Molecular modeling and SPRi investigations of interleukin 6 (IL6) protein and DNA aptamers

A point-of-care electrochemical biosensor for the rapid and sensitive detection of biomarkers in murine models with LPS-induced sepsis

Sepsis is a life-threatening condition, which is irreversible if diagnosis and intervention are delayed. The response of the immune cells towards an infection triggers widespread inflammation through the production of cytokines, which may result in multiple organ dysfunction and eventual death. Conventional detection techniques fail to provide a rapid diagnosis because of their limited sensitivity and tedious protocol. This study proposes a point-of-care (POC) electrochemical biosensor that overcomes the limitations of current biosensing technologies in the clinical setting by its integration with electrokinetics, enhancing the sensitivity to picogram level compared with the nanogram limit of current diagnostic technologies. This biosensor promotes the use of a microelectrode strip to address the limitations of conventional photolithographic fabrication methods. Tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and microRNA-155 (miR-155) were monitored in a lipopolysaccharide (LPS)-induced septic mouse model. The optimum target hybridization time in a high conductivity medium was observed to be 60 s leading to the completion of the whole operation within 5 min compared with the 4-h detection time of the traditional enzyme-linked immunosorbent assay (ELISA). The limit of detection (LOD) was calculated to be 0.84, 0.18, and 0.0014 pg mL-1, respectively. This novel sensor may have potential for the early diagnosis of sepsis in the clinical setting.

"Clickable" graphene nanoribbons for biosensor interfaces

We report on the synthesis of "clickable" graphene nanoribbons (GNRs) and their application as a versatile interface for electrochemical biosensors. GNRs are successfully deposited on gold-coated working electrodes and serve as a platform for the covalent anchoring of a bioreceptor (i.e., a DNA aptamer), enabling selective and sensitive detection of Interleukin 6 (IL6). Moreover, when applied as the intermediate linker on reduced graphene oxide (rGO)-based field-effect transistors (FETs), the GNRs provide improved robustness compared to conventional aromatic bi-functional linker molecules. GNRs enable an orthogonal and covalent attachment of a recognition unit with a considerably higher probe density than previously established methods. Interestingly, we demonstrate that GNRs introduce photoluminescence (PL) when applied to rGO-based FETs, paving the way toward the simultaneous optical and electronic probing of the attached biointerface.

Organic Electrochemical Transistor Aptasensor for Interleukin-6 Detection

We demonstrate an organic electrochemical transistor (OECT) biosensor for the detection of interleukin 6 (IL6), an important biomarker associated with various pathological processes, including chronic inflammation, inflammaging, cancer, and severe COVID-19 infection. The biosensor is functionalized with oligonucleotide aptamers engineered to bind specifically IL6. We developed an easy functionalization strategy based on gold nanoparticles deposited onto a poly(3,4-ethylenedioxythiophene) doped with polystyrenesulfonate (PEDOT:PSS) gate electrode for the subsequent electrodeposition of thiolated aptamers. During this functionalization step, the reduction of sulfide bonds allows for simultaneous deposition of a blocking agent. A detection range from picomolar to nanomolar concentrations for IL6 was achieved, and the selectivity of the device was assessed against Tumor Necrosis Factor (TNF), another cytokine involved in the inflammatory processes.

Nucleic Acid Aptamer-Based Biosensors: A Review

Aptamers, short strands of either DNA, RNA, or peptides, known for their exceptional specificity and high binding affinity to target molecules, are providing significant advancements in the field of health. When seamlessly integrated into biosensor platforms, aptamers give rise to aptasensors, unlocking a new dimension in point-of-care diagnostics with rapid response times and remarkable versatility. As such, this review aims to present an overview of the distinct advantages conferred by aptamers over traditional antibodies as the molecular recognition element in biosensors. Additionally, it delves into the realm of specific aptamers made for the detection of biomarkers associated with infectious diseases, cancer, cardiovascular diseases, and metabolomic and neurological disorders. The review further elucidates the varying binding assays and transducer techniques that support the development of aptasensors. Ultimately, this review discusses the current state of point-of-care diagnostics facilitated by aptasensors and underscores the immense potential of these technologies in advancing the landscape of healthcare delivery.

Successes and Failures of Static Aptamer-Target 3D Docking Models

While Molecular Dynamics simulation programs are probably superior for predicting the binding and affinity of aptamers and their cognate ligands, such molecular dynamics programs require more computing power and analysis time than static docking programs that are more widely accessible to the scientific community on the internet. Static docking programs can be used to investigate the geometric fit of rigid DNA or RNA aptamer 3D structures and their ligands to aid in predicting the relative affinities and cross-reactivity of various potential ligands. Herein, the author describes when such static 3D docking analysis has worked well to produce useful predictions or confirmation of high-affinity aptamer interactions or successful aptamer beacon behavior and when it has not worked well. The analysis of why failures may occur with static 3D computer models is also discussed.

