1
|
Pala D, Clark DE. Caught between a ROCK and a hard place: current challenges in structure-based drug design. Drug Discov Today 2024; 29:104106. [PMID: 39029868 DOI: 10.1016/j.drudis.2024.104106] [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: 04/11/2024] [Revised: 06/27/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
Abstract
The discipline of structure-based drug design (SBDD) is several decades old and it is tempting to think that the proliferation of experimental structures for many drug targets might make computer-aided drug design (CADD) straightforward. However, this is far from true. In this review, we illustrate some of the challenges that CADD scientists face every day in their work, even now. We use Rho-associated protein kinase (ROCK), and public domain structures and data, as an example to illustrate some of the challenges we have experienced during our project targeting this protein. We hope that this will help to prevent unrealistic expectations of what CADD can accomplish and to educate non-CADD scientists regarding the challenges still facing their CADD colleagues.
Collapse
Affiliation(s)
- Daniele Pala
- Medicinal Chemistry and Drug Design Technologies Department, Chiesi Farmaceutici S.p.A, Research Center, Largo Belloli 11/a, 43122 Parma, Italy
| | - David E Clark
- Charles River, 6-9 Spire Green Centre, Flex Meadow, Harlow CM19 5TR, UK.
| |
Collapse
|
2
|
Zhang C, Liu YC, Wang D, Wang Y. Discovery of a novel ROCK2 ATP competitive inhibitor by DNA-encoded library selection. Biochem Biophys Res Commun 2024; 699:149537. [PMID: 38280309 DOI: 10.1016/j.bbrc.2024.149537] [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: 11/22/2023] [Revised: 12/23/2023] [Accepted: 01/14/2024] [Indexed: 01/29/2024]
Abstract
Neurodegeneration disorders, such as Alzheimer's disease (AD), have garnered significant attention due to their impact on individuals and society as a whole. Understanding the mechanisms behind these disorders and developing effective therapy strategies is of utmost importance. One potential therapeutic target that has emerged is Rho-associated coiled-coil containing protein kinase 2 (ROCK2), as its accumulation and activity have been closely linked to memory loss. In this report, we present the findings of a recent discovery involving a new molecule that has the ability to competitively inhibit ROCK2 activity. This molecule was identified through the utilization of a DNA-encoded library (DEL) screening platform. Following selection against ROCK2, an off-DNA compound was synthesized and examined to ascertain its inhibitory properties, selectivity, mechanism of action, and binding mode analysis. From the screening, compound CH-2 has demonstrated an IC50 value of 28 nM against ROCK2, while exhibiting a 5-fold selectivity over ROCK1. Further analysis through molecular docking has provided insights into the specific binding modes of this compound. Our findings suggest that DEL selection offers a rapid method for identifying new inhibitors. Among these, the CH-2 compound shows promise as a potential ROCK2 inhibitor and warrants further investigation.
Collapse
Affiliation(s)
- Chenhua Zhang
- Institute for Cancer Research, School of Basic Medical Science, Health Science Center of Xi'an Jiaotong University, 76 YanTa XiLu, Xi'an, Shaanxi, 710061, China
| | - Yu-Chih Liu
- TandemAI Technology Shanghai Co., Ltd., Zhangjiang Hi-Tech Park, Shanghai, 201203, China
| | - Depu Wang
- Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Yili Wang
- Institute for Cancer Research, School of Basic Medical Science, Health Science Center of Xi'an Jiaotong University, 76 YanTa XiLu, Xi'an, Shaanxi, 710061, China.
| |
Collapse
|
3
|
Du S, Hu X, Menéndez-Arias L, Zhan P, Liu X. Target-based drug design strategies to overcome resistance to antiviral agents: opportunities and challenges. Drug Resist Updat 2024; 73:101053. [PMID: 38301487 DOI: 10.1016/j.drup.2024.101053] [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: 10/31/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Viral infections have a major impact in human health. Ongoing viral transmission and escalating selective pressure have the potential to favor the emergence of vaccine- and antiviral drug-resistant viruses. Target-based approaches for the design of antiviral drugs can play a pivotal role in combating drug-resistant challenges. Drug design computational tools facilitate the discovery of novel drugs. This review provides a comprehensive overview of current drug design strategies employed in the field of antiviral drug resistance, illustrated through the description of a series of successful applications. These strategies include technologies that enhance compound-target affinity while minimizing interactions with mutated binding pockets. Furthermore, emerging approaches such as virtual screening, targeted protein/RNA degradation, and resistance analysis during drug design have been harnessed to curtail the emergence of drug resistance. Additionally, host targeting antiviral drugs offer a promising avenue for circumventing viral mutation. The widespread adoption of these refined drug design strategies will effectively address the prevailing challenge posed by antiviral drug resistance.
