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Yang J, Tian E, Chen L, Liu Z, Ren Y, Mao W, Zhang Y, Zhang J. Development and therapeutic perspectives of CXCR4 antagonists for disease therapy. Eur J Med Chem 2024; 275:116594. [PMID: 38879970 DOI: 10.1016/j.ejmech.2024.116594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
Chemokine receptor 4 (CXCR4) is a subtype receptor protein of the GPCR family with a seven-transmembrane structure widely distributed in human tissues. CXCR4 is involved in diseases (e.g., HIV-1 infection), cancer proliferation and metastasis, inflammation signaling pathways, and leukemia, making it a promising drug target. Clinical trials on CXCR4 antagonists mainly focused on peptides and antibodies, with a few small molecule compounds, such as AMD11070 (2) and MSX-122 (3), showing promise in cancer treatment. This perspective discusses the structure-activity relationship (SAR) of CXCR4 and its role in diseases, mainly focusing on the SAR of CXCR4 antagonists. It also explores the standard structural features and target interactions of CXCR4 binding in different disease categories. Furthermore, it investigates various modification strategies to propose potential improvements in the effectiveness of CXCR4 drugs.
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Affiliation(s)
- Jun Yang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and Institute of Respiratory Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Erkang Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Li Chen
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and Institute of Respiratory Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Zihang Liu
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and Institute of Respiratory Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yijiu Ren
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Wuyu Mao
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and Institute of Respiratory Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Yiwen Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and Institute of Respiratory Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Jifa Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and Institute of Respiratory Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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2
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Meng Q, Zhu R, Mao Y, Zhu S, Wu Y, Huang L, Ciechanover A, An J, Xu Y, Huang Z. Biological and mutational analyses of CXCR4-antagonist interactions and design of new antagonistic analogs. Biosci Rep 2023; 43:BSR20230981. [PMID: 38131305 PMCID: PMC10987480 DOI: 10.1042/bsr20230981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/05/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
The chemokine receptor CXCR4 has become an attractive therapeutic target for HIV-1 infection, hematopoietic stem cell mobilization, and cancer metastasis. A wide variety of synthetic antagonists of CXCR4 have been developed and studied for a growing list of clinical applications. To compare the biological effects of different antagonists on CXCR4 functions and their common and/or distinctive molecular interactions with the receptor, we conducted head-to-head comparative cell-based biological and mutational analyses of the interactions with CXCR4 of eleven reported antagonists, including HC4319, DV3, DV1, DV1 dimer, V1, vMIP-II, CVX15, LY2510924, IT1t, AMD3100, and AMD11070 that were representative of different structural classes of D-peptides, L-peptide, natural chemokine, cyclic peptides, and small molecules. The results were rationalized by molecular modeling of CXCR4-antagonist interactions from which the common as well as different receptor binding sites of these antagonists were derived, revealing a number of important residues such as W94, D97, H113, D171, D262, and E288, mostly of negative charge. To further examine this finding, we designed and synthesized new antagonistic analogs by adding positively charged residues Arg to a D-peptide template to enhance the postulated charge-charge interactions. The newly designed analogs displayed significantly increased binding to CXCR4, which supports the notion that negatively charged residues of CXCR4 can engage in interactions with moieties of positive charge of the antagonistic ligands. The results from these mutational, modeling and new analog design studies shed new insight into the molecular mechanisms of different types of antagonists in recognizing CXCR4 and guide the development of new therapeutic agents.
