X-ray Crystallography Research Articles

Calix[2]azolium[2]benzimidazolone hosts for selective binding of neutral substrates in water

The separation and purification of chemical raw materials, particularly neutral compounds with similar physical and chemical properties, represents an ongoing challenge. In this study, we introduce a class of water-soluble macrocycle compound, calix[2]azolium[2]benzimidazolone (H), comprising two azolium and two benzimidazolone subunits. The heterocycle subunits form a hydrophobic binding pocket that enables H1 to encapsulate a series of neutral guests in water with 1:1 or 2:1 stoichiometry, including aldehydes, ketones, and nitrile compounds. The host-guest complexation in the solid state was further confirmed through X-ray crystallography. Remarkably, H1 was shown to be a nonporous adaptive crystal material to separate valeraldehyde from the mixture of valeraldehyde/2-methylbutanal/pentanol with high selectivity and recyclability in the solid states. This work not only demonstrates that azolium-based macrocycles are promising candidates for the encapsulation of organic molecules but also shows the potential application in separation science.

Cinquefoil Knot Possessing Dynamic and Tunable Metal Coordination.

While the majority of knots are made from the metal-template approach, the use of entangled, constrained knotted loops to modulate the coordination of the metal ions remains inadequately elucidated. Here, we report on the coordination chemistry of a 140-atom-long cinquefoil knotted strand comprising five tridentate and five bidentate chelating vacancies. The knotted loop is prepared through the self-assembly of asymmetric "3 + 2" dentate ligands with copper(II) ions that favor five-coordination geometry. The formation of the copper(II) pentameric helicate is confirmed by X-ray crystallography, while the corresponding copper(II) knot is characterized by XPS and LR-/HR ESI-MS. Upon removal of the original template, the knotted ligand facilitates zinc(II) ions, which typically form four- or six-coordination geometries, resulting in the formation of an otherwise inaccessible zinc(II) metallic knot with coordinatively unsaturated metal centers. The coordination numbers and geometries of the zinc(II) cations are undoubtedly determined by X-ray crystallography. Despite the kinetically labile nature and high reversibility of the zinc(II) complex preventing the detection of 5-to-6 coordination equilibrium in solution, the effects on metal-ion coordination induced by knotting hold promise for fine-tuning the coordination of metal complexes.

Vibrational properties of heme-nitrosoalkane complexes in comparison with those of their HNO analogs, and reactivity studies towards nitric oxide and Lewis acids.

C-Nitroso compounds (RNO, R = alkyl and aryl) are byproducts of drug metabolism and bind to heme proteins, and their heme-RNO adducts are isoelectronic to ferrous nitroxyl (NO-/HNO) complexes. Importantly, heme-HNO compounds are key intermediates in the reduction of NO to N2O and nitrite to ammonium in the nitrogen cycle. Ferrous heme-RNO complexes act as stable analogs of these species, potentially allowing for the investigation of the vibrational and electronic properties of unstable heme-HNO intermediates. In this paper, a series of six-coordinate ferrous heme-RNO complexes (where R = iPr and Ph) were prepared using the TPP2- and 3,5-Me-BAFP2- co-ligands, and tetrahydrofuran, pyridine, and 1-methylimidazole as the axial ligands (bound trans to RNO). These complexes were characterized using different spectroscopic methods and X-ray crystallography. The complex [Fe(TPP)(THF)(iPrNO)] was further utilized for nuclear resonance vibrational spectroscopy (NRVS), allowing for the detailed assignment of the Fe-N(R)O vibrations of a heme-RNO complex for the first time. The vibrational properties of these species were then correlated with those of their HNO analogs, using DFT calculations. Our studies support previous findings that RNO ligands in ferrous heme complexes do not elicit a significant trans effect. In addition, the complexes are air-stable, and do not show any reactivity of their RNO ligands towards NO. So although ferrous heme-RNO complexes are suitable structural and electronic models for their HNO analogs, they are unsuitable to model the reactivity of heme-HNO complexes. We further investigated the reaction of our heme-RNO complexes with different Lewis acids. Here, [Fe(TPP)(THF)(iPrNO)] was found to be unreactive towards Lewis acids. In contrast, [Fe(3,5-Me-BAFP)(iPrNO)2] is reactive towards all of the Lewis acids investigated here, but in most cases the iron center is simply oxidized, resulting in the loss of the iPrNO ligand. In the case of the Lewis acid B2(pin)2, the reduced product [Fe(3,5-Me-BAFP)(iPrNH2)(iPrNO)] was identified by X-ray crystallography.

