ABSTRACT
Herein, we describe the design and synthesis of γ-secretase modulator (GSM) clinical candidate PF-06648671 (22) for the treatment of Alzheimer's disease. A key component of the design involved a 2,5-cis-tetrahydrofuran (THF) linker to impart conformational rigidity and lock the compound into a putative bioactive conformation. This effort was guided using a pharmacophore model since crystallographic information was not available for the membrane-bound γ-secretase protein complex at the time of this work. PF-06648671 achieved excellent alignment of whole cell in vitro potency (Aß42 IC50 = 9.8 nM) and absorption, distribution, metabolism, and excretion (ADME) parameters. This resulted in favorable in vivo pharmacokinetic (PK) profile in preclinical species, and PF-06648671 achieved a human PK profile suitable for once-a-day dosing. Furthermore, PF-06648671 was found to have favorable brain availability in rodent, which translated into excellent central exposure in human and robust reduction of amyloid ß (Aß) 42 in cerebrospinal fluid (CSF).
Subject(s)
Alzheimer Disease , Amyloid Precursor Protein Secretases , Amyloid beta-Peptides , Amyloid Precursor Protein Secretases/antagonists & inhibitors , Amyloid Precursor Protein Secretases/metabolism , Alzheimer Disease/drug therapy , Humans , Animals , Amyloid beta-Peptides/metabolism , Rats , Structure-Activity Relationship , Mice , Male , Drug Discovery , Furans/pharmacology , Furans/pharmacokinetics , Furans/chemical synthesis , Furans/chemistry , Furans/therapeutic use , Rats, Sprague-Dawley , Brain/metabolismABSTRACT
Bispecific degraders (PROTACs) of ERα are expected to be advantageous over current inhibitors of ERα signaling (aromatase inhibitors/SERMs/SERDs) used to treat ER+ breast cancer. Information from DNA-encoded chemical library (DECL) screening provides a method to identify novel PROTAC binding features as the linker positioning, and binding elements are determined directly from the screen. After screening â¼120 billion DNA-encoded molecules with ERα WT and 3 gain-of-function (GOF) mutants, with and without estradiol to identify features that enrich ERα competitively, the off-DNA synthesized small molecule exemplar 7 exhibited nanomolar ERα binding, antagonism, and degradation. Click chemistry synthesis on an alkyne E3 ligase engagers panel and an azide variant of 7 rapidly generated bispecific nanomolar degraders of ERα, with PROTACs 18 and 21 inhibiting ER+ MCF7 tumor growth in a mouse xenograft model of breast cancer. This study validates this approach toward identifying novel bispecific degrader leads from DECL screening with minimal optimization.
Subject(s)
DNA/chemistry , Estrogen Receptor alpha/metabolism , Small Molecule Libraries/chemistry , Animals , Breast Neoplasms/drug therapy , Cell Line, Tumor , Cell Survival/drug effects , Click Chemistry , DNA/metabolism , Estrogen Antagonists/chemistry , Estrogen Antagonists/metabolism , Estrogen Antagonists/pharmacology , Estrogen Antagonists/therapeutic use , Estrogen Receptor alpha/chemistry , Estrogen Receptor alpha/genetics , Female , Half-Life , Humans , Indoles/chemistry , Indoles/metabolism , Kinetics , Mice , Small Molecule Libraries/metabolism , Small Molecule Libraries/pharmacology , Small Molecule Libraries/therapeutic use , Structure-Activity Relationship , Xenograft Model Antitumor AssaysABSTRACT
Herein we describe the design and synthesis of a series of pyridopyrazine-1,6-dione γ-secretase modulators (GSMs) for Alzheimer's disease (AD) that achieve good alignment of potency, metabolic stability, and low MDR efflux ratios, while also maintaining favorable physicochemical properties. Specifically, incorporation of fluorine enabled design of metabolically less liable lipophilic alkyl substituents to increase potency without compromising the sp(3)-character. The lead compound 21 (PF-06442609) displayed a favorable rodent pharmacokinetic profile, and robust reductions of brain Aß42 and Aß40 were observed in a guinea pig time-course experiment.
ABSTRACT
Herein we describe the design and synthesis of a novel series of γ-secretase modulators (GSMs) that incorporates a pyridopiperazine-1,6-dione ring system. To align improved potency with favorable ADME and in vitro safety, we applied prospective physicochemical property-driven design coupled with parallel medicinal chemistry techniques to arrive at a novel series containing a conformationally restricted core. Lead compound 51 exhibited good in vitro potency and ADME, which translated into a favorable in vivo pharmacokinetic profile. Furthermore, robust reduction of brain Aß42 was observed in guinea pig at 30 mg/kg dosed orally. Through chemical biology efforts involving the design and synthesis of a clickable photoreactive probe, we demonstrated specific labeling of the presenilin N-terminal fragment (PS1-NTF) within the γ-secretase complex, thus gaining insight into the binding site of this series of GSMs.