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Affiliation(s)
- Qian Meng
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ruohan Zhu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yujia Mao
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Siyu Zhu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yi Wu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lina S.M. Huang
- Division of Infectious Diseases and Global Public Heath, Department of Medicine, School of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, U.S.A
| | - Aaron Ciechanover
- The Rapport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3109601, Israel
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Jing An
- Division of Infectious Diseases and Global Public Heath, Department of Medicine, School of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, U.S.A
| | - Yan Xu
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Ziwei Huang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Division of Infectious Diseases and Global Public Heath, Department of Medicine, School of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, U.S.A
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
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3
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Discovery of Bis-Imidazoline Derivatives as New CXCR4 Ligands. Molecules 2023; 28:molecules28031156. [PMID: 36770826 PMCID: PMC9920567 DOI: 10.3390/molecules28031156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
The chemokine receptor CXCR4 and its ligand CXCL12 regulate leukocyte trafficking, homeostasis and functions and are potential therapeutic targets in many diseases such as HIV-1 infection and cancers. Here, we identified new CXCR4 ligands in the CERMN chemical library using a FRET-based high-throughput screening assay. These are bis-imidazoline compounds comprising two imidazole rings linked by an alkyl chain. The molecules displace CXCL12 binding with submicromolar potencies, similarly to AMD3100, the only marketed CXCR4 ligand. They also inhibit anti-CXCR4 mAb 12G5 binding, CXCL12-mediated chemotaxis and HIV-1 infection. Further studies with newly synthesized derivatives pointed out to a role of alkyl chain length on the bis-imidazoline properties, with molecules with an even number of carbons equal to 8, 10 or 12 being the most potent. Interestingly, these differ in the functions of CXCR4 that they influence. Site-directed mutagenesis and molecular docking predict that the alkyl chain folds in such a way that the two imidazole groups become lodged in the transmembrane binding cavity of CXCR4. Results also suggest that the alkyl chain length influences how the imidazole rings positions in the cavity. These results may provide a basis for the design of new CXCR4 antagonists targeting specific functions of the receptor.
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4
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Jecs E, Tahirovic YA, Wilson RJ, Miller EJ, Kim M, Truax V, Nguyen HH, Akins NS, Saindane M, Wang T, Sum CS, Cvijic ME, Schroeder GM, Burton SL, Derdeyn CA, Xu L, Jiang Y, Wilson LJ, Liotta DC. Synthesis and Evaluation of Novel Tetrahydronaphthyridine CXCR4 Antagonists with Improved Drug-like Profiles. J Med Chem 2022; 65:4058-4084. [PMID: 35179893 DOI: 10.1021/acs.jmedchem.1c01564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Our first-generation CXCR4 antagonist TIQ15 was rationally modified to improve drug-like properties. Introducing a nitrogen atom into the aromatic portion of the tetrahydroisoquinoline ring led to several heterocyclic variants including the 5,6,7,8-tetrahydro-1,6-naphthyridine series, greatly reducing the inhibition of the CYP 2D6 enzyme. Compound 12a demonstrated the best overall properties after profiling a series of isomeric tetrahydronaphthyridine analogues in a battery of biochemical assays including CXCR4 antagonism, CYP 2D6 inhibition, metabolic stability, and permeability. The butyl amine side chain of 12a was substituted with various lipophilic groups to improve the permeability. These efforts culminated in the discovery of compound 30 as a potent CXCR4 antagonist (IC50 = 24 nM) with diminished CYP 2D6 activity, improved PAMPA permeability (309 nm/s), potent inhibition of human immunodeficiency virus entry (IC50 = 7 nM), a cleaner off-target in vitro safety profile, lower human ether a-go-go-related gene channel activity, and higher oral bioavailability in mice (% FPO = 27) compared to AMD11070 and TIQ15.
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Affiliation(s)
- Edgars Jecs
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Yesim A Tahirovic
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Robert J Wilson
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Eric J Miller
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Michelle Kim
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Valarie Truax
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Huy H Nguyen
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Nicholas S Akins
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Manohar Saindane
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Tao Wang
- Bristol-Myers Squibb Research & Development, Princeton, New Jersey 08543, United States
| | - Chi S Sum
- Bristol-Myers Squibb Research & Development, Princeton, New Jersey 08543, United States
| | - Mary E Cvijic
- Bristol-Myers Squibb Research & Development, Princeton, New Jersey 08543, United States
| | - Gretchen M Schroeder
- Bristol-Myers Squibb Research & Development, Princeton, New Jersey 08543, United States
| | - Samantha L Burton
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, United States
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30322, United States
