1
|
Li F, Zhuo L, Xie F, Luo H, Li Y, Lin H, Li X. Exploration of small molecule compounds targeting abdominal aortic aneurysm based on CMap database and molecular dynamics simulation. Vascular 2024:17085381241273289. [PMID: 39155144 DOI: 10.1177/17085381241273289] [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: 08/20/2024]
Abstract
OBJECTIVE The mitigation of abdominal aortic aneurysm (AAA) growth through pharmaceutical intervention offers the potential to avert the perils associated with AAA rupture and the subsequent need for surgical intervention. Nevertheless, the existing effective drugs for AAA treatment are limited, necessitating a pressing exploration for novel therapeutic medications. METHODS AAA-related transcriptome data were downloaded from GEO, and differentially expressed genes (DEGs) in AAA tissue were screened for GO and KEGG enrichment analyses. Small molecule compounds and their target proteins with negative connectivity to the AAA expression profile were predicted in the Connectivity Map (CMap) database. Molecular docking and molecular dynamics simulation were performed to predict the binding of the target protein to the small molecule compound, and the MM/GBSA method was used to calculate the binding free energy. Cluster analysis was performed using the cluster tool in the GROMACS package. An AAA cell-free model was built, and CETSA experiments were used to demonstrate the binding ability of small molecules to the target protein in cells. RESULTS A total of 2244 DEGs in AAA were obtained through differential analysis, and the DEGs were mainly enriched in the tubulin binding biological function and cell cycle pathway. The CMap results showed that Apicidin had a potential therapeutic effect on AAA with a connectivity score of -97.74, and HDAC4 was the target protein of Apicidin. Based on literature, HDAC4-Apicidin was selected as the subsequent research object. The lowest affinity of Apicidin-HDAC4 molecular docking was -8.218 kcal/mol. Molecular dynamics simulation results indicated that Apicidin-HDAC4 could form a stable complex. MM/GBSA analysis showed a total binding free energy of -55.40 ± 0.79 kcal/mol, and cluster analysis showed that there were two main conformational clusters during the binding process, accounting for 22.4% and 57.8%, respectively. Apicidin could form hydrogen bonds with surrounding residues for stable binding. CETSA experiment proved the stable binding ability of Apicidin and HDAC4. CONCLUSION Apicidin inhibited HDAC4 in AAA and exhibited favorable protein-ligand interactions and stability, making it a potential candidate drug for treating AAA.
Collapse
Affiliation(s)
- Fushan Li
- Department of Vascular, Sanming First Hospital Affiliated to Fujian Medical University, Sanming, China
| | - Liqing Zhuo
- Department of Electrocardiography, Sanming First Hospital Affiliated to Fujian Medical University, Sanming, China
| | - Fangtao Xie
- Department of Vascular, Sanming First Hospital Affiliated to Fujian Medical University, Sanming, China
| | - Haiping Luo
- Department of Vascular, Sanming First Hospital Affiliated to Fujian Medical University, Sanming, China
| | - Ying Li
- Department of Vascular, Sanming First Hospital Affiliated to Fujian Medical University, Sanming, China
| | - Huyu Lin
- Department of Vascular, Sanming First Hospital Affiliated to Fujian Medical University, Sanming, China
| | - Xiaoguang Li
- Department of Vascular, Sanming First Hospital Affiliated to Fujian Medical University, Sanming, China
| |
Collapse
|
2
|
Tan YQ, Zhang W, Xie ZC, Li J, Chen HW. CaMK II in Cardiovascular Diseases, Especially CaMK II-δ: Friends or Enemies. Drug Des Devel Ther 2024; 18:3461-3476. [PMID: 39132626 PMCID: PMC11314529 DOI: 10.2147/dddt.s473251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/05/2024] [Indexed: 08/13/2024] Open
Abstract
Cardiovascular diseases (CVDs) tend to affect the young population and are associated with a significant economic burden and psychological distress to the society and families. The physiological and pathological processes underlying CVDs are complex. Ca2+/calmodulin-dependent kinase II (CaMK II), a protein kinase, has multiple biological functions. It participates in multiple pathological processes and plays a central role in the development of CVDs. Based on this, this paper analyzes the structural characteristics and distribution of CaMK II, the mechanism of action of CaMK II, and the relationship between CaMK II and CVDs, including ion channels, ischemia-reperfusion injury, arrhythmias, myocardial hypertrophy, cardiotoxicity, hypertension, and dilated cardiomyopathy. Given the different regulatory mechanisms of different isoforms of CaMK II, the clinical use of specific targeted inhibitors or novel compounds should be evaluated in future research to provide new directions.
