Process for purifying glycopeptide phosphonate derivatives

1. A method of purifying a compound of formula I:

wherein:

R 19 is hydrogen;

R 20 is —R a —Y—R b -(Z) x , R f , —C(O)R f , or —C(O)—R a —Y—R b -(Z) x ;

R 3 is —OR c , —NR c R c , —O—R a —Y—R b -(Z) x , —NR c —R a —Y—R b -(Z) x , —NR c R e , or —O—R e ; or R 3 is a nitrogen-linked, oxygen-linked, or sulfur-linked substituent that comprises one or more phosphono groups;

R 5 is selected from the group consisting of hydrogen, halo, —CH(R c )—NR c R c , —CH(R c )—NR c R e , —CH(R c )—NR c —R a —Y—R b -(Z) x , —CH(R c )—R x , —CH(R c )—NR c —R a —C(═O)—R x , and a substituent that comprises one or more phosphono groups;

each R a is independently selected from the group consisting of alkylene, substituted alkylene, alkenylene, substituted alkenylene, alkynylene and substituted alkynylene;

each R b is independently selected from the group consisting of a covalent bond, alkylene, substituted alkylene, alkenylene, substituted alkenylene, alkynylene and substituted alkynylene, provided R b is not a covalent bond when Z is hydrogen;

each R c is independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, heteroaryl, heterocyclic and —C(O)R d ;

each R d is independently selected from the group consisting of alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, heteroaryl and heterocyclic;

R e is a saccharide group;

each R f is independently alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, heteroaryl, or heterocyclic;

R x is an N-linked amino saccharide or an N-linked heterocycle;

each Y is independently selected from the group consisting of oxygen, sulfur, —S—S—, —NR c —, —S(O)—, —SO 2 —, —NR c C(O)—, —OSO 2 —, —OC(O)—, —NR c SO 2 —, —C(O)NR c —, —C(O)O—, —SO 2 NR c —, —SO 2 O—, —P(O)(OR c )O—, —P(O)(OR c )NR c —, —OP(O)(OR c )O—, —OP(O)(OR c )NR c —, —OC(O)O—, —NR c C(O)O—, —NR c C(O)NR c —, —OC(O)NR c —, —C(═O)—, and —NR c SO 2 NR c —;

each Z is independently selected from hydrogen, aryl, cycloalkyl, cycloalkenyl, heteroaryl and heterocyclic; and

x is 1 or 2;

or a pharmaceutically acceptable salt, stereoisomer, or prodrug thereof;

provided at least one of R 3 and R 5 is a substituent comprising one or more phosphono groups; the method comprising the steps of:

(a) contacting a first acidified aqueous solution comprising a compound of formula I with a polystyrene divinyl benzene resin;

(b) eluting the contacted resin with a second acidified aqueous solution comprising a polar organic solvent to form an eluate; and

(c) isolating the compound of formula I from the eluate.

2. The method of claim 1 wherein the polar organic solvent present in the second acidified aqueous solution comprises acetonitrile.

3. The method of claim 1 wherein the polar organic solvent present in the second acidified aqueous solution is in a ratio of about 1:4 to about 1:15 polar organic solvent:water.

4. The method of claim 1 wherein the acid present in the second acidified aqueous solution comprises acetic acid.

5. The method of claim 1 wherein the acid present in the second acidified aqueous solution comprises hydrochloric acid.

6. The method of claim 1 wherein the acid in the solution of the polar organic solvent present in the second acidified aqueous solution is in a concentration of from about 5 millimolar to about 50 millimolar.

7. The method of claim 1 wherein in step (a) the polystyrene divinyl benzene resin has a pore size of from about 50 Å to about 1000 Å.

8. The method of claim 1 wherein step (c) comprises isolating the compound of formula I by lyophilization.

9. The method of claim 1 wherein step (c) comprises isolating the compound of formula I by a process comprising precipitation.

10. The method of claim 1 wherein step (c) further comprises forming a solution with a higher concentration of the compound of formula I than the eluate.

11. The method of claim 1 wherein the purity of the compound of formula I in a product of step (c) is greater than about 80%.

12. The method of claim 1 wherein step (b) comprises washing the contacted resin with an aqueous solution comprising a polar organic solvent a plurality of times to form a plurality of fractions and combining the fractions to form the eluate.

