Computer-aided nanodrug discovery: recent progress and future prospects.

Nanodrugs, which utilise nanomaterials in disease prevention and therapy, have attracted considerable interest since their initial conceptualisation in the 1990s. Substantial efforts have been made to develop nanodrugs for overcoming the limitations of conventional drugs, such as low targeting efficacy, high dosage and toxicity, and potential drug resistance. Despite the significant progress that has been made in nanodrug discovery, the precise design or screening of nanomaterials with desired biomedical functions prior to experimentation remains a significant challenge. This is particularly the case with regard to personalised precision nanodrugs, which require the simultaneous optimisation of the structures, compositions, and surface functionalities of nanodrugs. The development of powerful computer clusters and algorithms has made it possible to overcome this challenge through in silico methods, which provide a comprehensive understanding of the medical functions of nanodrugs in relation to their physicochemical properties. In addition, machine learning techniques have been widely employed in nanodrug research, significantly accelerating the understanding of bio-nano interactions and the development of nanodrugs. This review will present a summary of the computational advances in nanodrug discovery, focusing on the understanding of how the key interfacial interactions, namely, surface adsorption, supramolecular recognition, surface catalysis, and chemical conversion, affect the therapeutic efficacy of nanodrugs. Furthermore, this review will discuss the challenges and opportunities in computer-aided nanodrug discovery, with particular emphasis on the integrated "computation + machine learning + experimentation" strategy that can potentially accelerate the discovery of precision nanodrugs.

Significant Roles of a Particularly Stable Two-Center Two-Electron Lu-Lu σ Bond in Lu2@C86: Electronic Structure of Lu and Radius of Lu2.

There is still dispute over the stability of endohedral metallofullerenes (EMFs) M2C2n, and recently, multiform lutetium-based dimetallofullerenes have been dropped in experiments. The thermodynamic stabilities of Lu2C86 EMFs are revealed by density functional theory (DFT) in conjunction with statistical thermodynamic analyses. Inevitably, besides the experimentally reported Lu2@C2v(63751)-C86, Lu2@Cs(63750)-C86, and Lu2@Cs(63757)-C86, other three metal carbide clusterfullerenes, Lu2C2@D2d(51591)-C84, Lu2C2@C1(51383)-C84, and Lu2C2@Cs(id207430)-C84, rather than Lu2@C86 are first characterized as thermodynamically stable isomers of Lu2C86. Specially, the Cs(id207430)-C84 is a newly non-classical fullerene containing one heptagon, which is stabilized via encaging Lu2C2. Another interesting phenomenon is that the outer fullerene cages of thermodynamically stable Lu2C82-88 molecules are geometrically connected through C2 addition/loss and Stone-Wales (SW) transformation, suggesting a special relationship between thermodynamic stabilities and geometries of Lu2C82-88 EMFs. Furthermore, the electronic configurations of (Lu2)4+@C864- and (Lu2C2)4+@C844- were confirmed. A significantly stable two-center two-electron (2c-2e) Lu-Lu σ single bond is formed in Lu2@C86. By comparing M-M bonds in M2@C2v(63751)-C86 (M = Sc, Y, La, and Lu), two significant factors, the valence atomic orbital (ns) of metal atoms and radius of M2+, are found to determine the stability of the M-M bond in the C2v(63751)-C86. Additionally, the simulated UV-vis-NIR spectra of thermodynamically stable Lu2C86 isomers were simulated, which further disclose their electronic features.

Magnesiation of Aryl Fluorides Catalyzed by a Rhodium-Aluminum Complex.

We report the magnesiation of aryl fluorides catalyzed by an Al-Rh heterobimetallic complex. We show that the complex is highly reactive to cleave the C-F bonds across the polarized Al-Rh bond under mild conditions. The reaction allows the use of an easy-to-handle magnesium powder to generate a range of arylmagnesium reagents from aryl fluorides, which are conventionally inert to such metalation compared with other aryl halides.

