Design of new quinolin-2-one-pyrimidine hybrids as sphingosine kinases inhibitors.

Sphingosine-1-phosphate is now emerging as an important player in cancer, inflammation, autoimmune, neurological and cardiovascular disorders. Abundance evidence in animal and humans cancer models has shown that SphK1 is linked to cancer. Thus, there is a great interest in the development new SphK1 inhibitors as a potential new treatment for cancer. In a search for new SphK1 inhibitors we selected the well-known SKI-II inhibitor as the starting structure and we synthesized a new inhibitor structurally related to SKI-II with a significant but moderate inhibitory effect. In a second approach, based on our molecular modeling results, we designed new structures based on the structure of PF-543, the most potent known SphK1 inhibitor. Using this approach, we report the design, synthesis and biological evaluation of a new series of compounds with inhibitory activity against both SphK1 and SphK2. These new inhibitors were obtained incorporating new connecting chains between their polar heads and hydrophobic tails. On the other hand, the combined techniques of molecular dynamics simulations and QTAIM calculations provided complete and detailed information about the molecular interactions that stabilize the different complexes of these new inhibitors with the active sites of the SphK1. This information will be useful in the design of new SphK inhibitors.

A new series of antibacterial nitrosopyrimidines: synthesis and structure-activity relationship.

New nitrosopyrimidines were synthesized and evaluated as potential antibacterial agents. Different compounds structurally related with 4,6-bis(alkyl or arylamino)-5-nitrosopyrimidines were evaluated. Some of these nitrosopyrimidines displayed significant antibacterial activity against human pathogenic bacteria. Among them compounds 1c, 2a-c, and 9a-c exhibited remarkable activity against methicillin-sensitive and -resistant Staphylococcus aureus, Escherichia coli, Yersinia enterocolitica, and Salmonella enteritidis. A detailed structure-activity relationship study, supported by theoretical calculations, aided us to identify and understand the minimal structural requirements for the antibacterial action of the nitrosopyrimidines reported here. Thus, our results have led us to identify a topographical template that provides a guide for the design of new nitrosopyrimidines with antibacterial effects.

Structure-activity relationship study of nitrosopyrimidines acting as antifungal agents.

The design, synthesis, in vitro evaluation, and conformational study of nitrosopyrimidine derivatives acting as antifungal agents are reported. Different compounds structurally related with 4,6-bis(alkyl or arylamino)-5-nitrosopyrimidines were evaluated. Some of these nitrosopyrimidines have displayed a significant antifungal activity against human pathogenic strains. In this paper, we report a new group of nitrosopyrimidines acting as antifungal agents. Among them, compounds 2a, 2b and 15, the latter obtained from a molecular modeling study, exhibited antifungal activity against Candida albicans, Candida tropicalis and Cryptococcus neoformans. We have performed a conformational and electronic analysis on these compounds by using quantum mechanics calculations in conjunction with Molecular Electrostatic Potentials (MEP) obtained from B3LYP/6-31G(d) calculations. Our experimental and theoretical results have led us to identify a topographical template which may provide a guide for the design of new nitrosopyrimidines with antifungal effects.

2-Amino-6-methoxy-4-(4-methylanilino)-5-nitrosopyrimidine and ethyl N-[4-(adamantan-1-ylamino)-2-amino-5-nitrosopyrimidin-6-yl]-3-aminopropionate: polarized electronic structures and hydrogen-bonded supramolecular assembly in one and two dimensions.

In both 2-amino-6-methoxy-4-(4-methylanilino)-5-nitrosopyrimidine, C(12)H(13)N(5)O(2), (I), and ethyl N-[4-(1-adamantylamino)-2-amino-5-nitrosopyrimidin-6-yl]-3-aminopropionate, C(19)H(28)N(6)O(3), (II), the nitrosopyrimidine unit is planar and the bond distances provide evidence for significant polarization of the electronic structures. In (II), the ethoxycarbonyl fragment of the molecule is disordered over two sets of sites with occupancies of 0.910 (4) and 0.090 (4). In the molecules of both compounds, there is an intramolecular N-H···O hydrogen bond. The molecules of (I) are linked into a chain of rings by a combination of N-H···O and C-H···O hydrogen bonds, while the molecules of (II) are linked by a two-centre N-H···N hydrogen bond and a three-centre N-H···(N,O) hydrogen bond to form sheets containing four distinct types of ring.

