# Patent

## Title
Heterocyclic aspartyl protease inhibitors

## Abstract

Disclosed are compounds of the formula I




or a stereoisomer, tautomer, or pharmaceutically acceptable salt or solvate thereof,

wherein

    
    
        W is a bond, —C(═S)—, —S(O)—, —S(O)2—, —C(═O)—, —O—, —C(R6)(R7)—, —N(R5)— or —C(═N(R5))—;
        X is —O—, —N(R5)— or —C(R6)(R7)—; provided that when X is —O—, U is not —O—, —S(O)—, —S(O)2—, —C(═O)— or —C(═NR5)—;
        U is a bond, —S(O)—, —S(O)2—, —C(O)—, —O—, —P(O)(OR15)—, —C(═NR5)—, —(C(R6)(R7))b— or —N(R5)—; wherein b is 1 or 2; provided that when W is —S(O)—, —S(O)2—, —O—, or —N(R5)—, U is not —S(O)—, —S(O)2—, —O—, or —N(R5)—; provided that when X is —N(R5)— and W is —S(O)—, —S(O)2—, —O—, or —N(R5)—, then U is not a bond;
        and R1, R2, R3, R4, R5, R6, and R7 are as defined in the specification;

and pharmaceutical compositions comprising the compounds of formula I.

    
    


Also disclosed is the method of inhibiting aspartyl protease, and in particular, the methods of treating cardiovascular diseases, cognitive and neurodegenerative diseases, and the methods of inhibiting of Human Immunodeficiency Virus, plasmepins, cathepsin D and protozoal enzymes.
Also disclosed are methods of treating cognitive or neurodegenerative diseases using the compounds of formula I in combination with a cholinesterase inhibitor or a muscarinic m1 agonist or m2 antagonist.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a Divisional of co-pending application U.S. Ser. No. 12/331,787, filed Dec. 10, 2008, which is a Divisional of U.S. Ser. No. 11/149,027, filed Jun. 9, 2005, U.S. Pat. No. 7,700,603, which is a Continuation-in-Part of application U.S. Ser. No. 11/010,772, filed Dec. 13, 2004, U.S. Pat. No. 7,592,348, which claims the benefit of U.S. Provisional Application No. 60/529,535, filed Dec. 15, 2003, each of which is incorporated herein by reference.


FIELD OF THE INVENTION
This invention relates to heterocyclic aspartyl protease inhibitors, pharmaceutical compositions comprising said compounds, their use in the treatment of cardiovascular diseases, cognitive and neurodegenerative diseases, and their use as inhibitors of the Human Immunodeficiency Virus, plasmepsins, cathepsin D and protozoal enzymes.
BACKGROUND
Eight human aspartic proteases of the A1 (pepsin-like) family are known to date: pepsin A and C, renin, BACE, BACE 2, Napsin A, cathepsin D in pathological conditions.
The role of renin-angiotensin system (RAS) in regulation of blood pressure and fluid electrolyte has been well established (Oparil, S, et al. N Engl J Med 1974; 291:381-401/446-57). The octapeptide Angiotensin-II, a potent vasoconstrictor and stimulator for release of adrenal aldosterone, was processed from the precursor decapeptide Angiotensin-I, which in turn was processed from angiotensinogen by the renin enzyme. Angiotensin-II was also found to play roles in vascular smooth muscle cell growth, inflammation, reactive oxygen species generation and thrombosis, influence atherogenesis and vascular damage. Clinically, the benefit of interruption of the generation of angiotensin-II through antagonism of conversion of angiotensin-I has been well known and there are a number of ACE inhibitor drugs on the market. The blockade of the earlier conversion of angiotensinogen to angiotensin-I, i.e. the inhibition of renin enzyme, is expected to have similar but not identical effects. Since renin is an aspartyl protease whose only natural substrate is angiotensinogen, it is believed that there would be less frequent adverse effect for controlling high blood pressure and related symptoms regulated by angiotensin-II through its inhibition.
Another protease, Cathepsin-D, is involved in lysosomal biogenesis and protein targeting, and may also be involved in antigen processing and presentation of peptide fragments. It has been linked to numerous diseases including, Alzheimer's, disease, connective tissue disease, muscular dystrophy and breast cancer.
Alzheimer's disease (AD) is a progressive neurodegenerative disease that is ultimately fatal. Disease progression is associated with gradual loss of cognitive function related to memory, reasoning, orientation and judgment. Behavioral changes including confusion, depression and aggression also manifest as the disease progresses. The cognitive and behavioral dysfunction is believed to result from altered neuronal function and neuronal loss in the hippocampus and cerebral cortex. The currently available AD treatments are palliative, and while they ameliorate the cognitive and behavioral disorders, they do not prevent disease progression. Therefore there is an unmet medical need for AD treatments that halt disease progression.
Pathological hallmarks of AD are the deposition of extracellular β-amyloid (Aβ) plaques and intracellular neurofibrillary tangles comprised of abnormally phosphorylated protein tau. Individuals with AD exhibit characteristic Aβ deposits, in brain regions known to be important for memory and cognition. It is believed that Aβ is the fundamental causative agent of neuronal cell loss and dysfunction which is associated with cognitive and behavioral decline. Amyloid plaques consist predominantly of Aβ peptides comprised of 40-42 amino acid residues, which are derived from processing of amyloid precursor protein (APP). APP is processed by multiple distinct protease activities. Aβ peptides result from the cleavage of APP by β-secretase at the position corresponding to the N-terminus of Aβ, and at the C-terminus by γ-secretase activity. APP is also cleaved by α-secretase activity resulting in the secreted, non-amyloidogenic fragment known as soluble APP.
An aspartyl protease known as BACE-1 has been identified as the β-secretase activity responsible for cleavage of APP at the position corresponding to the N-terminus of Aβ peptides.
Accumulated biochemical and genetic evidence supports a central role of Aβ in the etiology of AD. For example, Aβ has been shown to be toxic to neuronal cells in vitro and when injected into rodent brains. Furthermore inherited forms of early-onset AD are known in which well-defined mutations of APP or the presenilins are present. These mutations enhance the production of Aβ and are considered causative of AD.
Since Aβ peptides are formed as a result β-secretase activity, inhibition of BACE-1 should inhibit formation of Aβ peptides. Thus inhibition of BACE-1 is a therapeutic approach to the treatment of AD and other cognitive and neurodegenerative diseases caused by Aβ plaque deposition.
Human immunodeficiency virus (HIV), is the causative agent of acquired immune deficiency syndrome (AIDS). It has been clinically demonstrated that compounds such as indinavir, ritonavir and saquinavir which are inhibitors of the HIV aspartyl protease result in lowering of viral load. As such, the compounds described herein would be expected to be useful for the treatment of AIDS. Traditionally, a major target for researchers has been HIV-1 protease, an aspartyl protease related to renin.
In addition, Human T-cell leukemia virus type I (HTLV-I) is a human retrovirus that has been clinically associated with adult T-cell leukemia and other chronic diseases. Like other retroviruses, HTLV-I requires an aspartyl protease to process viral precursor proteins, which produce mature virions. This makes the protease an attractive target for inhibitor design. (Moore, et al. Purification of HTLV-I Protease and Synthesis of Inhibitors for the treatment of HTLV-I Infection 55th Southeast Regional Meeting of the American Chemical Society, Atlanta, Ga., US Nov. 16-19, 2003 (2003), 1073. CODEN; 69EUCH Conference, AN 2004:137641 CAPLUS.)
Plasmepsins are essential aspartyl protease enzymes of the malarial parasite. Compounds for the inhibition of aspartyl proteases plasmepsins, particularly I, II, IV and HAP, are in development for the treatment of malaria. (Freire, et al. WO 2002074719. Na Byoung-Kuk, et al. Aspartic proteases of Plasmodium vivax are highly conserved in wild isolates Korean Journal of Prasitology (2004 June), 42 (2) 61-6, Journal code: 9435800) Furthermore, compounds used to target aspartyl proteases plasmepsins (e.g. I, II, IV and HAP), have been used to kill malarial parasites, thus treating patients thus afflicted.
SUMMARY OF THE INVENTION
The present invention relates to compounds having the structural formula I




or a stereoisomer, tautomer, or pharmaceutically acceptable salt or solvate thereof, wherein

W is a bond, —C(═S)—, —S(O)—, —S(O)2—, —C(═O)—, —O—, —C(R6)(R7)—, —N(R5)— or —C(═N(R5))—;
X is —O—, —N(R5)— or —C(R6)(R7); provided that when X is —O—, U is not —O—, —S(O)—, —S(O)2—, —C(═O)— or —C(═NR5)—;
U is a bond, —S(O)—, —S(O)2—, —C(O)—, —O— —P(O)(OR15)—, —C(═NR5)—, —(C(R6)(R7))b— or —N(R5)—; wherein b is 1 or 2; provided that when W is —S(O)—, —S(O)2—, —O—, or —N(R5)—, U is not —S(O)—, —S(O)2—, —O—, or —N(R5)—; provided that when X is —N(R15)— and W is —S(O)—, —S(O)2—, —O—, or —N(R5)—, then U is not a bond;
R1, R2 and R5 are independently selected from the group consisting of H, alkyl, alkenyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, arylcycloalkyl, —OR15, —CN, —C(O)R8, —C(O)OR9, —S(O)R10, —S(O)2R10, —C(O)N(R11)(R12), —S(O)N(R11)(R12), —S(O)2N(R11)(R12), —NO2, —N═C(R8)2 and —N(R8)2, provided that R1 and R5 are not both selected from —NO2, —N═C(R8)2 and —N(R8)2;
R3, R4, R6 and R7 are independently selected from the group consisting of H, alkyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, halo, —CH2—O—Si(R9)(R10)(R19), —SH, —CN, —OR9, —C(O)R8, —C(O)OR9, —C(O)N(R11)(R12), —SR19, —S(O)N(R11)(R12), —S(O)2N(R11)(R12), —N(R11)(R12), —N(R11)C(O)R8, —N(R11)S(O)R10, —N(R11)C(O)N(R12)(R13), —N(R11)C(O)OR9 and —C(═NOH)R8; provided that when U is —O— or —N(R5)—, then R3, R4, R6 and R7 are not halo, —SH, —OR9, —SR19, —S(O)N(R11)(R12), —S(O)2N(R11)(R12), —N(R11)(R12), —N(R11)C(O)R8, —N(R11)S(O)R10, —N(R11)C(O)N(R12)(R13), or —N(R11)C(O)OR9; provided that when W is —O— or —N(R5)—, then R3 and R4 are not halo, —SH, —OR9, —SR19, —S(O)N(R11)(R12), —S(O)2N(R11)(R12), —N(R11)(R12), —N(R11)C(O)R8, —N(R11)S(O)R10, —N(R11)C(O)N(R12)(R13), or —N(R11)C(O)OR9; and provided that when X is —N(R5)—, W is —C(O)— and U is a bond, R3 and R4 are not halo, —CN, —SH, —OR9, —SR19, —S(O)N(R11)(R12) or —S(O)2N(R11)(R12); or R3, R4, R6 and R7, together with the carbon to which they are attached, form a 3-7 membered cycloalkyl group optionally substituted by R14 or a 3-7 membered cycloalkylether optionally substituted by R14;
or R3 and R4 or R6 and R7 together with the carbon to which they are attached, are combined to form multicyclic groups such as




wherein M is —CH2—, S, —N(R19)— or O, A and B are independently aryl or heteroaryl and q is 0, 1 or 2 provided that when q is 2, one M must be a carbon atom and when q is 2, M is optionally a double bond; and with the proviso that when R3, R4, R6 and R7 form said multicyclic groups





then adjacent R3 and R4 or R6 and R7 groups cannot be combined to form said multicyclic groups;

R8 is independently selected from the group consisting of H, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkylalkyl, cycloalkenyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, —OR15, —N(R15)(R16), —N(R15)C(O)R16, —N(R15)S(O)R16, —N(R15)S(O)2R16, —N(R15)S(O)2N(R16)(R17), —N(R15)S(O)N(R16)(R17), —N(R15)C(O)N(R16)(R17) and —N(R15)C(O)OR16;
R9 is independently selected from the group consisting of H, alkyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl and heteroarylalkyl;
R10 is independently selected from the group consisting of H, alkyl, alkenyl, cycloalkyl, cycloalkylalkyl, cycloalkenyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl and —N(R15)(R16);
R11, R12 and R13 are independently selected from the group consisting of H, alkyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, —C(O)R8, —C(O)OR9, —S(O)R10, —S(O)2R10, —C(O)N(R15)(R16), —S(O)N(R15)(R16), —S(O)2N(R15)(R16) and —CN;
R14 is 1-5 substituents independently selected from the group consisting of alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkylalkyl, cycloalkenyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, halo, —CN, —OR15, —C(O)R15, —C(O)OR15, —C(O)N(R15)(R16), —SR15, —S(O)N(R15)(R16), —S(O)2N(R15)(R16), —C(═NOR15)R16, —P(O)(OR15)(OR16), —N(R15)(R16), —N(R15)C(O)R16, —N(R15)S(O)R16, —N(R15)S(O)2R16, —N(R15)S(O)2N(R16)(R17), —N(R15)S(O)N(R16)(R17), —N(R15)C(O)N(R16)(R17) and —N(R15)C(O)OR16;
R15, R16 and R17 are independently selected from the group consisting of H, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, arylcycloalkyl, arylheterocycloalkyl, R18-alkyl, R18-cycloalkyl, R18-cycloalkylalkyl, R18-heterocycloalkyl, R18-heterocycloalkylalkyl, R18-aryl, R18-arylalkyl, R18-heteroaryl and R18-heteroarylalkyl; or
R15, R16 and R17 are




wherein R23 numbers 0 to 5 substituents, m is 0 to 6 and n is 1 to 5;

R18 is 1-5 substituents independently selected from the group consisting of alkyl, alkenyl, aryl, arylalkyl, arylalkenyl, arylalkynyl, —NO2, halo, heteroaryl, HO-alkyoxyalkyl, —CF3, —CN, alkyl-CN, —C(O)R19, —C(O)OH, —C(O)OR19, —C(O)NHR20, —C(O)NH2, —C(O)NH2—C(O)N(alkyl)2, —C(O)N(alkyl)(aryl), —C(O)N(alkyl)(heteroaryl), —SR19, —S(O)2R20, —S(O)NH2, —S(O)NH(alkyl), —S(O)N(alkyl)(alkyl), —S(O)NH(aryl), —S(O)2NH2, —S(O)2NHR19, —S(O)2NH(heterocycloalkyl), —S(O)2N(alkyl)2, —S(O)2N(alkyl)(aryl), —OCF3, —OH, —OR20, —O-heterocycloalkyl, —O-cycloalkylalkyl, —O-heterocycloalkylalkyl, —NH2, —NHR20, —N(alkyl)2, —N(arylalkyl)2, —N(arylalkyl)-(heteroarylalkyl), —NHC(O)R20, —NHC(O)NH2, —NHC(O)NH(alkyl), —NHC(O)N(alkyl)(alkyl), —N(alkyl)C(O)NH(alkyl), —N(alkyl)C(O)N(alkyl)(alkyl), —NHS(O)2R20, —NHS(O)2NH(alkyl), —NHS(O)2N(alkyl)(alkyl), —N(alkyl)S(O)2NH(alkyl) and —N(alkyl)S(O)2N(alkyl)(alkyl);
or two R18 moieties on adjacent carbons can be linked together to form




R19 is alkyl, cycloalkyl, aryl, arylalkyl or heteroarylalkyl;
R20 is alkyl, cycloalkyl, aryl, halo substituted aryl, arylalkyl, heteroaryl or heteroarylalkyl;
and wherein each of the alkyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, alkenyl and alkynyl groups in R1, R2, R3, R4, R5, R6, R7, R8, R9, R10, R11, R12, R13 and R14 are independently unsubstituted or substituted by 1 to 5 R21 groups independently selected from the group consisting of alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkylalkyl, cycloalkenyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, halo, —CN, —OR15, —C(O)OR15, —C(O)OR15, —C(O)N(R15)(R16), —SR15, —S(O)N(R15)(R16), —CH(R15)(R16), —S(O)2N(R15)(R16), —C(═NOR5)R16, —P(O)(OR15)(OR16), —N(R15)(R16), -alkyl-N(R15)(R16), —N(R15)C(O)R16, —CH2—N(R15)C(O)R16, —CH2—N(R15)C(O)N(R16)(R17), —CH2—R15; —CH2N(R15)(R16), —N(R15)S(O)R16, —N(R15)S(O)2R16, —CH2—N(R15)S(O)2R16, —N(R15)S(O)2N(R16)(R17), —N(R15)S(O)N(R16)(R17), —N(R15)C(O)N(R16)(R17), —CH2—N(R15)C(O)N(R16)(R17), —N(R15)C(O)OR16, —CH2—N(R15)C(O)OR16, —S(O)R15, ═NOR15, —N3, —NO2 and —S(O)2R15; and wherein each of the alkyl, cycloalkenyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, alkenyl and alkynyl groups in R21 are independently unsubstituted or substituted by 1 to 5 R22 groups independently selected from the group consisting of alkyl, cycloalkyl, cycloalkenyl, heterocycloalkyl, aryl, heteroaryl, halo, —CF3, —CN, —OR15, —C(O)R15, C(O)OR15, -alkyl-C(O)OR15, C(O)N(R15)(R16), —SR15, —S(O)N(R15)(R16), —S(O)2N(R15)(R16)C(═NOR15)R16—P(O)(OR15)(OR16), —N(R15)(R16), -alkyl-N(R15)(R16), —N(R15)C(O)R16, —CH2—N(R15)C(O)R16, —N(R15)S(O)R16, —N(R15)S(O)2R16, —CH2—N(R15)S(O)2R16, —N(R15)S(O)2N(R16)(R17), —N(R15)S(O)N(R16)(R17), —N(R15)C(O)N(R16)(R17), —CH2—N(R15)C(O)N(R16)(R17), —N(R15)C(O)OR16, —CH2—N(R15)C(O)OR16, —N3, ═NOR15, —NO2, —S(O)R15 and —S(O)2R15;
or two R21 or two R22 moieties on adjacent carbons can be linked together to form




and when R21 or R22 are selected from the group consisting of —C(═NOR15)R16, —N(R15)C(O)R16, —CH2—N(R15)C(O)R16, —N(R15)S(O)R31, —N(R15)S(O)2R16, —CH2—N(R15)S(O)2R16, —N(R15)S(O)2N(R16)(R17), —N(R15)S(O)N(R16)(R17), —N(R15)C(O)N(R16)(R17), —CH2—N(R15)C(O)N(R16)(R17), —N(R15)C(O)OR16 and —CH2—N(R15)C(O)OR16, R15 and R16 together can be a C2 to C4 chain wherein, optionally, one, two or three ring carbons can be replaced by —C(O)— or —N(H)— and R15 and R16, together with the atoms to which they are attached, form a 5 to 7 membered ring, optionally substituted by R23;
R23 is 1 to 5 groups independently selected from the group consisting of alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkylalkyl, cycloalkenyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, halo, —CN, —OR24, —C(O)R24, —C(O)OR24, —C(O)N(R24)(R25), —SR24, —S(O)N(R24)(R25), —S(O)2N(R24)(R25), —C(═NOR24)R25, —P(O)(OR24)(OR25), —N(R24)(R25), -alkyl-N(R24)(R25), —N(R24)C(O)R25, —CH2—N(R24)C(O)R25, —N(R24)S(O)R25, —N(R24)S(O)2R25, —CH—N(R24)S(O)2R25, —N(R24)S(O)2N(R25)(R26), —N(R24)S(O)N(R25)(R26), —N(R24)C(O)N(R25)(R26), —CH2—N(R24)C(O)N(R25)(R26), —N(R24)C(O)OR25, —CH2—N(R24)C(O)OR25, —S(O)R24 and —S(O)2R24; and wherein each of the alkyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, alkenyl and alkynyl groups in R23 are independently unsubstituted or substituted by 1 to 5 R27 groups independently selected from the group consisting of alkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, halo, —CF3, —CN, —OR24, —C(O)R24, —C(O)OR24, alkyl-C(O)OR24, C(O)N(R24)(R25), —SR24, —S(O)N(R24)(R25), —S(O)2N(R24)(R25), —C(═NOR24)R25, —P(O)(OR24)(OR25), —N(R24)(R25), -alkyl-N(R24)(R25), —N(R24)C(O)R25, —CH2—N(R24)C(O)R25, —N(R24)S(O)R25, —N(R24)S(O)2R25, —CH2—N(R24)S(O)2R25, —N(R24)S(O)2N(R25)(R26), —N(R24)S(O)N(R25)(R26), —N(R24)C(O)N(R25)(R26), —CH2—N(R24)C(O)N(R25)(R26), —N(R24)C(O)OR25, —CH2—N(R24)C(O)OR25, —S(O)R24 and —S(O)2R24;
R24, R25 and R26 are independently selected from the group consisting of H, alkyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, arylcycloalkyl, R27-alkyl, R27-cycloalkyl, R27-cycloalkylalkyl, R27-heterocycloalkyl, R27-heterocycloalkylalkyl, R27-aryl, R27-arylalkyl, R27-heteroaryl and R27-heteroarylalkyl;
R27 is 1-5 substituents independently selected from the group consisting of alkyl, aryl, arylalkyl, —NO2, halo, —CF3, —CN, alkyl-CN, —C(O)R28, —C(O)OH, —C(O)OR28, —C(O)NHR29, —C(O)N(alkyl)2, —C(O)N(alkyl)(aryl), —C(O)N(alkyl)(heteroaryl), —SR28, —S(O)2R29, —S(O)NH2, —S(O)NH(alkyl), —S(O)N(alkyl)(alkyl), —S(O)NH(aryl), —S(O)2NH2, —S(O)2NHR28, —S(O)2NH(aryl), —S(O)2NH(heterocycloalkyl), —S(O)2N(alkyl)2, —S(O)2N(alkyl)(aryl), —OH, —OR29, —O-heterocycloalkyl, —O-cycloalkylalkyl, —O-heterocycloalkylalkyl, —NH2, —NHR29, —N(alkyl)2, —N(arylalkyl)2, —N(arylalkyl)(heteroarylalkyl), —NHC(O)R29, —NHC(O)NH2, —NHC(O)NH(alkyl), —NHC(O)N(alkyl)(alkyl), —N(alkyl)C(O)NH(alkyl), —N(alkyl)C(O)N(alkyl)(alkyl), —NHS(O)2R29, —NHS(O)2NH(alkyl), —NHS(O)2N(alkyl)(alkyl), —N(alkyl)S(O)2NH(alkyl) and —N(alkyl)S(O)2N(alkyl)(alkyl);
R28 is alkyl, cycloalkyl, arylalkyl or heteroarylalkyl; and
R29 is alkyl, cycloalkyl, aryl, arylalkyl, heteroaryl or heteroarylalkyl;
provided that when W is —C(O)— and U is a bond, R1 is not optionally substituted phenyl, and that when U is —C(O)— and W is a bond, R5 is not optionally substituted phenyl;
provided that neither R1 nor R5 is —C(O)-alkyl-azetidinone or alkyl di-substituted with (—COOR15 or —C(O)N(R15)(R16)) and (—N(R15)(R16), —N(R15)C(O)R16, —N(R15)S(O)R16, —N(R15)S(O)2R16, —N(R15)S(O)2N(R16)(R17), —N(R15)S(O)N(R16)(R17), —N(R15)C(O)N(R16)(R17), or —N(R15)C(O)OR16);
provided that when R1 is methyl, X is —N(R5)—, R2 is H, W is —C(O)— and U is a bond, (R3, R4) is not (H, H), (phenyl, phenyl), (H, phenyl), (benzyl, H), (benzyl, phenyl), (i-butyl, H), (i-butyl, phenyl), (OH-phenyl, phenyl), (halo-phenyl, phenyl), or (CH3O-phenyl, NO2-phenyl); and when W is a bond and U is —C(O)—, (R3, R4) is not (H, H), (phenyl, phenyl), (H, phenyl), (benzyl, H), (benzyl, phenyl), (i-butyl, H), (i-butyl, phenyl), (OH-phenyl, phenyl), (halo-phenyl, phenyl), or (CH3O-phenyl, NO2-phenyl);
provided that when X is —N(R5)—, R1 and R5 are each H, W is —C(O)— and U is a bond, (R3, R4) is not (optionally substituted phenyl, optionally substituted benzyl), (optionally substituted phenyl, heteroarylalkyl) or (heteroaryl, heteroarylalkyl);
provided that when U is a bond, W is —C(O)—, and R3 and R4 form a ring with the carbon to which they are attached, R1 is not 2-CF3-3-CN-phenyl;
provided that when X is —N(R5)—, U is —O— and W is a bond or —C(R6)(R7)—, (R3,R4) is not (H, —NHC(O)-alkyl-heteroaryl) or (H, alkyl-NHC(O)-alkyl-heteroaryl); and
provided that when X is —N(R5)—, R1 and R5 are not -alkylaryl-aryl-SO2—N(R15)(R16) wherein R15 is H and R16 is heteroaryl;
provided that when R1 is R21-aryl or R21-arylalkyl, wherein R21 is —OCF3, —S(O)CF3, —S(O)2CF3, —S(O)alkyl, —S(O)2alkyl, —S(O)2CHF2, —S(O)2CF2CF3, —OCF2CHF2, —OCHF2, —OCH2CF3, —SF5 or —S(O)2NR15R16;
wherein R15 and R16 are independently selected from the group consisting of H, alkyl, alkenyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl, R18-alkyl, R18-cycloalkyl, R18-heterocycloalkyl, R18-aryl and R18-heteroaryl; U is a bond or —CH2; and X is —N(R5)—; then R5 is H;
provided that when U is a bond,
R3 and R4 are alkyl,




where R21 is halo, —CN, alkyl, alkoxy, haloalkyl or haloalkoxy, or R3 and R4, together with the carbon to which they are attached, form a 3-7 membered cycloalkyl group,

and R1 is




where a is 0 to 6 and R22 is alkyl, alkoxy, halo, —CN, —OH, —NO2 or haloalkyl;

then R21a is not H, —C(O)2R15, wherein R15 is selected from the group consisting of alkyl, cycloalkyl and alkyl substituted with phenyl, alkyl or alkyl-R22, wherein R22 is selected from the group consisting of
phenyl,
phenyl substituted with alkyl,
and




wherein R22 is selected from the group consisting of H, methoxy, nitro, oxo, —OH, halo and alkyl,





In another aspect, the invention relates to a pharmaceutical composition comprising at least one compound of formula I and a pharmaceutically acceptable carrier.
In another aspect, the invention comprises the method of inhibiting aspartyl protease comprising administering at least one compound of formula I to a patient in need of such treatment.
More specifically, the invention comprises: the method of treating a cardiovascular disease such as hypertension, renal failure, or a disease modulated by renin inhibition; the method of treating Human Immunodeficiency Virus; the method of treating a cognitive or neurodegenerative disease such as Alzheimer's Disease; the method of inhibiting plasmepins I and II for treatment of malaria; the method of inhibiting Cathepsin D for the treatment of Alzheimer's Disease, breast cancers and ovarian cancer; and the method of inhibiting protozoal enzymes, for example inhibition of plasmodium falciparnum, for the treatment of fungal infections. Said method of treatment comprise administering at least one compound of formula I to a patient in need of such treatment. In particular, the invention comprises the method of treating Alzheimer's disease comprising administering at least one compound of formula I to a patient in need of such treatment.
In another aspect, the invention comprises the method of treating Alzheimer's disease comprising administering to a patient I need of such treatment a combination of at least one compound of formula I and a cholinesterase inhibitor or a muscarinic m1 agonist or m2 antagonist.
In a final aspect, the invention relates to a kit comprising in separate containers in a single package pharmaceutical compositions for use in combination, in which one container comprises a compound of formula I in a pharmaceutically acceptable carrier and a second container comprises a cholinesterase inhibitor or a muscarinic m1 agonist or m2 antagonist in a pharmaceutically acceptable carrier, the combined quantities being an effective amount to treat a cognitive disease or neurodegenerative disease such as Alzheimer's disease.


DETAILED DESCRIPTION
Compounds of formula I wherein X, W and U are as defined above include the following independently preferred structures:




In compounds of formulas IA to IF, U is preferably a bond or —C(R6)(R7)—. In compounds of formula IG and IH, U is preferably —C(O)—.
It will be understood that since the definition of R1 is the same as the definition of R5, when X is —N(R5)—, compounds of formula I wherein W is a bond and U is a bond, —S(O)—, —S(O)2—, —C(O)—, —O—, —C(R6)(R7)— or —N(R5)— are equivalent to compounds of formula I wherein U is a bond and W is a bond, —S(O)—, —S(O)2—, —C(O)—, —O—, —C(R6)(R7)— or —N(R5)—.
More preferred compounds of the invention are those of formula IB wherein U is a bond or those of formula IB wherein U is —C(R6)(R7)—.
Another group of preferred compounds of formula I is that wherein R2 is H.
R3, R4, R6 and R7 are preferably selected from the group consisting of alkyl, cycloalkyl, cycloalkylalkyl, heterocycloalkyl, heterocycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, halo, —CH2—O—Si(R9)(R10)(R19), —SH, —CN, —OR9, —C(O)R8, —C(O)OR9, —C(O)N(R11)(R12), —SR19, —S(O)N(R11)(R12), —S(O)2N(R11)(R12), —N(R11)(R12), —N(R11)C(O)R8, —N(R11)S(O)R10, —N(R11)C(O)N(R12)(R13), —N(R11)C(O)OR9 and —C(═NOH)R8.
R3, R4, R6 and R7 are preferably selected from the group consisting of aryl, heteroaryl, heteroarylalkyl, arylalkyl, cycloalkyl, heterocycloalkyl, heterocycloalkylalkyl, alkyl and cycloalkylalkyl.
In a group of preferred compounds
U is a bond or —C(O)—;
W is a bond or —C(O)—;
X is —N(R5)—;
R1 is H, alkyl, R21-alkyl, arylalkyl, R21-arylalkyl, cycloalkylalkyl, R21-cycloalkylalkyl, heterocycloalkylalkyl or R21-heterocycloalkylalkyl,
R2 is H;
R3 is alkyl, cycloalkylalkyl, cycloalkyl, aryl, arylalkyl, R21-alkyl, R21-cycloalkylalkyl, R21-cycloalkyl, R21-aryl or R21-arylalkyl;
R4 is alkyl, cycloalkylalkyl, cycloalkyl, aryl, arylalkyl, R21-alkyl, R21-cycloalkylalkyl, R21-cycloalkyl, R21-aryl or R21-arylalkyl;
R5 is H, alkyl, R21-alkyl, arylalkyl, R21-arylalkyl, cycloalkylalkyl, R21-cycloalkylalkyl, heterocycloalkylalkyl or R21-heterocycloalkylalkyl;
R6 is alkyl, cycloalkylalkyl, cycloalkyl, aryl, arylalkyl, R21-alkyl, R21-cycloalkylalkyl, R21-cycloalkyl, R21-aryl or R21-arylalkyl;
R7 is alkyl, cycloalkylalkyl, cycloalkyl, aryl, arylalkyl, R21-alkyl, R21-cycloalkylalkyl, R21-cycloalkyl, R21-aryl or R21-arylalkyl;
R15, R16 and R17 is H, R18-alkyl, alkyl or




R21 is alkyl, aryl, halo, —OR15, —NO2, —C(O)R15, —CH2—N(R15)C(O)N(R16)(R17) or —CH(R15)(R16);
n is 1;
m is 1;
R18 is —OR20 
R20 is aryl;
and
R23 is alkyl.
In a group of preferred compounds
R3, R4, R6 and R7 are




and

R1 and R5 is H, CH3,




In an additional group of preferred compounds;
U is a bond or —C(O)—;
W is a bond or —C(O)—;
X is —N(R5)—;
R1 is H, alkyl, R21-alkyl, arylalkyl, R21-arylalkyl, cycloalkylalkyl, R21-cycloalkylalkyl, heterocycloalkylalkyl or R21-heterocycloalkylalkyl,
R2 is H;
R3 is alkyl, cycloalkylalkyl, cycloalkyl, aryl, arylalkyl, R21-alkyl, R21-cycloalkylalkyl, R21-cycloalkyl, R21-aryl, R21-arylalkyl, heteroarylalkyl, heteroaryl, heterocycloalkyl, heterocycloalkylalkyl, R21-heteroarylalkyl, R21-heteroaryl, R21-heterocycloalkyl or R21-heterocycloalkylalkyl;
R4 is alkyl, cycloalkylalkyl, cycloalkyl, aryl, arylalkyl, R21-alkyl, R21-cycloalkylalkyl, R21-cycloalkyl, R21-aryl, R21-arylalkyl, heteroarylalkyl, heteroaryl, heterocycloalkyl, heterocycloalkylalkyl, R21-heteroarylalkyl, R21-heteroaryl, R21-heterocycloalkyl or R21-heterocycloalkylalkyl;
R5 is H, alkyl, R21-alkyl, arylalkyl, R21-arylalkyl, cycloalkylalkyl, R21-cycloalkylalkyl, heterocycloalkylalkyl or R21-heterocycloalkylalkyl;
R6 is alkyl, cycloalkylalkyl, cycloalkyl, aryl, arylalkyl, R21-alkyl, R21-cycloalkylalkyl, R21-cycloalkyl, R21-aryl, R21-arylalkyl, heteroarylalkyl, heteroaryl, heterocycloalkyl, heterocycloalkylalkyl, R21-heteroarylalkyl, R21-heteroaryl, R21-heterocycloalkyl or R2-heterocycloalkylalkyl;
R7 is alkyl, cycloalkylalkyl, cycloalkyl, aryl, arylalkyl, R21-alkyl R21-cycloalkylalkyl, R21-cycloalkyl, R21-aryl, R21-arylalkyl, heteroarylalkyl, heteroaryl, heterocycloalkyl, heterocycloalkylalkyl, R21-heteroarylalkyl, R21-heteroaryl, R21-heterocycloalkyl or R21-heterocycloalkylalkyl;
R15, R16 and R17 is H, cycloalkyl, cycloalkylalkyl, R18-alkyl, alkyl, aryl, R18-aryl, R18-arylalkyl, arylalkyl,




n is 1 or 2;
m is 0 or 1;
R18 is —OR20 or halo;
R20 is aryl or halo substituted aryl;
R21 is alkyl, aryl, heteroaryl, R22-alkyl, R22-aryl, R22-heteroaryl, halo, heterocycloalkyl, —N(R15)(R16), —OR15, —NO2, —C(O)R15, —N(R15)C(O)R16, —N(R15)S(O)2R16, —CH2—N(R15)C(O)N(R16)(R17), —N(R15)C(O)N(R16)(R17) or —CH(R15)(R16);
R22 is —OR15 or halo
and
R23 is H or alkyl.
It is noted that the carbons of formula I may be replaced with 1 to 3 silicon atoms so long as all valency requirements are satisfied.
As used above, and throughout the specification, the following terms, unless otherwise indicated, shall be understood to have the following meanings:
“Patient” includes both human and animals.
“Mammal” means humans and other mammalian animals.
“Alkyl” means an aliphatic hydrocarbon group which may be straight or branched and comprising about 1 to about 20 carbon atoms in the chain. Preferred alkyl groups contain about 1 to about 12 carbon atoms in the chain. More preferred alkyl groups contain about 1 to about 6 carbon atoms in the chain. Branched means that one or more lower alkyl groups such as methyl, ethyl or propyl, are attached to a linear alkyl chain. “Lower alkyl” means a group having about 1 to about 6 carbon atoms in the chain which may be straight or branched. Non-limiting examples of suitable alkyl groups include methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, n-pentyl, heptyl, nonyl and decyl. R21-substituted alkyl groups include fluoromethyl, trifluoromethyl and cyclopropylmethyl.
“Alkenyl” means an aliphatic hydrocarbon group containing at least one carbon-carbon double bond and which may be straight or branched and comprising about 2 to about 15 carbon atoms in the chain. Preferred alkenyl groups have about 2 to about 12 carbon atoms in the chain; and more preferably about 2 to about 6 carbon atoms in the chain. Branched means that one or more lower alkyl groups such as methyl, ethyl or propyl, are attached to a linear alkenyl chain. “Lower alkenyl” means about 2 to about 6 carbon atoms in the chain which may be straight or branched. Non-limiting examples of suitable alkenyl groups include ethenyl, propenyl, n-butenyl, 3-methylbut-2-enyl, n-pentenyl, octenyl and decenyl.
“Alkynyl” means an aliphatic hydrocarbon group containing at least one carbon-carbon triple bond and which may be straight or branched and comprising about 2 to about 15 carbon atoms in the chain. Preferred alkynyl groups have about 2 to about 12 carbon atoms in the chain; and more preferably about 2 to about 4 carbon atoms in the chain. Branched means that one or more lower alkyl groups such as methyl, ethyl or propyl, are attached to a linear alkynyl chain. “Lower alkynyl” means about 2 to about 6 carbon atoms in the chain which may be straight or branched. Non-limiting examples of suitable alkynyl groups include ethynyl, propynyl, 2-butynyl, 3-methylbutynyl, n-pentynyl, and decynyl.
“Aryl” means an aromatic monocyclic or multicyclic ring system comprising about 6 to about 14 carbon atoms, preferably about 6 to about 10 carbon atoms. The aryl group can be optionally substituted with one or more substituents (e.g., R18, R21, R22, etc.) which may be the same or different, and are as defined herein or two substituents on adjacent carbons can be linked together to form




Non-limiting examples of suitable aryl groups include phenyl and naphthyl.

