Catalytic Osmylation and Antiviral Activity of Some Garbocyclic 5-Substituted Uridine and Cytidine Analogues

Abstract

Some carbocyclic uridines and cytidines have been dihydroxylated in an osmium catalyzed reaction. Besides the nucleoside analogues, the anti forms, the diastereomeric syn forms were formed. These could be separated and tested with regard to antiviral activity.     

Palladium-Catalyzed Animation of 6-Chloropurine. Synthesis of N6-Substituted Adenosine Analogues

Abstract

Room-temperature treatment of persilylated 6-chloro-9-β-D-ribofuranosyl-purine with a variety of aliphatic and aromatic amines, in the presence of Pd₂(dba)₃, BINAP and base, leads to N⁶-substituted adenosine analogues in fair to good yields. Coupling of chloropurine with a chiral aziridinyl diester is applied in the synthesis of a potential adenylosuccinate lyase inhibitor.     

Conformational Characteristics and Correlations in Crystal Structures of Nucleic Acid Oligonucleotides: Evidence for Sub-states

Abstract

Sugar phosphate backbone conformations are a structural element inextricably involved in a complete understanding of specific recognition nucleic acid ligand interactions, from early stage discrimination of the correct target to complexation per se, including any structural adaptation on binding. The collective results of high resolution DNA, RNA and protein/DNA crystal structures provide an opportunity for an improved and enhanced statistical analysis of standard and unusual sugar-phosphate backbone conformations together with corresponding dinucleotide sequence effects as a basis for further exploration of conformational effects on binding. In this study, we have analyzed the conformations of all relevant crystal structures in the nucleic acids data base, determined the frequency distribution of all possible ?, ζ, α, β and γ backbone angle arrangements within four nucleic acid categories (A-RNA and A-DNA, free and bound B-DNA) and explored the relationships between backbone angles, sugar puckers and selected helical parameters. The trends in the correlations are found to be similar regardless of the nucleic acid category. It is interesting that specific structural effects exhibited by the different unusual backbone sub-states are in some cases contravariant. Certain α/γ changes are accompanied by C3′ endo (north) sugars, small twist angles and positive values of base pair roll, and favor a displacement of nucleotide bases towards the minor groove compared to that of canonical B form structures. Unusual ?/ζ combinations occur with C2′ (south) sugars, high twist angles, negative values of base pair roll, and base displacements towards the major groove. Furthermore, any unusual backbone correlates with a reduced dispersion of equilibrium structural parameters of the whole double helix, as evidenced by the reduced standard deviations of almost all con- formational parameters. Finally, a strong sequence effect is displayed in the free oligomers, but reduced somewhat in the ligand bound forms. The most variable steps are GpA and CpA, and, to a lesser extent, their partners TpC and TpG. The results provide a basis for considering if the variable and non-variable steps within a biological active sequence precisely determine morphological structural features as the curvature direction, the groove depth, and the accessibility of base pair for non covalent associations.     

Crystal Structures of CusC Review Conformational Changes Accompanying Folding and Transmembrane Channel Formation

Gram-negative bacteria, such as Escherichia coli, frequently utilize tripartite efflux complexes in the RND (resistance–nodulation–cell division) family to expel diverse toxic compounds from the cell. These complexes span both the inner and outer membranes of the bacterium via an α-helical, inner membrane transporter; a periplasmic membrane fusion protein; and a β-barrel, outer membrane channel. One such efflux system, CusCBA, is responsible for extruding biocidal Cu(I) and Ag(I) ions. To remove these toxic ions, the CusC outer membrane channel must form a β-barrel structural domain, which creates a pore and spans the entire outer membrane. We here report the crystal structures of wild-type CusC, as well as two CusC mutants, suggesting that the first N-terminal cysteine residue plays an important role in protein–membrane interactions and is critical for the insertion of this channel protein into the outer membrane. These structures provide insight into the mechanisms on CusC folding and transmembrane channel formation. It is found that the interactions between CusC and membrane may be crucial for controlling the opening and closing of this β-barrel, outer membrane channel.     

4-Substituted carbamazepine derivatives: Conformational analysis and sodium channel-blocking properties

The physicochemical properties of 4-substituted carbamazepine derivatives were investigated. It was elucidated that the 4-substitution is not effective in reducing the rotations (E/Z) about the N—C1′ axes around the outer carbamoyl moiety. However, the atropisomers were isolated with high stereochemical stability, meaning that the 4-substitution reduced the butterfly motion of the tricyclic ring system efficiently. The Cl/CH₃-substituted carbamazepine derivatives showed greater inhibitory effects on hNa_v1.2 channel currents compared with carbamazepine, although no difference in the activity between enantiomers was observed.     