| | - Cynthia A Derdeyn
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, United States
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30322, United States
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Lingjie Xu
- Hangzhou Junrui Biotechnology, Hangzhou, Zhejiang 310000, China
| | - Yi Jiang
- Hangzhou Junrui Biotechnology, Hangzhou, Zhejiang 310000, China
| | - Lawrence J Wilson
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Dennis C Liotta
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
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5
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A fragment integrational approach to GPCR inhibition: Identification of a high affinity small molecule CXCR4 antagonist. Eur J Med Chem 2022; 231:114150. [DOI: 10.1016/j.ejmech.2022.114150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 11/23/2022]
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6
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Speranta A, Manoliu L, Sogor C, Mernea M, Seiman CD, Seiman DD, Chifiriuc C. Structural bioinformatics used to predict the protein targets of remdesivir and flavones in SARS-CoV-2 infection. Med Chem 2021; 18:382-393. [PMID: 34365955 DOI: 10.2174/1573406417666210806154129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/30/2020] [Accepted: 03/21/2021] [Indexed: 01/18/2023]
Abstract
BACKGROUND During the current SARS-CoV-2 pandemic, the identification of effective antiviral drugs is crucial. Unfortunately, no specific treatment or vaccine is available to date. OBJECTIVE Here, we aimed to predict the interactions between SARS-CoV-2 proteins and protein targets from the human body for some flavone molecules (kaempferol, morin, pectolinarin, myricitrin, and herbacetin) in comparison to synthetic compounds (hydroxychloroquine, remdesivir, ribavirin, ritonavir, AMD-070, favipiravir). METHODS Using MOE software and advanced bioinformatics and cheminformatics portals, we conducted an extensive analysis based on various structural and functional features of compounds, such as their amphiphilic field, flexibility, and steric features. The structural similarity analysis of natural and synthetic compounds was performed using Tanimoto coefficients. The interactions of some compounds with SARS-CoV-2 3CLprotease or RNA-dependent RNA polymerase were described using 2D protein-ligand interaction diagrams based on known crystal structures. The potential targets of considered compounds were identified using the SwissTargetPrediction web tool. RESULTS Our results showed that remdesivir, pectolinarin, and ritonavir present a strong structural similarity which may be correlated to their similar biological activity. As common molecular targets of compounds in the human body, ritonavir, kaempferol, morin, and herbacetin can activate multidrug resistance-associated proteins, while remdesivir, ribavirin, and pectolinarin appear as ligands for adenosine receptors. CONCLUSION Our evaluation recommends remdesivir, pectolinarin, and ritonavir as promising anti-SARS-CoV-2 agents.
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Affiliation(s)
- Avram Speranta
- University of Bucharest, Faculty of Biology, Department of Anatomy, Animal Physiology and Biophysics, 36-46 Bd. M. Kogalniceanu, 050107, Bucharest. Romania
| | - Laura Manoliu
- University of Bucharest, Faculty of Biology, Department of Anatomy, Animal Physiology and Biophysics, 36-46 Bd. M. Kogalniceanu, 050107, Bucharest. Romania
| | - Catalina Sogor
- University of Bucharest, Faculty of Biology, Department of Anatomy, Animal Physiology and Biophysics, 36-46 Bd. M. Kogalniceanu, 050107, Bucharest. Romania
| | - Maria Mernea
- University of Bucharest, Faculty of Biology, Department of Anatomy, Animal Physiology and Biophysics, 36-46 Bd. M. Kogalniceanu, 050107, Bucharest. Romania
| | - Corina Duda Seiman
- West University of Timisoara, Faculty of Chemistry, Biology, Geography, Department of Chemistry and Biology, 16 Pestalozzi, 300115, Timisoara. Romania
| | - Daniel Duda Seiman
- Victor Babes University of Medicine and Pharmacy Timisoara, 2 Piata Eftimie Murgu, 300041, Timisoara. Romania
| | - Carmen Chifiriuc
- University of Bucharest, Faculty of Biology, Department of Botanics and Microbiology, 1-3 Aleea Portocalelor Str, 60101 Bucharest. Romania
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7
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Discovery of novel aminopiperidinyl amide CXCR4 modulators through virtual screening and rational drug design. Eur J Med Chem 2020; 201:112479. [PMID: 32534343 DOI: 10.1016/j.ejmech.2020.112479] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/08/2020] [Accepted: 05/16/2020] [Indexed: 12/29/2022]
Abstract
The C-X-C chemokine receptor type 4 (CXCR4) is a potential therapeutic target for HIV infection, metastatic cancer, and inflammatory autoimmune diseases. In this study, we screened the ZINC chemical database for novel CXCR4 modulators through a series of in silico guided processes. After evaluating the screened compounds for their binding affinities to CXCR4 and inhibitory activities against the chemoattractant CXCL12, we identified a hit compound (ZINC 72372983) showing 100 nM affinity and 69% chemotaxis inhibition at the same concentration (100 nM). To increase the potency of our hit compound, we explored the protein-ligand interactions at an atomic level using molecular dynamics simulation which enabled us to design and synthesize a novel compound (Z7R) with nanomolar affinity (IC50 = 1.25 nM) and improved chemotaxis inhibition (78.5%). Z7R displays promising anti-inflammatory activity (50%) in a mouse edema model by blocking CXCR4-expressed leukocytes, being supported by our immunohistochemistry study.
