Enzyme inhibiting compounds and methods

Abstract

The invention provides compounds, compositions, and methods for studying the Rohmer pathway and for treating bacterial infections or parasitic infections. The parasitic infection can be a protozoan infection, such as malaria. The compounds and compositions can also be used as antibiotics, for example, to kill bacteria or parasites, or to inhibit bacterial or parasite growth. The invention further provides inhibitors of isoprenoid biosynthesis enzymes, and methods of inhibiting the activity of isoprenoid biosynthesis enzymes. The compounds can be, for example, alkynes or allenes that bind to a unique Fe of an Fe 4 S 4 cluster of an isoprenoid biosynthesis enzyme.

What is claimed is: 
     
         1 . A method of treating a bacterial infection or parasitic infection in a mammal, wherein the bacterial infection or parasitic infection is caused by a bacteria or parasite that has of an isoprenoid biosynthesis enzyme that includes an Fe 4 S 4  cluster, comprising administering to a mammal in need of such treatment an effective amount of a compound of Formula I: 
       
         
           
           
               
               
           
         
       
       wherein
 A is H; OH; halo; (C 1 -C 4 )alkyl; (C 3 -C 8 )cycloalkyl; CF 3 ; N(R x ) 2 ; (C 1 -C 4 )alkyl substituted by hydroxy, halo, amino, or nitro; 2-oxirane; —CO 2 R y ; —CH(CO 2 R y ) 2 ; —C(═O)CO 2 R y ; (hydroxylamino)carbonyl; hydroxylamino(sulfonyl); —S(═NH) 2 -Me; N-carbaldehye-hydroxylamino; aryl, aroyl, heteroaryl, or heterocycle; or A is —(CH 2 ) n —C═C≡R 1  where n is 0-3 and R 1  is H, OH, (C 1 -C 4 )alkyl, (C 3 -C 8 )cycloalkyl, CF 3 , or N(R x ) 2 ; 
 U is —C≡C—, —C═C═C—, or optionally absent if A is —(CH 2 ) n —C≡C—R 1 ; 
 L is a direct bond or a divalent radical of the formula —W—Z—W—;
 wherein each W is independently —N(R′)C(═O)—, —C(═O)N(R′)—, —OC(═O)—, —C(═O)O—, —O—, —S—, —S(O)—, —S(O) 2 —, —N(R′)‘ 3 , —C(═O)—, —(CH 2 ) n — where n is 1-3, —(CX* 2 )—, —(CH 2 ) n —(CX* 2 )— where n is 1-3, or a direct bond; and 
 Z is a divalent moiety selected from (C 1 -C 12 )alkyl, (C 2 -C 12 )alkenyl, (C 2 -C 12 )alkynyl, (C 3 -C 8 )cycloalkyl, (C 6 -C 10 )aryl, —N(R′)C(═O)—, —C(═O)N(R′)—, —OC(═O)—, —C(═O)O—, —N(R′)—, —C(═O)—, —(CX* 2 )—, —(CH 2 ) n —(CX* 2 )— where n is 1-3, —(OCH 2 -CH 2 ) n — where n is 1 to about 10, —C(O)NH(CH 2 ) n — where n is 1 to about 6, —OP(O)(OH)O—, —OP(O)(OH)O(CH 2 ) n — where n is 1 to about 6, —OP(O)(OH)OCH 2 CH(OH)CH 2 ‘ 3 , —N + (Me) 2 (CH 2 ) n — where n is 1 to about 6; or (C 1 -C 12 )alkyl, (C 2 -C 12 )alkenyl, (C 2 -C 12 )alkynyl, or —(OCH 2 —CH 2 ) n — optionally interrupted between two carbons, or between a carbon and an oxygen, with a (C 3 -C 8 )cycloalkyl, heteroaryl, heterocycle, or (C 6 -C 10 )aryl group, where n is 1 to about 6; or Z is a direct bond; 
 
 B is pyrophosphate; phosphonic acid; a moiety of Formula I-A; a moiety of Formula I-B; a drug moiety; or an independently defined moiety A; 
 each R x  is independently H, (C 1 -C 4 )alkyl, (C 1 -C 4 )alkanoyl, or —(C 1 -C 4 )alkyl(aryl); 
 each R y  is independently H, (C l -C 4 )alkyl, or (C 3 -C 8 )cycloalkyl; 
 each X* is independently H, OH, NH 2 , halo, (C 1 -C 4 )alkyl, or —(CH 2 ) n —CO 2 R y  wherein n is 0-2; or the two X* groups together are ═C—CO 2 R y ; and 
 each R′ is independently H, (C 1 -C 6 )alkyl, or a nitrogen protecting group; 
 the moiety of Formula I-A is: 
 
