We have examined sequence diversity of 147 co-crystal structures of proteins utilizing NAD as a cofactor or as a substrate. Most of these proteins bind NAD in an extended conformation (e.g. the distance between the adenine 6-amino group of NAD and the nicotinamide amide carbon is 16 Å or more). However, there are clear exceptions to this general trend. Several bacterial reductases bind NAD in an extremely folded conformation (the distance of 6 Å) and NAD kinases bind NAD in bent (compact) conformations with the distance of 11-12 Å. Although NAD can be accommodated in all of the above conformations it is likely that compact NAD mimics (with the distance of 11-12 Å) should not fit to the binding domains of majority of NAD-utilizing enzymes that require an extended conformation of NAD. It may be expected, therefore, that such compounds could be selective against NAD kinases. Tiazofurin adenine dinucleotide (TAD) is a potent inhibitor (Ki = 100 nM) of NAD-dependent IMP-dehydrogenase. This NAD mimic binds at the cofactor binding domain in the extended conformation. As a proof of concept, we prepared tiazofurin-5’-yl adenosine-5’-yl disulfide (1) by replacing the pyrophosphate (-O-P-O-P-O-) linkage by a short (-S-S-) disulfide bridge. We found that this compact disulfide analogue of TAD has lost its activity against IMPDH and became a moderate inhibitor of M. tuberculosis (IC50 = 80 μM) NAD kinase. We also found that di(adenosine-5’yl) disulfide (2), a by-product in the synthesis of 1, showed slightly better activity against mycobacterium (IC50 = 45 μM) as well as human (IC50 = 87 μM) NAD kinase. Introduction of bromine at the C-8 of adenine ring results in restriction of conformation of 8-bromo-adenosine to the syn conformation. We prepared the corresponding 8-bromo disulfide (3) and found further improvement in the inhibitory activity against human (IC50 = 6 μM) and mycobacterium (IC50 = 14) NAD kinase. Compound 3 is the most potent inhibitor of NAD kinases reported so far. Using a simple method for preparation of disulfide 2 we synthesized a number of nucleobase and sugar modified analogues that have been evaluated against these enzymes, and we will discuss our results.

Compact NAD mimics as selective inhibitors of NAD kinases

PETRELLI, Riccardo;
2009-01-01

Abstract

We have examined sequence diversity of 147 co-crystal structures of proteins utilizing NAD as a cofactor or as a substrate. Most of these proteins bind NAD in an extended conformation (e.g. the distance between the adenine 6-amino group of NAD and the nicotinamide amide carbon is 16 Å or more). However, there are clear exceptions to this general trend. Several bacterial reductases bind NAD in an extremely folded conformation (the distance of 6 Å) and NAD kinases bind NAD in bent (compact) conformations with the distance of 11-12 Å. Although NAD can be accommodated in all of the above conformations it is likely that compact NAD mimics (with the distance of 11-12 Å) should not fit to the binding domains of majority of NAD-utilizing enzymes that require an extended conformation of NAD. It may be expected, therefore, that such compounds could be selective against NAD kinases. Tiazofurin adenine dinucleotide (TAD) is a potent inhibitor (Ki = 100 nM) of NAD-dependent IMP-dehydrogenase. This NAD mimic binds at the cofactor binding domain in the extended conformation. As a proof of concept, we prepared tiazofurin-5’-yl adenosine-5’-yl disulfide (1) by replacing the pyrophosphate (-O-P-O-P-O-) linkage by a short (-S-S-) disulfide bridge. We found that this compact disulfide analogue of TAD has lost its activity against IMPDH and became a moderate inhibitor of M. tuberculosis (IC50 = 80 μM) NAD kinase. We also found that di(adenosine-5’yl) disulfide (2), a by-product in the synthesis of 1, showed slightly better activity against mycobacterium (IC50 = 45 μM) as well as human (IC50 = 87 μM) NAD kinase. Introduction of bromine at the C-8 of adenine ring results in restriction of conformation of 8-bromo-adenosine to the syn conformation. We prepared the corresponding 8-bromo disulfide (3) and found further improvement in the inhibitory activity against human (IC50 = 6 μM) and mycobacterium (IC50 = 14) NAD kinase. Compound 3 is the most potent inhibitor of NAD kinases reported so far. Using a simple method for preparation of disulfide 2 we synthesized a number of nucleobase and sugar modified analogues that have been evaluated against these enzymes, and we will discuss our results.
2009
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11581/202518
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