“Heteroaryl” means an aromatic monocyclic or multicyclic ring system comprising about 5 to about 14 ring atoms, preferably about 5 to about 10 ring atoms, in which one to eight of the ring atoms is an element other than carbon, for example nitrogen, oxygen or sulfur, alone or in combination. Preferred heteroaryls contain about 5 to about 6 ring atoms. The “heteroaryl” can be optionally substituted by one or more R21 substituents which may be the same or different, and are as defined herein. The prefix aza, oxa or thia before the heteroaryl root name means that at least a nitrogen, oxygen or sulfur atom respectively, is present as a ring atom. A nitrogen atom of a heteroaryl can be optionally oxidized to the corresponding N-oxide. Non-limiting examples of suitable heteroaryls include pyridyl, pyrazinyl, furanyl, thienyl, pyrimidinyl, isoxazolyl, isothiazolyl, oxazolyl, thiazolyl, pyrazolyl, furazanyl, pyrrolyl, pyrazolyl, triazolyl, 1,2,4-thiadiazolyl, pyrazinyl, pyridazinyl, quinoxalinyl, phthalazinyl, imidazo[1,2-a]pyridinyl, imidazo[2,1-b]thiazolyl, benzofurazanyl, indolyl, azaindolyl, benzimidazolyl, benzothienyl, quinolinyl, imidazolyl, thienopyridyl, quinazolinyl, thienopyrimidyl, pyrrolopyridyl, imidazopyridyl, isoquinolinyl, benzoazaindolyl, 1,2,4-triazinyl, benzothiazolyl and the like.
“Cycloalkyl” means a non-aromatic mono- or multicyclic ring system comprising about 3 to about 10 carbon atoms, preferably about 5 to about 10 carbon atoms. Preferred cycloalkyl rings contain about 5 to about 7 ring atoms. The cycloalkyl can be optionally substituted with one or more R21 substituents which may be the same or different, and are as defined above. Non-limiting examples of suitable monocyclic cycloalkyls include cyclopropyl, cyclopentyl, cyclohexyl, cycloheptyl and the like. Non-limiting examples of suitable multicyclic cycloalkyls include 1-decalin, norbornyl, adamantyl and the like. Further non-limiting examples of cycloalkyl include the following




“Cycloalkylether” means a non-aromatic ring of 3 to 7 members comprising an oxygen atom and 2 to 7 carbon atoms. Ring carbon atoms can be substituted, provided that substituents adjacent to the ring oxygen do not include halo or substituents joined to the ring through an oxygen, nitrogen or sulfur atom.
“Cycloalkenyl” means a non-aromatic mono or multicyclic ring system comprising about 3 to about 10 carbon atoms, preferably about 5 to about 10 carbon atoms which contains at least one carbon-carbon double bond. The cycloalkenyl ring can be optionally substituted with one or more R21 substituents which may be the same or different, and are as defined above. Preferred cycloalkenyl rings contain about 5 to about 7 ring atoms. Non-limiting examples of suitable monocyclic cycloalkenyls include cyclopentenyl, cyclohexenyl, cycloheptenyl, and the like. Non-limiting example of a suitable multicyclic cycloalkenyl is norbornylenyl.
“Heterocyclenyl” means a non-aromatic monocyclic or multicyclic ring system comprising about 3 to about 14 ring atoms, preferably about 5 to about 10 ring atoms, in which one or more of the atoms in the ring system is an element other than carbon, for example nitrogen, oxygen or sulfur atom, alone or in combination, and which contains at least one carbon-carbon double bond or carbon-nitrogen double bond. There are no adjacent oxygen and/or sulfur atoms present in the ring system. Preferred heterocyclenyl rings contain about 5 to about 6 ring atoms. The prefix aza, oxa or thia before the heterocyclenyl root name means that at least a nitrogen, oxygen or sulfur atom respectively is present as a ring atom. The heterocyclenyl can be optionally substituted by one or more ring system substituents, wherein “ring system substituent” is as defined above. The nitrogen or sulfur atom of the heterocyclenyl can be optionally oxidized to the corresponding N-oxide, S-oxide or S,S-dioxide. Non-limiting examples of suitable monocyclic azaheterocyclenyl groups include 1,2,3,4-tetrahydropyridine, 1,2-dihydropyridyl, 1,4-dihydropyridyl, 1,2,3,6-tetrahydropyridine, 1,4,5,6-tetrahydropyrimidine, 2-pyrrolinyl, 3-pyrrolinyl, 2-imidazolinyl, 2-pyrazolinyl, and the like. Non-limiting examples of suitable oxaheterocyclenyl groups include 3,4-dihydro-2H-pyran, dihydrofuranyl, fluorodihydrofuranyl, and the like. Non-limiting example of a suitable multicyclic oxaheterocyclenyl group is 7-oxabicyclo[2.2.1]heptenyl. Non-limiting examples of suitable monocyclic thiaheterocyclenyl rings include dihydrothiophenyl, dihydrothiopyranyl, and the like.
“Halo” means fluoro, chloro, bromo, or iodo groups. Preferred are fluoro, chloro or bromo, and more preferred are fluoro and chloro.
“Haloalkyl” means an alkyl as defined above wherein one or more hydrogen atoms on the alkyl is replaced by a halo group defined above.
“Heterocyclyl” (or heterocycloalkyl) means a non-aromatic saturated monocyclic or multicyclic ring system comprising about 3 to about 14 ring atoms, preferably about 5 to about 10 ring atoms, in which 1-3, preferably 1 or 2 of the atoms in the ring system is an element other than carbon, for example nitrogen, oxygen or sulfur, alone or in combination. There are no adjacent oxygen and/or sulfur atoms present in the ring system. Preferred heterocyclyls contain about 5 to about 6 ring atoms. The prefix aza, oxa or thia before the heterocyclyl root name means that at least a nitrogen, oxygen or sulfur atom respectively is present as a ring atom. The heterocyclyl can be optionally substituted by one or more R21 substituents which may be the same or different, and are as defined herein. The nitrogen or sulfur atom of the heterocyclyl can be optionally oxidized to the corresponding N-oxide, S-oxide or S,S-dioxide. Non-limiting examples of suitable monocyclic heterocyclyl rings include piperidyl, pyrrolidinyl, piperazinyl, morpholinyl, thiomorpholinyl, thiazolidinyl, 1,3-dioxolanyl, 1,4-dioxanyl, tetrahydrofuranyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, and the like.
“Arylalkyl” means an aryl-alkyl- group in which the aryl and alkyl are as previously described. Preferred aralkyls comprise a lower alkyl group. Non-limiting examples of suitable aralkyl groups include benzyl, 2-phenethyl and naphthalenylmethyl. The bond to the parent moiety is through the alkyl.
“Arylcycloalkyl” means a group derived from a fused aryl and cycloalkyl as defined herein. Preferred arylcycloalkyls are those wherein aryl is phenyl and cycloalkyl consists of about 5 to about 6 ring atoms. The arylcycloalkyl can be optionally substituted by 1-5 R21 substituents. Non-limiting examples of suitable arylcycloalkyls include indanyl and 1,2,3,4-tetrahydronaphthyl and the like. The bond to the parent moiety is through a non-aromatic carbon atom.
“Arylheterocycloalkyl” means a group derived from a fused aryl and heterocycloalkyl as defined herein. Preferred arylcycloalkyls are those wherein aryl is phenyl and heterocycloalkyl consists of about 5 to about 6 ring atoms. The arylheterocycloalkyl can be optionally substituted by 1-5 R21 substituents. Non-limiting examples of suitable arylheterocycloalkyls include




The bond to the parent moiety is through a non-aromatic carbon atom.
Similarly, “heteroarylalkyl” “cycloalkylalkyl” and “heterocycloalkylalkyl” mean a heteroaryl-, cycloalkyl- or heterocycloalkyl-alkyl- group in which the heteroaryl, cycloalkyl, heterocycloalkyl and alkyl are as previously described. Preferred groups contain a lower alkyl group. The bond to the parent moiety is through the alkyl.
“Acyl” means an H—C(O)—, alkyl-C(O)—, alkenyl-C(O)—, alkynyl-C(O)— or cycloalkyl-C(O)— group in which the various groups are as previously described. The bond to the parent moiety is through the carbonyl. Preferred acyls contain a lower alkyl. Non-limiting examples of suitable acyl groups include formyl, acetyl, propanoyl, 2-methylpropanoyl, butanoyl and cyclohexanoyl.
“Alkoxy” means an alkyl-O— group in which the alkyl group is as previously described. Non-limiting examples of suitable alkoxy groups include methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy and heptoxy. The bond to the parent moiety is through the ether oxygen.
“Alkyoxyalkyl” means a group derived from an alkoxy and alkyl as defined herein. The bond to the parent moiety is through the alkyl.
“Arylalkenyl” means a group derived from an aryl and alkenyl as defined herein. Preferred arylalkenyls are those wherein aryl is phenyl and the alkenyl consists of about 3 to about 6 atoms. The arylalkenyl can be optionally substituted by one or more R27 substituents. The bond to the parent moiety is through a non-aromatic carbon atom.
“Arylalkynyl” means a group derived from a aryl and alkynyl as defined herein. Preferred arylalkynyls are those wherein aryl is phenyl and the alkynyl consists of about 3 to about 6 atoms. The arylalkynyl can be optionally substituted by one or more R27 substituents. The bond to the parent moiety is through a non-aromatic carbon atom.
The suffix “ene” on alkyl, aryl, heterocycloalkyl, etc. indicates a divalent moiety, e.g., —CH2CH2— is ethylene, and




is para-phenylene.

The term “optionally substituted” means optional substitution with the specified groups, radicals or moieties, in available position or positions.
Substitution on a cycloalkylalkyl, heterocycloalkylalkyl, arylalkyl, or heteroarylalkyl moiety includes substitution on the ring portion and/or on the alkyl portion of the group.
When a variable appears more than once in a group, e.g., R8 in —N(R8)2, or a variable appears more than once in the structure of formula I, e.g., R15 may appear in both R1 and R3, the variables can be the same or different.
With reference to the number of moieties (e.g., substituents, groups or rings) in a compound, unless otherwise defined, the phrases “one or more” and “at least one” mean that there can be as many moieties as chemically permitted, and the determination of the maximum number of such moieties is well within the knowledge of those skilled in the art. With respect to the compositions and methods comprising the use of “at least one compound of formula I,” one to three compounds of formula I can be administered at the same time, preferably one.
As used herein, the term “composition” is intended to encompass a product comprising the specified ingredients in the specified amounts, as well as any product which results, directly or indirectly, from combination of the specified ingredients in the specified amounts.
The wavy line  as a bond generally indicates a mixture of, or either of, the possible isomers, e.g., containing (R)- and (S)-stereochemistry. For example,




means containing both





Lines drawn into the ring systems, such as, for example:




indicate that the indicated line (bond) may be attached to any of the substitutable ring carbon atoms.

As well known in the art, a bond drawn from a particular atom wherein no moiety is depicted at the terminal end of the bond indicates a methyl group bound through that bond to the atom, unless stated otherwise. For example:




represents





It should also be noted that any heteroatom with unsatisfied valences in the text, schemes, examples, structural formulae, and any Tables herein is assumed to have the hydrogen atom or atoms to satisfy the valences.
Those skilled in the art will recognize that certain compounds of formula I are tautomeric, and all such tautomeric forms are contemplated herein as part of the present invention. For example, a compound wherein X is —N(R5)— and R1 and R5 are each H can be represented by any of the following structures:




When R21 and R22, are, for example, —N(R15)C(O)N(R16)(R17) and R15 and R16 form a ring, the moiety formed, is, for example,




Prodrugs and solvates of the compounds of the invention are also contemplated herein. The term “prodrug”, as employed herein, denotes a compound that is a drug precursor which, upon administration to a subject, undergoes chemical conversion by metabolic or chemical processes to yield a compound of formula I or a salt and/or solvate thereof. A discussion of prodrugs is provided in T. Higuchi and V. Stella, Pro-drugs as Novel Delivery Systems (1987) Volume 14 of the A.C.S. Symposium Series, and in Bioreversible Carriers in Drug Design, (1987) Edward B. Roche, ed., American Pharmaceutical Association and Pergamon Press, both of which are incorporated herein by reference thereto.
“Solvate” means a physical association of a compound of this invention with one or more solvent molecules. This physical association involves varying degrees of ionic and covalent bonding, including hydrogen bonding. In certain instances the solvate will be capable of isolation, for example when one or more solvent molecules are incorporated in the crystal lattice of the crystalline solid. “Solvate” encompasses both solution-phase and isolatable solvates. Non-limiting examples of suitable solvates include ethanolates, methanolates, and the like. “Hydrate” is a solvate wherein the solvent molecule is H2O.
“Effective amount” or “therapeutically effective amount” is meant to describe an amount of compound or a composition of the present invention effective in inhibiting aspartyl protease and/or inhibiting BACE-1 and thus producing the desired therapeutic effect in a suitable patient.
The compounds of formula I form salts which are also within the scope of this invention. Reference to a compound of formula I herein is understood to include reference to salts thereof, unless otherwise indicated. The term “salt(s)”, as employed herein, denotes acidic salts formed with inorganic and/or organic acids, as well as basic salts formed with inorganic and/or organic bases. In addition, when a compound of formula I contains both a basic moiety, such as, but not limited to a pyridine or imidazole, and an acidic moiety, such as, but not limited to a carboxylic acid, zwitterions (“inner salts”) may be formed and are included within the term “salt(s)” as used herein. Pharmaceutically acceptable (i.e., non-toxic, physiologically acceptable) salts are preferred, although other salts are also useful. Salts of the compounds of the formula I may be formed, for example, by reacting a compound of formula I with an amount of acid or base, such as an equivalent amount, in a medium such as one in which the salt precipitates or in an aqueous medium followed by lyophilization. Acids (and bases) which are generally considered suitable for the formation of pharmaceutically useful salts from basic (or acidic) pharmaceutical compounds are discussed, for example, by S. Berge et al, Journal of Pharmaceutical Sciences (1977) 66 (1) 1-19; P. Gould, International J. of Pharmaceutics (1986) 33 201-217; Anderson et al, The Practice of Medicinal Chemistry (1996), Academic Press, New York; in The Orange Book (Food & Drug Administration, Washington, D.C. on their website); and P. Heinrich Stahl, Camille G. Wermuth (Eds.), Handbook of Pharmaceutical Salts: Properties, Selection, and Use, (2002) Int'l. Union of Pure and Applied Chemistry, pp. 330-331. These disclosures are incorporated herein by reference thereto.
Exemplary acid addition salts include acetates, adipates, alginates, ascorbates, aspartates, benzoates, benzenesulfonates, bisulfates, borates, butyrates, citrates, camphorates, camphorsulfonates, cyclopentanepropionates, digluconates, dodecylsulfates, ethanesulfonates, fumarates, glucoheptanoates, glycerophosphates, hemisulfates, heptanoates, hexanoates, hydrochlorides, hydrobromides, hydroiodides, 2-hydroxyethanesulfonates, lactates, maleates, methanesulfonates, methyl sulfates, 2-naphthalenesulfonates, nicotinates, nitrates, oxalates, pamoates, pectinates, persulfates, 3-phenylpropionates, phosphates, picrates, pivalates, propionates, salicylates, succinates, sulfates, sulfonates (such as those mentioned herein), tartarates, thiocyanates, toluenesulfonates (also known as tosylates), undecanoates, and the like.
Exemplary basic salts include ammonium salts, alkali metal salts such as sodium, lithium, and potassium salts, alkaline earth metal salts such as calcium and magnesium salts, aluminum salts, zinc salts, salts with organic bases (for example, organic amines) such as benzathines, diethylamine, dicyclohexylamines, hydrabamines (formed with N,N-bis(dehydroabietyl)ethylenediamine), N-methyl-D-glucamines, N-methyl-D-glucamides, t-butyl amines, piperazine, phenylcyclohexylamine, choline, tromethamine, and salts with amino acids such as arginine, lysine and the like. Basic nitrogen-containing groups may be quarternized with agents such as lower alkyl halides (e.g. methyl, ethyl, propyl, and butyl chlorides, bromides and iodides), dialkyl sulfates (e.g. dimethyl, diethyl, dibutyl, and diamyl sulfates), long chain halides (e.g. decyl, lauryl, myristyl and stearyl chlorides, bromides and iodides), aralkyl halides (e.g. benzyl and phenethyl bromides), and others.
All such acid salts and base salts are intended to be pharmaceutically acceptable salts within the scope of the invention and all acid and base salts are considered equivalent to the free forms of the corresponding compounds for purposes of the invention.
All stereoisomers (for example, geometric isomers, optical isomers and the like) of the present compounds (including those of the salts, solvates and prodrugs of the compounds as well as the salts and solvates of the prodrugs), such as those which may exist due to asymmetric carbons on various substituents, including enantiomeric forms (which may exist even in the absence of asymmetric carbons), rotameric forms, atropisomers, and diastereomeric forms, are contemplated within the scope of this invention. Individual stereoisomers of the compounds of the invention may, for example, be substantially free of other isomers, or may be admixed, for example, as racemates or with all other, or other selected, stereoisomers. The chiral centers of the present invention can have the S or R configuration as defined by the IUPAC 1974 Recommendations. The use of the terms “salt”, “solvate” “prodrug” and the like, is intended to equally apply to the salt, solvate and prodrug of enantiomers, stereoisomers, rotamers, tautomers, racemates or prod rugs of the inventive compounds.
Polymorphic forms of the compounds of formula I, and of the salts, solvates and prodrugs of the compounds of formula I, are intended to be included in the present invention
Compounds of formula I can be made using procedures known in the art. Preparative methods for preparing starting materials and compounds of formula I are show below as general reaction schemes (Method A, Method B, etc.) followed by specific procedures, but those skilled in the art will recognize that other procedures can also be suitable. In the Schemes and in the Examples below, the following abbreviations are used:

    
    
        methyl: Me; ethyl: Et; propyl: Pr; butyl: Bu; benzyl: Bn; tertiary butyloxycarbonyl: Boc or BOC
        high pressure liquid chromatography: HPLC
        liquid chromatography mass spectroscopy: LCMS
        room temperature: RT or rt
        day: d; hour: h; minute: min
        retention time: Rt 
        microwave: μW
        saturated: sat.; anhydrous: anhyd.
        1-hydroxybenzotriazole: HOBt
        1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride: EDCl
        ethyl acetate: EtOAc
        Benzyloxycarbonyl: CBZ
        [1-(chloromethyl)-4-fluoro-1,4-diazoniabicyclo[2.2.2]octane bis(tetrafluoro-borate)]:Selectfluor
        1,8-diazabicyclo[5,4,0]undec-7-ene: DBU
        tetrahydrofuran: THF; N,N-dimethylformamide: DMF; methanol: MeOH; diethyl ether: Et2O; acetic acid: AcOH; acetonitrile: MeCN; trifluoroacetic acid: TFA; dichloromethane: DCM; dimethoxyethane: DME; diphenylphosphinoferrocene (dppf);
        n-butyllithium: n-BuLi; lithium diisopropylamide: LDA
        1-hydroxy-7-azabenzotriazole: HOAt
        4-N,N-dimethylaminopyridine: DMAP; diisopropylethylamine: DIEA; N-methylmorpholine: NMM
        Microporous Toluene sulfonic acid resin (MP-TsOH resin)
        tris-(2-aminoethyl)aminomethyl polystyrene (PS-trisamine)
        methylisocyanate polystyrene (PS-NCO)
        Saturated (sat.); anhydrous, (anhyd); room temperature (rt); hour (h); Minutes (Min), Retention Time (Rt); molecular weight (MW); milliliter (mL); gram (g). milligram (mg); equivalent (eq); day (d); microwave (μW); microliter (μL);
    
    


All NMR data were collected on 400 MHz NMR spectrometers unless otherwise indicated. LC-Electrospray-Mass spectroscopy with a C-18 column and 5% to 95% MeCN in water as the mobile phase was used to determine the molecular mass and retention time. The tables contain the compounds with retention time/observed MW and/or NMR data.
For internal consistency in the reaction schemes shown in Methods A to DF, the product of each method is shown as structure A4, B4, C3, etc., wherein certain variables are as defined for that method, but it will be apparent that, for example, A4 has the same structure as C3. That is, different methods can be used to prepare similar compounds.
The compounds in the invention may be produced by processes known to those skilled in the art and as shown in the following reaction schemes and in the preparations and examples described below. The tables contain the compounds with observed m/e values from mass spectroscopy and/or NMR data. These compounds can be obtained with synthetic methods similar to these listed in the last column using appropriate reagents.




Method A
Step 1
To a solution of A1 (R3=CH3 & R4=CH2CH(CH3)2) (10 mmol, 1 eq) in 30 ml of anhyd. CH2Cl2 was added thiocarbonyl dipyridone (1.2 eq). After stirring overnight the solution was diluted with CH2Cl2, washed with 1N HCl, H2O (2×), and a saturated aqueous NaCl solution (2×). The organic solution was dried over Na2SO4, filtered and concentrated. The crude material was purified via flash chromatography to afford A2 (R3=CH3 & R4=CH2CH(CH3)2).
Method A
Step 2
A solution of 3,5-difluorobenzyl amine (0.15 mmol, 1.5 eq) in THF (0.15 mL) was added to a solution of A2 (R3=CH3 & R4=CH2CH(CH3)2) (0.1 mmol, 1 eq) in anhydrous CH2Cl2 (1 mL). The reaction mixture was refluxed overnight. The reaction solution was added to MP-TsOH resin (2-3 eq) and diluted with CH3CN. The suspension was agitated overnight. The mixture was filtered and the filtrate was concentrated to afford A3 (R1=3,5-difluorobenzyl, R3=CH3, & R4=CH2CH(CH3)2).
Method A
Step 3
To a solution of A3 (R1=3,5-difluorobenzyl, R3=CH3, & R4=CH2CH(CH3)2) (10 mg) in CH3OH (1 mL) was added NH4OH (0.44 mL) and t-butyl hydrogen peroxide (0.1 mL) and the reaction mixture was agitated for 2 d. The solution was concentrated, the resulting residue was dissolved in CH3OH (1.2 mL) and was treated with sulfonic acid resin. The suspension was agitated overnight and the resin was washed with CH3OH (4×10 min) before it was treated with 2 N NH3 in CH3OH for 1 h. The suspension was filtered and the filtrate was concentrated to give the crude material which was purified by preparative HPLC/LCMS eluting with a CH3CN/H2O gradient to afford A4 (R1=3,5-difluorobenzyl, R2=H, R3=CH3, & R4=CH2CH(CH3)2). NMR (CD3OD): δ6.9, m, 3H; δ4.8-4.9, m; δ1.75, d, 2H; δ1.5, m, 1H; δ1.42, s, 3H; δ0.85, d, 3H; δ0.65, d, 3H. ES_LCMS (m/e) 296.1.
The following compounds were synthesized using similar methods:
















Obs.


#
Structure
MW
m/e


















1




223
224


 


2




223
224


 


3




225
226


 


4




225
226


 


5




227
228


 


6




237
238


 


7




239
240


 


8




239
240


 


9




239
240


 


10




240
241


 


11




241
242


 


12




241
242


 


13




251
252


 


14




253
254


 


15




254
255


 


16




255
256


 


17




255
256


 


18




255
256


 


19




260
261


 


20




260
261


 


21




265
266


 


22




265
266


 


23




265
266


 


24




267
268


 


25




268
269


 


26




268
269


 


27




269
270


 


28




273
274


 


29




273
274


 


30




274
275


 


31




274
275


 


32




274
275


 


33




277
278


 


34




279
280


 


35




280
281


 


36




280
281


 


37




280
281


 


38




280
281


 


39




281
282


 


40




282
283


 


41




282
283


 


42




282
283


 


43




283
284


 


44




285
286


 


45




287
288


 


46




287
288


 


47




289
290


 


48




293
294


 


49




294
295


 


50




294
295


 


51




295
296


 


52




296
297


 


53




301
302


 


54




303
304


 


55




304
305


 


56




304
305


 


57




305
306


 


58




307
308


 


59




307
308


 


60




308
309


 


61




310
311


 


62




317
318


 


63




319
320


 


64




322
323


 


65




324
325


 


66




327
328


 


67




327
328


 


68




327
328


 


69




327
328


 


70




328
329


 


71




330
331


 


72




331
332


 


73




331
332


 


74




335
336


 


75




335
336


 


76




337
338


 


77




337
338


 


78




342
343


 


79




345
346


 


80




345
346


 


81




349
350


 


82




349
350


 


83




351
352


 


84




351
352


 


85




351
352


 


86




359
360


 


87




361
362


 


88




361
362


 


89




361
362


 


90




363
364


 


91




363
364


 


92




363
364


 


93




363
364


 


94




363
364


 


95




363
364


 


96




369
370


 


97




374
375


 


98




375
376


 


99




375
376


 


100




377
378


 


101




377
378


 


102




377
378


 


103




381
382


 


104




382
383


 


105




385
386


 


106




385
386


 


107




386
387


 


108




389
390


 


109




391
392


 


110




391
392


 


111




391
392


 


112




391
392


 


113




393
394


 


114




393
394


 


115




400
401


 


116




401
402


 


117




401
402


 


118




401
402


 


119




401
402


 


120




403
404


 


121




403
404


 


122




403
404


 


123




405
406


 


124




405
406


 


125




409
410


 


126




409
410


 


127




409
410


 


128




409
410


 


129




411
412


 


130




413
414


 


131




413
414


 


132




414
415


 


133




415
416


 


134




415
416


 


135




415
416


 


136




417
418


 


137




419
420


 


138




421
422


 


139




423
424


 


140




425
426


 


141




425
426


 


142




425
426


 


143




427
428


 


144




429
430


 


145




430
431


 


146




430
431


 


147




431
432


 


148




433
434


 


149




437
438


 


150




439
440


 


151




440
441


 


152




440
441


 


153




441
442


 


154




441
442


 


155




442
443


 


156




447
448


 


157




449
450


 


158




455
456


 


159




463
464


 


160




463
464


 


161




471
472


 


162




473
474


 


163




481
482


 


164




481
482


 


165




487
488


 


166




488
489


 


167




499
500


 


168




504
505


 


169




523
524


 


170




525
526


 


171




525
526


 


172




527
528


 


173




528
529


 


174




535
536


 


175




535
536


 


176




535
536


 


177




535
536


 


178




550
551


 


179




554
555


 


180




556
557


 


181




569
570


 


182




581
582


 


183




374
NA


 


184




388
NA


 


185




337
NMR


 


186




351
NMR













A modified literature procedure was used (Ugi, I. Angew. Chem. 1962, 74 9-22).

Method B
Step 1
To a solution of B1 (HCl salt, R1=3-chlorophenethyl) (1.1 g, 5.73 mmol) in anhydrous CH3OH (15 mL) was added potassium thiocyanate (0.56 g, 5.73 mmol). The reaction mixture was heated to 60° C. for 1 h. The suspension was filtered and the filtrate was added to B5 (R3=Me, R4=iBu) (0.72 mL, 5.73 mmol) and benzyl isocyanide (0.77 mL, 6.3 mmol). The mixture was stirred overnight before the solution was concentrated and the residue was purified via flash chromatography eluting with ethyl acetate in hexane to yield 0.28 g of B2 (R3=CH3, R4=CH2CH(CH3)2, and R1=3-Chlorophenethyl).
Method B
Step 2
A solution of 40% concentrated HCl in CH3CH2OH was added to B2 (R3=CH3, R4=CH2CH(CH3)2, and R1=3-Chlorophenethyl) and the solution was heated in a microwave at 160° C. for 30 min. The solution was concentrated and purified via reverse phase preparative HPLC eluting with a CH3CN/H2O (with 0.1% formic acid) gradient to afford B3 (R3=CH3, R4=CH2CH(CH3)2, and R1=3-Chlorophenethyl).
Method B
Step 3
Compound B4 (R2=H, R3=CH3, R4=CH2CH(CH3)2, and R1=3-Chlorophenethyl) was prepared from B3 (R3=CH3, R4=CH2CH(CH3)2, and R1=3-Chlorophenethyl) following a procedure similar to Method A, Step 3.
NMR (CD3OD): δ 8.1, br, 1H; δ 7.35, s, 1H; δ 7.25, m, 3H; δ 3.6, m, 1H; δ 3.4, m, 1 H; δ 3.0, m, 1H; δ 2.8, m, 1 H; δ 1.75, m, 1H; δ 1.6, m, 1H; δ 1.35, m, 1H; δ 1.2 s, 3H; δ 0.8, m, 6H. ES_LCMS (m/e): 308.1
The following compounds were prepared using similar methods
















Obs.


#
Structure
MW
m/e







545




251
252


 


546




293
294


 


547




307
308


 


548




357
358


 


549




371
372


 


550




413



 


551




265













Method C
Step 1
A solution of C1 (R3=R4=CH2CH2CH2CH3) (50 mg, 0.25 mmol) and C4 (R1=3-chlorophenyl) (38 μL, 0.26 mmol) was refluxed overnight. Trisamine resin (2 eq) and polystyrene isocyanate resin (2 eq) was added and the mixture was agitated. After 3 h, the suspension was filtered and the resin was washed with CH2Cl2 (3×) and CH3OH (3×). The filtrate was concentrated to afford C2 (R1=3-Cl—C6H4, R3=R4=CH2CH2CH2CH3) (60 mg, 68%).
Method C
Step 2
Compound C3 (R1=3-Cl—C6H4, R2=H, R3=R4=CH2CH2CH2CH3) was prepared from C2 (R1=3-Cl—C6H4, R3=R4=CH2CH2CH2CH3) following a procedure similar to Method A, Step 3. NMR (CDCl3): δ 7.4, m, 2H; δ 7.2, m, 2H; δ 5.0, s, 2H; δ 1.7, m, 4H; δ 1.1, m, 8H; δ 0.7; m, 6H. ES-LCMS (m/e): 336.1.
The following compounds were prepared using similar method.
















Obs.


#
Structure
MW
m/e







641




209
210


 


642




211
212


 


643




215
216


 


644




225
226


 


645




239
240


 


646




245
246


 


647




246
247


 


648




251
252


 


649




267
268


 


650




309
310


 


651




317
318


 


652




319
320


 


653




323
324


 


654




324
325


 


655




329
330


 


656




329
330


 


657




335
336


 


658




335
336


 


659




335
336


 


660




335
336


 


661




335
336


 


662




352
353


 


663




352
353


 


664




377
378


 


665




385
386


 


666




391
392


 


667




420
421


 


668




420
421













Method D
Step 1
A mixture of D1 (R3=R4=CH2C6H5) (20 g), potassium cyanide (40 g) and ammonium carbonate (15 g) in ethanol (100 mL) and H2O (200 mL) was heated in a sealed flask at 130° C. overnight to yield 25 g of D2 (R3=R4=CH2C6H5) after filtration followed by washing with water.
Method D
Step 2
A solution of 2 N KOH (3 eq) was added to D2 (R3=R4=CH2C6H5) (1 eq) and irradiated via microwave at 185° C. for 3 h followed by addition of concentrated HCl to the solution until a pH=2-3 was obtained. The solid was filtered and washed with water to afford D3 (R3=R4=CH2C6H5).
Method D
Step 3
A solution of trimethylsilyldiazomethane in hexane (2 N) (2 eq) was added drop wise to a solution of D3 (R3=R4=CH2C6H5) (1 eq) in anhydrous CH3OH (30 mL). After 1 h, an additional 2 eq of trimethylsilyldiazomethane in hexane (2 N) was added and the reaction was stirred for 20 minutes before it was concentrated. The residue was dissolved in a 0.2 N HCl solution (25 mL) and washed with ether (3×). A saturated solution of Na2CO3 was added to the aqueous phase until the pH of the solution was basic. The solution was extracted with ethyl acetate (3×). The organic extracts were combined, dried over Na2SO4, and concentrated to afford D4 (R3=R4=CH2C6H5).
The following amino esters were prepared using a similar method.











Method E
Step 1
Thionyl chloride (0.47, 6.38 mmol) was added drop wise to a solution of E1 (R3=CH2CH2C6H5) (2 g, 6.38 mmol) and benzaldehyde dimethyl acetal (0.96 mL, 6.38 mmol) in anhydrous THF at 0° C. under N2. After 5 min, ZnCl2 (0.87 g, 6.38 mmol) was added and the reaction mixture was stirred at 0° C. After 3 h, an additional amount of ZnCl2 (0.18 g, 1.28 mmol) and thionyl chloride (0.1 mL, 1.28 mmol) were added and stirred for 1 h at 0° C. The reaction mixture was poured into a stirred suspension of ice/H2O. The mixture was stirred occasionally until the ice melted. The aqueous solution was extracted with ether (3×). The combined organic extracts were washed with H2O (3×), a sat. aqueous solution of NaHCO3 (1×), and H2O (2×). The organic solution was dried over Na2SO4, filtered and concentrated. The crude material was purified via flash chromatography eluting with ethyl acetate in hexane to yield compound E2 (R3=CH2CH2C6H5).
Method E
Step 2
A solution of lithium hexamethyldisilazide in hexane (1.0 M, 1.65 mL, 1.64 mmol) was added drop wise to a solution of E2 (R3=CH2CH2C6H5) (600 mg, 1.49 mmol) and HMPA (0.85 mL) in THF (6.5 mL) cooled at −78° C. under N2. After 15 min, isobutyl iodide (0.52 mL, 4.48 mmol) was added drop wise and the reaction mixture was stirred at −78° C. for 3 h. The reaction was warmed to −65° C., stirred for 2 h and warmed to rt overnight. The reaction solution was poured into a mixture of sat. NaHCO3 (aq)/ether/ice. The aqueous layer was extracted with ether (3×). The organic extracts were combined and washed with brine (2×). The organic solution was dried over Na2SO4, filtered and concentrated. The crude material was purified via flash chromatography eluting with ethyl acetate in hexane to yield compound E3 (R3=CH2CH2C6H5, R4=CH2CH(CH3)2).
Method E
Step 3
A solution of lithium methoxide (1 N in CH3OH) (0.36 mL, 0.36 mmol) was added to compound E3 (R3=CH2CH2C6H5, R4=CH2CH(CH3)2). The reaction mixture was shaken at rt for 50 min. An additional 0.55 eq of lithium methoxide were added. After 2.5 h, a sat. aqueous solution of NaHSO3 (0.75 mL) and ethyl acetate (3 mL) was added to the reaction mixture and shaken for 15 min. The suspension was filtered. The resulting white solid was washed with a sat. aqueous solution of NaHSO3 (1×) and ethyl acetate (1×). The aqueous phase of the filtrate was separated and extracted with ethyl acetate (2×). The organic extracts were combined and washed with a sat. aqueous solution of NaHSO3 (8×). The organic solution was dried over Na2SO4, filtered and concentrated to afford E4 (R3=CH2CH2C6H5, R4=CH2CH(CH3)2) (109 mg, 87%).
Method E
Step 4
To a solution of E4 (R3=CH2CH2C6H5, R4=CH2CH(CH3)2) (109 mg, 0.28 mmol) in CH3OH (4 mL) was added 1 N HCl (0.28 mL, 0.28 mmol) and 20% palladium hydroxide on carbon (22 mg). The reaction mixture was hydrogenated at 40 psi. After 2.5 h, the reaction was filtered and the catalyst was washed with CH3OH (3×). The filtrate was concentrated to afford E5 (R3=CH2CH2C6H5, R4=CH2CH(CH3)2) (78 mg, 96%).
The following aminoesters were prepared using similar method.














A 500 mL methanol solution of 20 g of D5 (R3=benzyl, n=1) with 1.5 eq of HCl was hydrogenated with 1 g of Rh/C (5% w/w) and 2 g of Pt/C (5% w/w) at 60 psi for 2 days. The solid was filtered and washed with excessive methanol. The combined solution was evaporated to give 20 g of F1 (R3=cyclohexylmethyl, n=1) as HCl salt.
The following amino esters were examples prepared using similar method.











Method G
Step 1
To a solution of G1 (R1=CH2(3-ClC6H4) and R3=CH3) (400 mg, 1.23 mmol, generated following a procedure similar to Method C, Step 1) in ethanol (5 mL) was added lithium hydroxide monohydrate (100 mg, 2.45 mmol) in H2O (0.5 mL). After 2.5 h, another portion of lithium hydroxide monohydrate (100 mg, 2.45 mmol) was added. After 5.5 h, the reaction mixture was diluted with H2O (15 mL) and extracted with ether (2×). A solution of 30% HCl was added to the aqueous phase until its pH=1 to 2. The solution was saturated with NaCl and extracted with ethyl acetate (3×). The organic solution was dried over Na2SO4, filtered and concentrated to afford G2 (R1=CH2(3-ClC6H4) and R3=CH3) (357 mg, 93%).
Method G
Step 2
A solution of benzyl amine (1.2 eq) was added to G2 (R1=CH2(3-ClC6H4) and R3=CH3) (1 eq), HOBT (1.5 eq) and polystyrene EDC resin (94 mg, 1.53 mmol/g, 3 eq) in 1:1 THF:CH3CN (1 mL). The reaction mixture was shaken overnight at rt. Trisamine resin (85 mg, 3.38 mmol/g, 6 eq) and isocyanate resin (100 mg, 1.47 mmol/g, 3 eq) was added. After 6 h, the suspension was filtered and the filtrate was concentrated to afford G3 (R1=CH2(3-ClC6H4), R3=CH3, R15=CH2C6H5 and R16=H).
Method G
Step 3
Compound G4 (R1=CH2(3-ClC6H4), R2=H, R3=CH3, R15=CH2C6H5 and R15=H) was prepared from G3 (R1=CH2(3-ClC6H4), R3=CH3, R15=CH2C6H5 and R16=H) following a procedure similar to Method A, Step 3.
The following compounds were prepared using similar methods.
















Obs.


#
Structure
MW
m/e







669




322
323


 


670




334
335


 


671




336
337


 


672




348
349


 


673




364
365


 


674




364
365


 


675




376
377


 


676




384
385


 


677




390
391


 


678




393
394


 


679




398
399


 


680




398
399


 


681




406
407


 


682




412
413


 


683




414
415


 


684




414
415


 


685




414
415


 


686




421
422


 


687




428
429


 


688




434
435


 


689




442
443


 


690




449
450


 


691




461
462


 


692




511
512


 


693




511
512













Method H
Step 1
To a solution of H1 (R3=CH3) (5 g, 39 mmol) in a 1:1 mixture of 0.5 M NaHCO3:CH3CH2OH was added R1—NCS (R1=3-chlorobenzyl) (11.5 mL, 78 mmol). The reaction mixture was heated at 50° C. overnight. The reaction was cooled and diluted with water. The aqueous phase was extracted with ethyl acetate (5×). The organic extracts were combined, washed with water (2×) and dried over Na2SO4. The solution was filtered and solvent was removed to give a small volume of solution. Hexane was added and the resulting suspension was filtered to yield 6.8 g of a solid H2 (R3=CH3, R1=CH2(3-ClC6H4)) (61%).
Method H
Step 2
Compound H3 (R3=CH3, R1=CH2(3-ClC6H4)) was synthesized from H2 (R3=CH3, R1=CH2(3-ClC6H4)) following a procedure similar to Method A, Step 3.
Method H
Step 3
To a solution of crude H3 (R3=CH3, R1=CH2(3-ClC6H4)) (14 mmol) in a 1:3 mixture of CH3OH:THF was added 0.5 M NaHCO3 in H2O (28 mL, 14 mmol) and di-tert-butyl dicarbonate (3.69 g, 16.9 mmol). The reaction was stirred at rt for 2.5 h and then stored at −10° C. overnight. The reaction was diluted with brine and extracted with ethyl acetate (4×). The organic extracts were combined and washed with brine (1×). The organic solution was dried over Na2SO4, filtered and concentrated. The crude material was purified via flash chromatography eluting with ethyl acetate in hexane to afford 1.5 g of H4 (R1=CH2(3-ClC6H4) and R3=CH3).
Method H
Step 4
A solution of triflic anhydride (128 μL, 0.76 mmol) in CH2Cl2 (5 mL) was added drop wise to a solution of H4 (R1=CH2(3-ClC6H4) and R3=CH3) (200 mg, 0.55 mmol) and 2,6-lutidine (176 μL, 2.18 mmol) at −30° C. The reaction mixture was stirred for 1.5 h. Water (10 mL) was added at −20° C. and the ice bath was removed. The reaction was stirred until it reached 0° C. The organic layer was separated, dried over Na2SO4, filtered and concentrated to afford 310 mg of H5 (R1=CH2(3-ClC6H4) and R3=CH3).
Method H
Step 5
A solution of crude H5 (R1=CH2(3-ClC6H4) and R3=CH3) (0.11 mmol) and 7N ammonia in Methanol (R21—H=NH2—H) (10 eq) was stirred overnight at rt. The reaction solution was concentrated. The crude material was purified using reverse phase preparative HPLC eluting with a CH3CN/H20 gradient with 0.1% formic acid to yield H6 (R1=CH2(3-ClC6H4), R3=CH3, R21=NH2).
Method H
Step 6
A solution of 50% trifluoroacetic acid in CH2Cl2 (2 mL) was added to H6 (R1=CH2(3-ClC6H4), R3=CH3, R21=NH2). After 40 min the solvent was evaporated and residue purified by preparative HPLC/LCMS eluting with a CH3CN/H2O gradient to afford H7 (R1=CH2(3-ClC6H4), R3=CH3, R21=NH2).
NMR (CDCl3), δ 7.45, m, 3H; δ 7.35, m, 1H; δ 4.9, m, 2H; δ 3.5, m, 2H; δ 1.65, s, 3H. ES_LCMS (m/e) 267.07.
The following compounds were prepared using similar methods.
