Collapse
Affiliation(s)
- Shaoqing Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xueping Hu
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, PR China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| |
Collapse
|
4
|
Zaky YA, Rashad MW, Zaater MA, El Kerdawy AM. Discovery of dual rho-associated protein kinase 1 (ROCK1)/apoptosis signal-regulating kinase 1 (ASK1) inhibitors as a novel approach for non-alcoholic steatohepatitis (NASH) treatment. BMC Chem 2024; 18:2. [PMID: 38172941 PMCID: PMC10765837 DOI: 10.1186/s13065-023-01081-3] [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: 07/13/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024] Open
Abstract
In the current study we suggest a novel approach to curb non-alcoholic steatohepatitis (NASH) progression, and we suggest privileged scaffolds for the design of novel compounds for this aim. NASH is an advanced form of non-alcoholic fatty liver disease that can further progress into fibrosis, cirrhosis, and hepatocellular carcinoma. It is a widely emerging disease affecting 25% of the global population and has no current approved treatments. Protein kinases are key regulators of cellular pathways, of which, Rho-associated protein kinase 1 (ROCK1) and apoptosis signal-regulating kinase 1 (ASK1) play an important role in the progression of NASH and they stand out as promising targets for NASH therapy. Interestingly, their kinase domains are found to be similar in sequence and topology; therefore, dual inhibition of ROCK1 and ASK1 is expected to be amenable and could achieve a more favourable outcome. To reach this goal, a training set of ROCK1 and ASK1 protein structures co-crystalized with type 1 (ATP-competitive) inhibitors was constructed to manually generate receptor-based pharmacophore models representing ROCK1 and ASK1 inhibitors' common pharmacophoric features. The models produced were assessed using a test set of both ROCK1 and ASK1 actives and decoys, and their performance was evaluated using different assessment metrics. The best pharmacophore model obtained, showing a Mathew's correlation coefficient (MCC) of 0.71, was then used to screen the ZINC purchasable database retrieving 6178 hits that were filtered accordingly using several medicinal chemistry and pharmacokinetics filters returning 407 promising compounds. To confirm that these compounds are capable of binding to the target kinases, they were subjected to molecular docking simulations at both protein structures. The results were then assessed individually and filtered, setting the spotlight on various privileged scaffolds that could be exploited as the nucleus for designing novel ROCK1/ASK1 dual inhibitors.
Collapse
Affiliation(s)
- Yara A Zaky
- Department of Chemistry, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt.
| | - Mai W Rashad
- Department of Chemistry, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Marwa A Zaater
- Master Postgraduate Program, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ahmed M El Kerdawy
- Department of Chemistry, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- School of Pharmacy, College of Science, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, Lincolnshire, UK
| |
Collapse
|
5
|
Xu X, Yao L. Recent advances in the development of Rho kinase inhibitors (2015-2021). Med Res Rev 2024; 44:406-421. [PMID: 37265266 DOI: 10.1002/med.21980] [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: 12/23/2021] [Revised: 01/27/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023]
Abstract
Rho-associated coiled-coil kinases (ROCKs) are key downstream effectors of small GTPases. ROCK plays a central role in diverse cellular events with accumulating evidence supporting the concept that ROCK is important in tumor development and progression. Numerous ROCK inhibitors have been investigated for their therapeutic potential in the treatment of cancers. In this article, we review recent research progress on ROCK inhibitors, especially those with potential for the treatment of cancers, reported in the literature from 2015 to 2021. Most ROCK inhibitors show potent in vitro and in vivo antitumor activities and have potential in the treatment of cancers.
Collapse
Affiliation(s)
- Xiangrong Xu
- Yantai University Hospital, Yantai University, Yantai, China
| | - Lei Yao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| |
Collapse
|
6
|
Marciniak B, Kciuk M, Mujwar S, Sundaraj R, Bukowski K, Gruszka R. In Vitro and In Silico Investigation of BCI Anticancer Properties and Its Potential for Chemotherapy-Combined Treatments. Cancers (Basel) 2023; 15:4442. [PMID: 37760412 PMCID: PMC10526149 DOI: 10.3390/cancers15184442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/10/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND DUSP6 phosphatase serves as a negative regulator of MAPK kinases involved in numerous cellular processes. BCI has been identified as a potential allosteric inhibitor with anticancer activity. Our study was designed to test the anticancer properties of BCI in colon cancer cells, to characterize the effect of this compound on chemotherapeutics such as irinotecan and oxaliplatin activity, and to identify potential molecular targets for this inhibitor. METHODS BCI cytotoxicity, proapoptotic activity, and cell cycle distribution were investigated in vitro on three colon cancer cell lines (DLD1, HT-29, and Caco-2). In silico investigation was prepared to assess BCI drug-likeness and identify potential molecular targets. RESULTS The exposure of colorectal cancer cells with BCI resulted in antitumor effects associated with cell cycle arrest and induction of apoptosis. BCI exhibited strong cytotoxicity on DLD1, HT-29, and Caco-2 cells. BCI showed no significant interaction with irinotecan, but strongly attenuated the anticancer activity of oxaliplatin when administered together. Analysis of synergy potential further confirmed the antagonistic interaction between these two compounds. In silico investigation indicated CDK5 as a potential new target of BCI. CONCLUSIONS Our studies point to the anticancer potential of BCI but note the need for a precise mechanism of action.
Collapse
Affiliation(s)
- Beata Marciniak
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (M.K.); (K.B.); (R.G.)
| | - Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (M.K.); (K.B.); (R.G.)
