Analysis of three crystal structure determinations of a 5-methyl-6-N-methylanilino pyridopyrimidine antifolate complex with human dihydrofolate reductase
Analysis of three crystal structure determinations of a 5-methyl-6-N-methylanilino pyridopyrimidine antifolate complex with human dihydrofolate reductase
复制标题
DOI：
10.1107/s0907444903014963
复制
发表时间：
2003-09-01
期刊：
影响因子：
--
通讯作者：
Gangjee, A
中科院分区：
文献类型：
--
作者：
Cody, V;Luft, JR;Gangjee, A
首次报道了有效的抗叶酸抑制剂2,4-二氨基-5-甲基-6-[（3',4',5'-三甲氧基- n -甲基苯胺）甲基]吡啶[2,3-d]嘧啶(1)与人二氢叶酸还原酶（hDHFR）和NADPH配合物的结构数据。结晶条件的微小差异导致了两种不同形式的二元配合物的生长。本文还报道了在类似条件下生长的hDHFR与NADPH和(1)三元配合物的另一个晶体的结构测定。从NADPH和(1)的hDHFR三元配合物中获得的R3晶格的衍射数据为2.1埃分辨率，从二元配合物中获得的衍射数据为2.2埃分辨率。在第一个四边形P4(3)2(1)2晶格的例子中，从具有hDHFR和(1)的二元配合物中也收集了2.1 A分辨率的数据。这些结构的分子间接触比较揭示了柔性环区（残基40-46、77-83和103-107）的主链构象（1.9-3.2埃）的差异，反映了方面体和四边形空间基团之间填充环境的差异。堆积环境分析表明，四方晶格的堆积更加紧密，体现在其较小的V-M值和较低的溶剂含量上。抑制剂(1)的构象在所有结构上都相似，并且与母体喹唑啉化合物TMQ的构象相似。结果表明，与N-H或N-CHO类似物相比，N10-CH3取代物(1)对刚地弓形虫DHFR （tgDHFR）具有最大的效价和选择性。tgDHFR活性位点的模型表明，在人或卡氏肺囊虫DHFR结构中都不存在与(1)的优先接触。酸性残基（tgDHFR的Glu30和Asp）的差异影响了二氨基吡啶环的精确定位，而其他残基的变化，特别是在第60和64位（Leu与Met和Asn与Phe），涉及与三甲氧基取代基的相互作用。
Structural data are reported for the first example of the potent antifolate inhibitor 2,4-diamino-5-methyl-6-[(3',4',5'-trimethoxy-N-methylanilino) methyl] pyrido[2,3-d] pyrimidine (1) in complex with human dihydrofolate reductase (hDHFR) and NADPH. Small differences in crystallization conditions resulted in the growth of two different forms of a binary complex. The structure determination of an additional crystal of a ternary complex of hDHFR with NADPH and (1) grown under similar conditions is also reported. Diffraction data were collected to 2.1 Angstrom resolution for an R3 lattice from a hDHFR ternary complex with NADPH and (1) and to 2.2 Angstrom resolution from a binary complex. Data were also collected to 2.1 A resolution from a binary complex with hDHFR and (1) in the first example of a tetragonal P4(3)2(1)2 lattice. Comparison of the intermolecular contacts among these structures reveals differences in the backbone conformation (1.9-3.2 Angstrom) for flexible loop regions (residues 40-46, 77-83 and 103-107) that reflect differences in the packing environment between the rhombohedral and tetragonal space groups. Analysis of the packing environments shows that the tetragonal lattice is more tightly packed, as reflected in its smaller V-M value and lower solvent content. The conformation of the inhibitor (1) is similar in all structures and is also similar to that observed for TMQ, the parent quinazoline compound. The activity profile for this series of 5-deaza N-substituted non-classical trimethoxybenzyl antifolates shows that the N10-CH3 substituted (1) has the greatest potency and selectivity for Toxoplasma gondii DHFR (tgDHFR) compared with its N-H or N-CHO analogs. Models of the tgDHFR active site indicate preferential contacts with (1) that are not present in either the human or Pneumocystis carinii DHFR structures. Differences in the acidic residue (Glu30 versus Asp for tgDHFR) affect the precise positioning of the diaminopyrido-pyrimidine ring, while changes in other residues, particularly at positions 60 and 64 (Leu versus Met and Asn versus Phe), involve interactions with the trimethoxybenzyl substituents.