Attractive through-space S-O interaction in the DNA-cleaving antitumor antibiotic leinamycin

Exploiting the role of stereoelectronic effects to design the antagonists of the human complement C3a receptor

Stereoelectronic effects are crucial in governing the conformational behaviour of small molecules bearing heterocyclic rings adjacent to amides.

Nature of the E⋯E′ interactions (E, E′ = O, S, Se, and Te) at naphthalene 1,8-positions with fine details of the structures: experimental and theoretical investigations

The nature of E⋯E′ in 1-RE–8-R′E′C₁₀H₆ (E/E′ = O, S, Se and Te) is clarified with the QTAIM approach and NBO analysis, after structural determinations.

Multicomponent, Enantioselective Michael-Michael-Aldol-β-Lactonizations Delivering Complex β-Lactones

Optically active, tertiary amine Lewis bases react with unsaturated acid chlorides to deliver chiral, α,β-unsaturated acylammonium salts. These intermediates participate in a catalytic, enantioselective, three-component process delivering bi- and tricyclic β-lactones through a Michael-Michael-aldol-β-lactonization. In a single operation, the described multicomponent, organocascade process forms complex bi- and tricyclic β-lactones by generating four new bonds, two rings, and up to four contiguous stereocenters. In the racemic series, yields of 22-75% were achieved using 4-pyrrolidinopyridine as Lewis base. In the enantioselective series employing isothiourea catalysts, a kinetic resolution of the initially formed racemic Michael adduct appears operative, providing yields of 46% to quantitative (based on 50% max) with up to 94:6 er. Some evidence for a dynamic kinetic asymmetric transformation for tricyclic-β-lactone 1d was obtained following optimization (yields up to 61%, 94:6 er) through a presumed reversible Michael.

On the properties of S⋯O and S⋯π noncovalent interactions: the analysis of geometry, interaction energy and electron density

We report computational studies on the origin and magnitude of non-covalent S⋯O and S⋯π interactions.

Synthesis and characterization of a small analogue of the anticancer natural product leinamycin

Leinamycin (1) is a Streptomyces-derived natural product that displays nanomolar IC(50) values against human cancer cell lines. In the work described here, we report the synthesis and characterization of a small leinamycin analogue 19 that closely resembles the 'upper-right quadrant' of the natural product, consisting of an alicyclic 1,2-dithiolan-3-one 1-oxide heterocycle connected to an alkene by a two-carbon linker. The results indicate that this small analogue contains the core set of functional groups required to enable thiol-triggered generation of both redox active polysulfides and an episulfonium ion intermediate via the complex reaction cascade first seen in the natural product leinamycin. The small leinamycin analogue 19 caused thiol-triggered oxidative DNA strand cleavage in a manner similar to the natural product, but did not alkyate duplex DNA effectively. This highlights the central role of the 18-membered macrocycle of leinamycin in driving efficient DNA alkylation by the natural product.

The macrocycle of leinamycin imparts hydrolytic stability to the thiol-sensing 1,2-dithiolan-3-one 1-oxide unit of the natural product

Reaction of cellular thiols with the 1,2-dithiolan-3-one 1-oxide moiety of leinamycin triggers the generation of DNA-damaging reactive intermediates. Studies with small, synthetic analogues of leinamycin reveal that the macrocyclic portion of the natural product imparts remarkable hydrolytic stability to the 1,2-dithiolan-3-one 1-oxide heterocycle without substantially compromising its thiol-sensing property.

Thermal solid-state Z/E isomerization of 2-alkylidene-4-oxothiazolidines: Effects of non-covalent interactions

Configurational isomerization of stereo-defined 5-substituted and unsubstituted 2-alkylidene-4-oxothiazolidines 1 in the solid state, giving the Z/E mixtures in various ratios, was investigated by 1H-NMR spectroscopy, X-ray powder crystallography and differential scanning calorimetry (DSC). The Z/E composition can be rationalized in terms of non-covalent interactions, involving intermolecular and intramolecular hydrogen bonding and directional non-bonded 1,5-type S...O interactions. X-Ray powder crystallography, using selected crystalline (Z)-4- oxothiazolidine substrates, revealed transformation to the amorphous state during the irreversible Z ? E process. A correlation between previous results on the Z/E isomerization in solution and now in the solid state was established.

