Improving the permeability of the hydroxyethylamine BACE-1 inhibitors: Structure–activity relationship of P2′ substituents

Predicting Passive Permeability of Drug-like Molecules from Chemical Structure: Where Are We?

Intestinal absorption in human is routinely predicted in drug discovery using in vitro assays such as permeability in the Madin-Darby canine kidney cell line. In silico models trained on these data are used in drug discovery efforts to prioritize novel chemical targets for synthesis; however, their proprietary nature and the limited validation available, which is usually restricted to predicting in vitro permeability, are barriers to widespread adoption. Because of the categorical nature of the in vitro permeability assay, intrinsic assay variability, and the challenges often encountered when translating in vitro data to an in vivo drug property, validation based solely on in vitro data might not be a good characterization of the usefulness of the in silico tool. In this work, we analyze the performance of three different in silico models in predicting the in vitro and in vivo permeability of 300 marketed drugs and 86 discovery compounds. The models differ in their approach (mechanistic vs quantitative structure-activity relationship) and the degree of complexity; one of them is a linear equation based on seven simple physicochemical descriptors and is presented for the first time in this work. Results show that in silico models can be successfully used to complement the discovery toolbox for characterizing in vivo intestinal permeability, defined using fraction of dose absorbed in human (Fa) and human jejunal permeability (P_eff). While the in vitro permeability models outperformed the in silico approach at predicting each of the in vivo end points explored, the gap in predictivity between the in vitro and the in vivo data was generally comparable to the gap between in silico and in vitro data. The in vitro and in silico approaches shared many of the same outliers, which can often be explained by the route of drug absorption (paracellular vs transcellular, active vs passive). Data suggest that the discovery process can greatly benefit from an early adoption of in silico models for predicting permeability as well as from a careful analysis of the in silico to in vivo disconnects.

Determination of the protonation state for the catalytic dyad in β-secretase when bound to hydroxyethylamine transition state analogue inhibitors: A molecular dynamics simulation study

BACE1 is an aspartyl protease of pharmacological interest for its direct participation in Alzheimer's disease (AD) through β-amyloid peptide production. Two aspartic acid residues are present in the BACE1 catalytic region which can adopt multiple protonation states depending on the chemical nature of its inhibitors, i.e., monoprotonated, diprotonated and di-deprotonated states. In the present study a series of protein-ligand molecular dynamics (MD) simulations was carried out to identify the most feasible protonation state adopted by the catalytic dyad in the presence of hydroxyethylamine transition state analogue inhibitors. The MD trajectories revealed that the di-deprotonated state is most prefered in the presence of hydroxyethilamine (HEA) family inhibitors. This appears as a result after evaluating, for all 9 protonation state configurations during the simulation time, the deviations of a set of distances and dihedral angles measured on the ligand, protein and protein-ligand complex with reference to an X-ray experimental BACE1/HEA crystallographic structure. These results will help to clarify the phenomena related to the HEAs inhibitory pathway, and improve HEAs databases' virtual screening and ligand design processes targeting β-secretase protein.

Interaction mechanism exploration of HEA derivatives as BACE1 inhibitors by in silico analysis

The β-site amyloid precursor protein cleaving enzyme 1 (BACE1) initiates the generation of β-amyloid (Aβ) peptides which play a critical early role in the pathogenesis of Alzheimer's disease (AD), and thus it is a prime target for lowering the Aβ levels to treat AD.

One-Pot Synthesis of N-Substituted β-Amino Alcohols from Aldehydes and Isocyanides

A practical two-stage one-pot synthesis of N-substituted β-amino alcohols using aldehydes and isocyanides as starting materials has been developed. This method features mild reaction conditions, broad scope, and general tolerance of functional groups. Based on a less common central carbon-carbon bond disconnection, this protocol complements traditional approaches that involve amines and various carbon electrophiles (epoxides, α-halo ketones, β-halohydrins). Medicinally relevant products can be prepared in a concise and efficient way from simple building blocks, as demonstrated in the synthesis of the antiasthma drug salbutamol. Upgrading the synthesis to an enantioselective variant is also feasible.

