101
|
Reddy NC, Molla R, Joshi PN, T. K. S, Basu I, Kawadkar J, Kalra N, Mishra RK, Chakrabarty S, Shukla S, Rai V. Traceless cysteine-linchpin enables precision engineering of lysine in native proteins. Nat Commun 2022; 13:6038. [PMID: 36229616 PMCID: PMC9561114 DOI: 10.1038/s41467-022-33772-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
The maintenance of machinery requires its operational understanding and a toolbox for repair. The methods for the precision engineering of native proteins meet a similar requirement in biosystems. Its success hinges on the principles regulating chemical reactions with a protein. Here, we report a technology that delivers high-level control over reactivity, chemoselectivity, site-selectivity, modularity, dual-probe installation, and protein-selectivity. It utilizes cysteine-based chemoselective Linchpin-Directed site-selective Modification of lysine residue in a protein (LDMC-K). The efficiency of the end-user-friendly protocol is evident in quantitative conversions within an hour. A chemically orthogonal C-S bond-formation and bond-dissociation are essential among multiple regulatory attributes. The method offers protein selectivity by targeting a single lysine residue of a single protein in a complex biomolecular mixture. The protocol renders analytically pure single-site probe-engineered protein bioconjugate. Also, it provides access to homogeneous antibody conjugates (AFC and ADC). The LDMC-K-ADC exhibits highly selective anti-proliferative activity towards breast cancer cells.
Collapse
Affiliation(s)
- Neelesh C. Reddy
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Rajib Molla
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Pralhad Namdev Joshi
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Sajeev T. K.
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Ipsita Basu
- grid.452759.80000 0001 2188 427XDepartment of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700 106 W.B. India
| | - Jyotsna Kawadkar
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | | | - Ram Kumar Mishra
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Suman Chakrabarty
- grid.452759.80000 0001 2188 427XDepartment of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700 106 W.B. India
| | - Sanjeev Shukla
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Vishal Rai
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| |
Collapse
|
102
|
Awoonor-Williams E. Estimating the binding energetics of reversible covalent inhibitors of the SARS-CoV-2 main protease: an in silico study. Phys Chem Chem Phys 2022; 24:23391-23401. [PMID: 36128834 DOI: 10.1039/d2cp03080b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The main protease (Mpro) of the SARS-CoV-2 virus is an attractive therapeutic target for developing antivirals to combat COVID-19. Mpro is essential for the replication cycle of the SARS-CoV-2 virus, so inhibiting Mpro blocks a vital piece of the cell replication machinery of the virus. A promising strategy to disrupt the viral replication cycle is to design inhibitors that bind to the active site cysteine (Cys145) of the Mpro. Cysteine targeted covalent inhibitors are gaining traction in drug discovery owing to the benefits of improved potency and extended drug-target engagement. An interesting aspect of these inhibitors is that they can be chemically tuned to form a covalent, but reversible bond, with their targets of interest. Several small-molecule cysteine-targeting covalent inhibitors of the Mpro have been discovered-some of which are currently undergoing evaluation in early phase human clinical trials. Understanding the binding energetics of these inhibitors could provide new insights to facilitate the design of potential drug candidates against COVID-19. Motivated by this, we employed rigorous absolute binding free energy calculations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations to estimate the energetics of binding of some promising reversible covalent inhibitors of the Mpro. We find that the inclusion of enhanced sampling techniques such as replica-exchange algorithm in binding free energy calculations can improve the convergence of predicted non-covalent binding free energy estimates of inhibitors binding to the Mpro target. In addition, our results indicate that binding free energy calculations coupled with multiscale simulations can be a useful approach to employ in ranking covalent inhibitors to their targets. This approach may be valuable in prioritizing and refining covalent inhibitor compounds for lead discovery efforts against COVID-19 and other coronavirus infections.
Collapse
Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada.
| |
Collapse
|
103
|
Tang R, Liu J, Li S, Zhang J, Yu C, Liu H, Chen F, Lv L, Zhang Q, Yuan K, Shao H. A patent and literature review of CDK12 inhibitors. Expert Opin Ther Pat 2022; 32:1055-1065. [PMID: 36120913 DOI: 10.1080/13543776.2022.2126765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Cyclin-dependent kinase 12 (CDK12) belongs to the CDK family of serine/threonine protein kinases and associates with cyclin K to exert its biological functions, including regulating gene transcription, mRNA processing and translation. Increasing evidences demonstrate the importance of CDK12 in various human cancers, illustrating its potential as both biomarker and therapeutic target. In addition, CDK12 is also a promising target for the treatment of myotonic dystrophy type 1. Efforts have been taken to discover small molecule inhibitors to validate this important therapeutic target. AREAS COVERED This review covers the patented CDK12 inhibitors from 2016 to present, as well as these from peer-reviewed literature. It provides the reader an update of the discovery strategies, chemical structures and molecular profiling of all available CDK12 inhibitors. EXPERT OPINION CDK12 inhibitors with various mechanism of actions have been discovered and it is a great set of tools to evaluate the therapeutic potential of CDK12 in different disease models. CDK12 inhibitors have shown promising results in myotonic dystrophy type 1 mouse model and several preclinical cancer models either as single agent or combination with other anti-cancer agents. Its therapeutic value awaits more rigorous preclinical testing and further clinical investigation.
Collapse
Affiliation(s)
- Ruijun Tang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China.,Center for Clinical Biorepositories and Biospecimen & Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jing Liu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Shuyao Li
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Junjie Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Chunhong Yu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Honglu Liu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Fang Chen
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Lu Lv
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Qian Zhang
- Department of Chemistry, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China.,Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,The Biobank of Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Hao Shao
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| |
Collapse
|
104
|
Protein tyrosine kinase inhibitor resistance in malignant tumors: molecular mechanisms and future perspective. Signal Transduct Target Ther 2022; 7:329. [PMID: 36115852 PMCID: PMC9482625 DOI: 10.1038/s41392-022-01168-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/08/2022] [Accepted: 08/26/2022] [Indexed: 02/07/2023] Open
Abstract
AbstractProtein tyrosine kinases (PTKs) are a class of proteins with tyrosine kinase activity that phosphorylate tyrosine residues of critical molecules in signaling pathways. Their basal function is essential for maintaining normal cell growth and differentiation. However, aberrant activation of PTKs caused by various factors can deviate cell function from the expected trajectory to an abnormal growth state, leading to carcinogenesis. Inhibiting the aberrant PTK function could inhibit tumor growth. Therefore, tyrosine kinase inhibitors (TKIs), target-specific inhibitors of PTKs, have been used in treating malignant tumors and play a significant role in targeted therapy of cancer. Currently, drug resistance is the main reason for limiting TKIs efficacy of cancer. The increasing studies indicated that tumor microenvironment, cell death resistance, tumor metabolism, epigenetic modification and abnormal metabolism of TKIs were deeply involved in tumor development and TKI resistance, besides the abnormal activation of PTK-related signaling pathways involved in gene mutations. Accordingly, it is of great significance to study the underlying mechanisms of TKIs resistance and find solutions to reverse TKIs resistance for improving TKIs efficacy of cancer. Herein, we reviewed the drug resistance mechanisms of TKIs and the potential approaches to overcome TKI resistance, aiming to provide a theoretical basis for improving the efficacy of TKIs.
Collapse
|
105
|
Karaj E, Sindi SH, Kuganesan N, Perera L, Taylor W, Viranga Tillekeratne LM. Tunable Cysteine-Targeting Electrophilic Heteroaromatic Warheads Induce Ferroptosis. J Med Chem 2022; 65:11788-11817. [PMID: 35984756 PMCID: PMC10408038 DOI: 10.1021/acs.jmedchem.2c00909] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Once considered potential liabilities, the modern era witnesses a renaissance of interest in covalent inhibitors in drug discovery. The available toolbox of electrophilic warheads is limited by constraints on tuning reactivity and selectivity. Following our work on a class of ferroptotic agents termed CETZOLEs, we discovered new tunable heterocyclic electrophiles which are capable of inducing ferroptosis. The biological evaluation demonstrated that thiazoles with an alkyne electrophile at the 2-position selectively induce ferroptosis with high potency. Density functional theory calculations and NMR kinetic studies demonstrated the ability of our heterocycles to undergo thiol addition, an apparent prerequisite for cytotoxicity. Chemoproteomic analysis indicated several potential targets, the most prominent among them being GPX4 protein. These results were further validated by western blot analysis and the cellular thermal shift assay. Incorporation of these heterocycles into appropriate pharmacophores generated highly cytotoxic agents such as the analogue BCP-T.A, with low nM IC50 values in ferroptosis-sensitive cell lines.
Collapse
Affiliation(s)
- Endri Karaj
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43606
| | - Shaimaa H. Sindi
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43606
| | - Nishanth Kuganesan
- Department of Biological Sciences, College of Natural Sciences and Mathematics, University of Toledo, Toledo, OH 43606
| | - Lalith Perera
- Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - William Taylor
- Department of Biological Sciences, College of Natural Sciences and Mathematics, University of Toledo, Toledo, OH 43606
| | - L. M. Viranga Tillekeratne
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43606
| |
Collapse
|
106
|
Liu Y, Guo Q, Yang H, Zhang XW, Feng N, Wang JK, Liu TT, Zeng KW, Tu PF. Allosteric Regulation of IGF2BP1 as a Novel Strategy for the Activation of Tumor Immune Microenvironment. ACS CENTRAL SCIENCE 2022; 8:1102-1115. [PMID: 36032766 PMCID: PMC9413439 DOI: 10.1021/acscentsci.2c00107] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Tumor immune microenvironment (TIME) regulators are promising cancer immunotherapeutic targets. IGF2BP1, as a crucial N 6-methyladenosine (m6A) reader protein, recognizes m6A target transcripts, ultimately leading to cancer development. However, currently, the biological function of IGF2BP1 in regulating the TIME is not well-understood. In this study, we report that IGF2BP1 knockdown induces cancer cell apoptosis, thereby significantly not only activating immune cell infiltration including CD4+, CD8+ T cells, CD56+ NK cells, and F4/80+ macrophage but also decreasing PD-L1 expression in hepatocellular carcinoma (HCC). Then, chemical genetics identifies a small-molecule cucurbitacin B (CuB), which directly targets IGF2BP1 at a unique site (Cys253) in the KH1-2 domains. This leads to a pharmacological allosteric effect to block IGF2BP1 recognition of m6A mRNA targets such as c-MYC, which is highly associated with cell apoptosis and immune response. In vivo, CuB exhibits an obvious anti-HCC effect through inducing apoptosis and subsequently recruits immune cells to tumor microenvironment as well as blocking PD-L1 expression. Collectively, IGF2BP1 may serve as a novel pharmacological allosteric target for anticancer therapeutics via mediating TIME.