N6-substituted 2-amino-4-chloro-5-formylpyrimidines: puckered versus planar pyrimidine rings, and hydrogen-bonded aggregation in zero, one, two and three dimensions.

The structures of 12 new N(6)-substituted 2-amino-4-chloro-5-formylpyrimidines, where the N(6) substituent is of the type NHR or NR(1)R(2), have been determined. The intramolecular dimensions provide strong evidence for the development of polarized, charge-separated molecular-electronic structures, with the positive charge delocalized over the two exocyclic amino N atoms and with negative charge on the formyl O atom. This polarization appears to be independent of the significant puckering, in seven of the compounds, of the pyrimidine rings from planarity towards boat, twist-boat or screw-boat conformations. In 11 of the compounds studied here, N-H...N hydrogen bonds link pairs of molecules into centrosymmetric R2(2)(8) dimer units, and their overall crystal structures are determined by the patterns of hydrogen bonds by which these units are further linked. Examples are reported in which no further hydrogen bonding occurs; in which the R2(2)(8) dimers are linked into chains of rings, or into sheets; and in which sheets are formed by the pi-stacking of hydrogen-bonded chains of rings. In the sole structure lacking the R2(2)(8) dimer motif, N-H...O and N-H...N hydrogen bonds cooperate to generate a three-dimensional framework structure.

Anhydrous versus hydrated N4-substituted 1H-pyrazolo[3,4-d]pyrimidine-4,6-diamines: hydrogen bonding in two and three dimensions.

Ten new N(4)-substituted 1H-pyrazolo[3,4-d]pyrimidine-4,6-diamines have been synthesized and the structures of nine of them are reported here, falling into two clear groups, those which are stoichiometric hydrates and those which crystallize in solvent-free forms. In each of N(4)-methyl-N(4)-phenyl-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine, C(12)H(12)N(6) (I), N(4)-cyclohexyl-N(4)-methyl-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine, C(12)H(18)N(6) (II), and N(4)-(3-chlorophenyl)-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine, C(11)H(9)ClN(6) (III), the molecules are linked into hydrogen-bonded sheets. The molecules of 2-{4-(6-amino-1H-pyrazolo[3,4-d]pyrimidin-4-yl)piperazin-1-yl}ethanol, C(11)H(17)N(7)O (IV), are linked into a three-dimensional framework, while the structure of N(4)-methyl-N(4)-(4-methylphenyl)-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine monohydrate, C(13)H(14)N(6) x H(2)O (V), is only two-dimensional despite the presence of five independent hydrogen bonds. The stoichiometric hemihydrates N(4)-ethyl-N(4)-phenyl-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine hemihydrate, C(13)H(14)N(6) x 0.5 H(2)O (VI) and N(4)-(4-methoxyphenyl)-N(4)-methyl-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine hemihydrate, C(13)H(14)N(6)O x 0.5 H(2)O (VII), exhibit remarkably similar sheet structures, despite different space groups and Z' values, Z' = 0.5 in C2/c for (VI) and Z' = 1 in P1 for (VII). N(4)-4-Benzyl-N(4)-phenyl-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine monohydrate, C(18)H(16)N(6) x H(2)O (VIII), crystallizes with Z' = 2 in P2(1)/n, and the four independent molecular components are linked into sheets by a total of 11 intermolecular hydrogen bonds. The sheet structure in {4-(pyrrolidin-1-yl)-1H-pyrazolo[3,4-d]pyrimidine-6-amine} ethanol hemisolvate hemihydrate, C(9)H(12)N(6).0.5C(2)H(6)O x 0.5 H(2)O (IX), is built from the pyrimidine and water components only; it contains eight independent hydrogen bonds, and it very closely mimics the sheets in (VI) and (VII); the ethanol molecules are pendent from these sheets. The N(4)-alkyl-N(4)-aryl-4-aminopyrazolopyrimidine molecules in (I), (V)-(VIII) all adopt very similar conformations, dominated in each case by an intramolecular C-H...pi(arene) hydrogen bond: this interaction is absent from (III) where the molecular conformation is entirely different and probably dominated by the intermolecular hydrogen bonds.

