Mutants and molecular dockings reveal that the primary L-thyroxine binding site in human serum albumin is not the one which can cause familial dysalbuminemic hyperthyroxinemia

PLAS-5k: Dataset of Protein-Ligand Affinities from Molecular Dynamics for Machine Learning Applications

Computational methods and recently modern machine learning methods have played a key role in structure-based drug design. Though several benchmarking datasets are available for machine learning applications in virtual screening, accurate prediction of binding affinity for a protein-ligand complex remains a major challenge. New datasets that allow for the development of models for predicting binding affinities better than the state-of-the-art scoring functions are important. For the first time, we have developed a dataset, PLAS-5k comprised of 5000 protein-ligand complexes chosen from PDB database. The dataset consists of binding affinities along with energy components like electrostatic, van der Waals, polar and non-polar solvation energy calculated from molecular dynamics simulations using MMPBSA (Molecular Mechanics Poisson-Boltzmann Surface Area) method. The calculated binding affinities outperformed docking scores and showed a good correlation with the available experimental values. The availability of energy components may enable optimization of desired components during machine learning-based drug design. Further, OnionNet model has been retrained on PLAS-5k dataset and is provided as a baseline for the prediction of binding affinities.

Variations in the Human Serum Albumin Gene: Molecular and Functional Aspects

The human albumin gene, the most abundant serum protein, is located in the long arm of chromosome 4, near the centromere, position 4q11–3. It is divided by 14 intervening introns into 15 exons, the last of which is untranslated. To date, 74 nucleotide substitutions (mainly missense) have been reported, determining the circulating variants of albumin or pre-albumin. In a heterozygous state, this condition is known as alloalbuminaemia or bisalbuminaemia (OMIM # 103600). The genetic variants are not associated with disease, neither in the heterozygous nor in the homozygous form. Only the variants resulting in familial dysalbuminaemic hyperthyroxinaemia and hypertriiodothyroninaemia are of clinical relevance because affected individuals are at risk of inappropriate treatment or may have adverse drug effects. In 28 other cases, the pathogenic variants (mainly affecting splicing, nonsense, and deletions), mostly in the homozygous form, cause a premature stop in the synthesis of the protein and lead to the condition known as congenital analbuminaemia. In this review, we will summarize the current knowledge of genetic and molecular aspects, functional consequences and potential therapeutic uses of the variants. We will also discuss the molecular defects resulting in congenital analbuminaemia, as well as the biochemical and clinical features of this rare condition

Rapid molecular diagnosis of ALB gene variants prevents unnecessary interventions in familial dysalbuminemic hyperthyroxinemia

OBJECTIVES

Familial dysalbuminemic hyperthyroxinemia (FDH) is an autosomal dominant condition caused by heterozygous gain-of-function mutations in the human ALB gene.

CASE PRESENTATION

We report, a three-year-old boy with FDH due to p.R242P (or p.R218P without signal peptide) mutation in the ALB gene with a phenotype characterized by extremely high serum total and free thyroxine concentrations. His parents had normal thyroid function tests (TFT), so the mutation detected in this patient is assumed "de novo". Although the most frequent variant was p.R242H in Caucasians and p.R242P in Japanese, our patient had p.R242P variant.

CONCLUSIONS

Early identification of FDH is fundamental to prevent unnecessary repeats of TFT with different methods. We encourage the ALB gene hot spot sequencing initially and indicate that this molecular diagnosis is a rapid and simple method to diagnose FDH in individuals with euthyroid hyperthyroxinemia.