Collapse
Affiliation(s)
- Yang Liu
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, Beijing 100191, China
- Center
of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, 49 N. Garden Road, Haidian District, Beijing 100191, China
| | - Qiang Guo
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, Beijing 100191, China
| | - Heng Yang
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, Beijing 100191, China
| | - Xiao-Wen Zhang
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, Beijing 100191, China
| | - Na Feng
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, Beijing 100191, China
| | - Jing-Kang Wang
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, Beijing 100191, China
| | - Ting-Ting Liu
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, Beijing 100191, China
| | - Ke-Wu Zeng
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, Beijing 100191, China
- E-mail: (KW Zeng)
| | - Peng-Fei Tu
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, Beijing 100191, China
- (PF
Tu)
| |
Collapse
|
107
|
Chen C, Yin Y, Shi G, Zhou Y, Shao S, Wei Y, Wu L, Zhang D, Sun L, Zhang T. A highly selective JAK3 inhibitor is developed for treating rheumatoid arthritis by suppressing γc cytokine-related JAK-STAT signal. SCIENCE ADVANCES 2022; 8:eabo4363. [PMID: 35984890 PMCID: PMC9390995 DOI: 10.1126/sciadv.abo4363] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/07/2022] [Indexed: 05/28/2023]
Abstract
Janus kinases (JAKs) play a critical role in immune responses by relaying signals from more than 50 cytokines, making them attractive therapeutic targets for autoimmune diseases. Although approved JAK inhibitors have demonstrated clinical efficacy, they target a broad spectrum of cytokines, which results in side effects. Therefore, next-generation inhibitors maintain efficacy, while sparing adverse events need to be developed. Among members of the JAK family, JAK3 only regulates a narrow spectrum of γc cytokines and becomes a potentially ideal target. Here, a highly JAK3-selective inhibitor Z583 is developed, which showed a potent inhibition of JAK3 with an IC50 of 0.1 nM and exhibited a 4500-fold selectivity for JAK3 than other JAK subtypes. Furthermore, Z583 completely inhibited the γc cytokine signaling and sufficiently blocked the development of inflammatory response in RA model, while sparing hematopoiesis. Collectively, the highly selective JAK3 inhibitor Z583 is a promising candidate with significant therapeutic potential for autoimmune diseases.
Collapse
Affiliation(s)
- Chengjuan Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yuan Yin
- School of Science, China Pharmaceutical University, Nanjing 210009, China
| | - Gaona Shi
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yu Zhou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shuai Shao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yazi Wei
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Lei Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Dayong Zhang
- School of Science, China Pharmaceutical University, Nanjing 210009, China
| | - Lan Sun
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Tiantai Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| |
Collapse
|
108
|
Lovell AR, Jammal N, Bose P. Selecting the optimal BTK inhibitor therapy in CLL: rationale and practical considerations. Ther Adv Hematol 2022; 13:20406207221116577. [PMID: 35966045 PMCID: PMC9373150 DOI: 10.1177/20406207221116577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Bruton's tyrosine kinase (BTK) inhibitors have dramatically changed the treatment of newly diagnosed and relapsed/refractory chronic lymphocytic leukemia (CLL). Ibrutinib, acalabrutinib, and zanubrutinib are Food and Drug Administration (FDA)-approved BTK inhibitors that have all demonstrated progression-free survival (PFS) benefit compared with chemoimmunotherapy. The efficacy of these agents compared to one another is under study; however, current data suggest they provide similar efficacy. Selectivity for BTK confers different adverse effect profiles, and longer follow-up and real-world use have characterized side effects over time. The choice of BTK inhibitor is largely patient-specific, and this review aims to highlight the differences among the agents and guide the choice of BTK inhibitor in clinical practice.
Collapse
Affiliation(s)
- Alexandra R. Lovell
- Division of Pharmacy, The University of Texas
MD Anderson Cancer Center, Houston, TX, USA
| | - Nadya Jammal
- Division of Pharmacy, The University of Texas
MD Anderson Cancer Center, Houston, TX, USA
| | - Prithviraj Bose
- Department of Leukemia, The University of Texas
MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| |
Collapse
|
109
|
Dempe DP, Ji CL, Liu P, Brummond KM. Thiol Reactivity of N-Aryl α-Methylene-γ-lactams: Influence of the Guaianolide Structure. J Org Chem 2022; 87:11204-11217. [PMID: 35930660 DOI: 10.1021/acs.joc.2c01530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The α-methylene-γ-lactam offers promise as a complementary warhead for the development of targeted covalent inhibitors. However, an understanding of the factors governing its electrophilic reactivity is needed to promote the development of lead compounds utilizing this motif. Herein we synthesize a series of N-aryl-substituted α-methylene-γ-lactams installed within the framework of a bioactive guaianolide analog. To determine the effects of the guaianolide structure on the electrophilic reactivity, these compounds were reacted with glutathione under biomimetic conditions, and the rate constants were measured. A linear free-energy relationship was observed with the Hammett parameter of the N-aryl group within the cis- or trans-annulated isomeric series of compounds. However, the trans-annulated compounds exhibited a ca. 10-fold increase in reactivity relative to both the cis-annulated compounds and the corresponding N-arylated 3-methylene-2-pyrrolidinones. Density functional theory calculations revealed that the reactivity of the trans-annulated stereoisomers is promoted by the partial release of the ring strain of the fused seven-membered ring in the thio-Michael addition transition state.
Collapse
Affiliation(s)
- Daniel P Dempe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | | | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States.,Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Kay M Brummond
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
110
|
de Boer C, Armstrong Z, Lit VAJ, Barash U, Ruijgrok G, Boyango I, Weitzenberg MM, Schröder SP, Sarris AJC, Meeuwenoord NJ, Bule P, Kayal Y, Ilan N, Codée JDC, Vlodavsky I, Overkleeft HS, Davies GJ, Wu L. Mechanism-based heparanase inhibitors reduce cancer metastasis in vivo. Proc Natl Acad Sci U S A 2022; 119:e2203167119. [PMID: 35881786 PMCID: PMC9351465 DOI: 10.1073/pnas.2203167119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/22/2022] [Indexed: 01/30/2023] Open
Abstract
Heparan sulfate proteoglycans (HSPGs) mediate essential interactions throughout the extracellular matrix (ECM), providing signals that regulate cellular growth and development. Altered HSPG composition during tumorigenesis strongly aids cancer progression. Heparanase (HPSE) is the principal enzyme responsible for extracellular heparan sulfate catabolism and is markedly up-regulated in aggressive cancers. HPSE overactivity degrades HSPGs within the ECM, facilitating metastatic dissemination and releasing mitogens that drive cellular proliferation. Reducing extracellular HPSE activity reduces cancer growth, but few effective inhibitors are known, and none are clinically approved. Inspired by the natural glycosidase inhibitor cyclophellitol, we developed nanomolar mechanism-based, irreversible HPSE inhibitors that are effective within physiological environments. Application of cyclophellitol-derived HPSE inhibitors reduces cancer aggression in cellulo and significantly ameliorates murine metastasis. Mechanism-based irreversible HPSE inhibition is an unexplored anticancer strategy. We demonstrate the feasibility of such compounds to control pathological HPSE-driven malignancies.
Collapse
Affiliation(s)
- Casper de Boer
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Zachary Armstrong
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
- Current address: Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Vincent A. J. Lit
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Uri Barash
- Technion Integrated Cancer Center, The Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Gijs Ruijgrok
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Ilanit Boyango
- Technion Integrated Cancer Center, The Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Merle M. Weitzenberg
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Sybrin P. Schröder
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Alexi J. C. Sarris
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Nico J. Meeuwenoord
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Pedro Bule
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
- Current address: Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
| | - Yasmine Kayal
- Technion Integrated Cancer Center, The Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Neta Ilan
- Technion Integrated Cancer Center, The Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Jeroen D. C. Codée
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Israel Vlodavsky
- Technion Integrated Cancer Center, The Bruce Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Herman S. Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Gideon J. Davies
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Liang Wu
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
- The Rosalind Franklin Institute, Harwell, OX11 0FA, UK
| |
Collapse
|
111
|
Li S, Zhang P, Xu F, Hu S, Liu J, Tan Y, Tu Z, Sun H, Zhang ZM, He QY, Sun P, Ding K, Li Z. Ynamide Electrophile for the Profiling of Ligandable Carboxyl Residues in Live Cells and the Development of New Covalent Inhibitors. J Med Chem 2022; 65:10408-10418. [PMID: 35880853 DOI: 10.1021/acs.jmedchem.2c00272] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covalent inhibitors with an electrophilic warhead have received considerable attention due to their remarkable pharmacological properties. However, the electrophilic warhead in covalent drugs is often an α, β-unsaturated amide, and the targets are mainly cysteine or lysine residues. Thus, the development of novel electrophiles that can target other amino acids is highly desirable. Ynamide, a useful and versatile building block, is commonly employed in the construction of various compounds in organic synthesis. The performance of this functional group in a proteome-wide environment has been studied here for the first time, and it has been shown that it can efficiently modify carboxyl residues in situ and in vitro. Upon incorporation of this ynamide warhead into the pharmacophores of kinase inhibitors, the resulting compound showed moderate inhibition against the EGFR L858R mutant but not against EGFR WT. This novel electrophilic group can be used in the development of new types of covalent inhibitors.
Collapse
Affiliation(s)
- Shengrong Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Pengwei Zhang
- Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, Guangdong, China.,Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, Guangdong, China
| | - Fang Xu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Shengcao Hu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Jiacong Liu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Yi Tan
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Zhengchao Tu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Hongyan Sun
- Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Qing-Yu He
- Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, Guangdong, China.,MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510120, China
| | - Pinghua Sun
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632.,MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510120, China
| |
Collapse
|
112
|
de Oliveira MVD, Furtado RM, da Costa KS, Vakal S, Lima AH. Advances in UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) Covalent Inhibition. Front Mol Biosci 2022; 9:889825. [PMID: 35936791 PMCID: PMC9346081 DOI: 10.3389/fmolb.2022.889825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Peptidoglycan is a cross-linked polymer responsible for maintaining the bacterial cell wall integrity and morphology in Gram-negative and Gram-positive bacteria. The peptidoglycan pathway consists of the enzymatic reactions held in three steps: cytoplasmic, membrane-associated, and periplasmic. The Mur enzymes (MurA-MurF) are involved in a cytoplasmic stage. The UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) enzyme is responsible for transferring the enolpyruvate group from phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine (UNAG) to form UDP-N-acetylglucosamine enolpyruvate (EP-UNAG). Fosfomycin is a natural product analogous to PEP that acts on the MurA target enzyme via binding covalently to the key cysteine residue in the active site. Similar to fosfomycin, other MurA covalent inhibitors have been described with a warhead in their structure that forms a covalent bond with the molecular target. In MurA, the nucleophilic thiolate of Cys115 is pointed as the main group involved in the warhead binding. Thus, in this minireview, we briefly describe the main recent advances in the design of MurA covalent inhibitors.
