PhytoSelectDBT: A database for the molecular models of anti-diabetic targets docked with bioactive peptides from selected ethno-medicinal plants

It is of interest to assess the effectiveness of bioactive peptides derived from 41 ethno-medicinal plants, classify them according to their anti-diabetic protein targets (DPP-IV, alpha-amylase, alpha-glucosidase, GRK2, GSK3B, GLP-1R, and AdipoR1), and create a web tool named PhytoSelectDBT by using the top seven peptides per target. If one of the target-based medicinal plant suggestions made by PhytoSelectDBT is unsuccessful, alternative target-based possibilities are presented by PhytoSelectDBT for treating the condition and any other related complications. The results provide a useful resource for the management of type 2 diabetes and emphasize the significance of utilising ethnomedical knowledge for the identification of potent anti-diabetic plants and their peptides. We used molecular docking to investigate interactions between anti-diabetic targets (DPP-IV, alpha-amylase, alpha-glucosidase, GRK2, GSK3B, GLP-1R, and AdipoR1) and projected bioactive peptides from 41 ethnomedicinal plants. All bioactive peptides were cross-checked against several databases to determine their allergenicity, toxicity, and cross-reactivity. The presence of B and T cell epitopes was also examined in all simulated digested bioactive peptides for reference. This data is archived at the PhytoselectDBT database.


Background:
Diabetes Mellitus (DM) is a lifestyle disease and there is no cure.
-Globally, an estimated 422 million adults were living with Diabetes in 2014‖ -WHO Report [1].Type 2 diabetes mellitus (T2DM) accounts for around 90% of all cases of diabetes [2].For an adult with diabetes in a low-income Indian family, 25 percent of the family income goes to diabetes care [3].The cost burden is too high in the cases of complications [4].In remote areas like 'Northeast India', most people do not have access to proper medical facilities.So, people here prefer cheap medical healthcare sources due to the burden of expenditure on diabetes management.Here local ethnomedicinal practitioners with the traditional knowledge of ethnomedicinal plants play an important role in their life.Other than the knowledge of ethnomedicinal plants and disease association, they actually are not aware of what the molecular phytoconstituents that work or what their mechanism of action from antidiabetic plants is.In this scenario and without the knowledge of currently available scientific research conclusions about ethnomedicinal plants and their phyto constituents, there is a high probability that the selection of a wrong medicinal plant based on only current traditional knowledge of ethnomedicine can contribute to disease complications or drug resistance.
The treatment must not only be safe and effective but also improve the quality of life [5].In 2011 India was home to 61.3 million diabetes patients, according to IDF (International Diabetes Federation) Diabetes Atlas, and by 2030 this number of diabetes patients are predicted to reach 101.2 million [6].Type 1 diabetes mellitus results when the pancreas fails to produce enough insulin.Type 2 diabetes mellitus (T2D) -is a condition that appears when the body produces inadequate amounts of insulin or the insulin that is produced does not function correctly to control blood glucose level [7].In India management of this metabolic disorder faces multiple challenges, such as low levels of awareness, scarcity of trained medical and paramedical workers and unaffordability of prescription drugs and services [8].Novel involvement of existing resources promises to revolutionize the care of diabetic patients in India [8].
Several conventional antidiabetic plant treatments are employed worldwide and are also considered to have less side effects and less toxic than synthetic drug treatments [9].Although there are medicinal drugs to treat various forms of diabetes mellitus, other complimentary/traditional herbs are used in patients with diabetes [10].Studies conducted to explore patient preferences have shown that patients prefer less expensive treatment, have fewer side effects, and are more convenient and more effective [10].As per ancient literature, more than 800 plants are reported to have antidiabetic properties [11].To control hypoglycemia, ethano pharmacological survey reported more than 1200 plants used in traditional medicine [11].Indian Materia Medica has mentioned various dravyas effective in Madhumeha [11].Different ethnic groups have been unconsciously using plants possessing antidiabetic property.Some studies have shown that herbs can delay the progression of diabetic complications, while other studies have shown that some herbs used in diabetes management are not effective [10].Drugs with the potential to target more metabolic pathways are more promising than those targeting a single pathway, but also correlated with adverse effects are those drugs targeting several pathways [12].There is a great debate on the optimum risk-benefit profile about therapeutic strategies and treatment of diabetes due to side effects related to existing drugs.Ethnomedicinal plants target multiple pathways due to multiple phytochemicals present in them so there is a need of careful ©Biomedical Informatics (2023) Medicinal plants play a major role in controlling Diabetes progression and its associated complications by acting on molecular pathways and key therapeutic targets [16].The mechanism for phytochemicals' antidiabetic activity could be summed up as: reduction of insulin resistance and increasing of insulin sensitivity, stimulation of insulin secretion from pancreatic cells; stimulation of hepatic glycolysis and glycogenesis; activation of PPARgamma, anti-inflammatory and antioxidant effects, inhibition of alphaamylase, alpha-glucosidase, and beta-galactosidase, and inhibiting intestinal absorption of glucose [17] etc.After collection of all ethnomedicinal antidiabetic plants of Northeast India we searched the antidiabetic phytochemicals of the 41 selected plants in this study and their mechanism of action from different publication one by one.
Bioactive peptides are specific protein fragments that positively affect physiological functions and human health [18].These peptides exhibit the following characteristics: (i) targeted high bioactivity; (ii) low toxicity and reduction of the incidence of tissue aggregation in the body; (iii) high structural diversity; and (iv) small size (relative to antibodies) [19].These properties enable peptides to be applied as therapeutic agents for antidiabetic, antimicrobial, and antioxidant, antithrombotic and antihypertensive functions in human health [20].Bioactive peptides extracted from plants or microorganisms can control blood glucose levels, reduce insulin resistance and otherwise counter diabetes [21], [22], [23], [24], [25] and [26].These peptides can be classified according to their antidiabetic actions such as α-amylase and αglucosidase inhibitors, GLP-1 receptor agonists and DPP-IV inhibitors [27] 1), classify them according to their antidiabetic protein targets (DPP-IV, alpha-amylase, alpha-glucosidase, GRK2, GSK3B, GLP-1R, and AdipoR1), and create a web tool PhytoSelectDBT by using the top seven peptides per target.

