Accepted Manuscript

MAO enzymes inhibitory activity of new benzimidazole derivatives including

hydrazone and propargyl side chains

Özgür Devrim Can, Derya Osmaniye, Ümide Demir Özkay, Begüm Nurpelin Sağlık,
Serkan Levent, Sinem Ilgın, Merve Baysal, Yusuf Özkay, Zafer Asım Kaplancıklı

PII: S0223-5234(17)30158-7
DOI: 10.1016/j.ejmech.2017.03.009
Reference: EJMECH 9269

To appear in: European Journal of Medicinal Chemistry

Received Date: 2 November 2016

Revised Date: 22 February 2017
Accepted Date: 4 March 2017

Please cite this article as: E.D. Can, D. Osmaniye, E. Demir Özkay, B.N. Sağlık, S. Levent, S. Ilgın, M.
Baysal, Y. Özkay, Z.A. Kaplancıklı, MAO enzymes inhibitory activity of new benzimidazole derivatives
including hydrazone and propargyl side chains, European Journal of Medicinal Chemistry (2017), doi:
10.1016/j.ejmech.2017.03.009.

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 ACCEPTED MANUSCRIPT
MAO Enzymes Inhibitory Activity of New Benzimidazole Derivatives Including

Hydrazone and Propargyl Side Chains

Fifteen novel benzimidazole compounds were synthesized in order to investigate their

inhibitory potency against hMAO-A and hMAO-B enzymes. The compound 4e displayed

significant hMAO-B inhibition, notable interactions in the active site, non-cytotoxicity, non-

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genotoxicity and a good predicted ADME profile.

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Significant
hMAO-B Non-genotoxic
Good ADME Non-cytotoxic
inhibition
profile NIHI3T3A
IC50= 0.075 µM
prediction

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AN IC50= 316 µM

O N
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N NH N

Compound 4e
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N
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C EP
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Notable interactions in the active site

 ACCEPTED MANUSCRIPT
MAO Enzymes Inhibitory Activity of New Benzimidazole Derivatives Including

Hydrazone and Propargyl Side Chains

Özgür Devrim Cana, Derya Osmaniyeb, Ümide Demir Özkaya, Begüm Nurpelin Sağlık b,c,

Serkan Leventb,c, Sinem Ilgınd, Merve Baysald, Yusuf Özkay* b,c, Zafer Asım Kaplancıklıb

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Department of Pharmacology, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir,

Turkey

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b
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470

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Eskişehir, Turkey

c
Doping and Narcotic Compounds Analysis Laboratory, Faculty of Pharmacy, Anadolu

University, 26470 Eskişehir, Turkey

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d
Department of Toxicology, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir,
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Turkey
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* Corresponding author.
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E-mail address: yozkay@anadolu.edu.tr (Y. Özkay).

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Tel: +90-222-3350580/3779 Fax: +90-222-3350750.

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Address: Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical

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Chemistry, 26470, Eskişehir, Turkey.

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Abstract

In the present work, 15 new N’-(arylidene)-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-

yl)benzohydrazide (4a-4o) were designed and synthesized. The structures of the synthesized

compounds were elucidated using FT-IR, 1H-NMR, 13C-NMR, and HRMS spectral data. The

inhibitory activity of the compounds 4a-4o against hMAO-A and hMAO-B enzymes was

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evaluated by using in vitro Amlex Red® reagent based fluorometric method. Due to lots of

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high-cost kits including this assay, we determined the ingredients of the kits from the data

sheets of several suppliers, and adjusted a protocol by working with various concentrations

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and volumes of these ingredients. As a result, a fast and sensitive assay was applied as in the

commercially available MAO kits with lower costs and clearer ingredients than those of the

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kits. The enzyme inhibition assay revealed that synthesized compounds have selective

inhibition potency against hMAO-B. The compound 4e and 4f displayed IC50 values of
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0.0075 µM and 0.136 µM against hMAO-B, respectively. The reference drugs selegiline

(IC50=0.040 µM) and rasagiline (IC50=0.066 µM) also displayed a significant inhibition
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against hMAO-B. The enzyme kinetic study was performed in order to observe the effect of
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the most active compound 4e on substrate-enzyme relationship and non-competitive

inhibition of hMAO-B was determined. Cytotoxicity and genotoxicity studies were carried
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out and the compound 4e was found as non-cytotoxic and non-genotixic. Theoretical
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calculation of ADME properties suggested that compound 4e may have a good

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pharmacokinetic profile. The docking study of compound 4e revealed that there is a strong

interaction between the active sites of hMAO-B and analyzed compound.

Keywords: MAO-A; MAO-B; amplex red; benzimidazole; propargyl; hydrazone; docking.

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1. Introduction

Monoamine oxidases (MAOs) are the enzymes catalyzing oxidative deamination of

monoamines such as dopamine, noradrenaline, adrenaline, and serotonin [1]. MAOs are

placed in the mitochondrial outer membrane of neuronal, glial, and other cells [2]. This

enzyme exists in two forms, MAO-A and MAO-B. These two isoforms share almost 70%

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sequence identity at the amino acid level and were identified based on their substrate

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selectivity and inhibitor sensitivities. MAO-A preferentially breakdown serotonin,

noradrenaline, and adrenaline, and is irreversibly inhibited by clorgyline. On the other hand,

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MAO-B preferentially breakdown dopamine, β-phenetylamine, and benzylamine, and is

irreversibly inhibited by selegiline [3,4].

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Since inhibition of the enzyme activity prevents degradation of monoamine neurotransmitters,

and induces an increase in the levels of these neurotransmitters at the synaptic cleft, inhibitors
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of MAO enzymes have the notable therapeutic potential for the treatment of disorders caused

by deficiencies in monoaminergic neurotransmission of the brain [5]. For instance, reversible

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and selective MAO-A inhibitor moclobemide as well as non-selective and irreversible MAO
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inhibitor phenelzine, which induce a notable increase in the levels of noradrenaline and
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serotonin levels at the central synapses, are among the well-known antidepressant drugs. In

addition to major depressive disorder, numerous clinical studies have exhibited the
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therapeutic potential of MAO inhibitors against further emotional disorders such as atypical
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depression [6], dysthymic disorder [7], bipolar depression [8], bulimia [9] and also of some

anxiety disorders such as panic disorder [1] social phobia [10,11] and post-traumatic stress

disorder [12]. Monoamine oxidase B (MAO-B) is also a well-known target for

neuroprotective drugs as well as antidepressants [13, 14]. Irreversible and selective MAO-B

inhibitory drug selegiline, which raises dopamine levels in the synapses of basal ganglions, is

known to be beneficial for the palliative treatment of patients with Parkinson disease. Besides,

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MAO-B inhibitors are also used alone or in combination to treat Alzheimer’s disease due to

their protective effects on both vascular and neuronal tissues [15,16].

Although there is a wide therapeutic potential of MAO inhibitors for central nervous system

(CNS) disorders, these drugs have some early phase (such as orthostatic hypotension,

dizziness, drowsiness, insomnia, and nausea) and late phase (such as hepatotoxicity, weight

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gain, edema, muscle pains, myoclonus, paresthesias, and sexual dysfunction) adverse effects.

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Moreover, risks of drug-drug (serotonin syndrome) or drug-diet (cheese reaction) interaction

induced by some of the MAO inhibitors are seriously limited use of these drugs in psychiatry

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clinics [17]. Therefore, discovery and development of new, more potent and safer MAO

inhibitors are among the current scientific targets of the medicinal chemists.

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In terms of crystal structure, MAO isoforms differ in nature and volume of the catalytic site,

consenting to discover selective binders [13,18]. The hMAO-B enzyme has two cavities
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connected by the amino acid ILE199 that works as a ‘gate’. The entrance cavity has a volume

of 290 Å3 and, possesses very hydrophobic character. The second cavity, with a volume of
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390 Å3, includes the substrate binding site. The coenzyme FAD is located at the end of this
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cavity. Crystallographic data of the substrate cavity has indicated that the amino acid side
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chains, coating the cavity, are very hydrophobic and favorable to interact with an amine

moiety. The FAD and closely two parallel tyrosyl residues (398 and 435) constitute an
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‘aromatic cage’. In contrast hMAO-B, hMAO-A has only a single cavity of 550 Å3, in which
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FAD and two closely parallel tyrosyl residues (407 and 444) also form an ‘aromatic cage’.

The substrate binding sites of both hMAO-A and hMAO-B have quite hydrophobic nature

[19-23]. All these information simplify the understanding of the selective interactions

between these isoforms and their ligands. Hence, it is possible to observe the catalytic

mechanism and identify the pharmacophoric requirements for the rational design of new

inhibitors.

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In the light of above information, in this study we planned to synthesize some novel MAO

inhibitors. Based on the previous literature [2,24-26], demonstrating the inhibitory efficacy of

benzimidazole compounds against MAO enzyme, we decided to synthesize some novel

benzimidazole derivatives as potential MAO inhibitor candidates. Further, we designed the

side chains by using two other pharmacophore groups, which also have notable MAO enzyme

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inhibitory capacity. The first pharmacophore group was selected as “hydrazone”, because

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substrates and inhibitors of MAO enzyme usually carry an amino or imino group, which

seems to play an essential role in the orientation and complex formation at the active site of

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the enzyme. Iproniazide and isocarboxazid were the MAO inhibitors, bearing hydrazone

moiety (Figure 1). Based on this potential, numerous substituted hydrazones and hydrazides

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have been reported as MAO inhibitors [27-31]. The second pharmacophore group was chosen
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as “propargyl” due to the inhibitory potential of this moiety against MAO-A and/or MAO-B
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enzymes [32-34]. Some of the clinically prescribed MAO inhibitors such as rasagiline and

selegiline, are already known to carry the propargyl group in their chemical structures (Figure
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1) [35,36]. Moreover, neuroprotective capacity of the compounds, carrying a propargyl group,

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increases the importance of this moiety in drug design studies [32-34].

In the current work, a novel series of benzimidazole derivatives bearing “hydrazone” and
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“propargyl” side chains were synthesized to examine their activity against MAO enzyme
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isotypes, with the goal of developing safer and potent MAO-A and MAO-B inhibitors
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(Figure 1).

