Insight into crystal structures and identification of potential styrylthieno[2,3-b]pyridine-2-carboxamidederivatives against COVID-19 Mpro through structure-guided modeling and simulation approach

Anti-SARS-CoV-2 drugs are urgently needed to prevent the pandemic and for immunization. Their protease inhibitor treatment for COVID-19 has been used in clinical trials. In Calu-3 and THP1 cells, 3CL SARS-CoV-2 Mpro protease is required for viral expression, replication, and the activation of the cytokines IL-1, IL-6, and TNF-. The Mpro structure was chosen for this investigation because of its activity as a chymotrypsin-like enzyme and the presence of a cysteine-containing catalytic domain. Thienopyridine derivatives increase the release of nitric oxide from coronary endothelial cells, which is an important cell signaling molecule with antibacterial activity against bacteria, protozoa, and some viruses. Using DFT calculations, global descriptors are computed from HOMO-LUMO orbitals; the molecular reactivity sites are analyzed from an electrostatic potential map. NLO properties are calculated, and topological analysis is also part of the QTAIM studies. Both compounds 1 and 2 were designed from the precursor molecule pyrimidine and exhibited binding energies (-14.6708 kcal/mol and -16.4521 kcal/mol). The binding mechanisms of molecule 1 towards SARS-COV-2 3CL Mpro exhibited strong hydrogen bonding as well as Vdw interaction. In contrast, derivative 2 was bound to the active site protein's active studied that several residues and positions, including (His41, Cys44, Asp48, Met49, Pro52, Tyr54, Phe140, Leu141, Ser144, His163, Ser144, Cys145, His164, Met165, Glu166, Leu167, Asp187, Gln189, Thr190, and GLn192) are critical for the maintenance of inhibitors inside the active pocket. Molecular docking and 100 ns MD simulation analysis revealed that Both compounds 1 and 2 with higher binding affinity and stability toward the SARS-COV-2 3CL Mpro protein. Binding free energy calculations and other MD parameters support the finding.Communicated by Ramaswamy H. Sarma.

Exploration of Some Heterocyclic Compounds Containing Trifluoromethylpyridine Scaffold as Insecticides Toward Aphis gossypii Insects

Five types of heterocyclic compounds containing trifloromethylpyridine scaffold namely; 3-cyano-2-(N-phenyl)carbamoylmethylthio-6-(thiophen-2-yl)-4-trifluoromethyl-pyridine (6a), thieno[2,3-b]pyridines 3-5 and 7a-c, pyrido[3',2':4,5]thieno[3,2-d] pyrimidines 8-13 and 15a-c, pyrido[3',2':4,5]thieno[3,2-d][1,2,3]triazines 16a,b, and 9-(thiophen-2-yl)-7-(trifluoromethyl) pyrido [3',2':4,5]thieno[2,3-e][1,2,4]triazolo[1,5-c]pyrimidine (14) were synthesized in excellent yields and very pure state. The structures of these compounds were confirmed by elemental and spectral analyses. Most of the synthesized compounds were evaluated as insecticidal agents toward Aphis gossypii insects and promising results obtained. Among all tested compounds, only 6, 7a, 7c and 15c being the most potent compounds against nymphs and adults of Aphis gossypii and their activities are nearly to that of acetamiprid as a reference. The effect of 6a compounds 7a, 7c and 15c on the Aphis digestive system from histological point of view was also included.

Novel tetrahydroisoquinolines as DHFR and CDK2 inhibitors: synthesis, characterization, anticancer activity and antioxidant properties

In this study, we synthesized new 5,6,7,8-tetrahydroisoquinolines and 6,7,8,9-tetrahydrothieno[2,3-c]isoquinolines based on 4-(N,N-dimethylamino)phenyl moiety as expected anticancer and/or antioxidant agents. The structure of all synthesized compounds were confirmed by spectral date (FT-IR, 1H NMR, 13C NMR) and elemental analysis. We evaluated the anticancer activity of these compounds toward two cell lines: A459 cell line (lung cancer cells) and MCF7 cell line (breast cancer cells). All tested compounds showed moderate to strong anti-cancer activity towards the two cell lines. Compound 7e exhibited the most potent cytotoxic activity against A549 cell line (IC50: 0.155 µM) while compound 8d showed the most potent one against MCF7 cell line (IC50: 0.170 µM) in comparison with doxorubicin. In addition, we examined the effect of compounds 7e and 8d regarding the growth of A549 and MCF7 cell lines, employing flow cytometry and Annexin V-FITC apoptotic assay. Our results showed that compound 7e caused cell cycle arrest at the G2/M phase with a 79-fold increase in apoptosis of A459 cell line. Moreover, compound 8d caused cell cycle arrest at the S phase with a 69-fold increase in apoptosis of MCF7 cell line. Furthermore, we studied the activity of these compounds as enzyme inhibitors against several enzymes. Our findings by docking and experimental studies that compound 7e is a potent CDK2 inhibitor with IC50 of 0.149 µM, compared to the Roscovitine control drug with IC50 of 0.380 µM. We also found that compound 8d is a significant DHFR inhibitor with an IC50 of 0.199 µM, compared to Methotrexate control drug with IC50 of 0.131 µM. Evaluation of the antioxidant properties of ten compounds was also studied in comparison with Vitamin C. Compounds 1, 3, 6, 7c and 8e have higher antioxidant activity than Vitamin C which mean that these compounds can used as potent antioxidant drugs.