Coordination Flexibility of the Rh(PXP) Complex to NH3, CO, and C2H4 (PXP = Diphosphine-Based Pincer Ligand; X = B, Al, and Ga): Theoretical Insight.

The recently synthesized rhodium-aluminum bimetallic complex Rh(PAlP) 1 (PAlP = pincer-type diphosphino-aluminyl ligand Al{[N(C6H4)]2NMe}[CH2P(iPr)2]2) containing a unique Rh-Al direct bond exhibits coordination flexibility because Rh and Al can play the role of coordination site for the substrate. DFT calculations of NH3, CO, and C2H4 adducts with 1 show that the Rh atom is favorable for all these substrate but the Al atom is as favorable as the Rh atom for NH3 and unfavorable for CO and C2H4. NH3 and CO prefer the coordination at the Rh-axial (Ax) site to the Rh-equatorial (Eq) site, but C2H4 prefers coordination at the Rh-Eq site to the Rh-Ax site. Consequently, two CO and C2H4 molecules coordinate with 1 at the Rh-Ax and Rh-Eq sites to afford trigonal bipyramidal complexes Rh(PAlP)(CO)2 and Rh(PAlP)(C2H4)2, which is consistent with the experimental observation of Rh(PAlP)(CO)2. Energy decomposition analysis reveals that an electrostatic term plays an important role for NH3 coordination with the Al atom of 1, because Al has a significantly large positive charge and NH3 has a much negatively charged N atom and exhibits a considerably negative electrostatic potential at the Al position. In B and Ga analogues Rh(PBP) 2 and Rh(PGaP) 3, B and Ga atoms are not good for CO and C2H4 like the Al atom in 1. NH3 adducts with 2 and 3 at the B and Ga sites are less stable than those adducts at the Rh-Ax site unlike the NH3 adduct with 1 at the Al site. This difference in the NH3 adduct between Rh(PAlP) and others (Rh(PBP) and Rh(PGaP)) arises from much less positive charges of B and Ga and a smaller atomic size of B than that of Al. These results indicate that the significantly large electropositive nature and appropriate atomic size of Al are responsible for the characteristic coordination flexibility of Rh(PAlP).

Theoretical Investigations of Lu2C84: Unexpected Impact of Metal Electronic Configuration toward the Metal-Metal σ-Bond in Fullerene.

Recent experimental works recovered multiformity of lutetium-involved dimetallofullerenes. On the basis of density functional theory (DFT) combined with statistical thermodynamic analyses, the relative stabilities of Lu2C84 dimetallofullerene were clarified. Besides the experimentally acknowledged Lu2@D2d(51591)-C84 and Lu2@C2v(51575)-C84, another four isomers metallofullerenes, Lu2@C1(51580)-C84, Lu2C2@Cs(39715)-C82, Lu2C2@C3v(39717)-C82, and Lu2C2@C2v(39718)-C82, are first proposed as thermodynamically stable structures. Interestingly, the geometric relationships among the pristine cages of stable Lu2C84 isomers through Stone-Wales transformation or C2 lose/insertion reveal important clues of the fullerene formation mechanism. The ionic interaction in the stable Lu2C84 isomers is revealed, and their valence states are Lu24+@C844- or (Lu2C2)4+@C824-. In the Lu2@C84 isomers, the results of frontier molecular orbital and natural bond orbital analyses suggest that a Lu-Lu single bond is formed, which is mainly composed of the 6s and 6p orbitals of the Lu atoms. Further analyses of the M2@C84 (M = Sc, Y, La, and Yb) structures disclose the importance of the electron configuration of metal element toward the formation of a single metal-metal bond in C84. Moreover, the covalent interaction between the Lu2 moiety and the C84 cages is disclosed, which is a supplement to the ionic model.

Encapsulation of Monometal Uranium into Fullerenes C2n (2n = 70-74): Important Ionic U4+C2n4- Characters and Covalent U-Cage Bonding Interactions.