Polar coordinate representation of Hb(rc) versus (h2/8m)nabla2rhob(rc) at BCP in AIM analysis: classification and evaluation of weak to strong interactions

Polar coordinate (R, theta) representation is proposed for the plot of Hb(rc) versus (h2/8m)nabla2rhob(rc) in AIM analysis to classify, evaluate, and understand weak to strong interactions in a unified way and in more detail; Hb(rc) and nabla2rhob(rc) are total electron energy densities and the Laplacian of rhob(rc) at bond critical points (BCPs: rc), respectively, where rhob(rc) are electron densities at rc. Both the x- and y-axes of the plot are expressed in the common unit of energy since Hb(rc) = Gb(rc) + Vb(rc) and (h2/8m)nabla2rhob(rc) = Hb(rc) - Vb(rc)/2 (= Gb(rc) + Vb(rc)/2), where Gb(rc) and Vb(rc) are kinetic energy densities and potential energy densities, respectively. Data employed for the plot are calculated at BCPs for full-optimized structures and optimized structures with the fixed distances (r) of r = r(o) + wa(o), where r(o) are the full-optimized distances, a(o) is the Bohr radius, and w = +/-0.1 and +/-0.2. The plot draws a helical stream starting from near origin (Hb(rc) = (h2/8m)nabla2rhob(rc) = 0) for very weak interactions and turns to the right as interactions become stronger. The helical stream is well described by the polar coordinate representation with (R, theta); R is given in the energy unit, and theta in degrees is measured from the y-axis. The ratio of Vb(rc)/Gb(rc) (= k) controls theta, of which an acceptable range in the plot is 45.0 < theta < 206.6 degrees. Each plot for an interaction gives a curve, which supplies important information. It is expressed by theta(p) and kappa(p); theta(p) corresponds to the tangent line measured from the y-direction, and kappa(p) is the curvature of the plot at w = 0. The polar coordinate (R, theta) representation with (theta(p), kappa(p)) helps us to classify, evaluate, and understand the nature of weak to strong interactions in a unified way.

Crystal and molecular structures of diglycosyl disulfide derivatives

The crystal and molecular structures of S-(2,3,4,6-tetra-O-acetyl-beta-d-glucopyranosyl)-S'-(2,3,4,6-tetra-O-acetyl-beta-d-galactopyranosyl)disulfide (1) and the mono-sulfoxide (3) of bis(2,3,4,6-tetra-O-acetyl-beta-d-glucopyranosyl)disulfide (2) are described. Comparison of 2 and 3, containing -S-S- and -S-S(O)- bonds, respectively, allows to delineate structural differences brought about by the different oxidation states of one of the sulfur atoms in carbohydrate disulfides.

Radical/Ion Pair Formation in the Electrochemical Reduction of Arene Sulfenyl Chlorides

Important aspects of the electrochemical reduction of a series of substituted arene sulfenyl chlorides are investigated. A striking change is observed in the reductive cleavage mechanism as a function of the substituent on the aryl ring of the arene sulfenyl chloride. With p-substituted phenyl chlorides a "sticky" dissociative ET mechanism takes place where a concerted ET mechanism leads to the formation of a radical/anion cluster before decomposition. With o-nitropheyl sulfenyl substituted chlorides a stepwise mechanism is observed where through space S...O interactions play an important role stabilizing both the neutral molecules and their reduced forms. Disulfides are generated through a nucleophilic reaction of the two-electron reduction produced anion (arenethiolate) on the parent molecule. The dissociative electron transfer theory, as well as its extension to the case of strong in-cage interactions between the produced fragments, along with the gas phase chemical quantum calculations results helped rationalize both the observed change in the ET mechanism and the occurrence of the "sticky dissociative" ET mechanism. The radical/anion pair interactions have been determined both in solution as well as in gas phase. This study shows that despite the low magnitude of in-cage interactions in acetonitrile as compared to in the gas phase, their existence strongly affects the kinetics of the involved reactions. It also shows that, as expected, these interactions are reinforced by the existence of strong electron-withdrawing substituents.

Quantification of Intramolecular Nonbonding Interactions in Organochalcogens

Intramolecular nonbonding interactions between chalcogen atoms in a series of ortho substituted arylselenides (S/O...Se-Y, with Y = -Me, -CN, -Cl, and -F) are quantified using the coupled cluster CCSD(T)/cc-pVDZ level of theory. A homodesmic reaction method as well as an ortho-para approach are employed in evaluating the strength of intramolecular interactions. Comparison of the results obtained using the ab initio MP2 method and pure and hybrid density functional theories are performed with that of the coupled cluster values to assess the quality of different density functionals in evaluating the strength of nonbonding interactions. The interaction energies are found to be higher when the thioformyl group acts as the donor and the Se-F bond acts as the acceptor. In a given series with the same donor atom, the strength of the interaction follows the order Me < CN < Cl < F, exhibiting fairly high sensitivity to the group attached to selenium (Se-Y). Analysis of electron density at the S/O...Se bond critical point within the Atoms in Molecule framework shows a very good correlation with the computed intramolecular interaction energies.

