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Bhattacharjee A, Kar S, Ojha PK. Unveiling G-protein coupled receptor kinase-5 inhibitors for chronic degenerative diseases: Multilayered prioritization employing explainable machine learning-driven multi-class QSAR, ligand-based pharmacophore and free energy-inspired molecular simulation. Int J Biol Macromol 2024; 269:131784. [PMID: 38697440 DOI: 10.1016/j.ijbiomac.2024.131784] [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: 01/24/2024] [Revised: 04/02/2024] [Accepted: 04/21/2024] [Indexed: 05/05/2024]
Abstract
GRK5 holds a pivotal role in cellular signaling pathways, with its overexpression in cardiomyocytes, neuronal cells, and tumor cells strongly associated with various chronic degenerative diseases, which highlights the urgent need for potential inhibitors. In this study, multiclass classification-based QSAR models were developed using diverse machine learning algorithms. These models were built from curated compounds with experimentally derived GRK5 inhibitory activity. Additionally, a pharmacophore model was constructed using active compounds from the dataset. Among the models, the SVM-based approach proved most effective and was initially used to screen DrugBank compounds within the applicability domain. Compounds showing significant GRK5 inhibitory potential underwent evaluation for key pharmacophoric features. Prospective compounds were subjected to molecular docking to assess binding affinity towards GRK5's key active site amino acid residues. Stability at the binding site was analyzed through 200 ns molecular dynamics simulations. MM-GBSA analysis quantified individual free energy components contributing to the total binding energy with respect to binding site residues. Metadynamics analysis, including PCA, FEL, and PDF, provided crucial insights into conformational changes of both apo and holo forms of GRK5 at defined energy states. The study identifies DB02844 (S-Adenosyl-1,8-Diamino-3-Thiooctane) and DB13155 (Esculin) as promising GRK5 inhibitors, warranting further in vitro and in vivo validation studies.
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Affiliation(s)
- Arnab Bhattacharjee
- Drug Discovery and Development Laboratory (DDD Lab), Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Supratik Kar
- Chemometrics and Molecular Modeling Laboratory, Department of Chemistry and Physics, Kean University, 1000 Morris Avenue, Union, NJ, 07083, USA
| | - Probir Kumar Ojha
- Drug Discovery and Development Laboratory (DDD Lab), Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India.
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2
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Gupta A, Haldhar R, Agarwal V, Rajput DS, Chun KS, Han SB, Raj V, Lee S. Exploring the Potential of Natural Products as FoxO1 Inhibitors: an In Silico Approach. Biomol Ther (Seoul) 2024; 32:390-398. [PMID: 38586882 PMCID: PMC11063485 DOI: 10.4062/biomolther.2023.156] [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: 09/05/2023] [Revised: 10/14/2023] [Accepted: 10/21/2023] [Indexed: 04/09/2024] Open
Abstract
FoxO1, a member of the Forkhead transcription factor family subgroup O (FoxO), is expressed in a range of cell types and is crucial for various pathophysiological processes, such as apoptosis and inflammation. While FoxO1's roles in multiple diseases have been recognized, the target has remained largely unexplored due to the absence of cost-effective and efficient inhibitors. Therefore, there is a need for natural FoxO1 inhibitors with minimal adverse effects. In this study, docking, MMGBSA, and ADMET analyses were performed to identify natural compounds that exhibit strong binding affinity to FoxO1. The top candidates were then subjected to molecular dynamics (MD) simulations. A natural product library was screened for interaction with FoxO1 (PDB ID- 3CO6) using the Glide module of the Schrödinger suite. In silico ADMET profiling was conducted using SwissADME and pkCSM web servers. Binding free energies of the selected compounds were assessed with the Prime-MMGBSA module, while the dynamics of the top hits were analyzed using the Desmond module of the Schrödinger suite. Several natural products demonstrated high docking scores with FoxO1, indicating their potential as FoxO1 inhibitors. Specifically, the docking scores of neochlorogenic acid and fraxin were both below -6.0. These compounds also exhibit favorable drug-like properties, and a 25 ns MD study revealed a stable interaction between fraxin and FoxO1. Our findings highlight the potential of various natural products, particularly fraxin, as effective FoxO1 inhibitors with strong binding affinity, dynamic stability, and suitable ADMET profiles.
