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

Alternative Electron Sources for Cytochrome P450s Catalytic Cycle: Biosensing and Biosynthetic Application

The functional significance of cytochrome P450s (CYP) enzymes is their ability to catalyze the biotransformation of xenobiotics and endogenous compounds. P450 enzymes catalyze regio- and stereoselective oxidations of C-C and C-H bonds in the presence of oxygen as a cosubstrate. Initiation of cytochrome P450 catalytic cycle needs an electron donor (NADPH, NADH cofactor) in nature or alternative artificial electron donors such as electrodes, peroxides, photo reduction, and construction of enzymatic “galvanic couple”. In our review paper, we described alternative “handmade” electron sources to support cytochrome P450 catalysis. Physical-chemical methods in relation to biomolecules are possible to convert from laboratory to industry and construct P450-bioreactors for practical application. We analyzed electrochemical reactions using modified electrodes as electron donors. Electrode/P450 systems are the most analyzed in terms of the mechanisms underlying P450-catalyzed reactions. Comparative analysis of flat 2D and nanopore 3D electrode modifiers is discussed. Solar-powered photobiocatalysis for CYP systems with photocurrents providing electrons to heme iron of CYP and photoelectrochemical biosensors are also promising alternative light-driven systems. Several examples of artificial “galvanic element” construction using Zn as an electron source for the reduction of Fe3+ ion of heme demonstrated potential application. The characteristics, performance, and potential applications of P450 electrochemical systems are also discussed

The Use of Deep Machine Learning for the Automated Selection of Remote Sensing Data for the Determination of Areas of Arable Land Degradation Processes Distribution

Soil degradation processes are widespread on agricultural land. Ground-based methods for detecting degradation require a lot of labor and time. Remote methods based on the analysis of vegetation indices can significantly reduce the volume of ground surveys. Currently, machine learning methods are increasingly being used to analyze remote sensing data. In this paper, the task is set to apply deep machine learning methods and methods of vegetation indices calculation to automate the detection of areas of soil degradation development on arable land. In the course of the work, a method was developed for determining the location of degraded areas of soil cover on arable fields. The method is based on the use of multi-temporal remote sensing data. The selection of suitable remote sensing data scenes is based on deep machine learning. Deep machine learning was based on an analysis of 1028 scenes of Landsats 4, 5, 7 and 8 on 530 agricultural fields. Landsat data from 1984 to 2019 was analyzed. Dataset was created manually for each pair of “Landsat scene”/“agricultural field number”(for each agricultural field, the suitability of each Landsat scene was assessed). Areas of soil degradation were calculated based on the frequency of occurrence of low NDVI values over 35 years. Low NDVI values were calculated separately for each suitable fragment of the satellite image within the boundaries of each agricultural field. NDVI values of one-third of the field area and lower than the other two-thirds were considered low. During testing, the method gave 12.5% of type I errors (false positive) and 3.8% of type II errors (false negative). Independent verification of the method was carried out on six agricultural fields on an area of 713.3 hectares. Humus content and thickness of the humus horizon were determined in 42 ground-based points. In arable land degradation areas identified by the proposed method, the probability of detecting soil degradation by field methods was 87.5%. The probability of detecting soil degradation by ground-based methods outside the predicted regions was 3.8%. The results indicate that deep machine learning is feasible for remote sensing data selection based on a binary dataset. This eliminates the need for intermediate filtering systems in the selection of satellite imagery (determination of clouds, shadows from clouds, open soil surface, etc.). Direct selection of Landsat scenes suitable for calculations has been made. It allows automating the process of constructing soil degradation maps

Informativeness of the Long-Term Average Spectral Characteristics of the Bare Soil Surface for the Detection of Soil Cover Degradation with the Neural Network Filtering of Remote Sensing Data