The effects of hypothyroidism and hyperthyroidism on placental Hofbauer cells of pregnant rats

We investigated the effects of maternal thyroid disorders on Hofbauer cells of both the placenta and the fetus in pregnant rats. We divided 21 rats into three groups: control group, induced hypothyroidism (hypo) group and induced hyperthyroidism (hyper) group. Hypothyroidism was induced using propylthiouracil and hyperthyroidism was induced using L-thyroxine. We measured maternal weight, maternal free thyroxine, fetal weight, fetal viability and placental morphology. At the end of the experiment, fetuses of the hypo and hyper groups were less developed than those of the control group. In the hypo and hyper groups, the thickness of the labyrinth zone was decreased, but thickness of the basal zone and decidua basalis was increased. The number of Hofbauer cells was increased in both the hypo and hyper groups. Vascular endothelial growth factor expression was increased in both the hypo and hyper groups compared to controls. Our findings indicate that maternal thyroid disorders exert a negative effect on fetal growth and placental development.

A Chinese Family with Familial Dysalbuminemic Hyperthyroxinemia (FDH) due to R242H Mutation on Human Albumin Gene: Reevaluating the Role of FDH in Patients with Asymptomatic Hyperthyroxinemia

OBJECTIVE

Familial dysalbuminemic hyperthyroxinemia (FDH) has now become an established cause for spurious asymptomatic hyperthyroxinemia. Several different codon mutations on albumin gene had been identified. We here provided an established but rarely reported heterozygous mutation based on gene sequencing results from a Chinese family.

METHODS

The proband is a 14-year-old girl with light goiter and asymptomatic clinical presentations, whose thyroid function test by a one-step immunoassay showed increased free thyroxine (FT4) and free triiodothyronine (FT3) but nonsuppressed thyrotropin (TSH). All thyroid auto-antibodies were in the normal range. Blood samples were collected from her and most of her immediate family members for target gene sequencing and verification.

RESULTS

Hyperthyroxinemia was also confirmed in the proband's mother and one of her uncles and his son. In the proband and these three pedigrees, the high-throughput gene screening sequencing and the following Sanger sequencing disclosed a heterozygous mutation in the albumin gene, which located in its exon 7 (c.725G > A), and correspondingly leads to an arginine replacement with a histidine (R242H) in its protein. This is an established mutation named as R218H if present without signal peptide sequence.

CONCLUSIONS

For patients with asymptomatic hyperthyroxinemia, FDH should be clinically excluded before embarking on further investigations for other specific causes.

Aminophenols increase proliferation of thyroid tumor cells by inducing the transcription factor activity of estrogen receptor α

Aminophenols, which are widely used as components of hair dye and medicine, may function as environmental endocrine disruptors by regulating the proliferation of endocrine-related cancers. Estrogen receptor α (ERα) is a key regulator of breast cancer. Recently, it was found that ERα may also participate in the transformation and progression of thyroid tumors, but its interaction with aminophenols and its function in thyroid tumors is not clear. In this study, the transcription factor activity of ERα in BHP10-3 cells (a thyroid tumor cell line) was examined using luciferase assays. The promoter recruitment of ERα was examined using chromatin co-precipitation (ChIP). Additionally, in an in vivo study, BHP10-3 cells were transplanted into nude mice. Upon administration of aminophenols, the transcription factor activity of ERα was significantly increased in BHP10-3 cells, and the recruitment of ERα to the promoter of its target gene was increased. Aminophenols enhanced the in vitro and in vivo proliferation of BHP10-3 cells. By discovering that aminophenols induce the onco-promoting activity of ERα, our study extends the understanding of the function of aminophenols and suggests that ERα is a potential therapeutic target for the treatment of thyroid tumors.

Recent Developments and Applications of the MMPBSA Method

The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.

Clinical, Genetic, and Protein Structural Aspects of Familial Dysalbuminemic Hyperthyroxinemia and Hypertriiodothyroninemia