Bioactive prenylated phenyl derivatives derived from marine natural products: novel scaffolds for the design of BACE inhibitors

Bioassay guided-fractionation of active extracts from the sponge Sarcotragus sp. led to the isolation biochemical characterization and development of a chemistry program of bioactive prenylated phenyl derivatives.

Design and synthesis of hydroxyethylamine (HEA) BACE-1 inhibitors: prime side chromane-containing inhibitors

The structure activity relationship of the prime region of conformationally restricted hydroxyethylamine (HEA) BACE inhibitors is described. Variation of the P1' region provided selectivity over Cat-D with a series of 2,2-dioxo-isothiochromanes and optimization of the P2' substituent of chromane-HEA(s) with polar substituents provided improvements in the compound's in vitro permeability. Significant potency gains were observed with small aliphatic substituents such as methyl, n-propyl, and cyclopropyl when placed at the C-2 position of the chromane.

Structure-based design of β-site APP cleaving enzyme 1 (BACE1) inhibitors for the treatment of Alzheimer's disease

The amyloid hypothesis asserts that excess production or reduced clearance of the amyloid-β (Aβ) peptides in the brain initiates a sequence of events that ultimately lead to Alzheimer's disease and dementia. The Aβ hypothesis has identified BACE1 as a therapeutic target to treat Alzheimer's and led to medicinal chemistry efforts to design its inhibitors both in the pharmaceutical industry and in academia. This review summarizes two distinct categories of inhibitors designed based on conformational states of "closed" and "open" forms of the enzyme. In each category the inhibitors are classified based on the core catalytic interaction group or the aspartyl binding motif (ABM). This review covers the description of inhibitors in each ABM class with X-ray crystal structures of key compounds, their binding modes, related structure-activity data highlighting potency advances, and additional properties such as selectivity profile, P-gp efflux, pharmacokinetic, and pharmacodynamic data.

Small-molecule BACE1 inhibitors: a patent literature review (2006 - 2011)

INTRODUCTION

Alzheimer's disease is a devastating neurodegenerative disorder for which no disease-modifying therapy exists. The amyloid hypothesis, which implicates Aβ as the toxin initiating a biological cascade leading to neurodegeneration, is the most prominent theory concerning the underlying cause of the disease. BACE1 is one of two aspartyl proteinases that generate Aβ, thus inhibition of BACE1 has the potential to ameliorate the progression of Alzheimer's disease by abating the production of Aβ.

AREAS COVERED

This review chronicles small-molecule BACE1 inhibitors as described in the patent literature between 2006 and 2011 and their potential use as disease-modifying treatments for Alzheimer's disease. Over the past half a dozen years, numerous BACE1 inhibitors have been published in the patent applications, but often these contain a paltry amount of pertinent biological data (e.g. potency, selectivity, and efficacy). Fortunately, numerous relevant publications containing important data have appeared in the journal literature during this period. The goal in this effort was to create an amalgam of the two records to add value to this review.

EXPERT OPINION

The pharmaceutical industry has made tremendous progress in the development of small-molecule BACE1 inhibitors that lower Aβ in the central nervous system. Assuming the amyloid hypothesis is veracious, we anticipate a disease-modifying therapy to combat Alzheimer's disease is near.

Design of an orally efficacious hydroxyethylamine (HEA) BACE-1 inhibitor in a preclinical animal model

In this Letter, we describe our efforts to design HEA BACE-1 inhibitors that are highly permeable coupled with negligible levels of permeability-glycoprotein activity. These efforts culminate in producing 16 which lowers Αβ by 28% and 32% in the cortex and CSF, respectively, in the preclinical wild type Hartley guinea pig animal model when dosed orally at 30mpk BID for 2.5days.