Molecular Topology as Novel Strategy for Discovery of Drugs with Aβ Lowering and Anti-Aggregation Dual Activities for Alzheimer’s Disease

<div><p>Background and Purpose</p><p>In this study, we demonstrate the use of Molecular topology (MT) in an Alzheimer’s disease (AD) drug discovery program. MT uses and expands upon the principles governing the molecular connectivity theory of numerically characterizing molecular structures, in the present case, active anti-AD drugs/agents, using topological descriptors to build models. Topological characterization has been shown to embody sufficient molecular information to provide strong correlation to therapeutic efficacy.</p><p>Experimental Approach</p><p>We used MT to include multiple bioactive properties that allows for the identification of multi-functional single agent compounds, in this case, the dual functions of β-amyloid (Aβ) -lowering and anti-oligomerization. Using this technology, we identified and designed novel compounds in chemical classes unrelated to current anti-AD agents that exert dual Aβ lowering and anti-Aβ oligomerization activities in animal models of AD. AD is a multifaceted disease with different pathological features.</p><p>Conclusion and Implications</p><p>Our study, for the first time, demonstrated that MT can provide novel strategy for discovering drugs with Aβ lowering and anti-aggregation dual activities for AD.</p></div

Representative <i>in vitro</i> screening results for Aβ -lowering and anti-oligomerization activity.

<p>(A) Measurement of Aβ_1–42 and Aβ_1–40 in conditioned medium from Tg2576 primary neurons treated with different concentration of testing compound (B) Dose dependent inhibition of testing compound on synthetic Aβ_1–42 peptides aggregation into HMW oligomeric Aβ forms. Aβ_1–42 (final concentration 10 μM) was incubated with various concentrations of compound at 37°C for 24 hours. Bands were visualized by western blot analysis probed with 6E10 antibody. MW: molecular weight, CTRL is Aβ_1–42 without incubation, Lane 1–8, 0, 10, 20, 40, 80,160, 320 and 640 μM of compound. (C and D) SDS-PAGE of Aβ_1–42 (C) and Aβ_1–40 (D) in the presence or absence of testing compound following PICUP. Aβ_1–42 or Aβ_1–40 was cross-linked in the presence or absence of testing compound and the bands were visualized using silver staining. Lanes 1: molecular weight, lane 2: Aβ_1–42 or Aβ_1–40 peptides without PICUP reaction; lane 3: Aβ_1–42 or Aβ_1–40 peptides following PICUP reaction; Lanes 4 and 5: PICUP of Aβ peptides in the presence of an equimolar concentration (lane 4) or 10x molar excess (lane 5) of testing compound.</p

Schematic drug discovery procedure using molecular topology modeling.

<p>Schematic drug discovery procedure using molecular topology modeling.</p

Short-term feasibility studies of the 8 lead compounds in reducing Aβ neuropathology in Tg2576 mouse model of AD.

<p>Tg2576 mice were treated with 2 mg/kg/day of the candidate compound delivered through their drinking water for 4 weeks, Body weight, brain neuropathology including oligomeric Aβ as well as total brain Aβ were compared to vehicle-treated control Tg2576 mice (n = 5 per group, *p<0.05).</p

Molecular name, database identifier, empirical formula, 2-D structure, and topological indexes of HOMO and LUMO Gap (HLG) of the eight compounds that are able to exert dual Aβ -lowering and anti-oligomerization by <i>in vitro</i> testing.

<p>Molecular name, database identifier, empirical formula, 2-D structure, and topological indexes of HOMO and LUMO Gap (HLG) of the eight compounds that are able to exert dual Aβ -lowering and anti-oligomerization by <i>in vitro</i> testing.</p

Forward Engineering process schematic.

<p>Each model iteration consists of five steps: (1) compilation of a training set of active and inactive compounds with associated data, (2) mathematical translation of structure into TIs, (3) use of TIs to develop model descriptors, (4) compound libraries are screened using the model filters to identify compounds that fit the desired properties, (5) selection of pre-qualified lead compounds for evaluation.</p

Representative <i>in vitro</i> screening results for Aβ -lowering and anti-oligomerization activity.

<p>(A) Measurement of Aβ_1–42 and Aβ_1–40 in conditioned medium from Tg2576 primary neurons treated with different concentration of testing compound (B) Dose dependent inhibition of testing compound on synthetic Aβ_1–42 peptides aggregation into HMW oligomeric Aβ forms. Aβ_1–42 (final concentration 10 μM) was incubated with various concentrations of compound at 37°C for 24 hours. Bands were visualized by western blot analysis probed with 6E10 antibody. MW: molecular weight, CTRL is Aβ_1–42 without incubation, Lane 1–8, 0, 10, 20, 40, 80,160, 320 and 640 μM of compound. (C and D) SDS-PAGE of Aβ_1–42 (C) and Aβ_1–40 (D) in the presence or absence of testing compound following PICUP. Aβ_1–42 or Aβ_1–40 was cross-linked in the presence or absence of testing compound and the bands were visualized using silver staining. Lanes 1: molecular weight, lane 2: Aβ_1–42 or Aβ_1–40 peptides without PICUP reaction; lane 3: Aβ_1–42 or Aβ_1–40 peptides following PICUP reaction; Lanes 4 and 5: PICUP of Aβ peptides in the presence of an equimolar concentration (lane 4) or 10x molar excess (lane 5) of testing compound.</p