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M.G. Salem et al.
Bioorganic Chemistry 111 (2021) 104909
binding energy ꢀ 24.11 Kcal/mol, it formed 2H-bonds with His 110, and
Trp 111 and two arene-arene with Tyr 209 and Trp 111 as the co-
crystallized ligand NADP, but it was docked inside the 3H4G with
lower binding energy ꢀ 11.2 Kcal/mol, and it did not form any inter-
active hydrogen bond (H-bond) like NADP, it only formed week in-
teractions of one arene-arene with Trp 22. While compound 15C, was
docked inside the 4QR6 with a good binding energy ꢀ 16.43 Kcal/mol, it
formed 2H-bonds with His 110, and Tyr 48 and One arene-arene with
Trp 20 as the co-crystallized ligand NADP, but it was docked inside the
3H4G with lower binding energy ꢀ 11.9 Kcal/mol, and it did not form
any interactive H-bond like NADP, it only formed week interactions of
one arene-arene interaction with Trp 22.
Scheme I. Synthesis of 2-chloro-N-arylacetamide derivatives (intermediates) 3
Moreover, as seen in Fig. 3A, it was noticed that ligand 12B tightly
bounded itself inside the binding site by two distinct H-bonds with
His110 (with bond length 1.72 Å) and Trp11 (with bond length 1.45 Å)
through the oxygen atoms as H-bond acceptors of rhodamine and
acetamide, respectively. Also, compound 15C, as seen on Fig. 3B, tightly
bounded itself inside the binding site by two strong H-bonds with His110
(with bond length 1.82 Å) and Tyr48 (with bond length 2.06 Å) through
the oxygen atom as H-bond acceptor acetamide. These strong H-bond
interactions were deterministic in targeting ALR2. In addition, it showed
significant interactions with both polar and hydrophobic residues of
ALR2 that further increased its binding affinity.
(A-D).
So, from the strong interactive binding modes of the two docked
compounds inside the two rested proteins, we could conclude the over
selectivity against the 4QR6 over 3H4G, this in agreement with the in-
vitro inhibitory biological results of both compound 12B and 15C to-
wards ALR2 with IC50 of 0.29 and 0.35 µM, respectively compared to
Epalrestate (IC50 = 0.40 µM) and AlR1 with IC50 of 39.11 and 40.72 µM,
respectively compared to Valproic acid (IC50 = 57.4 µM).
To predict the mode of action of the docked compounds 12B and 15C
compared with the co-crystallized ligand (Repaglinide), they were
evaluated as agonists for their binding affinities towards the molecular
target (PDB: 6PZ9) as a SUR1 membrane protein in pancreatic B-cell to
stimulate insulin secretion [18]. As seen in Table 4 with the two- and
three-dimensional representation of the overall interaction inside the
binding site of the target molecule, compound 12B was docked inside
the receptor binding site with binding energy –22.63 Kcal/mol, to form
2H-bonds with Asn 437 (bond length 2.16 Å) and Arg 1248 (1.75 Å) as
Scheme II. Synthesis of 5-arylidenerhodanine compounds (intermediates) 5
(A-G).
of D and E series obtained N, N-dimethyl amino and nitro substituents at
para-position on benzylidene moiety respectively. The weakest com-
pounds were in series A, F and G. These series obtained no substitution
(series A) or contained m-substituents on benzylidene ring (series F and
G) which resulted in a decreased interaction with the active site of ALR2.
–
H-bond acceptors through (–OCH ) substituents and C O group of
–
3
acetamide group, respectively. While compound 15C, was docked inside
the receptor binding site with binding energy ꢀ 21.41 Kcal/mol, to form
1H-bonds with Asn 437 (bond length 2.34 Å) as H-bond acceptor
2.2.3. The selectivity indices of the novel compounds
The selective inhibition of the novel compounds was calculated in
terms of their IC50 values against ALR1 versus ALR2. In all series,
remarkable selectivity indices were observed for compounds 10B, 11B,
12B, 15C and 22E with 39, 45, 134, 116 and 38 folds, respectively.
These compounds were more selective towards ALR2. Therefore, com-
pounds of series B might be considered potent and selective inhibitors
with minor side effects. According to the previous three parameters, in-
vivo hypoglycemic activity, in-vitro ALR1 and ALR2 inhibitory activity
and the selectivity indices of the novel compounds, the most active
compounds were 12B and 15C.
–
through C O group of acetamide group.
–
So, the molecular docking study elucidates the feasible mechanism of
binding of both compounds 12B and 15C to act as agonist inside the
6PZ9 (SUR1) protein, which explains their high biological activity as a
hypoglycemic agent (87% and 82.3% reduction in blood glucose,
respectively).
3. Bioinformatics study
Bioinformatics studies were conducted to establish physicochemical
properties and drug-like properties for compounds 10B, 11B, 12B, 15C,
16C, 26F and 27F that exhibited the most potent hypoglycemic activ-
ities. The examined compounds showed promising drug-likeness grads
and good physicochemical properties according to Lipinsiki’s rule of five
[17]. These physicochemical properties included molecular weight,
number of rotatable bonds, H-bond donor and acceptors along with
number of violations. Furthermore, acceptable pharmacokinetics such
as permeability and intestinal absorption were observed too. For good
drug absorbance through intestine, the value of topological polar surface
area (TPSA) should be as low as 140. Blood brain barrier (BBB) should be
as low as 90 Å2 [18]. The examined compounds showed good absorption
and permeability. As shown in Table 5, the tested compounds had 1–2H-
bond donors and 5–6H-bond acceptors. Besides, all tested compounds
2.3. In silico studies
2.3.1. Molecular modeling
Molecular docking study was performed to rationalize the in-vivo and
in-vitro biological results and give insights into the possible binding
modes of compounds of the 7 series (A-G) together with the co-
crystallized ligands within the active sites of 6PZ9 (SUR1), aldose
reductase (4QR6) and aldehyde reductase enzymes (3H4G).
Among the highest active compounds 12B and 15C were highlighted
for their binding mode inside the 4QR6 (ALR2) and 3H4G (ALR1) to
elucidate their over selectivity towards the ALR2 over the AlR1. As seen
in Table 3, compound 12B was docked inside the 4QR6 with a strong
4