Synthesis, spectroscopic characterizations, DFT, molecular docking and molecular dynamics simulations of a novel 2-methyl-3H-benzimidazolo[1,2-b][1,2,4]triazepin-4(5H)-one

Article abstract of DOI:10.1016/j.molstruc.2019.127317

A novel compound named 2-methyl-3H-benzimidazolo[1,2-b][1,2,4]triazepin-4(5H)-one (C₁₁H₁₀N₄O) has been synthesized and characterized by spectroscopic techniques (FT-IR),UV–Vis,¹H NMR, ¹³C NMR and mass spectra. The optimized molecular structure analyses, vibrational wave numbers, ¹³C and ¹H NMR chemical shifts of the title molecule have been performed at DFT/B3LYP method with 6-31 + G(d,p) basis set. The electronic absorption wavelengths computed using B3LYP, B3P86 and PBE0 hybrid functional. The scaled vibrational modes, and the predicted ¹³C NMR and ¹H NMR chemical shifts are relatively in good agreement with the corresponding experimental ones. However, B3LYP, B3P86 and PBE0 hybrid functional fail in reproduction of experimental λ_MAX of the tilted compound and it is underestimated by the tested hybrid functionals with deviations to the experimental values of 30, 34 and 40 nm for B3LYP, B3P86 and PBE0, respectively. In addition, molecular docking and molecular dynamics simulations of titled compound were carried out to determine its binding modes and stability within the leucine-rich repeat kinase 2 active site.

Full text of DOI:10.1016/j.molstruc.2019.127317

Journal Pre-proof
Synthesis, spectroscopic characterizations, DFT, molecular docking and
molecular dynamics simulations of a novel 2-methyl-3H-benzimidazolo[1,2-b]
[1,2,4]triazepin-4(5H)-one
Youness El Bakri, El Hassane Anouar, Karthikeyan Subramani, Ali Ben-Yahya, El
Mokhtar Essassi
PII:
S0022-2860(19)31426-7
DOI:
https://doi.org/10.1016/j.molstruc.2019.127317
MOLSTR 127317
Reference:
To appear in: Journal of Molecular Structure
Received Date: 22 September 2019
Revised Date: 27 October 2019
Accepted Date: 29 October 2019
Please cite this article as: Y. El Bakri, E.H. Anouar, K. Subramani, A. Ben-Yahya, E.M. Essassi,
Synthesis, spectroscopic characterizations, DFT, molecular docking and molecular dynamics
simulations of a novel 2-methyl-3H-benzimidazolo[1,2-b][1,2,4]triazepin-4(5H)-one, Journal of Molecular
Structure (2019), doi: https://doi.org/10.1016/j.molstruc.2019.127317.
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Synthesis, spectroscopic characterizations, DFT, Molecular docking and Molecular
dynamics simulations of a novel 2-methyl-3H-benzimidazolo[1,2-b][1,2,4]triazepin-
4(5H)-one
Youness El Bakri,a,b,* El Hassane Anouar,c,* Subramani Karthikeyan,b Ali Ben-Yahya,a
and El Mokhtar Essassia
a Laboratoire de Chimie Organique Heterocyclique, URAC 21, Pôle de Compétences Pharmacochimie,
Universite Mohammed V, Faculte des Sciences, Av. IbnBattouta, BP 1014 Rabat, Maroc.
b Organic Chemistry Department, Science Faculty, RUDN University Miklukho-Maklaya st. 6, 117198
Moscow, Russian Federation.
c Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam bin Abdulaziz
University, Al-Kharj 11942, Saudi Arabia.
Corresponding authors
Dr. Youness El Bakri
Tel: +212677288857 Tel: +212677288857 / +79773560777
E-mail address: yns.elbakri@gmail.com
Dr. El Hassane ANOUAR
Tel: +966537237912
E-mail: anouarelhassane@yahoo.fr

