In-silico Characterization of the Phytochemicals of Phyllanthus Niruri Against Nephrolithiasis

Adeboye Omolara Olubunmi; Agboluaje Saheed Alabi; Salami Leke Peter

doi:doi:10.11648/j.jddmc.20261201.11

Research Article |

| Peer-Reviewed

In-silico Characterization of the Phytochemicals of Phyllanthus Niruri Against Nephrolithiasis

Adeboye Omolara Olubunmi^*

, Agboluaje Saheed Alabi

, Salami Leke Peter

Published in Journal of Drug Design and Medicinal Chemistry (Volume 12, Issue 1)

Received: 7 February 2026 Accepted: 21 February 2026 Published: 17 March 2026

Views: Downloads:

Download PDF

Share This Article

Twitter
Linked In
Facebook

Abstract

Nephrolithiasis, which is also known as kidney stone disease, is a regular urological disorder that came with the formation of crystalline deposits within the renal system. It is very significant that the regular and convention procedures for the prevention and treatment of kidney stone diseases including lithotripsy and pharmacotherapy have limitations ranging from recurrence, expensive and great adverse effects, which necessitate the search for safer and highly effective alternatives in phytochemicals with proven biological activities. Phyllanthus niruri is locally and traditionally recognized and active for its antiurolithiatic and nephroprotective effects, with its various diverse bioactive constituents such as flavonoids, alkaloids, tannins, and phenolic compounds. In this work we employed molecular docking and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analyses to screen phytochemicals generated from Phyllanthus niruri as potential inhibitors of nephrolithiasis associated proteins. 64 phytochemicals were retrieved from literature and was used to perform docking against the 7KLL protein target using AutoDock and AutoDock Vina integrated in PyRx. Binding affinities, inhibition constants as well as protein-ligands interactions were analyzed using Biovia Discovery Studio and PyMOL. ADMET predictions were performed using online softweb Admetsar2 to assess pharmacokinetic and safety profiles. Amariin (−8.8 kcal/mol), Ellagitannin (8.5 kcal/mol), Miquelianin (-8.6 kcal/mol) Nirurin (-8.5 kcal/mol), Quercetin 3-0-beta-D-glucuronopyranoside (-8.6 kcal/mol) demonstrated strong binding affinities comparable to or higher than standard drugs allopurinol (−5.9 kcal/mol), levofloxacin (−.6.7 kcal/mol), and nifedipine (−5. kcal/mol). used for comparison. The ADMET evaluation shown that the top ligands possess favorable drug-likeness, oral bioavailability, and non-toxicity. The results suggest that Phyllanthus niruri phytochemicals possess promising inhibitory potential against nephrolithiasis targets and may serve as leads for the development of safe, plant-based therapeutics.

Published in	Journal of Drug Design and Medicinal Chemistry (Volume 12, Issue 1)
DOI	10.11648/j.jddmc.20261201.11
Page(s)	1-18
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2026. Published by Science Publishing Group

Keywords

Phyllanthus Niruri, Nephrolithiasis, Molecular Docking, ADMET Analysis, Phytochemicals, Autodock Vina

1. Introduction

Nephrolithiasis, which is also known as kidney stone disease is a regular metabolical and urological disorder that came with the formation of crystalline deposits of insoluble salts, majorly calcium oxalate within the renal system. Over recent decades, kidney stone disease has been increased significantly globally with an estimated lifetime risk of 10–12% in men and 7–9% in women

[1]

. The disease causes considerable economic and healthcare burdens, most especially in the regions with very hot climates and inadequate access to medical facilities that can aid the prevention and treatment. Patho-physiologically, the formation of stone develops from the supersaturation of urinary tract with crystalline insoluble substances such as uric acid, calcium, oxalate and phosphate usually aggravated by metabolic disorders, dehydration as well as dietary factors

[2]

The existing management procedures not excluding pharmacological interventions like thiazide diuretics, allopurinol, and citrate therapy as well as minimally invasive surgical techniques like extracorporeal shock wave lithotripsy (ESWL) and ureteroscopy

[3]

With all their efficacy and potentiality towards inhibiting the disease, they are frequently resulted to high recurrence rates, postoperative pain, infection risks, and drugs induced toxicity

[4]

Consequent on the aforementioned there is need to explore the natural bioactive compounds as alternative or adjunct therapeutic agent to diminish the existence of this disease and it has gained enormous and increasing attention.

Phyllanthus niruri (Figure 1) belong to the family of Phyllanthaceae and it is commonly referred to as “stone breaker” or “chanca piedra,” has been reported that it is widely employed in traditional medicine systems in some area of the world such as Ayurveda and Chinese medicine for exhibiting hepatoprotective, antiviral, and nephroprotective properties [6,]. Studies on the Phytochemicals that are made up of the Phyllanthus niruri have revealed the presence of flavonoids, lignans, tannins, and alkaloids which possess diverse pharmacological activities including antioxidant, anti-inflammatory, and antiurolithiatic effects

[5]

Download: Download full-size image

Figure 1. The Phillanthus niruri (extracted from

[6]

Computational chemistry has made it easier and possible to screen and predict bioactive compounds with high precision through in-silico methods such as molecular docking and ADMET analysis etc

[7]

These tools enable us to identify the potential inhibitors through modeling interactions between ligands and target proteins while also predicting pharmacokinetic properties through the available computational tools. This study, therefore, aims to investigate the molecular dockings and pharmacokinetic potential of phytochemicals derived from Phyllanthus niruri against nephrolithiasis-associated targets.

2. Materials and Methods

2.1. Ligand Preparation

A total of sixty-four phytochemicals (Table 1) previously reported in Phyllanthus niruri were selected from literature databases alongside some standard pharmaceutical drugs used for the treatment of nephrolithiasis. The 3D structures of all ligands were retrieved from PubChem (https://pubchem.ncbi.nlm.nih.gov)

