Small Molecule X-ray Research Articles

Geometry of guanidinium groups in arginines.

The restraints in common usage today have been obtained based on small molecule X-ray crystal structures available 25 years ago and recent reports have shown that the values of bond lengths and valence angles can be, in fact, significantly different from those stored in libraries, for example for the peptide bond or the histidine ring geometry. We showed that almost 50% of outliers found in protein validation reports released in the Protein Data Bank on 23 March 2016 come from geometry of guanidine groups in arginines. Therefore, structures of small molecules and atomic resolution protein crystal structures have been used to derive new target values for the geometry of this group. The most significant difference was found for NE-CZ-NH1 and NE-CZ-NH2 angles, showing that the guanidinium group is not symmetric. The NE-CZ-NH1 angle is larger, 121.5(10)˚, than NE-CZ-NH2, 119.2(10)˚, due to the repulsive interaction between NH1 and CD1 atom.

Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules.

The Torsion Library contains hundreds of rules for small molecule conformations which have been derived from the Cambridge Structural Database (CSD) and are curated by molecular design experts. The torsion rules are encoded as SMARTS patterns and categorize rotatable bonds via a traffic light coloring scheme. We have systematically revised all torsion rules to better identify highly strained conformations and minimize the number of false alerts for CSD small molecule X-ray structures. For this new release, we added or substantially modified 78 torsion patterns and reviewed all angles and tolerance intervals. The overall number of red alerts for a filtered CSD data set with 130 000 structures was reduced by a factor of 4 compared to the predecessor. This is of clear advantage in 3D virtual screening where hits should only be removed by a conformational filter if they are in energetically inaccessible conformations.

Discovery of potent, orally bioavailable, small-molecule inhibitors of WNT signaling from a cell-based pathway screen.

WNT signaling is frequently deregulated in malignancy, particularly in colon cancer, and plays a key role in the generation and maintenance of cancer stem cells. We report the discovery and optimization of a 3,4,5-trisubstituted pyridine 9 using a high-throughput cell-based reporter assay of WNT pathway activity. We demonstrate a twisted conformation about the pyridine–piperidine bond of 9 by small-molecule X-ray crystallography. Medicinal chemistry optimization to maintain this twisted conformation, cognisant of physicochemical properties likely to maintain good cell permeability, led to 74 (CCT251545), a potent small-molecule inhibitor of WNT signaling with good oral pharmacokinetics. We demonstrate inhibition of WNT pathway activity in a solid human tumor xenograft model with evidence for tumor growth inhibition following oral dosing. This work provides a successful example of hypothesis-driven medicinal chemistry optimization from a singleton hit against a cell-based pathway assay without knowledge of the biochemical target.

Temperature dependence of Uiso constraints in riding hydrogen treatments

"Anisotropic parametrisation of the thermal displacements of hydrogen atoms in single-crystal X-ray structure refinement is not possible with independent atom model (IAM) scattering factors. This is due to the weak scattering contribution of hydrogen atoms. Only when aspherical scattering factors are used can carefully measured Bragg data provide such information. For conventional structure determinations parameters of ""riding"" hydrogen atoms are frequently constrained to values of their ""parent"" heavy atom. Usually values of 1.2 and 1.5 times X-U_eq are assigned to H-U_iso in these cases. Such constraints yield reasonable structural models for room-temperature data. However, todays small molecule X-Ray diffraction experiments are usually carried out at significantly lower temperatures. To further study the temperature dependence of ADPs we have evaluated several data sets of N-Acetyl-L-4-Hydroxyproline Monohydrate at temperatures ranging from 9 K to 250 K. Methods compared were HAR [1], Invariom refinement [2], time-of-flight Neutron diffraction and the TLS+ONIOM approach [3]. In the TLS+ONIOM approach non-hydrogen ADPs from Invariom refinement provided ADPs for the TLS-fit. Hydrogen atoms in all methods were grouped and analyzed according to their Invariom name. We reach a good agreement of the temperature dependence of H-U_iso/X-U_eq. At very low temperatures the ratio H-U_iso/X-U_eq can be as high as 4, e.g. for Hydrogen attached to a sp3 carbon atom with three non-Hydrogen atom neighbors. Since all methods consistently show that the H-U_iso/X-U_eq ratio is temperature dependent, this effect should be taken into account in conventional structure determinations."

