X-ray Crystal Structure Research Articles

X-ray Structure-Guided Discovery of a Potent Benzimidazole Glutaminyl Cyclase Inhibitor That Shows Activity in a Parkinson's Disease Mouse Model.

The secretory glutaminyl cyclase (sQC) and Golgi-resident glutaminyl cyclase (gQC) are responsible for N-terminal protein pyroglutamation and associated with various human diseases. Although several sQC/gQC inhibitors have been reported, only one inhibitor, PQ912, is currently undergoing clinic trials for the treatment of Alzheimer's disease. We report an X-ray crystal structure of sQC complexed with PQ912, revealing that the benzimidazole makes "anchor" interactions with the active site zinc ion and catalytic triad. Structure-guided design and optimization led to a series of new benzimidazole derivatives exhibiting nanomolar inhibition for both sQC and gQC. In a MPTP-induced Parkinson's disease (PD) mouse model, BI-43 manifested efficacy in mitigating locomotor deficits through reversing dopaminergic neuronal loss, reducing microglia, and decreasing levels of the sQC/gQC substrates, α-synuclein, and CCL2. This study not only offers structural basis and new leads for drug discovery targeting sQC/gQC but also provides evidence supporting sQC/gQC as potential targets for PD treatment.

Structural Insights into the Interaction of Terpenoids with Streptomyces avermitilis CYP107P2.

Streptomyces avermitilis genome includes 33 genes encoding monooxygenation-catalyzing cytochrome P450 enzymes. We investigated the structure of CYP107P2 and its interactions with terpenoid compounds. The recombinant CYP107P2 protein was expressed in Escherichia coli and the purified enzyme exhibited a typical P450 spectrum upon CO-binding in its reduced state. Type-I substrate-binding spectral titrations were observed with various terpenoid compounds, including α-pinene, β-pinene, α-terpinyl acetate, and (+)-3-carene. The calculated binding affinities (Kd) ranged from 15.9 to 50.8 μM. The X-ray crystal structure of CYP107P2 was determined at 1.99 Å resolution, with a well-conserved overall P450 folding conformation. The terpenoid compound docking models illustrated that the structural interaction between monoterpenes and CYP107P2, with the distance between heme and terpenes ranging from 3.4 to 5.4 Å, indicates potential substrate binding for P450 enzyme. This study suggests that CYP107P2 is a Streptomyces P450 enzyme capable of catalyzing terpenes as substrates, signifying noteworthy advancements in comprehending a novel P450 enzyme's involvement in terpene reactions.

In silico design of novel multitarget small molecule inhibitors to treat PTEN-mutant endometrial carcinoma.

e15119 Background: Previously we described triple CDK4/6-CDK9 inhibitor, LCI133 for the treatment of endometrial carcinoma (EC). We used in silico modeling to optimize LCI133’s physicochemical properties to increase PI3K p110α potency/ADME to better target epithelial-derived cancers, resulting in nanomolar potent LCI139. We characterized LCI139’s in vitro potency, target specificity, activity in in vitro EC models, safety in normal cell lines. Methods: LCI139 + analogs were designed using computational chemistry based on X-ray crystal structures of each target protein + validated chemistry using nuclear magnetic resonance + high-resolution mass spectrometry. Specific target inhibition was assessed by cell-free kinase hotspot/lipid kinase assay + selectivity profile. LCI139 (0.001-10μM) was screened against EC cell lines AN3CA, RL95-2, Ishikawa, KLE, HEC-1-A and -B for 48 hours; IC50 values determined by CellTiter-Glo Assay. EC cells were treated with LCI139 or single agent control for 24 hours + stained with Annexin V/7-AAD to assess apoptosis. Representative PTEN wildtype (HEC-1A) + mutant (AN3CA) EC cell lines were chosen for mechanistic studies + treated 6 to 24 hours with multitarget or single agent inhibitor. Cells were stained with Vybrant DyeCycle Violet to determine cell cycle arrest by cytometer. Cellular lysates were prepared for Western blot (WB). Results: LCI139’s has a molecular weight of 502.57Da + is a highly potent PI3Kα-CDK4/6-CDK9 inhibitor by cell-free kinase assays: 0.070µM (PI3Kα), 0.461µM (PI3Kγ), 0.214µM (PI3Kδ), 0.0015µM (CDK4), 0.0036µM (CDK6), 0.000039µM (CDK9). KINOMEscan revealed a favorable S(35) selectivity score of 0.221 screened against 403 non-mutant kinases. PTEN mutant AN3CA (IC50 216.0nM), RL95-2 (IC50 22.8nM), Ishikawa (IC50 2.5nM) had nanomolar LCI139 IC50 values. PTEN-wild type cell lines were insensitive up to 10μM; confirmed by dose-dependent apoptosis + colony-forming assays. WB revealed LCI139 treatment ablated MCL-1 expression, decreased phosphorylation of AKT, Rb, Rpb1 (Ser2), induced significant amounts of cPARP in PTEN mutant AN3CA. In PTEN-wildtype HEC1A WB, dose-dependent expression of pAKT in PTEN siRNA was noted. LCI139 generated heterogenous cell line specific effects on cell cycle progression + arrest. LCI139 displayed favorable toxicity against normal human kidney cells (HEK-293) compared to single agent controls. Conclusions: Triple PI3K-CDK4/6-CDK9 inhibitor, LCI139, is nanomolar potent against PTEN mutant EC cell lines + displays decreased toxicity compared with CDK9 inhibitor reference compounds, AZD4573 + flavopiridol. Our results merit mechanistic dissection of PTEN interaction with PI3K + CDK9 signaling pathways, cell cycle machinery, CDK9-mediated transcriptional control. These data support extensive in vivo potency, toxicity, PK/PD studies to assess LCI139’s clinical utility in treating EC.

