ABSTRACT
Plasmepsin X (PMX) is an essential aspartyl protease controlling malaria parasite egress and invasion of erythrocytes, development of functional liver merozoites (prophylactic activity), and blocking transmission to mosquitoes, making it a potential multistage drug target. We report the optimization of an aspartyl protease binding scaffold and the discovery of potent, orally active PMX inhibitors with in vivo antimalarial efficacy. Incorporation of safety evaluation early in the characterization of PMX inhibitors precluded compounds with a long human half-life (t1/2) to be developed. Optimization focused on improving the off-target safety profile led to the identification of UCB7362 that had an improved in vitro and in vivo safety profile but a shorter predicted human t1/2. UCB7362 is estimated to achieve 9â¯logâ¯10 unit reduction in asexual blood-stage parasites with once-daily dosing of 50 mg for 7 days. This work demonstrates the potential to deliver PMX inhibitors with in vivo efficacy to treat malaria.
Subject(s)
Antimalarials , Folic Acid Antagonists , Malaria , Animals , Humans , Antimalarials/pharmacology , Antimalarials/therapeutic use , Plasmodium falciparum/metabolism , Aspartic Acid Endopeptidases , Malaria/drug therapyABSTRACT
Vorapaxar is an approved drug for the reduction of thrombotic cardiovascular events in patients with a history of myocardial infarction or with peripheral arterial disease. Subsequent to the discovery of Vorapaxar, medicinal chemistry efforts were continued to identify structurally differentiated leads. Toward this goal, extensive structure-activity relationship studies using a C-ring-truncated version of Vorapaxar culminated in the discovery of three leads, represented as 13, 14, and 23. Among these leads, compound 14 possessed favorable pharmacokinetic properties and an off-target profile, which supported additional profiling in an exploratory rat toxicology study.
Subject(s)
Myocardial Infarction , Thrombosis , Animals , Humans , Lactones , Myocardial Infarction/drug therapy , Platelet Aggregation Inhibitors , Rats , Receptor, PAR-1 , Receptors, Proteinase-Activated , Thrombosis/chemically induced , Thrombosis/drug therapyABSTRACT
Herein, we disclose three structurally differentiated γ-secretase modulators (GSMs) based on an oxadiazine scaffold. The analogues from series I potently inhibit the generation of Aß42 in vitro when the substituents at 3 and 4 positions of the oxadiazine moiety adopt an α orientation (cf. 11). To address the concern around potential reactivity of the exocyclic double bond present in series I toward nucleophilic attack, compounds containing either an endocyclic double bond, such as 20 (series II), or devoid of an olefinic moiety, such as 27 (series III), were designed and validated as novel GSMs. Compound 11 and azepine 20 exhibit robust lowering of CSF Aß42 in rats treated with a 30 mg/kg oral dose.
Subject(s)
Amyloid Precursor Protein Secretases/antagonists & inhibitors , Amyloid Precursor Protein Secretases/metabolism , Alkenes/chemistry , Alkenes/pharmacology , Amyloid beta-Peptides/antagonists & inhibitors , Amyloid beta-Peptides/cerebrospinal fluid , Animals , Binding Sites/physiology , HEK293 Cells , Humans , Oxadiazoles/chemistry , Oxadiazoles/pharmacology , Peptide Fragments/antagonists & inhibitors , Peptide Fragments/cerebrospinal fluid , Rats , Structure-Activity RelationshipABSTRACT
Herein we describe structure-activity relationship (SAR) and metabolite identification (Met-ID) studies that provided insight into the origin of time-dependent inhibition (TDI) of cytochrome P450 3A4 (CYP3A4) by compound 1. Collectively, these efforts revealed that bioactivation of the fluoropyrimidine moiety of 1 led to reactive metabolite formation via oxidative defluorination and was responsible for the observed TDI. We discovered that substitution at both the 4- and 6-positions of the 5-fluoropyrimidine of 1 was necessary to ameliorate this TDI as exemplified by compound 19.
