Compounds and method for treatment of HIV

Description

FIELD OF THE INVENTION

The present invention relates generally to therapeutic compounds and compositions, as well as methods for treatment of HIV.

BACKGROUND OF THE INVENTION

Human immunodeficiency viruses (HIV) are lentiviruses from the family of retroviridae. Transmission is initiated by the passage of HIV across the mucosal barrier of sexual organs or placenta when exposed to infectious body fluids such as semen, vaginal secretions, or blood.

HIV, particularly the strains known as HIV type-1 (HIV-1) and type-2 (HIV-2) viruses, is the etiological agent of the complex disease that includes progressive destruction of the immune system AIDS (acquired immune deficiency syndrome) and degeneration of the central and peripheral nervous system. A common feature of retrovirus replication is the action of integrase, a viral enzyme that inserts the viral genome into the DNA of the mammal cell. Since integration is a vital step in retroviral replication, blocking it can halt further spread of the virus.

Toxicity or undesirable side effects of the common drugs for treating HIV infection, e.g., AZT or HIV protease inhibitors, are incompatible with their antiviral activity when used at an effective pharmaceutical concentration. Thus, there is still a need in the art for alternative compounds for treating HIV.

SUMMARY OF THE INVENTION

In an aspect, there is provided a compound of Formula I:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof;

X is selected from Se, N—OH, NH, NO₂, CN, N—CN, N═O, O or S, wherein:

when X is Se, N—OH, NH, or N—CN, custom character is a double bond, and

R¹, R², R³, R⁴and R⁵are each independently selected from H, halo, hydroxyl, amino, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted carbocyclic group, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group;

when X is selected from NO₂, CN or N═O, custom character is a single bond, and

when X is O or S, custom character is a double bond,

R¹, R², R³, and R⁴are each independently selected from H, halo, hydroxyl, amino, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted carbocyclic group, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group, and

R⁵is —(C═O)NR⁶R⁷or

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wherein R⁶and R⁷are each independently selected from H, halo, hydroxyl, amino, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted carbocyclic group, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group, and

wherein Z and A are each independently selected from CR⁹or N, and R⁸and R⁹are each independently selected from H, halo, hydroxyl, amino, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted carbocyclic group, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group.

In another aspect, R¹, R², R³, and R⁴are each independently selected from H, halo, hydroxyl, cyano, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted haloalkyl, substituted or unsubstituted hydroxyalkyl, substituted or unsubstituted alkoxy, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, a substituted or unsubstituted heteroaromatic group, carboxyl, alkylcarbonyl, arylcarbonyl, cycloalkylcarbonyl, heterocyclylcarbonyl, amino, aminoalkyl, alkylaminoalkyl, heterocyclylalkyl, aralkyl, arylalkenyl, arylalkynyl, alkylthio, alkylamino, arylamino, heteroarylamino, aralkylamino, alkylaminoalkylamino, arylthio, aralkylthio, aryloxy, aralkoxy, heterocyclylalkoxy, heterocyclyloxyalkyl, cycloalkyl, and cycloalkenyl.

In a further aspect, R¹, R², R³, and R⁴are each independently selected from H or substituted or unsubstituted alkyl. In another aspect, X is selected from Se, N—OH, NH, NO₂, CN, N—CN, or N═O; and R⁵is selected from H, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group. In yet another aspect, R⁵is —(C═O)Y and Y is selected from H, halo, hydroxyl, amino, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted carbocyclic group, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group. In still another aspect, Y is selected from H, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group. In another aspect, the —(C═O)Y is —(C═O)NR⁶R⁷and R⁶and R⁷are each independently selected from H or the substituted or unsubstituted hydrocarbon group. In another aspect, the substituted or unsubstituted hydrocarbon group is selected from a substituted or unsubstituted alkyl group. In another aspect, the substituted or unsubstituted alkyl group is a substituted or unsubstituted alkylaryl or a substituted or unsubstituted alkylheteroaryl. In another aspect, the substituted or unsubstituted alkylaryl is a substituted or unsubstituted alkylphenyl, wherein the phenyl group is substituted with a halo group.

In a further aspect, R⁵is —(C═O)OR⁶and R⁶is selected from H or a substituted or unsubstituted hydrocarbon group. In another aspect, R⁶is selected from a substituted or unsubstituted alkyl group. In yet another aspect, R⁶is H. In another aspect, R¹, R², R³, and R⁴are each independently selected from a substituted or unsubstituted alkylaryl. In another aspect, the substituted or unsubstituted alkylaryl is a substituted or unsubstituted alkylphenyl, wherein the phenyl group is substituted with a halo group. In another aspect, the compound is selected from:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof.

In another aspect, X is selected from Se, N—OH, NH, or N═O. In another aspect, X is O or S; and R⁶and R⁷are each independently selected from H or the substituted or unsubstituted hydrocarbon group. In another aspect, the substituted or unsubstituted hydrocarbon group is selected from a substituted or unsubstituted alkyl group. In yet another aspect, the substituted or unsubstituted alkyl group is a substituted or unsubstituted alkylaryl or a substituted or unsubstituted alkylheteroaryl. In another aspect, the substituted or unsubstituted alkylaryl is a substituted or unsubstituted alkylphenyl, wherein the phenyl group is substituted with a halo group. In another aspect, the halo group is selected from bromo, chloro, fluoro or iodo.

In another aspect, the compound is selected from:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof.

In another aspect, X is selected from Se, N—OH, NH, or N—CN; and R⁵is selected from H, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group. In another aspect, R⁵is selected from a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group. In another aspect, R⁵is a substituted or unsubstituted heteroaromatic group. In another aspect, R⁵is

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wherein Z and A are each independently selected from CR⁹or N, and R⁸and R⁹are each independently selected from H, halo, hydroxyl, amino, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted carbocyclic group, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group. In yet another aspect, at least one of Z and A is N. In another aspect, both Z and A are N. In another aspect, R⁸is a substituted or unsubstituted hydrocarbon group. In another aspect, R⁸is selected from a substituted or unsubstituted alkyl group. In another aspect, the substituted or unsubstituted alkyl group is a substituted or unsubstituted alkylaryl or a substituted or unsubstituted alkylheteroaryl. In another aspect, the substituted or unsubstituted alkylaryl is a substituted or unsubstituted alkylphenyl, wherein the phenyl group is substituted with a halo group. In another aspect, the halo group is selected from bromo, chloro, fluoro or iodo.

In yet another aspect, the compound is selected from:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof.

In still another aspect, there is provided a compound of Formula II:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof;

X is selected from Se, N—OH, NH, NO₂, CN, N—CN, N═O, O or S, wherein:

when X is Se, N—OH, NH, N—CN, or S, custom character is a double bond, and

R¹, R², and R³are each independently selected from H, halo, hydroxyl, amino, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted carbocyclic group, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group;

when X is selected from NO₂, CN or N═O, custom character is a single bond, and

when X is O, custom character is a double bond,

R¹and R²are each independently selected from H, halo, hydroxyl, amino, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted carbocyclic group, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group, and

R³is

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In another aspect, R¹and R²are each independently selected from H, halo, hydroxyl, cyano, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted haloalkyl, substituted or unsubstituted hydroxyalkyl, substituted or unsubstituted alkoxy, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, a substituted or unsubstituted heteroaromatic group, carboxyl, alkylcarbonyl, arylcarbonyl, cycloalkylcarbonyl, heterocyclylcarbonyl, amino, aminoalkyl, alkylaminoalkyl, heterocyclylalkyl, aralkyl, arylalkenyl, arylalkynyl, alkylthio, alkylamino, arylamino, heteroarylamino, aralkylamino, alkylaminoalkylamino, arylthio, aralkylthio, aryloxy, aralkoxy, heterocyclylalkoxy, heterocyclyloxyalkyl, cycloalkyl, and cycloalkenyl. In yet another aspect, R¹and R²are each independently selected from H or substituted or unsubstituted alkyl. In another aspect, X is selected from Se, N—OH, NH, NO₂, CN, N—CN, N═O, or S; and R³is selected from H, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group. In another aspect, R³is selected from a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group. In another aspect, R³is a substituted or unsubstituted heteroaromatic group. In still another aspect, R³is

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wherein Z and A are each independently selected from CR¹⁰or N, and R⁴and R¹⁰are each independently selected from H, halo, hydroxyl, amino, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted carbocyclic group, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group. In another aspect, X is O. In another aspect, at least one of Z and A is N. In another aspect, both Z and A are N. In another aspect, R⁴is a substituted or unsubstituted hydrocarbon group. In another aspect, R⁴is selected from a substituted or unsubstituted alkyl group. In another aspect, the substituted or unsubstituted alkyl group is a substituted or unsubstituted alkylaryl or a substituted or unsubstituted alkylheteroaryl. In another aspect, the substituted or unsubstituted alkylaryl is a substituted or unsubstituted alkylphenyl, wherein the phenyl group is substituted with a halo group. In another aspect, the halo group is selected from bromo, chloro, fluoro or iodo. In another aspect, X is selected from Se, N—OH, NH, N—CN, or S; and R³is selected from H, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group. In another aspect, R³is —(C═O)Y and Y is selected from H, halo, hydroxyl, amino, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted carbocyclic group, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group. In still another aspect, Y is selected from H, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group. In another aspect, the —(C═O)Y is —(C═O)NR⁸R⁹and R⁸and R⁹are each independently selected from H or the substituted or unsubstituted hydrocarbon group. In another aspect, the substituted or unsubstituted hydrocarbon group is selected from a substituted or unsubstituted alkyl group. In another aspect, the substituted or unsubstituted alkyl group is a substituted or unsubstituted alkylaryl or a substituted or unsubstituted alkylheteroaryl. In another aspect, the substituted or unsubstituted alkylaryl is a substituted or unsubstituted alkylphenyl, wherein the phenyl group is substituted with a halo group. In another aspect, the compound is selected from:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof.

In another aspect, wherein the compound above is an HIV integrase inhibitor.

In another aspect, there is provided a pharmaceutical composition comprising the compound above, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, optionally with a pharmaceutically acceptable carrier or diluent. In another aspect, there is provided the pharmaceutical composition in combination with at least one other anti-HIV agent.

In another aspect, there is provided a method for the treatment of HIV in a mammal comprising administering to said mammal an anti-HIV effective treatment amount of the compound above, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, optionally with a pharmaceutically acceptable carrier or diluent.

In another aspect, there is provided a method for salvage therapy in the treatment of HIV in a mammal comprising administering to said mammal an anti-HIV effective treatment amount of a compound above, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, optionally with a pharmaceutically acceptable carrier or diluent. In another aspect, the mammal is human. In another aspect, the method further comprises co-administering at least one other anti-HIV agent in combination and/or in alternation with the compound.

In yet another aspect, there is provided a use of an anti-HIV effective treatment amount of the compound above, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, optionally with a pharmaceutically acceptable carrier or diluent, in the manufacture of a medicament for the treatment of HIV in a mammal.

In another aspect, there is provided a use of an anti-HIV effective treatment amount of the compound above, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, optionally with a pharmaceutically acceptable carrier or diluent, in the manufacture of a medicament for salvage therapy in the treatment of HIV in a mammal.

In another aspect, there is provided a use of an anti-HIV effective treatment amount of the compound above, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, optionally with a pharmaceutically acceptable carrier or diluent, for salvage therapy in the treatment of HIV in a mammal.

In another aspect, the mammal is human. In another aspect, the use further comprises use of at least one other anti-HIV agent in combination and/or in alternation with the compound.

In yet another aspect, there is provided a method for making the compound of Formula III:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof;

X is selected from Se, N—OH, NH, NO₂, CN, N—CN, N═O, O or S, wherein:

when X is selected from Se, N—OH, NH, N—CN, O or S, custom character is a double bond,

when X is selected from NO₂, CN or N═O, custom character is a single bond,

Z and A are each independently selected from CR⁹or N, and R⁸and R⁹are each independently selected from H, halo, hydroxyl, amino, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted carbocyclic group, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group,

wherein the method comprises:

a) reacting a compound of Formula VII with an amine of NH₂AHC(O)R⁸to form an intermediate of Formula VIII:

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b) reacting the intermediate of Formula VIII with base to yield Formula III, whereby X is oxygen;

c) reacting Formula III, whereby X is oxygen, under conditions to replace the oxygen of the carbonyl group with any X group defined herein to form the compounds of Formula III. In yet another aspect, wherein c) comprises reacting Formula III, whereby X is oxygen, with NH₂OH to form the compound of Formula III, wherein X is N—OH.

In another aspect, there is provided a method for making the compound of Formula IV:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof;

X is selected from Se, N—OH, NH, NO₂, CN, N—CN, N═O, O or S, wherein:

when X is Se, N—OH, NH, or N—CN, custom character is a double bond,

when X is selected from NO₂, CN or N═O, custom character is a single bond,

when X is O or S, custom character is a double bond,

wherein the method comprises:

a) reacting a compound of Formula VII with an amine of NHR⁶R⁷to form an intermediate of Formula IX:

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b) reacting the intermediate of Formula IX under conditions to replace the oxygen of the carbonyl group in the ring with any X group defined herein to form the compound of Formula IV. In another aspect, wherein b) comprises reacting Formula IX with NH₂OH to form the compound of Formula IV, wherein X is N—OH.

In yet another aspect, there is provided a method for making the compound of Formula V:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof;

X is selected from Se, N—OH, NH, NO₂, CN, N—CN, N═O, O or S, wherein:

when X is Se, N—OH, NH, N—CN, or S, custom character is a double bond, and

when X is selected from NO₂, CN or N═O, custom character is a single bond,

wherein the method comprises:

a) reacting a compound of Formula XII with an amine of NHR⁶R⁷to form an intermediate of Formula XIII:

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b) reacting the intermediate of Formula XIII under conditions to replace the oxygen of the carbonyl group in the ring with any X group defined herein to form the compound of Formula V. In yet another aspect, wherein b) comprises reacting Formula XIII with NH₂OH to form the compound of Formula V, wherein X is N—OH.

In another aspect, there is provided a method for making the compound of Formula VI:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof;

X is N—OH and custom character is a double bond,

wherein the method comprises:

a) reacting a compound of Formula X, whereby R is a benzyl group, with an amine of NH₂AHC(O)R⁴to form an intermediate of Formula XI:

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b) reacting the intermediate of Formula XI with base to yield Formula VI, whereby X is oxygen;

c) reacting Formula VI, whereby X is oxygen, with Lawesson's reagent, to yield Formula VI, whereby X is sulfur;

d) reacting Formula VI, whereby X is sulfur and R is a benzyl group, with NH₂OCH₂Ar, to yield Formula VI, whereby X is N—O—CH₂Ar; and

e) reducing Formula VI, whereby X is N—O—CH₂Ar, to yield Formula VI, whereby X is N—OH and R is a H.

Other features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples while indicating embodiments of the invention are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from the detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

Certain embodiments of the present invention will now be described more fully with reference to the accompanying drawings:

FIG. 1 shows a graph of the effect of COTI-HIV1Doxo in an HIV-1 integrase assay; and

FIG. 2 shows plots of the log-transformation of drug concentrations and best-fit curve for COTI-HIV-1 (A), COTI-HIV28233 (B), COTI-HIV28236 (C), and two sodium azide controls (D & E) to allow calculation of IC₅₀using non-linear regression.

DETAILED DESCRIPTION

The present invention is directed to new compounds, compositions comprising such compounds, a method of administration thereof, and use thereof to treat HIV. The compounds of this invention may function as inhibitors of HIV integrase.

DEFINITIONS

When describing the compounds, compositions, methods and uses of this invention, the following terms have the following meanings unless otherwise indicated.

The term “therapeutically effective amount” as used herein means that amount of active compound or pharmaceutical agent that elicits the biological or medicinal response in a tissue, system, animal or human that is being sought by a researcher, veterinarian, medical doctor or other clinician.

The compounds of the present invention may have asymmetric centers, chiral axes, and chiral planes (as described, for example, in: E. L. Eliel and S. H. Wilen, Stereo-chemistry of Carbon Compounds, John Wiley & Sons, New York, 1994, pages 1119-1190), and occur as racemates, racemic mixtures, and as individual diastereomers, with all possible isomers and mixtures thereof, including optical isomers, E isomers, and Z isomers, being included in the present invention. In addition, the compounds disclosed herein may exist as tautomers and both tautomeric forms are intended to be encompassed by the scope of the invention, even though only one tautomeric structure may be depicted.

Generally, reference to a certain element such as hydrogen or H is meant to, if appropriate, include all isotopes of that element.

Where the term “alkyl group” is used, either alone or within other terms such as “haloalkyl group” and “alkylamino group”, it encompasses linear or branched carbon radicals having, for example, one to about twenty carbon atoms or, in specific embodiments, one to about twelve carbon atoms. In other embodiments, alkyl groups are “lower alkyl” groups having one to about six carbon atoms. Examples of such groups include, but are not limited thereto, methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, pentyl, iso-amyl, hexyl and the like. In more specific embodiments, lower alkyl groups have one to four carbon atoms.