- Doctoral School of Exact and Natural Sciences, University of Lodz, 90-237 Lodz, Poland
| | - Somdutt Mujwar
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India;
| | - Rajamanikandan Sundaraj
- Centre for Drug Discovery, Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India;
| | - Karol Bukowski
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (M.K.); (K.B.); (R.G.)
| | - Renata Gruszka
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (M.K.); (K.B.); (R.G.)
| |
Collapse
|
7
|
Xu QX, Guo L, Li Y, Wang ZW, Hu P, Yang GM, Pan Y. In silico screening-based discovery of benzamide derivatives as inhibitors of Rho-associated kinase-1 (ROCK1). J Biomol Struct Dyn 2023:1-18. [PMID: 37668086 DOI: 10.1080/07391102.2023.2253918] [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: 02/09/2023] [Accepted: 07/17/2023] [Indexed: 09/06/2023]
Abstract
As a pivotal node in modulating various cell behaviors, Rho-associated kinase-1 (ROCK1) has attracted significant attention as a promising therapeutic target in a variety of diseases. Benzamide has been widely reported as a ROCK1 inhibitors in recent years. To better understand its pharmacological properties and to explore its potential inhibitors, a series of ROCK1 inhibitors derived from N-methyl-4-(4-pyrazolidinyl) benzamides (MPBs) were investigated by using three-dimensional quantitative structure-activity relationship (3D-QSAR) models, pharmacophore models, molecular docking, and molecular dynamics (MD) simulation. The comparative Molecular Field Analysis (CoMFA) model (q2 = 0.616, R2 = 0.972, ONC = 4, and r2pred = 0.983) and the best Comparative Molecular Similarity Indices Analysis (CoMSIA) model (q2= 0.740, R2 = 0.982, ONC = 6, and r2pred = 0.824) exhibited reliable predictability with satisfactory validation parameters. In the subsequent virtual screening, VS03 and VS05 were identified to have superior predicted activities and higher docking scores, meanwhile they demonstrated to be reasonably stable in the binding pocket through MD simulations. These results provide a significant theoretical direction for the rational design and development of novel ROCK1 inhibitors.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Qi-Xuan Xu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Liang Guo
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuan Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhao-Wei Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Po Hu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Guang-Ming Yang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yang Pan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| |
Collapse
|
8
|
Qiao R, Tang W, Li J, Li C, Zhao C, Wang X, Li M, Cui Y, Chen Y, Cai G, Wu Q, Zhao X, Wang P. Structure-based virtual screening of ROCK1 inhibitors for the discovery of Enterovirus-A71 antivirals. Virology 2023; 585:205-214. [PMID: 37384967 DOI: 10.1016/j.virol.2023.06.011] [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: 04/29/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 07/01/2023]
Abstract
Human enterovirus A71 (EV-A71) is the major causative agent of hand, foot, and mouth disease (HFMD), which may lead to neurological sequelae and even death. Although EV-A71 seriously threatens public health, there remains no efficient drug for the treatment of EV-A71 infection. We previously demonstrated that ROCK1 is a novel host dependency factor for EV-A71 replication and can serve as a target for the development of anti-EV-A71 therapeutics. In this study, we identified a subset of inhibitors with potential anti-EV-A71 activity by virtual screening using ROCK1 as a target. Among the hits, Dasabuvir, an HCV polymerase inhibitor, was found to have the best antiviral activity which is consistent with the ranking scores in Autodock Vina and iGEMDOCK. We found that Dasabuvir efficiently suppressed EV-A71 replication in a dose-dependent manner. Moreover, Dasabuvir not only efficiently suppressed the replication of EV-A71 in RD cells, but also in multiple cell lines, including HEK-293T, Caco-2, HT-29, HepG2, and Huh7. Besides, Dasabuvir alleviated the release of proinflammatory cytokines caused by EV-A71 infection. Notably, Dasabuvir also exhibited antiviral activity of CVA10, indicating it may have broad-spectrum antiviral activity against species Enteroviruses A. Hence, our results further confirm that ROCK1 can be a potential drug target and suggest Dasabuvir could be a clinical candidate for the treatment of EV-A71 infection.
Collapse
Affiliation(s)
- Rui Qiao
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wanggang Tang
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, China
| | - Jiayan Li
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Chen Li
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Chaoyue Zhao
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xun Wang
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Minghui Li
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuchen Cui
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yanjia Chen
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Guonan Cai
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Qingyu Wu
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoyu Zhao
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China.
| | - Pengfei Wang
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China.
