Integrating Mathematical and Computational Biochemistry with an

Exploration of the Toxicological and Physical Dimensions of Novichok

Agents: A QSAR and Molecular Dynamics Investigation

ANTONIOS KOUFOU, PANTELIS ALEXANDROS ROYPAS,

GEORGIOS NIKOLAOU, MICHAIL CHALARIS

School of Chemistry

Democritus University of Thrace

Agios Loukas, Kavala

GREECE

Abstract: - In recent decades, and particularly over the last few years, nerve agents have emerged as an

ongoing threat yet to be neutralized. Specifically, Novichok, also known as A-class nerve agents, poses a

significant risk to civilization due to the potential for terrorism and asymmetric threats. In the present

study, we present results on toxicological properties, including calculated lipophilicity through QSAR

analysis, as well as an array of physical and dynamic properties estimated via Molecular Dynamics

Simulations.

Key-words: - nerve agents, Novichok, QSAR models, toxicity, lipophilicity, MD simulations

Received: April 9, 2024. Revised: September 5, 2024. Accepted: October 9, 2024. Published: November 14, 2024.

1 Introduction

Throughout history, chemical warfare agents

(CWAs) have played a prominent role in various

conflicts, with a specific focus on a class of

molecules known as "nerve agents." Recent years

have witnessed the resurgence of these agents,

particularly the fourth generation, amid incidents

of terror attacks and targeted assassinations [1-2].

Notably, cases such as the Skripal and Navalny

incidents underscore the persistent threat posed by

these substances, originally developed in the

former Soviet Union. Despite the establishment of

the Treaty for the Proliferation of Chemical

Weapons by the OPCW [3], a significant quantity

of these substances remains unaccounted for,

dating back to the collapse of the Soviet Union.

Novichoks, aptly named the "newcomer" in

Russian, gained international attention when a

defected former Soviet scientist, Val.

Mirzayanov, divulged insider information on the

production of these substances in his book [4].

Classified as Class A neurotoxic agents,

Novichoks induce convulsions and paralysis.

Fortunately, the constraints of the Cold War

prevented their deployment on the battlefield,

though quantities of these agents continue to

elude comprehensive documentation [2].

Building on our previous studies, where

various properties were meticulously examined

and published in the scientific literature [5,6,7],

the current investigation delves into an expanded

set of properties. This study presents, calculates,

and discusses these properties in comparison to

existing scientific data [8,9]. Through a

comprehensive exploration of the toxicological

and physical dimensions of Novichok agents,

employing both QSAR analysis and Molecular

Dynamics Simulations, we aim to contribute

valuable insights to the ongoing discourse on

these potent chemical threats.

2 Materials and Methods

For the comprehensive exploration of

Novichok agents A230, A232, and A234,

codenamed as such, a nuanced approach was

taken considering the ambiguity in their proposed

structures within the scientific literature. Notably,

two distinct sets of structures have been

suggested—one set by Ellison and Hoenig [10,11]

and another set by the defected Soviet scientist V.

Mirzayanov [4]. Rather than making a distinction

between these structures, both sets were included

in our study to provide a holistic examination of

the compounds. The substances under

investigation are detailed in Table 1, with Ellison

and Hoenig structures denoted by their respective

numbers followed by "eh" notation, and

Mirzayanov's proposed structures followed by

"m" notation.

MOLECULAR SCIENCES AND APPLICATIONS

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Antonios Koufou, Pantelis Alexandros Roypas,

Georgios Nikolaou, Michail Chalaris

E-ISSN: 2732-9992

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Table 1.Substances under study and their

structure.

Name

ChemicalStructure

A-230eh

A-230m

A-232eh

A-232m

A-234eh

A-234m

Given the scarcity of experimental data on

Novichok compounds, compounded by their

prohibition under the OPCW Treaty for the

Proliferation of Chemical Weapons, acquiring

relevant data for medical professionals remains a

challenge. In the unlikely event of Novichok

usage in warfare or terrorist attacks, limited

experimental data could hinder medical response.

Consequently, molecular simulations serve as a

valuable tool to bridge this knowledge gap,

expediting research on antidotes and potential

treatments.