Obs. 


#
Structure
MW
m/e







694




238
239


 


695




248
249


 


696




257
258


 


697




264
265


 


698




266
267


 


699




292
293


 


700




308
309


 


701




314
315


 


702




320
321


 


703




328
329


 


704




334
335


 


705




342
343


 


706




354
355


 


707




372
373


 


708




418
419


 


709




483
484













Method I
Step 1
Diethylaminomethyl polystyrene resin (5 eq) was added to a solution of the formate salt of I1 (R1=CH2(3-ClC6H4), R3=CH3 and R16=H) in CH2Cl2 and the suspension was agitated. After 15 min, the mixture was filtered and the resin was washed with CH2Cl2 (4×). The filtrate was concentrated to afford the free base I1 (R1=CH2(3-ClC6H4), R3=CH3 and R16=H).
A solution of R15COOH (R15=Phenethyl) (1.3 eq) was added to a mixture of EDC resin (41 mg, 1.53 mmol/g, 3 eq), HOBT (1.5 eq), and the free base of I1 (R1=CH2(3-ClC6H4), R3=CH3 and R16=H) (0.021 mmol) in 1:1 CH3CN:THF. The suspension was agitated overnight. Polystyrene isocyanate resin (45 mg, 3 eq), polystyrene trisamine resin (40 mg, 6 eq) and a 1:1 mixture of CH3CN:THF (0.5 mL) was added. The mixture was agitated for 6 h. The suspension was filtered and the filtrate was concentrated to afford I2 (R1=CH2(3-ClC6H4), R3=CH3, R16=H and R15=CH2CH2C6H5).
Method I
Step 2
I3 (R1=CH2(3-ClC6H4), R3=CH3, R16=H and R15=CH2CH2C6H5) was prepared from I2 (R1=CH2(3-ClC6H4), R3=CH3, R16=H and R15=CH2CH2C6H5) using method similar to method H step 6.
The following compounds were prepared using similar method.
















Obs. 


#
Structure
MW
m/e







710




280
281


 


711




308
309


 


712




308
309


 


713




334
335


 


714




342
343


 


715




362
363


 


716




372
373


 


717




376
377


 


718




398
399


 


719




406
407


 


720




410
 11


 


721




410
 11


 


722




414
 15


 


723




420
 21


 


724




428
 29


 


725




511
 12













Method J
Step 1
Diethylaminomethyl polystyrene resin (5 eq) was added to a solution of J1 (TFA salt, R1=CH2(3-ClC6H4) and R3=CH3) in CH2Cl2 and the suspension was agitated. After 15 min, the mixture was filtered and the resin was washed with CH2Cl2 (4×). The filtrate was concentrated to afford the free base. A solution of R15NCO (R15=butyl) (2 eq) in CH2Cl2 was added to the free base of J1 (R1=CH2(3-ClC6H4) and R3=CH3) (0.021 mmol) in 1:1 CH3CN:THF. The suspension was agitated overnight. Polystyrene isocyanate resin (45 mg, 3 eq), polystyrene trisamine resin (40 mg, 6 eq) and a 1:1 mixture of CH3CN:THF (0.5 mL) was added. The mixture was agitated for 6 h. The suspension was filtered and the filtrate was concentrated to afford J2 (R1=CH2(3-ClC6H4), R3=CH3, and R15=CH2CH2CH2CH3).
Method J
Step 2
Compound J3 (R1=CH2(3-ClC6H4), R3=CH3, and R15=CH2CH2CH2CH3) was prepared from J2 (R1=CH2(3-ClC6H4), R3=CH3, and R15=CH2CH2CH2CH3) following the procedure described in Method H, Step 2.
The following compounds were prepared using similar method.
















Obs. 


#
Structure
MW
m/e







726




323
324


 


727




337
338


 


728





352


 


729





358


 


730




365
366


 


731




377
378


 


732




413
414


 


733




417
418


 


734




421
422


 


735




425
426













Method K
Step 1
A solution of R15SO2Cl (R15=Propyl) (1.5 eq) was added to a suspension of polystyrene diisopropylethylamine resin (18 mg, 3.45 mmol/g, 3 eq) and the free base of K1 prepared using method H (R1=CH2(3-ClC6H4) and R3=CH3) (0.021 mmol) in 1:1 CH3CN:THF. The suspension was agitated overnight. Polystyrene isocyanate resin (45 mg, 3 eq), polystyrene trisamine resin (40 mg, 6 eq) and a 1:1 mixture of CH3CN:THF (0.5 mL) was added. The mixture was agitated for 6 h. The suspension was filtered and the filtrate was concentrated to afford K2 (R1=CH2(3-ClC6H4), R3=CH3, and R15=CH2CH2CH3).
Method K
Step 2
Compound K3 (R1=CH2(3-ClC6H4), R3=CH3, and R15=CH2CH2CH3) was prepared from K2 (R1=CH2(3-ClC6H4), R3=CH3, and R15=CH2CH2CH3) following the procedure described in Method H, Step 6.
The following compounds were prepared using similar method.
















Obs. 


#
Structure
MW
m/e







736




316
317


 


737




344
345


 


738




372
373


 


739




378
379


 


740




442
443


 


741




454
455


 


742




492
493













(In the scheme, —Z—NH—C(O)R16— is equivalent to R1 substituted by R21, or R1Substituted by alkyl-R22, wherein R21 and R22 are —N(R15)C(O)R16 and R15 is H, and wherein Z is optionally substituted alkylene-arylene, alkylene-arylene-alkylene, alkylene-heteroarylene, alkylene-heteroarylene-alkylene, alkylene-cycloalkylene, alkylene-cycloalkylene-alkylene, alkylene-heterocycloalkylene, alkylene-heterocycloalkylene-alkylene, arylene, heteroarylene, cycloalkylene or heterocycloalkylene)
Method L
Step 1
A solution of L1 (R3=CH3 and R4=CH2CH(CH3)2) (1 eq) and Z=para-methylene-benzyl) (1.05 eq) in CH2Cl2 was stirred at rt. The reaction solution was concentrated and purified via flash chromatography. The material was treated with 50% trifluoroacetic acid in CH2Cl2 for 30 min. The solution was concentrated. The residue was dissolved in 1 N HCl (10 mL) and washed with ether (2×) A saturated solution of Na2CO3 in H2O was added to the aqueous phase until the solution became basic. The solution was extracted with CH2Cl2 (3×). The CH2Cl2 extracts were combined, dried over Na2SO41 filtered and concentrated to yield L2 (R3=CH3, R4=CH2CH(CH3)2, Z=para-(CH2)C6H4(CH2)—).
Method L
Step 2
Compound L3 (R3=CH3, R4=CH2CH(CH3)2, Z=para-(CH2)C6H4(CH2)—, R16=CH2CH2CH2CH3) was prepared from L2 (R3=CH3, R4=CH2CH(CH3)2, Z=para-(CH2)C6H4(CH2)—) following the procedure described in Method I, Step 1.
Method L
Step 3
Compound L4 (R3=CH3, R4=CH2CH(CH3)2, Z=para-(CH2)C6H4(CH2)—, R1=CH2CH2CH2CH3) was prepared from (R3=CH3, R4=CH2CH(CH3)2, Z=para-(CH2)C6H4(CH2)—, R16=CH2CH2CH2CH3) following the procedure described in Method A, Step 3.
The following compounds were prepared using similar method.













#
Structure
MW
Obs. m/e


















743




316
317


 


744




316
317


 


745




330
331


 


746




330
331


 


747




344
345


 


748




344
345


 


749




358
359


 


750




358
359


 


751




386
387


 


752




386
387


 


753




386
387


 


754




400
401


 


755




400
401


 


756




420
421


 


757




434
435


 


758




434
435


 


759




436
437


 


760




436
437


 


761




450
451


 


762




450
451


 


763




450
451


 


764




450
451


 


765




464
465


 


766




464
465


 


767




470
471


 


768




478
479


 


769




478
479


 


770




484
485


 


771




484
485


 


772




492
493


 


773




492
493


 


774




519
520


 


775




519
520


 


776




533
534


 


777




533
534













(In the scheme, —Z—NH—C(O)—NHR15— is equivalent to R1 substituted by R21, or R1 Substituted by alkyl-R22, wherein R21 and R22 are —N(R16)—C(O)—NHR15 and R16 is H, and wherein Z is optionally substituted alkylene-arylene, alkylene-arylene-alkylene, alkylene-heteroarylene, alkylene-heteroarylene-alkylene, alkylene-cycloalkylene, alkylene-cycloalkylene-alkylene, alkylene-heterocycloalkylene, alkylene-heterocycloalkylene-alkylene, arylene, heteroarylene, cycloalkylene or heterocycloalkylene)
Method M
Step 1
Compound M2 (R3=CH3, R4=CH2CH(CH3)2, Z=para-(CH2)C6H4(CH2)—, R15=3,4-difluorophenyl) was prepared from M1 (R3=CH3, R4=CH2CH(CH3)2, Z=para-(CH2)C6H4(CH2)—) following the procedure described in Method J, Step 1.
Method M
Step 2
Compound M3 (R3=CH3, R4=CH2CH(CH3)2, Z=para-(CH2)C6H4(CH2)—, R15=3,4-difluorophenyl) was prepared from M2 (R3=CH3, R4=CH2CH(CH3)2, Z=para-(CH2)C6H4(CH2)—, R15=3,4-difluorophenyl) following the procedure described in Method A, Step 3. NMR (CD3OD) δ 7.45, m, 1H; δ 7.26, m, 4H; 7.24, m, 1H; δ 6.96, m, 1H; δ 4.8, m; δ 4.3, s, 2H; δ 1.69, m, 2H; δ 1.44, m, 1H; δ 1.37, s, 3H; δ 0.8, m, 3H; δ 0.63, m, 3H. ES_LCMS (m/e) 430.27
The following compounds were prepared using similar method.
















Obs.


#
Structure 
MW
m/e


















778




331
332


 


779




359
360


 


780




359
360


 


781




373
374


 


782




373
374


 


783




373
374


 


784




373
374


 


785




387
388


 


786




387
388


 


787




387
388


 


788




387
388


 


789




401
402


 


790




401
402


 


791




405
406


 


792




407
408


 


793




407
408


 


794




407
408


 


795




413
414


 


796




413
414


 


797




418
419


 


798




418
419


 


799




421
422


 


800




421
422


 


801




421
422


 


802




421
422


 


803




421
422


 


804




421
422


 


805




421
422


 


806




421
422


 


807




423
424


 


808




423
424


 


809




423
424


 


810




423
424


 


811




425
426


 


812




425
426


 


813




427
428


 


814




429
430


 


815




429
430


 


816




429
430


 


817




432
433


 


818




432
433


 


819




432
433


 


820




433
434


 


821




433
434


 


822




435
436


 


823




435
436


 


824




435
436


 


825




435
436


 


826




435
436


 


827




435
436


 


828




435
436


 


829




437
438


 


830




437
438


 


831




437
438


 


832




437
438


 


833




437
438


 


834




437
438


 


835




437
438


 


836




439
440


 


837




439
440


 


838




439
440


 


839




441
442


 


840




441
442


 


841




441
442


 


842




441
442


 


843




443
444


 


844




443
444


 


845




443
444


 


846




447
448


 


847




447
448


 


848




449
450


 


849




450
451


 


850




450
451


 


851




450
451


 


852




451
452


 


853




451
452


 


854




451
452


 


855




452
453


 


856




453
454


 


857




453
454


 


858




455
456


 


859




455
456


 


860




455
456


 


861




457
458


 


862




457
458


 


863




457
458


 


864




458
459


 


865




458
459


 


866




460
461


 


867




461
462


 


868




461
462


 


869




461
462


 


870




461
462


 


871




461
462


 


872




461
462


 


873




461
462


 


874




463
464


 


875




466
467


 


876




466
467


 


877




467
468


 


878




469
470


 


879




469
470


 


880




471
472


 


881




471
472


 


882




472
473


 


883




472
473


 


884




475
476


 


885




475
476


 


886




475
476


 


887




475
476


 


888




475
476


 


889




475
476


 


890




475
476


 


891




475
476


 


892




475
476


 


893




475
476


 


894




475
476


 


895




475
476


 


896




477
478


 


897




477
478


 


898




479
480


 


899




479
480


 


900




480
481


 


901




483
484


 


902




483
484


 


903




485
486


 


904




485
486


 


905




485
486


 


906




485
486


 


907




485
486


 


908




489
490


 


909




489
490


 


910




489
490


 


911




491
492


 


912




493
494


 


913




493
494


 


914




493 
494


 


915




493
494


 


916




496
497


 


917




496
497


 


918




497
498


 


919




497
498


 


920




499
500


 


921




501
502


 


922




501
502


 


923




502
503


 


924




502
503


 


925




502
503


 


926




502
503


 


927




503
504


 


928




505
506


 


929




507
508


 


930




507
508


 


931




507
508


 


932




509
510


 


933




509
510


 


934




509
510


 


935




510
511


 


936




511
512


 


937




511
512


 


938




514
515


 


939




515
516


 


940




515
516


 


941




519
520


 


942




519
520


 


943




522
523


 


944




523
524


 


945




523
524


 


946




525
526


 


947




527
528


 


948




529
530


 


949




533
534


 


950




537
538


 


951




539
540


 


952




543
544


 


953




545
546


 


954




545
546


 


955




547
548


 


956




549
550


 


957




553
554


 


958




555
556


 


959




559
560


 


960




559
560


 


961




387













(In the scheme, —Z—NH—S(O)2R16— is equivalent to R1 substituted by R21, or R1 Substituted by alkyl-R22, wherein R21 and R22 are —N(R16)—C(O)—NHR15 and R16 is H, and wherein Z is optionally substituted alkylene-arylene, alkylene-arylene-alkylene, alkylene-heteroarylene, alkylene-heteroarylene-alkylene, alkylene-cycloalkylene, alkylene-cycloalkylene-alkylene, alkylene-heterocycloalkylene, alkylene-heterocycloalkylene-alkylene, arylene, heteroarylene, cycloalkylene or heterocycloalkylene)
Method N
Step 1
Compound N2 (R3=CH3, R4=CH2CH(CH3)2, Z=para-(CH2)C6H4(CH2)—, R16=CH2CH(CH3)2) was prepared from N1 (R3=CH3, R4=CH2CH(CH3)2, Z=para-(CH2)C6H4(CH2)—) following the procedure described in Method K, Step 1.
Method N
Step 2
Compound N3 (R3=CH3, R4−CH2CH(CH3)2, Z=para-(CH2)C6H4(CH2)—, R16=CH2CH(CH3)2) was prepared from N2 (R3=CH3, R4=CH2CH(CH3)2, Z=para-(CH2)C6H4(CH2)—, R16=CH2CH(CH3)2) following the procedure described in Method A, Step 3.
The following compounds were prepared using similar method.
















Obs. 


#
Structure
MW
m/e







962




380
381


 


963




380
381


 


964




394
395


 


965




394
395


 


966




451
452


 


967




484
485


 


968




484
485


 


969




498
499


 


970




498
499
















Method O
Step 1
A solution of indole-6-methanol (400 mg, 2.72 mmol), tert-butyldimethylsilyl chloride (816 mg, 5.41 mmol) and imidazole (740 mg, 10.9 mmol) in CH2Cl2 was stirred at rt. overnight before the solvent was evaporated and residue chromatographed using ethylacetate/hexane to give product O2.
Method O
Step 2
To a solution of O2 (200 mg, 0.77 mmol) in THF (10 mL) at −78° C. was added butyl lithium (1.2 eq). The solution was stirred at −78° C. for 5 min and then warmed to rt. The reaction mixture was cooled to −78° C. and p-toluenesulfonyl chloride was added. The solution was warmed to rt and stirred overnight. The reaction was quenched with a saturated aqueous K2CO3 solution, extracted with ethyl acetate and CH2Cl2. The crude material was purified via flash chromatography using ethylacetate/hexane to afford 360 mg of O3.
Method O
Step 3
A solution butyl lithium (1.2 eq) was added to a solution of O3 (340 mg, 0.829 mmol) in THF (20 mL). The reaction mixture was stirred for 15 min at −78° C. then sulfur dioxide was bubbled through the solution for 15 min. Hexane (100 mL) was added to the reaction mixture. The reaction mixture was evaporated to afford O4 which was used in the next step without further purification.
Method O
Step 4
To a solution of O4 (0.829 mmol) in CH2Cl2 cooled to 0° C. was added N-chlorosuccinimide (220 mg, 1.66 mmol). After 2 h of stirring, the solution was filtered through a Celite plug. The filtrate was concentrated to afford O5.
Method O
Step 5
To a solution of O5 in anhydrous pyridine (3 mL) was added butyl amine (100 μL). The reaction was agitated at rt for 4 d. The reaction mixture was partitioned between 1 N HCl and CH2Cl2. The organic layer was separated and washed with 1 N HCl (3×). The organic solution was dried over Na2SO4, filtered and concentrated. The crude material was purified via flash chromatography using ethylacetate/hexane to yield O6.
Method O
Step 6
To a solution of O6 (70 mg) in THF was added TBAF. The reaction was stirred at rt. before the reaction mixture was chromatographed using ethylacetate/hexane to afforded 50 mg of O7 (95%).
Method O
Step 7
To a solution of O7 (50 mg) in CH2Cl2 (5 mL) was added thionyl chloride (1 mL) the reaction was stirred for 5 min and then evaporated to afford O8.
Method O
Step 8
To a solution of O8 in CH3OH (5 mL) was added sodium azide (50 mg). The solution was stirred at rt overnight and solvent evaporated. The residue was chromatographed using ethylacetate/hexane to afforded O9 after purification.
Method O
Step 9
To a suspension of O9 (70 mg) in CH3OH was added 1 eq HCl (aq) and palladium on carbon. The reaction mixture was hydrogenated at 1 atm for 20 min to yield 90 mg of crude product O10.
Method O
Step 10
A solution of lithium hydroxide (30 mg) in H2O was added to a solution of O10 (40 mg) in CH3OH (3 mL). The reaction was stirred at rt for 2 h and an additional portion of LiOH (40 mg) was added and solution was stirred for 2 more hours. The solvent was evaporated and residue chromatographed using ethylacetate/hexane to afforded O11.




Method P
Step 1
A 300 mL of THF solution of 100 g of P1 (R23=n-Pr) was added to a suspension of 38 g of LAH in 2 L of anhydrous THF at 0 C. The reaction mixture is stirred at r.t. for 1 h before 30 ml of H2O, 90 ml of 15% NaOH was added at 0° C. The mixture was stirred at r.t. for one hour before Na2SO4 (anh) was added, the mixture was filtered, and the solution evaporated to give a product which was dried under vacuo overnight. This product was dissolved in 600 ml of DCM and the solution was added into a solution of oxalyl chloride (37.3 ml) and DMSO (60.8 ml) in 1.4 L of DCM at −78° C. over 40 min before Diisopropylethylamine (299 ml) was added at −78° C. The reaction was allowed to reach −10° C. The reaction was quenched with 1 L H2O at −10° C. and the mixture was extracted with DCM. After removal of solvent, P2 (R23=Pr, 106 g) was obtained. The crude material was used for next step without purification.
Method P
Step 2
To a 1.5 L DOCM solution of P2 (R23=Pr, 106 g) was added p-Boc-aminomethylbenzylamine (1.1 eq) and sodium triacetoxyborohydride (1.1 eq) and the reaction was stirred at r.t. overnight. The reaction was quenched with H2O and content extracted with DCM. After removal of solvents the residue was chromatographed using a silica gel column eluted with 3% MeOH in DCM to give 42.5 g of P3 (R23=Pr).
Method P
Step 3
A 10 ml MeOH solution of P3 (R23=Pr, 110 mg) was hydrogenated using Pd/C (5%, 11 mg) at 1 atm of hydrogen to give product P4 (R23=Pr) after removal of solvent and catalyst.
Method P
Step 4
To a 10 ml DOCM solution of P4 at 0° C. (R23=Pr) was added triphosgene (1.2 eq) and triethylamine (2.4 eq) and the solution was stirred at 0 C for 2 h before the reaction was extracted with DCM/H2O. After removal of the solvent, the residue was chromatographed using a silica gel column eluted with EtOAc/Hexane to give a white solid which was treated with 2N HCl in dioxane for 2 h. After removal of the solvent, compound P5 (R23=Pr) as a white solid was obtained (80 mg).
The following compounds were synthesized using similar methods:








Method Q
Step 1
At room temperature, Q1 (R3=Me; R4=iBu) (1.00 g) and Q8 (n=1, p=2, m=1) (1.24 g) in dichloromethane (30 mL) were stirred for 42 h. This mixture was concentrated in vacuo to give an amber oil which was purified on a column of silica gel (200 mL) eluted with ethylacetate/hexane to give Q2 (n=1, p=2, m=1, R3=Me; R4=iBu), a colorless oil (1.59 g).
Method Q
Step 2
Compound Q3 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu) was prepared from Q2 (n=1, p=2, m=1, R3=Me; R4=iBu) using method similar to method A step 3.
Method Q
Step 3
Compound Q3 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu) (1.37 g) in anhydrous dichloromethane (25 mL) was treated with di-tert-butyl dicarbonate (0.68 g, 1.1 equiv.) and diisopropylethylamine (0.66 mL, 1.1.equiv.). The resulting solution was stirred at room temperature for 20 h before it was diluted with dichloromethane and washed with 1N hydrochloric acid. The dried dichloromethane solution was concentrated in vacuo to give a colorless film (1.32 g) which was purified on a column of silica gel (125 mL) and eluted with hexane:ethyl acetate to give compound Q4 (n=1, p=2, m=1, R2=H, R3=Me; R4=i-Bu) as a white foam (0.74 g).
Method Q
Step 4
Compound Q4 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu) (0.540 g) in absolute EtOH (20 mL) was hydrogenated with 10% Pd/C (0.400 g) at 1 atm for 2 h. The reaction mixture was filtered and the filtrate was concentrated in vacuo to give Q5 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu) as a colorless oil (0.35 g).
Method Q
Step 5
Compound Q5 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu) (0.012 g) and HOBt (0.005 g) dissolved in acetonitrile (0.8 mL) and tetrahydrofuran (0.25 mL) was treated with EDC resin (0.080 g, 3 eq., 1.53 mmol/g) in a microtiter plate well followed by addition of a 1M dichloroethane solution of R15—COOH (40 uL, 1.25 eq.). After the well was capped and shaken for 18 h, the mixture was filtered and the resin washed with acetonitrile (0.5 mL). The combined solution was treated with Trisamine resin (0.050 g, 6 eq., 4.23 mmol/g) and Isocyanate resin (0.067 g, 3 eq., 1.53 mmol/g) for 18 h before the solution was filtered and the solvent was removed in vacuo to give Q6 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu, R15=Me).
Method Q
Step 6
A dichloromethane solution (1.0 mL) of Q6 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu, R16=Me) was mixed with trifluoroacetic acid (1.0 mL) and the solution was shaken for 2 h before it was concentrated. Diethyl ether (0.5 mL) was added and then concentrated in vacuo to give a residue, which was purified on a Prep LCMS unit to give Q7 (=1, p=2, m=1, R2=H, R3=Me; R4=iBu, R15=Me). NMR (CDCl3): δ 8.38, br, 2H; δ 4.56, m, 1H; δ 3.79, m, 1H; δ 3.57, m, 2H; δ 2.99, m, 1H; δ 2.48, m, 1H; δ 2.04, s, 3H; δ 1.95, m, 1H; δ 1.5-1.8, m, 5H; δ 1.5, s, 3H; 1.25, m, 2H; δ 0.95, m, 3H; δ 0.85, m, 3H. ES_LCMS (m/e) 309.17.
The following compounds were prepared using similar methods:













#
Structure
MW
Obs. m/e


















971




308
309


 


972




308
309


 


973




310
311


 


974




322
323


 


975




324
325


 


976




334
335


 


977




336
337


 


978




348
349


 


979




348
349


 


980




0
351


 


981




350
351


 


982




350
351


 


983




360
361


 


984




360
361


 


985




362
363


 


986




362
363


 


987




364
365


 


988




364
365


 


989




364
365


 


990




370
371


 


991




370
371


 


992




376
377


 


993




376
377


 


994




376
377


 


995




378
379


 


996




378
379


 


997




378
379


 


998




378
379


 


999




379
380


 


1000




384
385


 


1001




384
385


 


1002




384
385


 


1003




386
387


 


1004




388
389


 


1005




389
390


 


1006




390
391


 


1007




390
391


 


1008




390
391


 


1009




390
391


 


1010




390
391


 


1011




390
391


 


1012




390
391


 


1013




390
391


 


1014




390
391


 


1015




392
393


 


1016




392
393


 


1017




392
393


 


1018




394
395


 


1019




398
399


 


1020




398
399


 


1021




398
399


 


1022




398
399


 


1023




398
399


 


1024




400
401


 


1025




400
401


 


1026




400
401


 


1027




400
401


 


1028




400
401


 


1029




400
401


 


1030




400
401


 


1031




400
401


 


1032




402
403


 


1033




402
403


 


1034




404
405


 


1035




404
405


 


1036




404
405


 


1037




404
405


 


1038




404
405


 


1039




404
405


 


1040




404
405


 


1041




404
405


 


1042




409
410


 


1043




410
411


 


1044




0
411


 


1045




410
411


 


1046




412
413


 


1047




412
413


 


1048




412
413


 


1049




414
415


 


1050




414
415


 


1051




414
415


 


1052




414
415


 


1053




414
415


 


1054




414
415


 


1055




414
415


 


1056




416
417


 


1057




416
417


 


1058




417
418


 


1059




418
419


 


1060




418
419


 


1061




418
419


 


1062




418
419


 


1063




418
419


 


1064




420
421


 


1065




423
424


 


1066




424
425


 


1067




424
425


 


1068




426
427


 


1069




426
427


 


1070




426
427


 


1071




426
427


 


1072




426
427


 


1073




427
428


 


1074




428
429


 


1075




428
429


 


1076




428
429


 


1077




428
429


 


1078




428
429


 


1079




430
431


 


1080




430
431


 


1081




430
431


 


1082




432
433


 


1083




432
433


 


1084




432
433


 


1085




432
433


 


1086




432
433


 


1087




432
433


 


1088




438
439


 


1089




438
439


 


1090




438
439


 


1091




438
439


 


1092




438
439


 


1093




440
441


 


1094




440
441


 


1095




440
441


 


1096




440
441


 


1097




442
443


 


1098




442
443


 


1099




442
443


 


1100




442
443


 


1101




442
443


 


1102




444
445


 


1103




444
445


 


1104




444
445


 


1105




446
447


 


1106




446
447


 


1107




446
447


 


1108




449
450


 


1109




451
452


 


1110




452
453


 


1111




452
453


 


1112




452
453


 


1113




456
457


 


1114




456
457


 


1115




456
457


 


1116




458
459


 


1117




460
461


 


1118




460
461


 


1119




460
461


 


1120




460
461


 


1121




462
463


 


1122




462
463


 


1123




462
463


 


1124




462
463


 


1125




462
463


 


1126




464
465


 


1127




466
467


 


1128




466
467


 


1129




470
471


 


1130




472
473


 


1131




474
475


 


1132




474
475


 


1133




476
477


 


1134




476
477


 


1135




478
479


 


1136




482
483


 


1137




482
483


 


1138




482
483


 


1139




488
489


 


1140




490
491


 


1141




500
501


 


1142




502
503


 


1143




502
503


 


1144




504
505


 


1145




504
505


 


1146




504
505


 


1147




511
512


 


1148




512
513


 


1149




512
513


 


1150




520
521


 


1151




520
521


 


1152




520
521


 


1153




520
521


 


1154




522
523


 


1155




522
523


 


1156




536
537


 


1157




536
537


 


1158




536
537


 


1159




538
539


 


1160




538
539


 


1161




540
541


 


1162




541
542


 


1163




542
543


 


1164




546
547


 


1165




546
547


 


1166




550
551


 


1167




550
551


 


1168




569
570


 


1169




582
583


 


1170




582
583


 


1171




584
585


 


1172




584
585


 


1173




594
595


 


1174




596
597


 


1175




596
597













Method R
Step 1
A solution of R1 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu) (0.010 g) in acetonitrile (0.85 mL) and dichloroethane (0.15 mL) was put into a microtiter plate well followed by addition of 0.12 ml of 0.5M phenylisocyanate solution in dichloroethane. The well was sealed and the plate shaken for 20 h before the mixture was filtered and the solid washed with acetonitrile (0.5 ml). The combined solution was treated with Trisamine resin (0.050 g, 6 eq., 4.23 mmol/g) and Isocyanate resin (0.067 g, 3 eq., 1.53 mmol/g) and the mixture was shaken for 18 h. The mixture was filtered and the solution was evaporated to give R2 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu and R15=Ph).
Method R
Step 2
Procedure similar to Method Q, step 6 was used for the transformation of R2 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu and R15=Ph) to R3 (n−1, p=2, m=1, R2=H, R3=Me; R4=iBu and R15=Ph).
The following compounds were prepared using similar methods:













#
Structure
MW
Obs. m/e







1176




309
310


 


1177




309
310


 


1178




311
312


 


1179




325
326


 


1180




337
338


 


1181




346
347


 


1182




351
352


 


1183




351
352


 


1184




351
352


 


1185




365
366


 


1186




365
366


 


1187




365
366


 


1188




367
368


 


1189




377
378


 


1190




381
382


 


1191




385
386


 


1192




391
392


 


1193




393
394


 


1194




395
396


 


1195




399
400


 


1196




399
400


 


1197




399
400


 


1198




399
400


 


1199




399
400


 


1200




401
402


 


1201




403
404


 


1202




403
404


 


1203




407
408


 


1204




407
408


 


1205




410
411


 


1206




410
411


 


1207




413
414


 


1208




413
414


 


1209




415
416


 


1210




415
416


 


1211




415
416


 


1212




415
416


 


1213




417
418


 


1214




419
420


 


1215




419
420


 


1216




419
420


 


1217




421
422


 


1218




421
422


 


1219




425
426


 


1220




427
428


 


1221




427
428


 


1222




429
430


 


1223




429
430


 


1224




431
432


 


1225




431
432


 


1226




433
434


 


1227




435
436


 


1228




441
442


 


1229




441
442


 


1230




441
442


 


1231




445
446


 


1232




449
450


 


1233




453
454


 


1234




453
454


 


1235




453
454


 


1236




453
454


 


1237




453
454


 


1238




455
456


 


1239




455
456


 


1240




457
458


 


1241




461
462


 


1242




463
464


 


1243




467
468


 


1244




467
468


 


1245




471
472


 


1246




475
476


 


1247




477
478


 


1248




477
478


 


1249




487
488


 


1250




487
488


 


1251




487
488


 


1252




491
492













Method S
Step 1
A solution of S1 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu) (0.010 g) in acetonitrile (0.85 mL) and dichloroethane (0.15 mL) was put into a microtiter plate followed by addition of DIPEA-MP resin (0.030 g, 4 eq) and phenylsulfonyl chloride in dioxane (1M, 45 μL, 0.045 mmol. The well was capped and shaken for 18 h before it was filtered and residue washed with acetonitrile (0.5 mL). The combined solution was treated with Trisamine resin (0.040 g, 6 eq., 4.23 mmol/g) and Isocyanate resin (0.060 g, 3 equiv., 1.53 mmol/g) and shaken for 18 h before the mixture was filtered and the solvent removed to give S2 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu and R15=Ph).
Method S
Step 2
Procedure similar to Method Q, step 6 was used for the transformation of S2 to S3 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu and R15=Ph).
The following compounds were prepared using similar methods:













#
Structure
MW
Obs. m/e







1253




344
345


 


1254




344
345


 


1255




358
359


 


1256




358
359


 


1257




360
361


 


1258




372
373


 


1259




372
373


 


1260




386
387


 


1261




406
407


 


1262




406
407


 


1263




406
407


 


1264




412
413


 


1265




416
417


 


1266




420
421


 


1267




420
421


 


1268




420
421


 


1269




420
421


 


1270




420
421


 


1271




420
421


 


1272




424
425


 


1273




424
425


 


1274




424
425


 


1275




431
432


 


1276




432
433


 


1277




434
435


 


1278




434
435


 


1279




436
437


 


1280




436
437


 


1281




438
439


 


1282




440
441


 


1283




440
441


 


1284




440
441


 


1285




442
443


 


1286




442
443


 


1287




442
443


 


1288




442
443


 


1289




442
443


 


1290




446
447


 


1291




448
449


 


1292




448
449


 


1293




448
449


 


1294




454
455


 


1295




456
457


 


1296




456
457


 


1297




458
459


 


1298




458
459


 


1299




458
459


 


1300




462
463


 


1301




464
465


 


1302




466
467


 


1303




466
467


 


1304




466
467


 


1305




466
467


 


1306




470
471


 


1307




474
475


 


1308




474
475


 


1309




474
475


 


1310




474
475


 


1311




474
475


 


1312




474
475


 


1313




474
475


 


1314




474
475


 


1315




474
475


 


1316




474
475


 


1317




476
477


 


1318




480
481


 


1319




482
483


 


1320




484
485


 


1321




484
485


 


1322




488
489


 


1323




490
491


 


1324




490
491


 


1325




492
493


 


1326




498
499


 


1327




508
509


 


1328




508
509


 


1329




508
509


 


1330




508
509


 


1331




542
543


 


1332




557
558













Method T
Step 1
To a microtiter plate well containing 1 ml solution of T1 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu) in DCM (0.010 g) and R15C(O)R16 (5 equiv, R15=H, R16=Ph) was added Sodium cyanoborohydride in dichloroethane (14.3 mg/mL, 2 equiv.). The well was capped and shaken for 20 h before MP-TsOH Resin (100 mg, 1.29 mmol/g) was added to the well followed by additional MP-TsOH resin (50 mg) after 2 h. After the mixture was shaken for another 1 h, the mixture was filtered and the resin washed with dichloroethane (1 mL) (3×), then MeOH (1 mL) (2×). The resin was treated with 7N ammonia in MeOH (1 mL) for 30 min (2×) followed by filtration and evaporation of solvent to give T2 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu and R15=Ph and R16=H).
Method T
Step 2
Procedure similar to Method Q, step 6 was used for the transformation of T2 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu and R15=Ph and R16=H) to T3 (n=1, p=2, m=1, R2=H, R3=Me; R4=iBu and R15=Ph and R16=H).
The following compounds were prepared using similar methods:
















Obs. 


#
Structure
MW
m/e







1333




348
349


 


1334




350
351


 


1335




350
351


 


1336




356
357


 


1337




362
363


 


1338




370
371


 


1339




384
385


 


1340




384
385


 


1341




400
401


 


1342




446
447


 


1343




448
449













Alternatively, similar synthetic method can be used for the generation of other types of compounds. i.e.





In a microwave vial was charged U1 (R2=H; R3=i-Bu, R4=Me) (0.025 g) in toluene (4 mL), potassium carbonate (0.035 g), Pd(dppf)Cl2 (0.020 g). water (0.02 mL) and R21B(OH)2 (R21=m-Methoxyphenyl) (3 eq.) were placed. The vial was placed in a microwave for 10 min. at 150° C. The reaction mixture was diluted with dichloromethane and extracted with 2.5N NaOH. The dried (MgSO4) dichloromethane solution was concentrated in vacuo to give a brown residue which was purified via a RP Prep LCMS system to give product U2 (R2=H; R3=iBu: R4=Me; R21=m-methoxyphenyl).
The following compounds were prepared using similar methods:













#
Structure
MW
Obs. m/e







1344




279
280


 


1345




285
286


 


1346




293
294


 


1347




299
300


 


1348




299
300


 


1349




304
305


 


1350




309
310


 


1351




313
314


 


1352




318
319


 


1353




323
324


 


1354




323
324


 


1355




323
324


 


1356




329
330


 


1357




335
336


 


1358




335
336


 


1359




337
338


 


1360




343
344


 


1361




347
348


 


1362




347
348


 


1363




347
348


 


1364




347
348


 


1365




347
348


 


1366




349
350


 


1367




349
350


 


1368




350
351


 


1369




351
352


 


1370




352
353


 


1371




357
358


 


1372




359
360


 


1373




360
361


 


1374




360
361


 


1375




360
361


 


1376




360
361


 


1377




360
361


 


1378




360
361


 


1379




365
366


 


1380




365
366


 


1381




365
366


 


1382




365
366


 


1383




366
367


 


1384




371
372


 


1385




371
372


 


1386




371
372


 


1387




372
373


 


1388




372
373


 


1389




375
376


 


1390




377
378


 


1391




377
378


 


1392




377
378


 


1393




377
378


 


1394




379
380


 


1395




379
380


 


1396




380
381


 


1397




381
382


 


1398




383
384


 


1399




384
385


 


1400




385
386


 


1401




385
386


 


1402




386
387


 


1403




387
388


 


1404




389
390


 


1405




389
390


 


1406




392
393


 


1407




395
396


 


1408




403
404


 


1409




403
404


 


1410




405
406


 


1411




406
407


 


1412




413
414


 


1413




419
420


 


1414




497
498


 


1415




398
TBD


 


1416




399
TBD













Method V
Step 1
Compound V1 (R3=R4=Me) (14.76 mmole), EDCl (14.76 mmole), HOAt (14.76 mmole), and DIEA (14.76 mmole) were mixed with 36 ml DCM. This mixture was stirred at RT for 15 min before 3-chlorobenzylamine was added. After the reaction solution was stirred at RT overnight, it was washed with sodium carbonate (3×), water, 1N HCl (4×), and aq sodium bicarbonate and dried over anhydrous sodium sulfate. The solvent was evaporated and the residue was purified on flash column to give the amide product V2 (R1=3-chlorobenzyl; R3=R4=Me).
Method V, step 2
Compound V2 (R1=3-chlorobenzyl; R3=R4=Me) (8.33 mmole) was dissolved in 35 ml anhydrous DCM, and cooled to 0-5° C. Thiophosgene (9.16 mmole) in 10 ml DCM was added dropwise under N2 followed by addition of DIEA (11.96 mmole). The solution was stirred in ice bath for 0.5 h before the reaction mixture was washed with saturated sodium bicarbonate (3×), brine, and dried over anhydrous sodium sulfate. The solvent was evaporated and residue purified on flash column using ethylacetate/hexane to give the thiohydantoin V3 (R1=3-chlorobenzyl; R3=R4=Me).
Method V
step 3
The thiohydantoin V3 (R1=3-chlorobenzyl; R3=R4=Me) was treated with t-butyl hydroperoxide and ammonium hydroxide in MeOH at RT for 48 h to give compound V4 (R1=3-chlorobenzyl; R2=H; R3=R4=Me).
The following compounds were prepared using similar method.


