| |
Collapse
|
9
|
Fu S, Wen Y, Peng B, Tang M, Shi M, Liu J, Yang Y, Si W, Guo Y, Li X, Yan T, Kang J, Pei H, Chen L. Discovery of indoline-based derivatives as effective ROCK2 inhibitors for the potential new treatment of idiopathic pulmonary fibrosis. Bioorg Chem 2023; 137:106539. [PMID: 37163811 DOI: 10.1016/j.bioorg.2023.106539] [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: 10/02/2022] [Revised: 03/06/2023] [Accepted: 04/09/2023] [Indexed: 05/12/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and devastating lung disease with a median survival of only 3-5 years. Due to the lack of effective therapy, IPF threatens human health. Recently, increasing reports have indicated that Rho-associated coiled-coil protein kinases (ROCKs) play important roles in the development of IPF and might represent a novel target for the treatment of IPF. Herein, a new series of selective ROCK2 inhibitors based on indoline were designed and synthesized. Structural modification resulted in optimized compound 9b with an IC50 value of 6 nM against ROCK2 and the inhibition of collagen gel contraction. Cellular assays demonstrated that 9b could significantly suppress the expression of collagen I and α-SMA, and inhibited ROCK signaling pathway. Oral administration of compound 9b (10 mg/kg) exerted more significant anti-pulmonary fibrosis effects than nintedanib (100 mg/kg) and KD025 (100 mg/kg) in a bleomycin-induced IPF rat model, suggesting that 9b could serve as a potential lead compound for the treatment of IPF.
Collapse
Affiliation(s)
- Suhong Fu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yi Wen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bin Peng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Minghai Tang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mingsong Shi
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jiang Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yingxue Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wenting Si
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Guo
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiandeng Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.; School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tingting Yan
- Sichuan Good Doctor Panxi Pharmaceutical Co.,Ltd., Xichang 615000, China
| | - Jie Kang
- Sichuan Key Laboratory for Medicinal American Cockroach, Chengdu 610031, China
| | - Heying Pei
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China..
| | - Lijuan Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.; Chengdu Zenitar Biomedical Technology Co., Ltd, Chengdu 610000, China.
| |
Collapse
|
10
|
Xie Y, Yue L, Shi Y, Su X, Gan C, Liu H, Xue T, Ye T. Application and Study of ROCK Inhibitors in Pulmonary Fibrosis: Recent Developments and Future Perspectives. J Med Chem 2023; 66:4342-4360. [PMID: 36940432 DOI: 10.1021/acs.jmedchem.2c01753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Abstract
Rho-associated coiled-coil-containing kinases (ROCKs), serine/threonine protein kinases, were initially identified as downstream targets of the small GTP-binding protein Rho. Pulmonary fibrosis (PF) is a lethal disease with limited therapeutic options and a particularly poor prognosis. Interestingly, ROCK activation has been demonstrated in PF patients and in animal PF models, making it a promising target for PF treatment. Many ROCK inhibitors have been discovered, and four of these have been approved for clinical use; however, no ROCK inhibitors are approved for the treatment of PF patients. In this article, we describe ROCK signaling pathways and the structure-activity relationship, potency, selectivity, binding modes, pharmacokinetics (PKs), biological functions, and recently reported inhibitors of ROCKs in the context of PF. We will also focus our attention on the challenges to be addressed when targeting ROCKs and discuss the strategy of ROCK inhibitor use in the treatment of PF.
Collapse
Affiliation(s)
- Yuting Xie
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Yue
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yaojie Shi
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xingping Su
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Cailing Gan
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongyao Liu
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Taixiong Xue
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Tinghong Ye
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| |
Collapse
|
11
|
Meanwell NA. The pyridazine heterocycle in molecular recognition and drug discovery. Med Chem Res 2023; 32:1-69. [PMID: 37362319 PMCID: PMC10015555 DOI: 10.1007/s00044-023-03035-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/06/2023] [Indexed: 03/17/2023]
Abstract
The pyridazine ring is endowed with unique physicochemical properties, characterized by weak basicity, a high dipole moment that subtends π-π stacking interactions and robust, dual hydrogen-bonding capacity that can be of importance in drug-target interactions. These properties contribute to unique applications in molecular recognition while the inherent polarity, low cytochrome P450 inhibitory effects and potential to reduce interaction of a molecule with the cardiac hERG potassium channel add additional value in drug discovery and development. The recent approvals of the gonadotropin-releasing hormone receptor antagonist relugolix (24) and the allosteric tyrosine kinase 2 inhibitor deucravacitinib (25) represent the first examples of FDA-approved drugs that incorporate a pyridazine ring. In this review, the properties of the pyridazine ring are summarized in comparison to the other azines and its potential in drug discovery is illustrated through vignettes that explore applications that take advantage of the inherent physicochemical properties as an approach to solving challenges associated with candidate optimization. Graphical Abstract
Collapse
|
12
|
You Y, Zhu K, Wang J, Liang Q, Li W, Wang L, Guo B, Zhou J, Feng X, Shi J. ROCK inhibitor: Focus on recent updates. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
|
13
|
Moreira NCDS, Tamarozzi ER, Lima JEBDF, Piassi LDO, Carvalho I, Passos GA, Sakamoto-Hojo ET. Novel Dual AChE and ROCK2 Inhibitor Induces Neurogenesis via PTEN/AKT Pathway in Alzheimer's Disease Model. Int J Mol Sci 2022; 23:ijms232314788. [PMID: 36499116 PMCID: PMC9737254 DOI: 10.3390/ijms232314788] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 11/29/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive and complex neurodegenerative disease. Acetylcholinesterase inhibitors (AChEIs) are a major class of drugs used in AD therapy. ROCK2, another promising target for AD, has been associated with the induction of neurogenesis via PTEN/AKT. This study aimed to characterize the therapeutic potential of a novel donepezil-tacrine hybrid compound (TA8Amino) to inhibit AChE and ROCK2 protein, leading to the induction of neurogenesis in SH-SY5Y cells. Experiments were carried out with undifferentiated and neuron-differentiated SH-SY5Y cells submitted to treatments with AChEIs (TA8Amino, donepezil, and tacrine) for 24 h or 7 days. TA8Amino was capable of inhibiting AChE at non-cytotoxic concentrations after 24 h. Following neuronal differentiation for 7 days, TA8Amino and donepezil increased the percentage of neurodifferentiated cells and the length of neurites, as confirmed by β-III-tubulin and MAP2 protein expression. TA8Amino was found to participate in the activation of PTEN/AKT signaling. In silico analysis showed that TA8Amino can stably bind to the active site of ROCK2, and in vitro experiments in SH-SY5Y cells demonstrate that TA8Amino significantly reduced the expression of ROCK2 protein, contrasting with donepezil and tacrine. Therefore, these results provide important information on the mechanism underlying the action of TA8Amino with regard to multi-target activities.