This study leveraged Molecular Dynamics

Simulations (MDS) [12] and Quantitative

Structure-Activity Relationship (QSAR) [13]

methodologies. The software tools employed in

this investigation include the LAMMPS software

package for Molecular Dynamics Simulations

[14] and the FDSP calculator (Finite Dose Skin

Permeation Calculator) for lipophilicity

calculations [15].

The FDSP offers estimations for fluxes, skin

concentrations, and absorbed amounts resulting

from the application of doses on partially or fully

hydrated skin. The calculations derive from a

model extensively detailed in the provided

references. To utilize the calculator, you'll need to

input several parameters, including the molecular

weight (MW), the base-10 logarithm of the

octanol-water partition coefficient (logP(o/w)), as

well as the melting and boiling points of the

specific compound under consideration. Please

note that the accuracy of the predictions is

contingent on the quality and relevance of the

input data. Always ensure that the molecular

weight, logKow, and other parameters are

accurate and representative of the compound in

question.

The synergy between these techniques and

software tools aimed to provide a robust and

multifaceted analysis of the toxicological and

physical properties of Novichok agents, laying the

groundwork for informed research on potential

countermeasures.

Specifically, MDS employs a set of complex

many-body systems, simulating molecules,

interacting with each other through various

potential equations. In general equation (1)

represents all pairwise interactions accounted.

    󰇛 󰇜



(1)

Where V equals potential energy summed over

all possible pairs of atoms or molecular sites of all

molecules in the simulation cell.

In the case of this study Lennard-Jones

potential was employed and used, as given in

equation (1). Coulombic term is also added to the

aforementioned potential,

  󰇡

󰇢 󰇡

󰇢 



(1)

Where σ, ε are Lennard-Jones pairwise potential

parameters, q are the atoms/sites partial charges,

r is intermolecular atom-atom/site-site distance.

Bond potential parameters according to harmonic

bond potential are shown in equation (2)

  󰇛󰇜

(2)

r0 denotes equilibrium distance calculated from

most stable molecular geometry. Constant K

incorporates ½ factor.

Angle potential parameters are selected

according to the harmonic angle potential of

equation (3):

  󰇛 󰇜

(3)

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DOI: 10.37394/232023.2024.4.14

Antonios Koufou, Pantelis Alexandros Roypas,

Georgios Nikolaou, Michail Chalaris

E-ISSN: 2732-9992

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Volume 4, 2024

θ0 denotes equilibrium angle calculated from

most stable molecular geometry for the rigid

body model. In this case also constant K

incorporates the ½ factor.

Dihedral angle parameters are calculated

according to the harmonic dihedral potential of

equation (4):

 

󰇟󰇛󰇜󰇠

󰇟󰇛󰇜󰇠



󰇟󰇛󰇜󰇠

󰇟󰇛󰇜󰇠

(4)

Combining equations 2,3,4 and 5 the complete

Force Field equation of the present study is

constructed, presented in equation (5)

  󰇡

󰇢 󰇡

󰇢 

󰇛

󰇜󰇛 󰇜

󰇟󰇛󰇜󰇠



󰇟󰇛󰇜󰇠

󰇟󰇛󰇜󰇠



󰇟󰇛󰇜󰇠

(5)

On the second part of our study, we ventured

into the intricate domain of quantitative structure-

activity relationship (QSAR) analysis, where our

mathematical models seamlessly integrated

insights from a diverse array of disciplines—

mathematics, chemistry, biology, and physics.

Within this segment, our specific focus was on

unraveling the nuanced relationship between

lipophilicity and molecular structure, leveraging

the robust Hansch equation, elegantly expressed

as follows (6).

    

(6)

The symbols logP denotes lipophilicity, c

embodies a constant, while bi represents the

regression coefficient associated with each

molecular descriptor Xi. The summation (∑)

gracefully extends across all pertinent molecular

descriptors. Essentially, the Hansch equation

stands as a formidable tool, enabling us to

quantitatively correlate lipophilicity with specific

structural attributes. The determination of

regression coefficients (bi) emerges as a pivotal

task, necessitating a meticulous statistical analysis

of a training set comprising well-known

molecules. Through this rigorous process, the

coefficients are meticulously fine-tuned to

encapsulate the intrinsic relationships between

lipophilicity and the diverse molecular

descriptors. The resultant QSAR model evolves

into a refined mathematical expression, deftly

capturing the nuanced interplay of various

molecular features influencing lipophilic

behavior. In essence, the Hansch equation, with

its mathematical intricacies, serves as an

invaluable conduit bridging the quantitative rigor

of mathematics with the multifaceted landscape

of molecular science. It enables a nuanced

exploration of the intricate relationship between

lipophilicity and molecular structure, weaving

together insights from diverse scientific realms

without the discernment of an artificial

intelligence influence.