[8]

in SDF format and converted to PDB using the SMILES Online Translator (https://cactus.nci.nih.gov/translate/). Energy minimization was performed to obtain the most stable conformers. The phytochemicals identified and examined include (-)-Fustin, (S)-2-Amino-7-Hydroxytetralin, 2-Hydroxycinnamic acid, 4-Coumaric acid, 4-Desmethoxypropoxyl-4-methoxy Rabeprazole, Ageratriol, Amariin, Ambrosic acid, Apigenin, Apocynin, Astragalin, Brevifolincarboxylic acid, Catechol Dimethylether-d6, Catechol, Citral, Corilagin, Corymboside, Diosgenin, Elaeocarpusin, Ellagic acid, Ellagitannin, Epicatechin, Fisetin, Fumaric acid, Fustin, Gallic acid, Gallocatechin, Hinokinin, Hyperoside, Hypophyllanthin, Isocitric acid, Isoleucine, Isolintetralin, Kaempferol, Limonene, Lintetralin, Lupeol, Maleic acid, Methyl brevifolincarboxylate, Miquelianin, Myricitrin, Niranthin, Nirphyllin, Nirtetralin, Nirurin, Norsecurinine, Orientin, P-Cymene, Phyllanthin, Phyllnirurin, Phyllochrysine, Phyltetralin, Protocatechuic acid, Pyrogallol, Quercetin, Quercetin-3-O-beta-D-glucuronopyranoside, Quercetol, Quercitrin, Repandusinic acid A, Repandusinic acid B, Rutin, Trifolin, Urinatetralin and Vitexin and three standard drugs Allopurinol, Levofloxacin and Nifedipine were employed for comparison in this study. Each of these compounds was evaluated based on its molecular weight, molecular formula, 2D structure, and molecular structure to assess their potential efficacy in treating nephrolithiasis.

Table 1. Shows the Identified compounds in PHYLLANTHUS NIRURI and three pharmaceutical drugs used to cure NEPHROLITHIASIS with their respective molecular weight, 2D structure and molecular structure.

S/N	Ligands/ Pubchem Cid	Molecular Weight (G/Mol)	Molecular Formular
L1	(-)-Fustin (12310641)	288.25	C₁₅H₁₂O₆
L2	(S)-2-Amino-7-Hydroxytetralin (14750918)	163.22	C₁₀H₁₃NO
L3	2-Hydroxycinnamic acid (637540)	164.16	C₉H₈O₃
L4	4-Coumaric acid (637542)	164.16	C₉H₈O₃
L5	4-Desmethoxypropoxyl-4-methoxy Rabeprazole (11558510)	301.4	C₁₅H₁₅N₃O₂S
L6	Ageratriol (181557)	252.35	C₁₅H₂₄O₃
L7	Amariin (5482103)	968.6	C₄₁H₂₈O₂₈
L8	Ambrosic acid (75368818)	264.32	C₁₅H₂₀O₄
L9	Apigenin (5280443)	270.24	C₁₅H₁₀O₅
L10	Apocynin (2214)	166.17	C₉H₁₀O₃
L11	Astragalin (5282102)	448.4	C₂₁H₂₀O₁₁
L12	Brevifolincarboxylic acid (9838995)	292.2	C₁₃H₈O₈
L13	Catechol Dimethylether-d6 (12209214)	144.2	C₈H₁₀O₂
L14	Catechol (289)	110.11	C₆H₆O₂
L15	Citral (638011)	152.23	C₁₀H₁₆O
L16	Corilagin (73568)	634.5	C₂₇H₂₂O₁₈
L17	Corymboside (13644660)	564.5	C₂₆H₂₈O₁₄
L18	Diosgenin (99474)	414.6	C₂₇H₄₂O₃
L19	Elaeocarpusin (3086477)	1110.8	C₄₇H₃₄O₃₂
L20	Ellagic acid (5281855)	302.18	C₁₄H₆O₈
L21	Ellagitannin (10033935	992.7	C₄₄H₃₂O₂₇
L22	Epicatechin (72276)	290.27	C₁₅H₁₄O₆
L23	Fisetin (5281614)	286.24	C₁₅H₁₀O₆
L24	Fumaric acid (444972)	116.07	C₄H₄O₄
L25	Fustin (5317435)	288.25	C₁₅H₁₂O₆
L26	Gallic acid (370)	170.12	C₇H₆O₅
L27	Gallocatechin (65084)	306.27	C₁₅H₁₄O₇
L28	Hinokinin (442879)	354.4	C₂₀H₁₈O₆
L29	Hyperoside (5281643)	464.4	C₂₁H₂₀O₁₂
L30	Hypophyllanthin (182140)	430.5	C₂₄H₃₀O₇
L31	Isocitric acid (1198)	192.12	C₆H₈O₇
L32	Isoleucine (6306)	131.17	C₆H₁₃NO₂
L33	Isolintetralin (101241675)	400.5	C₂₃H₂₈O₆
L34	Kaempferol (5280863)	286.24	C₁₅H₁₀O₆
L35	Limonene (2231)	136.23	C₁₀H₁₆
L36	Lintetralin (11361584)	400.5	C₂₃H₂₈O₆
L37	Lupeol (259846)	426.7	C₃₀H₅₀O
L38	Maleic acid (444266)	116.07	C₄H₄O₄
L39	Methyl brevifolincarboxylate (5319518)	306.22	C₁₄H₁₀O₈
L40	Miquelianin (5274585)	478.4	C₂₁H₁₈O₁₃
L41	Myricitrin (5281673)	464.4	C₂₁H₂₀O₁₂
L42	Niranthin (13989915)	432.5	C₂₄H₃₂O₇
L43	Nirphyllin (5491556)	448.5	C₂₄H₃₂O₈
L44	Nirtetralin (182644)	430.5	C₂₄H₃₀O₇
L45	Nirurin (125896)	664.6	C₃₂H₄₀O₁₅
L46	Norsecurinine (11106439)	203.24	C₁₂H₁₃NO₂
L47	Orientin (5281675)	448.4	C₂₁H₂₀O₁₁
L48	P-Cymene (7463)	134.22	C₁₀H₁₄
L49	Phyllanthin (358901)	418.5	C₂₄H₃₄O₆
L50	Phyllnirurin (179963)	342.4	C₂₀H₂₂O₅
L51	Phyllochrysine (267769)	217.26	C₁₃H₁₅NO₂
L52	Phyltetralin (11223782)	416.5	C₂₄H₃₂O₆
L53	Protocatechuic acid (72)	154.12	C₇H₆O₄
L54	Pyrogallol (1057)	126.11	C₆H₆O₃
L55	Quercetin (5280343)	302.23	C₁₅H₁₀O₇
L56	Quercetin-3-O-beta-D-glucuronopyranoside (5274585)	478.4	C₂₁H₁₈O₁₃
L57	Quercetol (5280343)	302.23	C₁₅H₁₀O₇
L58	Quercitrin (5280459)	448.4	C₂₁H₂₀O₁₁
L59	Repandusinic acid A (147900)	970.7	C₄₁H₃₀O₂₈
L60	Repandusinic acid B (16131091)	1138.8	C₄₈H₃₄O₃₃
L61	Rutin (5280805)	610.5	C₂₇H₃₀O₁₆
L62	Trifolin (5282149)	448.4	C₂₁H₂₀O₁₁
L63	Urinatetralin (11760779)	384.4	C₂₂H₂₄O₆
L64	Vitexin (5280441)	432.4	C₂₁H₂₀O₁₀
L65	Allopurinol (135401907)	136.11	C₅H₄N₄O
L66	Levofloxacin (149096)	361.4	C₁₈H₂₀FN₃O₄
L67	Nifedipine (4485)	346.3	C₁₇H₁₈N₂O₆