2. Result and Discussion

2.1. Chemistry

The compounds 4a-4o were synthesized as outlined in Scheme 1. Methyl 4-(1H-

benzo[d]imidazol-2-yl)benzoate (1) was prepared under microwave irradiation by reacting

1,2-phenylenediamine and methyl 4-formylbenzoate. Substitution of compound 1 by

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propargyl bromide gave the methyl 4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)benzoate

(2). Reaction of the compound 2 and hydrazine hydrate afforded 4-(1-(prop-2-yn-1-yl)-1H-

benzo[d]imidazol-2-yl)benzohydrazide (3), which was treated with corresponding aldehyde to

gain the compounds 4a-4o.

Structural elucidation of the synthesized compounds (4a-4o) was performed by spectral

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analyses. In the IR spectra, N-H, CC and C=O stretching bands were observed between

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3410-3213 cm-1, 2126-2091 cm-1 and 1672-1641 cm-1, respectively. In the 1H-NMR spectra,

acetylene proton recorded as singlet between 3.50 and 3.54 ppm. Methylene bridge protons

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between benzimidazole and acetylene group were recorded as a singlet at 5.22-5.23 ppm.

Amide proton gave a singlet between 11.70 and 12.37 ppm. In the 13C-NMR spectra, peaks of

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methylene and acetylene carbons were observed about 35 ppm, and 77-79 ppm, respectively.

Carbonyl carbon gave a peak about 160-165 ppm. All the other aromatic hydrogens and
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carbons were recorded at expected areas in the both 1H-NMR and 13

C-NMR spectra. All

measured mass and isotope ratios were compatible with theoretical values in HRMS spectra.
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2.2. MAO Inhibition

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The newly synthesized N’-(arylidene)-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-

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yl)benzohydrazide derivatives (4a-4o) were investigated for their hMAO-A and hMAO-B

inhibitory activity by an in vitro fluorometric method, being able to sensitively detect

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monoamine oxidase (MAO) activity. The assay is based on the detection of H2O2 in a
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horseradish peroxidase coupled reaction using 10-acetyl-3,7-dihydroxyphenoxazine (Amplex

Red reagent). There are lots of commercially available MAO-A and MAO-B kits including

this assay. The advantage of the kits is a fast and sensitive protocol implementation. However,

only limited numbers of inhibitor candidates could be studied using a kit, and several numbers

of kits are required to screen potency of a series of inhibitor candidates. Thus, using a kit

causes high costs for researchers. Furthermore, in user guide of many kits, there is only

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experimental procedure to carry out protocol that does not give any information about

concentration of some of the contents. From this point, we determined the ingredients of the

assay by examining various kits, and applied a protocol by working with different

concentrations and volumes of these ingredients. As a result, a fast and a sensitive assay was

performed as in the commercially available MAO kits with lower costs and clearer

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information of ingredients than those of the kits.

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The assay was performed in two steps. First, compounds 4a-4o were tested at 10-3 and 10-4 M

concentrations. Second step was performed by using 10-5-10-9 M concentrations of selected

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compounds that indicate more than 50% inhibitory activity at initial concentrations. Table 1

presents the hMAO-A and hMAO-B inhibitory activity of compounds 4a-4o. The compounds

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4a, 4c, 4j and 4l could not pass the first step test due to lower inhibitory activity against both

MAO isoforms. In addition, compounds 4d, 4g, 4k, and 4n were not evaluated in the second
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step hMAO-A assay because of lower than 50% inhibition potencies. Against hMAO-A, the

most active compound 4f displayed an IC50 of 0.851 µM, whereas reference drug clorgiline
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had an IC50 of 0.0054 µM. On the other hand, compound 4f showed an IC50 of 0.136 µM
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against hMAO-B. Compound 4e displayed an important inhibitory activity against hMAO-B.

It was the most active derivative against hMAO-B with an IC50 of 0.075 µM. The reference
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drugs selegiline (IC50=0.040 µM) and rasagiline (IC50=0.066 µM) also displayed a significant
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inhibition against hMAO-B. Selectivity indexes (SI) were expressed as IC50(MAO-A) / IC50(MAO-
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B). Selectivity towards MAO-A increases as the corresponding SI decreases while selectivity

towards MAO-B isoform increases as the corresponding SI increases. It was observed that

synthesized compounds have selective inhibition potency against hMAO-B. Compound 4e

displayed very significant SI of 127.813.

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2.3. Kinetic Studies of Enzyme Inhibition

The mechanism of hMAO-B inhibition was investigated by enzyme kinetics, following the

similar procedure of the MAO inhibition assay. The linear Lineweaver-Burk graphics were

used to estimate the type of inhibition. Enzyme kinetic was analysed by recording substrate-

velocity curves in absence and presence of the most potent compound 4e, which was prepared

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at concentrations of IC50/4 (0.01875 µM), IC50/2 (0.0375 µM), IC50 (0.075 µM), 2xIC50 (0.150

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µM), and 4xIC50 (0.300 µM). In each case, the initial velocity measurements were gained at

different substrate (tyramine) concentrations ranging from 20 µM to 0.625 µM. The Ki

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(intercept on the x-axis) value of compound 4e was determined from the secondary plot of the

1/V versus varying concentrations.

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The graphical analysis of steady-state inhibition data for compound 4e is shown in Figure 1.

The Lineweaver–Burk plot introduces the inhibition type as mixed-type, competitive or non-
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competitive. In the mix-typed inhibition, the lines cross neither x- nor y-axis at the same

point. Competitive inhibitors possess the same intercept on y-axis but there are diverse slopes
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and intercepts on x-axis between the two data sets. Non-competitive inhibition has plots with
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the same intercept on x-axis but there are different slopes and intercepts on y-axis, which is
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observed in Figure 1. Therefore, this pattern indicates that the mechanism of hMAO-B

inhibition of 4e is non-competitive, explaining that the inhibitor can bind to either the free
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enzyme or the enzyme–substrate complex. Ki value for compound 4e was calculated as 0.151
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µM for the inhibition of hMAO-B.

2.4. Cytotoxicity

Toxicity of compounds 4e and 4f was investigated by MTT assay, which is based on the

reduction of yellow MTT dye by metabolically active eukaryotic and prokaryotic cells to form

the purple formazan product. This assay is mainly preferred to form a view about cell viability

and to observe the growth of cell culture [37,38]. MTT assay was carried out using healthy
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NIH/3T3 mouse embryonic fibroblast cell lines (ATCC CRL1658), which is recommended

for cytotoxicity screening by ISO (10993-5, 2009) [39]. As seen in Table 2, the IC50 values of

4e and 4f against NIH/3T3 cells were found to be 316 µM and ≥1000 µM, which are

significantly higher than the IC50 values of compounds (0.075 µM and 0.136 µM) against

hMAO-B. Thus, it can be stated that these compounds are nontoxic at their effective

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concentrations against hMAO-B.

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2.5. Genotoxicity

Ames assay was performed to investigate the genotoxicity of compounds 4e and 4f. In the

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MPF
Ames assay, more than 25 positive wells were observed with positive controls, and

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negative control wells also showed less than 8 positive wells in the presence and absence of
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S9 with TA98 and TA100, which complied with the requirements for the validation of the

AmesMPF and also as described in previous studies [40]. The results are presented in Table 3.
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Compound 4e showed a baseline of 5.85 and 1.91 against TA98, in the absence and presence
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of S9, respectively. Fold inductions over baseline did not reach the mentioned values of the
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baseline and also did not show any dose-response tendency. Therefore, compound 4e was

classified as non-mutagenic against TA98 in the presence/absence of metabolic activation

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(S9) (Figure 2). Compound 4e had a baseline of 6.73 against TA100 in the absence of S9 and

baseline of 5.00 in the presence of S9. Furthermore, fold inductions over baseline were less
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than 1.5 in each concentrations of the compound and also did not show a dose-response
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tendency. Therefore, 4e was not genotoxic against TA100 with/without metabolic activation

(Figure 3).

Compound 4f showed a baseline of 5.85 and 2.82 against TA98 with and without S9,

respectively. Fold inductions over baseline did not reach values more than 1.5 and,

statistically different results did not reveal a dose-response tendency against TA98 without

S9. However, fold inductions over baseline were more than 2.5 and 5 mg/ml concentrations of
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compound 4f against TA 98 with S9. Also, adjacent doses were found to reach mentioned fold

increases with a dose-response tendency. Therefore, 4f was classified as a mutagen against

TA98 with metabolic activation (Figure 4). Compound 4f was found to show a baseline of

6.73 and 5.49 against TA100 with and without S9, respectively. Mentioned-fold increases

over the baseline according to the criteria were not determined with 4f against TA100 without

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S9. However, 2.5 and 5 mg/ml concentrations of 4f reached more than 1.5 fold-increase over

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baseline with a statistical significance and a dose-response tendency. Thus, compound 4f was

found to be non-mutagenic against TA100 in the absence of metabolic activation, whereas it

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may also be classified as a weak mutagen against TA100 in the presence of metabolic

activation (Figure 5).

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Assuming the results of the AmesMPF assay, compound 4e was classified as non-mutagenic.
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This result enhances the importance of compound 4e as a hMAO-B inhibitor. However,
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compound 4f was found to be a weak mutagen, which avoids it to become a drug candidate.

2.6. Prediction of ADME Parameters and BBB Permeability

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An intrinsic pharmacological activity and low toxicological effects are not enough for a

compound to become a drug candidate. A good pharmacokinetics profile is also very

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important for the new drug candidates that should be evaluated earlier in the process of drug

development. Thus, pharmacokinetics profiles of the new drug candidates should be evaluated
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as early as possible in the drug development process. In recent years, combinatorial chemistry
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has significantly increased the number of compounds, for which early data on absorption,

distribution, metabolism and excretion (ADME) are needed [41]. Hence, predictions of

ADME properties of the synthesized compounds (4a-4o) were performed by online

Molinspiration property program [42]. This program applies the Lipinski’s rule of five, which

evaluates the ADME properties of drug like compounds, and is important for the optimization

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of a biologically active compound. According to this rule, an orally effective drug does not

possess more than one violation [43].

