Prediction of H-Bonding Motifs for Pyrazoles and Oximes Using the Cambridge Structural Database

H-bonding motifs for pyrazoles and oximes have been examined in the Cambridge Structural Database. The accessible surface of the N atoms has been found to be useful as a discriminator to divide structures into dimer and catemer motifs for both pyrazoles and oximes. Low accessibility favors dimers and tetramers and high values favor catemers and trimers. Total molecular volume shows some correlation for oximes, while high values favor dimers. Empirical rules were successfully applied to predict the motifs of eight new structures in the subsequent release of the CSD.     

Crystal structures of four δ‐keto esters and a Cambridge Structural Database analysis of cyano–halogen interactions

The revived interest in halogen bonding as a tool in pharmaceutical cocrystals and drug design has indicated that cyano–halogen interactions could play an important role. The crystal structures of four closely related δ‐keto esters, which differ only in the substitution at a single C atom (by H, OMe, Cl and Br), are compared, namely ethyl 2‐cyano‐5‐oxo‐5‐phenyl‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₁₉H₂₂N₂O₃, (1), ethyl 2‐cyano‐5‐(4‐methoxyphenyl)‐5‐oxo‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₂₀H₂₄N₂O₄, (2), ethyl 5‐(4‐chlorophenyl)‐2‐cyano‐5‐oxo‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₁₉H₂₁ClN₂O₃, (3), and the previously published ethyl 5‐(4‐bromophenyl)‐2‐cyano‐5‐oxo‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₁₉H₂₁BrN₂O₃, (4) [Maurya, Vasudev & Gupta (2013). RSC Adv. 3 , 12955–12962]. The molecular conformations are very similar, while there are differences in the molecular assemblies. Intermolecular C—H...O hydrogen bonds are found to be the primary interactions in the crystal packing and are present in all four structures. The halogenated derivatives have additional aromatic–aromatic interactions and cyano–halogen interactions, further stabilizing the molecular packing. A database analysis of cyano–halogen interactions using the Cambridge Structural Database [CSD; Groom & Allen (2014). Angew. Chem. Int. Ed. 53 , 662–671] revealed that about 13% of the organic molecular crystals containing both cyano and halogen groups have cyano–halogen interactions in their packing. Three geometric parameters for the C—X...N[triple‐bond]C interaction (X = F, Cl, Br or I), viz. the N...X distance and the C—X...N and C—N...X angles, were analysed. The results indicate that all the short cyano–halogen contacts in the CSD can be classified as halogen bonds, which are directional noncovalent interactions.     

Design and Structural Evolution of Matrix Metalloproteinase Inhibitors

Matrix metalloproteinases (MMPs) are involved in a multitude of severe diseases. Despite MMPs being considered druggable targets, past drug-discovery programs have not delivered the anticipated clinical benefits. This review examines the latest structural evolution of small-molecule inhibitors of MMPs, with a focus on the development of novel chemical entities with improved affinity and selectivity profiles. X-ray crystallographic data of the protein targets and cocrystal structures with inhibitors proved to be key for the success achieved during this ambitious endeavor. An evolutionary view on the structural diversity generated for this class of molecules is provided. This encouraging development paves the way for the clinical utilization of this class of highly relevant therapeutic targets. The structure-based design of superior MMP inhibitors highlights the power of this technique and displays strategies for the development of treatment options based on the modulation of challenging drug targets.     

From molecules to visuals: Empowering drug discovery and development with mass spectrometry imaging

Over the past three decades, mass spectrometry imaging (MSI) has emerged as a valuable tool for the spatial localization of drugs and metabolites directly from tissue surfaces without the need for labels. MSI offers molecular specificity, making it increasingly popular in the pharmaceutical industry compared to conventional imaging techniques like quantitative whole-body autoradiography (QWBA) and immunohistochemistry, which are unable to distinguish parent drugs from metabolites. Across the industry, there has been a consistent uptake in the utilization of MSI to investigate drug and metabolite distribution patterns, and the integration of MSI with omics technologies in preclinical investigations. To continue the further adoption of MSI in drug discovery and development, we believe there are two key areas that need to be addressed. First, there is a need for accurate quantification of analytes from MSI distribution studies. Second, there is a need for increased interactions with regulatory agencies for guidance on the utility and incorporation of MSI techniques in regulatory filings. Ongoing efforts are being made to address these areas, and it is hoped that MSI will gain broader utilization within the industry, thereby becoming a critical ingredient in driving drug discovery and development.     