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Affiliation(s)
- Anugya Gupta
- Faculty of Medical and Paramedical Sciences, Madhyanchal Professional University, Bhopal 462044, Madhya Pradesh, India
| | - Rajesh Haldhar
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Vipul Agarwal
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, Uttar Pradesh, India
| | - Dharmendra Singh Rajput
- Faculty of Medical and Paramedical Sciences, Madhyanchal Professional University, Bhopal 462044, Madhya Pradesh, India
| | - Kyung-Soo Chun
- College of Pharmacy, Keimyung University, Daegu 42601, Republic of Korea
| | - Sang Beom Han
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Vinit Raj
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sangkil Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
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3
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Ahamad S, Hema K, Gupta D. Identification of Novel Tau-Tubulin Kinase 2 Inhibitors Using Computational Approaches. ACS OMEGA 2023; 8:13026-13037. [PMID: 37065061 PMCID: PMC10099139 DOI: 10.1021/acsomega.3c00225] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
Tau tubulin kinase 2 (TTBK2) associated with multiple diseases is one of the kinases which phosphorylates tau and tubulin. Numerous efforts have been made to understand the role of TTBK2 in protein folding mechanisms and misfolding behavior. The misfolded protein intermediates form polymers with unwanted aggregation properties that initiate several diseases, including Alzheimer's. The availability of TTBK2 inhibitors can enhance the understanding of the molecular mechanism of action of the kinase and assist in developing novel therapeutics. In the quest for TTBK2 inhibitors, this study focuses on screening two chemical libraries (ChEMBL and ZINC-FDA). The molecular docking, RO5/absorption, distribution, metabolism, and excretion/toxicity, density functional theory, molecular dynamics (MD) simulations, and molecular mechanics with generalized Born and surface area solvation techniques enabled shortlisting of the four most active compounds, namely, ChEMBL1236395, ChEMBL2104398, ChEMBL3427435, and ZINC000000509440. Moreover, 500 ns MD simulation was performed for each complex, which provided valuable insights into the structural changes in the complexes. The relative fluctuation, solvent accessible surface area, atomic gyration, compactness covariance, and free energy landscapes revealed that the compounds could stabilize the TTBK2 protein. Overall, this study would be valuable for the researchers targeting the development of novel TTBK2 inhibitors.
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Liao J, Wang Q, Wu F, Huang Z. In Silico Methods for Identification of Potential Active Sites of Therapeutic Targets. Molecules 2022; 27:7103. [PMID: 36296697 PMCID: PMC9609013 DOI: 10.3390/molecules27207103] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/12/2022] [Accepted: 08/25/2022] [Indexed: 07/30/2023] Open
Abstract
Target identification is an important step in drug discovery, and computer-aided drug target identification methods are attracting more attention compared with traditional drug target identification methods, which are time-consuming and costly. Computer-aided drug target identification methods can greatly reduce the searching scope of experimental targets and associated costs by identifying the diseases-related targets and their binding sites and evaluating the druggability of the predicted active sites for clinical trials. In this review, we introduce the principles of computer-based active site identification methods, including the identification of binding sites and assessment of druggability. We provide some guidelines for selecting methods for the identification of binding sites and assessment of druggability. In addition, we list the databases and tools commonly used with these methods, present examples of individual and combined applications, and compare the methods and tools. Finally, we discuss the challenges and limitations of binding site identification and druggability assessment at the current stage and provide some recommendations and future perspectives.
