# Patent

## Title
Tubulysins and processes for preparing

## Abstract

Processes are described for the preparation of tubulysins. The processes are useful for preparing predetermined mixtures of tubulysins, preparing single tubulysins from mixtures of tubulysins, and for converting one tubulysin into a different tubulysin. The tubulysins described herein are useful in treating diseases and disease states that include pathogenic cell populations.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation application of U.S. patent application Ser. No. 12/739,579, filed Apr. 23, 2010, which is a U.S. national application under 35 U.S.C. §371(b) of International Application Ser. No. PCT/US2008/080948 filed Oct. 23, 2008, which claims the benefit under 35 U.S.C. §119(e) of U.S. Provisional Application Ser. No. 60/982,595, filed Oct. 25, 2007, and U.S. Provisional Application Ser. No. 61/036,176, filed Mar. 13, 2008, the disclosures of which are hereby incorporated herein by reference.


TECHNICAL FIELD
The invention described herein pertains to tubulysins and tubulysin analogs, and processes for preparing tubulysins and tubulysin analogs.
BACKGROUND
Tubulysins are a group of powerful inhibitors of tubulin polymerization. Tubulysins are useful in treating diseases and disease states that include pathogenic cell populations, such as cancer. Generally, tubulysins are linear tetrapeptides consisting of N-methyl pipecolic acid (Mep), isoleucine (Ile), an unnatural aminoacid called tubuvalin (Tuv), and either an unnatural aminoacid called tubutyrosine (Tut, an analog of tyrosine) or an unnatural aminoacid called tubuphenylalanine (Tup, an analog of phenylalanine), as shown in the following table:
















 









Factor
R1
T





A
(CH3)2CHCH2
OH


B
CH3(CH2)2
OH


C
CH3CH2
OH


D
(CH3)2CHCH2
H


E
CH3(CH2)2
H


F
CH2CH3
H


G
(CH3)2C═CH
OH


H
CH3
H


I
CH3
OH









Two particular species of mycobacteria synthesize tubulysins in high titer during fermentation. However, each species generally synthesizes a mixture of tubulysin factors, and that mixture differs between each of those mycobacteria species. For example, one species, Archangium gephyra, produces as the main component factors tubulysins A, B, C, G, and I, each of which may be identified by its including the Tut residue. In contrast, another species, Angiococcus disciformis, produces as the main component factors tubulysins D, E, F, and H, each of which may be identified by its including the Tup residue.

Such bacterial fermentations are convenient sources of tubulysins. However, because the mycobacteria produce only certain tubulysins, and/or mixtures of tubulysins, processes are needed for interconverting those tubulysins to the desired factors for medicinal and pharmacological uses. In addition, processes are needed for preparing novel tubulysins, tubulysin analogs, and tubulysin derivatives for medicinal and pharmacological uses.
SUMMARY OF THE INVENTION
Described herein are processes for preparing tubulysins. Also described herein are analogs and derivatives of tubulysins. In one embodiment, processes are described for preparing one or more tubulysins from a mixture of tubulysins, such as a mixture of tubulysins produced by fermentation or some other process. In another embodiment, processes are described herein for preparing a mixture of tubulyins from one or more tubulysins. In another embodiment, processes are described herein for converting one tubulysin into another tubulysin. In another embodiment, processes are described herein for converting one or more, or a mixture of tubulysins into one or more, or a mixture of tubulysin analogs. It is to be understood that as used herein, the term tubulysin refers both collectively and individually to the naturally occurring tubulysin, and the analogs and derivatives of tubulysins described herein, or that may be prepared from the processes described herein.
In another embodiment, novel tubulysins, tubulysin analogs, and tubulysin derivatives are described herein along with processes for preparing such novel tubulysins, tubulysin analogs, and tubulysin derivatives. In one embodiment, the processes include treating one or more tubulysins with an acid to prepare an intermediate. In another embodiment, the processes include the step of subsequently reacting the intermediate with a reagent to prepare a mixture of tubulysins from a different mixture of tubulysins, a single tubulysin from a mixture of tubulysins, a mixture of tubulysins from a single tubulysin, or a single tubulysins from a different tubulysin.
In one embodiment of the processes described herein, the intermediate is a compound of formulae (1a), (1b), or (1c):




wherein R, R1, S, T, U, V, W, Y, and Z are as described hereinbelow in the various embodiments, aspects, and variations thereof.

It is understood that intermediate compounds of formulae (1a), (1b), and (1c) may form salts, such as salts with the residual acid conjugate base. In addition, it is understood that iminium intermediates, such as those of formulae (1a), (1b), and (1c) may also be in equilibrium with the corresponding acyl aminal, where the residual acid conjugate base adds to the iminium intermediate. It is further appreciated that the iminium intermediates may form solvates or hydrates, each of which may be in equilibrium with the iminium intermediates. In any case, without being bound by theory, it is believed that nucleophiles such as RCN, RXH and the corresponding anions and salts thereof react with iminium intermediates regardless of whether the iminium is in a salt, hydrate, solvate or acylaminal form to prepare the compounds described herein, such as the compounds of formulae (2a), (2b), and (2c), respectively:




wherein R, R1, R10, S, T, U, V, W, Y, and Z are as described hereinbelow in the various embodiments, aspects, and variations thereof.



DETAILED DESCRIPTION
Described herein are processes for converting a single tubulysin or a mixture of tubulysin compounds into a single tubulysin compound or a different mixture of tubulysin compounds. In one embodiment, tubulysins described herein refer generally to tetrapeptide compounds of the formula




and pharmaceutical salts thereof, where

n is 1-3;
V is H, OR2, or halo, and W is H, OR2, or alkyl, where R2 is independently selected in each instance from H, alkyl, and C(O)R3, where R3 is alkyl, cycloalkyl, alkenyl, aryl, or arylalkyl, each of which is optionally substituted; providing that R2 is not H when both V and W are OR2; or V and W are taken together with the attached carbon to form a carbonyl;
X═H, C1-4 alkyl, alkenyl, each of which is optionally substituted, or CH2QR9; where Q is —N—, —O—, or —S—; R9═H, C1-4 alkyl, alkenyl, aryl, or C(O)R10; and R10═C1-6 alkyl, alkenyl, aryl, or heteroaryl;
Z is alkyl and Y is O; or Z is alkyl or C(O)R4, and Y is absent, where R4 is alkyl, CF3, or aryl;
R1 is H, or R1 represents 1 to 3 substituents selected from halo, nitro, carboxylate or a derivative thereof, cyano, hydroxyl, alkyl, haloalkyl, alkoxy, haloalkoxy, phenol protecting groups, prodrug moieties, and OR6, where R6 is optionally substituted aryl, C(O)R7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation; and
R is OH or a leaving group, or R forms a carboxylic acid derivative.
In one variation, Z is methyl. In another variation, R1 is H. In another variation, R1 is OR6 at C(4), where R6 is H, alkyl, or COR7. In another variation, V is H, and W is OC(O)R3.
Illustrative leaving groups include, but are not limited to halides, sulfonates, such as triflates, and the like, optionally substituted phenoxy, such as pentafluorophenoxy and the like, intermediates formed from ester forming or amide forming reagents, such as isobutyl chloroformate, DCC, HOBt, EDC, PyBOP, BOP, BOP-Cl, and the like.
Illustrative carboxylic acid derivatives include, but are not limited to, esters, amides, imides, acylhydrazides, nitriles, and optionally substituted variations thereof.
In another embodiment, tubulysins of the following general formula are described