2.2. Target Protein Selection

We obtained the crystal structure of the nephrolithiasis associated receptor (PDB ID: 7KLL) (Figure 2)

[9]

from the Protein Data Bank (https://www.rcsb.org)

[10, 11]

. It was subjected to thorough cleaning and treatment by removing all water molecules, ligand and heteroatoms using Biovia Discovery Studio 4.5 to make the receptor ready and suitable for docking. The active site of the receptor was clearly defined based on the literature reported binding residues.

Download: Download full-size image

Figure 2. Crystal structure of the nephrolithiasis receptor (PDB ID: 7KLL).

2.3. Docking Simulation

Molecular docking simulations is an essential tool in computational chemistry for exploring ligand-receptor interactions in computer aided drug discovery, using specialized software tools, softwebs, and protocols to predict binding affinities and optimize molecular interactions. In this study, the molecular docking was carried out using the AutoDock and AutoDock Vina integrated inside the PyRx virtual screening platform

[12]

The grid box dimensions were set to 86.3271 × 97.6678 × 89.3663 Å in the X, Y, and Z axes while the grid center coordinates set to 9.1266, −2.2417, and 9.1787 Å. The exhaustiveness parameter was maintained at the default value of 8 to maintain speed and accuracy. Binding affinities were recorded in kcal/mol, the inhibition constant was calculated, and the docked complexes were visualized using PyMOL and Biovia Discovery Studio to identify hydrogen bonds, hydrophobic interactions, and π-π stacking.

2.4. Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) Prediction

The top-ranking ligands were subjected to ADMET property prediction using SwissADME (http://www.swissadme.ch) and AdmetSar2, Key pharmacokinetic parameters; absorption (GIT permeability, P-gp substrate), distribution (BBB permeability, plasma protein binding), metabolism (CYP450 inhibition), excretion, and toxicity (hepatotoxicity, carcinogenicity, AMES mutagenicity) were evaluated and identified. Drug-likeness was assessed according to Lipinski’s rule of five criteria.

2.5. Data

Docking scores were analyzed to determine ligand–protein affinities, with more negative binding energy values indicating stronger binding. Compounds were ranked and compared to standard drugs. ADMET parameters were used to identify the most promising candidates with optimal bioavailability and safety profiles.

3. Results

3.1. Molecular Docking Analysis

Molecular docking was conducted to predict the binding affinities and interaction profiles of 64 phytochemicals from Phyllanthus niruri against the nephrolithiasis-associated protein target (PDB ID: 7KLL). The docking results, Table 2 revealed that several compounds exhibited strong binding energies, suggesting favorable interactions within the active site of the receptor. Among the phytochemicals, Amariin (−8.8 kcal/mol), Ellagitannin (8.5 kcal/mol), Miquelianin (-8.6 kcal/mol) Nirurin (-8.5 kcal/mol), Quercetin 3-0-beta-D-glucuronopyranoside (-8.6 kcal/mol) demonstrated the lowest (most favorable) binding energies, outperforming standard drugs such as allopurinol (−5.9 kcal/mol), levofloxacin (−.6.7 kcal/mol), and nifedipine (−5.0 kcal/mol).

Table 2. Shows the ligands, their binding affinity values and their respective Inhibition Constant.

S/N	LIGANDS	BINDING AFFINITY (Kcal/Mol)	Inhibition Constant K₁(µM)
1	(-)-Fustin	-7	7.43
2	(S)-2-Amino-7-Hydroxytetralin	-6.1	33.92
3	2-Hydroxycinnamic acid	-6.9	8.80
4	4-Coumaric acid	-6.2	28.65
5	4-Desmethoxypropoxyl-4-methoxy Rabeprazole	-6.2	28.65
6	Ageratriol	-6.3	24.20
7	Amariin	-8.8	0.36
8	Ambrosic acid	-6.4	20.45
9	Apigenin	-7.9	1.63
10	Apocynin	-5.8	56.27
11	Astragalin	-7.8	1.93
12	Brevifolincarboxylic acid	-7.5	3.20
13	Catechol Dimethylether-d6	-4.9	256.86
14	Catechol	-4.8	304.07
15	Citral	-5.1	183.30
16	Corilagin	-7.9	1.63
17	Corymboside	-7.7	2.28
18	Diosgenin	-7.6	2.70
19	Elaeocarpusin	-7.3	4.48
20	Ellagic acid	-7.7	2.28
21	Ellagitannin	-8.5	0.59
22	Epicatechin	-7.4	3.78
23	Fisetin	-7.2	5.30
24	Fumaric acid	-5.3	130.80
25	Fustin	-7	7.43
26	Gallic acid	-6.8	10.41
27	Gallocatechin	-7.2	5.30
28	Hinokinin	-6.3	24.20
29	Hyperoside	-7.6	2.70
30	Hypophyllanthin	-5.8	56.27
31	Isocitric acid	-6	40.15
32	Isoleucine	-4.8	304.07
33	Isolintetralin	-5.9	47.53
34	Kaempferol	-7.6	2.70
35	Limonene	-5.5	93.34
36	Lintetralin	-6.4	20.45
37	Lupeol	-8.1	1.16
38	Maleic acid	-5.1	183.30
39	Methyl brevifolincarboxylate	-7.4	3.78
40	Miquelianin	-8.6	0.50
41	Myricitrin	-7.6	2.70
42	Niranthin	-4.7	359.95
43	Nirphyllin	-6	40.15
44	Nirtetralin	-5.9	47.53
45	Nirurin	-8.5	0.59
46	Norsecurinine	-7.1	6.28
47	Orientin	-7.6	2.70
48	P-Cymene	-5.7	66.61
49	Phyllanthin	-5.2	154.84
50	Phyllnirurin	-6.9	8.80
51	Phyllochrysine	-7.2	5.30
52	Phyltetralin	-6	40.15
53	Protocatechuic acid	-6.4	20.45
54	Pyrogallol	-5.2	154.84
55	Quercetin	-7.5	3.20
56	Quercetin-3-O-beta-D-glucuronopyranoside	-8.6	0.50
57	Quercetol	7.5	3.20
58	Quercitrin	-8.1	1.16
59	Repandusinic acid A	-7.5	3.20
60	Repandusinic acid B	-7.8	1.93
61	Rutin	-7.9	1.63
62	Trifolin	-7.2	5.30
63	Urinatetralin	-6.7	12.33
64	Vitexin	-7.6	2.70
65	Allopurinol	-5.9	47.53
66	Levofloxacin	-6.7	12.33
67	Nefedipine	-5.9	47.53

