Beyond Fang's fury: a computational study of the enzyme–membrane interaction and catalytic pathway of the snake venom phospholipase A2 toxin†

IF 7.6 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY
Juliana Castro-Amorim, Alexandre V. Pinto, Ashis K. Mukherjee, Maria J. Ramos and Pedro A. Fernandes
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引用次数: 0

Abstract

Snake venom-secreted phospholipases A2 (svPLA2s) are critical, highly toxic enzymes present in almost all snake venoms. Upon snakebite envenomation, svPLA2s hydrolyze cell membrane phospholipids and induce pathological effects such as paralysis, myonecrosis, inflammation, or pain. Despite its central importance in envenomation, the chemical mechanism of svPLA2s is poorly understood, with detrimental consequences for the design of small-molecule snakebite antidotes, which is highly undesirable given the gravity of the epidemiological data that ranks snakebite as the deadliest neglected tropical disease. We study a member of the svPLA2 family, the Myotoxin-I, which is part of the venom of the Central American pit viper terciopelo (Bothrops asper), a ubiquitous but highly aggressive and dangerous species responsible for the most problematic snakebites in its habitat. Furthermore, PLA2 enzymes are a paradigm of interfacial enzymology, as the complex membrane–enzyme interaction is as important as is crucial for its catalytic process. Here, we explore the detailed interaction between svPLA2 and a 1 : 1 POPC/POPS membrane, and how enzyme binding affects membrane structure and dynamics. We further investigated the two most widely accepted reaction mechanisms for svPLA2s: the ‘single-water mechanism’ and the ‘assisted-water mechanism’, using umbrella sampling simulations at the PBE/MM level of theory. We demonstrate that both pathways are catalytically viable. While both pathways occur in two steps, the single-water mechanism yielded a lower activation free energy barrier (20.14 kcal mol−1) for POPC hydrolysis, consistent with experimental and computational values obtained for human PLA2. The reaction mechanisms are similar, albeit not identical, and can be generalized to svPLA2 from most viper species. Furthermore, our findings demonstrate that the sole small molecule inhibitor currently undergoing clinical trials for snakebite is a perfect transition state analog. Thus, understanding snake venom sPLA2 chemistry will help find new, effective small molecule inhibitors with anti-snake venom efficacy.

Abstract Image

Abstract Image

超越方的愤怒:蛇毒磷脂酶A2毒素的酶-膜相互作用和催化途径的计算研究
蛇毒分泌的磷脂酶A2 (svPLA2s)是几乎所有蛇毒中都存在的关键的高毒性酶。在蛇咬中毒后,svPLA2s水解细胞膜磷脂并引起病理作用,如瘫痪、肌坏死、炎症或疼痛。尽管svPLA2s在毒杀中具有核心重要性,但其化学机制尚不清楚,这对设计小分子蛇咬伤解毒剂产生了不利影响,鉴于流行病学数据将蛇咬伤列为最致命的被忽视的热带病的严重性,这是非常不可取的。我们研究了svPLA2家族的一个成员,Myotoxin-I,它是中美洲蝮蛇terciopelo (Bothrops aspper)毒液的一部分,这是一种无处不在但具有高度攻击性和危险的物种,在其栖息地造成了最严重的蛇咬伤。此外,PLA2酶是界面酶学的一个范例,因为复杂的膜-酶相互作用对其催化过程同样重要。在这里,我们详细探讨了svPLA2与1:1 POPC/POPS膜之间的相互作用,以及酶结合如何影响膜结构和动力学。我们进一步研究了svPLA2s的两种最广泛接受的反应机制:“单水机制”和“辅助水机制”,采用PBE/MM水平的伞式采样模拟理论。我们证明这两种途径在催化上都是可行的。虽然这两种途径都分两步进行,但单水机制对POPC的水解产生了较低的激活自由能垒(20.14 kcal mol−1),与人类PLA2的实验和计算值一致。尽管不完全相同,但反应机制相似,并且可以推广到大多数毒蛇物种的svPLA2。此外,我们的研究结果表明,目前正在进行蛇咬伤临床试验的唯一小分子抑制剂是一种完美的过渡状态类似物。因此,了解蛇毒sPLA2的化学性质将有助于发现新的、有效的具有抗蛇毒功效的小分子抑制剂。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Chemical Science
Chemical Science CHEMISTRY, MULTIDISCIPLINARY-
CiteScore
14.40
自引率
4.80%
发文量
1352
审稿时长
2.1 months
期刊介绍: Chemical Science is a journal that encompasses various disciplines within the chemical sciences. Its scope includes publishing ground-breaking research with significant implications for its respective field, as well as appealing to a wider audience in related areas. To be considered for publication, articles must showcase innovative and original advances in their field of study and be presented in a manner that is understandable to scientists from diverse backgrounds. However, the journal generally does not publish highly specialized research.
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