=Paper=
{{Paper
|id=Vol-3309/short4
|storemode=property
|title=Biosafety and Biosafety of Health and the Environment on the Basis of Information Technologies Column
|pdfUrl=https://ceur-ws.org/Vol-3309/short4.pdf
|volume=Vol-3309
|authors=Sofiya Vasylyuk,Oleksa Shved,Zoriana Hubrii,Olena Vichko,Olha Shved
|dblpUrl=https://dblp.org/rec/conf/ittap/VasylyukSHVS22
}}
==Biosafety and Biosafety of Health and the Environment on the Basis of Information Technologies Column==
https://ceur-ws.org/Vol-3309/short4.pdf
Biosafety and Biosafety of Health and the Environment on the
Basis of Information Technologies
Sofiya Vasylyuka, Oleksa Shveda, Zoriana Hubriia, Olena Vichkob and Olha Shveda
a
Lviv Polytechnic National University, 12 Bandera street, Lviv, 79013, Ukraine
b
Ternopil Ivan Puluj National Technical University, 56 Ruska street, 46001, Ternopil, Ukraine
Abstract
An abstract logical and comparative analysis of the use of alternative methods using
information technologies and computer methods of molecular modeling and analysis of
“structure-activity” relationships in the construction of safe biosubstances with the
preservation of a safe environment in the production of drugs and products was conducted.
The possibility of bioremediation of pollutants based on data from literary sources and
experimental synthesis and screening of bioactivity of substances for their introduction into
technological processes of the food, pharmaceutical and chemical industry with the possible
utilization of waste through bioremediation was investigated.
Keywords 1
biosafety, bioremediation, bioactivity prediction, biologically active substances, biotesting,
bioutilization, bioactivity screening.
1. Introduction
The current state of scientific research projects of biotechnology and commercial bioindustry in
Ukraine regarding the development of bioengineering, as well as the level of development of
biotechnological products production, requires innovative ways of safe research, biosafe latest
technologies for the production, consumption and disposal of bioproducts waste, as side effects or
double use of such technologies are possible and products often become a source of public fears, the
subject of polar discussions and protests. Such a situation arises due to possible biothreats in the case
of unprofessional or criminal use of advances in pharmaceuticals, agriculture, food and other sectors
of the economy.
Scientific inquiries regarding the determination of the relationship between bioactivity and the
structure of compounds in the development of new synthetic or bioengineering agents (medical,
veterinary, and agricultural) obtained by various methods are relevant to this day [1]. methods, among
which the evaluation of the acute toxicity of the products is carried out on laboratory animals in vivo
[2]. However, such experimental studies are quite valuable, in addition, they are constantly criticized
for ethical reasons. Therefore, since 2007, documents have been developed, in particular the
Guidelines of the European Community on chemicals and their safe use (REACH), which provide for
the development of computerized methods for analyzing "structure-activity" relationships and
studying toxic effects [3]. In the light of solving this problem, the importance of using information
technologies for the determination of pollutants and toxins in the monitoring of the environment and
the safety of ecosystems for human health cannot be ignored.
ITTAP’2022: 2nd InternationalWorkshop on Information Technologies: Theoretical and Applied Problems, November 22–24, 2022,
Ternopil, Ukraine
EMAIL: sofiia.v.vasyliuk@lpnu.ua (A. 1); oleksa.shved@gmail.com (A. 2); zoriana.v.hubrii@lpnu.ua (A. 3); o.vichko.te@gmail.com (A.
4); olha.v.shved@lpnu.ua (A. 5)
ORCID: 0000-0003-2946-0513 (A. 1); 0000-0003-0914-3270 (A. 2); 0000-0003-2533-6857 (A. 3); 0000-0002-5440-548X (A. 4);
0000-0002-6023-8067 (A. 5)
2022 Copyright for this paper by its authors.
Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).
CEUR Workshop Proceedings (CEUR-WS.org)
The main purpose of the work it is the identification of promising bioactive substances and the
search and development of ways to eliminate pollutants and toxins on the basis of information
technologies using computer modeling of the bioactivity of compounds to create and real load the
most common pollutants, taking into account the principles of sustainable development.
