Novel inhibitors of prolyl 4-hydroxylase. Part 4 pyridine-2-carboxylic acid analogues with alternative 2-substituents

The Recycling of Substandard Rocket Fuel N,N-Dimethylhydrazine via the Involvement of Its Hydrazones Derived from Glyoxal, Acrolein, Metacrolein, Crotonaldehyde, and Formaldehyde in Organic Synthesis

"Heptil" (unsymmetrical dimethylhydrazine-UDMH) is extensively employed worldwide as a propellant for rocket engines. However, UDMH constantly loses its properties as a result of its continuous and uncontrolled absorption of moisture, which cannot be rectified. This situation threatens its long-term usability. UDMH is an exceedingly toxic compound (Hazard Class 1), which complicates its transportation and disposal. Incineration is currently the only method used for its disposal, but this process generates oxidation by-products that are even more toxic than the original UDMH. A more benign approach involves its immediate reaction with a formalin solution to form 1,1-dimethyl-2-methylene hydrazone (MDH), which is significantly less toxic by an order of magnitude. MDH can then be polymerized under acidic conditions, and the resulting product can be burned, yielding substantial amounts of nitrogen oxides. This review seeks to shift the focus of MDH from incineration towards its application in the synthesis of relatively non-toxic and readily available analogs of various pharmaceutical substances. We aim to bring the attention of the international chemical community to the distinctive properties of MDH, as well as other hydrazones (such as glyoxal, acrolein, crotonal, and meta-crolyl), wherein each structural fragment can initiate unique transformations that have potential applications in molecular design, pharmaceutical research, and medicinal chemistry.

Evaluating Metal-Ligand Interactions of Metal-Binding Isosteres Using Model Complexes

Bioisosteres are a useful approach to address pharmacokinetic liabilities and improve drug-like properties. Specific to developing metalloenzyme inhibitors, metal-binding pharmacophores (MBPs) have been combined with bioisosteres, to produce metal-binding isosteres (MBIs) as alternative scaffolds for use in fragment-based drug discovery (FBDD). Picolinic acid MBIs have been reported and evaluated for their metal-binding ability, pharmacokinetic properties, and enzyme inhibitory activity. However, their structural, electronic, and spectroscopic properties with metal ions other than Zn(II) have not been reported, which might reveal similarities and differences between MBIs and the parent MBPs. To this end, [M(TPA)(MBI)]⁺ (M = Ni(II) and Co(II), TPA = tris(2-pyridylmethyl)amine) is presented as a bioinorganic model system for investigating picolinic acid, four heterocyclic MBIs, and 2,2'-bipyridine. These complexes were characterized by X-ray crystallography as well as NMR, IR, and UV-vis spectroscopies, and their magnetic moments were accessed. In addition, [(Tp^Ph,Me)Co(MBI)] (Tp^Ph,Me = hydrotris(3,5-phenylmethylpyrazolyl)borate) was used as a second model compound, and the limitations and attributes of the two model systems are discussed. These results demonstrate that bioinorganic model complexes are versatile tools for metalloenzyme inhibitor design and can provide insights into the broader use of MBIs.

Understanding collagen interactions and their targeted regulation by novel drugs

Introduction: Among protein and fibers in the extracellular matrix (ECM), collagen is the most copious and widely employed in cosmetic, food, pharmaceutical, and biomedical industries due to its extensive biocompatible and versatile properties. In the last years, the knowledge about functions of collagens increased and expanded dramatically. Once considered only crucial for the ECM scaffolding and mechanotransduction, additional functional roles have now been ascribed to the collagen superfamily which are defined by other recently discovered domains, supramolecular assembly and receptors.Areas covered: Given the importance of each step in the collagen biosynthesis, folding and signaling, medicinal chemists have explored small molecules, peptides, and monoclonal antibodies to modulate enzymes, receptors and interactions with the physiological ligands of collagen. These compounds were also explored toward diseases and pathological conditions. The authors discuss this providing their expert perspectives on the subject area.Expert opinion: Understanding collagen protein properties and its interactome is beneficial for therapeutic drug design. Nevertheless, compounds targeting collagen-based interactome suffered from the presence of different isoforms for each target and the lack of specific 3D crystal structures able to guide properly drug design.

