Pyrrolo[2,3-d]pyrimidines and pyrido[2,3-d]pyrimidines as conformationally restricted analogues of the antibacterial agent trimethoprim

The crystal structure of 1-(2-iodo-benzo-yl)-4-(pyrimidin-2-yl)piperazine: a three-dimensional hydrogen-bonded framework, augmented by π-π stacking inter-actions and I⋯N halogen bonds

In 1-(2-iodo-benzo-yl)-4-(pyrimidin-2-yl)piperazine, C15H15IN4O, the central piperazine ring adopts an almost perfect chair conformation with the pyrimidine substituent in an equatorial site. The planar amide unit makes a dihedral angle of 80.44 (7)° with the phenyl ring. A combination of C-H⋯O and C-H⋯π(arene) hydrogen bonds links the mol-ecules into a complex three-dimensional network structure, augmented by a π-π stacking inter-action and an I⋯N halogen bond, all involving different pairs of inversion-related mol-ecules. Comparisons are made with the structures of a number of related compounds.

Structural and Dynamics Perspectives on the Binding of Substrate and Inhibitors in Mycobacterium tuberculosis DHFR

Dihydrofolate reductase (DHFR), an essential enzyme in the folate pathway, is a potential target for new anti-tuberculosis drugs. Fifteen crystal structures of Mycobacterium tuberculosis DHFR complexed with NADPH and various inhibitors are available in the RCSB Protein Data Bank, but none of them is a substrate binding structure. Therefore, we performed molecular dynamics simulations on ternary complexes of M. tuberculosis DHFR:NADPH with a substrate (dihydrofolate) and each of three competitive inhibitors in 2,4-diaminopyrimidine series (P1, P157, and P169), in order to gain insight into the inhibition-mechanism of DHFR in the folate pathway. The binding energy and thermodynamics values of each system were calculated by the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) method. The dynamics of the enzyme and the motion of each amino acid residue at the active site were examined. The key factors that promote the binding of P157 and P169 on M. tuberculosis DHFR (mtbDHFR) reveal opportunities for using these compounds as novel anti-tuberculosis drugs.

CsOH/γ-Al2O3: a heterogeneous reusable basic catalyst for one-pot synthesis of 2-amino-4,6-diaryl pyrimidines

Pyrimidine derivatives were synthesized in one pot using a novel heterogeneous reusable catalyst, and complete characterization of catalyst was performed.

Crystal structures of 4-(pyrimidin-2-yl)piperazin-1-ium chloride and 4-(pyrimidin-2-yl)piperazin-1-ium nitrate

The title salts, C8H13N4 (+)·Cl(-), (I), and C8H13N4 (+)·NO3 (-), (II), contain linked pyridinium-piperazine heterocycles. In both salts, the piperazine ring adopts a chair conformation with protonation at the N atom not linked to the other ring. In the crystal of (I), weak N-H⋯Cl inter-actions are observed, leading to zigzag chains along [100]. In the crystal of (II), both H atoms on the NH2 (+) group form bifurcated N-H⋯(O,O) hydrogen bonds. Weak C-H⋯O inter-actions are also observed. These bonds collectively link the components into infinite chains along [100].

Crystal structure of 3-[4-(pyrimidin-2-yl)piperazin-1-ium-1-yl]butano-ate

The title compound, C12H18N4O2, crystallizes in the zwitterionic form with protonation at the N atom of the piperazine ring bearing the carboxylate group. The piperazine ring adopts a slightly distorted chair conformation. In the crystal, N-H⋯O hydrogen bonds are observed, forming chains along [010]. The packing is consolidated by C-H⋯O inter-actions, which generate a three-dimensional network.

4-(Pyrimidin-2-yl)piperazin-1-ium (E)-3-carb-oxy-prop-2-enoate

In the cation of the title salt, C8H13N4 (+)·C4H3O4 (-), the piperazinium ring adopts a slightly distorteded chair conformation. In the crystal, a single strong O-H⋯O inter-molecular hydrogen bond links the anions, forming chains along the c-axis direction. The chains of anions are linked by the cations, via N-H⋯O hydrogen bonds, forming sheets parallel to (100). These layers are linked by weak C-H⋯O hydrogen bonds, forming a three-dimensional structure. In addition, there are weak π-π inter-actions [centroid-centroid distance = 3.820 (9) Å] present involving inversion-related pyrimidine rings.