Structural and biophysical analysis of cytochrome P450 2C9*14 and *27 variants in complex with losartan

The human cytochrome P450 (CYP) 1, 2 and 3 families of enzymes are responsible for the biotransformation of a majority of the currently available pharmaceutical drugs. The highly polymorphic CYP2C9 predominantly metabolizes many drugs including anticoagulant S-warfarin, anti-hypertensive losartan, anti-diabetic tolbutamide, analgesic ibuprofen, etc. There are >80 single nucleotide changes identified in CYP2C9, many of which significantly alter the clearance of important drugs. Here we report the structural and biophysical analysis of two polymorphic variants, CYP2C9*14 (Arg125His) and CYP2C9*27 (Arg150Leu) complexed with losartan. The X-ray crystal structures of the CYP2C9*14 and *27 illustrate the binding of two losartan molecules, one in the active site near heme and another on the periphery. Both losartan molecules are bound in an identical conformation to that observed in the previously solved CYP2C9 wild-type complex, however, the number of losartan differs from the wild-type structure, which showed binding of three molecules. Additionally, isothermal titration calorimetry experiments reveal a lower binding affinity of losartan with *14 and *27 variants when compared to the wild-type. Overall, the results provide new insights into the effects of these genetic polymorphisms and suggests a possible mechanism contributing to reduced metabolic activity in patients carrying these alleles.

A biologically inspired fluorescent probe with enhanced sensing performance for detection of Al3+ based on metal replacement strategy

Salicylaldehyde acyl-hydrazone derivatives have been widely applied to design fluorescent probe for Al3+ detection, but they are always restricted to detect Al3+ in water and actual samples by their poor solubility, low sensitivity, and long response time. Biologically inspired, four salicylaldehyde acyl-hydrazone compounds were designed and synthesized and H4L1 as one of them was selected for in-situ assembly of the ytterbium complex (FP-Al), which has been developed to be a new fluorescent probe for Al3+ detection by the central mental displacement process. The in-situ structure transformation from FP-Al to Al-L was fully characterized by X-ray crystal structure analysis, 1H NMR, FT-IR, and spectral analysis. The intrinsic driving force was explained and elaborated by theoretical calculation. FP-Al showed a significant visible fluorescence enhancement and near-infrared luminescence decreased upon the addition of Al3+. Compared with the ligand H4L1, FP-Al showed enhanced sensing performance during Al3+ detection, especially in improving water solubility and selectivity to Al3+, promoting response speed, reducing background fluorescence and increase cell-membrane permeability. The application of spontaneous metal replacement reaction might be able to provide a new strategy to develop high-performance optical chemo-sensors.

A Fluorinated Chaperone Gives X-ray Crystal Structures of Acyclic Natural Product Derivatives up to 338 Molecular Weight.