Abstract
A novel compound named 2-methyl-3H-benzimidazolo[1,2-b][1,2,4]triazepin-4(5H)-
one (C11H10N4O) has been synthesized and characterized by spectroscopic techniques (FT-
IR),UV-Vis,1H-NMR, 13C-NMR and mass spectra. The optimized molecular structure
1
analyses, vibrational wave numbers, 13C and H NMR chemical shifts of the title molecule
have been performed at DFT/B3LYP method with 6-31+G(d,p) basis set. The electronic
absorption wavelengths computed using B3LYP, B3P86 and PBE0 hybrid functional. The
1
scaled vibrational modes, and the predicted 13C-NMR and H-NMR chemical shifts are
relatively in good agreement with the corresponding experimental ones. However, B3LYP,
B3P86 and PBE0 hybrid functional fail in reproduction of experimental λMAX of the tilted
compound and it is underestimated by the tested hybrid functionals with deviations to the
experimental values of 30, 34 and 40 nm for B3LYP, B3P86 and PBE0, respectively. In
addition, molecular docking and molecular dynamics simulations of titled compound were
carried out to determine its binding modes and stability within the leucine-rich repeat kinase 2
active site.
Keywords: 1,2-diamino-1H-benzimidazole, 1,2,4-triazepine, DFT calculations, Molecular
docking, Molecular dynamics

1. Introduction
New synthetic methods continue to be developed to construct seven-membered
heterocyclic compounds containing one, two, or three of the heteroatoms N, O, or S. The
focus of much of the literature has been non aromatic systems containing at least 1 N atom
and has often been driven by adesire to prepare these heterocycles in a stereocontrolled
fashion, the search for new bioactives, and the synthesis of natural products. Prominent
synthetic methods include transition metal-catalyzed, cycloaddition/annulation, cascade-type,
and C-H functionalization processes. Review articles on the synthesis of seven-membered
nitrogen heterocycles through the Ugimul-ticomponent reaction [1], synthetic approaches, and
biological activities of benzodiazepines [2], the isolation, structure deter-mination, medicinal
properties, and total synthesis of marine natural prod-ucts containing an oxepanyl ring [3], the
synthesis and medicinal importance of benzoxepines[4], methods for the synthesis of 1,2,3-,
1,2,4-, 1,2,5-, and 1,3,5-triazepines[5], and the isolation, biosynthesis, and biological activity
of natural products that contain a seven-membered ring with three or more heteroatoms [6] as
well asindole-fused azepines and analogs as anticancer lead molecules [7] have been
published.
All the heterocyclic compounds are of great interest in pharmaceutical chemistry. Out of
these heterocyclic compounds the benzfused heterocyclic compound, i.e. benzimidazoleandits
derivatives have wide variety of biological activities like antimicrobial activity[8-12],
antiinflammatory-analgesic [13-15], anticancer [16], CNS depressant [17], androgen receptor
antagonist [18], antitubercular [19, 20] and anticonvulsant [21-25]. In addition the
benzimidazole have played a very important role in the development of theory in heterocyclic
chemistry and also extensively in organic synthesis. Due to its wide biological interest we
have performed Structural Activity Relationship (SAR) studies for the above titled compound
and we found that which is majorly active in kinase family. Based on Swiss target search we

have found leucine-rich repeat kinase 2 (LRRK2) target and this structure from ROC domain
from the Parkinson's disease-associated and which reveals a dimericGTPase [26].
As an extension of our research efforts on the design and synthesis of new heterocyclic
systems with potent pharmacological properties on 1,2,4-triazole, benzimidazole and 1,2,4-
triazepine derivatives [27-30], we describe in the present paper the synthesis, spectroscopic
characterizations and computational studies of 2-methyl-3H-benzimidazolo[1,2-
b][1,2,4]triazepin-4(5H)-one obtained by condensation reaction of 1,2-diamino-1H-
benzimidazole and ethylacetoacetate (Scheme 1).
Scheme 1. Schematic representation of synthesis of the title compound.
2. Experimental and Theoretical Methods
2.1.Synthesis
A mixture of 1,2-diamino-1H-benzimidazole (1 g, 6.75 mmol) and ethyl acetolacetate
(4.26mL, 33.78mmol) was heated to 453 K in solvent-free conditions until completion (TLC).
The solid product that precipitated was collected by filtration, washed with ethanol.
The FT-IR spectrum of the tilted compound (Figure S1) was recorded directly without
dilution in KBr pellets using JASCO FTIR-4160 spectrometer in the range of 4000 – 400 cm-1
at resolution of ± 2 cm-1.The UV/vis spectrum of the tilted compound (Figure S1) was
recorded on a JASCO V-670 spectrophotometer with a simple monochromator for more
energy. Our spectrophotometer has the option to cover a spectral range from 190 to 3200 nm.
The NMR spectra were measured on a Bruker Avance DPX300 instrument. The chemical
shifts (δ) of the tilted compound are expressed in ppm down field from TMS as an internal
reference (Figure S3 and S4). Mass spectra (Figure 1) were performed on a Perkin-Elmer

