1
|
Ma L, Li M, Lv J, Yuan Q, Yin X, Lu W, Lin W, Wang P, Cui J, Lv Q, Liu J, Hu L. Design, synthesis, and biological evaluation of novel sesquiterpene lactone derivatives as PKM2 activators with potent anti-ulcerative colitis activities. Eur J Med Chem 2024; 272:116426. [PMID: 38718622 DOI: 10.1016/j.ejmech.2024.116426] [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: 01/10/2024] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 05/27/2024]
Abstract
Pyruvate kinase isoform 2 (PKM2) is closely related to the regulation of Th17/Treg balance, which is considered to be an effective strategy for UC therapy. Parthenolide (PTL), a natural product, only possesses moderate PKM2-activating activity. Thus, five series of PTL derivatives are designed and synthesized to improve PKM2-activated activities and anti-UC abilities. Through detailed structure optimization, B4 demonstrates potent T-cell anti-proliferation activity (IC50 = 0.43 μM) and excellent PKM2-activated ability (AC50 = 0.144 μM). Subsequently, through mass spectrometry analysis, B4 is identified to interact with Cys423 of PKM2 via covalent-bond. Molecular docking and molecular dynamic simulation results reveal that the trifluoromethoxy of B4 forms a stronger hydrophobic interaction with Ala401, Pro402, and Ile403. In addition, B4 has a significant effect only on Th17 cell differentiation, thereby regulating the Th17/Treg balance. The effect of B4 on Th17/Treg imbalance can be attributed to inhibition of PKM2 dimer translocation and suppression of glucose metabolism. Finally, B4 can notably ameliorate the symptoms of dextran sulfate sodium (DSS)-induced colitis in mouse model in vivo. Thus, B4 is confirmed as a potent PKM2 activator, and has the potential to develop as a novel anti-UC agent.
Collapse
Affiliation(s)
- Lingyu Ma
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Mengting Li
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jiahao Lv
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qingxin Yuan
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xunkai Yin
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Wenyu Lu
- School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Weijiang Lin
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Ping Wang
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jian Cui
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qi Lv
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Jian Liu
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Lihong Hu
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| |
Collapse
|
2
|
Nandi A, Nigar T, Das A, Dey YN. Network pharmacology analysis of Plumbago zeylanica to identify the therapeutic targets and molecular mechanisms involved in ameliorating hemorrhoids. J Biomol Struct Dyn 2023:1-15. [PMID: 37948311 DOI: 10.1080/07391102.2023.2280681] [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: 08/02/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
Plumbago zeylanica is an important plant used in the Ayurvedic system of medicine for the treatment of hemorrhoids or piles. Despite its clinical uses, its molecular mechanism, for ameliorating hemorrhoids is not yet explored. Hence, the present study evaluated the plausible molecular mechanisms of P. zeylanica in the treatment of hemorrhoids using network pharmacology and other in silico analysis. Network pharmacology was carried out by protein, GO, and KEGG enrichment analysis. Further ADME/T, molecular docking and dynamics studies of the resultant bioactive compounds of P. zeylanica with the regulated proteins were evaluated. Results of the network pharmacology analysis revealed that the key pathways and plausible molecular mechanisms involved in the treatment effects of P. zeylanica on hemorrhoids are cell migration, proliferation, motility, and apoptosis which are synchronized by cancer, focal adhesion, and by signalling relaxin, Rap1, and calcium pathways which indicates the involvement of angiogenesis and vasodilation which are the characteristic features of hemorrhoids. Further, the molecular docking and dynamics studies revealed that the bio active ingredients of P. zeylanica strongly bind with the key target proteins in the ambiance of hemorrhoids. Hence, the study revealed the mechanism of P. zeylanica in ameliorating hemorrhoids.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Arijit Nandi
- Department of Pharmacology, Dr. B.C. Roy College of Pharmacy and Allied Health Sciences, West Bengal, India
| | - Tanzeem Nigar
- Department of Pharmacology, Dr. B.C. Roy College of Pharmacy and Allied Health Sciences, West Bengal, India
| | - Anwesha Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Ahmedabad, Palaj, Gandhinagar, Gujarat, India
| | - Yadu Nandan Dey
- Department of Pharmacology, Dr. B.C. Roy College of Pharmacy and Allied Health Sciences, West Bengal, India
| |
Collapse
|
3
|