Obs. 



#
Structure
MW
m/e







 
1417




251
252


 



1418




265
266


 



1419




293
294


 



1420




307
308


 



1421




357
358


 



1422




371
372













Compound W1 obtained using method A (n=1, R2=m-Cl-Bn, R3=Me) was hydrolyzed to W2 (n=1, R2=m-Cl-Bn, R3=Me) using two equivalent of LiOH in MeOH.
The following compounds were synthesized in similar fashion:
















Obs. 


#
Structure
MW
m/e







1423




295
296


 


1424




311
312


 


1425




325
326


 


1426




411
412


 


1427




425
426













(In the scheme, —Z—NH—C(O)—N(R16)(R17)— is equivalent to R1 substituted by R21, or R1 Substituted by alkyl-R22, wherein R21 and R22 are —NH—C(O)—N(R16)(R17) and R15 is H, and wherein Z is optionally substituted alkylene-arylene, alkylene-arylene-alkylene, alkylene-heteroarylene, alkylene-heteroarylene-alkylene, alkylene-cycloalkylene, alkylene-cycloalkylene-alkylene, alkylene-heterocycloalkylene, alkylene-heterocycloalkylene-alkylene, arylene, heteroarylene, cycloalkylene or heterocycloalkylene)
Method X
Step 1
To a mixture of the amine X1 obtained using method L (R3=Me; R4=i-Bu; Z=para-(CH2)C6H4(CH2)—) (10 mg) in DCM and sat. NaHCO3 (1.1 by volume) was added triphosgene (0.33 eq) at r.t. The solution was stirred vigorously for 40 minutes before the organic layer was separated and dried over anhydrous Na2SO4. The organic solution was evaporated to give compound X2 (R3=Me; R4=i-Bu; Z=para-(CH2)C6H4(CH2)—).
Method X
Step 2
Compound X3 (R15=H; R16=cyclopropylmethyl; R3=Me; R4=iBu; Z=para-(CH2)C6H4(CH2)—) was prepared from X2 (R3=Me; R4=i-Bu; Z=para-(CH2)C6H4(CH2)—) using method similar to method M, step 1.
Method X
Step 3
Compound X4 (R16=H; R17=cyclopropylmethyl; R2=H; R3=Me; R4=iBu; Z=para-(CH2)C6H4(CH2)—) was prepared from X3 (R16=H; R17=cyclopropylmethyl; R2H; R3=Me; R4=iBu; Z=para-(CH2)C6H4(CH2)—) using method similar to method A Step 3. NMR (CD3OD): δ 7.25, s, 4H; δ 4.8, m, 2H; δ 4.25, s, 2H; δ 2.9, m, 2H; δ 1.68, m, 2H; δ 1.44, m, 1H; δ 1.36, s, 3H; δ 0.9, m, 1H; δ 0.82, m, 3H; δ 0.66, m, 3H; δ 0.4, m, 2H; δ 0.12, m, 2H. ES_LCMS (m/e) 386.1.
The following compounds were prepared using a similar method.
















Obs.


#
Structure
MW
m/e







1428




385
386


 


1429




401
402


 


1430




401
402


 


1431




415
416


 


1432




427
428


 


1433




435
436


 


1434




435
436


 


1435




443
444


 


1436




449
450


 


1437




463
464


 


1438




471
472


 


1439




485
486


 


1440




496
497


 


1441




504
505


 


1442




513
514


 


1443




518
519


 


1444




518
519


 


1445




524
525


 


1446




524
525


 


1447




526
527


 


1448




532
533


 


1449




533
534


 


1450




537
538


 


1451




537
538


 


1452




545
546


 


1453




559
560


 


1454




570
571


 


1455




572
573


 


1456




598
599













(In the scheme,




is equivalent to R1 substituted by R21 or R1 Substituted by alkyl-R22, wherein R21 and R22 are —N(R15)—C(O)—N(R16)(R17) and R15 and R16 form a ring as defined above, and wherein Z is optionally substituted alkylene-arylene, alkylene-arylene-alkylene, alkylene-heteroarylene, alkylene-heteroarylene-alkylene, alkylene-cycloalkylene, alkylene-cycloalkylene-alkylene, alkylene-heterocycloalkylene, alkylene-heterocycloalkylene-alkylene, arylene, heteroarylene, cycloalkylene or heterocycloalkylene)

Method Y
Step 1
The reaction mixture of compound Y1 obtained from Method L (R3=Me; R4=i-Bu; Z=para-(CH2)C6H4(CH2)—) (0.1639 mmole), Y2 (R23=H; R23=Pr) (0.1967 mmole), PS-EDC resin (0.4917 mmole) and HOBT (0.2459 mmole) in 3.5 ml of mixture of THF, MeCN and DMF (1:1:0.3) was shaken overnight at RT before 6 eq of PS-trisamine resin 3 eq of PS-isocyanate resin were added. After 6 hrs the reaction mixture was filtered and the resin was washed with THF, DCM and MeOH. The combined filtrate was evaporated and the crude was treated with 40% TFA in DCM for 40 min before the solvent was evaporated and residue purified on RP HPLC system to give product Y3 (R3=Me; R4=i-Bu; Z=para-(CH2)C6H4(CH2)—, R23=H; R23=Pr).
Method Y
Step 2
The reaction solution of Y3 (R3=Me; R4=i-Bu; Z=para-(CH2)C6H4(CH2)—, R23=H; R23=Pr) (0.030 mmole), carbonyl diimidazole (0.032 mmole), and DIEA (0.09 mmole) in 0.5 ml DCM was shaken over weekend at RT. The crude was then purified on reverse column to give the thiohydantoin product which was converted into Y4 (R2=H; R3=Me; R4=iBu; Z=para-(CH2)C6H4(CH2)—, R23=H; R23=Pr).
The following compounds were prepared using similar method.
















Obs. 


#
Structure
MW
m/e







1457




413
414


 


1458




413
414


 


1459




427
428













(In the scheme, —Z—NH—C(O)—N(R16)(R17)— is equivalent to R1 substituted by R21, or R1 Substituted by alkyl-R22, wherein R21 and R22 are —N(R15)—C(O)—N(R16)(R17) and R15 is H, and wherein Z is optionally substituted alkylene-arylene, alkylene-arylene-alkylene, alkylene-heteroarylene, alkylene-heteroarylene-alkylene, alkylene-cycloalkylene, alkylene-cycloalkylene-alkylene, alkylene-heterocycloalkylene, alkylene-heterocycloalkylene-alkylene, arylene, heteroarylene, cycloalkylene or heterocycloalkylene)
Method Z
Step 1
To the solution of the PhoximeTM resin (1.23 mmol/g) in DCM was added the amine Z1 obtained from method L (R3=Me; R4=iBu; Z=para-(CH2)C6H4(CH2)—) (2 eq). The mixture was shaken overnight before the resin was filtered and washed with DCM, MeOH, THF (3 cycles), then DCM (×2), dried in vacuum to get resin Z2 (R3=Me; R4=iBu; Z=para-(CH2)C6H4(CH2)—).
Method Z
Step 2
To the resin Z2 (R3=Me; R4=iBu; Z=para-(CH2)C6H4(CH2)—), swelled in DCM, in toluene was added N-methylbenzylamine (4 eq). The mixture was heated at 80-90° C. overnight before MP-TSOH resin (1.3 mmol/g, 12 eq) was added. The mixture was shaken for 1.5 hours, the solution was filtered and the resin washed with DCM and MeOH. The combined organic solution was concentrated in vacuo to get Z3 (R3=Me; R4=iBu; Z=para-(CH2)C6H4(CH2)—; R16=Me; R17=Bn).
Method Z
Step 3
Compound Z4 (R3=Me; R4=iBu; Z=para-(CH2)C6H4(CH2)—; R16=Me; R17=Bn) was generated from Z3 (R3=Me; R4—=iBu; Z=para-(CH2)C6H4(CH2)—; R16=Me; R17=Bn) using method similar to Method A step 3.
The following compounds were prepared using similar method.
















Obs.


#
Structure
MW
m/e







1460




457
458


 


1461




469
470


 


1462




471
472


 


1463




471
472


 


1464




483
484


 


1465




485
486


 


1466




485
486


 


1467




495
496


 


1468




499
500


 


1469




501
502


 


1470




507
508


 


1471




509
510


 


1472




517
518


 


1473




517
518


 


1474




531
532


 


1475




533
534


 


1476




533
534


 


1477




538
539


 


1478




545
546


 


1479




547
548


 


1480




547
548


 


1481




547
548


 


1482




551
552


 


1483




568
569


 


1484




571
572


 


1485




593
594


 


1486




596
597


 


1487




607
608


 


1488




364
365


 


1489




377
377


 


1490




513
514













8,11-Dichloro-6,11-dihydro-5H-benzo[5,6]cyclohepta[1,2-b]pyridine (AA2) (18 mg) was reacted with AA1, obtained from method Q, and diisopropylethylamine (14 uL) in acetonitrile (2.5 mL). The resulting mixture was heated at 65° C. for 18 h. The reaction mixture was placed on a preparative silica gel plate and eluted with hexane:ethyl acetate 3:1 to give the desired product which was treated with 40% TFA. Evaporation of the solvent followed by purification afforded compound AA3.
The following compounds were prepared by similar methods:
















Obs. 


#
Structure
MW
m/e







187




491
492


 


188




493
494













Method AB
Step 1
To a solution of (R)-(+)-2-methyl-2-propane sulfinamide (1.0 g, 8.3 mmol, 1 eq) and AB1 (R6=Ph, R7=n-Bu) (3 mL, 9.1 mmol, 1.1 eq) in anhydrous THF (30 mL) at room temperature was added Ti(OEt)4 (7 mL, 17 mmol, 2 eq). The mixture was heated at 70° C. for 24 h. After cooling to room temperature, the mixture was poured into 30 mL of brine under vigorous stirring. The resulting suspension was filtered through a pad of Celite and the solid was washed with EtOAc (2×20 mL). The filtrate was washed with brine (30 mL), dried (Na2SO4), and concentrated in vacuo. The residue was chromatographed on silica by eluting with hexane/Et2O (5:1) to give 1.9 g (85%) of (R)-2-methyl-N-(1-phenylpentylidene)propane-2-sulfinamide. 1H NMR (CDCl3, 300 MHz): δ 7.91 (m, 2H), 7.52-7.37 (m, 3H), 3.27 (m, 1H), 3.15 (m, 1H), 1.73-1.61 (m, 2H), 1.47-1.38 (m, 2H), 1.31 (s, 9H), 0.95 (m, 3H). MS (ESI): MH+=265.9. HPLC tR=7.24, 7.58 min (E/Z=5.5:1).
To a solution of methyl acetate (0.6 mL, 6.9 mmol, 2 eq) in THF (5 mL), LDA (2M in heptane/THF, 3.4 mL, 6.9 mmol, 2 eq) was added dropwise via a syringe at −78° C. After stirring at −78° C. for 30 min, a solution of ClTi(Oi-Pr)3 (1.8 mL, 7.6 mmol, 2.2 eq) in THF (5 mL) was added dropwise. After stirring for another 30 min, a solution of (R)-2-methyl-N-(1-phenylpentylidene)propane-2-sulfinamide (0.9 g, 3.4 mmol, 1 eq) in THF (2 mL) was added dropwise via a syringe. The mixture was stirred at −78° C. for 3 h and TLC showed no starting material left. A saturated aqueous solution of NH4Cl (10 eq) was added and the suspension was warmed to room temperature. The mixture was diluted with H2O (50 mL) and stirred for 10 min. The mixture was then partitioned between H2O (50 mL) and EtOAc (50 mL). The organic layer was separated and the aqueous layer was extracted with EtOAc (3×50 mL). The combined organic layers were washed with brine, dried (MgSO4) and concentrated to give 1.1 g of a brown oil. Chromatography on silica gel using 50% EtOAc/hexanes as eluent gave 0.8 g (76%) of methyl 3-((R)-2-methylpropan-2-ylsulfinamido)-3-phenylheptanoate as a yellow oil. 1H NMR (CDCl3, 300 MHz): 7.15-7.07 (m, 5H), 3.35 (s, 1H), 3.19 (dd, J=16, 5.6 Hz, 1H), 3.01 (dd, J=15.8, 5.5 Hz, 1H), 2.07 (m, 2H), 1.71 (m, 2H), 1.35-1.26 (m, 4H), 1.17 (s, 9H), 0.89 (m, 3H). MS (ESI): MH+=339.9. HPLC tR=7.50, 7.6 min (E/Z=1.5:1)
To a solution of methyl 3-((R)-2-methylpropan-2-ylsulfinamido)-3-phenylheptanoate (0.4 g, 1.1 mmol) in 12 mL of MeOH was added 16 mL of 4N HCl/dioxane. After stirring for 30 min, the volatiles were removed in vacuo. The residue was re-dissolved in MeOH (6 mL), stirred for 5 min, and evaporated again to afford 0.30 g (97%) of AB2 (R6=Ph, R7=n-Bu) as a yellow solid. 1H NMR (CDCl3, 300 MHz): 9.01 (br s, 2H), 7.37-7.12 (m, 5H), 3.64 (m, 1H), 3.54 (s, 3H), 3.31 (m, 1H), 2.09 (m, 2H), 1.8 (m, 2H), 1.1 (m, 4H), 1.07 (s, 9H), 0.7 (m, 3H). MS (ESI): MH+=235.9. HPLC tR=4.72 min.
Method AB
Step 2
Treatment of compound AB2 (R6=Ph, R7=n-butyl) with thiophosgene in CH2Cl2 in the presence of aqueous NaHCO3 at 0° C. generates isothiocyanate AB3 (R6=Ph, R7=n-butyl) which was converted into final product using method similar to Method A Step 2 and Method A Step 3 to give product AB5 (R6=Ph, R7=n-butyl, R1=Me). 1H NMR (CDCl3, 300 MHz): δ 10.4 (br s, 1H), 7.25-7.11 (m, 5H), 3.23 (dd, J=16, 5.6 Hz, 1H), 3.03 (s, 3H), 2.8 (dd, J=15.8, 5.5 Hz, 1H), 2.49 (s, 1H), 1.78 (m, 2H), 1.1-1.0 (m, 4H), 0.99 (m, 3H), MS (ESI): MH+=260.2. HPLC tR=5.09 min.
The following compounds were synthesized using similar methods:
















Obs.


#
Structure
MW
m/e







189




239
240


 


190




253
254


 


191




259
260


 


192




333
334


 


193




333
334


 


194




349
350


 


195




443
444


 


196




463
464


 


197




537
538


 


198




537
538


 


199




295
296


 


200




295
296













The synthesis was adapted from a procedure by Hull, R. et al, J. Chem. Soc. 1963, 6028-6033. Thus, to a solution of AC2 (R1=Benzyl) (0.72 g, 5.9 mmol) in AC1 (R4=Me, R3=Me) (1.4 mL) was added a 50% aqueous solution of cyanamide (0.31 mL, 8.0 mmol). The reaction was heated with stirring at reflux ( ̃40° C.) for 0.5 h, then cooled to 25° C. and stirred for an additional 16 h. The volatiles were removed in vacuo and the residue was partitioned between ether and H2O. The organic layer was dried over Na2SO4, filtered and the volatiles were removed in vacuo. The residue was purified by column chromatography using 5-10% CH3OH/CH2Cl2 as eluent followed by reverse phase preparative HPLC to give 0.15 g (8.0%) of AC3 (R1=benzyl, R4=Me and R3=Me) as a white solid. 1H NMR (CH3OH, 300 MHz): δ7.35-7.33 (m, 5H), 4.71 (s, 2H), 1.46 (s, 6H); 13C NMR (CDCl3, 75 MHz) δ 157.8, 135.6, 129.1, 128.5, 127.9, 104.2, 59.6, 28.8. MS (ESI) m/e 206.1 (M+H)+.


















Obs. 



#
Structure
MW
m/e







 
201




205
206













Method AD
Step 1
AD2 (R3=Ph, R4=tButyl) was prepared from AD1 using method similar to Method AB, step 2.
Method AD
Step 2
The synthesis was adapted from a procedure by Hussein, A. Q. et al, Chem. Ber. 1979, 112, 1948-1955. Thus, to a mixture of AD2 (R3=Ph, R4=tert-Butyl) (0.56 g, 2.7 mmol) and boiling chips in CCl4 (25 mL) was added N-bromosuccinimide (0.49 g, 2.7 mmol). The mixture was irradiated with a 200 watt light source for 1 h. The reaction was cooled, the solid filtered off and the volatiles were removed in vacuo. Chromatography on silica gel by eluting with 5% EtOAc/hexane gave 0.57 g (73%) of 1-(1-bromo-1-isothiocyanato-2,2-dimethylpropyl)benzene as a beige powder. 1H NMR (CDCl3, 300 MHz): δ 7.63-7.61 (m, 2H), 7.37-7.26 (m, 3H), 1.17 (s, 9H); 13C NMR (CDCl3, 75 MHz): δ 139.1, 129.0, 128.9, 128.6, 127.5, 91.2, 45.6, 26.6. MS (ESI) m/e 284.9 (M+H)+.
To a solution of 1-(1-bromo-1-isothiocyanato-2,2-dimethylpropyl)benzene (0.13 g, 0.47 mmol) and the hydrochloride salt of N-methylhydroxylamine (0.047 g, 0.57 mmol) in THF (3 mL) was added triethylamine (0.18 mL, 1.32 mmol). The mixture was stirred at 25° C. for 16 h, filtered and the volatiles were removed in vacuo. The residue was purified by column chromatography using CH3OH/CH2Cl2 as eluent to give 0.050 g (42%) of AD3 (R3=Ph, R4=tert-Butyl) as a glassy solid. 1H NMR (CDCl3, 300 MHz): δ 7.35-7.26 (m, 5H), 3.38 (s, 3H), 1.0 (s, 9H); MS (ESI) m/e 251.1 (M+H)+.
Method AD
Step 3
To a solution of AD3 (R3=Ph, R4=tert-Butyl) (0.065 g, 0.26 mmol) in CH3OH (5 mL) at 0° C. was added a solution of aqueous ammonia (2 mL) followed by a 70% aqueous solution of t-butylhydroperoxide (2 mL). The reaction was allowed to warm to 25° C. and stirred for 16 h. The volatiles were removed and the residue was purified by reverse phase HPLC to give 2.0 mg (2.2%) of AD4 (R3=Ph, R4=tert-Butyl) as a colorless oil. 1H NMR (CDCl3, 300 MHz) δ 7.47-7.43 (m, 2H), 7.39-7.35 (m, 3H), 3.23 (s, 3H), 1.0 (s, 9H); MS (ESI) m/e 234.2 (M+H)+.
The following compounds were synthesized using similar methods:


















Obs. 



#
Structure
MW
m/e







 
202




213
214


 



203




233
234


 



204




309
310













Method AE
Step 1
TBDMS-Cl (5.3 g, 35.19 mmole) and imidazole (2.4 g, 35.19 mmole) were added to a suspension of H2 (R1=Me, R3=cyclohexylmethyl) (8.2 g, 31.99 mmole) in 220 ml DCM. The reaction mixture was stirred at room temperature overnight. The reaction mixture was filtered, and the filtrate was diluted with 1200 ml EtOAc. The organic phase was washed with saturated NaHCO3 3× and brine 3×, and dried over anhydrous Na2SO4 to give 12 g of AE2 (R1=Me, R3=cyclohexylmethyl), which was used for next step without further purification.
Method AE
Step 2
AE2 (R1=Me, R3=cyclohexylmethyl; 12 grams crude) was converted to iminohydantoin using conditions similar to Method A Step 3, which was subsequently treated with 75% TFA in DCM at room temperature for 24 hrs. The solvent was evaporated in vacuo to give 13.6 g of a product that was reacted with Boc anhydride to give 5.8 g AE3 (R1=Me, R3=cyclohexylmethyl) after column purification.
Method AE
Step 3
AE4 (R1=Me, R3=cyclohexylmethyl) (8.2 g) was obtained from AE3 (5.8 g) according to the step 4 of the method H.
Method AE
Step 4
To a solution of AE4 (R1=Me, R3=cyclohexylmethyl) (3.95 g, 8.38 mmol) in anhydrous THF (98 mL) was added diisopropylethylamine (7 mL, 40 mmol). The reaction was stirred under N2 (gas) at room temperature. After 5.5 h, the reaction was concentrated and the crude material was purified via flash chromatography eluting with a gradient of 0 to 75% ethyl acetate in hexane to afford AE5 (R1=Me, R3=cyclohexylmethyl) (2.48 g, 92%).
Method AE
Step 4
To a solution of R15OH(R15=cyclobutyl) (10 μl) and HBF4 (1 equiv) in anhydrous methylene chloride (0.5 mL) was added a solution of AE5 (R1=Me, R3=cyclohexylmethyl) (20 mg, 0.062 mmol) in methylene chloride (0.5 mL). The reaction was agitated overnight at rt. Trifluoroacetic acid (1 mL) was added to the reaction mixture and the solution was agitated for 1 h at rt. The reaction was concentrated and the crude material was purified via reverse phase preparative HPLC/MS eluting with a 7 min gradient of 5 to 95% CH3CN in H2O with 0.1% formic acid to afford AE5 (R1=Me, R3=cyclohexylmethyl, R15=cyclobutyl).
The following compounds were synthesized using similar method:
















Obs.


#
Structure
MW
m/e







205




267
268


 


206




293
294


 


207




295
296


 


208




295
296


 


209




295
296


 


210




295
296


 


211




305
306


 


212




307
308


 


213




307
308


 


214




309
310


 


215




309
310


 


216




309
310


 


217




309
310


 


218




321
322


 


219




321
322


 


220




321
322


 


221




322
323


 


222




329
330


 


223




333
334


 


224




335
336


 


225




335
336


 


226




335
336


 


227




335
336


 


228




335
336


 


229




335
336


 


230




335
336


 


231




335
336


 


232




335
336


 


233




337
338


 


234




337
338


 


235




349
350


 


236




349
350


 


237




349
350


 


238




349
350


 


239




353
354


 


240




361
362


 


241




363
364


 


242




363
364


 


243




363
364


 


244




389
390


 


245




321
NA













To a solution of tBuOK (9.5 mg, 0.0848 mmole) in 0.5 ml anhydrous THF was added ArOH (Ar=m-Chlorophenyl) (13 μl, 0.1273 mmole) in 0.5 ml anhydrous THF followed by addition of AE4 (R1=Me, R3=cyclohexylmethyl) (20 mg, 0.0424 mmole) in 0.5 ml anhydrous THF. The reaction mixture was stirred at room temperature for 2 days before it was diluted with 1 ml MeCN, treated with 100 mg MP-TsOH resin and 100 mg Amberlyst A26 resin. The resin was removed by filtration and the filtrate was evaporated down to give a product that was treated with 50% TFA for 1 hr. After evaporation of TFA in vacuo, the residue was dissolved in 2 ml MeCN, and treated with 100 mg MP-TsOH resin. The resin was washed thoroughly with THF, MeCN and MeOH, and then treated with 2M NH3 in MeoH to give AF2 (R1=Me, R3=cyclohexylmethyl and R15=3-chlorophenyl).
The following compounds were synthesized using similar method:
















Obs.


#
Structure
MW
m/e







246




316
317


 


247




316
317


 


248




316
317


 


249




329
330


 


250




329
330


 


251




329
330


 


252




330
331


 


253




331
332


 


254




331
332


 


255




333
334


 


256




333
334


 


257




333
334


 


258




333
334


 


259




333
334


 


260




340
341


 


261




340
341


 


262




340
341


 


263




343
344


 


264




343
344


 


265




343
344


 


266




343
344


 


267




344
345


 


268




344
345


 


269




345
346


 


270




345
346


 


271




345
346


 


272




345
346


 


273




347
348


 


274




347
348


 


275




349
350


 


276




349
350


 


277




349
350


 


278




349
350


 


279




351
352


 


280




351
352


 


281




351
352


 


282




351
352


 


283




351
352


 


284




351
352


 


285




351
352


 


286




351
352


 


287




355
356


 


288




355
356


 


289




357
358


 


290




357
358


 


291




357
358


 


292




357
358


 


293




358
359


 


294




358
359


 


295




358
359


 


296




358
359


 


297




359
360


 


298




359
360


 


299




359
360


 


300




359
360


 


301




359
360


 


302




360
361


 


303




360
361


 


304




360
361


 


305




363
364


 


306




363
364


 


307




363
364


 


308




363
364


 


309




365
366


 


310




365
366


 


311




366
367


 


312




366
367


 


313




366
367


 


314




366
367


 


315




366
367


 


316




366
367


 


317




366
367


 


318




367
368


 


319




367
368


 


320




367
368


 


321




369
370


 


322




371
372


 


323




371
372


 


324




371
372


 


325




372
373


 


326




372
373


 


327




372
373


 


328




372
373


 


329




373
374


 


330




373
374


 


331




375
376


 


332




375
376


 


333




375
376


 


334




377
378


 


335




377
378


 


336




377
378


 


337




383
384


 


338




383
384


 


339




383
384


 


340




383
384


 


341




383
384


 


342




383
384


 


343




383
384


 


344




383
384


 


345




383
384


 


346




383
384


 


347




385
386


 


348




385
386


 


349




386
387


 


350




387
388


 


351




387
388


 


352




393
394


 


353




393
394


 


354




393
394


 


355




393
394


 


356




399
400


 


357




399
400


 


358




400
401


 


359




400
401


 


360




400
401


 


361




401
402


 


362




401
402


 


363




401
402


 


364




405
406


 


365




411
412


 


366




414
415


 


367




417
418


 


368




417
418


 


369




421
422


 


370




434
435


 


371




451
452













Method AG
Step 1
R21—H(R21=PhS—) (33 μl, 0.318 mmole) was treated with NaH (10.2 mg, 60% in mineral oil) in 0.5 ml anhydrous THF. A solution of AE4 (R1=Me, R3=Cyclohexylmethyl) (20 mg, 0.0424 mmol) in 0.5 ml anhydrous THF was added. The reaction mixture was stirred at room temperature overnight before it was partitioned between ether and saturated NaHCO3 water solution. The aqueous phase was extracted with ether 2 times. The combined organic phase was washed with brine 2 times, and dried over anhydrous NaSO4. The crude was purified on flash column with EtOAc/hexane to give 9 mg of AG1 (R21=PhS—, R1=Me, R3=cyclohexylmethyl) (49.2% yield).
Method AG
Step 2
AG1 (R21=PhS—, R1=Me, R3=cyclohexylmethyl) was treated with 50% TFA according to the Step 6 of the method H to give AG2 (R21=PhS—, R1=Me, R3=cyclohexylmethyl).
The following compounds were synthesized using similar method:
















#
Structure
MW
Obs. m/e





















372




315
316



 



373




331
332



 



374




337
338














Method AH
Step 1
Benzophenone imine (3.27 g, 18.04 mmole) was added to a suspension of AH1 (R3=cyclohexylmethyl) (4 g, 18.04 mmole) in 65 ml DCM. The reaction mixture was stirred at room temperature overnight under N2 before the solid was filtered, and the solvent was evaporated. The residue was dissolved in 100 ml ether, washed with water 2× and dried over anhydrous MgSO4. The crude was purified on flash column to give 5.08 g (80.57% yield) of AH2 (R3=cyclohexylmethyl).
Method AH
Step 2
A solution of AH2 (R3=cyclohexylmethyl) (1 g, 2.86 mmole) in 12 ml anhydrous THF was added to a suspension of 18-crown-6 (0.76 g, 2.86 mmole) and 30% KH in mineral oil (1.16 g, 8.58 mmole) in 4 ml anhydrous THF under N2. The mixture was cooled in ice-bath and R4Br (R4=3-pyridylmethyl, as a hydrobromide salt) was then added. The reaction mixture was stirred in ice-bath for 30 min and at room temperature for 2 more hrs before the reaction was quenched with 2 ml of HOAc/THF/H2O (0.25:0.75:1). The mixture was diluted with 40 ml EtOAc/H2O (1:1). The aqueous phase was extracted with EtOAc 3 times. The combined organic phase was washed with brine 3 times and dried over anhydrous MgSO4. The crude was purified on flash column to give 0.44 g (35.14% yield) of product which was treated with 1N HCl (2.2 ml, 2.22 mmole) in 3 ml ether in ice-bath followed by stirred at r.t. overnight. The aqueous phase was evaporated and purified on C-18 reverse phase column to give 0.22 g (66% yield) of AH3 (R4=3-pyridylmethyl; R3=cyclohexylmethyl).




To a solution of compound AI1 (R1=Me, R3=n-Bu) (34 mg, 0.105 mmol) in methanol (1 ml) was added 10% Pd/C (5 mg). The mixture was kept under an H2 balloon for 1 hr. After filtration of the catalyst, the filtrate was concentrated to get crude product. This residue was purified by RP HPLC to get compound AI2 (R1=Me, R3=n-Bu) (25 mg, 100%). Observed MW (M+H) 246.1; exact mass 245.15. 1H NMR (400 MHz, CD3OD): δ=7.59 (m, 2H), 7.36 (m, 3H), 3.17 (s, 3H), 2.17 (m, 2H), 1.27 (m, 4H), 0.86 (t, 3H, J=7.2 Hz).
The following compounds were prepared using similar methods:













#
Structure
MW
Obs. m/e


















375




283
284


 


376




285
286


 


377




299
300


 


378




450
451


 


379




462
463


 


380




463
464


 


381




487
488


 


382




489
490


 


383




503
504


 


384




516
517













To a mixture of compound AJ1 (R1=Me, R3=n-Bu) (70 mg, 0.165 mmol) and butylzincbromide (1.32 ml, 0.6 mmol) was added Pd(dppf)Cl2. The mixture was degassed, sealed and heated at 55° C. for 1 day. The mixture was diluted with CH2Cl2 and NH3/H2O. The organic layer was separated, dried, concentrated, and purified by RP HPLC to get product which was then treated with 4N HCl/dioxane for 30 min to give compound AJ2 (R1=Me, R3=n-Bu) (12 mg, 25%). Observed MW (M+H) 302.1; 1H NMR (400 MHz, CD3OD): δ=7.32 (m, 3H), 7.22 (m, 1H), 3.19 (s, 3H), 2.65 (m, 2H), 2.20 (m, 2H), 1.60 (m, 2H), 1.38 (m, 4H), 1.24 (m, 2H), 0.92 (m, 6H).
The following compound was synthesized in a similar fashion:













#
Structure
MW
Obs. m/e


















386




518
519


 


385




301
302













To a solution of AK1 (R1=Me, R3=n-Butyl, R21=n-Bu) (9 mg, 0.03 mmol) in methanol (1 ml) was added 5% Pt/C (5 mg), Rh/C (5 mg) and conc. HCl (0.05 ml). The mixture was kept under H2 (50 psi) for 2 days. After the filtration of the catalyst, the filtrate was concentrated to get compound AK2 (R1=Me, R3=n-butyl, R21=n-Bu) Observed MW (M+H) 308.1. 1H NMR (CD3OD): δ=3.16 (s, 3H), 1.80 (m, 6H), 1.26 (m, 16H), 0.88 (m, 6H).
The following compounds were synthesized using similar method:













#
Structure
MW
Obs. m/e


















387




277
278


 


388




291
292


 


389




305
306


 


390




307
308


 


391




391
392


 


392




391
392













Method AL
Step 1
To a solution of compound AL1 (R3=n-Bu) (418 mg, 1.39 mmol) in methanol (8 ml) was added PtO2 (40 mg) and conc. HCl (0.4 ml). The mixture was hydrogenated (50 psi) for 1 day. After filtration of the catalyst, the filtrate was concentrated. The crude residue was basified to pH=11-12 by 1N NaOH. This mixture was extracted with ethyl acetate. The organic layer was separated, dried and concentrated to get compound AL2 (R3=n-Bu) (316 mg, 100%).
Method AL
Step 2
To a solution of compound AL2 (R3=n-Bu) (300 mg, 1.32 mmol) in dichloromethane (6 ml) was added (BOC)2O (316 mg, 1.45 mmol). The mixture was stirred at RT for 1.5 hr. It was diluted with water and dichloromethane. The organic layer was separated, dried and concentrated to get compound AL3 (R3=n-Bu) (464 mg, 100%).




Method AM
Step 1
Compound AM1 (R1=Me, R3=n-Butyl) was treated with 4N HCl in dioxane for 2 hr. The mixture was concentrated to get compound AM2 as an HCl salt (R1=Me, R3=n-Butyl). Observed MW (M+H) 470.1, 1H NMR (CD3OD): δ=7.28 (m, 2H), 6.96 (m, 3H), 4.80 (m, 2H), 4.56 (m, 1H), 4.00 (m, 1H), 3.64 (m, 4H), 3.37 (m, 2H), 3.12 (m, 1H), 3.00 (m, 1H), 2.90 (m, 1H), 2.72 (m, 1H), 2.38 (m, 1H), 2.12-1.62 (m, 8H), 1.35 (m, 6H), 1.12 (m, 1H), 0.91 (m, 3H).
Method AM
Step 2
To a solution of compound AM2 (R1=Me, R3=n-Butyl) (32 mg, 0.068 mmol) in dichloromethane (1 ml) was added acetyl chloride (5 ul, 0.072 mmol). The mixture was stirred for 2 hr. It was then diluted with CH2Cl2 and water. The organic layer was separated, dried, concentrated and purified by RP HPLC to get compound AM3 (R1=Me, R3=n-Butyl and R15=Me) Observed MW (M+H) 512.3; 1H NMR (400 MHz, CDCl3): δ=7.27 (m, 2H), 6.98 (m, 1H), 6.92 (m, 2H), 4.65 (s, 2H), 4.50 (m, 2H), 3.98 (m, 1H), 3.70 (m, 1H), 3.41 (m, 2H), 2.98 (m, 2H), 2.62 (m, 1H), 2.50 (m, 1H), 2.47 (m, 1H), 2.02 (m, 5H), 1.75 (m, 6H), 1.26 (m, 7H), 0.84 (m, 3H).
The following compounds were synthesized using similar method:













#
Structure
MW
Obs. m/e


















394




252
253


 


395




252
253


 


396




456
457


 


397




469
470


 


398




498
499


 


399




511
512













To a solution of compound AN2 (R1=4-N-(α-phenoxyacetyl)piperidinylmethyl, R3=n-Butyl) (28 mg, 0.06 mmol) in dichloroethane (2 ml) was added butyraldehyde (5.3 ul, 0.06 mmol), triethylamine (8.4 ul, 0.06 mmol) and NaBH(OAc)3 (18 mg, 0.084 mmol). The mixture was stirred overnight. It was then diluted with dichloromethane and water. The organic layer was separated, dried, concentrated and purified by RP HPLC to get AN2 (R1=4-N-(a-phenoxyacetyl)piperidinylmethyl, R3=n-Butyl, R15=propyl and R16=H) (5.4 mg, 17%). Observed MW (M+H) 526.1; exact mass 525.37. 1H NMR (CD3OD): δ=7.28 (m, 2H), 6.96 (m, 3H), 4.76 (m, 2H), 4.55 (m, 1H), 4.05 (m, 1H), 3.77 (m, 1H), 3.61 (m, 3H), 3.50 (m, 1H), 3.11 (m, 4H), 2.85 (m, 1H), 2.68 (m, 1H), 2.38 (m, 1H), 2.05 (m, 2H), 1.95 (m, 2H), 1.73 (m, 5H), 1.39 (m, 8H), 1.10 (m, 1H), 0.99 (m, 3H), 0.92 (m, 3H).
The following compound was synthesized using similar method:













#
Structure
MW
Obs. m/e


















400




308
309


 


401




308
309


 


402




525
526













A mixture of copper chloride (2.06 g, 20.8 mmol) and lithium chloride (1.76 g, 41.6 mmol) in 100 ml of THF was cooled down to −78° C. To this mixture, a 2.0M solution of AO1 (R3=n-butyl) (10 ml, 20 mmol) was added gradually. The reaction was warmed up to −60° C., and AO2 (R4=m-Br-Ph) (2.9 ml, 22 mmol) was injected. The mixture was stirred at −60° C. for 15 minutes and then quickly warmed up to RT by removing the dry-ice bath. The reaction was quenched with water and sat. NaHCO3. After addition of diethyl ether, a lot of precipitate formed and was filtered. From the biphasic filtrate, the organic layer was separated, dried, concentrated and purified by silica gel chromatography (10% EtOAc/hexane) to get ketone AO3 (R4=m-BrPh, R3=n-Bu) (3.93 g, 82%). Observed MW (M+H) 241.1; exact mass 240.01. 1H NMR (400 MHz, CDCl3): δ=8.07 (m, 1H), 7.88 (m, 1H), 7.64 (m, 1H), 7.34 (m, 1H), 2.94 (t, 3H, J=7.2 Hz), 1.71 (m, 2H), 1.40 (m, 2H), 0.95 (t, 3H, J=7.6 Hz).
The following ketones were made according to Method 9:
















Observed MW




Structure
(M + H)
Exact mass













242.1
241.01














Method AP
Step 1
To a solution of AP1 (R4=3-Bromophenyl) (5 g, 25 mmol) in dichloromethane (10 ml) were added N,O-dimethylhydroxylamine hydrochloride (2.56 g, 26.25 mmol) and 4-methylmorpholine (2.95 ml, 26.25 mmol). EDCl (5.04 g, 26.25 mmol) was then added portionwise. The reaction mixture was stirred at RT overnight and was then quenched with 1N HCl (60 ml). The mixture was extracted with dichloromethane. The organic layer was washed with 1N HCl and brine, dried over Na2SO4, and concentrated to give the Weinreb amide AP2 (R4=m-BromoPhenyl) (5.96 g, 98%). Observed MW (M+H) 244.1; exact mass 243.99. 1H NMR (CDCl3): δ=7.78 (m, 1H), 7.58 (m, 2H), 7.24 (m, 1H), 3.51 (s, 3H), 3.32 (s, 3H). This material was used in the next step without purification.
Method AP
Step 2
To a suspension of magnesium turnings (1.19 g, 48.8 mmol) in 30 ml of THF was added dropwise a solution of R3Br (R3=cyclohexylethyl) (5.73 ml, 36.6 mmol) in 24 ml of THF. After addition of half of the solution of bromide, several crystals of iodine were added to initiate the reaction. The mixture became cloudy and heat evolved. The rest of the solution of bromide was added dropwise. The mixture was stirred at RT for 30 minutes and then was cooled to 0° C., and the AP2 (R4=m-BromoPhenyl) (5.96 g, 24.4 mmol) was added. The mixture was stirred at RT for 3 hr and then quenched with 1N HCl until no residual Mg(0) was left. The phases was separated, and the water layer was extracted with ether. The combined organic layers were washed with brine, dried, and concentrated. The crude was purified by silica chromatography (15% EtOAc/hexane) to get ketone AP3 (R4=m-BromoPhenyl, R3=Cyclohexylethyl) (8.06 g, 100%). Observed MW (M+H) 295.2; exact mass 294.06. 1H NMR (400 MHz, CDCl3): δ=8.18 (m, 1H), 7.85 (m, 1H), 7.64 (m, 1H), 7.33 (m, 1H), 2.94 (t, 3H, J=7.2 Hz), 1.70 (m, 9H), 1.63 (m, 4H).