PhAI: A deep-learning approach to solve the crystallographic phase problem.

X-ray crystallography provides a distinctive view on the three-dimensional structure of crystals. To reconstruct the electron density map, the complex structure factors [Formula: see text] of a sufficiently large number of diffracted reflections must be known. In a conventional experiment, only the amplitudes [Formula: see text] are obtained, and the phases ϕ are lost. This is the crystallographic phase problem. In this work, we show that a neural network, trained on millions of artificial structure data, can solve the phase problem at a resolution of only 2 angstroms, using only 10 to 20% of the data needed for direct methods. The network works in common space groups and for modest unit-cell dimensions and suggests that neural networks could be used to solve the phase problem in the general case for weakly scattering crystals.

A new isocoumarin derivative from endophytic fungus Pezicula neosporulosa VDB39 from Vaccinium dunalianum

Four isocoumarin derivatives (1–4) and five phenols (5–9) were obtained from the endophytic fungus Pezicula neosporulosa VDB39, which was isolated from the branches of Vaccinium dunalianum Wight (Ericaceae). Compound 1 is a new derivative of isocoumarin. The structures were elucidated by spectroscopic methods. Single X-ray crystallography confirmed the absolute configuration of compound 1. Additionally, the antiphytopathogenic fungi activity of isocoumarin derivatives (1–4) was evaluated.

Binary and Halide-free Catalyst Systems Based on Al/Ga/In Aminopyridylbisphenolate Complexes for the Cycloaddition of Epoxides and CO2.

Group 13 complexes bearing an aminopyridylbisphenol ligand have been prepared [ML-X; L = ligand, M = Al (X = Cl and Br), Ga (X = Cl, Br, and I), or In (X = Cl)]. The structures of the complexes containing the chloride ligand (ML-Cl; M = Al, Ga, and In) have been directly compared through an X-ray crystallography study, with differences in the monomeric or dimeric nature of their structures observed. All of the complexes obtained have been studied as potential catalysts for the synthesis of cyclic carbonates from epoxides and CO2. It has been found that the indium complex, as part of a traditional binary catalyst system (catalyst + tetra-butylammonium halide cocatalyst), displays the highest catalytic activity and is active under rather mild reaction conditions (balloon pressure of CO2). Meanwhile, it has been found that the GaL-I complex is a competent single-component catalyst (no need for addition of a cocatalyst) at more elevated reaction temperatures and pressures. A full substrate scope has been performed with both developed catalyst systems to demonstrate their applicability. In addition to the experimental results, a density functional theory study was performed on both catalyst systems. These results explain both why the indium catalyst is the most active under binary catalyst system conditions and how the gallium catalyst with an iodide (GaL-I) is able to act as a single-component catalyst in contrast to the indium-based complex.

A transferable classical force field to describe glyme based lithium solvate ionic liquids.

A non-polarizable force field for lithium (Li+) and bis(trifluoromethanesulfonyl)imide (TFSI-) ions solvated in diglyme at around 0.2 mol fraction salt concentration was developed based on abinitio molecular dynamics (AIMD) simulations and a modified polymer consistent force field model. A force-torque matching based scheme, in conjunction with a genetic algorithm, was used to determine the Lennard-Jones (LJ) parameters of the ion-ion and ion-solvent interactions. This force field includes a partial charge scaling factor and a scaling factor for the 1-4 interactions. The resulting force field successfully reproduces the radial distribution function of the AIMD simulations and shows better agreement compared to the unmodified force field. The new force field was then used to simulate salt solutions with glymes of increasing chain lengths and different salt concentrations. The comparison of the MD simulations, using the new force field, with experimental data at different salt concentrations and AIMD simulations on equimolar concentrations of the triglyme system demonstrates the transferability of the force field parameters to longer glymes and higher salt concentrations. Furthermore, the force field appears to reproduce the features of the experimental x-ray structure factors, suggesting accuracy beyond the first solvation shell, for equimolar salt solutions using both triglyme and tetraglyme as the solvent. Overall, the new force field was found to accurately reproduce the molecular descriptions of LiTFSI-glyme systems not only at various salt concentrations but also with glymes of different chain lengths. Thus, the new force field provides a useful and accurate tool to perform in silico studies of this family of systems at the atomistic level.