Synthesis of triterpenoid triazine derivatives from allobetulone and betulonic acid with biological activities

The synthetic transformation and modification of natural products with the aim to improve the biological properties is an area of current interest. The triterpenoids betulin and betulinic acid are very abundant in nature and now are commercially available. In our study, starting from betulin and betulinic acid, we obtained allobetulone and betulonic acid in a few synthetic steps. The ketone function at the A-ring was used as the starting point for the synthesis of a series of 1,2,4-triazine-fused triterpenoids. The alkylation and Liebeskind-Srogl coupling were used for further substitution of 1,2,4-triazines, and the intramolecular hetero Diels-Alder reaction leads to interesting fused thienopyridine derivatives. All new compounds were tested for their cytostatic activities against murine leukemia L1210, human cervix carcinoma HeLa and human lymphoblast CEM tumor cells. The results show that some triterpenoid triazine betulonic acid derivatives have a promising cytostatic activity in vitro and could be used as potential leads for the development of new type of anti-cancer agents. Several compounds were also endowed with anti-HCMV activity in the low micromolar range.

Synthesis and anticancer activity of some fused pyrimidines and related heterocycles

On account of the reported anticancer of pyrimidine and condensed pyrimidine, a new pyrimido [3,2-b]-1,2,4,5-tetrazine 3a , b , 5c , d , 6, 9, pyrimido [3,2-b]-1,2,4-triazine 10, 11, pyrimido [3,2-b]-1,2,4-triazole 12 and pyrimidine derivatives 1,2a , b , 4c , d , 8, 13, 14, 15 and 16 were synthesized through different chemical reactions. Structures of all synthesized compounds were supported by spectral and elemental analyses. The obtained compounds were evaluated for their in vitro antitumor activity against human liver cancer cell line (HEPG2).

Thioxopyrimidine in Heterocyclic Synthesis I: Synthesis of Some Novel 6-(Heteroatom-substituted)-(thio)pyrimidine Derivatives

A series of novel N-cycloalkanes, morpholine, piperazines, pyrazole, pyrimidine, benzimidazolo[1,2-a]pyrimidine, 1,2,3,4-tetrazolo[1,5-a]pyrimidine, azopyrazolo[1,5- a]pyrimidine, pyrimido[4', 5':3,4]pyrazolo[1,5-a]pyrimidines and pyridine derivatives incorporating a 5-cyano-4-methyl-2-phenyl-(thio)pyrimidine moiety were obtained by the intramolecular cyclization of 6-methylthio-pyrimidine, 6-(benzoylmethyl)thio- pyrimidine and 2-[(5-cyano-4-methyl-2-phenylpyrimidin-6-yl)thio]-3-dimethyl- amino-1-phenyl-prop-2-en-1-one with appropriate amines and enaminone compounds, respectively. The structure of all new synthesized compounds was established from their spectral data, elemental analysis and the X-ray crystal analysis.

Exploration of antimicrobial and antioxidant potential of newly synthesized 2,3-disubstituted quinazoline-4(3H)-ones

A series of 2-(chloromethyl)-3-(4-methyl-6-oxo-5-[(E)-phenyldiazenyl]-2-thioxo-5,6-dihydropyrimidine-1(2H)-yl)quinazoline-4(3H)-ones 9a-j was synthesized by treating 2-(chloroacetyl)amino benzoic acid with 3-amino-6-methyl-5-[(E)-phenyldiazenyl]-2-thioxo-2,5-dihydropyrimidine-4(3H)-one 8a-j and was screened for in vitro antibacterial activities against a representative panel of Gram-positive and Gram-negative bacteria. The compounds were synthesized in excellent yields and the structures were corroborated on the basis of IR, (1)H NMR, Mass and elemental analysis data. All the synthesized compounds elicited the potent inhibitory action against all the tested bacterial stains. Furthermore, in order to explore the antioxidant potential of newly synthesized compounds, the free radical scavenging activity measurement were performed by the 1,1-diphenyl-2-picryl-hydrazyl (DPPH) assay method. It is revealed from the antioxidant screening results that the compounds 9c and f manifested profound antioxidant potential.