       
         
           
           
               
               
           
         
       
       wherein
 R 10  is —CO 2 H or P(O)(OH) 2 ; 
 each R 11  is independently H, OH, NH 2 , halo, (C 1 -C 4 )alkyl, —(CH 2 ) n —CO 2 R y  where n is 0-2, or one R 11  is absent when the dashed line is a bond; or the two R 11  groups together are ═C—CO 2 R y ; 
 the dashed line is an optional bond that forms a double bond to C* when the bond is present; and 
 C* is CH when the dashed line is a bond, and is absent when the dashed line is not present; and 
 the moiety of Formula I-B is: 
 
       
         
           
           
               
               
           
         
       
       wherein
 R 12  is H, OH, halo, or —(CH 2 ) n —CO 2 R y  wherein n is 0-2; and 
 A 2  and A 3  are each independently C, CH, N, N + (O − ), or N + (Me); 
 wherein any alkyl, cycloalkyl, aryl, heteroaryl, or heterocycle is optionally substituted with one or more hydroxy, halo, amino, nitro, trifluoromethyl, trifluoromethoxy, carboxy, carbonyl, thiocarbonyl, ═N-Me, (C 1 -C 4 )alkyl, or (C 1 -C 4 )alkoxy groups, or a combination thereof; 
 or an anion, cation, salt or solvate thereof; 
 wherein the compound forms a bioorganometallic complex with an iron atom of the Fe 4 S 4  cluster of the isoprenoid biosynthesis enzyme, thereby inhibiting the activity of the isoprenoid biosynthesis enzyme and treating the bacterial infection or parasitic infection. 
 
     
     
         2 . The method of  claim 1  wherein the compound of Formula I is a compound of one of Formulas I-1 to I-22: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
       wherein each n is independently 0, 1, 2, 3, 4, or 5. 
     
     
         3 . The method of  claim 1  wherein the compound of Formula I is a compound of Formula IC: 
       
         
           
           
               
               
           
         
       
       where n is 0 or 1 and the drug moiety is a residue of a drug, wherein the residue does not include the alkyne moiety of the parent drug, and wherein the drug is selected from alrazagline; selegiline; terbinafine; ethinyl estradiol; norethindrone acetate; desogestrel; levonorgestrel; efavirenz; etonogestrel; norgestimate; or erlotinib. 
     
     
         4 . The method of  claim 1  wherein the compound of Formula I is agrocybin, alfaprostol, azafenidin, barban, beraprost, carfimate, cicutoxin, clodinafop-propargyl, danazol, desogestrel, dimethisterone, efavirenz, enanthotoxin, eniluracil, ethchlorvynol, ethinamate, ethinyl estradiol, ethisterone, ethynodiol diacetate, etonogestrel, flumioxazin, gephyrotoxin, gestodene, gestrinone, haloprogin, helenynolic acid, hexapropymate, histrionicotoxin, iloprost, lynestrenol, mepanipyrim, meparfynol, mestranol, methohexital sodium, 2-methyl-3-butyn-2-ol, mifepristone, moxestrol, o-nitrophenylpropiolic acid, norethindrone, norethynodrel, norgestimate, norgestrel, norgestrienone, oxadiargyl, oxenin, oxotremorine, oxybutynin, pargyline, parsalmide, 1-pentol (3-methyl-2-penten-4-yn-1-ol), phthalofyne, pinazepam, prallethrin, propargite, propyzamide, quinestrol, selegiline, tazarotene, terbinafine, thiarubrine A, thiarubrine B, tibolone, tremorine, or xemilofiban, wherein when a terminal alkyne H is present, the H is optionally replaced by R 1 . 
     
     
         5 . The method of  claim 1  wherein the molecular weight of the compound is less than 500. 
     
     
         6 . The method of  claim 1  wherein the molecular weight of the compound is about 200 to about 450. 
     
     
         7 . The method of  claim 1  wherein the compound of Formula I is a compound of Formula II: 
       
         
           
           
               
               
           
         
       
       wherein
 P x1  is —P(O)OH 2  or absent; 
 P x2  is a direct bond when P x1  is —P(O)OH 2  or P x2  is —P(O)(OH) when P x1  is absent; 
 L is O, S, NR 2 , C(R 3 )(R 4 ) when P x1  is absent; or CH, C—OH, or C-Me when P x1  is —P(O)OH 2 ; 
 each R 2  is independently H or (C 1 -C 4 )alkyl; 
 each R 3  is independently H, halo, or (C 1 -C 4 )alkyl; 
 each R 4  is independently H, halo, or (C 1 -C 4 )alkyl; and 
 L x  is moiety IIA, IIB, or IIC: 
 