Crystallizing molecules with long flexible chains is a challenge, making it difficult to perform X-ray crystallography. Chaperones can assist in the crystallization of compounds that do not crystallize by themselves by producing solvate crystals that contain the analyte in their three-dimensional lattices. Among the most versatile chaperones for liquid analytes are tetraaryladamantanes (TAAs), but the size of the compounds that can be encapsulated is limited, and attempts to surpass this limit with known TAAs were unsuccessful. Here we report that 1,3,5,7-tetrakis(2-fluoro-4-methoxyphenyl)adamantane (TFM) is a crystallization chaperone for acyclic molecules up to the molecular weight of phytyl acetate (338 g/mol). Encapsulation of such a large acyclic compound was achieved when the analyte was esterified and when a two-step temperature protocol was used for crystallization. Exploratory work indicates that a drop to -20 °C allows for encapsulation of squalene (Mr 411 g/mol), albeit with positional disorder of the analyte. Our X-ray crystal structures of solvates with flexible analytes shed light on how crystalline order can be imposed on large acyclic analytes. The new, fluorinated TAA gives access to crystal structures that were inaccessible thus far.

A Practice Synthesis and X-Ray Crystal Structure of (E)-4-(1-naphthylvinyl)pyridine and Related Compounds

The synthesis, structure, and photoreactivity of (E)-4-(1-naphthylvinyl)pyridine ((E)-4-1-nvp; 1) and its coordination compounds has been investigated. Synthesis of (1) via Wittig olefination resulted in a challenging isomer separation and purification process. By synthesizing (1) via a Horner-Wadsworth-Emmons reaction, high stereoselectivity and purity was achieved. The crystal structure of (1) revealed significant intramolecular rotation facilitated by CH···π interactions, ultimately preventing olefin stacking in both the solid-state structure of (1) and a cocrystal with a structural isomer. Novel Ag(I) and Zn(II) coordination complexes that utilize (1) as a ligand were also synthesized and fully characterized, facilitating the examination of the relationship between molecular planarity and secondary bonding contributions via Hirshfeld surface analyses. These findings deepen our understanding of intermolecular interactions involving (E)-4-1-nvp and offer insights for designing novel photoresponsive materials capable of solid-state [2+2] cycloaddition.

Michaelis-like complex of mouse ketohexokinase isoform C.

Over the past forty years there has been a drastic increase in fructose-related diseases, including obesity, heart disease and diabetes. Ketohexokinase (KHK), the first enzyme in the liver fructolysis pathway, catalyzes the ATP-dependent phosphorylation of fructose to fructose 1-phosphate. Understanding the role of KHK in disease-related processes is crucial for the management and prevention of this growing epidemic. Molecular insight into the structure-function relationship in ligand binding and catalysis by KHK is needed for the design of therapeutic inhibitory ligands. Ketohexokinase has two isoforms: ketohexokinase A (KHK-A) is produced ubiquitously at low levels, whereas ketohexokinase C (KHK-C) is found at much higher levels, specifically in the liver, kidneys and intestines. Structures of the unliganded and liganded human isoforms KHK-A and KHK-C are known, as well as structures of unliganded and inhibitor-bound mouse KHK-C (mKHK-C), which shares 90% sequence identity with human KHK-C. Here, a high-resolution X-ray crystal structure of mKHK-C refined to 1.79 Å resolution is presented. The structure was determined in a complex with both the substrate fructose and the product of catalysis, ADP, providing a view of the Michaelis-like complex of the mouse ortholog. Comparison to unliganded structures suggests that KHK undergoes a conformational change upon binding of substrates that places the enzyme in a catalytically competent form in which the β-sheet domain from one subunit rotates by 16.2°, acting as a lid for the opposing active site. Similar kinetic parameters were calculated for the mouse and human enzymes and indicate that mice may be a suitable animal model for the study of fructose-related diseases. Knowledge of the similarity between the mouse and human enzymes is important for understanding preclinical efforts towards targeting this enzyme, and this ground-state, Michaelis-like complex suggests that a conformational change plays a role in the catalytic function of KHK-C.

Highly Selective Ratiometric Sensors for Pb2+ Based on Luminescent Zn(II)-Coordination Polymers with Thiophenedicarboxylate. Crystal Structures and Spectroscopic Studies.