Hydrogen-bonded ribbons in ethyl (E)-3-[2-amino-4,6-bis(dimethylamino)pyrimidin-5-yl]-2-cyanoacrylate and 2-[(2-amino-4,6-di-1-piperidylpyrimidin-5-yl)methylene]malononitrile.

The pyrimidine rings in ethyl (E)-3-[2-amino-4,6-bis(dimethylamino)pyrimidin-5-yl]-2-cyanoacrylate, C(14)H(20)N(6)O(2), (I), and 2-[(2-amino-4,6-di-1-piperidylpyrimidin-5-yl)methylene]malononitrile, C(18)H(23)N(7), (II), which crystallizes with Z' = 2 in the P1 space group, are both nonplanar with boat conformations. The molecules of (I) are linked by a combination of N-H...N and N-H...O hydrogen bonds into chains of edge-fused R(2)(2)(8) and R(4)(4)(20) rings, while the two independent molecules in (II) are linked by four N-H...N hydrogen bonds into chains of edge-fused R(2)(2)(8) and R(2)(2)(20) rings. This study illustrates both the readiness with which highly-substituted pyrimidine rings can be distorted from planarity and the significant differences between the supramolecular aggregation in two rather similar compounds.

Four products from the cyanoacetylation of pyrimidines: hydrogen-bonded dimers, pi-stacked hydrogen-bonded chains and hydrogen-bonded chains of edge-fused rings.

The molecules of 2-[6-amino-3-methyl-2-(methylsulfanyl)-4-oxo-3,4-dihydropyrimidin-5-ylcarbonyl]acetonitrile, C(9)H(10)N(4)O(2)S, (I), are linked in pairs by N-H...O hydrogen bonds to form cyclic centrosymmetric R(2)(2)(4) dimers. Similar dimers formed by 2-(6-amino-1,3-dimethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-ylcarbonyl)acetonitrile, C(9)H(10)N(4)O(3), (II), are reinforced by paired N-H...N hydrogen bonds and linked into chains of rings by C-H...O hydrogen bonds. The molecules of 2-cyano-N-[6-methoxy-2-(methylsulfanyl)pyrimidin-4-yl]acetamide, C(9)H(10)N(4)O(2)S, (III), are linked into simple C(6) chains by an N-H...N hydrogen bond, and the chains are weakly linked into sheets by a pi-pi stacking interaction. A combination of one two-centre N-H...N hydrogen bond and one three-centre C-H...(N,O) hydrogen bond links the molecules of 2-cyano-N-[6-chloro-2-(methylsulfanyl)pyrimidin-4-yl]acetamide, C(8)H(7)ClN(4)OS, (IV), into a chain of alternating edge-fused R(2)(1)(6) and R(1)(2)(6) rings. The crystal structures reported in this study, and those of some related examples from the recent literature, show a wide variation in hydrogen-bonded aggregation consequent upon rather small changes in molecular constitution.

A concise synthesis of a highly substituted 6-(1H-benzimidazol-1-yl)-5-nitrosopyrimidin-2-amine: synthetic sequence and the molecular and supramolecular structures of one product and two intermediates.