       
         
           
           
               
               
           
         
       
       where in moiety II-A:
 R 1  is H; CF 3 ; N(R x ) 2  where R x  is H or (C 1 -C 4 )alkyl; (C 1 -C 4 )alkyl; (C 3 -C 8 )cycloalkyl; or (C 1 -C 4 )alkyl substituted by hydroxy, halo, amino, or nitro; or R 1  is absent when X is N; 
 X is C or N; n is 0, 1, or 2; 
 L 1  is O, S, NR 2 , or C(R 3 )(R 4 ); 
 each R 2  is independently H or (C 1 -C 4 )alkyl; 
 each R 3  is independently H, halo, or (C 1 -C 4 )alkyl; and 
 each R 4  is independently H, halo, or (C 1 -C 4 )alkyl; 
 
       in moiety II-B:
 Y is 2-oxirane; —OH; —CO 2 R 5  where R 5  is H, (C 1 -C 4 )alkyl, or (C 3 -C 8 )cycloalkyl; —N(R 6 )(R 7 ) where R 6  and R 7  are each independently H or (C 1 -C 4 )alkyl; or aryl or heteroaryl wherein the aryl or heteroaryl is optionally substituted with one or more halo, nitro, amino, trifluoromethyl, trifluoromethoxy, or (C 1 -C 4 )alkyl groups, or a combination thereof; 
 n is 0, 1, or 2; 
 L 1  is O, S, NR 2 , or C(R 3 )(R 4 ); 
 each R 2  is independently H or (C 1 -C 4 )alkyl; 
 each R 3  is independently H, halo, or (C 1 -C 4 )alkyl; 
 each R 4  is independently H, halo, or (C 1 -C 4 )alkyl; and 
 L 3  is —(CH 2 ) m —S— where m is 0, 1, 2, or 3; —CR 8 ═CR 9 — where R 8  and R 9  are each independently H or Me; or a direct bond; and 
 
       in moiety II-C:
 Z is —SH; —N(R 6 )(R 7 ) where R 6  and R 7  are each independently H or (C 1 -C 4 )alkyl; aryl or heteroaryl wherein the aryl or heteroaryl is optionally substituted with one or more halo, nitro, amino, trifluoromethyl, trifluoromethoxy, or (C 1 -C 4 )alkyl groups, or a combination thereof; or — 57  C—R 1  where R 1  is H; CF 3 ; N(R x ) 2  where R x  is H or (C 1 -C 4 )alkyl; (C 1 -C 4 )alkyl; (C 3 -C 8 )cycloalkyl; or (C 1 -C 4 )alkyl substituted by hydroxy, halo, amino, or nitro; 
 n is 0, 1, 2, 3, or 4; 
 L 1  is O, S, NR 2 , or C(R 3 )(R 4 ); 
 R 2  is H or (C 1 -C 4 )alkyl; 
 R 3  is H, halo, or (C 1 -C 4 )alkyl; and 
 R 4  is H, halo, or (C 1 -C 4 )alkyl; 
 or a salt or solvate thereof; 
 
       wherein the compound forms a bioorganometallic complex with an iron atom of the Fe 4 S 4  cluster of the isoprenoid biosynthesis enzyme, thereby inhibiting the activity of the isoprenoid biosynthesis enzyme and treating the bacterial infection or parasitic infection. 
     
     
         8 . The method of  claim 7  wherein the compound includes at least one of an alkyne or an allene moiety. 
     
     
         9 . The method of  claim 7  wherein the compound of Formula II is a compound of Formula III: 
       
         
           
           
               
               
           
         
       
       wherein
 R 1  is H; CF 3 ; N(R x ) 2  where each R x  is independently H, (C 1 -C 4 )alkyl; (C 1 -C 4 )alkanoyl; or (C 1 -C 4 )alkyl substituted by hydroxy, halo, amino, or nitro; or R 1  is absent when X is N; 
 X is C or N; 
 n is 0, 1, or 2; 
 L 1  is O, S, NR 2 , or C(R 3 )(R 4 ); 
 L 2  is O, S, NR 2 , or C(R 3 )(R 4 ); 
 each R 2  is independently H or (C 1 -C 4 )alkyl; 
 each R 3  is independently H, halo, or (C 1 -C 4 )alkyl; and 
 each R 4  is independently H, halo, or (C 1 -C 4 )alkyl; 
 
       or a salt or solvate thereof. 
     
