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Verubecestat (MK-8931)

Merck Alzheimer’s drugs Verubecestat (MK-8931) is an oral β- amyloid precursor protein cleaving enzyme (BACE1 or β-secretase enzyme) inhibitor, is currently in Phase III clinical trials

MK 8931, MK-8931, SCH 900931
2-Pyridinecarboxamide, N- (3 – ((5R) -3-amino-5,6-dihydro-2,5-dimethyl-1 , 1-dioxido-2H-1,2,4-thiadiazin-5-yl) -4-fluorophenyl) -5-fluoro-


CAS : 1286770-55-5

C17 H17 F2 N5 O3 S, 409.41
Mechanism: Oral β- amyloid precursor protein cleavage enzyme (BACE) inhibitors
Indications: Alzheimer’s disease
Development progress: phase III clinical
Companies: Merck

Verubecestat (MK-8931) is a small-molecule inhibitor of beta-secretase cleaving enzyme (BACE) 1 and BACE2 in development by Merck for the treatment of Alzheimer’s Disease.

MK-8931 is a beta-secretase 1 (BACE1) inhibitor in phase III development for the treatment of amnestic mild cognitive impairment (aMCI) due to Alzheimer’s disease at Merck & Co. The company is also conducting phase II/III trials for the treatment of Alzheimer’s type dementia.

Alzheimer’s disease (AD) is a devastating, progressive neurodegenerative disease that is associated with up to 80% of the estimated 47 million cases of dementia worldwide and is a leading cause of death in the United States.(1, 2) As the elderly population increases, the worldwide incidence of dementia is expected to nearly triple to approximately 132 million by 2050, creating an unsustainable socioeconomic burden.(1) Currently available therapies, which include acetylcholinesterase inhibitors and the N-methyl-d-aspartate receptor antagonist memantine, produce modest and transient improvement in cognitive function but do not alter the progression of AD.(3) Treatments that delay or halt disease progression by targeting the underlying causes of AD would have lasting impacts on patient function and quality of life and would address an urgent unmet medical need.
Two histopathological hallmarks are invariably observed in the brains of AD patients, namely, extracellular amyloid plaques composed primarily of β-amyloid (Aβ) peptides and intraneuronal neurofibrillary tangles composed primarily of aggregates of abnormally phosphorylated tau protein. Aβ peptides are formed by two sequential cleavages of the amyloid precursor protein (APP), first by β-site amyloid precursor protein cleaving enzyme 1 (BACE1) followed by cleavage of the resulting C-terminal fragment C99 by γ-secretase. This cleavage sequence results in production of a family of Aβ peptides, of which Aβ40 is the most abundant isoform and Aβ42 is more highly prone to aggregate into neurotoxic, oligomeric species.(4) According to the amyloid hypothesis, aberrant production and/or accumulation of Aβ peptides, principally Aβ42, over a period of decades is causative of the underlying disease pathogenesis that ultimately leads to neuronal cell death.(4, 5) In addition to the invariant presence of amyloid plaques in the brains of AD patients, the amyloid hypothesis is underpinned by several other lines of evidence. First, many distinct neurodegenerative diseases are associated with the invariant presence of abnormal protein aggregates analogous to amyloid plaques. Second, low levels of Aβ42 in the CSF are a reasonably good diagnostic/prognostic biomarker for AD. Finally, and most significantly, early onset autosomal dominant familial AD is associated with mutations in APP and the presenilin proteins (which are components of the γ-secretase enzyme), and all of these mutations share the common phenotype of increasing total Aβ levels or the relative proportion of Aβ42.(6) Given this multifaceted evidence supporting the role of Aβ peptides in AD progression, substantial efforts have been invested in the development of amyloid-lowering therapies as a disease-modifying approach to AD treatment.(7) Prominent among these has been inhibition of BACE1 to reduce or prevent production of the Aβ peptides. This approach has been further supported by the recent finding that a rare mutation (A673T) near the BACE1 cleavage site in APP reduces Aβ peptide production and is associated with reduced risk of developing AD and improved cognitive function in the elderly.(8)
BACE1 is a membrane-bound aspartyl protease expressed primarily in the central nervous system (CNS), is the sole enzymatic activity responsible for the initial β-site APP cleavage, and is required for Aβ peptide production in vivo.(9) In the brain, BACE1 is expressed mainly in neurons and cleaves APP predominantly in the endosomal compartments where the acidic pH is near the optimum for its enzymatic activity (pH 5).(10) Since the characterization of BACE1 more than 15 years ago,(11) there have been intensive efforts to overcome the challenges of identifying small molecule inhibitors that can penetrate the CNS and inhibit the formation of centrally derived Aβ peptides.(12) These efforts have been driven by evidence that BACE1 inhibition, in comparison with γ-secretase inhibition and antiamyloid immunotherapy, may be an inherently safer amyloid-lowering approach,(7) a notion that has been informed by an evolving understanding of BACE1 biology. In this regard, Bace1 knockout mice have been reported to have a number of subtle phenotypes, including reduction of central and peripheral nerve myelination, and several putative BACE1 substrates other than APP have recently been proposed.(10, 13, 14) However, many of these phenotypes and substrates remain to be independently confirmed, have little if any functional consequence, are not recapitulated by pharmacological inhibition of BACE, or may be mitigated through partial BACE1 inhibition.(8, 10, 13-15)