2. Results and methodology
2.1. Methodology
In the research process, a number of methods were used: abstract-logical (to generalize the
methods of assessing the impact of harmful substances of enterprises on the environment), analysis
and synthesis (to determine a comprehensive index of assessment of negative impacts), systemic
analysis (to develop a system of pollution prevention measures). To predict the bioactivity of
substances of potential drugs, a study was conducted using online resources SwissTargetPrediction
and SuperPred and Molinspiration Cheminformatics [4,5,6]. To characterize the level of pollution in
ecosystems, we used the results of our own research, as well as data from the literature. In
experimental studies during biotesting and bioengineering of bioobjects, simulations of the real load
of the most common pollutants, in particular nitrogen-containing ones, were carried out on the basis
of biocomputing, which made it possible to find and develop ways to eliminate such pollution and
toxins by complex bioremediation.
2.2. Results
In the analysis of data on the use of information technologies in the design of drugs and in the
utilization of pollutants from industrial and household waste showed the need for new innovative
approaches to the careful study and implementation of mathematical modeling and forecasting in the
study of the bioactivity of substances and the performance of biotests in the study of biological
objects at laboratory, pilot and production locations taking into account the dual use of biosafety
results, knowledge of means of protection and elimination of biorisks in the production and
consumption of bioproducts. This is required by the sphere of production and the sphere of the market
of consumption and use of products of chemical, pharmaceutical or biological origin [7].
The development of effective bioactive substances for pharmaceuticals, agricultural technology,
veterinary medicine and food technology is a long process and requires enormous financial costs. The
majority of biosubstances were discovered as a result of systematic optimization of lead compounds
that were found when testing substances on animals in vivo, isolated organs or in vitro on models of
enzyme inhibition or binding to receptors. At the same time, one discovered biosubstance accounts for
hundreds of thousands, or even more, of studied compounds [8]. Therefore, nowadays, the initial
stage of leader-compound search among the data of combinatorial libraries of biologically active
compounds is the use of pre-experimental in silico methods, in particular, virtual screening [9]. Since
the initial data for such screening are only chemical structures and calculated properties of
compounds, it can be applied to virtual libraries of almost any size.
For pharmaceuticals, the use of "drug-like" characteristics in the search for potential candidates for
a medicinal substance and the prediction of the biological activity of compounds using the
Molinspiration Cheminformatics internet service should be singled out as effective methods of virtual
screening. The term "drug-like characteristics" began to be widely used after the publication of the
work of Lipinski and colleagues [10]. It covers the concept of some characteristics of the structure of
compounds that affect their biological effect and are related to properties that affect adsorption,
distribution, metabolism, excretion and toxicity.
Based on the observations that most medicinal substances are relatively small and lipophilic
molecules, Lipinski formulated empirical rules (Lipinski's rules or "rule of five") [10]. These rules are
a set of molecular descriptors obtained on the basis of the analysis and classification of key
physicochemical properties of medicinal products and biologically active compounds
Each of the parameters (Fig. 1) characterizes certain features of the structure. Molecular mass is a
parameter related to the size of the molecule. Lipophilicity characterizes the distribution of the substance
between the aqueous and lipid phases in the body and the ability of the substance to pass through the cell
membrane. Parameters C and D indicate the ability of the compound to form, as a rule, hydrogen bonds, at
the "appropriate" site of the biomolecule. Parameter E characterizes the "stiffness" of the structure and
indicates the volume of the bound substance.
Figure 1: Lipinski's rules
One of the ways to assess the potential of natural and synthetic molecules (real or virtual) as biosubstances
for safe protection of health or the environment is to determine their molecular targets. At the same time, the
search for new targets for existing biosubstances using information technologies, as opposed to traditional
experimental methods, can expand the limits of the application of these substances in a shorter time and at a
lower cost. On the other hand, newly discovered molecular targets of existing biosubstances may involve
potential side effects and drug toxicity, so efforts should be made to improve the safety of these substances.
Experimental methods for identifying targets from in vivo are extremely time-consuming, expensive, and
sometimes unsuccessful, because their implementation requires the development of effective experiments of
biochemical and genetic interaction [11].
The currently available in silico bioactivity prediction approaches can be broadly classified into three
groups: based on ligands (chemically similar compounds exhibit similar biological activity), based on
structure (use of available three-dimensional 3D structures of targets to assess the structural and chemical
suitability of the requested compound to the target ) and hybrid.
