Effect of PDGF-B aptamer on PDGFRβ/PDGF-B interaction: Molecular dynamics study

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.

Analysis of aptamer-target binding and molecular mechanisms by thermofluorimetric analysis and molecular dynamics simulation

Introduction: Aptamers are valuable for bioassays, but aptamer-target binding is susceptible to reaction conditions. In this study, we combined thermofluorimetric analysis (TFA) and molecular dynamics (MD) simulations to optimize aptamer-target binding, explore underlying mechanisms and select preferred aptamer. Methods: Alpha-fetoprotein (AFP) aptamer AP273 (as the model) was incubated with AFP under various experimental conditions, and melting curves were measured in a real-time PCR system to select the optimal binding conditions. The intermolecular interactions of AP273-AFP were analysed by MD simulations with these conditions to reveal the underlying mechanisms. A comparative study between AP273 and control aptamer AP-L3-4 was performed to validate the value of combined TFA and MD simulation in selecting preferred aptamers. Results: The optimal aptamer concentration and buffer system were easily determined from the dF/dT peak characteristics and the melting temperature (Tm) values on the melting curves of related TFA experiments, respectively. A high Tm value was found in TFA experiments performed in buffer systems with low metal ion strength. The molecular docking and MD simulation analyses revealed the underlying mechanisms of the TFA results, i.e., the binding force and stability of AP273 to AFP were affected by the number of binding sites, frequency and distance of hydrogen bonds, and binding free energies; these factors varied in different buffer and metal ion conditions. The comparative study showed that AP273 was superior to the homologous aptamer AP-L3-4. Conclusion: Combining TFA and MD simulation is efficient for optimizing the reaction conditions, exploring underlying mechanisms, and selecting aptamers in aptamer-target bioassays.

Targeting Tumor Necrosis Factor Receptor 1 with Selected Aptamers for Anti-Inflammatory Activity

Tumor necrosis factor-α (TNFα) inhibitors are widely used in treating autoimmune diseases like rheumatoid arthritis (RA). These inhibitors can presumably alleviate RA symptoms by blocking TNFα-TNF receptor 1 (TNFR1)-mediated pro-inflammatory signaling pathways. However, the strategy also interrupts the survival and reproduction functions conducted by TNFα-TNFR2 interaction and causes side effects. Thus, it is urgently needed to develop inhibitors that can selectively block TNFα-TNFR1 but not TNFα-TNFR2. Here, nucleic acid-based aptamers against TNFR1 are explored as potential anti-RA candidates. Through the systematic evolution of ligands by exponential enrichment (SELEX), two types of TNFR1-targeting aptamers were obtained, and their K_D values are approximately 100-300 nM. In silico analysis shows that the binding interface of aptamer-TNFR1 highly overlapped with natural TNFα-TNFR1 binding. On the cellular level, the aptamers can exert TNFα inhibitory activity by binding to TNFR1. The anti-inflammatory efficiencies of aptamers were assessed and further enhanced using divalent aptamer constructs. These findings provide a new strategy to block TNFR1 for potential anti-RA treatment precisely.

Platelet-Derived Growth Factors Affect Clinical Features and Prognosis of Gastric Cancer

Purpose. To investigate the association of platelet-derived growth factors (PDGFs), clinicopathological features, and prognosis in gastric cancer patients. Methods. Tumor specimens of 180 individuals with gastric cancer treated between 2016 and 2020 were collected. Immunohistochemical staining and Western blot (WB) were used to detect the expression of PDGF-B and PDGF-D. The relationship between the expression of PDGF-B and PDGF-D and relapse-free subsistence (RFS) time was assessed using Kaplan–Meier curves. Univariate and multivariate Cox proportional hazards regression models were used to evaluate the relationship between the expression of PDGF-B and PDGF-D and the prognosis and clinicopathological features in gastric cancer patients. Results. High expression of PDGF-B and PDGF-D was detected in 108 (60%) and 137 (76%) tumor specimens, respectively. The expressions of PDGF-B and PDGF-D were independent predictive indicators in multivariate analysis when compared to tumor depth, tumor stage, lymph node metastasis, and RFS ( $P<0.01$ ). Conclusion. The high expression of PDGF-B and PDGF-D in gastric cancer tissues is associated with poor prognosis and poor survival rate of the patients. The expression of PDGF-B and PDGF-D can be used as important indicators to evaluate the biological behavior and prognosis of gastric cancer.