and pharmaceutical salts thereof, where

n is 1-3;
V is H, OR2, or halo, and W is H, OR2, or alkyl, where R2 is independently selected in each instance from H, alkyl, or C(O)R3, where R3 is alkyl, alkenyl or aryl, providing that R2 is not H when both V and W are OR2; or V and W are taken together with the attached carbon to form a carbonyl;
X═H, C1-4 alkyl, alkenyl, each of which is optionally substituted, or CH2QR9; where Q is —N—, —O—, or —S—; R9═H, C1-4 alkyl, alkenyl, aryl, or C(O)R10; and R10═C1-6 alkyl, alkenyl, aryl, or heteroaryl;
Z is alkyl or C(O)R4, where R4 is alkyl, CF3, or aryl;
T is H or OR6, where R6 is H, alkyl, aryl, COR7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation, or R6 is a phenol protecting group, or a prodrug moiety;
S and U are each independently selected from the group consisting of H, halo, nitro, cyano, alkyl, haloalkyl, alkoxy, and haloalkoxy; and
R is OH or a leaving group, or R forms a carboxylic acid derivative.
In one embodiment, natural tubulysins, and the corresponding analogs and derivatives thereof are described. Such natural tubulysins are generally linear tetrapeptides consisting of N-methyl pipecolic acid (Mep), isoleucine (Ile), an unnatural aminoacid called tubuvalin (Tuv), and either an unnatural aminoacid called tubutyrosine (Tut, an analog of tyrosine) or an unnatural aminoacid called tubuphenylalanine (Tup, an analog of phenylalanine). In another embodiment, naturally occurring tubulysins, and analogs and derivatives thereof, of the following general formula are described




and pharmaceutical salts thereof, where R, R1, and R10 are as described in the various embodiments herein.

In one embodiment, a first tubulysin, or alternatively a mixture of tubulysins, is converted into a second tubulysin by preparing an intermediate compound of formula (1a), wherein
n is 1-3;
V is H, OR2, or halo, and W is H, OR2, or alkyl, where R2 is independently selected in each instance from H, alkyl, and C(O)R3, where R3 is alkyl, cycloalkyl, alkenyl, aryl, or arylalkyl, each of which is optionally substituted; providing that R2 is not H when both V and W are OR2; or V and W are taken together with the attached carbon to form a carbonyl;
X═H, C1-4 alkyl, alkenyl, each of which is optionally substituted, or CH2QR9; where Q is —N—, —O—, or —S—; R9═H, C1-4 alkyl, alkenyl, aryl, or C(O)R10; and R10═C1-6 alkyl, alkenyl, aryl, or heteroaryl;
Z is alkyl and Y is O; or Z is alkyl or C(O)R4, and Y is absent, where R4 is alkyl, CF3, or aryl;
R1 is H, or R1 represents 1 to 3 substituents selected from halo, nitro, carboxylate or a derivative thereof, cyano, hydroxyl, alkyl, haloalkyl, alkoxy, haloalkoxy, phenol protecting groups, prodrug moieties, and OR6, where R6 is optionally substituted aryl, C(O)R7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation; and
R is OH or a leaving group, or R forms a carboxylic acid derivative. The intermediate is prepared by mixing a tubulysin or mixture of tubulysins of formula (2b) with an acid under substantially anhydrous conditions:




and pharmaceutical salts thereof, where

n is 1-3;
V is H, OR2, or halo, and W is H, OR2, or alkyl, where R2 is independently selected in each instance from H, alkyl, and C(O)R3, where R3 is alkyl, cycloalkyl, alkenyl, aryl, or arylalkyl, each of which is optionally substituted; providing that R2 is not H when both V and W are OR2; or V and W are taken together with the attached carbon to form a carbonyl;
X═H, C1-4 alkyl, alkenyl, each of which is optionally substituted, or CH2QR9; where Q is —N—, —O—, or —S—; R9═H, C1-4 alkyl, alkenyl, aryl, or C(O)R10; and R10═C1-6 alkyl, alkenyl, aryl, or heteroaryl;
Z is alkyl and Y is O; or Z is alkyl or C(O)R4, and Y is absent, where R4 is alkyl, CF3, or aryl;
R1 is H, or R1 represents 1 to 3 substituents selected from halo, nitro, carboxylate or a derivative thereof, cyano, hydroxyl, alkyl, haloalkyl, alkoxy, haloalkoxy, phenol protecting groups, prodrug moieties, and OR6, where R6 is optionally substituted aryl, C(O)R7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation; and
R is OH or a leaving group, or R forms a carboxylic acid derivative.
The intermediate compound of formula (1a) is then treated with a compound of formula R10CO2H, where R10 is not the same as R10 present in the first tubulysin used to prepare the second compound of formula (2a).
In one variation, Z is methyl. In another variation, R1 is H. In another variation, R1 is OR6 at C(4), where R6 is H, alkyl, or COR7. In another variation, V is H, and W is OC(O)R3. In another variation, R is OH. In another variation, R forms an ester derivative. In another variation, R forms an amide derivative. In another variation, R forms an acylhydrazide derivative, such as the compound formed from hydrazine.
In another embodiment, a first tubulysin, or alternatively a mixture of tubulysins, is converted into a second tubulysin by preparing an intermediate compound of formula (1b), wherein V is H, OR2, or halo, and W is H, OR2, or alkyl, where R2 is independently selected in each instance from H, alkyl, or COR3, where R3 is alkyl, alkenyl or aryl, providing that R2 is not H when both V and W are OR2; or V and W are taken together with the attached carbon to form a carbonyl; Z is CH3 or COR4, and Y is absent; or Z is CH3 and, Y is O; where R4 is alkyl, CF3 or aryl; T is H or OR6, where R6 is H, alkyl, aryl, COR7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation; and S and U are each independently selected from the group consisting of H, halo, nitro, cyano, alkyl, haloalkyl, alkoxy, and haloalkoxy, or the corresponding carboxylic acid derivative thereof, where R is other than OH. The intermediate is prepared by mixing a tubulysin or mixture of tubulysins of formula (2b) with an acid under substantially anhydrous conditions:




wherein R10 is H, alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted; V is H, OR2, or halo, and W is H, OR2, or alkyl, where R2 is independently selected in each instance from H, alkyl, or COR3, where R3 is alkyl, alkenyl, cycloalkyl, aryl or arylalkyl, each of which is optionally substituted, providing that R2 is not H when both V and W are OR2; or V and W are taken together with the attached carbon to form a carbonyl; Z is CH3 or COR4, and Y is absent; or Z is CH3 and, Y is O; where R4 is alkyl, CF3 or aryl; T is H or OR6, where R6 is H, alkyl, aryl, COR7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation; and S and U are each independently selected from the group consisting of H, halo, nitro, cyano, alkyl, haloalkyl, alkoxy, and haloalkoxy, or the corresponding carboxylic acid derivative thereof, where R is other than OH. The intermediate compound of formula (1b) is then treated with a compound of formula R10CO2H, where R10 is not the same as R10 in the first tubulysin to prepare the second compound of formula (2b).

In another embodiment, a first tubulysin or a mixture of tubulysins is converted into a second tubulysin by preparing an intermediate compound of formula (1c), wherein T is H or OH. The intermediate is prepared by mixing a tubulysin or mixture of tubulysins of formula (2c) with an acid under substantially anhydrous conditions:




wherein T is H or OH and R10 is H, alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted, or the corresponding carboxylic acid derivative thereof, where R is other than OH. The intermediate compound of formula (1c) is then treated with a compound of formula R10CO2H where R10 is not the same as R1 present in the starting tubulysin used to prepare the second compound of formula (2c).