The term “alkenyl group” encompasses linear or branched carbon radicals having at least one carbon-carbon double bond. The term “alkenyl group” can encompass conjugated and non-conjugated carbon-carbon double bonds or combinations thereof. An alkenyl group, for example and without being limited thereto, can encompass two to about twenty carbon atoms or, in a particular embodiment, two to about twelve carbon atoms. In embodiments, alkenyl groups are “lower alkenyl” groups having two to about four carbon atoms. Examples of alkenyl groups include, but are not limited thereto, ethenyl, propenyl, allyl, propenyl, butenyl and 4-methylbutenyl. The terms “alkenyl group” and “lower alkenyl group”, encompass groups having “cis” and “trans” orientations, or alternatively, “E” and “Z” orientations.

The term “alkynyl group” denotes linear or branched carbon radicals having at least one carbon-carbon triple bond. The term “alkynyl group” can encompass conjugated and non-conjugated carbon-carbon triple bonds or combinations thereof. Alkynyl group, for example and without being limited thereto, can encompass two to about twenty carbon atoms or, in a particular embodiment, two to about twelve carbon atoms. In embodiments, alkynyl groups are “lower alkynyl” groups having two to about ten carbon atoms. Some examples are lower alkynyl groups having two to about four carbon atoms. Examples of such groups include propargyl, butynyl, and the like.

The term “halo” means halogens such as fluorine, chlorine, bromine or iodine atoms.

The term “haloalkyl group” encompasses groups wherein any one or more of the alkyl carbon atoms is substituted with halo as defined above. Specifically encompassed are monohaloalkyl, dihaloalkyl and polyhaloalkyl groups including perhaloalkyl. A monohaloalkyl group, for one example, may have either an iodo, bromo, chloro or fluoro atom within the group. Dihalo and polyhaloalkyl groups may have two or more of the same halo atoms or a combination of different halo groups. “Lower haloalkyl group” encompasses groups having 1-6 carbon atoms. In some embodiments, lower haloalkyl groups have one to three carbon atoms. Examples of haloalkyl groups include fluoromethyl, difluoromethyl, trifluoromethyl, chloromethyl, dichloromethyl, trichloromethyl, pentafluoroethyl, heptafluoropropyl, difluorochloromethyl, dichlorofluoromethyl, difluoroethyl, difluoropropyl, dichloroethyl and dichloropropyl.

The term “hydroxyalkyl group” encompasses linear or branched alkyl groups having, for example and without being limited thereto, one to about ten carbon atoms, any one of which may be substituted with one or more hydroxyl groups. In embodiments, hydroxyalkyl groups are “lower hydroxyalkyl” groups having one to six carbon atoms and one or more hydroxyl groups. Examples of such groups include hydroxymethyl, hydroxyethyl, hydroxypropyl, hydroxybutyl and hydroxyhexyl.

The term “alkoxy group” encompasses linear or branched oxy-containing groups each having alkyl portions of, for example and without being limited thereto, one to about ten carbon atoms. In embodiments, alkoxy groups are “lower alkoxy” groups having one to six carbon atoms. Examples of such groups include methoxy, ethoxy, propoxy, butoxy and tert-butoxy. In certain embodiments, lower alkoxy groups have one to three carbon atoms. The “alkoxy” groups may be further substituted with one or more halo atoms, such as fluoro, chloro or bromo, to provide “haloalkoxy” groups. In other embodiments, lower haloalkoxy groups have one to three carbon atoms. Examples of such groups include fluoromethoxy, chloromethoxy, trifluoromethoxy, trifluoroethoxy, fluoroethoxy, and fluoropropoxy.

The term “aromatic group” or “aryl group” means an aromatic group having one or more rings wherein such rings may be attached together in a pendent manner or may be fused. In particular embodiments, an aromatic group is one, two or three rings. Monocyclic aromatic groups may contain 4 to 10 carbon atoms, typically 4 to 7 carbon atoms, and more typically 4 to 6 carbon atoms in the ring. Typical polycyclic aromatic groups have two or three rings. Polycyclic aromatic groups having two rings typically have 8 to 12 carbon atoms, preferably 8 to 10 carbon atoms in the rings. Examples of aromatic groups include, but are not limited to, phenyl, naphthyl, tetrahydronaphthyl, indanyl, biphenyl, phenanthryl, anthryl or acenaphthyl.

The term “heteroatom” means an atom other than carbon. Typically, heteroatoms are selected from the group consisting of sulfur, phosphorous, nitrogen and oxygen atoms. Groups containing more than one heteroatom may contain different heteroatoms.

The term “heteroaromatic group” or “heteroaryl group” means an aromatic group having one or more rings wherein such rings may be attached together in a pendent manner or may be fused, wherein the aromatic group has at least one heteroatom. Monocyclic heteroaromatic groups may contain 4 to 10 member atoms, typically 4 to 7 member atoms, and more typically 4 to 6 member atoms in the ring. Typical polycyclic heteroaromatic groups have two or three rings. Polycyclic aromatic groups having two rings typically have 8 to 12 member atoms, more typically 8 to 10 member atoms in the rings. Examples of heteroaromatic groups include, but are not limited thereto, pyrrole, imidazole, thiazole, oxazole, furan, thiophene, triazole, pyrazole, isoxazole, isothiazole, pyridine, pyrazine, pyridazine, pyrimidine, triazine, indole, benzofuran, benzothiophene, benzimidazole, benzthiazole, quinoline, isoquinoline, quinazoline, quinoxaline and the like.

The term “carbocyclic group” means a saturated or unsaturated carbocyclic hydrocarbon ring. Carbocyclic groups are not aromatic. Carbocyclic groups are monocyclic or polycyclic. Polycyclic carbocyclic groups can be fused, spiro, or bridged ring systems. Monocyclic carbocyclic groups may contain 4 to 10 carbon atoms, typically 4 to 7 carbon atoms, and more typically 5 to 6 carbon atoms in the ring. Bicyclic carbocyclic groups may contain 8 to 12 carbon atoms, typically 9 to 10 carbon atoms in the rings.

The term “heterocyclic group” means a saturated or unsaturated ring structure containing carbon atoms and 1 or more heteroatoms in the ring. Heterocyclic groups are not aromatic. Heterocyclic groups are monocyclic or polycyclic. Polycyclic heterocyclic groups can be fused, spiro, or bridged ring systems. Monocyclic heterocyclic groups may contain 4 to 10 member atoms (i.e., including both carbon atoms and at least 1 heteroatom), typically 4 to 7, and more typically 5 to 6 in the ring. Bicyclic heterocyclic groups may contain 8 to 18 member atoms, typically 9 or 10 member atoms in the rings. Representative heterocyclic groups include, by way of example, pyrrolidine, imidazolidine, pyrazolidine, piperidine, 1,4-dioxane, morpholine, thiomorpholine, piperazine, 3-pyrroline and the like.

The term “heterogeneous group” means a saturated or unsaturated chain of non-hydrogen member atoms comprising carbon atoms and at least one heteroatom. Heterogeneous groups typically have 1 to 25 member atoms. More typically, the chain contains 1 to 12 member atoms, 1 to 10, and most typically 1 to 6. The chain may be linear or branched. Typical branched heterogeneous groups have one or two branches, more typically one branch. Typically, heterogeneous groups are saturated. Unsaturated heterogeneous groups may have one or more double bonds, one or more triple bonds, or both. Typical unsaturated heterogeneous groups have one or two double bonds or one triple bond. More typically, the unsaturated heterogeneous group has one double bond.

The term “hydrocarbon group” or “hydrocarbyl group” means a chain of 1 to 25 carbon atoms, typically 1 to 12 carbon atoms, more typically 1 to 10 carbon atoms, and most typically 1 to 8 carbon atoms. Hydrocarbon groups may have a linear or branched chain structure. Typical hydrocarbon groups have one or two branches, typically one branch. Typically, hydrocarbon groups are saturated. Unsaturated hydrocarbon groups may have one or more double bonds, one or more triple bonds, or combinations thereof. Typical unsaturated hydrocarbon groups have one or two double bonds or one triple bond; more typically unsaturated hydrocarbon groups have one double bond.

When the term “unsaturated” is used in conjunction with any group, the group may be fully unsaturated or partially unsaturated. However, when the term “unsaturated” is used in conjunction with a specific group defined herein, the term maintains the limitations of that specific group. For example, an unsaturated “carbocyclic group”, based on the limitations of the “carbocyclic group” as defined herein, does not encompass an aromatic group.

The terms “carboxy group” or “carboxyl group”, whether used alone or with other terms, such as “carboxyalkyl group”, denotes —(C═O)—O—.

The term “carbonyl group”, whether used alone or with other terms, such as “aminocarbonyl group”, denotes —(C═O)—.

The terms “alkylcarbonyl group” denotes carbonyl groups which have been substituted with an alkyl group. In certain embodiments, “lower alkylcarbonyl group” has lower alkyl group as described above attached to a carbonyl group.

The term “aminoalkyl group” encompasses linear or branched alkyl groups having one to about ten carbon atoms any one of which may be substituted with one or more amino groups. In some embodiments, the aminoalkyl groups are “lower aminoalkyl” groups having one to six carbon atoms and one or more amino groups. Examples of such groups include aminomethyl, aminoethyl, aminopropyl, aminobutyl and aminohexyl.

The term “alkylaminoalkyl group” encompasses aminoalkyl groups having the nitrogen atom independently substituted with an alkyl group. In certain embodiments, the alkylaminoalkyl groups are “loweralkylaminoalkyl” groups having alkyl groups of one to six carbon atoms. In other embodiments, the lower alkylaminoalkyl groups have alkyl groups of one to three carbon atoms. Suitable alkylaminoalkyl groups may be mono or dialkyl substituted, such as N-methylaminomethyl, N, N-dimethyl-aminoethyl, N, N-diethylaminomethyl and the like.

The term “aralkyl group” encompasses aryl-substituted alkyl groups. In embodiments, the aralkyl groups are “lower aralkyl” groups having aryl groups attached to alkyl groups having one to six carbon atoms. In other embodiments, the lower aralkyl groups phenyl is attached to alkyl portions having one to three carbon atoms. Examples of such groups include benzyl, diphenylmethyl and phenylethyl. The aryl in said aralkyl may be additionally substituted with halo, alkyl, alkoxy, haloalkyl and haloalkoxy.

The term “arylalkenyl group” encompasses aryl-substituted alkenyl groups. In embodiments, the arylalkenyl groups are “lower arylalkenyl” groups having aryl groups attached to alkenyl groups having two to six carbon atoms. Examples of such groups include phenylethenyl. The aryl in said arylalkenyl may be additionally substituted with halo, alkyl, alkoxy, haloalkyl and haloalkoxy.

The term “arylalkynyl group” encompasses aryl-substituted alkynyl groups. In embodiments, arylalkynyl groups are “lower arylalkynyl” groups having aryl groups attached to alkynyl groups having two to six carbon atoms. Examples of such groups include phenylethynyl. The aryl in said aralkyl may be additionally substituted with halo, alkyl, alkoxy, haloalkyl and haloalkoxy. The terms benzyl and phenylmethyl are interchangeable.

The term “alkylthio group” encompasses groups containing a linear or branched alkyl group, of one to ten carbon atoms, attached to a divalent sulfur atom. In certain embodiments, the lower alkylthio groups have one to three carbon atoms. An example of “alkylthio” is methylthio, (CH₃S—).

The term “alkylamino group” denotes amino groups which have been substituted with one alkyl group and with two alkyl groups, including terms “N-alkylamino” and “N,N-dialkylamino”. In embodiments, alkylamino groups are “lower alkylamino” groups having one or two alkyl groups of one to six carbon atoms, attached to a nitrogen atom. In other embodiments, lower alkylamino groups have one to three carbon atoms. Suitable “alkylamino” groups may be mono or dialkylamino such as N-methylamino, N-ethylamino, N,N-dimethylamino, N,N-diethylamino and the like.

The term “arylamino group” denotes amino groups which have been substituted with one or two aryl groups, such as N-phenylamino. The “arylamino” groups may be further substituted on the aryl ring portion of the group.

The term “heteroarylamino” denotes amino groups which have been substituted with one or two heteroaryl groups, such as N-thienylamino. The “heteroarylamino” groups may be further substituted on the heteroaryl ring portion of the group.

The term “aralkylamino group” denotes amino groups which have been substituted with one or two aralkyl groups. In other embodiments, there are phenyl-C₁-C₃-alkylamino groups, such as N-benzylamino. The “aralkylamino” groups may be further substituted on the aryl ring portion of the group.

The term “alkylaminoalkylamino group” denotes alkylamino groups which have been substituted with one or two alkylamino groups. In embodiments, there are C₁-C₃-alkylamino-C₁-C₃-alkylamino groups.

The term “arylthio group” encompasses aryl groups of six to ten carbon atoms, attached to a divalent sulfur atom. An example of “arylthio” is phenylthio. The term “aralkylthio group” encompasses aralkyl groups as described above, attached to a divalent sulfur atom. In certain embodiments there are phenyl-C₁-C₃-alkylthio groups. An example of “aralkylthio” is benzylthio.

The term “aryloxy group” encompasses optionally substituted aryl groups, as defined above, attached to an oxygen atom. Examples of such groups include phenoxy.

The term “aralkoxy group” encompasses oxy-containing aralkyl groups attached through an oxygen atom to other groups. In certain embodiments, aralkoxy groups are “lower aralkoxy” groups having optionally substituted phenyl groups attached to lower alkoxy group as described above.

The term “cycloalkyl group” includes saturated carbocyclic groups. In certain embodiments, cycloalkyl groups include C₃-C₆rings. In embodiments, there are compounds that include, cyclopentyl, cyclopropyl, and cyclohexyl.

The term “cycloalkenyl group” includes carbocyclic groups that have one or more carbon-carbon double bonds; conjugated or non-conjugated, or a combination thereof. “Cycloalkenyl” and “cycloalkyldienyl” compounds are included in the term “cycloalkenyl”. In certain embodiments, cycloalkenyl groups include C₃-C₆rings. Examples include cyclopentenyl, cyclopentadienyl, cyclohexenyl and cycloheptadienyl. The “cycloalkenyl” group may have 1 to 3 substituents such as lower alkyl, hydroxyl, halo, haloalkyl, nitro, cyano, alkoxy, lower alkylamino, and the like.

The term “suitable substituent”, “substituent” or “substituted” used in conjunction with the groups described herein refers to a chemically and pharmaceutically acceptable group, i.e., a moiety that does not negate the therapeutic activity of the inventive compounds. It is understood that substituents and substitution patterns on the compounds of the invention may be selected by one of ordinary skill in the art to provide compounds that are chemically stable and that can be readily synthesized by techniques known in the art, as well as those methods set forth below. If a substituent is itself substituted with more than one group, it is understood that these multiple groups may be on the same carbon/member atom or on different carbons/member atoms, as long as a stable structure results. Illustrative examples of some suitable substituents include, cycloalkyl, heterocyclyl, hydroxyalkyl, benzyl, carbonyl, halo, haloalkyl, perfluoroalkyl, perfluoroalkoxy, alkyl, alkenyl, alkynyl, hydroxy, oxo, mercapto, alkylthio, alkoxy, aryl or heteroaryl, aryloxy or heteroaryloxy, aralkyl or heteroaralkyl, aralkoxy or heteroaralkoxy, HO—(C═O)—, amido, amino, alkyl- and dialkylamino, cyano, nitro, carbamoyl, alkylcarbonyl, alkoxycarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, arylcarbonyl, aryloxycarbonyl, alkylsulfonyl, and arylsulfonyl. Typical substituents include aromatic groups, substituted aromatic groups, hydrocarbon groups including alkyl groups such as methyl groups, substituted hydrocarbon groups such as benzyl, and heterogeneous groups including alkoxy groups such as methoxy groups.

The term “fused” means in which two or more carbons/member atoms are common to two adjoining rings, e.g., the rings are “fused rings”.

The pharmaceutically acceptable salts of the compounds of this invention include the conventional non-toxic salts of the compounds of this invention as formed, e.g., from non-toxic inorganic or organic acids. For example, such conventional non-toxic salts include those derived from inorganic acids such as hydrochloric, hydrobromic, sulfuric, sulfamic, phosphoric, nitric and the like; and the salts prepared from organic acids such as acetic, propionic, succinic, glycolic, stearic, lactic, malic, tartaric, citric, ascorbic, pamoic, maleic, hydroxymaleic, phenylacetic, glutamic, benzoic, salicylic, sulfanilic, 2-acetoxy-benzoic, fumaric, toluenesulfonic, methanesulfonic, ethane disulfonic, oxalic, isethionic, trifluoroacetic and the like.

The pharmaceutically acceptable salts of the compounds of this invention can be synthesized from the compounds of this invention which contain a basic or acidic moiety by conventional chemical methods. Generally, the salts of the basic compounds are prepared either by ion exchange chromatography or by reacting the free base with stoichiometric amounts or with an excess of the desired salt-forming inorganic or organic acid in a suitable solvent or various combinations of solvents. Similarly, the salts of the acidic compounds are formed by reactions with the appropriate inorganic or organic base.

