Novel pyrrolyl 2-aminopyridines as potent and selective human β-secretase (BACE1) inhibitors

Multicolor, Cell-Impermeable, and High Affinity BACE1 Inhibitor Probes Enable Superior Endogenous Staining and Imaging of Single Molecules

The prevailing but not undisputed amyloid cascade hypothesis places the β-site of APP cleaving enzyme 1 (BACE1) center stage in Alzheimer's Disease pathogenesis. Here, we investigated functional properties of BACE1 with novel tag- and antibody-free labeling tools, which are conjugates of the BACE1-inhibitor IV (also referred to as C3) linked to different impermeable Alexa Fluor dyes. We show that these fluorescent small molecules bind specifically to BACE1, with a 1:1 labeling stoichiometry at their orthosteric site. This is a crucial property especially for single-molecule and super-resolution microscopy approaches, allowing characterization of the dyes' labeling capabilities in overexpressing cell systems and in native neuronal tissue. With multiple colors at hand, we evaluated BACE1-multimerization by Förster resonance energy transfer (FRET) acceptor-photobleaching and single-particle imaging of native BACE1. In summary, our novel fluorescent inhibitors, termed Alexa-C3, offer unprecedented insights into protein-protein interactions and diffusion behavior of BACE1 down to the single molecule level.

Promising heterocycle-based scaffolds in recent (2019-2021) anti-Alzheimer's drug design and discovery

Alzheimer's disease (AD) is one of the neurodegenerative diseases that led to morbidity and mortality world-wide. It is a complex disease whose etiology is not completely known that leads to difficulty in prevent or cure of the AD. Also, there are only few approved drugs for AD treatment. Apart from deaths due to AD, expenditure of treatment and care of AD patients is higher than that of treatment of HIV and cancer diseases combined. Hence, it leads to an economic burden also. Although research is being carried out on designing drugs for AD, most of them have ended up in poor inhibitors with high toxicity. Hence, researchers should shoulder a great responsibility of discovery of efficient drugs for AD treatment. In the field of drug discovery, heterocycles played an important role. Also, most of the heterocyclic scaffolds have been used in design of potent anti-AD agents. In view of this, heterocyclic molecules reported recently are compiled and evaluated comprehensively. Especially, the molecules which exhibited pronounced activity are emphasized and described with respect to structure-activity relationship (SAR) in brief.

Novel Anti-Alzheimer's Therapeutic Molecules Targeting Amyloid Precursor Protein Processing

Alzheimer's disease (AD) is the most common cause of dementia among older people, and the prevalence of this disease is estimated to rise quickly in the upcoming years. Unfortunately, almost all of the drug candidates tested for AD until now have failed to exhibit any efficacy. Henceforth, there is an increased necessity to avert and/or slow down the advancement of AD. It is known that one of the major pathological characteristics of AD is the presence of senile plaques (SPs) in the brain. These SPs are composed of aggregated amyloid beta (Aβ), derived from the amyloid precursor protein (APP). Pharmaceutical companies have conducted a number of studies in order to identify safe and effective anti-Aβ drugs to combat AD. It is known that α-, β-, and γ-secretases are the three proteases that are involved in APP processing. Furthermore, there is a growing interest in these proteases, as they have a contribution to the modulation and production of Aβ. It has been observed that small compounds can be used to target these important proteases. Indeed, these compounds must satisfy the common strict requirements of a drug candidate targeted for brain penetration and selectivity toward different proteases. In this article, we have focused on the auspicious molecules which are under development for targeting APP-processing enzymes. We have also presented several anti-AD molecules targeting Aβ accumulation and phosphorylation signaling in APP processing. This review highlights the structure-activity relationship and other physicochemical features of several pharmacological candidates in order to successfully develop new anti-AD drugs.

Exploring 2D-QSAR for prediction of beta-secretase 1 (BACE1) inhibitory activity against Alzheimer's disease

We have developed a robust quantitative structure-activity relationship (QSAR) model employing a dataset of 98 heterocycle compounds to identify structural features responsible for BACE1 (beta-secretase 1) enzyme inhibition. We have used only 2D descriptors for model development purpose thus avoiding the conformational complications arising due to 3D geometry considerations. Following the strict Organization for Economic Co-operation and Development (OECD) guidelines, we have developed models using stepwise regression analysis followed by the best subset selection, while the final model was developed by partial least squares regression technique. The model was validated using various internationally accepted stringent validation parameters. From the insights obtained from the developed model, we have concluded that heteroatoms (nitrogen, oxygen, etc.) present within to an aromatic nucleus and the structural features such as hydrophobic, ring aromatic and hydrogen bond acceptor/donor are responsible for the enhancement of the BACE1 enzyme inhibitory activity. Moreover, we have performed the pharmacophore modelling to unveil the structural requirements for the inhibitory activity against the BACE1 enzyme. Furthermore, molecular docking studies were carried out to understand the molecular interactions involved in binding, and the results are then correlated with the requisite structural features obtained from the QSAR and pharmacophore models.

