Immunotherapies Targeting Tumor-Associated Macrophages (TAMs) in Cancer.

Tumor-associated macrophages (TAMs) are one of the most plentiful immune compositions in the tumor microenvironment, which are further divided into anti-tumor M1 subtype and pro-tumor M2 subtype. Recent findings found that TAMs play a vital function in the regulation and progression of tumorigenesis. Moreover, TAMs promote tumor vascularization, and support the survival of tumor cells, causing an impact on tumor growth and patient prognosis. Numerous studies show that reducing the density of TAMs, or modulating the polarization of TAMs, can inhibit tumor growth, indicating that TAMs are a promising target for tumor immunotherapy. Recently, clinical trials have found that treatments targeting TAMs have achieved encouraging results, and the U.S. Food and Drug Administration has approved a number of drugs for use in cancer treatment. In this review, we summarize the origin, polarization, and function of TAMs, and emphasize the therapeutic strategies targeting TAMs in cancer treatment in clinical studies and scientific research, which demonstrate a broad prospect of TAMs-targeted therapies in tumor immunotherapy.

Potent inhibitors targeting cyclin-dependent kinase 9 discovered via virtual high-throughput screening and absolute binding free energy calculations.

Due to the crucial regulatory mechanism of cyclin-dependent kinase 9 (CDK9) in mRNA transcription, the development of kinase inhibitors targeting CDK9 holds promise as a potential treatment strategy for cancer. A structure-based virtual screening approach has been employed for the discovery of potential novel CDK9 inhibitors. First, compounds with kinase inhibitor characteristics were identified from the ZINC15 database via virtual high-throughput screening. Next, the predicted binding modes were optimized by molecular dynamics simulations, followed by precise estimation of binding affinities using absolute binding free energy calculations based on the free energy perturbation scheme. The binding mode of molecule 006 underwent an inward-to-outward flipping, and the new binding mode exhibited binding affinity comparable to the small molecule T6Q in the crystal structure (PDB ID: 4BCF), highlighting the essential role of molecular dynamics simulation in capturing a plausible binding pose bridging docking and absolute binding free energy calculations. Finally, structural modifications based on these findings further enhanced the binding affinity with CDK9. The results revealed that enhancing the molecule's rigidity through ring formation, while maintaining the major interactions, reduced the entropy loss during the binding process and, thus, enhanced binding affinities.

Rivaroxaban for the treatment of heparin-induced thrombocytopenia with thrombosis in a patient undergoing artificial hip arthroplasty: A case report.

BACKGROUND: Anticoagulation treatment after lower limb surgery is one of the key methods to avoid thrombosis, and low-molecular-weight heparin is the treatment that is most frequently used in clinical practice. But one uncommon side effect of low-molecular-weight heparin is heparin-induced thrombocytopenia (HIT), which can develop into thrombosis if not caught early or managed incorrectly. CASE SUMMARY: We present a case of a patient who underwent hip arthroplasty and experienced thrombocytopenia due to HIT on the 9th d following the application of low-molecular-weight heparin anticoagulation. We did not diagnose HIT in time and applied 1 unit of platelets to the patient, which led to thrombosis. Luckily, the patient recovered following effective and timely surgery and treatment with rivaroxaban. CONCLUSION: Patients using low-molecular-weight heparin after lower limb surgery need to have their platelet counts regularly checked. If HIT develops, platelet treatment should be given with caution.

Tracking the Early Stage of Triplet-Induced Photodamage in a DNA Dimer and Oligomer Containing 5-Methylcytosine.

Methylation at the C5 position of cytosine, a naturally occurring epigenetic modification on DNA, shows a high correlation with mutational hotspots in disease such as skin cancer. Due to its essential biological relevance, numerous studies were devoted to confirming that the methylated sites favor the formation of the cyclobutane pyrimidine dimer (CPD), a well-known UV-induced lesion. However, photophysical and photochemical properties of dinucleotides and polynucleotides containing 5-methylcytosine (5mC) remain elusive. Herein, a charge transfer (CT) triplet state, generated via intersystem crossing (ISC) from a CT singlet state that enhanced after methylation on cytosine, is directly observed by using femtosecond transient absorption (TA) and time-resolved mid-infrared (TRIR) spectroscopy together with quantum chemical calculations for the first time in the T5mC dimer. Such an ISC process is quenched due to limitations of the ground-state geometries in 5mC-containing single-strand oligomer d(T5mC)9. This mechanistic information is important for understanding the early stage of triplet state-induced CPD formation in 5mC containing DNA.

Ursolic acid augments the chemosensitivity of drug-resistant breast cancer cells to doxorubicin by AMPK-mediated mitochondrial dysfunction.