Xie F, Gan L, Lei L, Cai T, Gao Y, Liu X, Cai B, Zhou L. Clinical outcome and genotype analysis of four Chinese children with pyruvate kinase deficiency. Mol Genet Genomic Med 2023; 11:e2239. [PMID: 37466302 PMCID: PMC10655518 DOI: 10.1002/mgg3.2239] [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: 02/22/2023] [Revised: 06/26/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Pyruvate kinase deficiency (PKD) is a rare congenital hemolytic anemia. Here, we summarized the clinical features and laboratory examinations of four Chinese children with PKD and analyze genomic mutations. METHOD Collected and analyzed the clinical data of all children and their parents and completed the relevant laboratory examinations of all children. Analyzed the sequences of related genes in children by second-generation sequencing technology and verified the suspected mutations in children's family by Sanger sequencing method or second-generation sequencing technology. RESULTS A total of six mutations in gene PKLR were detected in four cases. Except for c.1510C>T (P1) and c.941T>C (P2 and P4), which had been reported in previous studies, the other four novel gene mutations were reported for the first time, including a rare homozygous mutation with large fragment deletion. All those gene mutations cause changes in the amino acids encoded by the gene, as well as subsequent changes in protein structure or loss of function. CONCLUSION Compound heterozygous or homozygous mutations in the coding region of PKLR gene are the causes of PKD in these four Chinese children. The second-generation sequencing technology is an effective means to diagnose PKD. The mutations of c.457-c.462delATCGCC, c.1297T>C, c.1096C>T and Exon4-10del of PKLR reported in this article have not been included in the Thousand Genome Database, dbSNP(v138) and ExAC Database. The PKLR gene mutations found in these children with PKD can provide references for further research of the genetic characteristics of PKD and subsequent gene therapy.
Collapse
Affiliation(s)
- Fei Xie
- Department of PediatricsThe First Affiliated Hospital of Naval Medical UniversityShanghaiChina
| | - Lu Gan
- Department of PediatricsThe First Affiliated Hospital of Naval Medical UniversityShanghaiChina
| | - Lei Lei
- Department of PediatricsThe First Affiliated Hospital of Naval Medical UniversityShanghaiChina
| | - Tengguang Cai
- Department of PediatricsThe First Affiliated Hospital of Naval Medical UniversityShanghaiChina
| | - Yu Gao
- Department of PediatricsThe First Affiliated Hospital of Naval Medical UniversityShanghaiChina
| | - Xiaoying Liu
- Department of PediatricsThe First Affiliated Hospital of Naval Medical UniversityShanghaiChina
| | - Bin Cai
- Department of PediatricsThe First Affiliated Hospital of Naval Medical UniversityShanghaiChina
| | - Lin Zhou
- Department of PediatricsThe First Affiliated Hospital of Naval Medical UniversityShanghaiChina
| |
Collapse
|
4
|
Çınaroğlu S, Biggin PC. Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems. J Chem Inf Model 2023; 63:6095-6108. [PMID: 37759363 PMCID: PMC10565830 DOI: 10.1021/acs.jcim.3c01041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Indexed: 09/29/2023]
Abstract
Understanding the thermodynamic signature of protein-peptide binding events is a major challenge in computational chemistry. The complexity generated by both components possessing many degrees of freedom poses a significant issue for methods that attempt to directly compute the enthalpic contribution to binding. Indeed, the prevailing assumption has been that the errors associated with such approaches would be too large for them to be meaningful. Nevertheless, we currently have no indication of how well the present methods would perform in terms of predicting the enthalpy of binding for protein-peptide complexes. To that end, we carefully assembled and curated a set of 11 protein-peptide complexes where there is structural and isothermal titration calorimetry data available and then computed the absolute enthalpy of binding. The initial "out of the box" calculations were, as expected, very modest in terms of agreement with the experiment. However, careful inspection of the outliers allows for the identification of key sampling problems such as distinct conformations of peptide termini not being sampled or suboptimal cofactor parameters. Additional simulations guided by these aspects can lead to a respectable correlation with isothermal titration calorimetry (ITC) experiments (R2 of 0.88 and an RMSE of 1.48 kcal/mol overall). Although one cannot know prospectively whether computed ITC values will be correct or not, this work shows that if experimental ITC data are available, then this in conjunction with computed ITC, can be used as a tool to know if the ensemble being simulated is representative of the true ensemble or not. That is important for allowing the correct interpretation of the detailed dynamics of the system with respect to the measured enthalpy. The results also suggest that computational calorimetry is becoming increasingly feasible. We provide the data set as a resource for the community, which could be used as a benchmark to help further progress in this area.
