二氢嘧啶并[4,5-d]嘧啶类衍生物作为集落刺激因子-1受体激酶抑制剂的分子对接和定量构效关系研究

集落刺激因子-1受体激酶（CSF-1R）属于Ⅲ型受体酪氨酸激酶家族成员,其在调控单核巨噬细胞系中发挥重要作用。CSF-1R及其配体异常表达与肿瘤发展过程密切相关。因此,CSF-1R信号传导可成为抗肿瘤治疗的有吸引力的靶标。本文用比较分子场分析法（CoMFA）和比较分子相似性指数分析法（CoMSIA）研究了54个二氢嘧啶并[4,5-d]嘧啶类CSF-1R激酶抑制剂的三维定量构效关系（3D-QSAR）。基于配体叠合,CoMFA和CoMSIA模型的交叉验证系数（q2）分别为0.725和0.636,拟合验证系数（r2）分别为0.960和0.958,结果表明这两种模型均具有较好的预测能力。所建模型的等势图能直观反映分子不同取代基对活性的影响,其中立体场和疏水场对活性的贡献较大。通过分子对接研究显示,氨基酸残基Cys666、Asp796在配体和受体结合过程中产生作用,分子对接的结合模式与3D-QSAR得到的结果一致。这些信息为进一步优化CSF-1R激酶抑制剂提供了理论基础。     

3D-QSAR and Docking Studies of Pyrido[2,3-d]pyrimidine Derivatives as Wee1 Inhibitors

In order to investigate the inhibiting mechanism and obtain some helpful information for de-signing functional inhibitors against Wee1, three-dimensional quantitative structure-activity relationship (3D-QSAR) and docking studies have been performed on 45 pyrido[2,3-d] pyrim-idine derivatives acting as Wee1 inhibitors. Two optimal 3D-QSAR models with significant statistical quality and satisfactory predictive ability were established, including the CoMFA model (q²=0.707, R²=0.964) and CoMSIA model (q²=0.645, R²=0.972). The external val-idation indicated that both CoMFA and CoMSIA models were quite robust and had high predictive power with the predictive correlation coefficient values of 0.707 and 0.794, essen-tial parameter r²_m values of 0.792 and 0.826, the leave-one-out r²_m(LOO) values of 0.781 and 0.809, r²_m(overall) values of 0.787 and 0.810, respectively. Moreover, the appropriate binding orientations and conformations of these compounds interacting with Wee1 were revealed by the docking studies. Based on the CoMFA and CoMSIA contour maps and docking analyses, several key structural requirements of these compounds responsible for inhibitory activity were identified as follows: simultaneously introducing high electropositive groups to the sub-stituents R1 and R5 may increase the activity, the substituent R2 should be smaller bulky and higher electronegative, moderate-size and strong electron-withdrawing groups for the substituent R3 is advantageous to the activity, but the substituent X should be medium-size and hydrophilic. These theoretical results help to understand the action mechanism and design novel potential Wee1 inhibitors.     

Synthesis of Functionally Substituted Pyrrolo[2,3-g]- and Pyrrolo[3,2-f]quinolines from 5-Amino-2-phenyl- and 5-Amino-1-methyl-2-phenylindoles

The behavior of 5-amino-2-phenyl- and 5-amino-1-methyl-2-phenylindoles in reactions with acetoacetic, trifluoroacetoacetic, and ethoxymethylenemalonic esters, leading to the preparation of pyrrolo[2,3-g]- and pyrrolo[3,2-f]quinolines with functional substituents has been studied.     

Synthesis,Characterization and Biological Activity of Tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidine Derivatives as Epidermal Growth Factor Receptor Inhibitors

Based on the molecular docking studies, which were performed to position Erlotinib and the target compounds into the active site of the epidermal growth factor receptor(EGFR) to determine the probable binding model, a novel series of 5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidine derivatives as the novel potential EGFR kinase inhibitors was designed and synthesized. The antitumor activity of all the target compounds against human pulmonary carcinoma cell line A549 has been screened. Of all the target compounds, 4-[2-(1-piperidyl)carbonylmethoxyl- phenthio]-5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidine(7j) demonstrated the most potent antitumor activity. Several of the target compounds exhibited moderate antitumor activity. The preliminary structure-activity relationships of some target compounds were summarized.     

