Pac13 is a Small,Monomeric Dehydratase that Mediates the Formation of the 3′‐Deoxy Nucleoside of Pacidamycins

The uridyl peptide antibiotics (UPAs), of which pacidamycin is a member, have a clinically unexploited mode of action and an unusual assembly. Perhaps the most striking feature of these molecules is the biosynthetically unique 3′‐deoxyuridine that they share. This moiety is generated by an unusual, small and monomeric dehydratase, Pac13, which catalyses the dehydration of uridine‐5′‐aldehyde. Here we report the structural characterisation of Pac13 with a series of ligands, and gain insight into the enzyme's mechanism demonstrating that H42 is critical to the enzyme's activity and that the reaction is likely to proceed via an E1cB mechanism. The resemblance of the 3′‐deoxy pacidamycin moiety with the synthetic anti‐retrovirals, presents a potential opportunity for the utilisation of Pac13 in the biocatalytic generation of antiviral compounds.     

Biogenesis of the unique 4',5'-dehydronucleoside of the uridyl peptide antibiotic pacidamycin

The pacidamycins belong to a class of antimicrobial nucleoside antibiotics that act by inhibiting the clinically unexploited target translocase I, a key enzyme in peptidoglycan assembly. As with other nucleoside antibiotics, the pacidamycin 4',5'-dehydronucleoside portion is an essential pharmacophore. Here we show that the biosynthesis of the pacidamycin nucleoside in Streptomyces coeruleorubidus proceeds through three steps from uridine. The transformations involve oxidation of the 5'-alcohol by Pac11, transamination of the resulting aldehyde by Pac5, and dehydration by the Cupin-domain protein Pac13.     

The Cupin Protein Pac13 is Suggested by the Data to Be a Homodimer

Cupin proteins share a double‐stranded β‐helix fold, form one of the largest protein superfamilies, and possess remarkable functional diversity. They usually exist in homooligomeric states. Goss and co‐workers recently reported that the cupin protein Pac13, which is a dehydratase that mediates the formation of the 3′‐deoxy nucleoside of pacidamycins, is an unusual small monomer. However, a careful analysis of the biophysical and structural data provided by the authors suggests that Pac13 is in fact a homodimer, similar to many other cupin proteins.     

7‐Amino‐1‐(2‐deoxy‐β‐erythro‐pentofuranosyl)‐1H‐1,2,3‐triazolo[4,5‐d]pyrimidine: an 8‐azaadenine nucleoside with the nucleobase in a syn conformation

The title compound, C₉H₁₂N₆O₃, shows a syn‐glycosylic bond orientation [χ = 64.17 (16)°]. The 2′‐deoxyfuranosyl moiety exhibits an unusual C1′‐exo–O4′‐endo (₁T⁰; S‐type) sugar pucker, with P = 111.5 (1)° and τ_m = 40.3 (1)°. The conformation at the exocyclic C4′—C5′ bond is +sc (gauche), with γ = 64.4 (1)°. The two‐dimensional hydrogen‐bonded network is built from intermolecular N—H...O and O—H...N hydrogen bonds. An intramolecular bifurcated hydrogen bond, with an amino N—H group as hydrogen‐bond donor and the ring and hydroxymethyl O atoms of the sugar moiety as acceptors, constrains the overall conformation of the nucleoside.     

4,4′‐Methylenediphenol–4,4′‐bipyridine (2/3): decarboxylation of 5,5′‐methylenedisalicylic acid under hydrothermal conditions

Reaction of 5,5′‐methylenedisalicylic acid (5,5′‐H₄mdsa) with 4,4′‐bipyridine (4,4′‐bipy) and manganese(II) acetate under hydrothermal conditions led to the unexpected 2:3 binary cocrystal 4,4′‐methylenediphenol–4,4′‐bipyridine (2/3), C₁₃H₁₂O₂·1.5C₁₀H₈N₂ or (4,4′‐H₂dhdp)(4,4′‐bipy)_1.5, which is formed with a concomitant decarboxylation. The asymmetric unit contains one and a half 4,4′‐bipy molecules, one of which straddles a centre of inversion, and one 4,4′‐H₂dhdp molecule. O—H...N interactions between the hydroxy and pyridyl groups lead to a discrete ribbon motif with an unusual 2:3 stoichiometric ratio of strong hydrogen‐bonding donors and acceptors. One of the pyridyl N‐atom donors is not involved in hydrogen‐bond formation. Additional weak C—H...O interactions between 4,4′‐bipy and 4,4′‐H₂dhdp molecules complete a two‐dimensional bilayer supramolecular structure.     