Pyridine Derivatives as Insecticides─Part 4: Synthesis, Crystal Structure, and Insecticidal Activity of Some New Thienylpyridines, Thienylthieno[2,3-b]pyridines, and Related Heterocyclic Derivatives

The reaction of ethyl 5-cyano-2-methyl-4-(thiophen-2-yl)-6-thioxo-1,6-dihydropyridine-3-carboxylate (1) with 2-chloroacetamide or its N-aryl derivatives gave ethyl 6-((2-amino-2-oxoethyl)thio)-5-cyano-2-methyl-4-(thiophen-2-yl) nicotinate (2a) or its N-aryl derivatives 2b-f, respectively. Cyclization of 2a-f into their isomers 3a-f was carried out by heating in absolute ethanol in the presence of a catalytic amount of sodium ethoxide. The o-aminoamide 3a was reacted with some aryl aldehydes in refluxing ethanol containing a few drops of conc. HCl to afford the corresponding tetrahydropyrimidinones 4a-d. The cyclocondensation reaction of 3a with some cycloalkanones such as cyclopentanone and cyclohexanone gave the corresponding spiro compounds 5a,b. The crystal structures of compounds 2a and 2d were determined by single-crystal X-ray diffraction techniques. All new compounds were evaluated for their insecticidal activity toward nymphs and adults of Aphis gossypi.

Thieno[2,3-c]isoquinolines: A novel chemotype of antiproliferative agents inducing cellular apoptosis while targeting the G2/M phase and Tubulin

In the era of modern synthetic methodology and advanced bio-evaluation techniques and considering the notorious history of hepatocellular carcinoma (HCC), hopeful expectations regarding novel bioactive chemotypes have grown dramatically. Among the widely versatile motifs in drug discovery studies are isoquinoline and thieno[2,3-b]pyridine. Herein, the molecular merging of both motifs evoked thieno[2,3-c]isoquinoline as a novel antiproliferative chemotype being hardly studied against HCC. Accordingly, compound series 4, 5, 7 and 8 were synthesized and bioevaluated against the HepG2 cell line. The role of C7-Ac/C8-OH substituents, C8-C9 unsaturation, 1H-pyrrol-1-yl ring closure at C1-NH₂ and C6-Ph p-halo-substitution were biologically studied and successfully furnished the lead 5b while showing safe profile against Vero cells. Further, flow cytometric and Annexin V-FITC/PI apoptotic bio-investigations of 5b unveiled remarkable cell cycle arrest at the G2/M phase besides a 60-fold increase in apoptosis. The use of a DFT conformational study followed by Molecular docking and molecular mechanics/generalized born surface area scoring evoked potential tubulin-targeting activity of 5b at colchicine-binding site, which was confirmed by experimental evidence (Tub Inhib IC₅₀  = 71 µM vs. 14 µM for colchicine). Accordingly, preserving C7-acetyl and optimizing halogen position while preserving [6S,7R]-stereochemistry is crucial for optimum binding to colchicine binding site of tubulin.

Synthesis, biological evaluation and molecular docking study of some new 4-aminosalicylic acid derivatives as anti-inflammatory and antimycobacterial agents

In this study, new derivatives of the antitubercular and anti-inflammatory drug, 4-aminosaliclic acids (4-ASA) were synthesized, characterized, and evaluated for these activities. In vivo and in viro evaluation of anti-inflammatory activity revealed that compounds 10, 19 and 20 are the most active with potent cyclooxygenase-2 (COX-2) and 5-lipooxgenase (5-LOX) inhibition and without causing gasric lesions. The minimum inhibitory concentrations (MIC) of the newly synthesized compound were, also, measured against Mycobacterium tuberculosis H37RV. Among the tested compounds 17, 19 and 20 exhibited significant activities against the growth of M. tuberculosis. 20 is the most potent with (MIC 1.04 µM) 2.5 folds more potent than the parent drug 4-ASA. 20 displayed low cytotoxicity against normal cell providing a high therapeutic index. Important structure features were analyzed by docking and structure-activity relationship analysis to give better insights into the structural determinants for predicting the anti-inflammatory and anti-TB activities. Our results indicated that compounds 19 and 20 are potential lead compounds for the discovery of dual anti-inflammatory and anti-TB drug candidates.

Apocynin and its chitosan nanoparticles attenuated cisplatin-induced multiorgan failure: Synthesis, characterization, and biological evaluation

Cisplatin (CDDP) is an effective chemotherapeutic drug that has been used successfully in treating various tumors. Although its higher antineoplastic agent activity, CDDP exhibited severe side effects that limit its use. CDDP-induced toxicity is attributed to oxidative stress and inflammation. Apocynin (APO) is a bioactive phytochemical with potent antioxidant and anti-inflammatory properties. However, pharmaceutical experts face significant hurdles due to the limited bioavailability and quick elimination of APO. Therefore, we synthesized a chitosan (CTS)-based nano delivery system using the ionic gelation method to enhance APO bioactivity. CTS-APO-NPs were characterized using different physical and chemical approaches, including FTIR, XRD, TGA, Zeta-sizer, SEM, and TEM. In addition, the protective effect of CTS-APO-NPs against CDDP-induced nephrotoxicity, hepatotoxicity, and cardiotoxicity in rats was evaluated. CTS-APO-NPs restored serum biomarkers and antioxidants to their normal levels. Also, histopathological examination was used to assess the recovery of heart, kidney, and liver tissues. CTS-APO-NPs attenuated the oxidative stress mediated by Nrf2 activation while it dampened inflammation mediated by NF-κB suppression. CTS-APO-NPs is a potentially attractive target for more therapeutic trials.

