1
|
Jana S, Banerjee S, Baidya SK, Ghosh B, Jha T, Adhikari N. A combined ligand-based and structure-based in silico molecular modeling approach to pinpoint the key structural attributes of hydroxamate derivatives as promising meprin β inhibitors. J Biomol Struct Dyn 2024:1-17. [PMID: 38165455 DOI: 10.1080/07391102.2023.2298394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 10/16/2023] [Indexed: 01/03/2024]
Abstract
Human meprin β is a Zn2+-containing multidomain metalloprotease enzyme that belongs to the astacin family of the metzincin endopeptidase superfamily. Meprin β, with its diverse tissue expression pattern and wide substrate specificity, plays a significant role in various biological processes, including regulation of IL-6R pathways, lung fibrosis, collagen deposition, cellular migration, neurotoxic amyloid β levels, and inflammation. Again, meprin β is involved in Alzheimer's disease, hyperkeratosis, glomerulonephritis, diabetic kidney injury, inflammatory bowel disease, and cancer. Despite a crucial role in diverse disease processes, no such promising inhibitors of meprin β are marketed to date. Thus, it is an unmet requirement to find novel promising meprin β inhibitors that hold promise as potential therapeutics. In this study, a series of arylsulfonamide and tertiary amine-based hydroxamate derivatives as meprin β inhibitors has been analyzed through ligand-based and structure-based in silico approaches to pinpoint their structural and physiochemical requirements crucial for exerting higher inhibitory potential. This study identified different crucial structural features such as arylcarboxylic acid, sulfonamide, and arylsulfonamide moieties, as well as hydrogen bond donor and hydrophobicity, inevitable for exerting higher meprin β inhibition, providing valuable insight for their further future development.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sandeep Jana
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Sandip Kumar Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| |
Collapse
|
2
|
Eltaib L, Alzain AA. Discovery of dual-target natural inhibitors of meprins α and β metalloproteases for inflammation regulation: pharmacophore modelling, molecular docking, ADME prediction, and molecular dynamics studies. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023:1-23. [PMID: 37955603 DOI: 10.1080/1062936x.2023.2277425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023]
Abstract
Meprins, zinc-dependent metalloproteinases belonging to the metzincin family, have been associated with various inflammatory diseases due to their abnormal expression and activity. In this study, we utilized pharmacophore modelling to identify crucial features for discovering potential dual inhibitors targeting meprins α and β. We screened four pharmacophoric features against a library of 270,540 natural compounds from the Zinc database, resulting in 84,092 matching compounds. Molecular docking was then performed on these compounds, targeting the active sites of meprins α and β. Docking results revealed six compounds capable of interacting with both isoforms, with binding affinities ranging from -10.0 to -10.5 kcal/mol and -6.9 to -9.9 kcal/mol for meprin α and β, respectively. Among these compounds, ZINC000008790788 and ZINC000095099469 displayed superior docking scores and MM-GBSA binding free energy compared to reference ligands. Furthermore, these two compounds exhibited acceptable predicted pharmacokinetic properties and stable interactions with meprins α and β during molecular dynamics simulations. This study presents a comprehensive approach for identifying potential dual inhibitors of meprin α and β, offering insights into the development of therapeutic interventions for inflammatory diseases associated with meprin dysregulation.
Collapse
Affiliation(s)
- L Eltaib
- Department of Pharmaceutics, Faculty of Pharmacy, Northern Border University, Arar, Saudi Arabia
| | - A A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, Sudan
| |
Collapse
|
3
|
Banerjee S, Baidya SK, Adhikari N, Jha T. An updated patent review of matrix metalloproteinase (MMP) inhibitors (2021-present). Expert Opin Ther Pat 2023; 33:631-649. [PMID: 37982191 DOI: 10.1080/13543776.2023.2284935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
INTRODUCTION Matrix metalloproteinases (MMPs) are strongly interlinked with the progression and mechanisms of several life-threatening diseases including cancer. Thus, novel MMP inhibitors (MMPIs) as promising drug candidates can be effective in combating these diseases. However, no MMPIs are marketed to date due to poor pharmacokinetics and lower selectivity. Therefore, this review was performed to study the newer MMPIs patented after the COVID-19 period for an updated perspective on MMPIs. AREAS COVERED This review highlights patents related to MMPIs, and their therapeutic implications published between January 2021 and August 2023 available in the Google Patents, Patentscope, and Espacenet databases. EXPERT OPINION Despite various MMP-related patents disclosed up to 2020, newer patent applications in the post-COVID-19 period decreased a lot. Besides major MMPs, other isoforms (i.e. MMP-3 and MMP-7) have gained attention recently for drug development. This may open up newer dimensions targeting these MMPs for therapeutic advancements. The isoform selectivity and bioavailability are major concerns for effective MMPI development. Thus, adopting theoretical approaches and experimental methodologies can unveil the development of novel MMPIs with improved pharmacokinetic profiles. Nevertheless, the involvement of MMPs in cancer, and the mechanisms of such MMPs in other diseases should be extensively studied for novel MMPI development.
