The promoter region is very GC-rich and contains multiple SP1, ETF and AP2 binding site consensus sequences.

Cloning, sequencing and expression of human TSH receptor

Complementary cDNA clones encoding the TSH (thyroid stimulatory hormone) receptor were isolated from a human thyroid lambda gt10 library using Iow stringency hybridization with LH/hCG (luteinizing hormone-human choriogonadotropic hormone) receptor probes. Sequencing of the clones showed a 764 amino acid open reading frame. The first 21 amino acids probably correspond to a signal peptide, the mature protein thus contains 743 amino acids (calculated molecular weight: 84,501 daltons). Its putative structure consists of a 394 amino acid extracellular domain, a 266 amino acid membrane spanning domain with 7 putative transmembrane segments and a 83 amino acid intracellular domain. A high degree of homology is observed with LH/hCG receptor suggesting the definition of a new subfamily of G-protein coupled receptors. Computer search showed the presence in the putative third intracellular loop of a motif resembling that described in the non receptor type protein tyrosine kinases (c-src, c-yes, c-fgr, etc...). RNA blots showed that the receptor messenger RNA consists of two major species of 4300 and 3900 nucleotides. The cDNA was inserted into an expression vector and after transfection into COS 7 cells it was shown to produce a functional TSH receptor.

Cloning and sequencing of porcine LH-hCG receptor cDNA: variants lacking transmembrane domain

Complementary DNA clones, encoding the LH-hCG (luteinizing hormone-human choriogonadotropic hormone) receptor were isolated by screening a lambda gt11 library with monoclonal antibodies. The primary structure of the protein was deduced from the DNA sequence analysis; the protein contains 696 amino acids with a putative signal peptide of 27 amino acids. Hydropathy analysis suggests the existence of seven transmembrane domains that show homology with the corresponding regions of other G protein-coupled receptors. Three other types of clones corresponding to shorter proteins were observed, in which the putative transmembrane domain was absent. These probably arose through alternative splicing. RNA blot analysis showed similar patterns in testis and ovary with a major RNA of 4700 nucleotides and several minor species. The messenger RNA was expressed in COS-7 cells, yielding a protein that bound hCG with the same affinity as the testicular receptor.

Mechanisms of nuclear localization of the progesterone receptor: evidence for interaction between monomers

Deletion mutants of the rabbit progesterone receptor were used to identify two major mechanisms of its nuclear localization. A putative signal sequence, homologous to that of the SV40 large T antigen, was localized around amino acids 638-642 and shown to be constitutively active. When amino acids 638-642 were deleted, the receptor became cytoplasmic but could be shifted into the nucleus by the addition of hormone (or anti-hormone); it was almost fully active. The second mechanism consisted of the activation of the DNA binding domain. By deleting epitopes recognized by monoclonal antibodies, it was possible to follow different receptor mutants inside the same cells. In the absence of ligand, the receptor was transferred into the nucleus as a monomer. After administration of hormone (or anti-hormone) a "cytoplasmic" monomer was transferred into the nucleus through interaction with a "nuclear" monomer. These interactions occurred through the steroid binding domains of both monomers.