Exploration of Dihydrothieno[2,3-c] Isoquinolines As Luminescent Materials and Corrosion Inhibitors

The reaction of the starting compound, 7-acetyl-4-cyano-1,6-dimethyl-8-phenyl-7,8-dihydroisoquinoline-3(2H)-thione, with some N-aryl-2-chloroacetamides or chloroacetonitrile, in the presence of sodium acetate trihydrate, gave the corresponding substituted 3-methylsulfanyl-7-acetyl-4-cyano-1,6-dimethyl-8-phenyl-7,8-dihydroisoquinolines. Upon heating of the latter compounds with sodium methoxide in methanol, they underwent intramolecular Thorpe-Zeigler cyclization, affording the target isomers 1-amino-2-(substituted)-5,8-dimethyl-6-phenyl-6,7-dihydrothieno[2,3-c]isoquinolines (DHTIQs). The chemical structures of all produced substances were characterized by elemental and spectral analyses. The photophysical characteristics of the produced DHTIIQs (He1-Ph-Cl, He2-Ph-CH₃, He3-Ph, and He4-CN) have been investigated as luminous compounds. Potentiodynamic, surface morphology, and theoretical calculations were used to study the behavior of the synthesized DHTIQs as corrosion inhibitors on mild steel in a 1.0 M sulfuric acid solution.

Pyridine Derivatives as Insecticides. Part 3. Synthesis, Crystal Structure, and Toxicological Evaluation of Some New Partially Hydrogenated Isoquinolines against Aphis gossypii (Glover, 1887)

Three new series of isoquinolines, that is, 7-acetyl-3-acetonylsulfanyl-8-aryl-1,6-dimethyl-6-hydroxy-5,6,7,8-tetrahydroisoquinoline-4-carbonitriles (3a-c); 3-acetonylsulfanyl-8-aryl-1,6-dimethyl-7,8-dihydroisoquinoline-4-carbonitriles (4a-c); and 7-acetyl-8-aryl-1,6-dimethyl-3-ethylsulfanyl-7,8-dihydroisoquinoline-4-carbo-nitriles (6a,b) were carefully synthesized. Also, pyrazoloisoquinoline 7 was used as a precursor for synthesis of 7-ethylsulfanyl-4-phenyl-1-thiocarbamoyl-3,5,9a-trimethyl-3a,4,9,9a-tetrahydro-1H-pyrazolo[3,4-g]isoquinoline-8-carbonitrile (8); 7-benzyl-sulfanyl-4-phenyl-1-thiocarbamoyl-3,5,9a-trimethyl-3a,4,9,9a-tetrahydro-1H-pyrazolo[3,4-g]isoquinoline-8-carbonitrile (9); and 7-ethylsulfanyl-1-(4-oxo-4,5-dihydrothiazol-2-yl)-4-phenyl-3,5,9a-trimethyl-3a,4,9,9a-tetrahydro-1H-pyrazolo[3,4-g]isoquinoline-8-carbonitrile (10). Moreover, the crystal structures of two representative compounds were determined. Eleven new compounds 3a, 4a, 3b, 4b, 3c, 4c, 6a, 6b, 8, 9, and 10 were screneed for their toxicological activity against nymphs and adults of Aphis gossypii by using acetamprid, as a reference. After 24 h of treatment, the bioefficacy results indicate that all tested isoquinolines exhibit toxicological activity that varied from very high to low against nymphs and adults of Aphis gossypii, some compounds showing activity near to that of acetampirid and only one compound which possesses higher activity against nymphs and adults of Aphis gossypii than that of acetampirid itself.

Nitrophenyl-Group-Containing Heterocycles. I. Synthesis, Characterization, Crystal Structure, Anticancer Activity, and Antioxidant Properties of Some New 5,6,7,8-Tetrahydroisoquinolines Bearing 3(4)-Nitrophenyl Group

Regioselective cyclocondensation of 2,4-diacetyl-5-hydroxy-5-methyl-3-(3-nitrophenyl/4-nitrophenyl)cyclohexanones 1a,b with cyanothioacetamide afforded the corresponding 7-acetyl-4-cyano-1,6-dimethyl-6-hydroxy-8-(3- and -4-nitrophenyl)-5,6,7,8-tetrahydrosoquinoline-3(2H)-thiones 2a,b. Reaction of compounds 2a,b with ethyl iodide, 2-chloroacetamide (4a), or its N-aryl derivatives 4b-e in the presence of sodium acetate trihydrate gave 3-ethylthio-5,6,7,8-tetrahydroisoquinoline 3 and (5,6,7,8-tetrahydroisoquinolin-3-ylthio)acetamides 5a-i, respectively. Cyclization of compounds 5b-d,f,g into their isomeric 1-amino-6,7,8,9-tetrahydrothieno[2,3-c]isoquinoline-2-carboxamides 6b-d,f,g was achieved by heating in ethanol containing a catalytic amount of sodium carbonate. Structures of all synthesized compounds were characterized on the basis of their elemental analyses and spectroscopic data. The crystal structure of 5,6,7,8-tetrahydroisoquinoline 5d was determined by X-ray diffraction analysis. In addition, the biological evaluation of some synthesized compounds as anticancer agents was performed, and only six compounds showed moderate to strong activity against PACA2 (pancreatic cancer cell line) and A549 (lung carcinoma cell line). Moreover, the antioxidant properties of most synthesized compounds were examined. The results revealed high antioxidant activity for the most tested compounds.