Substituted 2,2′‐Bis(2‐oxidobenzylideneamino)‐4,4′‐dimethyl‐1,1′‐biphenyl Complexes of Zinc

The condensation reaction of 2,2′‐diamino‐4,4′‐dimethyl‐6,6'‐dibromo‐1,1′‐biphenyl with 2‐hydroxybenzaldehyde as well as 5‐methoxy‐, 4‐methoxy‐, and 3‐methoxy‐2‐hydroxybenzaldehyde yields 2,2′‐bis(salicylideneamino)‐4,4′‐dimethyl‐6,6′‐dibromo‐1,1′‐biphenyl ( 1a ) as well as the 5‐, 4‐, and 3‐methoxy‐substituted derivatives 1b , 1c , and 1d , respectively. Deprotonation of substituted 2,2′‐bis(salicylideneamino)‐4,4′‐dimethyl‐1,1′‐biphenyls with diethylzinc yields the corresponding substituted zinc 2,2′‐bis(2‐oxidobenzylideneamino)‐4,4′‐dimethyl‐1,1′‐biphenyls ( 2 ) or zinc 2,2′‐bis(2‐oxidobenzylideneamino)‐4,4′‐dimethyl‐6,6′‐dibromo‐1,1′‐biphenyls ( 3 ). Recrystallization from a mixture of CH₂Cl₂ and methanol can lead to the formation of methanol adducts. The methanol ligands can either bind as Lewis base to the central zinc atom or as Lewis acid via a weak O–H ··· O hydrogen bridge to a phenoxide moiety. Methanol‐free complexes precipitate as dimers with central Zn₂O₂ rings.     

The N1‐(2′‐deoxyribofuranoside) of 3‐iodo‐5‐nitroindole: a universal nucleoside forming nitro–iodo interactions

The title compound [systematic name: 1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐3‐iodo‐5‐nitro‐1H‐indole], C₁₃H₁₃IN₂O₅, exhibits an anti glycosylic bond conformation with a χ torsion angle of −114.9 (3)°. The furanose moiety shows a twisted C2′‐endo sugar pucker (S‐type), with P = 141.3° and τ_m = 40.3°. The orientation of the exocyclic C4′—C5′ bond is +ap (gauche, trans), with a γ torsion angle of 177.4 (2)°. The extended crystal structure is stabilized by hydrogen bonding and I...O contacts, as well as by stacking interactions. The O atoms of the nitro group act as acceptors, forming bifurcated hydrogen bonds within the ac plane. Additionally, the iodo substituent forms an interplanar contact with an O atom of the nitro group, and another contact with the O atom of the 5′‐hydroxy group of the sugar moiety within the ac plane is observed. These contacts can be considered as the structure‐determining factors for the molecular packing in the crystal structure.     

Heterocyclization reaction of 2‐(2‐methylaziridin‐1‐yl)‐3‐ureidopyridines under appel's conditions

The reaction of 2‐(2‐methylaziridin‐1‐yl)‐3‐ureidopyridines 12 with triphenylphosphine, carbon tetra‐chloride, and triethylamine (Appel's conditions) led to the corresponding carbodiimides 13 , which underwent intramolecular cycloaddition reaction with aziridine under the reaction conditions to give the pyridine‐fused heterocycles, 2,3‐dihydro‐1H‐imidazo[2′,3′:2,3]imidazo[4,5‐b]pyridines 16 and 12,13‐dihydro‐5H‐1,3 ‐benzodiazepino [2′,3′:2,3] imidazo[4,5‐b]pyridines 17 .     