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Affiliation(s)
- Jianbo Liao
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory of Computer-Aided Drug Design of Dongguan City, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan 523808, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan 523808, China
| | - Qinyu Wang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory of Computer-Aided Drug Design of Dongguan City, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan 523808, China
| | - Fengxu Wu
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, School of Pharmaceutical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - Zunnan Huang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory of Computer-Aided Drug Design of Dongguan City, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan 523808, China
- Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang 524023, China
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5
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Yao H. Virtual Screening of Natural Chemical Databases to Search for Potential ACE2 Inhibitors. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27051740. [PMID: 35268841 PMCID: PMC8911956 DOI: 10.3390/molecules27051740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 11/25/2022]
Abstract
The angiotensin-converting enzyme II (ACE2) is a multifunctional protein in both health and disease conditions, which serves as a counterregulatory component of RAS function in a cardioprotective role. ACE2 modulation may also have relevance to ovarian cancer, diabetes, acute lung injury, fibrotic diseases, etc. Furthermore, since the outbreak of the coronavirus disease in 2019 (COVID-19), ACE2 has been recognized as the host receptor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The receptor binding domain of the SARS-CoV-2 S-protein has a strong interaction with ACE2, so ACE2 may be a potent drug target to prevent the virus from invading host cells for anti-COVID-19 drug discovery. In this study, structure- and property-based virtual screening methods were combined to filter natural product databases from ChemDiv, TargetMol, and InterBioScreen to find potential ACE2 inhibitors. The binding affinity between protein and ligands was predicted using both Glide SP and XP scoring functions and the MM-GBSA method. ADME properties were also calculated to evaluate chemical drug-likeness. Then, molecular dynamics (MD) simulations were performed to further explore the binding modes between the highest-potential compounds and ACE2. Results showed that the compounds 154-23-4 and STOCK1N-07141 possess potential ACE2 inhibition activities and deserve further study.
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Affiliation(s)
- Huiping Yao
- Department of Obstetrics and Gynecology, The First Hospital of Lanzhou University, Lanzhou 730013, China
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6
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Ganeshan S, Shakibaie MR, Rajagopal R. Insights from the molecular docking analysis of colistin with the PmrA protein model from Acinetobacter baumannii. Bioinformation 2022; 18:41-49. [PMID: 35815194 PMCID: PMC9200612 DOI: 10.6026/97320630018041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/03/2022] Open
Abstract
Acinetobacter baumannii (AB) is one of the most common causes of nosocomial infections. Therefore, it is of interest to design and develop drugs against Acinetobacter baumannii. A strain of AB showing MIC 32 µg/ml against colistin was isolated from a hospital environment in Iran. Hence, we document data to glean insights from the molecular docking analysis of colistin with the PmrA protein from this bacterium.
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Affiliation(s)
- Shalini Ganeshan
- Department of Biotechnology, Tips college of arts and science, Coimbatore, Tamil Nadu 641107, India
| | - Mohammad Reza Shakibaie
- Department of Microbiology and Virology, Kerman University of Medical Sciences, Kerman, Iran
- Environmental Health Engineering Research Center, Kerman University of Medical Science, Kerman, Iran
| | - Rajaguru Rajagopal
- Research Scholar Department of Pharmaceutics, Mother Theresa Post Graduate and Research Institute of Health Sciences, Pondicherry-605006, India
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7
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Wu WJ, Xia CL, Ou SJ, Yang Y, Ma YF, Hou YL, Yang QP, Zhang J, Li JW, Qi Y, Xu CP. Novel Elongator Protein 2 Inhibitors Mitigating Tumor Necrosis Factor- α Induced Osteogenic Differentiation Inhibition. BIOMED RESEARCH INTERNATIONAL 2021; 2021:3664564. [PMID: 34853789 PMCID: PMC8629650 DOI: 10.1155/2021/3664564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022]
Abstract
Tumor necrosis factor-α is a common cytokine that increases in inflammatory processes, slows the differentiation of bone formation, and induces osteodystrophy in the long-term inflammatory microenvironment. Our previous study confirmed that the Elongation protein 2 (ELP2) plays a significant role in osteogenesis and osteogenic differentiation, which is considered a drug discovery target in diseases related to bone formation and differentiation. In this study, we applied an in silico virtual screening method to select molecules that bind to the ELP2 protein from a chemical drug molecule library and obtained 95 candidates. Then, we included 11 candidates by observing the docking patterns and the noncovalent bonds. The binding affinity of the ELP2 protein with the candidate compounds was examined by SPR analysis, and 5 out of 11 compounds performed good binding affinity to the mouse ELP2 protein. After in vitro cell differentiation assay, candidates 2# and 5# were shown to reduce differentiation inhibition after tumor necrosis factor-α stimulation, allowing further optimization and development for potential clinical treatment of inflammation-mediated orthopedic diseases.