The present invention includes pharmaceutically acceptable salts, solvates and prodrugs of the compounds of the invention and mixtures thereof.

The terms “comprising”, “having” and “including”, and various endings thereof, are meant to be open ended, including the indicated component but not excluding other elements.

A compound of the invention is represented by a compound of Formula I:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof;

X is selected from Se, N—OH, NH, NO₂, CN, N—CN, N═O, O or S, wherein:

when X is Se, N—OH, NH, or N—CN, custom character is a double bond, and

when X is selected from NO₂, CN or N═O, custom character is a single bond, and

when X is O or S, custom character is a double bond,

R⁵is —(C═O)NR⁶R⁷or

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A compound of the invention is also represented by a compound of Formula II:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof;

X is selected from Se, N—OH, NH, NO₂, CN, N—CN, N═O, O or S, wherein:

when X is Se, N—OH, NH, N—CN, or S, custom character is a double bond, and

when X is selected from NO₂, CN or N═O, custom character is a single bond, and

when X is O, custom character is a double bond,

R³is

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- wherein Z and A are each independently selected from CR¹⁰or N, and R⁴and R¹⁰are each independently selected from H, halo, hydroxyl, amino, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted carbocyclic group, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group.

In one embodiment, there is provided a compound represented by a compound of Formula III:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof;

X is selected from Se, N—OH, NH, NO₂, CN, N—CN, N═O, O or S, wherein:

when X is selected from Se, N—OH, NH, N—CN, O or S, custom character is a double bond,

when X is selected from NO₂, CN or N═O, custom character is a single bond,

In another embodiment, both Z and A are N and R⁸is a substituted or unsubstituted hydrocarbon group. In a more specific embodiment, R⁸is selected from a substituted or unsubstituted alkyl group, such as a substituted or unsubstituted alkylaryl or a substituted or unsubstituted alkylheteroaryl. More specifically, the substituted or unsubstituted alkylaryl is a substituted or unsubstituted alkylphenyl, wherein the phenyl group is substituted with a halo group such as a 4-fluorobenzyl group. R¹, R², R³, and R⁴may be specifically H or substituted or unsubstituted alkyl groups.

In a further embodiment, there is provided a compound represented by a compound of Formula IV:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof;

X is selected from Se, N—OH, NH, NO₂, CN, N—CN, N═O, O or S, wherein:

when X is Se, N—OH, NH, or N—CN, custom character is a double bond,

when X is selected from NO₂, CN or N═O, custom character is a single bond,

when X is O or S, custom character is a double bond,

In another embodiment, R⁶and R⁷are each independently selected from a substituted or unsubstituted alkyl group. The substituted or unsubstituted alkyl group may be a substituted or unsubstituted alkylaryl or a substituted or unsubstituted alkylheteroaryl. More specifically, the substituted or unsubstituted alkylaryl is a substituted or unsubstituted alkylphenyl, wherein the phenyl group is substituted with a halo group such as a 4-fluorobenzyl group. R¹, R², R³, and R⁴may be specifically H or substituted or unsubstituted alkyl groups.

Specific embodiments include, without being limited thereto, compounds such as:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof.

In a further embodiment, there is provided a compound represented by a compound of Formula IVA:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof;

X is selected from Se, N—OH, NH, NO₂, CN, N—CN, N═O, O or S, wherein:

when X is Se, N—OH, NH, or N—CN, custom character is a double bond,

when X is selected from NO₂, CN or N═O, custom character is a single bond,

when X is O or S, custom character is a double bond,

wherein R⁶is selected from H, halo, a substituted or unsubstituted hydrocarbon group, a substituted or unsubstituted heterogeneous group, a substituted or unsubstituted carbocyclic group, a substituted or unsubstituted heterocyclic group, a substituted or unsubstituted aromatic group, or a substituted or unsubstituted heteroaromatic group.

In another embodiment, R⁶is selected from a substituted or unsubstituted alkyl group. In yet another embodiment, R⁶is H. In another embodiment, R¹, R², R³, and R⁴are each independently selected from a substituted or unsubstituted alkylaryl. In another embodiment, the substituted or unsubstituted alkylaryl is a substituted or unsubstituted alkylphenyl, wherein the phenyl group is substituted with a halo group.

In a further embodiment, the compound is selected from:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof.

In yet another embodiment, there is provided a compound represented by a compound of Formula V:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof;

X is selected from Se, N—OH, NH, NO₂, CN, N—CN, N═O, O or S, wherein:

when X is Se, N—OH, NH, N—CN, or S, custom character is a double bond, and

when X is selected from NO₂, CN or N═O, custom character is a single bond,

In another embodiment, R⁶and R⁷are each independently selected from a substituted or unsubstituted alkyl group. The substituted or unsubstituted alkyl group may be a substituted or unsubstituted alkylaryl or a substituted or unsubstituted alkylheteroaryl. More specifically, the substituted or unsubstituted alkylaryl is a substituted or unsubstituted alkylphenyl, wherein the phenyl group is substituted with a halo group such as a 4-fluorobenzyl group. R¹and R²may be specifically H or substituted or unsubstituted alkyl groups.

In another embodiment, there is provided a compound of Formula VI:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof;

X is selected from Se, N—OH, NH, NO₂, CN, N—CN, N═O, O or S, wherein:

when X is Se, N—OH, NH, N—CN, O or S, custom character is a double bond,

when X is selected from NO₂, CN or N═O, custom character is a single bond,

In another embodiment, both Z and A are N and R⁴is a substituted or unsubstituted hydrocarbon group. In a more specific embodiment, R⁴is selected from a substituted or unsubstituted alkyl group, such as a substituted or unsubstituted alkylaryl or a substituted or unsubstituted alkylheteroaryl. More specifically, the substituted or unsubstituted alkylaryl is a substituted or unsubstituted alkylphenyl, wherein the phenyl group is substituted with a halo group such as a 4-fluorobenzyl group. R¹and R²may be specifically H or substituted or unsubstituted alkyl groups.

Specific embodiments include, without being limited thereto, compounds such as:

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and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof.

The compounds of this invention may be prepared by employing reactions and standard manipulations that are known in the literature or exemplified herein.

The compounds of Formula III described herein can be prepared as follows:

a) reacting a compound of Formula VII with an amine of NH₂AHC(O)R⁸to form an intermediate of Formula VIII:

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b) reacting the intermediate of Formula VIII with base to yield Formula III, whereby X is oxygen;

c) reacting Formula III, whereby X is oxygen, with NH₂OH (or under conditions to replace the oxygen of the carbonyl group in the ring with any X group mentioned herein (e.g. Se, S, etc.)) to form the compounds of Formula III.

The compounds of Formula IV described herein can be prepared as follows:

a) reacting a compound of Formula VII with an amine of NHR⁶R⁷to form an intermediate of Formula IX:

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b) reacting the intermediate of Formula IX with NH₂OH (or under conditions to replace the oxygen of the carbonyl group in the ring with any X group mentioned herein (e.g. Se, S, etc.)) to form the compound of Formula IV.

The compounds of Formula V described herein can be prepared as follows:

a) reacting a compound of Formula XII with an amine of NHR⁶R⁷to form an intermediate of Formula XIII:

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b) reacting the intermediate of Formula XIII with NH₂OH (or under conditions to replace the oxygen of the carbonyl group in the ring with any X group mentioned herein (e.g. Se, S, etc.)) to form the compound of Formula V.

The compounds of Formula VI described herein can be prepared as follows:

a) reacting a compound of Formula X (R is a benzyl group) with an amine of NH₂AHC(O)R⁴to form an intermediate of Formula XI:

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b) reacting the intermediate of Formula XI with base to yield Formula VI, whereby X is oxygen and R is a benzyl group;

c) reacting Formula VI, whereby X is oxygen and R is a benzyl group, with Lawesson's reagent, to yield Formula VI, whereby X is sulfur and R is a benzyl group;

d) reacting Formula VI, whereby X is sulfur and R is a benzyl group, with NH₂OCH₂Ar, to yield Formula VI, whereby X is N—O—CH₂Ar and R is a benzyl group; and

e) reacting Formula VI, whereby X is N—O—CH₂Ar and R is a benzyl group, with H₂/Pd, to yield Formula VI, whereby X is N—O—H and R is a H.

The compounds of the present invention are useful in the treatment of HIV. Certain compounds of the present invention may exhibit reduced toxicity as compared with conventionally administered agents.

The methods and uses described herein can be specifically directed to inhibiting HIV integrase in a mammal in need thereof. Such methods and uses may prevent, treat or delay the onset of AIDS in a mammal in need thereof. The present invention also includes a compound of the present invention described herein, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof for use in, for use as a medicament for, and/or for use in the preparation of a medicament for: inhibiting HIV integrase, preventing or treating infection by HIV, or preventing, treating or delaying the onset of AIDS.

A composition can comprise the compound(s) of the present invention described herein, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, optionally in combination with a pharmaceutically acceptable carrier or diluent. The compounds of this invention may be administered, for example, to mammals, typically humans, either alone or, in combination with pharmaceutically acceptable carriers or diluents, optionally with known adjuvants, such as alum, in a pharmaceutical composition, according to standard pharmaceutical practice. The compounds can be administered orally or parenterally, including the intravenous, intramuscular, intraperitoneal, and subcutaneous routes of administration.

The term “administration” (e.g., “administering” a compound) in reference to a compound of the invention means introducing the compound or a prodrug of the compound into the system of the mammal in need of treatment. For the purpose of inhibiting HIV integrase, preventing or treating HIV infection or preventing, treating or delaying the onset of AIDS, the compounds of the present invention can be administered by any means that produces contact of the active agent with the agent's site of action. They can be administered by any conventional means available for use in conjunction with pharmaceuticals, either as individual therapeutic agents or in a combination of therapeutic agents. They can be administered alone, but typically are administered with a pharmaceutical carrier selected on the basis of the chosen route of administration and standard pharmaceutical practice. The compounds of the invention can, for example, be administered orally, parenterally (including subcutaneous injections, intravenous, intramuscular, intrasternal injection or infusion techniques), by inhalation spray, or rectally, in the form of a unit dosage of a pharmaceutical composition containing an effective amount of the compound and conventional non-toxic pharmaceutically-acceptable carriers, adjuvants and vehicles. Liquid preparations suitable for oral administration (e.g., suspensions, syrups, elixirs and the like) can be prepared according to techniques known in the art and can employ any of the usual media such as water, glycols, oils, alcohols and the like. Solid preparations suitable for oral administration (e.g., powders, pills, capsules and tablets) can be prepared according to techniques known in the art and can employ such solid excipients as starches, sugars, kaolin, lubricants, binders, disintegrating agents and the like. Parenteral compositions can be prepared according to techniques known in the art and typically employ sterile water as a carrier and optionally other ingredients, such as a solubility aid. Injectable solutions can be prepared according to methods known in the art wherein the carrier comprises a saline solution, a glucose solution or a solution containing a mixture of saline and glucose. Further description of methods suitable for use in preparing pharmaceutical compositions of the present invention and of ingredients suitable for use in said compositions is provided in Remington's Pharmaceutical Sciences, 18th edition, edited by A. R. Gennaro, Mack Publishing Co., 1990.

The compounds of this invention can be administered orally in a dosage range of 0.001 to 1000 mg/kg of mammal (e.g., human) body weight per day in a single dose or in divided doses. One preferred dosage range is 0.01 to 500 mg/kg body weight per day orally in a single dose or in divided doses. Another preferred dosage range is 0.1 to 100 mg/kg body weight per day orally in single or divided doses. For oral administration, the compositions can be provided in the form of tablets or capsules containing 1.0 to 500 milligrams of the active ingredient, particularly 1, 5, 10, 15, 20, 25, 50, 75, 100, 150, 200, 250, 300, 400, and 500 milligrams of the active ingredient for the symptomatic adjustment of the dosage to the patient to be treated. The specific dose level and frequency of dosage for any particular patient may be varied and will depend upon a variety of factors including the activity of the specific compound employed, the metabolic stability and length of action of that compound, the age, body weight, general health, sex, diet, mode and time of administration, rate of excretion, drug combination, the severity of the particular condition, and the host undergoing therapy.

The compounds of the present invention may be used with one or more agents useful in the treatment of HIV infection or AIDS. As the compounds of the present invention can be HIV integrase inhibitors, such compounds are also useful in salvage therapy for patients whose virus has mutated and acquired resistance to other drugs. Such inhibitors target a distinct step in the retroviral life cycle and therefore, may be taken in combination with other types of HIV drugs to minimize adaptation by the virus.

For example, the compounds of this invention may be effectively administered, whether at periods of pre-exposure and/or post-exposure, in combination with effective amounts of one or more HIV/AIDS antivirals, immunomodulators, antiinfectives, or vaccines useful for treating HIV infection or AIDS, such as those disclosed in Table 1 of International Patent Application No. WO 01/38332 or in the Table in International Patent Application WO 02/30930, incorporated herein by reference. Suitable HIV/AIDS antivirals for use in combination with the compounds of the present invention include, for example, HIV protease inhibitors (e.g., indinavir, atazanavir, lopinavir optionally with ritonavir, saquinavir, or nelfinavir), nucleoside HIV reverse transcriptase inhibitors (e.g., abacavir, lamivudine (3TC), zidovudine (AZT), or tenofovir), and non-nucleoside HIV reverse transcriptase inhibitors (e.g., efavirenz or nevirapine). It will be understood that the scope of combinations of the compounds of this invention with HIV/AIDS antivirals, immunomodulators, anti-infectives or vaccines is not limited to the foregoing substances or to the list in the above-referenced Tables, but includes in principle any combination with any pharmaceutical composition useful for the treatment of AIDS. The HIV/AIDS antivirals and other agents will typically be employed in these combinations in their conventional dosage ranges and regimens as reported in the art, including, for example, the dosages described in the Physicians' Desk Reference, 57th edition, Thomson PDR, 2003. The dosage ranges for a compound of the invention in these combinations are the same as those set forth above.

Other embodiments of the present invention include a pharmaceutical composition comprising an effective amount of a compound of the present invention described herein and a pharmaceutically acceptable carrier and/or diluent. The composition may further comprise an effective amount of an HIV infection/AIDS treatment agent selected from the group consisting of HIV/AIDS antiviral agents, immunomodulators, and anti-infective agents. The HIV infection/AIDS treatment agent is an antiviral selected from the group consisting of HIV protease inhibitors, non-nucleoside HIV reverse transcriptase inhibitors, and nucleoside HIV reverse transcriptase inhibitors. The HIV infection/AIDS treatment agent and the compound of the present invention can each be employed in an amount that renders the combination effective for inhibiting HIV integrase, for treating or preventing infection by HIV, or for preventing, treating or delaying the onset of AIDS.

Another embodiment includes a method for the treatment of HIV in a mammal comprising administering to the mammal an anti-HIV effective treatment amount of the compound of the present invention described herein, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, optionally with a pharmaceutically acceptable carrier or diluent. There is also a method for salvage therapy in the treatment of HIV in a mammal comprising administering to said mammal an anti-HIV effective treatment amount of a compound of the present invention described herein, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, optionally with a pharmaceutically acceptable carrier or diluent. The mammal is typically a human. If the compound of the present invention is co-administered with at least one other anti-HIV agent, this can be done in combination and/or in alternation with the compound.

In other embodiments, there is provided the use of an anti-HIV effective treatment amount of the compound of the present invention described herein, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, optionally with a pharmaceutically acceptable carrier or diluent, in the manufacture of a medicament for the treatment of HIV in a mammal. There is also the use of an anti-HIV effective treatment amount of the compound of the present invention described herein, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, optionally with a pharmaceutically acceptable carrier or diluent, in the manufacture of a medicament for salvage therapy in the treatment of HIV in a mammal.

In other embodiments, there is provided the use of an anti-HIV effective treatment amount of the compound of the present invention described herein, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, optionally with a pharmaceutically acceptable carrier or diluent, for the treatment of HIV in a mammal. There is also the use of an anti-HIV effective treatment amount of the compound of the present invention described herein, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, optionally with a pharmaceutically acceptable carrier or diluent, for salvage therapy in the treatment of HIV in a mammal.

With respect to the uses of the compound of the present invention described herein, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof, the mammal is typically a human. If the compound of the present invention described herein, and/or a pharmaceutically-acceptable salt, hydrate, solvate, tautomer, optical isomer, E-isomer, Z-isomer, or combination thereof is co-administered with at least one other anti-HIV agent, this can be done in combination and/or in alternation with the compound.

When introducing elements disclosed herein, the articles “a”, “an”, “the”, and “said” are intended to mean that there are one or more of the elements.

The above disclosure generally describes the present invention. A more complete understanding can be obtained by reference to the following specific Examples. These Examples are described solely for purposes of illustration and are not intended to limit the scope of the invention. Changes in form and substitution of equivalents are contemplated as circumstances may suggest or render expedient. Although specific terms have been employed herein, such terms are intended in a descriptive sense and not for purposes of limitation.