The development of luminescent coordination polymers for the selective sensing of Pb2+ in water constitutes an active area of research that impacts analytical, environmental, and inorganic chemistry. Herein, two novel water-stable 2D Zn-coordination polymers {[Zn2(H2O)2(tdc)2(bpy)]·(H2O)}n 1 and [Zn(tdc)(tmb)]n 2 (tdc = thiophenedicarboxylate; bpy = 4,4'-bipyridine and tmb = 4,4'-trimethylenebipyridine) were synthesized, structurally determined by single crystal X-ray diffraction, and studied in-depth as luminescent sensors for a series of cations (Ca2+, Mg2+, Mn2+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+ Cd2+, Hg2+ and Pb2+) in 20% aqueous ethanol. These Zn-polymers possess photostability in 20% aqueous ethanol with a strong emission at 410 upon excitation at 330nm and quantum yields of around Φ = 0.09. Under these conditions, Pb+2 can be efficiently sensed with polymer 2 through a fluorescent ratiometric response with selectivity over common interfering metal ions such as Cu2+, Cd2+ and Hg2+ in the micromolar concentration range (detection limit = 1.78 ± 10μM). Such selectivity/affinity of Pb2+ over Hg2+ for luminescent chemosensors is still rare. On the basis of spectroscopic tools (1H NMR, far ATR-IR, PXRD), the X-ray crystal structure of 2, and Scanning Electron Microscopy with Energy-Dispersive X-ray Spectroscopic analysis, the ratiometric fluorescent response is proposed via an efficient metal-ion exchange driven through interactions between thiophenedicarboxylate rings and Pb2+ ions. The use of flexible luminescent Zn-coordination polymers as sensors for selective and direct detection of Pb2+ in aqueous media has been unexplored until now.

A new framework for novel analogues of pazopanib as potent and selective human carbonic anhydrase inhibitors: Design, repurposing rational, synthesis, crystallographic, in vivo and in vitro biological assessments

Herein, we describe the design and synthesis of novel aryl pyrimidine benzenesulfonamides APBSs 5a-n, 6a-c, 7a-b, and 8 as pazopanib analogues to explore new potent and selective inhibitors for the CA IX. All APBSs were examined in vitro for their promising inhibition activity against a small panel of hCAs (isoforms I, II, IX, and XII). The X-ray crystal structure of CA I in adduct with a representative APBS analogue was solved. APBS-5m, endowed with the best hCA IX inhibitory efficacy and selectivity, was evaluated for antiproliferative activity against a small panel of different cancer cell lines, SK-MEL-173, MDA-MB-231, A549, HCT-116, and HeLa, and it demonstrated one-digit IC50 values range from 2.93 μM (MDA-MB-231) to 5.86 μM (A549). Furthermore, compound APBS-5m was evaluated for its influence on hypoxia-inducible factor (HIF-1α) production, apoptosis induction, and colony formation in MDA-MB-231 cancer cells. The in vivo efficacy of APBS-5m as an antitumor agent was additionally investigated in an animal model of Solid Ehrlich Carcinoma (SEC). In order to offer perceptions into the conveyed hCA IX inhibitory efficacy and selectivity in silico, a molecular docking investigation was also carried out.

Structural Determinants of Vibrio cholerae FeoB Nucleotide Promiscuity.

Ferrous iron (Fe2+) is required for the growth and virulence of many pathogenic bacteria, including Vibrio cholerae (Vc), the causative agent of the disease cholera. For this bacterium, Feo is the primary system that transports Fe2+ into the cytosol. FeoB, the main component of this system, is regulated by a soluble cytosolic domain termed NFeoB. Recent reanalysis has shown that NFeoBs can be classified as either GTP-specific or NTP-promiscuous, but the structural and mechanistic bases for these differences were not known. To explore this intriguing property of FeoB, we solved the X-ray crystal structures of VcNFeoB in both the apo and GDP-bound forms. Surprisingly, this promiscuous NTPase displayed a canonical NFeoB G-protein fold like GTP-specific NFeoBs. Using structural bioinformatics, we hypothesized that residues surrounding the nucleobase could be important for both nucleotide affinity and specificity. We then solved the X-ray crystal structures of N150T VcNFeoB in the apo and GDP-bound forms to reveal H-bonding differences surround the guanine nucleobase. Interestingly, isothermal titration calorimetry revealed similar binding thermodynamics of the WT and N150T proteins to guanine nucleotides, while the behavior in the presence of adenine nucleotides was dramatically different. AlphaFold models of VcNFeoB in the presence of ADP and ATP showed important conformational changes that contribute to nucleotide specificity among FeoBs. Combined, these results provide a structural framework for understanding FeoB nucleotide promiscuity, which could be an adaptive measure utilized by pathogens to ensure adequate levels of intracellular iron across multiple metabolic landscapes.

