World Journal of Traditional Chinese Medicine

: 2021  |  Volume : 7  |  Issue : 3  |  Page : 377--382

Molecular docking-based research on the potential anti-encephalopathy effect of gentianine

Awais Wahab1, Jian-Xin Chen1, Cai-Xia Jia1, Ghulam Murtaza2, Chuan-Hong Wu3, Na Wang1,  
1 School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
2 Department of Pharmacy, COMSATS University Islamabad, Lahore, Pakistan
3 School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing; The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China

Correspondence Address:
Dr. Chuan-Hong Wu
Beijing University of Chinese Medicine, Beijing; The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao
Dr. Na Wang
Beijing University of Chinese Medicine, Beijing


Objective: Encephalopathy is increasingly threatening human health. It is correspondingly one of the concerns of society and medical community. As a natural source, traditional Chinese medicine has tremendous beneficial outcomes in various diseases including encephalopathy. Gentianine, a Chinese herbal compound, shows effectiveness in many diseases exclusively in inflammation. Therefore, this in vitro research was carried out to find its effectiveness in encephalopathy. Methodology: Ligand and proteins were searched and downloaded from ChemDraw and protein database, respectively. Sybyl-X2.0 docking software and its various functions were used to prepare ligand and proteins. Finally, gentianine was docked with proteins using Sybyl-X2.0 docking software. Results: Gentianine was docked with 20 protein targets. Compounds with C-score of 5 were selected. A total of three kinds of protein docked with gentianine (ABCC1, C-reactive protein [CRP], and NKX5-2) were selected. ABCC1 was expressed in the brain and was related to seizures and stroke. CRP was an inflammatory biomarker and related to seizures, epilepsy, stroke, and Parkinson's disease. NKX2–5 was also known as cardiac transcription and related to cerebral palsy, Alzheimer's disease, and stroke. All these targets were related to encephalopathy. Conclusion: Molecular docking findings in this study lead to the suggestion that gentianine might be helpful in treating encephalopathy. This study is expected to provide a solution to find potential anti-encephalopathy compounds.

How to cite this article:
Wahab A, Chen JX, Jia CX, Murtaza G, Wu CH, Wang N. Molecular docking-based research on the potential anti-encephalopathy effect of gentianine.World J Tradit Chin Med 2021;7:377-382

How to cite this URL:
Wahab A, Chen JX, Jia CX, Murtaza G, Wu CH, Wang N. Molecular docking-based research on the potential anti-encephalopathy effect of gentianine. World J Tradit Chin Med [serial online] 2021 [cited 2022 May 17 ];7:377-382
Available from:

Full Text


Encephalopathy refers to disease with abnormal brain tissue structure and physiological functions,[1] such as brain atrophy,[2] seizures,[3] cerebral palsy,[4] Alzheimer's disease,[5] Parkinson's disease,[6] epilepsy,[7] sequelae of cerebral thrombosis,[8] and stroke hemiplegia.[9] The etiology of the above-mentioned encephalopathy is not only attributed to cranial nerve but also to cerebrovascular functions.[10] Due to the particularity of the blood–brain barrier and the complexity of the encephalopathy pathogenesis,[11],[12] the research and development of drugs for encephalopathy[13] has become a challenge in the medical community.[14],[15]

Traditional Chinese medicine (TCM) is mainly playing a vital role as a supplementary or alternative therapy in health-care systems and becoming well known in various countries. In the ancient medical system, Traditional Chinese herbal products were described as a therapy for encephalopathy.[16],[17],[18] Pharmacological studies have revealed that certain TCMs[19] have effects on anti-inflammatory,[20] antioxidant,[21] vasodilation,[22] anti-glutamic acid,[23] antiplatelet,[24] and have potential effects against encephalopathy.[25]

Gentianine is basically a pure alkaloid, which is isolated from Radix Gentianae Macrophy. Gentianine has been used for the treatment of various types of diseases such as anti-inflammatory,[26] antipyretic,[27] diuretic,[28] antidiabetic,[29] analgesic,[30] sedative-hypnotic,[31] antimutagenicity,[32] hepatic injury,[33] arthritis,[34] and antiphlogistic.[35] However, there are few literatures related to gentianine showing efficacy against encephalopathy.