Protein DEK and DTA Aptamers: Insight Into the Interaction Mechanisms and the Computational Aptamer Design

By blocking the DEK protein, DEK-targeted aptamers (DTAs) can reduce the formation of neutrophil extracellular traps (NETs) to reveal a strong anti-inflammatory efficacy in rheumatoid arthritis. However, the poor stability of DTA has greatly limited its clinical application. Thus, in order to design an aptamer with better stability, DTA was modified by methoxy groups (DTA_OMe) and then the exact DEK–DTA interaction mechanisms were explored through theoretical calculations. The corresponding 2′-OCH3-modified nucleotide force field was established and the molecular dynamics (MD) simulations were performed. It was proved that the 2′-OCH3-modification could definitely enhance the stability of DTA on the premise of comparative affinity. Furthermore, the electrostatic interaction contributed the most to the binding of DEK–DTA, which was the primary interaction to maintain stability, in addition to the non-specific interactions between positively-charged residues (e.g., Lys and Arg) of DEK and the negatively-charged phosphate backbone of aptamers. The H-bond network analysis reminded that eight bases could be mutated to probably enhance the affinity of DTA_OMe. Therein, replacing the 29th base from cytosine to thymine of DTA_OMe was theoretically confirmed to be with the best affinity and even better stability. These research studies imply to be a promising new aptamer design strategy for the treatment of inflammatory arthritis.

Protein recognition-initiated exponential amplification reaction (PRIEAR) and its application in clinical diagnosis

The isothermal exponential amplification technology have rarely been fabricated as the universal sensing platform for the detection of various proteins. To broaden its application, we here developed a strategy named protein recognition-initiated exponential amplification reaction (PRIEAR) using protein recognition to induce the DNA assembly which converts protein recognition events into ssDNA amplicons and combining two-stage amplification to achieve exponential amplification technology. Taking advantage of this principle, diverse biomarkers can be quantified at sub-picomolar concentrations in the homogenous manner, making the PRIEAR suitable for clinical practice. Therefore, this strategy can expand the powerful isothermal exponential amplification technology to protein targets and thus provide a new toolbox into the clinical and biomedical applications.

Downregulation of PDGF-D Inhibits Proliferation and Invasion in Breast Cancer MDA-MB-231 Cells

BACKGROUND

The platelet derived growth factor-D (PDGF-D) plays an important role in breast tumor aggressiveness. However, limited study has investigated the effect of silencing PDGF-D on the biological function of breast cancer. The purpose of this study is to clarify the potential value of PDGF-D as a target for breast cancer treatment.

METHODS

Reverse transcription-polymerase chain reaction and western blot were used to detect PDGF-D expression in 5 different breast cancer cells. The lentiviral vector was usd to silence PDGF-D in MDA-MB-231 cells. Then, Methyl Thiazolyl Tetrazolium was used to detect cell viability, 5-Ethynyl-2'- deoxyuridine and a soft agar assay were used to detect cell proliferation and clonality. Additionally, cell apoptosis after PDGF-D knockdown was measured by Annexin V/ Prodium Iodide staining, and cell migration was detected by trans-well assay. Survival rate and tumor size were measured by nude mice transplantation.

RESULTS

The MDA-MB-231 and SK-BR-3 cell lines showed higher PDGF-D expression than the MCF7 cell lines (P<.05). After the PDGF-D gene was silenced, the growth and colony forming abilitys ignificantly decreased (P<.05) together with the induction of apoptosis in MDA-MB-231 cells (P<.05). Moreover, MDA-MB-231 cells with PDGF-D silencing showed significantly diminished aggressive migration and invasion potential compared to other cells (P<.05). In vivo experiments also indicated that PDGF-D silencing inhibited tumor growth and improved the survival rate of tumor-bearing mice.

CONCLUSION

Downregulation of PDGF-D had dramatic effects on breast cancer cell proliferation, apoptosis and migration, which indicates that it plays an important role in breast cancer development and progression.

Biomaterials for protein delivery for complex tissue healing responses

Tissue repair requires a complex cascade of events mediated by a variety of cells, proteins, and matrix molecules; however, the healing cascade can be easily disrupted by numerous factors, resulting in impaired tissue regeneration. Recent advances in biomaterials for tissue regeneration have increased the ability to tailor the delivery of proteins and other biomolecules to injury sites to restore normal healing cascades and stimulate robust tissue repair. In this review, we discuss the evolution of the field toward creating biomaterials that precisely control protein delivery to stimulate tissue regeneration, with a focus on addressing complex and dynamic injury environments. We highlight biomaterials that leverage different mechanisms to deliver and present proteins involved in healing cascades, tissue targeting and mimicking strategies, materials that can be triggered by environmental cues, and integrated strategies that combine multiple biomaterial properties to improve protein delivery. Improvements in biomaterial design to address complex injury environments will expand our understanding of both normal and aberrant tissue repair processes and ultimately provide a better standard of patient care.