Crystal structure and Hirshfeld surface analysis of 5-acetyl-3-amino-6-methyl-N-phenyl-4-[(E)-2-phenylethenyl]thieno[2,3-b]pyridine-2-carboxamide

The asymmetric unit of the title mol­ecule consists of four mol­ecules that differ primarily in the orientations of the styryl and the N-phenyl­carboxamido groups.

The asymmetric unit of the title compound, C₂₅H₂₁N₃O₂S, comprises four mol­ecules. Their conformations differ primarily in the orientations of the styryl and the N-phenyl­carboxamido groups. In the crystal, inter­molecular N—H⋯N, C—H⋯O and C—H⋯S hydrogen-bonding contacts as well a C—H⋯π(ring) inter­actions lead to the formation of a layer structure parallel to (010). Hirshfeld surface analysis revealed that H⋯H inter­actions represent the main contributions to the crystal packing.

Crystal structure and Hirshfeld surface analysis of 2-{[7-acetyl-4-cyano-6-hydroxy-8-(4-methoxyphenyl)-1,6-dimethyl-5,6,7,8-tetrahydroisoquinolin-3-yl]sulfanyl}acetic acid ethyl ester

In the title molecule, C25H28N2O5S, (alternative name ethyl 2-{[7-acetyl-4-cyano-6-hydroxy-8-(4-methoxyphenyl)-1,6-dimethyl-5,6,7,8-tetrahydroisoquinolin-3-yl]sulfanyl}acetate) the 4-methoxyphenyl group is disposed on one side of the bicyclic core and the oxygen atoms of the hydroxyl and acetyl groups are disposed on the other side. In the crystal, a layered structure parallel to the ac plane is generated by O—H...O and C—H...O hydrogen bonds plus C—H...π(ring) interactions.

Crystal structure and Hirshfeld surface analysis of ethyl 2-({5-acetyl-3-cyano-6-methyl-4-[(E)-2-phenyl-ethen-yl]pyridin-2-yl}sulfan-yl)acetate

In the title mol-ecule, C21H20N2O3S, the styryl and ester substituents are displaced to opposite sides of the plane of the pyridine ring. In the crystal, C-H⋯O hydrogen bonds form chains extending parallel to the a-axis direction, which pack with partial inter-calation of the styryl and ester substituents. A Hirshfeld surface analysis indicates that the most significant contributions to the crystal packing are from H⋯H (43.6%), C⋯H/H⋯C (15.6%), O⋯H/H⋯O (14.9%) and N⋯H/H⋯N (11.2%) contacts.

Crystal structure and Hirshfeld surface analysis of 2-{[7-acetyl-4-cyano-6-hy-droxy-8-(4-meth-oxy-phen-yl)-1,6-dimethyl-5,6,7,8-tetra-hydro-iso-quino-lin-3-yl]sulfan-yl}-N-phenyl-acetamide

The title mol-ecule, C29H29N3O4S, adopts a conformation with the two phenyl substituents disposed on opposite sides of the mean plane of the iso-quinoline unit. In the crystal, corrugated layers of mol-ecules are formed by N-H⋯O, C-H⋯N and C-H⋯S hydrogen bonds together with C-H⋯π(ring) inter-actions. These layers are connected by C-H⋯O contacts. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (45.2%), C⋯H/H⋯C (20.2%), O⋯H/H⋯O (15.8%) and N⋯H/H⋯N (11.0%) inter-actions.

Crystal structure and Hirshfeld surface analysis of 2-{[7-acetyl-8-(4-chloro-phen-yl)-4-cyano-6-hy-droxy-1,6-dimethyl-5,6,7,8-tetra-hydro-isoquinolin-3-yl]sulfan-yl}-N-(4-chloro-phen-yl)acetamide

In the title mol-ecule, C28H25Cl2N3O3S, the heterocyclic portion of the tetra-hydro-iso-quinoline unit is planar while the cyclo-hexene ring adopts a twist-boat conformation. The two 4-chloro-phenyl groups extend away from one side of this unit while the hydroxyl and acetyl groups extend away from the opposite side and form an intra-molecular O-H⋯O hydrogen bond. The crystal packing consists of layers parallel to the bc plane. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H⋯H (37.3%), Cl⋯H/H⋯Cl (17.6%), O⋯H/H⋯O (11.1%), C⋯H/H⋯C (10.9%) and N⋯H/H⋯N (9.7%) inter-actions.