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8
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Oum YH, Shetty D, Yoon Y, Liang Z, Voll RJ, Goodman MM, Shim H. A benzenesulfonamide derivative as a novel PET radioligand for CXCR4. Bioorg Med Chem 2020; 28:115240. [PMID: 31843463 PMCID: PMC6942325 DOI: 10.1016/j.bmc.2019.115240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 12/24/2022]
Abstract
CXCR4 is involved in various diseases such as inflammation, tumor growth, and cancer metastasis through the interaction with its natural endogenous ligand, chemokine CXCL12. In an effort to develop imaging probes for CXCR4, we developed a novel small molecule CXCR4-targeted PET agent (compound 5) by combining our established benzenesulfonamide scaffold with a labeling component by virtue of click chemistry. 5 shows nanomolar affinity (IC50 = 6.9 nM) against a known CXCR4 antagonist (TN14003) and inhibits more than 65% chemotaxis at 10 nM in vitro assays. Radiofluorinated compound 5 ([18F]5) demonstrates a competitive cellular uptake against CXCL12 in a dose-dependent manner. Further, microPET images of [18F]5 exhibits preferential accumulation of radioactivity in the lesions of λ-carrageenan-induced paw edema, human head and neck cancer orthotopic xenograft, and metastatic lung cancer of each mouse model.
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Affiliation(s)
- Yoon Hyeun Oum
- Department of Radiation Oncology, Emory University School of Medicine, USA
| | - Dinesh Shetty
- Department of Radiology and Image Sciences, Emory University School of Medicine, USA
| | - Younghyoun Yoon
- Department of Radiation Oncology, Emory University School of Medicine, USA
| | - Zhongxing Liang
- Department of Radiation Oncology, Emory University School of Medicine, USA; Winship Cancer Institute, Atlanta, GA 30322, USA
| | - Ronald J Voll
- Department of Radiology and Image Sciences, Emory University School of Medicine, USA
| | - Mark M Goodman
- Department of Radiology and Image Sciences, Emory University School of Medicine, USA; Winship Cancer Institute, Atlanta, GA 30322, USA
| | - Hyunsuk Shim
- Department of Radiation Oncology, Emory University School of Medicine, USA; Department of Radiology and Image Sciences, Emory University School of Medicine, USA; Winship Cancer Institute, Atlanta, GA 30322, USA.
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9
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Zhu S, Meng Q, Schooley RT, An J, Xu Y, Huang Z. Structural and Biological Characterizations of Novel High-Affinity Fluorescent Probes with Overlapped and Distinctive Binding Regions on CXCR4. Molecules 2019; 24:molecules24162928. [PMID: 31412600 PMCID: PMC6720714 DOI: 10.3390/molecules24162928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/09/2019] [Accepted: 08/10/2019] [Indexed: 01/25/2023] Open
Abstract
CXC-type chemokine receptor 4 (CXCR4) is well known as a co-receptor for cellular entry and infection of human immunodeficiency virus type 1 (HIV-1). As an important member of the G protein-coupled receptor (GPCR) family, CXCR4 also mediates a variety of cellular processes and functions, such as cell chemotaxis, proliferation, and calcium signal transductions. Identification and characterization of molecular ligands or probes of CXCR4 have been an intensive area of investigations as such ligands or probes are of significant clinical values for the studies and treatments of HIV-1 infection and other human diseases mediated by the receptor. The crystal structures of CXCR4 in complex with different ligands have revealed two distinctive binding regions or subpockets. Thus, understanding the interactions of diverse ligands with these distinctive CXCR4 binding regions has become vital for elucidating the relationship between binding modes and biological mechanisms of ligand actions. Peptidic CVX15 is the only ligand that has been validated to bind one of these distinctive binding regions (or so called the major subpocket) of CXCR4. Therefore, in this study, we developed an efficient probe system including two high-affinity peptidic fluorescent probes, designated as FITC-CVX15 and FITC-DV1, with the aim of targeting distinctive CXCR4 subpockets. We conducted rational design and chemical characterization of the two CXCR4-specific probes and examined their application in biological experiments including competitive binding assays, flow cytometry analysis, and confocal imaging. Especially these two probes were applied in parallel CXCR4 competitive binding assays to detect and analyze potential binding modes of diverse CXCR4 ligands, together with molecular docking and simulations. Our results have indicated that these peptidic fluorescent probe systems provide novel ligand detecting tools, as well as present a new approach for analyzing distinctive binding modes of diverse CXCR4 ligands.