Smiles: C [C @] 1 (CS (= O) (= O) N (C (= N1) N) C) c2cc (ccc2F) NC (= O) c3ccc (cn3) F



Scheme 3b:

Figure CN102639135AD00931

The amine A (Scheme 3a, step 4) (13.7 g) in n-butanol (150 mL) was added a slurry solution of cyanogen bromide (5M, in MeCN). The resulting mixture was heated to reflux for 4 hours. The mixture was concentrated to 1/3 of original volume. To this mixture was added Et20 (200 mL). The resulting solid was removed by filtration, and the solid was washed with Et20 (2x). The solid was partitioned between EtOAc and saturated Na2CO3 (aq). The aqueous layer was extracted with EtOAc (3x). The combined organic layers were washed with brine, dried over Na2SO4, filtered and concentrated to give 10.6 g

Scheme 10:

Figure CN102639135AD00982

The nitro compound (Scheme 3b) (2. 50 g, 6. 0 mmol) of Et0H (150 mL) was degassed (To this solution was bubbled with nitrogen time 3 min). To this solution was added Pd / C (10% w / w, 50% water, 698 mg). The mixture was placed in a nitrogen atmosphere. Exhaust, and backfilled with H2 (3x). The obtained mixture at room temperature, followed by stirring under H2 balloon for 2 hours. Bubbling nitrogen gas, and the mixture was purged, filtered through Celite, and concentrated.Small plug filtered through a silica gel column, eluting with EtOAc, and the product was purified to give the aniline (2. 2g, 97%).

















FINAL COMPD Verubecestat












Steps 1-4:

These steps were performed using similar procedures to those described in steps 1-4 of Scheme 1a.

Step 5:

To a solution of the amine from step 4 (10.5 g, 36 mmol) in CH2Cl2 (200 mL) was added benzoylisothiocyanate (4.3 mL, 1.1 eq.). The resulting solution was stirred at RT for 2.5 days. Additional benzoylisothiocyanate (0.86 mL, 0.2 eq.) was added and the solution was stirred at RT for an additional 2 hours. The solution was then concentrated in vacuo.

A portion of this material (6.5 g, ˜14 mmol) was dissolved in MeOH (200 mL). To this solution was added Na2CO3 (s) (1.52 g, 14 mmol). The resultant mixture was stirred at RT for 45 min. After that time, a slight excess of HOAc was added to the solution. The mixture was then concentrated. The residue was partitioned between CH2Cl2 and ½ sat. NaHCO3 (aq.). The aqueous layer was extracted with CH2Cl2 (3×). The combined organic layers were dried over Na2SO4, filtered and concentrated. The thiourea (˜4.9 g) was carried onto the next reaction without further purification.