S. aureus Eap is a polyvalent inhibitor of neutrophil serine proteases

Staphylococcus aureus expresses three high-affinity neutrophil serine protease (NSP) inhibitors known as the extracellular adherence protein domain (EAPs) proteins. Whereas EapH1 and EapH2 are comprised of a single EAP domain, the modular extracellular adherence protein (Eap) from S. aureus strain Mu50 consists of four EAP domains. We recently reported that EapH2 can simultaneously bind and inhibit cathepsin-G (CG) and neutrophil elastase (NE), which are the two most abundant NSPs. This unusual property of EapH2 arises from independent CG and NE-binding sites that lie on opposing faces of its EAP domain. Here we used X-ray crystallography and enzyme assays to show that all four individual domains of Eap (i.e. Eap1, Eap2, Eap3, and Eap4) exhibit an EapH2-like ability to form ternary complexes with CG and NE that inhibit both enzymes simultaneously. We found that Eap1, Eap2, and Eap3 have similar functional profiles insofar as NSP inhibition is concerned, but that Eap4 displays an unexpected ability to inhibit two NE enzymes simultaneously. Using X-ray crystallography, we determined that this second NE-binding site in Eap4 arises through the same region of its EAP domain that also comprises its CG-binding site. Interestingly, small angle X-ray scattering data showed that stable tail-to-tail dimers of the NE/Eap4/NE ternary complex exist in solution. This arrangement is compatible with NSP-binding at all available sites in a two-domain fragment of Eap. Together, our work implies that Eap is a polyvalent inhibitor of NSPs. It also raises the possibility that higher-order structures of NSP-bound Eap may have unique functional properties.

Syntheses, structures and magnetisms of dimethyl phosphate-bridged dinuclear lanthanide complexes with pentadentate macrocyclic ligand

A series of air-stable dinuclear complexes, [HNEt3]2[Ln2(L)2((CH3O)2PO2)4](BPh4)4 (L = 2,14-dimethyl-3,6,10,13,19-pentaazabicyclo[13.3.1]nonadeca1(19), 2,13,15,17-pentene, Ln = Dy, 1-Dy; Tb, 2-Tb; Gd, 3-Gd), has been synthesized and characterized using single-crystal X-ray crystallography and magnetic measurements. The crystal structures disclose that two dimethyl phosphate anions act as bridging ligands, linking two Ln(III) ions. Each Ln(III) ion is eight-coordinated by five nitrogen atoms from a pentadentate Schiff based ligand L and three oxygen atoms from three dimethyl phosphates, forming a triangular dodecahedral coordination geometry. Direct-current magnetic susceptibility measurements indicate an extremely weak antiferromagnetic exchange between Gd(III) ions in 3-Gd. Complex 1-Dy exhibits slow magnetic relaxation with an effective energy barrier (Ueff) of 13 K under an applied field of 1000 Oe, whereas 2-Tb does not exhibit single-molecule magnet behavior. This work presents a novel strategy for constructing polynuclear single-molecular magnets by using a pentadetate macrocycle as magnetic building blocks integrated with replaceable axial ligands.

A class of geranylquinol-derived polycyclic meroterpenoids from Arnebia euchroma against heart failure by reducing excessive autophagy and apoptosis in cardiomyocytes

Ten new B-ring aromatized 6/6/6-tricyclic dearomatized benzocogeijerene-based meroterpenoids with unusual methyl 1,2-shift or demethylation (2–9b), and two new geranylquinol derivatives (1 and 10), together with two known compounds (11 and 12), were isolated from the roots of Arnebia euchroma. Their structures were elucidated by extensive spectroscopic methods, X-ray diffraction crystallography, and ECD calculations. The plausible biosynthetic pathways including the unusual methyl 1,2-shfit and demethylation for B-ring aromatized 6/6/6-tricyclic meroterpenoids were discussed. Compounds 1, 2, 5, 6, 11, and 12 showed significant cardioprotective activities comparable to diltiazem against isoprenaline (ISO)-induced H9C2 cell damage in vitro. Compound 11 probably exerted heart-protective effect on ISO-induced H9C2 cells by modulating the PI3K-AKT-mTOR pathway, reducing excessive autophagy, and decreasing myocardial apoptosis.