生物催化与新药研究和开发

生物催化具有条件温和、效率高、选择性强、副产物少等特点,因此生物催化在新药的研究和开发中得到广泛的应用;此外,利用生物技术对生物催化剂进行改造优化,将使其能够更好地应用于新颖的生产工艺。本文对此领域的进展作一简单介绍和概述。     

Structural Basis of Microtubule Stabilization by Laulimalide and Peloruside A

Laulimalide and peloruside A are microtubule‐stabilizing agents (MSAs), the mechanism of action on microtubules of which is poorly defined. Here, using X‐ray crystallography it is shown that laulimalide and peloruside A bind to a unique non‐taxane site on β‐tubulin and use their respective macrolide core structures to interact with a second tubulin dimer across protofilaments. At the same time, they allosterically stabilize the taxane‐site M‐loop that establishes lateral tubulin contacts in microtubules. Structures of ternary complexes of tubulin with laulimalide/peloruside A and epothilone A are also solved, and a crosstalk between the laulimalide/peloruside and taxane sites via the M‐loop of β‐tubulin is found. Together, the data define the mechanism of action of laulimalide and peloruside A on tubulin and microtubules. The data further provide a structural framework for understanding the synergy observed between two classes of MSAs in tubulin assembly and the inhibition of cancer cell growth.     

Binary polymorphic cocrystals: an update on the available literature in the Cambridge Structural Database,including a new polymorph of the pharmaceutical 1:1 cocrystal theophylline–3,4‐dihydroxybenzoic acid

An analysis and classification of the 2925 neutral binary organic cocrystals in the Cambridge Structural Database is reported, focusing specifically on those both showing polymorphism and containing an active pharmaceutical ingredient (API). The search was confined to molecules having only C, H, N, O, S and halogens atoms. It was found that 400 out of 2925 cocrystals can be classified as pharmaceutical cocrystals, containing at least one API, and that of those, 56 can be classified as being polymorphic cocrystals. In general, the total number of polymorphic cocrystal systems of any type stands at 125. In addition, a new polymorph of the pharmaceutical cocrystal theophylline–3,4‐dihydroxybenzoic acid (1/1), C₇H₈N₄O₂·C₇H₆O₄, is reported.     

Isolation and Structural Elucidation of Armeniaspirols A–C: Potent Antibiotics against Gram‐Positive Pathogens

In an antibiotic lead discovery program, the known strain Streptomyces armeniacus DSM19369 has been found to produce three new natural products when cultivated on a malt‐containing medium. The challenging structural elucidation of the isolated compounds was achieved by using three independent methods, that is, chemical degradation followed by NMR spectroscopy, a computer‐assisted structure prediction algorithm, and X‐ray crystallography. The compounds, named armeniaspirol A–C ( 2 – 4 ), exhibit a compact, hitherto unprecedented chlorinated spiro[4.4]non‐8‐ene scaffold. Labeling experiments with [1‐¹³C] acetate, [1,2‐¹³C2] acetate, and [U‐¹³C] proline suggest a biosynthesis through a rare two‐chain mechanism. Armeniaspirols displayed moderate to high in vitro activities against Gram‐positive pathogens such as methicillin‐resistant S. aureus (MRSA) or vancomycin resistant E. faecium (VRE). As analogue 2 was active in vivo in an MRSA sepsis model, and showed no development of resistance in a serial passaging experiment, it represents a new antibiotic lead structure.     

N-环丙甲基-7α-[(R)-1-羟基-1-甲基-3-(2-噻吩)丙基]-6,14-内乙基桥四氢去甲基蒂巴因(噻诺啡)合成和晶体结构

N-环丙甲基-7α-[(R)-1-羟基-1-甲基-3-(2-噻吩)丙基]-6,14-内乙基桥四氢去甲基蒂巴因(噻诺啡)是阿片受体部分激动剂.噻诺啡经过一步法合成其结构通过单晶X射线衍射分析确证,其结构保持吗啡"T"型主体结构.     

Crystal structure and electrostatic properties of prednisolone acetate studied using a transferred multipolar atom model

Prednisolone acetate {systematic name: 2‐[(8S ,9S ,10R ,13S ,14S ,17R )‐11,17‐dihydroxy‐10,13‐dimethyl‐3‐oxo‐6,7,8,9,10,11,12,13,14,15,16,17‐dodecahydro‐3H‐cyclopenta[a ]phenanthren‐17‐yl]‐2‐oxoethyl acetate}, is an ophthalmic drug that belongs to the class of corticosteroids. Its crystal structure was refined using the classical independent atom model (IAM) and a transferred multipolar atom model using the ELMAM2 database. The results of both refinements have been compared. The ELMAM2 refinement was found to be superior in terms of the refinement statistics. It has been shown that certain electron‐density‐derived properties can be calculated on the basis of the transferred parameters for crystals which diffract to ordinary resolution. The procedure proves helpful in understanding the mode of action of the drug molecule.     

