Design of inhibitors targeted to the CD4 binding site on HIV-1 gp120

针对 HIV-1 gp120 上 CD4 结合位点的抑制剂的设计

• 批准号: 8791298
• 负责人: Asim K Debnath
• 金额: $ 77万
• 依托单位: NEW YORK BLOOD CENTER
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-02-15 至 2016-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8791298
• 关键词: AIDS prevention; AIDS therapy; Acids; Affinity; Agonist; Antibodies; Antiviral Agents; Arginine; Aspartic Acid; Binding; Binding Sites; CD4 Antigens; Cell surface; Cells; Clinical Research; Collaborations; Complex; Computer Simulation; Data; Databases; Dissociation; Docking; Drug Design; Drug resistance; Electrostatics; Entropy; Evaluation; Glycoproteins; Goals; HIV Envelope Protein gp120; HIV-1; Half-Life; Health; Immunoglobulin Fragments; Infection; Inhibitory Concentration 50; Intervention; Kinetics; Lead; Measures; Mediating; Nature; Pharmaceutical Chemistry; Pharmaceutical Preparations; Phenylalanine; Positioning Attribute; Property; Receptor Cell; Reporting; Research; Resistance; Role; Site; Sodium Chloride; Structure; Thermodynamics; Toxic effect; United States National Institutes of Health; Virus; base; clinically relevant; design; enthalpy; flexibility; glycosylation; improved; inhibitor/antagonist; innovation; interfacial; microbicide; mimicry; mutant; neutralizing antibody; next generation; novel; piperidine; pre-clinical; prevent; prophylactic; scaffold; screening; small molecule; therapeutic target; virtual

DESCRIPTION (provided by applicant): The entry of HIV-1 into host cells is mediated by the binding of the envelope glycoprotein gp120 to the host cell receptor CD4. The structures of the gp120-CD4-17b complex indicate that the CD4 binding site (CD4BS) on gp120 is located in a hydrophobic cavity, termed "Phe43 cavity" where Phe43CD4 makes critical hydrophobic contacts. Studies of these structures also confirmed an important electrostatic interaction between Arg59CD4 and Asp368gp120. Similar structural mimicry of several potent broad neutralizing antibodies (bNAbs) has recently been reported. The highly conserved nature of the residues in the CD4BS of gp120 and their role in binding to CD4 and CD4BS targeted bNAbs validates this site as a promising target for therapeutic and prophylactic intervention. Despite th remarkable diversity of the HIV-1 envelope glycoprotein sequence, glycosylation and conformational flexibility, gp120 must retain conserved domains required for binding to CD4. However, the well-conserved CD4 binding site has yet to be exploited to its full potential as a target in designing drugs to prevent HIV-1 entry, which will be the focus of our research. We were the first to identify two small molecule inhibitors, NBD-556 and NBD-557, which target the CD4BS on gp120. These molecules show unprecedented ability to induce conformational changes in gp120 similar to that of CD4; thereby, acting as agonists. Recently, we solved the structure of NBD-556 in complex with the gp120 coree, confirming that NBD-556 binds to the cavity of gp120. We used this structure to design new leads with improved anti-HIV-1 activity. However, these lead compounds showed CD4 agonist properties. In additional studies, we confirmed that a newly designed lead, NBD-11021, is a CD4 antagonist. Moreover, a recent report showed that the bNAb PGV04 targets the CD4BS but induces distinct conformational changes in gp120 that are not recognized by the 17b antibody. PGV04 thus does not induce exposure of the coreceptor binding site, suggesting that it is a CD4 antagonist not an agonist. We hypothesize that lead compounds, including NBD-11021, can be optimized by incorporating the distinct binding features of PGV04 with gp120 to produce a more potent and selective new class of HIV-1 entry inhibitors with CD4 antagonist properties. The goals of the proposed studies will be accomplished by three highly integrated specific aims. In Aim-1, the leads will be optimized through structure-guided design and medicinal chemistry. In Aim-2, thermodynamic and kinetic properties such as enthalpy, entropy, on- and off-rates and binding affinity (KD) will be measured as well as their antiviral potency and toxicity. The x-ray structures of new inhibitors in complex with gp120 will be determined. In Aim-3, mechanism of action will be studied and the resistant mutants of the inhibitors will be selected. The data from these studies will be used in designing potent next-generation entry inhibitors that will potentially escape resistance and be clinically relevant. The long-term goal is to develop a new class of HIV-1 entry inhibitors for pre clinical and clinical studies.

描述（申请人提供）：HIV-1 进入宿主细胞是通过包膜糖蛋白 gp120 与宿主细胞受体 CD4 的结合介导的。 gp120-CD4-17b 复合物的结构表明 gp120 上的 CD4 结合位点 (CD4BS) 位于疏水腔中，称为“Phe43 腔”，其中 Phe43CD4 进行关键的疏水接触。对这些结构的研究还证实了 Arg59CD4 和 Asp368gp120 之间的重要静电相互作用。最近报道了几种有效的广泛中和抗体（bNAb）的类似结构模拟。 gp120 CD4BS 中残基的高度保守性质及其在与 CD4 和 CD4BS 靶向 bNAb 结合中的作用证实了该位点作为治疗和预防干预的有希望的靶点。尽管 HIV-1 包膜糖蛋白序列、糖基化和构象灵活性具有显着的多样性，但 gp120 必须保留与 CD4 结合所需的保守结构域。然而，保守的 CD4 结合位点尚未充分发挥其作为设计药物以防止 HIV-1 进入的目标的潜力，这将是我们研究的重点。我们是第一个鉴定出两种小分子抑制剂 NBD-556 和 NBD-557，它们靶向 gp120 上的 CD4BS。这些分子表现出前所未有的诱导 gp120 构象变化的能力，类似于 CD4；从而充当激动剂。最近，我们解析了NBD-556与gp120 coree复合物的结构，证实NBD-556与gp120空腔结合。我们利用这种结构设计了具有改进的抗 HIV-1 活性的新先导化合物。然而，这些先导化合物表现出 CD4 激动剂特性。在其他研究中，我们证实新设计的先导化合物 NBD-11021 是一种 CD4 拮抗剂。此外，最近的一份报告表明，bNAb PGV04 靶向 CD4BS，但会诱导 gp120 发生明显的构象变化，而 17b 抗体无法识别该变化。因此，PGV04 不会诱导辅助受体结合位点的暴露，表明它是 CD4 拮抗剂而不是激动剂。我们假设，可以通过结合 PGV04 与 gp120 的独特结合特征来优化包括 NBD-11021 在内的先导化合物，以产生更有效、更具选择性的新型 HIV-1 进入抑制剂，并具有 CD4 拮抗剂特性。拟议研究的目标将通过三个高度综合的具体目标来实现。在 Aim-1 中，将通过结构引导设计和药物化学来优化先导化合物。在 Aim-2 中，将测量热力学和动力学特性，例如焓、熵、结合速率和解离速率以及结合亲和力 (KD) 以及它们的抗病毒效力和毒性。新型抑制剂的X射线结构 与gp120的复合物将被确定。在Aim-3中，将研究作用机制并选择抑制剂的耐药突变体。这些研究的数据将用于设计有效的下一代进入抑制剂，这些抑制剂将有可能逃脱耐药性并具有临床相关性。长期目标是开发一类新的 HIV-1 进入抑制剂，用于预防 临床和临床研究。