XFEL Beamline Optical Instrumentation for Ultrafast Science.

Free electron lasers operating in the soft and hard X-ray regime provide capabilities for ultrafast science in many areas, including X-ray spectroscopy, diffractive imaging, solution and material scattering, and X-ray crystallography. Ultrafast time-resolved applications in the picosecond, femtosecond, and attosecond regimes are often possible using single-shot experimental configurations. Aside from X-ray pump and X-ray probe measurements, all other types of ultrafast experiments require the synchronized operation of pulsed laser excitation for resonant or nonresonant pumping. This Perspective focuses on the opportunities for the optical control of structural dynamics by applying techniques from nonlinear spectroscopy to ultrafast X-ray experiments. This typically requires the synthesis of two or more optical pulses with full control of pulse and interpulse parameters. To this end, full characterization of the femtosecond optical pulses is also highly desirable. It has recently been shown that two-color and two-pulse femtosecond excitation of fluorescent protein crystals allowed a Tannor-Rice coherent control experiment, performed under characterized conditions. Pulse shaping and the ability to synthesize multicolor and multipulse conditions are highly desirable and would enable XFEL facilities to offer capabilities for structural dynamics. This Perspective will give a summary of examples of the types of experiments that could be achieved, and it will additionally summarize the laser, pulse shaping, and characterization that would be recommended as standard equipment for time-resolved XFEL beamlines, with an emphasis on ultrafast time-resolved serial femtosecond crystallography.

Structurally intriguing rearranged bicyclogermacrene-type sesquiterpenoid from Aphania oligophylla

An investigation on the aqueous ethanol extract of the powdered twigs of Aphania oligophylla has afforded a skeletal new sesquiterpenoid aphanoid A (1) and one new aromadendrane-type sesquiterpenoid aphanoid B (2), as well as six known sesquiterpenoids (3–8). Their structures including the absolute configurations were characterized based on spectroscopic data analysis and X-ray crystallography. Compound 1 featuring an unprecedented tricyclo[6.3.1.03,5]dodecane scaffold, is likely rearranged from the bicyclogermacrene-type sesquiterpenoid. Among those compounds, 2 at 10 μL showed moderate antimalarial effect.

A Structure-based Data Set of Protein-peptide Affinities and its Nonredundant Benchmark: Potential Applications in Computational Peptidology.

Peptides play crucial roles in diverse cellular functions and participate in many biological processes by interacting with a variety of proteins, which have also been exploited as a promising class of therapeutic agents to target druggable proteins over the past decades. Understanding the intrinsic association between the structure and affinity of protein-peptide interactions (PpIs) should be considerably valuable for the computational peptidology area, such as guiding protein-peptide docking calculations, developing protein-peptide affinity scoring functions, and designing peptide ligands for specific protein receptors. We attempted to create a data source for relating PpI structure to affinity. By exhaustively surveying the whole protein data bank (PDB) database as well as the ontologically enriched literature information, we manually curated a structure- based data set of protein-peptide affinities, PpI[S/A]DS, which assembled over 350 PpI complex samples with both the experimentally measured structure and affinity data. The data set was further reduced to a nonredundant benchmark consisting of 102 culled samples, PpI[S/A]BM, which only selected those of structurally reliable, functionally diverse and evolutionarily nonhomologous. The collected structures were resolved at a high-resolution level with either Xray crystallography or solution NMR, while the deposited affinities were characterized by dissociation constant, i.e. Kd value, which is a direct biophysical measure of the intermolecular interaction strength between protein and peptide, ranging from subnanomolar to millimolar levels. The PpI samples in the set/benchmark were arbitrarily classified into α-helix, partial α-helix, β-sheet formed through binding, β-strand formed through selffolding, mixed, and other irregular ones, totally resulting in six classes according to the secondary structure of their peptide ligands. In addition, we also categorized these PpIs in terms of their biological function and binding behavior. The PpI[S/A]DS set and PpI[S/A]BM benchmark can be considered a valuable data source in the computational peptidology community, aiming to relate the affinity to structure for PpIs.