Collapse
Affiliation(s)
| | - Renan Machado Furtado
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | - Kauê S. da Costa
- Institute of Biodiversity, Federal University of Western Pará, Santarém, Brazil
| | - Serhii Vakal
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Anderson H. Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
- *Correspondence: Anderson H. Lima,
| |
Collapse
|
113
|
Baldwin ET, Götte M, Tchesnokov EP, Arnold E, Hagel M, Nichols C, Dossang P, Lamers M, Wan P, Steinbacher S, Romero DL. Human endogenous retrovirus-K (HERV-K) reverse transcriptase (RT) structure and biochemistry reveals remarkable similarities to HIV-1 RT and opportunities for HERV-K-specific inhibition. Proc Natl Acad Sci U S A 2022; 119:e2200260119. [PMID: 35771941 PMCID: PMC9271190 DOI: 10.1073/pnas.2200260119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/28/2022] [Indexed: 11/18/2022] Open
Abstract
Human endogenous retroviruses (HERVs) comprise nearly 8% of the human genome and are derived from ancient integrations of retroviruses into the germline. The biology of HERVs is poorly defined, but there is accumulating evidence supporting pathological roles in diverse diseases, such as cancer, autoimmune, and neurodegenerative diseases. Functional proteins are produced by HERV-encoded genes, including reverse transcriptases (RTs), which could be a contributor to the pathology attributed to aberrant HERV-K expression. To facilitate the discovery and development of HERV-K RT potent and selective inhibitors, we expressed active HERV-K RT and determined the crystal structure of a ternary complex of this enzyme with a double-stranded DNA substrate. We demonstrate a range of RT inhibition with antiretroviral nucleotide analogs, while classic nonnucleoside analogs do not inhibit HERV-K RT. Detailed comparisons of HERV-K RT with other known RTs demonstrate similarities to diverse RT families and a striking similarity to the HIV-1 RT asymmetric heterodimer. Our analysis further reveals opportunities for selective HERV-K RT inhibition.
Collapse
Affiliation(s)
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Egor P. Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854
| | | | - Charles Nichols
- Charles River Laboratory, Chesterford Research Park, Saffron Walden CB10 1XL, United Kingdom
| | - Pam Dossang
- Charles River Laboratory, Chesterford Research Park, Saffron Walden CB10 1XL, United Kingdom
| | - Marieke Lamers
- Charles River Laboratory, Chesterford Research Park, Saffron Walden CB10 1XL, United Kingdom
- DomainEx, Chesterford Research Park, Saffron Walden CB10 1XL United Kingdom
| | - Paul Wan
- Charles River Laboratory, Chesterford Research Park, Saffron Walden CB10 1XL, United Kingdom
| | | | | |
Collapse
|
114
|
Yaashikaa PR, Devi MK, Kumar PS. Advances in the application of immobilized enzyme for the remediation of hazardous pollutant: A review. CHEMOSPHERE 2022; 299:134390. [PMID: 35339523 DOI: 10.1016/j.chemosphere.2022.134390] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/03/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Nowadays, ecofriendly, low-cost, and sustainable alternatives techniques have been focused on the effective removal of hazardous pollutants from the water streams. In this context, enzyme immobilization seems to be of specific interest to several researchers to develop novel, effective, greener, and hybrid strategies for the removal of toxic contaminants. Immobilization is a biotechnological tool, anchoring the enzymes on support material to enhance the stability and retain the structural conformation of enzymes for catalysis. Recyclability and reusability are the main merits of immobilized enzymes over free enzymes. Studies showed that immobilized enzyme laccase can be used up to 7 cycles with 66% efficiency, peroxidase can be recycled to 2 cycles with 50% efficiency, and also cellulase to 3 cycles with 91% efficiency. In this review, basic concepts of immobilization, different immobilization techniques, and carriers used for immobilization are summarized. In addition to that, the potential of immobilized enzymes as the bioremediation agents for the effective degradation of pollutants from the contaminated zone and the impact of different operating parameters are summarized in-depth. Further, this review provides future trends and challenges that have to be solved shortly for enhancing the potential of immobilized systems for large-scale industrial wastewater treatment.
Collapse
Affiliation(s)
- P R Yaashikaa
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - M Keerthana Devi
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India.
| |
Collapse
|
115
|
Synthesis of Amino-Acid-Based Nitroalkenes. ORGANICS 2022. [DOI: 10.3390/org3020011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Fatty-acid-based nitroalkenes have recently received great attention because of their bioactivities. On the contrary, peptide- or amino-acid-based nitroalkenes have been scarcely explored so far, although they may exhibit interesting biological properties, for example, as enzyme inhibitors. In this work, we study protocols for the efficient synthesis of nitroalkenes based on natural amino acids. A variety of N-protected amino alcohols and Weinreb amides, derived from α-amino acids, were converted to the corresponding N-protected amino aldehydes, and, through a Henry reaction with nitroalkanes, produced the corresponding nitro alcohols. The subsequent elimination reaction led to the (E)-isomer of amino-acid-based nitroalkenes in moderate to high yields.
Collapse
|
116
|
Montaño JL, Wang BJ, Volk RF, Warrington SE, Garda VG, Hofmann KL, Chen LC, Zaro BW. Improved Electrophile Design for Exquisite Covalent Molecule Selectivity. ACS Chem Biol 2022; 17:1440-1449. [PMID: 35587148 DOI: 10.1021/acschembio.1c00980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Covalent inhibitors are viable therapeutics. However, off-target reactivity challenges the field. Chemists have attempted to solve this issue by varying the reactivity attributes of electrophilic warheads. Here, we report the development of an approach to increase the selectivity of covalent molecules that is independent of warhead reactivity features and can be used in concert with existing methods. Using the scaffold of the Bruton's tyrosine kinase (BTK) inhibitor Ibrutinib for our proof-of-concept, we reasoned that increasing the steric bulk of fumarate-based electrophiles on Ibrutinib should improve selectivity via the steric exclusion of off-targets but retain rates of cysteine reactivity comparable to that of an acrylamide. Using chemical proteomic techniques, we demonstrate that elaboration of the electrophile to a tert-butyl (t-Bu) fumarate ester decreases time-dependent off-target reactivity and abolishes time-independent off-target reactivity. While an alkyne-bearing probe analogue of Ibrutinib has 247 protein targets, our t-Bu fumarate probe analogue has only 7. Of these 7 targets, BTK is the only time-independent target. The t-Bu inhibitor itself is also more selective for BTK, reducing off-targets by 70%. We investigated the consequences of treatment with Ibrutinib and our t-Bu analogue and discovered that only 8 proteins are downregulated in response to treatment with the t-Bu analogue compared to 107 with Ibrutinib. Of these 8 proteins, 7 are also downregulated by Ibrutinib and a majority of these targets are associated with BTK biology. Taken together, these findings reveal an opportunity to increase cysteine-reactive covalent inhibitor selectivity through electrophilic structure optimization.
Collapse
Affiliation(s)
- José L. Montaño
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Brian J. Wang
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Regan F. Volk
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Sara E. Warrington
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Virginia G. Garda
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Katherine L. Hofmann
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Leo C. Chen
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Balyn W. Zaro
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| |
Collapse
|
117
|
Li L, Meyer C, Zhou ZW, Elmezayen A, Westover K. Therapeutic Targeting the Allosteric Cysteinome of RAS and Kinase Families. J Mol Biol 2022; 434:167626. [PMID: 35595166 DOI: 10.1016/j.jmb.2022.167626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/25/2022] [Accepted: 05/03/2022] [Indexed: 12/14/2022]
Abstract
Allosteric mechanisms are pervasive in nature, but human-designed allosteric perturbagens are rare. The history of KRASG12C inhibitor development suggests that covalent chemistry may be a key to expanding the armamentarium of allosteric inhibitors. In that effort, irreversible targeting of a cysteine converted a non-deal allosteric binding pocket and low affinity ligands into a tractable drugging strategy. Here we examine the feasibility of expanding this approach to other allosteric pockets of RAS and kinase family members, given that both protein families are regulators of vital cellular processes that are often dysregulated in cancer and other human diseases. Moreover, these heavily studied families are the subject of numerous drug development campaigns that have resulted, sometimes serendipitously, in the discovery of allosteric inhibitors. We consequently conducted a comprehensive search for cysteines, a commonly targeted amino acid for covalent drugs, using AlphaFold-generated structures of those families. This new analysis presents potential opportunities for allosteric targeting of validated and understudied drug targets, with an emphasis on cancer therapy.
Collapse
Affiliation(s)
- Lianbo Li
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390, USA
| | - Cynthia Meyer
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390, USA
| | - Zhi-Wei Zhou
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390, USA
| | - Ammar Elmezayen
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390, USA
| | - Kenneth Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390, USA.
| |
Collapse
|
118
|
Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins. Bioorg Med Chem 2022; 62:116721. [PMID: 35358862 DOI: 10.1016/j.bmc.2022.116721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022]
Abstract
Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.
Collapse
|
119
|
Hooper A, Burns AS. Thermal Stability and Utility of Dienes as Protecting Groups for Acrylamides. ACS Med Chem Lett 2022; 13:833-840. [PMID: 35586437 PMCID: PMC9109275 DOI: 10.1021/acsmedchemlett.2c00075] [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: 02/18/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Abstract
Acrylamides are privileged electrophiles used in targeted covalent therapies, often installed at the end of a synthetic sequence due to their reactive nature. Herein, we report several diene-acrylamide adducts with a range of thermal stabilities toward retro-Diels-Alder deprotection of the acrylamide, enabling this masked functionality to be introduced early in a synthetic route and deprotected in a specific temperature range. Through kinetic studies, we identify solvent and structural trends that impact the stability of trimethylsilyl cyclopentadiene (TMS-CP) acrylamide adducts. TMS-CP protected acrylamides were installed on several amine-containing drugs, whose acrylamides were thermally unveiled (T = 160 °C, time ≤ 1 h) in moderate to high yields. We also showcase the potential utility of this protection strategy by improving the yield of a base-promoted SNAr reaction when the acrylamide is masked.
Collapse
Affiliation(s)
- Annie
R. Hooper
- Rodger
Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Alexander S. Burns
- Discovery
Chemistry, Janssen Research & Development
L.L.C., San Diego, California 92121, United States
| |
Collapse
|
120
|
Lang PA, Raj R, Tumber A, Lohans CT, Rabe P, Robinson CV, Brem J, Schofield CJ. Studies on enmetazobactam clarify mechanisms of widely used β-lactamase inhibitors. Proc Natl Acad Sci U S A 2022; 119:e2117310119. [PMID: 35486701 PMCID: PMC9170034 DOI: 10.1073/pnas.2117310119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
β-Lactams are the most important class of antibacterials, but their use is increasingly compromised by resistance, most importantly via serine β-lactamase (SBL)-catalyzed hydrolysis. The scope of β-lactam antibacterial activity can be substantially extended by coadministration with a penicillin-derived SBL inhibitor (SBLi), i.e., the penam sulfones tazobactam and sulbactam, which are mechanism-based inhibitors working by acylation of the nucleophilic serine. The new SBLi enmetazobactam, an N-methylated tazobactam derivative, has recently completed clinical trials. Biophysical studies on the mechanism of SBL inhibition by enmetazobactam reveal that it inhibits representatives of all SBL classes without undergoing substantial scaffold fragmentation, a finding that contrasts with previous reports on SBL inhibition by tazobactam and sulbactam. We therefore reinvestigated the mechanisms of tazobactam and sulbactam using mass spectrometry under denaturing and nondenaturing conditions, X-ray crystallography, and NMR spectroscopy. The results imply that the reported extensive fragmentation of penam sulfone–derived acyl–enzyme complexes does not substantially contribute to SBL inhibition. In addition to observation of previously identified inhibitor-induced SBL modifications, the results reveal that prolonged reaction of penam sulfones with SBLs can induce dehydration of the nucleophilic serine to give a dehydroalanine residue that undergoes reaction to give a previously unobserved lysinoalanine cross-link. The results clarify the mechanisms of action of widely clinically used SBLi, reveal limitations on the interpretation of mass spectrometry studies concerning mechanisms of SBLi, and will inform the development of new SBLi working by reaction to form hydrolytically stable acyl–enzyme complexes.