A concise and efficient synthesis of 6-benzimidazolyl-5-nitrosopyrimidines has been developed using Schiff base-type intermediates derived from N4-(2-aminophenyl)-6-methoxy-5-nitrosopyrimidine-2,4-diamine. 6-Methoxy-N4-{2-[(4-methylbenzylidene)amino]phenyl}-5-nitrosopyrimidine-2,4-diamine, (I), and N4-{2-[(ethoxymethylidene)amino]phenyl}-6-methoxy-5-nitrosopyrimidine-2,4-diamine, (III), both crystallize from dimethyl sulfoxide solution as the 1:1 solvates C19H18N6O2·C2H6OS, (Ia), and C14H16N6O3·C2H6OS, (IIIa), respectively. The interatomic distances in these intermediates indicate significant electronic polarization within the substituted pyrimidine system. In each of (Ia) and (IIIa), intermolecular N-H...O hydrogen bonds generate centrosymmetric four-molecule aggregates. Oxidative ring closure of intermediate (I), effected using ammonium hexanitratocerate(IV), produced 4-methoxy-6-[2-(4-methylphenyl-1H-benzimidazol-1-yl]-5-nitrosopyrimidin-2-amine, C19H16N6O2, (II) [Cobo et al. (2018). Private communication (CCDC 1830889). CCDC, Cambridge, England], where the extent of electronic polarization is much less than in (Ia) and (IIIa). A combination of N-H...N and C-H...O hydrogen bonds links the molecules of (II) into complex sheets.

A three-dimensional hydrogen-bonded framework in 2-amino-4,6-bis[N-methyl-N-(4-methylphenyl)amino]pyrimidine-5-carbaldehyde and hydrogen-bonded sheets in 2-amino-4-(indolin-1-yl)-6-methoxypyrimidine-5-carbaldehyde.

The molecules of 2-amino-4,6-bis[N-methyl-N-(4-methylphenyl)amino]pyrimidine-5-carbaldehyde, C(21)H(23)N(5)O, (I), and 2-amino-4-(indolin-1-yl)-6-methoxypyrimidine-5-carbaldehyde, C(14)H(14)N(4)O(2), (II), which crystallizes with Z' = 2 in the space group P\overline{1}, exhibit polarized electronic structures. Molecules of (I) are linked by a combination of N-H...O, C-H...O and C-H...pi(arene) hydrogen bonds into a three-dimensional framework structure, while those of (II) are linked into sheets by a combination of two N-H...O hydrogen bonds and one N-H...pi(arene) hydrogen bond.

Synthesis and structure-activity relationship study of potent cytotoxic analogues of the marine alkaloid Lamellarin D.

The marine alkaloid, Lamellarin D (Lam-D), has shown potent cytotoxicity in numerous cancer cell lines and was recently identified as a potent topoisomerase I inhibitor. A library of open lactone analogues of Lam-D was prepared from a methyl 5,6-dihydropyrrolo[2,1-a]isoquinoline-3-carboxylate scaffold (1) by introducing various aryl groups through sequential and regioselective bromination, followed by Pd(0)-catalyzed Suzuki cross-coupling chemistry. The compounds were obtained in a 24-44% overall yield, and tested in a panel of three human tumor cell lines, MDA-MB-231 (breast), A-549 (lung), and HT-29 (colon), to evaluate their cytotoxic potential. From these data, the SAR study concluded that more than 75% of the open-chain Lam-D analogues tested showed cytotoxicity in a low micromolar GI50 range.

Modular total synthesis of lamellarin D.

[Chemical reaction: see text] A modular total synthesis of lamellarin D, a marine alkaloid with potent cytotoxic as well as topoisomerase I inhibition properties, has been accomplished. A sequential and regioselective bromination/Suzuki cross-coupling procedure was applied for the introduction of aryl groups at positions 1 and 2 of scaffold 1. Microwave-assisted 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) oxidation to yield pyrroloisoquinoline 15, followed by phenol group deprotection and subsequent lactonization, gave lamellarin D (18% in eight steps from 1).

2-amino-5-nitro-4,6-dipiperidinopyrimidinium hydrogensulfate monohydrate: hydrogen-bonded sheets containing highly distorted cations.

