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    Article

    Binding Analysis of Cholesterol and its Derivatives with 13 Chosen Respiratory Allergens: An In-silico Study

    Radhakrishnan Narayanaswamy1★, Biswajit Das1, B S Sachin1★ Corresponding author

    1. 1Department of Biochemistry, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (Deemed to be University), Saveetha University, Thandalam, Chennai, Tamil Nadu, INDIA.

    CORRESPONDENCE

    Radhakrishnan Narayanaswamy

    Department of Biochemistry, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (Deemed to be University), Saveetha University, Thandalam, Chennai-602 105, Tamil Nadu, INDIA.

    kishnanbio07@gmail.com

    Received: 06-02-2026; Revised: 24-04-2026; Accepted: 19-06-2026.

    Volume 18, Issue 4 · pp. 1268–1274 · PUBLISHED Oct-Dec 2026 · DOI: 10.5530/pres.20260217

    ABSTRACT

    Background and Objectives Respiratory allergens are generally non-parasite proteins in nature, which induces more amounts of Immunoglobulin E (Ig E) levels in atopic persons. A steady increasing prevalence of asthma and other allergy related disorders, which has been turn a huge public health issue throughout the globe. In the present investigation, we aimed to study four chosen cholesterol and its derivatives as potent modulating agents against 13 selected respiratory allergens using docking methods. Materials and Methods The 13 chosen respiratory allergens proteins were studied on the docking behaviour with four selected ligands namely i) cholesterol, ii) 17:1 cholesteryl ester, iii) cholesterol formate and iv) cholesterol palmitate by using the swissdock method. In addition to docking, physicochemical properties of 13 chosen allergens proteins were determined using ProtParam web server. Results With reference to physicochemical property analysis, three selected respiratory allergen proteins (Mite allergen Bio t5, Major allergen Can f 1 and Allergen Can f 1) have exhibited instability index value greater (˃) than 40. The docking results revealed that Mite allergen Der f 21.0101 has exhibited the Highest Binding Energy [HBE] with all four target ligands [i) cholesterol (-8.18 kcal/mol); ii) 17:1 cholesteryl ester (-10.48 kcal/mol); iii) cholesterol formate (-8.41 kcal/mol) and iv) cholesterol palmitate (-9.63 kcal/mol)]. Interestingly, Allergen Can f 1 has exhibited amino acids interaction with three target ligands [cholesterol (Pro55); 17:1 cholesteryl ester (Lys131); and cholesterol palmitate (Tyr97)]. Conclusion Thus, the present finding gives new knowledge about the four selected ligands (cholesterol and its derivatives) as potent modulating agents against 13 chosen respiratory allergens, which will aid in developing allergy mitigation strategies.

    KEYWORDS

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    FULL TEXT

    INTRODUCTION

    Allergens are generally non-parasite proteins in nature, which induces more amounts of Immunoglobulin E (Ig E) levels in atopic persons (Kausar et al., 2022; Lin et al.,, 2022). The i) outdoor pollen, ii) molds, iii) indoor mites and iv) air-pollution are the major source of allergens (Ichikawa et al.,, 2009). Apart from these few allergens are reported from “domesticated animals” [like cat, cow, dog, guinea pig, hamster, horse and rabbit] and “pets” [such as American (Periplaneta americana) and German (Blattella germanica) cockroach]. Moreover, mice and rat are also reported to cause occupational allergens in some laboratory animal handlers (Min et al.,, 2023).

    Majority of allergens are regarded as “respiratory allergens” (Min et al.,, 2023). According to recent publication, asthma and allergic rhinitis are the two most popular respiratory allergies and are constantly growing globally (Kausar et al.,, 2022). Blomia tropicallis (Blo t), Dermatophagoides farina (Der f), Dermatophagoides microceras (Der m) and Dermatophagoides pteronyssinus (Der p) are the major House Dust Mites (HDM) species that induce allergic immune reactions or responses which lead to asthma and dermatitis (Ichikawa et al.,, 2005; Tai et al.,, 2018; Hu et al.,, 2022). Moreover, Blattella germanica (Bla g) and Periplaneta americana (Per a) are the two main cockroach species that induce allergic immune reactions (Offermann et al.,, 2014). Furthermore cat (Fel d 7) and dog (Can f 1) are the two major indoor allergens that induce allergic immune responses (Min et al.,, 2023).

