Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
Research Laboratories for Rational Design of Drugs and Biomaterials, Isiphephelo Court, Tsakane, 1550, Brakpan, Johannesburg East Rand, Gauteng, South Africa.
Curr Top Med Chem. 2023;23(12):1065-1080. doi: 10.2174/1568026623666230125124433.
β-ketoacyl-ACP synthase I (KasA I) enzyme is crucial in mycolic acid synthesis catalytic condensation reactions, hence implicated in 's virulence and drug resistance. Presently, there is no known potent KasA inhibitor; thiolactomycin lacks potency. Recently reported indazole compounds JSF-3285/DG167 and 5G/DG167 inhibit the KasA through binding to the substrate cavity. However, the molecular mechanism is still unclear, and the unknown resistance mechanisms raise concerns about JSF-3285's novelty.
This study is the first to report the flap dimer opening and closing of the KasA pocket using combined metrics to define the symmetry impact of the flap-dimer motions and investigate the underlying inhibitory mechanism of DG167 andDG167 using all-atom MD simulation.
The distance/ between the flap (PRO147) and dimer (LEU205) residues; TriC-α angle (: PRO147-VAL83-LEU205 & : PRO147-GLU199-LEU205); and the dihedral angle () were applied to investigate the flap "twisting" and dimer shift closing due to concerted motion by adjacent glycine-rich and glutamic acid-rich loops around the active site during the binding pocket's opening. The full flap-dimer of the unbound opens at 230 ns (d1 = 21.51 Å), corresponding to the largest TriC-α angle 44.5° as is unreliable to describe the flap-dimer motion. The overall averages and for the bounds were ~23.13° and ~23.31°, respectively. Thus, the degree of KasA flap dimer opening is best investigated by distance and . BFE (Kcal/mol) of -44.05 (DG167) showed a higher affinity for the pocket than tr2DG167-KasA (-32.16). Both DG167 and DG167 formed hydrophobic interactions with LEU116, GLY117, ALA119, and tr1DG167 formed strong H-bonds with GLU199. The average RMSD of 2.80 Å (Apo) and RoG of 20.97 Å showed that KasA is less stable and less tightly packed without the inhibitors.
These findings provide a background for a new structure-based design of novel KasA inhibitors.
β-酮酰基-ACP 合酶 I（KasA I）酶在分枝菌酸合成的催化缩合反应中至关重要，因此与“结核分枝杆菌”的毒力和耐药性有关。目前，尚无已知的强效 KasA 抑制剂；硫内酯霉素缺乏效力。最近报道的吲唑化合物 JSF-3285/DG167 和 5G/DG167 通过与底物腔结合来抑制 KasA。然而，其分子机制尚不清楚，并且未知的耐药机制引起了对 JSF-3285 新颖性的关注。
本研究首次报告了使用组合度量来定义瓣状二聚体运动的对称性影响，并使用全原子 MD 模拟研究了 DG167 和 DG167 对 KasA 的抑制机制，从而研究了 KasA 口袋中瓣状结构的打开和关闭。
使用距离/瓣状（PRO147）和二聚体（LEU205）残基之间的距离；TriC-α 角（：PRO147-VAL83-LEU205 和：PRO147-GLU199-LEU205）；和二面角（）来研究瓣状结构“扭曲”和由于活性位点周围富含甘氨酸和谷氨酸的环的协同运动导致的二聚体移动关闭，从而导致结合口袋打开。在无配体结合时，完整的无约束瓣状二聚体在 230 ns 时打开（d1 = 21.51 Å），对应于最大的 TriC-α 角 44.5°，因为 对于描述瓣状二聚体运动是不可靠的。绑定的总体平均值 和 分别约为23.13°和23.31°。因此，KasA 瓣状二聚体的打开程度最好通过距离和 来研究。-44.05（DG167）的 BFE（千卡/摩尔）显示出比 tr2DG167-KasA（-32.16）更高的结合口袋亲和力。DG167 和 DG167 都与 LEU116、GLY117、ALA119 形成疏水性相互作用，而 tr1DG167 与 GLU199 形成强氢键。平均 RMSD 为 2.80 Å（Apo）和 RoG 为 20.97 Å，表明没有抑制剂时，KasA 稳定性较低，结合更不紧密。
这些发现为新型 KasA 抑制剂的基于结构的新设计提供了背景。