Examples of ligand-based methods include SEA, SuperPred, PASS, and TarPred. To improve prediction
performance, new techniques have emerged that use supervised (such as HitPick and Target Hunter) and
unsupervised machine learning (ML) (such as SPiDER) to improve model accuracy. In addition, some of the
previous methods, such as ChemProt and SwissTargetPrediction, have also updated their search engines to
use ML models that have shown better performance
Research of bioactivity and safety of substances on the basis of information technology is widely used by
the Department of Technology of Biologically Active Compounds, Pharmacy and Biotechnology of Lviv
Polytechnic National University in scientific areas and projects. as an alternative to traditional methods, it
was possible to establish the bioactivity of chemical compounds. The use of pre-experimental in silico
methods of studying the bioactivity of chemical substances allowed scientists to optimize the search for
promising substances among a large array (over 500) of thiosulfonate, quinone-containing and heterocyclic
structures synthesized at the department [12, 13], to classify compounds into biologically active (hit-
compound), similar to substance activity (analog-compound) and basic compounds with certain activity
(leader-compound), and quickly and efficiently select promising leader compounds for further experimental
in-depth biological research. In particular, the screening of the biological activity of newly synthesized
compounds by microbiological and physiological methods (1BT screening - the study of many substances in
one biological test and SBT test - the determination of two or three substances in a series of biological tests),
which make it possible to confirm the results of virtual biological screening.
Molinspiration Cheminformatics SuperPred and SwissTargetPrediction online resources were used in the
studies of predicting the biological activity of synthesized compounds.
SwissTargetPrediction is a web tool that allows you to predict the most likely protein targets for small
molecules based on the principle of similarity using reverse screening [4].
SuperPred is a web server for predicting the bioactivity of compounds according to the anatomic-
therapeutic chemical classification system proposed by WHO, for obtaining information about compounds in
the process of drug development [5].
Evidence of the effectiveness of these alternative technologies are the patented biosubstances
discovered with their help and confirmed by experimental research, in particular, an antitumor
substance [14], an antithrombotic substance [15], a veterinary drug [16], a restegulator and a biocide
for combating phytopathogenic microflora during phytoremediation of oil-contaminated soils [17 ]
and a number of substances (for the design of drugs, for the protection of agricultural products from
phytopathogens, for the purification of the aquatic ecosystem, for the bioutilization of waste) that are
undergoing preclinical and clinical trials or are at the patenting stage.
Scientific research in biotechnology and bioengineering, as well as the technology of pharmaceutical
preparations, involves understanding the peculiarities of compliance with safety standards during laboratory
experimental research and production processes, as well as the need to comply with bioethical and biosafety
principles in the scientific and industrial sphere, the introduction of the basic principles of biosecurity
regulation in the field of biotechnology, as well as the use of materials and methods that may cause an
unforeseen danger of dual use and have a negative impact on human safety and the environment
Biosafety problems, deepened by the lack of fundamental knowledge, imperfect modern technologies of
production and waste disposal, since any productions are potential sources of pollution, especially the water
and air ecosystem.
The biosecurity of the use of aquatic bioresources in the discharge of wastewater on the scale of
small towns deserves special attention, taking into account the economic and climatic conditions of
Ukraine. It is considered promising to treat wastewater using biotechnological methods that do not
require significant costs and can be applied on a large scale to save energy and obtain useful products
(environmentally friendly fertilizers, biogas, etc.), and the use of computer models of information
technologies would provide an opportunity to strengthen the complex bioremediation of the
ecosystem by obtaining virtual forecasts of the safety of wastewater pollution of enterprises with
further modeling of cleaning methods and correlation with the obtained experimental data.
The most acceptable today are the methods of cleaning domestic wastewater in artificial
purification ecosystems due to the passage of physical, chemical and biological processes according
to a typical system of cleaning and pollution control and determining the level of pollution by long-
term methods.
Regarding waste disposal, the analysis of literary sources of a number of high-tech and close to natural
domestic wastewater treatment technologies showed that the most promising for application on the scale of
small towns, taking into account the economic and climatic conditions of Ukraine, is the technology of
bioengineering ponds with a horizontal subsurface flow of wastewater and the development of structures
with phytoremediation at bioengineering treatment facilities such as Constructed Wetlands and aerated ponds
(lagoons) biological ponds waste stabilization ponds [18]. Bioengineering ponds in Ukraine are still often
called bioengineering structures or bioplateau structures [18]. However, these structures are characterized by
one significant drawback – the low efficiency of removing nitrogen compounds [19], which requires
additional research. The technology of complex bio-purification facilities of the type of bioengineering ponds
according to the principles of sustainable development is ecologically acceptable and economically the most
promising bio-safe direction in the system of domestic wastewater treatment, water treatment, and therefore
requires the use of information technologies for the careful determination and selection of the method of
cleaning this industrial or domestic effluent.