The Z isomer of 2,4-diaminofuro[2,3-d]pyrimidine antifolate promotes unusual crystal packing in a human dihydrofolate reductase ternary complex

The crystal structure of the ternary complex of human dihydrofolate reductase (hDHFR) with NADPH and the Z isomer of 2,4-diamino-5-[2-(2'-methoxyphenyl)propenyl]-furo[2,3-d]pyrimidine (Z1) shows that the Z isomer binds in the normal antifolate orientation in which the furo oxygen occupies the 8-amino position observed in the binding of 2,4-diaminopteridine antifolates such as methotrexate and with the methoxyphenyl moiety cis to and coplanar with the furo[2,3-d]pyrimidine ring. The hDHFR ternary complex crystallized in the orthorhombic space group P2(1)2(1)2(1) and its structure was refined to 1.7 A resolution. Although other hDHFR complexes crystallize in this space group, these data provide only the second example of an unusual packing arrangement in which the conserved active-site Arg70 forms a salt bridge to the side chain of Glu44 from a symmetry-related molecule. As a result, the conformations of Phe31 and Gln35 shift with respect to those observed in the structure of mouse DHFR bound to Z1, which crystallizes in the monoclinic space group P2(1) and shows that Gln35 interacts with Arg70.

New 3,7-dihydro-4H-pyrazolo[3′,4′:2,3]pyrido[4,5-d]pyrimidin-4-ones

Thirteen novel pyrazolo[3″,4″:2,3]pyrido[4,5-d]pyrimidin-4-ones 7a–m were synthesised via tandem aza-Wittig and annulation reactions of the corresponding iminophosphoranes 5, phenylisocyanate, and substituted amine in 56–86% yields. Their structures were verified by IR, 1H NMR, EI-MS spectroscopy and elemental analysis. Preliminary bioassay indicated that some compounds possess inhibition activity against Brassica napus (rape) and Echinochloa crusgalli (barnyard grass).

Synthesis and antibacterial activity of a new series of 2,3,5,7-substituted-pyrido[2,3-d]pyrimidin-4(3h)-one derivatives

A new series of 2,3,5,7-substituted-pyrido[2,3-d]pyrimidin-4(3H)-one derivatives were prepared from 2-amino-N,6-substituted phenyl-4-(trifluoromethyl or methyl)nicotinamides. The key intermediate 2-amino-N,6-substituted phenyl-4-(trifluoromethyl or methyl)nicotinamides were synthesized from 2-bromo-N,6-disubstituted phenyl-4-(trifluoromethyl or methyl)nicotinamides as well as from ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) coupling of 2-amino-4,6-substituted nicotinic acid and substituted arylamines. All the synthesized compounds were screened for antibacterial activity against Gram +ve and Gram -ve bacteria. Compound 7c showed better antibacterial activity against Gram +ve and Gram -ve bacteria.

Dual inhibitors of thymidylate synthase and dihydrofolate reductase as antitumor agents: design, synthesis, and biological evaluation of classical and nonclassical pyrrolo[2,3-d]pyrimidine antifolates(1)

We designed and synthesized a classical analogue N-[4-[(2-amino-6-ethyl-3,4-dihydro-4-oxo-7H-pyrrolo[2,3-d]pyrimidin-5-yl)thio]benzoyl]-L-glutamic acid (4) and thirteen nonclassical analogues 5-17 as potential dual thymidylate synthase (TS) and dihydrofolate reductase (DHFR) inhibitors and as antitumor agents. The key intermediate in their synthesis was 2-amino-6-ethyl-3,4-dihydro-4-oxo-7H-pyrrolo[2,3-d]pyrimidine, 22, to which various aryl thiols were conveniently attached at the 5-position via an oxidative addition reaction using iodine. For the classical analogue 4, the ester obtained from the reaction was deprotected and coupled with diethyl L-glutamate followed by saponification. Compound 4 was a potent dual inhibitor of human TS (IC(50) = 90 nM) and human DHFR (IC(50) = 420 nM). Compound 4 was not a substrate for human FPGS. Metabolite protection studies established TS as its principal target. Most of the nonclassical analogues were only inhibitors of human TS with IC(50) values of 0.23-26 microM.