Synthesis, X-ray crystal structure, Hirshfeld combined with DFT and anticancer efficacy of (Z)–N-methyl-C-aryl aldonitrones

(Z)–N-methyl-C-aryl aldonitrones –O+N(Me)=C(H)R (1R = 2-naphthyl, 2R = 2‑hydroxy-1-naphthyl, 3R = 1-naphthyl, 4R = 2-hydroxyphenyl) were synthesised and fully characterised by several methods. The supramolecular structure aspects of 1 and 2 were analysed utilizing Hirshfeld topology analysis. In 1, the most common contacts are the H…H (45.1 %), C…H (39.1 %) and O…H (13.0 %) interactions while the corresponding values in case of 2 are 47.7, 24.0 and 18.8 %, respectively. The C…H and O…H interactions have the characteristic features of short important contacts in 1 while only the O…H interaction is the most significant in case of 2. Based on DFT calculations, the HOMO, LUMO, natural charges, polarity as well as chemical reactivity descriptors were predicted and compared for both compounds. On the other hand, compounds 1–4 reduced the growth of MCF-7 and T47D. Compound 3, which has the lowest IC50 values against the MCF-7 and T47D cell lines, is thought to be the most promising applicant as an anticancer drug.

New polynuclear compounds based on N-methyliminodipropionic acid: Solution studies, synthesis and X-ray crystal structures

Six new polynuclear coordination compounds based on 3d transition metal ions (Cu(II), Ni(II)) and Zn(II) with the flexible dicarboxylate compound N-methyliminodipropionic acid (H2midp) were prepared and characterized by IR spectroscopy, elemental analysis and single-crystal X-ray diffraction. Four of these compounds are 1D coordination polymers, namely [Cu(midp)(H2O)] (1), [Cu3(midp)2(H2O)4](NO3)2·6H2O (2) [Cu3(midp)2(H2O)4](CF3SO3)2·4H2O (3) and [NaZn(Hmidp)2](CF3SO3) (6). The structural analysis revealed that the chain structure of 1 is composed of [Cu(midp)(H2O)] units connected by the free carboxylato oxygen atom of neighbor units, in an alternate fashion. In 2 and 3, on the other hand, there are two [Cu(midp)H2O] units, connected by a central Cu(II) ion coordinating again to the free oxygen atom of the carboxylato groups. The Zn(II) compound is heteronuclear and the complex adopts a 1D cationic polymeric structure with zinc and sodium ions connected by two Hmidp– anions. The two other compounds are dinuclear, [Cu2(Hmidp)2(μ-H2O)2(H2O)2](CF3SO3)2·6H2O (4) and ([Ni2(midp)2(H2O)4] (5). Additionally, a Co(II) and a Cu(II) coordination compound were obtained with the same ligand and characterized by IR spectroscopy, thermal analysis and elemental analysis including metal quantification. For the copper compound the formula [Cu(Hmidp)](ClO4)·3H2O (7) is proposed while for the Co(II) compound (8) the proposed formula is [Co(midp)(H2O)2]. Solution studies of the ligand–M(II) systems (M(II) = Mn, Fe, Co, Ni, Cu, Zn, Cd and Pb) were also carried out in order to help the selection of the best synthetic conditions and also to complement the structural knowledge in the exploration of the potential formation of coordination polymers in these systems.

SilE-R and SilE-S-DABB Proteins Catalying Enantiospecific Hydrolysis of Organosilyl Ethers.

Silyl ethers fulfil a fundamental role in synthetic organic chemistry as protecting groups and their selective cleavage is an important factor in their application. We present here for the first time two enzymes, SilE-R and SilE-S, which are able to hydrolyse silyl ethers. They belong to the stress-response dimeric A/B barrel domain (DABB) family and are able to cleave the Si-O bond with opposite enantiopreference. Silyl ethers containing aromatic, cyclic or aliphatic alcohols and, depending on the alcohol moiety, silyl functions as large as TBDMS are accepted. The X-ray crystal structure of SilE-R, determined to a resolution of 1.98 Å, in combination with mutational studies, revealed an active site featuring two histidine residues, H8 and H79, which likely act synergistically as nucleophile and Brønsted base in the hydrolytic mechanism, which has not previously been described for enzymes. Although the natural function of SilE-R and SilE-S is unknown, we propose that these 'silyl etherases' may have significant potential for synthetic applications.