EXAMPLES
Example 1

Synthesis of the compound of the following formula:

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is as follows:

Synthesis of Starting Materials

Oxalic Acid Tert-Butyl Ester Methyl Ester

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To a solution of methyl chlorooxoacetate in TBME (1 mmol/ml) was added at 0-5° C. tert-butanol (1.5 equiv.), followed by dropwise addition of pyridine (1.5 equiv.). The resulting mixture was stirred at room temperature for 20 h. Water (15 vol.) was added, the mixture was extracted with TBME twice. The combined organic extracts were washed with brine, dried over anhydrous Na₂SO₄and concentrated under vacuum to give a colorless oil.

Synthesis of Oxalic Acid Tert-Butyl Ester Methyl Ester

Starting material
Conditions
Isolated Product

1 g
1.5 eq. t-BuOH

¹HNMR conforms

chlorooxoacetate
1.5 eq. Pyridine

8 ml TBME

0° to rt 20 h

20 g
1.5 eq. t-BuOH
22.7 g (87% yield)

chlorooxoacetate
1.5 eq. Pyridine

¹HNMR conforms

160 ml TBME

0° to rt 20 h

40 g
1.5 eq. t-BuOH
41.5 g (79.3% yield)

chlorooxoacetate
1.5 eq. Pyridine

¹HNMR conforms

8 ml TBME

0° to rt 20 h

Benzyloxy-Acetic Acid Methyl Ester

Benzyloxyacetyl chloride was added slowly to 10 vol of MeOH at 0-5° C. The mixture was stirred at room temperature for 20 h. MeOH was removed under vacuum to give quantitatively the desired product.

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Synthesis of Benzyloxy-Acetic Acid Methyl Ester

Starting material
Conditions
Isolated Product

1 g
10 ml MeOH
0.98 g (100%)

Benzyloxyacetyl

¹HNMR conforms

chloride

20 g
200 ml MeOH
19.5 g (100% yield)

Benzyloxyacetyl

¹HNMR conforms

chloride

25 g
10 ml MeOH
24.5 g (100%)

benzyloxyacetyl

¹HNMR conforms

chlorid

Coupling of Oxalic Acid Tert-Butyl Ester Methyl Ester and Benzyloxyacetic Acid Methyl Ester

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Following the procedure described in U.S. Patent Publication No. 2005/0090668, a mixture of benzyloxy-acetic acid methyl ester (1 equiv.) and oxalic acid tert-butyl ester methyl ester (1.5 equiv.) in THF (12 vol.) was treated with 1.5 equiv. of LDA (prepared freshly from diisopropyl amine and n-BuLi in THF) at −78° C. for 1 h. The mixture was then warmed to room temperature for 1 h and quenched with cold HCl (1N, 11 vol.). The mixture was extracted with EtOAc (3×12 vol.), the organic extracts were washed with brine, dried over anhydrous Na₂SO₄and concentrated to an oil. Chromatography of the crude product on silica gel (eluted with 15-60% EtOAc/Hexane) gave 78% of the coupled product as a colorless oil. As described in the patent, the ¹HNMR is complex due to multiple enol tautomers and enol olefin configurations. TLC of the purified product showed a single spot. The results are summarized in the following table.

Coupling of Oxalic Acid Tert-Butyl Ester Methyl Ester and Benzyloxyacetic Acid Methyl Ester

Starting material
Conditions
Isolated Product

0.9 g Benzyloxyacetic
1.5 eq. LDA
Crude yield 1.35 g (87%)

acid methyl ester
12 vol THF
TLC 1 major spot

1.2 g Oxalic acid tert-
−78° C. 1 h to rt 1 h
Used in the next step without purification

butyl ester methyl ester

1.8 g Benzyloxyacetic
1.5 eq. LDA
Chromatographed on silica gel

acid methyl ester
12 vol THF
2.4 g (78% yield)

2.4 g Oxalic acid tert-
−78° C. 1 h to rt 1 h
TLC 1 single spot

butyl ester methyl ester

14.2 g Benzyloxyacetic
1.5 eq. LDA
Crude yield 23.8 g (98%)

acid methyl ester
12 vol THF
TLC 1 major spot

18.9 g Oxalic acid tert-
−78° C. 1 h to rt 1 h
3.3 g used in the next step without

butyl ester methyl ester

purification. 20.5 g Chromatographed on

silica gel to give 16 g product

14.2 g Benzyloxyacetic
1.5 eq. LDA
10 g of 2-Benzyloxy-3-hydroxy-but-2-

acid methyl ester
12 vol THF
enedioic acid 4-tert-butyl ester 1-methyl

18.9 g Oxalic acid tert-
−78° C. 1 h to rt 1 h
ester isolated after chromatography

butyl ester methyl ester

12 g Benzyloxyacetic
1.5 eq. LDA
Chromatographed on silica gel

acid methyl ester
12 vol THF
14 g (68.3% yield)

16 g Oxalic acid tert-
−78° C. 1 h to rt 1 h
TLC 1 single spot

butyl ester methyl ester

12 g Benzyloxyacetic
1.5 eq. LDA
Chromatographed on silica gel

acid methyl ester
12 vol THF
14.5 g (70.7% yield)

16 g Oxalic acid tert-
−78° C. 1 h to rt 1 h
TLC 1 single spot

butyl ester methyl ester

Synthesis of 5-Benzyloxy-6-oxo-1,6-dihydro-pyrimidine-4-carboxylic acid tert-butyl ester

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Initial exploratory work on the synthesis of 5-Benzyloxy-6-oxo-1,6-dihydro-pyrimidine-4-carboxylic acid tert-butyl ester was performed on the crude coupled product with potassium t-butoxide as base using the procedure described in U.S. Patent Publication No. 2005/0090668. A mixture of the coupled product (1 equiv.) and formamidine HCl (1.5 equiv.) in MeOH (10 vol.) was treated with 4.5 equiv. of t-BuOK (1M in t-BuOH) at 0° C. The resulting mixture was stirred at room temperature for 20 h, saturated NH₄Cl was added, the mixture was extracted with EtOAc. The combined organic extracts were washed with brine, dried and concentrated to give a beige solid. Chromatography of the crude product gave 30% yield of a white solid. ¹HNMR conforms except for small amount of unknown contaminant. Mass spec: m/z=247, 303, 605 corresponds to (M-tBu)+1, M+1 and 2M+1. The reaction was repeated in larger scale with NaOMe as base to give 30% yield of the desired product and 4% of the corresponding methyl ester. Subsequently, the yield was improved to 65.4% using NaOMe as base. The results are summarized in the following table.

Synthesis of 5-Benzyloxy-6-oxo-1,6-dihydro-pyrimidine-4-carboxylic acid tert-butyl ester

Starting material
Conditions
Isolated Product

885 mg 2-Benzyloxy-3-
12.75 ml t-BuOK (1M)
Chromatographed

hydroxy-but-2-enedioic acid
8 ml MeOH
250 mg (30%)

4-tert-butyl ester 1-methyl
0° C. 0.25 h to rt 20 h

¹HNMR conforms

ester

Mass spec:

342 mg formamidine HCl

m/z = 247 (M − tBu) + 1,

303 (M + 1) and 605 (2M + 1)

1.78 g 2-Benzyloxy-3-
3.97 ml NaOMe (25% w/w)
Chromatographed

hydroxy-but-2-enedioic acid
6 ml MeOH
517 mg (30%)

4-tert-butyl ester 1-methyl
0° C. 0.25 h to rt 20 h

¹HNMR conforms

ester

58 mg (4%) of the methyl ester

511.8 mg formamidine HCl

also isolated

3.3 g crude 2-Benzyloxy-3-
7.4 ml NaOMe (25% w/w)
Quench with 1N HCl, product

hydroxy-but-2-enedioic acid
12 ml MeOH
precipitate and filtered. Filtrate

4-tert-butyl ester 1-methyl
0° C. 0.25 h to rt 60 h
extracted with EtOAc and

ester

chromatographed. Combined

962 mg formamidine HCl

product swish with 20% EtOAc and

filtered to give 527 mg methyl ester

16 g purified 2-Benzyloxy-3-
35 ml NaOMe (25% w/w)
Quench with 1N HCl, extracted

hydroxy-but-2-enedioic acid
60 ml MeOH
with EtOAc. Concentrate to a solid,

4-tert-butyl ester 1-methyl
0° C. 0.25 h to rt 17 h
swished with 40% EtOAc and

ester

filtered: 6.45 g.

5.02 g formamidine HCl

Filtrate concentrated and

chromatographed to give 2.57 g t-

Bu ester and 0.73 g mixture of t-Bu

and Me ester.

8.4 g 2-Benzyloxy-3-
18.7 ml NaOMe (25% w/w)
5 g of 5-Benzyloxy-6-oxo-1,6-

hydroxy-but-2-enedioic acid
32 ml MeOH
dihydro-pyrimidine-4-carboxylic

4-tert-butyl ester 1-methyl
0° C. 0.25 h to rt 17 h
acid tert-butyl ester isolated plus

ester

3.3 g ML

2.92 g formamidine HCl

14 g purified 2-Benzyloxy-3-
32 ml NaOMe (25% w/w)
Quench with 1N HCl, extracted

hydroxy-but-2-enedioic acid
60 ml MeOH
with EtOAc. Concentrate to a solid,

4-tert-butyl ester 1-methyl
0° C. 0.25 h to rt 17 h
swished with 40% EtOAc and

ester

filtered: 7.75 g.

4.4 g formamidine HCl

56.3% yield + M.L.

14.3 g purified 2-Benzyloxy-
32 ml NaOMe (25% w/w)
Quench with 1N HCl, extracted

3-hydroxy-but-2-enedioic
60 ml MeOH
with EtOAc. Concentrate to a solid,

acid 4-tert-butyl ester 1-
0° C. 0.25 h to rt 17 h
swished with 40% EtOAc and

methyl ester

filtered: 9.0 g.

4.4 g formamidine HCl

65.4% yield + M.L.

Synthesis of 5-Benzyloxy-1-methyl-6-oxo-1,6-dihydro-pyrimidine-4-carboxylic acid tert-butyl ester

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Using a procedure described in U.S. Patent Publication No. 2005/0090668, a solution of 5-benzyloxy-6-oxo-1,6-dihydro-pyrimidine-4-carboxylic acid tert-butyl ester was first treated with NaH (1.3 equiv.) in DMF followed by the addition of dimethylsulfate (1.3 equiv.) to give mainly the desired product after 2 h at room temperature. The reaction mixture was quenched with cold HCl (1N, 30 vol.) and extracted with EtOAc (3×30 vol.). The combined organic extracts were washed with dilute HCl and brine, dried and concentrated to an oil. Chromatography of the crude product (eluted with 40-60% EtOAc/hexane) gave 88% yield of the N-methylated compound (Synthon A).

Synthesis of 5-Benzyloxy-1-methyl-6-oxo-1,6-dihydro-pyrimidine-4-carboxylic acid tert-butyl ester

Starting material
Conditions
Isolated Product

151 mg 5-benzyloxy-6-
26 mg NaH
TLC showed one major

oxo-1,6-dihydro-
(60% in oil)
product. Crude ¹HNMR

pyrimidine-4-carboxylic
2 ml DMF
conforms. Crude yield

acid tert-butyl ester
0° C. 0.25 h
173 mg

82 mg Me₂SO₄
to rt 1.5 h

273 mg 5-benzyloxy-6-
47 mg NaH
Crude product combined

oxo-1,6-dihydro-
(60% in oil)
with product above and

pyrimidine-4-carboxylic
4 ml DMF
chromatographed to give

acid tert-butyl ester
0° C. 0.25 h
392 mg (88%) yield of

148 mg Me₂SO₄
to rt 2 h
desired product. ¹HNMR

conforms

3.03 g 5-benzyloxy-6-
520 mg NaH
Chromatography gave

oxo-1,6-dihydro-
(60% in oil)
2.15 g Synthon A

pyrimidine-4-carboxylic
30 ml DMF
(64.7%)

acid tert-butyl ester
0° C. 0.25 h

1.64 g Me₂SO₄
to rt 1.5 h

Synthesis of 5-Benzyloxy-1-methyl-6-oxo-1,6-dihydro-pyrimidine-4-carboxylic acid N′-[2-(4-fluoro-phenyl)-acetyl]-hydrazide

Synthon A was reacted with 1 equiv. of 1N sodium hydroxide to yield the 5-benzyloxy-1-methyl-6-oxo-1,6-dihydro-pyrimidine-4-carboxylic acid.

Synthesis of 5-Benzyloxy-1-methyl-6-oxo-1,6-dihydro-pyrimidine-4-carboxylic acid

Starting material
Conditions
Isolated Product

50 mg of 5-
1 equiv. NaOH
5-Benzyloxy-1-methyl-6-

Benzyloxy-1-methyl-
(1N),
oxo-1,6-dihydro-

6-oxo-1,6-dihydro-
10 v EtOH
pyrimidine-4-carboxylic

pyrimidine-4-
25° C. for 20 h
acid isolated

carboxylic acid tert-

butyl ester

1.7 g of 5-Benzyloxy-
1 equiv. NaOH
1.34 g of 5-Benzyloxy-1-

1-methyl-6-oxo-1,6-
(1N),
methyl-6-oxo-1,6-dihydro-

dihydro-pyrimidine-4-
10 v EtOH
pyrimidine-4-carboxylic

carboxylic acid tert-
25° C. for 20 h
acid isolated

butyl ester

4.8 g of 5-Benzyloxy-
1 equiv. NaOH
3.38 g of 5-Benzyloxy-1-

1-methyl-6-oxo-1,6-
(1N),
methyl-6-oxo-1,6-dihydro-

dihydro-pyrimidine-4-
10 v EtOH
pyrimidine-4-carboxylic

carboxylic acid tert-
25° C. for 20 h
acid isolated

butyl ester

85.6% yield.

8.3 g of 5-Benzyloxy-
1 equiv. NaOH
6.7 g of 5-Benzyloxy-1-

1-methyl-6-oxo-1,6-
(1N),
methyl-6-oxo-1,6-dihydro-

dihydro-pyrimidine-4-
10 v EtOH
pyrimidine-4-carboxylic

carboxylic acid tert-
25° C. for 20 h
acid isolated

butyl ester

98.2% yield.

Synthesis of (4-Fluoro-phenyl)-acetic acid hydrazide

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(4-Fluoro-phenyl)-acetyl chloride was readily prepared from the corresponding acid by refluxing the acid in thionyl chloride for 1 h. However, the acid chloride was too reactive. Addition of hydrazine hydrate to a solution of the acid chloride gave only the dimer. Reverse addition of acid chloride to hydrazine hydrate at 0° C. gave the desired hydrazide with some dimer. The acid chloride was then transformed to the corresponding ethyl ester. Reaction of the ethyl ester with 2 equiv. of hydrazine hydrate in refluxing EtOH gave cleanly the (4-Fluoro-phenyl)-acetic acid hydrazide in 76% yield. The results are summarized below.

Synthesis of (4-Fluoro-phenyl)-acetic acid hydrazide

Starting material
Conditions
Isolated Product

2.5 g (4-Fluoro-
6 ml SOCl₂
2.78 g of (4-Fluoro-

phenyl)-acetic
80° C. for 1 h,
phenyl)-acetyl

acid
evaporate to dryness
chloride isolated

172 mg of (4-
Acid chloride added
114 mg (4-Fluoro-

Fluoro-phenyl)-
to H₂NNH₂•H₂O in 5
phenyl)-acetic

acetyl chloride
ml CH₂Cl₂at 0° C.
acid hydrazide

Stir at 0° C. for 1 h,
isolated plus 37

20° C. for 0.5 h
mg dimer

2.4 g of (4-
10 ml EtOH
2.55 g (4-Fluoro-

Fluoro-phenyl)-
20° C. for 1 h
phenyl)-acetic

acetyl chloride

acid ethyl ester

2.55 g (4-Fluoro-
2 equiv. of
1.8 g (4-Fluoro-

phenyl)-acetic acid
H₂NNH₂•H₂O, 4 v
phenyl)-acetic

ethyl ester
EtOH, stir at 85° C.
acid hydrazide

for 5 h
isolated

10 g (4-Fluoro-
18 ml SOCl₂
11.88 g of (4-Fluoro-

phenyl)-acetic
80° C. for 1 h,
phenyl)-acetyl

acid
evaporate to dryness
chloride isolated

11.88 g of (4-Fluoro-
50 ml EtOH
20° C. for 1 h

phenyl)-acetyl

11.3 g (4-Fluoro-

chloride

phenyl)-acetic

acid ethyl ester

CKL-3-44 11 g
2 equiv. of
9.2 g (4-Fluoro-

(4-Fluoro-phenyl)-
H₂NNH₂•H₂O, 4 v
phenyl)-acetic

acetic acid ethyl
EtOH, stir at 85° C.
acid hydrazide

ester
for 5 h
isolated

The carboxylic acid was transformed to the corresponding acid chloride by refluxing the latter in thionyl chloride. Reaction of the acid chloride with (4-fluoro-phenyl)-acetic acid hydrazide gave almost quantitatively the desired bishydrazide.