Anti-diabetic therapeutic peptide characterization:
The updated steps in the protocol for anti-diabetic therapeutic peptide characterization from selected plant protein are: [1] Plant protein gastrointestinal digestion [2] Cross reactivity and Toxicity checks of Peptides [3] Molecular docking approaches: Anti-diabetic protein target and plant peptide docking

Plant protein gastrointestinal digestion:
In vitro and in vivo studies regarding the bioactivity of peptides has generated strong evidence of their health benefits.Enzymatic hydrolysis has been the process most commonly used for bioactive peptide production [33].A combination of two to a maximum of three enzymes could be utilized in the hydrolysis simulation of the proteins.Plant protein hydrolysates represent an option for production of bioactive peptides

Prediction of bioactive peptides:
Peptides identified by plant protein gastrointestinal digestion were screened by PeptideRanker, a tool for the prediction of bioactive peptides based on a novel N-to-1 neural network [37].Peptides with the score ≥ 0.8 were selected as potential bioactive peptides.

Peptides cross reactivity and toxicity check:
Peptides cross reactivity and toxicity check studies were performed as per published protocol in BioDADpep Publication [28].

Molecular docking approaches: Anti-diabetic protein targets and plant peptide docking:
Bioactive peptides (predicted by PeptideRanker) molecular docking studies were performed using VLifeMDS 4.6.02032020software [38] with selected anti-diabetic protein therapeutic targets.Model 1 is selected and then energetically minimized with VLifeMDS 4.6.02032020.