To a −78° C. solution of AQ1 (R4=cyclopropyl) (2.55 g, 38.0 mmol) in diethyl ether (100 ml) was added AQ3 (R3=n-Bu) (38 ml, 1.5 M in hexanes, 57 mmol). After 45 min, the cooling bath was removed. After 3 h at RT, the reaction was quenched by dropwise addition of water and then diluted further with EtOAc and water. The phases were separated and the aqueous layer was extracted with EtOAc (2×). The organic portions were combined, washed with brine, dried over MgSO4, and concentrated. This crude residue was subjected to column chromatography (silica gel, 0%→100% CH2Cl2/hexanes) to provide the desired ketone AQ4 (R4=cyclopropyl, R3=n-Butyl) (2.57 g, 20.4 mmol, 54%). 1H NMR (CDCl3) δ 2.52 (t, J=7.2 Hz, 2 H), 1.90 (m, 1 H), 1.57 (m, 2H), 1.30 (m, 2H), 0.98 (m, 2 H), 0.89 (t, J=7.6 Hz, 3 H), 0.83 (m, 2 H).




Method AR
Compound B2 (R1=m-Cl-Phenethyl, R3=Me, R4=i-butyl and R5=benzyl) was converted into AR2 (R1=m-Cl-Phenethyl, R3=Me, R4=i-butyl and R5=benzyl) using method A step 3.
The following compounds were synthesized using similar methods:













#
Structure
MW
Obs. m/e







 










403




396
397


 


404




354
NA


 


405




477
NA


 


406




460
NA


 


407




340
NA


 


408




382
NA


 


409




446
NA













Method AS
Step 1
To a mixture of AS1 (R3=Ph) (3.94 g) in toluene (10 ml) was added thionyl chloride (1.61 ml) and the resulting mixture as heated under reflux for 6 h (until HCl evolution ceased). The reaction mixture was kept overnight at rt before it was concentrated in vacuo. Toluene (10 ml) was added and the mixture was concentrated in vacuo again. The reaction mixture was dissolved in CH2Cl2, solid sodium bicarbonate added, filtered and then the CH2Cl2 solution was concentrated in vacuo to give AS2 (R3=Ph).
Method AS
Step 2
To AS2 (R3=Ph) (0.645 g) and AS5 (R4=4-chlorophenyl) (0.464 g), and 1,3-dimethylimidazolium iodide (0.225 g) in anhydrous THF (20 ml) was added 60% sodium hydride in oil (0.132 g). The resulting mixture was stirred at rt for 18 h. The reaction mixture was concentrated and partitioned between H2O and Et2O. The dried Et2O solution was concentrated in vacuo to give a yellow residue which was placed on preparative silica gel plates and eluted with CH2Cl2 to give AS3 (R3=Ph, R4=p-ClPh). (Miyashita, A., Matsuda, H., Hiagaskino, T., Chem. Pharm. Bull., 1992, 40 (10), 2627-2631).
Method AS
Step 3
Hydrochloric acid (1N, 1.5 ml) was added to AS3 (R3=Ph, R4=p-ClPh) in THF (10 ml) and the resulting solution was stirred at rt for 20 h. The reaction mixture was concentrated in vacuo and then partitioned between CH2Cl2 and H2O. The dried CH2Cl2 was concentrated in vacuo to give a residue which was placed on preparative silica gel plates and eluted with CH2Cl2:hexane 1:1 to afford AS4 (R3=Ph, R4=p-ClPh).
Method AS
Step 4
AS4 (R3=Ph, R4=p-ClPh) (0.12 g) and methylguanidine, HCl (AS6, R1=Me) (0.055 g) were mixed in absolute EtOH (5 ml) with triethylamine (0.2 ml) and then heated under reflux for 20 h. The resulting mixture was concentrated and then partitioned between CH2Cl2 and H2O. The dried CH2Cl2 was concentrated in vacuo to give a residue which was placed on preparative silica gel plates and eluted with CH2Cl2:MeOH 9:1 to afford AS5 (R3=Ph, R4=p-ClPh and R1=Me).
The following compounds were synthesized using similar methods:













#
Structure
MW
Obs. m/e


















411




265
266


 


412




265
266


 


413




271
272


 


414




271
272


 


415




279
280


 


416




295
296


 


417




295
296


 


418




299
300


 


419




299
300


 


420




309
310


 


421




325
326


 


422




343
344


 


423




343
344


 


424




421
422


 


425




482
483


 


426




512
513


 


427




560
561













Method AT
Step 1
AT1, prepared using a method similar to Method H, Step 1, 2 and 3, (n=4, R3=R4=n-Bu) (0.146 g) in MeOH (3 ml) and 1N NaOH (0.727 ml) were stirred overnight at rt. The mixture was concentrated and then partitioned in water (pH  ̃3, adjusted using conc. HCl) and EtOAc. The dried EtOAc layer was concentrated in vacuo to afford AT2 (n=4, R3=R4=n-Bu).
Method AT
Step 2
Compound AT2 (n=4, R3=R4=n-Bu) (0.012 g) in MeCN (1 ml) was treated with EDC resin (0.12 g, 1.44 mmol/g), HOBT (0.004 g) in THF (1 ml), and n-butylamine (R15=H, R16=n-butyl) (0.007 ml). The reaction was carried out overnight at rt. before Argonaut PS-NCO resin (0.150 g), PS-polyamine resin (0.120 g) and THF (2 ml) were added and the mixture shaken for 4 h. The reaction mixture was filtered and resin washed with THF (2 ml). The combined organic phase was concentrated in vacuo before the residue was treated with 1N HCl in MeOH (1 ml) for 4 h followed by evaporation of solvent to give AT3 (n=4, R3=R4=n-Bu, R15=H and R16=n-Butyl).
The following compounds were synthesized using similar method:
















Obs.


#
Structure
MW
m/e







428




324
325


 


429




325
326


 


430




338
339


 


431




339
340


 


432




366
367


 


433




368
369


 


434




380
381


 


435




382
383


 


436




400
401


 


437




406
407


 


438




414
415


 


439




414
415


 


440




420
421


 


441




428
429


 


442




444
445


 


443




458
459













A published procedure was adapted (Varga, I.; Nagy, T.; Kovesdi, I.; Benet-Buchholz, J.; Dormab, G.; Urge, L.; Darvas, F. Tetrahedron, 2003, (59) 655-662).
AU1 (R15=H, R16=H) (0.300 g), prepared according to procedure described by Furniss, B. S.; Hannaford, A. J.; Smith, P. W. G.; Tatchell, A. R., (Vogel's Textbook of Practical Organic Chemistry 5th ed. Longman: new York, 1989; pp 1034-1035), AU2 (HCl salt, R1=Me) (0.237 g), 50% KOH (0.305 ml), 30% H2O2 (0.115 ml) and EtOH (4.6 ml) were heated in a sealed tube for 2 h. Reaction mixture was concentrated and extracted with CH2Cl2. The dried organic solution was concentrated in vacuo to give a residue which was placed on preparative silica gel plates eluting with CH2Cl2:MeOH 9:1 to afford AU3 (R15=H, R16=H, R1=Me).
The following compounds were synthesized using similar method:













#
Structure
MW
Obs. m/e


















444




265
266


 


446




280
281


 


447




285
286


 


448




285
286


 


449




309
310


 


450




309
310













Method AV
Step 1
In a microwave tube, AV1 (R3=Me, R4=Bu-i) (0.0012 g) and AV2 (R22=OPh) (0.0059 ml) in isopropanol (2 ml) was placed in a microwave at 125° C. for 5 min. The reaction mixture was concentrated in vacuo to give AV3 (R3=Me, R4=i-Bu, R22=OPh).
Method AV
Step 2
AV3 (R3=Me, R4=i-Bu, R22=OPh) in CH2Cl2 (1 ml) and TFA (1 ml) was shaken for 2 h and the concentrated in vacuo and purified on Prep LCMS to afford AV4 (R3=Me, R4=i-Bu, R22=OPh).
The following compounds were synthesized in a similar fashion.













#
Structure
MW
Obs. m/e


















451




378
379


 


452




396
397


 


453




416
417













Method similar to Method U was used for this transformation. The following compounds were generated using similar methods.
The following compounds were synthesized in a similar fashion:













#
Structure
MW
Obs. m/e


















454




341
342


 


455




341
342


 


456




342
343


 


457




342
343


 


458




347
348


 


459




359
360


 


460




323
324


 


461




294
295













Method AX
Step 1
A literature procedure was adapted. (J-Q Yu and E. J. Corey, Organic Letters, 2002, 4, 2727-2730).
To a 400 ml DCM solution of AX1 (n=1, R4=phenethyl) (52 grams) in a ice bath was added 5 g of Pd/C (5% w/w), 50 g of potassium carbonate and 100 ml of anhydrous t-BuOOH. The mixture was stirred in air for overnight before it was diluted with DCM and washed with water. The residue after removal of organic solvent and drying was chromatographed using ethylacetate/hexane to give 25 g of Ax2 (n=1, R4=phenethyl).
Method AX
Step 2
A solution of AX2 (4.5 g, n=1, R4=phenethyl) in MeOH (50 ml) was treated with 0.4 g of Sodium borohydride and the reaction was stirred for 30 min before the solvent was removed and residue chromatographed to give a mixture of AX3 (n=1, R4=phenethyl) and AX4 (n=1, R4=phenethyl) which was separated using an AS chiralpak column eluted with 8% IPA in Hexane (0.05% DEA) to give 2.1 g of AX3 (n=1, R4=phenethyl) as the first fraction and 2.2 g of AX4 (n=1, R4=phenethyl) as the second fraction.
Method AX
Step 3
A 100 ml methanolic solution of AX4 (n=1, R4=phenethyl) (2.2 g) and 1,1′-bis(di-i-propylphosphino)ferrocene (1,5-cyclooctadiene)rhodium (I) tetrafluoroborate (0.4 g, 0.57 mmol) was hydrogenated at 55 psi overnight. The reaction was concentrated, and the brown oil was purified by silica gel chromatography to yield AX6 (n=1, R4=phenethyl) (1.7 g).
The following compounds were generated using similar method.








A solution of AY1 (n=1; 1.5 g, 3.4 mmol), 5% Rh/C (1.5 g), 5% Pd/C (0.5 g) in AcOH (30 mL) was shaken in a Parr apparatus at 55 psi for 18 hours. The vessel was flushed with N2, and the reaction was filtered through a pad of celite. After concentration AY2 was obtained which was carried on without purification. MS m/e: 312.0 (M+H).
AY3 was generated using similar method.








Method AZ
Step 1
To a solution of AZ1 (n=1, R1=Me, R3=2-cyclohexylethyl) (0.441 g, 1.01 mmol), generated from AY2 using Method C and Method H Step 3, in DCM was added Dess-Martin Periodinane (0.880 g, 2.07 mmol). The reaction was stirred for 3 hours at room temperature. The reaction was quenched with H2O and diluted with EtOAc. After removal of the organic phase, the aqueous layer was extracted with EtOAc (3×). The combined organics were dried (Na2SO4), filtered, and concentrated. The residue was purified by silica gel chromatography (0-100% EtOAc/hexanes) to yield AZ2 (n=1, R1=Me, R3=2-cyclohexylethyl) (0.408 g, 0.94 mmol, 93% yield). MS m/e: 434.1 (M+H).
Method AZ
Step 2
To a solution of AZ2 (n=1, R1=Me, R3=2-cyclohexylethyl) (0.011 g, 0.025 mmol) and AZ5 (R15=H and R16=m-pyridylmethyl) (0.0067 mL, 0.066 mmol) in DCE (1.8 mL) and MeOH (0.2 mL) was added AcOH (4 drops) and MP-cyanoborohydride resin (0.095 g, 2.42 mmol/g). The reaction was agitated for 40 hours at room temperature. The reaction was treated with 7N NH3/MeOH, and solution was filtered. After concentration, the residue was purified by silica gel HPLC (0-4% [(5% 7N NH3/MeOH)/MeOH]/(50% DCM/hexanes) to furnish fraction 1 and fraction 2 which, after removal of solvent, were treated with 20% TFA in DCM for 3 h at r.t. to give AZ4 (n=1, R1=Me, R3=2-cyclohexylethyl, R15=H and R16=m-pyridylmethyl) (0.005 g, 0.009 mmol) and the AZ3 (n=1, R1=Me, R3=2-cyclohexylethyl, R15=H and R16=m-pyridylmethyl) (0.012 g, 0.022 mmol) respectively.
The following compounds were generated using similar methods:
















Obs.


#
Structure
MW
m/e







462




333
334


 


463




348
349


 


464




374
375


 


465




374
375


 


466




374
375


 


467




374 
375


 


468




376
377


 


469




376
377


 


470




376
377


 


471




376
377


 


472




377
378


 


473




377
378


 


474




378
379


 


475




378
379


 


476




388
389


 


477




388
389


 


478




388
389


 


479




388
389


 


480




388
389


 


481




388
389


 


482




388
389


 


483




388
389


 


484




390
391


 


485




390
391


 


486




390
391


 


487




390
391


 


488




391
392


 


489




391
392


 


490




391
392


 


491




391
392


 


492




392
393


 


493




392
393


 


494




392
393


 


495




392
393


 


496




402
403


 


497




402
403


 


498




402
403


 


499




405
406


 


500




406
407


 


501




406
407


 


502




406
407


 


503




406
407


 


504




406
407


 


505




410
411


 


506




410
411


 


507




410
411


 


508




411
412


 


509




411
412


 


510




411
412


 


511




416
417


 


512




416
417


 


513




416
417


 


514




416
417


 


515




417
418


 


516




417
418


 


517




424
425


 


518




424
425


 


519




424
425


 


520




424
425


 


521




425
426


 


522




425
426


 


523




425
426


 


524




425
426


 


525




425
426


 


526




425
426


 


527




425
426


 


528




425
426


 


529




425
426


 


530




425
426


 


531




425
426


 


532




425
426


 


533




428
429


 


534




428
429


 


535




439
440


 


536




439
440


 


537




442
443


 


538




442
443


 


539




442
443


 


540




442
443


 


541




444
445


 


542




445
446


 


543




459
460


 


544




459
460













Method BA
Step 1
BA1, prepared according to a literature procedure (Terao Y; Kotaki, H; Imai, N and Achiwa K. Chemical and Pharmaceutical Bulletin, 33 (7), 1985, 2762-2766) was converted to BA2 using a procedure described by Coldham, I; Crapnell, K. M; Fernandez, J-C; Moseley J. D. and Rabot, R. (Journal of Organic Chemistry, 67 (17), 2002, 6185-6187).
1H NMR (CDCl3) for BA2: 1.42 (s, 9H), 4.06 (d, 4H), 4.09 (s, 1H), 4.18 (s, 2H), 5.62 (d, 1H).
Method BA
Step 2
BA3 was generated from BA2 using a literature procedure described by Winkler J. D.; Axten J.; Hammach A. H.; Kwak, Y-S; Lengweiler, U.; Lucero, M. J.; Houk, K. N. (Tetrahedron, 54 1998, 7045-7056). Analytical data for compound BA3: MS m/e: 262.1, 264.1 (M+H). 1H NMR (CDCl3) 1.43 (s, 9H), 3.98 (s, 2H), 4.11 (d, 4H), 5.78 (d, 1H).




Method BB
Step 1
Compound BB1 (n=1, R1=Me, R3=cyclohexylethyl) was converted to BB2 (n=1, R1=Me, R3=cyclohexylethyl) and BB3 (n=1, R1=Me, R3=cyclohexylethyl) which were separated via a silica gel column eluted with EtOAc in Hexane (0-15%).
Method BB
Step 2
Compound BB4 (n=1, R1=Me, R3=cyclohexylethyl) was generated from BB2 (n=1, R1=Me, R3=cyclohexylethyl) using 20% TFA in DCM.
The following compounds were generated using similar method:








Method BC
Step 1
Compound BC2 (n=1, R1=Me, R3=cyclohexylethyl and R15=m-Pyridyl) was obtained from BC1 (n=1, R2=Me, R3=cyclohexylethyl) using method L step 2.
Method BC
Step 2
Compound BC3 (n=1, R1=Me, R3=cyclohexylethyl and R15=m-Pyridyl) was obtained from BC2 (n=1, R1=Me, R3=cyclohexylethyl and R15=m-Pyridyl) using method L step 3.
The following compounds were generated using a similar method:
















Obs.


#
Structure
MW
m/e







552




374
375


 


553




388
389


 


554




388
389


 


555




388
389


 


556




388
389


 


557




390
391


 


558




390
391


 


559




402
403


 


560




402
403


 


561




402
403


 


562




402
403


 


563




404
405


 


564




404
405


 


565




404
405


 


566




404
405


 


567




410
411


 


568




410
411


 


569




411
412


 


570




411
412


 


571




411
412


 


572




411
412


 


573




411
412


 


574




411
412


 


575




416
417


 


576




416
417


 


577




416
417


 


578




416
417


 


579




424
425


 


580




424
425


 


581




424
425


 


582




424
425


 


583




425
426


 


584




425
426


 


585




425
426


 


586




425
426


 


587




425
426


 


588




425
426


 


589




425
426


 


590




430
431


 


591




430
431


 


592




438
439


 


593




438
439


 


594




439
440













Method BD
Step 1
Compound BD2 (n=1, R1=Me, R3=cyclohexylethyl and R15=Ph) was obtained from BD1 (n=1, R2=Me, R3=cyclohexylethyl) using Method N, Step 1.
Method BD
Step 2
Compound BD3 (n=1, R1=Me, R3=cyclohexylethyl and R15=Ph) was obtained from BD2 (n=1, R1=Me, R3=cyclohexylethyl and R15=m-Pyridyl) using Method N, Step 2.
The following compounds were generated using a similar method:













#
Structure
MW
Obs. m/e


















595




440
441


 


596




460
461













Method similar to Method M was adapted for these transformations. The following compounds were generated similar methods.
















Obs. 


#
Structure
MW
m/e


















597




405
406


 


598




439
440













Method BF
Step 1
Method similar to Method T, Step 1 was used for the synthesis of BF2 (n=1, R1=Me and R3=phenethyl, R15=H and R16=n-propyl).
Method BF
Step 2
Method similar to method L Step 3 was adapted for this transformation.
The following compounds were generated using similar methods.
















Obs.


#
Structure
MW
m/e


















599




376
377


 


600




390
391


 


601




390
391


 


602




390
391


 


603




397
398


 


604




397
398


 


605




397
398


 


606




397
398


 


607




411
412













Method BG
To a solution of BG1 (n=1, R3=cyclohexylethyl) (0.136 g, 0.31 mmol) in CH2Cl2 was added 2,6-lutidine, AgOTf, and butyl iodide. The reaction was stirred at room temperature for 96 hours. The reaction was filtered through a pad of Celite, and the solution was concentrated. The residue was purified by silica chromatography (0-100% EtOAc/hexanes) to furnish BG2 (n=1, R3=cyclohexylethyl, R15=n-butyl) (0.124 g, 0.25 mmol, 80% yield). MS m/e: 426.1 (M-OBu).
The following compound was prepared using similar method:








Method BH
Step 1
Compound BH1 (n=1, R3=cyclohexylethyl and R15=n-butyl) (0.060 g, 0.12 mmol) and 5% Pd(OH)2/C (0.040 g) in EtOAc (1 mL)/MeOH (0.2 mL) was stirred under an atmosphere of H2 for 20 hours at room temperature. The reaction was filtered through a pad of Celite, and the solution was concentrated. The crude product mixture BH2 (n=1, R3=cyclohexylethyl and R15=n-butyl) was carried on to the next step without purification.
Method BH
Step 2
A solution of BH2 (n=1, R3=cyclohexylethyl and R15=n-butyl) was converted to a product mixture of BH4 and BH3 using a method similar to Method C Step 1. The mixture was purified by silica get chromatography using EtOAc/hexanes to yield BH4 (n=1, R2=Me, R3=cyclohexylethyl and R15=n-butyl) (0.032 g, 0.078 mmol, 56% yield) and BH3 (n=1, R2=Me, R3=cyclohexylethyl and R15=n-butyl) (0.008 g, 0.020 mmol, 14% yield). For BH4 (n=1, R2=Me, R3=cyclohexylethyl and R15=n-butyl), MS m/e: 409.1 M+H). For BH3 (n=1, R2=Me, R3=cyclohexylethyl and R15=n-butyl), MS m/e: 409.1 (M+H).
Method BH
Step 3
Compound BH4 (n=1, R2=Me, R3=cyclohexylethyl and R15=n-butyl) (0.032 g, 0.078 mmol) was converted to BH5 (n=1, R2=Me, R3=cyclohexylethyl and R15=n-butyl) (0.016 g, 0.043 mmol, 57% yield) using a method similar to Method A, step 3. MS m/e: 392.1 (M+H).
The following compound was generated using a similar method:













#
Structure
MW
Obs. m/e


















608




391
392


 


609




391
392


 


610




391
392













A solution of BI1 (0.020 g, 0.040 mmol) in DCM (1 mL) was degassed using freeze/pump/thaw (4×) method. At the end of the fourth cycle Crabtree's catalyst was added and the system was evacuated. While thawing, the system was charged with hydrogen gas, and the reaction was stirred at room temperature for 16 hours under an H2 atmosphere. The reaction was concentrated, and the brown oil was purified by reverse phase HPLC to furnish BI2 (0.011 g, 0.022 mmol, 55% yield). MS m/e: 368.2 (M+H).




Method BJ
Step 1
A mixture of 2 ml dioxane solution of BJ1 (R1=Me, R3=Me) (140 mg, 0.5 mmol) generated using Method BK Steps 1 & 2, indole (1.2 eq), potassium t-Butoxide (1.4 eq), Pd2(dba)3 (0.02 eq) and 2-di-t-butylphospinobiphenyl (0.04 eq) in a sealed tube was irradiated in a microwave oven at 120° C. for 10 min and the mixture was separated via a silica gel column to give BJ2 (R1=Me, R3=Me) (0.73 mg).
Method BJ
Step 2
BJ2 (R1=Me, R3=Me) was converted to BJ3 (R1=Me, R3=Me) using Method BK, Steps 3 & 4. Obs. Mass for BJ3 (R1=Me, R3—=Me): 319.2.
















#
Structure
MW
Obs. m/e





















614




318
319














Method BK
Step 1
Hydantoin BK2 (R3=N-benzyl-3-piperidyl, R4=n-Bu) was prepared according to Method D, Step 1 from the corresponding ketone BK1 (R3=N-benzyl-3-piperidyl, R4=n-Bu). Analytical data for BK2 (R3=N-benzyl-3-piperidyl, R4=n-Bu): (M+H)=330.1.
Method BK
Step 2
To a suspension of hydantoin BK2 (R3=N-benzyl-3-piperidyl, R4=n-Bu) (138 mg, 0.419 mmol) in DMF (1.5 ml) was added dimethylformamide dimethylacetal (0.11 ml, 0.84 mmol). The resulting mixture was heated in a 100° C. oil bath for 16 h and then cooled to RT and concentrated under vacuum. This crude residue was purified by column chromatography (MeOH/DCM) to give product BK3 (R3=N-benzyl-3-piperidyl, R4=n-Bu) (140 mg, 0.408 mmol, 97%), (M+H)=344.1.
Method BK
Step 3
To a solution of a portion of BK3 (R3=N-benzyl-3-piperidyl, R4=n-Bu) (70 mg, 0.20 mmol) in toluene (1 ml) was added Lawesson's reagent (107 mg, 0.26 mmol). The resulting mixture was placed in an oil bath at 60° C. for 16 h and then at 100° C. for 24 h. After cooling to RT, the reaction was quenched by addition of several drops of 1 N HCl and then diluted with EtOAc and 1 N KOH. The phases were separated and the aqueous layer extracted with EtOAc (2×). The organic portions were combined, washed with brine, dried over MgSO4, filtered, and concentrated. This crude residue was purified by preparative TLC (1000 μm silica, 15% EtOAc/DCM) to give two separated diastereomers BK4 (R3=N-benzyl-3-piperidyl, R4=n-Bu) (24 mg, 0.067 mmol, 33%, MS: (M+H)=360.2) and BK5 (R3=N-benzyl-m-piperidyl, R4=n-Bu) (22 mg, 0.062 mmol, 31%, MS: (M+H)=360.2).
Method BK
Step 4
Diastereomer BK5 (R3=N-benzyl-3-piperidyl, R4=n-Bu) was treated with NH4OH (2 ml) and t-butyl hydrogen peroxide (70% aqueous, 2 ml) in MeOH (4 ml) for 24 h. After concentration, the crude sample was purified by preparative TLC (1000 mm silica, 7.5% 7N NH3/MeOH in DCM). The resulting sample was dissolved in DCM (1 ml), treated with 4N HCl in dioxane for 5 min, and finally concentrated to give diastereomeric products BK7 (R3=N-benzyl-3-piperidyl, R4=n-Bu) (12 mg, 0.029 mmol, 43%). 1H NMR (CD3OD) δ 7.60 (m, 2H), 7.49 (m, 3 H), 4.39 (ABq, JAB=12.8 Hz, ΔνAB=42.1 Hz, 2 H), 3.69 (m, 1 H), 3.39 (br d, J=13.6 Hz, 1 H), 3.20 (s, 3 H), 2.96 (m, 2 H), 2.45 (m, 1 H), 1.99 (m, 1 H), 1.92-1.78 (m, 3 H), 1.68 (br d, J=12.4 Hz, 1 H), 1.50 (dq, Jd=3.6 Hz, Jq=12.8 Hz, 1 H), 1.36-1.22 (m, 4 H), 1.03 (m, 1 H), 0.90 (t, J=7.2 Hz, 3 H). LCMS: tR (doubly protonated)=0.52 min, (singly protonated)=2.79 min; (M+H) for both peaks=343.2.
The following compounds were synthesized using similar methods:
















#
Structure
MW
Obs. m/e





















615




281
282














To a 2 ml Methanolic solution of BL1 (n=1, R3=cyclohexylethyl, R1=Me) (10 mg) was added BL3 (HCl salt, R15=H, 2 eq) and NaOAc (2 eq) and the mixture was heated to 60 C for 16 h. After removal of solvent, the residue was treated with 20% TFA in DCM for 30 min before the solvent was evaporated and residue purified using a reverse phase HPLC to give BL2 (n=1, R3=cyclohexylethyl, R1=Me and R15=H).
The following compounds were synthesized using similar methods.
















Obs. 


#
Structure
MW
m/e


















616




348
349


 


617




388
389













Method BM
Step 1
To a toulene solution (3 ml) of BM1 (n=1, R3=cyclohexylethyl, R2=Me) (0.050 mg) was added 1.5 eq of diphenylphosphorylazide and 1.5 eq of DBU and the solution was stirred at r.t. overnight. The reaction mixture was diluted with EtOAc and washed with 1% aq HOAc before the organic layer was dried and solvent evaporated. The residue was chromatographed using EtOAc/Hex to give a product that was treated with triphenylphosphine (2 eq) in THF (1% water) overnight to give BM2 (n=1, R3=cyclohexylethyl, R2=Me) after reverse phase purification.
Method BM
Step 2
To a DCM solution of BM2 (n=1, R3=cyclohexylethyl, R2=Me) was added 1 eq of benzyloxycarbonyl-OSu and the reaction was stirred overnight before the solvent was evaporated and residue chromatographed to give BM3 (n=1, R3=cyclohexylethyl, R2=Me).
Compound BM4 (n=1, R3=cyclohexylethyl, R2=Me) and BM5 (n=1, R3=cyclohexylethyl, R2=Me) were generated from BM2 (n=1, R3=cyclohexylethyl, R2=Me) and BM3 (n=1, R3=cyclohexylethyl, R2=Me) through Boc-deprotection.
The following compounds were synthesized using similar method:













#
Structure
MW
Obs. m/e


















618




332
333


 


619




468
469













A mixture of Pd(OAc)2 (9 mg), triethylamine (17 microliter), triethylsilane (11 microliter) and BN1 (20 mg) in DCM was hydrogenated at 1 atm at rt for 1.5 h before the reaction was filtered through a Celite pad to give BN2 after removal of solvent.
Method BO
The following compounds were generated through boc-deprotection of the corresponding starting material using 50% TFA in DCM, rt 30 min.
















#
Structure
MW
Obs. m/e





















620




266
267



 



621




266
267



 



622




274
275



 



623




274
275



 



624




288
289



 



625




320
321



 



626




320
321














Method BP
Step 1
To a solution of BP1 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) (0.012 g, 0.028 mmol) in CH2Cl2 (0.5 mL) was added 2,6-lutidine (0.010 mL, 0.086 mmol), AgOTf (0.024 g, 0.093 mmol), and benzyl bromide (0.010 mL, 0.084 mmol). The reaction was stirred at room temperature for 16 hours. The solid was filtered, and after concentration the residue was purified by reverse phase HPLC to yield BP2 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) (0.010 g, 0.019 mmol). MS m/e: 526.1 (M+H).
Method BP
Step 2
BP3 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) was prepared from BP2 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) using 30% TFA/DCM. MS m/e: 426.1 (M+H).
















Obs.


#
Structure
MW
m/e







627




425
426













Method BQ
Step 1
BQ1 was prepared according to Method AZ.
To a solution of BQ1 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) (0.004 g, 0.007 mmol) in CH2Cl2 (0.3 mL) was added DIEA (0.007 mL, 0.040 mmol), acetic acid (0.001 mL, 0.017 mmol), HOBt (0.003 g, 0.019 mmol), and EDCl (0.003 g, 0.016 mmol). The reaction was stirred at room temperature for 16 hours. The reaction was concentrated and purified by reverse phase HPLC to provide BQ2 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) (0.003 g, 0.005 mmol). MS m/e: 627.1 (M+H).
Method BQ
Step 2
BQ2 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) (0.003 g, 0.005 mmol) was treated with 20% TFA/CH2Cl2 (1 mL) in the presence of PS-thiophenol resin (0.030 g, 1.42 mmol/g) for 3 hours. The solution was filtered and concentrated to produce BQ3 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) (0.002 g, 0.005 mmol). MS m/e: 377.2 (M+H).













#
Structure
MW
Obs. m/e







628




376
377













Method BR
Step 1
To a solution of BR1 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) (0.004 g, 0.007 mmol) in pyridine (0.2 ml) was added DMAP (a few crystals) and methylsulfonyl chloride (3 drops). The reaction was stirred at room temperature for 6 days. The reaction was quenched with water and diluted with CH2Cl2. The organic layer was removed, and the aqueous phase was extracted with CH2Cl2 (3×). After concentration, the brown residue was purified by reverse phase HPLC to yield BR2 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) (0.003 g, 0.004 mmol). MS m/e: 663.2 (M+H).
Method BR
Step 2
BR3 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) was prepared from BR2 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) following a procedure similar to Method BQ Step 2. MS m/e: 413.1 (M+H).













#
Structure
MW
Obs. m/e







629




412
413













Method BS
Step 1
To a solution of BS1 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) (0.003 g, 0.006 mmol) in CH2Cl2 (0.3 mL) was added phenyl isocyanate (2 drops). The reaction was stirred at room temperature for 16 hours. The reaction was concentrated and purified by reverse phase HPLC to provide BS2 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) (0.002 g, 0.002 mmol). MS m/e 823.5 (M+H).
Method BS
Step 2
Compound BS2 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) was subjected to the same conditions in Method BQ Step 2. The crude mixture prepared above was treated with LiOH (0.006 g, 0.25 mmol) in MeOH (0.3 mL) for 2 hours. The reaction was concentrated, and the residue was purified by reverse phase HPLC to furnish BS3 (n=1, R1=Me, R2=H, R3=cyclohexylethyl) (0.0012 g, 0.002 mmol). MS m/e: 454.1 (M+H).













#
Structure
MW
Obs. m/e







630




453
454













Method BT
To a round bottom flask were added compound BT1 (R1=Me, R3=Me) (100 mg, 0.29 mmol), anhydrous toluene (2 ml), 3-aminopyridine (55 mg, 0.58 mmol) and 2-(di-tert-butyl phosphino) biphenyl (17 mg, 0.058). The solution was then degassed by N2 for 2 minutes before NaO-t-Bu (61 mg, 0.638 mmol) and Pd2(dba)3 (27 mg, 0.029 mmol) were added. The reaction was stirred at 80° C. for 22 hours. After cooling down to room temperature, the reaction was poured to cold water and extracted by CH2Cl2. The combined organic layer was then dried over Na2SO4. After the filtration, the concentrated residue was separated by TLC (CH3OH:CH2Cl2=1:10) and reverse phase HPLC (10%-100% acetonitrile in water w/0.1% formic acid) to produce the desired compound BT2 (R1=Me, R3=Me and R21=m-pyridyl) as a formate salt (23.6 mg, white solid, 20%). 1H NMR (CDCl3) δ 7.50-6.90 (m, 13H), 3.14 (s, 3H) MS m/e 358 (M+H).













#
Structure
MW
Obs. m/e


















631




347
348


 


632




356
357


 


633




357
358


 


634




357
358


 


635




357
358


 


636




358
359













Method BU
Step 1
To a round bottomed flask containing BU1 (m=1, n=1, R1=Me, R3=Cyclohexylethyl) (99 mg, 0.307 mmol) of the trifluoroacetic acid salt of pyrollidine derivative in 5 ml of DCM was added (86 μL, 0.614 mmol) of triethylamine followed by addition of (76 mg, 0.307 mmol) N-(benzyloxycarbonyloxy)succinimide. Stir at room temperature for 18 h. Dilute the mixture with DCM and extract with sat'd NaHCO3 soln, then water. Collect the organic portion and dry over Na2SO4, filter and concentrate in vacuo. Purify by silica gel chromatography (eluting with 0 to 60% EtOAc/hexanes) to yield BU2 (m=1, n=1, R1=Me, R3=Cyclohexylethyl) (130 mg, 0.284 mmol, 93% yield). MS m/e: 458.1 (M+H).
Method BU
Step 2
To a solution of BU2 (m=1, n=1, R1=Me, R3=Cyclohexylethyl) (130 mg) in 1 ml of MeOH in a reaction vial was added 0.5 ml of a solution of 70% tBuOOH in water and 0.5 ml of NH4OH. Seal the vial and shake at room temperature for 72 h. The mixture was concentrated in vacuo. The mixture was diluted with 1 ml of MeOH and a mixture 30 mg of NaHCO3 and Boc2O (87 mg, 0.398 mmol) were added. The solution mixture was stirred at room temperature for 18 h before it was concentrated and the residue purified by silica gel chromatography using EtOAc/hexanes to yield the BU3 (m=1, n=1, R1=Me, R3=Cyclohexylethyl) (90 mg, 0.167 mmol, 58% yield). MS m/e: 541.1, 441.1 (M+H)
Method BU
Step 3
A solution of BU3 (m=1, n=1, R1=Me, R3=Cyclohexylethyl) (90 mg, 0.167 mmol) in 5 ml of MeOH was hydrogenated using 100 mg of Pd(OH)2—C (20% w/w) at 1 atm for 1 h. The reaction mixture was filtered through a pad of diatomaceous earth and the pad was washed with MeOH. Concentration of the collected organic portions in vacuo yielded BU4 (m=1, n=1, R1=Me, R3=Cyclohexylethyl) (47 mg 0.116 mmol, 70% yield). MS m/e: 407.1 (M+H).
Method BU
Step 4
To a vial containing 10 mg of powdered 4 4′ molecular sieves was added 3-methoxyphenyl boronic acid (60 mg, 0.395 mmol) then 3 ml of anhydrous MeOH. To this mixture was added pyridine (100 ml, 0.650 mmol), Cu(OAc)2 (7 mg, 0.038 mmol), and BU4 (m=1, n=1, R1=Me, R3=Cyclohexylethyl) (7.83 mg, 0.019 mmol) and the mixture was stirred at room temperature for 96 h before it was quenched with 0.25 ml of 7N ammonia in methanol solution. The reaction mixture was extracted with water and DCM and the organic layers were dried and concentrate in vacuo. The residue was purified via a reverse-phase HPLC to give a product which was treated with 5 ml of 40% of TFA in DCM for 5 h. After removal of the volatiles, the residue was purified using a reverse phase HPLC system to furnish BU5 (m=1, n=1, R1=Me, R3=Cyclohexylethyl and R21=m-MeOPh) as the formic acid salt (0.7 mg, 0.0015 mmol, 30.1% yield). MS m/e: 413.1 (M+H).
















Obs.


#
Structure
MW
m/e







637




358
359


 


638




412
413













Method BV
Step 1
The method was adapted from a literature procedure (Page et al., Tetrahedron 1992, 35, 7265-7274)
A hexane solution of nBuLi (4.4 mL, 11 mmol) was added to a −78 C solution of BV2 (R4=phenyl) (2.0 g, 10 mmol) in THF (47 mL). After 60 minutes at −78 C, a solution of BV1 (R3=3-bromo-4-fluorophenyl) (2.24 g, 11 mmol) was added and the reaction slowly warmed to RT over 18 h. The reaction mixture was quenched with saturated ammonium chloride solution and extracted with CH2CO2 (2×), dried over MgSO4 and concentrated under vacuum. The resulting oil was subjected to silica gel chromatography using 4-10% EtOAc/Hexanes to give a white solid BV3 (R3=3-bromo-4-fluorophenyl and R4=phenyl) (1.69 g, 4.23 mmol, 42%). 1H NMR (CDCl3) δ 7.61 (m, 2 H), 7.27 (m, 3 H), 6.94 (m, 1 H), 6.92 (m, 1 H), 6.68 (m, 1 H), 3.15 (bs, 1 H), 2.57-2.73 (m, 4 H), 1.89 (m, 2 H).
Method BV
Step 2
A solution of BV3 (R3=3-bromo-4-fluorophenyl and R4=phenyl) (1.69 g, 4.23 mmol) in acetone (40 mL) was slowly added via addition funnel to a 0° C. solution of N-bromosuccinimide (NBS, 11.3 g, 63.3 mmol) in acetone (200 mL) and water (7.5 mL). The mixture was slowly warmed to RT, and quenched after 60 minutes with 10% aqueous Na2SO3. After diluting with CH2Cl2, the layers were separated, and the organic layer washed with water (2×), brine (1×) and dried over MgSO4. Concentration under vacuum afforded an oil which was subjected to silica gel chromatography using 5% EtOAc/Hexanes to give a solid BV4 (R3=3-bromo-4-fluorophenyl and R4=phenyl) (690 mg, 2.24 mmol, 53%). 1H NMR (CDCl3)  8.19 (m, 1 H), 7.93 (m, 3 H), 7.66 (m, 1 H), 7.50 (m, 2 H), 7.20 (m, 1 H).
Method BV
Step 3
BV5 (R3=3-bromo-4-fluorophenyl and R4=phenyl and R1=Me and R2=H) was prepared from BV4 (R3=3-bromo-4-fluorophenyl and R4=phenyl) using Method AS, Step 4.
