The top ligands were stabilized through multiple hydrogen bonds, π–π stacking, and hydrophobic interactions with key active site residues of the 7KLL protein Table 3. For example, Amariin and Miquelianin formed hydrogen bonds with residues ASP 183 and HIS 141, which are critical for ligand anchorage and enzyme inhibition. Visualization in Biovia Discovery Studio confirmed well-defined hydrogen bond networks and aromatic stacking interactions, Table 4 that contribute to enhanced binding stability.

Table 3. The docking scores, inhibition constant and amino acids residues of Interaction between the selected Phytochemicals and standard drug against 7KLL based on their binding affinity and inhibition constant compare to the standard drug.

Ligands	Name	Binding Affinity ΔG (kcal/mol)	Inhibition constant K1 (µM)	Residue involved in the interaction
L7	Amariin	-8.8	0.36	ASP: 183, ASN: 139, THR: 136, HIS: 141
L21	Ellagitannin	-8.5	0.59	VAL: 182, GLU: 202, TYR: 197, LYS: 191, HIS: 187, SER: 199, THR: 201, ASP: 204
L40	Miquelianin	-8.6	0.50	ASP: 183, GLU: 186, SER: 137, GLY: 142, ASN: 130, ASP: 128, THR: 246, HIS: 141, PRO: 20
L45	Nirurin	-8.5	0.59	ARG: 222, ARG: 225, LYS: 172, TYR: 218, ASP: 173, PRO: 116, LYS: 150
L56	Quercetin 3-0-beta-D-glucuronopyranoside	-8.6	0.50	ASP: 181, ASP: 183, PRO: 20, SER: 137, ASN: 130, HIS: 141, THR: 246, ASP: 128
L65	Allopurinol (standard drug)	-5.9	47.53	GLU: 186, ASP: 183, ASP: 128
L66	Levofloxacin (standard drug)	-6.7	12.33	PRO: 20, ASN: 139, HIS: 141, SER: 137
L67	Nefedipine (standard drug)	-5.9	47.53	LYS: 17, SER: 16, PHE: 15, GLU: 25, PHE: 55

Table 4. 3D and 2D of bonded and non-bonded interaction with the receptors and ligand.

Receptor + Ligand	3D STRUCTURE	2D STRUCTURE
7KLL + L7
7KLL + L21
7KLL + L40
7KLL + L45
7KLL + L56

These findings indicate that the phytochemicals possess structural and functional complementarity to the nephrolithiasis-associated target, implying potential inhibitory activity relevant to the prevention or dissolution of kidney stones.

3.2. Admet Analysis and Pharmacokinetics

ADMET analysis of the top 5 ligands was conducted using SwissADME

[13]

and AdmeSar2

[14]

to predict their pharmacokinetic properties. The results, Table 5 showed that compounds such as Amariin,, Ellagitannin, Miquelianin, Nirurin, Quercetin-3-O-beta-D-glucuronopyranoside complied with Lipinski’s Rule of Five, indicating good oral bioavailability. All the top ligands demonstrated high gastrointestinal (GIT) absorption, non-inhibition of CYP2D6 and CYP3A4 enzymes, and non-hepatotoxic properties. None of the compounds exhibited AMES mutagenicity or carcinogenic potential. Furthermore, the compounds showed moderate plasma protein binding and low blood-brain barrier (BBB) permeability, which are desirable for drugs targeting renal tissues.

Table 5. Shows the ligands and their drug-like parameters.