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Affiliation(s)
- Wen-Jiao Wu
- Department of Medical Research Center, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Chang-Liang Xia
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Shuan-Ji Ou
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Yang Yang
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Yun-Fei Ma
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yi-Long Hou
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Qing-Po Yang
- Department of Orthopaedics, The First People's Hospital of Kashgar Prefecture, Kashgar, Xinjiang, China
| | - Jun Zhang
- Department of Orthopaedics, The First People's Hospital of Kashgar Prefecture, Kashgar, Xinjiang, China
| | - Jian-Wei Li
- Department of Orthopaedics, Shenzhen Shekou People's Hospital, Shenzhen, Guangdong, China
| | - Yong Qi
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Chang-Peng Xu
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
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8
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Targeting the Autophagy Specific Lipid Kinase VPS34 for Cancer Treatment: An Integrative Repurposing Strategy. Protein J 2021; 40:41-53. [PMID: 33400087 DOI: 10.1007/s10930-020-09955-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
The impact of autophagy on cancer treatment and its corresponding responsiveness has galvanized the scientific community to develop novel inhibitors for cancer treatment. Importantly, the discovery of inhibitors that targets the early phase of autophagy was identified as a beneficial choice. Despite the number of research in recent years, screening of the DrugBank repository (9591 molecules) for the Vacuolar protein sorting 34 (VPS34) has not been reported earlier. Therefore, the present study was designed to identify potential VPS34 antagonists using integrated pharmacophore strategies. Primarily, an energy-based pharmacophore and receptor cavity-based analysis yielded five (DHRRR) and seven featured (AADDHRR) pharmacophore hypotheses respectively, which were utilized for the database screening process. The glide score, the binding free energy, pharmacokinetics and pharmacodynamics properties were examined to narrow down the screened compounds. This analysis yielded a hit molecule, DB03916 that exhibited a better docking score, higher binding affinity and better drug-like properties in contrast to the reference compound that suffers from a toxicity property. Importantly, the result was validated using a 50 ns molecular dynamics simulation study. Overall, we conclude that the identified hit molecule DB03916 is believed to serve as a prospective antagonist against VPS34 for cancer treatment.