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Affiliation(s)
- Siyu Zhu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Department of Medicine, Division of Infectious Diseases and Global Public Health, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Qian Meng
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Robert T Schooley
- Department of Medicine, Division of Infectious Diseases and Global Public Health, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Jing An
- Department of Medicine, Division of Infectious Diseases and Global Public Health, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Yan Xu
- School of Life and Health Sciences, Chinese University of Hong Kong, Shenzhen 518172, China.
| | - Ziwei Huang
- School of Life Sciences, Tsinghua University, Beijing 100084, China.
- Department of Medicine, Division of Infectious Diseases and Global Public Health, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
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10
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Katzman BM, Cox BD, Prosser AR, Alcaraz AA, Murat B, Héroux M, Tebben A, Zhang Y, Schroeder GM, Snyder JP, Wilson LJ, Liotta DC. Tetrahydroisoquinoline CXCR4 Antagonists Adopt a Hybrid Binding Mode within the Peptide Subpocket of the CXCR4 Receptor. ACS Med Chem Lett 2019; 10:67-73. [PMID: 30655949 DOI: 10.1021/acsmedchemlett.8b00441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/30/2018] [Indexed: 01/22/2023] Open
Abstract
The rationale for the structural and mechanistic basis of a tetrahydroisoquinoline (THIQ) based series of CXCR4 antagonists is presented. Using the previously reported crystal structures which reveal two distinct binding sites of CXCR4 defined as the small molecule (IT1t or minor) binding pocket and peptide (CVX15 or major) binding pocket, we hypothesized our THIQ small molecule series could bind like either molecule in these respective receptor configurations (IT1t versus CVX15 based poses). To this end, a thorough investigation was performed through a combination of receptor mutation studies, medicinal chemistry, biological testing, conformational analysis, and flexible docking. Our findings showed that the CVX15 peptide-based CXCR4 receptor complexes (red pose) were consistently favored over the small molecule IT1t based CXCR4 receptor configurations (blue pose) to correctly explain the computational and mutational studies as well as key structural components of activity for these small molecules.
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Affiliation(s)
- Brooke M. Katzman
- Department of Chemistry, Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Bryan D. Cox
- Department of Chemistry, Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Anthony R. Prosser
- Department of Chemistry, Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Ana A. Alcaraz
- Department of Chemistry, Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Brigitte Murat
- Medicinal Chemistry platform, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Madeleine Héroux
- Medicinal Chemistry platform, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Andrew Tebben
- Bristol-Myers Squibb R&D, US Route 206 and Province Line Road, Princeton, New Jersey 08543-4000, United States
| | - Yong Zhang
- Bristol-Myers Squibb R&D, US Route 206 and Province Line Road, Princeton, New Jersey 08543-4000, United States
| | - Gretchen M. Schroeder
- Bristol-Myers Squibb R&D, US Route 206 and Province Line Road, Princeton, New Jersey 08543-4000, United States
| | - James P. Snyder
- Department of Chemistry, Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Lawrence J. Wilson
- Department of Chemistry, Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Dennis C. Liotta
- Department of Chemistry, Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, United States
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11
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Berg C, Daugvilaite V, Steen A, Jørgensen AS, Våbenø J, Rosenkilde MM. Inhibition of HIV Fusion by Small Molecule Agonists through Efficacy-Engineering of CXCR4. ACS Chem Biol 2018; 13:881-886. [PMID: 29461034 DOI: 10.1021/acschembio.8b00061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
CXC chemokine receptor 4 (CXCR4) is involved in multiple physiological and pathological processes, notably as a coreceptor for human immunodeficiency virus (HIV) cell entry. Its broad expression pattern and vital biological importance make CXCR4 a troublesome drug target, as disruption of the interaction with its endogenous ligand, CXC chemokine ligand 12 (CXCL12), has severe consequences. In fact, only one CXCR4 drug, the bicyclam antagonist and HIV entry inhibitor AMD3100 (Plerixafor/Mozobil), has been approved for clinical use, however only for stem cell mobilization-a consequence of CXCR4 antagonism. Here, we report the engineering of an efficacy switch mutation in CXCR4-F292A7.43 in the middle of transmembrane helix 7-that converted the antagonists AMD3100 and AMD11070 into partial agonists. As agonists on F292A CXCR4, AMD3100 and AMD11070 were less disruptive to CXCR4 signaling while they remained efficient inhibitors of HIV fusion. This demonstrates that small molecule CXCR4 agonists can have a therapeutic potential as HIV entry inhibitors.