Familial dysalbuminemic hyperthyroxinemia (FDH-T4) and hypertriiodothyroninemia (FDH-T3) are dominantly inherited syndromes characterized by a high concentration of thyroid hormone in the blood stream. The syndromes do not cause disease, because the concentration of free hormone is normal, but affected individuals are at risk of erroneous treatment. FDH-T4 is the most common cause of euthyroid hyperthyroxinemia in Caucasian populations in which its prevalence is about 1 in 10,000 individuals, but the prevalence can be much higher in some ethnic groups. The condition is caused by a genetic variant of human serum albumin (HSA); Arg218 is mutated to histidine, proline, or serine or Arg222 is changed to isoleucine. The disorder is characterized by greater elevation in serum l-thyroxine (T4) than in serum triiodothyronine (T3); T4 can be increased by a factor 8-15. The high serum concentration of T4 is due to modification of a binding site located in the N-terminal half of HSA (in subdomain IIA). Thus, mutating Arg218 or Arg222 for a smaller amino acid reduces the steric restrictions in the site and creates a high-affinity binding site. The mutations can also affect binding of other ligands and can perhaps cause modified pharmacokinetics of albumin-binding drugs. In normal HSA, the high-affinity site has another location (in subdomain IIIB). Different locations of these sites imply that persons with and without FDH-T4 can have different types of interactions, and thereby complications, when given albumin-binding drugs. FDH-T3 is caused by a leucine to proline mutation in position 66 of HSA, which results in a large increment of the binding affinity for T3 but not for T4. For avoiding unwanted treatment of euthyroid persons with hyperthyroxinemia or hypertriiodothyroninemia, protein sequencing and/or sequencing of the albumin gene should be performed.

Identifying the antiasthmatic target of doxofylline using immobilized β2 -adrenoceptor based high-performance affinity chromatography and site-directed molecular docking

As a xanthine derivative, doxofylline is believed to be dominant for fighting against asthma in practice. Unlike other xanthines, the antiasthmatic effects of doxofylline lack any definite proof of target and mediating mechanism according to previous reports. In this work, the interaction between doxofylline and β2 -AR was investigated by high performance affinity chromatography using frontal analysis and nonlinear model. The methodology involved the immobilization of β2 -AR on the silica gel by a random linking method, the determination of the binding parameters by frontal analysis and nonlinear chromatography and the exploration of the binding mechanism by site-directed molecular docking. The association constant for doxofylline binding to immobilized β2 -AR was determined to be 7.70 × 10(4)  M(-1) by nonlinear chromatography and 5.91 × 10(4)  M(-1) by frontal analysis. Ser(169) and Ser(173) were the binding sites for the receptor-drug interaction on which hydrogen bond was believed to be the main driven force during the interaction. These results indicated that the antiasthmatic effects of doxofylline may be behind the mediating mechanism of β2 -AR. High performance affinity chromatography based on immobilized receptor has potential to become an alternative for drug target confirmation and drug-receptor interaction analysis. Copyright © 2016 John Wiley & Sons, Ltd.

Unique albumin with two silent substitutions (540Thr→Ala and 546Ala→Ser): Insights into how albumin is recycled

OBJECTIVES

To determine the cause of an albumin abnormality detected by chance on electrospray time-of-flight mass spectrometry (TOF MS) of whole plasma, and to assess its physiological consequences.

METHOD

Plasma was examined by TOF MS and tryptic mapping was used to locate mutation sites and determine the relative expression level of the variant and normal albumins. DNA sequencing was used to precisely define mutations.

RESULTS

Whole protein electrospray TOF MS indicated a decrease of 14Da in the mass of albumin. Peptide mass mapping and DNA sequencing established the presence of two novel heterozygous point mutations (540Thr→Ala and 546Ala→Ser) whose combined mass changes (-30 and +16Da) indicated both mutations occurred on the same allele. Peptide ratios showed the variant albumin was present at a lower level than normal with an expression ratio of approximately 1:2 (variant:normal). Phylogenetic sequence alignments show Thr540 is highly conserved while Ala546 has wide species variation, suggesting 540Thr→Ala might compromise the protein.

CONCLUSION

Both mutations occur close together in domain IIIB, a region involved in albumin scavenging and recycling. In particular, Thr540 is close to His535, a residue directly involved in pH-dependent binding and release of albumin from its recycling neonatal Fc receptor. Compromised receptor binding would explain the low albumin (34g/l) concentration and the diminished variant expression level.