Ligands	Compound	Molecular weight (g/mol)	Hydrogen Bond acceptor (HBA)	Hydrogen bond donor (HBD)	Log P	Rule of five violation	Heavy atom
L1	(-)-Fustin	288.25	6	4	-0.10	0	21
L2	(S)-2-Amino-7-Hydroxytetralin	163.22	2	2	1.21	0	12
L3	2-Hydroxycinnamic acid	164.16	3	2	1.22	0	12
L4	4-Coumaric acid	164.16	3	2	0.96	0	12
L5	4-Desmethoxypropoxyl-4-methoxy Rabeprazole	301.4	4	1	0.96	0	21
L6	Ageratriol	252.35	3	3	1.24	0	18
L7	Amariin	968.6	28	13	-1.67	3	69
L8	Ambrosic acid	264.32	4	1	1.51	0	19
L9	Apigenin	270.24	5	3	0.52	0	20
L10	Apocynin	166.17	3	1	0.51	0	12
L11	Astragalin	448.4	11	7	-0.09	2	32
L12	Brevifolincarboxylic acid	292.2	8	4	-0.11	0	21
L13	Catechol Dimethylether-d6	144.2	2	0	1.48	0	10
L14	Catechol	110.11	2	2	0.79	0	8
L15	Citral	152.23	1	0	2.49	0	11
L16	Corilagin	634.5	18	11	-0.30	3	45
L17	Corymboside	564.5	14	10	-1.32	3	40
L18	Diosgenin	414.6	3	1	4.29	1	30
L19	Elaeocarpusin	1110.8	32	15	-2.59	3	79
L20	Ellagic acid	302.18	8	4	0.14	0	22
L21	Ellagitannin	992.7	27	13	-0.07	3	71
L22	Epicatechin	290.27	6	5	0.24	0	21
L23	Fisetin	286.24	6	4	-0.03	0	21
L24	Fumaric acid	116.07	4	2	-0.29	0	8
L25	Fustin	288.25	6	4	-0.10	0	21
L26	Gallic acid	170.12	5	4	-0.16	0	12
L27	Gallocatechin	306.27	7	6	-0.29	1	22
L28	Hinokinin	354.4	6	0	2.71	0	26
L29	Hyperoside	464.4	12	8	-0.38	2	33
L30	Hypophyllanthin	430.5	7	0	1.91	0	31
L31	Isocitric acid	192.12	7	4	-0.06	0	13
L32	Isoleucine	131.17	3	2	-0.15	0	9
L33	Isolintetralin	400.5	6	0	2.23	0	29
L34	Kaempferol	286.24	6	4	-0.03	0	21
L35	Limonene	136.23	0	0	2.72	0	10
L36	Lintetralin	400.5	6	0	2.23	0	29
L37	Lupeol	426.7	1	1	4.72	1	31
L38	Maleic acid	116.07	4	2	-0.29	0	8
L39	Methyl brevifolincarboxylate	306.22	8	3	-0.09	0	22
L40	Miquelianin	478.4	13	8	-0.45	2	34
L41	Myricitrin	464.4	12	8	-0.07	2	33
L42	Niranthin	432.5	7	0	1.91	0	31
L43	Nirphyllin	448.5	8	1	1.39	0	32
L44	Nirtetralin	430.5	7	0	1.91	0	31
L45	Nirurin	664.6	15	9	-0.04	3	47
L46	Norsecurinine	203.24	3	0	0.63	0	15
L47	Orientin	448.4	11	8	-0.14	2	32
L48	P-Cymene	134.22	0	0	2.51	1	10
L49	Phyllanthin	418.5	6	0	2.43	0	30
L50	Phyllnirurin	342.4	5	1	2.38	0	25
L51	Phyllochrysine	217.26	3	0	1.02	0	16
L52	Phyltetralin	416.5	6	0	2.03	0	30
L53	Protocatechuic acid	154.12	4	3	0.26	0	11
L54	Pyrogallol	126.11	3	3	0.18	0	9
L55	Quercetin	302.23	7	5	-0.56	0	22
L56	Quercetin-3-O-beta-D-glucuronopyranoside	478.4	13	8	-0.45	2	34
L57	Quercetol	302.23	7	5	-0.56	0	22
L58	Quercitrin	448.4	11	7	-1.84	2	32
L59	Repandusinic acid A	970.7	28	15	-0.21	3	69
L60	Repandusinic acid B	1138.8	33	18	-1.39	3	81
L61	Rutin	610.5	16	10	-0.33	3	43
L62	Trifolin	448.4	11	7	-0.06	2	32
L63	Urinatetralin	384.4	6	0	2.42	0	28
L64	Vitexin	432.4	10	7	-0.02	1	31
L65	Allopurinol	136.11	3	2	-0.35	0	10
L66	Levofloxacin	361.4	6	1	-0.39	0	26
L67	Nifedipine	346.3	6	1	0.52	0	25

Amariin, Ellagitannin and Miquelianin demonstrated superior pharmacokinetic behavior, exhibiting optimal solubility and permeability profiles, while phyllanthin displayed higher lipophilicity (LogP 3.9), suggesting effective membrane permeability. Collectively, the ADMET results, Table 6 confirmed the suitability of these compounds as drug-like candidates with minimal predicted toxicity and acceptable absorption and metabolism parameters.

Table 6. ADME analysis and Pharmacokinetics of the derivatives.

Parameter	Amariin	Ellagitannin	Miquelianin	Nirurin	Quercetin-3-O-beta-D-glucuronopyranoside
Molecular Weight (g/mol)	968.64	992.71	478.36	664.65	478.36
LogP (Lipophilicity)	-1.67	-0.07	-0.45	-0.04	-0.45
Hydrogen Bond Donors (HBD)	13	13	8	9	8
Hydrogen Bond Acceptors (HBA)	28	27	13	15	13
Topological Polar Surface Area (TPSA) (Å²)	456.32	447.09	227.58	245.29	227.58
Number of Rotatable Bonds	3	5	4	8	4
Lipinski’s Rule of Five Violations	3	3	2	3	2
Veber’s Rule Compliance (Yes/No)	No	No	No	No	No
Gastrointestinal (GI) Absorption (High/Low)	Low	Low	Low	Low	Low
Blood-Brain Barrier (BBB) Permeability (Yes/No)	No	No	No	No	No
P-glycoprotein (P-gp) Substrate (Yes/No)	Yes	Yes	Yes	Yes	Yes
CYP450 Enzyme Inhibition	CYP3A4, CYP1A2	CYP3A4, CYP1A2	CYP3A4	CYP3A4, CYP2D6	CYP3A4
Bioavailability Score	0.17	0.17	0.11	0.17	0.11
Water Solubility (Good/Poor)	Good	Poor	Good	Good	Good
LogS (Solubility Index)	-3.24	-5.95	-3.09	-3.11	-3.09
Human Intestinal Absorption (HIA) (%)	18%	22%	35%	27%	38%
Renal Clearance (Yes/No)	No	No	Yes	No	Yes
Hepatotoxicity	Inactive (0.98)	Inactive (0.75)	Inactive (0.75)	Inactive (0.98)	Inactive
Mutagenicity	Inactive (0.82)	Inactive (0.60)	Inactive (0.68)	Inactive (0.82)	Inactive (0.82)
Respiratory Toxicity	Inactive (0.99)	Active (0.71)	Active (0.83)	Inactive (0.77)	Inactive
Cardiotoxicity	Inactive (0.91)	Inactive (0.57)	Inactive (0.61)	Inactive (0.91)	Inactive
Immunotoxicity	Inactive (0.99)	Active (0.97)	Active (0.58)	Inactive (0.99)	Inactive (0.99)

4. Discussion

The integration of in-silico docking and ADMET evaluation in this study provided mechanistic insights into the potential antiurolithiatic properties of Phyllanthus niruri phytochemicals. The strong binding affinities exhibited by Amarin, Ellagitannin, and Miquelianin suggest their ability to interact effectively with the nephrolithiasis-related protein (7KLL). These interactions are likely to inhibit crystal formation or aggregation processes that underline renal stone development. Ellagitannin, a hydrolyzable tannin, has been reported in earlier studies to exhibit significant antioxidant and calcium oxalate crystal inhibitory activity

[15]

. Its multiple hydroxyl groups contribute to strong hydrogen bonding and chelating capacity, which may underlie its binding to active site residues of 7KLL. Similarly, Amarin and Miquelianin possess polyphenolic structures capable of modulating oxidative stress pathways and preventing lipid peroxidation, both implicated in nephrolithiasis progression

[16]

. The observed binding energies of the phytochemicals surpass those of standard drugs such as allopurinol, indicating that natural compounds could serve as competitive or adjunct inhibitors with lower toxicity risk. Furthermore, ADMET profiling confirmed that these phytochemicals possess favorable pharmacokinetic properties and meet key criteria for oral bioavailability and safety, this supports previous findings where Phyllanthus niruri extracts demonstrated renal protective, diuretic, and antioxidant activities

[13, 17]

Collectively, the study reinforces the ethnopharmacological use of Phyllanthus niruri as a natural remedy for kidney stones and validates the application of computational screening in identifying plant-derived lead compounds with therapeutic potential. Nevertheless, while molecular docking provides predictive insights, in vitro and in vivo validation remains necessary to establish precise inhibitory mechanisms, bioavailability, and efficacy in biological systems.

