Thermodynamic and Mechanistic Insights into Translesion DNA Synthesis Catalyzed by Y‐Family DNA Polymerase Across a Bulky Double‐Base Lesion of an Antitumor Platinum Drug

To determine how the Y‐family translesion DNA polymerase η (Polη) processes lesions remains fundamental to understanding the molecular origins of the mutagenic translesion bypass. We utilized model systems employing a DNA double‐base lesion derived from 1,2‐GG intrastrand cross‐links of a new antitumor Pt^II complex containing a bulky carrier ligand, namely [PtCl₂(cis‐1,4‐dach)] (DACH=diaminocyclohexane). The catalytic efficiency of Polη for the insertion of correct dCTP, with respect to the other incorrect nucleotides, opposite the 1,2‐GG cross‐link was markedly reduced by the DACH carrier ligand. This reduced efficiency of Polη to incorporate the correct dCTP could be due to a more extensive DNA unstacking and deformation of the minor groove induced in the DNA by the cross‐link of bulky [PtCl₂(cis‐1,4‐dach)]. The major products of the bypass of this double‐base lesion produced by [PtCl₂(cis‐1,4‐dach)] by Polη resulted from misincorporation of dATP opposite the platinated G residues. The results of the present work support the thesis that this misincorporation could be due to sterical effects of the bulkier 1,4‐DACH ligand hindering the formation of the Polη–DNA–incoming nucleotide complex. Calorimetric analysis suggested that thermodynamic factors may contribute to the forces that governed enhanced incorporation of the incorrect dATP by Polη as well.     

Factors Affecting DNA–DNA Interstrand Cross‐Links in the Antiparallel 3′–3′ Sense: A Comparison with the 5′–5′ Directional Isomer

Reported herein is a study of the unusual 3′–3′ 1,4‐GG interstrand cross‐link (IXL) formation in duplex DNA by a series of polynuclear platinum anticancer complexes. To examine the effect of possible preassociation through charge and hydrogen‐bonding effects the closely related compounds [{trans‐PtCl(NH₃)₂}₂(μ‐trans‐Pt(NH₃)₂{NH₂(CH₂)₆NH₂}₂)]⁴⁺ (BBR3464, 1 ), [{trans‐PtCl(NH₃)₂}₂(μ‐NH₂(CH₂)₆NH₂)]²⁺ (BBR3005, 2 ), [{trans‐PtCl(NH₃)₂}₂(μ‐H₂N(CH₂)₃NH₂(CH₂)₄)]³⁺ (BBR3571, 3 ) and [{trans‐PtCl(NH₃)₂}₂{μ‐H₂N(CH₂)₃‐N(COCF₃)(CH₂)₄}]²⁺ (BBR3571‐COCF₃, 4 ) were studied. Two different molecular biology approaches were used to investigate the effect of DNA template upon IXL formation in synthetic 20‐base‐pair duplexes. In the “hybridisation directed” method the monofunctionally adducted top strands were hybridised with their complementary 5′‐end labelled strands; after 24 h the efficiency of interstrand cross‐linking in the 5′–5′ direction was slightly higher than in the 3′–3′ direction. The second method involved “postsynthetic modification” of the intact duplex; significantly less cross‐linking was observed, but again a slight preference for the 5′–5′ duplex was present. 2D [¹H, ¹⁵N] HSQC NMR spectroscopy studies of the reaction of [¹⁵N]‐ 1 with the sequence 5′‐d{TATACATGTATA}₂ allowed direct comparison of the stepwise formation of the 3′–3′ IXL with the previously studied 5′–5′ IXL on the analogous sequence 5′‐d(ATATGTACATAT)₂. Whereas the preassociation and aquation steps were similar, differences were evident at the monofunctional binding step. The reaction did not yield a single distinct 3′–3′ 1,4‐GG IXL, but numerous cross‐linked adducts formed. Similar results were found for the reaction with the dinuclear [¹⁵N]‐ 2 . Molecular dynamics simulations for the 3′–3′ IXLs formed by both 1 and 2 showed a highly distorted structure with evident fraying of the end base pairs and considerable widening of the minor groove.     

Highly Efficient Regio- and Stereoselective Synthesis of β-（1 →6）-Branched β-（1 →3）-Linked Glucohexaose and Its Analogue

A β-（1→）6）-branched β-（1→）3）-linked glucohexaose （1） and its lauryl glycoside （2）, present in many biologically active polysaccharides from traditional herbal medicines such as Ganoderma lucidum, Schizophyllum commune and Lentinus edodes, were highly efficiently synthesized. Coupling of 2,3,4,6-tetra-O-benzoyl-β-D-glucopyranosyl- （1--）3）-2-O-benzoyl-4,6-O-benzylidene-a-D-glucopyranosyl trichloroacetimidate （7） with 3,6-branched acceptors 8 and 12 gave β-（1→）3）-linked pentasaccharides （9） and （13）, then via simple chemical transformation 4＇,6＇-OH pentasaccharide acceptors 10 and 14 were obtained. Regio- and stereoselective coupling of 3 with 10 and 14 gave β-（1→）3）-linked hexasaccharides （11） and （15） as the major products. Deprotection of 11 and 15 provided the target sugar 1 and 2. Thus, a new method for the preparation of this kind of compounds was developed.     