Collapse
Affiliation(s)
- Yu-Qing Tan
- Department of Cardiology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, People’s Republic of China
| | - Wang Zhang
- Department of Pharmacy, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, People’s Republic of China
| | - Zi-Cong Xie
- Department of Cardiology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, People’s Republic of China
| | - Jun Li
- Department of Cardiology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, People’s Republic of China
| | - Heng-Wen Chen
- New Drug Research and Development Office, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, People’s Republic of China
| |
Collapse
|
3
|
Liu M, Zhao X, Liang X, Zhou YG. Homogeneous and Label-Free Detection and Monitoring of Protein Kinase Activity Using the Impact Electrochemistry of Silver Nanoparticles. ACS Sens 2024; 9:110-117. [PMID: 38113272 DOI: 10.1021/acssensors.3c01703] [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] [Indexed: 12/21/2023]
Abstract
Protein kinase activity correlates closely with that of many human diseases. However, the existing methods for quantifying protein kinase activity often suffer from limitations such as low sensitivity, harmful radioactive labels, high cost, and sophisticated detection procedures, underscoring the urgent need for sensitive and rapid detection methods. Herein, we present a simple and sensitive approach for the homogeneous detection of protein kinase activity based on nanoimpact electrochemistry to probe the degree of aggregation of silver nanoparticles (AgNPs) before and after phosphorylation. Phosphorylation, catalyzed by protein kinases, introduces two negative charges into the substrate peptide, leading to alterations in electrostatic interactions between the phosphorylated peptide and the negatively charged AgNPs, which, in turn, affects the aggregation status of AgNPs. Via direct electro-oxidation of AgNPs in nanoimpact electrochemistry experiments, protein kinase activity can be quantified by assessing the impact frequency. The present sensor demonstrates a broad detection range and a low detection limit for protein kinase A (PKA), along with remarkable selectivity. Additionally, it enables monitoring of PKA-catalyzed phosphorylation processes. In contrast to conventional electrochemical sensing methods, this approach avoids the requirement of complex labeling and washing procedures.
Collapse
Affiliation(s)
- Meijuan Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou 511300, Guangdong, P. R. China
| | - Xihan Zhao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou 511300, Guangdong, P. R. China
| | - Xianghui Liang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, P. R. China
| | - Yi-Ge Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou 511300, Guangdong, P. R. China
| |
Collapse
|
4
|
Silnitsky S, Rubin SJS, Zerihun M, Qvit N. An Update on Protein Kinases as Therapeutic Targets-Part I: Protein Kinase C Activation and Its Role in Cancer and Cardiovascular Diseases. Int J Mol Sci 2023; 24:17600. [PMID: 38139428 PMCID: PMC10743896 DOI: 10.3390/ijms242417600] [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: 11/01/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Protein kinases are one of the most significant drug targets in the human proteome, historically harnessed for the treatment of cancer, cardiovascular disease, and a growing number of other conditions, including autoimmune and inflammatory processes. Since the approval of the first kinase inhibitors in the late 1990s and early 2000s, the field has grown exponentially, comprising 98 approved therapeutics to date, 37 of which were approved between 2016 and 2021. While many of these small-molecule protein kinase inhibitors that interact orthosterically with the protein kinase ATP binding pocket have been massively successful for oncological indications, their poor selectively for protein kinase isozymes have limited them due to toxicities in their application to other disease spaces. Thus, recent attention has turned to the use of alternative allosteric binding mechanisms and improved drug platforms such as modified peptides to design protein kinase modulators with enhanced selectivity and other pharmacological properties. Herein we review the role of different protein kinase C (PKC) isoforms in cancer and cardiovascular disease, with particular attention to PKC-family inhibitors. We discuss translational examples and carefully consider the advantages and limitations of each compound (Part I). We also discuss the recent advances in the field of protein kinase modulators, leverage molecular docking to model inhibitor-kinase interactions, and propose mechanisms of action that will aid in the design of next-generation protein kinase modulators (Part II).