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Synthesis of 5-Benzyloxy-1-methyl-6-oxo-1,6-dihydro-pyrimidine-4-carboxylic acid N′-[2-(4-fluoro-phenyl)-acetyl]-hydrazide

Starting material
Conditions
Isolated Product

1. 100 mg 5-Benzyloxy-
Reflux 1 h, concentrated
160 mg isolated,

1-methyl-6-oxo-1,6-
under vacuum, used as is.
NMR MS

dihydro-pyrimidine-4-
Add acid chloride
conformed.

carboxylic acid, 2 ml
solution in CH₂Cl₂(1 ml)
160 mg isolated,

SOCl₂
to a suspension of
NMR MS

2. 63.8 mg (4-Fluoro-
hydrazide in CH₂Cl₂(1
conformed

phenyl)-acetic acid
ml), at 0°. Stir at rt for 1 h.

hydrazide (1.0 equiv.),

72 mg Et₃N (2.0 equiv.)

1. 1.15 g 5-Benzyloxy-1-
Reflux 1 h, concentrated
1.8 g isolated

methyl-6-oxo-1,6-
under vacuum, used as is.
(99%), NMR

dihydro-pyrimidine-4-
Add acid chloride
conformed.

carboxylic acid, 10 ml
solution in CH₂Cl₂(10 ml)

SOCl₂
to a suspension of

2. 742 mg (4-Fluoro
hydrazide in CH₂Cl₂(10

phenyl)-acetic acid
ml), at 0°. Stir at rt for 1 h.

hydrazide (1.0 equiv.),

892 mg Et₃N (2.0 equiv.)

1. 3.3 g 5-Benzyloxy-1-
Reflux 1 h, concentrated
4.97 g isolated

methyl-6-oxo-1,6-
under vacuum, used as is.
yield 95.6%

dihydro-pyrimidine-4-
Add acid chloride
NMR conformed.

carboxylic acid, 30 ml
solution in CH₂Cl₂(10 ml)

SOCl₂
to a suspension of

2. 2.13 g (4-Fluoro-
hydrazide in CH₂Cl₂(10

phenyl)-acetic acid
ml), at 0°. Stir at rt for

hydrazide (1.0 equiv.),
over night.

3.5 mL Et₃N (2.0 equiv.)

1. 6.7 g 5-Benzyloxy-1-
Reflux 1 h, concentrated
9.44 g isolated

methyl-6-oxo-1,6-
under vacuum, used as is.
yield 89.3%

dihydro-pyrimidine-4-
Add acid chloride
NMR conformed.

carboxylic acid, 30 ml
solution in CH₂Cl₂(10 ml)

SOCl₂
to a suspension of

2. 4.33 g (4-Fluoro-
hydrazide in CH₂Cl₂(10

phenyl)-acetic acid
ml), at 0°. Stir at rt for

hydrazide (1.0 equiv.),
over night.

3.5 mL Et₃N (2.0 equiv.)

Synthesis of 5-Benzyloxy-6-[5-(4-fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-3-methyl-3H-pyrimidin-4-one

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Following the procedure described in European Patent No. 1698628, 5-benzyloxy-1-methyl-6-oxo-1,6-dihydro-pyrimidine-4-carboxylic acid N′-[2-(4-fluoro-phenyl)-acetyl]-hydrazide was treated with CCl₄(7 equiv.), Ph₃P (3 equiv.) and Et₃N (3 equiv.) in CH₃CN (10 vol) at room temperature for 1.5 h. TLC showed only one product formed. The reaction mixture was diluted with EtOAc, washed with aqueous NaHCO₃and brine, dried and concentrated to give a crude solid. For the 1.8 g scale reaction, chromatography (4 columns) plus recrystallization twice was needed to isolate the desired product without Ph₃P═O contamination. NMR and MS confirmed the structure.

Starting material
Conditions
Isolated Product

160 mg bis hydrazide
Ph₃P was added
40 mg of cyclised oxadiazole

0.262 ml CCl₄(7 eq.)
to a suspension of bis
contaminated by Ph₃P

0.164 mL Et₃N (3 eq.)
hydrazide, CCl₄
isolated after chromatography

306 mg Ph₃P (3 eq.)
and Et₃N at rt. Stir
(eluted with 100% EtOAc).

for 1 h at rt.
NMR, MS conformed.

1.8 g bis hydrazide 3 ml
Ph₃P was added
First column chromatography

CCl₄(7 eq.)
to a suspension of bis
gave 1.91 g of desired

1.8 mL Et₃N (3 eq.)
hydrazide, CCl₄
product contaminated by

3.45 g Ph₃P (3 eq.)
and Et₃N at rt. Stir
small amount of Ph₃P═O and

for 1.5 h at rt.
3.5 g of Ph₃P═O containing

small amount of product. The

Ph₃P═O fraction was

repurified by chromatography

to give more desired product.

All the impure fractions were

combined and

chromatographed, the product

isolated was first crystallized

from EtOAc and then

recrystallization in toluene

gave a combined yield of 1.3

g (75%) of product.

4.95 g bis hydrazide
Ph₃P was added
First column chromatography

8.13 ml CCl₄(7 eq.)
to a suspension of bis
gave 1.6 g of desired product

5.04 mL Et₃N (3 eq.)
hydrazide, CCl₄
contaminated by small

9.49 g Ph₃P (3 eq.)
and Et₃N at rt. Stir
amount of Ph₃P═O and 5.2 g

over night at rt.
of desired product with

Ph₃P═O.

Recrystallisation of 1.6 g with

toluene gives 1.3 g of pure product.

9.4 g bis hydrazide
Ph₃P was added
First column chromatography

8.13 ml CCl₄(7 eq.)
to a suspension of bis
gave 5.0 g of desired product

5.04 mL Et₃N (3 eq.)
hydrazide, CCl₄
contaminated by small

9.49 g Ph₃P (3 eq.)
and Et₃N at rt. Stir
amount of Ph₃P═O and 7.5 g

over night at rt.
of desired product with

Ph₃P═O.

Recrystallisation of 5.0 g with

toluene gives 4.1 g of pure product.

Synthesis of 5-Benzyloxy-6-[5-(4-fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-3-methyl-3H-pyrimidine-4-thione

5-Benzyloxy-6-[5-(4-fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-3-methyl-3H-pyrimidin-4-one was treated with 0.62 equiv of Lawesson's reagent at 80-85° C. in toluene for 5-7 h. TLC showed one major product formation with some substrate still present. Chromatography (eluted with 70%-90% EtOAc/hexane) gave ˜50% yield of the title compound.

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Starting material
Conditions
Isolated Product

100 mg 5-Benzyloxy-6-[5-(4-
3 ml toluene, 80-85° C.
50 mg of a yellow

fluoro-benzyl)-[1,3,4]oxadiazol-2-
for 5 h
powder. NMR, MS

yl]-3-methyl-3H-pyrimidin-4-one

conformed.

63 mg Lawesson's reagent (0.62 eq.)

392 mg 5-Benzyloxy-6-[5-(4-
3 ml toluene, 80-85° C.
50 mg of a yellow

fluoro-benzyl)-[1,3,4]oxadiazol-2-
for 5 h
powder. NMR, MS

yl]-3-methyl-3H-pyrimidin-4-one

conformed.

63 mg Lawesson's reagent (0.62 eq.)

350 mg 5-Benzyloxy-6-[5-(4-
10 ml toluene, 80-85° C.
269 mg (74%) of a

fluoro-benzyl)-[1,3,4]oxadiazol-2-
for 7 h
yellow powder

yl]-3-methyl-3H-pyrimidin-4-one

233 mg Lawesson's reagent (0.65 eq.)

190 mg 5-Benzyloxy-6-[5-(4-
6 ml toluene, 80-85° C.
150 mg (76%) of a

fluoro-benzyl)-[1,3,4]oxadiazol-2-
for 14 h
yellow powder. NMR,

yl]-3-methyl-3H-pyrimidin-4-one

MS conformed.

126 mg Lawesson's reagent (0.65 eq.)

2.0 g 5-Benzyloxy-6-[5-(4-fluoro-
55 ml toluene, 80-85° C.
1.2 g (57.7%) of a

benzyl)-[1,3,4]oxadiazol-2-yl]-3-
for 8 h, r.t. for 16 hrs.
yellow powder. NMR,

methyl-3H-pyrimidin-4-one

MS conformed.

1.28 g Lawesson's reagent (0.62 eq.)

3.75 g 5-Benzyloxy-6-[5-(4-
94 ml toluene, 80-85° C.
2.75 g (70.5%) of a

fluoro-benzyl)-[1,3,4]oxadiazol-2-
for 8 h, r.t. for 16 hrs.
yellow powder. NMR,

yl]-3-methyl-3H-pyrimidin-4-one

MS conformed.

2.51 g Lawesson's reagent (0.62 eq.)

Reaction of 5-Benzyloxy-6-[5-(4-fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-3-methyl-3H-pyrimidine-4-thione with N, O-bis(trimethylsilyl)hydroxylamine in the presence of Hg(OAc)₂

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Reaction of 5-Benzyloxy-6-[5-(4-fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-3-methyl-3H-pyrimidine-4-thione with N, O-bis(trimethylsilyl)hydroxylamine in the presence of Hg(OAc)₂, the desired amidoxime derivative was isolated as a mixture of syn- and anti-isomers. Mass spec: m/z=408 (M+1) conforms to structure expected.

Starting material
Conditions
Isolated Product

50 mg 5-benzyloxy-6-[5-(4-fluoro-benzyl)-
2.5 ml dioxane, 4 h rt
Small amount of expected

[1,3,4]oxadiazol-2-yl]-3-methyl-3H-

product as mixture of isomers.

pyrimidine-4-thione (75% pure)

MS: m/z = 408 (M + 1)

83 mg N,O-

bis(trimethylsilyl)hydroxylamine (5 equiv.)

40 mg Hg(Oac)2 1.4 equiv.

400 mg 5-benzyloxy-6-[5-(4-fluoro-
20 ml dioxane, 3 h rt
Small amount of expected

benzyl)-[1,3,4]oxadiazol-2-yl]-3-methyl-

product.

3H-pyrimidine-4-thione (pure)

MS: m/z = 408 (M + 1)

1.05 mL N,O-

~20 mg of pure product

bis(trimethylsilyl)hydroxylamine (5 equiv.)

400 mg Hg(Oac)2 1.4 equiv.

400 mg 5-benzyloxy-6-[5-(4-fluoro-
20 ml dioxane, 3 h rt
Small amount of expected

benzyl)-[1,3,4]oxadiazol-2-yl]-3-methyl-

product.

3H-pyrimidine-4-thione (pure)

MS: m/z = 408 (M + 1)

2.0 mL N,O-

~10 mg of pure product

bis(trimethylsilyl)hydroxylamine (10 equiv.)

400 mg Hg(Oac)2 1.4 equiv.

200 mg 5-benzyloxy-6-[5-(4-fluoro-
20 ml toluene, 2 h,
n/a

benzyl)-[1,3,4]oxadiazol-2-yl]-3-methyl-
90° C.

3H-pyrimidine-4-thione (pure)
same TLC

0.5 mL N,O-

bis(trimethylsilyl)hydroxylamine (5 equiv.)

200 mg Hg(Oac)2 1.4 equiv.

200 mg 5-benzyloxy-6-[5-(4-fluoro-
20 ml THF, 2 h, r.t.
Purification of above and this

benzyl)-[1,3,4]oxadiazol-2-yl]-3-methyl-
same TLC
one give ~50 mg of good

3H-pyrimidine-4-thione (pure)

product.

0.5 mL N,O-

bis(trimethylsilyl)hydroxylamine (5 equiv.)

200 mg Hg(Oac)2 1.4 equiv.

2.48 g 5-benzyloxy-6-[5-(4-fluoro-benzyl)
125 ml Dioxane, 1 h,
Purification by silica gives 190

[1,3,4]oxadiazol-2-yl]-3-methyl-3H-
r.t.
mg of desire product. (7.66%

pyrimidine-4-thione (pure)
same TLC
yield).

6.48 mL N,O-

bis(trimethylsilyl)hydroxylamine (5 equiv.)

2.66 g Hg(Oac)₂1.4 equiv.

6-[5-(4-Fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-5-hydroxy-3-methyl-3H pyrimidin-4-one oxime (COTI-HIV-1DOxime)

5-Benzyloxy-6-[5-(4-fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-3-methyl-3H-pyrimidin-4-one oxime was hydrogenated at 1 atmosphere of hydrogen in the presence of equal weight of 10% Pd/C to give 68% yield of 6-[5-(4-fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-5-hydroxy-3-methyl-3H-pyrimidin-4-one oxime (COTI-HIV-1DOxime or, also referred to as COTI-HIV-1). Results are summarized below.

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Synthesis of 6-[5-(4-fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-5-hydroxy-3-methyl-3H-pyrimidin-4-one oxime (COTI-HIV-1DOxime)

Starting material
Conditions
Isolated Product

~50 to 100 mg of 5-Benzyloxy-6-
25 ml
28 mg COTI-HIV-1 +

[5-(4-fluoro-benzyl)-
THF, rt
by-product

[1,3,4]oxadiazol-2-yl]-3-methyl-
1 atm
56 mg of +/−pure

3H-pyrimidin-4-one oxime
of H₂.
COTI-HIV-1DOxime

(+/−pure)

and by product

100% w/w Pd/C 10% and 50%

water.

190 mg of 5-Benzyloxy-6-[5-(4-
25 ml
The crude is purifying

fluoro-benzyl)-[1,3,4]oxadiazol-
THF, rt
by silica with the above

2-yl]-3-methyl-3H-pyrimidin-4-
1 atm
products to give 100 mg

one oxime (pure)
of H₂.
(68%) of pure desire

100% w/w Pd/C 10% and 50%

product. (M/Z = 318)

water.

NMR ¹H conform

Example 1A

Synthesis of the compound of the following formula:

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is as follows:

6-[5-(4-Fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-5-hydroxy-3-methyl-3H pyrimidin-4-one
a) Preparation of 6-[5-(4-Fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-5-hydroxy-3-methyl-3H-pyrimidin-4-one by acid catalyzed debenzylation

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Reaction of 5-benzyloxy-6-[5-(4-fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-3-methyl-3H-pyrimidin-4-one and a 1:1 mixture of TFA/CH₂Cl₂gave the debenzylated product in reasonable yield. Results are summarized below.

Preparation of 6-[5-(4-Fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-5-hydroxy-3-methyl-3H-pyrimidin-4-one

Starting material
Conditions
Isolated Product

24 mg 5-benzyloxy-6-
0.3 ml CH₂Cl₂, 0.3 ml
Beige solid, ¹HNMR and

[5-(4-fluoro-benzyl)-
TFA, 20 h, rt.
MS conformed to

[1,3,4]oxadiazol-2-yl]-
Concentrate under
expected product

3-methyl-3H-
vacuum, swished with

pyrimidin-4-one
20% EtOAc/hexane

109 mg 5-benzyloxy-
1 ml CH₂Cl₂, 1 ml
65 mg beige solid (77%),

6-[5-(4-fluoro-benzyl)-
TFA, 48 h, rt.

¹HNMR conformed.

[1,3,4]oxadiazol-2-yl]-
Concentrate under

3-methyl-3H-
vacuum, co-distill with

pyrimidin-4-one
EtOAc/heptane,

swished with 30%

EtOAc/hexane

100 mg 5-benzyloxy-
1 ml CH₂Cl₂, 1 ml
69 mg beige solid,

6-[5-(4-fluoro-benzyl)-
TFA, 48 h, rt.

¹HNMR showed an

[1,3,4]oxadiazol-2-yl]-
Concentrate under
unknown impurity.

3-methyl-3H-
vacuum, co-distill with
Re-purify by swishing in

pyrimidin-4-one
EtOAc/heptane,
4 ml pure EtOAc for

swished with 30%
20 h to give 56 mg of

EtOAc/hexane
pure product. ¹HNMR

for 20 h
conformed.

b) Preparation of 6-[5-(4-Fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-5-hydroxy-3-methyl-3H-pyrimidin-4-one by palladium catalyzed debenzylation

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Hydrogenation of 5-Benzyloxy-6-[5-(4-fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-3-methyl-3H-pyrimidin-4-one in THF with 25% w/w of 10% Pd/C gave 67.5% of the desired product. Results are shown below.

Preparation of 6-[5-(4-Fluoro-benzyl)-[1,3,4]oxadiazol-2-yl]-5-hydroxy-3-methyl-3H-pyrimidin-4-one by palladium catalyzed debenzylation

Starting material
Conditions
Isolated Product

1.0 g of 5-Benzyloxy-6-[5-(4-
200 ml THF,
0.52 g of pure

fluoro-benzyl)-[1,3,4]oxadiazol-
r.t.
product (67.5%)

2-yl]-3-methyl-3H-pyrimidin-
1 atm
0.35 g of +/−pure

4-one 250 mg mg 10% Pd/C
30 mins
product.