Collapse
Affiliation(s)
| | - Elvira Regina Tamarozzi
- Department of Biotechnology, School of Arts, Sciences and Humanities—USP, São Paulo 03828-000, Brazil
| | | | - Larissa de Oliveira Piassi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo—USP, Ribeirão Preto 14049-900, Brazil
| | - Ivone Carvalho
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo—USP, Ribeirão Preto 14040-900, Brazil
| | - Geraldo Aleixo Passos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo—USP, Ribeirão Preto 14049-900, Brazil
- Laboratory of Genetics and Molecular Biology, Department of Basic and Oral Biology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Elza Tiemi Sakamoto-Hojo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo—USP, Ribeirão Preto 14049-900, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo—USP, Ribeirão Preto 14040-901, Brazil
- Correspondence: ; Tel.: +55-16-3315-3827
| |
Collapse
|
14
|
Ladduwahetty T, Lee MR, Maillard MC, Cachope R, Todd D, Barnes M, Beaumont V, Chauhan A, Gallati C, Haughan AF, Kempf G, Luckhurst CA, Matthews K, McAllister G, Mitchell P, Patel H, Rose M, Saville-Stones E, Steinbacher S, Stott AJ, Thatcher E, Tierney J, Urbonas L, Munoz-Sanjuan I, Dominguez C. Identification of a Potent, Selective, and Brain-Penetrant Rho Kinase Inhibitor and its Activity in a Mouse Model of Huntington's Disease. J Med Chem 2022; 65:9819-9845. [PMID: 35816678 DOI: 10.1021/acs.jmedchem.2c00474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Rho kinase (ROCK) pathway is implicated in the pathogenesis of several conditions, including neurological diseases. In Huntington's disease (HD), ROCK is implicated in mutant huntingtin (HTT) aggregation and neurotoxicity, and members of the ROCK pathway are increased in HD mouse models and patients. To validate this mode of action as a potential treatment for HD, we sought a potent, selective, central nervous system (CNS)-penetrant ROCK inhibitor. Identifying a compound that could be dosed orally in mice with selectivity against other AGC kinases, including protein kinase G (PKG), whose inhibition could potentially activate the ROCK pathway, was paramount for the program. We describe the optimization of published ligands to identify a novel series of ROCK inhibitors based on a piperazine core. Morphing of the early series developed in-house by scaffold hopping enabled the identification of a compound exhibiting high potency and desired selectivity and demonstrating a robust pharmacodynamic (PD) effect by the inhibition of ROCK-mediated substrate (MYPT1) phosphorylation after oral dosing.
Collapse
Affiliation(s)
- Tammy Ladduwahetty
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Matthew R Lee
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Michel C Maillard
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Roger Cachope
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Daniel Todd
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Michael Barnes
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Vahri Beaumont
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Alka Chauhan
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Caroline Gallati
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Alan F Haughan
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Georg Kempf
- Proteros Biostructures GmbH, Bunsenstr. 7a, D-82152 Planegg-Martinsried, Germany
| | | | - Kim Matthews
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - George McAllister
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Philip Mitchell
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Hiral Patel
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Mark Rose
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | | | - Stefan Steinbacher
- Proteros Biostructures GmbH, Bunsenstr. 7a, D-82152 Planegg-Martinsried, Germany
| | - Andrew J Stott
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Emma Thatcher
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Jason Tierney
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Liudvikas Urbonas
- Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Ignacio Munoz-Sanjuan
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Celia Dominguez
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| |
Collapse
|
15
|
Zhang W, Zhao W, Li Q, Zhao D, Qu J, Yuan Z, Cheng Z, Zhu X, Zhuang X, Zhang Z. 3D-printing magnesium-polycaprolactone loaded with melatonin inhibits the development of osteosarcoma by regulating cell-in-cell structures. J Nanobiotechnology 2021; 19:263. [PMID: 34481503 PMCID: PMC8418751 DOI: 10.1186/s12951-021-01012-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/24/2021] [Indexed: 12/30/2022] Open
Abstract
Melatonin has been proposed as a potent anticarcinogen presents a short half-life for osteosarcoma (OS). Cell-in-cell (CIC) structures play a role in the development of malignant tumors by changing the tumor cell energy metabolism. This study developed a melatonin-loaded 3D printed magnesium-polycaprolactone (Mg-PCL) scaffold and investigated its effect and molecular mechanism on CIC in OS. Mg-PCL scaffold was prepared by 3D-printing and its characteristic was determined. The effect and molecular mechanism of Mg-PCL scaffold as well as melatonin-loaded Mg-PCL on OS growth and progression were investigated in vivo and in vitro. We found that melatonin receptor 1 (MT1) and CIC expressions were increased in OS tissues and cells. Melatonin treatment inhibit the key CIC pathway, Rho/ROCK, through the cAMP/PKA signaling pathway, interfering with the mitochondrial physiology of OS cells, and thus playing an anti-invasion and anti-metastasis role in OS. The Mg-PCL-MT could significantly inhibit distant organ metastasis of OS in the in vivo model. Our results showed that melatonin-loaded Mg-PCL scaffolds inhibited the proliferation, invasion and metastasis of OS cells through the CIC pathway. The Mg-PCL-MT could be a potential therapeutics for OS.