Subject(s)
Amyloid Precursor Protein Secretases/antagonists & inhibitors , Pyridazines/chemical synthesis , Pyridines/chemical synthesis , Amyloid Precursor Protein Secretases/chemistry , Amyloid beta-Peptides/metabolism , Animals , Binding Sites , CHO Cells , Cricetinae , Cricetulus , Drug Design , Guinea Pigs , HEK293 Cells , Humans , Peptide Fragments/metabolism , Presenilin-1/chemistry , Pyridazines/pharmacokinetics , Pyridazines/pharmacology , Pyridines/pharmacokinetics , Pyridines/pharmacology , Stereoisomerism , Structure-Activity RelationshipABSTRACT
A facile one-pot synthesis of 3,4-dihydro-1H-pyrido[1,2-a]pyrazine-1,6(2H)-diones (pyridopyrazine-1,6-diones) has been developed which employs a sequential coupling/cyclization reaction of 6-hydroxypicolinic acids and ß-hydroxylamines. The transformation proceeds in good yield under mild conditions using O-(7-aza-1H-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate (HATU) to both carry out the amide formation and activate the hydroxyl group for intramolecular alkylation.
Subject(s)
Heterocyclic Compounds, 2-Ring/chemical synthesis , Picolinic Acids/chemistry , Pyrazines/chemical synthesis , Pyridines/chemical synthesis , Catalysis , Combinatorial Chemistry Techniques , Cyclization , Heterocyclic Compounds, 2-Ring/chemistry , Molecular Structure , Pyrazines/chemistry , Pyridines/chemistryABSTRACT
A new and useful procedure for the macrocyclization of linear peptides is described. The natural amino acid side chains of tyrosine (phenol), lysine (alkylamine), and histidine (imidazole) react in an intramolecular fashion with a pendent pyridine-N-oxide-carboxamide, which is selectively activated by the phosphonium salt, PyBroP. The reaction is mild, rapid, and efficient with a potentially large substrate scope. Multiple examples are provided with full characterization and analyses, including a novel aza-variant of the C-O-D ring system of vancomycin.
Subject(s)
Chemistry, Organic/methods , Peptides, Cyclic/chemical synthesis , Peptides/chemistry , Cyclization , Histidine/chemistry , Lysine/chemistry , Models, Molecular , Molecular Structure , Peptides, Cyclic/chemistry , Vancomycin/chemistryABSTRACT
We report the discovery and optimization of a novel series of dihydrobenzofuran amides as γ-secretase modulators (GSMs). Strategies for aligning in vitro potency with drug-like physicochemical properties and good microsomal stability while avoiding P-gp mediated efflux are discussed. Lead compounds such as 35 and 43 have moderate to good in vitro potency and excellent selectivity against Notch. Good oral bioavailability was achieved as well as robust brain Aß42 lowering activity at 100 mg/kg po dose.
Subject(s)
Amides/chemical synthesis , Amides/pharmacology , Amyloid Precursor Protein Secretases/antagonists & inhibitors , Drug Design , Administration, Oral , Amides/chemistry , Animals , Benzofurans/chemical synthesis , Benzofurans/chemistry , Benzofurans/pharmacology , Enzyme Activation/drug effects , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Guinea Pigs , Inhibitory Concentration 50 , Molecular Structure , Protein Binding , RatsABSTRACT
We describe an optimized series of acyclic hydroxyethylamine transition state isosteres of beta-secretase that incorporates a variety of P(2) side chains that yield potent inhibitors with excellent cellular activity. A 2.2A crystal structure of compound 13 is shown.
Subject(s)
Alzheimer Disease/drug therapy , Amyloid Precursor Protein Secretases/antagonists & inhibitors , Carbamates/chemistry , Protease Inhibitors/chemistry , Sulfonamides/chemistry , Amyloid Precursor Protein Secretases/chemistry , Carbamates/chemical synthesis , Carbamates/pharmacology , Cells, Cultured , Drug Design , Humans , Molecular Structure , Protease Inhibitors/chemical synthesis , Protease Inhibitors/pharmacology , Structure-Activity Relationship , Sulfonamides/chemical synthesis , Sulfonamides/pharmacologyABSTRACT
We describe a novel series of potent inhibitors of human beta-secretase. These compounds possess the hydroxyethyl amine transition state isostere. A 2.5A crystal structure of inhibitor 32 bound to BACE is provided.
