Structure- and interaction-based design of anti-SARS-CoV-2 aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptorbinding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variant

Скрининг белков-биомаркеров рака легкого с помощью мультиплексной электрохимической сенсорной системы на основе аптамеров

The aim of this work is the development and demonstration of the method of simultaneous detection of several biomarkers of lung cancer in the blood plasma of patients using a multiplex electrochemical testing system based on DNA aptamers. DNA aptamers are a new class of synthetic affinity probes obtained by in vitro or in vivo selection procedure by the systematic evolution of ligands by exponential enrichment (SELEX).Materials and methods. A set of aptamers obtained previously by selection for postoperative lung cancer tissue was used to create a multiplex electrochemical biochip. Identification of aptamer target proteins was performed using a modified affinity enrichment method (AptaBID). Molecular targets for the used set of aptamers to lung cancer were defined as vimentin, defensin, a light chain of myosin, tubulin alpha 1-B, neutrophil elastase and A1 elongation factor 1.Measurements of the presence of these biomarker proteins in blood plasma were carried out using electrochemical detection. The difference between peak heights before and after plasma deposition on the electrodes modified by aptamers was considered as a response of the system to the presence of protein onco-markers in blood plasma. Blood plasma of healthy volunteers was used as control.Results. Research showed that in the blood plasma of all the patients with lung cancer the content of biomarker proteins that bind to aptamers on electrode surfaces was increased. The increased content of these proteins in the blood plasma of patients suggests the presence of invasiveness and metastasis of tumors and their chemo-resistance.Цель. Разработка и демонстрация метода одновременного определения нескольких биомаркеров рака легкого в плазме крови больных с помощью мультиплексной электрохимической сенсорной системы, основанной на ДНК-аптамерах. ДНК-аптамеры представляют собой новый класс синтетических аффинных реагентов, получаемых с помощью процедуры селекции in vitro или in vivo методом систематической эволюции лигандов экспоненциальным обогащением (SELEX).Материалы и методы. Для создания мультиплексного электрохимического биочипа использовалось несколько аптамеров, полученных ранее путем селекции к послеоперационным тканям рака легкого. Идентификацию белков-мишеней аптамеров проводили с помощью модифицированного метода аффинного обогащения (AptaBID). В качестве молекулярных мишеней для использованного набора аптамеров к раку легкого были определены виментин, дефензин, легкая цепь миозина, тубулин альфа 1-B, нейтрофил эластаза и фактор удлинения 1 A1. Определение наличия этих белков-биомаркеров в плазме крови проводили с помощью электрохимической детекции. В качестве отклика системы на присутствие белков-онкомаркеров в плазме крови выступала разница между величинами пиков на квадратно-волновой вольтамперограмме до и после нанесения плазмы на электроды с предварительно иммобилизированными на их поверхности аптамерами. Для контрольного сравнения использовалась плазма крови здоровых добровольцев.Результаты. Показано, что в плазме крови всех исследованных больных раком легкого повышено содержание белков-биомаркеров, связывающихся с аптамерами на поверхностях электродов. Повышенное содержание этих белков в плазме крови больных предполагает их химиорезистентность и высокую степень инвазивности и метастазирования опухолей

Monitoring of breast cancer progression via aptamer-based detection of circulating tumor cells in clinical blood samples

Introduction: Breast cancer (BC) diagnostics lack noninvasive methods and procedures for screening and monitoring disease dynamics. Admitted CellSearch® is used for fluid biopsy and capture of circulating tumor cells of only epithelial origin. Here we describe an RNA aptamer (MDA231) for detecting BC cells in clinical samples, including blood. The MDA231 aptamer was originally selected against triple-negative breast cancer cell line MDA-MB-231 using cell-SELEX.Methods: The aptamer structure in solution was predicted using mFold program and molecular dynamic simulations. The affinity and specificity of the evolved aptamers were evaluated by flow cytometry and laser scanning microscopy on clinical tissues from breast cancer patients. CTCs were isolated form the patients’ blood using the developed method of aptamer-based magnetic separation. Breast cancer origin of CTCs was confirmed by cytological, RT-qPCR and Immunocytochemical analyses.Results: MDA231 can specifically recognize breast cancer cells in surgically resected tissues from patients with different molecular subtypes: triple-negative, Luminal A, and Luminal B, but not in benign tumors, lung cancer, glial tumor and healthy epithelial from lungs and breast. This RNA aptamer can identify cancer cells in complex cellular environments, including tumor biopsies (e.g., tumor tissues vs. margins) and clinical blood samples (e.g., circulating tumor cells). Breast cancer origin of the aptamer-based magnetically separated CTCs has been proved by immunocytochemistry and mammaglobin mRNA expression.Discussion: We suggest a simple, minimally-invasive breast cancer diagnostic method based on non-epithelial MDA231 aptamer-specific magnetic isolation of circulating tumor cells. Isolated cells are intact and can be utilized for molecular diagnostics purposes