A particularly important task for improving the ecology of the environment when using bioengineered
ponds with microbial and phytoremediation is to increase the efficiency of removing nitrogen compounds
and xenobiotics from wastewater. Based on the use of bioremediation, a technological scheme was
developed for the treatment of water high-nitrogen effluents using a biocomplex by inoculation of active
biomass of anammox bacteria and colonization with higher plants, which made it possible to increase the
efficiency of removing pollutants and biogenic nitrogen in these ecosystems and improve the functional
parameters of wastewater by intensification in bioengineering ponds with subsurface flow. The advantages of
using the ANAMMOX technology are: reduction of energy costs compared to traditional nitrification -
denitrification up to 60–90%; lack of need for an additional carbon source; decrease in the level of CO2
formation up to 90%; reducing the amount of excess activated sludge; high nitrogen removal efficiency;
smaller water footprint of the process [18]
The initial stage of the proposed complex bioremediation of water effluents on the basis of information
technologies was the modeling of the process of biodestruction of nitrogen-containing pollutants with a bac
preparation based on anammox bacteria. Based on these results, a study was conducted to investigate the
content of archaea in the biofilm of developed pilot bioengineering ponds.
By modeling, designing and launching an experimental engineering installation of complex
phytoremediation and anamox remediation for the conditions of wastewater in a small settlement, it was
established that it is rational to use the nitrogen load as the main parameter for the design of treatment
facilities on the basis. And the optimal load values for polluting substances have been determined: for
nitrogen, no more than 780 mg N/(m2·day); according to COD oxygen up to 2253 mg / (m2 day), which is
necessary for effective removal of nitrogen compounds and organic substances from wastewater [20].
Sufficient attention is paid to the study of the influence of xenobiotic pollutants or waste of natural origin
on the microorganisms of water basins and on the ecology of water bodies in general, since the spread of
local pollution in the water ecosystem even in the world ocean has a step-by-step trend today.
The waste of technological productions usually must be detoxified when thrown out, but it can still
end up in sewage treatment plants, which are actually the main points of pollution, and also due to the
emission of household waste (including synthetic and even partially biodegradable plastic) get into
the water ecosystem, which negatively will affect people's well-being and health. Therefore, the study
of the effect of various types of pollution on biological cleaning products at pilot plants makes it
possible to simulate the process of bioremediation and, with the help of biocomputing, to predict the
process of biodegradation of pollutants and the survivability of biotransformers of pollution
decomposition.
The study of integrated bioremediation facilities showed the safety of using bioremediation through the
complex application of microbial remediants and phytoremediates, especially from excessive nitrogen
pollution based on pilot plants of bioengineering ponds [19].
During the study of complex bioremediation facilities by bioindication and biotesting of bioengineered
ponds, the safety of using microbial remediants of Anamox bacteria was determined. The presence of a
nitrogenous substrate in domestic sewage without prior disposal affects the growth and accumulation of
biomass of pathogenic bacteria. Therefore, the use of bacterial remediation of the water environment, at least
within the limits of the artificial ecosystem of treatment facilities, is promising for purification in the
conditions of Anaerobic ammonium oxidation (ANAMMOX-process) to free nitrogen [21].
To solve the issues of cleaning local water ecosystems, biomonitoring of the environment is carried out
using bioindication (higher plants) and biotesting of its individual components (anammox bacteria), which
involves disposal, storage and processing of waste. Biocomp'ting of activity for each substance is carried out
in comparison with the known physiological activity or toxicity of the corresponding substance.
When studying the composition of the microbial population by the PCR method in model and pilot
ecosystems of bioengineering ponds, a number of factors were taken into account on the dynamics of the
biofilm and the content of anammox bacteria. Non-specific (bacterial) as well as functional and group-
specific oligonucleotide primers were used for the analysis (16S rRNA gene of eubacteria, 16S rRNA gene
of anammox bacteria, 16S rRNA gene of aerobic ammonium-oxidizing bacteria, as well as functional genes:
nirS gene of cytochrome cd-1 nitrite reductase, the nosZ N2O reductase gene of denitrifying bacteria and the
Arch-amoA α-subunit ammonium monooxygenase gene of ammonium-oxidizing archaea). In all studied
biofilm samples, the number of genes of anammox bacteria significantly exceeded other groups of bacteria
capable of transforming nitrogen compounds. In all studied biofilm samples, the number of genes of
anammox bacteria significantly exceeded other groups of bacteria capable of transforming nitrogen
compounds.