Collapse
Affiliation(s)
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| |
Collapse
|
5
|
Qu H, Liu J, Zhang D, Xie R, Wang L, Hong J. Glycolysis in Chronic Liver Diseases: Mechanistic Insights and Therapeutic Opportunities. Cells 2023; 12:1930. [PMID: 37566009 PMCID: PMC10417805 DOI: 10.3390/cells12151930] [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: 06/01/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Chronic liver diseases (CLDs) cover a spectrum of liver diseases, ranging from nonalcoholic fatty liver disease to liver cancer, representing a growing epidemic worldwide with high unmet medical needs. Glycolysis is a conservative and rigorous process that converts glucose into pyruvate and sustains cells with the energy and intermediate products required for diverse biological activities. However, abnormalities in glycolytic flux during CLD development accelerate the disease progression. Aerobic glycolysis is a hallmark of liver cancer and is responsible for a broad range of oncogenic functions including proliferation, invasion, metastasis, angiogenesis, immune escape, and drug resistance. Recently, the non-neoplastic role of aerobic glycolysis in immune activation and inflammatory disorders, especially CLD, has attracted increasing attention. Several key mediators of aerobic glycolysis, including HIF-1α and pyruvate kinase M2 (PKM2), are upregulated during steatohepatitis and liver fibrosis. The pharmacological inhibition or ablation of PKM2 effectively attenuates hepatic inflammation and CLD progression. In this review, we particularly focused on the glycolytic and non-glycolytic roles of PKM2 in the progression of CLD, highlighting the translational potential of a glycolysis-centric therapeutic approach in combating CLD.
Collapse
Affiliation(s)
| | | | | | | | | | - Jian Hong
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou 510632, China; (H.Q.)
| |
Collapse
|
6
|
Kapoor S, Chatterjee DR, Chowdhury MG, Das R, Shard A. Roadmap to Pyruvate Kinase M2 Modulation - A Computational Chronicle. Curr Drug Targets 2023; 24:464-483. [PMID: 36998144 DOI: 10.2174/1389450124666230330103126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 01/14/2023] [Accepted: 02/10/2023] [Indexed: 04/01/2023]
Abstract
Pyruvate kinase M2 (PKM2) has surfaced as a potential target for anti-cancer therapy. PKM2 is known to be overexpressed in the tumor cells and is a critical metabolic conduit in supplying the augmented bioenergetic demands of the recalcitrant cancer cells. The presence of PKM2 in structurally diverse tetrameric as well as dimeric forms has opened new avenues to design novel modulators. It is also a truism to state that drug discovery has advanced significantly from various computational techniques like molecular docking, virtual screening, molecular dynamics, and pharmacophore mapping. The present review focuses on the role of computational tools in exploring novel modulators of PKM2. The structural features of various isoforms of PKM2 have been discussed along with reported modulators. An extensive analysis of the structure-based and ligand- based in silico methods aimed at PKM2 modulation has been conducted with an in-depth review of the literature. The role of advanced tools like QSAR and quantum mechanics has been established with a brief discussion of future perspectives.
Collapse
Affiliation(s)
- Saumya Kapoor
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Ahmedabad, Opposite Air force Station Palaj, Gandhinagar-382355, Gujarat, India
| | - Deep Rohan Chatterjee
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Ahmedabad, Opposite Air force Station Palaj, Gandhinagar-382355, Gujarat, India
| | - Moumita Ghosh Chowdhury
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Ahmedabad, Opposite Air force Station Palaj, Gandhinagar-382355, Gujarat, India
| | - Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Ahmedabad, Opposite Air force Station Palaj, Gandhinagar-382355, Gujarat, India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Ahmedabad, Opposite Air force Station Palaj, Gandhinagar-382355, Gujarat, India
| |
Collapse
|
7
|
Chatterjee DR, Kapoor S, Jain M, Das R, Chowdhury MG, Shard A. PROTACting the kinome with covalent warheads. Drug Discov Today 2023; 28:103417. [PMID: 36306996 DOI: 10.1016/j.drudis.2022.103417] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/19/2022] [Accepted: 10/19/2022] [Indexed: 02/02/2023]
Abstract
The dawn of targeted degradation using proteolysis-targeting chimeras (PROTACs) against recalcitrant proteins has prompted numerous efforts to develop complementary drugs. Although many of these are specifically directed against undruggable proteins, there is increasing interest in small molecule-based PROTACs that target intracellular pathways, and some have recently entered clinical trials. Concurrently, small molecule-based PROTACs that target protumorigenic pathways in cancer cells, the tumor microenvironment (TME), and angiogenesis have been found to have potent effects that synergize with the action of antibodies. This has led to the augmentation of PROTACs with variable substitution patterns. Several combinations with small molecules targeting undruggable proteins are now under clinical investigation. In this review, we discuss the recent milestones achieved as well as challenges encountered in this area of drug development, as well as our opinion on the best path forward.