Synthesis and Characterization of Novel Functionally Substituted Planar Pyrimidothienoisoquinolines and Nonplanar (3aR, 4S, 9aS)-pyrazolo[3,4-g]isoquinolines

7-Acetyl-8-aryl-4-cyano-1,6-dimethyl-6-hydroxy-5,6,7,8-tetrahydroisoquinolin-3(2H)-thiones 2a,b are prepared and dehydrated to give 7-acetyl-8-aryl-4-cyano-1,6-dimethyl-6-hydroxy-7,8-dihydrodroisoquinolin-3(2H)-thiones 6a,b via a novel method by heating with acetyl chloride in acetic acid. The reaction of both compounds 2a,b and 6a,b with N-aryl-2-chloroacetamides 7a-c under two different conditions gave the same corresponding products, 7-acetyl-8-aryl-3-(N-aryl)carbamoylmethylsulfanyl-4-cyano-1,6-dimethyl-7,8-dihydroisoquinolines 8a-e, in high yields. On treatment of compounds 8a,b,e in methanol with a slightly excess molar amount of sodium methoxide, they underwent intramolecular Thorpe-Ziegler cyclization followed by spontaneous aromatization, providing the planar 7-acetyl-1-amino-6-aryl-2-(N-aryl)carbamoyl-5,8-dimethyl-8,9-dihydrothieno[2,3-c] isoquinolines 9a,b,e in good yield. Cyclocondensation reactions of 6a,b with phenyl hydrazine, thiosemicarbazide, or hydrazine hydrate led to the formation of nonplanar (3aR, 4S, 9aS)-pyrazolo[3,4-g]isoquinolines 11a, 11b, and 13, respectively. The reaction of compound 13 with 2-chloromethylquinazolin-4(3H)-one in the presence of anhydrous sodium acetate gave the expected thienopyrazoloisoquinolone 14. Heating the latter compound (14) with triethyl orthoformate in glacial acetic acid afforded the fused heptacyclic compound 15. All of the synthesized compounds were characterized based on their full spectral analyses such as IR, ¹H nuclear magnetic resonance (NMR), and mass spectrometry (MS). Moreover, the crystal structure of compound 6a was elucidated by X-ray diffraction analysis.

Synthesis, Characterization, and Crystal Structure of Some New Tetrahydroisoquinolines and Related Tetrahydrothieno[2,3-c]isoquinolines

The starting compounds 7-acetyl-8-aryl-4-cyano-1,6-dimethyl-6-hydroxy-5,6,7,8-tetrahydroisoquinoline(2H)-3-thiones 3a,b were synthesized and reacted with some N-aryl-2-chloroacetamides 4a-e in the presence of sodium acetate to produce 7-acetyl-8-aryl-3-(N-arylcarbamoylmethylsulfanyl)-4-cyano-1,6-dimethyl-6-hydroxy-5,6,7,8-tetrahydroisoquinolines 5a-g. Upon heating in ethanol containing sodium ethoxide, they underwent intramolecular Thorpe-Zeigler cyclization, affording the corresponding 7-acetyl-1-amino-6-aryl-2-(N-arylcarbamoyl)-5,8-dimethyl-8-hydroxy-6,7,8,9-tetrahydrothieno[2,3-c]isoquinolines 6a-g. Compounds 6c,g,f were converted into the corresponding 1-(1-pyrrolyl) derivatives 7a-c by heating with 2,5-dimethoxytetrahydrofuran in glacial acetic acid. Structures of all synthesized compounds were characterized by elemental and spectral analyses. Also, the crystal structure of compounds 5a was determined by X-ray diffraction analysis.

Crystallographic and spectroscopic characterization of 2-[(7-acetyl-4-cyano-6-hy-droxy-1,6-dimethyl-8-phenyl-5,6,7,8-tetra-hydro-isoquinolin-3-yl)sulfan-yl]-N-phenyl-acetamide

In the title mol-ecule, C28H27N3O3S, the heterocyclic portion of the tetra-hydro-iso-quinoline unit is planar and an intra-molecular N-H⋯N hydrogen bond and a C-H⋯π(ring) inter-action help to determine the overall conformation. In the crystal, a layer structure with the layers parallel to (10) is generated by O-H⋯O and C-H⋯O hydrogen bonds.

A concise review on some synthetic routes and applications of pyridine scaffold compounds

Different methods for the synthesis of pyridine derivatives as well as the chemical reactivity profiles and structures of these substances are reviewed. The utility of these compounds as precursors is emphasized in the synthesis of many heterocycles that are pharmacologically active organic compounds and agrochemicals. This review results from a literature survey containing some synthetic methods and applications of pyridine derivatives.

Fluorine-containing Heterocycles: Part II Synthesis and Reactions of New Thieno[2,3-b]Pyridine Derivatives Bearing Trifluoromethyl Group

Ethyl [3-cyano-6-(2-thienyl)-4-trifluoromethylpyridin-2-ylthio]acetate (2) and ethyl 3-amino-6-(2-thienyl)-4-trifluoromethylthieno[2,3-b]pyridine-2-carboxylate (3) were prepared by reaction of 3-cyano-6-(2-thienyl)-4-trifluoromethylpyridine-2(1H)-thione (1) with ethyl chloroacetate. The reaction of both 2 and 3 with hydrazine hydrate under different conditions was studied. The main products were [3-cyano-6-(2-thienyl)-4-trifluoromethyl-2-pyridinylthio]acetohydrazide (4) and 3-amino-6-(2-thienyl)-4-trifluoromethylthieno[2,3-b]pyridine-2-carbohydrazide (5). The condensation of acethydrazide 4 with some aromatic or heterocyclic aldehydes yielded the corresponding hydrazones 6a–d which underwent intramolecular Thorpe–Ziegler cyclisation to give the N1-aryl or heteroaryl-methylene-3-amino-6-(2-thienyl)-4-trifluoromethylthieno[2,3-b]pyridine-2-carbohydrazides (7a–d). Treatment of 7a–d with triethyl orthoformate led to the formation of pyridothienopyrimidine derivatives 8a–d. Heating carbohydrazide 5 with acetic acid gave an unexpected product which was assigned as 3-amino-2-methyl-7-(2-thienyl)-9-trifluoromethylpyrido[3′,2′:4,5] thieno[3,2-d]pyrimidine-4(3H)-one (12). Moreover, the reaction of 5 with other reagents such as acetic anhydride, formic acid, acetylacetone and/or triethyl orthoformate were carried out and their products were identified. Diazotisation of 5 produced the corresponding acyl azide 18 which underwent Curtius rearrangement to furnish the imidazolone derivative 20. Hydrolysis of the ester 3 gave the aminoacid 21 which in turn was converted into the oxazinone derivatives 22 and 23. Recyclisation of 22 and 23 into some pyrimidinone derivatives (12 and 24–26) was carried out.

