1
|
Rashid ZA, Bardaweel SK. Novel Matrix Metalloproteinase-9 (MMP-9) Inhibitors in Cancer Treatment. Int J Mol Sci 2023; 24:12133. [PMID: 37569509 PMCID: PMC10418771 DOI: 10.3390/ijms241512133] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Matrix metalloproteinases (MMPs) belong to a family of zinc-dependent proteolytic metalloenzymes. MMP-9, a member of the gelatinase B family, is characterized as one of the most intricate MMPs. The crucial involvement of MMP-9 in extracellular matrix (ECM) remodeling underscores its significant correlation with each stage of cancer pathogenesis and progression. The design and synthesis of MMP-9 inhibitors is a potentially attractive research area. Unfortunately, to date, there is no effective MMP-9 inhibitor that passes the clinical trials and is approved by the FDA. This review primarily focuses on exploring the diverse strategies employed in the design and advancement of MMP-9 inhibitors, along with their anticancer effects and selectivity. To illuminate the essential structural characteristics necessary for the future design of novel MMP-9 inhibitors, the current narrative review highlights several recently discovered MMP-9 inhibitors exhibiting notable selectivity and potency.
Collapse
Affiliation(s)
| | - Sanaa K. Bardaweel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Jordan, Amman 11942, Jordan
| |
Collapse
|
2
|
Asirvatham RD, Hwang DH, Prakash RLM, Kang C, Kim E. Pharmacoinformatic Investigation of Silymarin as a Potential Inhibitor against Nemopilema nomurai Jellyfish Metalloproteinase Toxin-like Protein. Int J Mol Sci 2023; 24:ijms24108972. [PMID: 37240317 DOI: 10.3390/ijms24108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Jellyfish stings pose a major threat to swimmers and fishermen worldwide. These creatures have explosive cells containing one large secretory organelle called a nematocyst in their tentacles, which contains venom used to immobilize prey. Nemopilema nomurai, a venomous jellyfish belonging to the phylum Cnidaria, produces venom (NnV) comprising various toxins known for their lethal effects on many organisms. Of these toxins, metalloproteinases (which belong to the toxic protease family) play a significant role in local symptoms such as dermatitis and anaphylaxis, as well as systemic reactions such as blood coagulation, disseminated intravascular coagulation, tissue injury, and hemorrhage. Hence, a potential metalloproteinase inhibitor (MPI) could be a promising candidate for reducing the effects of venom toxicity. For this study, we retrieved the Nemopilema nomurai venom metalloproteinase sequence (NnV-MPs) from transcriptome data and modeled its three-dimensional structure using AlphaFold2 in a Google Colab notebook. We employed a pharmacoinformatics approach to screen 39 flavonoids and identify the most potent inhibitor against NnV-MP. Previous studies have demonstrated the efficacy of flavonoids against other animal venoms. Based on our analysis, Silymarin emerged as the top inhibitor through ADMET, docking, and molecular dynamics analyses. In silico simulations provide detailed information on the toxin and ligand binding affinity. Our results demonstrate that Silymarin's strong inhibitory effect on NnV-MP is driven by hydrophobic affinity and optimal hydrogen bonding. These findings suggest that Silymarin could serve as an effective inhibitor of NnV-MP, potentially reducing the toxicity associated with jellyfish envenomation.
Collapse
Affiliation(s)
- Ravi Deva Asirvatham
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Du Hyeon Hwang
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | | | - Changkeun Kang
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Euikyung Kim
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| |
Collapse
|
3
|
Preciado LM, Comer J, Núñez V, Rey-Súarez P, Pereañez JA. Inhibition of a Snake Venom Metalloproteinase by the Flavonoid Myricetin. Molecules 2018; 23:molecules23102662. [PMID: 30332829 PMCID: PMC6222685 DOI: 10.3390/molecules23102662] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/22/2018] [Accepted: 09/25/2018] [Indexed: 11/16/2022] Open
Abstract
Most of the snakebite envenomations in Central and South America are caused by species belonging to Bothrops genus. Their venom is composed mainly by zinc-dependent metalloproteinases, responsible of the hemorrhage characteristic of these envenomations. The aim of this study was to determine the inhibitory ability of ten flavonoids on the in-vitro proteolytic activity of Bothrops atrox venom and on the hemorrhagic, edema-forming and myonecrotic activities of Batx-I, the most abundant metalloproteinase isolated from this venom. Myricetin was the most active compound, exhibiting an IC 50 value of 150 μ M and 1021 μ M for the inhibition of proteolytic and hemorrhagic activity, respectively. Independent injection experiments, with a concentration of 1600 μ M of myricetin administered locally, immediately after toxin injection, demonstrated a reduction of 28 ± 6 % in the hemorrhagic lesion. Additionally, myricetin at concentrations 800, 1200 and 1600 μ M promoted a reduction in plasma creatine kinase activity induced by Batx-I of 21 ± 2 % , 60 ± 5 % and 63 ± 2 % , respectively. Molecular dynamics simulations coupled with the adaptive biasing method suggest that myricetin can bind to the metalloproteinase active site via formation of hydrogen bonds between the hydroxyl groups 3', 4' and 5' of the benzyl moiety and amino acid Glu143 of the metalloproteinase. The hydroxyl substitution pattern of myricetin appears to be essential for its inhibitory activity. Based on this evidence, myricetin constitutes a candidate for the development of inhibitors to reduce local tissue damage in snakebite envenomations.