Multidrug resistance remains the major obstacle to successful therapy for breast carcinoma. Ursolic acid (UA), a triterpenoid compound, has been regarded as a potential neoplasm chemopreventive drug in some preclinical studies since it exerts multiple biological activities. In this research, we investigated the role of UA in augmenting the chemosensitivity of drug-resistant breast carcinoma cells to doxorubicin (DOX), and we further explored the possible molecular mechanisms. Notably, we found that UA treatment led to inhibition of cellular proliferation and migration and cell cycle arrest in DOX-resistant breast cancers. Furthermore, combination treatment with UA and DOX showed a stronger inhibitory effect on cell viability, colony formation, and cell migration; induced more cell apoptosis in vitro; and generated a more potent inhibitory effect on the growth of the MCF-7/ADR xenograft tumor model than DOX alone. Mechanistically, UA effectively increased p-AMPK levels and concomitantly reduced p-mTOR and PGC-1α protein levels, resulting in impaired mitochondrial function, such as mitochondrial respiration inhibition, ATP depletion, and excessive reactive oxygen species (ROS) generation. In addition, UA induced a DNA damage response by increasing intracellular ROS production, thus causing cell cycle arrest at the G0/G1 phase. UA also suppressed aerobic glycolysis by prohibiting the expression and function of Glut1. Considered together, our data demonstrated that UA potentiated the susceptibility of DOX-resistant breast carcinoma cells to DOX by targeting energy metabolism through the AMPK/mTOR/PGC-1α signaling pathway, and it is a potential adjuvant chemotherapeutic candidate in MDR breast cancer.

Inhibitor of DNA-binding family regulates the prognosis of ovarian cancer.

Aim: The mechanistic role of inhibitor of DNA binding or differentiation (ID) family in ovarian cancer (OC) has remained unclear. Materials & methods: We used the Oncomine, GEPIA, Kaplan-Meier Plotter, cBioPortal, SurvExpress, PROGgene V2, TIMER, and FunRich to evaluate the prognostic value of IDs in patients with OC. Results: the mRNA transcripts of all IDs were markedly downregulated in OC compared with normal tissue. The prognostic value of IDs was also explored within the subtypes, pathological stages, clinical stages and TP53 mutational status. The group with low-risk IDs showed relatively good overall survival (OS) compared with the high-risk group. Conclusion: ID1/3/4 may be exploited as promising prognostic biomarkers and therapeutic targets in OC patients.

Glabridin resensitizes p-glycoprotein-overexpressing multidrug-resistant cancer cells to conventional chemotherapeutic agents.

Multidrug resistance (MDR) remains an obstacle to chemotherapy related with the overexpression of several efflux membrane proteins, and p-glycoprotein (P-gp) is the most studied among them. Thus, continuous investigational efforts are necessary to find valuable MDR reversal agents, and the flavonoid compound glabridin (GBD) seems to be a promising candidate. This study aimed to investigate the potential of GBD against MDR and explore the possible mechanisms. First, we found that GBD could decrease the half maximal inhibitory concentration of paclitaxel and doxorubicin (DOX) in breast cancer cells like MDA-MB-231/MDR1 cells and MCF-7/ADR cells. It was further explained that GBD enhanced the apoptosis of MDA-MB-231/MDR1 cells induced by DOX, due to the increased accumulation of DOX. Then, tests were performed to explore the possible MDR reversal mechanisms. On one hand, GBD can suppress the expression of P-gp. On the other hand, GBD can downregulate the activity of P-gp ATPase when cotreated with DOX or verapamil, revealing that GBD was a substrate of P-gp. Moreover, the obtained kinetic inhibition parameters proved that GBD was a competitive inhibitor of P-gp, and in molecular docking simulation modeling, GBD exhibited stronger binding affinity with P-gp than DOX. In conclusion, GBD can increase the accumulation of DOX in MDA-MB-231/MDR1 cells by suppressing the expression of P-gp and competitively inhibiting the P-gp efflux pump and enhance the apoptosis of MDA-MB-231/MDR1 cells induced by DOX, and thus realize reversal effects on MDR. Therefore, the combination therapy of anticancer drugs and flavonoid-like GBD is a promising strategy to overcome P-gp-mediated MDR.

Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins.