Design, synthesis, and biological activity evaluation of BACE1 inhibitors with antioxidant activity

The proteolytic enzyme β-secretase (BACE1) plays a central role in the synthesis of the pathogenic β-amyloid peptides (Aβ) in Alzheimer's disease (AD), antioxidants could attenuate the AD syndrome and prevent the disease progression. In this study, BACE1 inhibitors (D1-D18) with free radical-scavenging activities were synthesized by molecular hybridization of 2-aminopyridine with natural antioxidants. The biological activity evaluation showed that D1 had obvious inhibitory activity against BACE1, and strong antioxidant activity in 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulphonate) (ABTS^+• ) assay, which could be used as a lead compound for further study.

BACE-1 and γ-Secretase as Therapeutic Targets for Alzheimer's Disease

Alzheimer’s disease (AD) is a growing global health concern with a massive impact on affected individuals and society. Despite the considerable advances achieved in the understanding of AD pathogenesis, researchers have not been successful in fully identifying the mechanisms involved in disease progression. The amyloid hypothesis, currently the prevalent theory for AD, defends the deposition of β-amyloid protein (Aβ) aggregates as the trigger of a series of events leading to neuronal dysfunction and dementia. Hence, several research and development (R&D) programs have been led by the pharmaceutical industry in an effort to discover effective and safety anti-amyloid agents as disease modifying agents for AD. Among 19 drug candidates identified in the AD pipeline, nine have their mechanism of action centered in the activity of β or γ-secretase proteases, covering almost 50% of the identified agents. These drug candidates must fulfill the general rigid prerequisites for a drug aimed for central nervous system (CNS) penetration and selectivity toward different aspartyl proteases. This review presents the classes of γ-secretase and beta-site APP cleaving enzyme 1 (BACE-1) inhibitors under development, highlighting their structure-activity relationship, among other physical-chemistry aspects important for the successful development of new anti-AD pharmacological agents.

Multidisciplinary approaches for targeting the secretase protein family as a therapeutic route for Alzheimer's disease

The continual increase of the aging population worldwide renders Alzheimer's disease (AD) a global prime concern. Several attempts have been focused on understanding the intricate complexity of the disease's development along with the on- andgoing search for novel therapeutic strategies. Incapability of existing AD drugs to effectively modulate the pathogenesis or to delay the progression of the disease leads to a shift in the paradigm of AD drug discovery. Efforts aimed at identifying AD drugs have mostly focused on the development of disease-modifying agents in which effects are believed to be long lasting. Of particular note, the secretase enzymes, a group of proteases responsible for the metabolism of the β-amyloid precursor protein (βAPP) and β-amyloid (Aβ) peptides production, have been underlined for their promising therapeutic potential. This review article attempts to comprehensively cover aspects related to the identification and use of drugs targeting the secretase enzymes. Particularly, the roles of secretases in the pathogenesis of AD and their therapeutic modulation are provided herein. Moreover, an overview of the drug development process and the contribution of computational (in silico) approaches for facilitating successful drug discovery are also highlighted along with examples of relevant computational works. Promising chemical scaffolds, inhibitors, and modulators against each class of secretases are also summarized herein. Additionally, multitarget secretase modulators are also taken into consideration in light of the current growing interest in the polypharmacology of complex diseases. Finally, challenging issues and future outlook relevant to the discovery of drugs targeting secretases are also discussed.