Example 2
Synthesis of COTI-HIV28236

Synthesis of the compound of the following formula:

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was conducted according to the following synthetic methodology:

Synthesis of the Common Intermediate 4c

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Synthesis of Compound 63:

To a suspension of lithium 3-fluoropyridine-2-carboxylate (10.1 g; 69 mmol; 1 eq.) in methanol (170 mL) were successively added 1,2-dimethoxypropane (17.0 mL; 138 mmol; 2 eq.) and concentrated sulphuric acid (18.0 mL; 345 mmol; 5 eq.). The reaction mixture became homogeneous and turned yellow after addition of sulphuric acid. The mixture was then heated at reflux for 20 hours. After cooling down to room temperature, the solvent was removed under vacuum. The oily residue was slowly poured into a mixture of ethyl acetate (200 mL) and a saturated solution of NaHCO₃(400 mL). At the end of the addition, the aqueous layer was again saturated by addition of solid NaHCO₃. The layers were then separated and the aqueous phase was extracted with ethyl acetate (2×200 mL). The combined organic phases were dried over Na₂SO₄, filtered and evaporated to dryness to afford compound 63 as a light yellow solid (9.5 g; yield=89%).

Synthesis of Compound 66:

To a solution of LDA (1.8M in THF/heptane; 72.0 mL; 129 mmol; 2.1 eq.) in THF (60 mL) at −78° C. was added tert-butylacetate (20.0 mL; 148 mmol; 2.4 eq.). The deep red solution was stirred at −78° C. for 45 minutes and maintained at that temperature during the slow addition of a solution of compound 63 (9.5 g; 62 mmol; 1 eq.) in THF (60 mL). The reaction mixture was then stirred for an additional 2 hours and quenched at −78° C. by addition of MTBE (150 mL) and water/acetic acid (1:1; 150 mL). After warming up to room temperature, the layers were separated and the aqueous phase was extracted with MTBE (2×100 mL). The combined organic phases were washed with water (300 mL) and brine (300 mL), dried over Na₂SO₄, filtered and evaporated to dryness to afford compound 66 as an yellow oil (16.2 g; contaminated with 8.5% w/w of acetic acid; yield=100%).

Synthesis of Compound 67:

To a solution of crude compound 66 (16.2 g; 62 mmol; 1 eq.) in acetonitrile (190 mL) at 0° C. was successively added triethylamine (14.6 mL; 112 mmol; 1.8 eq.) and ABSA (16.3 g; 68 mmol; 1.1 eq.). At the end of the addition, the reaction mixture was allowed to warm up to room temperature. A white solid precipitated progressively from the orange solution. After 18 hours, the reaction mixture was filtered on a Büchner funnel. The white cake was washed with ethyl acetate (450 mL). The mother liquor was decanted and the layers were separated. The organic phase was washed with a saturated solution of NH₄Cl (400 mL) and brine (400 mL), dried over Na₂SO₄, filtered and evaporated to dryness. The orange oily residue was triturated in diethyl ether. After filtration of the brown solid, the evaporation of the mother liquor afforded compound 67 as an orange oil (18.9 g contaminated with 9% w/w of p-AcHN-Ph-SO₂NH₂, yield=100%).

Synthesis of Compound 68:

To a solution of crude compound 67 (18.9 g; 62 mmol; 1 eq.) in THF (125 mL) at room temperature was slowly added trimethylphosphine (1M/THF; 68.0 mL; 68 mmol; 1.1 eq.). At the end of the addition, the reaction mixture was stirred for 15 minutes and quenched by addition of water (11.0 mL; 616 mmol; 10 eq.). The mixture was stirred for an additional 15 minutes prior to the addition of silica gel (45 g). The solvent was then evaporated under vacuum and the residue, which was adsorbed on silica gel, was purified by flash chromatography on silica gel (eluent: dichloromethane/methanol, 100/0 to 96/4) to afford compound 68 as an orange oil (15.7 g; yield=96%).

Synthesis of Compound 4d:

To a solution of compound 68 (15.7 g; 59 mmol; 1 eq.) in acetonitrile (300 mL) at room temperature were successively added DBU (18.5 mL; 124 mmol; 2.1 eq.) and methyl iodide (3.8 mL; 62 mmol; 1.05 eq.). The reaction mixture became deep red. After stirring for 18 hours at room temperature, the reaction was quenched by addition of a saturated solution of NH₄Cl (500 mL). The resulting mixture was extracted with dichloromethane (3×500 mL) and the combined organic phases were washed with brine (1 L), dried over Na₂SO₄, filtered and evaporated to dryness. The purification of the residue by chromatography on silica gel (eluent: dichloromethane/methanol, 100/0 to 90/10) afforded two fractions containing compound 4d. After evaporation to dryness, the first one was triturated in diethyl ether to afford a first batch of pure compound 4d as a pale orange solid (2.6 g; yield=17%). The second one was dissolved in dichloromethane (500 mL) and the resulting solution was washed with a saturated solution of NH₄Cl (2×500 mL), dried over Na₂SO₄, filtered and evaporated to dryness to afford a second batch of pure compound 4d as a pale orange solid (3.1 g; yield=20%). The two batches were combined (yield=37%).

Synthesis of Compound 4c:

To a solution of compound 4d (3.1 g; 12 mmol; 1 eq.) in dichloromethane (110 mL) at room temperature was added trifuoroacetic acid (12.0 mL; 157 mmol; 13.3 eq.). The reaction mixture turned brown. After stirring at room temperature for 18 hours, the reaction mixture was diluted by addition of diethyl ether (150 mL). The solvent were then removed under vacuum. The beige residue was triturated in diethyl ether to afford compound 4c as a beige solid (2.4 g; yield=100%). ¹H NMR (DMSO, ppm): 4.29 (s, 3H); 8.02 (m, 1H); 8.52 (m, 1H); 9.01 (m, 1H); and 14.32 (m, COOH).

Synthesis of COTI-HIV28236:

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Synthesis of Compound 76:

To a solution of compound 4c (907 mg; 4.4 mmol; 1 eq.) in DMSO (6 mL) at room temperature was successively added triethylamine (2.4 mL; 17.6 mmol; 4 eq.), para-fluorobenzylamine (610 μL; 5.3 mmol; 1.2 eq.) and TBTU (1.70 g; 5.3 mmol; 1.2 eq.). After stirring the mixture at room temperature for 16 hours, the reaction was quenched by addition of a saturated solution of NH₄Cl (50 mL). The aqueous phase was then extracted with dichloromethane (5×100 mL). The combined organic phases were combined, dried over Na₂SO₄, filtered and evaporated to dryness. The residue was dissolved in ethyl acetate (100 mL) and the solution was washed with water (100 mL), brine (100 mL), dried over Na₂SO₄, filtered and evaporated to dryness. The residue was then triturated in diethyl ether to afford compound 76 as an yellow solid (480 mg; yield=35%). All aqueous layers were then combined and extracted with chloroform (3×250 mL). The combined chloroform phases were dried over Na₂SO₄, filtered and evaporated to dryness in the presence of silica gel (3 g). The purification by chromatography on silica gel (eluent: dichloromethane/methanol, 98/2 to 90/10) afforded compound 76 as an yellow solid (454 mg; yield=33%). The two batches were combined (yield=68%).

Synthesis of Compound COTI-HIV28236:

To a suspension of compound 76 (228 mg; 73 μmol; 1 eq.) in toluene (3.7 mL) at room temperature was added hydroxylamine hydrochloride (76 mg; 1.10 mmol; 1.5 eq.) and titanium (IV) isopropoxide (330 μL; 1.10 mmol; 1.5 eq.). The reaction mixture was refluxed for 72 hours and evaporated to dryness. The red residue is dissolved in a mixture of a saturated solution of NaHCO₃/ethyl acetate/methanol (5:5:1; 55 mL). After separation of the layers, the aqueous phase was extracted with ethyl acetate (3×50 mL). The combined organic phases were washed with brine (100 mL), dried over Na₂SO₄, filtered and evaporated to dryness. The purification of the residue on silica gel (eluent: dichloromethane/methanol, 100/0 to 98/2) followed by a trituration in methanol afforded compound COTI-HIV28236 as a yellow solid (42 mg; yield=17%). ¹H NMR (CDCl₃, ppm): 3.82 (s, 3H); 4.61 (s, 2H); 6.99 (m, 2H); 7.34 (m, 1H); 7.44 (m, 1H), 7.55 (m, 1H), 8.24 (m, 1H), 9.82 (m, 1H) and 15.71 (m, NOH). ¹³C NMR (CDCl₃, ppm): 42.3, 43.3, 115.3, 115.6, 121.4, 127.5, 129.7, 129.8, 134.3, 135.8, 138.1, 138.7, 139.7, 160.9, 161.6, and 163.4. MS (ES+IC): m/z (M+H)⁺328.

Example 3
Synthesis of COTI-HIV28233

Synthesis of the compound of the following formula:

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Synthesis of the compound of COTI-HIV28233 was conducted according to the following synthetic methodology. Synthesis of the common intermediate 4c is as described above with respect to Example 2.

Synthesis of COTI-HIV28233:

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Synthesis of Compound 78:

To a solution of compound 77 (5.0 g; 33 mmol; 1 eq.) in dichloromethane (100 mL) at room temperature was successively added triethylamine (13.0 mL; 100 mmol; 3 eq.), tert-butylcarbazate (4.8 g; 36 mmol; 1.1 eq.), EDCI (6.9 g; 36 mmol; 1.1 eq.) and HOBt (445 mg; 3.3 mmol; 0.1 eq.). After stirring the mixture for 18 hours at room temperature, the reaction was quenched by addition of a saturated solution of NH₄Cl (200 mL). The layers were separated and the aqueous phase was extracted with dichloromethane (3×200 mL). The combined organic phases were dried over Na₂SO₄, filtered and evaporated to dryness to afford compound 78 as a colourless oil (9.1 g; yield=100%).

Synthesis of Compound 79:

To a solution of compound 78 (9.1 g; 33 mmol; 1 eq.) in dichloromethane (300 mL) at room temperature was slowly added trifluoroacetic acid (33.0 mL; 434 mmol; 13.2 eq.). The reaction mixture turned light brown. After stirring for 3 hours, the reaction mixture was evaporated to dryness. The colourless residue was dissolved in ethyl acetate (400 mL) and the solution was washed with a saturated solution of NaHCO₃(3×500 mL), dried over Na₂SO₄, filtered and evaporated to dryness. The resulting white foam was triturated in diethyl ether to afford compound 79 as a white solid (3.2 g; yield=57%).

Synthesis of Compound 80:

To a solution of compound 4c (1.5 g; 7.3 mmol; 1 eq.) in DMSO (11 mL) at room temperature was successively added triethylamine (3.8 mL; 29 mmol; 4 eq.), compound 79 (1.5 g; 8.8 mmol; 1.2 eq.) and TBTU (2.8 g; 8.8 mmol; 1.2 eq.). The reaction mixture became homogeneous for a few minutes prior to the precipitation of a solid. After stirring for 16 hours at room temperature, the precipitate was filtered on a Büchner funnel. The cake was washed with ethyl acetate and dried to afford compound 80 as a yellow solid (1.7 g; yield=64%).

Synthesis of Compound 81:

To a suspension of compound 80 (1.7 g; 4.7 mmol; 1 eq.) in acetonitrile (33 mL) at room temperature was successively added N,N-diisopropylethylamine (4.7 mL; 28.2 mmol; 6 eq.), triphenylphosphine (2.2 g; 8.5 mmol; 1.8 eq.) and hexachloroethane (1.7 g; 7.0 mmol; 1.5 eq.). The reaction mixture became homogeneous for few minutes prior to the precipitation of a solid. After stirring for 16 hours at room temperature, the precipitate was filtered on a Büchner funnel. The cake was washed with diethyl ether to afford compound 81 as a beige solid (1.1 g; yield=71%).

Synthesis of Compound COTI-HIV28233:

To a suspension of compound 81 (236 mg; 700 μmol; 1 eq.) in toluene (3.5 mL) at room temperature was added hydroxylamine hydrochloride (73 mg; 1.05 mmol; 1.5 eq.) and titanium (IV) isopropoxide (310 μL; 1.10 mmol; 1.5 eq.). The reaction mixture was refluxed for 18 hours and evaporated to dryness. The red residue was dissolved in a mixture of a saturated solution of NaHCO₃/ethyl acetate/methanol (5:5:1; 55 mL). After separation of the layers, the aqueous phase was extracted with ethyl acetate (3×50 mL). The combined organic phases were washed with brine (100 mL), dried over Na₂SO₄, filtered and evaporated to dryness. The purification of the residue on silica gel (eluent: dichloromethane/methanol, 100/0 to 98/2) followed by a trituration in methanol afforded compound COTI-HIV28233 as an yellow solid (39 mg; yield=16%). ¹H NMR (CDCl₃, ppm): 3.71 (s, 3H); 4.27 (s, 2H); 7.00 (m, 2H); 7.35 (m, 3H); 7.52 (m, 1H), 8.22 (m, 1H), 15.23 (m, NOH). MS (ES+IC): m/z (M+H)⁺353.

Example 4
Synthesis of COTI-HIV28236-SA

Synthesis of the compound of COTI-HIV28236-SA can be conducted according to the following synthetic methodology:

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Example 5
Synthesis of COTI-HIV28236-SeA

Synthesis of the compound of COTI-HIV28236-SeA can be conducted according to the following synthetic methodology:

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Example 6
Computational Assessment of Properties

A computational assessment of the properties of compounds according to the present invention was performed using the CHEMSAS® computational platform. CHEMSAS® is a robust proprietary computational platform for accelerated drug discovery, optimization and lead selection based upon a unique combination of traditional and modern pharmacology principles, statistical modeling and machine learning technologies. At the centre of the CHEMSAS® platform is a hybrid machine learning technology that may be used to: find, profile and optimize new targeted lead compounds; find novel uses for known compounds; and, solve problems with existing or potential drugs. In using the CHEMSAS® platform, first a therapeutic target was selected, in this case HIV and more particularly the critical enzyme HIV integrase. The second step involved the design of a candidate molecule library containing thousands of potential compounds through the assembly of privileged molecular fragments. Thirdly, the candidate library was profiled and optimized using a combination of validated computational models and traditional expert medicinal chemistry. In this step, the CHEMSAS® platform developed about 315 molecular descriptors for each candidate therapeutic compound. For example, molecular properties relating to a candidate compound's therapeutic efficacy, expected human toxicity, oral absorption, cumulative cellular resistance and/or kinetics were assessed. In some instances, comparative properties relating to commercially relevant benchmark compounds were also assessed. Potential lead compounds were then selected from the candidate library using a proprietary decision making tool designed to identify candidates with the optimal physical chemical properties, efficacy, ADME/Toxicity profile, etc. according to a pre-determined set of design criteria. The lead compounds selected from the candidate library were then synthesized for further pre-clinical development.

The properties of certain compounds according to the present invention, specifically, those indicated in Tables 1-8 that were assessed using the CHEMSAS® computational platform are shown below. Some of the predicted properties are validated by the experimental data provided herein, while other properties have been validated elsewhere during the development of other clinical candidates. The CHEMSAS® platform therefore provides a means of determining, predicting and/or testing the properties of a compound, particularly when used to determine the properties of compounds according to the present invention. The CHEMSAS® platform is also particularly useful in comparing the properties of compounds according to the invention with prior art compounds on a relative basis in silico.

Tables 1A and 1B: Physical Chemical Properties

Tables 1A and 1B shows that the compounds are all “drug-like” with good drug like physical properties.