Subject(s)
Cytochrome P-450 CYP3A Inhibitors/chemistry , Cytochrome P-450 CYP3A Inhibitors/pharmacology , Cytochrome P-450 CYP3A/metabolism , Pyrimidines/chemistry , Pyrimidines/pharmacology , Animals , Cytochrome P-450 CYP3A Inhibitors/pharmacokinetics , Humans , Kinetics , Pyrimidines/pharmacokinetics , Rats , Structure-Activity Relationship , Tissue DistributionABSTRACT
The design and synthesis of a new series of tetrahydrobenzisoxazoles as modulators of γ-secretase activity and their structure-activity relationship (SAR) will be detailed. Several compounds are active γ-secretase modulators (GSMs) with good to excellent selectivity for the reduction of Aß42 in the cellular assay. Compound 14a was tested in vivo in a nontransgenic rat model and was found to significantly reduce Aß42 in the CNS compartment compared to vehicle-treated animals (up to 58% reduction of cerebrospinal fluid Aß42 as measured 3 h after an acute oral dosing at 30 mg/kg).
ABSTRACT
We describe successful efforts to optimize the in vivo profile and address off-target liabilities of a series of BACE1 inhibitors represented by 6 that embodies the recently validated fused pyrrolidine iminopyrimidinone scaffold. Employing structure-based design, truncation of the cyanophenyl group of 6 that binds in the S3 pocket of BACE1 followed by modification of the thienyl group in S1 was pursued. Optimization of the pyrimidine substituent that binds in the S2'-S2â³ pocket of BACE1 remediated time-dependent CYP3A4 inhibition of earlier analogues in this series and imparted high BACE1 affinity. These efforts resulted in the discovery of difluorophenyl analogue 9 (MBi-4), which robustly lowered CSF and cortex Aß40 in both rats and cynomolgus monkeys following a single oral dose. Compound 9 represents a unique molecular shape among BACE inhibitors reported to potently lower central Aß in nonrodent preclinical species.
Subject(s)
Amyloid Precursor Protein Secretases/antagonists & inhibitors , Amyloid beta-Peptides/metabolism , Amyloid beta-Protein Precursor/metabolism , Drug Design , Heterocyclic Compounds/chemistry , Imines/chemistry , Amyloid beta-Peptides/cerebrospinal fluid , Animals , Cerebral Cortex/metabolism , Enzyme Inhibitors/pharmacology , Macaca fascicularis , Molecular Structure , Rats , Structure-Activity RelationshipABSTRACT
The synthesis of a series of iminoheterocycles and their structure-activity relationships (SAR) as inhibitors of the aspartyl protease BACE1 will be detailed. An effort to access the S3 subsite directly from the S1 subsite initially yielded compounds with sub-micromolar potency. A subset of compounds from this effort unexpectedly occupied a different binding site and displayed excellent BACE1 affinities. Select compounds from this subset acutely lowered Aß40 levels upon subcutaneous and oral administration to rats.
Subject(s)
Alzheimer Disease/drug therapy , Amyloid Precursor Protein Secretases/therapeutic use , Aspartic Acid Endopeptidases/therapeutic use , Amyloid Precursor Protein Secretases/genetics , Amyloid Precursor Protein Secretases/metabolism , Animals , Aspartic Acid Endopeptidases/genetics , Aspartic Acid Endopeptidases/metabolism , Drug Design , Drug Discovery , Models, Molecular , Molecular Structure , Rats , Structure-Activity RelationshipABSTRACT
In an attempt to further improve overall profiles of the oxadiazine series of GSMs, in particular the hERG activity, conformational modifications of the core structure resulted in the identification of fused oxadiazepines such as 7i which had an improved hERG inhibition profile and was a highly efficacious GSM in vitro and in vivo in rats. These SAR explorations offer opportunities to identify potential drugs to treat Alzheimer's disease.
