Structural Basis of Single-Nucleotide Polymorphisms in Cytochrome P450 2C9

Single-nucleotide polymorphisms in drug-metabolizing cytochrome P450 (CYP) enzymes are important contributors to interindividual differences in drug metabolism leading to adverse drug reactions. Despite their extensive characterization and importance in pharmacogenetics of clinical drugs, the structural basis of CYP polymorphisms has remained scant. Here we report the crystal structures of human CYP2C9 and its polymorphic variants, *3 (I359L) and *30 (A477T), with an antihypertensive drug losartan. The structures show distinct interaction and occupation of losartan in the active site, the access channel, and the peripheral binding site. The I359L substitution located far from the active site remarkably altered the residue side chains near the active site and the access channel, whereas the T477 substitution illustrated hydrogen-bonding interaction with the reoriented side chain of Q214. The results yield structural insights into the reduced catalytic activity of the CYP2C9 variants and have important implications for understanding genetic polymorphisms in CYP-mediated drug metabolism

Structure Analysis and Derivation of Deformed Electron Density Distribution of Polydiacetylene Giant Single Crystal by the Combination of X‑ray and Neutron Diffraction Data

The crystal structure of polydiacetylene giant single crystal has been analyzed on the basis of the two different methods of wide-angle neutron diffraction and X-ray diffraction. The X-ray result gives us the total electron density distribution [<b>ρ</b>(<b>x</b>)] of polymer chain. The neutron result tells the positions of atomic nuclei, which can allow us to speculate the electron density distributions [<b>ρ</b>₀(<b>x</b>)] around the nonbonded isolated atoms. As a result, the so-called bonded (or deformed) electron density Δρ­(<b>x</b>) [≡ ρ­(<b>x</b>) – ρ₀(<b>x</b>) = ρ_X(<b>x</b>) – ρ_N(<b>x</b>)], i.e., the electron density distribution due to the conjugation among the covalently bonded atoms along the polymer chain, can be estimated using the two information obtained by the X-ray and neutron data analyses (the so-called X-ray–neutron subtraction (X<i>–</i>N) method). The present report is the first example of the application of X–N method to the synthetic polymer species. The Δρ­(<b>x</b>) derived for polydiacetylene was found similar to that of the low-molecular-weight model compound having the similar electronically conjugated chemical formula. The Δρ­(<b>x</b>) was calculated by the density functional theory, which was in a good agreement with the experimental result qualitatively

Structure Analysis and Derivation of Deformed Electron Density Distribution of Polydiacetylene Giant Single Crystal by the Combination of X‑ray and Neutron Diffraction Data

The crystal structure of polydiacetylene giant single crystal has been analyzed on the basis of the two different methods of wide-angle neutron diffraction and X-ray diffraction. The X-ray result gives us the total electron density distribution [<b>ρ</b>(<b>x</b>)] of polymer chain. The neutron result tells the positions of atomic nuclei, which can allow us to speculate the electron density distributions [<b>ρ</b>₀(<b>x</b>)] around the nonbonded isolated atoms. As a result, the so-called bonded (or deformed) electron density Δρ­(<b>x</b>) [≡ ρ­(<b>x</b>) – ρ₀(<b>x</b>) = ρ_X(<b>x</b>) – ρ_N(<b>x</b>)], i.e., the electron density distribution due to the conjugation among the covalently bonded atoms along the polymer chain, can be estimated using the two information obtained by the X-ray and neutron data analyses (the so-called X-ray–neutron subtraction (X<i>–</i>N) method). The present report is the first example of the application of X–N method to the synthetic polymer species. The Δρ­(<b>x</b>) derived for polydiacetylene was found similar to that of the low-molecular-weight model compound having the similar electronically conjugated chemical formula. The Δρ­(<b>x</b>) was calculated by the density functional theory, which was in a good agreement with the experimental result qualitatively

Structure Analysis and Derivation of Deformed Electron Density Distribution of Polydiacetylene Giant Single Crystal by the Combination of X‑ray and Neutron Diffraction Data

The crystal structure of polydiacetylene giant single crystal has been analyzed on the basis of the two different methods of wide-angle neutron diffraction and X-ray diffraction. The X-ray result gives us the total electron density distribution [<b>ρ</b>(<b>x</b>)] of polymer chain. The neutron result tells the positions of atomic nuclei, which can allow us to speculate the electron density distributions [<b>ρ</b>₀(<b>x</b>)] around the nonbonded isolated atoms. As a result, the so-called bonded (or deformed) electron density Δρ­(<b>x</b>) [≡ ρ­(<b>x</b>) – ρ₀(<b>x</b>) = ρ_X(<b>x</b>) – ρ_N(<b>x</b>)], i.e., the electron density distribution due to the conjugation among the covalently bonded atoms along the polymer chain, can be estimated using the two information obtained by the X-ray and neutron data analyses (the so-called X-ray–neutron subtraction (X<i>–</i>N) method). The present report is the first example of the application of X–N method to the synthetic polymer species. The Δρ­(<b>x</b>) derived for polydiacetylene was found similar to that of the low-molecular-weight model compound having the similar electronically conjugated chemical formula. The Δρ­(<b>x</b>) was calculated by the density functional theory, which was in a good agreement with the experimental result qualitatively