Collapse
Affiliation(s)
- Lina María Preciado
- Programa de Ofidismo/Escorpionismo, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia.
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - Vitelbina Núñez
- Programa de Ofidismo/Escorpionismo, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia.
- Escuela de Microbiología, Universidad de Antioquia, UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia.
| | - Paola Rey-Súarez
- Programa de Ofidismo/Escorpionismo, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia.
| | - Jaime Andrés Pereañez
- Programa de Ofidismo/Escorpionismo, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 050010, Colombia.
| |
Collapse
|
4
|
Hou J, Zou Q, Wang Y, Gao Q, Yao W, Yao Q, Zhang J. Screening for the selective inhibitors of MMP-9 from natural products based on pharmacophore modeling and molecular docking in combination with bioassay experiment, hybrid QM/MM calculation, and MD simulation. J Biomol Struct Dyn 2018; 37:3135-3149. [PMID: 30079817 DOI: 10.1080/07391102.2018.1509019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Matrix metalloproteinase-9 (MMP-9) has been considered as an attractive target involving cancer therapy. In this study, the 3D QSAR pharmacophore model of MMP-9 inhibitors is built, and its reliability is subsequently validated based on different methods. The built pharmacophore model consists of the four chemical features, including two hydrogen bond acceptors (HBA), one hydrophobic (HY), and one ring aromatic (RA). Among them, both HY and RA are found to be especially important features because they involve the interactions of inhibitors with the S1' pocket of MMP-9, which determines the selectivity of MMP-9 inhibitors. By combining pharmacophore model with molecular docking, the virtual screening is carried out to identify the selective MMP-9 inhibitors from natural products. The four potential selective MMP-9 inhibitors of natural products are found. One of them was used to carry out the bioassay experiment inhibiting MMP-9, and the estimated IC50 value of only 26.94 µM clearly shows its strongly inhibitory activity; besides, both the hybrid quantum mechanics/molecular mechanics (QM/MM) calculation and the molecular dynamics simulation are performed to examine the reliability regarding the binding mode of this inhibitor with MMP-9 active sites predicted by molecular docking. All the screened four natural products are found to well bind with the MMP-9 active sites by different kinds of interactions. Finally, the ADMET properties of screened four natural products are assessed. These screened MMP-9 inhibitors of natural products could be used as the lead compounds to perform structural modifications and optimizations in the future work. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Jiaying Hou
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Qing Zou
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Yijun Wang
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Qi Gao
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Wenhui Yao
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Qizheng Yao
- c School of Pharmacy , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Ji Zhang
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , People's Republic of China.,b State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing , People's Republic of China
| |
Collapse
|
5
|
Hydroxyl-related differences for three dietary flavonoids as inhibitors of human purine nucleoside phosphorylase. Int J Biol Macromol 2018; 118:588-598. [PMID: 29894785 DOI: 10.1016/j.ijbiomac.2018.06.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/07/2018] [Accepted: 06/09/2018] [Indexed: 01/19/2023]
Abstract
In this work, the hydroxyl-related differences of binding properties and inhibitory activities of dietary flavonoids, namely chrysin, baicalein and apigenin against purine nucleoside phosphorylase (PNP) were investigated. It was found that the hydroxylation on position C4' of chrysin (→apigenin) mildly decreased the binding affinities for PNP, whereas on the position C6 of chrysin (→baicalein) significantly increased binding affinities. Comparatively, the hydroxylation on position C4' and C6 greatly improved their PNP inhibitory effects. The IC50 values of apigenin and baicalein were 6.09 × 10-5 M and 8.94 × 10-5 M, respectively, which is significantly lower than that of chrysin (2.13 × 10-4 M). Results from molecular modeling revealed that there are two binding sites, i.e. active site (major) and tryptophan site (minor) on PNP, and the binding of these flavonoids might induce a serious conformational destabilization of PNP as a result of altering the micro-environment and morphology by flavonoids.