Efficient Solid Phase Synthesis of Cleavable Oligodeoxynucleotides Based on a Novel Strategy for the Synthesis of 5′‐S‐(4,4′‐Dimethoxytrityl)‐2′‐deoxy‐5′‐thionucleoside Phosphoramidites

The incorporation of a specific cleavage site into an oligodeoxynucleotide can be achieved by utilizing the four 5′‐S‐(4,4′‐dimethoxytrityl)‐2′‐deoxy‐5′‐thionucleoside 3′‐(2‐cyanoethyl diisopropylphosphoramidites) 5 and 15a – c (Fig. 1). Based on the silver ion assisted cleavage of P? S and C? S bonds, we synthesized oligodeoxynucleotides with an achiral 5′‐phosphorothioate linkage 3′–O–P–S–5′ by the solid‐phase phosphoramidite procedure. The efficient cleavage of these modified oligodeoxynucleotides can be detected by HPLC, PAGE, and surface plasmon resonance (SPR) spectrometry. The liberated 5′‐thiol moiety can be used directly for post‐reaction labeling with appropriately functionalized reporter groups.     

1,N6‐Etheno‐2′‐deoxytubercidin hemihydrate

The title compound [systematic name: 7‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐7H‐imidazo[1,2‐c]pyrrolo[2,3‐d]pyrimidine hemihydrate], 2C₁₃H₁₄N₄O₃·H₂O or (I)·0.5H₂O, shows two similar conformations in the asymmetric unit. These two conformers are connected through one water molecule by hydrogen bonds. The N‐glycosylic bonds of both conformers show an almost identical anti conformation with χ = −107.7 (2)° for conformer (I‐1) and −107.0 (2)° for conformer (I‐2). The sugar moiety adopts an unusual N‐type (C3′‐endo) sugar pucker for 2′‐deoxyribonucleosides, with P = 36.8 (2)° and τ_m = 40.6 (1)° for conformer (I‐1), and P = 34.5 (2)° and τ_m = 41.4 (1)° for conformer (I‐2). Both conformers and the solvent molecule participate in the formation of a three‐dimensional pattern with a `chain'‐like arrangement of the conformers. The structure is stabilized by intermolecular O—H...O and O—H...N hydrogen bonds, together with weak C—H...O contacts.     

Enzyme Modification and Oxidative Cross‐linking Using Carboxylate‐, Phenol‐ and Catechol‐Conjugated 1,8‐Naphthalimides

The ground‐ and excited‐state interactions of β‐alanine, tyrosine and l ‐dopa substituted 1,8 naphthalimides (NI‐Ala, NI‐Tyr and NI‐Dopa) with lysozyme and mushroom tyrosinase were evaluated to understand the mechanism of oxidative modification. Photooxidative cross‐linking of lysozyme was observed for all three conjugates. The yield was significantly reduced for NI‐Tyr and NI‐Dopa due to intramolecular electron transfer to the excited singlet state of the 1,8‐naphthalimide. Incubation of NI‐Tyr and NI‐Dopa with mushroom tyrosinase resulted in an increased fluorescence from the naphthalimide, suggesting that the phenol and catechol portion of the conjugates are oxidized by the enzyme. This result demonstrates that the compounds bind in the active site of mushroom tyrosinase. The catalytic activity of mushroom tyrosinase to oxidize both tyrosine (monophenolase) and l ‐dopa (diphenolase) was modified by NI‐Tyr and NI‐Dopa. Monophenolase activity was inhibited, and the diphenolase activity was enhanced in the presence of these conjugates. Detailed Michaelis–Menten studies show that both V_max and K_m are modified, consistent with a mixed inhibition mechanism. Collectively, the results show that the compounds interact in the enzyme's active site, but also modify the distribution of the enzyme's oxidation states that are responsible for catalysis.     

4‐Chloro‐3′‐methylsulfinyl‐5(6 or 8)‐nitro‐3,4′‐diquinolinyl sulfides

Reaction of 4‐chloro‐3′‐methylthio‐3,4′‐diquinolinyl sulfides 3, 9b, 9c with a nitrating mixture proceeds via the 3′‐methylthio group monooxidation and yields 3′‐methylsulfinyl diquinolinyl sulfides 4, 5b, 5c , respectively. Further treatment of 4 with a nitrating mixture followed as C₅‐ and C₈‐nitration and gives mixture of 5a and 5c. Treatment of 3′‐methylsulfinyl quinolines 6 and 7 with hydrochloric acid/potassium iodide system causes reduction of the sulfoxide group in 6 and 7 to the sulfide group yielding 8 , in case of 4‐methoxyquinolines 6 , hydrolysis of the 4‐methoxyquinoline moiety to the 4‐quinolinone moiety takes place simultaneously. The proton and carbon chemical shifts of 4 and 5a were completely assigned following COSY, HETCOR and INEPT or COLOC studies.     