Shaping suvorexant: application of experimental and theoretical methods for driving synthetic designs

Dual Orexin Receptor Antagonists (DORA) bind to both the Orexin 1 and 2 receptors. High resolution crystal structures of the Orexin 1 and 2 receptors, both class A GPCRs, were not available at the time of this study, and thus, ligand-based analyses were invoked and successfully applied to the design of DORAs. Computational analysis, ligand based superposition, unbound small-molecule X-ray crystal structures and NMR analysis were utilized to understand the conformational preferences of key DORAs and excellent agreement between these orthogonal approaches was seen in the majority of compounds examined. The predominantly face-to-face (F2F) interaction observed between the distal aromatic rings was the core 3D shape motif in our design principle and was used in the development of compounds. A notable exception, however, was seen between computation and experiment for suvorexant where the molecule exhibits an extended conformation in the unbound small-molecule X-ray structure. Even taking into account solvation effects explicitly in our calculations, we nevertheless find support that the F2F conformation is the bioactive conformation. Using a dominant states approximation for the partition function, we made a comprehensive assessment of the free energies required to adopt both an extended and a F2F conformation of a number of DORAs. Interestingly, we find that only a F2F conformation is consistent with the activities reported.Electronic supplementary materialThe online version of this article (doi:10.1007/s10822-014-9710-x) contains supplementary material, which is available to authorized users.

Analysis of Small Molecule X-Ray Crystal Structures: Chemical Crystallography with Undergraduate Students in a Teaching Laboratory

The molecular structures of six small molecule organic compounds have been studied by X-ray diffraction in collaboration with undergraduate students enrolled in an advanced integrated laboratory course. The structures of 3-chloro-2-fluorobenzonitrile (1) [orthorhombic, P212121, a = 3.7679(13) A, b = 12.546(4) A, c = 13.780(5) A], 5-chloro-2-fluorobenzonitrile (2) [monoclinic, P21/c, a = 3.7909(7) A, b = 14.265(3) A, c = 12.171(2) A, β = 92.314(3)°], 2-bromo-3′-hydroxyacetophenone (3) [triclinic, P-1, a = 7.7081(3) A, b = 9.8840(3) A, c = 10.7320(4) A, α = 98.4345(4)°, β = 90.6184(4)°, γ = 105.9259(4)°], 3-chlorobenzoylacetonitrile (4) [monoclinic, Cc, a = 4.8086(6) A, b = 32.929(4) A, c = 10.5855(13) A, β = 97.665(1)°], 4-bromo-1-indanone (5) [triclinic, P-1, a = 7.3731(4) A, b = 7.5419(4) A, c = 8.2370(4) A, α = 62.927(1)°, β = 71.160(1)°, γ = 71.521(1)°], and 4-bromo-1-indanol (6) [monoclinic, P21/c, a = 12.7914(9) A, b = 4.6949(4) A, c = 27.864(2) A, β = 94.707(1)°] reveal several different types of intermolecular interactions, such as hydrogen bonding, π-stacking, halogen–halogen interactions, and C–H···X (X = O, N, halogen) interactions. The molecular structures of six small molecule organic compounds have been studied by X-ray diffraction in collaboration with undergraduate students enrolled in an advanced integrated laboratory course. The structures reveal several different types of intermolecular interactions, such as hydrogen bonding, π-stacking, halogen–halogen interactions, and C–H···X (X = O, N, halogen) interactions.