The theoretical calculations of ADME parameters (molecular weight, log P, topological polar

surface area (tPSA), number of hydrogen donors (nON), number of hydrogen acceptors

(nOHNH) and molecular volume (MV)) are presented in Table 3 along with the violations of

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Lipinski’s rule. According to these data, all compounds (4a-4o) follow Lipinski’s rule by

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causing no more than one violation. Thus, it can be suggested that synthesized compounds

may possess a good pharmacokinetic profile, increasing their pharmacological importance.

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Drug-likeness score (DLS) was calculated for compounds (4a-4o) and reference agents

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selegiline and clorgiline based on the Molsoft's chemical fingerprints mode consisting of five
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thousand of marketed drugs from World Drug Index (positives) and ten thousand of carefully

selected non-drug compounds (negatives) [44]. In the software, DLS was found to be between
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0 and 2, suggesting good pharmacokinetics for drug candidates. In the Table 3, it is seen that

only compound 4c has a negative DLS. On the other hand, DLSs of the other compounds are
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between 0.26-1.07. Furthermore, DLS of the most active compound 4e (1.02) is very close to
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that of selegiline (1.07). As a result, DLS calculation confirms that synthesized compounds
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may have a good pharmacokinetics.

Drugs that specifically target the CNS must first pass the blood-brain barrier (BBB). Although
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the BBB is protective in nature, the inability for drug molecules to permeate the BBB is a
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significant impediment for CNS drug candidates and should be addressed early in the drug

discovery process. Thus, the task of predicting the BBB permeability of new compounds is of

a great importance [45]. From this point of view, BBB permeability of the synthesized

compounds (4a-4o) was calculated by a CBLigand-BBB prediction server [46]. This predictor

uses two different algorithms as AdaBoost and Support Vector Machine (SVM), combining

with four different fingerprints, employed to predict if a compound can pass (+) or cannot

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pass (-) the BBB. In each case, predictor scores higher than 0, if the compound can pass the

BBB. As presented in Table 3, all calculations for synthesized compounds resulted as BBB

(+), which is necessary for MAO inhibitors.

2.7. Molecular Docking

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As stated in MAO inhibition section, compound 4e was found to be the most active and

selective hMAO-B inhibitor. Although, compounds 4c and 4d had a structural similarity to

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4e, they displayed poorer activity than 4e. Hence, docking studies were performed in order to

gain more insight into the binding modes of compounds 4c, 4d and 4e, and to evaluate the

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effects of structural modifications on the inhibitory activity against hMAO-A and hMAO-B

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enzymes. In the docking studies, X-ray crystal structure of hMAO-A (PDB ID: 2BXR) [47]
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and hMAO-B (PDB ID: 1S2Q) [48] were obtained from Protein Data Bank server

(www.pdb.org). The docking poses of compounds 4c, 4d and 4e on hMAO-A and the poses
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of compounds 4c and 4d on hMAO-B enzyme are presented in Figures 5-7 and Figures 8, 9,

respectively. The docking poses of the most active compound 4e are presented in Figures
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10A and 10B, including general view of 4e at the active site and the binding modes of 4e to
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amino acid residues. The poses displaying van der Waals interactions and electrostatic
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interactions are presented in Figures 11A and 11B.

The docking poses on hMAO-A reveals that there are two main interactions for compounds
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4c, 4d and 4e (Figures 5-7). These are π-π interaction between phenyl of the compounds and
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phenyl of Tyr444, and formation of a hydrogen bond between the carbonyl of the compounds

and amino of Met445. Additionally, it is seen that nitrogen of pyridine in the compound 4e

forms a hydrogen bond with the amino group of Thr52 (Figure 7). Disappearance of this

interaction (Figures 5 and 6) in compounds 4c and 4d explains that compound 4e displays

stronger binding to hMAO-A, and thus it has higher activity against hMAO-A than

compounds 4c and 4d.

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In the poses of hMAO-B docking studies, there is a π-π interaction between phenyl of Tyr398

and phenyl of compounds 4c and 4d (Figures 8 and 9). The amino group of hydrazone moiety

in 4c forms a hydrogen bond with carbonyl of Gly434. The benzimidazole of 4d displays

cation-π interaction with the phenyl of Tyr435. The carbonyl of 4d creates a hydrogen bond

with the amino group of Ser59. The compound 4e snugly binds to amino acid residues lining

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the cavity, and is located very near the FAD cofactor (Figure 10B). The benzimidazole ring

of this compound interacts with phenyl of Tyr435 by a π-π interaction in the aromatic cage of

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the active site. There is a hydrogen bond between the carbonyl of compound 4e and the amino

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group of Ile14. In addition, two neighboring nitrogens in the guanidine moiety of Arg42

establish two different hydrogen bonds with the imino group of hydrazone and nitrogen of

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pyridine (Figure 10B). These interactions support the approach, which reveals that amino
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acid side chains, coating the cavity, are very favorable to interact with the amine moieties [19-
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23].

As stated above, comparing with compounds 4c and 4d, there are more interactions between
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compound 4e and the amino acid residues. Particularly, it may be suggested that pyridine ring
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in the compound 4e is very important in terms of high hMAO-B inhibition because the main

difference between compound 4e and other derivatives is the presence of this ring.
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Compounds 4c and 4d carry pyrrole instead of pyridine in 4e. At first sight, it can be thought

that nitrogens of pyrrole and pyridine can form similar interactions with the amino acid
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residues. However, it is well known that characters of pyrrole and pyridine nitrogens are quite

different [49]. The lone pair of nitrogen in pyrrole is in resonance and cannot be donated,

whereas the lone pair of nitrogen in pyridine is localized and ready for donation. Thus,

pyridine nitrogen acts as hydrogen acceptor and can interact with donor sites of amino acid

residues in an enzyme active site. On the other hand, pyrrole nitrogen acts as hydrogen donor

and can interact with acceptor sites of amino acid residues. This difference influences binding

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capability of the compounds 4c, 4d and 4e to enzyme active site and enzyme inhibition

potency.

The other important factors of binding to the active site of enzyme are the van der Waals

forces and electrostatic interactions. Thus, probable interactions of these types in the active

site of hMAO-B were evaluated for compound 4e (Figure 11A and 11B). Compound 4e has

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favorable van der waals interactions, displayed with pink and red colors as described in the

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user guide of Glide [50] (Figure 11A). Particularly, the propargyl and carbonyl moieties of

compound 4e are in the strongest van der waals interactions between Gly58 and Arg42,

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respectively. Pyridine and carbonyl moieties of 4e are also in an electrostatic interaction

between Arg42 and Arg36, respectively (Figure 11B).

3. Conclusion
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Synthesis of novel compounds including the significant pharmacophore groups of existing
M

drugs is an important approach in the development of novel agents. Based on this strategy, in

the present study, 15 new benzimidazole compounds that incorporate hydrazone and
D

propargyl pharmacophores were tested againts MAO isoforms. Pharmacological studies

TE

revealed the potency of the compound 4e as hMAO-B inhibitor. Toxicological and ADME

studies enhanced the biological importance of this compound. The docking studies clearly
EP

explained the molecular interactions between the compound 4e and hMAO-B. Consequently,
C

all this information may create an influence on medicinal chemists to synthesize more potent
AC

and safer hMAO-B inhibitors, which may be beneficial for the treatment of patients with

Parkinson and Alzheimer’s diseases.

4. Experimental

4.1. Chemistry

All reagents were purchased from commercial suppliers and were used without further

purification. Melting points (M.p.) were determined on Mettler Toledo-MP90 Melting Point
14
 ACCEPTED MANUSCRIPT
System and were uncorrected. IR spectra was recorded on an IR Affinity-1S Infrared

spectrophotometer (Shimadzu, Tokyo, Japan). 1H NMR and 13

C NMR spectra was recorded

on a Bruker Fourier 300 (Bruker Bioscience, Billerica, MA, USA) respectively, in DMSO-d6.

(Bruker, USA), respectively. Mass spectra were recorded on an LCMS-IT-TOF (Shimadzu,

Kyoto, Japan) by using ESI method.

PT
4.1.1. General procedure for the synthesis of the compounds

RI
4.1.1.1. Methyl 4-(1H-benzo[d]imidazol-2-yl)benzoate (1)

SC
Methyl-4-formylbenzoate (2) (4.8 g, 0.03 mol), sodium disulfite (5.7 g, 0.03 mol) and DMF

(5 mL) were added into a vial (30 mL) of microwave synthesis reactor (Anton-Paar,

U
Monowave 300, Austria). The reaction mixture, was heated under conditions of 240 oC and 10
AN
bar for 5 min. The mixture was cooled down, 1,2-phenylenediamine (3.24 g, 0.03 mol) was

added and then the final mixture was kept under the same reaction conditions in the
M

microwave reactor. After cooling, the mixture was poured into the iced-water, precipitated
D

product was washed with water, dried, and recrystallized from ethanol.
TE

4.1.1.2. Methyl 4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)benzoate (2)

Methyl 4-(1H-benzo[d]imidazol-2-yl)benzoate (1) (5.04 g, 0.02 mol) was dissolved in DMF

EP

(10 mL) and sodium hydride (0.576g, 0.024 mol) was added. The mixture was shaken until
C

hydrogen output completed. Propargyl bromide (2.596 g, 0.11 mol) was added and then the
AC

mixture was stirred for 20 h at room temperature. The reaction content was poured into the

iced-water, precipitated product was washed with water, filtered, dried, and recrystallized

from EtOH.

4.1.1.3. 4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)benzohydrazide (3)

Methyl 4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)benzoate (2) (2.90 g, 0.01 mol) in

ethanol (15 mL) and excess of hydrazine hydrate (3 mL) were put into a vial (30 mL) of

15
 ACCEPTED MANUSCRIPT
microwave synthesis reactor (Anton-Paar Monowave 300, Austria). The reaction mixture was

kept under the conditions of 150 oC and 10 bar for 10 min. After cooling, the mixture was

poured into the iced-water, precipitated product was washed with water, dried, and

recrystallized from ethanol.

