This thesis was undertaken to determine if there is any interrelationship between the two terminal enzymes of the haem biosynthetic pathway, protoporphyrinogen oxidase (PPO) and ferrochelatase, with particular reference to porphyria variegata (PV) and erythropoietic protoporphyria (EPP)• It has previously been found that both enzymes were deficient in PV and EPP, there being a qualitative difference in so far as ferrochelatase deficiency is concerned. / IT2018

There are different conformational states of proteins characterized by different Gibbs free energy levels, manifested in folding-unfolding dynamics, for example. Recently, a set of protein states, which require relatively small amount of folding energies, emerged as subjects of intensive research, and proteins or regions characterized by the presence of these states have been termed as ‘Intrinsically Disordered Proteins’ (IDP) and ‘Intrinsically Disordered Protein Regions’ (IDPR), respectively. Predisposition for intrinsic disorder of a query protein is encoded in its amino acid sequence and composition, and can be rather accurately predicted using several intrinsic disorder algorithms. Since pathology of many human diseases can be driven by proteins characterized by high intrinsic disorder scores, research on various disease-associated proteins is often started with the analysis of their intrinsic disorder propensities. In this work, I utilized computational approaches based on the concept of intrinsic disorder to address three health-related issues. To this end, I developed a novel computational platform for disorder-based drug discovery and applied this tool for finding inhibitors of the cancer-related MBD2-NuRD complex, utilized molecular dynamic simulations to explain the effects of mutations on the functionality of the X-linked protoporphyria-related protein ALAS, and used bioinformatics tools to examine the effects ofcardiomyopathy-related mutations in cardiac troponin. Since the complex between the Methyl-CpG-binding domain protein 2 (MBD2) and the Nucleosome Remodeling Deacetylase complex (NuRD) specifically binds to the mCpG-island and blocks tumor suppressor gene expression, finding an inhibitor of this MBD2-NuRD complex is hypothesized to be important for the development of novel anti-cancer drugs. I found that the site, which is responsible for the MBD2 interaction with thetranscriptional repressor p66-α (p66α, which is a part of the NuRD complex), is characterized by a specific disorder-to-order transition pattern, this pattern showed a remarkable similarity to the disorder-to-order pattern of the Myc transcription factor binding site for the Max transcription factor. Importantly, several inhibitors of the Myc-Max interaction targeting the disorder-to-order transition site of Myc were previously described. By applying molecular docking at the disorder-to-order transition site of MBD2, two compounds were identified and further evaluated through molecular dynamics simulations. Anti-leukemia and anti-metastasis effectiveness of these compounds was demonstrated in dedicated in vitro and in vivo experiments conducted by our collaborators. In relation to the defective protein associated with the X-linked protoporphyria (XLPP), the hepta-variant of mouse erythroid 5-aminolevulinate synthase (mALAS2), previously shown to be characterized by a remarkable acceleration of the reaction rate, was investigated through molecular dynamics simulations. In this study, a loop to β-strand transition was observed, and this observation was crucial for a better understanding of the previously described rate-enhancing effects of seven simultaneous variations in the active loop site of this protein. Finally, a wide spectrum of bioinformatics tools was applied to carefully analyze a potential role of intrinsic disorder in a set of cardiomyopathy-related mutations in the components of human cardiac troponin. This analysis revealed that, in comparison with the wild type troponin, chains containing the disease-associated mutations were typically characterized by a local decrease in intrinsic disorder propensity. These mutations affected some disorder-based protein-protein interaction sites and caused remarkable rearrangements of the complex pattern of post-translational modifications. Therefore, this work illustrates that inclusion of the protein intrinsic disorder analysis into the arsenal of techniques used by the biomedical researchers represents an important and promising approach that provides novel inputs for the better understanding of protein behavior in relation to human disease at the molecular level. Techniques and methods developed and utilized in this study will significantly contribute to future biomedical research.