Collapse
Affiliation(s)
- Pauline A. Lang
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Ritu Raj
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Christopher T. Lohans
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Patrick Rabe
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| |
Collapse
|
121
|
Mol’kova EA, Shchegravina ES, Otvagin VF, Kuzmina NS, Malysheva YB, Svirshchevskaya EV, Zaburdaeva EA, Fedorov AY. Synthesis and biological evaluation of colchicine and thiocolchicine derivatives bearing a Michael acceptor moiety in ring A. Russ Chem Bull 2022. [DOI: 10.1007/s11172-022-3449-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
122
|
Liberelle M, Toulotte F, Renault N, Gelin M, Allemand F, Melnyk P, Guichou JF, Cotelle P. Toward the Design of Ligands Selective for the C-Terminal Domain of TEADs. J Med Chem 2022; 65:5926-5940. [PMID: 35389210 DOI: 10.1021/acs.jmedchem.2c00075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Hippo signaling pathway plays a fundamental role in the control of organ growth, cell proliferation, and stem cell characters. TEADs are the main transcriptional output regulators of the Hippo signaling pathway and bind to YAP and TAZ co-activators. TEAD1-4 are expressed differently, depending on the tissue and developmental level, and can be overexpressed in certain pathologies. TEAD ligands mainly target the internal pocket of the C-terminal domain of TEAD, and the first ligands selective for TEAD1 and TEAD3 have been recently reported. In this paper, we focus on the topographic homology of the TEAD C-terminal domain both externally and in the internal pocket to highlight the possibility of rationally designing ligands selective for one of the TEAD family members. We identified a novel TEAD2-specific pocket and reported its first ligand. Finally, AlphaFold2 models of full-length TEADs suggest TEAD autoregulation and emphasize the importance of the interface 2.
Collapse
Affiliation(s)
- Maxime Liberelle
- INSERM, CHU Lille, UMR-S 1172, Lille Neuroscience and Cognition Research Center, Université de Lille, F-59000 Lille, France
| | - Florine Toulotte
- INSERM, CHU Lille, UMR-S 1172, Lille Neuroscience and Cognition Research Center, Université de Lille, F-59000 Lille, France
| | - Nicolas Renault
- INSERM, CHU Lille, U-1286 - INFINTE - Institute for Translational Research in Inflammation, Université de Lille, F-59000 Lille, France
| | - Muriel Gelin
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Université de Montpellier, F-34090 Montpellier, France
| | - Frédéric Allemand
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Université de Montpellier, F-34090 Montpellier, France
| | - Patricia Melnyk
- INSERM, CHU Lille, UMR-S 1172, Lille Neuroscience and Cognition Research Center, Université de Lille, F-59000 Lille, France
| | - Jean-François Guichou
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Université de Montpellier, F-34090 Montpellier, France
| | - Philippe Cotelle
- INSERM, CHU Lille, UMR-S 1172, Lille Neuroscience and Cognition Research Center, Université de Lille, F-59000 Lille, France.,CS 90108, ENSCL-Centrale Lille, F-59652 Villeneuve d'Ascq, France
| |
Collapse
|
123
|
Vázquez-Mendoza LH, Mendoza-Figueroa HL, García-Vázquez JB, Correa-Basurto J, García-Machorro J. In Silico Drug Repositioning to Target the SARS-CoV-2 Main Protease as Covalent Inhibitors Employing a Combined Structure-Based Virtual Screening Strategy of Pharmacophore Models and Covalent Docking. Int J Mol Sci 2022; 23:3987. [PMID: 35409348 PMCID: PMC8999907 DOI: 10.3390/ijms23073987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
The epidemic caused by the SARS-CoV-2 coronavirus, which has spread rapidly throughout the world, requires urgent and effective treatments considering that the appearance of viral variants limits the efficacy of vaccines. The main protease of SARS-CoV-2 (Mpro) is a highly conserved cysteine proteinase, fundamental for the replication of the coronavirus and with a specific cleavage mechanism that positions it as an attractive therapeutic target for the proposal of irreversible inhibitors. A structure-based strategy combining 3D pharmacophoric modeling, virtual screening, and covalent docking was employed to identify the interactions required for molecular recognition, as well as the spatial orientation of the electrophilic warhead, of various drugs, to achieve a covalent interaction with Cys145 of Mpro. The virtual screening on the structure-based pharmacophoric map of the SARS-CoV-2 Mpro in complex with an inhibitor N3 (reference compound) provided high efficiency by identifying 53 drugs (FDA and DrugBank databases) with probabilities of covalent binding, including N3 (Michael acceptor) and others with a variety of electrophilic warheads. Adding the energy contributions of affinity for non-covalent and covalent docking, 16 promising drugs were obtained. Our findings suggest that the FDA-approved drugs Vaborbactam, Cimetidine, Ixazomib, Scopolamine, and Bicalutamide, as well as the other investigational peptide-like drugs (DB04234, DB03456, DB07224, DB7252, and CMX-2043) are potential covalent inhibitors of SARS-CoV-2 Mpro.
Collapse
Affiliation(s)
- Luis Heriberto Vázquez-Mendoza
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Posgrado en Farmacología de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (L.H.V.-M.); (J.C.-B.)
| | - Humberto L. Mendoza-Figueroa
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Posgrado en Farmacología de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (L.H.V.-M.); (J.C.-B.)
| | - Juan Benjamín García-Vázquez
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Posgrado en Farmacología de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (L.H.V.-M.); (J.C.-B.)
- Cátedras CONACyT-Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Posgrado en Farmacología de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (L.H.V.-M.); (J.C.-B.)
| | - Jazmín García-Machorro
- Laboratorio de Medicina de la Conservación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico;
| |
Collapse
|
124
|
Koperniku A, Garcia AA, Mochly-Rosen D. Boosting the Discovery of Small Molecule Inhibitors of Glucose-6-Phosphate Dehydrogenase for the Treatment of Cancer, Infectious Diseases, and Inflammation. J Med Chem 2022; 65:4403-4423. [PMID: 35239352 PMCID: PMC9553131 DOI: 10.1021/acs.jmedchem.1c01577] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We present an overview of small molecule glucose-6-phosphate dehydrogenase (G6PD) inhibitors that have potential for use in the treatment of cancer, infectious diseases, and inflammation. Both steroidal and nonsteroidal inhibitors have been identified with steroidal inhibitors lacking target selectivity. The main scaffolds encountered in nonsteroidal inhibitors are quinazolinones and benzothiazinones/benzothiazepinones. Three molecules show promise for development as antiparasitic (25 and 29) and anti-inflammatory (32) agents. Regarding modality of inhibition (MOI), steroidal inhibitors have been shown to be uncompetitive and reversible. Nonsteroidal small molecules have exhibited all types of MOI. Strategies to boost the discovery of small molecule G6PD inhibitors include exploration of structure-activity relationships (SARs) for established inhibitors, employment of high-throughput screening (HTS), and fragment-based drug discovery (FBDD) for the identification of new hits. We discuss the challenges and gaps associated with drug discovery efforts of G6PD inhibitors from in silico, in vitro, and in cellulo to in vivo studies.
Collapse
Affiliation(s)
- Ana Koperniku
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, 269 Campus Dr, Stanford, CA 94305, USA
- Corresponding Author: Ana Koperniku,
| | - Adriana A. Garcia
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, 269 Campus Dr, Stanford, CA 94305, USA
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, 269 Campus Dr, Stanford, CA 94305, USA
| |
Collapse
|
125
|
Xie Z, Hou S, Yang X, Duan Y, Han J, Wang Q, Liao C. Lessons Learned from Past Cyclin-Dependent Kinase Drug Discovery Efforts. J Med Chem 2022; 65:6356-6389. [PMID: 35235745 DOI: 10.1021/acs.jmedchem.1c02190] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Inhibition of cyclin-dependent kinases (CDKs) has become an effective therapeutic strategy for treating various diseases, especially cancer. Over almost three decades, although great efforts have been made to discover CDK inhibitors, many of which have entered clinical trials, only four CDK inhibitors have been approved. In the process of CDK inhibitor development, many difficulties and misunderstandings have hampered their discovery and clinical applications, which mainly include inadequate understanding of the biological functions of CDKs, less attention paid to pan- and multi-CDK inhibitors, nonideal isoform selectivity of developed selective CDK inhibitors, overlooking the metabolic stability of early discovered CDK inhibitors, no effective resistance solutions, and a lack of available combination therapy and effective biomarkers for CDK therapies. After reviewing the mechanisms of CDKs and the research progress of CDK inhibitors, this perspective summarizes and discusses these difficulties or lessons, hoping to facilitate the successful discovery of more useful CDK inhibitors.
Collapse
Affiliation(s)
- Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Shuzeng Hou
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Xiaoxiao Yang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Yajun Duan
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Jihong Han
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Qin Wang
- Department of Otolaryngology─Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, P. R. China
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| |
Collapse
|
126
|
Ge R, Shen Z, Yin J, Chen W, Zhang Q, An Y, Tang D, Satz AL, Su W, Kuai L. Discovery of SARS-CoV-2 main protease covalent inhibitors from a DNA-encoded library selection. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:79-85. [PMID: 35063690 PMCID: PMC8767972 DOI: 10.1016/j.slasd.2022.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covalent inhibitors targeting the main protease (Mpro, or 3CLpro) of SARS-CoV-2 have shown promise in preclinical investigations. Herein, we report the discovery of two new series of molecules that irreversibly bind to SARS-CoV-2 Mpro. These acrylamide containing molecules were discovered using our covalent DNA-encoded library (DEL) screening platform. Following selection against SARS-CoV-2 Mpro, off-DNA compounds were synthesized and investigated to determine their inhibitory effects, the nature of their binding, and to generate preliminary structure-activity relationships. LC-MS analysis indicates a 1:1 (covalent) binding stoichiometry between our hit molecules and SARS-CoV-2 Mpro. Fluorescent staining assay for covalent binding in the presence of cell lysate suggests reasonable selectivity for SARS-CoV-2 Mpro. And lastly, inhibition of enzymatic activity was also observed against a panel of 3CLpro enzymes from different coronavirus strains, with IC50 values ranging from inactive to single digit micromolar. Our results indicate that DEL selection is a useful approach for identifying covalent inhibitors of cysteine proteases.