#
Structure
MW
Obs. m/e









639




361
362



 



640




361
NA














To an oven-dried vial was added Pd2(dba)3 (15.4 mg, 0.0168 mmol) and 2-(Di-t-butylphosphino)biphenyl (10.0 mg, 0.0336 mmol) followed by addition of a solution of BW1 (R4=Me; R1=Me and n=1) (56.8 mg, 0.168 mmol) in 2 mL of anhydrous THF. 2-Bromopyridine (17.0 mL, 0.178 mmol) was added followed by addition of 0.80 mL of 1.0 N LHMDS solution in THF. The reaction mixtures was stirred at 35° C. for 90 min followed by addition of MeOH and filtration through a silica gel pad. Purification by silica gel chromatography (0 to 100% EtOAc in hexanes) yielded the product which was treated with 5 mL of a 30% TFA in DCM solution to give BW2 after concentration and purification via a reverse phase column (R4=Me; R1=Me; R22=2-pyridyl and n=1) (69.3 mg, 99%). ES_LCMS (m/e): 416.2




Method BX
Step 1
To a solution of BX1 (R4=Me and n=1) (0.78 g, 3.63 mmol) in 10 mL of anhydrous DMF, was added N-Boc-N′-methyl thiourea (0.70 g, 3.70 mmol), EDCl.HCl (0.90 g, 4.71 mmol), and diisopropylethylamine (2.5 mL). The mixture was stirred at RT for 16 h before it was quenched with water and extracted with EtOAc (3×50 mL). The organic solution was dried, concentrated and the residue chromatographed via a silica gel column to yield BX2 (R1=R4=Me and n=1) (1.23 g, 100%). ES_LCMS (m/e): 340.1
Method BX
Step 2
To a solution of BX2 (R1=R4=Me and n=1) (1.23 g, 3.63 mmol in 40 mL of anhydrous THF was added triphenylphosphine (1.43 g, 5.44 mmol) and the mixture was cooled to 0° C. followed by slow addition of diisopropylcarbodiimide (1.07 mL, 5.44 mmol). After the mixture was stirred for 15 min at 0° C., nicotinoyl azide (Synthesis, 2004 (17), 2886) (0.66 g, 4.71 mmol) was added in one portion and the reaction was allowed to warm to RT and stir for 3 h. The reaction was diluted with EtOAc (200 mL) and washed with water (3×100 mL). The residue from the organic layer was purified through a silica gel column to yield the product azide which was hydrogenation using 20% Pd(OH)2/C (0.64 mg) in MeOH to give BX3 (R1=R4=Me and n=1). ES_LCMS (m/e): 339.1.
Method BY
The following compounds were synthesized using methods similar to Methods AO or AP.




Method BZ
The following aminoacids were generated using methods similar to Method D








Compound CA2 (R3=R4=Ph; Z=m-phenylene, R15=H and R16=cyclopentyl) was obtained from CA1 (R3=R4=Ph; Z=m-phenylene, R15=H and R16=cyclopentyl) using a method similar to Method G.
Method CB
The following compounds were synthesized using methods similar to Method E and/or AX.








Method CC
Step 1
To a methanol solution (20 mL) of CC1 (5 g) cooled to 0° C. was added sodium borohydride (1 eq) and the reaction was stirred for 30 min before the reaction mixture was evaporated to dryness then extracted with DCM/water. The DCM fractions were pooled, dried (MgSO4), filtered and concentrated to dryness. The crude product was dissolved in 20 mL. of anhydrous DCM. To this solution was added t-butyldimethylchlorosilane (2 eq.) and imidazole (2 eq.). The reaction was stirred overnight at RT before it was quenched DCM and saturated NaHCO3. The organic phase was dried (MgSO4), filtered and evaporated to dryness to give crude product CC2.
Method CC
Step 2
A literature procedure was adapted (Aust. J. Chem. 1990, 43 (7), 1195). Compound CC2 (50 g) in 80 mL. THF was added to mercuric oxide (1.5 eq.) and borontrifluoride etherate (1.6 eq.) in 540 mL. of THF/H2O (5:1) and the mixture was stirred under nitrogen for 2 h before the reaction was quenched with saturated NaHCO3 (aq.) and ether. The ether phase was dried over anhyd. Na2SO4, filtered through a silica pad and concentrated to give crude CC3.
Method CC
Step 3
To CC3 (10.4 grams) in 200 mL MeOH was added 1.1 eq. of sodium borohydride and the mixture was stirred for 30 min before the reaction mixture was concentrated and the residue partitioned in DCM/H2O. The organic phase was dried over Na2SO4, filtered and concentrated. The residue was chromatographed to give product CC4.
Method CC
Step 4
Compound CC4 (2.5) in 5 mL. anhydrous DCM was added Bis(1,2-diphenylphosphino)ethane (DPPE; 1.2 eq.) followed by carbon tetrabromide (1.1 eq.) at 0° C. and the reaction was stirred for 30 min. The reaction was quenched with hexane and poured over a silica pad. The organic solution was evaporated to give product CC5 as an oil. 1H-NMR (CDCl3) δ 5.72, br s, 1H; 4.18, t, 1H; 3.83, q, 2H; 2.00-2.10, m, 2H; 1.76-1.81, m, 2H; 1.43-1.56, m, 2H; 0.84, s, 9H; 0.03, s, 6H.
Method CC
Step 5
Compound CC6 was generated from CC5 using a similar procedure in Method E. Crude compound CC6 was purified by flash chromatography (gradient 0-10% EtOAc in hexane). Two isomers were isolated during purification isomer A which eluted first followed by isomer B.
ISOMER A: 1H-NMR (CDCl3) δ 7.26-7.37, m, 5H; 5.57, s, 1H; 5.38, s, 1H; 5.02, q, 2H; 4.08, br s, 1H; 3.67, s, 3H; 3.08, d, 1H; 2.58, d, 1H; 1.80-1.92, m, 1H; 1.60-1.75, m, 3H; 1.32-1.44, m, 3H; 0.83, s, 9H; 0.35-0.45, m, 4H; 0.01, s, 6H.
ISOMER B: 1H-NMR (CDCl3) δ 7.286-7.36, m, 5H; 5.56, s, 1H; 5.39, s, 1H; 5.06, q, 2H; 4.15, brs, 1H; 3.71, s, 3H; 3.06, d, 1H; 2.70, d, 1H, 1.60-1.90, m, 4H; 1.33-1.48, m, 3H; 0.87, s, 9H; 0.37-0.51, m, 4H; 0.03, s, 6H. Yield 26% isomer A and 22% isomer B.
Method CC
Step 6
Compound CC7 was obtained from CC6 (isomer B) through treatment with 1 N TBAF in THF for 30 min followed by extraction with ether/water. The organic phase was separated and washed four times with water. The aqueous phase was pooled and washed once with Et2O (pH  ̃6 to 7). The organic phase was dried over Na2SO4, filtered and evaporated to give product CC7 in 94% yield. 1H-NMR (CDCl3) δ 7.28-7.39, m, 5H; 5.58, brs, 1H; 5.49, brs, 1H; 5.10, d, 1H; 5.02 d, 1H; 4.09, brs, 1H; 3.72, s, 3H; 3.14, d, 1H; 2.70, s, 1H; 1.79-1.87, m, 2H; 1.67-1.79, m, 1H; 1.53-1.67, m, 2H; 1.44-1.53, m, 2H; 1.31-1.39, m, 1H; 0.35-0.54, m, 4H




Step 1: tert-Butyl 2-(3-bromophenyl)-1-oxopropan-2-ylcarbamate
To a solution of tert-butyl 2-(3-bromophenyl)-1-hydroxypropan-2-ylcarbamate (CD1; R4=Me) (1.5 g, 4.6 mmol) in EtOAc (150 mL) at reflux was added IBX (3.82 g, 13.6 mmol, 3 eq). Reflux was continued for another 2 h and then the mixture was cooled to RT. The white precipitate was filtered and the filtrate was concentrated. The residue was purified by chromatography on silica gel by eluting with EtOAc/hexanes to give 1.0 g (66%) of tert-butyl 2-(3-bromophenyl)-1-oxopropan-2-yl carbamate (CD2; R4=Me) as a colorless oil. 1H NMR (CDCl3) δ 9.42 (s, 1H), 7.69 (m, 1H), 7.60 (m, 1H), 7.55-7.40 (m, 2H), 5.85 (bs, 1H), 1.96 (s, 3H), 1.56 (s, 9H).
Step 2: tert-Butyl 2-(3-bromophenyl)-1-(methylamino)propan-2-ylcarbamate
To a solution of tert-butyl 2-(3-bromophenyl)-1-oxopropan-2-ylcarbamate (CD2; R4=Me) (1.0 g, 3 mmol) in dichloroethane (50 mL) was added methylamine (0.48 g, 6.1 mmol, 2 eq) in water (40%) and 1 mL of ACOH. The solution was allowed to stir at RT for 1 h followed by the addition of sodium triacetoxyborohydride (1.8 g, 8.5 mmol, 2.8 eq). The resulting mixture was stirred at RT for 16 h and quenched with MeOH. After stirring for 30 min the mixture was concentrated in vacuo. The residue was purified by chromatography on silica gel by eluting with EtOAc/MeOH to give 0.62 g (60%) of tert-butyl 2-(3-bromophenyl)-1-(methylamino)propan-2-ylcarbamate (CD3; R1=Me, R4=Me) as a colorless oil. 1H NMR (CDCl3) δ 7.47 (bs, 1H), 7.37 (m, 1H), 7.27 (m, 1H), 7.23 (m, 1H), 5.97 (bs, 1H), 3.18-2.82 (m, 2H), 2.45 (s, 3H), 1.74 (s, 3H), 1.40 (s, 9H). MS (ESI) m/e 342.9 (M+H)+.
Step 3: 4-(3-Bromophenyl)-1,4-dimethylimidazolidin-2-imine
tert-Butyl 2-(3-bromophenyl)-1-(methylamino)propan-2-ylcarbamate (CD3; R1=Me, R4=Me) (0.62 g, 1.8 mmol) was dissolved in 25% TFA in DCM (25 mL) and the mixture was left stirring at RT for 1 h. The mixture was concentrated in vacuo and the residue was redissolved in CHCl3 (20 mL). The solution was washed with 15% NaOH (10 mL) and the aqueous layer was extracted with CHCl3 (3×10 mL). The combined organic layer was dried over MgSO4 and concentrated in vacuo to give 0.33 g (76%) of crude 2-(3-bromophenyl)-N1-methylpropan-1,2-diamine as a colorless oil. 1H NMR (CDCl3) δ 7.65 (t, J=1.7 Hz, 1H), 7.41-7.34 (m, 2H), 7.21 (t, J=7.8 Hz, 1H), 2.86 (dd, J=11.7, 0.6 Hz, 1H), 2.64 (dd, J=11.7, 0.6 Hz, 1H), 2.38 (s, 3H), 1.54 (bs, 3H), 1.43 (s, 9H). MS (ESI) m/e 242.9 (M+H)+. The compound was used in the next step without further purification.
To a solution of 2-(3-bromophenyl)-N1-methylpropan-1,2-diamine (0.12 g, 0.50 mmol) in EtOH (10 mL) was added BrCN (0.073 g, 0.70 mmol, 1.4 eq). The mixture was stirred at RT for 16 h and then concentrated in vacuo. The residue was redissolved in CHCl3 (20 mL) and the solution was washed with 15% NaOH (10 mL). The aqueous layer was extracted with CdCl3 (3×10 mL) and the combined organic layer was dried (MgSO4), and concentrated to give 0.14 g (100%) of 4-(3-bromophenyl)-1,4-dimethylimidazolidin-2-imine (CD4; R1=Me, R4=Me) as a colorless oil. 1H NMR (CDCl3) δ 7.42 (t, J=1.7 Hz, 1H), 7.35 (dd, J=8.1, 1.7 Hz, 2H), 7.15 (t, J=8.1 Hz, 1H), 3.62 (d, J=9.3 Hz, 1H), 3.53 (d, J=9.0 Hz, 1H), 308 (s, 3H), 1.56 (bs, 3H). MS (ESI) m/e 268.1, 270.1 (M+H)+.
Step 4: 4-(3-(3,4-Difluorophenyl)phenyl)-1,4-dimethylimidazolidin-2-imine
A mixture of 4-(3-bromophenyl)-4-methyloxazolidin-2-imine (0.027 g, 0.1 mmol, 1 eq), 3,4-difluorophenyl boronic acid (0.020 g, 0.13 mmol, 1.3 eq), FibreCat (20 mg), anhydrous ethanol (2 mL), and a 1N K2CO3 aqueous solution (0.12 mL, 0.12 mmol, 1.2 eq) was heated in a microwave reactor (Emrys Optimizer) at 110° C. for 15 min. The mixture was transferred to a prepacked column of Si-carbonate (2 g, 0.79 mmol/g), which had been conditioned with MeOH/DCM (1:1). The column was eluted with 1:1 MeOH/DCM (3×3 mL) and the eluants were collected and concentrated to give 0.019 g (63%) of 4-(3-(3,4-difluorophenyl)phenyl)-1,4-dimethylimidazolidin-2-imine (CD5; R1=Me, R4=Me, R21=3,4-difluorophenyl) as a white solid. 1H NMR (CDCl3) δ 7.60 (s, 1H), 7.50-7.20 (m, 6H), 3.48 (m, 2H), 2.79 (s, 3H), 1.66 (s, 3H). MS (ESI) m/e 302.2 (M+H)+, HPLC (A) Rt=5.48 min.
Alternative for Method CD for Compound: R1=OR15 
Alternative Method CD
Step 2: tert-Butyl 2-(3-bromophenyl)-1-(methoxyamino)propan-2-ylcarbamate
To a solution of tert-butyl 2-(3-bromophenyl)-1-oxopropan-2-ylcarbamate (CD2; R4=Me) (2.7 g, 8.2 mmol) in dichloroethane (40 mL) was added methoxylamine hydrochloride (0.89 g, 10.7 mmol, 1.3 eq) and 1 mL of AcOH. The solution was allowed to stir at RT for 16 h. The reaction mixture was concentrated to give the oxime intermediate. The oxime was dissolved in EtOH (20 mL) and borane-pyridine complex (0.74 g, 7.9 mmol) was added dropwise. After stirring at r.t for 20 min, the reaction mixture was concentrated in vacuo. The residue was redissolved in DCM (50 mL) and washed with water (3×20 mL). The organic layer was dried (Na2SO4) and concentrated to give 1.6 g (54%) of tert-butyl 2-(3-bromophenyl)-1-(methoxyamino)propan-2-ylcarbamate (CD3; R1=OMe, R4=Me). 1H NMR (CDCl3) δ 7.60-7.10 (m, 4H), 5.82 (s, 1H), 3.90 (s, 3H), 3.70 (m, 2H), 1.80 (s, 3H), 1.40 (s, 9H). The crude compound was used in the next step without further purification.
Alternative Method CD
Step 3: 4-(3-Bromophenyl)-1-methoxy-4-methylimidazolidin-2-imine
tert-Butyl 2-(3-bromophenyl)-1-(methoxyamino)propan-2-yl carbamate (CD3; R1=OMe, R4=Me) (1.6 g, 4.4 mmol) was dissolved in 25% TFA in DCM (25 mL) and the mixture was left stirring at RT for 1 h. The mixture was concentrated in vacuo. The residue was redissolved in CHCl3 (20 mL) and washed with 15% NaOH (10 mL). The aqueous layer was extracted with CHCl3 (3×10 mL). The combined organic layer was dried over MgSO4 and concentrated in vacuo. The residue was dissolved in EtOH (10 mL) and BrCN (0.096 g, 0.91 mmol) was added. After stirring at RT for 16 h, the mixture was concentrated in vacuo. The residue was redissolved in CHCl3 (20 mL) and washed with 15% NaOH (10 mL). The aqueous layer was extracted with CHCl3 (3×10 mL). The combined organic layer was dried over MgSO4 and concentrated to give 0.2 g (16%) of 4-(3-bromophenyl)-1-methoxy-4-methylimidazolidin-2-imine (CD4; R1=OMe, R4=Me) as a colorless oil. 1H NMR (CDCl3) δ 7.65-7.35 (m, 4H), 4.02 (s, 3H), 3.98 (d, 1H), 3.91 (d, 1H), 1.94 (s, 3H).
Alternative Method CD
Step 4: 4-(3-(3-Chlorophenyl)phenyl)-1-methoxy-4-methylimidazolidin-2-imine
A mixture of 4-(3-bromophenyl)-4-methyloxazolidin-2-imine (CD4; R1=OMe, R4=Me) (0.027 g, 0.1 mmol, 1 eq), 3-chloro phenylboronic acid (0.023 g, 0.13 mmol, 1.3 eq), FibreCat (0.020 g), anhydrous ethanol (2 mL), and 1N K2CO3 aqueous solution (0.12 mL, 0.12 mmol, 1.2 eq) was heated in a microwave reactor (Emrys Optimizer) at 110° C. for 15 min. The mixture was transferred to a prepacked column of Si-carbonate (2 g, 0.79 mmol/g), which had been conditioned with MeOH/DCM (1:1). The column was eluted with 1:1 MeOH/DCM (3×3 mL) and the eluants were collected and concentrated to give 0.008 g (25%) of 4-(3-(3-chlorophenyl)phenyl)-1-methoxy-4-methylimidazolidin-2-imine (CD5; R1=OMe, R4=Me, R21=3-ClC6H4) as a white solid. 1H NMR (CDCl3) δ 7.75-7.60 (m, 5H), 7.58-7.42 (m, 3H), 4.00 (m, 2H), 3.97 (s, 3H), 1.97 (s, 3H). MS (ESI) m/e 316.0, 318.0 (M+H)+, HPLC (A) Rt=5.64 min.




Method CE
Step 1
The synthesis of CE2 (R1=R4=Me, R21=Br and R4=Me) was adapted from the procedure of Spanu, P. et. al. Tet. Lett., 2003, 44, 671-675. Thus, to a solution of (S)-tert-butyl 4-(3-bromophenyl)-1,4-dimethyl-6-oxo-tetrahydropyrimidin-2(1H)-ylidenecarbamate (CE1; R1=R6=Me, R21=Br) (0.24 g, 0.6 mmol, 1 eq) in THF (4 mL), LDA (2M in heptane/THF, 0.6 mL, 0.12 mmol, 2 eq) was added dropwise via a syringe at −78° C. After stirring at −78° C. for 30 min, a solution of iodomethane (0.080 mL, 0.12 mmol, 2 eq) in THF (4 mL) was added dropwise to form an orange-colored enolate solution. The mixture was stirred at −78° C. for 3 h. Water was added to quench the reaction and the suspension was warmed to RT. The mixture was then partitioned between H2O and Et2O. The organic layer was separated and the aqueous layer was extracted with Et2O (3×25 mL).
The combined organic layers were washed with brine, dried (MgSO4) and concentrated to give 0.38 g of a brown oil. Chromatography on silica gel using 50% EtOAc/hexanes as eluent gave 0.14 g (54%) of tert-butyl (4S,5R)-4-(3-bromophenyl)-1,4,5-trimethyl-6-oxo-tetrahydropyrimidin-2(1H)-ylidenecarbamate (CE2; R1=R4=Me, R21=Br and R6=Me) as a white solid. 1H NMR (CDCl3, 300 MHz):  10.16 (s, 1H), 7.46 (m, 2H), 7.26 (m, 2H), 3.21 (s, 1H), 3.01 (m, 3H), 3.02 (m, 1H), 1.51 (s, 12H), 1.17 (d, J=7.1 Hz, 3H). MS (ESI): MH+=441.7 HPLC (A) Rt=7.20 min.
Method CE
Step 2
A mixture of (S)-tert-butyl 4-(3-bromophenyl)-1,4-dimethyl-6-oxo-tetrahydropyrimidin-2(1H)-ylidene carbamate (CE2; R1=R4=Me, R1=Me, R21=Br) (0.25 g, 0.6 mmol), 5-cyanothien-1-ylboronic acid (0.2 g, 1.3 mmol, 2 eq), Fibrecat (4.26% Pd, 0.7 g), and 1N aq. K2CO3 (0.5 mL) was heated at 110° C. in a 20 mL Smith process vial using the Emrys microwave synthesizer. After cooling, the reaction mixture was transferred to a pre-packed column of Si-Carbonate column and eluted with MeOH/CH2Cl2 (1:1). The eluent was concentrated to give 0.32 g of a yellow oil, which was purified by silica gel chromatography (20-50% EtOAc/hexanes to give 0.13 g (0.3 mmol, 48% yield, syn:anti ratio: 5:1) of (S)-tert-butyl 4-(3-(5-cyanothien-1-yl)phenyl)-1,4-dimethyl-6-oxotetrahydro-pyrimidin-2(1H)-ylidenecarbamate as a white solid. 1H NMR (CDCl3, 300 MHz): δ 10.15 (s, 1H), 7.58-7.53 (m, 3H), 7.53-7.38 (m, 2H), 7.23 (m, 1H), 3.32 (s, 3H), 3.16 (m, 1H), 1.57 (s, 9H), 1.23 (d, J=6.9 Hz, 3H). MS (ESI): MH+=438.7; M+−56=383.1. HPLC Rt=7.28 min (syn isomer).
(S)-tert-Butyl 4-(3-(5-cyanothien-1-yl)phenyl)-1,4-dimethyl-6-oxo-tetrahydropyrimidin-2(1H)-ylidenecarbamate (23 mg, 0.05 mmol) was treated with 1 mL of 30% TFA/CH2Cl2 at RT for 30 min. The volatiles were removed in vacuo and the residue was re-dissolved in acetonitrile (5 mL) and evaporated again to afford 17 mg of crude iminopyrimidinone as a yellow solid. The crude product was purified by reverse phase HPLC (B) to provide 10 mg (60%) of (S)-6-(3-(5-cyanothien-1-yl)phenyl)-6-ethyl-2-imino-3-methyl-tetrahydropyrimidin-4(1H)-one (CE3; R1=R4=Me, R6=Me, R21=5-cyanothien-1-yl) as a white solid. 1H NMR (CDCl3, 300 MHz):  11.1 (br s, 1H), 10.0 (s, 1H), 7.58-7.53 (m, 3H), 7.44 (m, 1H), 7.40-7.26 (m, 2H), 3.30 (m, 1H), 3.16 (s, 3H), 1.60 (s, 3H), 1.27 (d, J=7.2 Hz, 3H). MS (ESI): MH+=438.7; M+−56=339.1. HPLC Rt=7.24 min (syn isomer).




Method CF
Step 1
To a solution of t-butylcarbamate (0.5 g, 4.3 mmol, 1 eq) in anhydrous THF (5.0 mL) at RT was added NaH (0.17 g, 4.3 mmol, 1 eq). The mixture was stirred at RT for 15 min. Then a solution of methyl isocyanate (0.3 g, 4.2 mmol, 1 eq.) in anhydrous THF (5.0 mL) was added dropwise. The reaction mixture was allowed to stir at 25° C. for 15 min. The mixture was then poured into 30 mL of ice-water under vigorous stirring. The reaction solution was extracted with Et2O (2×25 mL). The organic layers were combined and washed with brine (30 mL), dried (Na2SO4), and concentrated in vacuo to give 0.42 g (50% yield) of tert-butyl methylcarbamothioylcarbamate CF1 (R1=Me) as a white solid. 1H NMR (CDCl3, 300 MHz): δ 8.3 (br s, 1H), 3.19 (d, 3H, J=4.8 Hz), 1.8 (br s, 1H), 1.5 (s, 9H).
Method CF
Step 2
To a solution of an HCl salt of AB2 (R6=3-bromophenyl and R7=Me) (0.2 g, 0.7 mmol) and CF1 (R1=Me) in DMF (2 mL) at RT was added DIEA (0.5 mL, 2.8 mmol, 4 eq) and 1-[3-(dimethylamino)propyl]-3-ethylcarbodiimide HCl (EDCl, 0.2 g, 1.0 mmol, 1.4 eq). After stirring at RT for 16 h, the mixture was diluted with EtOAc (10 mL), washed with brine, dried (MgSO4), and filtered. The filtrate was evaporated under reduced pressure to afford 0.34 g of crude product as a yellow oil which was purified using silica gel chromatography by eluting with 20% EtOAc/hexanes to give 0.17 g (0.4 mmol, 60%) of (S)-tert-butyl 4-(3-bromophenyl)-1,4-dimethyl-6-oxo-tetrahydropyrimidin-2(1H)-ylidenecarbamate (CF2; R1=R6=Me) as a white solid. 1H NMR (CDCl3, 300 MHz): δ 10.63 (s, 1H), 7.42 (m, 2H) 7.24 (m, 2H), 3.21 (s, 3H), 3.2 (d, 1H, J=16.3 Hz), 2.87 (d, 1H, J=16.1 Hz), 1.65 (s, 3H), 1.55 (s, 9H). MS (ESI): MH+=395.7, 398.7. HPLC Rt=7.11 min.
Method CF
Step 3
A mixture of (S)-tert-butyl 4-(3-bromophenyl)-1,4-dimethyl-6-oxo-tetrahydropyrimidin-2(1H)-ylidenecarbamate (CF2; R1=R6=Me) (0.25 g, 0.6 mmol), 5-chloro-2-hydroxyphenylboronic acid (R21=5-chloro-2-hydroxyphenyl; 0.2 g, 1.2 mmol, 2 eq), Fibrecat (4.26% of Pd, 0.7 g) and 1N aq. K2CO3 (0.5 mL) in dimethoxyethane (DME, 10 mL) or tert-butanol (10 mL) in a 20 mL Smith process vial equipped with stir a bar was sealed and heated in an Emrys optimizer at 110° C. for 15 min. After cooling, the reaction mixture was transferred to a pre-packed Si-Carbonate column and eluted with MeOH/CH2Cl2 (1:1). The eluant was collected and concentrated under reduced pressure to give 0.32 g of the crude product as an oil. The crude product was purified by silica gel chromatography (20-50% EtOAc/hexanes gradient) to yield 0.13 g (0.3 mmol, 48%) of (S)-tert-butyl 4-(3-(3-chloro-6-hydroxyphenyl)-phenyl)-1,4-dimethyl-6-oxo-tetrahydropyrimidin-2(1H)-ylidenecarbamate (CF3; R1=R6=Me, R21=3-chloro-6-hydroxyphenyl) as a white solid. 1H NMR (CDCl3, 300 MHz): δ 7.48-4.32 (m, 2H), 7.20 (m, 3H), 6.84 (m, 2H), 5.68 (br s, 1H), 3.28 (d, J=15.7 Hz, 1H), 3.21 (s, 3H), 2.96 (d, J=15.3 Hz, 1H), 1.68 (s, 3H), 1.53 (s, 9H). MS (ESI): MH+=443.7, 445.7; M+−56=388.0. HPLC Rt (A)=6.99 min.
Method CF
Step 4
(S)-tert-butyl 4-(3-(3-chloro-6-hydroxyphenyl)phenyl)-1,4-dimethyl-6-oxo-tetrahydropyrimidin-2(1H)-ylidenecarbamate (CF3; R1=R6=Me, R21=3-chloro-6-hydroxyphenyl) (23 mg, 0.05 mmol) was treated with 1 mL of 30% TFA/CH2Cl2 at RT for 30 min. The volatiles were removed in vacuo. The residue was redissolved in acetonitrile (5 mL) and evaporated again to afford 17 mg of the crude product as a yellow solid. The crude product was purified via reverse phase HPLC to provide 10 mg (60%) of (S)-6-(3-(3-chloro-6-hydroxy-phenyl)phenyl)-6-ethyl-2-imino-3-methyl-tetrahydropyrimidin-4(1H)-one (CF4; R1=R6=Me, R21=3-chloro-6-hydroxyphenyl) as a white solid. 1H NMR (CDCl3, 300 MHz): 11.4 (br s, 1H), 7.6-4.25 (m, 3H), 7.24-6.84 (m, 3H), 3.68 (br s, 1H), 5.18 (br s, 1H), 3.39 (d, J=16.1 Hz, 1H), 3.20 (s, 3H), 2.95 (d, J=15.8 Hz, 1H), 1.74 (s, 3H). MS (ESI): MH+=344.1. HPLC (A) Rt=5.07 min.




Method CG
Step 1
A solution of CG1 (R21=Br, 12.29 g, 45 mmol) and NaOH (1.93 g, 49 mmol) in MeOH (70 mL) and water (10 mL) was refluxed for 3 h. After removal of MeOH under vacuum, the aqueous residue was adjusted to pH 3 and the resulting solid filtered off, dried under vacuum to give CG2 (R21=Br, 11.41 g, 98%). 1H NMR (400 MHz, CD3OD) δ 8.49 (m, 1 H), 8.27 (m, 1 H), 3.90 (s, 3 H).
Method CG
Step 2
A mixture of CG2 (R21=Br, 11.41 g, 44 mmol), EDCl (8.6 g, 45 mmol), dipropylamine (6.2 mL, 44.8 mmol), HOBt (6.0 g, 44.4 mmol) and NEt3 (10 mL, 72 mmol) in CH2Cl2 (100 mL) was stirred at RT for 48 h. The reaction was washed with sat. NaHCO3, water (1×), NH4Cl (1×), water (1×), brine (1×), dried over MgSO4, filtered and concentrated under vacuum. The resulting material was subjected to silica gel chromatography (0%→40% EtOAc/hexanes) to give CG3 (R21=Br, R15=R16=Pr, 3.62 g, 24%).
Method CG
Step 3
A mixture of CG3 (R21=Br, R15=R16=Pr, 3.6 g, 10.5 mmol), HN(Me)SO2Me (1.4 mL, 16.3 mmol), Pd(OAc)2 (355 mg, 1.58 mmol), Xantphos (1.41 g, 2.44 mmol), Cs2CO3 (5.17 g, 15.8 mmol) in toluene (40 mL) was degassed under a stream of N2 for 10 min, then heated at 95° C. for 18 h. The reaction was cooled to RT, filtered through celite, and the filtrate partitioned between EtOAc and water. The organic layer was washed with water (1×), brine (1×), dried over MgSO4, filtered, and evaporated under vacuum. The resulting residue was subjected twice to silica gel chromatography (0%→3%/MeOH/CH2Cl2) to give CG4 (R21=N(Me)SO2Me, R15=R16=Pr, 2.65 g, 68%).
Method CG
Step 4
LiBH4 (2 M THF, 8 mL, 16 mmol) was added to a solution of CG4 (R21=N(Me)SO2Me, R15=R16=Pr, 2.65 g, 7.15 mmol) in THF (40 mL) at 0° C. After 18 h at RT, the reaction was quenched with 1 M HCl and extracted with EtOAc. The organic layer was washed with brine (1×), dried over MgSO4, filtered, and evaporated under vacuum. The resulting residue was subjected to silica gel chromatography (0%→5% MeOH/CH2Cl2) to give CG5 (R21=N(Me)SO2Me, R15=R16=Pr, 1.77 g, 72%).
Method CG
Step 5
A mixture of CG5 (R21=N(Me)SO2Me, R15=R16=Pr, 1.77 g, 5.17 mmol), sodium azide (404 mg, 6.21 mmol), and PPh3 (2.85 g, 10.87 mmol) in CCl4 (5 mL) and DMF (20 mL) was stirred at 90° C. for 5 h, then at RT for 18 h. The reaction was stirred with water (10 mL) for 10 min, then diluted with Et2O. The organic layer was triturated with water, filtered, dried over MgSO4, and evaporated under vacuum. The resulting material was directly used in the next step (azide reduction).
Method CG
Step 6
The product from method CG, step 5 was dissolved in EtOH (5 mL) and stirred in the presence of 10% Pd/carbon under an atmosphere of hydrogen (50 psi) for 18 h at RT. The reaction mixture was passed through a PTFE-filter, and the filtrate evaporated under reduced pressure. The resulting material was subjected to preparative thin layer chromatography (5% MeOH/CH2Cl2) to give CG6 (R21=N(Me)SO2Me, R15=R16=Pr, 130 mg, 7.5% from CG5).
Method CG
Step 7
A mixture of CG6 (R21=N(Me)SO2Me, R15=R16=Pr, 130 mg, 0.38 mmol), 1,3-di(tert-butoxycarbonyl)-2-methylisothiourea (110 mg, 0.38 mmol), NEt3 (55 μL, 0.38 mmol) in DMF (1.5 mL) was stirred at RT for 48 h. After removal of the volatiles in vacuo, the resulting material was subjected to preparative thin layer chromatography (5% MeOH/CH2Cl2 as eluent). The resulting intermediate (140 mg, 0.24 mmol) was treated with 50% TFA/CH2Cl2 at RT for 3 h, followed by removal of all volatiles under vacuum to give CG7 (R21=N(Me)SO2Me, R15=R16=Pr, 140 mg, 74% from CG6).
Method CG
Step 8
A mixture of CG7 (R21=N(Me)SO2Me, R15=R16=Pr, 120 mg, 0.24 mmol), benzil (50 mg, 0.24 mmol) and NEt3 (134 μL, 0.96 mmol) in EtOH (5 mL) was heated at 100° C. for 18 h. After evaporating all volatiles, the residue was partitioned between water and CH2Cl2. The organic layer was washed with brine (1×), dried over MgSO4, filtered and evaporated. The resulting material was subjected to preparative thin layer chromatography (10% MeOH/CH2Cl2 as eluent) to give CG8 (R21=N(Me)SO2Me, R15=R16=Pr, R3=R4=Ph, 69 mg, 50%) as the formate salt. 1H NMR (400 MHz, CDCl3) δ 7.10-7.40 (m, 13 H), 4.72 (m, 2 H), 3.34 (m, 2 H), 3.08 (s, 3 H), 3.00 (m, 2H), 2.60 (s, 3 H), 1.59 (m, 2H), 1.39 (m, 2 H), 0.92 (m, 3 H), 0.64 (m, 3 H); LCMS: 576.3 (M+H).




A solution of 0.35 mL of 1 M BBr3 in DCM (0.35 mmole) was added dropwise to a solution of CH1 (52 mg, 0.11 mole) in 1.5 mL anhydrous DCM in ice bath. The reaction solution was stirred in ice bath for 10 min. and 2 hrs at RT. The reaction was quenched with 5 mL MeOH in ice bath. After concentration the crude was purified on C18 reverse phase column to give CH2 (37.3 mg, 67.% yield) as a formate.




A solution of CI1 (20 mg as a formate; 0.042 mmole) in 4 mL of DCM was treated with mCPBA (0.42 mmole) at RT for 2 hrs. The crude mixture was purified on C18 reverse phase column to give compound CI2.




To a solution of CJ1 (R1=R6=Me; 324 mg, 0.87 mmole) in 2.5 mL CHCl3 and 2.5 mL HOAc in ice bath was added NBS (312 mg, 1.75 mmole) and the reaction mixture was stirred at RT. Upon reaction completion, the crude mixture was diluted with DCM, and washed with saturated aqueous Na2S2O3, aqueous NaHCO3 and brine. The crude was purified on flash column to give a product which was treated with 50% TFA in DCM to give CJ2 (R1=R6=Me 220 mg, 56.% yield) after evaporation.




Method CK
Step 1
Similar to a literature procedure (Moloney et al., J. Med. Chem. 1997, 2347-2362), methyl bromomethylbenzoate (7.00 g, 30.5 mmol) was added to a suspension of CK1 (R3=R4=Ph, 7.00 g, 27.8 mmol) and K2CO3 (3.85 g, 27.8 mmol) in DMF (50 mL) at RT. After 18 h, the reaction mixture was diluted with water and extracted with CH2Cl2 (3×). The combined organic layers were washed with NaHCO3 (1×), water (3×), dried over MgSO4, filtered and concentrated under vacuum to give compound CK2 (12.7 g, 100%)
Method CK
Step 2
Compound CK3 was obtained from CK2 using method BK, step 3.
Method CK
Step 3;
CK3 (1.18 g, 2.83 mmol) in THF (15 mL) and 2 N LiOH (4 mL, 8 mmol) was stirred overnight at RT. The mixture was quenched with 6 N HCl (2 mL, 12 mmol) and then partitioned between water and EtOAc. The dried EtOAc layer was concentrated in vacuo and the residue subjected to reverse-phase HPLC (gradient from 10%→95% CH3CN/H2O with 0.1% HCO2H, 30 mL/min flow rate on a preparative C18 reverse-phase column) to afford CK4.
Method CK
Step 4
Compounds CK5 were obtained from CK4 using method G, step 2.
Method CK
Step 5
Compounds CK6 were obtained from CK5 using method A, step 3.




Method CL
Step 1
CL2 was obtained from CL1 (3-chlorophenyl boronic acid) following method AW.
Method CL
Step 2
Trimethylsiyidiazomethane (2 M hexanes, 2.5 mL, 5.0 mmol) was added to a solution of LDA (freshly prepared from DIPA and nBuLi) in THF at −78° C. After 30 min at −78° C., a solution of aldehyde CL2 (900 mg, 4.13 mmol) in THF (5 mL) was added and the reaction slowly warmed to RT over 3 h. The reaction was quenched with water, then extracted with Et2O (2×100 mL). The combined organic layers were washed with brine (1×), dried over MgSO4, filtered, and evaporated under vacuum. The resulting material was subjected to silica gel chromatography (100% hexanes) to give CL3 (752 mg, 86%). 1H NMR (400 MHz, CDCl3) δ 7.21-7.65 (m, 8 H), 3.08 (s, 1 H).
Method CL
Step 3
A mixture of CL3 (202 mg, 0.95 mmol), aryl bromide (Ar=3,5-pyrimidinyl, 181 my, 1.14 mmol), Pd(dba)2 (27 mg, 47.5 μmol), PPh3 (25 mg, 95 μmol), CuI (18 mg, 95 μmol) and DIPA (400 μL, 285 μmol) in DMF (2 mL) was degassed for 10 min under a stream of N2, then heated at 100° C. for 30 min in a Smith Synthesizer microwave. The reaction was cooled to RT, filtered and diluted with EtOAc. The organic layer was washed with water (1×), brine (1×), dried over MgSO4, filtered, and evaporated under vacuum. The resulting material was subjected to silica gel chromatography (0→20% EtOAc/hexanes) to give CL4 (R3=3,5-pyrimidinyl, 220 mg, 80%).
Method CL
Step 4
A mixture of CL4 (R3=3,5-pyrimidinyl, 210 mg, 0.72 mmol), KMnO4 (297 mg, 1.88 mmol), tetrabutylammonium bromide (TBAB, 55 mg, 0.17 mmol) in AcOH (263 μL) and CH2Cl2 (5 mL) was stirred for 3 h at RT. The reaction mixture was filtered through a plug of silica gel, eluting with MeOH, and the filtrate was concentrated under vacuum. The residue was subjected to preparative thin layer chromatography (5% MeOH/DCM) to give CL5 (R3=3,5-pyrimidinyl, 154 mg, 66%).
Method CL
Step 5
Diketone CL5 was converted into CL6 as described in Method CG, step 8. LCMS (CL6, R3=3,5-pyrimidinyl): 378.2 (M+H).