Subject(s)
Alzheimer Disease/drug therapy , Amyloid Precursor Protein Secretases/metabolism , Azepines/chemical synthesis , Drug Discovery , Ether-A-Go-Go Potassium Channels/antagonists & inhibitors , Animals , Azepines/chemistry , Azepines/pharmacology , ERG1 Potassium Channel , Enzyme Activation/drug effects , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Humans , Inhibitory Concentration 50 , Molecular Structure , Rats , Structure-Activity RelationshipABSTRACT
On the basis of our observation that the biaryl substituent of iminopyrimidinone 7 must be in a pseudoaxial conformation to occupy the contiguous S1-S3 subsites of BACE1, we have designed a novel fused bicyclic iminopyrimidinone scaffold intended to favor this bioactive conformation. Strategic incorporation of a nitrogen atom in the new constrained ring allowed us to develop SAR around the S2' binding pocket and ultimately resulted in analogues with low nanomolar potency for BACE1. In particular, optimization of the prime side substituent led to major improvements in potency by displacement of two conserved water molecules from a region near S2'. Further optimization of the pharmacokinetic properties of this fused pyrrolidine series, in conjunction with facile access to a rat pharmacodynamic model, led to identification of compound 43, which is an orally active, brain penetrant inhibitor that reduces Aß(40) in the plasma, CSF, and cortex of rats in a dose-dependent manner.
Subject(s)
Amyloid Precursor Protein Secretases/antagonists & inhibitors , Aspartic Acid Endopeptidases/antagonists & inhibitors , Bridged Bicyclo Compounds, Heterocyclic/chemical synthesis , Nitriles/chemical synthesis , Pyrimidines/chemical synthesis , Pyrimidinones/chemical synthesis , Thiophenes/chemical synthesis , Administration, Oral , Amyloid Precursor Protein Secretases/chemistry , Amyloid beta-Peptides/metabolism , Animals , Aspartic Acid Endopeptidases/chemistry , Bridged Bicyclo Compounds, Heterocyclic/pharmacokinetics , Bridged Bicyclo Compounds, Heterocyclic/pharmacology , Cerebral Cortex/metabolism , Crystallography, X-Ray , HEK293 Cells , Humans , Macaca fascicularis , Models, Molecular , Molecular Conformation , Nitriles/pharmacokinetics , Nitriles/pharmacology , Peptide Fragments/metabolism , Permeability , Pyrimidines/pharmacokinetics , Pyrimidines/pharmacology , Pyrimidinones/pharmacokinetics , Pyrimidinones/pharmacology , Quantum Theory , Rats , Stereoisomerism , Structure-Activity Relationship , Thermodynamics , Thiophenes/pharmacokinetics , Thiophenes/pharmacologyABSTRACT
Beta-secretase 1 (BACE1) is a central nervous system (CNS) aspartyl protease required for production of amyloid beta (Aß) peptides. Brain-penetrant BACE1 inhibitors are central to test the 'amyloid hypothesis', which suggests that a reduction of Aß species in the CNS would halt or even reverse Alzheimer's disease. Discovery of the iminoheterocycle class of BACE1 inhibitors (which show robust efficacy in reduction of CNS Aß species in animal models) marked an important milestone. These discoveries arose independently from multiple research laboratories that took different paths to end at the same scaffolds. These druggable motifs should be applicable to other aspartyl proteases of therapeutic importance and also to other protein targets involving crucial interactions with carboxylic acid side chains. Here, a comparison of these approaches to BACE1 discovery will showcase how it is important to pay attention to the intrinsic physicochemical properties of the lead series, even at the very early stage of drug discovery.
Subject(s)
Amyloid Precursor Protein Secretases/antagonists & inhibitors , Amyloid Precursor Protein Secretases/chemistry , Aspartic Acid Endopeptidases/antagonists & inhibitors , Aspartic Acid Endopeptidases/chemistry , Protease Inhibitors/chemistry , Animals , Drug Design , Heterocyclic Compounds/chemistry , HumansABSTRACT
From an initial lead 1, a structure-based design approach led to identification of a novel, high-affinity iminohydantoin BACE1 inhibitor that lowers CNS-derived Aß following oral administration to rats. Herein we report SAR development in the S3 and F' subsites of BACE1 for this series, the synthetic approaches employed in this effort, and in vivo data for the optimized compound.