In the title compound, C(14)H(23)N(6)O(2)(+) x HSO(4)(-) x H(2)O, the pyrimidinium ring of the cation adopts a twist-boat conformation, induced by steric clashes between adjacent ring substituents; the anions and the water molecules are linked by three O-H.O hydrogen bonds [H...O = 1.70-1.78 A, O...O = 2.548 (2)-2.761 (2) A and O-H...O = 161-168 degrees ] into chains of edge-fused R(4)(4)(12) rings, which are linked into sheets by the cations, via three N-H...O hydrogen bonds [H...O = 1.96-2.17 A, N...O = 2.820 (2)-2.935 (2) A and N-H...O = 145-173 degrees ].

Benzylation and nitrosation of 4-amino-2-(methylsulfanyl)pyrimidin-6(1H)-one: two P2(1)/c polymorphs of 4-amino-1-benzyl-2-(methylsulfanyl)pyrimidin-6(1H)-one with Z' = 1 and 2, 4-amino-6-benzyloxy-2-(methylsulfanyl)pyrimidine and 4-amino-1-benzyl-2-(methylsulfanyl)-5-nitrosopyrimidin-6(1H)-one all give different hydrogen-bonded supramolecular structures.

4-Amino-1-benzyl-2-(methylsulfanyl)pyrimidin-6(1H)-one, C(12)H(13)N(3)OS, crystallizes in two polymorphic forms, both having space group P2(1)/c, with Z' = 1 for form (I) and Z' = 2 for form (II). In (I), the molecules are linked by a single N-H.O hydrogen bond into simple C(6) chains, which are themselves linked into sheets by aromatic pi-pi interactions, while in (II), chains of edge-fused R(4)(2)(8) and R(4)(4)(24) rings are generated by four distinct N-H.O hydrogen bonds. In 4-amino-1-benzyl-2-(methylsulfanyl)-5-nitrosopyrimidin-6(1H)-one, C(12)H(12)N(4)O(2)S, (III), where Z' = 2, two independent three-centre N-H.(N,O) hydrogen bonds generate a C(5)C(6)[R(1)(2)(5)] chain of rings. In 4-amino-6-benzyloxy-2-(methylsulfanyl)pyrimidine, C(12)H(13)N(3)OS, (IV), which is isomeric with (I) and (II), a combination of N-H.N and N-H.O hydrogen bonds generates a sheet of alternating R(2)(2)(8) and R(6)(6)(28) rings.

Hydrogen bonding in 2-amino-4,6-dimethoxypyrimidine, 2-benzylamino-4,6-bis(benzyloxy)pyrimidine and 2-amino-4,6-bis(N-pyrrolidino)pyrimidine: chains of fused rings and a centrosymmetric dimer.

Molecules of 2-amino-4,6-dimethoxypyrimidine, C(6)H(9)N(3)O(2), (I), are linked by two N-H.N hydrogen bonds [H.N 2.23 and 2.50 A, N.N 3.106 (2) and 3.261 (2) A, and N-H.N 171 and 145 degrees ] into a chain of fused rings, where alternate rings are generated by centres of inversion and twofold rotation axes. Adjacent chains are linked by aromatic pi-pi-stacking interactions to form a three-dimensional framework. In 2-benzylamino-4,6-bis(benzyloxy)pyrimidine, C(25)H(23)N(3)O(2), (II), the molecules are linked into centrosymmetric R(2)(2)(8) dimers by paired N-H.N hydrogen bonds [H.N 2.13 A, N.N 2.997 (2) A and N-H.N 170 degrees ]. Molecules of 2-amino-4,6-bis(N-pyrrolidino)pyrimidine, C(12)H(19)N(5), (III), are linked by two N-H.N hydrogen bonds [H.N 2.34 and 2.38 A, N.N 3.186 (2) and 3.254 (2) A, and N-H.N 163 and 170 degrees ] into a chain of fused rings similar to that in (I).