     
         10 . The method of  claim 7  wherein the compound of Formula II is a compound of Formula IV: 
       
         
           
           
               
               
           
         
       
       wherein
 Y is 2-oxirane; —OH; —CO 2 R 5  where R 5  is H or (C 1 -C 4 )alkyl; —N(R 6 )(R 7 ) where R 6  and R 7  are each independently H or (C 1 -C 4 )alkyl; or aryl or heteroaryl wherein the aryl or heteroaryl is optionally substituted with one or more halo, nitro, amino, trifluoromethyl, trifluoromethoxy, or (C 1 -C 4 )alkyl groups, or a combination thereof; 
 n is 0, 1, or 2; 
 L 1  is O, S, NR 2 , or C(R 3 )(R 4 ); 
 L 2  is O, S, NR 2 , or C(R 3 )(R 4 ); 
 each R 2  is independently H or (C 1 -C 4 )alkyl; 
 each R 3  is independently H, halo, or (C 1 -C 4 )alkyl; 
 each R 4  is independently H, halo, or (C 1 -C 4 )alkyl; and 
 L 3  is —(CH 2 ) m —S— where m is 0, 1, 2, or 3; —CR 8 ═CR 9 — where R 8  and R 9  are each independently H or Me; or a direct bond; 
 
       or a salt or solvate thereof. 
     
     
         11 . The method of  claim 10  wherein Y is 2-oxirane, —OH, —CO 2 H, —CO 2 Me, —NMe 2 , phenyl, 1-pyridinium, 2-pyridyl, 3-pyridyl, or 4-pyridyl, wherein the phenyl, pyridinium, or pyridyl is optionally substituted by one to five halo groups. 
     
     
         12 . The method of  claim 10  wherein the compound is: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
       or a salt or solvate thereof. 
     
     
         13 . The method of  claim 7  wherein the compound of Formula II is a compound of Formula V: 
       
         
           
           
               
               
           
         
       
       wherein
 Z is —SH; —N(R 6 )(R 7 ) where R 6  and R 7  are each independently H or (C 1 -C 4 )alkyl; aryl or heteroaryl wherein the aryl or heteroaryl is optionally substituted with one or more halo, nitro, amino, trifluoromethyl, trifluoromethoxy, or (C 1 -C 4 )alkyl groups, or a combination thereof; or —C≡C—R 1  where R 1  is H; CF 3 ; N(R x ) 2  where R x  is H or (C 1 -C 4 )alkyl; (C 1 -C 4 )alkyl; or (C 1 -C 4 )alkyl substituted by hydroxy, halo, amino, or nitro; 
 n is 0, 1, 2, 3, or 4; 
 L 1  is O, S, NR 2 , C(R 3 )(R 4 )or —NH—C(R 3 )(R 4 ); 
 R 2  is H or (C 1 -C 4 )alkyl; 
 R 3  is H, halo, or (C 1 -C 4 )alkyl; 
 R 4  is H, halo, or (C 1 -C 4 )alkyl; and 
 R 10  is H, OH, or Me; 
 
       or a salt or solvate thereof. 
     
     
         14 . The method of  claim 13  wherein L 1  is —CH 2 — or —NH—; and Z is —SH, —NMe 2 , phenyl, 1-pyridinium, 2-pyridyl, 3-pyridyl, or 4-pyridyl, wherein the phenyl, pyridinium, or pyridyl is optionally substituted by one to five halo, methyl, or nitro groups, or a combination thereof. 
     
     
         15 . The method of  claim 13  wherein the compound is: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
       or a salt or solvate thereof. 
     
     
         16 . The method of  claim 1  wherein the isoprenoid biosynthesis enzyme is E-4-Hydroxy-3-methyl-but-2-enyl diphosphate reductase. 
     
     
         17 . The method of  claim 16  wherein the K i  of the compound is less than 20 μM. 
     
     
         18 . A method of inhibiting the activity of an isoprenoid biosynthesis enzyme that has an Fe 4 S 4  cluster with one uniquely bonded Fe, comprising contacting the enzyme with a compound that has an alkyne or allene moiety, wherein the compound forms a bioorganometallic complex with the unique iron atom of the Fe 4 S 4  cluster of the isoprenoid biosynthesis enzyme, thereby inhibiting the activity of the enzyme. 
     
     
         19 . A method of inhibiting the activity of an isoprenoid biosynthesis enzyme that has an Fe 4 S 4  cluster, comprising contacting the enzyme with a compound of  claim 1 , wherein the compound forms a bioorganometallic complex with an iron atom of the Fe 4 S 4  cluster of the isoprenoid biosynthesis enzyme, thereby inhibiting the activity of the enzyme. 
     
     
         20 . A pharmaceutical composition comprising a compound of  claim 1  and a pharmaceutically acceptable diluent or carrier.