Intrinsically disordered proteins (IDPs) carry out crucial biological functions in essential biological processes of life. Because of the highly dynamic and conformationally heterogeneous nature of the disordered states of IDPs, molecular dynamics simulations are becoming an indispensable tool for the investigation of the conformational ensembles and dynamic properties of IDPs. Nevertheless, there is still no consensus on the most reliable force field in molecular dynamics simulations for IDPs hitherto. In this work, the recently proposed AMBER99SB2D force field is evaluated in modeling some disordered polypeptides and proteins by checking its ability to reproduce experimental NMR data. The results highlight that when the ildn side-chain corrections are included, AMBER99SB2D-ildn exhibits reliable results that agree with experiments compared with its predecessors, the AMBER14SB, AMBER99SB, AMBER99SB-ildn, and AMBER99SB2D force fields, and that decreasing the overall magnitude of protein-protein interactions in favor of protein-water interactions is a key ingredient behind the improvement.

Oxygen-sulfur exchange and the gas-phase reactivity of cobalt sulfide cluster anions with molecular oxygen.

We present here a study of gas-phase reactivity of cobalt sulfide cluster anions Co(m)S(n)(-) with molecular oxygen. Nascent Co(m)S(n)(-) clusters were prepared via a laser ablation source and reacted with oxygen in a fast flow reactor under thermal collision conditions. We chose (18)O2 in place of (16)O2 to avoid mass degeneration with sulfur, and a time-of-flight (TOF) mass spectrometer was used to detect the cluster distributions in the absence and presence of the reactant. It was found that oxygen-sulfur exchange occurs in the reactions for those with specific compositions (CoS)(n)(-) and (CoS)(n)S(-) (n = 2-5) according to a consistent pathway, "Co(m)S(n)(-) + (18)O2 → Co(m)S(n-1)(18)O(-) + S(18)O". Typically, for "Co2S2(-) + (18)O2" we have calculated the reaction coordinates by employing the density functional theory (DFT), where both the oxygen-sulfur exchange and SO molecule release are thermodynamically and kinetically favorable. It is noteworthy that the reaction with molecular oxygen (triplet ground state) needs to overcome a spin excitation as well as a large O-O activation energy. This study sheds light on the activation of molecular oxygen by cobalt sulfides on one hand and also provides insight into the regeneration mechanism of cobalt oxides from the counterpart sulfides in the presence of oxygen gas on the other hand.

Equilibrium and folding simulations of NS4B H2 in pure water and water/2,2,2-trifluoroethanol mixed solvent: examination of solvation models.

The structural stability and preference of a protein are highly sensitive to the environment accommodating it. In this work, the solvation effect on the structure and folding dynamics of a small peptide, NS4B H2, was studied by computer simulation. The native structure of NS4B H2 was solved previously in 50 % v/v water/2,2,2-trifluoroethanol (TFE) mixed solvent. In this work, both pure water and water/TFE cosolvent were utilized. The force field parameters for water were taken from the TIP3P water model, and those for TFE were generated following the routine of the general AMBER force field (GAFF). The simulated structure of NS4B H2 in the mixed solvent is quite in line with experimental data, while in pure water it undergoes a large structural deformation. The generalized Born (GB) model was also investigated by tuning the dielectric constant to match experimental measurements. However, the results show that its performance was less satisfactory. Two independent direct folding simulations of NS4B H2 in explicit water/TFE cosolvent were carried out, both of which resulted in successful folding. Investigation of the distribution of solvent molecules around the peptide indicates that folding is triggered by the aggregation of TFE on the peptide surface.

A numerically stable restrained electrostatic potential charge fitting method.

Inspired by the idea of charge decomposition in calculation of the dipole preserving and polarization consistent charges (Zhang et al., J. Comput. Chem. 2011, 32, 2127), we have proposed a numerically stable restrained electrostatic potential (ESP)-based charge fitting method for protein. The atomic charge is composed of two parts. The dominant part is fixed to a predefined value (e.g., AMBER charge), and the residual part is to be determined by restrained fitting to residual ESP on grid points around the molecule. Nonuniform weighting factors as a function of the dominant charge are assigned to the atoms. Because the residual part is several folds to several orders smaller than the dominant part, the impact of ill-conditioning is alleviated. This charge fitting method can be used in quantum mechanical/molecular mechanical (QM/MM) simulations and similar studies, where QM calculated electronic properties are frequently mapped to partial atomic charges.

Case-control study of diet in patients with cervical cancer or precancerosis in Wufeng, a high incidence region in China.

