TY - JOUR
T1 - An alternative conformation of the N-terminal loop of human dihydroorotate dehydrogenase drives binding to a potent antiproliferative agent
AU - Alberti, Marta
AU - Poli, Giulio
AU - Broggini, Luca
AU - Sainas, Stefano
AU - RIZZI, Menico
AU - Boschi, Donatella
AU - FERRARIS, DAVIDE MARIA
AU - Martino, Elena
AU - Ricagno, Stefano
AU - Tuccinardi, Tiziano
AU - Lolli, Marco L
AU - MIGGIANO, RICCARDO
PY - 2024
Y1 - 2024
N2 - : Over the years, human dihydroorotate dehydrogenase (hDHODH), which is a key player in the de novo pyrimidine-biosynthesis pathway, has been targeted in the treatment of several conditions, including autoimmune disorders and acute myelogenous leukaemia, as well as in host-targeted antiviral therapy. A molecular exploration of its inhibitor-binding behaviours yielded promising candidates for innovative drug design. A detailed description of the enzymatic pharmacophore drove the decoration of well-established inhibitory scaffolds, thus gaining further in vitro and in vivo efficacy. In the present work, using X-ray crystallography, an atypical rearrangement was identified in the binding pose of a potent inhibitor characterized by a polar pyridine-based moiety (compound 18). The crystal structure shows that upon binding compound 18 the dynamics of a protein loop involved in a gating mechanism at the cofactor-binding site is modulated by the presence of three water molecules, thus fine-tuning the polarity/hydrophobicity of the binding pocket. These solvent molecules are engaged in the formation of a hydrogen-bond mesh in which one of them establishes a direct contact with the pyridine moiety of compound 18, thus paving the way for a reappraisal of the inhibition of hDHODH. Using an integrated approach, the thermodynamics of such a modulation is described by means of isothermal titration calorimetry coupled with molecular modelling. These structural insights will guide future drug design to obtain a finer Kd/logD7.4 balance and identify membrane-permeable molecules with a drug-like profile in terms of water solubility.
AB - : Over the years, human dihydroorotate dehydrogenase (hDHODH), which is a key player in the de novo pyrimidine-biosynthesis pathway, has been targeted in the treatment of several conditions, including autoimmune disorders and acute myelogenous leukaemia, as well as in host-targeted antiviral therapy. A molecular exploration of its inhibitor-binding behaviours yielded promising candidates for innovative drug design. A detailed description of the enzymatic pharmacophore drove the decoration of well-established inhibitory scaffolds, thus gaining further in vitro and in vivo efficacy. In the present work, using X-ray crystallography, an atypical rearrangement was identified in the binding pose of a potent inhibitor characterized by a polar pyridine-based moiety (compound 18). The crystal structure shows that upon binding compound 18 the dynamics of a protein loop involved in a gating mechanism at the cofactor-binding site is modulated by the presence of three water molecules, thus fine-tuning the polarity/hydrophobicity of the binding pocket. These solvent molecules are engaged in the formation of a hydrogen-bond mesh in which one of them establishes a direct contact with the pyridine moiety of compound 18, thus paving the way for a reappraisal of the inhibition of hDHODH. Using an integrated approach, the thermodynamics of such a modulation is described by means of isothermal titration calorimetry coupled with molecular modelling. These structural insights will guide future drug design to obtain a finer Kd/logD7.4 balance and identify membrane-permeable molecules with a drug-like profile in terms of water solubility.
KW - DHODH
KW - X-ray crystallography
KW - human dihydroorotate dehydrogenase
KW - pyrimidine biosynthesis
KW - structure-based drug discovery
KW - DHODH
KW - X-ray crystallography
KW - human dihydroorotate dehydrogenase
KW - pyrimidine biosynthesis
KW - structure-based drug discovery
UR - https://iris.uniupo.it/handle/11579/180824
U2 - 10.1107/S2059798324004066
DO - 10.1107/S2059798324004066
M3 - Article
SN - 2059-7983
VL - 80
JO - ACTA CRYSTALLOGRAPHICA. SECTION D, STRUCTURAL BIOLOGY
JF - ACTA CRYSTALLOGRAPHICA. SECTION D, STRUCTURAL BIOLOGY
IS - 6
ER -