Method CM
Step 1
To a round bottom flask were added CM1 (R1=Me, R3=Ph; 500 mg, 1.22 mmol), methanol (20 mL) and 10% Pd/C (200 mg). The mixture was hydrogenated by a hydrogen balloon for 3 hour 40 min at stirring. After filtration, the concentrated residue was purified by Analogix flash column chromatography (EtOAc/Hexane=0%-50%) to produce CM2 (R1=Me, R3=Ph; 443 mg, 92%) as white solid. Observed MW (M+H) 381.2. (400 MHz, CD3OD): δ=9.13 (s, br, 1H), 7.36-7.26 (m, 5H), 7.09 (m, 1H), 6.68-6.57 (m, 3H), 3.13 (s, 3H), 1.49 (s, 9H).




To an Ace pressure tube were added CN1 (R3=phenyl; R1=Me; 100 mg, 0.290 mmol), bis(pinacolato)diboron (81.0 mg, 0.319 mmol), KOAc (85.0 mg, 0.87 mmol), PdCl2(dppf)2.CH2Cl2 (24 mg, 0.029 mmol) and anhydrous DMSO (1.0 mL). The reaction was then heated to 120° C. (oil bath temperature) at stirring for 2 hour 15 min. After cooling down to RT, the reaction were added 3,5-dibromo pyridine (206 mg, 0.87 mmol), anhydrous DMSO (1.0 mL) and 1M aq. K2CO3 (1.45 mL, 1.45 mmol). The reaction was then heated to 120° C. at stirring for 45 min. After cooling down to RT, the reaction was poured to cold water. The aqueous layer was extracted by DCM (3×50 mL) and the combined organic layer was dried over Na2SO4. The concentrated residue was purified first by preparative TLC (7M NH3/MeOH:DCM=1:10) and then preparative HPLC (reverse phase, C-18 column, 0.1% HCOOH/CH3CN: 0.1% HCOOH/H2O=10%-100%) to afford the desired product CN2 (formic acid salt; R3=phenyl; R1=Me; R21=3′-(5-bromopyridyl; 53.5 mg, 40%) as a white solid. Observed MW (M+H) 421.1. (400 MHz, CD3OD): δ=8.83-8.50 (m, br. 2H), 8.21 (s, 1H), 7.65 (m, 2H), 7.50 (m, 2H), 7.37 (m, 5H), 3.22 (s, 3H).




A microwave tube was charged with CO1 (R1=Me, R2H; R3=cyclopropyl, n=0) (30 mg, 0.097 mmol), PS-Ph3P—Pd (49 mg, 0.12 mmol), and R21SnBu3 (R21=2-pyrazinyl) (43 mg, 0.12 mmol) as a solution in 1 mL of PhCF3. The tube was sealed, and evacuated and back-filled with N2 (5×). The mixture was then exposed to microwave irradiation (110° C., 30 min). The resulting mixture was filtered with copious MeOH washes. Concentration of the filtrate gave a crude product that was subjected to RP-HPLC to give CO2 (R1=Me, R2=H; R3=c-Pr, n=0, R21=2-pyrazinyl) as a formate salt (12 mg, 0.063 mmol, 35%). LCMS Rt=3.58 min, m/e 308.2 (M+H).




Method CP
Step 1: 1,4,2-Diazaphospholidin-5-one, 2-methoxy-1-methyl-3,3-diphenyl-2-oxide (CP3)
Using methods similar to those described by I. V. Konovalova et al. (Zhurnal Obshchei Khimii, 50 (7), 1653-1654), 1.0 equivalent of phosphorisocyanatidous acid dimethyl ester (CP2), is added to a solution of benzophenone imine (CP1) in toluene and the mixture is warmed to reflux for 4 h. Removal of solvent and purification by flash chromatography provides the title compound (CP3).
Method CP
Step 2: 1,4,2-Diazaphospholidin-5-thione, 2-methoxy-1-methyl-3,3-diphenyl-2-oxide (CP4)
To a solution of CP3 in toluene (or xylene) is added Lawesson's reagent (1.2 equivalents), and the mixture is stirred at reflux for 2 h. The mixture is cooled and poured into cold water. The organic phase is dried (MgSO4) and filtered, and solvent is removed. The crude product is purified by flash chromatography to provide the title compound (CP4).
Method P1
Step 3: 1,4,2-Diazaphospholidin-5-imine, 2-methoxy-1-methyl-3,3-diphenyl-2-oxide (CP5)
Using a route similar to that described in Method A, step 3, CP4 is used to prepare the title compound (CP5).
As a variant of Method CP, benzophenone imine (CP1) is treated with 1.0 equivalent of phosphorisocyanatidous acid dimethyl ester [(CH3O)2P—N═C═S], giving directly CP4, which is converted to CP5 as described in Method CP, Step 3.




Method CQ
Step 1: 1,4,2-Diazaphospholidin-5-thione, 2-methoxy-1-methyl-3-methyl-3-(4-chloro)phenyl-2-oxide (CQ2)
Using an approach similar to that described by R. Merten et al. [(Chem. Ber., 102, 2143 (1969)], methylisothiocyanate (1.2 equivalents) is added to a solution of dimethyl [1-amino-1-(4-chloro)phenyl]ethylphosphonate (CQ1) in chloroform and the mixture is gradually warmed to reflux. After 2 h at reflux, the mixture is cooled and solvent is removed by evaporation. Purification of the crude product by flash chromatography provides the title compound.
Method CQ
Step 2: 1,4,2-Diazaphospholidin-5-imine, 2-methoxy-1-methyl-3-methyl-3-(4-chloro)phenyl-2-oxide (CQ3)
Using a route similar to that described in Method A, step 3, CQ2 is used to prepare the title compound.




Method CR
Step 1: 1,4,2-Diazaphospholidin-5-one, 2-methoxy-1-methyl-3-methyl-3-(4-bromo)phenyl-2-oxide (CR2)
Using an approach similar to that described by R. Merten et al. [(Chem. Ber., 102, 2143 (1969)), methylisocyanate (1.2 equivalents) is added to a solution of dimethyl [1-amino-1-(4-bromo)phenyl]ethylphosphonate (CR1) in chloroform and the mixture is gradually warmed to reflux. After 2 h at reflux, the mixture is cooled and solvent is removed by evaporation. Purification of the crude product by flash chromatography provides the title compound (CR2).
Method CR
Step 2: 1,4,2-Diazaphospholidin-5-thione, 2-methoxy-1-methyl-3-methyl-3-(4-bromo)phenyl-2-oxide (CR3)
To a solution of CR2 in toluene or xylene is added Lawesson's reagent (1.2 equivalents), and the mixture is stirred at reflux for 2 h. The mixture is cooled and poured into cold water. The organic phase is dried (MgSO4) and filtered, and solvent is removed. The crude product is purified by flash chromatography to provide the title compound.
Method CR
Step 3: 1,4,2-Diazaphospholidin-5-imine, 2-methoxy-1-methyl-3-methyl-3-(4-bromo)phenyl-2-oxide (CR4)
Using a route similar to that described in Method A, step 3, CR3 is used to prepare the title compound.




Method CS
Step 1: 1,4,2-Diazaphospholidin-5-thione, 2-methoxy-4-(4-methoxy)phenylmethyl)-1-methyl-3-phenylmethyl-2-oxide (CS2)
Using an approach similar to that described by R. Merten et al. [(Chem. Ber., 102, 2143 (1969)), methylisothiocyanate (1.2 equivalents) is added to a solution of dimethyl [1-(4-methoxy)phenylmethylamino-2-(4-bromo)phenyl]ethylphosphonate (CS1) in chloroform and the mixture is gradually warmed to reflux. After 2 h at reflux, the mixture is cooled and solvent is removed by evaporation. Purification of the crude product by flash chromatography provide the title compound.
Method CS
Step 2: 1,4,2-Diazaphospholidin-5-imine, 2-methoxy-4-(4-methoxy)phenylmethyl)-1-methyl-3-phenylmethyl-2-oxide (CS3)
Using a route similar to that described in Method A, step 3, CS2 is used to prepare the title compound.
Method CS
Step 3: 1,4,2-Diazaphospholidin-5-imine, 2-methoxy-1-methyl-3-phenylmethyl-2-oxide (CS4)
A solution of CS3 in methanol is hydrogenated at 1 atm in the presence of 5 mol % Pd/C, yielding the title compound after filtration and purification by flash chromatography.




Method CT
Step 1: Dimethyl-[(4-bromophenyl)-1-isothiocyanato]ethylphosphonate
To a mixture of CT1 in DCM and 0.1 N aqueous sodium bicarbonate (1.0 equivalent) is added thiophosgene (1.5 equivalents), and the mixture is stirred for 4 h at RT. Water is added, and the organic phase is dried (MgSO4), filtered and concentrated to give the product CT2 which is used without purification.
Method CT
Step 2: 1,4,2-Diazaphospholidin-5-thione, 2-methoxy-1-ethyl-3-(4-bromo)phenyl-2-oxide (CT3)
To a solution of CT2 in acetonitrile is added ethylamine (2 equivalents) and diisopropylethylamine (2 equivalents) and the solution is slowly warmed to reflux for 2 h. After removal of solvent, the product is purified by flash chromatography to give the title product.
Method CT
Step 3: 1,4,2-Diazaphospholidin-5-imine, 2-methoxy-1 ethyl-3-(4-bromo)phenyl-2-oxide (CT4)
Using a route similar to that described in Method A, step 3, CT3 is used to prepare the title compound.




Method CU
Step 1: 1,5,2-Diazaphosphorine-6(1H)-thione, 1-methyl-2-methoxy-3-phenyl-2-oxide (CU2)
Using an approach similar to that described by R. Merten et al. [(Chem. Ber., 102, 2143 (1969)), methylisothiocyanate (1.2 equivalents) is added to a solution of dimethyl (2-amino-1-phenyl)ethylphosphonate (CU1) in chloroform and the mixture is gradually warmed to reflux. After 2 h at reflux, the mixture is cooled and solvent is removed by evaporation. Purification of the crude product by flash chromatography provides the title compound.
Method CU
Step 2: 1,5,2-Diazaphosphorine-6(1H)-imine, 1-methyl-2-methoxy-3-phenyl-2-oxide (CU3)
Using a route similar to that described in Method A, step 3, CU2 is used to prepare the title compound.




Method CV
Step 1: Dimethyl (2-isothiocyanato-1-phenyl)ethylphosphonate (CV2)
To a mixture of CV1 in methylene chloride and 0.1 N aqueous sodium bicarbonate (1.0 equivalent) is added thiophosgene (1.5 equivalents), and the mixture is stirred for 4 h at RT. Water is added, and the organic phase is dried (MgSO4), filtered and concentrated to give the product which is used without purification.
Method CV
Step 2: 1,5,2-Diazaphosphorine-6(1H)-thione, 1-cyclopropyl-2-methoxy-3-phenyl-2-oxide (CV3)
To a solution of CV2 in acetonitrile is added cyclopropylamine (2 equivalents) and diisopropylethylamine (2 equivalents) and the solution is heated at reflux for 2 h. After removal of solvent, the product is purified by flash chromatography to give the title product.
Method CV
Step 3: 1,4,2-Diazaphospholidin-5-imine, 2-methoxy-1-cyclopropyl-3-(4-bromo)phenyl-2-oxide (CV4)
Using a route similar to that described in Method A, step 3, CV3 is used to prepare the title compound.




Method CW
Step 1: Boc-1,5,2-diazaphosphorine-5-imine, 2-methoxy-1-methyl-4-(3-arylphenyl)-2-oxides (CW2)
Reaction of tert-butyl methylcarbamothioylcarbamate with CW1 (R6=Me) using EDCl and DIEA in DMF affords CW2 (R6=Me) after purification.
Method CW
Step 2: 1,5,2-Diazaphosphorine-5-imine, 2-methoxy-1-methyl-4-(3-(m-cyanophenyl)phenyl)-2-oxides (CW3)
Following the procedure of Sauer, D. R. et al., Org. Lett., 2004, 6, 2793-2796, Suzuki reaction of CW2 (R6=Me) with aryl boronic acids using polymer-support Pd catalysts such as Fibre Cat or PS—PPh3-Pd under microwave heating conditions provides CW3 (R6=Me and R21=m-CN-Ph) of the invention after subsequent Boc-deprotection.




Method CX
Step 1, (S)-2-(tert-Butoxycarbonyl)-1,4-dimethyl-6-oxo-hexahydropyrimidine-4-carboxylic acid
To a solution of (S)-tert-butyl 4-(furan-2-yl)-1,4-dimethyl-6-oxo-tetrahydropyrimidin-2(1H)-ylidenecarbamate CX1 (R6=Me) (1.12 g, 3.64 mmol, prepared using Method CF) in DCM (7 mL) was added MeCN (7 mL) and H2O (10.5 mL), followed by RuCl3.H2O (7.6 mg, 0.036 mmol, 1 mol %), and NaIO4 (11.6 g, 54.2 mmol, 15 eq). The mixture was stirred at RT for 2 h. The mixture was diluted with DCM (100 mL) and the organic layer was separated, dried (Na2SO4), and concentrated to give 0.90 g (86%) of (S)-2-(tert-butoxycarbonyl)-1,4-dimethyl-6-oxo-hexahydropyrimidine-4-carboxylic acid CX2 (R6=Me) as a brown solid. 1H NMR (CD3OD):  3.17 (s, 3H), 3.02 (m, 2H), 1.63 (s, 9H), 1.57 (s, 3H).
Method CX
Step 2, (6S)-2-Imino-3,6-dimethyl-6-(3-(3-(trifluoromethyl)phenyl)-1,2,4-oxadiazol-5-yl)-tetrahydropyrimidin-4(1H)-one (CX3)
To a solution of (S)-2-(tert-butoxycarbonyl)-1,4-dimethyl-6-oxo-hexahydropyrimidine-4-carboxylic acid (CX2, R6=Me, 0.035 g, 0.12 mmol) in DMF (0.24 mL) was added TBTU (0.040 mg, 0.12 mmol, 1 eq), HOBt (0.0035 mg, 0.024 mmol, 0.2 eq), and DIEA (0.107 mL, 0.60 mmol, 5 eq). The mixture was stirred at RT for 10 min and then N′-hydroxy-3-(trifluoromethyl)benzamidine (0.028 mg, 0.13 mmol, 1.1 eq) was added. After stirring for another 2 h, the reaction mixture was diluted with EtOAc (20 mL), washed with H2O (10 mL) and saturated brine (10 mL), and concentrated in vacuo. The crude residue was dissolved in THF (0.4 mL) and then TBAF (1M in THF, 0.099 mL, 0.9 eq) was added. The mixture was stirred at RT for 2 h. EtOAc (20 mL) was added to the reaction mixture, which was washed with H2O (10 mL) and saturated brine (10 mL), and concentrated in vacuo. The residue was treated with 30% TFA/DCM (1 mL) at RT for 1. The reaction mixture was concentrated in vacuo and the crude product was purified on reverse phase HPLC (B) to give 0.015 g (26%) of (6S)-2-imino-3,6-dimethyl-6-(3-(3-(trifluoromethyl)phenyl)-1,2,4-oxadiazol-5-yl)-tetrahydropyrimidin-4(1H)-one (CX3; R6=Me, R7=3-(3-(trifluoromethyl)phenyl)-1,2,4-oxadiazol-5-yl)) as a white solid. 1H NMR (CD3OD): 8.40 (m, 2H), 8.04 (d, 1H, J=6.9 Hz), 7.90 (t, 1H, J=8.1 Hz), 3.81 (m, 2H), 3.39 (s, 3H), 1.82 (s, 3H). MS (ESI): MH+=354.2, HPLC (A) Rt=6.234 min.




(S)-2-(tert-Butoxycarbonyl)-1,4-dimethyl-6-oxo-hexahydropyrimidine-4-carbohydrazide
To a solution of (S)-2-(tert-butoxycarbonyl)-1,4-dimethyl-6-oxo-hexahydropyrimidine-4-carboxylic acid CX2 (R6=Me) (0.357 g, 1.25 mmol) in 1:5 MeOH/toluene (3 mL) was added TMSCHN2 (2M in hexane, 1.9 mL, 3.8 mmol, 3 eq). The mixture was stirred at RT for 2 h. The mixture was concentrated in vacuo to give 0.37 g (100%) of (S)-methyl 2-(tert-butoxycarbonyl)-1,4-dimethyl-6-oxo-hexahydropyrimidine-4-carboxylate as a brown solid. 1H NMR (CDCl3):  8.80 (s, 1H), 3.70 (s, 3H), 3.14 (s, 1H), 2.79 (s, 2H), 1.53 (s, 9H), 1.50 (s, 3H).
To a solution of (S)-methyl 2-(tert-butoxycarbonyl)-1,4-dimethyl-6-oxo-hexahydropyrimidine-4-carboxylate (0.074 g, 0.25 mmol) in EtOH (0.5 mL) was added NH2NH2 (0.023 mL, 0.75 mmol, 3 eq) and the mixture was stirred at RT for 4 h. The mixture was concentrated in vacuo to give 0.074 g (100%) of (S)-2-(tert-butoxycarbonyl)-1,4-dimethyl-6-oxo-hexahydropyrimidine-4-carbohydrazide (CY1, R6=Me) as a yellow solid. 1H NMR (CDCl3) 8.95 (s, 1H), 3.11 (s, 3H), 2.28 (m, 2H), 1.50 (s, 9H), 1.47 (s, 3H).




3-(5-((S)-2-Imino-1,4-dimethyl-6-oxo-hexahydropyrimidin-4-yl)-1,3,4-oxadiazol-2-yl)benzonitrile
To a solution of (S)-2-(tert-butoxycarbonyl)-1,4-dimethyl-6-oxo-hexahydropyrimidine-4-carbohydrazide (CY1; R6=Me, 0.037 g, 0.12 mmol) in DCM (0.3 mL) at 0° C. was added Et3N (0.035 mL, 0.24 mmol, 2 eq) followed by 3-cyanobenzoyl chloride (0.027 g, 0.16 mmol, 1.3 eq). The mixture was stirred at RT for 6 h. The mixture was diluted with DCM (20 mL), washed with H2O (10 mL) and saturated brine (10 mL), and concentrated in vacuo. The residue was then treated with TsCl (0.035 g, 0.18 mmol, 1.5 eq), Et3N (0.046 mL, 0.31 mmol, 2.6 eq), and DMAP (0.002 g, 0.016 mmol, 0.13 eq) in DCM (0.25 mL) at RT for 16 h. The mixture was diluted with DCM (20 mL), washed with H2O (10 mL) and saturated brine (10 mL), and concentrated in vacuo. The residue was treated with 30% TFA/DCM (1 mL) at RT for 1 h. The mixture was concentrated in vacuo and the residue was purified on reverse phase HPLC (B) to give 0.006 g (12%) of 3-(5-((S)-2-imino-1,4-dimethyl-6-oxo-hexahydropyrimidin-4-yl)-1,3,4-oxadiazol-2-yl)benzonitrile as a white solid (CZ1; R6=Me). 1H NMR (CD3OD, 300 MHz):  8.49 (m, 2H), 8.12 (d, 1H), 7.92 (t, 1H), 3.75 (m, 2H), 3.36 (s, 3H), 1.82 (s, 3H). MS (ESI): MH+=311.2, HPLC (A) Rt=4.175 min.




(S)-6-(5-(3-Chlorophenylamino)-1,3,4-oxadiazol-2-yl)-2-imino-3,6-dimethyl-tetrahydropyrimidin-4(1H)-one
To a solution of (S)-2-(tert-butoxycarbonyl)-1,4-dimethyl-6-oxo-hexahydropyrimidine-4-carbohydrazide (CY1, R6=Me, 0.030 g, 0.10 mmol) in DCM (0.25 mL) was added 3-chlorophenylisocyanate (0.015 mL, 0.20 mmol, 2 eq). The mixture was stirred at RT for 3 h and volatiles were then removed in vacuo. The residue was treated with TsCl (0.020 g, 0.10 mmol, 1 eq), Et3N (0.083 mL, 0.60 mmol, 6 eq), and DMAP (0.002 g, 0.016 mmol, 0.16 eq) in DCM (0.25 mL) at RT for 16 h. The mixture was diluted with DCM (20 mL), washed with H2O (10 mL) and saturated brine (10 mL), and concentrated in vacuo. The residue was treated with 30% TFA/DCM (1 mL) at RT for 1 h. The mixture was concentrated in vacuo and the residue was purified on reverse phase HPLC (B) to give 0.006 g (10%) of (S)-6-(5-(3-chlorophenylamino)-1,3,4-oxadiazol-2-yl)-2-imino-3,6-dimethyl-tetrahydropyrimidin-4(1H)-one (DA1; R6=Me). 1H NMR (CD3OD, 300 MHz):  7.78 (t, 1H), 7.47 (m, 2H), 7.17 (dt, 1H), 3.53 (m, 2H), 3.36 (s, 3H), 1.78 (s, 3H). MS (ESI): MH+=335.3, HPLC (A) Rt=5.710 min.




Method DB
Step 1; (1-(3-Bromophenyl)ethylidene)cyanamide (DB1, R4=Me)
Following the procedure of Cuccia, S. J.; Fleming, L. B.; France, D. J. Synth. Comm. 2002, 32 (19), 3011-3018: 3-Bromoacetophenone (2.0 g, 10 mmol, 1 eq), was dissolved in 20 mL DCM. A 1.0 N solution of titanium tetrachloride in DCM (20 mL, 20 mmol, 2 eq) was added dropwise over 15 min and the resulting mixture was stirred at 25° C. for 1 h. Bis-trimethylsilylcarbodiimide (5.0 mL, 22 mmol, 2.2 eq) in 5 mL of DCM was added over 15 min and the reaction was stirred for 16 h under argon. The reaction was poured onto 200 mL of an ice/water mixture and extracted with 3×200 mL of DCM. The combined organic phase was dried over MgSO4, filtered, and concentrated to give 2.3 g (100%) of (1-(3-bromophenyl)ethylidene)cyanamide (DB1, R4=Me) as a white solid: 1H NMR (CDCl3)  8.16 (t, J=1.8 Hz, 1H), 7.94 (dd, J=1.7, 1.1 Hz, 1H), 7.76 (dd, J=1.7, 1.1 Hz, 1H), 7.38 (t, J=8.0 Hz, 1H), 2.82 (s, 3H).
Method DB
Step 2; 5-(3-Bromophenyl)-2,5-dimethyl-1,2,4-oxadiazolidin-3-imine (DB2, R4=Me)
To a solution of the HCl salt of methylhydroxylamine (0.19 g, 2.2 mmol, 1 eq) in ethanol (25 mL) at 25° C. was added a 21% solution of NaOEt in ethanol (0.75 mL, 2.0 mmol, 0.9 eq) followed by (1-(3-bromophenyl)ethylidene)cyanamide (0.50 g, 2.2 mmol, 1 eq). After stirring at 25° C. for 10 min, the solvent was removed in vacuo. The residue was redissolved in CH2Cl2 (25 mL), the mixture was filtered, and the solvent was removed in vacuo to give 0.5 g (83%) of 5-(3-bromophenyl)-2,5-dimethyl-1,2,4-oxadiazolidin-3-imine (DB2, R1=Me, R4=Me) as a colorless oil: 1H NMR (CDCl3) δ 7.63 (t, J=1.8 Hz, 1H), 7.52 (dd, J=2.0, 1.1 Hz, 1H), 7.38 (dd, J=2.0, 1.1 Hz, 1H), 7.29 (t, J=7.9 Hz, 1H), 3.28 (s, 3H), 1.88 (s, 3H). MS (ESI) m/e 270.0, 272.0 (M+H)+.
Method DB
Step 3; 5-(3-(3-Chlorophenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazolidin-3-imine
To a solution of 5-(3-bromophenyl)-2,5-dimethyl-1,2,4-oxadiazolidin-3-imine (25 mg, 0.093 mmol) and 3-chlorophenyl boronic acid (17 mg, 0.11 mmol) in ethanol (1 mL) was added a 1 M aqueous solution of K2CO3 (0.22 mL, 0.22 mmol) and PS—PPh3-Pd (46 mg, 0.0046 mmol). The sample was heated in an Emrys Optimizer Microwave at 110° C. for 10 min. The resin was filtered off and rinsed alternately three times with CH2Cl2 (5 mL) and CH3OH (5 mL). The combined filtrates were concentrated and the residue was purified by reverse phase prep-HPLC to give 12.3 mg (44%) of 5-(3-(3′-chlorophenyl)-phenyl)-2,5-dimethyl-1,2,4-oxadiazolidin-3-imine (DB3; R1=Me, R4=Me, R21=3-chlorophenyl) as a colorless oil: 1H NMR (CDCl3)  7.69 (s, 1H), 7.58 (m, 2H), 7.49 (m, 3H), 7.37 (m, 2H), 3.29 (s, 3H), 1.94 (s, 3H). MS (ESI) m/e 302.0, 304.0 (MH+)+.
Using a similar procedure, the following compounds were also prepared.
5-(3-(3-Methoxyphenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazolidin-3-imine




1H NMR (CDCl3)  7.72 (s, 1H), 7.62 (dt, 1H), 7.49 (m, 2H), 7.38 (t, J=8.2 Hz, 1H), 7.20 (m, 1H), 7.14 (t, 1H), 6.93 (m, 1H), 3.88 (s, 3H), 3.27 (s, 3H), 1.95 (s, 3H). MS m/e 298.1 (M+H)
5-(3-(2,5-Dimethoxyphenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazolidin-3-imine




1H NMR (CDCl3)  7.67 (s, 1H), 7.57 (m, 1H), 7.45 (m, 2H), 6.92 (m, 3H), 3.82 (s, 3H), 3.77 (s, 3H), 3.27 (s, 3H), 1.95 (s, 3H). MS m/e 328.1 (M+H)
5-(3-(3-Fluorophenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazolidin-3-imine




1H NMR (CDCl3)  7.71 (s, 1H), 7.60 (m, 1H), 7.50 (m, 2H), 7.41 (m, 2H), 7.31 (m, 1H), 7.08 (m, 1H), 3.29 (s, 3H), 1.94 (s, 3H). MS m/e 286.0 (M+H)
5-(3-(3-Trifluoromethoxyphenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazolidin-3-imine




1H NMR (CDCl3)  7.70 (s, 1H), 7.59 (m, 1H), 7.55 (m, 1H), 7.50 (m, 2H), 7.46-7.48 (m, 2H), 7.26 (m, 1H), 3.29 (s, 3H), 1.95 (s, 3H). MS m/e 352.1 (M+H)
5-(3-(3-Pyridyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazolidin-3-imine




1H NMR (CD3OD)  9.17 (s, 1H), 8.84 (m, 2H), 8.08 (m, 1H), 7.99 (s, 1H), 7.88 (m, 1H), 7.72 (m, 2H), 3.37 (s, 3H), 2.00 (s, 3H). MS m/e 269.1 (M+H)
5-(3-(3,5-Dichlorophenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazolidin-3-imine




1H NMR (CDCl3)  7.66 (s, 1H), 7.54 (m, 1H), 7.52 (m, 2H), 7.47 (m, 2H), 7.38 (m, 1H), 3.30 (s, 3H), 1.94 (s, 3H). MS m/e 336.1 (M+H)
5-(3-(2-Chlorophenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazolidin-3-imine




1H NMR (CDCl3)  7.59 (m, 1H), 7.50 (m, 4H), 7.34 (m, 3H), 3.28 (s, 3H), 1.95 (s, 3H). MS m/e 302.1 (M+H)
5-(3-(3-Chloro-4-fluorophenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazolidin-3-imine




1H NMR (CDCl3)  7.65 (m, 2H), 7.48-7.54 (m, 4H), 7.22 (m, 1H), 3.30 (s, 3H), 1.94 (s, 3H). MS m/e 320.1 (M+H)




Method DC
Step 1, 5-(3-Bromophenyl)-5-methylimidazolidine-2,4-dione
A mixture of 3-bromoacetophenone (10 g, 50 mmol), KCN (8.16 g, 130 mmol, 2.5 eq) and (NH4)2CO3 (21.7 g, 225 mmol, 4.5 eq) in EtOH/H2O (1:1, 110 mL) was heated at 60° C. for 16 h. The reaction mixture was cooled to 0° C. The resulting precipitate was filtered, washed with water, hexane, and then dried to give 12.6 g (93%) of 5-(3-bromophenyl)-5-methylimidazolidine-2,4-dione as an off-white solid (DC1; R6=Me). 1H NMR (CD3OD)  7.64 (s, 1H), 7.45 (t, J=9.7 Hz, 2H), 7.26 (t, J=7.6 Hz, 1H), 1.68 (s, 3H).
Method DC
Step 2, 2-Amino-2-(3-bromophenyl)propanoic acid
5-(3-Bromophenyl)-5-methylimidazolidine-2,4-dione (DC1; R6=Me) (1.5 g, 5.6 mmol) was dissolved in 15 mL of 1N KOH, heated to 185° C. in a microwave reactor (Emrys Optimizer) for 2 h. Afterward, the mixture was carefully acidified using conc. HCl to pH  ̃2. The mixture was extracted once with Et2O (20 mL). The aqueous layer was concentrated in vacuo to give 1.6 g (100%) of 2-amino-2-(3-bromophenyl)-2-propanoic acid (DC2; R6=Me) as an off white solid. 1H NMR (CO3OD)  7.75 (t, J=2.0, 1H), 7.66 (m, 1H), 7.56 (m, 1H), 7.45 (t, J=8.1 Hz, 1H), 1.99 (s, 3H).
Method DC
Step 3, 2-(3-Bromophenyl)-2-(tert-butoxycarbonyl)propanoic acid
To a solution of 2-amino-2-(3-bromophenyl)-propanoic acid (DC2; R6=Me) (10.5 g, 43 mmol) in 1N KOH (105 mL) and dioxane (70 mL) at 0° C. was added (Boc)2O (20.6 g, 95 mmol, 2.2 eq). The mixture was stirred at RT for 16 h. The reaction mixture was concentrated to 100 mL. EtOAc (100 mL) was added and the mixture was cooled to 0° C. After acidifying with 2N KHSO4 to pH 2-3, the aqueous layer was extracted with EtOAc (3×50 mL). The combined EtOAc layer was washed with H2O (2×50 mL), dried (Na2SO4), and concentrated to give 11.7 g (79%) of 2-(3-bromophenyl)-2-(tert-butoxycarbonyl)propanoic acid as a white solid. 1H NMR (CDCl3)  7.61 (s, 1H), 7.41 (m, 2H), 7.24 (m, 1H), 1.98 (s, 3H), 1.44 (s, 9H).
To a solution of 2-(3-bromophenyl)-2-(tert-butoxycarbonyl)propanoic acid (11.3 g, 32.8 mmol) in MeOH (35 mL) was added toluene (175 mL) followed by TMSCHN2 (2M in hexane, 44 mL, 98 mmol, 3 eq). The mixture was stirred at RT for 16 h. Solvents were evaporated and the residue was chromatographed on silica by eluting with EtOAc/hexanes to give 11.8 g (100%) of methyl 2-(3-bromophenyl)-2-(tert-butoxycarbonyl)propanoate as a yellow oil. 1H NMR (CDCl3)  7.59 (t, J=1.8 Hz, 1H), 7.36-7.44 (m, 2H), 7.21 (t, J=8.0 Hz, 1H), 5.92 (s, 1H), 3.70 (s, 3H), 1.97 (s, 3H), 1.36 (br s, 9H).
To a solution of methyl 2-(3-bromophenyl)-2-(tert-butoxycarbonyl)propanoate (11.8 g, 33 mmol) in THF (150 mL) at −78° C. was added LAH powder (3.1 g, 82.0 mmol, 2.5 eq). The mixture was stirred at −78° C. and allowed to warm to RT over 16 h. The mixture was cooled to 0° C. and the reaction was quenched by slowly adding 3 mL of H2O. The mixture was diluted with DCM (500 mL) followed by the addition of 1N NaOH (6 mL) and H2O (9 mL). After stirring at 0° C. for 30 min, the mixture was filtered and the filtrate was concentrated to give 10 g (95%) of tert-butyl 2-(3-bromophenyl)-1-hydroxypropan-2-ylcarbamate (DC3; R6=Me) as a colorless oil. 1H NMR (CDCl3)  7.49 (t, J=1.8 Hz, 1H), 7.35-7.39 (m, 1H), 7.27-7.30 (m, 1H), 7.21 (t, J=7.8 Hz, 1H), 3.72 (m, 2H), 1.57 (s, 3H), 1.41 (br s, 9H).
Method DC
Step 4; 3-(tert-Butoxycarbonyl)-4-(3-bromophenyl)-4-methyl-[1,2,3]-oxathiazolidine-2,2-dioxide
To a solution of SOCl2 (5.7 mL, 2.5 eq) in dry CH3CN (37 mL) under argon was cooled to −40° C. was added tert-butyl 2-(3-bromophenyl)-1-hydroxypropan-2-ylcarbamate (DC3; R4=Me) (10.3 g, 31 mmol) in dry CH3CN (27 mL) was added dropwise, followed by the addition of dry pyridine (12.4 mL, 160 mmol, 5 eq). The mixture was then allowed to warm to RT in 1 h. The mixture was concentrated to about 30 mL. EtOAc (30 mL) was added and the precipitate was filtered off. The filtrate was concentrated in vacuo to give 10.4 g (89%) of 3-(tert-butoxycarbonyl)-4-(3-bromophenyl)-4-methyl-[1,2,3]-oxathiazolidine-2-oxide as a colorless oil. 1H NMR (CDCl3)  7.64 (t, J=2.0 Hz, 1H), 7.36-7.53 (m, 2H), 7.24 (m, 1H), 4.52 (q, J=9.5 Hz, 2H), 1.86 (s, 3H), 1.42 (br s, 9H).
To a solution of 3-(tert-butoxycarbonyl)-4-(3-bromophenyl)-4-methyl-[1,2,3]-oxathiazolidine-2-oxide (10.4 g, 28 mmol) in CH3CN (50 mL) at 0° C. was added RuO4 (0.5% in stabilized aq., 50 mg, 0.1% by weight) in H2O (10 mL) and NaIO4 (8.9 g, 41.5 mmol, 1.5 eq) in H2O (35 mL). The mixture was stirred at RT for 2 h. The mixture was partitioned between Et2O (200 mL) and H2O (50 mL). The organic layer was separated and the aqueous layer was extracted with Et2O (3×50 mL). The combined organic layer was dried (Na2SO4), and concentrated to give 10.8 g (100%) of 3-(tert-butoxycarbonyl)-4-(3-bromophenyl)-4-methyl-[1,2,3]-oxathiazolidine-2,2-dioxide (DC4; R6=Me) as a white solid ( ̃10.8 g, yield: 100%). 1H NMR (CDCl3)  7.56 (t, J=1.8 Hz, 1H), 7.48-7.52 (m, 1H), 7.38-7.44 (m, 1H), 7.30 (t, J=8.0 Hz, 1H), 4.41 (dd, J1=9.3 Hz, J2=20.4 Hz, 2H), 2.01 (s, 3H), 1.39 (s, 9H).
Method DC
Step 5; 3-Allyl-4-(3-bromophenyl)-4-methyl-[1,2,3]-oxathiazolidine-2,2-dioxide
3-(tert-Butoxycarbonyl)-4-(3-bromophenyl)-4-methyl-[1,2,3]-oxathiazolidine-2,2-dioxide (DC4; R6=Me) (10.8 g, 28 mmol) was dissolved in 25% TFA in DCM (40 mL, 5 eq) and the mixture was left standing at RT for 3 h. The mixture was concentrated in vacuo to give 7.3 g (91%) of 4-(3-bromophenyl)-4-methyl-[1,2,3]-oxathiazolidine-2,2-dioxide as a yellow oil. 1H NMR (CDCl3)  7.59 (t, J=1.8 Hz, 1H), 7.48-7.52 (m, 1H), 7.39-7.42 (m, 1H), 7.30 (t, J=8.1 Hz, 1H), 4.59 (m, 2H), 1.82 (s, 3H).
To a solution of 4-(3-bromophenyl)-4-methyl-[1,2,3]-oxathiazolidine-2,2-dioxide (7.3 g, 25 mmol) in DCM (77 mL) was added allyl iodide (9.1 mL, 100 mmol, 4 eq), followed by BnBu3NCl (0.39 g, 1.3 mmol) and 40% NaOH (28 mL). The mixture was stirred at RT for 16 h. The organic layer was separated and the solvent was evaporated. Silica gel chromatography using 5-20% EtOAc/hexanes gave 8.3 g (100%) of 3-allyl-4-(3-bromophenyl)-4-methyl-[1,2,3]-oxathiazolidine-2,2-dioxide (DC5; R6=Me) as a colorless oil. 1H NMR (CDCl3)  7.64 (t, J=1.8 Hz, 1H), 7.46-7.54 (m, 2H), 7.31 (t, J=8.0 Hz, 1H), 5.77-5.89 (m, 1H), 5.19-5.33 (m, 2H), 4.38 (dd, J1=8.7 Hz, J2=23.7 Hz, 2H), 3.46-3.68 (m, 2H), 1.83 (s, 3H).
Method DC
Step 6; N-(2-(3-bromophenyl)-2-amino)prop-1-oxy)-methylamine
To a suspension of NaH (60%, 0.14 g, 1.5 eq) in 0.5 mL of anhydrous DMF was added tert-butyl hydroxy(methyl)carbamate (0.52 g, 1.5 eq) in 1.5 mL of DMF. After stirring at RT for 15 min, a solution of 3-allyl-4-(3-bromophenyl)-4-methyl-[1,2,3]-oxathiazolidine-2,2-dioxide (DC5; R6=Me) (0.78 g, 2.3 mmol) in 6 mL of anhydrous DMF was added dropwise. The mixture was stirred at RT for 16 h. The mixture was partitioned between EtOAc (10 mL) and 1N HCl (3 mL). The organic layer was separated and the aqueous layer was extracted with EtOAc (3×5 mL). The combined organic layer was dried over Na2SO4 and concentrated to give 0.45 g (41%) of a product which was used without purification.
To a solution of the above product (3.86 g, 8.1 mmol) in THF (30 mL) was added a pre-stirred (15 min) mixture of Pd2(dba)3 (0.51 g, 0.41 mmol) and 1,4-bis(diphenylphosphino)butane (0.25 g, 0.41 mmol) in THF (5 mL), followed by thiosalicyliacid (2.2 g, 1.2 eq). The mixture was stirred at RT for 16 h. Solvent was evaporated and the residue was chromatographed on silica by eluting with 50% EtOAc/hexanes to give 1.3 g (37%) product as a oil which was dissolved in 4M HCl/dioxane (11 mL) and the mixture was stirred at RT for 2 h. Solvent was evaporated in vacuo and the residue was diluted with CHCl3 (10 mL) followed by treatment with 1N NaOH tol pH ̃12. The organic layer was separated and the aqueous layer was extracted with CHCl3 (3×10 mL). The combined organic layer was dried (Na2SO4) and concentrated to give 0.56 g (76%) of N-(2-(3-bromophenyl)-2-amino)prop-1-oxy)-methylamine (DC6; R6=Me, R1=Me) as a colorless oil. 1H NMR (CDCl3)  7.74 (t, J=1.8 Hz, 1H), 7.41-7.50 (m, 2H), 7.26 (t, J=8.0 Hz, 1H), 3.85 (dd, J1=9.6 Hz, J2=28.8 Hz, 2H), 2.72 (s, 3H), 1.48 (s, 3H).
Method DC
Step 7; 5-(3-Bromophenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine
To a solution of N-(2-(3-bromophenyl)-2-amino)prop-1-oxy)-methylamine (DC6; R6=Me, R1=Me) (0.76 g, 2.9 mmol) in EtOH (10 mL) was added BrCN (0.46 g, 4.4 mmol, 1.5 eq). After stirring at RT for 16 h, the mixture was concentrated. The residue was redissolved in CHCl3 (20 mL) and washed with 2N NaOH (10 mL). The aqueous layer was extracted with CHCl3 (3×10 mL). The combined organic layer was dried over Na2SO4 and concentrated to give 0.82 g (100%) of 5-(3-bromophenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine (DC7; R6=Me, R1=Me) as a light yellow oil. 1H NMR (CDCl3) δ 10.59 (s, 1H), 8.12 (br s, 1H), 7.46 (m, 2H), 7.29 (m, 2H), 4.14 (dd, J1=11.5 Hz, J2=57.7 Hz, 2H), 3.39 (s, 3H), 1.69 (s, 3H).
Method DC
Step 8; 5-(3-(3-Cyanophenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine
A mixture of 5-(3-bromophenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine (DC7; R6=Me, R1=Me) (0.025 g, 0.088 mmol, 1 eq), 3-cyanophenylboronic acid (0.019 g, 0.13 mmol, 1.5 eq), FibreCat (40 mg), anhydrous ethanol (1.5 mL), and a 1N K2CO3 aqueous solution (0.12 mL, 0.12 mmol, 1.4 eq) in a microwave vial was heated in a microwave reactor (Emrys Optimizer) at 110° C. for 15 min. The mixture was filtered, concentrated and purified by prep HPLC (B) to give 0.012 g (44%) of 5-(3-(3-cyanophenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine (DC8; R6=Me, R1=Me, R21=3-cyanophenyl) as a white solid. 1H NMR (CDCl3) 10.67 (s, 1H), 8.05 (br s, 1H), 7.85 (m, 2H), 7.50-7.66 (m, 5H), 7.35 (m, 1H), 4.22 (dd, J1=11.8 Hz, J2=48.6 Hz, 2H), 3.40 (s, 3H), 1.76 (s, 3H). MS m/e 307.3 (M+H)
Using a similar procedure, the following compounds were also prepared:
5-(3-(3-Pyridyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3)  10.85 (s, 1H), 9.13 (s, 1H), 8.76 (m, 1H), 8.65 (m, 1H), 7.92 (m, 2H), 7.81 (s, 1H), 7.60 (m, 2H), 7.44 (m, 1H), 4.26 (dd, J1=11.8 Hz, J2=37.4 Hz, 2H), 3.41 (s, 3H), 1.77 (s, 3H). MS m/e 283.2 (M+H)
5-(3-(5-Pyrimidyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3)  10.77 (br s, 1H), 10.42 (s, 1H), 9.26 (s, 1H), 9.07 (s, 1H), 7.84 (br s, 1H), 7.57-7.63 (m, 3H), 7.46 (m, 1H), 4.23 (dd, J1=11.5 Hz, J2=45.9 Hz, 2H), 3.41 (s, 3H), 1.77 (s, 3H). MS m/e 284.2 (M+H)
5-(3-(3-Chlorophenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3) 10.63 (s, 1H), 8.00 (br s, 1H), 746-7.55 (m, 5H), 7.31-7.7.40 (m, 3H), 4.20 (dd, J1=11.5 Hz, J2=54.4 Hz, 2H), 3.39 (s, 3H), 1.76 (s, 3H). MS m/e 316.2 (M+H)
5-(3-(3-Trifluoromethoxyphenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3)  10.72 (s, 1H), 8.03 (br s, 1H), 7.55 (m, 1H), 7.51 (m, 2H), 7.46 (m, 2H), 7.41 (m, 1H), 7.32-7.34 (dt, J1=1.6 Hz, J2=7.2 Hz, 1H), 7.21-7.23 (m, 1H), 4.21 (dd, J1=11.8 Hz, J2=53.0 Hz, 2H), 3.39 (s, 3H), 1.76 (s, 3H). MS m/e 366.2 (M+H)
5-(3-(3-Toluyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3)  10.61 (s, 1H), 8.07 (br s, 1H), 7.53 (m, 2H), 7.45 (m, 1H), 7.33-7.37 (m, 3H), 7.28-7.32 (m, 1H), 7.17-7.19 (m, 1H), 4.20 (dd, J1=11.8 Hz, J2=58.2 Hz, 2H), 3.38 (s, 3H), 2.42 (s, 3H), 1.76 (s, 3H). MS m/e 296.4 (M+H)
5-(3-(3,5-Dichlorophenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3) δ 10.71 (s, 1H), 8.06 (br s, 1H), 7.47 (m, 3H), 7.43 (m, 2H), 7.35 (m, 2H), 4.20 (dd, J1=11.7 Hz, J2=54.9 Hz, 2H), 3.40 (s, 3H), 1.76 (s, 3H). MS m/e 350.2 (M+H)
5-(3-(2-Fluoro-5-cyanophenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3)  10.50 (s, 1H), 7.86 (br s, 1H), 7.77 (dd, J1=2.1 Hz, J2=6.9 Hz, 1H), 7.65 (m, 1H), 7.50 (m, 2H), 7.42 (m, 1H), 7.27 (t, J=5.0 Hz, 2H), 4.20 (dd, J1=12.0 Hz, J2=50.4 Hz, 2H), 3.40 (s, 3H), 1.76 (s, 3H). MS m/e 325.1 (M+H)
5-(3-(2-Fluoro-5-methoxyphenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3)  10.53 (s, 1H), 7.94 (br s, 1H), 7.47 (m, 3H), 7.37 (m, 1H), 7.07 (t, J=9.5 Hz, 1H), 6.93 (m, 1H), 6.86 (m, 1H), 4.19 (dd, J1=11.7 Hz, J2=58.5 Hz, 2H), 3.82 (s, 3H), 3.38 (s, 3H), 1.75 (s, 3H). MS m/e 330.1 (M+H)
5-(3-(3-Dimethylaminocarbonylphenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3)  10.58 (s, 1H), 7.95 (br s, 1H), 7.26-7.65 (m, 8H), 4.20 (dd, J1=11.5 Hz, J2=54.7 Hz, 2H), 3.38 (s, 3H), 3.14 (s, 3H), 3.02 (s, 3H), 1.75 (s, 3H). MS m/e 353.2 (M+H)
5-(3-(2,5-Dimethoxyphenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3)  10.50 (s, 1H), 7.99 (br s, 1H), 7.40-7.50 (m, 3H), 7.29-7.33 (m, 1H), 6.84-6.94 (m, 3H), 4.18 (dd, J1=11.5 Hz, J2=65.4 Hz, 2H), 3.80 (s, 3H), 3.74 (s, 3H), 3.37 (s, 3H), 1.74 (s, 3H). MS m/e 342.2 (M+H)
5-(3-(3-Hydroxyphenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3)  9.75 (s, 1H), 7.39-7.54 (m, 3H), 7.21-7.30 (m, 2H), 7.10-7.12 (m, 2H), 6.82-6.84 (m, 1H), 5.83 (br s, 2H), 4.15 (dd, J1=11.5 Hz, J2=35.7 Hz, 2H), 3.36 (s, 3H), 1.74 (s, 3H). MS m/e 298.3 (M+H)
5-(3-(3-Fluorophenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3)  10.77 (s, 1H), 8.15 (s, 1H), 7.25-7.56 (m, 7H), 7.01-7.08 (m, 1H), 4.20 (dd, J1=11.5 Hz, J2=53.0 Hz, 2H), 3.40 (s, 3H), 1.76 (s, 3H). MS m/e 300.2 (M+H)
5-(3-(4-Cyanophenyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3)  10.67 (s, 1H), 8.01 (br s, 1H), 7.74 (s, 4H), 7.63 (s, 1H), 7.48-7.56 (m, 2H), 7.33-7.35 (m, 1H), 4.23 (dd, J1=11.5 Hz, J2=47.2 Hz, 2H), 3.40 (s, 3H), 1.76 (s, 3H). MS m/e 307.2 (M+H)
5-(3-(4-Methoxy-3-pyridyl)phenyl)-2,5-dimethyl-1,2,4-oxadiazinan-3-imine