4-Amino-6-benzyloxy-2-(methylsulfanyl)-5-nitrosopyrimidine: hydrogen-bonded dimers linked into pi-stacked chains.

The title compound, C(12)H(12)N(4)O(2)S, crystallizes with Z' = 2 in space group P2(1)/c. The intramolecular dimensions are consistent with a highly polarized electronic structure. Each of the independent molecules forms a centrosymmetric dimer linked by paired N-H.N hydrogen bonds, and these dimers are linked into a single type of chain by aromatic pi-pi-stacking interactions.

Symmetrically 4,6-disubstituted 2-aminopyrimidines and 2-amino-5-nitrosopyrimidines: interplay of molecular, molecular-electronic and supramolecular structures.

The structures of six symmetrically 4,6-disubstituted 2-aminopyrimidines, four of them containing a 5-nitroso substituent, have been determined. The nitroso compounds, in particular, exhibit polarized molecular-electronic structures leading to extensive charge-assisted hydrogen bonding. The intermolecular interactions observed include hard hydrogen bonds of N-H...N and N-H...O types together with O-H...O and O-H...N types in 2-amino-4,6-bis(2-hydroxyethylamino)-5-nitrosopyrimidine; soft hydrogen bonds of the C-H...O type in both 2-amino-4,6-bis(morpholino)-5-nitrosopyrimidine (3) and 2-amino-4,6-bis(benzylamino)-5-nitrosopyrimidine (4), and of the C-H...pi(arene) type in both 2-amino-4,6-bis(piperidino)pyrimidine (1) and 2-amino-5-nitroso-4,6-bis(3-pyridylmethoxy)pyrimidine (5); and aromatic pi...pi stacking interactions in 2-amino-5-nitroso-4,6-bis(3-pyridylmethoxy)pyrimidine. The supramolecular structures formed by the hard hydrogen bonds are finite, zero-dimensional in (1), one-dimensional in 2-amino-4,6-bis(3-pyridylmethoxy)pyrimidine (2), two-dimensional in both (3) and (4), and three-dimensional in both (5) and 2-amino-4,6-bis(2-hydroxyethylamino)-5-nitrosopyrimidine.

2-Amino-4,6-dimethoxy-5-nitrosopyrimidine-water (4/3): seven independent molecular components are linked into a three-dimensional framework by six three-centre and eight two-centre hydrogen bonds.

In the title compound, 4C(6)H(8)N(4)O(3).3H(2)O, the pyrimidine molecules all exhibit a polarized molecular electronic structure; the seven-component asymmetric unit can be selected as a closed cyclic aggregate and the linking of these aggregates can be analysed in terms of translational chain motifs running parallel to [110], [210] and [011], which combine to generate a single three-dimensional framework.

Amino-substituted O(6)-benzyl-5-nitrosopyrimidines: interplay of molecular, molecular-electronic and supramolecular structures.

The structures of eight 2,4,6-trisubstituted-5-nitrosopyrimidines (one of which crystallizes in two polymorphs) have been determined, including seven O(6)-benzyl derivatives which are potential, or proven, in vitro inhibitors of the human DNA-repair protein O(6)-alkylguanine-DNA-transferase. In the derivatives having an amino substituent at the 4-position, an intramolecular N-H.O hydrogen bond with the nitroso O as an acceptor leads to an overall molecular shape similar to that of substituted purines. There is a marked propensity for these nitroso compounds to crystallize with Z' = 2. The structure of an analogue with no nitroso group is also reported for comparative purposes. Compounds containing the N-alkyl substituents -NHCH(2)COOEt, -NHCH(2)CH(2)COOEt and -NHCH(CH(2)Ph)COOEt, derived from amino acid esters, exhibit a rich variety of conformational behaviour, and in all of the nitroso compounds the bond lengths provide strong evidence for a highly polarized electronic structure. Associated with this polarization is extensive charge-assisted hydrogen bonding between the molecules, leading to supramolecular aggregation in the form of finite (zero-dimensional) aggregates, chains, molecular ladders, sheets and frameworks.