2′‐Deoxy‐5‐methylisocytidine

In the title compound, 2‐amino‐1‐(2‐deoxy‐β‐d ‐erythro‐pento­furan­osyl)‐5‐methyl­pyrimidin‐4(1H)‐one, C₁₀H₁₅N₃O₄, the conformation of the N‐glycosidic bond is syn and the 2‐deoxy­ribo­furan­ose moiety adopts an unusual ^OT₁ sugar pucker. The orientation of the exocyclic C4′—C5′ bond is +sc (+gauche).     

7‐Iodo‐5‐aza‐7‐deazaguanine ribonucleoside: crystal structure,physical properties,base‐pair stability and functionalization

The positional change of nitrogen‐7 of the RNA constituent guanosine to the bridgehead position‐5 leads to the base‐modified nucleoside 5‐aza‐7‐deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson–Crick proton donor site N3—H becomes a proton‐acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all‐purine' DNA and DNA with silver‐mediated base pairs. The present work reports the single‐crystal X‐ray structure of 7‐iodo‐5‐aza‐7‐deazaguanosine, C<sub>10</sub>H<sub>12</sub>IN<sub>5</sub>O<sub>5</sub> ( 1 ). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4′‐endo) for the ribose moiety, with an antiperiplanar orientation of the 5′‐hydroxy group. Crystal packing is controlled by interactions between nucleobase and sugar moieties. The 7‐iodo substituent forms a contact to oxygen‐2′ of the ribose moiety. Self‐pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O—H…O and N—H…O). The concept of pK‐value differences to evaluate base‐pair stability was applied to purine–purine base pairing and stable base pairs were predicted for the construction of `all‐purine' RNA. Furthermore, the 7‐iodo substituent of 1 was functionalized with benzofuran to detect motional constraints by fluorescence spectroscopy.     

Organocatalytic Asymmetric Conjugate Addition of 3‐Monosubstituted Oxindoles to (E)‐1,4‐Diaryl‐2‐buten‐1,4‐diones: A Strategy for the Indirect Enantioselective Furanylation and Pyrrolylation of 3‐Alkyloxindoles

An asymmetric conjugate addition of 3‐monosubstituted oxindoles to a range of (E)‐1,4‐diaryl‐2‐buten‐1,4‐diones, catalyzed by commercially available cinchonine, is described. This organocatalytic asymmetric reaction affords a broad range of 3,3′‐disubstituted oxindoles that contain a 1,4‐dicarbonyl moiety and vicinal quaternary and tertiary stereogenic centers in high‐to‐excellent yields (up to 98 %), with excellent diastereomeric and moderate‐to‐high enantiomeric ratios (up to 99:1 and 95:5, respectively). Subsequently, cyclization of the 1,4‐dicarbonyl moiety in the resultant Michael adducts under different Paal–Knorr conditions results in two new kinds of 3,3′‐disubstituted oxindoles—3‐furanyl‐ and 3‐pyrrolyl‐3‐alkyl‐oxindoles—in high yields and good enantioselectivities. Notably, the studies presented here sufficiently confirm that this two‐step strategy of sequential conjugate addition/Paal–Knorr cyclization is not only an attractive method for the indirect enantioselective heteroarylation of 3‐alkyloxindoles, but also opens up new avenues toward asymmetric synthesis of structurally diverse 3,3′‐disubstituted oxindole derivatives.     

Synthesis of (2′S)‐2′‐Deoxy‐2′‐C‐methylpurine Nucleosides and Their Phosphoramidites

We describe the stereoselective synthesis of (2′S)‐2′‐deoxy‐2′‐C‐methyladenosine ( 12 ) and (2′S)‐2′‐deoxy‐2′‐C‐methylinosine ( 14 ) as well as their corresponding cyanoethyl phosphoramidites 16 and 19 from 6‐O‐(2,6‐dichlorophenyl)inosine as starting material. The methyl group at the 2′‐position was introduced via a Wittig reaction (→ 3 , Scheme 1) followed by a stereoselective oxidation with OsO₄ (→ 4 , Scheme 2). The primary‐alcohol moiety of 4 was tosylated (→ 5 ) and regioselectively reduced with NaBH₄ (→ 6 ). Subsequent reduction of the 2′‐alcohol moiety with Bu₃SnH yielded stereoselectively the corresponding (2′S)‐2′‐deoxy‐2′‐C‐methylnucleoside (→ 8a ).     