Molecular docking is an in silico method for drug designing, based on structural molecular biology.[36] The objective of docking is to predict fit optimization of ligand to the tri-dimensional protein structure.[37] The key function of docking is effectively search high-dimensional spaces and correct ranking of interaction (ligand-protein) based on scoring function. It allows screening of compounds, results based on ranking and structural prediction (how a protein target can be inhibited by ligand molecule) which helps in optimizing and developing new compounds.[38] The current study aims to explore the potential anti-encephalopathy effect of gentianine based on molecular docking.


Symptom-disease network of gentianine using SymMap

SymMap ( is a database which shows interrelations among herb, ingredient, TCM symptom, modern medicine symptom (MM symptom), target, and disease. In this study, we used the database to construct a symptom–disease network of gentianine.

Protein preparation

The targeted proteins Protein data bank identification (PDB-ID) and their gene names, as shown in [Table 1], were downloaded from the protein database. Molecular dynamics simulation (1000fs) was applied to these complexes using SYBL-X software. SYBL-X is a docking software based on network pharmacology, which permits molecular pathway maps and docking simulation to identify ligand role in complex proteins.[39] Before docking, the structural optimization and energy minimization of the selected proteins were processed into active capsules (processing including removal of excess chains, excess small molecules, excess water molecules, and addition of hydrogen).{Table 1}

Binding analysis

For further screening the interactions between encephalopathy-related human protein targets and gentianine, Sybyl X2.0 by tripos international Certara company, USA was used for docking. Default docking parameters were selected and the C-score was considered as the criteria for active sites and ligand affinity. C-score is the sum of separate terms (Van der Waals interaction, H-bonding, de-solvation effects, etc.) which explains its contributions to binding.[40] The C-score is worth to be considered from 0 to 5, where 5 indicates good affinity, 3 and 4 indicate further consideration, and 0 indicates unstable binding.

 Results and Discussion

Gentianine is basically a pure alkaloid, which is isolated from the Radix Gentianae Macrophy. According to SymMap, the TCM symptom-MM symptom–disease network of gentianine was constructed, as shown in [Figure 1]. Radix Gentianae Macrophy associated with encephalopathy, such as epileptic encephalopathy, Parkinsonism-dystonia, Aβ amyloidosis, and seizures. These encephalopathies were connected with three MM symptoms (fever convulsions, hemiparesis, and stroke) and three TCM symptoms (infantile fever, stroke, and hemiplegia). The network suggested that gentianine might have a potential effect on encephalopathy. However, the specific correlation between gentianine and encephalopathy remains unclear.{Figure 1}

Structure of gentianine was downloaded from the PubChem database, as shown in [Figure 2]. Overall, 20 protein crystal structures were downloaded from the PDB database, and their binding scores were obtained according to the surflex-dock function in Sybyl-X2.0 software. The docking results and PDB-ID are shown [Table 2].{Table 2}{Figure 2}

It can be seen from the above table that ABCC1, C-reactive protein (CRP), and NKX2-5 have a good affinity with gentianine. The docking of gentianine with ABBC1 showed a good C-score of 5 and two hydrogen bonds at TRP16 and ARG780, as shown in [Figure 3]. According to reports, ABCC1 (multi-drug resistance-associated protein 1) was expressed in the brain and can mildly downregulated in response to focal cerebral ischemia and seizures.[41] Kilic et al. reported that ABCC1 acts as a transporter for pharmacological active compound to the brain. Binding of pharmacologically active compounds to abluminal ABC transporter facilitates drug therapy.[41] Binding of gentianine to ABCC1 might facilitate the transportation of various pharmacologically active compounds through the blood–brain barrier into the brain.{Figure 3}

CRP docking with gentianine also gave us a high docking score of 5 and one hydrogen bond at GLU85, as shown in [Figure 4]. CRP is an inflammatory biomarker associated with a high risk of seizures, epilepsy, stroke, and Parkinson's disease.[42] Tian et al. study showed that CRP links to transient ischemic stroke or cerebrovascular attack.[43] CRP is an acute-phase protein, its level increases in various inflammatory states.[44] Various reports illustrated that during ischemia, there is an increased level of inflammatory mediators and CRP.[45] High levels of CRP relate to various vascular events like cerebrovascular accident and myocardial infarction, as reported in various studies. An earlier study demonstrated an elevated level of CRP during encephalopathy[46] (seizures, epilepsy, stroke, and Parkinson's disease) which, in turn, causes further inflammation and brain injury.[47] Inflammation acts a vital role in physiopathology of encepalopathy.[48]{Figure 4}

