An In-Silico Molecular Docking Analysis of Phytochemicals from Carica papaya, Moringa oleifera, and Tinospora cordifolia as Potential Dengue Virus Inhibitors

Introduction

Dengue virus

Dengue is a globally prevalent arboviral disease transmitted by Aedes mosquitoes, with clinical manifestations ranging from asymptomatic infection to severe dengue characterized by hemorrhage, organ dysfunction, and vascular leakage.¹ Increasing evidence highlights the central role of platelets in dengue pathogenesis. Dengue virus (DENV)–infected platelets actively participate in inflammatory and immunological responses by releasing mediators such as RANTES, macrophage migration inhibitory factor (MIF), and interleukin-1β (IL-1β).^2,3 Elevated levels of these mediators in severe dengue promote leukocyte activation, platelet–leukocyte aggregation, and endothelial dysfunction, ultimately contributing to vascular leakage.^4–9 Thrombocytopenia is a hallmark hematological feature of dengue and correlates strongly with disease severity.^12,13 It is associated with enhanced platelet activation, increased platelet leukocyte interactions, and accelerated clearance of activated or apoptotic platelets by monocytes and macrophages.^4,14,15 These processes collectively underscore the importance of platelet dysfunction in dengue-associated complications.

History and Epidemiology

Historical records indicate that dengue-like illness was first documented in China between 265 and 420 AD, with later outbreaks reported in the West Indies, Central America, and parts of Africa and Asia between the 17th and 18th centuries.⁴⁷ The four classical dengue virus serotypes (DENV-1 to DENV-4) are thought to have evolved through both sylvatic transmission cycles involving non-human primates and mosquitoes, and urban transmission between humans and Aedes mosquitoes, facilitated by human migration and trade.^45,47,48 While some evidence suggests an African origin with global dissemination via historical trade routes, other studies propose emergence from sylvatic cycles in Southeast Asia.^45,47,48 A genetically distinct fifth serotype (DENV-5) was later identified in Malaysia in 2007, with a probable sylvatic origin.^46,50,51

Currently, dengue is endemic in more than 100 countries across tropical and subtropical regions, with a marked increase in incidence over recent decades.^46,52 Southeast Asia remains a hyperendemic region, with all serotypes co-circulating and a large population at risk.^53,54 Countries such as India and Sri Lanka experience recurrent outbreaks, with regional variation in circulating serotypes and significant disease burden.^53–56

Clinical Aspects

DENV infection presents with a broad clinical spectrum ranging from mild dengue to severe disease. Following an incubation period of 4–10 days, patients typically develop acute febrile illness accompanied by myalgia, headache, and malaise.^1,16 Disease progression in severe cases is marked by leukopenia, thrombocytopenia, systemic inflammation, and increased plasma leakage, which may lead to hypotension, bleeding, and organ failure.^1,17 Platelet activation and apoptosis are prominent during dengue infection and are more pronounced in severe disease. Activated platelets exhibit surface expression of P-selectin, CD63, and phosphatidylserine, facilitating interactions with leukocytes and endothelial cells and promoting inflammatory and thrombo-inflammatory responses.^4,15,32 These platelet-mediated processes play a key role in disease severity.

Cycle of Replication

DENV infects multiple host cell types, including monocytes, macrophages, endothelial cells, and platelets, through receptors such as DC-SIGN, heparan sulfate proteoglycans, and mannose receptors.^18–21 Viral entry is mediated by the envelope glycoprotein, followed by endocytosis and translation of viral RNA into structural and non-structural proteins.^22,23 In platelets, DENV binding results in viral RNA accumulation and NS1 expression; however, productive viral replication does not occur. Instead, platelets undergo an abortive infection that triggers inflammatory signaling, platelet activation, and cytokine release, contributing to vascular dysfunction without the production of infectious virions.^2,19,20