7‐Deaza‐2′‐deoxyinosine: a nucleoside showing ambiguous base‐pairing properties against the four canonical DNA constituents

The title compound [systematic name: 7‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐3,7‐dihydro‐4H‐pyrrolo[2,3‐d]pyrimidin‐4‐one], C₁₁H₁₃N₃O₄, represents an acid‐stable derivative of 2′‐deoxyinosine. It exhibits an anti glycosylic bond conformation, with a χ torsion angle of 113.30 (15)°. The furanose moiety adopts an S‐type sugar pucker ⁴T₃, with P = 221.8 (1)° and τ_m = 40.4 (1)°. The conformation at the exocyclic C4′—C5′ bond of the furanose ring is ap (trans), with γ = 167.14 (10)°. The extended structure forms a three‐dimensional hydrogen‐bond network involving O—H...O, N—H...O and C—H...O hydrogen bonds. The title compound forms an uncommon hydrogen bond between a CH group of the pyrrole system and the ring O atom of the sugar moiety of a neighbouring molecule.     

Synthesis of 3′‐Thioamido‐Modified 3′‐Deoxythymidine 5′‐Triphosphates by Regioselective Thionation and Their Use as Chain Terminators in DNA Sequencing

The thioamide derivatives 3′‐deoxy‐5′‐O‐(4,4′‐dimethoxytrityl)‐3′‐[(2‐methyl‐1‐thioxopropyl)amino]thymidine ( 4a ) and 3′‐deoxy‐5′‐O‐(4,4′‐dimethoxytrityl)‐3′‐{{6‐{[(9H‐(fluoren‐9‐ylmethoxy)carbonyl]amino}‐1‐thioxohexyl}amino}thymidine ( 4b ) were synthesized by regioselective thionation of the corresponding amides 3a and 3b with 2,4‐bis(4‐methoxyphenyl)‐1,3,2,4‐dithiadiphosphetane 2,4‐disulfide (Lawesson's reagent). The addition of exact amounts of pyridine to the reaction mixture proved to be essential for an efficient transformation. The thioamides were converted into the corresponding 5′‐triphosphates 6a and 6b . Compound 6a was chosen for DNA sequencing experiments, and 6b was further labelled with fluorescein (→ 8 ).     

2′‐Deoxy‐7‐propynyl‐7‐deaza­adenosine: a DNA duplex‐stabilizing nucleoside

In the title compound, 2′‐deoxy‐7‐propynyl‐7‐deaza­adenosine, C₁₄H₁₆N₄O₃, the torsion angle of the N‐glycosylic bond is anti [χ = −130.7 (2)°]. The sugar pucker of the 2′‐deoxy­ribo­furanosyl moiety is C2′‐endo–C3′‐exo, ²T₃ (S‐type), with P = 185.9 (2)° and τ_m = 39.1 (1)°, and the orientation of the exocyclic C4′—C5′ bond is −ap (trans). The 7‐substituted propynyl group is nearly coplanar with the heterocyclic base moiety. Mol­ecules of the nucleoside form a layered network in which the heterocyclic bases are stacked head‐to‐tail with a closest distance of 3.197 (1) Å. The crystal structure of the nucleoside is stabilized by three inter­molecular hydrogen bonds of types N—H⋯ O, O—H⋯ N and O—H⋯ O.     

The α‐d anomer of 5‐aza‐7‐deaza‐2′‐deoxyguanosine

In the monohydrate of 2‐amino‐8‐(2‐deoxy‐α‐d ‐erythro‐pento­furan­osyl)‐8H‐imidazo­[1,2‐a]­[1,3,5]­triazin‐4‐one, C₁₀H₁₃N₅O₄·H₂O, denoted (I) or αZ_d, the conformation of the N‐gly­cosyl­ic bond is in the high‐anti range [χ = 87.5 (3)°]. The 2′‐deoxy­ribo­furan­ose moiety adopts a C2′‐endo,C3′‐exo(^2′T_3′) sugar puckering (S‐type sugar) and the conformation at the C4′—C5′ bond is ?sc (trans).