Co(III)–Co(II)–Co(III) edge-Sharing trinuclear complexes having the doubly methoxido-Bridged core bridged by acetato ligand

Two trinuclear cobalt complexes with the edge-sharing linear-type framework having benzylbis(2-pyridylmethyl)amine (bbpma), [{CoIII(bbpma)(μ-O2CCH3)(μ-OCH3)2}2CoII](X)2 (X=ClO4; [1](ClO4)2, X =PF6; [1](PF6)2), and one corresponding complex having ethylbis(2-pyridylmethyl)amine (ebpma), [{CoIII(ebpma)(μ-O2CCH3)(μ-OCH3)2}2CoII](PF6)2 ([2](PF6)2), were synthesized and the crystallographic and electronic structures were investigated. X-ray crystallography and magnetic measurements suggested that [1](PF6)2 and [2](PF6)2 were in the mixed-valent state and the mixed-spin state of Co(III)–Co(II)–Co(III) (LS-HS-LS), in which the electron spins were much localized on the central Co(II).

Synthetic V(V)-peroxido-zwitterionic species catalyze benzene oxidation under mild reaction conditions

A series of dinuclear complexes were synthesized, involving vanadium with N-methylglycine (sarcosine)/N,N’-dimethylglycine in aqueous media and H2O2, capable of exerting catalytic activity. Specifically, the ternary V(V) tetraperoxido dinuclear species (NH4)2[V2O2(O2)4(CH3NH2CH2COO)] (symmetric conformer) (1), (NH4)2[V2O2(O2)4(CH3NH2CH2COO)] (asymmetric conformer) (2), K2(Η2Ο)[V2O2(O2)4(CH3NH2CH2COO)] . H2O (3) (asymmetric conformer), and K2(Η2Ο)2[V2O2(O2)4{(CH3)2NHCH2COO)}] (4) (asymmetric conformer) were synthetically isolated in crystalline form. Compounds 1 and 2 are the same, whilst with profound conformational differences exemplified through pH-specific chemistries. The new materials 1-4 were characterized by elemental analysis, FT-IR, Raman, NMR, and UV-Visible spectroscopy, cyclic voltammetry, thermogravimetric analysis (TGA-DTG), and X-ray crystallography. Further support of the spectroscopic and structural profile was achieved through Bond Valence Sum (BVS) and Hirshfeld molecular mapping calculations. In all of the studied compounds, pH appears to be a crucial factor in the synthesis and isolation. The physicochemical characterization of the hybrid materials justified further use of compound 3 as a potential hydroxylation catalyst of benzene under a variable set of mild reaction conditions. The products of the catalytic reaction systems investigated were identified and quantified by gas chromatography–mass spectrometry (GC-MS) and gas chromatography–flame ionization detection (GC-FID), respectively. The results a) exemplify the involvement of the hybrid dinuclear vanadium compounds in the pursued benzene transformations, and b) distinctly demonstrate the structural and chemical characteristics justifying the emergence of catalytic action of vanadium under mild conditions (40 °C) in reactions toward organic substrates (e.g. benzene) as the basis for the pursuit of selective industrial applications, affording readily available useful compounds.

Experimental and theoretical studies of pyrazole-4-carbaldehyde derivatives by X-ray crystallography, DFT, molecular docking, and molecular dynamics simulation studies

Nitrogen-containing heterocycles play a crucial role in drug design and discovery. Pyrazole derivatives have garnered attention due to their unique and intriguing features. This study investigates the structure and properties of two pyrazole-4-carbaldehyde derivatives (3 and 4). We report the single crystal structure of one of the intermediate compounds, 1-(1-(4-bromophenyl)ethylidene)-2-(2-chlorophenyl)hydrazine (2), and a final compound, 1-(2-chlorophenyl)-3-phenyl-1H-pyrazole-4-carbaldehyde (3). We analysed the non-covalent interactions within the crystal using Hirshfeld surface analysis and 2D fingerprint plots. We also used density functional theory (DFT) at the B3LYP/6–311G(d,p) level to optimise the structures and understand electronic properties, transitions and vibrational frequencies. To predict the anti-inflammatory potentials and selectivity of 3 and 4, molecular docking and molecular dynamics (MD) simulation studies against COX1 (PDB ID: 1EQG) and COX2 (PDB ID: 1CX2) receptors were conducted. Overall, this study sheds light on the structural, chemical, and biochemical features of these two pyrazole-4-carbaldehyde derivatives.