4.1.1.4. General procedure for the N’-(arylidene)-4-(1-(prop-2-yn-1-yl)-1H-

PT
benzo[d]imidazol-2-yl)benzohydrazide (4a-4o)

RI
4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)benzohydrazide (0.29 g, 0.001 mol)

appropriate aldehyde (0.01 mol) and catalytic amount of glacial acetic acid were refluxed in

SC
ethanol for 2 h. The mixture was cooled, precipitated product was filtered, dried, and

U
recrystallized from ethanol.
AN
4.1.1.4.1. N'-[(thiophen-2-yl)methylene]-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)

benzohydrazide (4a)
M

Yield: 78 %, M.P. = 154.9 °C, FTIR (ATR, cm-1 ): 3229 (N-H), 2122 (CC), 1647 (C=O),
D

862, 704. 1H-NMR (300 MHz, DMSO-d6): δ = 3.50 (1H, s, CCH), 5.22 (2H, s, –CH2-),
TE

7.16 (1H, s, thiophene –CH-), 7.29-7.40 (2H, m, benzimidazole –CH-), 7.50 (1H, s, thiophene

–CH-), 7.69-7.76 (3H, m, benzimidazole –CH-, thiophene –CH-), 8.02 (2H, d, J= 7.75 Hz,
EP

disubstituted benzene –CH-), 8.11 (2H, d, J= 7.75 Hz, disubstituted benzene –CH-), 8.69 (1H,
13
s, imine –CH-), 11.99 (1H, s,–NH-). C-NMR (75 MHz, DMSO-d6): δ = 34.85 (–CH2-),
C
AC

76.75 (CCH), 78.95 (CCH), 111.42 (benzimidazole –CH-), 119.91 (benzimidazole –

CH-), 123.19 (benzimidazole –CH-), 123.69 (benzimidazole –CH-), 128.41 (imine –CH-),

128.58 (Ar-CH), 129.53 (Ar-CH), 129.63 (Ar-CH), 131.67 (Ar-CH), 133.08 (Ar-CH), 134.87

(Ar-CH), 135.95 (benzimidazole –CH-), 139.46 (Ar-CH), 142.86 (benzimidazole –CH-),

143.77 (Ar-CH), 151.96 (benzimidazole –CH-), 162.85 (C=O). HRMS (m/z): [M+H]+ calcd

for C22H16N4OS: 385.1118; found 385.1105.

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4.1.1.4.2. N'-[(5-nitrothiophen-2-yl)methylene)]-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-

2-yl) benzohydrazide (4b)

Yield: 82 %, M.P. = 167.8 °C, FTIR (ATR, cm-1 ): 3283 (N-H), 2091 (CC), 1672 (C=O),

1555, 1339 (NO2), 864. 1H-NMR (300 MHz, DMSO-d6): δ = 3.53 (1H, s, CCH), 5.23

(2H, s, –CH2-), 7.29-7.40 (2H, m, benzimidazole –CH-), 7.61 (1H, d, J= 4.20 Hz, thiophene

PT
–CH-), 7.72-7.76 (2H, m, benzimidazole –CH-), 8.04 (2H, d, J= 8.20 Hz, disubstituted

RI
benzene –CH-), 8.12-8.14 (3H, m, disubstituted benzene –CH-, thiophene –CH-), 8.71 (1H, s,
13
imine –CH-), 12.39 (1H, s,–NH-). C-NMR (75 MHz, DMSO-d6): δ = 34.86 (–CH2-),

SC
76.78 (CCH), 78.97 (CCH), 111.44 (benzimidazole –CH-), 119.94 (benzimidazole –

CH-), 123.17 (benzimidazole –CH-), 123.69 (benzimidazole –CH-), 128.75 (imine –CH-),

U
AN
129.59 (Ar-CH), 130.36 (Ar-CH), 130.99 (Ar-CH), 132.84 (Ar-CH), 133.50 (Ar-CH), 134.32

(Ar-CH), 136.00 (benzimidazole –CH-), 142.01 (Ar-CH), 142.90 (benzimidazole –CH-),

M

147.06 (Ar-CH), 151.87 (benzimidazole –CH-), 160.24 (C=O). HRMS (m/z): [M+H]+ calcd

for C22H15N5O3S: 430.0968; found 430.0954.

D

4.1.1.4.3. N'-[(1H-pyrrol-2-yl)methylene]-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)
TE

benzohydrazide (4c)

Yield: 80 %, M.P. = 105.4 °C, FTIR (ATR, cm-1 ): 3377, 3221 (N-H), 2120 (CC), 1653
EP

(C=O), 860, 743. 1H-NMR (300 MHz, DMSO-d6): δ = 3.51 (1H, s, CCH), 5.22 (2H, s,
C

–CH2-), 6.16 (1H, s, pyrrol –CH-), 6.52 (1H, s, pyrrol –CH-), 6.94 (1H, s, pyrrol –CH-), 7.29-
AC

7.40 (2H, m, benzimidazole –CH-), 7.74 (2H, br. s, benzimidazole –CH-), 8.01 (2H, d, J=

7.75 Hz, disubstituted benzene –CH-), 8.12 (2H, d, J= 7.75 Hz, disubstituted benzene –CH-),

8.32 (1H, s, imine –CH-), 11.58 (1H, s,–NH-). 13C-NMR (75 MHz, DMSO-d6): δ = 34.85 (–

CH2-), 76.75 (CCH), 78.98 (CCH), 109.79 (Ar-CH), 111.41 (benzimidazole –CH-),

113.99 (Ar-CH), 115.29 (Ar-CH), 119.90 (benzimidazole –CH-), 123.14 (benzimidazole –

CH-), 123.63 (benzimidazole –CH-), 127.47 (Ar-CH), 128.51 (Ar-CH), 129.45 (Ar-CH),

17
 ACCEPTED MANUSCRIPT
132.83 (Ar-CH), 135.30 (Ar-CH), 135.98 (benzimidazole –CH-), 141.69 (imine –CH-),

142.91 (benzimidazole –CH-), 152.04 (benzimidazole –CH-), 162.42 (C=O). HRMS (m/z):

[M+H]+ calcd for C22H17N5O: 368.1506; found 368.1488.

4.1.1.4.4. N'-[1-methyl-1H-pyrrol-2-yl)methylene]-4-(1-(prop-2-yn-1-yl)-1H-

benzo[d]imidazol-2-yl)benzohydrazide (4d)

PT
Yield: 82 %, M.P. = 115.3 °C, FTIR (ATR, cm-1 ): 3267 (N-H), 2120 (CC), 1668 (C=O),

RI
856, 741. 1H-NMR (300 MHz, DMSO-d6): δ = 3.52 (1H, s, CCH), 3.90 (3H, s, N-CH3),

5.22 (2H, s, –CH2-), 6.13 (1H, s, pyrrol–CH-), 6.54 (1H, s, pyrrol –CH-), 7.00 (1H, s, pyrrol

SC
–CH-), 7.29-7.40 (2H, m, benzimidazole –CH-), 7.72-7.76 (2H, m, benzimidazole –CH-),

8.02 (2H, d, J= 7.90 Hz, disubstituted benzene –CH-), 8.11 (2H, d, J= 7.90 Hz, disubstituted

U
benzene –CH-), 8.42 (1H, s, imine –CH-), 11.70 (1H, s,–NH-). 13
C-NMR (75 MHz, DMSO-
AN
d6): δ = 34.86 (–CH2-), 36.40 (-CH3), 76.77 (CCH), 78.99 (CCH), 108.89 (Ar-CH),
M

111.41 (benzimidazole –CH-), 115.11 (Ar-CH), 119.90 (benzimidazole –CH-), 123.14

(benzimidazole –CH-), 123.63 (benzimidazole –CH-), 127.51 (Ar-CH), 128.44 (Ar-CH),

D

128.63 (Ar-CH), 129.48 (Ar-CH), 132.86 (Ar-CH), 135.23 (Ar-CH), 135.98 (benzimidazole –
TE

CH-), 141.78 (imine –CH-), 142.91 (benzimidazole –CH-), 152.03 (benzimidazole –CH-),

162.33 (C=O). HRMS (m/z): [M+H]+ calcd for C23H19N5O: 382.1662; found 382.1677.
EP

4.1.1.4.5. N'-[(pyridin-3-yl)methylene]-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)
C

benzohydrazide (4e)
AC

Yield: 79 %, M.P. = 208.5 °C, FTIR (ATR, cm-1 ): 3410 (N-H), 2106 (CC), 1651 (C=O),

853, 735. 1H-NMR (300 MHz, DMSO-d6): δ = 3.52 (1H, s, CCH), 5.23 (2H, s, –CH2-),

7.29-7.40 (2H, m, benzimidazole –CH-), 7.51 (1H, br. s, pyridine –CH-), 7.73-7.76 (2H, m,

benzimidazole –CH-), 8.04 (2H, d, J= 7.70 Hz, disubstituted benzene –CH-), 8.13-8.19 (3H,

m, disubstituted benzene –CH-, pyridine –CH-), 8.55 (1H, s, imine –CH-), 8.63 (1H, br. s,
13
pyridine –CH-), 8.90 (1H, s, pyridine –CH-), 12.19 (1H, s,–NH-). C-NMR (75 MHz,

18
 ACCEPTED MANUSCRIPT
DMSO-d6): δ = 34.86 (–CH2-), 76.78 (CCH), 78.98 (CCH), 111.43 (benzimidazole –

CH-), 119.83 (benzimidazole –CH-), 123.16 (benzimidazole –CH-), 123.67 (benzimidazole –

CH-), 124.52 (Ar-CH), 128.69 (Ar-CH), 129.55 (Ar-CH), 130.64 (Ar-CH), 133.26 (Ar-CH),

134.00 (Ar-CH), 134.70 (Ar-CH), 135.99 (benzimidazole –CH-), 142.90 (benzimidazole –

CH-), 145.91 (Ar-CH), 149.30 (imine –CH-), 151.29, 151.94 (benzimidazole –CH-), 163.09

PT
(C=O). HRMS (m/z): [M+H]+ calcd for C23H17N5O: 380.1506; found 380.1484.

