In Silico Molecular Docking Analysis, Cytotoxicity, and Antibacterial Activities of Constituents of Fruits of Cucumis dipsaceus

Teshale Assefa; Hailemichael Tesso; Venkatesha Perumal Ramachandran; Leta Guta; Taye B Demissie; Japheth O Ombito; Rajalakshmanan Eswaramoorthy; Yadessa Melaku

doi:10.1021/acsomega.3c08866

In Silico Molecular Docking Analysis, Cytotoxicity, and Antibacterial Activities of Constituents of Fruits of Cucumis dipsaceus

ACS Omega. 2023 Dec 19;9(1):1945-1955. doi: 10.1021/acsomega.3c08866. eCollection 2024 Jan 9.

Authors

Teshale Assefa¹, Hailemichael Tesso¹, Venkatesha Perumal Ramachandran¹, Leta Guta², Taye B Demissie³, Japheth O Ombito³, Rajalakshmanan Eswaramoorthy⁴, Yadessa Melaku¹

Affiliations

¹ Department of Applied Chemistry, Adama Science and Technology University, P.O. Box, Adama 1888, Ethiopia.
² Department of Applied Biology, Adama Science and Technology University, P.O. Box, Adama 1888, Ethiopia.
³ Department of Chemistry, University of Botswana, Gaborone P/Bag 00704, Botswana.
⁴ Department of Biomaterials, S Aveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600 077, India.

Abstract

Cucumis dipsaceus (Cucurbitaceae) is a plant traditionally used against diarrhea, teeth-ach, wounds, stomach ache, meningitis, and cancer. The extracts of C. dipsaceus after silica gel column chromatography gave nine compounds identified using spectroscopic methods such as hexacosane (1), octadecane (2), 17-(-5-ethyl-2,6-dihydroxy-6-methylhept-3-en-2-yl)-9-(hydroxymethyl)-13-methylcyclopenta[α]phenanthren-3-ol (3), erythrodiol (4), (9,12)-propyl icosa-9,12-dienoate (5), α-spinasterol (6), 16-dehydroxycucurbitacin (7), cucurbitacin D (8), and 23,24-dihydroisocucurbitacin D (9). Compounds 3 and 4 are new to the genus Cucumis. α-Spinasterol showed better inhibition zone diameter = 13.67 ± 0.57, 15.00 ± 0.10, and 13.33 ± 0.57 mm against Escherichia coli, Pseudomonas aeruginosa, and Streptococcus pyogenes compared with the other tested samples. α-Spinasterol (-8.0 kcal/mol) and 3 (-7.6 kcal/mol) displayed high binding affinity against DNA Gyrase compared to ciprofloxacin (-7.3 kcal/mol). α-Spinasterol and 16-dehydroxycucurbitacin showed better binding affinity against protein kinase. The cytotoxicity results revealed that the EtOAc extract showed the highest potency with IC₅₀ = 16.05 μg/mL. 16-Dehydroxycucurbitacin showed a higher binding affinity (-7.7 kcal/mol) against human topoisomerase IIβ than etoposide. The cytotoxicity and antibacterial activities and in silico molecular docking analysis displayed by the constituents corroborate the traditional use of the plant against bacteria and cancer.