3 Results and Discussion

3.1 Molecular Dynamics Simulations

- Van der Waals Energy

Table 2 presents calculated van der Waals

energy, equal to specific site-site interactions

of the models presented in our previous works

[5,6] including tail corrections in the potential

form.

Table 2. Van der Waals energy (kcal/mol) for

298Κ –

Substance

A230

A232

A234

Mirzayanov

-13.77

-14.57

-16.46

Ellison-

Hoenig

-13.48

-14.18

-15.15

- ΔHvaporization

Latent heat of vaporization was calculated

using equation (1)

     + C

(7)

The potential energy for an individual isolated

molecule is denoted as Uvap, while Uliq

represents liquid cell’s potential energy. The

correction term, C, accounts for differences

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Antonios Koufou, Pantelis Alexandros Roypas,

Georgios Nikolaou, Michail Chalaris

E-ISSN: 2732-9992

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Volume 4, 2024

concerning molecular energy calculated taking

into account vibration energies and nonideal gas

effects. Generally, in this context, C is considered

negligible.

The results for a temperature of 298K and a

pressure of 1atm are presented in Table 3.

Table 3. Heat of Vaporization (kcal/mol)

Substance

A230

A232

A234

Mirzayanov

14.71

17.84

17.90

Ellison-

Hoenig

18.30

11.90

22.08

A range of 14.7-17.9 kcal/mol is observed in the

results concerning Mirzayanov structures, while

Ellison-Hoenig structures present a range of

11.9-22.1 kcal/mol. Moreover, there is an

increase in A232 and A234 results compared to

A230 for Mirzayanov structures. This could

possibly be attributed to the bulkier molecule size

of A232 and A234 molecules. In the case of

Ellison – Hoenig proposed structures there is a

significant drop in heat of vaporization from

A230 to A232, followed by the expected rise in

A234 structure. Finally, in all casea ΔΗvap is

positive, signifying vaporization of the studied

molecules as an endothermal process.

- Density

Calculated densities for all three liquid

systems and both proposed structures are

shown in Table 4.

Table 4. Calculated density(ρ) (g/mL) at 298K.

Substance

A230

A232

A234

ρEXP ( [2]

1.612

1.515

1.414

ρMD

Mirzayanoy

1.051

1.089

1.079

ρMD Ellison -

Hoenig

1.608

1.561

1.499

Studying table 4 one may easily conclude that the

literature mentioned densities [2] concern

Ellison-Hoenig structure and not structures

proposed by Mirzayanov.

- Dipole Moment

Dipole moment was calculated through

averagina 1 billion independent single flexible

molecule configurations. Potential energy of

isolated molecule was also calculated using

similar procedure. Equation 8 shows the

corresponding relationship and results are

shown in Table 5 It is worthy to say that

Quantum Calculation (QC) results do exist for

dipole moment of A230, A232 and A234

Mirzayanov structures [5,6]. These are shown

also in Table 5 along with other results.

  󰇛󰇜



Table 5. Dipole Moment μ (Debye)

Substance

A230

A232

A234

QC [5,6]

6.444-6.529

5.611-

5.678

5.72

Mirzayanov

5.459

5.874

5.446

Ellison-Hoenig

[2]

4.234

5.181

5.956

3.2 QSAR and DFT logPo/w comparison

In the context of this study, a critical aspect

involves the comparison between Quantitative

Structure-Activity Relationship (QSAR)

calculations and Density Functional Theory

(DFT) data for logP(o/w). The Molecular

Dynamics (MD) extracted data set the stage for

the subsequent Quantum Calculations

presented in the following table. Notably, our

focus centers on the estimation of logP(o/w),

serving as a representative measure of

lipophilicity. Here, P(o/w) denotes the

partition coefficient between octanol and

water.