Computational Approaches for the Design of Novel Anticancer Compounds Based on Pyrazolo[3,4-d]pyrimidine Derivatives as TRAP1 Inhibitor

In the present in-silico study, various computational techniques were applied to determine potent compounds against TRAP1 kinase. The pharmacophore hypothesis DHHRR_1 consists of important features required for activity. The 3D QSAR study showed a statistically significant model with R² = 0.96 and Q² = 0.57. Leave one out (LOO) cross-validation (R² CV = 0.58) was used to validate the QSAR model. The molecular docking study showed maximum XP docking scores (−11.265, −10.532, −10.422, −10.827, −10.753 kcal/mol) for potent pyrazole analogs (42, 46, 49, 56, 43), respectively, with significant interactions with amino acid residues (ASP 594, CYS 532, PHE 583, SER 536) against TRAP1 kinase receptors (PDB ID: 5Y3N). Furthermore, the docking results were validated using the 100 ns MD simulations performed for the selected five docked complexes. The selected inhibitors showed relatively higher binding affinities than the TRAP1 inhibitor molecules present in the literature. The ZINC database was used for a virtual screening study that screened ZINC05297837, ZINC05434822, and ZINC72286418, which showed similar binding interactions to those shown by potent ligands. Absorption, distribution, metabolism, and excretion (ADME) analysis showed noticeable results. The results of the study may be helpful for the further development of potent TRAP1 inhibitors     

Potential Stereoselective Binding of Trans-(±)-Kusunokinin and Cis-(±)-Kusunokinin Isomers to CSF1R

Breast cancer cell proliferation and migration are inhibited by naturally extracted trans-(−)-kusunokinin. However, three additional enantiomers of kusunokinin have yet to be investigated: trans-(+)-kusunokinin, cis-(−)-isomer and cis-(+)-isomer. According to the results of molecular docking studies of kusunokinin isomers on 60 breast cancer-related proteins, trans-(−)-kusunokinin was the most preferable and active component of the trans-racemic mixture. Trans-(−)-kusunokinin targeted proteins involved in cell growth and proliferation, whereas the cis-(+)-isomer targeted proteins involved in metastasis. Trans-(−)-kusunokinin targeted CSF1R specifically, whereas trans-(+)-kusunokinin and both cis-isomers may have bound AKR1B1. Interestingly, the compound’s stereoisomeric effect may influence protein selectivity. CSF1R preferred trans-(−)-kusunokinin over trans-(+)-kusunokinin because the binding pocket required a ligand planar arrangement to form a π-π interaction with a selective Trp550. Because of its large binding pocket, EGFR exhibited no stereoselectivity. MD simulation revealed that trans-(−)-kusunokinin, trans-(+)-kusunokinin and pexidartinib bound CSF1R differently. Pexidartinib had the highest binding affinity, followed by trans-(−)-kusunokinin and trans-(+)-kusunokinin, respectively. The trans-(−)-kusunokinin-CSF1R complex was found to be stable, whereas trans-(+)-kusunokinin was not. Trans-(±)-kusunokinin, a potential racemic compound, could be developed as a selective CSF1R inhibitor when combined.     

2,3-Dihydro-5,6-tetramethylenespiro(cyclohexane-2-thieno[2,3-d]pyrimidine)-4(1H)-thione. A Novel Synthetic Route and Crystalline Structure

Self-condensation of cyclohexylidenecyanothioacetamide gave 2,3-dihydro-5,6-tetramethylenespiro(cyclohexane-2-thieno[2,3-d]pyrimidine)-4(1H)-thione, the structure of which was proved by X-ray analysis. A mechanism is proposed for its formation and its alkylation has been studied.     