5. Conclusions

This study explored the molecular interactions and pharmacokinetic potential of phytochemicals derived from Phyllanthus niruri for the prevention and treatment of nephrolithiasis using in silico methods. The docking analysis revealed that compounds such as Amarin, Ellagitannin, Miquelianin, Nirurin, Quercetin-3-O-beta-D-glucuronopyranoside exhibited superior binding affinities compared with standard nephrolithiasis drugs. ADMET evaluations further confirmed their drug-likeness, safety, and favorable absorption and metabolism characteristics. The findings highlight Phyllanthus niruri as a promising natural source of bioactive compounds capable of modulating nephrolithiasis-associated targets. These results provide a foundation for subsequent experimental validation and potential drug development aimed at safer, cost-effective, and plant-based interventions for kidney stone disease.

Abbreviations

ADMET

Absorption, Distribution, Metabolism, Excretion, and Toxicity

Author Contributions

Adeboye Omolara Olubunmi: Conceptualization, Resources, Supervision, Writing – review & editing

Agboluaje Saheed Alabi: Formal Analysis, Investigation, Methodology, Software, Validation

Salami Leke Peter: Data Curation, Project Administration, Visualization, Writing – original draft

Conflicts of Interest

There are no conflicts of interest.

References

[1]	Kai Wang, Jing Ge, Wenlong Han, Dong Wang, Yinjuan Zhao, Yanhao Shen, Jiexun Chen, Dongming Chen, Jing Wu, Ning Shen, Shuai Zhu, Bin Xue & Xianlin Xu (2022). Risk factors for kidney stone disease recurrence: a comprehensive meta-analysis. BMC Urol 22, 62, https://doi.org/10.1186/s12894-022-01017-4
[2]	Leonardo Ferreira Fontenelle, Thiago Dias Sarti (2019), Kidney Stones: Treatment and Prevention. Am Fam Physician. 2019 Apr 15; 99(8): 490-496.
[3]	Wales R, Munshi F, Penukonda S, Sanford D, Pareek G (2023). The Surgical Management of Urolithiasis: A Review of Literature. R I Med J (2013). 106(11): 36-40.
[4]	Leslie, S. W., Sajjad, H. & Murphy, P. B. (2024). Urolithiasis. In: StatPearls [Internet]. StatPearls Publishing, Treasure Island (FL).
[5]	Kamruzzaman, M., Hoque, M. A., Islam, M. N. & Rahman, M. M. (2016). Phytochemical screening and antiurolithiatic potential of Phyllanthus niruri Linn. Journal of Medicinal Plants Research, 10(30), 478-484.
[6]	Navneet Kaur, Baljinder Kaur & Geetika Sirhindi (2017), Phytochemistry and Pharmacology of Phyllanthus niruri L.: A Review, Phytother. Res. https://doi.org/10.1002/ptr.5825
[7]	Trott, O. & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455-461.
[8]	Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2025). PubChem 2025 update. Nucleic Acids Res., 53(D1), D1516-D1525. https://doi.org/10.1093/nar/gkae1059
[9]	Lu, Hongjun Zhang, Derun Li, Matthew Childers, Qinglin Pu, Rachel L. Palte, Symon Gathiaka, Thomas W. Lyons, Anandan Palani, Peter W. Fan, Peter Spacciapoli, J. Richard Miller, Hyelim Cho, Mangeng Cheng, Kalyan Chakravarthy, Jennifer O’Neil, Padmanabhan Eangoor, Adam Beard, Hai-Young Kim, Josep Saurí, Hakan Gunaydin, David L. Sloman, Phieng Siliphaivanh, Jared Cumming, and Christian Fischer (2021). Structure-Based Discovery of Proline-Derived Arginase Inhibitors with Improved Oral Bioavailability for Immuno-OncologyMin. ACS Medicinal Chemistry Letters, 12(9), 1380-1388 https://doi.org/10.1021/acsmedchemlett.1c00195
[10]	H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne, (2000) The Protein Data Bank Nucleic Acids Research 28: 235-242 https://doi.org/10.1093/nar/28.1.235
[11]	H. M. Berman, K. Henrick, H. Nakamura Announcing the worldwide Protein Data Bank (2003) Nature Structural Biology 10: 980 https://doi.org/10.1038/nsb1203-980
[12]	Dallakyan, S. & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. In: Hempel, J. E. et al. (eds) Chemical Biology: Methods and Protocols. Methods in Molecular Biology, vol. 1263. Humana Press, New York, NY.
[13]	Daina, A., Michielin, O. & Zoete, V. (2017). SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 7, 42717 https://doi.org/10.1038/srep42717
[14]	Yang, H., Lou, C., Sun, L., Li, J., Cai, Y., Wang, Z., Li, W., Liu, G., & Tang, Y. (2019). admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties. Bioinformatics (Oxford, England), 35(6), 1067-1069. https://doi.org/10.1093/bioinformatics/bty707
[15]	Campos, A. H. & Schor, N. (1999). Phyllanthus niruri inhibits calcium oxalate endocytosis by renal tubular cells role of free radicals. Scandinavian Journal of Urology and Nephrology, 33(5), 293-297.
[16]	Pandey, K. B. & Rizvi, S. I. (2009). Plant polyphenols as dietary antioxidants in human health and disease. Oxidative Medicine and Cellular Longevity, 2(5), 270-278.
[17]	Santos, D. R., Rao, V. S. N. & Silveira, E. R. (1995). Antiurolithiatic activity of the aqueous extract of Phyllanthus niruri in rats. Phytotherapy Research, 9(6), 403-405.