The long-term spectral characteristics of the bare soil surface (BSS) in the BLUE, GREEN, RED, NIR, SWIR1, and SWIR2 Landsat spectral bands are poorly studied. Most often, the RED and NIR spectral bands are used to analyze the spatial heterogeneity of the soil cover; in our opinion, it is outmoded and seems unreasonable. The study of multi-temporal spectral characteristics requires the processing of big remote sensing data based on artificial intelligence in the form of convolutional neural networks. The analysis of BSS belongs to the direct methods of analysis of the soil cover. Soil degradation can be detected by ground methods (field reconnaissance surveys), modeling, or digital methods, and based on the remote sensing data (RSD) analysis. Ground methods are laborious, and modeling gives indirect results. RSD analysis can be based on the principles of calculation of vegetation indices (VIs) and on the BSS identification. The calculation of VIs also provides indirect information about the soil cover through the state of vegetation. BSS analysis is a direct method for analyzing soil cover heterogeneity. In this work, the informativeness of the long-term (37 years) average spectral characteristics of the BLUE, GREEN, RED, NIR, SWIR1 and SWIR2 bands of the Landsat 4–8 satellites for detecting areas of soil degradation with recognition of the BSS using deep machine learning methods was estimated. The objects of study are the spectral characteristics of kastanozems (dark chestnut soils) in the south of Russia in the territory of the Morozovsky district of the Rostov region. Soil degradation in this area is mainly caused by erosion. The following methods were used: retrospective monitoring of soil and land cover, deep machine learning using convolutional neural networks, and cartographic analysis. Six new maps of the average long-term spectral brightness of the BSS have been obtained. The information content of the BSS for six spectral bands has been verified on the basis of ground surveys. The informativeness was determined by the percentage of coincidences of degradation facts identified during the RSD analysis, and those determined in the field. It has been established that the spectral bands line up in the following descending order of information content: RED, NIR, GREEN, BLUE, SWIR1, SWIR2. The accuracy of degradation maps by band was determined as: RED—84.6%, NIR—82.9%, GREEN—78.0%, BLUE—78.0%, SWIR1—75.5%, SWIR2—62.2%

Recognition of the Bare Soil Using Deep Machine Learning Methods to Create Maps of Arable Soil Degradation Based on the Analysis of Multi-Temporal Remote Sensing Data

The detection of degraded soil distribution areas is an urgent task. It is difficult and very time consuming to solve this problem using ground methods. The modeling of degradation processes based on digital elevation models makes it possible to construct maps of potential degradation, which may differ from the actual spatial distribution of degradation. The use of remote sensing data (RSD) for soil degradation detection is very widespread. Most often, vegetation indices (indicative botany) have been used for this purpose. In this paper, we propose a method for constructing soil maps based on a multi-temporal analysis of the bare soil surface (BSS). It is an alternative method to the use of vegetation indices. The detection of the bare soil surface was carried out using the spectral neighborhood of the soil line (SNSL) technology. For the automatic recognition of BSS on each RSD image, computer vision based on deep machine learning (neural networks) was used. A dataset of 244 BSS distribution masks on 244 Landsat 4, 5, 7, and 8 scenes over 37 years was developed. Half of the dataset was used as a training sample (Landsat path/row 173/028). The other half was used as a test sample (Landsat path/row 174/027). Binary masks were sufficient for recognition. For each RSD pixel, value “1” was set when determining the BSS. In the absence of BSS, value “0” was set. The accuracy of the machine prediction of the presence of BSS was 75%. The detection of degradation was based on the average long-term spectral characteristics of the RED and NIR bands. The coefficient Cmean, which is the distance of the point with the average long-term values of RED and NIR from the origin of the spectral plane RED/NIR, was calculated as an integral characteristic of the mean long-term values. Higher long-term average values of spectral brightness served as indicators of the spread of soil degradation. To test the method of constructing soil degradation maps based on deep machine learning, an acceptance sample of 133 Landsat scenes of path/row 173/026 was used. On the territory of the acceptance sample, ground verifications of the maps of the coefficient Cmean were carried out. Ground verification showed that the values of this coefficient make it possible to estimate the content of organic matter in the plow horizon (R2 = 0.841) and the thickness of the humus horizon (R2 = 0.8599). In total, 80 soil pits were analyzed on an area of 649 ha on eight agricultural fields. Type I error (false positive) of degradation detection was 17.5%, and type II error (false negative) was 2.5%. During the determination of the presence of degradation by ground methods, 90% of the ground data coincided with the detection of degradation from RSD. Thus, the quality of machine learning for BSS recognition is sufficient for the construction of soil degradation maps. The SNSL technology allows us to create maps of soil degradation based on the long-term average spectral characteristics of the BSS

Improving the Efficiency of Electrocatalysis of Cytochrome P450 3A4 by Modifying the Electrode with Membrane Protein Streptolysin O for Studying the Metabolic Transformations of Drugs

