Computational approach to design of aptamers to the receptor binding domain of sars-cov-2

The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, the only one aptamer (Apt16) was selected from the library as a starting aptamer to the RBD protein. For Apt16/RBD complex, molecular dynamic and quantum chemical calculations revealed the pairs of nucleotides and amino acids whose contribution to the binding between aptamer and RBD is the largest. Taking into account these data, Apt16 was subjected to the structure modifications in order to increase the binding with the RBD. Thus, a new aptamer Apt25 was designed. The procedure of 1) aptamer structure modeling/modification, 2) molecular docking, 3) molecular dynamic simulations, 4) quantum chemical calculations was performed sev-eral times. As a result, four aptamers (Apt16, Apt25, Apt27, Apt31) to the RBD were designed in silico without any preliminary experimental data. Binding of the each modeled aptamer to the RBD was studied in terms of interactions between residues in protein and nucleotides in the aptamers. Based on the simulation results, the strongest binding with the RBD was predicted for two Apt27 and Apt31aptamers. The calculated results are in good agreement with experimental data obtained by flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods. Conclusion. The proposed computational approach to selection and refinement of aptamers is universal and can be used for wide range of molecular ligands and targets. Key words

Армирование грунтов основания вертикальными столбами из щебня в криолитозоне

Stabilization of permafrost soils of the roadbed base, constructed with assumption of thawing, thanks to improvement of their strength characteristics, requires development and selection of rational structural and technological solutions. The objective of the study was to analyze the effectiveness of use of vertical columns of crushed stone in the permafrost zone and their influence on strength characteristics of the soil base. The study has used general scientific methods, modeling, simulation and comparative analysis. This article proposes a method for improving strength properties of soil of the roadbed base within Obskaya–Salekhard section of the Northern Latitudinal Railway thanks to reinforcement of the roadbed base made with vertical columns of crushed stone, which increases stability of the structure. The proposed basic technological model of construction of the roadbed includes the following main stages: preparatory stage, 1 stage – arrangement of vertical columns of crushed stone and granular subbases, 2 stage – additional compaction with a vibratory roller in case of mismatch of stability of bearing capacity and precipitation of the base to operating standards. The studied object of the transport infrastructure was simulated both without the use of technology for reinforcing it with vertical columns of crushed stone and with its use. The stability coefficient was calculated, and the theoretical surface of embankment collapse was obtained using Midas GTS NX and Plaxis 2D software packages. The stability test of this structure was carried out both in a flat and in a threedimensional setting. The efficiency of using vertical columns of crushed stone to strengthen the embankments constructed on permafrost soils has been shown.Стабилизация многолетнемёрзлых грунтов основания земляного полотна, сооружаемого с допущением оттаивания, за счёт улучшения их прочностных характеристик требует разработки и выбора рациональных конструктивно-технологических решений. Целью исследования является анализ эффективности использования вертикальных столбов из щебня в криолитозоне и их влияния на прочностные характеристики грунтов основания. В исследовании использовались общенаучные методы, моделирование и сравнительный анализ. Предлагается метод улучшения прочностных свойств грунтов основания земляного полотна на участке Обская–Салехард Северного широтного хода за счёт армирования вертикальными столбами из щебня, что повышает устойчивость сооружения. Обосновывается принципиальная технологическая схема сооружения земляного полотна, которая включает в себя следующие основные этапы: подготовительный этап, 1 стадия – устройство вертикальных столбов из щебня и щебёночной подушки, 2 стадия – дополнительное уплотнение виброкатком в случае несоответствия устойчивости несущей способности и осадки основания нормам эксплуатации. Выполнено моделирование исследуемого объекта транспортной инфраструктуры как без использования технологии армирования вертикальными столбами из щебня, так и с её применением. Рассчитан коэффициент устойчивости иполучена теоретическая поверхность обрушения насыпи с использованием программных комплексов Midas GTS NX и Plaxis 2D. Проверка устойчивости данного сооружения велась как в плоской, так и в трёхмерной постановке. Показана эффективность использования вертикальных столбов из щебня для усиления насыпей, сооружаемых на многолетнемёрзлых грунтах

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

System of Forest Insect Pheromone Communication: Stability of «Information» Molecules to Environmental Factors

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.Features of external environmental factors (such as electromagnetic radiation in certain spectral bands) influencing pheromone molecules, which are carriers of information for forest insects in the search of the opposite sex, were examined. Stability of pheromone molecules for external influences has been studied for siberian moth Dendrolimus superans sibiricusTschetv., pine moth Dendrilimus piniL., gypsy moth Lymantria disparL., for xylophages Ips typographus L., Monochamus urussovi Fish. and Monochamus galloprovincialis Oliv. Properties of pheromone molecules were evaluated by calculations using quantum-chemical method B3LYP. Existing methods of quantum-chemical calculations are useful for analyzing the properties of quite small and uncomplicated molecules of forest insect pheromones. The calculations showed that the molecules of insect pheromones are able to absorb light in the ultraviolet range and move into an excited state. The values of dipole moments, the wavelengths of the absorption, atomic and molecular electronic properties of pheromones in the ground and excited states were calculated. The calculations showed that for the reaction of pheromones with oxygen an energy barrier is somewhat higher than for reactions of pheromones with water vapor. The worst reaction of pheromones with water molecules likely to pheromones such molecules whose dipole moment is comparable to the dipole moment of water. Quantum-chemical characteristics of the pheromone molecules can be linked to specific behavior of the insects