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9
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Marwaha TK, Madgulkar A, Bhalekar M, Asgaonkar K. Molecular docking, synthesis, and characterization of chitosan‐graft‐2‐mercaptobenzoic acid derivative as potential drug carrier. J Appl Polym Sci 2020. [DOI: 10.1002/app.49551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | - Ashwini Madgulkar
- Department of Pharmaceutics AISSMS College of Pharmacy Pune Maharashtra India
| | - Mangesh Bhalekar
- Department of Pharmaceutics AISSMS College of Pharmacy Pune Maharashtra India
| | - Kalyani Asgaonkar
- Department of Pharmaceutics AISSMS College of Pharmacy Pune Maharashtra India
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10
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Todd GM, Gao Z, Hyvönen M, Brazil DP, Ten Dijke P. Secreted BMP antagonists and their role in cancer and bone metastases. Bone 2020; 137:115455. [PMID: 32473315 DOI: 10.1016/j.bone.2020.115455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/23/2020] [Accepted: 05/23/2020] [Indexed: 02/08/2023]
Abstract
Bone morphogenetic proteins (BMPs) are multifunctional secreted cytokines that act in a highly context-dependent manner. BMP action extends beyond the induction of cartilage and bone formation, to encompass pivotal roles in controlling tissue and organ homeostasis during development and adulthood. BMPs signal via plasma membrane type I and type II serine/threonine kinase receptors and intracellular SMAD transcriptional effectors. Exquisite temporospatial control of BMP/SMAD signalling and crosstalk with other cellular cues is achieved by a series of positive and negative regulators at each step in the BMP/SMAD pathway. The interaction of BMP ligand with its receptors is carefully controlled by a diverse set of secreted antagonists that bind BMPs and block their interaction with their cognate BMP receptors. Perturbations in this BMP/BMP antagonist balance are implicated in a range of developmental disorders and diseases, including cancer. Here, we provide an overview of the structure and function of secreted BMP antagonists, and summarize recent novel insights into their role in cancer progression and bone metastasis. Gremlin1 (GREM1) is a highly studied BMP antagonist, and we will focus on this molecule in particular and its role in cancer. The therapeutic potential of pharmacological inhibitors for secreted BMP antagonists for cancer and other human diseases will also be discussed.
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Affiliation(s)
- Grace M Todd
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, UK
| | - Zhichun Gao
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Derek P Brazil
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, UK.
| | - Peter Ten Dijke
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
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Divyashri G, Krishna Murthy TP, Sundareshan S, Kamath P, Murahari M, Saraswathy GR, Sadanandan B. In silico approach towards the identification of potential inhibitors from Curcuma amada Roxb against H. pylori: ADMET screening and molecular docking studies. ACTA ACUST UNITED AC 2020; 11:119-127. [PMID: 33842282 PMCID: PMC8022237 DOI: 10.34172/bi.2021.19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/05/2020] [Accepted: 03/16/2020] [Indexed: 12/13/2022]
Abstract
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Introduction: The present study attempts to identify potential targets of H. pylori for novel inhibitors from therapeutic herb, mango ginger (Curcuma amada Roxb.). Methods: Crystal structure of all the selected drug targets obtained from Protein Data Bank (PDB) were subjected to molecular docking against a total of 130 compounds (found to have biological activity against H. pylori ) were retrieved from public databases. Compounds with good binding affinity were selected for Prime MM-GBSA rescoring and molecular dynamics (MD) simulation. Final list of compounds were taken for ADMET predictions. Results: Based on binding affinity denoted by glide score and ligand efficiency, mango ginger compounds were found selective to shikimate kinase and type II dehydroquinase through hydrogen bonding and salt bridge interactions. Stability of the interactions and free energy calculations by Prime MM-GBSA results confirmed the affinity of mango ginger compounds towards both shikimate kinase and type II dehydroquinase. From the above results, 15 compounds were calculated for ADMET parameters, Lipinski’s rule of five, and the results were found promising without any limitations. MD simulations identified gentisic acid as hit compound for shikimate kinase of H. pylori. Conclusion: Current study could identify the in silico potential of mango ginger compounds against shikimate kinase and type II dehydroquinase targets for H. pylori infections and are suitable for in vitro and in vivo evaluation.
