Trends Sci. 2026; 23(8): 13647

Introduction

Calophyllum is a widely recognized genus consisting of over 200 species of shrubs and evergreen trees and has ecological and medicinal value. These tropical trees are found all over the regions of Asia, Africa, the Pacific Islands, and America, which are usually grown in mangroves, lowland forests, and coastal areas. Morphologically, Calophyllum species are characterized by glossy, leathery leaves, round-shaped fruits, and resinous latex, which have been used for various purposes and in traditional medicine for ages. The timber is also used in construction and furniture owing to its strength and beauty in its aesthetic value [1,2].

Calophyllum species were cultivated to produce different bioactive compounds, including xanthones, coumarins, triterpenoids, and flavonoids. These chemicals have different uses in medicine. However, researchers have pointed out that coumarins have significant antiviral, antibacterial, anti-inflammatory, and anticancer properties [3-5]. Coumarins, mostly located in the leaves, bark, and seeds of these plants, have been the subject of both modern pharmacological research and traditional medicine. For instance, C. inophyllum species plants, known in the local community as "Bintangor Laut,” have properties for healing wounds, burns, and skin infections [6]. Additionally, the seeds have skin-healing properties and reduce scarring.

Recent studies have validated the medicinal properties of several Calophyllum coumarins. One of the most innovative prototypes in anti-AIDS research, Calanolide A (2), was identified back in 1992 from C. lanigerum var. austrocoriaceum and has been proven to inhibit Human Immunodeficiency Virus-1 (HIV-1) reverse transcriptase (RT) [7]. This antiviral activity of HIV-1 RT stems from its dependency on non-nucleoside reverse transcriptase inhibitors (NNRTIs) and is known to inhibit HIV-1 RT severely. Its structure with the hydrophobic benzopyran core and other substituent groups has bested the resonance cavities of RT, thus calanolides have turned the enzyme HIV replication into a dead-end pathway. This has positioned Calanolide A (2) to be sought for further development as an NNRTI and has brought attention to Calophyllum species to be further explored for their compounds as a novel antiviral framework [8,9].

HIV is a specialized type of retrovirus that breaks into the immune system by infecting CD4⁺ T-cells, which slowly leads to Acquired Immunodeficiency Syndrome (AIDS), if untreated. The virus propagates by assimilating its genome into a host cell DNA sequence through the actions of RT, IN, and other viral enzymes. With the introduction of antiretroviral therapy (ART), like NNRTIs, protease (PR) and integrase (IN) inhibitors, it has significantly extended the lifespan of people with HIV [10]. However, issues like drug resistance and the presence of dormant viral reservoirs demand constant evolution of treatment techniques [11,12]. One avenue of cross-disciplinary research employs monoclonal antibodies, therapeutic vaccines, natural compounds derived from plants, and gene-editing technologies such as CRISPR/Cas9, aimed at deeper suppression of vital HIV proteins and scaffolding for future drugs. Although a definitive treatment standard remains elusive, the objective transitions to achieving a conclusive cure. However, there is optimism that subsequent advancements in research, together with future technological innovations, will enable the permanent inhibition or inactivation of the virus [13-15].

Considering this, there is growing interest in finding small molecules that can specifically target viral enzymes. Natural products are especially interesting for this goal because they exhibit a wide range of structures and their biological activities are well known. Computational methods, particularly molecular docking, provide an effective method to anticipate the interactions of these drugs with essential viral proteins and to rank the most promising candidates before experimental validation. These in silico techniques allow researchers to better understand the different parts of the NNRTI-binding pocket and identify the most promising ones to explore further. The integration of docking studies with conventional methodologies and experimental assays has augmented the understanding of Calophyllum coumarins as potential antiviral agents, thereby establishing the Calophyllum genus as a central focus for the development of innovative pharmaceuticals and therapeutics.