Exploring a solvated dimer of Gefitinib: a quantitative analysis

Gefitinib or Iressa is an orally administered anilinoquinazoline used in cancer chemotherapy for the treatment of lung and breast cancer. It is reported to exist in two polymorphic forms, a stable form I and a metastable form II. Both of the forms belong to the triclinic P space group. In this work, we report the crystallization of Gefitinib to form a methanol solvate [systematic name: N‐(3‐chloro‐4‐fluorophenyl)‐7‐methoxy‐6‐[3‐(morpholin‐4‐yl)propoxy]quinazolin‐4‐amine methanol hemisolvate, C₂₂H₂₄ClFN₄O₃·0.5CH₃OH] that was theoretically and experimentally investigated. The unit cell is composed of two independent Gefitinib molecules (A and B) that form a stable molecular complex with methanol in the crystal lattice. To understand the crystal lattice stabilization, a combination of techniques, namely X‐ray diffraction, IR spectroscopy, thermogravimetric/differential scanning calorimetry (TG‐DSC), Hirshfeld surface analysis and CLP‐PIXEL methods were used. The analysis of the crystal structure of this dimer revealed a three‐dimensional isostructurality with the already reported form II. The A and B molecules are connected via trifurcated C—H…O and N—H…O hydrogen bonding. In addition, the presence of the methanol molecule stabilizes the crystal structure via C—H…O, N—H…O and C—H…Cl interactions between the two monomers. The IR analysis of the dimer has shown characteristic fingerprint values when compared to the commercial form. The TG‐DSC analysis of the solvated dimer is in good agreement with the patent reporting cocrystals of Gefitinib. Finally, theoretical calculations by the CLP‐PIXEL method and Hirshfeld surface and two‐dimensional (2D) fingerprint plot analysis were carried out in order to quantify the different intermolecular interactions and their energies in the crystal packing.     

Structural Effects on Defects and Growth in Crystals of Urea

1INTRODUCTIONThecrystalofureaisanonlinearopticalmaterial(13andcanbeprepareanopticalparameterocillator(OPO)element[2).LargeperfectcrystalshavebeengrownbysO.lutionmethod[3i,v!'athez-directionrestrictedgrowth..thed,thedirectionwiththehighestgrowthspeed.However,nodetailedinformationwasgivenondislocationsandstrainfeaturesrevealedbyX-raydiffractiontopography"'.Weconcentrateonstudyofthestructuraleffectsonthedefectiveformationandgrowthmorphology.foeureacrystalcrystallizesinthete-tragonalsystem"…     

Alkaloids Used as Medicines: Structural Phytochemistry Meets Biodiversity—An Update and Forward Look

Selecting candidates for drug developments using computational design and empirical rules has resulted in a broad discussion about their success. In a previous study, we had shown that a species’ abundance [as expressed by the GBIF (Global Biodiversity Information Facility)] dataset is a core determinant for the development of a natural product into a medicine. Our overarching aim is to understand the unique requirements for natural product-based drug development. Web of Science was queried for research on alkaloids in combination with plant systematics/taxonomy. All alkaloids containing species demonstrated an average increase of 8.66 in GBIF occurrences between 2014 and 2020. Medicinal Species with alkaloids show higher abundance compared to non-medicinal alkaloids, often linked also to cultivation. Alkaloids with high biodiversity are often simple alkaloids found in multiple species with the presence of ’driver species‘ and are more likely to be included in early-stage drug development compared to ‘rare’ alkaloids. Similarly, the success of an alkaloid containing species as a food supplement (‘botanical’) is linked to its abundance. GBIF is a useful tool for assessing the druggability of a compound from a certain source species. The success of any development programme from natural sources must take sustainable sourcing into account right from the start.     

含杂环卡宾碳的铁羰基簇合物的结构化学研究Ⅱ．—Fe_3(CO)_8[:CNHC(S)C(CH_3)_2NH]的合成和晶体结构

Ｆｅ３（ＣＯ）＿（１２）和取代２，４＿二硫代乙内酰脲反应，得到新的取代物Ｆｅ３（ＣＯ）＿８－［：ＣＮＨＣ（Ｓ）Ｃ（ＣＨ＿３）＿２ＮＨ］（μ＿３－Ｓ）＿２，并进行了ＩＲ、１￣ＨＮＭＲ、ＭＳ表征，测定了它的分子和晶体结构，讨论了杂环卡宾碎片：ＣＮＨＣ（Ｓ）Ｃ（ＣＨ＿３）＿２ＮＨ的取代位置，它是通过卡宾碳原子与Ｆｅ配位。     

Applicability of bioanalysis of multiple analytes in drug discovery and development: review of select case studies including assay development considerations