Structure-Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease

Metalloenzymes represent an important target space for drug discovery. A limitation to the early development of metalloenzyme inhibitors has been the lack of established structure-activity relationships (SARs) for molecules that bind the metal ion cofactor(s) of a metalloenzyme. Herein, we employed a bioinorganic perspective to develop an SAR for inhibition of the metalloenzyme influenza RNA polymerase PA_N endonuclease. The identified trends highlight the importance of the electronics of the metal-binding pharmacophore (MBP), in addition to MBP sterics, for achieving improved inhibition and selectivity. By optimization of the MBPs for PA_N endonuclease, a class of highly active and selective fragments was developed that displays IC₅₀ values <50 nM. This SAR led to structurally distinct molecules that also displayed IC₅₀ values of ∼10 nM, illustrating the utility of a metal-centric development campaign in generating highly active and selective metalloenzyme inhibitors.

Metal-Binding Isosteres as New Scaffolds for Metalloenzyme Inhibitors

The principle of isosteres or bioisosteres in medicinal chemistry is a central and essential concept in modern drug discovery. For example, carboxylic acids are often replaced by bioisosteres to mitigate issues related to lipophilicity or acidity while retaining acidic characteristics in addition to hydrogen bond donor/acceptor abilities. Separately, the development of metal-binding pharmacophores (MBPs) for binding to the active site metal ion in metalloenzymes of therapeutic interest is an emerging area in the realm of fragment-based drug discovery (FBDD). The direct application of the bioisostere concept to MBPs has not been well-described or systematically investigated. Herein, the picolinic acid MBP is used as a case study for the development of MBP isosteres (so-called MBIs). Many of these isosteres are novel compounds, and data on their physicochemical properties, metal binding capacity, and metalloenzyme inhibition characteristics are presented. The results show that MBIs of picolinic acid generally retain metal coordinating properties and exhibit predictable metalloenzyme inhibitory activity while possessing a broad range of physicochemical properties (e.g., p Ka, log P). These findings demonstrate the use of bioisosteres results in an untapped source of metal binding functional groups suitable for metalloenzyme FBDD. These MBIs provide a previously unexplored route for modulating the physicochemical properties of metalloenzyme inhibitors and improving their drug-likeness.

Collagen Prolyl 4-Hydroxylase as a Therapeutic Target

Collagen is the dominant protein of the extracellular matrix. Its distinguishing feature is a three-stranded helix of great tensile strength. (2 S,4 R)-4-Hydroxyproline residues are essential for the stability of this triple helix. These residues arise from the post-translational modification of (2 S)-proline residues by collagen prolyl 4-hydroxylases (CP4Hs), which are members of the Fe(II)- and α-ketoglutarate (AKG)-dependent dioxygenase family. Here, we provide a framework for the inhibition of CP4Hs as the basis for treating fibrotic diseases and cancer metastasis. We begin with a summary of the structure and enzymatic reaction mechanism of CP4Hs. Then, we review the metal ions, metal chelators, mimetics of AKG and collagen strands, and natural products that are known to inhibit CP4Hs. Our focus is on inhibitors with potential utility in the clinic. We conclude with a prospectus for more effective inhibitors.

Active methylenes in the synthesis of a pyrrole motif: an imperative structural unit of pharmaceuticals, natural products and optoelectronic materials

Pyrrole is one of the most important azaheterocycles, due to its wide range of applications in pharmaceuticals and optoelectronic materials, coupled with its utility as an intermediate in natural products.