Coumarins are widespread in nature and appear in many plant families; species of Calophyllum are a well-known example. Their parent framework, C₉H₆O₂, belongs to the benzo-α-pyrone group, or sometimes referred to as 1,2-benzopyrones. Chemically, a coumarin arises when a benzene ring fuses with a pyrone ring carrying a carbonyl group. This union creates the lactone skeleton that defines the compound’s reactivity and much of its biological behavior [16]. With minor structural modifications such as a methyl or hydroxyl substituent at different ring positions, many related molecules are generated, with each showing its own physical or pharmacological character [17,18]. Researchers usually classify plant-derived coumarins by their core structure: simple, prenylated, geranylated, pyrano, furano, sesquiterpenyl, oligomeric, and a few miscellaneous coumarins, as summarized in Figure 1 [19,20]. These structural groups account for much of the biological activity observed in Calophyllum extracts. Historically, the word “Coumarin” itself comes from the French “Coumarou” the old name for the Tonka bean (Dipteryx odorata), where Vogel first isolated the compound in 1820 [19].

Figure 1 Chemical structures of isolated coumarins.

Coumarins have been of interest for many years since they smell pleasant and have a wide range of medicinal uses [17]. Extracts from Calophyllum species exhibit intricate molecular patterns and are frequently employed as chemical identifiers for the genus [21]. Among them, calanolides and inophyllums stand out for their significant antiviral and anticancer actions. Several dipyrano-tetracyclic coumarins, such as calanolides, inophyllums, and cordatolides, also inhibit HIV through the NNRTI site of the virus [22]. The coexistence of these metabolites makes Calophyllum a promising source of new therapeutic candidates. In traditional healing, Calophyllum preparations have long been used to relieve inflammation and infections, and modern pharmacological work has confirmed many of those early observations. Demonstrated antiviral, anticancer, and anti-inflammatory effects now provide scientific backing for their ethnomedicinal use. Previous studies have suggested that certain structural features, such as the presence of aromatic substituents at the C-3 position of the coumarin core connected through an amide linkage, may enhance anti-inflammatory activity [23]. Biosynthesis of these compounds proceeds through the shikimate-derived phenylpropanoid route. Key enzymes such as phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), and coumarin synthases are involved in crucial reactions, including hydroxylation, cyclization, and methylation, that diversify the skeletons [24]. The pathway begins with phenylalanine, converted by PAL into cinnamic acid, which is then transformed through a series of steps into coumarins and related phenolics. Most of these compounds accumulate in the leaves of Calophyllum [21].

The objective of this review is to critically evaluate the current knowledge on coumarin compounds derived from the genus Calophyllum and their potential as anti-HIV agents. This study aims to compile and analyse reported phytochemical data, experimental bioassays, and molecular docking investigations related to Calophyllum coumarins and their interactions with key HIV targets such as reverse transcriptase (RT), and integrase (IN). By integrating findings from both experimental and computational studies, this review highlights important structural features that may influence binding interactions and biological activity. Furthermore, the review highlights existing research gaps and proposes future directions for the development of Calophyllum-derived coumarins as promising candidates for anti-HIV drug discovery and design.

Materials and methods

Search strategy

A systematic literature search was conducted to identify relevant studies on Calophyllum coumarins and their biological activities. The databases PubMed, Scopus, Web of Science, and Google Scholar were searched using Boolean operators combining the keywords (“Calophyllum” OR “Calophyllum coumarins”) AND (“anti-HIV” OR “antiviral”) AND (“molecular docking” OR “reverse transcriptase” OR “integrase” OR “1FK9” OR “3LPT”). The search was limited to peer-reviewed articles published in English between June 1968 and October 2025. Titles and abstracts were screened to assess their relevance to the topic, and the reference lists of selected articles were manually examined to identify additional relevant publications that may not have been captured during the initial database search.