In silico approach for Post-SELEX DNA aptamers: A mini-review

Aptamers are short oligonucleotides that possess high specificity and affinity against their target. Generated via Systematic Evolution of Ligands by Exponential Enrichment, (SELEX) in vitro, they were screened and enriched. This review covering the study utilizing bioinformatics tools to analyze primary sequence, secondary and tertiary structure prediction, as well as docking simulation for various aptamers and their ligand interaction. Literature was pooled from Web of Science (WoS) and Scopus databases until December 18, 2020 using specific search string related to DNA aptamers, in silico, structure prediction, and docking simulation. Out of 330 published articles, 38 articles were assessed in the analysis based on the predefined inclusion and exclusion criteria. It was found that Mfold and RNA Composer web server is the most popular tool in secondary and tertiary structure prediction of DNA aptamers, respectively. Meanwhile, in docking simulation, ZDOCK and AutoDock are preferred to analyze binding interaction in the aptamer-ligand complex. This review reports a brief framework of recent developments of in silico approaches that provide predictive structural information of ssDNA aptamer.

In silico molecular docking in DNA aptamer development

Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that exhibit binding affinity and specificity against a wide variety of target molecules. Compared to RNA aptamers, DNA aptamers are much more stable and therefore are widely adopted in a number of applications especially in diagnostics. The tediousness and rigor associated with certain steps of the SELEX intensify the efforts to adopt in silico molecular docking approaches together with in vitro SELEX procedures in developing DNA aptamers. Inspired by these endeavors, we carry out an overview of the in silico molecular docking approaches in DNA aptamer generation, by detailing the stepwise procedures as well as shedding some light on the various softwares used. The in silico maturation strategy and the limitations of the in silico approaches are also underscored.

Computational predictive approaches for interaction and structure of aptamers

Aptamers are short single-strand sequences that can bind to their specific targets with high affinity and specificity. Usually, aptamers are selected experimentally via systematic evolution of ligands by exponential enrichment (SELEX), an evolutionary process that consists of multiple cycles of selection and amplification. The SELEX process is expensive, time-consuming, and its success rates are relatively low. To overcome these difficulties, in recent years, several computational techniques have been developed in aptamer sciences that bring together different disciplines and branches of technologies. In this paper, a complementary review on computational predictive approaches of the aptamer has been organized. Generally, the computational prediction approaches of aptamer have been proposed to carry out in two main categories: interaction-based prediction and structure-based predictions. Furthermore, the available software packages and toolkits in this scope were reviewed. The aim of describing computational methods and tools in aptamer science is that aptamer scientists might take advantage of these computational techniques to develop more accurate and more sensitive aptamers.

Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches

The stochastic tunneling-basin hopping method (STUN-BH) was utilized to obtain the most stable peptide S7 configuration (Ac-Ser-Ser-Phe-Pro-Gln-Pro-Asn-CONH2) adsorbed on Au(111) facet. After the most stable S7 configuration was found, molecular dynamics (MD) simulation was conducted to investigate the thermal stability between S7 and Au facet at 300 K in both vacuum and water environment. Moreover, further design sets of peptide sequences on Au(111) facet were used to compare with S7. All molecular simulations were carried out by the large-scale atomic/molecular massively parallel simulator (LAMMPS). The Amber99sb-ILDN force field was employed for modeling the interatomic interaction of peptides, and the TIP3P water was used for the water environment. The CHARMM-METAL force field was introduced to model the S7, PF8 (Ac-Pro-Phe-Ser-Pro-Phe-Ser-Pro-Phe-CONH2) and FS8 (Ac-Phe-Ser-Phe-Ser-Phe-Ser-Phe-Ser-CONH2) interactions with Au(111). The MD simulation results demonstrate that the morphology of Pro affects the adsorption stability of Phe. Therefore, we designed two sequences, PF8 and FS8, to confirm our simulation result through experiment. The present study also develops a novel low-temperature plasma synthesis method to evaluate the facet selecting performance of the designed peptide sequences of S7, PF8, and FS8. The experimental results suggest that the reduced Au atom seed is captured with the designed peptide sequences and slowing growing under room temperature for 72 hours. The experimental results are in the excellent agreement with the simulation finding that the Pro in the designed peptide sequences plays a critical role in the facet selection for Au atom stacking.