Unconventional Magnetic Transition in Na x CoO2 (x>0.7) Single Crystals

NaxCoO2 (x>0.7) single crystals with a typical dimension of 0.4×0.4 mm2 have been prepared by a “rapid heat-up” technique. By the Benchtop Small Molecule X-ray Crystallography System, the samples have been confirmed to be a single phase of the hexagonal γ-NaxCoO2. Magnetic data from the crystal indicate a magnetic phase transition around T=30 K, and the transition is sensitive to the applied magnetic fields. This is most consistent with the formation of an antiferromagnetic spin-density-wave (SDW) with the easy axis for magnetization nearly along the c-axis. Weak and soft ferromagnetism has also been observed from the crystal at low temperature. This unconventional magnetic property may be ascribed to the effect of the small moments of Co4−x−δ sites at low temperature.

Isolation and characterization of main group and late transition metal complexes using orthometallated imine ligands

Several late transition metal and main group orthometallated imine complexes were synthesized by utilizing ortholithiated imine precursors. Magnesium, aluminum, zinc, copper(I), and tin(IV) complexes were isolated and characterized. Subsequent reactions with electrophiles such as Ph(2)PCl, MeI and I(2) yielded several functionalized products, including a new iminophosphine ligand and its corresponding copper(I) complex. The coordination modes of the orthometallated imine ligands, as well as the structures of the metal complexes, were studied in the solid state using small molecule X-ray diffraction when possible.

Discovery and Characterization of Atropisomer PH‐797804, a p38 MAP Kinase Inhibitor, as a Clinical Drug Candidate

PH-797804 ((aS)-3-{3-bromo-4-[(2,4-difluorobenzyl)oxy]-6-methyl-2-oxopyridin-1(2H)-yl}-N,4-dimethylbenzamde) is a diarylpyridinone inhibitor of p38 mitogen-activated protein (MAP) kinase derived from a racemic mixture as the more potent atropisomer (aS), first proposed by molecular modeling and subsequently confirmed by experiments. Due to steric constraints imposed by the pyridinone carbonyl group and the 6- and 6'-methyl substituents of PH-797804, rotation around the connecting bond of the pyridinone and the N-phenyl ring is restricted. Density functional theory predicts a remarkably high rotational energy barrier of >30 kcal mol(-1), corresponding to a half-life of more than one hundred years at room temperature. This gives rise to discrete conformational spaces for the N-phenylpyridinone group, and as a result, two atropic isomers that do not interconvert under ambient conditions. Molecular modeling studies predict that the two isomers should differ in their binding affinity for p38α kinase; whereas the atropic S (aS) isomer binds favorably, the opposite aR isomer incurs significant steric interference with p38α kinase. The two isomers were subsequently identified and separated by chiral chromatography. IC50 values from p38α kinase assays confirm that one atropisomer is >100-fold more potent than the other. It was ultimately confirmed by small-molecule X-ray diffraction that the more potent atropisomer, PH-797804, is the aS isomer of the racemic pair. Extensive pharmacological characterization supports that PH-797804 carries most activity both in vitro and in vivo, and it has a stability profile compatible with oral formulation and delivery options.

A geometry force field which converts low‐resolution X‐ray models to structures with properties found at ultra high resolution

A geometry optimization force field was developed using ultra high-resolution structures and tested using high- and low-resolution X-ray structures. Protein and small molecule X-ray data was used. When applied to ultra high-resolution structures the force field conserves the internal geometry and local strain energy. When applied to low-resolution structures there is a small change in geometry accompanied by a large drop in local strain energy. Although optimization causes only small structural changes in low-resolution X-ray models, it dramatically modifies profiles for hydrogen bonding, Van der Waals contact, bonded geometry, and local strain energy, making them almost indistinguishable from those found at high resolution. Further insight into the effect of the force field was obtained by comparing geometries of homologous proteins before and after geometry optimization. Optimization causes homologous regions of structures to become similar in internal geometry and energies. Once again, the changes only require small atomic movements. These findings provide insights into the structure of molecular complexes. The new force field contains only short-range interatomic potential functions. Its effectiveness shows that local geometries are determined by short-range interactions which are well modeled by the force field. Potential applications of this study include detection of possible structural errors, correction of errors with minimal change in geometry, improved understanding and prediction of the effects of modifying ligands or proteins, and computational addition of structural water.