TABLE 1A

MolID
Formula
MolWt
ALogP
HBndAcc

COTI-HIV1oxo
C17H12FN5O2
337.31
2.45
7

COTI-HIV1thio
C17H12FN5OS
353.38
3.35
6

COTI-HIV1Se
C17H12FN5OSe
400.27
2.48
6

COTI-HIV1imine
C17H13FN6O
336.33
2.51
7

COTI-HIV1Oxime
C17H13FN6O2
352.33
2.54
8

COTI-HIV2oxo
C16H13FN4O2
312.30
1.98
6

COTI-HIV28236-
C16H13FN4OS
328.37
2.88
5

SA

COTI-HIV28236-
C16H13FN4OSe
375.26
2.00
5

SeA

COTI-HIV2imine
C16H14FN5O
311.32
2.03
6

COTI-HIV28236
C16H14FN5O2
327.32
2.06
7

COTI-HIV1DOxime
C14H12FN5O3
317.28
1.15
8

COTI-HIV1Doxo
C14H11FN4O3
302.26
0.54
7

COTI-HIV1Dthio
C14H11FN4O2S
318.33
1.96
6

COTI-HIV1Dcyano
C15H11FN6O2
326.29
1.35
8

COTI-HIV1Dimino
C14H12FN5O2
301.28
1.12
7

COTI-HIV2DOxime
C13H13FN4O3
292.27
0.68
7

COTI-HIV2Doxo
C13H12FN3O3
277.25
0.07
6

COTI-HIV2Dthio
C13H12FN3O2S
293.32
1.49
5

COTI-HIV2Dcyano
C14H12FN5O2
301.28
0.89
7

COTI-HIV2Dimino
C13H13FN4O2
276.27
0.65
6

TABLE 1B

MolID
Formula
HBndDon
RotBnds
TPSA

COTI-HIV1oxo
C17H12FN5O2
0
3
78.31

COTI-HIV1thio
C17H12FN5OS
0
3
61.01

COTI-HIV1Se
C17H12FN5OSe
0
3
61.01

COTI-HIV1imine
C17H13FN6O
1
3
84.10

COTI-HIV1Oxime
C17H13FN6O2
1
4
93.15

COTI-HIV2oxo
C16H13FN4O2
1
4
73.35

COTI-HIV28236-
C16H13FN4OS
1
4
56.05

SA

COTI-HIV28236-
C16H13FN4OSe
1
4
56.05

SeA

COTI-HIV2imine
C16H14FN5O
2
4
79.14

COTI-HIV28236
C16H14FN5O2
2
5
88.19

COTI-HIV1DOxime
C14H12FN5O3
2
5
102.71

COTI-HIV1Doxo
C14H11FN4O3
1
4
87.87

COTI-HIV1Dthio
C14H11FN4O2S
1
4
70.57

COTI-HIV1Dcyano
C15H11FN6O2
1
5
104.83

COTI-HIV1Dimino
C14H12FN5O2
2
4
93.66

COTI-HIV2DOxime
C13H13FN4O3
3
6
97.74

COTI-HIV2Doxo
C13H12FN3O3
2
5
82.90

COTI-HIV2Dthio
C13H12FN3O2S
2
5
65.60

COTI-HIV2Dcyano
C14H12FN5O2
2
6
99.86

COTI-HIV2Dimino
C13H13FN4O2
3
5
88.69

Legend for Table 1:

MolWt stands for Molecular Weight measured in Daltons and is a size descriptor;

A Log P is calculated lipophilicity/solubility estimates;

HBndDon stands for Hydrogen Bond Donor and refers to the number of atoms able to donate electrons to potentially form Hydrogen bonds;

HBndAcc stands for Hydrogen Bond Acceptor and refers to the number of atoms able to accept electrons to potentially form Hydrogen bonds;

TPSA stands for Topological Polar Surface Area and is a measure of Molecular Surface Charge/Polarity; and

RotBnds stands for Rotatable Bonds which is a count of freely rotatable single bonds in the molecule.

Table 2: Solubility Properties

Table 2 shows that all of the compounds are expected to have acceptable solubility values for drug-like compounds.

TABLE 2A

MolID
Formula
LogD(pH 7.4)
LogSw

COTI-HIV1oxo
C17H12FN5O2
2.52
−3.94

COTI-HIV1thio
C17H12FN5OS
2.60
−4.35

COTI-HIV1Se
C17H12FN5OSe
2.15
−4.22

COTI-HIV1imine
C17H13FN6O
1.79
−3.89

COTI-HIV1Oxime
C17H13FN6O2
2.03
−3.94

COTI-HIV2oxo
C16H13FN4O2
2.66
−3.46

COTI-HIV28236-
C16H13FN4OS
2.87
−3.65

SA

COTI-HIV28236-
C16H13FN4OSe
1.97
−3.55

SeA

COTI-HIV2imine
C16H14FN5O
2.00
−3.52

COTI-HIV28236
C16H14FN5O2
1.93
−3.42

COTI-HIV1DOxime
C14H12FN5O3
1.47
−3.44

COTI-HIV1Doxo
C14H11FN4O3
1.57
−3.19

COTI-HIV1Dthio
C14H11FN4O2S
1.84
−3.75

COTI-HIV1Dcyano
C15H11FN6O2
1.58
−3.71

COTI-HIV1Dimino
C14H12FN5O2
0.15
−3.36

COTI-HIV2DOxime
C13H13FN4O3
1.76
−2.63

COTI-HIV2Doxo
C13H12FN3O3
0.54
−2.45

COTI-HIV2Dthio
C13H12FN3O2S
1.17
−3.04

COTI-HIV2Dcyano
C14H12FN5O2
1.88
−2.73

COTI-HIV2Dimino
C13H13FN4O2
−1.05
−2.59

Legend for Table 2:

Log D(7.4) is a measure of relative solubility in octanol vs water at a specific pH, in this case pH=7.4; and

Log Sw is the logarithm of the calculated solubility in pure water usually measured at 25° C.

Table 3: Efficacy (Log IC50)

Referring to Table 3, compounds with a high value for Prob_Log IC50<−6 (meaning a value that is greater than 0.70, preferably greater than 0.80, more preferably greater than 0.90) are predicted to have a high likelihood of sub-micromolar activity against HIV Integrase. Similarly, Prob_Log IC50<−7 represents the probability that the IC50 is less than or equal to 100 nM. In-silico comparative data is also shown for compounds described in PCT Publication No. WO2003/062204: Compound A; PCT Publication No. WO 2004/101512: Compound B; and Laquinimod™. These compounds are as follows:

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TABLE 3

MolID
Formula
Prob_LogIC50 <- 6
Prob_LogIC50 <- 7

COTI-HIV1oxo
C17H12FN5O2
0.911
0.000

COTI-HIV1thio
C17H12FN5OS
0.202
0.000

COTI-HIV1Se
C17H12FN5OSe
0.000
0.000

COTI-HIV1imine
C17H13FN6O
0.944
0.934

COTI-HIV1Oxime
C17H13FN6O2
0.935
0.912

COTI-HIV2oxo
C16H13FN4O2
0.986
0.000

COTI-HIV28236-
C16H13FN4OS
0.018
0.000

SA

COTI-HIV28236-
C16H13FN4OSe
0.000
0.000

SeA

COTI-HIV2imine
C16H14FN5O
0.938
0.000

COTI-HIV28236
C16H14FN5O2
0.965
0.973

COTI-HIV1DOxime
C14H12FN5O3
0.989
0.947

COTI-HIV1Doxo
C14H11FN4O3
0.996
0.957

COTI-HIV1Dthio
C14H11FN4O2S
0.776
0.000

COTI-HIV1Dcyano
C15H11FN6O2
0.829
0.011

COTI-HIV1Dimino
C14H12FN5O2
0.979
0.895

COTI-HIV2DOxime
C13H13FN4O3
0.996
0.581

COTI-HIV2Doxo
C13H12FN3O3
0.995
0.994

COTI-HIV2Dthio
C13H12FN3O2S
0.203
0.000

COTI-HIV2Dcyano
C14H12FN5O2
0.980
0.001

COTl-HIV2Dimino
C13H13FN4O2
0.985
0.955

Compound A
C17H14N3O3
0.999
0.996

Compound B
C18H13FN4O2
0.946
0.076

Laquinimod ™
C18H17N3O3
0.897
0.000

Legend for Table 3:

Prob_Log IC50<−6 is the probability that the IC50 value of the compound (i.e. the amount required to reduce the initial concentration by 50%) will be less than 10⁻⁶(i.e. sub-micromolar activity against the chosen target).

Prob_Log IC50<−7 is the probability that the IC50 value of the compound (i.e. the amount required to reduce the initial concentration by 50%) will be less than 10⁻⁷(i.e. less than or equal to 100 nM activity against the chosen target).

Tables 4A and 4B: Oral Absorption and BBB Penetration

Referring to Tables 4A and 4B, compounds with a high P_OrlAvail>30% are likely to have acceptable oral absorption. Compounds with a high P_Clr<30 ml/min/kg are expected to have an acceptable clearance rate and are therefore expected to remain in circulation longer than those with a low P_Clr<30 ml/min/kg. All compounds were predicted to be acceptable in both attributes. EST_PPB % is the estimated percentage plasma protein binding of the compound. Estimates of greater than 95% plasma protein binding would be considered to be highly protein bound. P_BBBPenetration is an estimate of the probability that the drug will penetrate the blood brain barrier and enter the central nervous system (CNS). Predicted values of greater than 0.7 P_ indicate that the drug is likely to pass the blood brain barrier and enter the central nervous system (CNS).

TABLE 4A

P_Clr <

P_OrlAvail >
30 ml/

MolID
Formula
30%
min/kg

COTI-HIV1oxo
C17H12FN5O2
0.970
0.961

COTI-HIV1thio
C17H12FN5OS
0.954
0.925

COTI-HIV1Se
C17H12FN5OSe
0.980
0.906

COTI-HIV1imine
C17H13FN6O
0.970
0.934

COTI-HIV1Oxime
C17H13FN6O2
0.933
0.917

COTI-HIV2oxo
C16H13FN4O2
0.971
0.981

COTI-HIV28236-
C16H13FN4OS
0.968
0.980

SA

COTI-HIV28236-
C16H13FN4OSe
0.975
0.980

SeA

COTI-HIV2imine
C16H14FN5O
0.973
0.967

COTI-HIV28236
C16H14FN5O2
0.966
0.957

COTI-HIV1DOxime
C14H12FN5O3
0.992
0.966

COTI-HIV1Doxo
C14H11FN4O3
0.992
0.984

COTI-HIV1Dthio
C14H11FN4O2S
0.993
0.984

COTI-HIV1Dcyano
C15H11FN6O2
0.992
0.928

COTI-HIV1Dimino
C14H12FN5O2
0.992
0.966

COTI-HIV2DOxime
C13H13FN4O3
0.950
0.976

COTI-HIV2Doxo
C13H12FN3O3
0.940
0.994

COTI-HIV2Dthio
C13H12FN3O2S
0.959
0.994

COTI-HIV2Dcyano
C14H12FN5O2
0.960
0.952

COTI-HIV2Dimino
C13H13FN4O2
0.955
0.986

TABLE 4B

EST_PPB
P_BBBPene-

MolID
Formula
%
tration

COTI-HIV1oxo
C17H12FN5O2
94.10
0.605

COTI-HIV1thio
C17H12FN5OS
95.83
0.817

COTI-HIV1Se
C17H12FN5OSe
95.42
0.863

COTI-HIV1imine
C17H13FN6O
86.83
0.777

COTI-HIV1Oxime
C17H13FN6O2
93.92
0.640

COTI-HIV2oxo
C16H13FN4O2
48.00
0.694

COTI-HIV28236-
C16H13FN4OS
89.71
0.887

SA

COTI-HIV28236-
C16H13FN4OSe
86.05
0.984

SeA

COTI-HIV2imine
C16H14FN5O
50.21
0.713

COTI-HIV28236
C16H14FN5O2
51.05
0.275

COTI-HIV1DOxime
C14H12FN5O3
94.53
0.927

COTI-HIV1Doxo
C14H11FN4O3
65.97
0.966

COTI-HIV1Dthio
C14H11FN4O2S
94.37
0.842

COTI-HIV1Dcyano
C15H11FN6O2
93.61
0.946

COTI-HIV1Dimino
C14H12FN5O2
91.38
0.971

COTI-HIV2DOxime
C13H13FN4O3
53.38
0.928

COTI-HIV2Doxo
C13H12FN3O3
50.40
0.920

COTI-HIV2Dthio
C13H12FN3O2S
71.37
0.134

COTI-HIV2Dcyano
C14H12FN5O2
58.95
0.915

COTI-HIV2Dimino
C13H13FN4O2
50.41
0.895

Legend for Table 4:

P_OrlAvail>30% is the probability that the oral availability of the compound will be greater than 30%.

P_Clr<30 ml/min/kg is the probability that the compound will be cleared from circulation at a rate of less than 30 ml/min/kg.

EST_PPB % is the estimated percentage plasma protein binding of the compound.

P_BBBPenetration is an estimate of the probability that the drug will penetrate the blood brain barrier and enter the central nervous system (CNS).

TABLE 5

Metabolic Stability (Percent remaining at 60

minutes and calculated half life in hours)

MolID
Formula
Est_T½(Hrs)

COTI-HIV1oxo
C17H12FN5O2
12.5

COTI-HIV1thio
C17H12FN5OS
12.1

COTI-HIV1Se
C17H12FN5OSe
14.5

COTI-HIV1imine
C17H13FN6O
16.0

COTI-HIV1Oxime
C17H13FN6O2
13.3

COTI-HIV2oxo
C16H13FN4O2
5.6

COTI-HIV28236-
C16H13FN4OS
8.2

SA

COTI-HIV28236-
C16H13FN4OSe
7.2

SeA

COTI-HIV2imine
C16H14FN5O
6.4

COTI-HIV28236
C16H14FN5O2
6.1

COTI-HIV1DOxime
C14H12FN5O3
8.5

COTI-HIV1Doxo
C14H11FN4O3
7.0

COTI-HIV1Dthio
C14H11FN4O2S
12.8

COTI-HIV1Dcyano
C15H11FN6O2
16.5

COTI-HIV1Dimino
C14H12FN5O2
8.2

COTI-HIV2DOxime
C13H13FN4O3
7.0

COTI-HIV2Doxo
C13H12FN3O3
6.0

COTI-HIV2Dthio
C13H12FN3O2S
6.7

COTI-HIV2Dcyano
C14H12FN5O2
8.4

COTI-HIV2Dimino
C13H13FN4O2
6.7

Table 5 shows that in vitro metabolic stability is expected to be adequate for all compounds. The compounds with a high Est_T½ (Hrs) are expected to take longer to be reduced to one half of their initial concentration than those with a low Est_T½ (Hrs). All predicted half lives were considered to be acceptable.

Legend for Table 5:

Est_T½ (hrs) is a calculated estimate of the half life of the drug measured in hours.

TABLE 6

Probability of Toxicity

AcuteLD50

MolID
Formula
(oral)
HepToxProb

COTI-HIV1oxo
C17H12FN5O2
698.32
0.131

COTI-HIV1thio
C17H12FN5OS
1063.08
0.109

COTI-HIV1Se
C17H12FN5OSe
760.55
0.155

COTI-HIV1imine
C17H13FN6O
682.51
0.106

COTI-HIV1Oxime
C17H13FN6O2
790.04
0.077

COTI-HIV2oxo
C16H13FN4O2
1276.26
0.022

COTI-HIV28236-
C16H13FN4OS
1157.14
0.028

SA

COTI-HIV28236-
C16H13FN4OSe
839.67
0.023

SeA

COTI-HIV2imine
C16H14FN5O
1101.07
0.033

COTI-HIV28236
C16H14FN5O2
2362.44
0.070

COTI-HIV1DOxime
C14H12FN5O3
1226.94
0.147

COTI-HIV1Doxo
C14H11FN4O3
1805.56
0.059

COTI-HIV1Dthio
C14H11FN4O2S
1256.64
0.091

COTI-HIV1Dcyano
C15H11FN6O2
1148.98
0.311

COTI-HIV1Dimino
C14H12FN5O2
1356.28
0.048

COTI-HIV2DOxime
C13H13FN4O3
1985.67
0.017

COTI-HIV2Doxo
C13H12FN303
658.87
0.322

COTI-HIV2Dthio
C13H12FN3O2S
953.29
0.040

COTI-HIV2Dcyano
C14H12FN5O2
1417.21
0.115

COTI-HIV2Dimino
C13H13FN4O2
1202.51
0.011

The low values provided in Table 6 for HepToxProb show that none of the compounds are expected to cause any Hepatic Toxicity. The compounds with a low AcuteLD50 (oral) are potentially more toxic than those with a high AcuteLD50 (oral). It takes more of a compound with a high AcuteLD50 (oral) to cause death in 50% of the rats to which it is administered, therefore such compounds are less toxic than those with a low AcuteLD50 (oral). Compounds with an LD50 of greater than 500 mg/kg are predicted to have acceptable toxicity for further development.

Legend for Table 6:

AcuteLD50 (oral) is the calculated point estimate of the dose of the drug in mg/kg that would cause death in 50% of healthy test lab rats when the drug is given orally.

HepToxProb is the average calculated probability from an ensemble of models that the drug in question will cause any liver toxicity.