    The earlier reports engaged us to carry out the current investigation on 13 chosen respiratory allergens proteins which includes i) House dust mite allergen (Der f 2), ii) Mite allergen Der f 2, iii) Mite allergen Der f 21.0101, iv) Der p 2 allergen, v) Group 2 allergen Bio t2 isoform 1, vi) Peptidase 1 (DERF1), vii) Group 2 allergen Bio t2 isoform 9, viii) Mite allergen Bio t5, ix) Allergen Bla g 4, x) Per a 4 allergen, xi) Major allergen Can f 1, xii) Per a 2 allergen and xiii) Allergen Can f 1

    These above said respiratory allergens proteins were aimed to investigate on the docking behaviour with four selected ligands namely i) cholesterol, ii) 17:1 cholesteryl ester, iii) cholesterol formate and iv) cholesterol palmitate by using the swissdock method, which may help in developing allergy mitigation strategies.

    MATERIALS AND METHODS

    Ligand preparation

    The chemical structures of four selected ligands i) cholesterol (CIDᴑ 5997); ii) 17:1 cholesteryl ester (CIDᴑ 24779603); iii) cholesterol formate (CIDᴑ 165217) and iv) cholesteryl palmitate (CIDᴑ 246520) were downloaded from ᴑPubChem compound database. The ligands structures were drawn and prepared by utilizing ChemDraw 2D and 3D softwares. Thus, these prepared three-dimensional structures were utilized for further swissdock analysis (Srinivasan et al.,, 2023; Victor et al.,, 2023).

    Preparation of target proteins

    The three-dimensional (3-D) structure of respiratory allergens proteins i) House dust mite allergen -Der f 2 (PDB◊ ID: 2FO8 with a resolution of 2.20 Aᵒ); ii) Mite allergen-Der f 2 (UniProt◊◊ ID: Q5TIW2 • Q5TIW2_DERFA); iii) Mite allergen- Der f 21.0101 (UniProt◊◊ ID: B2GM84 · ALL21_DERFA); iv) Der p 2 allergen (UniProt◊◊ ID: Q1H8P8 · Q1H8P8_DERPT); v) Group 2 allergen Bio t2 isoform 1 (UniProt◊◊ ID: A6XEN8 · A6XEN8_BLOTA); vi) Peptidase 1-DERF1 (UniProt◊◊ ID: P16311 · PEPT1_DERFA); vii) Group 2 allergen Bio t2 isoform 9 (UniProt◊◊ ID: A6XEP6 · A6XEP6_BLOTA); viii) Mite allergen Bio t5 (UniProt◊◊ ID: O96870 · ALL5_BLOTA); ix) Allergen Bla g 4 (UniProt◊◊ ID: P54962 · BLG4_BLAGE); x) Per a 4 allergen (UniProt◊◊ ID: Q1M0Y5 · Q1M0Y5_PERAM); xi) Major allergen Can f 1 (UniProt◊◊ ID: O18873 · ALL1_CANLF); xii) Per a 2 allergen (UniProt◊◊ ID: E7BQV5 · E7BQV5_PERAM); and xiii) Allergen Can f 1 (PDB◊ ID: 7DRU with a resolution of 2.50 Aᵒ) was downloaded from Protein Data Bank (PDB◊) and UniProt◊◊ databases respectively. ‘A’ chain of these two proteins (House dust mite allergen -Der f 2 and Allergen Can f 1) were prepared independently by removing other chains, ligands (heteroatoms), and even the crystallographically observed ‘water’ (H2O) molecules by utilizing UCSF Chimera software tool (Vishnupriya et al.,, 2024).