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Affiliation(s)
- G Divyashri
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bangalore, Karnataka, India
| | - T P Krishna Murthy
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bangalore, Karnataka, India
| | - Subramaniam Sundareshan
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bangalore, Karnataka, India
| | - Pavan Kamath
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bangalore, Karnataka, India
| | - Manikanta Murahari
- Pharmacological Modelling and Simulation Centre, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - G R Saraswathy
- Pharmacological Modelling and Simulation Centre, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India.,Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Bindu Sadanandan
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bangalore, Karnataka, India
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12
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Yang L, Liu S, Wang Y. Role of bone morphogenetic protein-2/4 in astrocyte activation in neuropathic pain. Mol Pain 2019; 15:1744806919892100. [PMID: 31726923 PMCID: PMC6886276 DOI: 10.1177/1744806919892100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Bone morphogenetic protein-2/4 (BMP2/4) has been recognized as promoters of astrocyte activity. Substantial evidence suggests that BMP2/4 may be elevated and plays a critical role in astrocyte activation upon spinal cord injury. Although neuropathic pain is similarly associated with astrocyte activation, the participation of BMP2/4 in this regard still remains unclear. Methods A rat model of neuropathic pain achieved by spinal nerve ligation at L5 was used to evaluate the expression of glial fibrillary acidic protein and BMP2/4 in the spinal cord in days 1, 4, 7, 10, and 14. Next, normal rats received intrathecal exogenous BMP2/4 and the antagonist Noggin to assess the effect of BMP2/4 on astrocyte activation. In both experiments, von Frey filaments were used to evaluate the changes in paw withdrawal threshold. In addition, Western blotting and immunofluorescence were performed to assess the expression of glial fibrillary acidic protein, BMP2/4, p-Smad 1/5/8, and phospho-signal transducer and activator of transcription-3 (p-STAT3) in the spinal cord. Results Firstly, spinal nerve ligation caused a significant increase in the expression of BMP4, while BMP2 levels remained unchanged. Secondly, exogenous BMP4 but not BMP2 induced a significant decrease in paw withdrawal threshold, along with the upregulation of glial fibrillary acidic protein. Moreover, exogenous BMP4 stimulated both p-Smad 1/5/8 and p-STAT3, while BMP2 only upregulated p-Smad 1/5/8. Finally, exogenous Noggin alleviated the decrease in paw withdrawal threshold induced by BMP4 and reduced astrocyte activation, as well as p-STAT3 upregulation. Conclusions Our results indicate only BMP4—and not BMP2—intervened in allodynia in rats by eliciting glial activation probably through both p-Smad 1/5/8 and p-STAT3 signaling.
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Affiliation(s)
- Lin Yang
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Province Center for Clinical Anesthesia and Anesthesiology, Research Institute of Central South University, Changsha, China
| | - Shuxin Liu
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Province Center for Clinical Anesthesia and Anesthesiology, Research Institute of Central South University, Changsha, China
| | - Yaping Wang
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Province Center for Clinical Anesthesia and Anesthesiology, Research Institute of Central South University, Changsha, China
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13
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Implementation of pharmacophore-based 3D QSAR model and scaffold analysis in order to excavate pristine ALK inhibitors. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02410-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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14
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Xu CP, Qi Y, Cui Z, Yang YJ, Wang J, Hu YJ, Yu B, Wang FZ, Yang QP, Sun HT. Discovery of novel elongator protein 2 inhibitors by compound library screening using surface plasmon resonance. RSC Adv 2019; 9:1696-1704. [PMID: 35518050 PMCID: PMC9059734 DOI: 10.1039/c8ra09640f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 12/26/2018] [Indexed: 12/13/2022] Open
Abstract
Tumour necrosis factor-α (TNF-α) is a pleiotropic cytokine that becomes elevated in chronic inflammatory states, including slowing down osteogenic differentiation, which leads to bone dysplasia in long-term inflammatory microenvironments. The elongator complex plays a role in gene regulation and association with various cellular activities, including the downstream signal transduction of TNF-α in osteogenic cells. To find an inhibitor of Elongator Protein 2 (Elp2), we performed a compound library screen and verified the pharmaceutical effects of candidate compounds on the mouse myoblast cell (C2C12) and mouse osteoblastic cells (MC3T3-E1). The commercial FDA-approved drug (FD) library and the bioactive compound (BC) library were used as candidate libraries. After a label-free, high-throughput affinity measurement with surface plasmon resonance (SPRi), seven kinds of compounds showed binding affinity with mouse Elp2 protein. The seven candidates were then used to perform an inhibition test with TNF-α-induced C2C12 and MC3T3-E1 cell lines. One candidate compound reduced the differentiation suppression caused by TNF-α with resuscitated alkaline phosphatase (ALP) activity, mineralization intensity and expression of osteogenic differentiation marker genes. The results of our study provide a competitive candidate to mitigate the TNF-α-induced osteogenic differentia.