Возможности компьютерно-то쬬¬¬¬¬¬ографической ангиопульмонографии в диагностике тромбоэмболии легочной артерии

The purpose of this search is to evaluate diagnostic capability of CT pulmonary angiography (CTPAG) in patients with pulmonary embolism. Examination results of 45 patients with suspected pulmonary embolism provided. Pulmonary embolism symptoms and frequency of their occurrence in study group described. The modification of technical CTPAG protocol proposed for to improve visualization and to reduce radiation exposure.С целью оценки диагностических возможностей компьютерно-томографической ангиопульмонографии (КТАПГ) в выявлении тромбоэмболии легочных артерий (ТЭЛА) приведены результаты обследования 45 пациентов с подозрением на тромбоэмболию легочной артерии (ТЭЛА). Описаны компьютерно-томографические симптомы ТЭЛА и частота их встречаемости в обследуемой группе. Предложена модификация технического протокола КТАПГ, позволяющая повысить качество визуализации, снизить лучевую нагрузку

Аптамеры для диагностики и лечения глиальных опухолей человека

Purpose of the study: to evaluate the feasibility of using functional analogues of protein antibodies – dNa/ RNa aptamers in diagnostics, treatment and prognosis of human brain glial tumors.Material and Methods. The relevant literature sources were searched in scopus, Web of science, pubmed, elibrary with inclusion of publications from 2000 to 2023. sixty articles are presented in the review.Results. The analysis of the literature devoted to classification, diagnostics and therapy of brain glioblastomas was carried out and the feasibility of using for in vivo diagnostics and therapy of this disease aptamers, which are molecular recognition elements based on DNA/RNA oligonucleotides, capable of binding to the given molecular targets and distinguishing even separate functional groups in them, was studied. A list of aptamers to human glial brain tumors and their molecular targets that can be used for diagnostics and therapy of glioblastoma, including tumor imaging by pet/ct, mRi, plasmon resonance, fluorescence and confocal microscopy, etc., is presented. literature data suggest that DNA/RNA aptamers can be used to search for circulating tumor cells in the blood of glioblastoma patients, to target therapeutic drugs to the tumor and to inhibit tumor growth.Conclusion. Brain glioblastoma is a heterogeneous tumor consisting of cells at different stages of malignancy and, accordingly, with a different set of oncogenes. For this reason, a multitarget strategy that includes combined suppression of angiogenesis, invasion, metastasis, proliferation and survival of tumor cells should be proposed for the therapy of this disease. DNA/RNA aptamers tailored to key proteins involved in oncogenic transformation may be suitable candidates for the implementation of multitarget therapy for brain glioblastoma.Цель исследования – оценить возможность использования функциональных аналогов белковых антител – ДНК/РНК-аптамеров в диагностике, лечении и прогнозировании развития глиальных опухолей головного мозга человека.Материал и методы. Поиск соответствующих источников литературы проводили в системах scopus, Web of science, pubmed, elibrary с включением публикаций с 2000 по 2023 г. В обзоре представлены данные из 60 статей.Результаты. Проведен анализ литературы, посвященной классификации, диагностике и терапии глиобластом головного мозга и изучению возможности использования для in vivo диагностики и терапии этого заболевания аптамеров, которые представляют собой молекулярные распознающие элементы на основе ДНК/РНК-олигонуклеотидов, способных связываться с заданными молекулярными мишенями и различать в них даже отдельные функциональные группы. Приведен список из аптамеров к глиальным опухолям головного мозга человека и их молекулярных мишеней, которые могут быть использованы для диагностики и терапии глиобластомы, в том числе для визуализации опухоли методами ПЭТ/КТ, МРТ, плазмонного резонанса, флуоресцентной и конфокальной микроскопии и др. Данные литературы свидетельствуют о том, что с помощью ДНК/РНК-аптамеров можно осуществлять поиск циркулирующих опухолевых клеток в крови больных глиобластомой, адресную доставку к опухоли терапевтических препаратов и подавлять опухолевый рост.Заключение. Глиобластома головного мозга – гетерогенная опухоль, состоящая из клеток, находящихся на разной стадии злокачественности и, соответственно, с различным набором онкогенов. Именно поэтому для терапии этого заболевания должна быть предложена мультитаргетная стратегия, которая включает в себя комбинированное подавление ангиогенеза, инвазии, метастазирования, пролиферации и выживаемости опухолевых клеток. Подходящими кандидатами для реализации мультитаргетной терапии глиобластомы головного мозга могут стать ДНК/РНК-аптамеры, подобранные к ключевым белкам, участвующим в онкогенной трансформации

