BACE1 inhibitors with a pyridine scaffold.
Abstract
Pyridine is a unique aromatic ring. Although pyridines are used industrially, pyridine moieties are present in many natural products, such as vitamins, coenzymes, and alkaloids, and also in many drugs and pesticides. Pyridine moieties are often used in drugs because of their characteristics such as basicity, water solubility, stability, and hydrogen bond-forming ability, and their small molecular size. Because pyridine rings are able to act as the bioisosteres of amines, amides, heterocyclic rings containing nitrogen atoms, and benzene rings, their replacement by pyridine moieties is important in drug discovery. Recently, we synthesized a series of BACE1 inhibitors by in silico conformational structure-based drug design and found an important role of pyridine moiety as a scaffold. In this chapter, we describe the important role of pyridines in medicinal chemistry and the development of β-secretase inhibitors possessing a pyridine scaffold for the treatment of Alzheimer’s disease.
Keywords
- Alzheimer’s disease
- BACE1 inhibitor
- bioisostere
- drug design
- in silico conformational structure-based design
1. Introduction
Alzheimer’s disease (AD) is the most common cause of dementia. AD is characterized by progressive intellectual deterioration. In 1906, Alois Alzheimer, a psychiatrist and a neuropathologist, reported on a 51-year-old female at the Frankfurt Asylum. The patient showed strange behavioral symptoms and loss of short-term memory, which was later called “AD.” The cause of AD has only been clarified relatively recently, and there have been no therapeutic agents since that first report by Dr. Alzheimer over 100 years ago. Recently, the development of many drug candidates based on the amyloid hypothesis has been reported. β-Secretase (BACE1; β-site amyloid precursor protein-cleaving enzyme 1) is a promising molecular target for the development of anti-Alzheimer’s drugs. BACE1 triggers the formation of the amyloid β (Aβ) peptide that is the main component of the senile plaques found in the brain of AD patients. We designed a series of peptidomimetic inhibitors possessing a substrate transition-state analog. We followed this with the design of nonpeptidic BACE1 inhibitors possessing a pyridine scaffold, using an approach based on a conformer of the docked ligand in the target biomolecule—the “
2. Conventional roles of pyridine in medicinal chemistry
Pyridine rings are present in many natural products including vitamins such as niacins and vitamin B6, coenzymes such as nicotinamide adenine dinucleotide (NAD), and alkaloids such as trigonelline. Trigonelline is an alkaloid that is the product of niacin metabolism. Many drugs and pesticides contain a pyridine moiety. Examples include antimicrobial agents, antiviral agents, antioxidants, antidiabetic agents, anti-malarial agents, anti-inflammatory agents, psychopharmacological antagonists, and antiamoebic agents [1]. These pyridine moieties play critical roles in medicinal chemistry because of their abovementioned characteristics. One role of pyridine in medicinal chemistry is to improve water solubility because of its weak basicity. Although many drugs and pesticides possessing a pyridine ring had been designed for improved water solubility, this improvement is often pH-dependent. For example, the sulfa drug, sulfapyridine
Bioisosteres have an important role in the pyridine ring for medicinal chemistry [4]. Bioisosteres are functional or atomic groups with similar physiochemical properties to the parent functional/atomic groups.
Compounds associated with them exhibit similar biological or physiochemical properties as the parent compound. In medicinal chemistry, a portion of a candidate drug is replaced with other functional/atomic groups with the goal of improving drug efficacy,
Matrix metalloproteinases (MMPs) are calcium- and zinc-containing endopeptidases that have diverse roles in cell behaviors including cell proliferation, migration, and differentiation. Some MMP family subtypes, which include MMP2, MMP3, and MMP9, can degrade the extracellular matrix, resulting in the accelerated infiltration and migration of cancer cells. Inhibitors of some MMP subtypes had been reported for anticancer activity. Most MMP inhibitors have a hydroxamic acid that can bind to the zinc-containing sites of MMPs [7]. The second-generation MMP inhibitors such as batimastat
3. Design of BACE1 inhibitors
3.1. Pathology of AD and design of peptidomimetic inhibitors
AD is the most common cause of dementia. Its cause has been unclear. A breakthrough was made through the genetic study of some familial AD (FAD) patients with a mutation of the gene encoding amyloid precursor protein (APP) or presenilin gene. As these mutations caused an increase in Aβs that are the main components of senile plaques in the brain of patients with AD, it indicates their involvement in the pathogenesis of AD [9, 10, 11, 12]. Aβs are produced from APP by two processing enzymes, β-secretase (BACE1; β-site APP-cleaving enzyme 1) and γ-secretase, which are potential molecular targets for anti-AD drugs [13, 14, 15, 16]. The cleavage sites of APP are shown in Figure 3A. The full-length APP (APP770) and its isoforms, APP695 and APP751, result from the alternative splicing of its mRNA. BACE1 is a type I transmembrane aspartic protease with 501 amino acids, which triggers Aβ formation in the rate-limiting first step by cleaving at the N-terminus (β-site) of the Aβ domain of APP. Next, the aspartic protease, γ-secretase, cleaves at the C-terminus of the Aβ domain, releasing Aβs that consists mainly of two molecular