Mechanisms of Thrombocytopenia

Dengue-associated thrombocytopenia results from a combination of reduced platelet production and enhanced peripheral platelet clearance.^24,25 Early in infection, transient suppression of megakaryopoiesis may occur due to bone marrow dysfunction, while disease progression is dominated by peripheral mechanisms.^26–28 Peripheral platelet clearance is driven by platelet activation, apoptosis, immune-mediated opsonization, complement activation, and increased platelet adhesion to leukocytes and endothelial cells.^{15,27,32–34} Additional mechanisms, including von Willebrand factor–mediated platelet desialylation and antibody-dependent platelet destruction, further exacerbate platelet loss and correlate with disease severity.^36–41 Collectively, these processes highlight the multifactorial nature of dengue-associated thrombocytopenia and support the exploration of host-targeted molecular strategies aimed at modulating platelet-related pathways involved in dengue pathophysiology.⁴⁴ 

Figure 1: Mechanisms for dengue thrombocytopenia. Thrombocytopenia might be caused by a reduction in megakaryopoiesis or peripheral platelet consumption.     Click here to view Figure

Platelet counts in dengue reach their lowest levels around defervescence and disease progression, even though recovery from acute bone marrow suppression and restoration of hematopoiesis occur before the critical phase, with platelet count normalization seen only during convalescence.^27,32 This temporal mismatch suggests that peripheral platelet clearance plays a major role in dengue-associated thrombocytopenia.^15,21 During infection, platelets exhibit marked activation and apoptotic features, including Translocation of P-selectin and CD63, activation of integrin αIIbβ3, exposure to phosphatidylserine, and mitochondrial dysfunction.^15,21 These changes are more pronounced in severe dengue and are closely linked to enhanced monocyte and macrophage mediated phagocytosis of apoptotic platelets via phosphatidylserine recognition, and platelet-monocyte interactions are facilitated by surface P-selectin and platelet activation.^4,15,32 

Figure 2: The Dengue inflammatory response is significantly influenced by platelets. 2(a) DENV’s genome is translated and duplicated when it binds to platelets via DC-SIGN, resulting in the buildup of viral proteins and fresh viral RNA copies.     Click here to view Figure

Thrombocytopenia in dengue is strongly associated with enhanced platelet interactions with monocytes, other leukocytes, and endothelial cells, leading to increased platelet activation and clearance.^4,10,33,34 Elevated platelet–monocyte and platelet–neutrophil aggregates, platelet adhesion to endothelial cells in organs such as the liver, spleen, and heart, and increased platelet deposition in the microvasculature contribute to disease severity.^4,33–35 DENV infection also promotes endothelial release of von Willebrand factor (vWF), increasing platelet binding, desialylation via GPIbα, and subsequent hepatic clearance.^15,36,37 Antibody-mediated mechanisms further exacerbate thrombocytopenia, as platelet-associated IgG and IgM—particularly anti-NS1 antibodies—cross-react with platelet integrins, enhancing opsonization, complement activation, and platelet destruction.^38–41 Additionally, direct binding of NS1 to platelets activates the complement system, with increased complement activity correlating inversely with platelet counts.^2,42,43 Collectively, dengue-associated thrombocytopenia results from a combination of bone marrow suppression and peripheral mechanisms including platelet activation, immune-mediated clearance, complement lysis, aggregation, and platelet–cell interactions.^15,44

Carica papaya

Carica papaya L. is a fast-growing herbaceous plant of the family Caricaceae, widely cultivated in tropical and subtropical regions. The plant is characterized by a soft, unbranched stem, palmately lobed leaves, and a large fleshy fruit containing numerous seeds. C. papaya is rich in bioactive compounds, including alkaloids (notably carpaine), flavonoids, phenolic acids, and proteolytic enzymes such as papain.⁶² These phytochemicals are reported to exhibit antioxidant, anti-inflammatory, and platelet-modulating properties, which have attracted attention for their potential role in dengue-associated thrombocytopenia. Owing to its diverse pharmacological profile and traditional use in managing febrile illnesses, C. papaya represents a promising source of host-targeted compounds for dengue-related therapeutic exploration.

