Computational Mapping of Conformational Dynamics and Interaction Hotspots of Human VISTA with pH-Selective Antibodies

The V-domain Ig suppressor of T-cell activation (VISTA)
is a critical
negative immune checkpoint protein that regulates T-cell-mediated
anticancer immune responses, making it a promising target for immunotherapy.
Unlike other checkpoint proteins, VISTA activity is moderated by pH
and engages with distinct ligands under variable pH conditions to
promote immune suppression. Understanding the structural dynamics
of VISTA and developing pH-selective antibodies to disrupt its interactions
remain significant areas of research. Recently, two X-ray crystal
structures of VISTA bound to pH-selective monoclonal antibodies have
been reported. In this study, we probed the structural stability,
conformational dynamics, and molecular interactions of VISTA in its
apo state and when bound to these antibodies. A combination of atomistic
modeling, molecular dynamics simulations, binding free energy calculations,
energy decomposition analyses, and computational alanine scanning
was employed. The results revealed the critical roles of key arginine
residues (R90 and R74) that shield the hydrophobic core of VISTA,
maintaining its structural integrity. Distinct VISTA regions, including
the CC′ loop, C′C″ segments, and FG loop, were
found to play pivotal roles in antibody binding. Electrostatic interactions
involving R86, R159, and E157, alongside an extensive π–π
stacking network facilitated by Y69, Y73, and F94, were identified
as key contributors to the complex stability and binding affinity.
Overall, this study provides detailed insights into the structural
dynamics and molecular interactions of VISTA with pH-selective antibodies.
These findings enhance our understanding of VISTA’s molecular
mechanisms and lay a foundation for the rational design of improved
therapeutics targeting immune checkpoint proteins.

T细胞活化V结构域免疫球蛋白抑制因子（V-domain Ig suppressor of T-cell activation, VISTA）是一类关键的负向免疫检查点蛋白，可调控T细胞介导的抗肿瘤免疫应答，因此成为免疫治疗的极具潜力的靶点。与其他免疫检查点蛋白不同，VISTA的活性受pH值调控，且会在不同pH条件下结合不同配体以介导免疫抑制。解析VISTA的结构动力学并开发可阻断其相互作用的pH选择性抗体，仍是该领域的重要研究方向。近期已有两项关于VISTA与pH选择性单克隆抗体结合的X射线晶体结构被报道。本研究针对VISTA的脱辅基状态（apo state）及其与上述抗体结合的复合物状态，探究了其结构稳定性、构象动力学与分子相互作用机制。研究采用了全原子建模、分子动力学模拟、结合自由能计算、能量分解分析以及丙氨酸扫描突变计算等多种计算生物学方法。结果揭示了关键精氨酸残基R90与R74的核心作用：它们可包裹VISTA的疏水核心，维持其结构完整性。研究发现VISTA的多个特定区域，包括CC'环、C'C''段以及FG环，在抗体结合过程中发挥关键作用。由R86、R159与E157参与的静电相互作用，以及由Y69、Y73与F94介导的广泛π-π堆积网络，被证实是维持复合物稳定与提升结合亲和力的关键因素。总体而言，本研究详细阐明了VISTA与pH选择性抗体结合的结构动力学与分子相互作用机制。这些发现加深了我们对VISTA分子作用机制的理解，为靶向免疫检查点蛋白的优化治疗药物的理性设计奠定了坚实基础。