Collapse
Affiliation(s)
- Deep Rohan Chatterjee
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Saumya Kapoor
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Meenakshi Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Moumita Ghosh Chowdhury
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India.
| |
Collapse
|
8
|
Gupta A, Das R, Chamoli A, Choithramani A, Kumar H, Patel S, Khude D, Bothra G, Wangdale K, Ghosh Chowdhury M, Rathod R, Mandoli A, Shard A. A Series of Ferrocene-Containing Pyrazolo[1,5- a]pyrimidines Induce a Strong Antiproliferative Effect against Oral Cancer Cells. Organometallics 2022. [DOI: 10.1021/acs.organomet.2c00348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Astha Gupta
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research−Ahmedabad, Opposite Airforce Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research−Ahmedabad, Opposite Airforce Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Ambika Chamoli
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research−Ahmedabad, Opposite Airforce Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Asmita Choithramani
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research−Ahmedabad, Opposite Airforce Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Hansal Kumar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research−Ahmedabad, Opposite Airforce Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Sagarkumar Patel
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research−Ahmedabad, Opposite Airforce Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Datta Khude
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research−Ahmedabad, Opposite Airforce Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Gourav Bothra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research−Ahmedabad, Opposite Airforce Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Khushal Wangdale
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research−Ahmedabad, Opposite Airforce Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Moumita Ghosh Chowdhury
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research−Ahmedabad, Opposite Airforce Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Rajeshwari Rathod
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research−Ahmedabad, Opposite Airforce Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Amit Mandoli
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research−Ahmedabad, Opposite Airforce Station, Palaj, Gandhinagar, Gujarat 382355, India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research−Ahmedabad, Opposite Airforce Station, Palaj, Gandhinagar, Gujarat 382355, India
| |
Collapse
|
9
|
Das R, Ghosh Chowdhury M, Raundal S, Jadhav J, Kumar N, Patel S, Shard A. Objective assessment of adrenocortical carcinoma driver genes and their correlation with tumor pyruvate kinase M2. Gene 2022; 822:146354. [PMID: 35189247 DOI: 10.1016/j.gene.2022.146354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023]
Abstract
Glandular cancers have a significant share of the total cancer patients all over the world. In the case of adrenocortical carcinomas (ACCs), although the benign form is more frequent and common, the malignant form provides a very less percentage of patients with five or more than five years of survival rate. There are gene alterations that are involved as a crucial factor behind the occurrence of ACCs. Out of these, the most prominent genetic alterations (PRKAR-1A, CTNNB1, ZNRF3, TP53, CCNE1 and TERF2 genes) are linked with a glycolytic enzyme pyruvate kinase M2 (PKM2), which converts phosphoenolpyruvate (PEP) to pyruvate in the glycolytic pathway. The involvementof PKM2 renders a cumulative effect through different pathways that may result in the onset of ACCs. Thus, this review aims to establish a link between ACCs, alterations of specific genes and PKM2.