Protein-peptide docking:
For Docking Lenovo computer, i5 equivalent processor (AMD A9 7 th Gen) with Windows 10 operating system is used.Peptide screening was performed with selection of appropriate protein structure.Batch docking simulation was done using GRIP batch docking to generate dock score and interactions.
Step 2: Selected the protein file to be used for docking.
Step 3: Specified the cavity for docking either by selecting the pre saved co-crystal ligand or selecting the cavity number based on residues of active site.
Step 4: Selected the folder of Ligands and to save docking results.
Step 5: Selected docking parameters and clicked ok, checked the docking job in Task manager.After docking simulation, the best docked conformer of each peptide/ligand was checked for interactions with receptor like hydrogen bonding and other interactions using LigPlot+.LigPlot+ is a successor to original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams [44].LigPlot + runs from an intuitive java interface which allows on-screen editing of the plots via mouse click-and-drag operations.

Problem with ethno-medicinal plant practices:
Type 2 Diabetes treatment should be prioritized according to existing evidence [45].Knowledge of cautiously using ethnomedicinal Plants in Diabetes management is very important using the latest scientific findings so that it is not only useful in Diabetes management but also useful in the management of Diabetes complications.Due to the burden of disease management, people with Type 2 Diabetes prefer ethno-medicinal plants although preclinical/clinical trial data with human subjects are limited and preliminary.
[1] ‗Multiple phytochemicals' -‗multiple target' -‗Single plant'.[2] Phyto-peptides are not well characterized based on mechanism of action on multiple on and off anti-diabetic targets.[3] There is a high probability that the selection of a wrong medicinal plant-based on traditional knowledge can contribute to disease complications or drug resistance.
So, a tool named PhytoSelectDBT version 2.0 is developed to encounter these problems using functional peptide classification of anti-diabetic plants based on Diabetes and its complication.Scientists can search presented plant data through (A) and (B), strengthen the confirmation and addition of data to improve ethnomedicinal practices and reduce healthcare burden.After selecting desired check box (s), clicking on ‗Filter' button will retrieve results with one or more plant name (s).Clicking on -Read More‖ hyperlink in the search resulted plant name (s)/Images (s) will popup the page with following details: (1) Image, (2) Plant name, ( We utilized systematic bioinformatics methods to understand and predict the (mechanism of action of) anti-diabetic peptides.All predicted bioactive Peptides from forty-one plant species were screened against seven anti-diabetic targets.The plant species screened in this study have previously been tested against diabetes in animal models.In this research, we found bioactive anti-diabetic peptides in all selected plants against all selected anti-diabetic human therapeutic targets.After docking simulation, the best docked conformer of each peptide was checked for various interactions with receptor like hydrogen bonding, hydrophobic bonding interaction.Docking of each bioactive peptide resulted in 10 conformations.The docking results were analysed and a pose was selected based on lowest binding energy and H-bond interactions.The peptide forming most stable peptide-receptor complex is the one which is having minimum dock score.

Results and Discussion
H-bond with active side residues in protein cavity were considered to be vital for the selective therapeutic interactions, interaction stability and selective therapeutic agonistic or antagonistic effect, resulting in higher activity of bioactive peptides.So, in further analysis bioactive peptides those formed H-bond inside the selected target protein cavity with known active site residues interactions are preferred to understand their binding modes.Several hydrogen bonds mediate the interactions between the peptides and protein targets as previously reported.Peptides cross-reactivity check revealed that 54 of our bioactive peptides matched with AHTPDB, BioPepDB, SATPdb, BioDADPep and IEDB (see excel file in website: https://omicsbase.com/PhytoselectDBT/bioactivepeptides-and-iedb-database/).

Conclusion:
PhytoSelectDBT is useful for understanding multifunctional therapeutic applications and their molecular mechanisms of the anti-diabetic effects.Data will be of help in the understanding the nature of bioactive peptides, their structural properties required for the selection of plants in management of diabetes and its complications; and for designing new anti-diabetic formulations with improved accuracy and precision.However, extensive pharmacology and toxicological studies in animal and human models are further warranted.