Preparation of ligands

A total of 60 coumarins that have been isolated from the Malaysian genus Calophyllum were retrieved from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/), and ChemDraw Ultra 12.0 was used to hand sketch the structures of compounds that were not found in PubChem; all these ligands were drawn, saved as SDF (Structure Data File) format and transformed into 3-dimensional structures, and geometry-optimized using Chem3D 23.1.1 (64-bit) before docking. The reference compounds Efavirenz (PubChem CID: 64139) and Raltegravir (PubChem CID: 54671008) were retrieved from the PubChem database in SDF format and then converted to PDB files using Open Babel integrated in PyRx 0.9.8 software. The openbabel tool embedded in PyRx was used to perform energy minimization for each ligand separately using the default parameters of steepest descent steps 100 with step size 0.02 (Å) and conjugate gradient steps 100 with step size 0.02 (Å), whereas the update interval was fixed at 10 [53]. Before or during molecular docking, energy minimization is an important step to make the structure less rigid and get rid of any steric interference for more accurate results [54].

Preparation of the target protein

The crystal structures of HIV-1 RT and IN were sourced from the Protein Data Bank with PDB IDs: 1F9K and 3LPT, respectively. Before docking, water molecules, other atoms, and ligand cocrystallized with the protein were removed with the Biovia Discovery Studio 2021 Client. The protein structure was minimized by using the conjugate gradient algorithm and the AMBER force field with UCSF Chimera 1.10.1 [55].

Molecular docking

The PyRx virtual screening tool and the AutoDock Vina Wizard 4.2 were used for molecular docking. The grid box was adjusted to cover the binding sites, with the center size set to X: 23.5181, Y: 22.1833, Z: 21.1452 for 1FK9 and X: Y: Z: 15.4789 for 3LPT. This made sure that the ligand could fit into the pocket where it would bind. An exhaustive number of 8 was employed to make the docking results more accurate. The docked compounds were then evaluated based on their lowest binding energy (kJ/mol). The binding energy (ΔG) in kJ/mol of isolated ligands and standard drugs was determined by duplicating the docking experiments. The 2D and 3D depictions of the docking complexes were generated using Discovery Studio 2021 [54].

Drug-likeness and ADMET prediction

The drug-likeness properties of the selected compounds were evaluated using Lipinski’s rule of five through the SwissADME web server (www.swissadme.ch) [56,57]. Their pharmacokinetic properties, including absorption, distribution, metabolism, excretion, and toxicity (ADMET), were further assessed using the pkCSM platform (https://biosig.lab.uq.edu.au/pkcsm/) [58].

Results and discussion

Coumarins from Calophyllum species

The Calophyllum genus is known to contain various coumarin derivatives from its plant components, including stem bark, leaves, latex, and even fruits. From the species of this genus, many of these compounds have already been isolated, proving the inherent chemical diversity of Calophyllum. One of the most common coumarin compounds in C. recurvatum, C. andersonii, and C. inophyllum is Soulattrolide (1), which is found in stem bark and latex, making it more abundant in different species and parts of the plant. In addition, Inophyllum A (2), Inophyllum B (3), and Inophyllum P (5), which have been isolated in the leaves and fruit kernels of C. inophyllum, are the other most significant coumarin types. This suggests that some species of Calophyllum not only have multiple coumarins but also readily distribute them in various parts of the plant. Such distribution may be associated with the plant’s ecological adaptations or as a means of defense mechanism as coumarins have a vital role in protecting the plant against herbivore and pathogen invasion [59].

Calanolide A (6) and Calanolide B (7) are dominant in Calophyllum species. Such compounds were obtained from the latex, twigs, fruits, and stem bark of C. lanigerum and C. teysmannii. The fact that these calanolide types are frequently found in plant parts and in various studies highlights their significance for the genus. A pattern of chemical conservation among the many Calophyllum species is highlighted by this recurrent isolation, indicating that specific biosynthetic pathways are continuously active in several of the genus’s members [28].