Collapse
Affiliation(s)
- Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research- Ahmedabad, Gandhinagar, Gujarat 380054, India
| | - Moumita Ghosh Chowdhury
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research- Ahmedabad, Gandhinagar, Gujarat 380054, India
| | - Sonal Raundal
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research- Ahmedabad, Gandhinagar, Gujarat 380054, India
| | - Jyotika Jadhav
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research- Ahmedabad, Gandhinagar, Gujarat 380054, India
| | - Navin Kumar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research- Ahmedabad, Gandhinagar, Gujarat 380054, India
| | - Sagarkumar Patel
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research- Ahmedabad, Gandhinagar, Gujarat 380054, India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research- Ahmedabad, Gandhinagar, Gujarat 380054, India.
| |
Collapse
|
10
|
Jadhav J, Das R, Kamble S, Chowdhury MG, Kapoor S, Gupta A, Vyas H, Shard A. Ferrocene-Based Modulators of Cancer-Associated Tumor Pyruvate Kinase M2. J Organomet Chem 2022. [DOI: 10.1016/j.jorganchem.2022.122338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
11
|
Arora S, Joshi G, Chaturvedi A, Heuser M, Patil S, Kumar R. A Perspective on Medicinal Chemistry Approaches for Targeting Pyruvate Kinase M2. J Med Chem 2022; 65:1171-1205. [PMID: 34726055 DOI: 10.1021/acs.jmedchem.1c00981] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The allosteric regulation of pyruvate kinase M2 (PKM2) affects the switching of the PKM2 protein between the high-activity and low-activity states that allow ATP and lactate production, respectively. PKM2, in its low catalytic state (dimeric form), is chiefly active in metabolically energetic cells, including cancer cells. More recently, PKM2 has emerged as an attractive target due to its role in metabolic dysfunction and other interrelated conditions. PKM2 (dimer) activity can be inhibited by modulating PKM2 dimer-tetramer dynamics using either PKM2 inhibitors that bind at the ATP binding active site of PKM2 (dimer) or PKM2 activators that bind at the allosteric site of PKM2, thus activating PKM2 from the dimer formation to the tetrameric formation. The present perspective focuses on medicinal chemistry approaches to design and discover PKM2 inhibitors and activators and further provides a scope for the future design of compounds targeting PKM2 with better efficacy and selectivity.
Collapse
Affiliation(s)
- Sahil Arora
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
| | - Gaurav Joshi
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
- School of Pharmacy, Graphic Era Hill University, Dehradun, Uttarakhand 248171, India
| | - Anuhar Chaturvedi
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover 30625, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover 30625, Germany
| | - Santoshkumar Patil
- Discovery Services, Syngene International Ltd., Biocon Park, SEZ, Bommasandra Industrial Area-Phase-IV, Bommasandra-Jigani Link Road, Bengaluru, Karnataka 560099, India
| | - Raj Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
| |
Collapse
|
12
|
A non-canonical role for pyruvate kinase M2 as a functional modulator of Ca 2+ signalling through IP 3 receptors. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119206. [PMID: 35026348 DOI: 10.1016/j.bbamcr.2021.119206] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 12/22/2022]
Abstract
Pyruvate kinase isoform M2 (PKM2) is a rate-limiting glycolytic enzyme that is widely expressed in embryonic tissues. The expression of PKM2 declines in some tissues following embryogenesis, while other pyruvate kinase isozymes are upregulated. However, PKM2 is highly expressed in cancer cells and is believed to play a role in supporting anabolic processes during tumour formation. In this study, PKM2 was identified as an inositol 1,4,5-trisphosphate receptor (IP3R)-interacting protein by mass spectrometry. The PKM2:IP3R interaction was further characterized by pull-down and co-immunoprecipitation assays, which showed that PKM2 interacted with all three IP3R isoforms. Moreover, fluorescence microscopy indicated that both IP3R and PKM2 localized at the endoplasmic reticulum. PKM2 binds to IP3R at a highly conserved 21-amino acid site (corresponding to amino acids 2078-2098 in mouse type 1 IP3R isoform). Synthetic peptides (denoted 'TAT-D5SD' and 'D5SD'), based on the amino acid sequence at this site, disrupted the PKM2:IP3R interaction and potentiated IP3R-mediated Ca2+ release both in intact cells (TAT-D5SD peptide) and in a unidirectional 45Ca2+ flux assay on permeabilized cells (D5SD peptide). The TAT-D5SD peptide did not affect the enzymatic activity of PKM2. Reducing PKM2 protein expression using siRNA increased IP3R-mediated Ca2+ signalling in intact cells without altering the ER Ca2+ content. These data identify PKM2 as an IP3R-interacting protein that inhibits intracellular Ca2+ signalling. The elevated expression of PKM2 in cancer cells is therefore not solely connected to its canonical role in glycolytic metabolism, rather PKM2 also has a novel non-canonical role in regulating intracellular signalling.
Collapse
|