Step 6:

Example 15 was prepared using a method similar to that described in Scheme 1a step 6.

To a shiny of amine A (Scheme 3a step 4) (13.7 grams) in n-butanol (150 mL) was added a solution of cyanogen bromide (5M in MeCN). The resultant mixture was heated to reflux for 4 hours. The mixture was concentrated to ⅓ of the original volume. To the mixture was added Et2O (200 mL). The resultant solid was removed via filtration and the solid was washed with Et2O (2×). The solid was partitioned between EtOAc and sat. Na2CO3 (aq.). The aqueous layer was extracted with EtOAc (3×). The combined organic layers were washed with brine, dried over Na2SO4, filtered and concentrated to afford 10.6 grams of Ex. 15. This material was converted to the t-butyl carbamate using a procedure similar to that described in Scheme 3.

Step 7:

A mixture of the bromide (3.00 g, 6.92 mmol), benzophenone imine (1.39 mL, 8.30 mmol), Pd2(dba)3 (0.634 g, 0.692 mmol), John-Phos (0.413 g, 1.38 mmol), sodium tert-butoxide (2.13 g, 22.1 mmol), and toluene (51 mL) was degassed (vacuum/N2). The mixture was then stirred at 65° C. under nitrogen for 3 h. After this time, the reaction mixture was cooled to room temperature and filtered through a pad of Celite and rinsed with ethyl acetate (100 mL). The filtrate was concentrated under reduced pressure. The residue was then dissolved in methanol (76 mL) and the resulting solution was charged with hydroxyl amine hydrochloride (2.16 g, 31.1 mmol) and sodium acetate (2.55 g, 31.1 mmol). The reaction mixture was stirred at room temperature for 40 min. After this time, the reaction mixture was concentrated under reduced pressure. The resulting residue was dissolved in ethyl acetate (200 mL) and washed with saturated aqueous sodium bicarbonate (100 mL), water (100 mL), and brine (100 mL). The organic layer was then dried over anhydrous sodium sulfate, filtered, and concentrated under reduced pressure. The residue was purified by column chromatography (silica, 0-100% ethyl acetate/heptane) to afford the amino pyridine (0.880 g, 34%).

To a flame-dried flask was added a pyridyl bromide (Table IIb, Entry 15, 1.5 g, 3.3 mmol), Pd2(dba)3 (305 mg, 0.3 mmol), (2-biphenyl)di-tert-butylphosphine (200 mg, 0.7 mmol), sodium tert-butoxide (1.02 g, 0.011 mmol), benzophenone imine (670 ul, 4 mmol), and toluene (21 mL). The mixture was evacuated under vacuum and back-filled with N2 (3×). The mixture was stirred at 60° C. for 1 h. After filtration through celite, the filtrate was concentrated. The crude residue was dissolved in 36 mL of methanol, and hydroxyl amine hydrochloride (458 mg, 6.6 mmol) and sodium acetate (541 mg, 6.6 mmol) were added. The reaction was stirred for 35 min and then quenched with saturated aqueous sodium bicarbonate. The mixture was extracted with ethyl acetate, and the combined organic portions were dried over magnesium sulfate and concentrated. The crude residue was purified by a flash silica column (50% ethyl acetate/hexane) to get an aminopyridine product (730 mg, 68%).

A solution of the nitro compound (Scheme 3b) (2.50 g, 6.0 mmol) in EtOH (150 mL) was degassed by bubbling N2 through the solution for 3 min. To this solution was added Pd/C (10% w/w, 50% H2O, 698 mg.). The mixture was placed under an atmosphere of N2. The atmosphere was evacuated and back-filled with H2 (3×). The resulting mixture was stirred at RT under a H2 balloon for 2 h. The mixture was purged by bubbling N2 through it, filtered through Celite and concentrated. The product was purified by filtering through a small plug of silica gel column eluting with EtOAc to afford the aniline (2.2 g, 97%).