N- versus O-alkylation: utilizing NMR methods to establish reliable primary structure determinations for drug discovery

A classic synthetic issue that remains unresolved is the reaction that involves the control of N- versus O-alkylation of ambident anions. This common chemical transformation is important for medicinal chemists, who require predictable and reliable protocols for the rapid synthesis of inhibitors. The uncertainty of whether the product(s) are N- and/or O-alkylated is common and can be costly if undetermined. Herein, we report an NMR-based strategy that focuses on distinguishing inhibitors and intermediates that are N- or O-alkylated. The NMR strategy involves three independent and complementary methods. However, any combination of two of the methods can be reliable if the third were compromised due to resonance overlap or other issues. The timely nature of these methods (HSQC/HMQC, HMBC. ROESY, and (13)C shift predictions) allows for contemporaneous determination of regioselective alkylation as needed during the optimization of synthetic routes.

Inhibition of 2-oxoglutarate dependent oxygenases

2-Oxoglutarate (2OG) dependent oxygenases are ubiquitous iron enzymes that couple substrate oxidation to the conversion of 2OG to succinate and carbon dioxide. In humans their roles include collagen biosynthesis, fatty acid metabolism, DNA repair, RNA and chromatin modifications, and hypoxic sensing. Commercial applications of 2OG oxygenase inhibitors began with plant growth retardants, and now extend to a clinically used pharmaceutical compound for cardioprotection. Several 2OG oxygenases are now being targeted for therapeutic intervention for diseases including anaemia, inflammation and cancer. In this critical review, we describe studies on the inhibition of 2OG oxygenases, focusing on small molecules, and discuss the potential of 2OG oxygenases as therapeutic targets (295 references).

Synthesis of 5-(2,2'-bipyridinyl and 2,2'-bipyridinediiumyl)-2'-deoxyuridine nucleosides: precursors to metallo-DNA conjugates

The synthesis of 2,2'-bipyridinyl-2'-deoxyuridine metal-chelator nucleosides (Bipy-dU) with either ethynyl or ethylenyl linkers was now been accomplished. These new nucleosides will permit the construction of a number of corresponding metallo-DNA conjugates where many types of metals can be complexed to the 2,2'-bipyridinyl chelator group and the resulting metallo-dU conjugates incorporated into DNA oligonucleotides. Additionally this paper also reports the synthesis of a di-N-alkylated bipyridinediiumyl-2'-deoxyuridine nucleoside (Bipy(2+)-dU) with an ethylenyl linker. The Bipy(2+)-dU nucleoside was found to decompose under basic conditions precluding its use in standard automated DNA-synthesis by the phosphoramidite method. No such restrictions apply to the two Bipy-dU nucleosides reported here for use as metal chelators.

One-step synthesis of 3,5-disubstituted-2-pyridylpyrroles from the condensation of 1,3-diones and 2-(aminomethyl)pyridine

3,5-Disubstituted- and 3,4,5-trisubstituted-2-(2-pyridyl)pyrroles may be synthesized efficiently from the novel condensation of 2-(aminomethyl)pyridine and 1,3-diones. The cyclization reaction was found to proceed through the intermediacy of a (2-pyridyl)methylimine. A marked dependence of the regioselectivity in the reaction of unsymmetrical diones on the presence of additional aminomethylpyridine suggests that two pathways to the product pyrroles are available.

Present status of hepatoprotectants

Perpetual exposure of liver to xenobiotics and therapeutic agents leads to toxic manifestations of a complex and diverse nature. Not a single curative therapeutic agent has been found so far which could provide lasting remedy to patients suffering from hepatic disorders. In fact, the remedies available in the modern system of medicine provide only symptomatic relief without any significant changes on the disease process. Moreover, their use is associated with severe side effects and chances of relapses. Except some natural products claimed to be effective, no safe synthetic product is yet available for the management of hepatic disorders. Lack of effective, least toxic and curative hepatoprotectants made the task difficult to discover newer drugs. This review is an attempt to provide an overall view of the development of synthetic and natural products as hepatoprotective agents.