SCIEX API unit 300. The samples are ionized by the ion spray technique (IS).Elemental
analysis was performed on a Euro EA - CHNSO Elemental Analyzer. TLC and column
chromatography were carried out, respectively, on silica plates (Merck 60 F254) and silica gel
(Merck 60, 230-400 mesh).
Yield: 50% mp: 290-293°C IR (νmax, cm−1): 3517(N-H), 3122(C-H, aromatic), 1648(C=O),
1604(C=N), 1437(C-H, CH3), 1371(C=C, aromatic). UV (λmax = 292nm). 1H NMR 300 MHz,
(DMSO-d6), δ(ppm): 2.28 (s, 3H, CH3), 3.55 (s, 2H, CH2), 8.71 (s, 1H, NH). 13C NMR75
MHz, (DMSO-d6) δ (ppm): δ 24.94, 42.8437, 141.42, 144.08, 164.78, 168.99. HRMS (IE)
Calculated for C11H10N4O: [M+H+]=214.2310, Found: [M+H+]=214.1911. Elemental analysis
Calculated: C, 61.67%; H, 4.71%; N, 26.15%; O, 7.47%, Found: C, 61.70%; H, 4.65%; N,
26.20%; O, 7.45%.
2.2 DFT calculations
Geometry optimization of the ground state (GS) of the tilted compound has been carried
out at the DFT level of theory by using the hybrid functionals B3LYP, B3P86 and PBE0
hybrid functionals combined with the double basis set 6-31+G(d,p) as implemented in the
Gaussian 16 software package [31]. Polarization and diffuse functions on heavy and hydrogen
atoms were added to the double basis set to obtain better accuracy of the results. The ground
state minimum for the tilted compound was confirmed by the frequency calculations at the
same levels of theory [31]. The calculated vibrational modes were scaled by 0.9679 [32]. The
FT-IR and Raman spectra of the tilted compound were calculated using the hybrid functionals
B3LYP, B3P86 and PBE0 hybrid functionals combined with the double basis set 6-31+G(d,p)
1
(Figures S5-S7). The predicted H and 13C NMR chemical shifts were obtained within the
GIAO approach [33, 34] by calculating the isotropic chemical shielding constants at the same
level of theory. The isotropic shielding constants were used to calculate the isotropic chemical
shifts, δcal, with respect to tetramethylsilane (TMS).δiso = ρTMS – ρiso, whereδiso, ρisoand ρTMS

are the chemical shift, the absolute shielding and the absolute shielding of TMS, respectively.
The solvent effects were taken into account implicitly by using the polarizable continuum
model (PCM), for which integral equation formalism is used (IEF-PCM). In the PCM model,
the substrate is embedded into a cavity surrounded by a dielectric continuum characterized by
its dielectric constant (εDMSO = 46.826) [35].
2.3 Molecular docking & dynamics studies
The chemical structure of above titled compound was drawn using chem. Draw pro 12
and further energetically minimized using conjugate gradient algorithm using impact panel
which is in-built in Schrödinger 2018-2 program. The target molecule of LRRK2 (PDB ID:
2ZEJ) was found based on Swiss target search [36]. The LRRK2 molecule further prepared
for using protein preparation wizard for docking studies. The induced fit docking analysis was
performed once both small molecule and macromolecule prepared and active site residues
were picked up from the co-crystal binding site of LRRK2. Once docking finished, 20
different binding poses were generated and best binding complex were taken based on binding
energy and interacting residues for further analysis. For the molecular dynamics studies, best
LRRK2 with titled compound was taken and the complex system was built using a periodic
boundary condition with a 10 Å3 cubic box from the centre of mass of the LRRK2 complex. A
TIP3P water solvation system was used in a buffer system with charged ions placed
isotropically to neutralise the Ewald charge summation of the solvated LRRK2complex
entity. The system was minimized with maximum iterations of 5000 steps with a gradient
convergence threshold of 1.0 kcal mol−1 Å−1.Once the system was minimized the system was
subjected to Newtonian dynamics of the model system to evaluate energy of the system. A
series of 2ps steps was integrated to record the simulation. A six stage NPT ensemble default
relaxation process was carried out before performing the molecular dynamics simulation. In
the first stage a solute-restrained Brownian dynamics of the ensemble was carried out while