    Determination of physicochemical properties

    ProtParam web server was utilized to determine the physicochemical properties of 13 respiratory allergen proteins [House dust mite allergen (Der f 2), Mite allergen Der f 2, Mite allergen Der f 21.0101, Der p 2 allergen, Group 2 allergen Bio t2 isoform 1, Peptidase 1 (DERF1), Group 2 allergen Bio t2 isoform 9, Mite allergen Bio t5, Allergen Bla g 4, Per a 4 allergen, Major allergen Can f 1, Per a 2 allergen and Allergen Can f 1] Whole protein sequence of 13 allergens proteins (expect House dust mite allergen -Der f 2 and Allergen Can f 1, where “A” chain) was given separately as input data (Vishnupriya et al.,, 2024; Narayanaswamy et al.,, 2024).

    Docking study

    The molecular docking analysis was carried out for 13 chosen respiratory allergens proteins with four target ligands (cholesterol, 17:1 cholesteryl ester, cholesterol formate and cholesteryl palmitate) using the Swissdock free web server. Finally, “PyMOL” software was used to determine the binding site of best-docked pose for each ligand (Prakash et al.,, 2023). Docking protocol was validated using quercetin as standard drug. And the root mean square deviation [RMSD◊◊] analysis of all the docked complexes (four target ligands) was separately compared with that of quercetin (standard drug) docked complex for each chosen respiratory allergen protein by utilizing the ‘align’ command in “PyMOL” software (Ramsbottom et al.,, 2018; Narayanaswamy et al.,, 2024).

    RESULTS

    In the current investigation, only one chosen respiratory allergen protein (Der p 2 allergen) has exhibited theoretical Isoelectric Point (PI) value greater (˃) than 7.0 (as shown in Table 1). Interestingly, three selected allergen proteins (Mite allergen Bio t5, Major allergen Can f 1 and Allergen Can f 1) have shown instability index value greater (˃) than 40. Similarly, in the present investigation all the chosen respiratory allergen proteins (except four- Group 2 allergen Bio t2 isoform 1, Group 2 allergen Bio t2 isoform 9, Mite allergen Der f 2, Der p 2 allergen) have exhibited lowest grand average of hydropathicity (GRAVY) value.

    Table 1: Represents the physicochemical properties of 13 chosen respiratory allergen proteins using ProtParam web server.
    Protein nameMW◘P1◊NR■PRᴑׁExt.co1▲▲Ext.co2▼▼Instability IndexAliphatic IndexGRAVY҉
    Allergen Bla g 4209276.482523276402739028.0272.42-0.567
    Allergen Can f 1178535.662118130751295045.9876.01-0.571
    Der p 2 allergen158907.591617118351146031.56105.480.055
    Group 2 allergen Bio t2 isoform 1151806.1716144845447020.7893.310.128
    Group 2 allergen Bio t2 isoform 9152756.1716144845447024.2999.510.182
    House dust mite allergen (Der f 2)140446.4517168855848021.0894.42-0.181
    Major allergen Can f 1192485.952119130751295043.4587.47-0.349
    Mite allergen Bio t5156425.2726193105298041103.43-0.548
    Mite allergen Der f 2158076.93171710345997026.56105.480.062
    Mite allergen Der f 21.0101159654.9727209970997032.6692.5-0.285
    Peptidase 1 (DERF1)364355.663730536655329038.5379.31-0.389
    Per a 2 allergen381905.463225330703232029.7781.88-0.005
    Per a 4 allergen205173.99268431104286016.469.23-0.262

    The current Swissdock investigation showed that Mite allergen Der f 21.0101 has shown the Maximum Binding Energy [MBE] (-8.18 kcal/mol) with the first target ligand cholesterol. On the other hand, Mite allergen Bio t5 has exhibited the minimum binding energy (-6.03 kcal/mol) with cholesterol (as shown in Table 2). Surprisingly, only two respiratory allergen proteins (Allergen Can f 1 and per a 4 allergen) have shown amino acid interactions with the cholesterol (as shown in Table ).