Seven Cysteine-Deficient Mutants Depict the Interplay between Thermal and Chemical Stabilities of Individual Cysteine Residues in Mitogen-Activated Protein Kinase c‑Jun N‑Terminal Kinase 1

Intracellular proteins can have free cysteines that may contribute to their structure, function, and stability; however, free cysteines can lead to chemical instabilities in solution because of oxidation-driven aggregation. The MAP kinase, c-Jun N-terminal kinase 1 (JNK1), possesses seven free cysteines and is an important drug target for autoimmune diseases, cancers, and apoptosis-related diseases. To characterize the role of cysteine residues in the structure, function, and stability of JNK1, we prepared and evaluated wild-type JNK1 and seven cysteine-deficient JNK1 proteins. The nonreduced sodium dodecyl sulfate–polyacrylamide gel electrophoresis experiments showed that the chemical stability of JNK1 increased as the number of cysteines decreased. The contribution of each cysteine residue to biological function and thermal stability was highly susceptible to the environment surrounding the particular cysteine mutation. The mutations of solvent-exposed cysteine to serine did not influence biological function and increased the thermal stability. The mutation of the accessible cysteine involved in the hydrophobic pocket did not affect biological function, although a moderate thermal destabilization was observed. Cysteines in the loosely assembled hydrophobic environment moderately contributed to thermal stability, and the mutations of these cysteines had a negligible effect on enzyme activity. The other cysteines are involved in the tightly filled hydrophobic core, and mutation of these residues was found to correlate with thermal stability and enzyme activity. These findings about the role of cysteine residues should allow us to obtain a stable JNK1 and thus promote the discovery of potent JNK1 inhibitors

Identification of Highly Potent Human Immunodeficiency Virus Type‑1 Protease Inhibitors against Lopinavir and Darunavir Resistant Viruses from Allophenylnorstatine-Based Peptidomimetics with P2 Tetrahydrofuranylglycine

The emergence of drug-resistant HIV from a widespread antiviral chemotherapy targeting HIV protease in the past decades is unavoidable and provides a challenge to develop alternative inhibitors. We synthesized a series of allophenylnorstatine-based peptidomimetics with various P₃, P₂, and P₂́ moieties. The derivatives with P₂ tetrahydrofuranylglycine (Thfg) were found to be potent against wild type HIV-1 protease and the virus, leading to a highly potent compound <b>21f</b> (KNI-1657) against lopinavir/ritonavir- or darunavir-resistant strains. Co-crystal structures of <b>21f</b> and the wild-type protease revealed numerous key hydrogen bonding interactions with Thfg. These results suggest that the strategy to design allophenylnorstatine-based peptidomimetics combined with Thfg residue would be promising for generating candidates to overcome multidrug resistance

Identification of Highly Potent Human Immunodeficiency Virus Type‑1 Protease Inhibitors against Lopinavir and Darunavir Resistant Viruses from Allophenylnorstatine-Based Peptidomimetics with P2 Tetrahydrofuranylglycine

The emergence of drug-resistant HIV from a widespread antiviral chemotherapy targeting HIV protease in the past decades is unavoidable and provides a challenge to develop alternative inhibitors. We synthesized a series of allophenylnorstatine-based peptidomimetics with various P₃, P₂, and P₂́ moieties. The derivatives with P₂ tetrahydrofuranylglycine (Thfg) were found to be potent against wild type HIV-1 protease and the virus, leading to a highly potent compound <b>21f</b> (KNI-1657) against lopinavir/ritonavir- or darunavir-resistant strains. Co-crystal structures of <b>21f</b> and the wild-type protease revealed numerous key hydrogen bonding interactions with Thfg. These results suggest that the strategy to design allophenylnorstatine-based peptidomimetics combined with Thfg residue would be promising for generating candidates to overcome multidrug resistance

Insights into the Proton Transfer Mechanism of a Bilin Reductase PcyA Following Neutron Crystallography

Phycocyanobilin, a light-harvesting and photoreceptor pigment in higher plants, algae, and cyanobacteria, is synthesized from biliverdin IXα (BV) by phycocyanobilin:ferredoxin oxidoreductase (PcyA) via two steps of two-proton-coupled two-electron reduction. We determined the neutron structure of PcyA from cyanobacteria complexed with BV, revealing the exact location of the hydrogen atoms involved in catalysis. Notably, approximately half of the BV bound to PcyA was BVH⁺, a state in which all four pyrrole nitrogen atoms were protonated. The protonation states of BV complemented the protonation of adjacent Asp105. The “axial” water molecule that interacts with the neutral pyrrole nitrogen of the A-ring was identified. His88 Nδ was protonated to form a hydrogen bond with the lactam O atom of the BV A-ring. His88 and His74 were linked by hydrogen bonds via H₃O⁺. These results imply that Asp105, His88, and the axial water molecule contribute to proton transfer during PcyA catalysis