keeping the energy constant using the NVT condition. In the second stage the Berendsen
thermostat was used and the NVT (canonical) ensemble was allowed to relax with respect to
temperature with velocity resembling of every 1ps applied to non-hydrogen solute sample.
Subsequently, the NVT ensemble was changed to an NPT ensemble with a Berendsenbarostat
and the system was kept at 1 atm pressure followed by system equilibration of 1ns. Then the
ensemble was subjected to a 50 ns molecular dynamics run [37, 38].
3. Results and Discussion
3.1. Mass spectrum
Mass spectrometry (MS) helps identifying the amount and type of fragments present in
a sample. Mass spectrum is generally pre-sented as a vertical bar graph, in which each bar
represents an ion having a specific mass-to-charge ratio (m/z) and the length of each bar
shows the relative abundance of that ion. Most of the ions formed in a mass spectrometer have
a single charge; therefore, the m/z value is equivalent to mass itself. The most intense peak is
assigned as the base peak corresponding to the abundance of 100%.
In this paper, mass spectrum of the title compound was investigated to analyze possible
ionic fragmentations and their stabilities. The experimental mass spectrum of the title
molecule is given in Figure 1. The possible fragments were identified by their mass-to-charge
ratio (m/z).

Fig. 1. Mass spectrum of the title compound
The structure of the title compound was also confirmed on the basis of a study in mass
spectrometry, using as ionization mode: the electronic impact (scheme 2).

6
N
7
8
9
NH
5
O
N
4
3
11
10
1
2
N
m/z=214
CH3
H3C
.
- CHO
- CO
N
- CH2=C=O
- NH=C=O
-
N
N
N
N
N
H
NH
N
NH
N
N
N
NH
N
H
N
N
N
CH3
m/z=172
O
m/z=185
m/z=186
CH3
CH3
C
m/z=159
- CH3-CN
H3C
-
- CO
N
N
H
N
N
N
N
N
N
N
NH
N
H
H
N
N
N
C
m/z=131
N
NH
H
N
m/z=144
m/z=131
H
H
-
H3C
C
CH
m/z=145
N
N
H
-
N
H
m/z=171
CH3
-
H
C
H
N
N
N
N
N
m/z=131
N
H
N
N
N
m/z=117
H
- H-CN
(- C2HN)
- N2
m/z=118
N
H
CH3
N
N
N
-
(- C2HN)
N
H
H
m/z=103
m/z=104
N
CH3
N
H
m/z=132
Scheme 2. Proposed fragmentation pathway of the title compound.
The molecular ion undergoes mainly five fragmentations:
1-Loss of a ketene molecule to lead to an ion m/z = 172 corresponding to a
triazolobenzimidazolium structure. This fragmentation is characteristic of the seven-
membered compounds having a -CH2-C=O moiety.
2-Elimination of a carbon monoxide molecule giving rise to an ion at m/z = 186 which loses a
molecule of acetonitrile to give an ion at m/z = 145. The latter undergoes a rearrangement
after loss of a molecule of hydrocyanic acid to lead to the benzimidazolium ion at m/z = 118

3-Ejection of a molecule of 3-methyl-2H-azirine after disruption of the N1-N11 and C3-C4
bonds of the tricyclic system, leading to the ion at m/z = 159 of diazetobenzimidazolium
structure which loses a molecule of carbon monoxide to lead to the ion at m / z = 131.
4-Loss of a radical CHO, giving rise to an ion with m/z = 185 of structure
triazinobenzimidazolium which loses a molecule of acetonitrile to give an ion at m/z = 144 of
structure diazetobenzimidazolium which loses a molecule d hydrogen cyanide to give the
benzimidazolium ion at m/z = 117.
5-Elimination of an isocyanic acid molecule creating an ion at m/z = 171 of
pyrazolobenzimidazolium structure likely to be in two tautomeric forms. The latter loses a
molecule of propyne to lead to an ion at m/z = 131 which can be in the form of two isomeric
structures: diaziridinobenzimidazolium or benzotriazinium. The latter, more stable ejects a
molecule of nitrogen and a molecule of hydrogen cyanide to lead respectively to the ions at
m/z = 103 and m/z = 104.
It should be noted that the ion at m/z = 131 can also come from the ion at m/z = 172, after loss
of a molecule of acetonitrile. Similarly, the losses of CO, CHO and an isocyanic acid
molecule make it possible to show the presence, in the molecule studied, of the lactam
function.
A mechanism can be proposed to explain the formation of the benzimidazolium ion at
m/z = 118, from the ion at m/z = 145 (scheme 3).