RI
4.1.1.4.6. N'-(4-fluorobenzylidene)-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)

benzohydrazide (4f)

SC
Yield: 85 %, M.P. = 153.3 °C, FTIR (ATR, cm-1 ): 3300 (N-H), 2126 (CC), 1644 (C=O),

841, 733. 1H-NMR (300 MHz, DMSO-d6): δ = 3.52 (1H, s, CCH), 5.23 (2H, s, –CH2-),

U
AN
7.30-7.40 (4H, m, benzimidazole –CH-, fluorophenyl –CH-), 7.74 (2H, br. s, benzimidazole –

CH-), 7.82 (2H, br. s, fluorophenyl –CH-), 8.04 (2H, d, J= 7.65 Hz, disubstituted benzene –
M

CH-), 8.13 (2H, d, J= 7.65 Hz, disubstituted benzene –CH-), 8.50 (1H, s, imine –CH-), 12.04
13
(1H, s,–NH-). C-NMR (75 MHz, DMSO-d6): δ = 34.86 (–CH2-), 76.78 (CCH), 78.98
D

(CCH), 111.43 (benzimidazole –CH-), 116.43 (JCF-2=21.8 Hz) (Ar-CH), 119.92

TE

(benzimidazole –CH-), 123.15 (benzimidazole –CH-), 123.66 (benzimidazole –CH-), 128.62

EP

(Ar-CH), 129.52 (Ar-CH), 129.82 (JCF-3=8.3 Hz) (Ar-CH), 131.35 (JCF-4=3.1 Hz) (Ar-CH),

133.15 (Ar-CH), 134.87 (Ar-CH), 135.99 (benzimidazole –CH-), 142.91 (benzimidazole –

C

CH-), 147.49 (imine –CH-), 151.97 (benzimidazole –CH-), 162.96 (C=O), 163.66 (JCF-
AC

1=245.7 Hz) (Ar-CH). HRMS (m/z): [M+H]+ calcd for C24H17N4OF: 397.1459; found

397.1455.

4.1.1.4.7. N'-(4-chlorobenzylidene)-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)

benzohydrazide (4g)

Yield: 82 %, M.P. = 222.9 °C, FTIR (ATR, cm-1 ): 3279 (N-H), 2124 (CC), 1643 (C=O),

837, 733. 1H-NMR (300 MHz, DMSO-d6): δ = 3.52 (1H, s, CCH), 5.23 (2H, s, –CH2-),

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 ACCEPTED MANUSCRIPT
7.29-7.40 (2H, m, benzimidazole –CH-), 7.55 (2H, d, J= 7.80 Hz, chlorophenyl –CH-), 7.74-

7.80 (4H, m, benzimidazole –CH-, chlorophenyl –CH-), 8.04 (2H, d, J= 7.50 Hz,

disubstituted benzene –CH-), 8.14 (2H, d, J= 7.50 Hz, disubstituted benzene –CH-), 8.49 (1H,
13
s, imine –CH-), 12.09 (1H, s,–NH-). C-NMR (75 MHz, DMSO-d6): δ = 34.86 (–CH2-),

76.78 (CCH), 78.98 (CCH), 111.43 (benzimidazole –CH-), 119.92 (benzimidazole –

PT
CH-), 123.15 (benzimidazole –CH-), 123.66 (benzimidazole –CH-), 128.65 (Ar-CH), 129.27

RI
(Ar-CH), 129.46 (Ar-CH), 129.52 (Ar-CH), 133.21 (Ar-CH), 133.68 (Ar-CH), 134.80 (Ar-

CH), 135.08 (Ar-CH), 135.99 (benzimidazole –CH-), 142.90 (benzimidazole –CH-), 147.28

SC
(imine –CH-), 151.95 (benzimidazole –CH-), 163.01 (C=O). HRMS (m/z): [M+H]+ calcd for

C24H17N4OCl: 413.1164; found 413.1145.

4.1.1.4.8.
U
N'-(4-hydroxybenzylidene)-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)
AN
benzohydrazide (4h)
M

Yield: 83 %, M.P. = 151.8 °C, FTIR (ATR, cm-1 ): 3385 (O-H), 3238 (N-H), 2120 (CC),

1643 (C=O), 862, 831, 734. 1H-NMR (300 MHz, DMSO-d6): δ = 3.52 (1H, s, CCH),
D

5.23 (2H, s, –CH2-), 6.86 (2H, d, J= 7.85 Hz, hydroxyphenyl –CH-), 7.29-7.40 (2H, m,
TE

benzimidazole –CH-), 7.59 (2H, d, J= 7.85 Hz, hydroxyphenyl –CH-), 7.74 (2H, br. s,

benzimidazole –CH-), 8.02 (2H, d, J= 7.75 Hz, disubstituted benzene –CH-), 8.12 (2H, d, J=
EP

7.75 Hz, disubstituted benzene –CH-), 8.39 (1H, s, imine –CH-), 9.96 (1H, s, -OH), 11.82
C

13
(1H, s,–NH-). C-NMR (75 MHz, DMSO-d6): δ = 34.86 (–CH2-), 76.78 (CCH), 78.99
AC

(CCH), 111.42 (benzimidazole –CH-), 116.22 (Ar-CH), 119.91 (benzimidazole –CH-),

123.14 (benzimidazole –CH-), 123.64 (benzimidazole –CH-), 125.67 (Ar-CH), 128.54 (Ar-

CH), 129.43 (Ar-CH), 129.48 (Ar-CH), 132.95 (Ar-CH), 135.15 (Ar-CH), 135.98

(benzimidazole –CH-), 142.90 (benzimidazole –CH-), 148.96 (imine –CH-), 152.01

(benzimidazole –CH-), 160.02 (Ar-CH), 162.64 (C=O). HRMS (m/z): [M+H]+ calcd for

C24H18N4O2: 395.1503; found 395.1487.

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4.1.1.4.9. N'-(4-methoxybenzylidene)-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-

yl)benzohydrazide (4i)

Yield: 89 %, M.P. = 201.0 °C, FTIR (ATR, cm-1 ): 3256 (N-H), 2124 (CC), 1647 (C=O),

858, 837. 1H-NMR (300 MHz, DMSO-d6): δ = 3.52 (1H, s, CCH), 3.82 (3H, s, -OCH3),

5.23 (2H, s, –CH2-), 7.04 (2H, d, J= 8.00 Hz, methoxyphenyl –CH-), 7.29-7.40 (2H, m,

PT
benzimidazole –CH-), 7.69-7.80 (4H, m, benzimidazole –CH-, methoxyphenyl –CH-), 8.02

RI
(2H, d, J= 7.90 Hz, disubstituted benzene –CH-), 8.14 (2H, d, J= 7.90 Hz, disubstituted
13
benzene –CH-), 8.46 (1H, s, imine –CH-), 12.02 (1H, s,–NH-). C-NMR (75 MHz, DMSO-

SC
d6): δ = 34.86 (–CH2-), 55.80 (-OCH3), 76.78 (CCH), 78.99 (CCH), 111.42

(benzimidazole –CH-), 112.80 (Ar-CH), 114.83 (Ar-CH), 119.91 (benzimidazole –CH-),

U
AN
123.14 (benzimidazole –CH-), 123.64 (benzimidazole –CH-), 127.31 (Ar-CH), 128.60 (Ar-

CH), 129.25 (Ar-CH), 129.47 (Ar-CH), 135.09 (Ar-CH), 135.98 (benzimidazole –CH-),
M

142.91 (benzimidazole –CH-), 148.59 (imine –CH-), 152.01 (benzimidazole –CH-), 161.36

(Ar-CH), 162.79 (C=O). HRMS (m/z): [M+H]+ calcd for C25H20N4O2: 409.1659; found
D

409.1648.
TE

4.1.1.4.10. N'-(2-methoxybenzylidene)-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)

benzohydrazide (4j)
EP

Yield: 81 %, M.P. = 127.7 °C, FTIR (ATR, cm-1 ): 3275 (N-H), 2120 (CC), 1672 (C=O),
C

846, 746. 1H-NMR (300 MHz, DMSO-d6): δ = 3.53 (1H, s, CCH), 3.88 (3H, s, -OCH3),
AC

5.23 (2H, s, –CH2-), 7.02-7.13 (2H, m, methoxyphenyl –CH-), 7.29-7.46 (3H, m,

benzimidazole –CH-, methoxyphenyl –CH-), 7.73-7.77 (2H, m, benzimidazole –CH-), 7.92

(1H, d, J= 7.50 Hz, methoxyphenyl –CH-), 8.03 (2H, d, J= 7.80 Hz, disubstituted benzene –

CH-), 8.16 (2H, d, J= 7.60 Hz, disubstituted benzene –CH-), 8.87 (1H, s, imine –CH-), 12.03
13
(1H, s,–NH-). C-NMR (75 MHz, DMSO-d6): δ = 34.87 (–CH2-), 56.18 (-OCH3),

76.78(CCH), 78.98 (CCH), 111.42 (benzimidazole –CH-), 112.34 (Ar-CH), 119.92

21
 ACCEPTED MANUSCRIPT
(benzimidazole –CH-), 121.25 (Ar-CH), 122.71 (Ar-CH), 123.15 (benzimidazole –CH-),

123.65 (benzimidazole –CH-), 126.02 (Ar-CH), 128.62 (Ar-CH), 129.49 (Ar-CH), 132.17

(Ar-CH), 133.08 (Ar-CH), 134.89 (Ar-CH), 135.98 (benzimidazole –CH-), 142.92

(benzimidazole –CH-), 144.12 (imine –CH-), 152.00 (benzimidazole –CH-), 158.29 (Ar-CH),

162.75 (C=O). HRMS (m/z): [M+H]+ calcd for C25H20N4O2: 409.1659; found 409.1652.