Conformational Requirements of Acetylcholine Analogues and Local Anaesthetics

ATTEMPTS have been made to view the roles of acetylcholine and of cholinergic agonists as triggering permeability changes in excitable membranes through attachment to acetylcholine receptor biopolymers^1,2. Similarly, it has been proposed that local anaesthetics might block nerve conduction through attachment to axonal acetylcholine receptors^3,4. These considerations raise a number of questions. Are certain specific conformations essential for molecules related to acetylcholine either to “trigger” or to “block” depolarization of excitable membranes ? Are the conformations of such molecules identical in the crystal and in solution ? What are the rotational barriers to conformational alteration of such molecules ?     

Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA

The reliable repair of pre-mutagenic U/G mismatches that originated from hydrolytic cytosine deamination is crucial for the maintenance of the correct genomic information. In most organisms, any uracil base in DNA is attacked by uracil DNA glycosylases (UDGs), but at least in Methanothermobacter thermautotrophicus ΔH, an alternative strategy has evolved. The exonuclease III homologue Mth212 from the thermophilic archaeon M. thermautotrophicus ΔH exhibits a DNA uridine endonuclease activity in addition to the apyrimidinic/apurinic site endonuclease and 3′ → 5′exonuclease functions. Mth212 alone compensates for the lack of a UDG in a single-step reaction thus substituting the two-step pathway that requires the consecutive action of UDG and apyrimidinic/apurinic site endonuclease.In order to gain deeper insight into the structural basis required for the specific uridine recognition by Mth212, we have characterized the enzyme by means of X-ray crystallography. Structures of Mth212 wild-type or mutant proteins either alone or in complex with DNA substrates and products have been determined to a resolution of up to 1.2 Å, suggesting key residues for the uridine endonuclease activity. The insertion of the side chain of Arg209 into the DNA helical base stack resembles interactions observed in human UDG and seems to be crucial for the uridine recognition. In addition, Ser171, Asn153, and Lys125 in the substrate binding pocket appear to have important functions in the discrimination of aberrant uridine against naturally occurring thymidine and cytosine residues in double-stranded DNA.     

Conformational Preferences of the CalliFMRFamides and their Free-Acid Analogues

Abstract

A molecular dynamics study was undertaken to determine the conformational basis for the differing activities of the insect neuropeptide hormones calliFMRFamide 3 (SPSQDFMRF-NH₂), calliFMRFamide 5 (APGQDFMRF-NH₂) and their corresponding free-acid analogues (SPSQDFM- RF-OH and APGQDFMRF-OH) in two insect bioassays. A simulated annealing protocol was used to determine the range of conformers available to the linear peptides. Analysis of the conformers obtained indicated that all the peptides exhibited distinct secondary structure preferences. These, when correlated with their biological activities, enabled the formulation of putative conformation- activity relationships for the peptides.     

New Analogues of Uridine as Possible Anti-Viral Agents Specific to SARS-CoV-2

Molecular Biology - The development of specific drugs against SARS-CoV-2 infection is a major challenge facing global science and healthcare. Despite numerous attempts, there are still no truly...     

Crystal Structures of Cytochrome P450 105P1 from Streptomyces avermitilis: Conformational Flexibility and Histidine Ligation State

The polyene macrolide antibiotic filipin is widely used as a probe for cholesterol in biological membranes. The filipin biosynthetic pathway of Streptomyces avermitilis contains two position-specific hydroxylases, C26-specific CYP105P1 and C1′-specific CYP105D6. In this study, we describe the three X-ray crystal structures of CYP105P1: the ligand-free wild-type (WT-free), 4-phenylimidazole-bound wild-type (WT-4PI), and ligand-free H72A mutant (H72A-free) forms. The BC loop region in the WT-free structure has a unique feature; the side chain of His72 within this region is ligated to the heme iron. On the other hand, this region is highly disordered and widely open in WT-4PI and H72A-free structures, respectively. Histidine ligation of wild-type CYP105P1 was not detectable in solution, and a type II spectral change was clearly observed when 4-phenylimidazole was titrated. The H72A mutant showed spectroscopic characteristics that were almost identical to those of the wild-type protein. In the H72A-free structure, there is a large pocket that is of the same size as the filipin molecule. The highly flexible feature of the BC loop region of CYP105P1 may be required to accept a large hydrophobic substrate.     

