In silico extension on the antidiabetic potential of Euonymus laxiflorus natural compounds onto the inhibitability against protein tyrosine phosphatase 1B

. Euonymus laxiflorus bioactive compounds 1-β -D-glucopyranosyloxy-3,5-dimethoxy-4-hydroxybenzene ( 1 ), Walterolactone A/B β -D-pyranoglucoside ( 2 ), Gallocatechin ( 3 ), Leonuriside A ( 4 ), Methyl galloate ( 5 ), and Catechin ( 6 ) were experimentally evidenced for their multi-inhibition against α - glucosidase and α -amylase. In this work, they were subjected to a combination of computational platforms on tyrosine phosphatase 1B (UniProtKB-PTP1B). As the results, the overall potentiality for bio-inhibitory applications is primarily evaluated by the order: 1 (DS average -12.2 kcal.mol -1 ; polarisability 45.5 Å; no toxicity; ground-state energy -1222.73 a.u.; dipole moment 0.989 Debye) > 2 (DS average -9.7 kcal.mol - 1 ; polarisability 39.4 Å; no toxicity; ground-state energy -1070.08 a.u.; dipole moment 6.726 Debye) > 4 (DS average -9.1 kcal.mol -1 ; polarisability 45.1 Å; no toxicity; ground-state energy -1222.73 a.u.; dipole moment 4.895 Debye). Altogether, the retrievals encourage further attempts to test the inhibitory effects of 2 against tyrosine phosphatase 1B and improve the dipole moment of 1 to enhance its biological applicability.


Introduction
Diabetes mellitus, a chronic glucose-related metabolic disorder, has risen as a worldwide health concern and is putting pressure on med-care systems worldwide.It not only creates hyperglycemia-related conditions but also induces further complications, which have been widely reported by preceding studies and clinical trials [1][2][3][4][5].The mechanisms have also been wellestablished in the existing literature, including pancreatic β-cells deterioration (type 1) and insulin-metabolic abnormal activity (type 2); especially, the latter is responsible for 90-95 % of diagnoses [6].Despite this well-rounded understanding, the cause is still highly uncertain; possible, genetic abnormalities, pathologic disorders, clinical conditions, or gestational failures are commonly referred and agreed by scientific community [7].
Up-to-date, there is no cure for this disease; the medicinal products on the market often only provide the temporary inhibition of undesirable biological activities, as symptomatic remedies rather than therapeutic treatments.The targets often relate to glucose-and insulin-based enzymes.
For example, α-glucosidase is the bio-catalyst for the hydrolysis of -(1/4) and -(1/6) bonds in starch and disaccharide molecules; meanwhile, αamylase is the major form of salivary and pancreatic amylase found in humans and other mammals, responsible for the hydrolysis of αlinked polysaccharides (e.g.starch and glycogen) into shorter chains (e.g.dextrins and maltose).
Their physiochemical roles induce the postprandial spikes from digestive carbohydrates [8,9].From another view, protein tyrosine phosphatase 1B (PTP1B) catalyses the phosphorylation process, which further activates the glucose uptake of the insulin responsive cell [10].Therefore, an effective bio-inhibitor against these proteins can provide negative regulatory effects on the hyperglycemic activity or insulin signaling pathway; consequently, a reduction of glucose uptake ensues.On the commercial market, there are various hypoglycemic drugs targeting αglucosidase and α-amylase, e.g.Sulfonylureas, Biguanides, or Acarbose; however, the substances are also known either less effective towards the latter or with mild-serious side effects, e.g.
diarrhea or flatulence [11,12].Regarding the insulin-related enzyme, Trodusquemine, an aminosterol isolated from dogfish sharks, is the commonly known inhibitor with considerable efficacy [13]; however, the substance is only recently developed and also known for its expensive price.Therefore, looking for new and safe antidiabetic agents, especially those with multi-protein inhibitory effects, is still necessary.
Natural sources, especially herbs and medicinal plants, are the subjects of research interest given their bioavailability and biodiversity.
(the Celastraceae family) is a subtropical shrub (biome), native to South India, South China, Taiwan and the Indochinese peninsula.The plant is known by the local folk experiences for its medicinal value and has been long exploited in-practice as the remediation for osteoarthritis, inflammatory arthritis, and haemostasis.Nevertheless, only very recently, its anti-oxidant [14], anti-inflammatory [15], anti-cancerous [16], and anti-diabetic [17] activities have been proven scientifically by In this extension, candidates with multiple inhibitory effects against α-glucosidase and αamylase experimentally reported by Nguyen et al.
in 2018 [19] were selected for a computational screening for their potential towards protein tyrosine phosphatase 1B.In particular, the ligands  for the computational screening in this study.and in-pose arrangements (3D).

ADMET analysis
Pharmacological potentiality of the compounds was also assessed by a combinational model, including (i) ADMET properties: absorption, distribution, metabolism, excretion, and toxicity; (ii) Reference: Pires' theoretical interpretations [27].

Density functional theory calculation
Molecular chemical properties of the investigated structures were given by density functional theory (DFT) calculation using Gaussian 09 without symmetry constraints [28].Level of theory M052X/6-311++G(d,p) and basis set def2-TZVPP [29] were selected.The converged geometries were checked for the structural global minimum on the potential energy surface (PES) by vibrational frequencies.The frozen-core approximation for non-valence-shell electrons was applied.The resolution-of-identity (RI) approximation was set.
The frontier orbital analysis was carried out by NBO 5.1 at the level of theory M052X/def2-TZVPP.[30].