    Table 2: The Swissdock binding energy analysis of 13 selected respiratory allergen proteins with the cholesterol ligand using Swissdock method.
    Protein nameSwissdock binding energy (-kcal/mol)Interactions of amino acids residuesBond distance (Aᵒ)RMSD◊◊ compared with quercetin docked complex (Aᵒ) value
    Allergen Bla g 47.19NHBI◘-0
    Allergen Can f 17.3Pro5520
    Der p 2 allergen6.6NHBI◘-0
    Group 2 allergen Bio t2 isoform 17.33NHBI◘-0
    Group 2 allergen Bio t2 isoform 96.58NHBI◘-0
    House dust mite allergen (Derf 2)6.14NHBI◘-0
    Major allergen Can f 17.06NHBI◘-0
    Mite allergen Bio t56.03NHBI◘-0
    Mite allergen Der f 26.73NHBI◘-0
    Mite allergen Der f 21.01018.18NHBI◘-0
    Peptidase 1 (DERF1)7.08NHBI◘-0
    Per a 2 allergen7.84NHBI◘-0
    Per a 4 allergen7.17Lys353.50

    The present Swissdock analysis showed that Mite allergen Der f 21.0101 has exhibited the Highest Binding Energy [HBE] (-10.48 kcal/mol) with the second target ligand 17:1 cholesteryl ester. On the other hand, Mite allergen Der f 2 has shown the least binding energy (-6.95 kcal/mol) with the 17:1 cholesteryl ester (as shown in Table 3). Interestingly, only four respiratory allergen proteins (Allergen Bla g 4, Allergen Can f 1, Mite allergen Bio t5 and Peptidase 1 (DERF1)) have shown amino acid interactions with the 17:1 cholesteryl ester (as shown in Table ).

    Table 3: The Swissdock binding energy analysis of 13 selected respiratory allergen proteins with the 17:1 cholesteryl ester ligand using Swissdock method.
    Protein nameSwissdock binding energy (-kcal/mol)Interactions of amino acids residuesBond distance (Aᵒ)RMSD◊◊ compared with quercetin docked complex (Aᵒ) value
    Allergen Bla g 47.17Lys145 Gln1493.3 2.82.01
    Allergen Can f 19.43Lys1312.94.98
    Der p 2 allergen7.99NHBI◘-2.42
    Group 2 allergen Bio t2 isoform 16.92NHBI◘-2.49
    Group 2 allergen Bio t2 isoform 97.38NHBI◘-3.13
    House dust mite allergen (Derf 2)7.05NHBI◘-4.92
    Major allergen Can f 17.94NHBI◘-2.67
    Mite allergen Bio t57.52Lys213.43.3
    Mite allergen Der f 26.95NHBI◘-2.07
    Mite allergen Der f 21.010110.48NHBI◘-2.38
    Peptidase 1 (DERF1)8.56Arg1033.31.54
    Per a 2 allergen8.32NHBI◘-1.51
    Per a 4 allergen7.39NHBI◘-7.47

    The current Swissdock investigation showed that Mite allergen Der f 21.0101 has shown the Maximum Binding Energy [MBE] (-8.41 kcal/mol) with the third target ligand cholesterol formate. On the other hand, House dust mite allergen (Derf 2) has exhibited the minimum binding energy (-6.44 kcal/mol) with the cholesterol formate (as shown in Table 4a). Surprising, only three respiratory allergen proteins (Allergen Bla g 4, Der p 2 allergen and Group 2 allergen Bio t2 isoform 9) have shown amino acid interactions with the cholesterol formate (as shown in Table 4a).

    Table 4a: The Swissdock binding energy analysis of 13 selected respiratory allergen proteins with the cholesterol formate ligand using Swissdock method.
    Protein nameSwissdock binding energy (-kcal/mol)Interactions of amino acids residuesBond distance (Aᵒ)RMSD◊◊ compared with quercetin docked complex (Aᵒ) value
    Allergen Bla g 47.37Gln693.30.59
    Allergen Can f 16.91NHBI◘-5.59
    Der p 2 allergen7.4Ala13 Val153.3 3.40.95
    Group 2 allergen Bio t2 isoform 16.62NHBI◘-2.06
    Group 2 allergen Bio t2 isoform 96.52Val113.44.99
    House dust mite allergen (Derf 2)6.44NHBI◘-1.57
    Major allergen Can f 16.65NHBI◘-1.71
    Mite allergen Bio t56.86NHBI◘-6.05
    Mite allergen Der f 26.47NHBI◘-2.53
    Mite allergen Der f 21.01018.41NHBI◘-2.32
    Peptidase 1 (DERF1)7.27NHBI◘-0.77
    Per a 2 allergen7.87NHBI◘-2.93
    Per a 4 allergen6.51NHBI◘-10.5