Collapse
|
6
|
Wang Y, Yang L, Hou J, Zou Q, Gao Q, Yao W, Yao Q, Zhang J. Hierarchical virtual screening of the dual MMP-2/HDAC-6 inhibitors from natural products based on pharmacophore models and molecular docking. J Biomol Struct Dyn 2018; 37:649-670. [PMID: 29380672 DOI: 10.1080/07391102.2018.1434833] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The dual-target inhibitors tend to improve the response rate in treating tumors, comparing with the single-target inhibitors. Matrix metalloproteinase-2 (MMP-2) and histone deacetylase-6 (HDAC-6) are attractive targets for cancer therapy. In this study, the hierarchical virtual screening of dual MMP-2/HDAC-6 inhibitors from natural products is investigated. The pharmacophore model of MMP-2 inhibitors is built based on ligands, but the pharmacophore model of HDAC-6 inhibitors is built based on the experimental crystal structures of multiple receptor-ligand complexes. The reliability of these two pharmacophore models is validated subsequently. The hierarchical virtual screening, combining these two different pharmacophore models of MMP-2 and HDAC-6 inhibitors with molecular docking, is carried out to identify the dual MMP-2/HDAC-6 inhibitors from a database of natural products. The four potential dual MMP-2/HDAC-6 inhibitors of natural products, STOCK1 N-46177, STOCK1 N-52245, STOCK1 N-55477, and STOCK1 N-69706, are found. The studies of binding modes show that the screened four natural products can simultaneously well bind with the MMP-2 and HDAC-6 active sites by different kinds of interactions, to inhibit the MMP-2 and HDAC-6 activities. In addition, the ADMET properties of screened four natural products are assessed. These found dual MMP-2/HDAC-6 inhibitors of natural products could serve as the lead compounds for designing the new dual MMP-2/HDAC-6 inhibitors having higher biological activities by carrying out structural modifications and optimizations in the future studies.
Collapse
Affiliation(s)
- Yijun Wang
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Limei Yang
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Jiaying Hou
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Qing Zou
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Qi Gao
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Wenhui Yao
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Qizheng Yao
- c School of Pharmacy , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| | - Ji Zhang
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China.,b State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing , 210009 , People's Republic of China
| |
Collapse
|
7
|
Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 332] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
Collapse
Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
| |
Collapse
|
8
|
Multiple receptor-ligand based pharmacophore modeling and molecular docking to screen the selective inhibitors of matrix metalloproteinase-9 from natural products. J Comput Aided Mol Des 2017. [PMID: 28623487 DOI: 10.1007/s10822-017-0028-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Matrix metalloproteinase-9 (MMP-9) is an attractive target for cancer therapy. In this study, the pharmacophore model of MMP-9 inhibitors is built based on the experimental binding structures of multiple receptor-ligand complexes. It is found that the pharmacophore model consists of six chemical features, including two hydrogen bond acceptors, one hydrogen bond donor, one ring aromatic regions, and two hydrophobic (HY) features. Among them, the two HY features are especially important because they can enter the S1' pocket of MMP-9 which determines the selectivity of MMP-9 inhibitors. The reliability of pharmacophore model is validated based on the two different decoy sets and relevant experimental data. The virtual screening, combining pharmacophore model with molecular docking, is performed to identify the selective MMP-9 inhibitors from a database of natural products. The four novel MMP-9 inhibitors of natural products, NP-000686, NP-001752, NP-014331, and NP-015905, are found; one of them, NP-000686, is used to perform the experiment of in vitro bioassay inhibiting MMP-9, and the IC50 value was estimated to be only 13.4 µM, showing the strongly inhibitory activity of NP-000686 against MMP-9, which suggests that our screening results should be reliable. The binding modes of screened inhibitors with MMP-9 active sites were discussed. In addition, the ADMET properties and physicochemical properties of screened four compounds were assessed. The found MMP-9 inhibitors of natural products could serve as the lead compounds for designing the new MMP-9 inhibitors by carrying out structural modifications in the future.
Collapse
|
9
|
Abstract
Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP. Based on previous computational experience, we provide in this chapter technical and methodological guidelines that may be useful to and stimulate other researchers to perform molecular dynamics simulations to help address unresolved questions concerning the molecular mode of action of MMPs.
Collapse
Affiliation(s)
- Natalia Díaz
- Dpto. Química Física y Analítica, Universidad de Oviedo, Oviedo, Spain.
| | - Dimas Suárez
- Dpto. Química Física y Analítica, Universidad de Oviedo, Oviedo, Spain
| |
Collapse
|
10
|
Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chem Rev 2016; 116:5520-66. [DOI: 10.1021/acs.chemrev.5b00630] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|