Role of sulfur chirality in the chemical processes of biology

Chiral structures profoundly influence chemical and biological processes. While chiral carbon biomolecules have received much attention, chirality is also possible in certain sulfur compounds; just as with carbon, there can be differences in the physiological behavior of chiral sulfur compounds. For instance, one drug enantiomer, Nexium (esomeprazole, a chiral sulfoxide), is used for its superior clinical properties as a proton pump inhibitor over the racemic mixture, Prilosec (Losec, omeprazole). This critical review introduces sulfur stereochemistry and nomenclature, and provides a comprehensive approach to chiral sulfur compounds and their enzymatic reactions in general and secondary metabolism. The major structural types of biological interest are sulfonium salts, sulfoxides, and sulfoximines. (103 references).

Orthogonal Multipolar Interactions in Structural Chemistry and Biology

The past few decades of molecular recognition studies have greatly enhanced our knowledge on apolar, ion-dipole, and hydrogen-bonding interactions. However, much less attention has been given to the role that multipolar interactions, in particular those with orthogonal dipolar alignment, play in organizing a crystal lattice or stabilizing complexes involving biological receptors. By using results from database mining, this review attempts to give an overview of types and structural features of these previously rather overlooked interactions. A number of illustrative examples of these interactions found in X-ray crystal structures of small molecules and protein-ligand complexes demonstrate their propensity and thus potential importance for both, chemical and biological molecular recognition processes.

The Role of Nonbonded Sulfur−Oxygen Interaction in the Dissociative Electron Transfer to Nitro-Substituted Arenesulfenyl Chlorides

The electrochemical reduction of p-nitrophenyl sulfenyl chloride, o-nitrophenyl sulfenyl chloride as well as bis(4-nitrophenyl) disulfide and bis(2-dinitrophenyl) disulfide was investigated in acetonitrile at an inert electrode. Reduction standard potentials as well standard heterogeneous electron-transfer rate constants have been determined using convolution analysis. An unexpected big difference in the thermodynamics and kinetics of the initial electron-transfer process as well as a striking change in the reductive cleavage mechanism of the S-Cl bond as a function of the nitro group position on the aryl ring of the aryl sulfenyl chloride is observed. A computational study at the B3LYP level shows that this difference in behavior is due to the through-space nonbonded S...O interaction in the o-nitrophenyl sulfenyl chloride.

Synthesis and antitumor activity of novel C-8 ester derivatives of leinamycin

A novel series of C-8 ester derivatives of leinamycin are described. Condensation of N-substituted amino acids or carboxylic acids containing polyether moiety with leinamycin resulted in the C-8 ester derivatives with good antitumor activity in several experimental models. Among these derivatives, compound 4e, which has five ethylene glycol ether units in the C-8 acyl group, showed potent antitumor activity against human tumor xenograft. Combination with the modification of the dithiolanone moiety was applied to these C-8 ester derivatives and some of them also showed good antitumor activity.

The role of amine in the mechanism of pentathiepin (polysulfur) antitumor agents

A computational and experimental study is presented, which provides the first evidence that amine has an opportunity to engage in bonding with pentathiepin to promote its decomposition. The study provides mechanistic insight into the process that gives rise to pentathiepin biological activity. Primary or secondary amine will allow for an intramolecular addition to the pentathiepin ring at the nearest sulfur (S1). In contrast, tertiary amine adds reversibly to S1, because nitrogen cannot lose its positive charge by deprotonation. This precludes the amine promotion step. An energetically low-lying process is characterized, corresponding to S3-loss triggered by nucleophilic activation with a primary or secondary amine. Pentathiepin desulfurization via S3-unit transfer is supported by a trapping study with norbornene. That the amine may confer an enhanced reactivity in the natural products varacin, 1, and lissoclinotoxin A, 2, adds to the understanding of the pathway for pentathiepin activation and may provide new design concepts that have potential applications for this class of biocides.

Computational characterization of sulfur-cxygen-bonded sulfuranyl radicals derived from alkyl- and (carboxyalkyl)thiopropionic acids: evidence for sigma-type radicals

Sulfide radical cations are known to stabilize via sulfur-oxygen bond formation with carboxylic acid functions. However, structural information on the resulting sulfuranyl radicals has so far only been provided by ESR spectroscopy for more stable, aromatic-substituted species, while the rather short-lived aliphatic sulfuranyl radicals have largely been characterized by time-resolved UV spectroscopy only. Therefore, we have obtained theoretical structural information on S-O-bonded sulfuranyl radicals from three model compounds, tert-butyl 2-(methylthio)peroxybenzoate, 3-methylthiopropionic acid, and 3,3'-thiodipropionic acid, using density functional theory, semiempirical, and molecular mechanics methods. All S-O-bonded species exist predominantly as three-electron-bonded sigma-radicals with an estimated heterolytic bond dissociation energy of the S therefore O bond on the order of 23-27 kcal mol(-1). Characteristic optical absorption bands, vibrational frequencies, and hyperfine coupling tensors are evaluated to facilitate the identification of such radicals by time-resolved UV, IR, and ESR spectroscopy.