By using density functional theory calculations combined with statistical thermodynamic analyses, the stabilization performance of a series of fullerene cages C2n (2n = 70-74) via encapsulating monometal uranium was systematically and thoroughly investigated. Results indicate that fullerene cages D5h(8149)-C70 and D3h(14246)-C74 obeying the isolated pentagon rule and C2(10612)-C72 featured with one pentalene moiety were the most promising candidates to encage uranium. Subsequent Mulliken spin density distribution and frontier molecular orbital analyses suggest that four formal electron transfer occurs from monometal U to above the carbon cages. There also exists a high degree of covalent character between the atom U and fullerenes C2n based on Mayer bond order and quantum theory of atoms in molecule (QTAIM) analyses, indicative of the cooperative stabilization by both ionic and covalent bonding interactions. In addition, investigations on the above-mentioned U@C2n isomers and other favorable candidates (U@Cs(8094)-C70, U@C1(10610)-C72, U@C1(13393)-C74, and U@C1(14049)-C74) reveal that these isomers could be closely linked via simple C2 addition and Stone-Wales transformation. These results will provide a systematic understanding on U-based endohedral metallofullerenes (EMFs) and also might be helpful for further exploration of EMF growth mechanisms.

La-La bonded dimetallofullerenes [La2@C2n]-: species for stabilizing C2n (2n = 92-96) besides La2C2@C2n.

Recent reports pointed out that the formal La2C2n (2n = 92-106) series can exist stably as carbide cluster metallofullerenes (CCMFs) La2C2@C2n-2 with their successful crystallographic characterization. Herein, we suggest that the corresponding dimetallofullerenes (di-EMFs) La2@C2n possessing the lowest potential energies are also plausible candidates because of their favorability in statistical thermodynamics. This can be demonstrated in our present theoretical investigations on La2C94 and previously reported other La2C2n (2n = 92, 96-100) series by density functional theory calculations and statistical mechanics analyses. Nevertheless, it was noted that these thermodynamically favorable La2@C2n isomers turned out to be kinetically unstable radicals due to the presence of one unpaired electron on the carbon cage, making them missing fullerenes and difficult to be captured in their pristine forms, except for the experimentally obtained La2@D5(450)-C100 that has no unpaired electron. Such kinetic instability could be modified by electron reduction (the products were denoted as [La2@C2n]-) or other similar exterior functionalization with ˙CF3 and benzyl radicals, resulting in La-La bonded and paramagnetic species capable of being captured. On the basis of these approaches, carbon cages D3(85)-C92, Cs(120)-C94, D2(186)-C96, and C2(157)-C96 are predicted to be feasibly captured as both pristine CCMF species and electron reduced di-EMF derivatives.

Epoxy and Oxidoannulene Oxidation Mechanisms of Fused-Pentagon Chlorofullerenes: Oxides Linked by a Pirouette-Type Transition State.

Recently, the oxidative functionalization of double-fused-pentagon (DFP)-containing chlorofullerenes #271C50Cl10 and #913C56Cl10 was carried out, resulting in two monoepoxides with the oxygen atom added at the ortho site of pentalene on the DFP moiety. To uncover the reactivity of isolated-pentagon-rule violating fullerenes upon oxidation, two possible formation processes (ozone molecule and oxygen radical served as oxidation reagents) of these two oxides were systematically investigated through density functional theory calculations. For the ozone oxidation, two possible pathways were explored, and the results indicate that the biradical mechanism Pathos-RACDP is kinetically more favorable than Pathos-RABP, where R, A, and P represent reactants, ozonide intermediates, and oxidation products and B, C, and D represent another three oxygen-containing intermediates. The products obtained by ozone oxidation ([6,6]-55-closed epoxides P-C3-C29 for #271C50Cl10 and P-C42-C43 for #913C56Cl10 with oxygen atom added at the shortest and highest HOMO-contribution bonds) are consistent with experimental observations. However, the oxygen radical additions on these two chlorofullerenes favor generation of the [5,6]-66-open oxidoannulene adducts P-C3-C2 and P-C42-C54, respectively. Subsequent analyses of their geometrical features and structural stabilities suggest that these two oxidoannulene adducts are energetically unfavorable and could be converted to more stable epoxides mentioned above by undergoing a pirouette-type transition state. In these two diverse oxidation procedures, the favorable C-C bonds for ozone attacking and C atoms for oxygen-adsorption are rationalized in terms of their bond lengths and HOMO contributions as well as pyramidalization angles.