La protoporphyrie érythropoïétique (PPE) est une maladie héréditaire rare caractérisée par un déficit en activité FECH responsable d’une accumulation de PPIX. Elle se manifeste par une photosensibilité très invalidante. Il n’existe pas de traitement efficace pour la PPE. 95 % des malades présentent un allèle FECH hypomorphe (c.315-48C) en trans d'une mutation FECH délétère, ce qui entraine une diminution de l'activité FECH résiduelle dans les érythroblastes en dessous d'un seuil critique d'environ 35 % de l'activité normale. L’allèle hypomorphe (c.315-48C) favorise l'utilisation d'un site cryptique d'épissage situé en -63 de l’intron 3 générant un ARNm FECH incluant une partie de l’intron 3 et possédant un codon stop prématuré. L’ARN est alors dégradé par NMD pendant sa maturation. Nous avons déjà identifié un oligonucléotide antisens (ASO-V1) qui redirige l'épissage vers le site accepteur physiologique de l’intron 3 et augmente la production d’ARN FECH WT. Nous avons développé par ce travail une nouvelle stratégie d’adressage d’ASO-V1 en utilisant des peptides ciblant le récepteur de la transferrine (RTf1) qui est exprimé à un niveau très élevé dans les progéniteurs érythroïdes en différenciation concomitamment à la FECH. Nous avons développé des peptides bifonctionnels à partir des séquences peptidiques ciblant le RTf1 tout en les couplant à des séquences Cell Penetrating Peptide (CPP) qui facilitent la sortie de l’ASO-V1 de la vésicule endosomale. Après la transfection des lignées lymphoblastoïdes de malades PPE par différents nanocomplexes RTf1-CPP/ASO-V1, nous avons pu montrer que plusieurs des peptides bifonctionnels utilisés permettaient une redirection efficace et prolongée de l’épissage cryptique vers l’épissage physiologique exon3-exon4 et que cela permettait une correction des taux d’ARN FECH WT. Nous avons ensuite testé l’effet des nanocomplexes RTf1-CPP/ASO-V1, ex vivo, dans les progéniteurs érythroïdes en différenciation de différents sujets atteints de PPE et nous sommes arrivés à augmenter l’ARN FECH WT et diminuer significativement l’accumulation de la PPIX dans ces cellules par rapport à celles transfectées par des nanocomplexes RTf1-CPP/ASO-Mock. La prochaine étape de notre étude serait d’apporter la preuve de concept, in vivo, dans un modèle murin humanisé de PPE après l'administration de nanocomplexes RTf1-CPP/ASOV1 / Erythropoietic protoporphyria (EPP) is a rare hereditary disease characterized by a deficiency in FECH activity responsible for the accumulation of PPIX. EPP is manifested by a very disabling photosensitivity. There is no effective treatment for EPP. 95% of the patients present a hypomorphic FECH allele (c.315-48C) in trans of a deleterious FECH mutation, resulting in a decrease in residual FECH activity in erythroblasts below a critical threshold of about 35% of normal activity. The hypomorphic allele (c.315-48C) promotes the use of a cryptic splicing site located at -63 of the intron 3 generating a FECH mRNA including a part of the intron 3 and possessing a premature stop codon. The RNA is then degraded by NMD during its maturation. We have previously identified an antisense oligonucleotide (ASO-V1) that redirects splicing to the physiological acceptor site of intron 3 and increases the production of WT FECH mRNA. Here, we developed a new ASO-V1 addressing strategy using transferrin receptor (TRf1) targeted peptides. TfR1 is expressed at a very high level in differentiating erythroid progenitors concomitantly with FECH. We developed bifunctional peptides from peptide sequences targeting TfR1 while coupling them to Cell Penetrating Peptide (CPP) sequences that facilitate the release of ASO-V1 from the endosomal vesicle. We transfected the lymphoblastoid cell lines from EPP patients by different TfR1-CPP/ASO-V1 nanocomplexes and we demonstated that several of the bifunctional peptides allowed an efficient and prolonged redirection of the cryptic splicing towards the exon3-exon4 physiological splicing and the correction of the WT FECH mRNA levels. Then, we tested the effect of TfR1-CPP/ASO-V1 nanocomplexes, ex vivo, in differentiating erythroid progenitors of different EPP subjects and we were able to increase WT FECH mRNA and decrease significantly the accumulation of the PPIX in these cells compared to those transfected by TfR1-CPP/ASO-Scr nanocomplexes. The next step of our study would be to provide a proof of concept, in vivo, in a humanized murine model of EPP after the administration of TfR1-CPP/ASOV-1 nanocomplexes