[ 34 ].
Predicting possible sites of cleavage for individual proteases is an important task to be completed during drug-design process of peptide therapeutics to improve their stability and availably as a promising drug[34].For endogenous proteins secreted in the small intestine, only small intestinal digestion was simulated taking into account the reported specificity of trypsin and chymotrypsin only[35].simulated digestion was conducted using Proteolytic Cleavage tool in CLC Genomics Workbench 12[36].A combination of two to a maximum of three enzymes could be utilized in the hydrolysis simulation of the proteins.Protein sequences are digested by the proteolytic enzyme selected (trypsin and chymotrypsin) in below combination to generate peptides: START Trypsin, Trypsin END, Trypsin Trypsin, START Chymotrypsin-low spec., Chymotrypsinlow spec.END, Chymotrypsin-low spec.Chymotrypsin-low spec., START Chymotrypsin-high spec., Chymotrypsin-high spec.END, Chymotrypsin-high spec.Chymotrypsin-high spec., Trypsin Chymotrypsin-low spec., Chymotrypsin-low spec.Trypsin, Trypsin Chymotrypsin-high spec., Chymotrypsin-high spec.Trypsin, Chymotrypsin-high spec.Chymotrypsin-low spec., Chymotrypsinlow spec.Chymotrypsin-high spec.Here, Start: First amino acid of protein sequence; End: Last amino acid of protein sequence.
[15] were carefully gathered from a number of sources and published works of literature[15].We found that 284 different ethnomedical plants are used to treat diabetes in Northeast India.From the list, 39 recognised antidiabetic plants were chosen for this study.Additionally, instead of the plants from the previously mentioned list of antidiabetic plants from northeast India, two ethnomedicinal plants Murraya paniculata and Achyranthes aspera were chosen which are proved to be antidiabetic in in vivo experiments.

28].
. A comprehensive list of Antidiabetic Plant Derived Bioactive Peptides from varied sources can be searched in our work BioDADPep database [Complications from diabetes can be classified into microvascular or macrovascular [2].Hyperglycemia encourages glucose autoxidation to form free radicals.The generation of free radicals beyond the scavenging abilities of endogenous antioxidant defenses results in macro-and microvascular dysfunction [31].peripheral vascular disease, and stroke.The latter may lead to bruises or injuries that do not heal, gangrene, and, ultimately, amputation [2].Therefore, it is of interest to assess the effectiveness of bioactive peptides derived from 41 ethnomedicinal plants (Table

Table 1 :
List of selected ethnomedicinal antidiabetic plants, ranked & prioritized in PhytoSelectDBT for diabetes management.and ‗Meghalaya' were used in all combinations in Pubmed search.Ethnic terms such as Garo, Khasi, Bengali, and Assamese were also used with the above terms in all combinations to search literature in Pubmed.
[32]rials and Methods: Data collection and organization:An extensive literature search was undertaken to identify antidiabetic plants of Northeast India from publications.Keywords such as ‗antidiabetic plants', ‗antidiabetic phytochemicals', ‗Diabetes, ethnomedicinal plants', ‗Northeast India', ‗Assam', ‗Nagaland', ‗Tripura', ‗Mizoram', ‗Sikkim', ‗Manipur', 'Arunachal Pradesh', animal studies have reported the in vivo antidiabetic effects of peptides, but the mechanisms have not been completely elucidated[32].It is meaningful to enlarge the bioactive peptide database and further explain the mechanisms of these proteins through detailed animal studies[32]especially results out of all bioactive peptides in the selected plants mode.

Table 2 :
Top peptides against anti-diabetic targets and their interactions is shown.Based on top docking score per peptide per anti-diabetic target selected anti-diabetic plants are ranked & prioritized in PhytoSelectDBT.