In each of the foregoing embodiments, it is understood that in certain configurations, the tubulysins may instead be converted into different mixtures of tubulysins rather than a single tubulysin. In such embodiments, a single starting tubulysin, or mixture of tubulysins, may be first converted into a common intermediate compound or a mixture of intermediate compounds of formulae (1a), (1b), or (1c), then those intermediate compounds are reacted with a mixture of carboxylic acids to provide the desired mixture of tubulysins. For example, if a mixture of tubulysins B and C, or the corresponding analogs or derivatives thereof, is desired, a single starting tubulysin, such as tubulysin A, or the corresponding analog or derivative thereof, or alternatively a mixture of tubulysins, may be first converted into the corresponding compound of formulae (1a), (1b), or (1c), wherein T is OH, then reacted with a mixture of carboxylic acids, such as butanoic acid and propanoic acid, corresponding to the appropriate groups on tubulysin B and C, respectively. It is appreciated that a statistical mixture may result based on the relative proportion of carboxylic acids used in the second step. Alternatively, it is also appreciated that kinetic and thermodynamic factors may influence the final proportion of tubulysins obtained in the second step and thus a statistical mixture of tubulysins based on the ratio of carboxylic acids will not result. In either case, it is understood that routine optimization of the relative ratios of carboxylic acid mixtures will afford the desired mixture of tubulysins from common intermediates of formulae (1a), (1b), and (1c).
In another embodiment, intermediate compound of formula (1b) can be treated with a compound of formula R9QH or the anion prepared therefrom to give a compound of the following formula:




wherein Q is —N—, —O—, or —S—; R9 is H, alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted, or R9 is C(O)R20, S(O)2R20, or P(O)(OR20)2; where R20 is independently selected in each instance from the group consisting of H, alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted, or R20 is a metal cation; V is H, OR2, or halo, and W is H, OR2, or alkyl, where R2 is independently selected in each instance from H, alkyl, or COR3, where R3 is alkyl, alkenyl, cycloalkyl, aryl or arylalkyl, each of which is optionally substituted, providing that R2 is not H when both V and W are OR2; or V and W are taken together with the attached carbon to form a carbonyl Z is CH3 or COR4, and Y is absent; or Z is CH3 and, Y is O; where R4 is alkyl, CF3 or aryl; T is H or OR6, where R6 is H, alkyl, aryl, COR7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation; and S and U are each independently selected from the group consisting of H, halo, nitro, cyano, alkyl, haloalkyl, alkoxy, and haloalkoxy, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, intermediate compound of formula (1c) can be treated with a compound of formula R9QH or an anion thereof to give a compound of the following formula:




wherein Q is —N—, —O—, or —S—; R9 is H, alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted, or R9 is C(O)R20, S(O)2R20, or P(O)(OR20)2; where R20 is independently selected in each instance from the group consisting of H, alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted, or R20 is a metal cation: and T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

It is to be understood that the corresponding compounds of formula (2a) may be similarly prepared via the corresponding intermediate of formula (1a) and R9QH.
In another embodiment, intermediate compound of formula (1b) can be treated with a nitrile compound, R21CN, to give a compound of the following formula:




wherein R21 is alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted; V is H, OR2, or halo, and W is H, OR2, or alkyl, where R2 is independently selected in each instance from H, alkyl, or COR3, where R3 is alkyl, alkenyl, cycloalkyl, aryl or arylalkyl, each of which is optionally substituted, providing that R2 is not H when both V and W are OR2; or V and W are taken together with the attached carbon to form a carbonyl Z is CH3 or COR4, and Y is absent; or Z is CH3 and, Y is O; where R4 is alkyl, CF3 or aryl; T is H or OR6, where R6 is H, alkyl, aryl, COR7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation; and S and U are each independently selected from the group consisting of H, halo, nitro, cyano, alkyl, haloalkyl, alkoxy, and haloalkoxy, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, intermediate compound of formula (1c) can be treated with a nitrile compound, R21CN, to give a compound of the following formula:




wherein R21 is alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted and T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

It is to be understood that the corresponding compounds of formula (2a) may be similarly prepared via the corresponding intermediate of formula (1a) and R21CN.
In another embodiment, intermediate compound of formula (1b) can be treated with an alkenylsilane of formula R22(TMS)CCH2 to give a compound of the following formula:




wherein R22 is alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted; V is H, OR2, or halo, and W is H, OR2, or alkyl, where R2 is independently selected in each instance from H, alkyl, or COR3, where R3 is alkyl, alkenyl, cycloalkyl, aryl or arylalkyl, each of which is optionally substituted, providing that R2 is not H when both V and W are OR2; or V and W are taken together with the attached carbon to form a carbonyl; Z is CH3 or COR4, and Y is absent; or Z is CH3 and, Y is O; where R4 is alkyl, CF3 or aryl; T is H or OR6, where R6 is H, alkyl, aryl, COR7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation; and S and U are each independently selected from the group consisting of H, halo, nitro, cyano, alkyl, haloalkyl, alkoxy, and haloalkoxy, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, intermediate compound of formula (1c) can be treated with an alkenylsilane of formula R22(TMS)CCH2 to give a compound of the following formula:




wherein R22 is alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted; and T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

It is to be understood that the corresponding compounds of formula (2a) may be similarly prepared via the corresponding intermediate of formula (1a) and R22(TMS)CCH2.
It is understood that in the preceding embodiments other olefins may form by isomerization, depending on the conditions of the reaction and the identity of R22. For example, when R22 is alkyl, it is appreciated that under the reaction conditions, the double bond can migrate to other carbon atoms along the alkenyl chain, including to form the terminal or ω-olefin.
In another embodiment, intermediate compound of formula (1b) is treated with a compound of formula R23C(O)CH2Ra to give a compound of the following formula:




wherein R23 is H, alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted; Ra is C(O)R9, C(O)OR9 or CN; R9 is selected from the group consisting of H, alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted; V is H, OR2, or halo, and W is H, OR2, or alkyl, where R2 is independently selected in each instance from H, alkyl, or COR3, where R3 is alkyl, alkenyl, cycloalkyl, aryl or arylalkyl, each of which is optionally substituted, providing that R2 is not H when both V and W are OR2; or V and W are taken together with the attached carbon to form a carbonyl; Z is CH3 or COR4, and Y is absent; or Z is CH3 and, Y is O; where R4 is alkyl, CF3 or aryl; T is H or OR6, where R6 is H, alkyl, aryl, COR7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation; and S and U are each independently selected from the group consisting of H, halo, nitro, cyano, alkyl, haloalkyl, alkoxy, and haloalkoxy, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, intermediate compound of formula (1c) is treated with a compound of formula R23C(O)CH2Ra to give a compound of the following formula:




wherein R23 is H, alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted; Ra is C(O)R9, C(O)OR9 or CN; R9 is selected from the group consisting of H, alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted: and T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