System of Forest Insect Pheromone Communication: Stability of «Information» Molecules to Environmental Factors

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.Features of external environmental factors (such as electromagnetic radiation in certain spectral bands) influencing pheromone molecules, which are carriers of information for forest insects in the search of the opposite sex, were examined. Stability of pheromone molecules for external influences has been studied for siberian moth Dendrolimus superans sibiricusTschetv., pine moth Dendrilimus piniL., gypsy moth Lymantria disparL., for xylophages Ips typographus L., Monochamus urussovi Fish. and Monochamus galloprovincialis Oliv. Properties of pheromone molecules were evaluated by calculations using quantum-chemical method B3LYP. Existing methods of quantum-chemical calculations are useful for analyzing the properties of quite small and uncomplicated molecules of forest insect pheromones. The calculations showed that the molecules of insect pheromones are able to absorb light in the ultraviolet range and move into an excited state. The values of dipole moments, the wavelengths of the absorption, atomic and molecular electronic properties of pheromones in the ground and excited states were calculated. The calculations showed that for the reaction of pheromones with oxygen an energy barrier is somewhat higher than for reactions of pheromones with water vapor. The worst reaction of pheromones with water molecules likely to pheromones such molecules whose dipole moment is comparable to the dipole moment of water. Quantum-chemical characteristics of the pheromone molecules can be linked to specific behavior of the insects

Estimation of the thermal and photochemical stabilities of pheromones Estimation of the thermal and photochemical stabilities of pheromones

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.The correlation between the kinetic stability of molecules against temperature and variations in their geometric structure under optical excitation is investigated by the example of different organic pheromone molecules sensitive to temperature or ultraviolet radiation using the density functional theory. The kinetic stability is determined by the previously developed method based on the calculation of the probability of extension of any structural bond by a value exceeding the limit value Lмах corresponding to the breaking of the bond under temperature excitation. The kinetic stability calculation only requires the eigenfrequencies and vibrational mode vectors in the molecule ground state to be calculated, without determining the transition states. The weakest bonds in molecules determined by the kinetic stability method are compared with the bond length variations in molecules in the excited state upon absorption of light by a molecule. Good agreement between the results obtained is demonstrated and the difference between them is discussed. The universality of formulations within both approaches used to estimate the stability of different pheromone molecules containing strained cycles and conjugated, double, and single bonds allows these approaches to be applied for studying other molecules

Computational approach to design of aptamers to the receptor binding domain of SARS-CoV-2

The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, the only one aptamer (Apt16) was selected from the library as a starting aptamer to the RBD protein. For Apt16/RBD complex, molecular dynamic and quantum chemical calculations revealed the pairs of nucleotides and amino acids whose contribution to the binding between aptamer and RBD is the largest. Taking into account these data, Apt16 was subjected to the structure modifications in order to increase the binding with the RBD. Thus, a new aptamer Apt25 was designed. The procedure of 1) aptamer structure modeling/modification, 2) molecular docking, 3) molecular dynamic simulations, 4) quantum chemical calculations was performed sev-eral times. As a result, four aptamers (Apt16, Apt25, Apt27, Apt31) to the RBD were designed in silico without any preliminary experimental data. Binding of the each modeled aptamer to the RBD was studied in terms of interactions between residues in protein and nucleotides in the aptamers. Based on the simulation results, the strongest binding with the RBD was predicted for two Apt27 and Apt31aptamers. The calculated results are in good agreement with experimental data obtained by flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods. Conclusion. The proposed computational approach to selection and refinement of aptamers is universal and can be used for wide range of molecular ligands and targets.nonPeerReviewe

Action of the Atomic and Electronic Structure of Pheromone Molecules on the Effectiveness of Communication in Xylophagous Insects

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.The B3LYР/6-31(p,d) density functional method is applied to pheromones of the forest xylophagous insects Ips typographus L., Monochamus urussovi Fisch., and Monochamus galloprovincialis Oliv. to calculate the absorption spectra and find excited states. The calculated results are used to assess the possible activity of the molecules when they are affected by solar radiation

The Stability of the Pheromones of Xylophagous Insects to Environmental Factors: An Evaluation by Quantum Chemical Analysis

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.Abstract—The ground and excited states of the pheromone molecules produced by xylophagous insects (the bark beetle Ips typographus L., the black fir sawyer beetle Monochamus urussovi Fisch., and the black pine sawyer M. galloprovincialis Oliv.) were modeled using a quantum chemical method utilizing DFT (density functional theory) with the B3LYP functional. The absorption wavelengths (energies) and dipole moments were calculated; the transitions of electrons from occupied to empty molecular orbitals were considered. The computed data were used to assess the stability of pheromone molecules exposed to environmental factors, such as solar radiation and humidity

Action of the Atomic and Electronic Structure of Pheromone Molecules on the Effectiveness of Communication in Xylophagous Insects

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.The B3LYР/6-31(p,d) density functional method is applied to pheromones of the forest xylophagous insects Ips typographus L., Monochamus urussovi Fisch., and Monochamus galloprovincialis Oliv. to calculate the absorption spectra and find excited states. The calculated results are used to assess the possible activity of the molecules when they are affected by solar radiation