Scheme 3. Plausible mechanism for the formation of benzimidazolium ion.
The ion at m/z = 171 can also lose a molecule of formula C2HN to give the ion at m/z =
132 of 2-methyl-benzimidazolium structure. A mechanism for forming this ion is shown in
Scheme 4.
H
H
N
N
N
H
H
CH3
CH2
N
N
NH
N
N
N
H
m/z = 145
H
H
N
-
N
H
HN
CH3
NH
C2HN
HN
N
H
m/z = 132
Scheme 4. Mechanism for the formation of 2-methyl-benzimidazolium.
3.2.1H-NMR and 13C-NMR spectra
1
The experimental and predicted H and 13C NMR chemical shifts for the tilted
compound are shown in Table 1. Relatively good correlations were obtained between the
predicted and experimental chemical shifts of titled compound, with the correlation

1
13
coefficients of 99.89 and 99.1% for H-NMR and C NMR, respectively (Figure 2). Mean
1
13
13
average deviations for H NMR and C NMR are 0.11 and 4.37 ppm, respectively. For C
NMR, the minimal deviation is obtained for the reproduction of the chemical shift of methyl
group with a deviation of 1.29 ppm, while the maximal deviation is obtained for –CH-
functional with a deviation of 12.24 ppm. For 1H NMR, the minimal deviation is obtained for
the reproduction of the chemical shift of amine group (-NH-) with a deviation of 0.02 ppm,
while the maximal deviation is obtained for –CH2- protons with a deviation of 0.12 ppm.
1
Table 1. Experimental and predicted H and 13C NMR chemical shifts (ppm) for the tilted
compound.
1H-NMR
Predicted Experimental
(CH3, s, 3H,)
(CH2, s, 2H,)
(NH, s, 1H)
MAE
Max. Dev.
Min. Dev.
13C-NMR
(CH3)
(-CH2-)
(-CH-)
(C=N)
CH3-(C=N)
(C=O)
2.38
3.43
8.73
0.11
0.12
0.02
2.28
3.55
8.71
26.23
44.65
129.18
148.02
167.34
171.66
26.23
44.65
129.18
148.02
4.37
24.94
42.84
141.42
144.08
164.78
168.99
24.94
42.84
141.42
144.08
(CH3)
(-CH2-)
(-CH-)
(-CH-)
MAE
Max. Dev.
Min. Dev.
12.24
1.29

200
180
160
140
120
100
80
δExp. (ppm) = δPred. (ppm) + 3*10-5
R² = 99.5%
60
40
20
0
0
20 40 60 80 100 120 140 160 180 200
δPred. (ppm)
Fig. 2. Correlation curve between the predicted and experimental 13C NMR chemical shifts
of the tilted compound.
3.3. Vibration Spectrum
Some of the main experimental, calculated and scaled vibrations modes of the tilted
compound, and their corresponding calculated intensities and Raman scattering activities are
given in Table 2. The calculated vibration modes are scaled with a factor of 0.9613. The
reproduction of the experimental vibration modes depends on the type of vibration mode itself
and the hybrid functional used. Mean average deviations, maximal and minimal deviations
obtained using with the tested functional are shown in Table 2. Accordingly, the best
reproduction is obtained with B3LYP with an MAE of 30 cm-1. For this functional, the
lowest deviation is obtained for νC-H (CH3) with a deviation of 4 cm-1 with respect to the
observed value. All the tested hybrid functional fail in the reproduction of νC=O with lowest
maximal deviation obtained with B3LYP of 80 cm-1. As can be seen in Table 2, the correction
of the calculated vibration is improved the reproduction of the experimental values. For
instance, the deviation of νC-H (ar) obtained with B3LYP functional before and after