It is to be understood that the corresponding compounds of formula (2a) may be similarly prepared via the corresponding intermediate of formula (1a) and R23C(O)CH2Ra.
In another embodiment, intermediate compound of formula (1b) is treated with water to give a second intermediate compound of the following formula (3b)




wherein V is H, OR2, or halo, and W is H, OR2, or alkyl, where R2 is independently selected in each instance from H, alkyl, or COR3, where R3 is alkyl, alkenyl, cycloalkyl, aryl or arylalkyl, each of which is optionally substituted, providing that R2 is not H when both V and W are OR2; or V and W are taken together with the attached carbon to form a carbonyl; Z is CH3 or COR4, and Y is absent; or Z is CH3 and, Y is O; where R4 is alkyl, CF3 or aryl; T is H or OR6, where R6 is H, alkyl, aryl, COR7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation; and S and U are each independently selected from the group consisting of H, halo, nitro, cyano, alkyl, haloalkyl, alkoxy, and haloalkoxy, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, intermediate compound of formula (1c) is treated with water to give a second intermediate compound of formula (3c):




wherein T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

It is to be understood that the corresponding compounds of formula (3a) may be similarly prepared via the corresponding intermediate of formula (1a) and water.
In another embodiment, intermediate compound of formula (3b) is treated with a halogenating, sulfonylating, phosphonylating or phosphorylation reagent to give a compound of the following formula:




wherein X3 is halogen, OS(O)2R24, OP(O)(OR24)R24, or OP(O)(OR24)2; where R24 is independently selected in each instance from the group consisting of H, alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted, or R24 is a metal cation; V is H, OR2, or halo, and W is H, OR2, or alkyl, where R2 is independently selected in each instance from H, alkyl, or COR3, where R3 is alkyl, alkenyl, cycloalkyl, aryl or arylalkyl, each of which is optionally substituted, providing that R2 is not H when both V and W are OR2; or V and W are taken together with the attached carbon to form a carbonyl; Z is CH3 or COR4, and Y is absent; or Z is CH3 and, Y is O; where R4 is alkyl, CF3 or aryl; T is H or OR6, where R6 is H, alkyl, aryl, COR7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation; and S and U are each independently selected from the group consisting of H, halo, nitro, cyano, alkyl, haloalkyl, alkoxy, and haloalkoxy, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, intermediate compound of formula (3c) is treated with a halogenating, sulfonylating, phosphonylating or phosphorylation reagent to give a compound of the following formula:




wherein X3 is halogen, OS(O)2R24, OP(O)(OR24)R24, or OP(O)(OR24)2; where R24 is independently selected in each instance from the group consisting of H, alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted, or R24 is a metal cation; and T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

It is to be understood that the corresponding compounds of formula (3a) may be similarly prepared via the corresponding intermediate of formula (1a) and treatment with a halogenating, sulfonylating, phosphonylating or phosphorylation reagent.
In another embodiment, a compound of the following formula (2d):




is described, wherein R10 is H, alkyl, cycloalkyl, alkenyl, aryl or arylalkyl, each of which is optionally substituted: and T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH; is treated with trifluoroacetic acid and the mixture is concentrated under reduced pressure to give an intermediate iminium compound. It is understood that such iminium compounds may be present as the corresponding trifluoroacetate salt compounds, and other hydrates and solvates, and as the acylaminal compound, and other addition adducts, as is illustrated by the following formulae:





Mixing the compound of those formulae, or other corresponding intermediates described herein and prepared by treatment of compound (2d) with TFA, and with an alcohol gives the corresponding N,O-acetal compound of the following formula:





wherein R9 is H, alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted, or R9 is C(O)R20, S(O)2R20, or P(O)(OR20)2; where R20 is independently selected in each instance from the group consisting of H, alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted, or R20 is a metal cation: and T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, mixing a compound of formula (2d) with trifluoroacetic acid and concentrating the mixture under reduced pressure, followed by mixing the concentrated mixture with a thiol gives a N,S-acetal compound of the following formula:




wherein R9 is H, alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted, or R9 is C(O)R20, S(O)2R20, or P(O)(OR20)2; where R20 is independently selected in each instance from the group consisting of H, alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted, or R20 is a metal cation: and T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, mixing a compound of formula (2d) with trifluoroacetic acid and concentrating the mixture under reduced pressure, followed by mixing the concentrated mixture with a nitrile gives a compound of the following formula:




wherein R21 is alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted; and T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, mixing a compound of formula (2d) with trifluoroacetic acid and concentrating the mixture under reduced pressure, followed by mixing the concentrated mixture with a ketone, in a Biginelli-type reaction, gives a compound of the following formula:




wherein R23 is H, alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted; Ra is C(O)R8, C(O)OR8 or CN; R8 is selected from the group consisting of H, alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted; and T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, mixing a compound of formula (2d) with trifluoroacetic acid and concentrating the mixture under reduced pressure, followed by mixing the concentrated mixture with an alkenylsilane gives a compound of the following formula:




wherein R22 is alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted; and T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, mixing a compound of formula (2d) with trifluoroacetic acid and concentrating the mixture under reduced pressure, followed by mixing the concentrated mixture with water gives a compound of formula (3d):




which may also be referred to as hydroxytubulysin D when T is OH, or hydroxytubulysin A when T is OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, N-hydroxymethytubulysin A or N-hydroxymethytubulysin D is treated with a sulfonyl halide and a base to give a compound of the following formula:




wherein R24 is alkyl, cycloalkyl, alkenyl, aryl or arylalkyl, each of which is optionally substituted; and T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, N-hydroxymethytubulysin A or N-hydroxymethytubulysin D is treated with a bromine or iodine in the presence of triphenylphospine and imidazole to give a compound of the following formula:




wherein X4 is Br or I; and T is H or OH, or the corresponding carboxylic acid derivative thereof, where R is other than OH.

In another embodiment, conjugates of tubulysins of the following formula are described:




and pharmaceutical salts thereof, where n is 1-3; T is H or OR6, where R6 is H, alkyl, aryl, COR7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation, or R6 is a phenol protecting group, or a prodrug moiety; Z is alkyl or C(O)R4, where R4 is alkyl, CF3, or aryl; and R is OH or a leaving group, or R forms a carboxylic acid derivative. Illustrative examples of such compounds, and their preparation are described in J. Med. Chem. 51, 1530-1533 (2008), the disclosure of which is incorporated herein by reference. It is understood that the conjugates may be formed at any heteroatom in the foregoing formula by removing the corresponding hydrogen or other group, including but not limited to conjugates formed by removing the hydrogen from R when R═OH, from T when T=OH, and the like. Conjugates described herein may include spacer linkers and/or releasable linkers as generally described in US Patent Application Publication 2005/0002942, the disclosure of which is incorporated herein by reference. In addition, conjugates described herein may include targeting ligands, including but not limited to folate and analogs and derivatives of folate, for targeting the conjugates to pathogenic cell populations, such as generally described in US Patent Application Publication 2005/0002942.

In another embodiment, tubulysins of the following general formula are described




and pharmaceutical salts thereof, where

n is 1-3;
V is H, OR2, or halo, and W is H, OR2, or alkyl, where R2 is independently selected in each instance from H, alkyl, or COR3, where R3 is alkyl, alkenyl or aryl, providing that R2 is not H when both V and W are OR2; or V and W are taken together with the attached carbon to form a carbonyl;
X═H, C1-4 alkyl, alkenyl, each of which is optionally substituted, or CH2QR9; where Q is —N—, —O—, or —S—; R9═H, C1-4 alkyl, alkenyl, aryl, or C(O)R10; and R10═C1-6 alkyl, alkenyl, aryl, or heteroaryl;
Z is CH3 or COR4, and Y is absent; or Z is CH3 and, Y is O; where R4 is alkyl, CF3 or aryl;
T is H or OR6, where R6 is H, alkyl, aryl, COR7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation;
S and U are each independently selected from the group consisting of H, halo, nitro, cyano, alkyl, haloalkyl, alkoxy, and haloalkoxy; and
R is OH or a leaving group, or R forms a carboxylic acid derivative. Additional tubulysins are described in US patent application publication Nos. 2006/0128754 and 2005/0239713, the disclosures of which are incorporated herein by reference.
In another embodiment, tubulysins of the following formula are described:




and pharmaceutical salts thereof, where n is 1-3; T is H or OR6, where R6 is H, alkyl, aryl, COR7, P(O)(OR8)2, or SO3R8, where R7 and R8 are independently selected in each instance from H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl, each of which is optionally substituted, or R8 is a metal cation, or R6 is a phenol protecting group, or a prodrug moiety; Z is alkyl or C(O)R4, where R4 is alkyl, CF3, or aryl; and R is OH or a leaving group, or R forms a carboxylic acid derivative. Illustrative examples of such compounds, and their preparation are described in J. Med. Chem. 51, 1530-1533 (2008), the disclosure of which is incorporated herein by reference.

