Enzymes involved in lipid A biosynthesis are promising antibacterial drug targets in Gram-negative bacteria. In this study, we use a structure-based design approach to develop a series of novel tetrazole ligands with low μM affinity for LpxA, the first enzyme in the lipid A pathway. Aided by previous structural data, X-ray crystallography, and surface plasmon resonance bioanalysis, we identify 17 hit compounds. Two of these hits were subsequently modified to optimize interactions with three regions of the LpxA active site. This strategy ultimately led to the discovery of ligand L13, which had a KD of 3.0 μM. The results reveal new chemical scaffolds as potential LpxA inhibitors, important binding features for ligand optimization, and protein conformational changes in response to ligand binding. Specifically, they show that a tetrazole ring is well-accommodated in a small cleft formed between Met169, the "hydrophobic-ruler" and His156, both of which demonstrate significant conformational flexibility. Furthermore, we find that the acyl-chain binding pocket is the most tractable region of the active site for realizing affinity gains and, along with a neighboring patch of hydrophobic residues, preferentially binds aliphatic and aromatic groups. The results presented herein provide valuable chemical and structural information for future inhibitor discovery against this important antibacterial drug target.

Michael D. Sacco

Kyle Defrees

Xiujun Zhang

William Lawless

Emeka Nwanochie

Amelia Balsizer

Sophie E. Darch

Adam R. Renslo

Yu Chen

ACS Infectious Diseases

ACS INFECTIOUS DISEASES 将成为第一本强调化学及其在这一多学科和合作研究领域中的作用的期刊。该杂志将涵盖各种主题，包括但不限于：*发现和开发新的抗菌药物——通过基于靶点或表型的方法以及与抗菌药物产生协同作用的化合物进行鉴定。*药物的表征和验证靶点或通路——使用单一靶点和全基因组敲除和敲除、生化研究、结构生物学、促进潜在药物靶点的表征和优先排序的新技术。* 耐药性机制——促进我们对耐药性理解的基础研究；预防耐药性的策略。* 作用机制——使用遗传、代谢组学和基于活性和亲和力的蛋白质分析来阐明临床和实验性抗菌剂的作用机制。* 宿主-病原体相互作用——研究宿主-病原体的工具相互作用，宿主和病原体的细胞生物化学，以及病原体与宿主微生物群的分子相互作用。*传染病的小分子疫苗佐剂。*病毒和细菌生物化学和分子生物学。

ACS Infectious Diseases is a journal that emphasizes the role of chemistry in this multidisciplinary and collaborative research field. The journal covers a variety of topics, including but not limited to: * Discovery and development of new antibacterial agents—identifying compounds that act synergistically with antibacterial drugs through target-based or phenotypic approaches. * Characterization of drugs and validation of targets or pathways—using single-target and whole-genome knockout and knockdown, biochemical studies, structural biology, and new technologies to facilitate the characterization and prioritization of potential drug targets. * Mechanisms of resistance—basic research that enhances our understanding of resistance; strategies for preventing resistance. * Mechanisms of action—elucidating the mechanisms of clinical and experimental antibacterial agents using genetics, metabolomics, and activity- and affinity-based protein analyses. * Host-pathogen interactions—studying the interactions between host and pathogen, the cell biochemistry of hosts and pathogens, and the molecular interactions between pathogens and host microbiomes. * Small molecule vaccine adjuvants for infectious diseases. * Biochemistry and molecular biology of viruses and bacteria.

《ACS Infectious Diseases》是一本专注于化学及其在多学科合作研究领域中作用的期刊。该杂志涵盖多个主题，包括但不限于：* 新抗菌药物的发现与开发——通过靶点或表型的方法，识别与抗菌药物协同作用的化合物。* 药物的表征与靶点或通路的验证——采用单一靶点和全基因组敲除、敲除、生化研究、结构生物学等新技术，促进潜在药物靶点的表征与优先排序。* 耐药机制——基础研究促进我们对耐药性的理解；预防耐药性的策略。* 作用机制——利用遗传学、代谢组学及基于活性和亲和力的蛋白质分析，阐明临床和实验性抗菌剂的作用机制。* 宿主-病原体相互作用——研究宿主与病原体之间的相互作用、宿主和病原体的细胞生物化学，以及病原体与宿主微生物群的分子相互作用。* 传染病的小分子疫苗佐剂。* 病毒和细菌的生物化学与分子生物学。

Structure-Based Ligand Design Targeting <i>Pseudomonas aeruginosa</i> LpxA in Lipid A Biosynthesis

The results reveal new chemical scaffolds as potential LpxA inhibitors, important binding features for ligand optimization, and protein conformational changes in response to ligand binding, and show that a tetrazole ring is well-accommodated in a small cleft formed between Met169, the "hydrophobic-ruler" and His156, both of which demonstrate significant conformational flexibility.

Category	Quartile
医学	2
医学, 药物化学	2
医学, 传染病学	2

Structure-Based Ligand Design Targeting Pseudomonas aeruginosa LpxA in Lipid A Biosynthesis

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