6-Substituted Derivatives of Carbovir: Anti-HIV Activity

Abstract

A series of 6-alkoxy and 6-alkylamino carbovir derivatives were synthesized in order to evaluate prodrug approaches to increased bioavailability of the anti-HIV agent, carbovir. All of the compounds were active against HIV with the N-alkyl derivatives less active than the corresponding O-alkyl derivatives. The adenosine deaminase inhibitor, EHNA, had no effect on the anti-HIV activity of 6-propoxycarbovir, while the adenylic acid deaminase inhibitor, 2′-deoxycoformycin, significantly decreased antiviral activity. These observations suggest that the 6-alkoxycarbovirs are metabolized directly to the monophosphates and are subsequently converted to carbovir monophosphate via adenylic acid deaminase     

Iodine Monochloride Facilitated Deglycosylation,Anomerization, and Isomerization of 3-Substituted Thymidine Analogues

The reaction of thymidine, 3-mono-, and 3,3′,5′-trialkylsubstitued thymidine analogues with iodine monochloride (ICl) was investigated. Treatment with ICl resulted in rapid deglycosylation, anomerization, and isomerization of thymidine and 3-substituted thymidine analogues under various reaction conditions leading to the formation of the nucleobases as the major products accompanied by minor formation of α-furanosidic-, α-pyranosidic-, and β-pyranosidic nucleosides. On the other hand, 3,3′,5′-trisubstitued thymidine analogues were only deglycosylated and anomerized. These results are similar to those observed for the acidic hydrolysis of the glycoside bond in nucleosides, but were presumably caused by the Lewis acid character of an iodine electrophile.     

Synthesis and Antiviral Activity of Carbocyclic Nucleosides Incorporating a Modified Cyclopentane Ring. Part 3: Adenosine and Uridine Analogues

Abstract

Six new carbocyclic nucleosides were prepared by mounting a purine (compounds 4–6), 8-azapurine (7 and 8) or undine (9) base on the ammo group of (1S,3R)-3-amino-2,2,3-trimethylcyclopentylmethanol (10). At subtoxic concentrations, compounds 5-9 showed at best marginal antiviral activity.     

Conformational Changes in a Plant Ketol-Acid Reductoisomerase upon Mg and NADPH Binding as Revealed by Two Crystal Structures

Ketol-acid reductoisomerase (KARI; EC 1.1.1.86) is an enzyme in the branched-chain amino acid biosynthesis pathway where it catalyzes the conversion of 2-acetolactate into (2R)-2,3-dihydroxy-3-isovalerate or the conversion of 2-aceto-2-hydroxybutyrate into (2R,3R)-2,3-dihydroxy-3-methylvalerate. KARI catalyzes two reactions—alkyl migration and reduction—and requires Mg²⁺ and NADPH for activity. To date, the only reported structures for a plant KARI are those of the spinach enzyme-Mn²⁺-(phospho)ADP ribose-(2R,3R)-2,3-dihydroxy-3-methylvalerate complex and the spinach KARI-Mg²⁺-NADPH-N-hydroxy-N-isopropyloxamate complex, where N-hydroxy-N-isopropyloxamate is a predicted transition-state analog. These studies demonstrated that the enzyme consists of two domains, N-domain and C-domain, with the active site at the interface of these domains. Here, we have determined the structures of the rice KARI-Mg²⁺ and rice KARI-Mg²⁺-NADPH complexes to 1.55 Å and 2.80 Å resolutions, respectively. In comparing the structures of all the complexes, several differences are observed. Firstly, the N-domain is rotated up to 15° relative to the C-domain, expanding the active site by up to 4 Å. Secondly, an α-helix in the C-domain that includes residues V510-T519 and forms part of the active site moves by ∼ 3.9 Å upon binding of NADPH. Thirdly, the 15 C-terminal amino acid residues in the rice KARI-Mg²⁺ complex are disordered. In the rice KARI-Mg²⁺-NADPH complex and the spinach KARI structures, many of the 15 residues bind to NADPH and the N-domain and cover the active site. Fourthly, the location of the metal ions within the active site can vary by up to 2.7 Å. The new structures allow us to propose that an induced-fit mechanism operates to (i) allow substrate to enter the active site, (ii) close over the active site during catalysis, and (iii) open the active site to facilitate product release.     

Crystal Structures of PRK1 in Complex with the Clinical Compounds Lestaurtinib and Tofacitinib Reveal Ligand Induced Conformational Changes

Protein kinase C related kinase 1 (PRK1) is a component of Rho-GTPase, androgen receptor, histone demethylase and histone deacetylase signaling pathways implicated in prostate and ovarian cancer. Herein we describe the crystal structure of PRK1 in apo form, and also in complex with a panel of literature inhibitors including the clinical candidates lestaurtinib and tofacitinib, as well as the staurosporine analog Ro-31-8220. PRK1 is a member of the AGC-kinase class, and as such exhibits the characteristic regulatory sequence at the C-terminus of the catalytic domain – the ‘C-tail’. The C-tail fully encircles the catalytic domain placing a phenylalanine in the ATP-binding site. Our inhibitor structures include examples of molecules which both interact with, and displace the C-tail from the active site. This information may assist in the design of inhibitors targeting both PRK and other members of the AGC kinase family.     