Aptamers Targeting Cardiac Biomarkers as an Analytical Tool for the Diagnostics of Cardiovascular Diseases: A Review

The detection of cardiac biomarkers is used for diagnostics, prognostics, and the risk assessment of cardiovascular diseases. The analysis of cardiac biomarkers is routinely performed with high-sensitivity immunological assays. Aptamers offer an attractive alternative to antibodies for analytical applications but, to date, are not widely practically implemented in diagnostics and medicinal research. This review summarizes the information on the most common cardiac biomarkers and the current state of aptamer research regarding these biomarkers. Aptamers as an analytical tool are well established for troponin I, troponin T, myoglobin, and C-reactive protein. For the rest of the considered cardiac biomarkers, the isolation of novel aptamers or more detailed characterization of the known aptamers are required. More attention should be addressed to the development of dual-aptamer sandwich detection assays and to the studies of aptamer sensing in alternative biological fluids. The universalization of aptamer-based biomarker detection platforms and the integration of aptamer-based sensing to clinical studies are demanded for the practical implementation of aptamers to routine diagnostics. Nevertheless, the wide usage of aptamers for the diagnostics of cardiovascular diseases is promising for the future, with respect to both point-of-care and laboratory testing.

Exploring the most stable aptamer/target molecule complex by the stochastic tunnelling-basin hopping-discrete molecular dynamics method

The stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to the search for the most stable biomolecular complexes in water by using the MARTINI coarse-grained (CG) model. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as an EpCAM adaptor for an EpA (Apt_EpA) benchmark target molecule. The effects of two adsorption positions on the EpCAM were analysed, and it is found that the Apt_EpA adsorption configuration located within the EpCAM pocket-like structure is more stable and the energy barrier is lower due to the interaction with water. By the root mean square deviation (RMSD), the configuration of EpCAM in water is more conservative when the Apt_EpA binds to EpCAM by attaching to the pocket space of the EpCAM dimer. For Apt_EpA, the root mean square fluctuation (RMSF) analysis result indicates Nucleobase 1 and Nucleobase 2 display higher flexibility during the CGMD simulation. Finally, from the binding energy contour maps and histogram plots of EpCAM and each Apt_EpA nucleobase, it is clear that the binding energy adsorbed to the pocket-like structure is more continuous than that energy not adsorbed to the pocket-like structure. This study has proposed a new numerical process for applying the STUN-BH-DMD with the CG model, which can reduce computational details and directly find a more stable Apt_EpA/EpCAM complex in water.

Computer-Aided aptamer design for sulfadimethoxine antibiotic: step by step mutation based on MD simulation approach

This study introduces a computational method to design a new aptamer with higher binding affinity to a special target in comparison with the experimentally available aptamers. The method is called step by step mutation based on MD simulation, which includes some steps. First, MD simulation is performed for the SELEX-introduced (native) aptamer in the presence of the target. Afterwards, conformational factor (P_i) is calculated for the simulated system, which obtains the affinity of the aptamer residues to the target. A nucleotide exchange is done for the residue with the least P_i parameter to the nucleotide with the highest P_i value that results in a mutant aptamer. MD simulation is performed for the target-mutant complex, and P_i values are calculated again. The nucleotide exchange is performed similarly, and the designing process is proceeded repeatedly that results in a mutant with the improved specificity to the target. The aptamer affinity to the target is also determined in each step through calculating the binding Gibbs energy (ΔG_Bind) as a reliable parameter. The introduced strategy is utilized efficiently to design a mutant aptamer with improved specificity toward sulfadimethoxine (SDM) antibiotic as a case study. The great difference in the ΔG_Bind values about 579.856 kJ mol^-1 highlights that the M5 mutant possesses the improved specificity toward SDM in comparison with the native aptamer. Besides, the selectivity of the M5 aptamer toward SDM is examined among some conventional interfering compounds by using MD simulation that confirms the applicability of the designed aptamer for further experimental studies.

Statistical analysis of intermolecular interactions in trypsin-inhibitor complexes

Communicated by Ramaswamy H. Sarma.

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.

The investigation of the G-quadruplex aptamer selectivity to Pb2+ ion: a joint molecular dynamics simulation and density functional theory study

The aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb²⁺ in comparison with some ions. The Free Energy Landscape (FEL) analysis indicates that Pb²⁺ has remained inside the aptamer during the MD simulation, while the other ions have left it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energies prove that the conformational stability of the aptamer is the highest in the presence of Pb²⁺. According to the compaction parameters, the greatest compressed ion-aptamer complex, and hence, the highest ion-aptamer interaction have been induced in the presence of Pb²⁺. The contact maps clarify the closer contacts between the nucleotides of the aptamer in the presence of Pb²⁺. The density functional theory (DFT) results show that Pb²⁺ forms the most stable complex with the aptamer, which is consistent with the MD results. The QM calculations reveal that the N-H bonds and the O…H distances are the longest and the shortest, respectively, in the presence of Pb²⁺. The obtained results verify that the strongest hydrogen bonds (HBs), and hence, the most compressed aptamer structure are induced by Pb²⁺. Besides, atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm the results.Communicated by Ramaswamy H. Sarma.