Collapse
Affiliation(s)
- Rui Ge
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Zuyuan Shen
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Jian Yin
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wenhua Chen
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Qi Zhang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yulong An
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Dewei Tang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | | | - Wenji Su
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.
| | - Letian Kuai
- WuXi AppTec(,) 55 Cambridge Parkway, 8th Floor(,) Cambridge, MA 02142, USA.
| |
Collapse
|
127
|
Mustafa M, Winum JY. The importance of sulfur-containing motifs in drug design and discovery. Expert Opin Drug Discov 2022; 17:501-512. [PMID: 35193437 DOI: 10.1080/17460441.2022.2044783] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Sulfur-containing functional groups are privileged motifs that occur in various pharmacologically effective substances and several natural products. Various functionalities are found with a sulfur atom at diverse oxidation states, as illustrated by thioether, sulfoxide, sulfone, sulfonamide, sulfamate, and sulfamide functions. They are valuable scaffolds in the field of medicinal chemistry and are part of a large array of approved drugs and clinical candidates. AREA COVERED Herein, the authors review the current research on the development of organosulfur-based drug discovery. This article also covers details of their roles in the new lead compounds reported in the literature over the past five years 2017-2021. EXPERT OPINION Given its prominent role in medicinal chemistry and its importance in drug discovery, sulfur has attracted continuing interest and has been used in the design of various valuable compounds that demonstrate a variety of biological and pharmacological feature activities. Overall, sulfur's role in medicinal chemistry continues to grow. However, many sulfur functionalities remain underused in small-molecule drug discovery and deserve special attention in the armamentarium for treating diverse diseases. Research efforts are also still required for the development of a synthetic methodology for direct access to these functions and late-stage functionalization.
Collapse
Affiliation(s)
- Muhamad Mustafa
- IBMM, Univ. Montpellier, CNRS, ENSCM, Montpellier, France.,Department of Medicinal Chemistry, Faculty of Pharmacy, Deraya Unuversity, Minia, Egypt
| | | |
Collapse
|
128
|
Li Y, Han L, Zhang Z. Understanding the influence of AMG 510 on the structure of KRAS G12C empowered by molecular dynamics simulation. Comput Struct Biotechnol J 2022; 20:1056-1067. [PMID: 35284050 PMCID: PMC8894142 DOI: 10.1016/j.csbj.2022.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/07/2023] Open
Abstract
The KRASG12C mutant is often associated with human cancers, and AMG 510 as a promising covalent inhibitor of KRASG12C has achieved surprising efficacy in clinical trials. However, the interaction mechanism between KRASG12C and AMG 510 is not completely understood. Here, we performed all-atom molecular dynamics simulations on the complex of KRASG12C-AMG 510 to explore the influence of this covalent inhibitor on the conformational change of KRASG12C. A PCA (Principal Component Analysis) model was constructed based on known KRAS crystal structures to distinguish different conformations (active, inactive, and other). By mapping simulation trajectories onto the PCA model, we observed that the conformations of KRASG12C bound with AMG 510 were mainly concentrated in the inactive conformation. Further analysis demonstrated that AMG 510 reduced the flexibility of two switch regions to make the complex of KRASG12C-AMG 510 restricted in the inactive conformation. In the meantime, we also identified key interacting residues between KRASG12C and AMG 510 through the calculation of binding energy. Finally, we built a series of KRAS second-site mutation systems (i.e. KRASG12C/mutations) to conduct large-scale screening of potential resistance mutations. By further combining MD simulations and the PCA model, we not only recapitulated the currently known resistance mutations of AMG 510 successfully but also proposed some novel potential resistant mutations. Taken together, these results broaden our insight into the influence of AMG 510 on the conformational change of the KRASG12C mutant at the atomic level, thereby providing crucial hints for the improvement and optimization of drug candidates.
Collapse
Affiliation(s)
- Yu Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lei Han
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| |
Collapse
|
129
|
Rothweiler EM, Brennan PE, Huber KVM. Covalent fragment-based ligand screening approaches for identification of novel ubiquitin proteasome system modulators. Biol Chem 2022; 403:391-402. [PMID: 35191283 DOI: 10.1515/hsz-2021-0396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/07/2022] [Indexed: 12/19/2022]
Abstract
Ubiquitination is a key regulatory mechanism vital for maintenance of cellular homeostasis. Protein degradation is induced by E3 ligases via attachment of ubiquitin chains to substrates. Pharmacological exploitation of this phenomenon via targeted protein degradation (TPD) can be achieved with molecular glues or bifunctional molecules facilitating the formation of ternary complexes between an E3 ligase and a given protein of interest (POI), resulting in ubiquitination of the substrate and subsequent proteolysis by the proteasome. Recently, the development of novel covalent fragment screening approaches has enabled the identification of first-in-class ligands for E3 ligases and deubiquitinases revealing so far unexplored binding sites which highlights the potential of these methods to uncover and expand druggable space for new target classes.
Collapse
Affiliation(s)
- Elisabeth M Rothweiler
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK
| | - Paul E Brennan
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, Oxford OX3 7FZ, UK
| | - Kilian V M Huber
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK
| |
Collapse
|
130
|
Jamshidiha M, Lanyon-Hogg T, Sutherell CL, Craven GB, Tersa M, De Vita E, Brustur D, Pérez-Dorado I, Hassan S, Petracca R, Morgan RM, Sanz-Hernández M, Norman JC, Armstrong A, Mann DJ, Cota E, Tate EW. Identification of the first structurally validated covalent ligands of the small GTPase RAB27A. RSC Med Chem 2022; 13:150-155. [PMID: 35308027 PMCID: PMC8864489 DOI: 10.1039/d1md00225b] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022] Open
Abstract
Rab27A is a small GTPase, which mediates transport and docking of secretory vesicles at the plasma membrane via protein-protein interactions (PPIs) with effector proteins. Rab27A promotes the growth and invasion of multiple cancer types such as breast, lung and pancreatic, by enhancing secretion of chemokines, metalloproteases and exosomes. The significant role of Rab27A in multiple cancer types and the minor role in adults suggest that Rab27A may be a suitable target to disrupt cancer metastasis. Similar to many GTPases, the flat topology of the Rab27A-effector PPI interface and the high affinity for GTP make it a challenging target for inhibition by small molecules. Reported co-crystal structures show that several effectors of Rab27A interact with the Rab27A SF4 pocket ('WF-binding pocket') via a conserved tryptophan-phenylalanine (WF) dipeptide motif. To obtain structural insight into the ligandability of this pocket, a novel construct was designed fusing Rab27A to part of an effector protein (fRab27A), allowing crystallisation of Rab27A in high throughput. The paradigm of KRas covalent inhibitor development highlights the challenge presented by GTPase proteins as targets. However, taking advantage of two cysteine residues, C123 and C188, that flank the WF pocket and are unique to Rab27A and Rab27B among the >60 Rab family proteins, we used the quantitative Irreversible Tethering (qIT) assay to identify the first covalent ligands for native Rab27A. The binding modes of two hits were elucidated by co-crystallisation with fRab27A, exemplifying a platform for identifying suitable lead fragments for future development of competitive inhibitors of the Rab27A-effector interaction interface, corroborating the use of covalent libraries to tackle challenging targets.
Collapse
Affiliation(s)
- Mostafa Jamshidiha
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | - Thomas Lanyon-Hogg
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | | | - Gregory B Craven
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - Montse Tersa
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - Elena De Vita
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | - Delia Brustur
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | | | - Sarah Hassan
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | - Rita Petracca
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | - Rhodri M Morgan
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | | | - Jim C Norman
- Beatson Institute for Cancer Research, Garscube Estate Glasgow G61 1BD UK
| | - Alan Armstrong
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | - David J Mann
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - Ernesto Cota
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - Edward W Tate
- Department of Chemistry, Imperial College London London W12 0BZ UK
| |
Collapse
|
131
|
Therapeutic peptides: current applications and future directions. Signal Transduct Target Ther 2022; 7:48. [PMID: 35165272 PMCID: PMC8844085 DOI: 10.1038/s41392-022-00904-4] [Citation(s) in RCA: 478] [Impact Index Per Article: 239.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Peptide drug development has made great progress in the last decade thanks to new production, modification, and analytic technologies. Peptides have been produced and modified using both chemical and biological methods, together with novel design and delivery strategies, which have helped to overcome the inherent drawbacks of peptides and have allowed the continued advancement of this field. A wide variety of natural and modified peptides have been obtained and studied, covering multiple therapeutic areas. This review summarizes the efforts and achievements in peptide drug discovery, production, and modification, and their current applications. We also discuss the value and challenges associated with future developments in therapeutic peptides.
Collapse
|
132
|
Rocho FR, Bonatto V, Lameiro RF, Lameira J, Leitão A, Montanari CA. A patent review on cathepsin K inhibitors to treat osteoporosis (2011 - 2021). Expert Opin Ther Pat 2022; 32:561-573. [PMID: 35137661 DOI: 10.1080/13543776.2022.2040480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Cathepsin K (CatK) is a lysosomal cysteine protease and the predominant cathepsin expressed in osteoclasts, where it degrades the bone matrix. Hence, CatK is an attractive therapeutic target related to diseases characterized by bone resorption, like osteoporosis. AREAS COVERED This review summarizes the patent literature from 2011 to 2021 on CatK inhibitors and their potential use as new treatments for osteoporosis. The inhibitors were classified by their warheads, with the most explored nitrile-based inhibitors. Promising in vivo results have also been disclosed. EXPERT OPINION As one of the most potent lysosomal proteins whose primary function is to mediate bone resorption, cathepsin K remains an excellent target for therapeutic intervention. Nevertheless, there is no record of any approved drug that targets CatK. The most notable cases of drug candidates targeting CatK were balicatib and odanacatib, which reached Phase II and III clinical trials, respectively, but did not enter the market. Further developments include exploring new chemical entities beyond the nitrile-based chemical space, with improved ADME and safety profiles. In addition, CatK's role in cancer immunoexpression and its involvement in the pathophysiology of osteo- and rheumatoid arthritis have raised the race to develop activity-based probes with excellent potency and selectivity.