MH+: 410.0, HPLC1.79 min, LCMSMETHOD D

Method D:

  • Column: Agilent Zorbax SB-C18 (3.0×50 mm) 1.8 uM

Mobile phase: A: 0.05% Trifluoroacetic acid in water

    • B: 0.05% Trifluoroacetic acid in acetonitrile

Gradient: 90:10 (A:B) for 0.3 min, 90:10 to 5:95 (A:B) over 1.2 min, 5:95 (A:B) for 1.2 min.

Flow rate: 1.0 mL/min

UV detection: 254 and 220 nm

Mass spectrometer: Agilent 6140 quadrupole



Discovery of the 3-Imino-1,2,4-thiadiazinane 1,1-Dioxide Derivative Verubecestat (MK-8931)–A β-Site Amyloid Precursor Protein Cleaving Enzyme 1 Inhibitor for the Treatment of Alzheimer’s Disease

Departments of Discovery Chemistry, Neuroscience, §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, ΔTranslational Medicine, #Structural Chemistry, Molecular and Materials Characterization, Pharmaceutical Sciences and Clinical Supply, and Toxicological Sciences, MRL, Merck & Co. Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
Albany Molecular Research Inc., 26 Corporate Circle, Albany, New York 12203, United States
J. Med. Chem., Article ASAP
DOI: 10.1021/acs.jmedchem.6b00307
Publication Date (Web): November 18, 2016
Copyright © 2016 American Chemical Society
*Phone: 908-740-4729. E-mail:, *Phone: 973-868-2088. E-mail:

ACS Editors’ Choice – This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.


Abstract Image

Verubecestat 3 (MK-8931), a diaryl amide-substituted 3-imino-1,2,4-thiadiazinane 1,1-dioxide derivative, is a high-affinity β-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitor currently undergoing Phase 3 clinical evaluation for the treatment of mild to moderate and prodromal Alzheimer’s disease. Although not selective over the closely related aspartyl protease BACE2, verubecestat has high selectivity for BACE1 over other key aspartyl proteases, notably cathepsin D, and profoundly lowers CSF and brain Aβ levels in rats and nonhuman primates and CSF Aβ levels in humans. In this annotation, we describe the discovery of 3, including design, validation, and selected SAR around the novel iminothiadiazinane dioxide core as well as aspects of its preclinical and Phase 1 clinical characterization.


N-[3-[(5R)-3-Amino-5,6-dihydro-2,5-dimethyl-1,1-dioxido-2H-1,2,4-thiadiazin-5-yl]-4-fluorophenyl]-5-fluoro-2-pyridinecarboxamide (3)

 3 (2.70 g, 89% yield) as a white solid. 1H NMR (400 MHz, DMSO-d6) δ 10.57 (s, 1H), 8.73 (d, J = 2.8 Hz, 1H), 8.22 (dd, J = 8.8, 4.8 Hz, 1H), 8.03–7.95 (m, 2H), 7.79 (m, 1H), 7.14 (dd, J = 11.6, 8.8 Hz, 1H), 6.03 (br s, 2H), 3.78 (s, 1H), 3.34 (s, 1H), 3.05 (s, 3H), 1.61 (s, 3H). ESI MS m/z 410.2 [M + H]+. [α]D20 37.2° (c 0.367, CH3OH).
To generate its hydrochloride salt, 3prepared above was added to CH2Cl2 (50 mL) followed by a solution of HCl (2 N in Et2O, 3.6 mL, 7.2 mmol), and the mixture was concentrated in vacuo. The product was slurried in distilled water (50 mL) and lyophilized to afford the HCl monohydrate salt of 3 (2.58 g, 79% yield, 3 steps) as a white solid. 1H NMR (400 MHz, CD3OD) δ 8.59 (d, J = 2.8 Hz, 1H), 8.26 (dd, J = 8.8, 4.8 Hz, 1H), 8.02 (dd, J = 7.6, 2.8 Hz, 1H), 7.82–7.75 (m, 2H), 7.22 (dd, J = 12.0, 8.8 Hz, 1H), 4.49 (dd, J = 14.4, 0.8 Hz, 1H), 4.30 (d, J = 14.4 Hz, 1H), 3.30 (s, 3H), 1.96 (s, 3H). ESI MS m/z410.2 [M + H]+. Anal. Calcd (C17H20ClF2N5O4S): C, 44.02; H, 4.35; N, 15.10; Cl, 7.64; S, 6.91. Found: C, 43.77; H, 4.32; N, 14.81; Cl, 7.84; S, 7.04.