Collapse
Affiliation(s)
- Weilin Zhang
- Department of Orthopedics, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, Liaoning, China
| | - Wei Zhao
- Department of Orthopedics, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, Liaoning, China
| | - Qin Li
- Translational Medicine Center, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Duoyi Zhao
- Department of Orthopedics, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, Liaoning, China
| | - Junxing Qu
- Department of Orthopedics, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, Liaoning, China
| | - Ziyang Yuan
- Department of Orthopedics, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, Liaoning, China
| | - Zhihong Cheng
- Department of Orthopedics, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, Liaoning, China
| | - Xiaojuan Zhu
- Key Laboratory of Molecular Epigenetics, Ministry of Education and Institute of Cytology and Genetics, Northeast Normal University, Changchun, Jilin, China
| | - Xiuli Zhuang
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry Chinese Academy of Sciences, Changchun, Jilin, China
| | - Zhiyu Zhang
- Department of Orthopedics, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, Liaoning, China.
| |
Collapse
|
16
|
Ghosh S, Keretsu S, Cho SJ. Designing of the N-ethyl-4-(pyridin-4-yl)benzamide based potent ROCK1 inhibitors using docking, molecular dynamics, and 3D-QSAR. PeerJ 2021; 9:e11951. [PMID: 34434664 PMCID: PMC8359802 DOI: 10.7717/peerj.11951] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/20/2021] [Indexed: 01/20/2023] Open
Abstract
Rho-associated kinase-1 (ROCK1) has been recognized for its pivotal role in heart diseases, different types of malignancy, and many neurological disorders. Hyperactivity of ROCK phosphorylates the protein kinase-C (PKC), which ultimately induces smooth muscle cell contraction in the vascular system. Inhibition of ROCK1 has been shown to be a promising therapy for patients with cardiovascular disease. In this study, we have conducted molecular modeling techniques such as docking, molecular dynamics (MD), and 3-Dimensional structure-activity relationship (3D-QSAR) on a series of N-ethyl-4-(pyridin-4-yl)benzamide-based compounds. Docking and MD showed critical interactions and binding affinities between ROCK1 and its inhibitors. To establish the structure-activity relationship (SAR) of the compounds, 3D-QSAR techniques such as Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) were used. The CoMFA (q 2 = 0.774, r 2 = 0.965, ONC = 6, and r p r e d 2 = 0.703) and CoMSIA (q 2 = 0.676, r 2 = 0.949, ONC = 6, and r p r e d 2 = 0.548) both models have shown reasonable external predictive activity, and contour maps revealed favorable and unfavorable substitutions for chemical group modifications. Based on the contour maps, we have designed forty new compounds, among which, seven compounds exhibited higher predictive activity (pIC50). Further, we conducted the MD study, ADME/Tox, and SA score prediction using the seven newly designed compounds. The combination of docking, MD, and 3D-QSAR studies helps to understand the coherence modification of existing molecules. Our study may provide valuable insight into the development of more potent ROCK1 inhibitors.
Collapse
Affiliation(s)
- Suparna Ghosh
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju, South Korea
| | - Seketoulie Keretsu
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju, South Korea
| | - Seung Joo Cho
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju, South Korea.,Department of Cellular and Molecular Medicine, College of Medicine, Chosun University, Gwangju, South Korea
| |
Collapse
|
17
|
Hu Z, Wang C, Glunz PW, Li J, Cheadle NL, Chen AY, Chen XQ, Myers JE, Guarino VR, Rose A, Sack JS, Sitkoff D, Taylor DS, Xu S, Yan C, Zhang H, Zhang L, Hennan J, Adam LP, Wexler RR, Quan ML. Discovery of a phenylpyrazole amide ROCK inhibitor as a tool molecule for in vivo studies. Bioorg Med Chem Lett 2020; 30:127495. [PMID: 32798651 DOI: 10.1016/j.bmcl.2020.127495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 11/25/2022]
Abstract
Structure-activity relationship optimization on a series of phenylpyrazole amides led to the identification of a dual ROCK1 and ROCK2 inhibitor (25) which demonstrated good potency, kinome selectivity and favorable pharmacokinetic profiles. Compound 25 was selected as a tool molecule for in vivo studies including evaluating hemodynamic effects in telemeterized mice, from which moderate decreases in blood pressure were observed.