Moringa oleifera

Moringa oleifera Lam., commonly known as the drumstick tree, is a rapidly growing deciduous plant belonging to the family Moringaceae and distributed across tropical and subtropical regions. The plant contains a wide spectrum of bioactive constituents, including flavonoids (quercetin, kaempferol), isothiocyanates, phenolic acids, vitamins, and essential amino acids.⁶⁴ These compounds are known for their antioxidant, anti-inflammatory, hematopoietic, and immunomodulatory activities. Given the involvement of oxidative stress and immune dysregulation in dengue pathogenesis, M. oleifera phytochemicals are of particular interest as potential modulators of host inflammatory and platelet-related pathways relevant to dengue infection.

Tinospora cordifolia

Tinospora cordifolia (Willd.) Miers is a medicinal climber of the family Menispermaceae, widely distributed in tropical regions of India. The plant is characterized by succulent climbing stems with aerial roots and heart-shaped leaves. It possesses a rich phytochemical profile comprising alkaloids (berberine, palmatine), diterpenoids, glycosides (tinosporaside, cordifolide), flavonoids, and immunomodulatory polysaccharides.⁶³ Traditionally known as “Amrita,” T. cordifolia has been reported to exhibit antipyretic, anti-inflammatory, antioxidant, and immunomodulatory properties. These biological activities support its selection for in-silico evaluation as a potential source of host-directed compounds in dengue-associated inflammatory and immune responses.

In-silico approaches such as molecular docking offer a rapid and cost-effective strategy to predict molecular interactions between viral or host targets and bioactive compounds prior to experimental validation. Medicinal plants such as Carica papaya, Moringa oleifera, and Tinospora cordifolia have been traditionally used in dengue management, particularly for thrombocytopenia and immune modulation. However, limited information is available regarding their molecular interactions with dengue-associated targets. Therefore, the present study aims to computationally evaluate selected phytochemicals from these plants against dengue-related gene targets to identify potential inhibitors and provide a rational basis for further experimental investigation^[60,61].

Given the involvement of plasminogen in platelet dysfunction during dengue infection, targeting PLG through phytochemical-based molecular docking offers a rational in-silico strategy

Materials and Methods

Identification of target genes of both Disease and Phytochemicals

The Disease target genes of Dengue virus are identified and taken from the Mala cards data base website. The plant phytochemical compounds present in Carica papaya, Moringa Oleifera and Tinospora Cordifolia are identified from the website IMPPAT and they further scrutinized based on the Drug likeliness and ADME analysis. The Gene targets of these phytochemical compounds are identified and taken from the Swiss Target predictor website.

Identification of common genes

Using the VENNY 2.0 website, the disease genes from the mala cards and the phytochemical target genes from the Swiss target predictor are used for the Venn analysis to determine the shared target genes.

Identification of proteins and Ligands

The Protein Data Bank website (PDB) is used to identify the proteins associated with the common target genes that were retrieved from Venny. Proteins are chosen for further processing based on their characteristics, such as Organism, Mutations, and Resolution, among others. For molecular docking research, proteins found in humans with resolutions greater than 2.0 and no mutations are often recommended. The phytochemical compounds used in docking research are called ligands, and they may be found on the Pubchem website.

Molecular docking

The molecular docking of these identified proteins are done using the PyRx-0.8 software and the results of binding affinity are obtained from it. The Visualization of the docking study is done using the Biovia discovery studio 2025 software. And at sometimes CB-Dock an online blind docking tool which is used to identify the cur pockets in proteins which are suitable for Flex and Rigid docking.^57,58,59 It is important to emphasize that molecular docking provides predictive insights into binding affinity and interaction patterns, but does not confirm biological efficacy.

Results

Dengue virus Genes

These Dengue virus genes are identified from the Mala card data base website from the Gene cards.

Plant Phytochemicals

These Phytochemicals are obtained from the IMPPAT website and later Scrutinized based on drug likeliness score and ADME analysis data.

Table 1: Selected Plant phytochemicals of Carica papaya, Moringa oleifera and Tinospora cordifolia.

Identification of common genes

The common genes of the disease targets and the selected phytochemical compounds of Carica papaya, Moringa oleifera and Tinospora cordifolia is identified by drawing VENN diagrams for the disease genes and the plant phytochemical targets. The Venn diagram was drawn in the website VENNY 2.0 between disease genes and the selected plant phytochemical target compounds. Venn diagram drawn between disease genes and Carpaine, Palmitic acid, Lauric acid, Hesperetin and Pentadecanoic acid.