Cite This Article

Plain Text BibTeX RIS

APA Style

Olubunmi, A. O., Alabi, A. S., Peter, S. L. (2026). In-silico Characterization of the Phytochemicals of Phyllanthus Niruri Against Nephrolithiasis. Journal of Drug Design and Medicinal Chemistry, 12(1), 1-18. https://doi.org/10.11648/j.jddmc.20261201.11

Copy | Download

ACS Style

Olubunmi, A. O.; Alabi, A. S.; Peter, S. L. In-silico Characterization of the Phytochemicals of Phyllanthus Niruri Against Nephrolithiasis. J. Drug Des. Med. Chem. 2026, 12(1), 1-18. doi: 10.11648/j.jddmc.20261201.11

Copy | Download

AMA Style

Olubunmi AO, Alabi AS, Peter SL. In-silico Characterization of the Phytochemicals of Phyllanthus Niruri Against Nephrolithiasis. J Drug Des Med Chem. 2026;12(1):1-18. doi: 10.11648/j.jddmc.20261201.11

Copy | Download

@article{10.11648/j.jddmc.20261201.11,
  author = {Adeboye Omolara Olubunmi and Agboluaje Saheed Alabi and Salami Leke Peter},
  title = {In-silico Characterization of the Phytochemicals of Phyllanthus Niruri Against Nephrolithiasis},
  journal = {Journal of Drug Design and Medicinal Chemistry},
  volume = {12},
  number = {1},
  pages = {1-18},
  doi = {10.11648/j.jddmc.20261201.11},
  url = {https://doi.org/10.11648/j.jddmc.20261201.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.jddmc.20261201.11},
  abstract = {Nephrolithiasis, which is also known as kidney stone disease, is a regular urological disorder that came with the formation of crystalline deposits within the renal system. It is very significant that the regular and convention procedures for the prevention and treatment of kidney stone diseases including lithotripsy and pharmacotherapy have limitations ranging from recurrence, expensive and great adverse effects, which necessitate the search for safer and highly effective alternatives in phytochemicals with proven biological activities. Phyllanthus niruri is locally and traditionally recognized and active for its antiurolithiatic and nephroprotective effects, with its various diverse bioactive constituents such as flavonoids, alkaloids, tannins, and phenolic compounds. In this work we employed molecular docking and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analyses to screen phytochemicals generated from Phyllanthus niruri as potential inhibitors of nephrolithiasis associated proteins. 64 phytochemicals were retrieved from literature and was used to perform docking against the 7KLL protein target using AutoDock and AutoDock Vina integrated in PyRx. Binding affinities, inhibition constants as well as protein-ligands interactions were analyzed using Biovia Discovery Studio and PyMOL. ADMET predictions were performed using online softweb Admetsar2 to assess pharmacokinetic and safety profiles. Amariin (−8.8 kcal/mol), Ellagitannin (8.5 kcal/mol), Miquelianin (-8.6 kcal/mol) Nirurin (-8.5 kcal/mol), Quercetin 3-0-beta-D-glucuronopyranoside (-8.6 kcal/mol) demonstrated strong binding affinities comparable to or higher than standard drugs allopurinol (−5.9 kcal/mol), levofloxacin (−.6.7 kcal/mol), and nifedipine (−5. kcal/mol). used for comparison. The ADMET evaluation shown that the top ligands possess favorable drug-likeness, oral bioavailability, and non-toxicity. The results suggest that Phyllanthus niruri phytochemicals possess promising inhibitory potential against nephrolithiasis targets and may serve as leads for the development of safe, plant-based therapeutics.},
 year = {2026}
}

Copy | Download

TY  - JOUR
T1  - In-silico Characterization of the Phytochemicals of Phyllanthus Niruri Against Nephrolithiasis
AU  - Adeboye Omolara Olubunmi
AU  - Agboluaje Saheed Alabi
AU  - Salami Leke Peter
Y1  - 2026/03/17
PY  - 2026
N1  - https://doi.org/10.11648/j.jddmc.20261201.11
DO  - 10.11648/j.jddmc.20261201.11
T2  - Journal of Drug Design and Medicinal Chemistry
JF  - Journal of Drug Design and Medicinal Chemistry
JO  - Journal of Drug Design and Medicinal Chemistry
SP  - 1
EP  - 18
PB  - Science Publishing Group
SN  - 2472-3576
UR  - https://doi.org/10.11648/j.jddmc.20261201.11
AB  - Nephrolithiasis, which is also known as kidney stone disease, is a regular urological disorder that came with the formation of crystalline deposits within the renal system. It is very significant that the regular and convention procedures for the prevention and treatment of kidney stone diseases including lithotripsy and pharmacotherapy have limitations ranging from recurrence, expensive and great adverse effects, which necessitate the search for safer and highly effective alternatives in phytochemicals with proven biological activities. Phyllanthus niruri is locally and traditionally recognized and active for its antiurolithiatic and nephroprotective effects, with its various diverse bioactive constituents such as flavonoids, alkaloids, tannins, and phenolic compounds. In this work we employed molecular docking and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analyses to screen phytochemicals generated from Phyllanthus niruri as potential inhibitors of nephrolithiasis associated proteins. 64 phytochemicals were retrieved from literature and was used to perform docking against the 7KLL protein target using AutoDock and AutoDock Vina integrated in PyRx. Binding affinities, inhibition constants as well as protein-ligands interactions were analyzed using Biovia Discovery Studio and PyMOL. ADMET predictions were performed using online softweb Admetsar2 to assess pharmacokinetic and safety profiles. Amariin (−8.8 kcal/mol), Ellagitannin (8.5 kcal/mol), Miquelianin (-8.6 kcal/mol) Nirurin (-8.5 kcal/mol), Quercetin 3-0-beta-D-glucuronopyranoside (-8.6 kcal/mol) demonstrated strong binding affinities comparable to or higher than standard drugs allopurinol (−5.9 kcal/mol), levofloxacin (−.6.7 kcal/mol), and nifedipine (−5. kcal/mol). used for comparison. The ADMET evaluation shown that the top ligands possess favorable drug-likeness, oral bioavailability, and non-toxicity. The results suggest that Phyllanthus niruri phytochemicals possess promising inhibitory potential against nephrolithiasis targets and may serve as leads for the development of safe, plant-based therapeutics.
VL  - 12
IS  - 1
ER  -