Ultrastructural localisation and further biochemical characterisation of prolyl 4-hydroxylase from Phaseolus vulgaris: comparative analysis

Prolyl 4-hydroxylase (EC 1.14.11.2), the enzyme responsible for the post-translational hydroxylation of peptide proline, has been well described in animals but has been little studied in plants. The best characterised example is the enzyme from French bean (Phaseolus vulgaris). In this study, the biochemical properties of this plant enzyme were examined in more detail and, using specific polyclonal antibodies, the localisation of the enzyme was determined. Both alpha- and beta-subunits did not show multiple forms, suggesting a relatively broad specificity of the enzyme complex with respect to the target hydroxylated amino acid sequences. Antibodies to the mammalian and Chlamydomonas enzymes cross-react with the higher plant subunits, indicating that some epitopes are highly conserved. The P. vulgaris enzyme was inhibited by analogues of oxoglutarate, but was not susceptible to doxorubicin. Inhibition of the bean enzyme by an oxaloglycine derivative resulted in the retention of the target (hydroxy)proline-rich protein in the endomembrane system. Immunolocalisation of the enzyme showed close association with the endoplasmic reticulum and Golgi apparatus in root tip cells of P. vulgaris or Tropaeolum majus. This localisation was particularly pronounced in Golgi-associated vesicles of young root tip cells of T. majus, cell types where rapid synthesis and deposition of wall material was observed. These data are consistent with the hypothesis, proposed by Bolwell [G.P. Bolwell, Dynamic aspects of the plant extracellular matrix, Int. Rev. Cytol. 146 (1993) 261-324], that protein hydroxylation must be completed before the glycosylation of the target (hydroxy)proline-rich glycoproteins in the Golgi stack.

Collagen hydroxylases and the protein disulfide isomerase subunit of prolyl 4-hydroxylases

Prolyl 4-hydroxylases catalyze the formation of 4-hydroxyproline in collagens and other proteins with an appropriate collagen-like stretch of amino acid residues. The enzyme requires Fe(II), 2-oxoglutarate, molecular oxygen, and ascorbate. This review concentrates on recent progress toward understanding the detailed mechanism of 4-hydroxylase action, including: (a) occurrence and function of the enzyme in animals; (b) general molecular properties; (c) intracellular sites of hydroxylation; (d) peptide substrates and mechanistic roles of the cosubstrates; (e) insights into the development of antifibrotic drugs; (f) studies of the enzyme's subunits and their catalytic function; and (g) mutations that lead to Ehlers-Danlos Syndrome. An account of the regulation of collagen hydroxylase activities is also provided.

Prolyl 4-hydroxylases and their protein disulfide isomerase subunit

Prolyl 4-hydroxylases (EC 1.14,11.2) catalyze the formation of 4-hydroxyproline in collagens and other proteins with collagen-like sequences. The vertebrate type I and type II enzymes are [alpha (I)]2 beta 2 and [alpha (II)]2 beta 2 tetramers, respectively, whereas the enzyme from the nematode Caenorhabditis elegans is an alpha beta dimer. The type I enzyme is the major form in most but not all vertebrate tissues. The catalytic properties of the various enzyme forms are highly similar, but there are distinct, although small, differences in K(m) values for various peptide substrates between the enzyme forms and major differences in Ki values for the competitive inhibitor, poly(L-proline). Prolyl 4-hydroxylase requires Fe2+, 2-oxoglutarate, O2 and ascorbate. Kinetic studies and theoretical considerations have led to elucidation of the reaction mechanism, and recent extensive site-directed mutagenesis studies have identified five critical residues at the cosubstrate binding sites. A number of compounds have been characterized that inhibit it competitively with respect to some of the cosubstrates, and three groups of suicide inactivators have also been identified. The beta subunit in all forms of prolyl 4-hydroxylase is identical to protein disulfide isomerase (PDI), a multifunctional polypeptide that also serves as a subunit in the microsomal triglyceride transfer protein, as a chaperone-like polypeptide that probably assists folding of a number of newly synthesized proteins, and in several other functions. The main role of the PDI polypeptide as a protein subunit is probably related to its chaperone function. Recent expression studies of recombinant human prolyl 4-hydroxylase subunits in a yeast have indicated that the formation of a stable enzyme tetramer in vivo requires coexpression of collagen polypeptide chains.