Subject(s)
Alzheimer Disease/drug therapy , Amyloid Precursor Protein Secretases/antagonists & inhibitors , Amyloid beta-Peptides/antagonists & inhibitors , Anticonvulsants/chemical synthesis , Aspartic Acid Endopeptidases/antagonists & inhibitors , Enzyme Inhibitors/chemical synthesis , Hydantoins/chemical synthesis , Administration, Oral , Alzheimer Disease/blood , Alzheimer Disease/cerebrospinal fluid , Amyloid Precursor Protein Secretases/metabolism , Amyloid beta-Peptides/blood , Amyloid beta-Peptides/cerebrospinal fluid , Animals , Anticonvulsants/pharmacology , Aspartic Acid Endopeptidases/metabolism , Binding Sites , Computer Simulation , Crystallography, X-Ray , Disease Models, Animal , Drug Design , Enzyme Inhibitors/pharmacology , Humans , Hydantoins/pharmacology , Models, Molecular , Protein Binding , Rats , Rats, Sprague-DawleyABSTRACT
Fused oxadiazines (3) were discovered as selective and orally bioavailable γ-secretase modulators (GSMs) based on the structural framework of oxadiazoline GSMs. Although structurally related, initial modifications showed that structure-activity relationships (SARs) did not translate from the oxadiazoline to the oxadiazine series. Subsequent SAR studies on modifications at the C3 and C4 positions of the fused oxadiazine core helped to identify GSMs such as compounds 8r and 8s that were highly efficacious in vitro and in vivo in a number of animal models with highly desirable physical and pharmacological properties. Further improvements of in vitro activity and selectivity were achieved by the preparation of fused morpholine oxadiazines. The shift in specificity of APP cleavage rather than a reduction in overall γ-secretase activity and the lack of changes in substrate accumulation and Notch processing as observed in the animal studies of compound 8s confirm that the oxadiazine series of compounds are potent GSMs.
ABSTRACT
Inhibition of BACE1 to prevent brain Aß peptide formation is a potential disease-modifying approach to the treatment of Alzheimer's disease. Despite over a decade of drug discovery efforts, the identification of brain-penetrant BACE1 inhibitors that substantially lower CNS Aß levels following systemic administration remains challenging. In this report we describe structure-based optimization of a series of brain-penetrant BACE1 inhibitors derived from an iminopyrimidinone scaffold. Application of structure-based design in tandem with control of physicochemical properties culminated in the discovery of compound 16, which potently reduced cortex and CSF Aß40 levels when administered orally to rats.
ABSTRACT
Fragment-based drug discovery (FBDD) has become increasingly popular over the last decade. We review here how we have used highly structure-driven fragment-based approaches to complement more traditional lead discovery to tackle high priority targets and those struggling for leads. Combining biomolecular nuclear magnetic resonance (NMR), X-ray crystallography, and molecular modeling with structure-assisted chemistry and innovative biology as an integrated approach for FBDD can solve very difficult problems, as illustrated in this chapter. Here, a successful FBDD campaign is described that has allowed the development of a clinical candidate for BACE-1, a challenging CNS drug target. Crucial to this achievement were the initial identification of a ligand-efficient isothiourea fragment through target-based NMR screening and the determination of its X-ray crystal structure in complex with BACE-1, which revealed an extensive H-bond network with the two active site aspartate residues. This detailed 3D structural information then enabled the design and validation of novel, chemically stable and accessible heterocyclic acylguanidines as aspartic acid protease inhibitor cores. Structure-assisted fragment hit-to-lead optimization yielded iminoheterocyclic BACE-1 inhibitors that possess desirable molecular properties as potential therapeutic agents to test the amyloid hypothesis of Alzheimer's disease in a clinical setting.
Subject(s)
Amyloid Precursor Protein Secretases/antagonists & inhibitors , Drug Discovery , Enzyme Inhibitors/analysis , Enzyme Inhibitors/pharmacology , Nuclear Magnetic Resonance, Biomolecular , Small Molecule Libraries/pharmacology , Amyloid Precursor Protein Secretases/metabolism , Crystallography, X-Ray , Enzyme Inhibitors/chemistry , High-Throughput Screening Assays , Models, Molecular , Small Molecule Libraries/analysis , Small Molecule Libraries/chemistry , Structure-Activity RelationshipABSTRACT
Cyclic hydroxyamidines were designed and validated as isosteric replacements of the amide functionality. Compounds with these structural motifs were found to be metabolically stable and to possess highly desirable pharmacokinetic profiles. These designs were applied in the identification of γ-secretase modulators leading to highly efficacious agents for reduction of central nervous system Aß(42) in various animal models.