Advancing Aptamers as Molecular Probes for Cancer Theranostic Applications-The Role of Molecular Dynamics Simulation

Theranostics cover emerging technologies for cell biomarking for disease diagnosis and targeted introduction of drug ingredients to specific malignant sites. Theranostics development has become a significant biomedical research endeavor for effective diagnosis and treatment of diseases, especially cancer. An efficient biomarking and targeted delivery strategy for theranostic applications requires effective molecular coupling of binding ligands with high affinities to specific receptors on the cancer cell surface. Bioaffinity offers a unique mechanism to bind specific target and receptor molecules from a range of non-targets. The binding efficacy depends on the specificity of the affinity ligand toward the target molecule even at low concentrations. Aptamers are fragments of genetic materials, peptides, or oligonucleotides which possess enhanced specificity in targeting desired cell surface receptor molecules. Aptamer-target binding results from several inter-molecular interactions including hydrogen bond formation, aromatic stacking of flat moieties, hydrophobic interaction, electrostatic, and van der Waals interactions. Advancements in Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assay has created the opportunity to artificially generate aptamers that specifically bind to desired cancer and tumor surface receptors with high affinities. This article discusses the potential application of molecular dynamics (MD) simulation to advance aptamer-mediated receptor targeting in targeted cancer therapy. MD simulation offers real-time analysis of the molecular drivers of the aptamer-receptor binding and generate optimal receptor binding conditions for theranostic applications. The article also provides an overview of different cancer types with focus on receptor biomarking and targeted treatment approaches, conventional molecular probes, and aptamers that have been explored for cancer cells targeting.

In Silico Design of Novel Mutant Anti-MUC1 Aptamers for Targeted Cancer Therapy

The transmembrane glycoprotein mucin 1 (MUC1) is an attractive tumor marker for cancer therapy and diagnosis. The nine amino acid extracellular epitope APDTRPAPG of this protein is selectively recognized by the S2.2 single-stranded DNA anti-MUC1 aptamer, which has emerged as a promising template for designing novel targeting agents for MUC1-directed therapy. In this work, 100 ns molecular dynamics (MD) simulations, MM/GBSA binding free energy calculations, and conformational analysis were employed to propose a novel prospective anti-MUC1 aptamer with increased affinity toward the MUC1 epitope resulting from the double mutation of the T11 and T12 residues with PSU and U nucleosides, respectively. The double mutant aptamer exhibits a tight interaction with the MUC1 epitope and adopts a groove conformation that structurally favors the intermolecular contact with the epitope through the intermediate T11-A18 region leaving the 3' and 5' ends free for further chemical conjugation with a nanocarrier or pharmaceutical. These results are valuable to gain understanding about the molecular features governing aptamer-epitope interactions and constitute a first key step for the design of novel aptamer-based nanocarriers for MUC1-targeted cancer therapy.

Predicting the Most Stable Aptamer/Target Molecule Complex Configuration Using a Stochastic-Tunnelling Basin-Hopping Discrete Molecular Dynamics Method: A Novel Global Minimum Search Method for a Biomolecule Complex

This study proposed a novel global minimum search method for predicting the most stable biomolecule complex, which combines the strengths of three global minimum search methods (stochastic tunnelling, basin hopping, and discrete molecular dynamics) to efficiently improve the spatial domain search ability of the stochastic tunnelling-basin hopping (STUN-BH) method from our previous study. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as a benchmark target molecule for the EpCAM aptamer EpA (Apt_EpA). For the most stable Apt_EpA/EpCAM complex predicted by our new method, the Apt_EpA was attached to the entangling loop fragments of the two EpCAM molecules with the most Apt_EpA residues. After the Apt_EpA/EpCAM complex had equilibrated with the water environment through a molecular dynamics simulation at 300 K for 10 ns, stable hydrogen bonds formed between the bases of Apt_EpA and EpCAM residues of the secondary structures, which included the alpha helix and beta sheet becoming less stable in the water environment. Those hydrogen bonds formed between the bases of Apt_EpA and EpCAM loop fragment residues remained stable in the water environment.