Metal fluorides—multi-functional tools for the study of phosphoryl transfer enzymes, a practical guide

Enzymes facilitating the transfer of phosphate groups constitute the most extensive protein families across all kingdoms of life. They make up approximately 10% of the proteins found in the human genome. Understanding the mechanisms by which enzymes catalyze these reactions is essential in characterizing the processes they regulate. Metal fluorides can be used as multifunctional tools to study these enzymes. These ionic species bear the same charge as phosphate and the transferring phosphoryl group and, in addition, allow the enzyme to be trapped in catalytically important states with spectroscopically sensitive atoms interacting directly with active site residues. The ionic nature of these phosphate surrogates also allows their removal and replacement with other analogs. Here, we describe the best practices to obtain these complexes, their use in NMR, X-ray crystallography, cryo-EM, and SAXS and describe a new metal fluoride, scandium tetrafluoride, which has significant anomalous signal using soft X-rays.

Exploring the Ligand Binding and Conformational Dynamics of the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ.

The adenosine triphosphate (ATP)-binding cassette (ABC) importer GlnPQ from Lactococcus lactis has two sequential covalently linked substrate-binding domains (SBDs), which capture the substrates and deliver them to the translocon. The two SBDs differ in their ligand specificities, binding affinities and the distance to the transmembrane domain; interestingly, both SBDs can bind their ligands simultaneously without affecting each other. In this work, we studied the binding of ligands to both SBDs using X-ray crystallography and molecular dynamics simulations. We report three high-resolution structures of SBD1, namely, the wild-type SBD1 with bound asparagine or arginine, and E184D SBD1 with glutamine bound. Molecular dynamics (MD) simulations provide a detailed insight into the dynamics associated with open-closed transitions of the SBDs.

Pd(II), Pt(II), and novel Hg(II) metal complexes of N-(diphenylphosphinothioyl)-2-(4-methylpyridyl) amine chelating ligand: Synthesis, characterization, X-ray structures and catalytic activity of Pd(II) derivative in the Suzuki cross-coupling reaction

The reaction of monooxidized thioyl (4-CH3)C6H3N-2-NH(P(S)Ph2) (1) ligand with MCl2(COD)(M = Pd, Pt) in equimolar ratio resulted in cis-[MCl2{1-κ2S,Npy}] (M = Pd (2), Pt(3)) complexes. Also, The reaction of 1 with HgX2 (X = Cl, I) produced cis-[HgX2{1-κ2S,Npy }] (X = Cl(4), I(5)). Complexes 2–5 have been isolated and characterized by multinuclear NMR (1H, 13C, and 31P) and IR spectroscopy. The molecular structures of 2, 4, and 5 were determined using single X-ray crystallography. 4 and 5 are the first structurally defined instances of this type of κ2S,Npy -bidentate ligand with Hg(II) metal complexes. The new palladium(II) complex 2 as a pre-catalyst in the Suzuki cross-coupling process was also investigated.

Unusual norcucurbitacin glycosides from the roots of Siraitia grosvenorii

Siraitia grosvenorii Swingle is one of the first approved medicine food homology species in China, and it has been used as a natural sweetener in the food industry and as a traditional medicine to relieve cough and reduce phlegm. However, many S. grosvenorii roots are discarded yearly, which results in a great waste of resources. Twelve undescribed norcucurbitacin-type triterpenoid glycosides, siraitiaosides A-L (1-12), and six known analogs (13-18) were isolated from the roots of S. grosvenorii. The structures of isolated norcucurbitacin glycosides were elucidated by comprehensive data analyses, including HRESIMS, UV, IR, NMR, ECD calculations, and X-ray crystallography analysis. Siraitiaosides A-E (1-5) featured an unusual 19,29-norcucurbitacin framework while siraitiaosides F-L (6-12) featured a rare 29-norcucurbitacin framework. Notably, compound 4 displayed moderate anti-acetylcholinesterase (AChE) activity with an IC50 of 21.0 μM, meanwhile, compounds 16 and 18 exhibited pronounced cytotoxic activities against MCF-7, CNE-1, and HeLa cancer cell lines with IC50 values of 2.1-15.2 μM. In silico studies showed that compound 4 bound closely to AChE with a binding energy of -5.04 kcal/mol, and compound 18 could tightly bind to PI3K, AKT1, ERK2, and MMP9 proteins that related to autophagy, apoptosis, migration/invasion, and growth/proliferation. In summary, the roots of Siraitia grosvenorii have potential medicinal values due to the multiple bioactive components.