PT
4.1.1.4.11. N'-(3-methoxybenzylidene)-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)

RI
benzohydrazide (4k)

Yield: 80 %, M.P. = 224.7 °C, FTIR (ATR, cm-1 ): 3213 (N-H), 2120 (CC), 1667 (C=O),

SC
860, 744. 1H-NMR (300 MHz, DMSO-d6): δ = 3.53 (1H, s, CCH), 3.83 (3H, s, -OCH3),

5.23 (2H, s, –CH2-), 7.03 (1H, d, J= 7.60 Hz, methoxyphenyl –CH-), 7.32-7.40 (5H, m,

U
benzimidazole –CH-, methoxyphenyl –CH-), 7.73 (2H, br. s, benzimidazole –CH-), 8.04 (2H,
AN
d, J= 7.60 Hz, disubstituted benzene –CH-), 8.14 (2H, d, J= 7.60 Hz, disubstituted benzene –
M

13
CH-), 8.48 (1H, s, imine –CH-), 12.04 (1H, s,–NH-). C-NMR (75 MHz, DMSO-d6): δ =

34.86 (–CH2-), 55.68 (-OCH3), 76.79 (CCH), 78.98 (CCH), 111.42 (benzimidazole –
D

CH-), 111.71 (Ar-CH), 116.83 (Ar-CH), 119.93 (benzimidazole –CH-), 120.62 (Ar-CH),
TE

123.15 (benzimidazole –CH-), 123.66 (benzimidazole –CH-), 128.64 (Ar-CH), 129.52 (Ar-

CH), 130.47 (Ar-CH), 133.16 (Ar-CH), 134.90 (Ar-CH), 135.99 (benzimidazole –CH-),
EP

136.16 (Ar-CH), 142.92 (benzimidazole –CH-), 148.55 (imine –CH-), 151.97 (benzimidazole
C

–CH-), 160.04 (Ar-CH), 162.99 (C=O). HRMS (m/z): [M+H]+ calcd for C25H20N4O2:
AC

409.1659; found 409.1649.

4.1.1.4.12. N'-(3-hydroxybenzylidene)-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)

benzohydrazide (4l)

Yield: 85 %, M.P. = 137.2 °C, FTIR (ATR, cm-1 ): 3244 (N-H), 3192 (O-H), 2126 (CC),

1641 (C=O), 860, 769, 738. 1H-NMR (300 MHz, DMSO-d6): δ = 3.52 (1H, s, CCH),

5.23 (2H, s, –CH2-), 6.86 (1H, d, J= 7.85 Hz, hydroxyphenyl –CH-), 6.96 (1H, d, J= 7.85

22
 ACCEPTED MANUSCRIPT
Hz, hydroxyphenyl –CH-), 7.27-7.40 (4H, m, benzimidazole –CH-, hydroxyphenyl –CH-),

7.74 (2H, br. s, benzimidazole –CH-), 8.02 (2H, d, J= 7.80 Hz, disubstituted benzene –CH-),

8.12 (2H, d, J= 7.75 Hz, disubstituted benzene –CH-), 8.30 (1H, s, imine –CH-), 11.77 (1H,
13
s,–NH-). C-NMR (75 MHz, DMSO-d6): δ = 34.86 (–CH2-), 76.78 (CCH), 78.97

(CCH), 111.42 (benzimidazole –CH-), 113.16 (Ar-CH), 118.04 (Ar-CH), 119.10 (Ar-CH),

PT
119.37 (Ar-CH), 119.92 (benzimidazole –CH-), 123.16 (benzimidazole –CH-), 123.67

RI
(benzimidazole –CH-), 128.63 (Ar-CH), 129.52 (Ar-CH), 130.39 (Ar-CH), 133.11 (Ar-CH),

134.93 (Ar-CH), 135.98 (benzimidazole –CH-), 142.90 (benzimidazole –CH-), 148.76 (imine

SC
–CH-), 151.98 (benzimidazole –CH-), 158.18 (Ar-CH), 162.93 (C=O). HRMS (m/z): [M+H]+

calcd for C24H18N4O2: 395.1503; found 395.1509.

4.1.1.4.13.
U
N'-(3,5-dihydroxybenzylidene)-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)
AN
benzohydrazide (4m)
M

Yield: 86 %, M.P. = 163.2 °C, FTIR (ATR, cm-1 ): 3275 (N-H), 3202 (O-H), 2126 (CC),

1649 (C=O), 856, 769, 740. 1H-NMR (300 MHz, DMSO-d6): δ = 3.52 (1H, s, CCH),
D

5.22 (2H, s, –CH2-), 6.80 (1H, d, J= 7.85 Hz, dihydroxyphenyl –CH-), 6.96 (1H, d, J= 7.85
TE

Hz, dihydroxyphenyl –CH-), 7.27-7.40 (3H, m, benzimidazole –CH-, dihydroxyphenyl –CH-

), 7.74 (2H, br. s, benzimidazole –CH-), 8.02 (2H, d, J= 7.80 Hz, disubstituted benzene –CH-
EP

), 8.12 (2H, d, J= 7.75 Hz, disubstituted benzene –CH-), 8.30 (1H, s, imine –CH-), 11.77 (1H,
C

13
s,–NH-). C-NMR (75 MHz, DMSO-d6): δ = 34.86 (–CH2-), 76.76 (CCH), 78.99
AC

(CCH), 111.42 (benzimidazole –CH-), 113.18 (Ar-CH), 116.06 (Ar-CH), 119.91

(benzimidazole –CH-), 121.19 (Ar-CH), 123.14 (benzimidazole –CH-), 123.64

(benzimidazole –CH-), 126.13 (Ar-CH), 128.53 (Ar-CH), 129.47 (Ar-CH), 132.93 (Ar-CH),

135.17 (Ar-CH), 135.98 (benzimidazole –CH-), 142.90 (benzimidazole –CH-), 147.18 (imine

–CH-), 152.04 (benzimidazole –CH-), 162.59 (C=O). HRMS (m/z): [M+H]+ calcd for

C24H18N4O3: 411.1452; found 411.1434.

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4.1.1.4.14. N'-(3,5-dimethoxybenzylidene)-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)

benzohydrazide (4n)

Yield: 86 %, M.P. = 124.5 °C, FTIR (ATR, cm-1 ): 3219 (N-H), 2118 (CC), 1653 (C=O),

762, 745.1H-NMR (300 MHz, DMSO-d6): δ = 3.52 (1H, s, CCH), 3.82 (3H, s, -OCH3),

3.84 (3H, s, -OCH3), 5.23 (2H, s, –CH2-), 7.03-7.06 (1H, m, dimethoxyphenyl –CH-), 7.22-

PT
7.25 (1H, m, dimethoxyphenyl –CH-), 7.29-7.40 (2H, m, benzimidazole –CH-), 7.61 (1H, s,

RI
dimethoxyphenyl –CH-), 7.74 (2H, br. s, benzimidazole –CH-), 8.04 (2H, d, J= 7.45 Hz,

disubstituted benzene –CH-), 8.13 (2H, d, J= 7.45 Hz, disubstituted benzene –CH-), 8.70 (1H,

SC
13
s, imine –CH-), 12.37 (1H, s,–NH-). C-NMR (75 MHz, DMSO-d6): δ = 34.85 (–CH2-),

55.95 (-OCH3), 56.04 (-OCH3), 76.77 (CCH), 78.99 (CCH), 108.71 (Ar-CH), 111.42

U
AN
(benzimidazole –CH-), 111.95 (Ar-CH), 119.91 (benzimidazole –CH-), 122.49 (Ar-CH),

123.15 (benzimidazole –CH-), 123.65 (benzimidazole –CH-), 127.41 (Ar-CH), 128.57 (Ar-
M

CH), 129.50 (Ar-CH), 133.02 (Ar-CH), 135.08 (Ar-CH), 135.98 (benzimidazole –CH-),

142.91 (benzimidazole –CH-), 148.85 (imine –CH-), 149.56 (Ar-CH), 151.32 (Ar-CH),
D

152.00 (benzimidazole –CH-), 162.79 (C=O). HRMS (m/z): [M+H]+ calcd for C26H22N4O3:
TE

439.1765; found 439.1753.

4.1.1.4.15. N'-(2,3-dimethoxybenzylidene)-4-(1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-yl)
EP

benzohydrazide (4o)
C

Yield: 76 %, M.P. = 99.3 °C, FTIR (ATR, cm-1 ): 3219 (N-H), 2120 (CC), 1643 (C=O),
AC

792, 763.1H-NMR (300 MHz, DMSO-d6): δ = 3.52 (1H, s, CCH), 3.82 (3H, s, -OCH3),

3.85 (3H, s, -OCH3), 5.23 (2H, s, –CH2-), 7.14 (2H, br. s, dimethoxyphenyl –CH-), 7.29-7.40

(2H, m, benzimidazole –CH-), 7.50-7.52 (1H, m, dimethoxyphenyl –CH-), 7.72-7.77 (2H, m,

benzimidazole –CH-), 8.04 (2H, d, J= 7.95 Hz, disubstituted benzene –CH-), 8.16 (2H, d, J=
13
7.95 Hz, disubstituted benzene –CH-), 8.79 (1H, s, imine –CH-), 12.06 (1H, s,–NH-). C-

NMR (75 MHz, DMSO-d6): δ = 34.86 (–CH2-), 56.25 (-OCH3), 61.73 (-OCH3), 76.77

24
 ACCEPTED MANUSCRIPT
(CCH), 78.98 (CCH), 111.42 (benzimidazole –CH-), 114.82 (Ar-CH), 117.50 (Ar-CH),

119.92 (benzimidazole –CH-), 123.16 (benzimidazole –CH-), 123.67 (benzimidazole –CH-),

124.90 (Ar-CH), 128.16 (Ar-CH), 128.63 (Ar-CH), 129.50 (Ar-CH), 133.13 (Ar-CH), 134.84

(Ar-CH), 135.98 (benzimidazole –CH-), 142.90 (benzimidazole –CH-), 144.26 (Ar-CH),

148.55 (imine –CH-), 151.98 (benzimidazole –CH-), 153.16 (Ar-CH), 162.83 (C=O). HRMS

PT
(m/z): [M+H]+ calcd for C26H22N4O3: 439.1765; found 439.1749.