Automated Solid‐Phase Synthesis of a β‐(1,3)‐Glucan Dodecasaccharide

β‐Glucans are a group of structurally heterogeneous polysaccharides found in bacteria, fungi, algae and plants. β‐(1,3)‐D ‐Glucans have been studied in most detail due to their impact on the immune system of vertebrates. The studies into the immunomodulatory properties of these glucans are typically carried out with isolates that contain a heterogeneous mixture of polysaccharides of different chain lengths and varying degrees of branching. In order to determine the structure–activity relationship of β‐(1,3)‐glucans, access to homogeneous, structurally‐defined samples of these oligosaccharides that are only available through chemical synthesis is required. The syntheses of β‐glucans reported to date rely on the classical solution‐phase approach. We describe the first automated solid‐phase synthesis of a β‐glucan oligosaccharide that was made possible by innovating and optimizing the linker and glycosylating agent combination. A β‐(1,3)‐glucan dodecasaccharide was assembled in 56 h in a stereoselective fashion with an average yield of 88 % per step. This automated approach provides means for the fast and efficient assembly of linker‐functionalized mono‐ to dodecasaccharide β‐(1,3)‐glucans required for biological studies.     

A Redox‐Activated G‐Quadruplex DNA Binder Based on a Platinum(IV)–Salphen Complex

There has been increasing interest in the development of small molecules that can selectively bind to G‐quadruplex DNA structures. The latter have been associated with a number of key biological processes and therefore are proposed to be potential targets for drug development. Herein, we report the first example of a reduction‐activated G‐quadruplex DNA binder. We show that a new octahedral platinum(IV)–salphen complex does not interact with DNA in aqueous media at pH 7.4; however, upon addition of bioreductants such as ascorbic acid or glutathione, the compound is readily reduced to the corresponding square planar platinum(II) complex. In contrast to the parent platinum(IV) complex, the in situ generated platinum(II) complex has good affinity for G‐quadruplex DNA.     

Stereoselective Synthesis of the Halaven C14–C26 Fragment from D‐Quinic Acid: Crystallization‐Induced Diastereoselective Transformation of an α‐Methyl Nitrile

Crystallization‐induced diastereoselective transformation (CIDT) of an α‐methyl nitrile completes an entirely non‐chromatographic synthesis of the halichondrin B C14–C26 stereochemical array. The requisite α‐methyl nitrile substrate is derived from D ‐quinic acid through a series of substrate‐controlled stereoselective reactions via a number of crystalline intermediates that benefit from a rigid polycyclic template. Therefore, all four stereogenic centers in the Halaven C14–C26 fragment were derived from the single chiral source D ‐quinic acid.     

A Telomerase‐Responsive DNA Icosahedron for Precise Delivery of Platinum Nanodrugs to Cisplatin‐Resistant Cancer

A telomerase‐responsive DNA icosahedron was designed to precisely release caged platinum nanodrugs into cisplatin‐resistance tumor cells for effective therapy. This DNA icosahedron was constructed from two pyramidal DNA cages connected with telomerase primers and telomeric repeats, and platinum nanodrugs were then encapsulated into the DNA structure. In the presence of telomerase, the primers are extended, leading to inner‐chain substitution of the DNA icosahedron and subsequent release of the caged nanodrugs. This DNA icosahedron can precisely release caged nanodrugs in response to telomerase in tumor cells, giving enhanced anticancer efficacy in drug‐resistant carcinoma and with reduced toxicity to normal tissues. We speculate that this precisely designed, well controlled DNA cage could be generalized to diverse anticancer drugs.     

Synthesis and Crystal Structure of [1‐(η5‐9‐Fluorenyl)‐2‐(η5‐1‐indenyl)ethane]hafnium Dimethyl

The synthesis and characterization of the unsymmetric hafnium dialkyl [1‐(η⁵‐9‐fluorenyl)‐2‐(η⁵‐1‐indenyl)ethane]HfCl₂ ( 2 ) and corresponding dimethyl complex [1‐(η⁵‐9‐fluorenyl)‐2‐(η⁵‐1‐indenyl)ethane]Hf(CH₃)₂ ( 3 ) is described. The dialkyl hafnocene ( 3 ) crystallizes in monoclinic space group P2₁/c (No. 14) with a = 9.458(8), b = 8.541(8), c = 23.733(11) Å, β = 93.16(5) deg., V = 1914(3) ų, Z = 4. Further on, complex 3 was activated with methylaluminiumoxane (MAO) and utilized as a catalyst in ethene polymerization.     