Fluorine-Containing Heterocycles: Part I. Synthesis of New 7-(2-thienyl)-9-Trifluoromethylpyrido[3′,2′:4,5]Thieno[3,2-d]Pyrimidines and Related Fused Tetracyclic Systems

3-amino-6-(2-thienyl)-4-trifluoromethylthieno[2,3-b]pyridine-2-carboxamide (3) and 2-carbonitrile analogue 5 were prepared by reaction of 3-cyano-6-(2-thienyl)-4-trifluoromethylpyridine-2(1H)-thione (1) with chloroacetamide or chloroacetonitrile respectively. Heating compound 3 with triethyl orthoformate led to the formation of pyridothienopyrimidinone derivative 6. Reaction of 6 with phosphorus oxychloride produced 4-chloropyrimidine derivative 7 which underwent some nucleophilic displacements upon treatment with thiourea, piperidine, morpholine or hydrazine hydrate to give the target 4-substituted pyridothienopyrimidines 8, 10a, 10b and 11 respectively. Reaction of compound 8 with methyl iodide or ethyl chloroacetate gave compounds 9a,b. The condensation of 3-amino-6-(2-thienyl)-4-trifluoromethyl-thieno[2,3-b]pyridine-2-carbonitrile (5) with triethyl orthoformate led to the formation of methanimidate derivative 21 which upon treatment with hydrazine hydrate gave the target 3-amino-3,4-dihydro-4-imino-7-(2-thienyl)-9-trifluoromethylpyrido[3′,2′:4,5] thieno[3,2-d]pyrimidine (22). The reactions of compounds 11 and 22 with some reagents namely; triethyl orthoformate, acetic anhydride, formic acid, acetic acid, acetylacetone benzaldehyde and/or diethyl malonate were carried out and their products were identified, in most cases as [1,2,4]triazolopyridothienopyrimidines via Dimroth rearrangement.

Synthesis of New Thiopyridines, Thienopyridines, Pyridothienopyrimidines and Pyranothienopyridines with Anticipated Biological Activity

(5-Acetyl-4-aryl-3-cyano-6-methylpyridin-2-ylthio)acethydrazides (4a,b), 5-acetyl-3-amino-4-aryl-6-methylthieno[2,3- b]pyridine-2-carbohydrazides (5a,b) and 5-acetyl-3-amino-6-methyl-4-phenylthieno[2,3- b]pyridine-2-carboxylic acid (13) were synthesised and used as key intermediates in the synthesis of the target compounds.

5-Acetyl-3-amino-4-(4-methoxyphenyl)-6-methylthieno[2,3-b]pyridine-2-carbonitrile

The asymmetric unit of the title compound, C18H15N3O2S, comprises two independent molecules, which differ primarily in the orientations of the acetyl andp-anisyl substituents, each being rotated in opposite directions from the mean plane of the pyridine ring. The major feature of the molecular packing is the formation of a two-dimensional network parallel to the (110) plane, being mediated by amine-N—H...O(carbonyl) hydrogen bonds involving one amine H atom of each independent molecule. The remaining amine-H atoms form significantly weaker N—H...O(methoxy) interactions.

N′-[(1Z)-1-(3-Methyl-5-oxo-1-phenyl-4,5-dihydro-1H-pyrazol-4-ylidene)ethyl]-2-[(4-methylphenyl)sulfanyl]acetohydrazide

In the title compound, C21H22N4O2S, the dihedral angle between the pyrazole ring and adjacent benzene ring is 6.4 (1)°. The molecular conformation is influenced by intramolecular N—H...O and C—H...O hydrogen bonds. In the crystal, N—H...O hydrogen bonds plus C—H...π and π–π stacking interactions form chains extending in thea-axis direction. The chains are linked by complementary pairs of C—H...π interactions.

Ethyl 3-amino-2-cyano-4-(4-methoxyphenyl)-6- methylthieno[2,3-b]pyridine-5-carboxylate

In the title molecule, C19H17N3O3S, the bicyclic core is planar [maximum deviation = 0.0205 (1) Å] In the crystal, the molecules stack along thea-axis direction through π–π-stacking interactions between the bicyclic units with a small alternation in the interplanar distances along the stack. The stacks are held together by N—H...N and C—H...O hydrogen bonds. The carboethoxy substituent is disordered over several closely spaced sites and was modeled as having two-component disorder [occupancy ratio 0.548 (16):0.452 (16)]. The final refinement was as a two-component twin.

