将动力学嵌入到市场阶段抗体类生物治疗药物的固有物理化学特征中。

Embedding Dynamics in Intrinsic Physicochemical Profiles of Market-Stage Antibody-Based Biotherapeutics.

机构信息

Early Stage Pharmaceutical Development, Pharmaceutical Development Biologicals & In silico Team, Boehringer Ingelheim International GmbH & Co. KG, Biberach/Riss 88397, Germany.

Biotherapeutics Discovery & In silico Team, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States.

出版信息

Mol Pharm. 2023 Feb 6;20(2):1096-1111. doi: 10.1021/acs.molpharmaceut.2c00838. Epub 2022 Dec 27.

Abstract

Adequate stability, manufacturability, and safety are crucial to bringing an antibody-based biotherapeutic to the market. Following the concept of holistic in silico developability, we introduce a physicochemical description of 91 market-stage antibody-based biotherapeutics based on orthogonal molecular properties of variable regions (Fvs) embedded in different simulation environments, mimicking conditions experienced by antibodies during manufacturing, formulation, and in vivo. In this work, the evaluation of molecular properties includes conformational flexibility of the Fvs using molecular dynamics (MD) simulations. The comparison between static homology models and simulations shows that MD significantly affects certain molecular descriptors like surface molecular patches. Moreover, the structural stability of a subset of Fv regions is linked to changes in their specific molecular interactions with ions in different experimental conditions. This is supported by the observation of differences in protein melting temperatures upon addition of NaCl. A DEvelopability Navigator In Silico (DENIS) is proposed to compare mAb candidates for their similarity with market-stage biotherapeutics in terms of physicochemical properties and conformational stability. Expanding on our previous developability guidelines (Ahmed et al. , (37), e2020577118), the hydrodynamic radius and the protein strand ratio are introduced as two additional descriptors that enable a more comprehensive in silico characterization of biotherapeutic drug candidates. Test cases show how this approach can facilitate identification and optimization of intrinsically developable lead candidates. DENIS represents an advanced computational tool to progress biotherapeutic drug candidates from discovery into early development by predicting drug properties in different aqueous environments.

摘要

充分的稳定性、可制造性和安全性对于将抗体生物疗法推向市场至关重要。遵循整体计算可开发性的概念,我们根据不同模拟环境中嵌入的可变区 (Fv) 的正交分子特性,为 91 种处于市场阶段的抗体生物疗法提供了一种物理化学描述,模拟了抗体在制造、配方和体内过程中所经历的条件。在这项工作中,分子特性的评估包括使用分子动力学 (MD) 模拟对 Fv 的构象灵活性进行评估。静态同源模型和模拟之间的比较表明,MD 显著影响某些分子描述符,如表面分子斑块。此外,Fv 区域的结构稳定性与其在不同实验条件下与离子的特定分子相互作用的变化有关。在添加 NaCl 时蛋白质熔点的变化支持了这一点。提出了一种用于计算的可开发性导航仪 (DENIS),用于根据物理化学性质和构象稳定性,比较单抗候选物与其在市场上的生物疗法的相似性。在我们之前的可开发性指南 (Ahmed 等人,(37),e2020577118) 的基础上,引入了流体力学半径和蛋白质链比作为两个额外的描述符,这使得更全面的生物治疗候选药物的计算特性成为可能。案例研究展示了如何通过在不同水相环境中预测药物特性,该方法可以促进内在可开发的先导候选物的鉴定和优化。DENIS 是一种先进的计算工具,通过预测不同水相环境中的药物特性,可将生物治疗候选药物从发现推进到早期开发阶段。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/780d/9906779/0de172dcea53/mp2c00838_0002.jpg

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