Collapse
Affiliation(s)
- Fernanda R Rocho
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 13566-590, São Carlos/SP, Brazil
| | - Vinícius Bonatto
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 13566-590, São Carlos/SP, Brazil
| | - Rafael F Lameiro
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 13566-590, São Carlos/SP, Brazil
| | - Jerônimo Lameira
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 13566-590, São Carlos/SP, Brazil.,On leave from Drug Designing and Development Laboratory. Federal University of Pará, Rua Augusto Correa S/N, Belém, PA, Brazil
| | - Andrei Leitão
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 13566-590, São Carlos/SP, Brazil
| | - Carlos A Montanari
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 13566-590, São Carlos/SP, Brazil
| |
Collapse
|
133
|
Labarre A, Stille JK, Patrascu MB, Martins A, Pottel J, Moitessier N. Docking Ligands into Flexible and Solvated Macromolecules. 8. Forming New Bonds─Challenges and Opportunities. J Chem Inf Model 2022; 62:1061-1077. [PMID: 35133156 DOI: 10.1021/acs.jcim.1c00701] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the years, structure-based design programs and specifically docking small molecules to proteins have become prominent in drug discovery. However, many of these computational tools have been developed to primarily dock enzyme inhibitors (and ligands to other protein classes) relying heavily on hydrogen bonds and electrostatic and hydrophobic interactions. In reality, many drug targets either feature metal ions, can be targeted covalently, or are simply not even proteins (e.g., nucleic acids). Herein, we describe several new features that we have implemented into Fitted to broaden its applicability to a wide range of covalent enzyme inhibitors and to metalloenzymes, where metal coordination is essential for drug binding. This updated version of our docking program was tested for its ability to predict the correct binding mode of drug-sized molecules in a large variety of proteins. We also report new datasets that were essential to demonstrate areas of success and those where additional efforts are required. This resource could be used by other program developers to assess their own software.
Collapse
Affiliation(s)
- Anne Labarre
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal H3A 0B8, Quebec, Canada
| | - Julia K Stille
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal H3A 0B8, Quebec, Canada
| | - Mihai Burai Patrascu
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal H3A 0B8, Quebec, Canada
| | - Andrew Martins
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal H3A 0B8, Quebec, Canada
| | - Joshua Pottel
- Molecular Forecaster Inc., 7171, rue Frederick-Banting, Montreal H4S 1Z9, Quebec, Canada
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal H3A 0B8, Quebec, Canada.,Molecular Forecaster Inc., 7171, rue Frederick-Banting, Montreal H4S 1Z9, Quebec, Canada
| |
Collapse
|
134
|
Ye Z, Wang K, Chen L, Jin X, Chen H, Tang G, Yao SQ, Feng Z, Zhang CJ. A targeted covalent inhibitor of p97 with proteome-wide selectivity. Acta Pharm Sin B 2022; 12:982-989. [PMID: 35256959 PMCID: PMC8897041 DOI: 10.1016/j.apsb.2021.09.003] [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: 06/01/2021] [Revised: 08/28/2021] [Accepted: 09/02/2021] [Indexed: 11/17/2022] Open
Abstract
A resurging interest in targeted covalent inhibitors (TCIs) focus on compounds capable of irreversibly reacting with nucleophilic amino acids in a druggable target. p97 is an emerging protein target for cancer therapy, viral infections and neurodegenerative diseases. Extensive efforts were devoted to the development of p97 inhibitors. The most promising inhibitor of p97 was in phase 1 clinical trials, but failed due to the off-target-induced toxicity, suggesting the selective inhibitors of p97 are highly needed. We report herein a new type of TCIs (i.e., FL-18) that showed proteome-wide selectivity towards p97. Equipped with a Michael acceptor and a basic imidazole, FL-18 showed potent inhibition towards U87MG tumor cells, and in proteome-wide profiling, selectively modified endogenous p97 as confirmed by in situ fluorescence scanning, label-free quantitative proteomics and functional validations. FL-18 selectively modified cysteine residues located within the D2 ATP site of p97. This covalent labeling of cysteine residue in p97 was verified by LC‒MS/MS-based site-mapping and site-directed mutagenesis. Further structure–activity relationship (SAR) studies with FL-18 analogs were established. Collectively, FL-18 is the first known small-molecule TCI capable of covalent engagement of p97 with proteome-wide selectivity, thus providing a promising scaffold for cancer therapy.
Collapse
Affiliation(s)
- Zi Ye
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Ke Wang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Lianguo Chen
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Xiaofeng Jin
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Hao Chen
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Shao Q. Yao
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Zhiqiang Feng
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
- Corresponding authors. Tel.: +86 10 63165311, fax: +86 10 63017757.
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
- Corresponding authors. Tel.: +86 10 63165311, fax: +86 10 63017757.
| |
Collapse
|
135
|
Sexton M, Malachowski WP, Yap GPA, Rachii D, Feldman G, Krasley AT, Chen Z, Tran MA, Wiley K, Matei A, Petersen S, Tien ST. Catalytic Enantioselective Birch-Heck Sequence for the Synthesis of Phenanthridinone Derivatives with an All-Carbon Quaternary Stereocenter. J Org Chem 2022; 87:1154-1172. [PMID: 34985891 PMCID: PMC9382569 DOI: 10.1021/acs.joc.1c02523] [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] [Indexed: 01/23/2023]
Abstract
Novel phenanthridinone analogues with an all-carbon quaternary stereocenter have been enantioselectively synthesized using the Birch-Heck sequence. Flat phenanthridinone structures have extensive bioactivity but consequently also suffer from poor therapeutic selectivity. The addition of a quaternary center to the phenanthridinone skeleton has the potential to generate more complex analogues with improved selectivity. Unfortunately, no general synthetic pathway to such derivatives exists. Herein we report a four-step process that transforms inexpensive benzoic acid into 22 different quaternary carbon-containing phenanthridinone analogues with a variety of substituents on all three rings: alkyl groups at the quaternary center; methyl, methoxymethyl, or para-methoxybenzyl on the amide nitrogen; and halogen and methyl substituents on the aryl ring. Good to very good enantioselectivity was demonstrated in the key intramolecular desymmetrizing Mizoroki-Heck reaction. Transformations of the Heck reaction products into molecules with potentially greater therapeutic relevance were also accomplished.
Collapse
Affiliation(s)
- Mary Sexton
- Bryn Mawr College, Chemistry Department, Bryn Mawr,
Pennsylvania 19010
| | | | - Glenn P. A. Yap
- University of Delaware, Department of Chemistry and
Biochemistry, Newark, Delaware 19716
| | - Diana Rachii
- Bryn Mawr College, Chemistry Department, Bryn Mawr,
Pennsylvania 19010
| | - Greg Feldman
- Bryn Mawr College, Chemistry Department, Bryn Mawr,
Pennsylvania 19010
| | - Andrew T. Krasley
- Bryn Mawr College, Chemistry Department, Bryn Mawr,
Pennsylvania 19010
| | - Zhilin Chen
- Bryn Mawr College, Chemistry Department, Bryn Mawr,
Pennsylvania 19010
| | - My Anh Tran
- Bryn Mawr College, Chemistry Department, Bryn Mawr,
Pennsylvania 19010
| | - Kalyn Wiley
- Bryn Mawr College, Chemistry Department, Bryn Mawr,
Pennsylvania 19010
| | - Alexandra Matei
- Bryn Mawr College, Chemistry Department, Bryn Mawr,
Pennsylvania 19010
| | - Samantha Petersen
- Bryn Mawr College, Chemistry Department, Bryn Mawr,
Pennsylvania 19010
| | - Sabrina Tran Tien
- Bryn Mawr College, Chemistry Department, Bryn Mawr,
Pennsylvania 19010
| |
Collapse
|
136
|
He S, Dong G, Cheng J, Wu Y, Sheng C. Strategies for designing proteolysis targeting chimaeras (PROTACs). Med Res Rev 2022; 42:1280-1342. [PMID: 35001407 DOI: 10.1002/med.21877] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 12/18/2022]
Abstract
Proteolysis targeting chimaeras (PROTACs) is a cutting edge and rapidly growing technique for new drug discovery and development. Currently, the largest challenge in the molecular design and drug development of PROTACs is efficient identification of potent and drug-like degraders. This review aims to comprehensively summarize and analyse state-of-the-art methods and strategies in the design of PROTACs. We provide a detailed illustration of the general principles and tactics for designing potent PROTACs, highlight representative case studies, and discuss the advantages and limitations of these strategies. Particularly, structure-based rational PROTAC design and emerging new types of PROTACs (e.g., homo-PROTACs, multitargeting PROTACs, photo-control PROTACs and PROTAC-based conjugates) will be focused on.
Collapse
Affiliation(s)
- Shipeng He
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Guoqiang Dong
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Junfei Cheng
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Ying Wu
- School of Pharmacy, Second Military Medical University, Shanghai, China.,Department of Pharmacy, 920th Hospital of Joint Logistics Support Force, Kunming, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai, China
| |
Collapse
|
137
|
Ojida A. [Covalent drug discovery exploiting the new warheads]. Nihon Yakurigaku Zasshi 2022; 157:361-365. [PMID: 36047154 DOI: 10.1254/fpj.22052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Covalent drug forms a covalent bond with desease-related target proteins irreversibly inhibits their function. In order to develop a safe and non-toxic covalent drug, it is important to device new reaction chemistry that realizes a sufficient reactivity and high target selectivity for targeted protein under the complicated biological systems such as our body. Currently, new reaction chemistry is being actively developed all over the world to achieve excellent target selectivity of covalent drugs. In this essay, we intoroduce α-chlorofluoroacetamide and bicyclobutane amide as the new reactive groups for proteineous cysteine of targeted protein and their application to develop targeted covalent inhibitors for the treatment of cancer and infecsious deseases.
Collapse
Affiliation(s)
- Akio Ojida
- Graduate School of Pharmcaeutical Sceinces, Kyushu Universitiy
| |
Collapse
|
138
|
Knight S, Gianni D, Hendricks A. Fragment-based screening: A new paradigm for ligand and target discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:3-7. [PMID: 35058174 DOI: 10.1016/j.slasd.2021.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Significant advances in fragment-based screening, including the emergence of Fully Functionalised Fragments (FFFs) and innovations in Covalent Fragment screening are providing a new paradigm for ligand and target discovery. FFFs offer some key distinct advantages over other screening modalities such as small molecules and genetic screens, including 1) An ability to access diverse chemical space employing a relatively small compound set 2) Ease of screen optimisation given there is no requirement for genetic manipulation and 3) Built-in proteomics tools to facilitate rapid target deconvolution directly in cells. Covalent fragments enable exploration of novel druggable nodes through irreversible fragment-cysteine interactions, complementing their fully functionalized counterparts. Both FFFs and Covalent fragments present the phenotypic screening community with an additional and complementary approach for disease centric target identification.