Collapse
Affiliation(s)
- Zilun Hu
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA.
| | - Cailan Wang
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Peter W Glunz
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Julia Li
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Nathan L Cheadle
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Alice Y Chen
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Xue-Qing Chen
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Joseph E Myers
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Victor R Guarino
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Anne Rose
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - John S Sack
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Doree Sitkoff
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - David S Taylor
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Songmei Xu
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Chunhong Yan
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Hongwei Zhang
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Lisa Zhang
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - James Hennan
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Leonard P Adam
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Ruth R Wexler
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| | - Mimi L Quan
- Research & Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, NJ 08543-5400, USA
| |
Collapse
|
18
|
Song L, Zhu C, Zheng W, Lu D, Jiao H, Zhao R, Bao Z. Computational systematic selectivity of the Fasalog inhibitors between ROCK-I and ROCK-II kinase isoforms in Alzheimer's disease. Comput Biol Chem 2020; 87:107314. [PMID: 32619776 DOI: 10.1016/j.compbiolchem.2020.107314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/31/2022]
Abstract
Human Rho-associated coiled-coil forming kinase (ROCK) is a class of essential neurokinases that consists of two structurally conserved isoforms ROCK-I and ROCK-II; they have been revealed to play distinct roles in the pathogenesis of Alzheimer's disease (AD) and other neurological disorders. Selective targeting of the two kinase isoforms with small-molecule inhibitors is a great challenge due to the surprisingly high homology in kinase domain (92 %) and the full identity in kinase active site (100 %). Here, we describe a computational protocol to systematically profile the selectivity of Fasudil and its 25 analogs (termed as Fasalogs) between the two kinase isoforms. It is suggested that the substitution of Fasudil's 1,4-diazepane moiety with rigid ring such as Ripasudil and Dimehtylfasudil would render the resulting inhibitors of ROCK-II over ROCK-I (II-o-I) selectivity, while the substitution with long, flexible group such as H-89 and BDBM92607 tends to have I-o-II selectivity. Structural analysis reveals that the inhibitor affinity is not only determined by the identical active site, but also contributed from the non-identical first and second shells of the site as well as other non-conserved kinase regions, which can indirectly influence the active site and inhibitor binding through allosteric effect. A further kinase assay basically confirms the computational findings, which also exhibits a good consistence with theoretical selectivity over 10 tested samples (Rp = 0.89). In particular, the Fasalog compounds Dimehtylfasudil and H-89 are identified as II-o-I and I-o-II selective inhibitors. They can be considered as promising lead molecular entities to develop new specific ROCK isoform-selective Fasalog inhibitors.
Collapse
Affiliation(s)
- Laijun Song
- Department of Neurology, Daqing Oil Field General Hospital, Daqing, 163001, China
| | - Chunyu Zhu
- Department of Neurology, Daqing Oil Field General Hospital, Daqing, 163001, China
| | - Wenxin Zheng
- Department of Neurology, Daqing Oil Field General Hospital, Daqing, 163001, China
| | - Dan Lu
- Department of Neurology, Daqing Oil Field General Hospital, Daqing, 163001, China
| | - Hong Jiao
- Department of Neurology, Second Affiliated Hospital, Harbin Medical University, Harbin, 150086, China
| | - Rongbing Zhao
- Department of Neurology, Daqing Oil Field General Hospital, Daqing, 163001, China.
| | - Zhonglei Bao
- Department of Neurology, Daqing Oil Field General Hospital, Daqing, 163001, China.
| |
Collapse
|
19
|
Keretsu S, Bhujbal SP, Joo Cho S. Computational study of paroxetine-like inhibitors reveals new molecular insight to inhibit GRK2 with selectivity over ROCK1. Sci Rep 2019; 9:13053. [PMID: 31506468 PMCID: PMC6736929 DOI: 10.1038/s41598-019-48949-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/19/2019] [Indexed: 01/08/2023] Open
Abstract
The G-protein coupled receptor kinase 2 (GRK2) regulates the desensitization of beta-adrenergic receptors (β-AR), and its overexpression has been implicated in heart failure. Hence, the inhibition of GRK2 is considered to be an important drug target for the treatment of heart failure. Due to the high sequence similarity of GRK2 with the A, G, and C family (AGC family) of kinases, the inhibition of GRK2 also leads to the inhibition of AGC kinases such as Rho-associated coiled-coil kinase 1 (ROCK1). Therefore, unraveling the mechanisms to selectively inhibit GRK2 poses an important challenge. We have performed molecular docking, three dimensional quantitative structure activity relationship (3D-QSAR), molecular dynamics (MD) simulation, and free energy calculations techniques on a series of 53 paroxetine-like compounds to understand the structural properties desirable for enhancing the inhibitory activity for GRK2 with selectivity over ROCK1. The formation of stable hydrogen bond interactions with the residues Phe202 and Lys220 of GRK2 seems to be important for selective inhibition of GRK2. Electropositive substituents at the piperidine ring and electronegative substituents near the amide linker between the benzene ring and pyrazole ring showed a higher inhibitory preference for GRK2 over ROCK1. This study may be used in designing more potent and selective GRK2 inhibitors for therapeutic intervention of heart failure.