Discovery of Potent and Highly Selective Thienopyridine Janus Kinase 2 Inhibitors

Developing Janus kinase 2 (Jak2) inhibitors has become a significant focus for small molecule drug discovery programs in recent years due to the identification of a Jak2 gain-of-function mutation in the majority of patients with myeloproliferative disorders (MPD). Here, we describe the discovery of a thienopyridine series of Jak2 inhibitors that culminates with compounds showing 100- to >500-fold selectivity over the related Jak family kinases in enzyme assays. Selectivity for Jak2 was also observed in TEL-Jak cellular assays, as well as in cytokine-stimulated peripheral blood mononuclear cell (PBMC) and whole blood assays. X-ray cocrystal structures of 8 and 19 bound to the Jak2 kinase domain aided structure-activity relationship efforts and, along with a previously reported small molecule X-ray cocrystal structure of the Jak1 kinase domain, provided structural rationale for the observed high levels of Jak2 selectivity.

Stereochemical Requirements for the Mineralocorticoid Receptor Antagonist Activity of Dihydropyridines

A number of known 1,4-dihydropyridine CCBs were identified as having comparable potency to the steroidal MR antagonist eplerenone. Chiral resolution of mebudipine revealed that MR and CCB activity reside in opposite enantiomers. Small molecule X-ray crystal structures showed that the C4 stereochemistry of optimized selective MR analogues, e.g. 5, is consistent with MR-active mebudipine. Molecular modeling supports a binding pose consistent with that previously proposed for DHP diesters.

Titanium imido complexes utilizing orthometallated derivatized acetophenone and piperonal imine ligands: synthesis, isolation, and characterization

A series of five ortho-lithiated imines (Li-L(n); n = 1-5) was synthesized via the reaction of an aryl or alkyl acetophenone imine with n-butyllithium. The ortho-lithiated imines were subsequently reacted with Ti(NR)Cl(2)py(3) (R = C(CH(3))(3), 2,6-Me(2)C(6)H(3), 2,6-Et(2)C(6)H(3), or 2,6-(i)Pr(2)C(6)H(3)), yielding complexes of the form (L(n))(2)Ti(NR). Several of the resulting complexes [(L(1))(2)Ti(NC(CH(3))(3)), 1a; (L(3))(2)Ti(N-2,6-Me(2)C(6)H(3)), 3b; and (L(5))(2)Ti(NC(CH(3))(3)), 5a] were structurally characterized using small molecule X-ray diffraction. The C(2) symmetric complexes produced in these reactions displayed a distorted square pyramidal geometry. In each complex the titanium center was located above the square plane of the two coordinated bidentate ligands and the chelating C approximately N ligands were folded away from the metal center. When a less sterically demanding alkylimine was used (L(4)), the resulting complex was isolated as an equilibrium mixture of cis and trans isomers of the empirical formula (L(4))(2)Ti(NC(CH(3))(3))py (cis/trans 4a).

Bruker AXS announces novel APEX™ DUO, the most versatile system for small molecule X-ray crystallography

Bruker AXS announces novel APEX™ DUO, the most versatile system for small molecule X-ray crystallography

Focus on materials

Focus on materials

A user interface toolkit for small molecule X-ray structure determination and analysis

A user interface toolkit for small molecule X-ray structure determination and analysis

Fluorine interactions at the thrombin active site: protein backbone fragments H-C(alpha)-C=O comprise a favorable C-F environment and interactions of C-F with electrophiles.