Collapse
Affiliation(s)
- Sinéad Knight
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK; Bioscience, Sygnature Discovery Ltd, Alderley Park, Cheshire, UK.
| | - Davide Gianni
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Adam Hendricks
- Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, Boston, USA; Civetta Therapeutics, 10 Wilson Road, Cambridge, MA 02140
| |
Collapse
|
139
|
Zhang MY, Yang H, Ortiz G, Trnka MJ, Petronikolou N, Burlingame AL, DeGrado WF, Fujimori DG. Covalent labeling of a chromatin reader domain using proximity-reactive cyclic peptides. Chem Sci 2022; 13:6599-6609. [PMID: 35756531 PMCID: PMC9172573 DOI: 10.1039/d2sc00555g] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/10/2022] [Indexed: 11/21/2022] Open
Abstract
Chemical probes for chromatin reader proteins are valuable tools for investigating epigenetic regulatory mechanisms and evaluating whether the target of interest holds therapeutic potential. Developing potent inhibitors for the plant homeodomain (PHD) family of methylation readers remains a difficult task due to the charged, shallow and extended nature of the histone binding site that precludes effective engagement of conventional small molecules. Herein, we describe the development of novel proximity-reactive cyclopeptide inhibitors for PHD3—a trimethyllysine reader domain of histone demethylase KDM5A. Guided by the PHD3–histone co-crystal structure, we designed a sidechain-to-sidechain linking strategy to improve peptide proteolytic stability whilst maintaining binding affinity. We have developed an operationally simple solid-phase macrocyclization pathway, capitalizing on the inherent reactivity of the dimethyllysine ε-amino group to generate scaffolds bearing charged tetraalkylammonium functionalities that effectively engage the shallow aromatic ‘groove’ of PHD3. Leveraging a surface-exposed lysine residue on PHD3 adjacent to the ligand binding site, cyclic peptides were rendered covalent through installation of an arylsulfonyl fluoride warhead. The resulting lysine-reactive cyclic peptides demonstrated rapid and efficient labeling of the PHD3 domain in HEK293T lysates, showcasing the feasibility of employing proximity-induced reactivity for covalent labeling of this challenging family of reader domains. We describe the development of covalent cyclic peptide ligands which target a chromatin methylation reader domain using a proximity-reactive sulfonyl fluoride moiety.![]()
Collapse
Affiliation(s)
- Meng Yao Zhang
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Hyunjun Yang
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Gloria Ortiz
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Nektaria Petronikolou
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
- Quantitative Biosciences Institute, University of California San Francisco San Francisco CA 94158 USA
| |
Collapse
|
140
|
Svenningsen EB, Ottosen RN, Jørgensen KH, Nisavic M, Larsen CK, Hansen BK, Wang Y, Lindorff-Larsen K, Tørring T, Hacker SM, Palmfeldt J, Poulsen TB. The covalent reactivity of functionalized 5-hydroxy-butyrolactams is the basis for targeting of fatty acid binding protein 5 (FABP5) by the neurotrophic agent MT-21. RSC Chem Biol 2022; 3:1216-1229. [PMID: 36320884 PMCID: PMC9533406 DOI: 10.1039/d2cb00161f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/02/2022] [Indexed: 11/21/2022] Open
Abstract
Covalently acting compounds experience a strong interest within chemical biology both as molecular probes in studies of fundamental biological mechanisms and/or as novel drug candidates. In this context, the identification of new classes of reactive groups is particularly important as these can expose novel reactivity modes and, consequently, expand the ligandable proteome. Here, we investigated the electrophilic reactivity of the 3-acyl-5-hydroxy-1,5-dihydro-2H-pyrrole-2-one (AHPO) scaffold, a heterocyclic motif that is e.g. present in various bioactive natural products. Our investigations were focused on the compound MT-21 – a simplified structural analogue of the natural product epolactaene – which is known to have both neurotrophic activity and ability to trigger apoptotic cell death. We found that the central N-acyl hemiaminal group of MT-21 can function as an electrophilic centre enabling divergent reactivity with both amine- and thiol-based nucleophiles, which furthermore translated to reactivity with proteins in both cell lysates and live cells. We found that in live cells MT-21 strongly engaged the lipid transport protein fatty acid-binding protein 5 (FABP5) by direct binding to a cysteine residue in the bottom of the ligand binding pocket. Through preparation of a series of MT-21 derivatives, we probed the specificity of this interaction which was found to be strongly dependent on subtle structural changes. Our study suggests that MT-21 may be employed as a tool compound in future studies of the biology of FABP5, which remains incompletely understood. Furthermore, our study has also made clear that other natural products containing the AHPO-motif may likewise possess covalent reactivity and that this property may underlie their biological activity. In this work, it is shown that an N-acyl hemiaminal motif present in many natural products can function as an electrophilic centre, mediating covalent reactivity in biological systems, reacting with both thiols and amines.![]()
Collapse
Affiliation(s)
| | - Rasmus N. Ottosen
- Department of Chemistry, Aarhus University, DK-8000, Aarhus C, Denmark
| | | | - Marija Nisavic
- Department of Chemistry, Aarhus University, DK-8000, Aarhus C, Denmark
- Department of Clinical Medicine – Research Unit for Molecular Medicine, Aarhus University Hospital, DK-8200 Aarhus N, Denmark
| | - Camilla K. Larsen
- Department of Engineering – Microbial Biosynthesis, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Bente K. Hansen
- Department of Chemistry, Aarhus University, DK-8000, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark
| | - Yong Wang
- Copenhagen Biocenter, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | | | - Thomas Tørring
- Department of Engineering – Microbial Biosynthesis, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Stephan M. Hacker
- Leiden Institute of Chemistry, Leiden University, NL-2333 CC Leiden, The Netherlands
| | - Johan Palmfeldt
- Department of Clinical Medicine – Research Unit for Molecular Medicine, Aarhus University Hospital, DK-8200 Aarhus N, Denmark
| | - Thomas B. Poulsen
- Department of Chemistry, Aarhus University, DK-8000, Aarhus C, Denmark
| |
Collapse
|
141
|
Huang KW, Chen JW, Hua TY, Chu YY, Chiu TY, Liu JY, Tu CI, Hsu KC, Kao YT, Chu JW, Hsiao YY. Targeted Covalent Inhibitors Allosterically Deactivate the DEDDh Lassa Fever Virus NP Exonuclease from Alternative Distal Sites. JACS AU 2021; 1:2315-2327. [PMID: 34977900 PMCID: PMC8715546 DOI: 10.1021/jacsau.1c00420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Indexed: 06/14/2023]
Abstract
For using targeted covalent inhibitors (TCIs) as anticancer and antiviral drugs, we establish that the model compounds PCMPS (p-chloromercuriphenyl sulfate) and PCMB (p-chloromercuribenzoate) are inhibitors of the DEDDh family of exonucleases. The underlying mechanism is analyzed by X-ray crystallography, activity/nucleic acid-binding assays, and all-atom molecular dynamics (MD) simulations. The first TCI-complexed structures of a DEDDh enzyme, the Lassa fever virus NP exonuclease (NPexo), are resolved to elucidate that the Cys409 binding site is away from the active site and the RNA-binding lid. The NPexo C409A structures indicate Cys461 as the alternative distal site for obstructing the equally active mutant. All-atom MD simulations of the wild type and mutant NPexos in explicit solvent uncover an allosteric inhibition mechanism that the local perturbation induced by PCMPS sulfonate propagates to impact the RNA-binding lid conformation. Binding assay studies confirm that PCMPS does affect the RNA binding of NPexo. The predicted relative potency between PCMPS and PCMB is also in line with experiments. The structural data and inhibition mechanism established in this work provide an important molecular basis for the drug development of TCIs.
Collapse
Affiliation(s)
- Kuan-Wei Huang
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jing-Wen Chen
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
| | - Tzu-Yu Hua
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
| | - Yu-Yu Chu
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
| | - Tsai-Yuan Chiu
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jung-Yu Liu
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Chun-I Tu
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Kai-Cheng Hsu
- Graduate
Institute of Cancer Biology and Drug Discovery, College of Medical
Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program
for Cancer Molecular Biology and Drug Discovery, College of Medical
Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D.
Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
- Biomedical
Commercialization Center, Taipei Medical
University, Taipei 11031, Taiwan
| | - Ya-Ting Kao
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
- Center
for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jhih-Wei Chu
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
- Center
for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yu-Yuan Hsiao
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
- Center
for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Drug
Development and Value Creation Research Center, Center for Cancer
Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| |
Collapse
|
142
|
Genetically encoding latent bioreactive amino acids and the development of covalent protein drugs. Curr Opin Chem Biol 2021; 66:102106. [PMID: 34968810 DOI: 10.1016/j.cbpa.2021.102106] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/07/2021] [Accepted: 11/25/2021] [Indexed: 12/11/2022]
Abstract
As natural proteins generally do not bind targets in a covalent mode, the therapeutic potential of covalent protein drugs remains largely unexplored. Recently, latent bioreactive amino acids have been incorporated into proteins through genetic code expansion, which selectively react with nearby natural residues via proximity-enabled reactivity, generating diverse covalent linkages for proteins in vitro and in cells. These new covalent linkages provide novel avenues for protein research and engineering. In addition, a general platform technology, proximity-enabled reactive therapeutics (PERx), has been established for the development of covalent protein drugs. The first covalent protein drug demonstrates advantageous features in cancer immunotherapy in mice. Selective introduction of covalent bonds into proteins will advance biological studies, synthetic biology, and biotherapeutics with the power of biocompatible covalent chemistries.
Collapse
|
143
|
Zhang Z, Wang Y, Chen X, Song X, Tu Z, Chen Y, Zhang Z, Ding K. Characterization of an aromatic trifluoromethyl ketone as a new warhead for covalently reversible kinase inhibitor design. Bioorg Med Chem 2021; 50:116457. [PMID: 34670167 DOI: 10.1016/j.bmc.2021.116457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 12/28/2022]
Abstract
An aromatic trifluoromethyl ketone moiety was characterized as a new warhead for covalently reversible kinase inhibitor design to target the non-catalytic cysteine residue. Potent and selective covalently reversible inhibitors of FGFR4 kinase were successfully designed and synthesized by utilizing this new warhead. The binding mode of a representative inhibitor was fully characterized by using multiple technologies including MALDI-TOF mass spectrometry, dialysis assay and X-ray crystallographic studies etc. This functional group was also successfully applied to discovery of a new JAK3 inhibitor, suggesting its potential application in designing other kinase inhibitors.
Collapse
Affiliation(s)
- Zhen Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yongjin Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xiaojuan Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiaojuan Song
- Drug Discovery Pipeline & Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou 510530, China
| | - Zhengchao Tu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China; Drug Discovery Pipeline & Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou 510530, China
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhimin Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China; The First Affiliated Hospital, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
| |
Collapse
|
144
|
de Rosa M, Nonnis S, Aliverti A. Covalent inhibition of P. falciparum ferredoxin-NADP + reductase: Exploring alternative strategies for the development of new antimalarial drugs. Biochem Biophys Res Commun 2021; 577:89-94. [PMID: 34509083 DOI: 10.1016/j.bbrc.2021.09.008] [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: 08/07/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 11/20/2022]
Abstract
The protozoan Plasmodium falciparum is the main aetiological agent of tropical malaria. Characteristic of the phylum is the presence of a plastid-like organelle which hosts several homologs of plant proteins, including a ferredoxin (PfFd) and its NADPH-dependent reductase (PfFNR). The PfFNR/PfFd redox system is essential for the parasite, while mammals share no homologous proteins, making the enzyme an attractive target for novel and much needed antimalarial drugs. Based on previous findings, three chemically reactive residues important for PfFNR activity were identified: namely, the active-site Cys99, responsible for hydride transfer; Cys284, whose oxidation leads to an inactive dimeric form of the protein; and His286, which is involved in NADPH binding. These amino acid residues were probed by several residue-specific reagents and the two cysteines were shown to be promising targets for covalent inhibition. The quantitative and qualitative description of the reactivity of few compounds, including a repurposed drug, set the bases for the development of more potent and specific antimalarial leads.