Structural Studies of a Complex of a CAG/CTG Repeat Sequence-Specific Binding Molecule and A-A-Mismatch-Containing DNA.

Triplet repeat diseases are caused by the abnormal elongation of repeated sequences comprising three bases. In particular, the elongation of CAG/CTG repeat sequences is thought to result in conditions such as Huntington's disease and myotonic dystrophy type 1. Although the causes of these diseases are known, fundamental treatments have not been established, and specific drugs are expected to be developed. Pyrrole imidazole polyamide (PIP) is a class of molecules that binds to the minor groove of the DNA duplex in a sequence-specific manner; because of this property, it shows promise in drug discovery applications. Earlier, it was reported that PIP designed to bind CAG/CTG repeat sequences suppresses the genes that cause triplet repeat diseases. In this study, we performed an X-ray crystal structure analysis of a complex of double-stranded DNA containing A-A mismatched base pairs and a cyclic-PIP that binds specifically to CAG/CTG sequences. Furthermore, the validity and characteristics of this structure were analyzed using in silico molecular modeling, ab initio energy calculations, gel electrophoresis, and surface plasmon resonance. With our direct observation using atomic force microscopy and DNA origami, we revealed that the PIP caused structural changes in the DNA strands carrying the expanded CAG/CTG repeat. Overall, our study provides new insight into PIP from a structural perspective.

Myxococcus xanthus encapsulin cargo protein EncD is a flavin-binding protein with ferric reductase activity

Encapsulins are protein nanocompartments that regulate cellular metabolism in several bacteria and archaea. Myxococcus xanthus encapsulins protect the bacterial cells against oxidative stress by sequestering cytosolic iron. These encapsulins are formed by the shell protein EncA and three cargo proteins: EncB, EncC, and EncD. EncB and EncC form rotationally symmetric decamers with ferroxidase centers (FOCs) that oxidize Fe+2 to Fe+3 for iron storage in mineral form. However, the structure and function of the third cargo protein, EncD, have yet to be determined. Here, we report the x-ray crystal structure of EncD in complex with flavin mononucleotide. EncD forms an α-helical hairpin arranged as an antiparallel dimer, but unlike other flavin-binding proteins, it has no β-sheet, showing that EncD and its homologs represent a unique class of bacterial flavin-binding proteins. The cryo-EM structure of EncA-EncD encapsulins confirms that EncD binds to the interior of the EncA shell via its C-terminal targeting peptide. With only 100 amino acids, the EncD α-helical dimer forms the smallest flavin-binding domain observed to date. Unlike EncB and EncC, EncD lacks a FOC, and our biochemical results show that EncD instead is a NAD(P)H-dependent ferric reductase, indicating that the M. xanthus encapsulins act as an integrated system for iron homeostasis. Overall, this work contributes to our understanding of bacterial metabolism and could lead to the development of technologies for iron biomineralization and the production of iron-containing materials for the treatment of various diseases associated with oxidative stress.

Library Screening, In Vivo Confirmation, and Structural and Bioinformatic Analysis of Pentapeptide Sequences as Substrates for Protein Farnesyltransferase.

Protein farnesylation is a post-translational modification where a 15-carbon farnesyl isoprenoid is appended to the C-terminal end of a protein by farnesyltransferase (FTase). This process often causes proteins to associate with the membrane and participate in signal transduction pathways. The most common substrates of FTase are proteins that have C-terminal tetrapeptide CaaX box sequences where the cysteine is the site of modification. However, recent work has shown that five amino acid sequences can also be recognized, including the pentapeptides CMIIM and CSLMQ. In this work, peptide libraries were initially used to systematically vary the residues in those two parental sequences using an assay based on Matrix Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). In addition, 192 pentapeptide sequences from the human proteome were screened using that assay to discover additional extended CaaaX-box motifs. Selected hits from that screening effort were rescreened using an in vivo yeast reporter protein assay. The X-ray crystal structure of CMIIM bound to FTase was also solved, showing that the C-terminal tripeptide of that sequence interacted with the enzyme in a similar manner as the C-terminal tripeptide of CVVM, suggesting that the tripeptide comprises a common structural element for substrate recognition in both tetrapeptide and pentapeptide sequences. Molecular dynamics simulation of CMIIM bound to FTase further shed light on the molecular interactions involved, showing that a putative catalytically competent Zn(II)-thiolate species was able to form. Bioinformatic predictions of tetrapeptide (CaaX-box) reactivity correlated well with the reactivity of pentapeptides obtained from in vivo analysis, reinforcing the importance of the C-terminal tripeptide motif. This analysis provides a structural framework for understanding the reactivity of extended CaaaX-box motifs and a method that may be useful for predicting the reactivity of additional FTase substrates bearing CaaaX-box sequences.