Collapse
Affiliation(s)
- Seketoulie Keretsu
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Swapnil P Bhujbal
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Seung Joo Cho
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju, 501-759, Republic of Korea. .,Department of Cellular Molecular Medicine, College of Medicine, Chosun University, Gwangju, 501-759, Republic of Korea.
| |
Collapse
|
20
|
Dayal N, Mikek CG, Hernandez D, Naclerio GA, Yin Chu EF, Carter-Cooper BA, Lapidus RG, Sintim HO. Potently inhibiting cancer cell migration with novel 3H-pyrazolo[4,3-f]quinoline boronic acid ROCK inhibitors. Eur J Med Chem 2019; 180:449-456. [PMID: 31330446 DOI: 10.1016/j.ejmech.2019.06.089] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 06/28/2019] [Accepted: 06/28/2019] [Indexed: 01/01/2023]
Abstract
Rho-associated protein kinases (ROCKs) are ubiquitously expressed in most adult tissues, and are involved in modulating the cytoskeleton, protein synthesis and degradation pathways, synaptic function, and autophagy to list a few. A few ROCK inhibitors, such as fasudil and netarsudil, are approved for clinical use. Here we present a new ROCK inhibitor, boronic acid containing HSD1590, which is more potent than netarsudil at binding to or inhibiting ROCK enzymatic activities. This compound exhibits single digit nanomolar binding to ROCK (Kds < 2 nM) and subnanomolar enzymatic inhibition profile (ROCK2 IC50 is 0.5 nM for HSD1590. Netarsudil, an FDA-approved drug, inhibited ROCK2 with IC50 = 11 nM under similar conditions). Whereas netarsudil was cytotoxic to breast cancer cell line, MDA-MB-231 (greater than 80% growth inhibition at concentrations greater than 5 μM), HSD1590 displayed low cytotoxicity to MDA-MB-231. Interestingly, at 1 μM HSD1590 inhibited the migration of MDA-MB-231 whereas netarsudil did not.
Collapse
Affiliation(s)
- Neetu Dayal
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Clinton G Mikek
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Delmis Hernandez
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - George A Naclerio
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Elizabeth Fei Yin Chu
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Brandon A Carter-Cooper
- Translational Core Laboratory, University of Maryland Greenebaum Cancer Center, 655 W Baltimore Street, Baltimore, MD, 21201, USA
| | - Rena G Lapidus
- Translational Core Laboratory, University of Maryland Greenebaum Cancer Center, 655 W Baltimore Street, Baltimore, MD, 21201, USA
| | - Herman O Sintim
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA; Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN, 47907, USA; Purdue Institute of Inflammation and Infectious Diseases, Purdue University, West Lafayette, IN, 47907, USA.
| |
Collapse
|
21
|
Montaruli M, Alberga D, Ciriaco F, Trisciuzzi D, Tondo AR, Mangiatordi GF, Nicolotti O. Accelerating Drug Discovery by Early Protein Drug Target Prediction Based on a Multi-Fingerprint Similarity Search. Molecules 2019; 24:molecules24122233. [PMID: 31207991 PMCID: PMC6631269 DOI: 10.3390/molecules24122233] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/08/2019] [Accepted: 06/12/2019] [Indexed: 01/06/2023] Open
Abstract
In this continuing work, we have updated our recently proposed Multi-fingerprint Similarity Search algorithm (MuSSel) by enabling the generation of dominant ionized species at a physiological pH and the exploration of a larger data domain, which included more than half a million high-quality small molecules extracted from the latest release of ChEMBL (version 24.1, at the time of writing). Provided with a high biological assay confidence score, these selected compounds explored up to 2822 protein drug targets. To improve the data accuracy, samples marked as prodrugs or with equivocal biological annotations were not considered. Notably, MuSSel performances were overall improved by using an object-relational database management system based on PostgreSQL. In order to challenge the real effectiveness of MuSSel in predicting relevant therapeutic drug targets, we analyzed a pool of 36 external bioactive compounds published in the Journal of Medicinal Chemistry from October to December 2018. This study demonstrates that the use of highly curated chemical and biological experimental data on one side, and a powerful multi-fingerprint search algorithm on the other, can be of the utmost importance in addressing the fate of newly conceived small molecules, by strongly reducing the attrition of early phases of drug discovery programs.
Collapse
Affiliation(s)
- Michele Montaruli
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via E. Orabona, 4, I-70125 Bari, Italy.
| | - Domenico Alberga
- Cineca, Via Magnanelli 6/3, 40033 Casalecchio di Reno, Bologna, Italy.
| | - Fulvio Ciriaco
- Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", via E. Orabona, 4, I-70125 Bari, Italy.
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via E. Orabona, 4, I-70125 Bari, Italy.
| | - Anna Rita Tondo
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via la Masa 19, 20156 Milano, Italy.
| | | | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via E. Orabona, 4, I-70125 Bari, Italy.
| |
Collapse
|