In another embodiment, tubulysins of the following formula are described:




and pharmaceutical salts thereof, where n, S, T, U, V, W, Z, R, and R10 are as described in the various embodiments herein.

In another embodiment, tubulysins of the following formula are described:




and pharmaceutical salts thereof, where n, S, T, U, V, W, Z, QR9, and R are as described in the various embodiments herein. In one variation, Q is —N—, —O—, or —S—; and R9 is H, alkyl, alkenyl, cycloalkyl, aryl, or arylalkyl, each of which is optionally substituted. In another variation, QR9 are taken together to form C(O)R10, S(O)2R10, P(O)(OR10a)2, where R10 and OR10a are independently selected in each instance from the group consisting of H, alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted, or R10a is a metal cation.

In another embodiment, tubulysins of the following formula are described:




and pharmaceutical salts thereof, where R12 represents 1 or more substituents selected from alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted; and where n, S, T, U, V, W, Z, and R are as described in the various embodiments herein. It is to be understood that other olefins may form by isomerization, depending on the conditions of the reaction and the identity of R1. For example, when R1 is alkyl, it is appreciated that under the reaction conditions, the double bond can migrate to other carbon atoms along the alkenyl chain, including to form the terminal or wω-olefin.

In another embodiment, tubulysins of the following formula are described:




and pharmaceutical salts thereof, where R13 is C(O)R10, C(O)OR10 or CN; and where n, S, T, U, V, W, Z, R, and R10 are as described in the various embodiments herein, where R10 is independently selected in each instance.

In another embodiment, tubulysins of the following formula are described:




and pharmaceutical salts thereof, where n, S, T, U, V, W, Z, and R are as described in the various embodiments herein.

In another embodiment, tubulysins of the following formula are described:




and pharmaceutical salts thereof, where X3 is halogen, OS(O)2R10, OP(O)(OR10a)R10, or OP(O)(OR10a)2; where R10 and R10a are independently selected in each instance from the group consisting of H, alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl, each of which is optionally substituted, or R10a is a metal cation; and where n, S, T, U, V, W, Z, and R are as described in the various embodiments herein.

Additional tubulysins useful in preparing the conjugates described herein are described in Peltier et al., “The Total Synthesis of Tubulysin D,” J. Am. Chem. Soc. 128:16018-19 (2006), the disclosure of which is incorporated herein by reference.
In each of the foregoing embodiments, it is understood that in one variation, the compounds of the various formulae have the following absolute configuration:




at the indicated asymmetric backbone carbon atoms.

As described herein, the tubulysin compounds may be inhibitors of tubulin polymerization, and also may be DNA-alkylators. Accordingly, methods for treating diseases and disease states including pathogenic cell populations, such as cancer, are described herein.
EXAMPLES
General Procedures
Trifluoroacetic acid (TFA, 0.20 mL) was added via syringe into a light brown solution of a tubulysin mixture (20 mg, containing tubulysins A, B, C, G, I and hydroxytubulysin) in anhydrous dichloromethane (DCM, 0.80 mL). After stirring for 40 minutes at room temperature and under argon, to the solution was added the correspondending nucleophile (for example, but not limited to, H2O, MeOH, 1-propanol, ethylene glycol, 3-methylbutanol, 1-propanethiol, 2-sulfanylethanol, 1,2-ethanedithiol, acetic acid, butyric acid, trans-4-chloro-2-butenoic acid), 0.20 mL was used for all thiols and 0.50 mL was used for all the others, and the solution was concentrated at reduced pressure on a Büchi Rotavapor and then further concentrated by means of an oil pump. The crude product was dissolved in dimethyl sulfoxide (DMSO, 1.0 mL) and purified by preparative HPLC to afford the product as a white solid.
GENERAL PREPARATIVE HPLC PARAMETERS
Column: Waters XTerra Prep MS C18 10 μm, 19×250 mm; Mobile phase A: 2.0 mM sodium phosphate buffer, pH 7.0; Mobile phase B: acetonitrile; Method: 10% B to 80% B over 30 minutes, flow rate=26 mL/min.
Example
Interconversion of natural tubulysins
TFA (1.0 mL) was added to a light brown solution of a mixture of tubulysins (105 mg tubulysins A, B, C, G, I and hydroxy-tubulysin A) in dry DCM (5.0 mL) and the resulting light brown-greenish solution was stirred at room temperature under argon for 50 minutes. LC/MS indicated that the tubulysin mixture was converted to hydroxy-tubulysin. To the solution was added butyric acid (10 mL) and the solution was first concentrated by evaporation to a small volume to remove TFA and DCM, and then further concentrated to a thick oil under vacuum over about 1 hour. HPLC analysis indicated a complete conversion of the hydroxy tubulysin intermediate to tubulysin B. The crude product was dissolved in DMSO (1.2 mL) and purified by preparative HPLC on a Waters XTerra Prep MS C18 10 μm 19×250 mm column using a 25% B to 50% B gradient over 20 minutes (A: 2.0 mM phosphate buffer, pH 7.0; B: ACN) at 25 mL/minute. Fractions from 11.5 to 13.5 minutes were collected and lyophilized to 86 mg of a white solid containing 77 mg of tubulysin B and 9.0 mg of sodium phosphate salts. Monitoring the interconversion throughout the experiment by HPLC showed conversion only to tubulysin B, as compared to a reference standard sample. It is to be understood that other mixtures of tubulysins can be similarly converted into a single tubulysin. It is further to be understood that this and other mixtures of tubulysins can be similarly converted into a different tubulysin than tubulysin B.
Example
Interconversion of natural tubulysins
The conditions of the previous Example were repeated to (a) convert tubulysin A into tubulysin B, (b) convert tubulysin A into tubulysin I, (c) convert a mixture of tubulysins A and B into tubulysin B, and (d) convert a mixture of tubulysins A, B, and I into tubulysin B. In each case, the yield of tubulysin B was ≧90%. It is to be understood that in each of examples (a) to (d), the corresponding tubulysin can be converted into a different tubulysin than tubulysin B. It is further to be understood that tubulysin B can be similarly converted into a different tubulysin. In some cases, N-hydroxymethyl substituted tubulysin was also isolated. It was surprisingly discovered that this hemiaminal was stable at neutral pH, and did not decompose to the free amine and formaldehyde.




The 1H NMR spectrum of hydroxytubulysin A was consistent with the structure; the MS had an m/z=760. The 1H NMR spectrum of tubulysin B obtained in this experiment was consistent with the structure; the MS had an m/z=830.