Photoreactions of Endohedral Metallofullerene with Siliranes: Electronic Properties of Carbosilylated Lu3N@Ih-C80.

Photochemical carbosilylation of Lu3N@Ih-C80 was performed using siliranes (silacyclopropanes) to afford the corresponding [5,6]- and [6,6]-adducts. Electrochemical studies indicated that the redox potentials of the carbosilylated derivatives were shifted cathodically in comparison with those of the [5,6]-pyrrolidino adducts. The electronic effect of the silirane addends on Lu3N@Ih-C80 was verified on the basis of density functional theory calculations.

Stabilization of a Chlorinated (#4348)C66:C2v Cage by Encapsulating Monometal Species: Coordination between Metal and Double Hexagon-Condensed Pentalenes.

Carbon cages in endohedral and exohedral fullerene derivatives are usually different. A recent report suggested that chlorofullerene C66Cl10:Cs and endohedral metallofullerene (EMF) Sc2@C66 shared the same cage (#4348)C66:C2v, while it was denied by the definitive characterization of Sc2@C66, which actually possesses the (#4059)C66:C2v isomer. Here, we show that a (#4348)C66:C2v cage with a double hexagon-condensed pentalene (DHCP) moiety, which was captured by exohedral chlorination, is also capable of being stabilized by encapsulating tri- or divalent monometal (M) species. On the basis of density functional theory calculations combined with statistical mechanics analyses, (#4348)C66:C2v-based mono-EMFs M@C2v(4348)-C66 (M = Tb, La, Y, and Yb) were demonstrated to be the most stable and predominant isomers at the fullerene formation temperature region, while another chlorinated cage (#4169)C66:Cs, featured with triple sequentially fused pentagon (TSFP) moiety, is less favorable to be obtained in the form of EMFs, although these two cages can be interconverted by a simple Stone-Wales transformation. The superiority of M@C2v(4348)-C66 over M@Cs(4169)-C66 comes from the stronger interaction of M-DHCP over that of M-TSFP in both ionic and covalent bonding aspects. In addition, size-selective complexation of host [n]cycloparaphenylene ([n]CPP) and Tb@C2v(4348)-C66 was simulated, showing that [10]CPP exhibits the best affinity toward Tb@C66, which provides a new opportunity for isolation and characterization of C66-based mono-EMFs.

Boosting activation of oxygen molecules on C60 fullerene by boron doping.

The activation of oxygen molecules on boron-doped C60 fullerene (C59 B) and the subsequent water formation reaction are systematically investigated by using hybrid density functional calculations. Results indicate that C59 B shows a favorable ability to activate oxygen molecules both kinetically and thermodynamically. The oxygen molecule is first adsorbed on the boron atom, which is identified to be the most reactive site in C59 B for O2 adsorption because of its high positive charge and spin density. The adsorption structure C59 BO2 can further isomerize to form two products with small reaction barriers. Water formation reactions upon these two structures are energetically favorable and suggest a four-electron mechanism for the oxygen reduction reaction catalyzed by C59 B. This work provides a reliable theoretical insight into the catalytic properties of boron-doped fullerene, which is believed to be helpful to explore fullerene catalysts.

Azide addition to Sc2@C66: favorable activity on unsaturated linear triquinanes and dramatic reactivity difference compared with the free C66 cage.

Density functional theory calculations on methyl azide additions to C66 and Sc2@C2v(4059)-C66 suggest that the best addition sites type E[5,6]-56 bond e2 and the new type D[5,6]-55 bond d for C66 and type G[5,5]-66 bond g for Sc2@C66 are located on the unsaturated linear triquinane moieties.

Expressions of Toll-like receptors 3, 4, 7, and 9 in cervical lesions and their correlation with HPV16 infection in Uighur women.

Recent findings show that Toll-like receptors (TLRs) expressed in immune cells play a crucial role in the innate immune response and the subsequent induction of adaptive immune responses against microbial infection on tissue injury. Furthermore, expression of TLRs in cancer cells is associated with tumor proliferation and invasion. To explore the role of TLRs expression in cervical carcinogenesis in Uighur women, we detected the expressions of TLR3, TLR4, TLR7, and TLR9 in 25 normal cervical tissues, 64 cervical intraepithelial neoplasia (CIN) tissues, and 63 cervical squamous cell carcinoma (CSCC) tissues using immunohistochemical staining, as well as human papillomavirus type 16 (HPV16) infection using PCR. All samples used in this study were from Xinjiang Uighur women. We found the expression levels of TLR4, TLR7, and TLR9 were significantly higher in CIN and CSCC than in normal controls (P < 0.05). Up-regulation of TLR4 and TLR7 were correlated with tumor differentiation but not FIGO stage or lymph node metastasis (P > 0.05). Up-regulation of TLR9 was correlated with lymph node metastasis (P < 0.05) but not tumor differentiation or FIGO stage (P > 0.05). We also analyzed the correlation between the expressions of TLRs and HPV16 infection and found that the expressions of TLR4 and TLR9 significantly correlated with HPV16 infection in CIN (r = 7.434, P = 0.006; r = 7.123, P = 0.008) and CSCC (r = 6.423, P = 0.001; r = 8.478, P = 0.004), whereas the expression of TLR3 was not significantly different in any of the three groups and had no significant correlation with HPV16 infection. Our results suggest that high expression of TLR4, TLR7, and TLR9 may play important roles in the development and progression of CIN and CSCC in Uighur women, and the expressions of TLR4 and TLR9 can be up-regulated by HPV16 infection.

Association between micronucleus frequency and cervical intraepithelial neoplasia grade in Thinprep cytological test and its significance.

A micronucleus is an additional small nucleus formed due to chromosomes or chromosomal fragments fail to be incorporated into the nucleus during cell division. In this study, we assessed the utility of micronucleus counting as a screening tool in cervical precancerous lesions in Thinprep cytological test smears under oil immersion. High risk HPV was also detected by hybrid capture-2 in Thinprep cytological test smears. Our results showed that micronucleus counting was significantly higher in high-grade squamous intraepithelial lesion (HSIL) and invasive carcinoma cases compared to low-grade squamous intraepithelial lesion (LSIL) and non-neoplastic cases. Receiver operating characteristic (ROC) curve analysis revealed that micronucleus counting possessed a high degree of sensitivity and specificity for identifying HSIL and invasive carcinoma. Cut-off of 7.5 for MN counting gave a sensitivity of 89.6% and a specificity of 66.7% (P = 0.024 and AUC = 0.892) for detecting HSIL and invasive carcinoma lesions. Multiple linear regression analysis showed that only HSIL and invasive cancer lesions not age, duration of marital life and number of pregnancy are significantly associated with MN counting. The positive rate of high risk HPV was distinctly higher in LSIL, HSIL and invasive cancer than that in non-neoplstic categories. In conclusions, MN evaluation may be viewed as an effective biomarker for cervical cancer screening. The combination of MN count with HPV DNA detection and TCT may serve as an effective means to screen precancerous cervical lesions in most developing nations.

miR-101 suppresses tumor proliferation and migration, and induces apoptosis by targeting EZH2 in esophageal cancer cells.

AIM: To investigate the role of miR-101 in the regulation of tumor proliferation, invasion, apoptosis and to its target gene in human ESCC. METHODS: The expression level of miR-101 in Eca109 cell line was determined by real-time polymerase chain reaction (PCR). After transfected with miR-101 mimics and inhibitor, proliferation, migration and apoptosis in ESCC cell line (Eca109) were detected by MTT, cell wound healing assay and flow cytometry, respectively. The expression of EZH2 in Eca109 cell was examined by immunohistochemical staining. RESULTS: We found that miR-101 was significantly down-regulated in ESCC cell than in matched normal esophageal epithelium cell. The expression level of miR-101 was inversely correlated to EZH2 protein expression in ESCC cell. In Eca109 cells, over-expression of miR-101 significantly inhibited the migration and invasion of ESCC cells, and promotes cell apoptosis. CONCLUSIONS: These findings suggest that decreased expression of miR-101 might promote metastasis of human ESCC by inducing accumulation of EZH2 protein.