correction are of 99 and 4 cm-1 with respect to the experimental value. The root-mean-square
deviation (RMS) between the calculated and scaled vibration modes and the observed ones
were determined for each tested hybrid functional (Table 2). The lowest RMS value is
obtained with B3LYP of 35 cm-1.
Table 2. Calculated and experimental vibrational modes of the tilted compound.
Calc.
Scal.
IIR
RA*
Exp
B3LYP
νN-H
νC-H (ar)
νC=O
νC=N (C=C)
νC-H (CH3)
νC=C(ar)
3597
3221
1785
1695
1483
1394
30
137
23
35
3482
3118
1728
1640
1432
1349
30
80
4
35
72.44
5.67
721.03
29.65
6.59
1.62
-
-
-
-
127.11 3523
168.86 3123
79.84
1770
145.03 1676
13.2
1429
22.1
1378
MAE
-
-
-
-
-
-
-
-
Max. Dev.
Min. Dev.
RMS
B3P86
νN-H
νC-H (ar)
νC=O
νC=N (C=C)
νC-H (CH3)
νC=C(ar)
3621
3217
1813
1715
1476
1417
34
165
39
41
3505
3114
1755
1660
1429
1372
32
107
1
41
78.25
11.31
722.61
26.54
6.98
10.35
125.98 3517
170.06 3122
74.64
1648
149.87 1604
15.35
1437
10.23
1371
MAE
-
-
-
-
-
-
-
-
-
-
-
-
Max. Dev.
Min. Dev.
RMS
PBE0
νN-H
νC-H (ar)
νC=O
νC=N (1,2,4-triazepine)
νC-H (CH3)
νC=C(arc)
MAE
3640
3227
1829
1732
1476
1424
39
181
39
46
3523
3123
1770
1676
1429
1378
36
122
1
46
81.57
9.96
729.9
27.95
5.36
5.46
-
122.00 3517
164.31 3122
72.22
1648
152.62 1604
19.72
1437
5.70
1371
-
-
-
-
-
-
-
-
Max. Dev.
Min. Dev.
RMS
-
-
-
* Raman scattering activity

3.4. Electronic absorption spectrum
The experimental and calculated maximum absorption bands of the tilted compound are
shown in Table 3. The calculated maximum absorption bands were obtained using B3LYP,
B3P86 and PBE0 in gas and IEF-PCM phases. The experimental absorption band at 292 nm
corresponds to π →π* electronic transition. As can been seen from Table 3, the reproduction
of MAXmay depends on the type of the hybrid functional, and the media. In gas phase, the
λ
experimental λMAX of the tilted compound is underestimated by tested hybrid functional with
deviation with respect to the experimental of 30, 34 and 40 nm for B3LYP, B3P86 and PBE0,
respectively. The solvent has no effect on the position of the absorption bands (Table 3).
However, λMAX is strongly affect in PCM. The solvent-solute interaction induce
anhyperchromic shift, i.e., an increase in the absorption intensity. The absorption λMAX is
attributed to H→L+1 electronic transition in gas phase, and to H-1→L electronic transition
(Figure 3).
Table 3. λMAX (nm), EMAX (eV), electronic Transition (ET) and oscillator strength (f) of
maximum absorption band of the titled compound. The calculations are performed using
B3LYP, B3P86 and PBE0 hybrid functional in gas and IEF-PCM phases.
Experimental
Calculated
λMAX EMAX ET
f
λMAX EMAX
Gas
B3LYP
B3P86
PBE0
262 4.74 H→L+1 0.61
258 4.81 H→L+1 0.37
252 4.92 H→L+1 0.85
292
4.26
IEF-PCM
B3LYP
B3P86
261 4.75 H-1→L 0.66
258 4.81 H-1→L 0.67
251 4.93 H-1→L 0.66
PBE0