Methyl 2-{[(6S*,7R*,8S*)-7-acetyl-8-(4-chlorophenyl)-4-cyano-6-hydroxy-1,6-dimethyl-5,6,7,8-tetrahydroisoquinolin-3-yl]sulfanyl}acetate

In the title compound, C23H23ClN2O4S, the 4-chlorophenyl ring is inclined to the pyridine ring of the isoquinoline group by 71.86 (13)°. In the crystal, molecules are linked by pairs of O—H...O hydrogen bonds, forming inversion dimers, which stack along theb-axis direction. The methyl acetate group attached to the S atom is disordered over two sites in a 50:50 ratio, which appears to prevent close intermolecular contacts between the methyl groups.

7-Acetyl-8-(4-chlorophenyl)-3-ethylsulfanyl-6-hydroxy-1,6-dimethyl-5,6,7,8-tetrahydroisoquinoline-4-carbonitrile

In the title compound, C22H23ClN2O2S, the chlorophenyl ring is inclined to the pyridine ring of the isoquinoline ring system by 79.78 (4)°. The cyclohexane ring adopts a flattened boat conformation. In the crystal, dimers form through complementary sets of inversion-related O—H...O and C—H...O hydrogen bonds. These are connected into zigzag chains along the c-axis direction by pairwise C—H...N interactions that also form inversion dimers.

Ethyl 8-amino-7-(furan-2-yl)-5,6-dihydrothieno[2,3-b]benzo[h]quinoline-9-carboxylate

In the title compound, C22H18N2O3S, the two independent molecules in the asymmetric unit form a dimerviaN—H...O hydrogen bonds. In the crystal, the molecular layers can be found in the (110) plane, connected by C—H...π interactions. Atoms of the furan ring of one independent molecule are disordered over two sets of sites with an occupancy ratio 0.735 (3):0.265 (3).

Ethyl 3-amino-2-carbamoyl-4-(4-methoxyphenyl)-6-methylthieno[2,3-b]pyridine-5-carboxylate dimethyl sulfoxide monosolvate

The conformation of the title molecule, C19H19N3O4S·C2H6OS, which crystallized as a DMSO solvate, is partially determined by an intramolecular N—H...O hydrogen bond, forming anS(6) loop. The thienopyridine bicyclic system is almost planar, with an r.m.s. deviation of 0.002 Å. The benzene ring makes a dihedral angle of 65.44 (8)° with the mean plane of the thienopyridine bicyclic system. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with anR22(8) ring motif. Within the dimers, which stack along thea-axis direction, there is a weak π–π interaction [centroid-to-centroid distance = 3.5428 (11) Å] involving inversion-related thiophene rings. In addition, N—H...O and C—H...O hydrogen bonds help to consolidate the packing,viathe solvent molecules.

Ethyl 13-(4-chlorophenyl)-11-methyl-6-oxo-5-phenyl-8-thia-3,4,5,10-tetraazatricyclo[7.4.0.02,7]trideca-1(9),2(7),3,10,12-pentaene-12-carboxylate

In the title molecule, C24H17ClN4O3S, the central tricyclic moiety is twisted slightly, as indicated by the dihedral angles of 4.86 (5) and 0.97 (6)°, respectively, between the five-membered ring and the C3N3and pyridyl rings. Additionally, the chlorobenzene ring makes a dihedral angle of 65.80 (5)° with the pyridyl ring. Weak C—H...O, C—Cl...N [3.0239 (13) Å] and π–π stacking interactions [inter-centroid distance between thienyl rings = 3.6994 (8) Å, and between thienyl and pyridyl rings = 3.7074 (8) Å] contribute to the molecular packing. The ethyl group in the ester moiety is disordered over two sets of sites, with the major component having an occupancy of 0.567 (11).

Piperidinium 4-(4-chlorophenyl)-3-cyano-5-ethoxycarbonyl-6-methylpyridine-2-thiolate

In the crystal of the title salt, C5H12N+·C16H12ClN2O2S−, the cation adopts a chair conformation, and N—H...N and N—H...S hydrogen bonds form chains of alternating cations and anions running parallel to thecaxis. The crystal structure contains a solvent-accessible void of 50 Å3, but no solvent molecule is located there.

Ethyl 3-amino-4-(4-chlorophenyl)-2-[(4-methoxyphenyl)carbamoyl]-6-phenylthieno[2,3-b]pyridine-5-carboxylate

The conformation of the title molecule, C30H24ClN3O4S, is partially determined by an intramolecular N—H...O hydrogen bond, forming anS(6) loop, and an N—H...π interaction involving the centroid of the 4-chlorophenyl ring. The thienopyridine bicyclic system is almost planar with an r.m.s. deviation of 0.019 Å. Its mean plane is inclined to the phenyl ring, the 4-chlorophenyl ring and the 4-methoxyphenyl ring by 36.19 (7), 81.67 (7) and 12.75 (7)°, respectively. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with anR22(20) ring motif. Within the dimers, which stack along theb-axis direction, there is a weak π–π interaction [centroid-to-centroid distance = 3.7936 (9) Å] involving inversion-related thiophene and pyridine rings.