The development of sound bioanalytical method(s) is of paramount importance during the process of drug discovery and development culminating in a marketing approval. Although the bioanalytical procedure(s) originally developed during the discovery stage may not necessarily be fit to support the drug development scenario, they may be suitably modified and validated, as deemed necessary. Several reviews have appeared over the years describing analytical approaches including various techniques, detection systems, automation tools that are available for an effective separation, enhanced selectivity and sensitivity for quantitation of many analytes. The intention of this review is to cover various key areas where analytical method development becomes necessary during different stages of drug discovery research and development process. The key areas covered in this article with relevant case studies include: (a) simultaneous assay for parent compound and metabolites that are purported to display pharmacological activity; (b) bioanalytical procedures for determination of multiple drugs in combating a disease; (c) analytical measurement of chirality aspects in the pharmacokinetics, metabolism and biotransformation investigations; (d) drug monitoring for therapeutic benefits and/or occupational hazard; (e) analysis of drugs from complex and/or less frequently used matrices; (f) analytical determination during in vitro experiments (metabolism and permeability related) and in situ intestinal perfusion experiments; (g) determination of a major metabolite as a surrogate for the parent molecule; (h) analytical approaches for universal determination of CYP450 probe substrates and metabolites; (i) analytical applicability to prodrug evaluations-simultaneous determination of prodrug, parent and metabolites; (j) quantitative determination of parent compound and/or phase II metabolite(s) via direct or indirect approaches; (k) applicability in analysis of multiple compounds in select disease areas and/or in clinically important drug-drug interaction studies. A tabular representation of select examples of analysis is provided covering areas of separation conditions, validation aspects and applicable conclusion. A limited discussion is provided on relevant aspects of the need for developing bioanalytical procedures for speedy drug discovery and development. Additionally, some key elements such as internal standard selection, likely issues of mass detection, matrix effect, chiral aspects etc. are provided for consideration during method development.     

Synthesis of molecular magnetics based on cobalt trisoxalate. Structural and magnetic properties of NBun 4[MnIICoIII(C2O4)3]

Bimetallic oxalate-bridged complexes Q[M^IICo(C₂O₄)₃] (Q=Me₄N⁺, Buⁿ ₄P⁺; M^II=Mn, Co, Ni, Cu, Zn) were synthesized. Single crystals of [NBuⁿ ₄][Mn^IICo^III(C₂O₄)₃] were studied by XRD. Unit cell parametersa=b=9.242(3) Å,c=54.524(13) Å; space groupR3c. Magnetic measurements indicate the absence of a magnetic phase transition up to the temperature of liquid helium. The XRD data confirm the presence of Co^III ions with a low-spin configuration in the crystal.     

水热条件下坡缕石在NaOH溶液中的行为及结构变化

分别用1,2和3 mol·L^-1的NaOH溶液,在不同的温度条件下对坡缕石进行了侵蚀实验。对反应后的固相产物进行了XRD和SEM分析,对浸出液中的金属阳离子进行了原子吸收光谱分析。讨论了反应温度和碱溶液浓度对碱溶后产物的影响。XRD和SEM结果表明,c_NaOH≤2 mol·L^-1时,坡缕石经碱溶液侵蚀后,可以生成蒙脱石和方沸石,其中反应温度的升高有利于方沸石的形成,碱溶液浓度的升高有利于蒙脱石的形成。当碱溶液浓度达到3 mol·L^-1,反应温度为200 ℃时,最终产物为SiO₂。浸出液的定量分析结果显示,坡缕石与碱溶液的反应过程中,Na⁺对八面体阳离子的置换具有选择性,置换顺序为：Al³⁺＞Fe³⁺(Fe²⁺)＞Mg²⁺。     

Optical Properties and Structural Perfection of Chicago Sky Blue 6B-doped KDP Crystals

KDP crystals doped with Chicago Sky Blue 6B(CSB-6B) were grown by traditional lowering temperature method.The optical properties and structural perfection of KDP crystals were investigated by transmittance spectra and high-resolution X-ray diffraction,respectively.The results indicate that CSB-6B tends to be incorporated into the pyramidal sector of KDP crystals(PyS-KDP) and lead to inclusions parallel to(101) face.Additionally,the transmittance of as-grown KDP crystals decreases as the amount of CSB-6B increases.Moreover,the rocking curves of PyS-KDP suggest that CSB-6B can deteriorate the structural perfection of PyS-KDP.     

Syntheses and Structural Characterizations of [Co~Ⅲ(TPA)(N_3)_2]·(ClO_4) and [Cu~Ⅱ(TPA)(N_3)]·(ClO_4) (TPA=Tris(2-pyridylmethyl)amine)

1 INTRODUCTION As a versatile ligand, N3- has been attracted great interest for several decades. In addition to mono- dentate coordination through a single N-donor, the azide group is not only an efficient antiferromag- netic coupler in the 1,3-fashion…