5-Aminolevulinate synthase (ALAS; EC 2.3.1.37) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the first committed step of heme biosynthesis in animals, the condensation of glycine and succinyl-CoA yielding 5-aminolevuliante (ALA), CoA, and CO2. Murine erythroid-specific ALAS (mALAS2) variants that cause high levels of PPIX accumulation provide a new means of targeted, and potentially enhanced, photosensitization. Transfection of HeLa cells with expression plasmids for mALAS2 variants, specifically for those with mutated mitochondrial presequences and a mutation in the active site loop, caused significant cellular accumulation of PPIX, particularly in the membrane. Light treatment of HeLa cells expressing mALAS2 variants revealed that mALAS2 expression results in an increase in cell death in comparison to aminolevulinic acid (ALA) treatment producing a similar amount of PPIX. Generation of PPIX is a crucial component in the widely used photodynamic therapies (PDT) of cancer and other dysplasias. The delivery of stable and highly active mALAS2 variants has the potential to expand and improve upon current PDT regimes. Mutations in the C-terminus of human ALAS2 (hALAS2) can increase hALAS2 activity and are associated with X-linked erythropoietic protoporphyria (XLEPP), a disease phenotypically characterized by elevated levels or PPIX and zinc protoporphyrin in erythroblasts. This is apparently due to enhanced cellular hALAS2 activity, but the biochemical relationship between these C-terminal mutations and increased hALAS2 activity is not well understood. HALAS2 and three XLEPP variants were studied both in vitro to compare kinetic and structural parameters and ex vivo in HeLa and K562 cells. Two XLEPP variants, delAGTG, and Q548X, exhibited higher catalytic rates and affinity for succinyl-CoA than wild-type hALAS2, had increased transition temperatures, and caused porphyrin accumulation in HeLa and K562 cells. Another XLEPP mutation, delAT, had an increased transition temperature and caused porphyrin accumulation in mammalian cells, but exhibited a reduced catalytic rate at 37[deg]C in comparison to wild-type hALAS2. The XLEPP variants, unlike wild-type hALAS2, were more structurally responsive upon binding of succinyl-CoA, and adopted distinct features in tertiary and PLP cofactor-binding site. These results imply that the C-terminus of hALAS2 is important for regulating its structural integrity, which affects kinetic activity and stability. XLEPP has only recently been identified as a blood disorder, and thus there are no specific treatments. One potential treatment involves the use of the antibiotic isonicotinic acid hydrazide (isoniazid, INH), commonly used to treat tuberculosis. INH can cause sideroblastic anemia as a side-effect and has traditionally been thought to do so by limiting PLP availability to hALAS2 via direct inhibition of pyridoxal kinase, and reacting with pyridoxal to form pyridoxal isonicotinoyl hydrazone. We postulated that in addition to PLP-dependent inhibition of hALAS2, INH directly acts on hALAS2. Using FACS and confocal microscopy, we show here that INH reduces protoporphyrin IX accumulation in HeLa cells expressing either wild-type human hALAS2 or XLEPP variants. In addition, PLP and pyridoxamine 5'-phosphate (PMP) restored cellular hALAS2 activity in the presence of INH. Kinetic analyses with purified hALAS2 demonstrated non-competitive or uncompetitive inhibition with an apparent Ki of 1.5 uM. Circular dichroism studies revealed that INH triggers structural changes in hALAS2 that interfere with the association of hALAS2 with its PLP cofactor. These studies demonstrate that hALAS2 can be directly inhibited by INH, provide insight into the mechanism of inhibition, and support the prospective use of INH in treating patients with XLEPP and potentially other cutaneous porphyrias.