    The present Swissdock analysis showed that Mite allergen Der f 21.0101 has exhibited the Highest Binding Energy [HBE] (-9.63 kcal/mol) with the fourth target ligand cholesteryl palmitate. On the other hand, Mite allergen Bio t5 has shown the least binding energy (-6.50 kcal/mol) with the cholesterol palmitate. Interestingly, only three respiratory allergen proteins (Allergen Can f 1, Major allergen Can f 1 and Peptidase 1 (DERF1)) have shown amino acid interactions with the cholesterol palmitate (as shown in Table 4b).

    Table 4b: The Swissdock binding energy analysis of 13 selected respiratory allergen proteins with the cholesterol palmitate ligand using Swissdock method.
    Protein nameSwissdock binding energy (-kcal/mol)Interactions of amino acids residuesBond distance (Aᵒ)RMSD◊◊ compared with quercetin docked complex (Aᵒ) value
    Allergen Bla g 48.78NHBI◘-2.5
    Allergen Can f 18.94Tyr973.55.13
    Der p 2 allergen7.74NHBI◘-3.14
    Group 2 allergen Bio t2 isoform 17.56NHBI◘-7.54
    Group 2 allergen Bio t2 isoform 98.65NHBI◘-6.07
    House dust mite allergen (Derf 2)7.47NHBI◘-4.84
    Major allergen Can f 18.96Thr823.22.81
    Mite allergen Bio t56.5NHBI◘-6.75
    Mite allergen Der f 27.76NHBI◘-2.19
    Mite allergen Der f 21.01019.63NHBI◘-2.14
    Peptidase 1 (DERF1)8.52Lys353.56.98
    Per a 2 allergen8.68NHBI◘-2.05
    Per a 4 allergen7.32NHBI◘-6.8

    DISCUSSION

    Respiratory allergens come across two lipid-based barriers namely pulmonary surfactant and luminal plasma membrane of airway (respiratory tract) epithelial cells (Min et al.,, 2023). Recent year’s theory reveals that “epithelial barrier disruptions” leads to both allergy and auto-immune responses (Akdis, 2021).

    Bienboire-Frosini and colleagues (2020) had demonstrated that steroids [i) Androstenone, ii) Androstenedione, iii) Androstenol, iv) Corticosterone, v) Dehydroepiandrosterone, vi) Deoxycorticosterone, vii) Dihydrotestosterone, viii) Estradiol, ix) Estrone, x) Hydroxyprogesterone, xi) Pregnenolone, xii Progesterone and xiii) Testosterone] and fatty acids [i) Capric acid, ii) Dodecanal, iii) Dodecanol, iv) Ethyl laurate, v) Hexadecanamide, vi) Isobutyric acid, vii) Lauric acid, viii) Linoleic acid, ix) Methyl palmitate, x) Myristic acid, xi) Nonanamide, xii) Octadecanamide, xiii) Oleic acid, xiv) Palmitic acid and xv) Tetradecanol] bind with the major cat allergen Fel d1.

    Similarly, Min and co-workers (2023) had reported that 88 fatty acids bind with Can f 1 and Fel d7. Thus, in the present investigation, four target ligands namely i) cholesterol, ii) 17:1 cholesteryl ester, iii) cholesterol formate and iv) cholesterol palmitate was chosen for the docking study.