In the leaves of C. lanigerum, other coumarins such as Cordatolide A (14) and Cordatolide B (15) have been identified, whereas the fruits and twigs of the same species also produced 12-Methoxycalanolide A (10) and 12-Methoxycalanolide B (11). Such intraspecific variation regarding the sources and types of coumarins suggests that species of Calophyllum have biosynthetic pathways that can synthesize diverse forms of coumarins in different tissues and organs of the plant. Table 1 provides a systematic summary of the coumarins extracted from Calophyllum species which illustrates a clear variety in both the types of compounds and parts of the plant. The widespread occurrence of some coumarins in many species and tissues indicates the great chemical potential of the genus. These results demonstrate that Calophyllum deserves intense attention and exploration for future research.

Table 1 Coumarins isolated from several Calophyllum species.

Biological activities of coumarins

Calanolide C (8), Calanolide F (13), along with Calanolide E2 (30), represent another group of Calophyllum coumarins with notable anti-HIV activity. Although their binding affinities are somewhat lower than those of Calanolide A (6) and B (7), these compounds still demonstrate meaningful inhibition of HIV-1 reverse transcriptase. Their inclusion in studies broadens the range of Calophyllum compounds that may be optimized and developed into effective antiviral agents. Moreover, their diverse structural characteristics offer valuable data for designing next-generation inhibitors [32-34]. The biological activities described in Table 2 include significant cytotoxic, anti-inflammatory, and antibacterial properties. Calophyllolide (17) and Inophyllum E (19), for instance, exhibit significant toxicity to human epidermoid cancer cells [60]. These results suggest that coumarins derived from Calophyllum may possess applications beyond antiviral therapy. The documented actions create avenues for further investigation into their roles as anticancer and antibacterial agents, along with their therapeutic efficacy in inflammatory conditions. In summary, the bioactivity highlights the exceptional potential of Calophyllum coumarins, particularly in the context of HIV treatment. Some of the compounds that have been proven to inhibit HIV-1 RT significantly are Soulattrolide (1), Calanolide A (6), and Calanolide B (7). These drugs have low IC₅₀ and EC₅₀ values [33,34,61,62]. Inophyllum derivatives also have a high potency and distinctive structure, further substantiating that Calophyllum is a valuable source of bioactive compounds. Studies to date cover a range of coumarins isolated from different Calophyllum species, underscoring how important this genus has become in natural-product chemistry and the ongoing search for new therapeutic agents.

Table 2 Biological activities of several Calophyllum phytochemicals.

Molecular docking

In this study, molecular docking was employed to explore whether coumarins from Calophyllum could play a part in suppressing HIV replication. The approach allowed a closer examination of the key protein-ligand contacts that define how these molecules interact with their targets. From such analyses, researchers can infer the chemical traits that appear to make certain coumarins more reactive or selective than others. During the viral life cycle, the enzymes RT and IN act in sequence, where RT converts the viral RNA into DNA, while IN inserts that DNA into the host genome. Interfering with either step effectively halts replication. The docking evaluation of 60, therefore, provides a useful starting point for designing anti-HIV candidates. Table 3 summarizes the binding affinities of the tested coumarin derivatives, and Figures 2 and 3 illustrate the corresponding 2D and 3D ligand-protein complexes.

Table 3 Binding energies (in kJ/mol) of coumarin derivatives against 1F9K and 3LPT.

Figure 2 2D and 3D conformation view of (36); (A), (19) (B), (18) (C), (41) (D) (20) (E) and Efavirenz (F) against 1F9K.

Figure 3 2D and 3D conformation view of (43) (A), (20) (B), (42) (C), (28) (D), (19) (E), and Raltegravir (F) against 3LPT.

HIV-1 RT target

Docking with RT demonstrated that Efavirenz (−27.20 kJ/mol) interacted mainly through π-π and hydrophobic contacts with residues Tyr181, Lys101, Val179, and Ile180, forming a representative non-nucleoside inhibitor (NNRTI) binding profile. In comparison, Calophyllum coumarins exhibited comparable with remarkable affinities.