Porphyria is a group of inherited metabolic disorders due to enzymatic defect of the heme biosynthesis resulting in the overproduction of the heme precursors' porphyrins in different body organs. The enzymes of the heme biosynthesis are encoded by corresponding genes in which any defect in any of these genes lead to a specific type of porphyria. Numerous mutations were detected in these genes leading to impairment in the enzyme function and therefore developing of the clinical manifestations of porphyria. The aim of the present work was to investigate the UROD gene in patients with porphyria cutanea tarda (PCT) and hepatoerythropoietic protoporphyria (HEP) as well as the FECH gene in patients with erythropoietic protoporphyria (EPP) on a molecular level. We identified numerous mutations in the FECH and the UROD genes in three different populations, Czech, Slovak, and Egyptian. We described the novel mutations in the UROD gene in HEP Arabic patients from Egypt as well in the FECH gene in patients with EPP of Czech and Slovak origin. We expressed mutatted UROD protein in prokaryotic system and found 19 % of the wild-type enzymatic activity. Moreover, the current study presents for the first time the frequency of the low expression allele IVS3-48c in the FECH gene in healthy controls from the Czech...

Porphyria is a group of inherited metabolic disorders due to enzymatic defect of the heme biosynthesis resulting in the overproduction of the heme precursors' porphyrins in different body organs. The enzymes of the heme biosynthesis are encoded by corresponding genes in which any defect in any of these genes lead to a specific type of porphyria. Numerous mutations were detected in these genes leading to impairment in the enzyme function and therefore developing of the clinical manifestations of porphyria. The aim of the present work was to investigate the UROD gene in patients with porphyria cutanea tarda (PCT) and hepatoerythropoietic protoporphyria (HEP) as well as the FECH gene in patients with erythropoietic protoporphyria (EPP) on a molecular level. We identified numerous mutations in the FECH and the UROD genes in three different populations, Czech, Slovak, and Egyptian. We described the novel mutations in the UROD gene in HEP Arabic patients from Egypt as well in the FECH gene in patients with EPP of Czech and Slovak origin. We expressed mutatted UROD protein in prokaryotic system and found 19 % of the wild-type enzymatic activity. Moreover, the current study presents for the first time the frequency of the low expression allele IVS3-48c in the FECH gene in healthy controls from the Czech...

ABSTRACT The porphyrias are a diverse group of metabolic disorders arising from diminished activity of enzymes in the heme biosynthetic pathway. They can present with acute neurovisceral symptoms, cutaneous symptoms, or both. The complexity of these disorders is demonstrated by the fact that some acute porphyria patients with the underlying genetic defect(s) are latent and asymptomatic while others present with severe symptoms. This indicates that there is at least one other risk factor required in addition to the genetic defect for symptom manifestation. A systematic review of the heme biosynthetic pathway highlighted the involvement of a number of micronutrient cofactors. An exhaustive review of the medical literature uncovered numerous reports of micronutrient deficiencies in the porphyrias as well as successful case reports of treatments with micronutrients. Many micronutrient deficiencies present with symptoms similar to those in porphyria, in particular vitamin B6. It is hypothesized that a vitamin B6 deficiency and related micronutrient deficiencies may play a major role in the pathogenesis of the acute porphyrias. In order to further investigate the porphyrias, a computational model of the heme biosynthetic pathway was developed based on kinetic parameters derived from a careful analysis of the literature. This model demonstrated aspects of normal heme biosynthesis and illustrated some of the disordered biochemistry of acute intermittent porphyria (AIP). The testing of this model highlighted the modifications necessary to develop a more comprehensive model with the potential to investigated hypotheses of the disordered biochemistry of the porphyrias as well as the discovery of new methods of treatment and symptom control. It is concluded that vitamin B6 deficiency might be the risk factor necessary in conjunction with the genetic defect to trigger porphyria symptoms.