13. The method of claim 1 wherein, in the compound of formula I, R 3 is —OH.

14. The method of claim 1 wherein, in the compound of formula I, R 3 is a nitrogen-linked, oxygen-linked, or sulfur-linked substituent that comprises one or more phosphono groups.

15. The method of claim 1 wherein, in the compound of formula I, R 3 is a group of the formula —O—R a —P(O)(OH) 2 , —S—R a —P(O)(OH) 2 , or —NR c —R a —P(O)(OH) 2 .

16. The method of claim 1 wherein, in the compound of formula I, R 5 is a group of the formula —(CH(R 21 )—N(R c )—R a —P(O)(OH) 2 ; wherein R 21 is hydrogen or R d .

17. The method of claim 1 wherein, in the compound of formula I, R 20 is —CH 2 CH 2 —NH—(CH 2 ) 9 CH 3 ; —CH 2 CH 2 CH 2 —NH—(CH 2 ) 8 CH 3 ; —CH 2 CH 2 CH 2 CH 2 —NH—(CH 2 ) 7 CH 3 ; —CH 2 CH 2 —NHSO 2 —(CH 2 ) 9 CH 3 ; —CH 2 CH 2 —NHSO 2 —(CH 2 ) 11 CH 3 ; —CH 2 CH 2 —S—(CH 2 ) 8 CH 3 ; —CH 2 CH 2 —S—(CH 2 ) 9 CH 3 ; —CH 2 CH 2 —S—(CH 2 ) 10 CH 3 ; —CH 2 CH 2 CH 2 —S—(CH 2 ) 8 CH 3 ; —CH 2 CH 2 CH 2 —S—(CH 2 ) 9 CH 3 ; —CH 2 CH 2 CH 2 —S—(CH 2 ) 3 —CH═CH—(CH 2 ) 4 CH 3 (trans); —CH 2 CH 2 CH 2 CH 2 —S—(CH 2 ) 7 CH 3 ; —CH 2 CH 2 —S(O)—(CH 2 ) 9 CH 3 ; —CH 2 CH 2 —S—(CH 2 ) 6 Ph; —CH 2 CH 2 —S—(CH 2 ) 8 Ph; —CH 2 CH 2 CH 2 —S—(CH 2 ) 8 Ph; —CH 2 CH 2 —NH—CH 2 -4-(4-Cl-Ph)-Ph; —CH 2 CH 2 —NH—CH 2 -4-[4-(CH 3 ) 2 CHCH 2 -]-Ph; —CH 2 CH 2 —NH—CH 2 -4-(4-CF 3 -Ph)-Ph; —CH 2 CH 2 —S—CH 2 -4-(4-Cl-Ph)-Ph; —CH 2 CH 2 —S(O)—CH 2 -4-(4-Cl-Ph)-PH; —CH 2 CH 2 CH 2 —S—CH 2 -4-(4-Cl-Ph)-Ph; —CH 2 CH 2 CH 2 —S(O)—CH 2 -4-(4-Cl-Ph)-Ph; —CH 2 CH 2 CH 2 —S—CH 2 -4-[3,4-di-Cl-PhCH 2 O-)-Ph; —CH 2 CH 2 —NHSO 2 —CH 2 -4-[4-(4-Ph)-Ph]-Ph; —CH 2 CH 2 CH 2 —NHSO 2 —CH 2 -4-(4-Cl-Ph)-Ph; —CH 2 CH 2 CH 2 —NHSO 2 —CH 2 -4-(Ph-C≡C-)-Ph; —CH 2 CH 2 CH 2 —NHSO 2 -4-(4-Cl-Ph)-Ph; or —CH 2 CH 2 CH 2 —NHSO 2 -4-(naphth-2-yl)-Ph.

18. The method of claim 1 wherein, in the compound of formula I, R 3 is —OH; R 5 is N-(phosphonomethyl)-aminomethyl; R 19 is hydrogen, and R 20 is —CH 2 CH 2 —NH—(CH 2 ) 9 CH 3 ; or a pharmaceutically acceptable salt thereof.

19. The method of claim 1 wherein, in the compound of formula I, R 3 is —OH; R 5 is N-(phosphonomethyl)-aminomethyl; R 19 is hydrogen, and R 20 is —CH 2 CH 2 —NH—(CH 2 ) 9 CH 3 .