|
1
|
Pang J, Yu Q, Wei H, Xia X, Lin Z, Du X, Wang C. Theoretical study on the structures and pharmacokinetic evaluation of verticillane-type diterpenes from soft coral Heteroxenia ghardaqensis. BMC Chem 2025; 19:122. [PMID: 40350455 PMCID: PMC12067919 DOI: 10.1186/s13065-025-01499-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Accepted: 05/02/2025] [Indexed: 05/14/2025] Open
Abstract
The density functional theory (DFT) method ωB97XD/6-311++G(2d, p) was applied to calculate and analyze the geometric structures, spectral properties, frontier molecular orbitals, and molecular electrostatic potentials of 14 novel verticillane-type diterpenoids isolated from the soft coral Heteroxenia ghardaqensis. Additionally, reaction index analysis was conducted using conceptual density functional theory, and the drug-likeness of these compounds was evaluated using two different pharmacokinetic prediction platforms. The results showed that the hydroxyl hydrogen, secondary amine hydrogen, carbonyl oxygen, and hydroxyl oxygen in the molecules of these compounds have relatively high reactivity. Compounds 5, 8, and 9 exhibit significant anti-inflammatory activity and have similar electronic delocalization distribution characteristics, showing good stability and excellent biological activity, among which compound 5 demonstrates more significant drug potential. For compounds 2, 8, and 12 with hepatoprotective activity, through the analysis of comprehensive pharmacokinetic parameters and molecular docking data, compound 12 is considered more suitable as a potential hepatoprotective drug.
Collapse
Affiliation(s)
- Jiangmei Pang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Qinzhe Yu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Huining Wei
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Xiaoyun Xia
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zishan Lin
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Xiandong Du
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Chaojie Wang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| |
Collapse
|
|
2
|
Progress and Impact of Latin American Natural Product Databases. Biomolecules 2022; 12:biom12091202. [PMID: 36139041 PMCID: PMC9496143 DOI: 10.3390/biom12091202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Natural products (NPs) are a rich source of structurally novel molecules, and the chemical space they encompass is far from being fully explored. Over history, NPs have represented a significant source of bioactive molecules and have served as a source of inspiration for developing many drugs on the market. On the other hand, computer-aided drug design (CADD) has contributed to drug discovery research, mitigating costs and time. In this sense, compound databases represent a fundamental element of CADD. This work reviews the progress toward developing compound databases of natural origin, and it surveys computational methods, emphasizing chemoinformatic approaches to profile natural product databases. Furthermore, it reviews the present state of the art in developing Latin American NP databases and their practical applications to the drug discovery area.
Collapse
|
|
3
|
Shao S, Wang X, She J, Zhang H, Pang X, Lin X, Zhou X, Liu Y, Li Y, Yang B. Diversified Chaetoglobosins from the Marine-Derived Fungus Emericellopsis sp. SCSIO41202. Molecules 2022; 27:molecules27061823. [PMID: 35335187 PMCID: PMC8948984 DOI: 10.3390/molecules27061823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 11/16/2022] Open
Abstract
Two undescribed cytochalasins, emeriglobosins A (1) and B (2), together with nine previously reported analogues (3–11) and two known tetramic acid derivatives (12, 13) were isolated from the solid culture of Emericellopsis sp. SCSIO41202. Their structures, including the absolute configurations of their stereogenic carbons, were fully elucidated based on spectroscopic analysis and the calculated ECD. Some of the isolated compounds were evaluated for their cytotoxicity and enzyme inhibitory activity against acetylcholinesterase (AChE) in vitro. Among them, 8 showed potent AChE inhibitory activity, with an IC50 value of 1.31 μM, and 5 showed significant cytotoxicity against PC-3 cells, with an IC50 value of 2.32 μM.
Collapse
Affiliation(s)
- Surun Shao
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica/Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (S.S.); (X.W.); (J.S.); (X.P.); (X.L.); (X.Z.)
- Pharmacy School, Guilin Medical University, Guilin 541004, China;
| | - Xueni Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica/Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (S.S.); (X.W.); (J.S.); (X.P.); (X.L.); (X.Z.)
| | - Jianglian She
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica/Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (S.S.); (X.W.); (J.S.); (X.P.); (X.L.); (X.Z.)
| | - Han Zhang
- Pharmacy School, Guilin Medical University, Guilin 541004, China;
| | - Xiaoyan Pang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica/Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (S.S.); (X.W.); (J.S.); (X.P.); (X.L.); (X.Z.)
| | - Xiuping Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica/Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (S.S.); (X.W.); (J.S.); (X.P.); (X.L.); (X.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xuefeng Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica/Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (S.S.); (X.W.); (J.S.); (X.P.); (X.L.); (X.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yonghong Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica/Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (S.S.); (X.W.); (J.S.); (X.P.); (X.L.); (X.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Correspondence: (Y.L.); (Y.L.); (B.Y.); Tel.: +86-20-89023174 (B.Y.)
| | - Yunqiu Li
- Pharmacy School, Guilin Medical University, Guilin 541004, China;
- Correspondence: (Y.L.); (Y.L.); (B.Y.); Tel.: +86-20-89023174 (B.Y.)
| | - Bin Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica/Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (S.S.); (X.W.); (J.S.); (X.P.); (X.L.); (X.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Correspondence: (Y.L.); (Y.L.); (B.Y.); Tel.: +86-20-89023174 (B.Y.)
| |
Collapse
|
|
4
|
Zhao L, Zhang LL, Miao XX, Li JX, Lin HW, Jiao WH. New NF-κB Inhibitory Steroids from the Marine Sponge Dysidea avara Collected from the South China Sea. Chem Biodivers 2021; 18:e2100578. [PMID: 34499797 DOI: 10.1002/cbdv.202100578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/20/2021] [Indexed: 11/07/2022]
Abstract
Chemical investigation of the marine sponge Dysidea avara, collected from the South China Sea, yielded 13 steroids, including nine new (1-9) and four known (10-13) ones. The new structures were elucidated as (3S,14R)-3,14-dihydroxycholesta-5,8-dien-7-one (1), (22E,24R)-7α-ethoxy-5α,6α-epoxyergosta-8(14),22-dien-3β-ol (2), 3β-hydroxy-7α-ethoxy-5α,6α-epoxy-8(14)-cholestene (3), 3β,5α-dihydroxy-6α-ethoxychofesta-7,9(11)-diene (4), 3β,5α-dihydroxy-6β-ethoxycholest-7-ene (5), (22E,24R)-24-ethoxy-3β,5α-dihydroxy-6β-ethoxyergosta-7,22-diene (6), (22E)-3β,5α-dihydroxy-6β-ethoxycholesta-7,22-diene (7), 24-ethoxy-3β,5α-dihydroxy-6β-ethoxycholest-7-ene (8 and 9), by extensive spectroscopic analyses, such as HR-ESI-MS, 1D and 2D NMR data. The absolute configuration of 1 was assigned by comparison the experimental ECD spectra with the calculated ones. Among the 13 metabolites, compounds 1, 4, 11, 12, and 13 showed NF-κB inhibitory activities in human HER-293 cells with IC50 values of 6.4, 18.7, 8.1, 9.6, and 7.5 μM, respectively. Preliminary structure-activity relationship analysis unveiled that the conjugated ketones or unsaturated double bonds might be the functional groups for the five active steroids.
Collapse
Affiliation(s)
- Lu Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Li-Ling Zhang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Xian-Xian Miao
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jia-Xin Li
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Hou-Wen Lin
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Wei-Hua Jiao
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| |
Collapse
|