Docking-based inhibitability
The most susceptible sites of the targeted protein are highlighted in Generally speaking, this indicates that all the candidates are highly promising as pervasive bioinhibitors against the structure.The most stable complexes regarding each ligand-protein system are selected for more indetail presentation, whose data is given in Table 2.
These should be considered as the main inhibitory

QSARIS-based physicochemical properties
The physicochemical properties of the compounds (retrieved from the QSARIS) and the number of hydrogen bonds (counted from docking-based results) are given in Table 3. Overall, all the candidates well satisfy Lipinski's criteria for the argument on drug-likeness, i.e.: molecular mass < 500 amu; hydrogen-like donors < 5; hydrogen-like acceptors < 10; partition coefficient logP < +5.From the view of biological compatibility, 1, 2, 4 are considered as most promising given by their lowest octane-water partition ratios (logP < 0).
From the view of biological interactability, the potential can be ranked by the order of polarisability: 1 ≈ 4 (ca.45 Å) > 2 ≈ ≈ 6 (ca.40 Å) > 5 (22.8 Å).The property represents the sensitivity of a structure to external electric fields such as those created by other polarised agents (e.g.amino-acid-based protein structures); the unit conversion is given by Claussius-Mossotti relation:  3), the model expects 3, 5, and 6 might act as carcinogens.This means that if the latter three were selected for further consideration, they should be subjected to more in-depth assessments of mutagenicity.

Quantum-based chemical properties
The

A
typical procedure of molecular docking simulation (by MOE 2015.10 [22]) follows three steps, i.e.: (i) Input preparation (configuration: protein active range 4.5 Å, ligand charge-assigning using Gasteiger-Huckel method); (ii) Docking simulation (configuration: retaining poses 10; solutions per iteration 1000; solutions per fragmentation 200); (iii) Re-docking iteration (threshold: root-mean-square deviation (RMSD) values < 2 Å).Given theoretical interpretation, the inhibitory effectiveness of a ligand towards the targeted protein structure can be primarily evaluated by docking score (DS) energy of the associated inhibitory system, which represents pseudo-Gibbs free energy (formed by hydrophilic binding and hydrophobic interaction); also, RMSD values and number of hydrogen-like interactions can be considered for arguments on bioconformational rigidity and binding strength, respectively.In addition, MOE can provide visual rendering for ligand-protein interaction maps (2D)

Figure 3 .
The results from docking simulation can be utilized for argument on the inhibitory effects of each compound(1)(2)(3)(4)(5)(6) against the protein structure for tyrosine-protein phosphatase type 1 (PTP1B).In this scope, the total docking score (DS) values and the number of hydrogen-like bonds are selected as the main indicators for inhibitory effectiveness, which respectively represent pseudo values for Gibbs free energy of ligand-protein complex formation and their strong intermolecular bonds.The primary docking parameters are summarised in Table1; the control drug (D) is Trodusquemine.Overall, different compounds exhibit different affinities toward the sites of PTP1B, especially Site 1 (majority of candidates) and Site 4 (1 and D).The average values are considered as the representative for in-practice inhibitory effectiveness since the biological process is often based on multi-site inhibition rather than single-site selectiveness.In principle, sufficient distortion forces channelling on a variety of protein sites would result in denaturation of enzyme shape, thus enzymatic cease ensuing in overall.Given this argument, the most effective inhibitors against PTP1B are predicted by the order: 1-PTP1B (DSaverage -12.2 kcal.mol - ) > 3-PTP1B (DSaverage -10.4 kcal.mol - ) > 2-PTP1B ≈ 5-PTP1B (DSaverage ca.-9.5 kcal.mol - ) > 4-PTP1B ≈ 6-PTP1B (DSaverage ca.-9.1 kcal.mol - ).These figures are significantly elevated cf. that of D-PTP1B (DSaverage -8.7 kcal.mol - ).

2 DS:Fig. 4 .
Fig. 4. Visual presentation and in-pose interaction map of ligand-PTP1B (ligand: 1-6 and D) inhibitory structures 7237 109 intake given by their high absorbability (intestinal absorption > 30 %) and low resistance (Caco2 permeability < 8 × 10 −8 cm.s −1 ); none of them is predicted to inhibit the activity of P-glycoprotein family, thus no effect on the extrusion of the toxins and xenobiotics out of cells.The compounds do not show noticeable tendency of accumulation to either tissue or plasma (by relatively balanced VDss); in addition, they are unlikely to cross the blood-brain barrier (logBB < -1) or penetrate the central nervous system (logPS < -3).None of them is predicted to either inhibit the activity of the cytochromes P450 family or be oxidised by the liver (as their substrates); also, they are unlikely to be rapidly excreted by the kidney (carried by organic cation transporter 2).These bio-kinetic behaviour might be conducive to their prolong circulation in the body, thus longer medicinal effects.However, toxicity-based predictions pose certain precautions for pharmacological development.While 1, 2, and 4 are particularly safe for medicinal use, i.e.: (i) no mutagenic potentials; (ii) no potential for fatal ventricular arrhythmia as hERG inhibitors; (ii) no hepatotoxicity; (iv) no skin sensitisation; (v) toxicity to bacterium T. Pyriformis (pIGC50 > -0.5 log μg.L -1 ) yet safety to animal organisms, e.g.fish Flathead Minnows (LC50 > -0. results from quantum calculation provide another view on the bio-medium compatibility and intermolecular interactability of the candidates based on ab initio insights of their chemical properties.The optimised geometries of the bioactive compounds are shown in Figure 5. Overall, the input structures can be self-consistently converged easily without any geometrical constraints or abnormal bonding parameters (i.e.angles and length).This is often of the characteristics of natural compounds; thereby in-turn also validating their spectroscopic characterisation and structural elucidation from the preceding works.

Table 1 .
Results on inhibitability of 1-6 and D toward PTP1B sites

Table 2 .
Docking results for most effective ligands-PTP1B inhibitory complexes

Table 5 .
Ground state electronic energy and dipole moment values of 1-6