Gear Up for a pH Shift: A Responsive Iron(II) 2-Amino-6-picolyl-Appended Macrocyclic paraCEST Agent That Protonates at a Pendent Group

Two high-spin Fe(II) and Co(II) complexes of 1,4,7,10-tetraazacyclododecane (CYCLEN) appended with four 2-amino-6-picolyl groups, denoted as [Fe(TAPC)]²⁺ and [Co(TAPC)]²⁺, are reported. These complexes demonstrate C₂-symmetrical geometry from coordination of two pendents, and they are present in a single diastereomeric form in aqueous solution as shown by ¹H NMR spectroscopy and by a single-crystal X-ray structure for the Co(II) complex. A highly shifted but low-intensity CEST (chemical exchange saturation transfer) signal from NH groups is observed at -118 ppm for [Co(TAPC)]²⁺ at pH 6.0 and 37 °C. A higher intensity CEST peak is observed for [Fe(TAPC)]²⁺, which demonstrates a pH-dependent frequency shift from -72 to -79 ppm at pH 7.7 to 4.8, respectively, at 37 °C. This shift in the CEST peak correlates with the protonation of the unbound 2-amino-6-picolyl pendents, as suggested by UV-vis and ¹H NMR spectroscopy studies at different pH values. Phantom imaging demonstrates the challenges and feasibility of using the [Fe(TAPC)]²⁺ agent on a low-field MRI scanner. The [Fe(TAPC)]²⁺ complex is the first transition-metal-based paraCEST agent that produces a pH-induced CEST frequency change toward the development of probes for concentration-independent imaging of pH.

Current pharmacotherapy and putative disease-modifying therapy for Alzheimer's disease

Alzheimer's disease (AD) is an age-related neurodegenerative disease of the central nervous system correlated with the progressive loss of cognition and memory. β-Amyloid plaques, neurofibrillary tangles and the deficiency in cholinergic neurotransmission constitute the major hallmarks of the AD. Two major hypotheses have been implicated in the pathogenesis of AD namely the cholinergic hypothesis which ascribed the clinical features of dementia to the deficit cholinergic neurotransmission and the amyloid cascade hypothesis which emphasized on the deposition of insoluble peptides formed due to the faulty cleavage of the amyloid precursor protein. Current pharmacotherapy includes mainly the acetylcholinesterase inhibitors and N-methyl-D-aspartate receptor agonist which offer symptomatic therapy and does not address the underlying cause of the disease. The disease-modifying therapy has garnered a lot of research interest for the development of effective pharmacotherapy for AD. β and γ-Secretase constitute attractive targets that are focussed in the disease-modifying approach. Potentiation of α-secretase also seems to be a promising approach towards the development of an effective anti-Alzheimer therapy. Additionally, the ameliorative agents that prevent aggregation of amyloid peptide and also the ones that modulate inflammation and oxidative damage associated with the disease are focussed upon. Development in the area of the vaccines is in progress to combat the characteristic hallmarks of the disease. Use of cholesterol-lowering agents also is a fruitful strategy for the alleviation of the disease as a close association between the cholesterol and AD has been cited. The present review underlines the major therapeutic strategies for AD with focus on the new developments that are on their way to amend the current therapeutic scenario of the disease.

BACE1 (β-secretase) inhibitors for the treatment of Alzheimer's disease

BACE1 (β-secretase, memapsin 2, Asp2) has emerged as a promising target for the treatment of Alzheimer's disease. BACE1 is an aspartic protease which functions in the first step of the pathway leading to the production and deposition of amyloid-β peptide (Aβ). Its gene deletion showed only mild phenotypes. BACE1 inhibition has direct implications in the Alzheimer's disease pathology without largely affecting viability. However, inhibiting BACE1 selectively in vivo has presented many challenges to medicinal chemists. Since its identification in 2000, inhibitors covering many different structural classes have been designed and developed. These inhibitors can be largely classified as either peptidomimetic or non-peptidic inhibitors. Progress in these fields resulted in inhibitors that contain many targeted drug-like characteristics. In this review, we describe structure-based design strategies and evolution of a wide range of BACE1 inhibitors including compounds that have been shown to reduce brain Aβ, rescue the cognitive decline in transgenic AD mice and inhibitor drug candidates that are currently in clinical trials.

Study on the active mechanism of β-secretase inhibitors by molecular simulations

The proteolytic enzyme β-secretase (BACE-1) is one of potential drug targets for treating Alzheimers's disease. First, the reliable and accurate models of three-dimensional quantitative structure-activity relationship for the BACE-1 inhibitors were established, and the several important structural factors that mainly influence the inhibitory activity were obtained. Second, the results of molecular docking presented the binding mode between BACE-1 and its inhibitors, and molecular dynamic simulations provided the details of the receptor-ligand interactions. Furthermore, several new derivatives were designed and validated based on these theoretical analyses. Our studies revealed the binding mechanism between BACE-1 and its inhibitors, and provide some insights into the further structural modification and the design of new inhibitors with higher activity.