Ethyl 4-(4-chlorophenyl)-5-cyano-2-methyl-6-sulfanylidene-1,6-dihydropyridine-3-carboxylate

In the title compound, C16H13ClN2O2S, the dihedral angle between the 4-chlorophenyl ring and the pyridine ring is 63.53 (6)°. There is an intramolecular C—H...O contact present. In the crystal, molecules are linked by pairs of N—H...S hydrogen bonds, forming inversion dimers. The dimers are linked by C—H...O and C—H...N hydrogen bonds, forming slabs parallel to theabplane.

N′-Benzylidene-2-({5-[(4-chlorophenoxy)methyl]-4-phenyl-4H-1,2,4-triazol-3-yl}sulfanyl)acetohydrazide hemihydrate

The title compound, C24H20ClN5O2S·0.5H2O, has three independent molecules in the asymmetric unit and two water molecules of crystallization, one of which is equally disordered over two sites. The three unique organic molecules differ in the conformations of the substituents on the pyrazole ring. In the crystal, extensive O—H...O, O—H...N, N—H...O and C—H...O hydrogen bonding generates a three-dimensional network and C—H...π interactions are also observed.

3-Phenoxymethyl-6-phenyl-1,2,4-triazolo[3,4-b][1,3,4]thiadiazole

In the title compound, C16H12N4OS, the bicyclic triazolothiadiazole core is approximately planar, with an r.m.s. deviation of 0.018 Å. The phenyl rings are inclined to its mean plane by 7.66 (7) and 71.79 (7)°. In the crystal, molecules are linkedviaa C—H...π interaction and a π–π interaction [intercentroid distance = 3.2942 (9) Å] involving inversion-related triazole rings. These interactions result in the formation of chains propagating along [10-1].

2-({5-[(4-Chlorophenoxy)methyl]-4-phenyl-4H-1,2,4-triazol-3-yl}sulfanyl)-N-phenylacetamide

The title molecule, C23H19ClN4O2S, is in an `extended' conformation. In the crystal, pairwise N—H...N and C—H...O hydrogen bonds lead to the formation of `stair-step' chains. C—H...π interactions further contribute to the consolidation of the molecular packing. The 4-chlorophenyl group is disordered over two sets of sites in a 0.948 (2):0.052 (2) ratio. The dihedral angle between the two components of the disordered chloro-substituted benzene ring is 15.76 (9) °.

2-{[5-(4-Chlorophenoxymethyl)-4-phenyl-4H-1,2,4-triazol-3-yl]sulfanyl}-N-(4-nitrophenyl)acetamide

The title molecule, C23H18ClN5O4S, is in an `extended' conformation. The central triazole ring makes dihedral angles of 58.14 (6), 86.29 (6) and 41.99 (6)°, respectively, with the adjacent phenyl, chlorophenyl and nitrophenyl rings. In the crystal, molecules are linkedviaa pair of N—H...N hydrogen bonds with anR22(16) ring motif, forming an inversion dimer. The dimers are connected by C—H...O hydrogen bonds into a tape structure along [011]. C—H...π interactions between the tapes are also observed.

Ethyl 3-({[(4-methylphenyl)carbamoyl]methyl}sulfanyl)-5,6-diphenylpyridazine-4-carboxylate

The packing in the crystal of the title molecule, C28H25N3O3S, is aided by intermolecular N—H...O and C—H...O hydrogen bonds. In the crystal, the ethyl group of the ester is disordered over two sets of sites with refined occupancies of 0.760 (8) and 0.240 (8).

Crystal structure of ethyl 3-amino-6-methyl-2-[(4-methylphenyl)carbamoyl]-4-[(E)-2-phenylethenyl]thieno[2,3-b]pyridine-5-carboxylate monohydrate

In the crystal, complementary N—H⋯O hydrogen bonds form dimers which are then associated into chains parallel to the c axis through O—H⋯N hydrogen bonds involving the lattice water mol­ecule.

In the title mol­ecule, C₂₇H₂₅N₃O₃S·H₂O, the dihedral angle between the planes of the thienyl ring and the pendant p-tolyl group is 39.25 (6)°, while that between the pyridine ring and the pendant phenyl ring is 44.37 (6)°. In addition, there is a slight twist in the bicyclic core, with a dihedral angle of 2.39 (4)° between the thienyl and pyridine rings. The conformation of the carbamoyl moiety is partially determined by an intra­molecular N—H⋯O hydrogen bond. In the crystal, complementary N—H⋯O hydrogen bonds form dimers which are then associated into chains parallel to the c axis through O—H⋯N hydrogen bonds involving the water mol­ecule of crystallization. Electron density associated with an additional solvent mol­ecule of partial occupancy and disordered about a twofold axis was removed with the SQUEEZE procedure in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9–18]. The given chemical formula and other crystal data do not take into account the unknown solvent molecule(s).

Diethyl 3-amino-6-methyl-4-[(E)-2-phenylethenyl]thieno[2,3-b]pyridine-2,5-dicarboxylate

In the title molecule, C22H22N2O4S, the bicyclic core is slightly folded [1.9 (1)°], while pairwise intermolecular N—H...O hydrogen bonding forms dimers across centers of symmetry. The dihedral angle between the phenyl ring an the six-membered ring of the bicyclic core is 75.50 (4)°. The molecular conformation is stabilized by an intramolecular N—H...O hydrogen bond with graph-set motifS(6) and by a weak C—H...O contact, forming anS(7) motif. In the crystal, π–π interactions [centroid-to-centroid distance = 3.7484 (10) Å] between phenyl rings and two weak C—H...π interactions are also observed.