Lewis acid-promoted transformation of 2-alkoxypyridines into 2-aminopyridines and their antibacterial activity. Part 2: Remarkably facile C–N bond formation

2-Alkoxy-3-cyano-4,6-diarylpyridines 1a,b which were synthesized by condensation of alpha,beta-unsaturated ketones with malononitrils were subjected to Lewis acid-catalyzed nucleophilic displacement reaction with various amines to afford the corresponding 2-aminopyridines 3-21. The potency of the results as antibacterial agents has been evaluated. The structure of the newly prepared compounds was assessed by microanalysis, IR, and NMR spectra. Molecular modeling and QSAR methods are used to study the antibacterial activity of the active compounds by means of the molecular mechanic method.

Adaptive neuro-fuzzy inference system: an instant and architecture-free predictor for improved QSAR studies

The application of an adaptive neuro-fuzzy inference system (ANFIS) has been developed for obtaining sufficient quantitative structure-activity relationships (QSAR) with high accuracy. To this end, a data set of 68 pyrimidines derivatives as DHFR inhibitors, described first in the excellent independent studies of Hansch et al. (J. Med. Chem. 1982, 25, 777-784 and J. Med. Chem. 1991, 34, 46-54) and later by So and Richards (J. Med. Chem. 1992, 35, 3201-3207), was examined. The ANFIS system, first time applied in the literature to QSAR studies, was trained using a hybrid algorithm consisting of back-propagation and least-squares estimation while the optimum number and shape of membership functions were obtained through the subtractive clustering algorithm. Prior to the development and evaluation of the ANFIS system, geometry optimization of the examined compounds was performed, deriving a series of diverse descriptors from which the best subset was selected by using a hybrid genetic algorithm system. The predictive abilities of the resulting models compared to those produced from classical multivariate regression such as linear and nonlinear (quadratic) partial least squares regression (PLS and QPLS, respectively). The ANFIS method outperformed both the PLS models as well as the published results, leading to substantial gain in both the prediction ability and the computation speed (almost instant training).

Design, synthesis, and X-ray crystal structure of a potent dual inhibitor of thymidylate synthase and dihydrofolate reductase as an antitumor agent

A novel N-¿2-amino-4-methyl[(pyrrolo[2, 3-d]pyrimidin-5-yl)ethyl]benzoyl¿-L-glutamic acid (3a) was designed and synthesized as a potent dual inhibitor of thymidylate synthase (TS) and dihydrofolate reductase (DHFR) and as an antitumor agent. Compound 3b, the N7-benzylated analogue of 3a, was also synthesized as an antitumor agent. The synthesis of 3a was accomplished via a 12-step sequence which involved the synthesis of 2-amino-4-methylpyrrolo[2,3-d]pyrimidine (10) in 5 steps from 2-acetylbutyrolactone. Protection of the 2-amino group of 10 and regioselective iodination at the 5-position followed by palladium-catalyzed coupling afforded intermediate 14 which was converted to 3a by reduction and saponification. Similar synthetic methodology was used for 3b. X-ray crystal structure of the ternary complex of 3a, DHFR, and NADPH showed that the pyrrolo[2, 3-d]pyrimidine ring binds in a "2,4-diamino mode" in which the pyrrole nitrogen mimics the 4-amino moiety of 2,4-diaminopyrimidines. This is the first example of a classical pyrrolo[2,3-d]pyrimidine antifolate shown to have this alternate mode of binding to DHFR. Compounds 3a and 3b were more inhibitory than LY231514 against TS from Lactobacillus casei and Escherichia coli. Analogue 3a was also more inhibitory against DHFR from human, Toxoplasma gondii, and Pneumocystis carinii. Evaluation of 3a against methotrexate (MTX)-resistant cell lines with defined mechanisms indicated that cross-resistance of 3a was much lower than that of MTX. Metabolite protection studies and folylpoly-gamma-glutamate synthetase studies suggest that the antitumor activity of 3a against the growth of tumor cells in culture is a result of dual inhibition of TS and DHFR. Compound 3a inhibited the growth of CCRF-CEM and FaDu cells in culture at ED(50) values of 12.5 and 7.0 nM, respectively, and was more active against FaDu cells than MTX. In contrast, compound 3b was inactive against both cell lines. Compound 3a was evaluated in the National Cancer Institute in vitro preclinical antitumor screening program and afforded IG(50) values in the nanomolar range against a number of tumor cell lines.