Copy | Download

Author Information

Adeboye Omolara Olubunmi

Department of Chemistry, Emmanuel Alayande University of Education, Oyo, Nigeria

Contact Email

http://orcid.org/0000-0001-5232-1779
Agboluaje Saheed Alabi

Faculty of Chemistry, Higher School of Economics, Moscow, Russia

http://orcid.org/0000-0001-8699-8008
Salami Leke Peter

Department of Integrated Science, Ekiti State University, Ekiti, Nigeria

http://orcid.org/0009-0001-5833-1895

Download PDF

Submit an Article

Plain Text BibTeX RIS

APA Style

Olubunmi, A. O., Alabi, A. S., Peter, S. L. (2026). In-silico Characterization of the Phytochemicals of Phyllanthus Niruri Against Nephrolithiasis. Journal of Drug Design and Medicinal Chemistry, 12(1), 1-18. https://doi.org/10.11648/j.jddmc.20261201.11

Copy | Download

ACS Style

Olubunmi, A. O.; Alabi, A. S.; Peter, S. L. In-silico Characterization of the Phytochemicals of Phyllanthus Niruri Against Nephrolithiasis. J. Drug Des. Med. Chem. 2026, 12(1), 1-18. doi: 10.11648/j.jddmc.20261201.11

Copy | Download

AMA Style

Olubunmi AO, Alabi AS, Peter SL. In-silico Characterization of the Phytochemicals of Phyllanthus Niruri Against Nephrolithiasis. J Drug Des Med Chem. 2026;12(1):1-18. doi: 10.11648/j.jddmc.20261201.11

Copy | Download

@article{10.11648/j.jddmc.20261201.11,
  author = {Adeboye Omolara Olubunmi and Agboluaje Saheed Alabi and Salami Leke Peter},
  title = {In-silico Characterization of the Phytochemicals of Phyllanthus Niruri Against Nephrolithiasis},
  journal = {Journal of Drug Design and Medicinal Chemistry},
  volume = {12},
  number = {1},
  pages = {1-18},
  doi = {10.11648/j.jddmc.20261201.11},
  url = {https://doi.org/10.11648/j.jddmc.20261201.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.jddmc.20261201.11},
  abstract = {Nephrolithiasis, which is also known as kidney stone disease, is a regular urological disorder that came with the formation of crystalline deposits within the renal system. It is very significant that the regular and convention procedures for the prevention and treatment of kidney stone diseases including lithotripsy and pharmacotherapy have limitations ranging from recurrence, expensive and great adverse effects, which necessitate the search for safer and highly effective alternatives in phytochemicals with proven biological activities. Phyllanthus niruri is locally and traditionally recognized and active for its antiurolithiatic and nephroprotective effects, with its various diverse bioactive constituents such as flavonoids, alkaloids, tannins, and phenolic compounds. In this work we employed molecular docking and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analyses to screen phytochemicals generated from Phyllanthus niruri as potential inhibitors of nephrolithiasis associated proteins. 64 phytochemicals were retrieved from literature and was used to perform docking against the 7KLL protein target using AutoDock and AutoDock Vina integrated in PyRx. Binding affinities, inhibition constants as well as protein-ligands interactions were analyzed using Biovia Discovery Studio and PyMOL. ADMET predictions were performed using online softweb Admetsar2 to assess pharmacokinetic and safety profiles. Amariin (−8.8 kcal/mol), Ellagitannin (8.5 kcal/mol), Miquelianin (-8.6 kcal/mol) Nirurin (-8.5 kcal/mol), Quercetin 3-0-beta-D-glucuronopyranoside (-8.6 kcal/mol) demonstrated strong binding affinities comparable to or higher than standard drugs allopurinol (−5.9 kcal/mol), levofloxacin (−.6.7 kcal/mol), and nifedipine (−5. kcal/mol). used for comparison. The ADMET evaluation shown that the top ligands possess favorable drug-likeness, oral bioavailability, and non-toxicity. The results suggest that Phyllanthus niruri phytochemicals possess promising inhibitory potential against nephrolithiasis targets and may serve as leads for the development of safe, plant-based therapeutics.},
 year = {2026}
}

Copy | Download

TY  - JOUR
T1  - In-silico Characterization of the Phytochemicals of Phyllanthus Niruri Against Nephrolithiasis
AU  - Adeboye Omolara Olubunmi
AU  - Agboluaje Saheed Alabi
AU  - Salami Leke Peter
Y1  - 2026/03/17
PY  - 2026
N1  - https://doi.org/10.11648/j.jddmc.20261201.11
DO  - 10.11648/j.jddmc.20261201.11
T2  - Journal of Drug Design and Medicinal Chemistry
JF  - Journal of Drug Design and Medicinal Chemistry
JO  - Journal of Drug Design and Medicinal Chemistry
SP  - 1
EP  - 18
PB  - Science Publishing Group
SN  - 2472-3576
UR  - https://doi.org/10.11648/j.jddmc.20261201.11
AB  - Nephrolithiasis, which is also known as kidney stone disease, is a regular urological disorder that came with the formation of crystalline deposits within the renal system. It is very significant that the regular and convention procedures for the prevention and treatment of kidney stone diseases including lithotripsy and pharmacotherapy have limitations ranging from recurrence, expensive and great adverse effects, which necessitate the search for safer and highly effective alternatives in phytochemicals with proven biological activities. Phyllanthus niruri is locally and traditionally recognized and active for its antiurolithiatic and nephroprotective effects, with its various diverse bioactive constituents such as flavonoids, alkaloids, tannins, and phenolic compounds. In this work we employed molecular docking and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analyses to screen phytochemicals generated from Phyllanthus niruri as potential inhibitors of nephrolithiasis associated proteins. 64 phytochemicals were retrieved from literature and was used to perform docking against the 7KLL protein target using AutoDock and AutoDock Vina integrated in PyRx. Binding affinities, inhibition constants as well as protein-ligands interactions were analyzed using Biovia Discovery Studio and PyMOL. ADMET predictions were performed using online softweb Admetsar2 to assess pharmacokinetic and safety profiles. Amariin (−8.8 kcal/mol), Ellagitannin (8.5 kcal/mol), Miquelianin (-8.6 kcal/mol) Nirurin (-8.5 kcal/mol), Quercetin 3-0-beta-D-glucuronopyranoside (-8.6 kcal/mol) demonstrated strong binding affinities comparable to or higher than standard drugs allopurinol (−5.9 kcal/mol), levofloxacin (−.6.7 kcal/mol), and nifedipine (−5. kcal/mol). used for comparison. The ADMET evaluation shown that the top ligands possess favorable drug-likeness, oral bioavailability, and non-toxicity. The results suggest that Phyllanthus niruri phytochemicals possess promising inhibitory potential against nephrolithiasis targets and may serve as leads for the development of safe, plant-based therapeutics.
VL  - 12
IS  - 1
ER  -

Copy | Download