RI
4.2. MAO-A and MAO-B Inhibition Assay

Ampliflu™ Red (10-Acetyl-3,7-dihydroxyphenoxazine), peroxidase from horseradish,

SC
hMAO-A, hMAO-B, H2O2, tyramine hydrochloride, selegiline, rasagiline and clorgiline were

U
purchased from Sigma-Aldrich (Steinheim, Germany) and retained under the suggested
AN
conditions by supplier. All pipetting processes were performed using a Biotek Precision XS

robotic system (USA). Measurements were carried out by a BioTek-Synergy H1 microplate

M

reader (USA) based on the fluorescence generated (excitation, 535 nm, emission, 587 nm)

over a 30 min period, in which the fluorescence increased linearly.

D

In the enzymatic assay, three different daily prepared solutions were used. I) Inhibitor
TE

solutions: Synthesized compounds and reference agents were prepared in 2% DMSO in 10-3-
EP

10-9 M concentrations (10 mL for each concentration). II) Enzyme solutions: Recombinant

hMAO-A (0.5 U/mL) and recombinant hMAO-B (0.64 U/mL) enzymes were dissolved in the
C

phosphate buffer and final volumes were adjusted to 10 mL. III) Working solution:
AC

Horseradish peroxidase (200 U/mL, 100 µL), Ampliflu™ Red (20 mM, 200 µL) and tyramine

(100 mM, 200 µL) were dissolved in the phosphate buffer and final volume was adjusted to

10 mL.

The solutions of inhibitor (20 µL/well) and hMAO-A (100 µL/well) or hMAO-B (100

µL/well) were added to the flat black bottom 96-well micro test plate, and incubated at 37°C

for 30 min. After this incubation period, the reaction was started by adding a working solution

25
 ACCEPTED MANUSCRIPT
(100 µL/well). The mixture was incubated at 37°C for 30 min and the fluorescence (Ex/Em =

535/587 nm) was measured at 5 min intervals. Control experiments were carried out

simultaneously by replacing the inhibitor solution with 2% DMSO (20 µL). To check the

probable inhibitory effect of inhibitors on horseradish peroxidase, a parallel reading was

performed by replacing enzyme solutions with %3 H2O2 solution (20 mM 100 µL/well). In

PT
addition, the possible capacity of the inhibitors to modify the fluorescence generated in the

RI
reaction mixture due to non-enzymatic inhibition was determined by mixing inhibitor and

working solutions.

SC
The specific fluorescence emission (used to obtain the final results) was calculated after

subtraction of the background activity, which was determined from vials containing all

U
AN
components except the hMAO isoforms, which were replaced by phosphate buffer (100

µL/well). Blank, control and all concentrations of inhibitors were analyzed in quadruplicate
M

and inhibition percent was calculated by using following equation:

(     )  (    )
D

% Inhibition =     
 100
TE

FCt2: Fluorescence of a control well measured at t2 time, FCt1: Fluorescence of a control well

measured at t2 time, FIt2: Fluorescence of an inhibitor well measured at t2 time, FIt1:

EP

Fluorescence of an inhibitor well measured at t1 time,

C

The IC50 values were calculated from a dose-response curve obtained by plotting the
AC

percentage inhibition versus the log concentration with the use of GraphPad ‘PRISM’

software (version 5.0). The results were displayed as mean ±standard deviation (SD).

Selectivity index (SI) was calculated as IC50(hMAO-A)/ IC50(hMAO-B).

4.3. Enzyme Kinetic Studies

The same materials were used in the MAO inhibition assay. The most active compound 4e

was tested at five different concentrations (IC50/4, IC50/2, IC50, 2 x IC50 and 4 x IC50/4). The

26
 ACCEPTED MANUSCRIPT
solutions of inhibitor (20 µL/well) and enzyme were added to the flat black bottom 96-well

micro test plate, and incubated at 37°C for 30 min. After incubation period, the working

solution, including various concentrations (20, 10, 5, 2.5, 1.25, and 0.625µM) of tyramine

(100 µL/well) was added. The increase of the fluorescence (Ex/Em = 535/587 nm) was

recorded for 30 min. A parallel experiment was carried out without inhibitor. All processes

PT
were assayed in quadruplicate. The results were analyzed as Lineweaver-Burk plots using

RI
Microsoft Office Excel 2013. The Vmax values of the Lineweaver-Burk plots were replotted

versus the inhibitor concentration, and the Ki values were determined from the x-axis

SC
intercept as -Ki.

4.4. Cytotoxicity Assay

U
AN
Cytotoxicity of compounds 4e and 4f was tested using the NIH/3T3 mouse embryonic

fibroblast cell line (ATCC® CRL-1658™, London, UK). NIH/3T3 cells were incubated
M

according to the supplier’s recommendations. NIH/3T3 cells were seeded at 1x104 cells into

each well of 96-well plates. MTT assay was performed as previously described [51, 52]. The
D

compounds were tested between 0.0316-1000 µM concentrations. The IC50 values were
TE

determined by plotting a dose-response curve of inhibition % versus compound

EP

concentrations tested [53].

4.5. Genotoxicity Assay

C

The genotoxicity of the most effective compounds (4e and 4f) was determined by Ames assay
AC

using AmesMPF 98/100 mutagenicity assay sample kit (Xenometrix AG, Switzerland) as

previously described [54]. Salmonella typhimurium strains, TA98 (frameshift mutations) and

TA100 (base-pair substitutions), are used in this assay. Concentration range of the compounds

was between 16 and 5000 µg/mL according to the previous guidelines [40]. Compounds were

prepared in six different concentrations (5, 2.5, 1.25, 0.625, 0.3125, 0.156 mg/mL) in DMSO.

Mutagenic potential was determined in absence and presence of Aroclor™-1254 induced

27
 ACCEPTED MANUSCRIPT
male Sprague–Dawley rat liver microsomal enzyme (S9) mix (Xenometrix AG, Switzerland).

Positive controls without S9 mix were 2-Nitrofluorene (2 µg/mL) and 4-nitroquinoline N-

oxide (0.1 µg/mL) whereas 1 µg/mL and 2.5 µg/mL of 2-aminoanthracene solutions were

used as positive controls with S9 against TA 98 and TA100, respectively. Solvent control was

prepared with 4% DMSO. At the end of the experiment, revertant bacteria drops the pH of

PT
solution and indicator medium colour was changed to yellow. Yellow wells were counted as

RI
positive and compared with the negative control. Fold induction over the negative control and

fold induction over the baseline were calculated. Fold induction over the negative control is

SC
the ratio of the mean number of positive wells for the dose concentration divided by the mean

number of positive wells for the zero dose (negative) control. Fold induction over the baseline

U
is the ratio of the mean number of positive wells for the dose concentration divided by zero
AN
dose baseline. The zero dose baseline is obtained by adding one standard deviation to the
M

mean number of positive wells of the zero dose control. Mutagenicity was determined

according to the criteria from previous studies [55]. For a baseline value ≤ 3, significant
D

increases between 2 and 3-fold the baseline were classified as weak mutagen, and increases ≥
TE

3-fold the baseline were classified as mutagen. For a baseline was >3, significant increases

between 1.5 and 2.5-fold the baseline were classified as weak mutagen, and increases ≥ 2.5-
EP

fold the baseline, were classified as mutagen. As a rule, at least two adjacent doses with

significant increases or a significant increase at the highest dose level should be observed for
C
AC

a mutagenic compound. All doses were compared according to Student’s t-test at p < 0.05 for

statistical significance. The compounds were classified as a non-mutagenic if they did not

have any of the properties mentioned above.

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4.6. Prediction of ADME Parameters and BBB Permeability

Physicochemical parameters of compounds (4a-4o) were analysed by online Molinspiration

property calculation program [42]. DLSs were calculated by MolSoft software [44]. BBB

permeability of the compounds was assigned by an online BBB Predictor [46].

PT
4.7. Molecular Docking

A structure based in silico procedure was applied to discover the binding modes of

RI
compounds 4c, 4d and 4e to hMAO-A and hMAO-B enzyme active sites. The crystal

SC
structures of hMAO-A (PDB ID: 2BXR) [47,56,57] and hMAO-B (PDB ID: 1S2Q) [48],

which were crystallized with the reference drugs (chlorgiline and rasagiline) of enzyme

U
inhibition assay, were retrieved from the Protein Data Bank server (www.pdb.org).
AN
The structures of ligands were built using the Schrödinger Maestro [58] interface and then

were submitted to the Protein Preparation Wizard protocol of the Schrödinger Suite 2016
M

Update 2 [59]. The ligands were prepared by the LigPrep 3.8 [60] to assign the protonation
D

states at pH 7.4±1.0 and the atom types, correctly. Bond orders were assigned and hydrogen
TE

atoms were added to the structures. In order to observe all probable conformations of ligands,

an additional conformational search was performed by using the Mixed torsional/Low-mode

EP

sampling presented in Macromodell 11.2 [61]. The grid generation was formed using Glide

7.1 [62]. The grid box with dimensions of 20 Å x 20 Å x 20 Å was centered in the vicinity of
C

the flavin (FAD) N5 atom on the catalytic site of the protein to cover all binding sites and
AC

neighboring residues [63-65]. Flexible docking runs were performed with single precision

docking mode (SP). Electrostatic and van der Waalls interactions in the active site of hMAO-

B were evaluated by a per-residue interactions panel of Glide 7.1 [62].

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Acknowledgement

This study was financially supported by Anadolu University Scientific Projects Fund, Project

No: 1605S309.

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El-Faham, H. E. A. Ahmed, A. Amer, Eur. J. Med. Chem. 93 (2015) 308-320.

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Med. Chem. 93 (2015) 481-491.

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[63] M. Toprakçı, K. Yelekçi, Bioorg. Med. Chem. Lett. 15 (2005) 4438-4446.

[64] N. Gökhan-Kelekçi, Ö. Ö. Şimşek, A. Ercan, K. Yelekçi, Z. S. Şahin, Ş. Işık, G. Uçar, A.

A. Bilgin, Bioorg. Med. Chem. 17 (2009) 6761-6772.

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Chem. Lett. 24 (2014) 3278–3284.