Gentianine was docked with NKX2-5 with a docking score of 5 and one hydrogen bond at ARG190, as shown in [Figure 5]. NKX2-5 (homeobox protein NKX-2.5) also known as cardiac transcription and it was identified to play a role in stroke, cerebral palsy, and Alzheimer's disease.[49] Binding of gentianine to NKX2-5 provided clues that gentianine might be effective in treating encephalopathy.{Figure 5}

All the protein targets of Gentianine obtained through molecular docking and their activity in various pathological condition as shoen in [Figure 6].{Figure 6}


Gentianine has a good affinity with ABCC1, CRP, and NKX2-5, which suggests that gentianine might have a great potential in the treatment of encephalopathy. However, limitations of the effects of gentianine still remain to be explored. These three target proteins are in three different aspects and related to different types of encephalopathy. Further pharmacological experiments were needed to provide further evidence for gentianine in the treatment of encephalopathy in future.

Financial support and sponsorship

This work was supported by the National Natural Science Foundation of China (No. 82004085), the Double First-Class Personnel Office-Research Fund of Scientific Research Team (1000061020051), University Nursing Program for Young Scholars with Creative Talents in Heilongjiang Province (UNPYSCT-2018032), and Chunhui program from Ministry of Education (HLJ2019039).

Conflicts of interest

Prof. Jian-Xin Chen is an editorial Board member of World Journal of Traditional Chinese Medicine. The article was subject to the journal's standard procedures, with peer review handled independently of this editorial board member and their research groups.


