Transition state structure of 5′-methylthioadenosine/s-adenosylhomocysteine nucleosidases
View Patent ↗Provided are methods of designing a putative inhibitor of a 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase. The methods comprise designing a chemically stable compound that resembles the charge and geometry of the 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase transition state. Also provided are methods of inhibiting 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidases using the inhibitors found by the above methods.
1. A method of screening for an inhibitor of a 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) having 5′methylthioadenosine and S-adenosylhomocysteine substrates, the method comprising the steps of:
(i) measuring kinetic isotope effects on the MTAN catalyzed hydrolysis of 5′-methylthioadenosine to obtain the MTAN transition state structure,
wherein the MTAN transition state comprises the structure
where R is CH 3 or homocysteine;
(ii) determining the molecular electrostatic potential at the van der Waals surface computed from the wave function of the MTAN transition state and the geometric atomic volume of the MTAN transition state;
(iii) obtaining a chemically stable compound that resembles the molecular electrostatic potential at the van der Waals surface computed from the wave function of the MTAN transition state and the geometric atomic volume of the MTAN transition state,
wherein the compound comprises a moiety resembling the molecular electrostatic potential surface of the ribosyl group at the transition state,
wherein the moiety resembling the molecular electrostatic potential surface of the ribosyl group at the transition state is a substituted iminoribitol, a substituted hydroxypyrrolidine, a substituted pyridine or a substituted imidazole,
wherein the compound comprises an atomic moiety inserted into the inhibitor providing a compound that mimics the C1′-N9 ribosyl bond distance of a 5′-methylthioadenosine or S-adenosylhomocysteine at the transition state,
wherein the atomic moiety inserted into the inhibitor that provides a compound that mimics the C1′-N9 ribosyl bond distance of a 5′-methylthioadenosine or S-adenosylhomocysteine at the transition state is a methylene, a substituted methylene, an ethyl, or a substituted ethyl bridge, and
wherein the compound comprises a purine moiety or a deazapurine moiety; and
(iv) testing the compound for inhibitory activity to MTAN by determining if the compound inhibits MTAN-catalyzed hydrolysis of 5′-methylthioadenosine to generate adenine and 5-methylthioribose or if the compound inhibits MTAN-catalyzed hydrolysis of S-adenosylhomocysteine to generate adenine and S-ribosylhomocysteine,
wherein a compound that inhibits MTAN-catalyzed hydrolysis of 5′-methylthioadenosine or S-adenosylhomocysteine is an inhibitor of MTAN.
2. The method of claim 1 , wherein the compound comprises a purine moiety.
3. The method of claim 1 , wherein the compound comprises a deazapurine moiety.
4. The method of claim 1 , wherein the compound comprises a moiety resembling methylthioribose at the transition state.
5. The method of claim 1 , wherein the compound comprises a moiety resembling S-homocysteinyl ribose at the transition state.
6. The method of claim 1 , wherein the substituent is an aryl- or alkyl-substituted thiol group.
7. The method of claim 6 , wherein the substituent is a methylthiol group.
8. The method of claim 1 , wherein the compound exhibits a similarity value S e to the transition state greater than to either substrate.
9. The method of claim 1 , wherein the 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase is from a bacterial pathogen.
10. The method of claim 9 , wherein the bacterial pathogen is a mammalian pathogen.
11. The method of claim 10 , wherein the mammalian pathogen is an E. coli , a Staphylococcus sp., a Streptococcus sp., an Enterococcus sp., a Bacillus sp., Bifidobacterium bifidum , a Lactobacillus sp., Listeria monocytogenes , a Nocardia sp., Rhodococcus equi, Erysipelothrix rhusiopathiae, Corynebacterium diptheriae, Propionibacterium acnes , an Actinomyces sp., a Clostridium sp., a Mobiluncus sp., a Peptostreptococcus sp., a Neisseria ap., Moraxella catarrhalis , a Veillonella sp. Actinobacillus actinomycetemcomitans, Acinetobacter baumannii, Bordetella pertussis , a Brucella sp., a Campylobacter sp., a Capnocytophaga sp., Cardiobacterium hominis, Eikenella corrodens, Francisella tularensis , a Haemophilus sp., Helicobacter pylori, Kingella Kingae , a Pasteurella , a Klebsiella sp., an Enterobacter sp., a Proteus sp., a Salmonella sp., a Shigella sp., Serratia marcescens , a Yersinia sp. an Aeromonas sp., Plesiomonas shigelloides , a Vibrio sp., an Acinetobacter sp., a Flavobacterium sp., a Pseudomonas sp., a Burkholderia sp., a Xanthomonas sp., a Bacteroides sp., a Prevotella sp., a Fusobacterium sp., Spirillum minus , a Borrelia sp., Bartonella henselae , a Chlamydia sp., a Chlamydophila sp., Coxiella burnetii , an Ehrlichia sp., an Anaplasma sp., a Legionella sp., a Leptospira sp., a Mycobacterium sp., a Rickettsia sp., an Orientia sp., or Treponema pallidum.
12. The method of claim 10 , wherein the mammalian pathogen is an E. coli.
13. The method of claim 10 , wherein the mammalian pathogen is a Streptococcus pneumoniae.
14. The method of claim 1 , wherein the 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase transition state comprises properties as set forth in Table 2 or Table 7.
15. The method of claim 1 , wherein the 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase transition state is highly dissociative with very low bond order to the leaving group, no significant bond order to the attacking water nucleophile and the ribosyl moiety to have significant oxacarbenium ion character.
16. The method of claim 1 , wherein a reaction catalyzed by 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase undergoes a dissociative (D N *A N ) (S N 1) mechanism with little involvement of the leaving group or participation of the attacking nucleophile at the transition state, causing the transition state to have significant ribooxacarbenium ion character.
17. The method of claim 1 , wherein the 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase transition state has a small bond order to the leaving group and little participation of the attacking nucleophile.
18. The method of claim 1 , wherein the 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase transition state exhibits significant cationic character with low Pauling bond order to the leaving group and insignificant bond order to the attacking nucleophile.
19. The method of claim 1 , wherein the 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase transition state is a dissociative transition state with oxacarbenium ion character.
20. The method of claim 1 , wherein the 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase transition inhibitor resembles 5′-methylthioadenosine (MTA) with riboxacarbenium features in the ribosyl group and elevated pK a values in the leaving group adenine analogue.