1H NMR (CDCl3)  10.55 (s, 1H), 8.74 (d, J=6.0 Hz, 1H), 8.64 (s, 1H), 7.83 (br s, 1H), 7.49-7.53 (m, 3H), 7.37-7.42 (m, 2H), 4.20 (dd, J1=11.5 Hz, J2=49.4 Hz, 2H), 4.11 (s, 3H), 3.39 (s, 3H), 1.76 (s, 3H). MS m/e 313.2 (M+H)




Method DD
Step 1
To a 10 mL MeOH solution of DD1 (R3=R6=H, R7=Me, 1 g) was added p-methoxybenzaldehyde (1 eq) and 4 A molecular sieves (4 g). The solution was stirred overnight before sodium borohydride (1 eq) was added and reaction stirred for 1 h. The reaction mixture was filtered and solvent evaporated. The residue was chromatographed using MeOH/DCM to afford compound DD2 (R3=R6=H, R7=Me).
Method DD
Step 2
Procedure similar to Method CF, step 2 was used for generation of DD3 (R1=Me, R3=R6=H, R7=Me).
Method DD
Step 3
Procedure similar to Method CF, step 3 was used for generation of DD4 (R1=Me, R3=R6=H, R7=Me) from DD3
Method DD
Step 4
Compound DD4 was hydrogenated using Pd(OH)2/C in Methanol. After removal of the catalyst and solvent the crude product was treated with 20% TFA in DCM to give product DD5 (R1=Me, R3=R6=H, R7=Me) after purification.




Method DE
Step 1: 5-(4-Chlorophenyl)-3-methylsulfanyl-5,6-dihydro-4H-[1,2,4]thiadiazine 1,1-dioxide
2-(4-Chlorophenyl)ethenesulfonyl chloride DE1 is treated with 1.2 equivalents of S-methyl isothiourea hemisulfate and a slight excess of 1N NaOH in acetone. After 12 h at RT the mixture is concentrated in vacuo and the precipitate collected to give the title compound.
Method DE
Step 2: N-(2-(4-Chlorophenyl)ethene-1-sulfonyl)-S-methylisothiourea
Using a method similar to that described by K. Hasegawa and S. Hirooka (Bull. Chem. Soc. Jap., 1972, 45, 1893), N-(2-(4-chlorophenyl)ethylene-1-sulfonyl)thiourea DE2 in DMF is treated with 1N NaOH (2.4 equivalents) and dimethyl sulfate (1.2 equivalents) at 0-10° C. After 3 h at RT, the reaction mixture is poured into ice water. The precipitate is collected, washed with water and dried to give the title compound DE3.
Method DE
Step 2: 5-(4-Chlorophenyl)-1,1-dioxo-[1,2,4]thiadiazinan-3-one
Using a method similar to that described by K. Hasegawa and S. Hirooka (Bull. Chem. Soc. Jap., 1972, 45, 1893), 5-(4-chlorophenyl)-3-methylsulfanyl-5,6-dihydro-4H-[1,2,4]thiadiazine 1,1-dioxide DE2 in acetone is treated with 1N NaOH and the mixture is refluxed for 2 h. The acetone is evaporated and the mixture is acidified with conc. HCl to afford the title compound DE3.
Method DE
Step 3: 5-(4-Chlorophenyl)-2-methyl-1,1-dioxo-[1,2,4]thiadiazinan-3-one
Using a method similar to that described by A. Etienne et al. (Bull. Soc. Chim. Fr., 1974, 1395) 5-(4-chlorophenyl)-1,1-dioxo-[1,2,4]thiadiazinan-3-one DE3 is treated with sodium methoxide (1 equivalent) in methanol. Add methyl iodide (1.2 equivalent) in DMF and allow to stir for 12 h. Pour the mixture into ice water and collect the precipitate of the title compound DE4.
Method DE
Step 4: 5-(4-Chlorophenyl)-2-methyl-1,1-dioxo-[1,2,4]thiadiazinan-3-thione
To a solution of DE4 in toluene (or xylene) is added Lawesson's reagent (1.2 equivalents), and the mixture is stirred at reflux for 2 h. The mixture is cooled and poured into cold water. The organic phase is dried (MgSO4) and filtered, and solvent is removed. The crude product is purified by flash chromatography to provide the title compound (DE5).
Method DE
Step 5: 5-(4-Chlorophenyl)-2-methyl-1,1-dioxo-[1,2,4]thiadiazinan-3-ylideneamine
Using a route similar to that described in Method A, step 3, DE5 is used to prepare the title compound (DE6).
As a variant of this method, DE2 is treated with ammonia and the resultant product is treated with sodium hydride and methyl iodide in DMF to give the product DE6




Method DF
Step 1: 2-Hydrazinocarbonylpropane-2-sulfonic acid Cyclohexylamide
Using a method similar to that described by S. Paik and E. H. White (Tetrahedron, 1996, 52, 5303), 2-cyclohexylsulfamoyl-2-methylpropionic acid ethyl ester DF1 (which is prepared by the method of A. De Blic et al. (Synthesis, 1982, 281)) in ethanol is treated with 1.2 equivalent of 95% hydrazine under N2 and the mixture is allowed to stand at RT for 12 h. The reaction mixture is concentrated to give the title compound DF2 which is used directly in Step 2.
Method DF
Step 2: 2-Cyclohexyl-5,5-dimethyl-1,2,4-thiadiazolidin-3-one-1,1-dioxide
A solution of DF2 in CH2Cl2 is refluxed under a N2 for 10 h. The solvent is removed in vacuo and the crude product is purified by flash chromatography to provide the title compound DF3.
Method DF
Step 3: 2-Cyclohexyl-5,5-dimethyl-1,2,4-thiadiazolidin-3-thione-1,1-dioxide
To a solution of DF3 in toluene (or xylene) is added Lawesson's reagent (1.2 equivalents), and the mixture is stirred at reflux for 2 h. The mixture is cooled and poured into cold water. The organic phase is dried (MgSO4) and filtered, and solvent is removed. The crude product is purified by flash chromatography to provide the title compound (DF4).
Method DF
Step 4: 2-Cyclohexyl-5,5-dimethyl-1,2,4-thiadiazolidin-3-imine-1,1-dioxide
Using a route similar to that described in Method A, step 3, DF4 is used to prepare the title compound (DF5).
The following table contains example compounds which were synthesized with procedure(s) similar to methods listed in the corresponding column and whose LCMS data (obs. mass) are also listed.
















Obs.


#
Compounds
Method
Mass


















1491




CF
297


 


1492




CF
333.9


 


1493




CF
329.9


 


1494




CF
367.9


 


1495




AW
281


 


1496




CF
306


 


1497




AB
307


 


1498




CF
314


 


1499




CF
318


 


1500




CF
325


 


1501




CF
325


 


1502




CF
330


 


1503




CF
336


 


1504




CF
336


 


1505




AB
340


 


1506




CE
342


 


1507




CF
343


 


1508




CF
344


 


1509




CF
344


 


1510




CF
344


 


1511




AB
354


 


1512




A
354


 


1513




CF
358


 


1514




CF
358


 


1515




BS
358


 


1516




A
364


 


1517




A
366


 


1518




A
366


 


1519




A
368


 


1520




A
370


 


1521




AB
374


 


1522




A
380


 


1523




A
382


 


1524




A
382


 


1525




BS
383


 


1526




CF
384


 


1527




A
384


 


1528




A
384


 


1529




A
384


 


1530




A
384


 


1531




A
396


 


1532




A
396


 


1533




A
397


 


1534




A
398


 


1535




A
398


 


1536




A
398


 


1537




A
398


 


1538




A
398


 


1539




A
400


 


1540




A
402


 


1541




AB
404


 


1542




A
406


 


1543




A
406


 


1544




BS
408


 


1545




A
410


 


1546




A
410


 


1547




A
411


 


1548




A
412


 


1549




A
412


 


1550




A
414


 


1551




CE
415


 


1552




A
416


 


1553




A
417


 


1554




A
417


 


1555




A
419


 


1556




A
420


 


1557




A
421


 


1558




A
422


 


1559




A
422


 


1560




A
422


 


1561




A
423


 


1562




A
423


 


1563




CE
424


 


1564




A
425


 


1565




A
426


 


1566




A
426


 


1567




A
426


 


1568




A
431


 


1569




A
431


 


1570




A
431


 


1571




A
433


 


1572




A
434


 


1573




A
437


 


1574




A
439


 


1575




A
465


 


1576




CG
470


 


1577




CG
470


 


1578




CG
470


 


1579




CG
470


 


1580




CE
474


 


1581




CG
484


 


1582




CG
484


 


1583




BR
489


 


1584




CF
274.1


 


1585




AW
311.1


 


1586




AB
312.1


 


1587




AB
319.1


 


1588




CF
320.1


 


1589




CF
325.1


 


1590




AB
328.1


 


1591




AW
332.1


 


1592




CE
333.1


 


1593




CF
336.1


 


1594




AW
337.1


 


1595




CF
337.1


 


1596




CF
337.1


 


1597




CF
337.1


 


1598




AB
338.1


 


1599




AB
338.1


 


1600




CE
338.1


 


1601




CF
339.1


 


1602




CE
339.1


 


1603




AB
342.1


 


1604




AW
343.1


 


1605




AB
345.1


 


1606




AB
346.1


 


1607




AB
350.1


 


1608




CF
350.1


 


1609




AW
356.1


 


1610




AW
357.1


 


1611




AW
359.1


 


1612




AB
362.1


 


1613




CE
364.1


 


1614




CE
365.1


 


1615




AW
367.1


 


1616




AW
368.1


 


1617




AW
372.1


 


1618




CF
373.1


 


1619




AB
378.1


 


1620




AW
378.1


 


1621




CF
379.1


 


1622




CF
384.1


 


1623




BQ
386.1


 


1624




BQ
387.1


 


1625




AB
388.1


 


1626




CO
399.1


 


1627




BW
412.1


 


1628




BW
412.1


 


1629




CE
414.1


 


1630




BQ
419.1


 


1631




AW
421.1


 


1632




AM
425.1


 


1633




AW
425.1


 


1634




BW
426.1


 


1635




AW
436.1


 


1636




BQ
439.1


 


1637




BQ
440.1


 


1638




BQ
453.1


 


1639




CH
455.1


 


1640




BW
463.1


 


1641




Q
468.1


 


1642




BS
478.1


 


1643




BS
478.1


 


1644




BS
484.1


 


1645




BS
484.1


 


1646




BQ
492.1


 


1647




BW
492.1


 


1648




BW
495.1


 


1649




BW
496.1


 


1650




Q
560.1


 


1651




AW
569.1


 


1652




BW
573.1


 


1653




AW
470.1


 


1654




AW
307.2


 


1655




AW
308.2


 


1656




CP
308.2


 


1657




AW
315.2


 


1658




AW
321.2


 


1659




CO
321.2


 


1660




AW
325.2


 


1661




AW
326.2


 


1662




AW
328.2


 


1663




AW
331.2


 


1664




CE
335.2


 


1665




AW
336.2


 


1666




AW
337.2


 


1667




CF
339.2


 


1668




AW
340.2


 


1669




CO
341.2


 


1670




AW
342.2


 


1671




AW
346.2


 


1672




AW
350.2


 


1673




CJ
352.2


 


1674




AW
354.2


 


1675




AW
355.2


 


1676




CE
359.2


 


1677




AW
361.2


 


1678




AW
361.2


 


1679




AW
361.2


 


1680




AW
362.2


 


1681




AW
368.2


 


1682




AW
372.2


 


1683




AW
374.2


 


1684




BQ
375.2


 


1685




CL
377.2


 


1686




BK
377.2


 


1687




AW
377.2


 


1688




CG
378.2


 


1689




AW
383.2


 


1690




CO
385.2


 


1691




BQ
386.2


 


1692




AW
406.2


 


1693




CL
408.2


 


1694




BS
409.2


 


1695




BW
412.2


 


1696




BW
413.2


 


1697




BW
413.2


 


1698




BS
420.2


 


1699




R
425.2


 


1700




R
425.2


 


1701




BQ
429.2


 


1702




BQ
430.2


 


1703




R
434.2


 


1704




R
434.2


 


1705




BW
437.2


 


1706




AW
439.2


 


1707




BQ
440.2


 


1708




BQ
441.2


 


1709




BQ
441.2


 


1710




BW
442.2


 


1711




BQ
445.2


 


1712




BQ
446.2


 


1713




R
446.2


 


1714




R
446.2


 


1715




BS
448.2


 


1716




R
448.2


 


1717




BQ
450.2


 


1718




BQ
450.2


 


1719




BW
451.2


 


1720




CI
452.2


 


1721




BQ
454.2


 


1722




BQ
454.2


 


1723




AW
419.2


 


1724




AW
423.2


 


1725




AW
430.2


 


1726




AW
431.2


 


1727




AW
435.2


 


1728




CK
439.2


 


1729




AW
441.2


 


1730




AW
450.3


 


1731




CK
453.3


 


1732




CK
453.3


 


1733




AW
453.3


 


1734




CK
455.3


 


1735




L
467.3


 


1736




L
467.3


 


1737




CK
469.3


 


1738




CK
481.3


 


1739




CK
483.3


 


1740




CK
497.3


 


1741




CK
525.3


 


1742




BQ
515.3


 


1743




BQ
516.3


 


1744




BQ
519.3


 


1745




BS
522.3


 


1746




BQ
525.3


 


1747




BQ
532.3


 


1748




CG
576.3


 


1749




BQ
455.3


 


1750




BW
456.3


 


1751




BQ
456.3


 


1752




BQ
456.3


 


1753




BS
456.3


 


1754




BQ
456.3


 


1755




AW
456.3


 


1756




BQ
548.3


 


1757




BQ
458.3


 


1758




BQ
458.3


 


1759




BQ
458.3


 


1760




BS
460.3


 


1761




R
460.3


 


1762




BW
462.3


 


1763




BW
462.3


 


1764




BW
463.3


 


1765




BQ
464.3


 


1766




BQ
464.3


 


1767




BW
465.3


 


1768




BQ
467.3


 


1769




Q
467.3


 


1770




BS
468.3


 


1771




BW
468.3


 


1772




Q
468.3


 


1773




BQ
469.3


 


1774




BQ
469.3


 


1775




CG
469.3


 


1776




BQ
470.3


 


1777




BQ
470.3


 


1778




BS
472.3


 


1779




BQ
473.3


 


1780




BQ
473.3


 


1781




BS
473.3


 


1782




Q
473.3


 


1783




AW
473.3


 


1784




BQ
474.3


 


1785




BQ
478.3


 


1786




AZ
478.3


 


1787




AZ
478.3


 


1788




BS
479.3


 


1789




Q
481.3


 


1790




BS
482.3


 


1791




Q
482.3


 


1792




R
482.3


 


1793




R
482.3


 


1794




R
482.3


 


1795




R
482.3


 


1796




BS
484.3


 


1797




R
486.3


 


1798




R
486.3


 


1799




CK
487.3


 


1800




BS
488.3


 


1801




BS
488.3


 


1802




BS
488.3


 


1803




BQ
488.3


 


1804




BW
488.3


 


1805




R
488.3


 


1806




BQ
489.3


 


1807




BQ
489.3


 


1808




AW
489.3


 


1809




BQ
492.3


 


1810




Q
493.3


 


1811




BS
497.3


 


1812




CG
497.3


 


1813




BS
498.3


 


1814




R
498.3


 


1815





498.3


 


1816





498.3


 


1817




R
500.3


 


1818




R
502.3


 


1819




R
502.3


 


1820




BS
504.3


 


1821




BS
504.3


 


1822




BQ
504.3


 


1823




BQ
508.3


 


1824




CF
329.1, 331.1


 


1825




CF
334.0, 336.0


 


1826




CF
342.1, 344.1


 


1827




CF
352.0, 353.9


 


1828




CF
358.1, 360.1


 


1829




CF
363.1, 365.1


 


1830




CF
367.9, 369.9


 


1831




A
501.1 499


 


1832




CE
309









Human Cathepsin D FRET Assay
This assay can be run in either continuous or endpoint format. The substrate used below has been described (Y. Yasuda et al., J. Biochem., 125, 1137 (1999)). Substrate and enzyme are commercially available.
The assay is run in a 30 ul final volume using a 384 well Nunc black plate. 8 concentrations of compound are pre-incubated with enzyme for 30 mins at 37 C followed by addition of substrate with continued incubation at 37 C for 45 mins. The rate of increase in fluorescence is linear for over 1 h and is measured at the end of the incubation period using a Molecular Devices FLEX station plate reader. Kis are interpolated from the IC50s using a Km value of 4 uM and the substrate concentration of 2.5 uM.
Reagents
Na-Acetate pH 5
1% Brij-35 from 10% stock (Calbiochem)
DMSO
Purified (>95%) human liver Cathepsin D (Athens Research & Technology Cat#16-12-030104)
Peptide substrate (Km=4 uM) Mca-Gly-Lys-Pro-Ile-Leu-Phe-Phe-Arg-Leu-Lys(Dnp)-D-Arg-NH2 Bachem Cat # M-2455
Pepstatin is used as a control inhibitor (Ki ̃0.5 nM) and is available from Sigma.
Nunc 384 well black plates
Final Assay Buffer Conditions
100 mM Na Acetate pH 5.0
0.02% Brij-35
1% DMSO
Compound is diluted to 3× final concentration in assay buffer containing 3% DMSO. 10 ul of compound is added to 10 ul of 2.25 nM enzyme (3×) diluted in assay buffer without DMSO, mixed briefly, spun, and incubated at 37 C for 30 mins. 3× substrate (7.5 uM) is prepared in 1× assay buffer without DMSO. 10 ul of substrate is added to each well mixed and spun briefly to initiate the reaction. Assay plates are incubated at 37 C for 45 mins and read on 384 compatible fluorescence plate reader using a 328 nm Ex and 393 nm Em.
Compounds of the present invention exhibit hCathD Ki data ranges from about 0.1 to about 500 nM, preferably about 0.1 to about 100 nM more preferably about 0.1 to about 75 nM.
The following are examples of compounds that exhibit hCathD Ki data under 75 nM.










structure













 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 















The following compound




has a hCath D Ki value of 0.45 nM.

BACE-1 Cloning, Protein Expression and Purification
A predicted soluble form of human BACE1 (sBACE1, corresponding to amino acids 1-454) was generated from the full length BACE1 cDNA (full length human BACE1 cDNA in pcDNA4/mycHisA construct; University of Toronto) by PCR using the advantage-GC cDNA PCR kit (Clontech, Palo Alto, Calif.). A HindIII/PmeI fragment from pcDNA4-sBACE1myc/His was blunt ended using Klenow and subcloned into the Stu I site of pFASTBACl(A) (Invitrogen). A sBACE1mycHis recombinant bacmid was generated by transposition in DH10Bac cells (GIBCO/BRL). Subsequently, the sBACE1mycHis bacmid construct was transfected into sf9 cells using CellFectin (Invitrogen, San Diego, Calif.) in order to generate recombinant baculovirus. Sf9 cells were grown in SF 900-II medium (Invitrogen) supplemented with 3% heat inactivated FBS and 0.5× penicillin/streptomycin solution (Invitrogen). Five milliliters of high titer plaque purified sBACEmyc/His virus was used to infect 1 L of logarithmically growing sf9 cells for 72 hours. Intact cells were pelleted by centrifugation at 3000×g for 15 minutes. The supernatant, containing secreted sBACE1, was collected and diluted 50% v/v with 100 mM HEPES, pH 8.0. The diluted medium was loaded onto a Q-sepharose column. The Q-sepharose column was washed with Buffer A (20 mM HEPES, pH 8.0, 50 mM NaCl).
Proteins, were eluted from the Q-sepharose column with Buffer B (20 mM HEPES, pH 8.0, 500 mM NaCl). The protein peaks from the O-sepharose column were pooled and loaded onto a Ni-NTA agarose column. The Ni-NTA column was then washed with Buffer C (20 mM HEPES, pH 8.0, 500 mM NaCl). Bound proteins were then eluted with Buffer D (Buffer C+250 mM imidazole). Peak protein fractions as determined by the Bradford Assay (Biorad, CA) were concentrated using a Centricon 30 concentrator (Millipore). sBACE1 purity was estimated to be  ̃90% as assessed by SDS-PAGE and Commassie Blue staining. N-terminal sequencing indicated that greater than 90% of the purified sBACE1 contained the prodomain; hence this protein is referred to as sproBACE1
Peptide Hydrolysis Assay
The inhibitor, 25 nM EuK-biotin labeled APPsw substrate (EuK-KTEEISEVNLDAEFRHDKC-biotin; CIS-Bio International, France), 5 μM unlabeled APPsw peptide (KTEEISEVNLDAEFRHDK; American Peptide Company, Sunnyvale, Calif.), 7 nM sproBACE1, 20 mM PIPES pH 5.0, 0.1% Brij-35 (protein grade, Calbiochem, San Diego, Calif.), and 10% glycerol were preincubated for 30 min at 30° C. Reactions were initiated by addition of substrate in a 5 μl aliquot resulting in a total volume of 25 μl. After 3 hr at 30° C. reactions were terminated by addition of an equal volume of 2× stop buffer containing 50 mM Tris-HCl pH 8.0, 0.5 M KF, 0.001% Brij-35, 20 μg/ml SA-XL665 (cross-linked allophycocyanin protein coupled to streptavidin; CIS-Bio International, France) (0.5 μg/well). Plates were shaken briefly and spun at 1200×g for 10 seconds to pellet all liquid to the bottom of the plate before the incubation. HTRF measurements were made on a Packard Discovery® HTRF plate reader using 337 nm laser light to excite the sample followed by a 50 μs delay and simultaneous measurements of both 620 nm and 665 nm emissions for 400 μs.
IC50 determinations for inhibitors, (I), were determined by measuring the percent change of the relative fluorescence at 665 nm divided by the relative fluorescence at 620 nm, (6651620 ratio), in the presence of varying concentrations of I and a fixed concentration of enzyme and substrate. Nonlinear regression analysis of this data was performed using GraphPad Prism 3.0 software selecting four parameter logistic equation, that allows for a variable slope. Y=Bottom+(Top-Bottom)/(1+10^(LogEC50−X)*Hill Slope)); X is the logarithm of concentration of I, Y is the percent change in ratio and Y starts at bottom and goes to top with a sigmoid shape.
Compounds of the present invention have an IC50 range from about 0.001 to about 500 μM, preferably about 0.001 to about 100 μM, more preferably about 0.001 to about 20 μM.
Examples of compounds with human BACE 1 IC50<1 μM are listed below:





































Human Mature Renin Enzyme Assay:

Human Renin was cloned from a human kidney cDNA library and C-terminally epitope-tagged with the V5-6His sequence into pcDNA3.1. pCNDA3.1-Renin-V5-6His was stably expressed in HEK293 cells and purified to >80% using standard Ni-Affinity chromatography. The prodomain of the recombinant human renin-V5-6His was removed by limited proteolysis using immobilized TPCK-trypsin to give mature-human renin. Renin enzymatic activity was monitored using a commercially available fluorescence resonance energy transfer (FRET) peptide substrate, RS-1 (Molecular Probes, Eugene, Oreg.) in 50 mM Tris-HCl pH 8.0, 100 mM NaCl, 0.1% Brij-35 and 5% DMSO buffer for 40 mins at 30 degrees celsius in the presence or absence of different concentrations of test compounds. Mature human Renin was present at approximately 200 nM. Inhibitory activity was defined as the percent decrease in renin induced fluorescence at the end of the 40 min incubation compared to vehicle controls and samples lacking enzyme.












I% of 



hRenin



at


Compound
100 μM











68.8


 






75.3


 






76.9









In the aspect of the invention relating to a combination of at least one compound of formula I with at least one cholinesterase inhibitor, acetyl- and/or butyrylcholinesterase inhibitors can be used. Examples of cholinesterase inhibitors are tacrine, donepezil, rivastigmine, galantamine, pyridostigmine and neostigmine, with tacrine, donepezil, rivastigmine and galantamine being preferred. Preferably, these combinations are directed to the treatment of Alzheimer's disease.
In the aspect of the invention relating to a combination of at least one compound of formula I with at least one muscarinic m1 agonist or m2 antagonist can be used. Examples of m1 agonists are known in the art. Examples of m2 antagonists are also known in the art; in particular, m2 antagonists are disclosed in U.S. Pat. Nos. 5,883,096; 6,037,352; 5,889,006; 6,043,255; 5,952,349; 5,935,958; 6,066,636; 5,977,138; 6,294,554; 6,043,255; and 6,458,812; and in WO 03/031412, all of which are incorporated herein by reference.
In other aspects of the invention relating to a combination of at least one compound of formula I and at least one other agent, for example a beta secretase inhibitor; a gamma secretase inhibitor; an HMG-CoA reductase inhibitor such as atorvastatin, lovastatin, simvistatin, pravastatin, fluvastatin and rosuvastatin; non-steroidal anti-inflammatory agents such as, but not necessarily limited to ibuprofen, relafen or naproxen; N-methyl-D-aspartate receptor antagonists such as memantine; anti-amyloid antibodies including humanized monoclonal antibodies; vitamin E; nicotinic acetylcholine receptor agonists; CB1 receptor inverse agonists or CB1 receptor antagonists; antibiotics such as doxycycline; growth hormone secretagogues; histamine H3 antagonists; AMPA agonists; PDE4 inhibitors; GABAA inverse agonists; inhibitors of amyloid aggregation; glycogen synthase kinase beta inhibitors; promoters of alpha secretase activity. Preferably, these combinations are directed to the treatment of Alzheimer's disease.
For preparing pharmaceutical compositions from the compounds described by this invention, inert, pharmaceutically acceptable carriers can be either solid or liquid. Solid form preparations include powders, tablets, dispersible granules, capsules, cachets and suppositories. The powders and tablets may be comprised of from about 5 to about 95 percent active ingredient. Suitable solid carriers are known in the art, e.g. magnesium carbonate, magnesium stearate, talc, sugar or lactose. Tablets, powders, cachets and capsules can be used as solid dosage forms suitable for oral administration. Examples of pharmaceutically acceptable carriers and methods of manufacture for various compositions may be found in A. Gennaro (ed.), Remington's Pharmaceutical Sciences, 18th Edition, (1990), Mack Publishing Co., Easton, Pa.
Liquid form preparations include solutions, suspensions and emulsions. As an example may be mentioned water or water-propylene glycol solutions for parenteral injection or addition of sweeteners and opacifiers for oral solutions, suspensions and emulsions. Liquid form preparations may also include solutions for intranasal administration.
Aerosol preparations suitable for inhalation may include solutions and solids in powder form, which may be in combination with a pharmaceutically acceptable carrier, such as an inert compressed gas, e.g. nitrogen.
Also included are solid form preparations which are intended to be converted, shortly before use, to liquid form preparations for either oral or parenteral administration. Such liquid forms include solutions, suspensions and emulsions.
The compounds of the invention may also be deliverable transdermally. The transdermal compositions can take the form of creams, lotions, aerosols and/or emulsions and can be included in a transdermal patch of the matrix or reservoir type as are conventional in the art for this purpose.
Preferably the compound is administered orally.
Preferably, the pharmaceutical preparation is in a unit dosage form. In such form, the preparation is subdivided into suitably sized unit doses containing appropriate quantities of the active component, e.g., an effective amount to achieve the desired purpose.
The quantity of active compound in a unit dose of preparation may be varied or adjusted from about 1 mg to about 100 mg, preferably from about 1 mg to about 50 mg, more preferably from about 1 mg to about 25 mg, according to the particular application.
The actual dosage employed may be varied depending upon the requirements of the patient and the severity of the condition being treated. Determination of the proper dosage regimen for a particular situation is within the skill of the art. For convenience, the total daily dosage may be divided and administered in portions during the day as required.
The amount and frequency of administration of the compounds of the invention and/or the pharmaceutically acceptable salts thereof will be regulated according to the judgment of the attending clinician considering such factors as age, condition and size of the patient as well as severity of the symptoms being treated. A typical recommended daily dosage regimen for oral administration can range from about 1 mg/day to about 300 mg/day, preferably 1 mg/day to 50 mg/day, in two to four divided doses.
When a compound of formula I is used in combination with a cholinesterase inhibitor to treat cognitive disorders, these two active components may be co-administered simultaneously or sequentially, or a single pharmaceutical composition comprising a compound of formula I and a cholinesterase inhibitor in a pharmaceutically acceptable carrier can be administered. The components of the combination can be administered individually or together in any conventional oral or parenteral dosage form such as capsule, tablet, powder, cachet, suspension, solution, suppository, nasal spray, etc. The dosage of the cholinesterase inhibitor can be determined from published material, and may range from 0.001 to 100 mg/kg body weight.
When separate pharmaceutical compositions of a compound of formula I and a cholinesterase inhibitor are to be administered, they can be provided in a kit comprising in a single package, one container comprising a compound of formula I in a pharmaceutically acceptable carrier, and a separate container comprising a cholinesterase inhibitor in a pharmaceutically acceptable carrier, with the compound of formula I and the cholinesterase inhibitor being present in amounts such that the combination is therapeutically effective. A kit is advantageous for administering a combination when, for example, the components must be administered at different time intervals or when they are in different dosage forms.
While the present invention has been described in conjunction with the specific embodiments set forth above, many alternatives, modifications and variations thereof will be apparent to those of ordinary skill in the art. All such alternatives, modifications and variations are intended to fall within the spirit and scope of the present invention.

## Claims

1. A compound, or an enantiomer thereof, or a tautomer or a pharmaceutically acceptable salt of said compound, said enantiomer, or said tautomer, said compound selected from the group consisting of:

2. A pharmaceutical composition comprising an effective amount of a compound of claim 1 and a pharmaceutically effective carrier.

3. A pharmaceutical composition according to claim 2, further comprising at least one additional active agent selected from:
a cholinesterase inhibitor; a muscarinic m1 agonist; a muscarinic m2 antagonist; a N-methyl-D-aspartate receptor antagonist; a beta secretase inhibitor other than a compound of claim 1; a gamma secretase inhibitor; an HMG-CoA reductase inhibitor; a cholesterol absorption inhibitor; a non-steroidal anti-inflammatory agent; an anti-amyloid antibody; vitamin E; a nicotinic acetylcholine receptor agonist; a CB1 receptor inverse agonist; a CB1 receptor antagonist; an antibiotic; a growth hormone secretagogue; a histamine H3 antagonist; an AMPA agonist; a PDE4 inhibitor; a GABAA inverse agonist; an inhibitor of amyloid aggregation; a glycogen synthase kinase beta inhibitor; and a promoter of alpha secretase activity; and a pharmaceutically acceptable carrier.

4. A method of inhibiting BACE 1 comprising administering an effective amount of a compound according to claim 1, or an enantiomer thereof, or a tautomer or a pharmaceutically acceptable salt of said compound, said enantiomer, or said tautomer.