In a systematic fluorine scan of a rigid inhibitor to map the fluorophilicity/fluorophobicity of the active site in thrombin, one or more F substituents were introduced into the benzyl ring reaching into the D pocket. The 4-fluorobenzyl inhibitor showed a five to tenfold higher affinity than ligands with other fluorination patterns. X-ray crystal-structure analysis of the protein-ligand complex revealed favorable C-F...H-C(alpha)-C=O and C-F...C=O interactions of the 4-F substituent of the inhibitor with the backbone H-C(alpha)-C=O unit of Asn98. The importance of these interactions was further corroborated by the analysis of small-molecule X-ray crystal-structure searches in the Protein Data Base (PDB) and the Cambridge Structural Database (CSD). In the C--F...C=O interactions that are observed for both aromatic and aliphatic C-F units and a variety of carbonyl and carboxyl derivatives, the F atom approaches the C=O C atom preferentially along the pseudotrigonal axis of the carbonyl system. Similar orientational preferences are also seen in the dipolar interactions C--F.C[triple chemical bond]N, C-F.C-F, and C-F...NO(2), in which the F atoms interact at sub-van der Waals distances with the electrophilic centers.

A fluorine scan of the phenylamidinium needle of tricyclic thrombin inhibitors: effects of fluorine substitution on pKa and binding affinity and evidence for intermolecular C-F...CN interactions.

The H-atoms of the phenylamidinium needle of tricyclic thrombin inhibitors, which interacts with Asp189 at the bottom of the selectivity pocket S1 of the enzyme, were systematically exchanged with F-atoms in an attempt to improve the pharmacokinetic properties by lowering the pK(a) value. Both the pK(a) values and the inhibitory constants K(i) against thrombin and trypsin were decreased upon F-substitution. Interestingly, linear free energy relationships (LFERs) revealed that binding affinity against thrombin is much more affected by a decrease in pK(a) than the affinity against trypsin. Surprising effects of F-substitutions in the phenylamidinium needle on the pK(a) value of the tertiary amine centre in the tricyclic scaffold of the inhibitors were observed and subsequently rationalised by X-ray crystallographic analysis and ab initio calculations. Evidence for highly directional intermolecular C-F...CN interactions was obtained by analysis of small-molecule X-ray crystal structures and investigations in the Cambridge Structural Database (CSD).

A Fluorine Scan of Thrombin Inhibitors to Map the Fluorophilicity/Fluorophobicity of an Enzyme Active Site: Evidence for CF⋅⋅⋅CO Interactions

A highly fluorophilic environment comprising the HCαCO unit of Asn 98 in the active site of thrombin was identified by X-ray crystallography of a complex formed between the enzyme and a synthetic inhibitor (see partial X-ray structure, distances are in Angstroms). Short CF⋅⋅⋅HCα and CF⋅⋅⋅CO contacts involving HCαCO fragments were also frequently observed in small-molecule X-ray crystal structures.

Azepanone-based inhibitors of human and rat cathepsin K.

The synthesis, in vitro activities, and pharmacokinetics of a series of azepanone-based inhibitors of the cysteine protease cathepsin K (EC 3.4.22.38) are described. These compounds show improved configurational stability of the C-4 diastereomeric center relative to the previously published five- and six-membered ring ketone-based inhibitor series. Studies in this series have led to the identification of 20, a potent, selective inhibitor of human cathepsin K (K(i) = 0.16 nM) as well as 24, a potent inhibitor of both human (K(i) = 0.0048 nM) and rat (K(i,app) = 4.8 nM) cathepsin K. Small-molecule X-ray crystallographic analysis of 20 established the C-4 S stereochemistry as being critical for potent inhibition and that unbound 20 adopted the expected equatorial conformation for the C-4 substituent. Molecular modeling studies predicted the higher energy axial orientation at C-4 of 20 when bound within the active site of cathepsin K, a feature subsequently confirmed by X-ray crystallography. Pharmacokinetic studies in the rat show 20 to be 42% orally bioavailable. Comparison of the transport of the cyclic and acyclic analogues through CaCo-2 cells suggests that oral bioavailability of the acyclic derivatives is limited by a P-glycoprotein-mediated efflux mechanism. It is concluded that the introduction of a conformational constraint has served the dual purpose of increasing inhibitor potency by locking in a bioactive conformation as well as locking out available conformations which may serve as substrates for enzyme systems that limit oral bioavailability.