Recent Advances in Degradable Hybrids of Biomolecules and NGs for Targeted Delivery

Recently, the fast development of hybrid nanogels dedicated to various applications has been seen. In this context, nanogels incorporating biomolecules into their nanonetworks are promising innovative carriers that gain great potential in biomedical applications. Hybrid nanogels containing various types of biomolecules are exclusively designed for: improved and controlled release of drugs, targeted delivery, improvement of biocompatibility, and overcoming of immunological response and cell self-defense. This review provides recent advances in this rapidly developing field and concentrates on: (1) the key physical consequences of using hybrid nanogels and introduction of biomolecules; (2) the construction and functionalization of degradable hybrid nanogels; (3) the advantages of hybrid nanogels in controlled and targeted delivery; and (4) the analysis of the specificity of drug release mechanisms in hybrid nanogels. The limitations and future directions of hybrid nanogels in targeted specific- and real-time delivery are also discussed.

Inhibition of Colorectal Cancer Cell Proliferation by Regulating Platelet-Derived Growth Factor B Signaling with a DNA Aptamer

Background:

Overexpression of platelet-derived growth factor-BB (PDGF-BB) is associated with colorectal carcinogenesis. PDGF-BB plays a role in the autocrine growth stimulation of cancer cells. Aptamers are short single-stranded oligonucleotides that can bind to cellular targets with high affinity and specificity and offer the advantage of non-immunogenicity, non-toxicity and high stability. Thus, they receive interest as potential therapeutic agents.

Methods:

The endogenous level of PDGF-BB in Caco-2 and SW480, colorectal cancer (CRC) cells, was evaluated using ELISA. The effect of the PDGF-BB aptamer on cell proliferation was investigated in two CRC cell lines and CCD841 CoN, normal colon cells. The effective molar ratio between PDGF-BB and PDGF-BB aptamer was further explored. Cell viability in all experiments was analyzed using MTS assay. Western blotting was performed to examine the alteration of relevant signaling pathways.

Results:

Caco-2 and SW480 cells endogenously synthesized and secreted PDGF-BB to stimulate their growth. Cells treated with the PDGF-BB aptamer proliferated at a slower rate, but CCD841 CoN did not. Pre-incubation of PDGF-BB with the corresponding aptamer at the molar ratio 1:1 could significantly silence its proliferative effect on CRC cells. Western blot analysis revealed that the phosphorylation level of ERK1/2, a key component in PDGF downstream signaling pathway, was down-regulated by the aptamer, indicating the underlying mechanism of inhibition of CRC cell proliferation.

Conclusions:

This study demonstrated that using a DNA aptamer to interfere with the binding of PDGF-BB to its receptor suppressed CRC cell proliferation in part via down-regulation of the Ras/Raf/MEK/ERK signaling pathway. It raised the possibility that the PDGF-BB-specific aptamer could be a promising therapeutic agent for CRC targeted therapy.

Effect of platelet-derived growth factor-BB on gap junction and connexin43 in rat penile corpus cavernosum smooth muscle cells

We explored whether platelet-derived growth factor (PDGF)-BB regulates corpus cavernosum smooth muscle cell gap junctions and can ameliorate erectile dysfunction and how it modulates connexin43 (CX43) after bilateral cavernous neurectomy. Primary cultured rat corpus cavernosum smooth muscle cells were treated with PDGF-BB with or without a PDGFR inhibitor, Akt siRNA or the depletion or promotion of β-catenin. PDGF-BB improved CCSMCs gap junction coupling and increased CX43 and PDGFRβ expression; inhibition of PDGFR activity down-regulated CX43 and decreased Akt and nuclear β-catenin. Knockdown or promotion of β-catenin down-regulated and up-regulated CX43 expression respectively. Moreover, β-catenin activation induced CX43 nuclear accumulation, which impeded CX43 down-regulation induced by PDGFR inhibition, suggesting that CX43 expression is positively correlated with nuclear β-catenin expression. Furthermore, CX43 promoter luciferase and chromatin immunoprecipitation assays indicated that β-catenin regulates CX43 transcription by directly interacting with its promoter. Male rats underwent bilateral cavernous neurectomy. After 12 weeks, they were injected with PDGF-BB, CX43 and PDGFRβ expression was significantly lower than in the control group, which was reversed by PDGF-BB injection. These results suggested that PDGF-BB contributed to the improvement of gap junction intracellular communication among corpus cavernosum smooth muscle cells, increased CX43 through PDGFRβ/Akt/nuclear β-catenin signalling, and ameliorated cavernous nerve injury-induced erectile dysfunction.