species, Aβ1–42 and Aβ1–40. γ-Secretase cleaves two cleavage sites “γ-sites” forming Aβ1–40 and Aβ1–42. Two processing enzymes, BACE1 and γ-secretase, are categorized as aspartic proteases. They have an acidic optimum pH. Furthermore, BACE1 and γ-secretase, and their substrate, APP, are located in the same intracellular granules, such as endosomes and the trans-Golgi network, which have an acidic environment, suggesting that Aβs are produced in these locations [17]. Aβ1–42 displays more potent neurotoxicity and aggregation behavior than Aβ1–40 and appears to be critical in the pathogenesis of AD. By contrast, α-secretase is a disintegrin and metalloprotease (ADAM) family metalloprotease, for example, ADAM9, ADAM10, and TNF-α-converting enzyme (TACE, also known as ADAM17), which cleaves APP at the α-site between Lys16 and Leu17 in the Aβ domain [17]. A homolog enzyme of BACE1, BACE2, cleaves at two sites (θ-sites) between Phe19 and Phe20, and between Phe20 and Ala21 in the Aβ domain [18]. Because the α-site and θ-sites are located at the center of the Aβ domain, their cleavage does not lead to Aβ production. According to the amyloid hypothesis, BACE1 and γ-secretase are the molecular targets for anti-AD drugs. However, because γ-secretase can cleave other single-pass transmembrane proteins
As BACE1 is an aspartic protease, early BACE1 inhibitors are peptidomimetic with a substrate transition-state analog. They were designed on the basis of an inhibitor design approach as well as other aspartic proteases such as renin and human immunodeficiency virus protease [20, 21, 22, 23, 24, 25, 26]. Many mutations in the APP gene that affect Aβ formation, Aβ1–42/Aβ1–40 ratio or Aβ toxicity have been reported. Among them, the Swedish mutation (K670 N, M671 L double mutation, Figure 3A) around the β-site induces β-cleavage by BACE1, increasing the Aβ1–42 and Aβ1–40 levels in the brains of AD patients. Because the Swedish-mutant APP is cleaved faster than the wild-type APP, early BACE1 inhibitors were designed on the basis of the Swedish-mutant APP amino acid sequence. In 1999, Sinha et al. at Elan Pharmaceuticals succeeded in purifying BACE1 from the human brain using a transition-state analog based on the Swedish-mutant sequence and cloned the BACE1 enzyme [16]. In 2000 and 2001, Ghosh and Tang described the potent inhibitors, compounds
We have also reported a series of peptidomimetic BACE1 inhibitors possessing a norstatine-type transition-state analog, phenyl norstatine (Pns: (
3.2. Design of nonpeptidic BACE1 inhibitors with a pyridine scaffold
We designed and synthesized nonpeptidic BACE1 inhibitors from our peptidic BACE1 inhibitors
Next, we focused on a proton of the P2-isophthalic ring of inhibitor
3.3. Design based on quantum chemical interaction and electron donor bioisostere
The first reported coordinate set of crystal structure of BACE1-inhibitor (OM99–2) complex is 1FKN by Gosh et al. [27, 28, 29]. The P2 moiety of the inhibitor interacts with the Arg235 side chain of BACE1 by hydrogen bonding in the crystal structure. We compared the publicly available X-ray crystal structures of BACE1-inhibitor complexes and discovered that most inhibitors did not interact with Arg235 by hydrogen bonding [41]. Surprisingly, the guanidino group of BACE1-Arg235 in most crystal structures, except 1FKN, showed the similar “flopping over” feature of the P2 region of the inhibitors, and the nearest distances between the guanidino plane of Arg235 side chain and the P2 region of the inhibitor showed similar values of approximately 3 Å. The P2 moieties in many crystal structures that interact with the BACE1-Arg235 side chain are a methyl group, carbonyl oxygen atom, or aromatic ring. They appear to interact with the guanidine plane of Arg235 side chain by CH-π, O-π, or π-π stacking interactions. This suggests that the π-orbital on the guanidino plane can interact with the P2 region of the inhibitors by a weak quantum force. The only exception was the interaction in the first reported X-ray crystal structure, 1FKN. Although the P2 moiety of OM99–2 in the crystal structure of 1FKN appeared to interact with the BACE1-Arg235 side chain via hydrogen bonding, the P2-moiety of OM00–3 that was structurally similar to OM99–2 interacted with the π-orbital on the guanidine plane of the BACE1-Arg235 side chain via O-π interaction (PDB ID: 1M4H). Many early BACE1 inhibitors that possess a hydrogen bond receptor at the P2 position were designed using the 1FKN crystal structure. However, the hydrogen-bonding interaction between most of the inhibitors and the BACE1-Arg235 side chain was not shown in their crystal structures. For instance, inhibitor
We hypothesized that the quantum chemical interaction between an inhibitor and the side chain of BACE1-Arg235 plays a critical role in the inhibition mechanism. Therefore, we focused on the optimization around the P2 region. The finding of a structure–activity relationship study focusing on the inhibitor’s P2 region is shown in Table 1 [39, 40, 41, 44]. Inhibitors
4. Conclusion
Pyridines are important in medicinal chemistry because of their properties, which include weak basicity, water solubility,
Acknowledgments
This study was supported in part by the Grants in Aid for Scientific Research from MEXT (Ministry of Education, Culture, Sports, Science and Technology), Japan (KAKENHI No. 23590137 and No. 26460163), and a donation from Professor Emeritus Tetsuro Fujita of Kyoto University. Prof. Fujita passed away on January 1 of last year. Prof. Fujita was my teacher. We dedicate this chapter to Prof. Fujita.
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