The Utility of Isothiocyanato Thiophenes in the Synthesis of Thieno[2,3-d]pyrimidine Derivatives as Possible Radioprotective and Anticancer Agents

The synthesis of novel thioureido derivatives 3, 8, and 10; biscompounds 7, 9, and 11; and tetracyclic compounds 5, 6, and 16 utilizing 5-isothiocyanato-3-methyl-thiophene-2,4-dicarboxylic acid diethyl ester 2 are reported. The structures of these compounds were confirmed by microanalyses and IR, ¹H NMR, and mass spectroscopy. Preliminary biological studies of some of the synthesized compounds showed promising radioprotective and anticancer activities.     

A Convenient Method for the Preparation of Substituted Naphtho[2,3-b]-1,4-dioxin by the Diels-Alder Reaction.

The naphtho-fused systems 3 and 4 were synthesized from the hydroxy-acetal1 through deacetylation, formation of unstable diene 2 and Diels-Alder cycloaddition with the appropriate dienophile in acidic media.     

Unusual dihydrazone formation in the fischer-indole cyclization. The synthesis of novel nonclassical annulated 2,4-Diamino-pyrrolo[2,3-d]pyrimidine antifolates

The synthesis of seven novel tetracyclic 2,4-diaminopyrrolo[2,3-d]pyrimidines as conformationally restricted nonclassical antifolates was achieved via an unusual Fischer-indole cyclization of dihydrazones. An attempted synthesis of 2,4-diamino-6-hydrazinopyrimidine afforded 2-amino-4,6-dihydrazinopyrimidine which when reacted with appropriate ketones gave the dihydrazones. The dihydrazones in turn under Fischer-indole cyclization conditions afforded target conformationally restricted tetracyclic products.     

Exploiting the Multidentate Nature of Chiral Disulfonimides in a Multicomponent Reaction for the Asymmetric Synthesis of Pyrrolo[1,2‐a]indoles: A Remarkable Case of Enantioinversion

A new multicomponent coupling reaction for the enantioselective synthesis of pyrrolo[1,2‐a]indoles under the catalysis of a chiral disulfonimide is described. The high specificity of the reaction is a consequence of the multidentate character of the Brønsted acid catalyst. Insights from DFT calculations helped explain the unexpected high enantioselectivity observed with the simplest 3,3′‐unsubstituted binaphthyl catalyst as a result of transition‐state stabilization by a network of cooperative noncovalent interactions. The remarkable enantioinversion resulting from the simple introduction of substituents at 3‐ and 3′‐positions, the first reported example of this phenomenon in the context of binaphthalene‐derived Brønsted acid catalysis, was instead attributed to destabilizing steric interactions.     

Methyl 2-benzoylamino-3-dimethylaminopropenoate in the synthesis of heterocyclic systems. The synthesis of benzoyl- amino substituted 7H-pyrano[2,3-d]pyrimidine, 1H,6H-pyrano- [2,3-c]pyrazole and 2H-1-benzopyran derivatives

Methyl 2-benzoylamino-3-dimethylaminopropenoate (6) reacts with heterocyclic compounds containing an active methylene group or potential methylene group in the ring system, such as barbituric acid derivatives 1 and 2, pyrazolones 3 and 4, and resorcinol, in acetic acid to afford the corresponding benzoylamino substituted pyranopyrimidinones 7 and 8 , pyranopyrazolones 9 and 10 , and 2H-1-benzopyranone 11 . The method represents a novel procedure for the preparation of condensed pyranones.     

First Asymmetric Total Synthesis of (R,E)-1-[4-(3-Hydroxyprop-1-enyl)phenoxyl]-3-methylbutane-2,3-diol

A new anti-inflammatory active phenylpropenoid, (R,E)-1-[4-(3-hydroxyprop-1-enyl) phenoxyl]-3-methylbutane-2,3-diol (1), isolated from the stem wood of Zanthoxylum integrifoliolum, has been synthesized for the first time using commercially available 4-hydroxy benzaldehyde (2). The key step involves the Sharpless asymmetric dihydroxylation of olefin (3).