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Affiliation(s)
- Chang-Peng Xu
- Department of Orthopaedics, Guangdong Second Provincial General Hospital Guangzhou Guangdong P. R. China
| | - Yong Qi
- Department of Orthopaedics, Guangdong Second Provincial General Hospital Guangzhou Guangdong P. R. China
| | - Zhuang Cui
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University Guangzhou Guangdong P. R. China
| | - Ya-Jun Yang
- Department of Pharmacology, Guangdong Medical College Zhanjiang Guangdong P. R. China
| | - Jian Wang
- Department of Orthopaedics, The Inner Mongolia People's Hospital Hohhot Inner Mongolia P. R. China
| | - Yan-Jun Hu
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University Guangzhou Guangdong P. R. China
| | - Bin Yu
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University Guangzhou Guangdong P. R. China
| | - Fa-Zheng Wang
- Department of Orthopaedics, The First People's Hospital of Kashgar Prefecture Kashgar Xinjiang P. R. China
| | - Qing-Po Yang
- Department of Orthopaedics, The First People's Hospital of Kashgar Prefecture Kashgar Xinjiang P. R. China
| | - Hong-Tao Sun
- Department of Orthopaedics, Guangdong Second Provincial General Hospital Guangzhou Guangdong P. R. China
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Low-intensity pulsed ultrasound stimulation facilitates in vitro osteogenic differentiation of human adipose-derived stem cells via up-regulation of heat shock protein (HSP)70, HSP90, and bone morphogenetic protein (BMP) signaling pathway. Biosci Rep 2018; 38:BSR20180087. [PMID: 29789443 PMCID: PMC6048203 DOI: 10.1042/bsr20180087] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/28/2018] [Accepted: 04/10/2018] [Indexed: 02/01/2023] Open
Abstract
Low-intensity pulsed ultrasound (LIPUS) has positive effects on osteogenic differentiation. However, the effect of LIPUS on osteogenic differentiation of human adipose-derived stem cells (hASCs) is unclear. In the present study, we investigated whether LIPUS could promote the proliferation and osteogenic differentiation of hASCs. hASCs were isolated and osteogenically induced with LIPUS stimulation at 20 and 30 mW cm-2 for 30 min day-1 Cell proliferation and osteogenic differentiation potential of hASCs were respectively analyzed by cell counting kit-8 assay, Alizarin Red S staining, real-time polymerase chain reaction, and Western blotting. The results indicated that LIPUS stimulation did not significantly affect the proliferation of hASCs, but significantly increased their alkaline phosphatase activity on day 6 of culture and markedly promoted the formation of mineralized nodules on day 21 of culture. The mRNA expression levels of runt-related transcription factor, osteopontin, and osteocalcin were significantly up-regulated by LIPUS stimulation. LIPUS stimulation did not affect the expression of heat shock protein (HSP) 27, HSP40, bone morphogenetic protein (BMP)-6 and BMP-9, but significantly up-regulated the protein levels of HSP70, HSP90, BMP-2, and BMP-7 in the hASCs. Further studies found that LIPUS increased the mRNA levels of Smad 1 and Smad 5, elevated the phosphorylation of Smad 1/5, and suppressed the expression of BMP antagonist Noggin. These findings indicated that LIPUS stimulation enhanced osteogenic differentiation of hASCs possibly through the up-regulation of HSP70 and HSP90 expression and activation of BMP signaling pathway. Therefore, LIPUS might have the potential to promote the repair of bone defect.
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