    With regard to physiochemical properties, only one chosen respiratory allergen protein (Der p 2 allergen) has exhibited theoretical isoelectric point (PI) value greater (˃) than 7.0. This result reveals that Der p 2 allergen protein is basic in nature, which was in good agreement with earlier reports (Kausar et al.,, 2022; Vishnupriya et al.,, 2024). Similarly, three selected respiratory allergen proteins (Mite allergen Bio t5, Major allergen Can f 1 and Allergen Can f 1) have shown instability index value greater (˃) than 40. This finding suggests these are instability protein in nature, which was in good correlation with previous reports (Kausar et al.,, 2022; Vishnupriya et al.,, 2024).

    With reference to docking, Mite allergen Der f 21.0101 has exhibited the Highest Binding Energy [HBE] with all four target ligands [i) cholesterol (-8.18 kcal/mol); ii) 17:1 cholesteryl ester (-10.48 kcal/mol); iii) cholesterol formate (-8.41 kcal/mol) and iv) cholesterol palmitate (-9.63 kcal/mol). In contrast, Mite allergen Bio t5 has shown the least binding energy with two target ligands [i) cholesterol (-6.03 kcal/mol) and ii) cholesterol palmitate (-6.50 kcal/mol)] respectively. This finding was on par with earlier report, where 13 steroids have docked with major cat allergen Fel d1 (Bienboire-Frosini et al.,, 2020). Similarly, cholesterol ligand has shown interaction with Pro55 and Lys35 amino acid residues of Allergen Can f 1 and per a 4 allergen respectively.

    Interestingly, 17:1 cholesteryl ester ligand has shown interaction with Lys145 and Gln149; Lys131; Lys21 and Arg103 amino acid residues of Allergen Bla g 4; Allergen Can f 1; Mite allergen Bio t5 and Peptidase 1 (DERF1). This result was in good correlation with previous report, where 88 fatty acids bind with Lys131 amino acid residue of Can f 1 allergen (Min et al.,, 2023).

    Similarly, cholesterol formate ligand has shown interaction with Gln69; Ala13 and Val15; Val11 amino acid residues of Allergen Bla g 4; Der p 2 allergen and Group 2 allergen Bio t2 isoform 9. This result was in close correlation with previous report, where replacement (mutation) of valine (Val) instead of alanine (Ala) at 16th amino acid position in wild-type Der p2 allergen showed significant increase in cholesterol binding capacity (Reginald & Chew, 2019).

    Furthermore, cholesterol palmitate ligand has shown interaction with Tyr97; Thr82; Lys35 amino acid residues of Allergen Can f 1; Major allergen Can f 1 and Peptidase 1 (DERF1). This finding was in close agreement with previous report, where Cys35 was reported instead of Lys35 in Der f 1 allergen (Chruszcz et al.,, 2009; Lin et al.,, 2023).

    The present finding is only based on docking (in silico) method which gives new insight into the four chosen ligands and their interactions with 13 selected respiratory allergen proteins. However, further in vitro ANS (8-anilino-1-naphthalene sulfonate) binding assay experiments are needed to confirm allergen proteins interactions with four chosen ligands.

    CONCLUSION

    In the current investigation, the four chosen ligands (cholesterol, 17:1 cholesteryl ester, cholesterol formate and cholesterol palmitate) have shown the potential to dock with 13 selected respiratory allergen proteins. Interestingly, Allergen Can f 1 has exhibited amino acids interaction with three target ligands [cholesterol (Pro55); 17:1 cholesteryl ester (Lys131); and cholesterol palmitate (Tyr97)]. Similarly, Allergen Bla g 4 has exhibited amino acids interaction with two target ligands [17:1 cholesteryl ester (Lys145, Gln149); and cholesterol formate (Gln69)]. Furthermore Peptidase 1 (DERF1) has exhibited amino acids interaction with two target ligands [17:1 cholesteryl ester (Arg103); and cholesterol palmitate (Lys35)]. Thus, the current finding gives new understanding about the four chosen ligands as binding agents with 13 selected respiratory allergen proteins, which may help in developing allergy mitigation approaches.

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    Narayanaswamy, R., Das, B., & Sachin, B. S. (2026). Binding Analysis of Cholesterol and its Derivatives with 13 Chosen Respiratory Allergens: An In-silico Study. Pharmacognosy Research, 18(4), 1268–1274. https://doi.org/10.5530/pres.20260217