Based on the results of PCR-RF, conclusions were made about the importance of the role of anammox
bacteria in the installations of bioengineering ponds with horizontal subsurface flow. In all studied biofilm
samples, the number of genes of anammox bacteria significantly outweighed the number of genes of aerobic
ammonia-oxidizing and other groups of bacteria capable of transforming nitrogen compounds. The average
share of anammox bacteria in the total population of eubacteria in the biofilm on the surface of the gravel in
the filter layer for pilot plants with BVR was 18.5 ± 6.0% for the entire period of the experiment. Based on
the results of PCR-RF, conclusions are made about the importance of the role of anammox, which makes it
possible to assess biological risks, in addition, it is possible to obtain information about microorganisms and
strains, their location, as well as about the safety of personnel who need access to pathogens or toxins, or to
assess threats of their improper use.
At the same time, during the biotreatment of waste water, artificial ecosystems (water treatment plants)
carry out anaerobic treatment with the additional production of the energy product biogas, the production of
which is harmed by the products of the oxidative decomposition of nitrogen- and sulfur-containing
compounds - ammonia and hydrogen sulfide. In particular, it negatively affects the production of hydrogen
sulfide (H2S) biogas, which is formed during the decomposition of sulfur-containing substrates and mainly
proteins. Control of the content of hydrogen sulfide can usually be carried out by biological (in situ
microaeration) and physico-chemical methods of absorption by scrubbing with water and adsorption with
activated carbon. Nitrogen-containing substrates, especially rich in proteins, can form ammonia (NH3) as a
result of decomposition, the level of which is regulated depending on the value of temperature and acidity
(the pH level is high and the temperature is high, then the balance changes in the direction of ammonia).
Methods of removing and controlling ammonia can be different . It is more practical to use zeolites by
previously adding NaCl to it, while the experimental method of removing ammonia - the process of
anaerobic oxidation of ammonium (ANAMMOX-process) needs additional research in the field of biogas
production.
Also, with this cleaning, other pollutants slow down the production of biogas, including oxygen that can
penetrate with an insufficiently enriched crushed substrate and harm methane bacteria, and especially high
concentrations of chemical substances (antibiotics, chemotherapeutic agents, and disinfectants) can restrain
the fermentation process and lead to its complete failure. stops, especially with their high concentration. A
restraining effect can be given by the accumulation of organic acids, which are formed during the anaerobic
decomposition of organic substances in the corresponding departments of treatment plants. With a stable
process of biogas formation, the amount of organic acids (they are also called acetic acid equivalents) is
normally below 2000 mg/l). If fresh or very easily decomposing substrates are fed too quickly, rapid
oxidation and accumulation of acids up to the level of 16,000 mg/l can occur, as well as a negative ratio of
acetic to propionic acid, which leads to a whole series of reactions, starting with the fact that high
concentrations of acids restrain themselves bacteria in such a way that the pH level decreases, which causes a
delay in the development of methane bacteria until the decomposition process is completely stopped. This
can be countered only by a complete reduction in substrate supply. Mathematical modeling of the biorefining
process and optimization of methane fermentation will help the economic benefit of the biogas production
process.
Of course, in order to ensure rational surface water use and biomonitoring based on spatial and temporal
changes of bioindicator components of the water ecosystem, we believe that it would also be effective to use
information technologies to study the symbiosis of microflora (phyto-, bacteria-, zooplankton and benthos)
and higher aquatic plants ( phytocenosis) and self-restoration of phytocenoses in the next vegetation cycle,
which involves the introduction of phytoremediation bioengineering ponds (BS), which can contribute to the
restoration of the biological balance of the water ecosystem or the improvement of the ecological situation in
the region.
The use of complex methods of thematic processing of digital images for the monitoring of the water
ecosystem, in particular, the synthesis of cartographic models, the synthesis of water bodies and their
technological load, the introduction of remote sensing technologies using models, methods and technologies
of information support for the management and monitoring of the ecological safety of water bodies ,
prevention and elimination of the consequences of man-made disasters have already been proposed by
scientists [22, 23].
Therefore, the combination of in silico biological activity prediction methods and in vitro microbiological
testing in the context of biosafety and biosecurity allowed us to optimize the selection of basic compounds in
order to increase their activity and determine the specificity of action, as well as the use of biocomputing
methods made it possible to propose effective antibacterial compounds for protection against pathogenic
infections, which will help protect human health. Biomonitoring can be an effective tool for pollution
mapping and trend monitoring in real time and retrospective analysis. Simple and inexpensive sampling
procedures allow a very large number of sites to be included in one survey. The development of modular
systems and mathematical modeling in the process of bioremediation will help to identify and eliminate
pollution during wastewater treatment, and waste disposal will obviously contribute to the economic benefit
of the process and the biosafety of the environment.
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