Teysmanone A (36) (−33.05 kJ/mol) established conventional hydrogen bonds between its carbonyl group and Arg172 (5.65 Å) and van der Waals interactions with Tyr181 and Ile180, complemented by π-alkyl contacts with Val179 (5.08 Å) and Lys101 (5.96 Å). Its extended conjugation and prenylated ring contribute to amide π-stacking and van der Waals stabilization within the NNRTI pocket. Such contacts mediate the relevant conformational flexibility of the domain polymerase, allowing for the proper positioning of incoming nucleotides.

Inophyllum E (19) (−31.38 kJ/mol) donated hydrogen bonds to Arg172 (3.92 - 6.38 Å) through conventional hydrogen interaction. Tyr181 (4.85 Å) and formed π-π T-shaped stacking with the aromatic system, while Val179 (6.15 Å) anchors the coumarin core within the π-alkyl linking.

Inophyllum C (18) and Inophyllum G-1 (41) (−31.38 kJ/mol) engaged in π-π stacking with Tyr181 and hydrophobic contacts with Val179 and Lys101 (4.27 - 4.96 Å). These interactions are known to allosterically restrict the conformational flexibility of the thumb subdomain of HIV-1 RT, a region responsible for positioning the nucleic acid duplex during polymerization.

Soulattrolone (20) (−30.96 kJ/mol) displayed a bonding within the carbonyl of ligands and Arg172 (4.20 Å) through conventional hydrogen linkage and other interactions as well. These ligands collectively occupied the NNRTI allosteric pocket by exhibiting significant RT inhibitory activity through a combination of polar and hydrophobic interactions.

HIV-1 IN target

For HIV-1 IN, the control ligand raltegravir (−26.36 kJ/mol) interacted through conventional hydrogen bonding with Thr125 (3.77 - 4.76 Å) and Gln95 (4.38 Å), alongside π-alkyl and π-sigma, which interacted with Ala129 (4.21 Å) and Ala128 (4.50 Å), respectively. Typically, it is inhibitors that chelate or block the DDE catalytic triad that is responsible for DNA-strand transfer. In contrast, several coumarin analogues displayed stronger affinities.

Inophyllum A 4-bromobenzoate (43) (−29.71 kJ/mol) formed a carbon-hydrogen bond between carbonyl oxygen and Thr125 (3.65 Å), while π-π stacking with Tyr99 (4.61 Å). Several alkyl and π-alkyl interactions were observed within the range 4.28 - 5.66 Å. While the bromophenyl substituent enhanced π-electron delocalization, strengthening hydrophobic and van der Waals interactions that could hinder access to the viral DNA-binding groove.

Soulattrolone (20) (−29.29 kJ/mol) formed a conventional hydrogen bond with Thr125 (4.09 Å) and π-alkyl contacts with Tyr99 and Leu102 (4.28 - 5.41 Å), occupying the catalytic loop that initiates strand transfer. At the same time, Ala128 formed an alkyl interaction within the active site cleft of the aromatic system of the coumarin core.

Inophyllum G-2 (42) (−29.29 kJ/mol) showed π-π stacking with Trp132 and π-alkyl contacts with Ala98, including alkyl interaction with Leu102 and Ala128. These interactions suggest that its prenylated side chain fits into the hydrophobic DNA-binding channel, potentially disrupting the coordination geometry of the Mg²⁺ cofactors required for catalytic activity.

Mammea A/AB dioxalanocyclo F (28) (−28.87 kJ/mol) displayed a carbon-hydrogen bond with Ala129 (3.61 Å) and π-alkyl interactions with Tyr99, Ala129, and Ala128 (4.20 - 4.84 Å), indicating stabilization of the dioxolane ring system through this interaction.

Inophyllum E (19) (−28.87 kJ/mol) exhibited a conventional hydrogen bond with Thr125 and several π-alkyl interactions with Ala128 and Tyr99 together with van der Waals contacts, suggesting a close aromatic fit within the catalytic pocket of integrase.