Figure 3: 3(a) Venn diagram for the common genes identification between the Dengue virus genes and the Plant phytochemicals of Lauric acid, Hesperetin and Pentadecanoic acid. 3(b)Venn diagram of common genes of Carpaine and Disease targets. 3(c) Venn Diagram of common genes of Palmitic acid and Disease targets.     Click here to view Figure

Table 2: Identified common genes of the plant phytochemicals.

Protein Selection

Plasminogen (PLG) as the common gene target among all the three plants and Protein are identified according to their characters and 8UQ6 with (pdb_00008uq6) id The Human plasminogen protein which bind to the streptococcal surface enolase is selected for further molecular docking studies. This protein has a Resolution of 3.60A with no mutations in Humans. Without mutations and a high resolution value it is easy to use for the studies without any disturbances. The protein is cleaned by removing the Hetero and Water atoms present if any and after used for molecular docking process. 

Figure 4: Structure of the cleaned protein 8UQ6 (pdb_00008uq6) used for the docking Study.     Click here to view Figure

Molecular Docking

The Molecular docking process of the obtained Phytochemical (ligand) compounds Carpaine, Lauric acid, Palmitic acid, Hesperetin and Pentadecanoic acid as they have a similar gene targets PLG and the obtained protein 8UQ6 is commonly used for the 3 ligands. The molecular docking done by using the software’s PyRx and the Biovia Discovery studio 2025. The PyRx software provides the docking data and the binding affinity of the ligand and protein, where the discovery studio is used to visualize the actual site of docking of the Ligand inside the protein chain. The protein 8UQ6 got bind with the 5 ligand compounds. It is important to emphasize that molecular docking provides predictive insights into binding affinity and interaction patterns, but does not confirm biological efficacy.

Table 3: Binding Affinity of the compounds

Visualization Analysis

The Visualization analysis for the 5 different ligands with the 1 targeted protein is done by using the Biovia Discovery studio 2025 software.

Figure5: 5(a-b) Representing the Docking of the ligand Carpaine with the protein chain 8UQ6 along the Hydrogen bonds based on the donor and the acceptor. 5(c) Represents the 2D image of the docking process of Ligand and Protein chain.     Click here to view Figure

Figure6: 6(a-b) Representing the Docking of the ligand Hesperetin with the protein chain 8UQ6 along the Hydrogen bonds based on the donor and the acceptor. 6(c) Represents the 2D image of the docking process of Ligand and Protein chain.     Click here to view Figure

Figure7: 7(a-b) Representing the Docking of the ligand Pentadecanoic acid with the protein chain 8UQ6 along the Hydrogen bonds based on the donor and the acceptor. 7(c) Represents the 2D image of the docking process of Ligand and Protein chain.     Click here to view Figure

Figure8: 8(a-b) Representing the Docking of the ligand Palmitic acid with the protein chain 8UQ6 along the Hydrogen bonds based on the donor and the acceptor. 8(c) Represents the 2D image of the docking process of Ligand and Protein chain.     Click here to view Figure

Figure9: 9(a-b) Representing the Docking of the ligand Lauric acid with the protein chain 8UQ6 along the Hydrogen bonds based on the donor and the acceptor. 9(c) Represents the 2D image of the docking process of Ligand and Protein chain.     Click here to view Figure

Discussion

The present in-silico investigation explored the interaction potential of phytochemicals from Carica papaya, Moringa oleifera, and Tinospora cordifolia with host factors relevant to dengue pathogenesis. Network-based target analysis identified plasminogen (PLG) as a shared molecular target associated with dengue-related pathways and the selected phytochemicals, highlighting its potential relevance in host-directed therapeutic strategies.