Coronary Vasoactivity of Novel N6-Substituted Adenosines

Abstract

Previous studies of the structure-coronary vasoactivity relationships of adenosines substituted at N-6 identified certain simple alkyl and aralkyl groups that can promote activity and others that reduce activity. The present study shows that such alkyl and aryl moieties, when combined in an N-6 substituent, can contribute additively to coronary vasoactivity.     

Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site

Efforts to develop therapeutic agents that inhibit HIV-1 entry have led to the identification of several small molecule leads. One of the most promising is the NBD series, which binds within a conserved gp120 cavity and possesses para-halogen substituted aromatic rings, a central oxalamide linker, and a tetramethylpiperidine moiety. In this study, we characterized structurally the interactions of four NBD analogues containing meta-fluoro substitution on the aromatic ring and various heterocyclic ring replacements of the tetramethylpiperidine group. The addition of a meta-fluorine to the aromatic ring improved surface complementarity and did not alter the position of the analogue relative to gp120. By contrast, heterocyclic ring replacements of the tetramethylpiperidine moiety exhibited diverse positioning and interactions with the vestibule of the gp120 cavity. Overall, the biological profile of NBD-congeners was modulated by ligand interactions with the gp120-cavity vestibule. Herein, six co-crystal structures of NBD-analogues with gp120 provide a structural framework for continued small molecule-entry inhibitor optimization.     

Synthesis,Antiviral and Cytostatic Activities of Carbocyclic Nucleosides Incorporating a Modified Cyclopentane Ring. Part 2:1 Adenosine and Uridine Analogues

Abstract

Six new carbocyclic nucleosides were prepared by mounting a purine (compounds 5–7), 8-azapurine (compounds 9 and 10) or pyrimidine (compound 13) base on the amino group of (1R,cis)-3-(aminornethyl)-1,2,2-trimethylcyclopentylmethanol (2). The antiviral activity of compounds 5–7, 10 and 13, and their cytostatic activity, were evaluated. At subtoxic concentrations, the compounds showed no or marginal antiviral activity. Compound 5 showed moderate inhibition on tumor cell proliferation.     

The Physio1ogical Activity of 2 : 6-Substituted Phenoxyacetic Acids

Anumber of 2 : 6-substituted phenoxyacetic acids in which theside chain had been substituted by ailcyl groups to form -propionic,-n-butyric and -n-valeric acids were investigated to assesstheir ability to act as growth-regulators. Besides employingstandard tedmiques of bioassay, further experiments were undertaken to determine the effects of these compounds on the vegetativegrowth and development of intact plants of Helianthus annuus. It has been established that all the compounds tested inducedcurvature in the Went pea curvature test and that without exceptionthe activity of the parent phenoxyacetic acid (2:6-dichloro-,2:4:6-trichloro-,2:6-dimethyl-, and 2:4-dichloro-6-methyl-)was increased by side chain substitution. In the Avena straight growth assay, the a 2:6-dichloro- and2:6-dimethyl- phenoxypropionic and butyric acids brought aboutstatistically significant increases in length of the coleoptilesections, when measurements were made at the end of 24 hours.Their activity was of the same order as that exhibited by a2:4-dichlorophenoxyacetic acid. Investigations were carried out on the uptake of water by sectionsof pea internode and the extension growth of Avena coleoptileaectiona when both the concentration and the length of treatmentwere varied. For some compounds it was found that over a certainrange of concentration water uptake and extension growth wereaccelerated in the initial 6–8 hours. Subsequent to this,inhibition occurred so that no significant increases above controlvalues were apparent at the end of 24 hours, and in some casesan actual loss of water or shrinkage in length took place. Itwas thus possible to demonstrate that 2:6-dimethylphenoxyaceticacid acts as a growth regulator in pea extension growth andthat 2:6-dichiorophenoxyacetic acid is active in the Avena test. The changes in the leaf area of individual pairs of leaves,together with the lengths of the internodes and shoot weightwere followed after application of measured amounts of eachcompound to the first pair of leaves of H. annuus. A numberof the 2:6-compounds were capable of modifying growth in wayssimilar to 2:4-dichlorophenoxyacetlc acid. However, much higherconcentration had to be applied in order to produce effectscomparable to those caused by the 2:4-dichloro- compound. Measurementsof the percentage of applied compound which penetrated intothe leaf showed that there were no marked differences in thisrespect between the different phenoxy acids. On the other hand,experiments in which the treated leaves were left on the plantfor varying periods of time led to the conclusion that the a: 6-substituted compounds are less readily translocated than2:4-dichlorophenoxyacetic acid.