In addition to this study, calanolide A (6), a known anti-HIV coumarin from C. lanigerum, exhibited moderate binding toward both HIV-1 RT (−6.6) and IN (−5.9) compared to the newly evaluated analogues. Its lower affinity is likely due to a limited hydrophobic surface and a lack of prenyl or brominated substituents that enhance π-stacking stabilization. Nevertheless, its conserved binding orientation supports its role as a reliable benchmark for validating the docking outcomes of Calophyllum coumarins. Overall, the docking analysis of Calophyllum-derived compounds shows significant affinity for both the HIV-1 reverse-transcriptase (RT) and integrase (IN) binding pockets, in several instances performing even better than the reference drugs Efavirenz and Raltegravir. Interaction maps reveal a mix of π–π stacking, π–alkyl, and hydrogen-bond contacts. Residues which include Tyr181, Lys101, and Arg172 in RT, as well as Thr125, Ala128, and Trp132 in IN, seem to be crucial for keeping these complexes stable. Molecules with larger conjugated aromatic systems or prenyl-type side groups tend to bind better.

Drug-likeness and ADMET prediction

The drug-likeness of the selected 12 phytocompounds, chosen based on their docking scores, was evaluated using Lipinski’s rule of five (RO5) to estimate their potential suitability as orally active drug candidates. The calculated physicochemical parameters, including molecular weight (MW), lipophilicity (LogP), number of rotatable bonds (NORTB), hydrogen bond acceptors (HBA), hydrogen bond donors (HBD), and Lipinski’s rule violations, are summarized in Table 4. Efavirenz and Raltegravir were included as reference drugs for comparison. Several of the investigated phytocompounds showed drug-likeness profiles comparable to those of these reference compounds.

Table 4 Predicted drug-likeness ability for some chosen compounds.

^aMW: Molecular weight, ^bLogP: Partition coefficient, ^cNORTB: Rotatable bonds, ^dHBA: H-bond acceptors, ^eHBD: H-bond donors, ^fLipinski’s violation: 0 = good

Most of the studied phytocompounds, Calanolide A (6), Inophyllum C (18), Inophyllum E (19), Soulattrolone (20), Mammea A/AB dioxalanocyclo F (28), Teysmanone A (36), Isocalanone (38), Inophyllum G-1 (41), and Inophyllum G-2 (42), exhibited favorable drug-likeness characteristics and satisfied the RO5 criteria, including LogP ≤ 5, MW ≤ 500 Da, HBAs ≤ 10, and HBDs ≤ 5. However, Inophyllum A 4-bromobenzoate (43) showed 2 violations of Lipinski’s rule, mainly due to its higher MW and increased lipophilicity (LogP = 6.23). These features may limit its oral bioavailability. However, such deviations do not necessarily exclude its potential as a bioactive molecule, particularly if alternative formulation or delivery approaches are considered. Overall, the results suggest that most of the selected phytocompounds possess physicochemical properties consistent with drug-like molecules, supporting their further investigation in pharmacokinetic and biological studies.

The ADMET properties of the selected 12 phytocompounds were further evaluated to gain further insight into their predicted pharmacokinetic behavior and safety profiles. Parameters related to absorption, distribution, metabolism, excretion, and toxicity are summarized in Table 5. Efavirenz and Raltegravir were included as reference compounds to facilitate comparison. All phytocompounds exhibited relatively low predicted aqueous solubility, with water solubility values ranging from −3.01 to −5.35 log mol/L. Despite this, the compounds showed consistently high predicted human intestinal absorption, with most values exceeding 95%. This suggests that, although solubility may be limited, efficient oral absorption is still likely. Low aqueous solubility may therefore be addressed through appropriate formulation strategies to support oral bioavailability [58,70]. The detailed distribution indicated that most phytocompounds showed negative log BB values, indicating limited ability to cross the blood-brain barrier. This was supported by low predicted CNS permeability values, suggesting minimal central nervous system exposure. Note that, Efavirenz exhibited higher BBB permeability, consistent with its known pharmacological profile.

Table 5 Predicted ADMET characteristics for some selected compounds.