Plasminogen is a key regulator of fibrinolysis, inflammation, and vascular integrity, processes that are markedly dysregulated during dengue infection and contribute to thrombocytopenia and plasma leakage. Modulation of PLG activity may therefore influence platelet stability and endothelial function, both of which are central to dengue disease severity. Based on structural quality and biological relevance, human plasminogen (PDB ID: 8UQ6) was selected for molecular docking to evaluate ligand–protein interactions.

Docking analysis demonstrated that carpaine, an alkaloid from Carica papaya, exhibited the highest binding affinity toward PLG, indicating a stable and energetically favorable interaction. This observation provides a plausible molecular basis for previous clinical and experimental reports describing the platelet-supportive effects of C. papaya in dengue-associated thrombocytopenia. Hesperetin from Moringa oleifera also showed a strong binding interaction, suggesting that flavonoid-mediated modulation of host inflammatory or fibrinolytic pathways may contribute to its reported therapeutic potential. Although Tinospora cordifolia is widely recognized for its immunomodulatory and antiviral properties, its phytochemicals displayed comparatively weaker binding affinities toward PLG in the present model, indicating that its effects may be mediated through alternative molecular targets or pathways not captured in this analysis.

Despite these promising findings, the study has inherent limitations. Molecular docking provides predictive insights into ligand–protein interactions but does not confirm biological activity or therapeutic efficacy. The identification of a single common host target does not fully capture the complexity of dengue pathogenesis, which involves multiple viral and host-mediated mechanisms. Furthermore, docking studies do not account for pharmacokinetic behavior, bioavailability, metabolism, or cellular context. Consequently, the results should be interpreted as preliminary evidence supporting further in vitro, in vivo, and clinical investigations to validate the role of these phytochemicals in dengue management. 

Conclusion

The present in-silico study investigated phytochemicals from Carica papaya, Moringa oleifera, and Tinospora cordifolia for their potential interactions with a dengue-associated host target. Molecular docking analysis identified plasminogen as a common target, with carpaine from Carica papaya exhibiting the highest binding affinity, followed by hesperetin from Moringa oleifera. These interactions suggest a favorable molecular basis for the reported platelet-supportive and anti-inflammatory properties of these plants in dengue-associated complications.

While phytochemicals from Tinospora cordifolia showed comparatively weaker interactions with plasminogen in this model, their established immunomodulatory effects may involve alternative molecular pathways. Overall, the findings highlight Carica papaya and Moringa oleifera as promising sources of host-directed compounds relevant to dengue pathophysiology and provide a rational computational framework to support further experimental exploration.

Future studies should prioritize experimental validation of the identified phytochemicals using in vitro assays, including antiviral activity and platelet function models, followed by evaluation in suitable in vivo dengue models. Detailed pharmacokinetic, toxicological, and bioavailability studies will be essential to assess the translational potential of carpaine and hesperetin. Additionally, exploring multi-target host pathways and synergistic phytochemical combinations may provide deeper insight into their therapeutic relevance. Such investigations could facilitate the development of evidence-based, phytochemical-derived adjunct strategies for dengue management.

The promising in silico interactions observed for carpaine and hesperetin warrant further experimental validation through in vitro and in vivo models to confirm their biological relevance and therapeutic potential in dengue-associated complications.

Acknowledgement

The authors sincerely thank Mrs. V. Jhansi Lakshmi for guidance and Vignan Institute of Pharmaceutical Technology for providing necessary facilities.

Funding Sources

The author(s) received no financial support for the research, authorship, and/or publication of this article.

Conflict of Interest

The authors do not have any conflict of interest.

Data Availability Statement

This statement does not apply to this article.

Ethics Statement

This research did not involve human participants, animal subjects, or any material that requires ethical approval.

Informed Consent Statement

This study did not involve human participants, and therefore, informed consent was not required.

Clinical Trial Registration

This research does not involve any clinical trials.

Permission to reproduce material from other sources

Not Applicable 

Author Contributions

Jhansi Lakshmi Varanasi: Guidance and Supervision.

Naga Bharathi Marni: Methodology and Conceptualization.

Sai Sudheer Thatavarthi: Data Collection, Analysis, Molecular Docking, Visualization, Writing – Original Draft.

Mounika Matcha: Review & Editing. 

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