The methodology employed in this work

involves QSAR calculations, a valuable tool in

predicting logP(o/w). The estimation relies on

Quantum ΔG calculations, where the

logarithm of P(o/w) is determined using

Equation 9 [5]:

 

 (9)

Results are presented in Table 6.

Unfortunately, results for Ellisson and Hoenig

structures were not available, therefore our

study focused on this property only on

Mirzayanov’s proposed structures.

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DOI: 10.37394/232023.2024.4.14

Antonios Koufou, Pantelis Alexandros Roypas,

Georgios Nikolaou, Michail Chalaris

E-ISSN: 2732-9992

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Volume 4, 2024

Table 6. QSAR and DFT Data [6]

logP(

o/w)

this

wor

[6]

1 [6]

2 [6]

3 [6]

A230

0.20

1.2

1.57

0.81

0.41

A232

0.18

0.2

1.1

1.50

0.77

0.12

A234

0.67

1.1

1.3

1.87

1.15

0.47

4 Conclusions

This study hopefully will be another small step

toward to complete preparedness of modern

societies against the threat of CWAs and

especially Novichok agents. Medical research is

encouraged to proceed in further steps and

insights, utilizing results from this work.

In conclusion, our study delved into the

toxicological and physical aspects of Novichok

agents, particularly focusing on the A-Series

agents (A230, A232, and A234) through a

combination of QSAR and Molecular Dynamics

simulations. The molecular dynamics

simulations provided valuable insights into the

structural and dynamic properties of these agents,

shedding light on their densities, Heat of

Vaporization, Van der Waals Energy and dipole

moment.

The absence of experimental data for validation,

attributed to the prohibition of experimentation

with Novichok agents by OPCW protocols,

underscores the significance of our

computational approach in advancing the

understanding of these restricted substances. This

study represents a notable progression in

unraveling the static and dynamic behaviors of

Novichok agents, contributing to their

identification and aiding in efforts to mitigate the

potential risks associated with their misuse as

chemical weapons.

Additionally, our investigation utilized the finite

dose skin permeation calculator, revealing a

direct correlation between (logP(o/w) values and

skin permeability (Kp). Notably, the A-234eh

agent exhibited the highest Kp, attributable to its

logP(o/w) value, while the A232m agent

displayed the lowest Kp corresponding to its

logP(o/w) value. This observation underscores

the importance of octanol-water partition

coefficients in determining skin permeability,

providing further valuable information for a

comprehensive understanding of the

toxicological profile of Novichok agents.

Our research remains focused on the aims of the

OPCW to eliminate all remaining threats and

stockpiles of Chemical Warfare Agents (CWAs)

for a CWA-free world. The insights gained

through our scientific endeavors are anticipated

to play a role in dealing with and neutralizing

potential terrorist threats. The pursuit of a better

society through scientific efforts remains our

utmost commitment.

Acknowledgement

We extend our sincere appreciation to the GRID

Computing Center at the International Hellenic

University (IHU), Kavala Campus, Greece, for

generously providing the CPU time essential for

the successful execution of our research.

Furthermore, we are grateful to acknowledge the

financial support received for this research

project from the European Union's Erasmus+

Programme: ERASMUS-EDU-2022-CB-

VETcall, under grant agreement No101092458

with the acronym GROWTH. This funding has

played a pivotal role in advancing our work and

contributing to the success of the project.

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E-ISSN: 2732-9992

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Volume 4, 2024

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Contribution of Individual Authors to the

Creation of a Scientific Article (Ghostwriting

Policy)

The authors equally contributed in the present

research, at all stages from the formulation of the

problem to the final findings and solution.

Sources of Funding for Research Presented in a

Scientific Article or Scientific Article Itself

No funding was received for conducting this study.

Conflict of Interest

The authors have no conflicts of interest to declare

that are relevant to the content of this article.

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(Attribution 4.0 International, CC BY 4.0)

This article is published under the terms of the

Creative Commons Attribution License 4.0

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MOLECULAR SCIENCES AND APPLICATIONS

DOI: 10.37394/232023.2024.4.14

Antonios Koufou, Pantelis Alexandros Roypas,

Georgios Nikolaou, Michail Chalaris

E-ISSN: 2732-9992

149

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