Isolation of Intermediates in the Synthesis of Thieno[2,3-d]pyrimidine-2,4(1H,3H)-diones Using Microwave Irradiation

A simple and fast method for the isolation of intermediates in the synthesis of 3-arylthieno[2,3-d]pyrimidine-2,4(1H,3H)-diones has been developed by microwave-assisted condensation of ethyl 2-amino-4,5-dimethylthiophene-3-carboxylate with aryl isocyanates. The intermediates, subsequently, underwent cyclization in t-butanol in the presence of potassium t-butoxide on heating to reflux to give the desired bicyclic products, 3-arylthieno[2,3-d]pyrimidine-2,4(1H,3H)-diones.     

Contractive Annulation: A Strategy for the Synthesis of Small,Strained Cyclophanes and Its Application in the Synthesis of [2](6,1)Naphthaleno[1]paracyclophane

A new synthetic strategy (contractive annulation) for the synthesis of highly strained cyclophanes has been conceived and its viability has been demonstrated through a nine‐step synthesis of [2](6,1)naphthaleno[1]paracyclophane from [2.2]paracyclophane.     

Preparation of brassylic acid from 5,6,7,8,9,10,11,12,13,14-decahydrocyclododeca[1,2-d]pyrimidine(1H, 3H)-2,4-dione obtained by the condensation of cyclododecanone and urea or biuret

A simple method is proposed for the preparation of brassylic acid by the alkaline hydrolysis of 5,6,7,8,9,10,11,12,13,14-decahydrocyclododeca[1,2-d]pyrimidine(1H, 3H)dione-2,4, which is the product of the condensation of cyclododecanone with urea or biuret. The condensation of the cyclododecanone with thiourea proceeds differently, leading to 5,6,7,8,9,10,11,12,13,14-decahydrocyclododeca[1,2-d]pyrimidine(1H, 3H)spirocyclododecane-2-thione-4.A. N. Nesmeyanov Institute of Organometallic Compounds, Russian Academy of Sciences, 117813 Moscow. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 1, pp. 226–229, January, 1992.     

Synthesis of tri- or tetrasubstituted pyrimidine derivatives through the [5+1] annulation of enamidines with either N,N-dimethylformamide dialkyl acetals or orthoesters and their application in a ring transformation of pyrimidines to pyrido[2,3-d]pyrimidin-5-one derivatives

The [5+1] annulation of enamidines, which were prepared from functionalized silanes, organolithium compounds and two nitriles, with N,N-dimethylformamide dialkyl acetals as the C1 unit is described, leading to the synthesis of tri- and tetrasubstituted pyrimidine derivatives under catalyst- and solvent-free reaction conditions. Furthermore, the [5+1] annulation of enamidines by using orthoesters as the C1 unit is described, in which catalytic amounts of ZnBr(2) catalyze the annulation to produce polysubstituted pyrimidines under toluene or xylene reflux conditions. Moreover, the combination of a reductive ring-opening reaction with [Mo(CO)(6)] and a subsequent intramolecular cyclization with tBuOK effectively causes a skeletal transformation from the pyrimidines containing an isoxazolyl and an ethoxy substituent to form pyrido[2,3-d]pyrimidin-5-one frameworks in excellent yield.     

Reversal of the Regiochemistry in the Rhodium‐Catalyzed [4+3] Cycloaddition between Vinyldiazoacetates and Dienes

A regio‐, diastereo‐, and enantioselective [4+3] cycloaddition between vinylcarbenes and dienes has been achieved using the dirhodium tetracarboxylate catalyst [Rh₂(S‐BTPCP)₄]. This methodology provides facile access to 1,4‐cycloheptadienes that are regioisomers of those formed from the tandem cyclopropanation/Cope rearrangement reaction of vinylcarbenes with dienes.