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  14. 17.

    The CAS name represents the 3-aminothiadiazine tautomer, and the structures depicted in the manuscript represent the 3-iminothiadiazinane tautomer.

सुकून उतना ही देना प्रभू, जितने से जिंदगी चल जाये। औकात बस इतनी देना, कि औरों का भला हो जाये।

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He was only in first standard in school when I was hit by a deadly one in a million spine stroke called acute transverse mylitis, it made me 90% paralysed and bound to a wheel chair, Now I keep him as my source of inspiration and helping millions, thanks to millions of my readers who keep me going and help me to keep my son happy
सुकून उतना ही देना प्रभू, जितने से
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कि औरों का भला हो जाये।


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DR ANTHONY MELVIN CRASTO, Born in Mumbai in 1964 and graduated from Mumbai University, Completed his Ph.D from ICT, 1991,Matunga, Mumbai, India, in Organic Chemistry, The thesis topic was Synthesis of Novel Pyrethroid Analogues, Currently he is working with AFRICURE PHARMA, ROW2TECH, NIPER-G, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India as ADVISOR, earlier assignment was with GLENMARK LIFE SCIENCES LTD, as CONSUlTANT, Retired from GLENMARK in Jan2022 Research Centre as Principal Scientist, Process Research (bulk actives) at Mahape, Navi Mumbai, India. Total Industry exp 32 plus yrs, Prior to joining Glenmark, he has worked with major multinationals like Hoechst Marion Roussel, now Sanofi, Searle India Ltd, now RPG lifesciences, etc. He has worked with notable scientists like Dr K Nagarajan, Dr Ralph Stapel, Prof S Seshadri, etc, He did custom synthesis for major multinationals in his career like BASF, Novartis, Sanofi, etc., He has worked in Discovery, Natural products, Bulk drugs, Generics, Intermediates, Fine chemicals, Neutraceuticals, GMP, Scaleups, etc, he is now helping millions, has 9 million plus hits on Google on all Organic chemistry websites. His friends call him Open superstar worlddrugtracker. His New Drug Approvals, Green Chemistry International, All about drugs, Eurekamoments, Organic spectroscopy international, etc in organic chemistry are some most read blogs He has hands on experience in initiation and developing novel routes for drug molecules and implementation them on commercial scale over a 32 PLUS year tenure till date Feb 2023, Around 35 plus products in his career. He has good knowledge of IPM, GMP, Regulatory aspects, he has several International patents published worldwide . He has good proficiency in Technology transfer, Spectroscopy, Stereochemistry, Synthesis, Polymorphism etc., He suffered a paralytic stroke/ Acute Transverse mylitis in Dec 2007 and is 90 %Paralysed, He is bound to a wheelchair, this seems to have injected feul in him to help chemists all around the world, he is more active than before and is pushing boundaries, He has 100 million plus hits on Google, 2.5 lakh plus connections on all networking sites, 100 Lakh plus views on dozen plus blogs, 227 countries, 7 continents, He makes himself available to all, contact him on +91 9323115463, email, Twitter, @amcrasto , He lives and will die for his family, 90% paralysis cannot kill his soul., Notably he has 38 lakh plus views on New Drug Approvals Blog in 227 countries...... , He appreciates the help he gets from one and all, Friends, Family, Glenmark, Readers, Wellwishers, Doctors, Drug authorities, His Contacts, Physiotherapist, etc He has total of 32 International and Indian awards

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