Example
Methoxy Tubulysin (EC0313)




TFA (0.20 mL) was added to a solution of tubulysin B (21.0 mg) in dry DCM (0.80 mL) and the mixture was stirred at room temperature under argon for 1 hour. MeOH (1.0 mL) was added to the stirring solution and the solvent was evaporated after 1 h. The residue was purified by preparative HPLC on a Waters XTerra Prep MS C18 10 μm 19×250 mm column using a 20% B to 50% B gradient over 25 minutes (A: 1.0 mM phosphate buffer, pH 7.0; B: ACN) at 10 mL/minute. Fractions from 18.8 to 22.3 minutes were collected and lyophilized to 18.0 mg of a white solid containing 15.5 mg of title compound and 2.5 mg of sodium phosphate salts. The 1H NMR spectrum of methoxy tubulysin obtained in this experiment was consistent with the structure; the MS had an m/z=774.
Example
2-Hydroxyethoxy Tubulysin (EC0346)




TFA (75 μL) was added to a solution of tubulysin B (4.8 mg) in dry DCM (0.30 mL) and the mixture was stirred at room temperature under argon for 1 hour. Ethylene glycol (0.30 mL) was added to the stirring solution and the solvent was evaporated after 30 min. The residue was purified by a preparative HPLC on a Waters Phenomenex Luna C18 10 μm 4.6×250 mm column using a 10% B to 80% B gradient over 20 minutes (A: 1.0 mM phosphate buffer, pH 7.0; B: ACN) at 2.5 mL/minute. Fractions from 6.3 to 6.7 minutes were collected and lyophilized to 4.9 mg of a white solid containing 4.8 mg of title compound and 0.1 mg of sodium phosphate salts. The 1H NMR spectrum of 2-hydroxyethoxy tubulysin obtained in this experiment was consistent with the structure; the MS had an m/z=804.
Example
2-Mercaptoethylthio Tubulysin (EC0374)




TFA (60 μL) was added to a solution of tubulysin B (6.9 mg) in dry DCM (0.54 mL) and the mixture was stirred at room temperature under argon for 30 minutes. 1,2-Ethanedithiol (2.0 μL) was added to the stirring solution and the solvent was evaporated after 5 h. The residue was purified by preparative HPLC on a Waters XTerra Prep MS C18 10 μm 19×250 mm column using a 10% B to 80% B gradient over 20 minutes (A: 2.0 mM phosphate buffer, pH 7.0; B: ACN) at 25 mL/minute. Fractions from 9.5 to 10.7 minutes were collected and lyophilized to 7.7 mg of a white solid containing 3.4 mg of title compound and 4.3 mg of sodium phosphate salts. The 1H NMR spectrum of 2-mercaptoethylthio tubulysin obtained in this experiment was consistent with the structure; the MS had an m/z=836.
Example
iso-Butyrylamidotubulysin (EC0585)




A mixture of tubulysins containing factors A, B, C, G, I, and hydroxy tubulysin (R═C(O)CH2CH(CH3)2, C(O)CH2CH2CH3, C(O)CH2CH3, C(O)CH═C(CH3)2, C(O)CH3, and H, respectively) was converted to a single tubulysin. To a solution of the tubulysin mixture (25 mg) in isovaleronitrile (150 μL) was added a solution containing TFA (30 μL), concentrated H2SO4 (20 μL), and isovaleronitrile (150 μL). After stirring at room temperature for 22 hours, the reaction was quenched with 2.0 mM sodium phosphate buffer (pH=7.0, 15 mL) and injected into a preparative HPLC for purification. Column: Waters XTerra Prep MS C18 10 μm, 19×250 mm; Mobile phase A: 2.0 mM sodium phosphate buffer, pH 7.0; Mobile phase B: acetonitrile; Method: 10% B to 80% B over 30 minutes, flow rate=26 mL/min. Fractions from 17.22-18.36 minutes were collected and lyophilized to produce EC0585 as a white solid (16 mg). The 1H NMR spectrum of iso-butyrylamidotubulysin obtained in this experiment was consistent with the structure; the MS had an m/z=843.
Example
N-Homoallyl Tubulysin EC0550




A mixture of tubulysins containing factors A, B, C, G, I, and hydroxy tubulysin (R═C(O)CH2CH(CH3)2, C(O)CH2CH2CH3, C(O)CH2CH3, C(O)CH═C(CH3)2, C(O)CH3, and H, respectively) was converted to a single tubulysin. TFA (0.15 mL) was added to a solution of the tubulysin mixture (19 mg) in anhydrous DCM (0.60 mL) at room temperature. After stirring for 40 minutes at room temperature under argon, the reaction was quenched with anhydrous MeOH (0.50 mL). The solution was concentrated on a Büchi Rotavapor, co-evaporated with anhydrous MeOH (2×) and anhydrous DCM (2×), vacuumed for 30 minutes, co-evaporated again with anhydrous MeOH and anhydrous DCM (2×), and vacuumed for an additional 1.5 hours. The residue was dissolved in anhydrous DCM (0.75 mL), to which was added allyltrimethylsilane (0.30 mL), cooled in an ice-bath, and to which was added BF3.Et2O (0.23 mL). The reaction mixture was stirred under argon in an ice-bath for 30 minutes, and then the cooling was removed and the reaction mixture was stirred at room temperature for an additional 2 hours and 50 minutes. The reaction mixture was concentrated and the residue was purified by a preparative HPLC. Column: Waters XTerra Prep MS C18 10 μm, 19×250 mm; Mobile phase A: 2.0 mM sodium phosphate buffer, pH 7.0; Mobile phase B: acetonitrile; Method: 15% B to 80% B over 30 minutes, flow rate=26 mL/min. Fractions from 14.41-15.17 minutes were collected and lyophilized to afford EC0550 as a white solid (10 mg). The 1H NMR spectrum of N-homoallyl tubulysin obtained in this experiment was consistent with the structure; the MS had an m/z=784.
Example
Synthesis of Tubulysin B Hydrazide EC0347




N,N-Diisopropylethylamine (DIPEA, 6.1 μL) and isobutyl chloroformate (3.0 μL) were added with the help of a syringe in tandem into a solution of tubulysin B (0.15 mg) in anhydrous EtOAc (2.0 mL) at −15° C. After stirring for 45 minutes at −15° C. under argon, the reaction mixture was cooled down to −20° C. and to which was added anhydrous hydrazine (5.0 μL). The reaction mixture was stirred under argon at −20° C. for 3 hours, quenched with 1.0 mM sodium phosphate buffer (pH 7.0, 1.0 mL), and injected into a preparative HPLC for purification. Column: Waters XTerra Prep MS C18 10 μm, 19×250 mm; Mobile phase A: 1.0 mM sodium phosphate buffer, pH 7.0; Mobile phase B: acetonitrile; Method: 10% B to 80% B over 20 minutes, flow rate=25 mL/min. Fractions from 15.14-15.54 minutes were collected and lyophilized to produce EC0347 as a white solid (2.7 mg). The 1H NMR spectrum of tubulysin B hydrazide obtained in this experiment was consistent with the structure; the MS had an m/z=844.
Example
Synthesis of EC0311




DIPEA (0.60 mL) was added to a suspension of HOBt-A (685 mg, 91%) in anhydrous DCM (5.0 mL) at 0° C., stirred under argon for 2 minutes, and to which was added anhydrous hydrazine (0.10 mL). The reaction mixture was stirred under argon at 0° C. for 10 minutes and room temperature for an additional 30 minutes, filtered, and the filtrate was purified by flash chromatography (silica gel, 2% MeOH in DCM) to afford EC0311 as a clear thick oil (371 mg), solidified upon standing.
Example
Synthesis of EC0312




DIPEA (36 μL) and isobutyl chloroformate (13 μL) were added with the help of a syringe in tandem into a solution of tubulysin B (82 mg) in anhydrous EtOAc (2.0 mL) at −15° C. After stirring for 45 minutes at −15° C. under argon, to the reaction mixture was added a solution of EC0311 in anhydrous EtOAc (1.0 mL). The resulting solution was stirred under argon at −15° C. for 15 minutes and room temperature for an additional 45 minutes, concentrated, and the residue was purified by flash chromatography (silica gel, 2 to 8% MeOH in DCM) to give EC0312 as a white solid (98 mg). The 1H NMR spectrum of EC0312 obtained in this experiment was consistent with the structure; the MS had an m/z=1057.
Example
The following compounds were prepared according to the procedures described herein.