Electrochemical aptasensor for lung cancer-related protein detection in crude blood plasma samples

The development of an aptamer-based electrochemical sensor for lung cancer detection is presented in the work.A highly specific DNA-aptamer, LC-18, selected to postoperative lung cancer tissues was immobilized onto a gold microelectrode and electrochemical measurements were performed in a solution contaning the redox marker ferrocyanide/ferricyanide. As a result, the electrochemical aptasensor was able to detect cancer-related targets in crude blood plasma of lung cancer patients

Bioluminescent aptamer-based solid-phase microassay to detect lung tumor cells in plasma

Two high-affinity DNA aptamers for lung tumor cells were applied as biospecific elements in bioluminescent assay of patient blood. The oligonucleotide complementary to the 5' end of both aptamers carrying either biotin or Ca2+-regulated photoprotein obelin was used to form a sandwich-type analytical complex on the surfaces of magnetic streptavidin-activated microspherical particles. Clinical blood samples from cases of morphologically confirmed lung cancer and control samples were analyzed applying the developed assay. From the receiver operator curve (ROC) analysis, the chosen threshold value as clinical decision limit offers the sensitivity of 91.5% and the specificity of 75% (p<0.001). The area under ROC curve with the value of 0.901 distinguishes well between the two groups under investigation

Development of a Biosensor for Electrochemical Detection of Tumor-Associated Proteins in Blood Plasma of Cancer Patients by Aptamers

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.A molecular biosensor based on DNA aptamers (aptasensors) for the diagnosis of lung cancer in blood plasma samples was designed. To create the aptasensor, aptamer 17_80, obtained in the study of postoperative material, was used. The affinity and binding selectivity of the aptamer 17_80 to the lung tumor tissue was confirmed on histological sections of postmortem samples of lung tissue. Using affinity enrichment and mass spectrometry, a possible target molecular of the aptamer 17_80, vimentin, was found

Magnetic Field Parameters Determination for the Magneto-mechanical Activation of Ehrlich Ascites Carcinoma Cells Using Aptamers with Magnetic Nanoparticles

Magneto-mechanical activation in nonheating low-frequency magnetic field is a promising method for cancer therapy. It is contactless with very high penetration depth (>1 m) and a minimum of side effects and risks. Nevertheless, there is still no developed theory and a sufficient amount of experimental data. The aim of this study was to determine the parameters of magnetic field oscillation frequency and signal waveform to perform the magneto-mechanical activation of Ehrlich ascites carcinoma cells using aptamers with magnetic nanoparticles

Development of a Biosensor for Electrochemical Detection of Tumor-Associated Proteins in Blood Plasma of Cancer Patients by Aptamers

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.A molecular biosensor based on DNA aptamers (aptasensors) for the diagnosis of lung cancer in blood plasma samples was designed. To create the aptasensor, aptamer 17_80, obtained in the study of postoperative material, was used. The affinity and binding selectivity of the aptamer 17_80 to the lung tumor tissue was confirmed on histological sections of postmortem samples of lung tissue. Using affinity enrichment and mass spectrometry, a possible target molecular of the aptamer 17_80, vimentin, was found