Graduation Year

2022

Document Type

Dissertation

Degree

Ph.D.

Degree Name

Doctor of Philosophy (Ph.D.)

Degree Granting Department

Chemistry

Major Professor

Haitao (Mark) Ji, Ph. D.

Co-Major Professor

Xiaodong (Mike) Shi, Ph. D.

Committee Member

Jianfeng Cai, Ph.D.

Committee Member

Vincent Luca, Ph.D.

Keywords

Molecular Modeling, Medicinal Chemistry, Bioinformatics, Chemical Biology

Abstract

α-Helix accounts for the largest class of protein secondary structures and plays a key role in mediating protein-protein interactions (PPIs). Small-molecule α-helix mimetics mimic the structural features of α-helical hot spots and offer a powerful tool to unravel complex signaling networks and mitigate aberrant PPIs. In this dissertation, the side-chain conformational convergence of α-helical hot spots was disclosed, and insights into the side-chain convergence were exploited to instruct the design of small-molecule α-helix mimetics. The first chapter of this dissertation provides an overview of the characteristics of α-helical hot spots and current strategies to design small-molecule α-helix mimetics. In chapter two, the conformational convergence of hydrophobic α-helical hot spots was revealed by analyzing α-helix-mediated PPI complex structures. The pharmacophore models were derived for hydrophobic α-helical hot spots at positions i, i + 3 and i + 7. These provide the foundation to designing generalizable scaffolds that can directly mimic the binding mode of the side chains of α-helical hot spots, offering a new class of small-molecule α-helix mimetics. For the first time, the protocol was developed to identify the PPI targets that have similar binding pockets, allowing evaluation of inhibitor selectivity between α-helix-mediated PPIs. The mimicry efficiency of the previously designed scaffold 2.1 was disclosed. The close positioning of this scaffold to the additional α-helical hot spots suggests that the decoration of this series of generalizable scaffolds can conveniently reach the binding pockets of additional α-helical hot spots to produce potent small-molecule PPI inhibitors. In chapter three, a computational protocol was developed to design scaffolds to mimic the key binding features of α-helix-mediated PPIs. The integration of pharmacophore-based virtual screening to fragment hopping ensures the construction of a group of structurally diverse scaffolds by selecting and combining graph frameworks, rings, and linkers, which offers an objective approach for designing scaffolds of novel small-molecule α-helix mimetics with desired mimicry efficiency, synthetic accessibility, and physiochemical properties. This protocol was applied to design scaffolds 3.2 and 3.3, and scaffold 3.2 was selected and functionalized based on the key binding features of β-catenin/BCL9 PPI and MCL-1/Bak PPI. Biological studies and cell-based studies have confirmed the ability of 3.5 and 3.7 to disrupt β-catenin/BCL9 PPI and MCL-1/Bak PPI, respectively. These results suggest that the developed protocol enables the design of small molecules solely based on the interaction between α-helical hot spots and its accommodating pockets. The fourth chapter of this dissertation characterized the hydrophilic α-helical hot spots and α-helix-mediated PPIs with hydrophilic hot spots. The cooperativity index, Kc, was developed to reveal the binding synergy between hot spots of the ligand protein. For the first time the convergence of the side-chain spatial arrangements of hydrophilic α-helical hot spots Thr, Tyr, Asp, Asn, Ser, Cys, and His in protein-protein interaction (PPI) complex structures were disclosed and quantified by developing novel clustering models. In-depth analyses disclosed the driving force for the PPI binding conformation convergence of hydrophilic α-helical hot spots. This observation allows deriving pharmacophore models to design new mimetics for hydrophilic α-helical hot spots. A computational protocol was developed to search amino acid analogs and small-molecule mimetics for each hydrophilic α-helical hot spot. As a pilot study, diverse building blocks of commercially available non-standard L-type α-amino acids and the phenyl ring-containing small-molecule fragments were obtained, which serve as a fragment collection to mimic hydrophilic α-helical hot spots for improvement of binding affinity, selectivity, physicochemical properties, and synthesis accessibility of α-helix mimetics.

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