The 1H NMR spectrum of EC0575 obtained in this experiment was consistent with the structure; the MS had an m/z=862.




The 1H NMR spectrum of EC0560 obtained in this experiment was consistent with the structure; the MS had an m/z=820.




The 1H NMR spectrum of EC0356 obtained in this experiment was consistent with the structure; the MS had an m/z=817.




The 1H NMR spectrum of EC0611 obtained in this experiment was consistent with the structure; the MS had an m/z=802.




The 1H NMR spectrum of EC0623 obtained in this experiment was consistent with the structure; the MS had an m/z=818.
It is appreciated that the foregoing Examples are merely illustrative of the processes described herein and that many routine modifications may be made to prepare additional tubulysin compounds, and analogs and derivatives thereof. For example, additional ether forming alcohols may be used, including but not limited to alcohols, such as ethanol, propanol, sec-butanol, and the like, polyols, such as ethylene glycols, polyethylene glycols, propylene glycols, polypropylene glycols, glycerol, and the like, including alkyl, and acyl derivatives thereof, aminoalcohols, such as aminoethanol, aminopropanol, polyaminoalkylethanol, and the like, including alkyl, and acyl derivatives thereof, and others. Similarly, additional thiols, carboxylic acids, amino acids, amines, and the like may be used as nucleophiles to trap the intermediate iminium compounds of formulae (1) and (3).
Method Example
Inhibition of Cellular DNA Synthesis
The compounds described herein are evaluated using an in vitro cytotoxicity assay that predicts the ability of the drug to inhibit the growth of folate receptor-positive KB cells. The KB cells are exposed for up to 7 h at 37° C. over a range of concentrations of folate-drug conjugate in the absence or presence of at least a 100-fold excess of folic acid. The cells are then rinsed once with fresh culture medium and incubated in fresh culture medium for 72 hours at 37° C. Cell viability is assessed using a 3H-thymidine incorporation assay.
Method Example
In vitro concentration-dependent cytotoxic activity
Cells were heavily seeded in 24-well Falcon plates and allowed to form nearly confluent monolayers overnight. Thirty minutes prior to the addition of test article, spent medium was aspirated from all wells and replaced with fresh folate-free RPMI (FFRPMI). Note, designated wells received media containing 100 μM folic acid; and, cells within the latter wells were used to determine the targeting specificity, since cytotoxic activity produced in the presence of excess folic acid (enables competition for FR binding) would signify the portion of the total activity that was unrelated to FR-specific delivery. Following one rinse with 1 mL of fresh FFRPMI containing 10% heat-inactivated fetal calf serum, each well received 1 mL of media containing increasing concentrations of test article (4 wells per sample) in the presence or absence of 100 μM free folic acid (a binding site competitor). Treated cells were pulsed for 2 h at 37° C., rinsed 4 times with 0.5 mL of media, and then chased in 1 mL of fresh media up to 70 h. Spent media was aspirated from all wells and replaced with fresh media containing 5 μCi/mL 3H-thymidine. Following a further 2 h 37° C. incubation, cells were washed 3 times with 0.5 mL of PBS and then treated with 0.5 mL of ice-cold 5% trichloroacetic acid per well. After 15 min, the trichloroacetic acid was aspirated and the cell material solubilized by the addition of 0.5 mL of 0.25 N sodium hydroxide for 15 min. Four hundred and fifty μL of each solubilized sample were transferred to scintillation vials containing 3 mL of Ecolume scintillation cocktail and then counted in a liquid scintillation counter. Final results are expressed as the percentage of 3H-thymidine incorporation relative to untreated controls.
As shown in the following table, dose-dependent cytotoxicity is measurable, and in most cases, the IC50 values (concentration of drug conjugate required to reduce 3H-thymidine incorporation into newly synthesized DNA by 50%) are in the low nanomolar range. Furthermore, the cytotoxicities of these conjugates are reduced in the presence of excess free folic acid, indicating that the observed cell killing was mediated by binding to the folate receptor.














Example
Cytotoxicity IC50 (nM)



















Tubulysin A
2



Tubulysin B
2.6



EC0313
9



EC0346
18



EC0550
2



EC0356
12



EC0374
24



EC0585
8



EC0386
42



EC0623
0.48



EC0346
18










Method Example
Tumor models and therapy
Four to seven week-old mice (Balb/c or nu/nu strains) are purchased from Harlan Sprague Dawley, Inc. (Indianapolis, Ind.). Since normal rodent chow contains a high concentration of folic acid (6 mg/kg chow), mice used in these studies are maintained on the folate-free diet (Harlan diet #TD00434) for 1 week before tumor implantation to achieve serum folate concentrations close to the range of normal human serum. For tumor cell inoculation, 1×106 M109 cells or 1×106 KB cells in 100 μL are injected in the subcutis of the dorsal medial area. Tumors are measured in two perpendicular directions every 2-3 days using a caliper, and their volumes were calculated as 0.5×L×W2, where L=measurement of longest axis in mm and W=measurement of axis perpendicular to L in mm. Log cell kill (LCK) and treated over control (T/C) values are then calculated according to published procedures (see, e.g., Lee et al., “BMS-247550: a novel epothilone analog with a mode of action similar to paclitaxel but possessing superior antitumor efficacy” Clin Cancer Res 7:1429-1437 (2001); Rose, “Taxol-based combination chemotherapy and other in vivo preclinical antitumor studies” J Natl Cancer Inst Monogr 47-53 (1993)). Dosing solutions are prepared fresh each day in PBS and administered through the lateral tail vein of the mice. Importantly, dosing is initiated when the s.c. tumors were between 50-100 mm3 in volume.
Persistent drug toxicity is assessed by collecting blood via cardiac puncture and submitting the serum for independent analysis of blood urea nitrogen (BUN), creatinine, total protein, AST-SGOT, ALT-SGPT plus a standard hematological cell panel at Ani-Lytics, Inc. (Gaithersburg, Md.). In addition, histopathologic evaluation of formalin-fixed heart, lungs, liver, spleen, kidney, intestine, skeletal muscle and bone (tibia/fibula) is conducted by board-certified pathologists at Animal Reference Pathology Laboratories (ARUP; Salt Lake City, Utah).

## Claims

1. A process for converting a compound of the formula (I)




wherein:
n is an integer from 1 to 3;
V is selected from the group consisting of H, OR2, and halo, and W is selected from the group consisting of H, OR2, and alkyl; or V and W are taken together with the attached carbon to form a carbonyl;
Z is alkyl, and Y is O; or Z is alkyl or C(O)R4, and Y is absent;
R is OH or a leaving group; or R forms a carboxylic acid derivative selected from the group consisting of an ester, an amide, an imide, and an acylhydrazide;
R1 is H; or R1 represents 1 to 3 substituents each independently selected from the group consisting of halo, nitro, carboxylate, cyano, hydroxyl, alkyl, haloalkyl, alkoxy, haloalkoxy, and OR6;
each R2 is independently selected from the group consisting of H, alkyl, and C(O)R5, provided that R2 is not H when both V and W are OR2;
R4 is selected from the group consisting of alkyl, CF3, and aryl;
each R5 is independently selected from the group consisting of alkyl, cycloalkyl, alkenyl, arylalkyl and aryl;
R6 is selected from the group consisting of aryl, C(O)R7, P(O)(OR8)2, SO3R8, and a phenol protecting group;
each R7 and R8 is independently selected from the group consisting of H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl; or R8 is a metal cation;
and
R10 is alkyl or alkenyl, each of which is optionally substituted;
into a compound of the formula (II)





wherein:
n, V, W, Z, Y, R, R1, R2, R4, R5, R6, R7, R8, and R10 are as defined in formula I;
X is CH2QR9;
Q is —NH— or —S—, and each R9 is independently selected from the group consisting of hydrogen, C1-4 alkyl, alkenyl, aryl, and C(O)R11; or Q is —O—, and R9 is C(O)R11 or C5 alkyl; and
each R11 is independently selected from the group consisting of C1-6 alkyl, alkenyl, aryl, and heteroaryl;
the process comprising
(a) mixing the compound of the formula (I) with an acid to form an intermediate; and
(b) reacting the intermediate with a nucleophile.

2. The process of claim 1, wherein the nucleophile is selected from the group consisting of 3-methylbutanol, 1-propanethiol, 2-sulfanylethanol, 1,2-ethanedithiol, acetic acid, butyric acid, trans-4-chloro-2-butenoic acid, and isovaleronitrile.

3. The process of claim 1, wherein the acid is trifluoroacetic acid.

4. A process for converting a compound of the formula (I)




wherein:
n is an integer from 1 to 3;
V is selected from the group consisting of H, OR2, and halo, and W is selected from the group consisting of H, OR2, and alkyl; or V and W are taken together with the attached carbon to form a carbonyl;
Z is alkyl, and Y is O; or Z is alkyl or C(O)R4, and Y is absent;
R is OH or a leaving group; or R forms a carboxylic acid derivative selected from the group consisting of an ester, an amide, an imide, and an acylhydrazide;
R1 is H; or R1 represents 1 to 3 substituents each independently selected from the group consisting of halo, nitro, carboxylate, cyano, hydroxyl, alkyl, haloalkyl, alkoxy, haloalkoxy, and OR6;
each R2 is independently selected from the group consisting of H, alkyl, and C(O)R5, provided that R2 is not H when both V and W are OR2;
R4 is selected from the group consisting of alkyl, CF3, and aryl;
each R5 is independently selected from the group consisting of alkyl, cycloalkyl, alkenyl, arylalkyl and aryl;
R6 is selected from the group consisting of aryl, C(O)R7, P(O)(OR8)2, SO3R8, and a phenol protecting group;
each R7 and R8 is independently selected from the group consisting of H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl; or R8 is a metal cation;
and
R10 is alkyl or alkenyl;
into a compound of the formula (II)





wherein:
n, V, W, Z, Y, R, R1, R2, R4, R5, R6, R7, R8, and R10 are as defined in formula I;
X is selected from the group consisting of C1-4 alkyl, alkenyl, and CH2QR9;
Q is selected from the group consisting of —NH—, —O—, and —S—;
each R9 is independently selected from the group consisting of hydrogen, C1-5 alkyl, alkenyl, aryl, and C(O)R11; and
each R11 is independently selected from the group consisting of C1-6 alkyl, alkenyl, aryl, and heteroaryl;
the process comprising
(a) mixing the compound of the formula (I) with trifluoroacetic acid to form an intermediate and
(b) reacting the intermediate with a nucleophile.

5. The process of claim 4, wherein the nucleophile is a compound of the formula R11CO2H or an anion thereof, wherein R11 is as defined in formula II; or the nucleophile is a compound of the formula R9OH or an anion thereof, wherein R9 is as defined in formula II; or the nucleophile is a compound of the formula R21CN, wherein R21 is selected from the group consisting of alkyl, alkenyl, cycloalkyl, aryl, and arylalkyl.

6. The process of claim 4, wherein the nucleophile is selected from the group consisting of methanol, 1-propanol, ethylene glycol, 3-methylbutanol, 1-propanethiol, 2-sulfanylethanol, 1,2-ethanedithiol, acetic acid, butyric acid, trans-4-chloro-2-butenoic acid, isovaleronitrile, and allyltrimethylsilane.

7. The process of claim 4, wherein the second compound is tubulysin B and the nucleophile is butyric acid.

8. A process for converting a compound of the formula (I)




wherein:
n is an integer from 1 to 3;
V is selected from the group consisting of H, OR2, and halo, and W is selected from the group consisting of H, OR2, and alkyl; or V and W are taken together with the attached carbon to form a carbonyl;
Z is alkyl, and Y is O; or Z is alkyl or C(O)R4, and Y is absent;
R is OH or a leaving group; or R forms a carboxylic acid derivative selected from the group consisting of an ester, an amide, an imide, and an acylhydrazide;
R1 is H; or R1 represents 1 to 3 substituents each independently selected from the group consisting of halo, nitro, carboxylate, cyano, hydroxyl, alkyl, haloalkyl, alkoxy, haloalkoxy, and OR6;
each R2 is independently selected from the group consisting of H, alkyl, and C(O)R5, provided that R2 is not H when both V and W are OR2;
R4 is selected from the group consisting of alkyl, CF3, and aryl;
each R5 is independently selected from the group consisting of alkyl, cycloalkyl, alkenyl, arylalkyl and aryl;
R6 is selected from the group consisting of aryl, C(O)R7, P(O)(OR8)2, SO3R8, and a phenol protecting group;
each R7 and R8 is independently selected from the group consisting of H, alkyl, alkenyl, cycloalkyl, heterocyclyl, aryl, and arylalkyl; or R8 is a metal cation;
and
R10 is alkyl or alkenyl;
into a compound of the formula (II)





wherein:
n, V, W, Z, Y, R, R1, R2, R4, R5, R6, R7, R8, and R10 are as defined in formula I;
X is CH2OR9;
each R9 is independently selected from the group consisting of C1-5 alkyl, alkenyl, aryl, and C(O)R11; and
each R11 is independently selected from the group consisting of C1-6 alkyl, alkenyl, aryl, or heteroaryl;
the process comprising
(a) mixing the compound of the formula (I) with trifluoroacetic acid to form an intermediate; and
(b) reacting the intermediate with a nucleophile.

9. The process of claim 8, wherein the nucleophile is a compound of the formula R11CO2H or an anion thereof, wherein R11 is as defined in formula II; or the nucleophile is a compound of the formula R9OH or an anion thereof, wherein R9 is as defined in formula II.

10. The process of claim 8, wherein the nucleophile is selected from the group consisting of methanol, 1-propanol, ethylene glycol, 3-methylbutanol, acetic acid, and butyric acid.

11. The process of claim 8, wherein R9 is C1-5 alkyl.

12. The process of claim 8, wherein R9 is C(O)R11, and R11 is C1-6 alkyl.

13. The process of claim 8, wherein R9 is C(O)R11, R11 is —CH2CH2CH3, and the nucleophile is butyric acid.

14. The process of claim 8, wherein the first compound is mixed with trifluoroacetic acid under substantially anhydrous conditions.

15. The process of claim 8, wherein R is OH or forms an acylhydrazide.

16. The process of claim 8, wherein n is 2.

17. The process of claim 8, wherein V is H, W is OR2, R2 is C(O)R5, and R5 is alkyl.

18. The process of claim 8, wherein Z is alkyl, and Y is absent.

19. The process of claim 10, wherein R1 represents 1 substituent that is OH, or R1 is H.

20. The process of claim 10, wherein the compound of the formula I is of the formula (III)




wherein:
R, R1, R6, R7, R8, and R10 are as defined in formula I.