Collapse
Affiliation(s)
- Matteo de Rosa
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy.
| | - Simona Nonnis
- DIMEVET - Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milano, Italy; CRC "Innovation for Well-Beeing and Environment" (I-WE), Università degli Studi di Milano, Milano, Italy
| | | |
Collapse
|
145
|
Kwong AJ, Pham TND, Oelschlager HE, Munshi HG, Scheidt KA. Rational Design, Optimization, and Biological Evaluation of Novel MEK4 Inhibitors against Pancreatic Adenocarcinoma. ACS Med Chem Lett 2021; 12:1559-1567. [PMID: 34676038 DOI: 10.1021/acsmedchemlett.1c00376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 01/05/2023] Open
Abstract
Growth, division, and development of healthy cells relies on efficient response to environmental survival cues. The conserved mitogen-activated protein kinase (MAPK) family of pathways interface extracellular stimuli to intracellular processes for this purpose. Within these pathways, the MEK family has been identified as a target of interest due to its clinical relevance. Particularly, MEK4 has drawn recent attention for its indications in pancreatic and prostate cancers. Here, we report two potent MEK4 inhibitors demonstrating significant reduction of phospho-JNK and antiproliferative properties against pancreatic cancer cell lines. Furthermore, molecular inhibition of MEK4 pathway activates the MEK1/2 pathway, with the combination of MEK1/2 and MEK4 inhibitors demonstrating synergistic effects against pancreatic cancer cells. Our inhibitors provided insight into the crosstalk between MAPK pathways and new tools for elucidating the roles of MEK4 in disease states, findings which will pave the way for better understanding of the MAPK pathways and development of additional probes.
Collapse
Affiliation(s)
- Ada J. Kwong
- Department of Chemistry, Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Thao N. D. Pham
- Department of Medicine, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Chicago, Illinois 60611, United States
| | - Hannah E. Oelschlager
- Department of Chemistry, Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Hidayatullah G. Munshi
- Department of Medicine, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Chicago, Illinois 60611, United States
| | - Karl A. Scheidt
- Department of Chemistry, Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| |
Collapse
|
146
|
Gao M, Moumbock AFA, Qaseem A, Xu Q, Günther S. CovPDB: a high-resolution coverage of the covalent protein-ligand interactome. Nucleic Acids Res 2021; 50:D445-D450. [PMID: 34581813 PMCID: PMC8728183 DOI: 10.1093/nar/gkab868] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/07/2021] [Accepted: 09/15/2021] [Indexed: 01/14/2023] Open
Abstract
In recent years, the drug discovery paradigm has shifted toward compounds that covalently modify disease-associated target proteins, because they tend to possess high potency, selectivity, and duration of action. The rational design of novel targeted covalent inhibitors (TCIs) typically starts from resolved macromolecular structures of target proteins in their apo or holo forms. However, the existing TCI databases contain only a paucity of covalent protein–ligand (cP–L) complexes. Herein, we report CovPDB, the first database solely dedicated to high-resolution cocrystal structures of biologically relevant cP–L complexes, curated from the Protein Data Bank. For these curated complexes, the chemical structures and warheads of pre-reactive electrophilic ligands as well as the covalent bonding mechanisms to their target proteins were expertly manually annotated. Totally, CovPDB contains 733 proteins and 1,501 ligands, relating to 2,294 cP–L complexes, 93 reactive warheads, 14 targetable residues, and 21 covalent mechanisms. Users are provided with an intuitive and interactive web interface that allows multiple search and browsing options to explore the covalent interactome at a molecular level in order to develop novel TCIs. CovPDB is freely accessible at http://www.pharmbioinf.uni-freiburg.de/covpdb/ and its contents are available for download as flat files of various formats.
Collapse
Affiliation(s)
- Mingjie Gao
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Aurélien F A Moumbock
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Ammar Qaseem
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Qianqing Xu
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| |
Collapse
|
147
|
Bonatto V, Shamim A, Rocho FDR, Leitão A, Luque FJ, Lameira J, Montanari CA. Predicting the Relative Binding Affinity for Reversible Covalent Inhibitors by Free Energy Perturbation Calculations. J Chem Inf Model 2021; 61:4733-4744. [PMID: 34460252 DOI: 10.1021/acs.jcim.1c00515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covalent inhibitors are assuming central importance in drug discovery projects, especially in this pandemic scenario. Many research groups have focused their attention on inhibiting viral proteases or human proteases such as cathepsin L (hCatL). The inhibition of these critical enzymes may impair viral replication. However, molecular modeling of covalent ligands is challenging since covalent and noncovalent ligand-bound states must be considered in the binding process. In this work, we evaluated the suitability of free energy perturbation (FEP) calculations as a tool for predicting the binding affinity of reversible covalent inhibitors of hCatL. Our strategy relies on the relative free energy calculated for both covalent and noncovalent complexes and the free energy changes have been compared with experimental data for eight nitrile-based inhibitors, including three new inhibitors of hCatL. Our results demonstrate that the covalent complex can be employed to properly rank the inhibitors. Nevertheless, a comparison of the free energy changes in both noncovalent and covalent states is valuable to interpret the effect triggered by the formation of the covalent bond on the interactions played by functional groups distant from the warhead. Overall, FEP can be employed as a powerful predictor tool in developing and understanding the activity of reversible covalent inhibitors.
Collapse
Affiliation(s)
- Vinícius Bonatto
- Medicinal & Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil
| | - Anwar Shamim
- Medicinal & Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil
| | - Fernanda Dos R Rocho
- Medicinal & Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil
| | - Andrei Leitão
- Medicinal & Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain
| | - Jerônimo Lameira
- Medicinal & Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil.,Institute of Biological Science, Federal University of Pará, Rua Augusto Correa S/N, 66075-110 Belém, Pará, Brazil
| | - Carlos A Montanari
- Medicinal & Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil
| |
Collapse
|
148
|
Friday SN, Cheng DW, Zagler SG, Zanella BS, Dietz JD, Calbat CN, Roach LT, Bagnal C, Faile IS, Halkides CJ, Viola RE. Design and testing of selective inactivators against an antifungal enzyme target. Drug Dev Res 2021; 83:447-460. [PMID: 34469014 DOI: 10.1002/ddr.21875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/03/2021] [Accepted: 08/19/2021] [Indexed: 11/10/2022]
Abstract
Systemic infections from fungal organisms are becoming increasingly difficult to treat as drug resistance continues to emerge. To substantially expand the antifungal drug landscape new compounds must be identified and developed with novel modes of action against previously untested drug targets. Most drugs block the activity of their targets through reversible, noncovalent interactions. However, a significant number of drugs form irreversible, covalent bonds with their selected targets. While more challenging to develop, these irreversible inactivators offer some significant advantages as novel antifungal agents. Vinyl sulfones contain a potentially reactive functional group that could function as a selective enzyme inactivator, and members of this class of compounds are now being developed as inactivators against an antifungal drug target. The enzyme aspartate semialdehyde dehydrogenase (ASADH) catalyzes a key step in an essential microbial pathway and is essential for the survival of every microorganism examined. A series of vinyl sulfones have been designed, guided by molecular modeling and docking studies to enhance their affinity for fungal ASADHs. These newly synthesized compounds have been examined against this target enzyme from the pathogenic fungal organism Candida albicans. Vinyl sulfones containing complementary structural elements inhibit this enzyme with inhibition constants in the low-micromolar range. These inhibitors have also led to the rapid and irreversible inactivation of this enzyme, and show some initial selectivity when compared to the inactivation of a bacterial ASADH. The best inactivators will serve as lead compounds for the development of potent and selective antifungal agents.
Collapse
Affiliation(s)
- Samantha N Friday
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, USA
| | - Daniel W Cheng
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Sebastian G Zagler
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Brady S Zanella
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Jordan D Dietz
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Christopher N Calbat
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Logan T Roach
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Cindy Bagnal
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Ian S Faile
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Christopher J Halkides
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Ronald E Viola
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, USA
| |
Collapse
|
149
|
Kumar M, Reddy NC, Rai V. Chemical technologies for precise protein bioconjugation interfacing biology and medicine. Chem Commun (Camb) 2021; 57:7083-7095. [PMID: 34180471 DOI: 10.1039/d1cc02268g] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins provide an excellent means to monitor and regulate biological processes. Hence, a precise chemical toolbox for their modification becomes indispensable. In this perspective, this feature article outlines our efforts to establish the core principles of chemoselectivity, site-selectivity, site-specificity, site-modularity, residue-modularity, and protein-specificity. With the knowledge to systematically regulate these parameters, the field has access to technological platforms that can address multiple challenges at the interface of chemistry, biology, and medicine.
Collapse
Affiliation(s)
- Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| | - Neelesh C Reddy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| |
Collapse
|
150
|
Franz M, Mörchen B, Degenhart C, Gülden D, Shkura O, Wolters D, Koch U, Klebl B, Stoll R, Helfrich I, Scherkenbeck J. Sequence-Selective Covalent CaaX-Box Receptors Prevent Farnesylation of Oncogenic Ras Proteins and Impact MAPK/PI3 K Signaling. ChemMedChem 2021; 16:2504-2514. [PMID: 33899342 PMCID: PMC8453727 DOI: 10.1002/cmdc.202100167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 01/21/2023]
Abstract
Oncogenic Ras proteins are implicated in the most common life-threatening cancers. Despite intense research over the past two decades, the progress towards small-molecule inhibitors has been limited. One reason for this failure is that Ras proteins interact with their effectors only via protein-protein interactions, which are notoriously difficult to address with small organic molecules. Herein we describe an alternative strategy, which prevents farnesylation and subsequent membrane insertion, a prerequisite for the activation of Ras proteins. Our approach is based on sequence-selective supramolecular receptors which bind to the C-terminal farnesyl transferase recognition unit of Ras and Rheb proteins and covalently modify the essential cysteine in the so-called CaaX-box.
Collapse
Affiliation(s)
- Matthias Franz
- Faculty of Mathematics and Natural SciencesUniversity of Wuppertal42119WuppertalGermany
| | - Britta Mörchen
- Vascular Oncology & MetastasisUniversity Hospital Essen45147EssenGermany
| | | | - Daniel Gülden
- Faculty of Mathematics and Natural SciencesUniversity of Wuppertal42119WuppertalGermany
| | - Oleksandr Shkura
- Faculty of Chemistry and BiochemistryRuhr-University Bochum44780BochumGermany
| | - Dirk Wolters
- Faculty of Chemistry and BiochemistryRuhr-University Bochum44780BochumGermany
| | - Uwe Koch
- Lead Discovery Center GmbH44227DortmundGermany
| | - Bert Klebl
- Lead Discovery Center GmbH44227DortmundGermany
| | - Raphael Stoll
- Faculty of Chemistry and BiochemistryRuhr-University Bochum44780BochumGermany
| | - Iris Helfrich
- Vascular Oncology & MetastasisUniversity Hospital Essen45147EssenGermany
| | - Jürgen Scherkenbeck
- Faculty of Mathematics and Natural SciencesUniversity of Wuppertal42119WuppertalGermany
| |
Collapse
|