Structural Basis for Parallel G-Quadruplex Recognition by an Ankyrin Protein.

G-Quadruplex (G4) structures formed by guanine-rich DNA and RNA sequences are implicated in various biological processes. Understanding the mechanisms by which proteins recognize G4 structures is crucial for elucidating their functional roles. Here we present the X-ray crystal structure of an ankyrin protein bound to a parallel G4 structure. Our findings reveal a new specific recognition mode in which a bundle of α-helices and loops of the ankyrin form a flat surface to stack on the G-tetrad core. The protein employs a combination of hydrogen bonds and hydrophobic contacts to interact with the G4, and electrostatic interaction is used to enhance the binding affinity. This binding mechanism provides valuable insights into understanding G4 recognition by proteins.

Stereoisomers of oxime ethers of 1,4-naphthoquinone: Synthesis, characterization, X-ray crystal structures, and DFT studies

In the present work, we use the C-3 substituted 2-hydroxy-1,4-naphthoquinones viz. 2-hydroxynaphthalene-1,4-dione (1), 2-hydroxy-3-methylnaphthalene-1,4-dione (2), and 2-chloro-3-hydroxynaphthalene-1,4-dione (3) as starting materials and obtained naphthoquinoneoxime ethers viz. 3-hydroxy-4-(methoxyimino)naphthalen-1(4H)-one (4), 3-hydroxy-4-(methoxyimino)-2-methylnaphthalen-1(4H)-one (5) and 2-chloro-3-hydroxy-4-(methoxyimino)naphthalen-1(4H)-one (6) via a facile and efficient synthesis involving condensation with methoxyamine hydrochloride. X-ray structure showed that 4 belongs to the orthorhombic (P212121) space group, whereas 5 and 6 (P21/c) crystalize in the monoclinic crystal system. The isomer ratios derived from NMR experiments elucidating stereoisomerism in compounds comprised of carbon-nitrogen double bonds have been analyzed; the naphthoquinone oxime ethers 4, 5, and 6 were also characterized employing the ωB97x-D/6–311++G (d, p) level of density functional theory. Theoretical studies reveal different conformational isomers with the ‘amphi’ and ‘syn’ isomers as low-lying structures along their energy hierarchy in accordance with the X-ray crystallography data. The spectral characterization of vibrational frequencies and 1H /13C NMR chemical shifts in unison with experiments and theory has been presented.

Bridging the maytansine and vinca sites: Cryptophycins target β-tubulin’s T5-loop

Cryptophycins are microtubule-targeting agents (MTAs) that belong to the most potent antimitotic compounds known to date; however, their exact molecular mechanism of action remains unclear. Here, we present the 2.2 Å resolution X-ray crystal structure of a potent cryptophycin derivative bound to the αβ-tubulin heterodimer. The structure addresses conformational issues present in a previous 3.3 Å resolution cryo-electron microscopy structure of cryptophycin-52 bound to the maytansine site of β-tubulin. It further provides atomic details on interactions of cryptophycins, which had not been described previously, including ones that are in line with structure-activity relationship (SAR) studies. Interestingly, we discovered a second cryptophycin-binding site that involves the T5-loop of β-tubulin, a critical secondary structure element involved in the exchange of the guanosine nucleotide and in the formation of longitudinal tubulin contacts in microtubules. Cryptophycins are the first natural ligands found to bind to this new "βT5-loop site” that bridges the maytansine and vinca sites. Our results offer unique avenues to rationally design novel MTAs with the capacity to modulate T5-loop dynamics and to simultaneously engage multiple β-tubulin binding sites.