Synthesis of α‐(Fluorophenyl)pyridine by Palladium‐Catalyzed Cross‐Coupling Reaction

A series of α‐(fluoro‐substituted phenyl)pyridines have been synthesized by means of a palladium‐catalyzed cross‐coupling reaction between fluoro‐substituted phenylboronic acid and 2‐bromopyridine or its derivatives. The reactivities of the phenylboronic acids containing di‐ and tri‐fluoro substituents with α‐pyridyl bromide were investigated in different catalyst systems. Unsuccessful results were observed in the Pd/C and PPh₃ catalyst system due to phenylboronic acid containing electron‐withdrawing F atom(s). For the catalyst system of Pd(OAc)₂/PPh₃, the reactions gave moderate yields of 55% –80%, meanwhile, affording 10% –20% of dimerisation (self‐coupling) by‐products, but trace products were obtained in coupling with 2,4‐difluorophenylboronic acids because of steric hinderance. Pd(PPh₃)₄ was more reactive for boronic acids with sterically hindering F atom(s), and the coupling reactions gave good yields of 90% and 91% without any self‐coupling by‐product.     

Enzymatic Synthesis of 7′,5′‐Bicyclo‐DNA Oligonucleotides

The selection of artificial genetic polymers with tailor‐made properties for their application in synthetic biology requires the exploration of new nucleosidic scaffolds that can be used in selection experiments. Herein, we describe the synthesis of a bicyclo‐DNA triphosphate (i.e., 7′,5′‐bc‐TTP) and show its potential to serve for the generation of new xenonucleic acids (XNAs) based on this scaffold. 7′,5′‐bc‐TTP is a good substrate for Therminator DNA polymerase, and up to seven modified units can be incorporated into a growing DNA chain. In addition, this scaffold sustains XNA‐dependent DNA synthesis and potentially also XNA‐dependent XNA synthesis. However, DNA‐dependent XNA synthesis on longer templates is hampered by competitive misincorporation of deoxyadenosine triphosphate (dATP) caused by the slow rate of incorporation of 7′,5′‐bc‐TTP.     

具有β-(1→6)-半乳吡喃糖骨架和α-L-(1→3)-阿拉伯呋喃糖侧链的阿拉伯半乳寡糖的简易合成

4-Methoxyphenyl glycoside of β-D-Galp-(1→6)-[α-L-Araf-(1→3)-]β-D-Galp-(1→6)-β-D-Galp-(1→6)-{β-D-Galp-(1→6)-[α-L-Araf-(1→3)-]β-D-Galp-(1→6)-β-D-Galp-(1→6)-}2β-D-Galp-(1→6)-[α-L-Araf-(1→)3)-]β-D-Galp-(1→)6)-β-D-Galp was synthesized with 2,3,4,6-tetra-O-benzoyl-α-D-galactopyranosyl trichloroacetimidate (1), 6-O-acetyl-2,3,4-tri-O-benzoyl-α-D-galactopyranosyl trichloroacetimidate (11), 4-methoxyphenyl 3-O-allyl-2,4-tri-O-benzoyl-β-D-galactopyranoside (2),isopropyl 3-O-allyl-2,4-tri-O-benzoyl--thio-β-D-galactopyranoside (12),4-methoxyphenyl 2,3,4-tri-O-benzoyl-β-D-galactopyranoside (5), and 2,3,5-tri-O-benzoyl-α-L-arabinofuranosyl trichloroacetimidate (8) as the key synthons.     

Catalytic Enantioselective Synthesis of a 3‐Aryl‐3‐benzyloxindole (=3‐Aryl‐3‐benzyl‐1,3‐dihydro‐2H‐indol‐2‐one) Exhibiting Antitumor Activity

A palladium‐catalyzed intramolecular α‐arylation of an amide in the presence of a bulky chiral N‐heterocyclic carbene ligand is the key step in the first catalytic synthesis of (3R)‐6‐chloro‐3‐(3‐chlorobenzyl)‐1,3‐dihydro‐3‐(3‐methoxyphenyl)‐2H‐indol‐2‐one ((R)‐ 5 ). This oxindole, in racemic form, had been shown previously to be an anticancer agent. (R)‐ 5 was obtained with an overall yield of 45% and with 96% enantioselectivity.     

The Structure of an Archaeal B‐Family DNA Polymerase in Complex with a Chemically Modified Nucleotide

Archaeal B‐family DNA polymerases (DNA pols) are the driving force of cutting‐edge biotechnological applications like next‐generation sequencing. The acceptance of chemically modified nucleotides by DNA pols is key to these technologies. Until now, no structural data have been available for these DNA pols in complex with modified substrates, which could build the basis for understanding interactions between the enzyme and the chemically modified nucleotide and for the further development of next‐generation nucleotides. For the first time, we crystallized an exonuclease‐deficient variant of the wild‐type B‐family KOD DNA pol with a modified nucleotide in a closed, ternary complex. We also crystalized the A‐family DNA pol KlenTaq with the same nucleotide. The reported structural data reveal how the protein and the DNA modulate two distinct conformations of the appended moiety in the A‐ and B‐family DNA pols and how these influence the processing of the modified nucleotide. Overall, this study provides first insight into the interplay between B‐family DNA pols and relevant modified substrates.