Collapse
Affiliation(s)
- Shmuel Silnitsky
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel; (S.S.); (M.Z.)
| | - Samuel J. S. Rubin
- Department of Medicine, School of Medicine, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA;
| | - Mulate Zerihun
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel; (S.S.); (M.Z.)
| | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel; (S.S.); (M.Z.)
| |
Collapse
|
5
|
Ahsan R, Khan MM, Mishra A, Noor G, Ahmad U. Protein Kinases and their Inhibitors Implications in Modulating Disease Progression. Protein J 2023; 42:621-632. [PMID: 37768476 DOI: 10.1007/s10930-023-10159-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2023] [Indexed: 09/29/2023]
Abstract
Protein phosphorylation plays an important role in cellular pathways, including cell cycle regulation, metabolism, differentiation and survival. The protein kinase superfamily network consists of 518 members involved in intrinsic or extrinsic interaction processes. Protein kinases are divided into two categories based on their ability to phosphorylate tyrosine, serine, and threonine residues. The complexity of the system implies its vulnerability. Any changes in the pathways of protein kinases may be implicated in pathological processes. Therefore, they are regarded as having an important role in human diseases and represent prospective therapeutic targets. This article provides a review of the protein kinase inhibitors approved by the FDA. Finally, we summarize the mechanism of action of protein kinases, including their role in the development and progression of protein kinase-related roles in various pathological conditions and the future therapeutic potential of protein kinase inhibitors, along with links to protein kinase databases. Further clinical studies aimed at examining the sequence of protein kinase inhibitor availability would better utilize current protein kinase inhibitors in diseases. Additionally, this review may help researchers and biochemists find new potent and selective protein kinase inhibitors and provide more indications for using existing drugs.
Collapse
Affiliation(s)
- Rabiya Ahsan
- Department of pharmacology, Faculty of Pharmacy, Integral University, Lucknow, India
| | - Mohd Muazzam Khan
- Department of pharmacology, Faculty of Pharmacy, Integral University, Lucknow, India.
| | - Anuradha Mishra
- Department of pharmacology, Amity Institute of Pharmacy, Amity University, sector 125, Noida, Uttar Pradesh, 201313, India
| | - Gazala Noor
- Department of pharmacology, Faculty of Pharmacy, Integral University, Lucknow, India
| | - Usama Ahmad
- Department of pharmaceutics, Faculty of Pharmacy, Integral University, Lucknow, India
| |
Collapse
|
6
|
Godbole SS, Dokholyan NV. Allosteric regulation of kinase activity in living cells. eLife 2023; 12:RP90574. [PMID: 37943025 PMCID: PMC10635643 DOI: 10.7554/elife.90574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023] Open
Abstract
The dysregulation of protein kinases is associated with multiple diseases due to the kinases' involvement in a variety of cell signaling pathways. Manipulating protein kinase function, by controlling the active site, is a promising therapeutic and investigative strategy to mitigate and study diseases. Kinase active sites share structural similarities, making it difficult to specifically target one kinase, and allosteric control allows specific regulation and study of kinase function without directly targeting the active site. Allosteric sites are distal to the active site but coupled via a dynamic network of inter-atomic interactions between residues in the protein. Establishing an allosteric control over a kinase requires understanding the allosteric wiring of the protein. Computational techniques offer effective and inexpensive mapping of the allosteric sites on a protein. Here, we discuss the methods to map and regulate allosteric communications in proteins, and strategies to establish control over kinase functions in live cells and organisms. Protein molecules, or 'sensors,' are engineered to function as tools to control allosteric activity of the protein as these sensors have high spatiotemporal resolution and help in understanding cell phenotypes after immediate activation or inactivation of a kinase. Traditional methods used to study protein functions, such as knockout, knockdown, or mutation, cannot offer a sufficiently high spatiotemporal resolution. We discuss the modern repertoire of tools to regulate protein kinases as we enter a new era in deciphering cellular signaling and developing novel approaches to treat diseases associated with signal dysregulation.
Collapse
Affiliation(s)
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of MedicineHersheyUnited States
- Department of Biomedical Engineering, Penn State University, University ParkHersheyUnited States
- Department of Engineering Science and Mechanics, Penn State University, University ParkHersheyUnited States
- Department of Biochemistry & Molecular Biology, Penn State College of MedicineHersheyUnited States
- Department of Chemistry, Penn State University, University ParkHersheyUnited States
| |
Collapse
|