In the present work, screen-printed electrodes (SPE) modified with a synthetic surfactant, didodecyldimethylammonium bromide (DDAB) and streptolysin O (SLO) were prepared for cytochrome P450 3A4 (CYP3A4) immobilization, direct non-catalytic and catalytic electrochemistry. The immobilized CYP3A4 demonstrated a pair of redox peaks with a formal potential of −0.325 ± 0.024 V (vs. the Ag/AgCl reference electrode). The electron transfer process showed a surface-controlled mechanism (“protein film voltammetry”) with an electron transfer rate constant (ks) of 0.203 ± 0.038 s−1. Electrochemical CYP3A4-mediated reaction of N-demethylation of erythromycin was explored with the following parameters: an applied potential of −0.5 V and a duration time of 20 min. The system with DDAB/SLO as the electrode modifier showed conversion of erythromycin with an efficiency higher than the electrode modified with DDAB only. Confining CYP3A4 inside the protein frame of SLO accelerated the enzymatic reaction. The increases in product formation in the reaction of the electrochemical N-demethylation of erythromycin for SPE/DDAB/CYP3A4 and SPE/DDAB/SLO/CYP3A4 were equal to 100 ± 22% and 297 ± 7%, respectively. As revealed by AFM images, the SPE/DDAB/SLO possessed a more developed surface with protein cavities in comparison with SPE/DDAB for the effective immobilization of the CYP3A4 enzyme

Recognition of the Bare Soil Using Deep Machine Learning Methods to Create Maps of Arable Soil Degradation Based on the Analysis of Multi-Temporal Remote Sensing Data

The detection of degraded soil distribution areas is an urgent task. It is difficult and very time consuming to solve this problem using ground methods. The modeling of degradation processes based on digital elevation models makes it possible to construct maps of potential degradation, which may differ from the actual spatial distribution of degradation. The use of remote sensing data (RSD) for soil degradation detection is very widespread. Most often, vegetation indices (indicative botany) have been used for this purpose. In this paper, we propose a method for constructing soil maps based on a multi-temporal analysis of the bare soil surface (BSS). It is an alternative method to the use of vegetation indices. The detection of the bare soil surface was carried out using the spectral neighborhood of the soil line (SNSL) technology. For the automatic recognition of BSS on each RSD image, computer vision based on deep machine learning (neural networks) was used. A dataset of 244 BSS distribution masks on 244 Landsat 4, 5, 7, and 8 scenes over 37 years was developed. Half of the dataset was used as a training sample (Landsat path/row 173/028). The other half was used as a test sample (Landsat path/row 174/027). Binary masks were sufficient for recognition. For each RSD pixel, value “1” was set when determining the BSS. In the absence of BSS, value “0” was set. The accuracy of the machine prediction of the presence of BSS was 75%. The detection of degradation was based on the average long-term spectral characteristics of the RED and NIR bands. The coefficient Cmean, which is the distance of the point with the average long-term values of RED and NIR from the origin of the spectral plane RED/NIR, was calculated as an integral characteristic of the mean long-term values. Higher long-term average values of spectral brightness served as indicators of the spread of soil degradation. To test the method of constructing soil degradation maps based on deep machine learning, an acceptance sample of 133 Landsat scenes of path/row 173/026 was used. On the territory of the acceptance sample, ground verifications of the maps of the coefficient Cmean were carried out. Ground verification showed that the values of this coefficient make it possible to estimate the content of organic matter in the plow horizon (R2 = 0.841) and the thickness of the humus horizon (R2 = 0.8599). In total, 80 soil pits were analyzed on an area of 649 ha on eight agricultural fields. Type I error (false positive) of degradation detection was 17.5%, and type II error (false negative) was 2.5%. During the determination of the presence of degradation by ground methods, 90% of the ground data coincided with the detection of degradation from RSD. Thus, the quality of machine learning for BSS recognition is sufficient for the construction of soil degradation maps. The SNSL technology allows us to create maps of soil degradation based on the long-term average spectral characteristics of the BSS

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 using small-angle X-ray scattering, cytometry, and fluorescence polarization. Using a new iterative design procedure, Interaction Based Drug Design (SIBDD), a highly specific aptamer to the receptor-binding 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 variants.peerReviewe