HOMO
LUMO
HOMO-1
LUMO+1
Fig. 3. Molecular orbitals correspond to λMAX electronic absorption.
3.5. Molecular docking & dynamics analysis
The docking and dynamics studies reveal the information about the binding interaction
mechanism between titled compound and LRRK2 (Figure 4). The binding energy for LRRK2
–compound complex is -25.45 kcal/mol and which shows the good binding affinity between
compound and LRRK2. From the Figure 4c the ligand plot, two hydrogen bonding formation
between residues GLN 1352 bonded with N atom and THR 1368 bonded with O atom of
titled compound. Also, ASP 1372 and LYS 1374 residues were contact with negatively and
positively charged in titled compound binding environment. Mostly polar residues THR 1368,
THR 1348, THR 1349 and GLN 1352 were in contact with the titled compound molecule
binding environment and VAL 1369 is only having hydrophobic contact with titled
compound. The molecular dynamics simulations were carried for to understand the stability of
LRRK2- titled compound complex system during 50 ns simulation time The docking and
dynamics studies reveal the information about the binding interaction mechanism between

titled compound and LRRK2 (Figure 4). The binding energy for LRRK2 –compound complex
is -25.45 kcal/mol and which shows the good binding affinity between compound and
LRRK2. From the Figure 2c the ligand plot, two hydrogen bonding formation between
residues GLN 1352 bonded with N atom and THR 1368 bonded with O atom of titled
compound. Also, ASP 1372 and LYS 1374 residues were contact with negatively and
positively charged in titled compound binding environment. Mostly polar residues THR 1368,
THR 1348, THR 1349 and GLN 1352 were in contact with the titled compound molecule
binding environment and VAL 1369 is only having hydrophobic contact with titled
compound. The molecular dynamics simulations were carried for to understand the stability of
LRRK2- titled compound complex system during 50 ns simulation time.
Fig. 4. (a) Best binding pose of titled compound with LRRK2 (b) Ligand plot for LRRK2 –
titled compound complex.

As shown in the Figures 5a and 5b Root Mean Square Deviation (RMSD), Root Mean
Square Fluctuation (RMSF) analysis will help to understand the LRRK2 – titled compound
complex system equilibration and fluctuation thought the end of simulation time. In Figure 5a
RMSD result shows that LRRK2 –titled compound are converged at greater than 3Å, which
means the system has large confirmation rather than small or globular protein and ligand
RMSD (Lig fit Protein) was stable during the thought the simulation time. In Figures 5b
RMSF plot will help to understand local changes of LRRK2 along with protein chain and the
green color lines were titled compound binding site residues of LRRK2 during the simulation.
Fig. 5. (a) RMSD (b) RMSF plot of LRRK2 – titled compound complex.
Figures 6a and 6b shows the final molecular dynamics output of LRRK2 – titled
compound complex. From that Figure 6a TRP 1376 alone participating above 50 % and
remaining residues were contributes below 50 % hydrophobic force with titled compound and

Figure 6b clearly shows that most of the residues were in the form of hydrophobic after
molecular dynamics simulation and the overall result concludes that the LRRK2 – titled
compound complex system was stable during the 50 ns simulation [39, 40].
Fig. 6. (a) interaction fraction plot (b) detailed ligand interaction contact of LRRK2 – titled
compound complex.

Conclusions
We have reported herein the synthesis of 2-methyl-3H-benzimidazolo[1,2-
b][1,2,4]triazepin-4(5H)-one. We have fully characterized them using FT-IR spectroscopies,
13
UV-Vis, MS and NMR (1H, C). Subsequently, the optimized structure of the molecule was
determined based on DFT calculations by the B3LYP method using Gaussian 16 software
package. Molecular docking result concludes that there was good binding affinity between
LRRK2 – titled compound and molecular dynamics result suggest that LRRK2 – titled
compound complex system was stable during 50 ns simulation time.
Acknowledgements
The publication was prepared with the support of the “RUDN University Program 5-100”.
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1. 2-methyl-3H-benzimidazolo[1,2-b][1,2,4]triazepin-4(5H)-one was synthesized and
characterized.
2. Molecular structure is characterized by using spectroscopic techniques.
3. DFT calculations at B3LYP allow a better reproduction of the experimental data.
4. Molecular docking and molecular dynamics analysis were carried with leucine-rich
repeat kinase 2 complex

Declaration of interests
☒ The authors declare that they have no known competing financial interests or personal relationships
that could have appeared to influence the work reported in this paper.
☐The authors declare the following financial interests/personal relationships which may be considered
as potential competing interests: