Currently much effort has been
Currently, much effort has been made to design and synthesize ThDP analogs (such as ThTDP, ThTTDP, and triazole-ThDP in Fig. 2)8, 9, 10, 11, 12 as PDHc E1 inhibitors. These ThDP analog inhibitors, such as ThTDP and ThTTDP, can block the ThDP binding site, and exhibit significantly stronger binding affinities for PDHc E1 than ThDP.13, 14 However, these ThDP analogs exhibit no potential utility and display poor bioavailability, due to their complex structure with highly charged pyrophosphate groups. They also showed poor enzyme-selective inhibition between microorganisms and mammals.
To the best of our knowledge, the crystal structures of the PDHc E1/ThDP or inhibitor complex from E. coli (PDB ID: 1L8A and 1RP7) have been determined. The crystal structures enable structure-based design of novel inhibitors against PDHc E1. On that basis, we selected E. coli PDHc E1 as the target pattern to design new cofactor ThDP analogs as inhibitors of PDHc E1. In our laboratory, we recently had got preliminary progress for finding an effective E. coli PDHc E1 inhibitor I by structure-based rational design.17, 18 The mechanism was predicted with theory. Base on this work, the linker of I was further optimized affording ThDP analogs II, III, IV, V and VI as E. coli PDHc E1 inhibitors (Fig. 2).19, 20, 21, 22, 23 Some of them were demonstrated to be effective inhibition (IC50>0.65µM) of E. coli PDHc E1 with moderate antibacterial or antifungal activity. The results convinced us that the linker (Fig. 2) of parent structure I plays a vital role in the biological activity of these ThDP analogs. The findings encouraged us to further find useful PDHc E1 inhibitors out with antibacterial or antifungal activity by further optimization of lead structure I.
Structure–activity relationship (SAR) indicated the introduction of Cy5 amine (non-sulfonated) acceptor or hydrogen bond donor structural unit into the linker in parent structure I could increase the inhibitory activity against E. coli PDHc E1 and antifungal activity.22, 23 Aiming to explore more optimizing linkages, the N-acylhydrazone moiety (CONHNCH), which not only had well-known biological activities,24, 25, 26 but also included hydrogen bond acceptor and hydrogen bond donor structural unit, was introduced to the structure I as a ‘open-chain’ linker to form a new structural class A as potential E. coli PDHc E1 inhibitors. Furthermore, the effect of Me group on pyrimidine ring was firstly studied, which was replaced by H or NH2 group. Therefore, three new structural classes of PDHc E1 inhibitors were formed (Fig. 3). Considering the binding site of diphosphate of ThDP in the active site of E. coli PDHc E1, various chemical groups as Ar were incorporated into the parent compounds A, B, and C to investigate their preliminary SAR.
Herein, the chemical synthesis of these new N-acylhydrazone pyrimidine derivatives A, B, and C as E. coli PDHc E1 inhibitors is described in details. The inhibitory activities on E. coli PDHc E1 are presented along with their SAR analysis as follows. Interaction between mode of inhibitor and target PDHc E1 was also explored by molecular docking study to identify the critical binding sites of the target PDHc E1. The enzyme-selectivity of representative compounds between microorganisms and mammals was also examined.
Chemistry The synthetic route of A, B, and C is depicted in Scheme 1. Substituted-amidine and 2-(ethoxymethylene)malononitrile as starting material was used to prepare 4-amino-2-substitutedpyrimidine-5-carbaldehyde 2 according to the literature method.2 is the key intermediate for the preparation of title compounds A, B, and C. The title compounds could be synthesized by a five-step sequence starting from starting material. Various substituted benzoic acid reacted with ethanol in the presence of concentrated sulfuric acid to produce substituted ethyl benzoate 3, which reacted with hydrazine hydrate in ethanol to produce corresponding hydrazide 4. Finally, the new N-acylhydrazone pyrimidine derivatives A, B, and C were prepared in good yields by condensing compound 2 with a variety of substituted benzoyl hydrazine in ethanol at reflux. All synthesized compounds were characterized by 1H NMR, 13C NMR, mass spectrometry and elementary analysis.