TABLE 7

Animal and Human Toxicity Predictions

hMRTD

hERG

(mg/kg/

(IC50 >

MolID
Formula
day)
VentTach
10 umol)

COTI-HIV1oxo
C17H12FN5O2
1.29
0.018
0.934

COTI-HIV1thio
C17H12FN5OS
0.87
0.469
0.907

COTI-HIV1Se
C17H12FN5OSe
1.23
0.526
0.771

COTI-HIV1imine
C17H13FN6O
1.18
0.008
0.835

COTI-HIV1Oxime
C17H13FN6O2
1.64
0.012
0.814

COTI-HIV2oxo
C16H13FN4O2
1.85
0.013
0.988

COTI-HIV28236-
C16H13FN4OS
2.46
0.086
0.932

SA

COTI-HIV28236-
C16H13FN4OSe
2.16
0.040
0.896

SeA

COTI-HIV2imine
C16H14FN5O
1.56
0.031
0.959

COTI-HIV28236
C16H14FN5O2
2.15
0.009
0.969

COTI-
C14H12FN5O3
7.62
0.002
0.978

HIV1DOxime

COTI-HIV1Doxo
C14H11FN4O3
7.81
0.003
0.993

COTI-HIV1Dthio
C14H11FN4O2S
1.01
0.007
0.981

COTI-HIV1Dcyano
C15H11FN6O2
4.01
0.009
0.928

COTI-HIV1Dimino
C14H12FN5O2
5.04
0.006
0.987

COTI-
C13H13FN4O3
14.49
0.003
0.998

HIV2DOxime

COTI-HIV2Doxo
C13H12FN3O3
12.39
0.002
1.000

COTI-HIV2Dthio
C13H12FN3O2S
7.62
0.007
0.995

COTI-HIV2Dcyano
C14H12FN5O2
6.34
0.009
0.994

COTI-HIV2Dimino
C13H13FN4O2
7.15
0.003
0.998

The expected maximum recommended therapeutic daily dose in humans is provided in the column labeled hMRTD and is measured in mg/kg/d. hERG (IC50>10 umol) is the probability that the IC50 value (i.e. the amount required to produce a 50% decrease in initial concentration) for hERG will be greater than 10 umol. A high value indicates that it is likely that the compound will have little hERG channel activity. All of the compounds met the acceptance criterion of the probability being greater than 0.70. A high predicted hERG 1050 value is associated with a low probability of ventricular tachycardia (VentTach).

Legend for Table 7:

hMRTD is the calculated maximum recommended therapeutic daily dose of the drug in milligrams per kg per day for the average 60 Kg human adult; VentTach is the probability that the drug would produce ventricular trachycardia, which is a potentially lethal cardiac rhythm disturbance. hERG (IC50>10 umol) is the probability that the IC50 value (i.e. the amount required to produce a 50% decrease in initial concentration) for hERG will be greater than 10 umol. A high value indicates that it is likely that the compound will have little activity against hERG.

TABLE 8

Predicted Bio-pharmaceutical Classification (BCS)

P_Class
P_Class
P_Class
P_Class

MolID
Formula
1
2
3
4

COTI-HIV1oxo
C17H12FN5O2
0.000
0.994
0.000
0.005

COTI-HIV1thio
C17H12FN5OS
0.010
0.983
0.000
0.006

COTI-HIV1Se
C17H12FN5OSe
0.000
0.993
0.000
0.006

COTI-HIV1imine
C17H13FN6O
0.005
0.986
0.000
0.009

COTI-HIV1Oxime
C17H13FN6O2
0.008
0.983
0.000
0.009

COTI-HIV2oxo
C16H13FN4O2
0.000
0.079
0.000
0.921

COTI-HIV28236-
C16H13FN4OS
0.000
0.741
0.000
0.259

SA

COTI-HIV28236-
C16H13FN4OSe
0.010
0.537
0.008
0.445

SeA

COTI-HIV2imine
C16H14FN5O
0.001
0.316
0.003
0.680

COTI-HIV28236
C16H14FN5O2
0.000
0.831
0.000
0.169

COTI-HIV1DOxime
C14H12FN5O3
0.000
0.197
0.000
0.803

COTI-HIV1Doxo
C14H11FN4O3
0.000
0.523
0.000
0.476

COTI-HIV1Dthio
C14H11FN4O2S
0.000
0.995
0.000
0.004

COTI-HIV1Dcyano
C15H11FN6O2
0.003
0.991
0.000
0.007

COTI-HIV1Dimino
C14H12FN5O2
0.000
0.656
0.000
0.343

COTI-HIV2DOxime
C13H13FN4O3
0.004
0.838
0.001
0.157

COTI-HIV2Doxo
C13H12FN3O3
0.001
0.710
0.000
0.288

COTI-HIV2Dthio
C13H12FN3O2S
0.000
0.255
0.001
0.744

COTI-HIV2Dcyano
C14H12FN5O2
0.003
0.774
0.001
0.222

COTl-HIV2Dimino
C13H13FN4O2
0.002
0.817
0.001
0.180

Table 8 shows the predicted BCS for all of the structures. Referring to the Legend below, the probability of belonging to a given BCS class is provided. The majority of the compounds are predicted to be in Class 2. This implies that the compounds are predicted to have good permeability and low solubility and provides guidance for formulation and further development.

Legend for Table 8:

P_Class 1 is the probability that the compound would be in BCS Class 1 and have a high solubility and a high permeability.

P_Class 2 is the probability that the compound would be in BCS Class 2 and have a low solubility and a high permeability.

P_Class 3 is the probability that the compound would be in BCS Class 3 and have a high solubility and a low permeability.

P_Class 4 is the probability that the compound would be in BCS Class 4 and have a low solubility and a low permeability.

Example 7
HIV Integrase Assay In Vitro

The purpose of this study was to analyze the capacity of the COTI-HIV1Doxo (a COTI-HIV1 Ketone Derivative) to inhibit HIV-1 integrase in an in vitro assay. It should be noted that this compound is a precursor to all of the COTI-HIV1D-structures. The structure of COTI-HIV1Doxo is shown below:

embedded image

Methods:

The capacity of the compound to inhibit HIV integrase in a cell-free system was assessed. An HIV Integrase Assay System (XpressBio Life Science Products; Thurmont, Md., www.expressbio.com) was used. In brief, double-stranded HIV-1 donor substrate (the U5 long terminal repeat) was immobilized in 96-well plates. Recombinant HIV-1 integrase protein was added, along with an oligonucleotide target substrate. The integrase cleaves the donor substrate and integrates it into the target substrate, which is now in solution phase—the integrated product (the amount is indicative of integrase activity) was detected using an antibody specific for the recombinant target/donor sequence. Inhibitors added along with the donor substrate reduced the amount of product. The degree of inhibition by the compound at each concentration tested (from 1 nM to 100 μM) was determined and, if sufficient inhibition was achieved, an IC50 of the inhibitor was determined. The capacity of a compound known to inhibit HIV integrase activity (NaN3) was assessed as a positive control. All assessed inhibitions were compared to controls treated with vehicle only (compounds dissolved in 100% DMSO, then diluted in buffer to a maximum DMSO concentration of 0.1% DMSO). Concentrations of DMSO up to 5% have no significant effect on HIV integrase activity.

An advantage of the assay is that the capacity of a test compound to directly inhibit HIV integrase can be determined, without complications arising from the effects of the test compound on cell viability that are a complicating factor when testing effects on integration in living cells. However, it should be kept in mind that indirect HIV integrase inhibition (which might possibly occur in living cells) will not be detected.

Results and Discussion:

COTI-HIV1Doxo was assayed for HIV-1 integrase activity, as described above. All measurements were made in quadruplicate (n=4) to allow statistical analysis of significance. NaN₃(1.0% or 3.3%), a known HIV-1 integrase inhibitor, effectively decreased HIV-1 integrase activity in vitro, indicating the reliability of the assay (FIG. 1). COTI-HIV1Doxo inhibited HIV-1 integrase at a concentration of 100 nM (p<0.001, Student's t-test) but not at 10 nM (Rank Sum Test, p=1.000, performed after failure of an equal variance test on the raw data). All higher tested compound concentrations (up to 100 μM) significantly decreased HIV-1 integrase activity (p<0.001 in all cases). Interestingly, a low concentration of COTI-HIV-1 ketone derivative (1 nM) enhanced HIV-1 integrase activity, for unknown reasons (p<0.001).

Overall, COTI-HIV1Doxo appears to be an effective inhibitor of HIV-1 integrase in vitro with capacity to significantly reduce HIV-1 integrase activity at a nanomolar (100 nM) concentration. Complete inhibition of integrase activity was not observed, indicating that increasing COTI-HIV1Doxo concentrations did not reduce integrase function in a linear fashion. In fact, 50% reduction in HIV-1 integrase activity was not achieved until the compound concentrations were in the 10 μM range. Finally, very low concentrations of COTI-HIV-1 ketone derivative (1 nM) slightly but significantly enhanced HIV-1 integrase activity. It did so in a reproducible fashion, in 3 independent experiments. This is consistent with the computational predictions provided for Prob_Log IC50<−6 in Table 3, above.

Example 8
HIV-1 Integrase Assay of COTI-HIV-1, COTI-HIV28233, and COTI-HIV28236

The purpose of this study was to analyze the capacity of COTI-HIV-1 (COTI-HIV1DOxime), COTI-HIV28233 (COTI-HIV1oxime), and COTI-HIV28236, to inhibit HIV-1 integrase in a cell-free/in-vitro assay system.

embedded image

Methods:

Compound Preparation:

COTI-HIV-1 (8 mg; MW: 317.27; Lot # JFM-16-177-FIN) COTI-HIV28233 (8 mg; Lot # ND10/CO04164D) and COTI-HIV28236 (20 mg; MW: 327.31; Lot # ND10/CO04139I) were received at room temperature in lyophilized form. Both compounds were kept in this form at room temperature prior to testing (<1 week).

Test Samples:

Integrase only negative control; No integrase negative control; Sodium azide positive control: a known HIV-1 integrase inhibitor; COTI-HIV-1 (100.000 μM, 10.000 μM, 1.000 μM, 0.100 μM, 0.010 μM, 0.001 μM); COTI-HIV28233 (100.000 μM, 10.000 μM, 1.000 μM, 0.100 μM, 0.010 μM, 0.001 μM); COTI-HIV28236 (100.000 μM, 10.000 μM, 1.000 μM, 0.100 μM, 0.010 μM, 0.001 μM)

HIV-1 Integrase Assay Kit Procedure:

The effect of each compound on HIV integrase activity was assayed using the “HIV-1 Integrase Assay Kit” version 2.0, catalogue number EZ-1700 obtained from XpressBio Life Science Products. Immediately prior to the start of the assay, both compounds were dissolved in dimethyl sulfoxide (DMSO) and used immediately in the HIV integration assay. The assay was performed according to the instructions listed by the manufacturer (XpressBio Life Science Products, Maryland, USA). In brief, the required streptavidin-coated strip wells were coated with DS oligo and placed overnight at 4° C. The plates were then incubated with integrase and followed by the addition of test articles at the desired concentration. The plates were developed using the supplied HRP antibody and TMB peroxidase substrate as per the manufacturer's instructions. The reactions were stopped with TMB stop solution and immediately read (<10 min) using a VICTOR XXX. The absorbance of each well was read at 450 nm for 0.5 sec. All measurements were performed in triplicate. Sodium azide, a known HIV-1 integrase inhibitor, was used as a positive control for inhibiting HIV integrase activity and was found to effectively decrease HIV-1 integrase activity in vitro, indicating the reliability of the assay.

Data Analysis:

The background absorbance was subtracted from the raw data of each sample to yield “background corrected” absorbance values. The mean absorbance of the test samples divided by the mean integrase control activity multiplied by the associated CV yielded the percent adjusted SD. The CV=% SD for the 100% integrase alone control.

Results and Discussion:

To determine the IC₅₀of each test compound, non-linear regression analysis was used. The concentration data (x-axis) was log-transformed (FIG. 2) and analyzed using the equation log(inhibitor) vs. normalized response (Y=100/(1+10^((X−Log IC₅₀))) to determine the IC₅₀(Table 1). Since the data was compared to the integrase alone activity, it was presented as a percent of the control activity. Therefore, the activity observed with the integrase alone control was defined at 100% and the activity observed in the absence of integrase as 0%. Since we have a well-defined 0% and 100% and good control data, the response of the test samples were normalized to run between 0% and 100%.

FIGS. 2D and 2E show the results of the sodium azide control, which was run in parallel with the test samples. As observed, in the absence of sodium azide, the percent control activity was 100% and with increasing concentration of sodium azide, the percent control activity decreased, reaching 0% activity with 10% sodium azide. The calculated IC₅₀for both sodium azide controls were similar, 0.12% and 0.14%. The data obtained from all test compounds did not form a full sigmoidal curve reaching 0% control activity (FIG. 2). Because the top and the bottom plateaus can be defined by solid control data (eg. sodium azide), the data was fitted to a normalized model in order to calculate the IC₅₀. This model assumes that the dose response curve has a standard slope, equal to a Hill slope of −1.0. Since 6 compound concentrations were tested in triplicate, the data was analyzed using the standard slope model, in contrast with the variable slope model. The IC₅₀values for COTI-HIV-1, COTI-HIV28233 and COTI-HIV28236 were 58.7 μM, 23.9 μM and 14.0 μM (Table 9). COTI-HIV-1 and COTI-HIV28236 both significantly inhibited HIV-1 integrase at all concentrations tested (P<0.03 and P<0.02 t-test, respectively). COTI-HIV28233 significantly inhibited HIV-1 integrase at 100 μM (P=0.039). Of the three compounds, COTI-HIV28233 achieved the lowest percent of the total control activity (34.82%; P=0.039) at a concentration of 100 μM.

TABLE 9

Summary of the IC50 values for COTI-HIV-1,

COTI-HIV28233 and COTI-HIV28236

IC50

Test Sample
(μM)

COTI-HIV-1
58.7

COTI-HIV28233
23.9

COTI-HIV28236
14.0

Overall, COTI-HIV-1, COTI-HIV28233 and COTI-HIV28236 appear to be effective inhibitors of HIV-1 integrase in vitro with capacity to significantly reduce HIV-1 integrase activity. COTI-HIV-1 and COTI-HIV28236 were found to significantly inhibit HIV-1 integrase activity in vitro at all concentrations tested, with the lowest concentration being 1 nM. COTI-HIV28233 was found to modestly inhibit HIV-1 integrase activity at low concentrations, but to significantly reduce activity in the range of 100 μM. The lack of attaining statistical significance at lower concentrations of COTI-HIV28233 can likely be attributed to higher standard deviations in the values obtained.

At least 50% reduction in HIV-1 integrase activity was achieved at 100 μM for both COTI-HIV28233 and COTI-HIV28236. Non-linear regression analysis of the data from COTI-HIV-1, COTI-HIV28233 and COTI-HIV28236 allowed for the calculation of their IC₅₀values, which were 58.7 μM, 23.9 μM and 14.0 μM respectively. Overall, it appears as though COTI-HIV28236 was the most potent drug of the three compounds tested.

The above-described embodiments of the present invention are intended to be examples only. Alterations, modifications and variations may be effected to the particular embodiments by those of skill in the art without departing from the scope of the invention, which is defined solely by the claims appended hereto.

Claims

1. A method for making the compound of Formula III:
2. The method of claim 1, wherein c) comprises reacting Formula III, whereby X is oxygen, with NH2OH to form the compound of Formula III, wherein X is N—OH.
3. A method for making the compound of Formula IV:
4. The method of claim 3, wherein b) comprises reacting Formula IX with NH2OH to form the compound of Formula IV, wherein X is N—OH.
5. The method of claim 1, wherein R1, R2, R3, and R4 are each independently selected from H or substituted or unsubstituted alkyl.
6. The method according to claim 1, wherein X is Se, N—OH, NH, NO2, CN, N—CN, or N═O.
7. The method according to claim 1, wherein X is O or S.
8. The method according to claim 1, wherein the compound of Formula III is selected from:
9. The method according to claim 1, wherein at least one of Z and A is N.
10. The method according to claim 1, wherein both Z and A are N.
11. The method according to claim 1, wherein R8 is a substituted or unsubstituted hydrocarbon group.
12. The method according to claim 11, wherein R8 is a substituted or unsubstituted alkyl group.
13. The method according to claim 1, wherein the compound of Formula III is selected from:
14. The method of claim 3, wherein R1, R2, R3, and R4 are each independently selected from H or substituted or unsubstituted alkyl.
15. The method according to claim 3, wherein X is Se, N—OH, NH, NO2, CN, N—CN, or N═O.
16. The method according to claim 3, wherein R6 and R7 are each independently selected from H or a substituted or unsubstituted hydrocarbon group.
17. The method according to claim 16, wherein the substituted or unsubstituted hydrocarbon group is a substituted or unsubstituted alkyl group.
18. The method according to claim 17, wherein the substituted or unsubstituted alkyl group is a substituted or unsubstituted alkylaryl or a substituted or unsubstituted alkylheteroaryl.
19. The method according to claim 3, wherein X is O or S; and R6 and R7 are each independently selected from H or a substituted or unsubstituted alkyl group.
20. The method according to claim 3, wherein the compound of Formula IV is selected from:

Parent Case Info

This application is a division of U.S. application Ser. No. 14/618,986 filed Feb. 10, 2015, now allowed, which is a division of U.S. application Ser. No. 13/638,597 filed May 7, 2013, now U.S. Pat. No. 8,987,272, which is a national phase filing under 35 U.S.C. §371 of International Application No. PCT/CA2011/000357 filed Apr. 1, 2011, which claims the benefit of provisional U.S. Application No. 61/320,223, filed Apr. 1, 2010.

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Child	14618986		US

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