Computational Organic Chemistry and Biochemistry Group , Ruđer Bošković Institute , Bijenička cesta 54 , HR-10000 Zagreb , Croatia.
ACS Chem Neurosci. 2019 Aug 21;10(8):3532-3542. doi: 10.1021/acschemneuro.9b00147. Epub 2019 Jul 2.
Monoamine oxidases (MAOs) are flavin adenine dinucleotide containing flavoenzymes that catalyze the degradation of a range of brain neurotransmitters, whose imbalance is extensively linked with the pathology of various neurological disorders. This is why MAOs have been the central pharmacological targets in treating neurodegeneration for more than 60 years. Still, despite this practical importance, the precise chemical mechanisms underlying the irreversible inhibition of the MAO B isoform with clinical drugs rasagiline (RAS) and selegiline (SEL) remained unknown. Here we employed a combination of MD simulations, MM-GBSA binding free energy evaluations, and QM cluster calculations to show the MAO inactivation proceeds in three steps, where, in the rate-limiting first step, FAD utilizes its N5 atom to abstracts a hydride anion from the inhibitor α-CH group to ultimately give the final inhibitor-FAD adduct matching crystallographic data. The obtained free energy profiles reveal a lower activation energy for SEL by 1.2 kcal mol and a higher reaction exergonicity by 0.8 kcal mol, with the former being in excellent agreement with experimental ΔΔ = 1.7 kcal mol, thus rationalizing its higher in vivo reactivity over RAS. The calculated Δ energies confirm SEL binds better due to its bigger size and flexibility allowing it to optimize hydrophobic C-H···π and π···π interactions with residues throughout both of enzyme's cavities, particularly with FAD, Gln206 and four active site tyrosines, thus overcoming a larger ability of RAS to form hydrogen bonds that only position it in less reactive orientations for the hydride abstraction. Offered results elucidate structural determinants affecting the affinity and rates of the inhibition reaction that should be considered to cooperate when designing more effective compounds devoid of untoward effects, which are of utmost significance and urgency with the growing prevalence of brain diseases.
单胺氧化酶（MAO）是一种黄素腺嘌呤二核苷酸（flavin adenine dinucleotide，FAD）结合的黄素酶，可催化一系列脑神经递质的降解，其失衡与多种神经退行性疾病的病理广泛相关。这就是为什么 MAO 作为治疗神经退行性疾病的药理学靶点已经超过 60 年。尽管具有这种实际重要性，但与临床药物雷沙吉兰（rasagiline，RAS）和司来吉兰（selegiline，SEL）不可逆抑制 MAO-B 同工型相关的精确化学机制仍不清楚。在这里，我们结合使用 MD 模拟、MM-GBSA 结合自由能评估和 QM 簇计算，表明 MAO 失活分三个步骤进行，在限速的第一步中，FAD 利用其 N5 原子从抑制剂的α-CH 基团中提取氢阴离子，最终生成与晶体数据匹配的最终抑制剂-FAD 加合物。所得的自由能曲线表明，SEL 的反应活化能较低，为 1.2 kcal/mol，反应的反应熵变较高，为 0.8 kcal/mol，这与实验测定的ΔΔ=1.7 kcal/mol 非常吻合，从而解释了其在体内更高的反应活性。计算得到的ΔE 值证实，SEL 具有更好的结合能力，这是由于其较大的尺寸和灵活性使其能够优化与酶的两个腔室中的残基的疏水 C-H···π 和 π···π 相互作用，特别是与 FAD、Gln206 和四个活性位点酪氨酸，从而克服了 RAS 形成氢键的能力更大，这仅使其处于不利于氢化物提取的反应性较差的取向。所提供的结果阐明了影响抑制反应亲和力和速率的结构决定因素，在设计没有不良影响的更有效化合物时应考虑这些因素，这对于大脑疾病日益流行的情况下具有至关重要和紧迫的意义。