Three-dimensional structure of M. tuberculosis dihydrofolate reductase reveals opportunities for the design of novel tuberculosis drugs

Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate and is essential for the synthesis of thymidylate, purines and several amino acids. Inhibition of the enzyme's activity leads to arrest of DNA synthesis and cell death. The enzyme has been studied extensively as a drug target for bacterial, protozoal and fungal infections, and also for neoplastic and autoimmune diseases. Here, we report the crystal structure of dihydrofolate reductase from Mycobacterium tuberculosis, a human pathogen responsible for the death of millions of human beings per year. Three crystal structures of ternary complexes of M. tuberculosis DHFR with NADP and different inhibitors have been determined, as well as the binary complex with NADP, with resolutions ranging from 1.7 to 2.0 A. The three DHFR inhibitors are the anticancer drug methotrexate, the antimicrobial trimethoprim and Br-WR99210, an analogue of the antimalarial agent WR99210. Structural comparison of these complexes with human dihydrofolate reductase indicates that the overall protein folds are similar, despite only 26 % sequence identity, but that the environments of both NADP and of the inhibitors contain interesting differences between the enzymes from host and pathogen. Specifically, residues Ala101 and Leu102 near the N6 of NADP are distinctly more hydrophobic in the M. tuberculosis than in the human enzyme. Another striking difference occurs in a region near atoms N1 and N8 of methotrexate, which is also near atom N1 of trimethoprim, and near the N1 and two methyl groups of Br-WR99210. A glycerol molecule binds here in a pocket of the M. tuberculosis DHFR:MTX complex, while this pocket is essentially filled with hydrophobic side-chains in the human enzyme. These differences between the enzymes from pathogen and host provide opportunities for designing new selective inhibitors of M. tuberculosis DHFR.

Conformationally restricted analogues of trimethoprim: 2,6-diamino-8-substituted purines as potential dihydrofolate reductase inhibitors from Pneumocystis carinii and Toxoplasma gondii

Twenty-two 2,6-diamino-8-substituted purines (2-23) were synthesized, in which rotation around the two flexible bonds of trimethoprim (TMP), linking the pyrimidine ring to the side chain phenyl ring, was restricted by incorporation into a purine ring, in an attempt to increase the potency and selectivity of TMP against dihydrofolate reductase (DHFR) from the organisms that often cause fatal opportunistic infections in patients with AIDS, i.e., Pneumocystis carinii (pc) and Toxoplasma gondii (tg). The syntheses of analogues 2-20 were achieved via a one-pot reaction of 2,4,5,6-tetraaminopyrimidine and the appropriately substituted benzaldehyde or phenyl acetaldehyde, in acidic methoxyethanol. Analogues 21-23 were synthesized via nucleophilic displacement of 2,6-diamino-8-(chloromethyl)purine with the appropriate anilines or 2-naphthalenethiol. The compounds were evaluated as inhibitors of pcDHFR and tgDHFR with rat liver (rl) DHFR as the mammalian reference enzyme. Compound 11, the 3',4'-dichlorophenyl analogue, was as potent as TMP and had a selectivity ratio of 13 for pcDHFR, which ranked it as one of the three most selective inhibitors of pcDHFR (compared to rlDHFR) known to date. It also displayed a selectivity ratio of 38 for tgDHFR. None of the other analogues showed any improvement compared to TMP in potency or selectivity. In the preclinical in vitro screening program of the National Cancer Institute, compound 11 showed a GI50 of 10(-6) M for the inhibition of the growth of 17 tumor cell lines.