1Campbell BC, De Silva DA, Macleod MR, Coutts SB, Schwamm LH, Davis SM, et al. Ischaemic stroke. Nat Rev Dis Primers 2019;5:70.
2Towfighi A, Saver JL. Stroke declines from third to fourth leading cause of death in the United States: Historical perspective and challenges ahead. Stroke 2011;42:2351-5.
3Bell RD, Zlokovic BV. Neurovascular mechanisms and blood–brain barrier disorder in Alzheimer's disease. Acta Neuropathol 2009;118:103-13.
4Paolucci S, Antonucci G, Grasso MG, Bragoni M, Coiro P, De Angelis D, et al. Functional outcome of ischemic and hemorrhagic stroke patients after inpatient rehabilitation: A matched comparison. Stroke 2003;34:2861-5.
5Behl C, Moosmann B. Oxidative nerve cell death in Alzheimer's disease and stroke: Antioxidants as neuroprotective compounds. Biol Chem 2002;383:521-36.
6Ritz MF, Curin Y, Mendelowitsch A, Andriantsitohaina R. Acute treatment with red wine polyphenols protects from ischemia-induced excitotoxicity, energy failure and oxidative stress in rats. Brain Res 2008;1239:226-34.
7Osborne NN, Casson RJ, Wood JP, Chidlow G, Graham M, Melena J. Retinal ischemia: Mechanisms of damage and potential therapeutic strategies. Prog Retin Eye Res 2004;23:91-147.
8Taylor RA, Sansing LH. Microglial responses after ischemic stroke and intracerebral hemorrhage. Clin Dev Immunol 2013;2013:746068.
9O'Keefe JH, Bell DS. Postprandial hyperglycemia/hyperlipidemia (postprandial dysmetabolism) is a cardiovascular risk factor. Am J Cardiol 2007;100:899-904.
10Daulatzai MA. Cerebral hypoperfusion and glucose hypometabolism: Key pathophysiological modulators promote neurodegeneration, cognitive impairment, and Alzheimer's disease. J Neurosci Res 2017;95:943-72.
11Jauch EC, Saver JL, Adams HP Jr, Bruno A, Connors JJ, Demaerschalk BM, et al. Guidelines for the early management of patients with acute ischemic stroke: A guideline for healthcare professionals from the American Heart Association/American Stroke Association. Stroke 2013;44:870-947.
12Adams HP Jr., Brott TG, Furlan AJ, Gomez CR, Grotta J, Helgason CM, et al. Guidelines for thrombolytic therapy for acute stroke: A supplement to the guidelines for the management of patients with acute ischemic stroke. A statement for healthcare professionals from a Special Writing Group of the Stroke Council, American Heart Association. Circulation 1996;94:1167-74.
13Marder VJ, Jahan R, Gruber T, Goyal A, Arora V. Thrombolysis with plasmin: Implications for stroke treatment. Stroke 2010;41:S45-9.
14Kidwell CS, Liebeskind DS, Starkman S, Saver JL. Trends in acute ischemic stroke trials through the 20th century. Stroke 2001;32:1349-59.
15Madhavan R, Jacobs BS, Levine SR. Stroke trials: What have we learned? Neurol Res 2002;24 Suppl 1:S27-32.
16Harris S, Sungkar S, Rasyid A, Kurniawan M, Mesiano T, Hidayat R. TOAST subtypes of ischemic stroke and its risk factors: A hospital-based study at cipto mangunkusumo hospital, Indonesia. Stroke Res Treat 2018;2018:9589831.
17Ay H, Furie KL, Singhal A, Smith WS, Sorensen AG, Koroshetz WJ. An evidence-based causative classification system for acute ischemic stroke. Ann Neurol 2005;58:688-97.
18Han SW, Kim SH, Lee JY, Chu CK, Yang JH, Shin HY, et al. A new subtype classification of ischemic stroke based on treatment and etiologic mechanism. Eur Neurol 2007;57:96-102.
19Chang CC, Lee YC, Lin CC, Chang CH, Chiu CD, Chou LW, et al. Characteristics of traditional Chinese medicine usage in patients with stroke in Taiwan: A nationwide population-based study. J Ethnopharmacol 2016;186:311-21.
20Gong X, Sucher NJ. Stroke therapy in traditional Chinese medicine (TCM): Prospects for drug discovery and development. Phytomedicine 2002;9:478-84.
21Chen C, Venketasubramanian N, Gan RN, Lambert C, Picard D, Chan BP, et al. Danqi Piantang Jiaonang (DJ), a traditional Chinese medicine, in poststroke recovery. Stroke 2009;40:859-63.
22Kim H. Neuroprotective herbs for stroke therapy in traditional eastern medicine. Neurol Res 2005;27:287-301.
23Fu Y, Wang Y, Zhang B. Systems pharmacology for traditional Chinese medicine with application to cardio-cerebrovascular diseases. J Tradit Chinese Med Sci 2014;1:84-91.
24Chen YF. Traditional Chinese herbal medicine and cerebral ischemia. Front Biosci (Elite Ed) 2012;4:809-17.