Screen3D: a novel fully flexible high-throughput shape-similarity search method

3D shape- or volume-based virtual screening is a broadly used approach in drug discovery. In recent years a large number of publications have appeared in which these tools were compared not only to competitive methods but to docking studies as well. Studies often showed that the effectiveness of docking could be highly variable due to a large number of possible confounding factors, while ligand-based, shape-based approaches were more consistent. Here, we describe a novel, fully flexible shape-based virtual screening algorithm that does not require previous 3D conformation or conformer generation. Due to its solid consistency it can easily be used on desktop computers by non-expert scientists. The algorithm is demonstrated in a study for the investigation of β-secretase inhibitors and benchmarked on the Directory of Useful Decoys data set.

Computational methods in drug discovery

Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature.

Microsecond molecular dynamics simulation of Aβ42 and identification of a novel dual inhibitor of Aβ42 aggregation and BACE1 activity

AIM

To study the conformational changes of Aβ42 and discover novel inhibitors of both Aβ42 aggregation and β-secretase (BACE1).

METHODS

A molecular dynamics (MD) simulation at a microsecond level was performed to explore stable conformations of Aβ42 monomer in aqueous solution. Subsequently, structure-based virtual screening was used to search for inhibitors of both Aβ42 aggregation and BACE1. Protein purification and in vitro activity assays were performed to validate the inhibition of the compounds identified via virtual screening.

RESULTS

The initial α-helical conformation of Aβ42, which was unstable in aqueous solution, turned into a β-sheet mixed with a coil structure through a transient and fully random coil. The conformation of Aβ42 mainly comprising β-sheets and coils structure was used for further virtual screening. Five compounds were identified as inhibitors for Aβ42 aggregation, and one of them, AE-848, was discovered to be a dual inhibitor of both Aβ42 aggregation and BACE1, with IC50 values of 36.95 μmol/L and 22.70 μmol/L, respectively.

CONCLUSION

A helical to β-sheet conformational change in Aβ42 occurred in a 1.8 microsecond MD simulation. The resulting β-sheet structure of the peptide is an appropriate conformation for the virtual screening of inhibitors against Aβ42 aggregation. Five compounds were identified as inhibitors of Aβ42 aggregation by in vitro activity assays. It was particularly interesting to discover a dual inhibitor that targets both Aβ42 aggregation and BACE1, the two crucial players in the pathogenesis of Alzheimer's disease.

The structural evolution of β-secretase inhibitors: a focus on the development of small-molecule inhibitors

Effective treatment of Alzheimer's disease (AD) remains a critical unmet need in medicine. The lack of useful treatment for AD led to an intense search for novel therapies based on the amyloid hypothesis, which states that amyloid β-42 (Aβ42) plays an early and crucial role in all cases of AD. β-Secretase (also known as BACE-1 β-site APP-cleaving enzyme, Asp-2 or memapsin-2) is an aspartyl protease representing the rate limiting step in the generation of Aβ peptide fragments, therefore it could represent an important target in the steady hunt for a disease-modifying treatment. Generally, β-secretase inhibitors are grouped into two families: peptidomimetic and nonpeptidomimetic inhibitors. However, irrespective of the class, serious challenges with respect to blood-brain barrier (BBB) penetration and selectivity still remain. Discovering a small molecule inhibitor of β-secretase represents an unnerving challenge but, due to its significant potential as a therapeutic target, growing efforts in this task are evident from both academic and industrial laboratories. In this frame, the rising availability of crystal structures of β-secretase-inhibitor complexes represents an invaluable opportunity for optimization. Nevertheless, beyond the inhibitory activity, the major issue of the current research approaches is about problems associated with BBB penetration and pharmacokinetic properties. This review follows the structural evolution of the early β-secretase inhibitors and gives a snap-shot of the hottest chemical templates in the literature of the last five years, showing research progress in this field.

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.

What has polar surface area ever done for drug discovery?

Over the last decade, polar surface area (PSA) has become a ubiquitous term in medicinal and computational chemistry circles. This article charts the development of the increasingly efficient methods for the calculation of PSA before illustrating its usefulness through selected examples drawn from the medicinal chemistry literature. Consideration of PSA is shown to assist in the improvement of cellular potency, intestinal absorption and blood-brain barrier permeation or restriction to the peripheral circulation.