Subject(s)
Amidines/chemical synthesis , Amyloid Precursor Protein Secretases/metabolism , Oxadiazoles/chemical synthesis , Oxazines/chemical synthesis , Amidines/pharmacokinetics , Amidines/pharmacology , Amyloid beta-Peptides/metabolism , Animals , Brain/metabolism , Dogs , HEK293 Cells , Humans , Macaca fascicularis , Male , Oxadiazoles/pharmacokinetics , Oxadiazoles/pharmacology , Oxazines/pharmacokinetics , Oxazines/pharmacology , Peptide Fragments/metabolism , Rats , Stereoisomerism , Structure-Activity RelationshipABSTRACT
We herein report the discovery of four series of fused 5,6-bicyclic heterocycles as γ-secretase modulators. Synthesis and SAR of these series are discussed. These compounds represent a new class of γ-secretase modulators that demonstrate moderate to good in vitro potency in inhibiting Aß(42) production.
Subject(s)
Amyloid Precursor Protein Secretases/metabolism , Amyloid beta-Peptides/antagonists & inhibitors , Bridged Bicyclo Compounds, Heterocyclic/chemistry , Bridged Bicyclo Compounds, Heterocyclic/pharmacology , Alzheimer Disease/drug therapy , Amyloid beta-Peptides/metabolism , Animals , Bridged Bicyclo Compounds, Heterocyclic/pharmacokinetics , Humans , Rats , Structure-Activity RelationshipABSTRACT
The synthesis and structure-activity relationship of a novel series of pyrazolopyridines are reported. These compounds represent a new class of γ-secretase modulators that demonstrate good in vitro potency in inhibiting Aß42 production. Examples with statistically significant in vivo efficacy in reducing the production of rat cerebrospinal fluid Aß42 were also identified.
ABSTRACT
The synthesis of a novel series of iminoheterocycles and their structure-activity relationship (SAR) as modulators of gamma-secretase activity will be detailed. Encouraging SAR generated from a monocyclic core led to a structurally unique bicyclic core. Selected compounds exhibit good potency as gamma-secretase modulators, excellent rat pharmacokinetics, and lowering of Abeta42 levels in various in vivo models.
Subject(s)
Alzheimer Disease/drug therapy , Amyloid Precursor Protein Secretases/metabolism , Amyloid beta-Peptides/metabolism , Imines/chemistry , Imines/therapeutic use , Peptide Fragments/metabolism , Amyloid beta-Peptides/antagonists & inhibitors , Animals , Brain/metabolism , Bridged Bicyclo Compounds, Heterocyclic/chemistry , Bridged Bicyclo Compounds, Heterocyclic/pharmacokinetics , Bridged Bicyclo Compounds, Heterocyclic/therapeutic use , Humans , Imines/pharmacokinetics , Mice , Mice, Transgenic , Peptide Fragments/antagonists & inhibitors , Rats , Structure-Activity RelationshipABSTRACT
The syntheses and structure-activity relationships of the tartrate-based TACE inhibitors are discussed. The optimization of both the prime and non-prime sites led to compounds with picomolar activity. Several analogs demonstrated good rat pharmacokinetics.
Subject(s)
ADAM Proteins/antagonists & inhibitors , Protease Inhibitors/chemistry , Tartrates/chemistry , ADAM Proteins/metabolism , ADAM17 Protein , Animals , Binding Sites , Computer Simulation , Protease Inhibitors/chemical synthesis , Protease Inhibitors/pharmacokinetics , Rats , Structure-Activity Relationship , Tartrates/chemical synthesis , Tartrates/pharmacokineticsABSTRACT
A series of novel dopamine D(1) antagonists derived from functionalization of the D-ring of SCH 39166 were prepared. A number of these compounds displayed subnanomolar D(1) activity and more than 1000-fold selectivity over D(2). We found C-3 derivatization afforded compounds with superior overall profile in comparison to the C-2 and C-4 derivatization. A number of highly potent D(1) antagonists were discovered which have excellent selectivity over other dopamine receptors and improved PK profile compared to SCH 39166.