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Table 1: IC50 (µM) values of the compounds 4a-4o derivatives against hMAO isoforms.

Compound IC50 (µM) IC50 (µM) *SI Selectivity

hMAO-A hMAO-B
4a ≥1000 ≥100 - -
4b 27.075±2.462 0.881±0.139 30.732 MAO-B

4c ≥1000 ≥1000 - MAO-B

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4d ≥100 12.162±2.782 ≥8.222 MAO-B

4e 9.586±2.236 0.075±0.009 127.813 MAO-B

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4f 0.851±0.053 0.136±0.051 6.257 MAO-B

4g ≥100 10.151±1.790 ≥9.851 MAO-B

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4h 2.819±0.340 1.967±0.029 1.433 MAO-B

4i 43.317±2.800 1.945±0.161 22.271 MAO-B

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4j ≥1000 ≥1000 - MAO-B

4k ≥100 12.615±1.472 ≥7.927 MAO-B

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4l ≥1000 ≥1000 - MAO-B

4m 19.606±1.580 10.333±2.892 1.897 MAO-B

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4n ≥100 25.235±3.712 3.963 MAO-B

4o 53.513±3.086 18.489±1.627 2.894 MAO-B

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Chlorgiline 0.0054±0.0004 - - MAO-A

Selegiline - 0.040±0.002 - MAO-B

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Rasagiline - 0.066±0.004 - MAO-B

*The selectivity index (SI) was calculated as IC50 (MAO-A) / IC50 (MAO-B).
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Table 2: IC50 (µM) values of the compounds 4e and 4f derivatives against NIH/3T3 cell
line.
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Compound 4e 4f
IC50 (mM) 0.316 1<
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Table 3. The AMESMPF results of the compounds

REVERTANTS Fold increase (over baseline)

Compound Concentration TA 98 TA 100

(mg/mL)
S9+ S9- S9+ S9-

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4e 0.156 0.35 1.03 0.53 0.74

0.3125 0.35 0.74 0.27 0.99

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0.625 0.35 0.51 0.27 0.84

1.25 0.52 0.68 0.33 0.64

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2.5 0.52 0.40 0.27 0.74

5 0.00* 0.46 0.07* 0.89

4f 0.156

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1.30 0.68 0.79 0.89
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0.3125 2.13* 0.46 0.49 0.79

0.625 2.01 0.23 1.15 0.69

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1.25 2.13* 0.28 1.46* 0.59

2.5 2.95* 0.28 1.88* 1.78

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5 3.07* 0.34 1.94* 1.63

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* t test p value (unpaired 1-sided) < 0.05 , *** t test p value (unpaired 1-sided) < 0.001
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Table 4. Calculated ADME parameters, DLS, and BBB permeability of the compounds
(4a-4o) and reference drugs.

BBB
Comp. MW logP tPSA nON nOHNH MV Vio DLS
(+/-)

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4a 384.46 4.83 59.29 5 1 336.48 0 0.32 +

4b 429.46 4.92 105.11 8 1 359.81 0 0.26 +

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4c 367.41 4.09 75.08 6 2 330.75 0 -0.07 +

4d 381.44 4.16 64.22 6 1 347.70 1 0.67 +

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4e 379.42 3.70 72.18 6 1 341.61 0 1.07 +

4f 396.43 5.10 59.29 5 1 350.70 1 0.56 +

4g 412.88 5.61 59.29

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4h 394.43 4.45 79.52 6 2 353.79 0 0.51 +

4ı 408.46 4.99 68.52 6 1 371.31 0 0.37 +

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4j 408.46 4.94 68.52 6 1 371.31 0 0.10 +

4k 408.46 4.97 68.52 6 1 371.31 0 0.56 +

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4l 394.43 4.43 79.52 6 2 353.79 0 0.63 +

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4m 410.43 3.90 99.74 7 3 361.81 0 0.27 +

4n 438.49 4.97 77.76 7 1 396.86 0 0.37 +

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4o 438.49 4.75 77.76 7 1 396.86 0 0.79 +

Selegiline 187.29 2.64 3.24 1 0 202.64 0 1.03 +

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Rasagiline 171.10 210 12.03 1 1 175.10 0 0.55 +

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Clorgiline 272.18 3.74 12.47 2 0 238.91 0 0.82 +

MW: Molecular weight; log P: log octanol/water partition coefficient; tPSA: Total Polar Surface Area;

nON: number of Hydrogen acceptors; nOHNH: number of Hydrogen donors and MV: Molecular

Volume were calculated using Molinspiration Calculation of Molecular Properties toolkit. DLS: Drug

Likeness Model Score was calculated using MolSoft 2016 Drug-Likeness and molecular property

prediction toolkit. BBB (+/-): Blood-Brain Barier Permeability was calculated by a CBLigand-BBB

prediction server.
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O
O
H
H N N
N
N
N O H
H

N
Iproniazid Isocarboxazid

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N
N Ar
N
H
N

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The synthesized compounds 4a-4o

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NH

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N
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Selegiline
Rasagiline

Figure 1: Structures of some MAO inhibitors and synthesized compounds (4a-4o).

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NH2 H
O O N O
a

H O N O
NH2
(1)

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N O N O
c

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N N O
HN NH2
(2)
(3)

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O N O
d
Ar
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H Ar HN N
N

(4a-4o)
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Scheme 1: Synthesis way of the compounds 4a-4o. Ar: 4a: Thiophen-2-yl; 4b: 5-Nitro-
thiophen-2-yl; 4c: Pyrrol-2-yl; 4d: 1-Methyl-pyrrol-2-yl; 4e: Pyridin-3-yl; 4f: 4-
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Fluorophenyl; 4g: 4-Chlorophenyl; 4h: 4-Hydroxyphenyl; 4i: 4-Methoxyphenyl; 4j: 2-

Methoxyphenyl; 4k: 3-Methoxyphenyl; 4l: 3-Hydoxyphenyl; 4m: 3,5-Dihydoxyphenyl; 4n:
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3,5-Dimethoxyphenyl; 4o: 2,3-Dimethoxyphenyl. Reagents and Conditions: a: Na2S2O5

/DMF, Microwave irradiation, 240 oC, 10 bar, 5 + 5 min. b: NaH/DMF, propargyl bromide,
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r.t, 20 h. c: NH2NH2.H2O (%100), Microwave irradiation, 150oC, 10 bar, 10 min. d:

EtOH/CH3COOH, reflux, 2 h.
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(A)

Control 14.00

1/V (nmol/min/mg protein)-1

IC50/4 (0.01875 µM)
12.00
IC50/2 (0.0375 µM)
10.00
IC50 (0.075 µM)

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2 x IC50 (0.150 µM) 8.00

4 x IC50 (0.300 µM) 6.00

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4.00

2.00

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0.00
-3 -2 -1 0 1 2 3
-2.00 1/[S] µM-1

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(B)
1/Vmax (nmol/min/mg protein)-1

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0
-0.2 -0.15 -0.1 -0.05 0 0.05 0.1 0.15 0.2 0.25 0.3
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-2 µM)
Compound 4e (µ
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-4

Figure 2. (A) Lineweaver–Burk plots for the inhibition of hMAO-B by compound 4e. [S],
substrate concentration (µM); V, reaction velocity (nmol/min/mg protein). Inhibitor
concentrations are shown at the left. Vmax values from 4 x IC50 to Control; 0.146, 0.197, 0.255,
0.320, 0.399 and 0.506 (nmol/min/mg protein). Km value of the non-competitive inhibition;
0.499±0.005 (µM). (B) Secondary plot for calculation of steady-state inhibition constant (Ki)
of compound 4e. Ki was calculated as 0.150 µM.
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Figure 3. Dose-response curve of 4e against TA98 and TA100 in the presence and absence of
S9 according to AMES MPF test. * t test p value (unpaired 1-sided) < 0.05 with a fold-
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induction over baseline > 2; -------: 2-fold induction over baseline.
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Figure 4. Dose-response curve of compound 4f against TA98 and TA100 in the presence and
absence of S9 according to AMES MPF test. * t test p value (unpaired 1-sided) < 0.05 with a
fold-induction over baseline > 2; -------: 2-fold induction over baseline.
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Figure 5. The interacting mode of compound 4c in the active region of hMAO-A. The

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inhibitor and the important residues in the active site of the enzyme are presented by tube
model. The FAD molecule is colored purple with ball and stick model.
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Figure 6. The interacting mode of compound 4d in the active region of hMAO-A. The
inhibitor and the important residues in the active site of the enzyme are presented by tube
model. The FAD molecule is colored purple with ball and stick model.
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Figure 7. The interacting mode of compound 4e in the active region of hMAO-A. The

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inhibitor and the important residues in the active site of the enzyme are presented by tube
model. The FAD molecule is colored purple with ball and stick model.
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Figure 8. The interacting mode of compound 4c in the active region of hMAO-B. The
inhibitor and the important residues in the active site of the enzyme are presented by tube
model. The FAD molecule is colored purple with ball and stick model.
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Figure 9. The interacting mode of compound 4d in the active region of hMAO-B. The
inhibitor and the important residues in the active site of the enzyme are presented by tube

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model. The FAD molecule is colored purple with ball and stick model.
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(A)

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(B)
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Figure 10. (A) The view of compound 4e at the active site of hMAO-B. (B) The interacting
mode of compound 4e in the active region. The inhibitor and the important residues in the
active site of the enzyme are presented by tube model. The FAD molecule is colored purple
with ball and stick model.
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(A)

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(B)
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Figure 11. (A) The van der Waals interaction of compound 4e. The active ligand has a lot of
favorable van der Waals interactions (red and pink). (B) The electrostatic interaction of
compound 4e. The residues are colored (blue, red, and pink) according to the distance from
ligand by Per-Residue Interaction panel.
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Highlights

15 New benzimidazole derivatives were synthesized.

Compounds 4e and 4f indicated important inhibitory activity against hMAO-B

enzyme.

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Compound 4e was found to be non-cytotoxic and non-genotoxic.

A good ADME profile was predicted for the compound 4e.

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Interaction modes between the hMAO-B and compound 4e were determined by

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docking studies.

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