PURPOSE: To investigate the diet of patients with cervical cancer and precancerosis in the Wufeng area, a high- incidence region in China. METHODS: In the case group, 104 patients diagnosed with cervical cancer or cervical intraepithelial neoplasias (CINII/III) were recruited from the Wufeng area. Nine hundred thirty-six healthy women were selected from the same area as the matched controls. A questionnaire, which included questions about general lifestyle conditions, smoking and alcohol status, source of drinking water, green tea intake, and diet in the past year, was presented to all participants. RESULTS: Green tea intake (P=0.022, OR=0.551, 95% CI=0.330-0.919) and vegetable intake (P=0.035, OR=0.896, 95% CI=0.809-0.993) were identified as protective factors against cervical cancer or CINII/III. There was no indication of any associations of other lifestyle factors (smoking status, alcohol status, source of drinking water) or diet (intake of fruit, meat/egg/milk, soybean food, onion/garlic, staple food and pickled food) with cervical cancer. CONCLUSIONS: The results suggest that eating more fresh vegetables and drinking more green tea may help to reduce the risk of cervical cancer or CINII/III in people of the Wufeng area.

Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water.

Multiple single-trajectory molecular dynamics (MD) simulation at room temperature (300 K) in explicit water was carried out to study the folding dynamics of an α-helix (PDB 2I9M ) using a polarized charge scheme that includes electronic polarization of backbone hydrogen bonds. Starting from an extended conformation, the 17-residue peptide was successfully folded into the native structure (α-helix) between 80 and 130 ns with a root-mean-square deviation of ~1.0 Å. Analysis of the time-dependent trajectories revealed that helix formation of the peptide started at the terminals and progressed toward the center of the peptide. For comparison, MD trajectories generated under various versions of standard AMBER force fields failed to show any significant or stable helix formation in our simulation. Our result shows clear evidence that the electronic polarization of backbone hydrogen bonds energetically stabilizes the helix formation and is critical to the stable folding of the short helix structure.

Communication: The electrostatic polarization is essential to differentiate the helical propensity in polyalanine mutants.

The folding processes of three polyalanine peptides with composition of Ac-(AAXAA)(2)-GY-NH(2) (where X is chosen to be Q, K, and D) are studied by molecular dynamics simulation in solvent of 40% trifluoroethanol using both polarized and unpolarized force fields. The simulations reveal the critical role of polarization effect for quantitative description of helix formation. When polarized force field is used, peptides with distinctive helical propensity are correctly differentiated and the calculated helical contents are in close agreement with experimental measurement, indicating that consideration of polarization effect can correctly predict the effect of sequence variation on helix formation.

Quantum mechanical studies of residue-specific hydrophobic interactions in p53-MDM2 binding.

Quantum chemistry calculations at the levels of MP2/cc-pVDZ and MP2/cc-PVTZ have been carried out to study residue-specific interactions at the hydrophobic p53-MDM2 binding interface. The result of the calculation, based on structures from nanosecond molecular dynamics simulation, revealed that (19)Phe, (22)Leu, and (23)Trp of p53 have the strongest binding interaction with MDM2 followed by (26)Leu and (27)Pro. The specific residues of MDM2 that have dominant binding interactions with p53 are specifically identified to be (51)Lys, (54)Leu, (62)Met, (67)Tyr, (72)Gln, (94)Lys, (96)His, and (100)Tyr. The p53-MDM2 binding interaction is dominated by van der Waals interaction and to a lesser degree by electrostatic interaction. The MP2 results are in generally good agreement with those from the force field calculation while the DFT/B3LYP calculation failed to give attractive interaction energies for certain residue-residue interactions due to the lack of dispersion energy.

Quantum study of HIV-1 protease-bridge water interaction.

We present a fully quantum mechanical calculation for binding interaction between HIV-1 protease (PR) and the water molecule W301 which bridges the flaps of the protease with the inhibitors of PR. The quantum calculation is made possible by applying a recently developed molecular fractionation with conjugate caps (MFCC) method which divides a protein molecule into capped amino acid-based fragments and their conjugate caps. These individual fragments are properly treated to preserve the chemical property of bonds that are cut. Ab initio methods at HF, B3LYP, and MP2 levels with a fixed basis set 6-31+G* have been employed in the present calculation. The MFCC calculation produces a quantum mechanical interaction "map" representing interactions between individual residues of PR and W301. This enables a detailed quantitative analysis on binding of W301 to specific residues of PR at quantum mechanical level.

New method for direct linear-scaling calculation of electron density of proteins.

A new scheme for direct linear-scaling quantum mechanical calculation of electron density of protein systems is developed. The new scheme gives much improved accuracy of electron density for proteins than the original MFCC (molecular fractionation with conjugate caps) approach in efficient linear-scaling calculation for protein systems. In this new approach, the error associated with each cut in the MFCC approach is estimated by computing the two neighboring amino acids in both cut and uncut calculations and is corrected. Numerical tests are performed on six oligopeptide taken from PDB (protein data bank), and the results show that the new scheme is efficient and accurate.