Epigenetic regulation of human riboflavin transporter 2(hRFT2) in cervical cancers from Uighur women.

In the present study, we studied the hypermethylation of the human riboflavin transporter 2 (hRFT2) gene and regulation of protein expression in biopsies from resected tissues from Uighur cervical squamous cell carcinoma (CSCC) patients and their neighboring normal tissues. hRFT2 gene promoter region methylation sequences were mapped in cervical cancer cell line SiHa by bisulfite-sequencing PCR and quantitative detection of methylated DNA from 30 pairs of Uighur's CSCCs and adjacent normal tissues by MassARRAY (Sequenom, San Diego, CA, USA) and hRFT2 protein expression was analyzed by immunohistochemistry. In SiHa, we identified 2 CG sites methylated from all of 12CpG sites of the hRFT2 gene. Analysis of the data from quantitative analysis of single CpG site methylation by Sequenom MassARRAY platform showed that the methylation level between two CpG sites (CpG 2 and CpG 3) from CpG 1~12 showed significant differences between CSCC and neighboring normal tissues. However, the methylation level of whole target CpG fragments demonstrated no significant variation between CSCC (0.476 ± 0.020) and neighboring normal tissues (0.401 ± 0.019, p>0.05). There was a tendency for translocation the hRFT2 proteins from cytoplasm/membrane to nucleus in CSCC with increase in methylation of CpG 2 and CpG 3 in hRFT2gene promoter regions, which may relate to the genesis of CSCC. Our results suggested that epigenetic modifications are responsible for aberrant expression of the hRFT2 gene, and may help to understand mechanisms of cervical carcinogenesis.

Metabonomic signature analysis of cervical carcinoma and precancerous lesions in women by (1)H NMR spectroscopy.

(1)H nuclear magnetic resonance (NMR)-based metabonomics has been used to characterize the metabolic profiles of cervical intraepithelial neoplasia (CIN) and cervical squamous cell carcinoma (CSCC). Principal component analysis (PCA) and orthogonal partial least-squares discriminant analysis (OPLS-DA) were used to model the systematic variation related to patients with CIN or CSCC with healthy controls. Potential metabolic biomarkers were identified using database comparisons, and the one-way analysis of variance (ANOVA) test was used to examine the significance of the metabolites. Compared with plasma obtained from the healthy controls, plasma from patients with CIN had higher levels of very-low density lipoprotein (VLDL), acetone, unsaturated lipid and carnitine, together with lower levels of creatine, lactate, isoleucine, leucine, valine, alanine, glutamine, histidine, glycine, acetylcysteine, myo-inositol, choline and glycoprotein. Plasma from patients with CSCC had higher levels of acetate and formate, together with lower levels of creatine, lactate, isoleucine, leucine, valine, alanine, glutamine, histidine and tyrosine compared with the plasma of the healthy controls. In addition, compared with the plasma of patients with CIN, the plasma of CSCC patients had higher levels of acetate, formate, lactate, isoleucine, leucine, valine, alanine, glutamine, histidine, tyrosine, acetylcysteine, myo-inositol, glycoprotein, α-glucose and ß-glucose, together with lower levels of acetone, unsaturated lipid and carnitine. Moreover, the profiles showed high feasibility and specificity by statistical analysis with OPLS-DA compared to the Thinprep cytology test (TCT) by setting the histopathological outcome as standard. The metabolic profile obtained for cervical cancer is significant, even for the precancerous disease. This suggests a systemic metabolic response to cancer, which may be used to identify potential early diagnostic biomarkers of the cancer and to establish clinical diagnostic methods.