Collapse
Affiliation(s)
| | | | | | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| |
Collapse
|
4
|
Li Q, Feng K, Liu J, Ren Y. Molecular modeling studies of novel naphthyridine and isoquinoline derivatives as CDK8 inhibitors. J Biomol Struct Dyn 2020; 39:6355-6369. [PMID: 32723012 DOI: 10.1080/07391102.2020.1797537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Cell cycle is an important part of cellular activities. The selective inhibition of cyclin-dependent kinases (CDK) activity in tumor cells can lead to continuous cell proliferation. Thirty-nine CDK8 inhibitors were systematically investigated on the basis of a three-dimensional quantitative structure-activity relationship (3D-QSAR). Models for comparative molecular field analysis (q2=0.64, r2=0.98) and comparative molecular similarity index analysis (q2=0.609, r2=0.952) were obtained. Contour maps illustrated that bioactivity of inhibitors is most affected by steric, electrostatic, hydrogen bond donor, and receptor interactions of molecular groups. Twenty new CDK8 inhibitors (DS01-DS20) were designed based on the contour maps. The results of ADME prediction illustrated that the designed compounds had potential druggability. The binding mode between a ligand and receptor was explored through molecular docking and molecular dynamics. Results revealed that the hydrogen bond interaction with residue LYS52 remarkably affected the activity of these compounds. Further analysis indicated that the introduction of fluorine to an amino naphthyridine ring of compound 28 contributes to the improvement of molecular activities. Pharmacophore-based virtual screening and Surflex-Sim in the ZINC database of 1,30,000 molecules demonstrated that 14 compounds with an indazole ring might be antitumor inhibitors. 3D-QSAR, molecular docking, molecular dynamics and pharmacophore results are consistent. These findings can be used as a reference for the design and discovery of new CDK8 inhibitors that can reduce design errors.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Qunlin Li
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Kairui Feng
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Jianxin Liu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Yujie Ren
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| |
Collapse
|
5
|
Ramsbeck D, Hamann A, Richter G, Schlenzig D, Geissler S, Nykiel V, Cynis H, Schilling S, Buchholz M. Structure-Guided Design, Synthesis, and Characterization of Next-Generation Meprin β Inhibitors. J Med Chem 2018; 61:4578-4592. [PMID: 29694039 DOI: 10.1021/acs.jmedchem.8b00330] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The metalloproteinase meprin β emerged as a current drug target for the treatment of a number of disorders, among those fibrosis, inflammatory bowel disease and Morbus Alzheimer. A major obstacle in the development of metalloprotease inhibitors is target selectivity to avoid side effects by blocking related enzymes with physiological functions. Here, we describe the structure-guided design of a novel series of compounds, based on previously reported highly active meprin β inhibitors. The bioisosteric replacement of the sulfonamide scaffold gave rise to a next generation of meprin inhibitors. Selected compounds based on this novel amine scaffold exhibit high activity against meprin β and also remarkable selectivity over related metalloproteases, i.e., matrix metalloproteases and A disintegrin and metalloproteinases.
Collapse
Affiliation(s)
- Daniel Ramsbeck
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Antje Hamann
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Georg Richter
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Dagmar Schlenzig
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Stefanie Geissler
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Vera Nykiel
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Holger Cynis
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Stephan Schilling
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| | - Mirko Buchholz
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Department of Drug Design and Target Validation MWT , Biocenter, Weinbergweg 22 , 06120 Halle (Saale) , Germany
| |
Collapse
|