25Bei W, Peng W, Zang L, Xie Z, Hu D, Xu A. Neuroprotective effects of a standardized extract of Diospyros kaki leaves on MCAO transient focal cerebral ischemic rats and cultured neurons injured by glutamate or hypoxia. Planta Med 2007;73:636-43.
26Kwak WJ, Kim JH, Ryu KH, Cho YB, Jeon SD, Moon CK. Effects of gentianine on the production of pro-inflammatory cytokines in male Sprague-Dawley rats treated with lipopolysaccharide (LPS). Biol Pharm Bull 2005;28:750-3.
27Khan MA, Wadud A, Tariq M, Nazamuddin M. Antipyretic activity of crude and aqueous extract of Gule ghaafis (GENTIANA OLIVIERI GRISEB) on yeast induced pyrexia in animal model. Int J Pharm Sci Res 2015;6:3528.
28Mansoor A, Huda S, Asrar M. Evaluation of diuretic activity of extracts of Gentiana oliveri and gentianine in rats. Res Rev J Pharm Pharm Sci 2015;4:240-9.
29Vaidya H, Goyal RK, Cheema SK. Anti-diabetic activity of swertiamarin is due to an active metabolite, gentianine, that upregulates PPAR-γ gene expression in 3T3-L1 cells. Phytother Res 2013;27:624-27.
30Wenjin C, Jianwei W. Protective effect of Gentianine, a compound from Du Huo Ji Sheng Tang, against Freund's complete adjuvant-induced arthritis in rats. Inflammation 2017;40:1401-8.
31Liu XW, Liu SM, Liu CF. Sedative-hypnotic effect of gentianine and its influence on the content of 5-HT, GABA in mouse brain. Lishizhen Med Mater Med Res 2012;2:741-52.
32Tian CW, Cheng YT, Zhang TJ, Yang XW. Anti-mutagenicity of swertiamarin and its metabolite in incubated system of human intestinal flora. Chinese Herb Med 2017;9:92-5.
33Wang AY, Lian LH, Jiang YZ, Wu YL, Nan JX. Gentiana manshurica Kitagawa prevents acetaminophen-induced acute hepatic injury in mice via inhibiting JNK/ERK MAPK pathway. World J Gastroenterol 2010;16:384-91.
34Shabi MM, Uthrapathy S, Raj CD, Krishnamoorthy G, Ravindhran D, Joseph J, et al. Analgesic and anti-arthritic effect of Enicostemma littorale Blume. Adv Biosci Biotechnol 2014;5:1018.
35Oztürk N, Korkmaz S, Oztürk Y, Başer KH. Effects of gentiopicroside, sweroside and swertiamarine, secoiridoids from gentian (Gentiana lutea ssp. symphyandra), on cultured chicken embryonic fibroblasts. Planta Med 2006;72:289-94.
36de Ruyck J, Brysbaert G, Blossey R, Lensink MF. Molecular docking as a popular tool in drug design, an in silico travel. Adv Appl Bioinform Chem 2016;9:1.
37Grebner C, Iegre J, Ulander J, Edman K, Hogner A, Tyrchan C. Binding mode and induced fit predictions for prospective computational drug design. J Chem Inf Model 2016;56:774-87.
38Morris GM, Lim-Wilby M. Molecular docking. Methods Mol Biol 2008;443:365-82.
39Hsin KY, Matsuoka Y, Asai Y, Kamiyoshi K, Watanabe T, Kawaoka Y, et al. systemsDock: A web server for network pharmacology-based prediction and analysis. Nucleic Acids Res 2016;44:W507-13.
40Ballester PJ, Mitchell JB. A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking. Bioinformatics 2010;26:1169-75.
41Kilic E, Spudich A, Kilic U, Rentsch KM, Vig R, Matter CM, et al. ABCC1: A gateway for pharmacological compounds to the ischaemic brain. Brain 2008;131:2679-89.
42Evans CR, Long DL, Howard G, McClure LA, Zakai NA, Jenny NS, et al. C-reactive protein and stroke risk in blacks and whites: The reasons for geographic and racial differences in stroke cohort. Am Heart J 2019;217:94-100.
43Tian YF, Zhou YP, Zhong CK, Buren B, Xu T, Li HM, et al. C-reactive protein level, apolipoprotein B-to-apolipoprotein A-1 ratio, and risks of ischemic stroke and coronary heart disease among inner Mongolians in China. Biomed Environ Sci 2016;29:467-74.
44Pay JB, Shaw AM. Towards salivary C-reactive protein as a viable biomarker of systemic inflammation. Clin Biochem 2019;68:1-8.
45Chen W, Lin A, Yu Y, Zhang L, Yang G, Hu H, et al. Serum soluble ST2 as a novel inflammatory marker in acute ischemic stroke. Clin Lab 2018;64:1349-56.
46Luo Y, Wang Z, Li J, Xu Y. Serum CRP concentrations and severity of ischemic stroke subtypes. Can J Neurol Sci 2012;39:69-73.
47Hamidon BB, Sapiah S, Nawawi H, Raymond AA. The prognostic value of C-reactive protein (CRP) levels in patients with acute ischaemic stroke. Med J Malaysia 2004;59:631-7.
48Słomka A, Świtońska M, Sinkiewicz W, Żekanowska E. Haemostatic factors do not account for worse outcomes from ischaemic stroke in patients with higher C-reactive protein concentrations. Ann Clin Biochem 2017;54:378-85.
49Zhang Q, Chen W, Chen S, Li S, Wei D, He W. Identification of key genes and upstream regulators in ischemic stroke. Brain Behav 2019;9:e01319.