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Affiliation(s)
- Christian Berg
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
- Infectious Diseases Unit, Department of Medicine, Herlev−Gentofte Hospital, Herlev Ringvej 75, 2730 Herlev, Denmark
| | - Viktorija Daugvilaite
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Anne Steen
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Astrid Sissel Jørgensen
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Jon Våbenø
- Helgeland Hospital Trust, Prestmarkveien 1, 8800 Sandnessjøen, Norway
| | - Mette Marie Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
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12
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Grande F, Giancotti G, Ioele G, Occhiuzzi MA, Garofalo A. An update on small molecules targeting CXCR4 as starting points for the development of anti-cancer therapeutics. Eur J Med Chem 2017; 139:519-530. [PMID: 28826086 DOI: 10.1016/j.ejmech.2017.08.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 12/19/2022]
Abstract
CXCR4 (C-X-C Chemokine Receptor type 4) and its natural ligand SDF-1α (Stromal-Derived-Factor-1α) are involved in a number of physiological and pathological processes including cancer spread and progression. Over the past few years, numerous CXCR4 antagonists have been identified and currently are in different development stages as potential agents for the treatment of several diseases involving the CXCR4/SDF-1α axis. Herein, we focus on small molecules reported in literature between 2013 and 2017, claimed as CXCR4 antagonists and potentially useful in the treatment of cancer and other diseases where this receptor is involved. Most of the compounds resulted from a chemical optimization of previously identified molecules and some of them could represent suitable candidates for the development of advanced anticancer agents.
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Affiliation(s)
- Fedora Grande
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, 87036 Rende (CS), Italy.
| | - Gilda Giancotti
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, UK
| | - Giuseppina Ioele
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, 87036 Rende (CS), Italy
| | - Maria A Occhiuzzi
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, 87036 Rende (CS), Italy
| | - Antonio Garofalo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, 87036 Rende (CS), Italy
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13
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Design and computational support for the binding stability of a new CCR5/CXCR4 dual tropic inhibitor: Computational design of a CCR5/CXCR4 drug. J Mol Graph Model 2017; 75:71-79. [PMID: 28575798 DOI: 10.1016/j.jmgm.2017.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/21/2017] [Accepted: 02/21/2017] [Indexed: 02/05/2023]
Abstract
The human immunodeficiency virus (HIV) infects healthy human cells by binding to the glycoprotein cluster of differentiation 4 receptors on the surface of helper T-cells, along with either of two chemokine receptors, CC chemokine receptor type 5 (CCR5) or C-X-C chemokine receptor type 4 (CXCR4). Recently, a pyrazolo-piperdine ligand was synthesized and the corresponding biological data showed good binding to both chemokine receptors, effectively blocking HIV-1 entry. Here, we exhaustively assess the atomistic binding interactions of this compound with both CCR5 and CXCR4, and we find that binding is driven by π-stacking interactions between aromatic rings on the ligand and receptor residues, as well as electrostatic interactions involving the protonated piperidine nitrogen. However, these favorable binding interactions were partially offset by unfavorable desolvation of active site glutamates and aspartates, prompting our proposal of a new, synthetically-accessible derivative designed to increase the electrostatic interactions without compromising the π-stacking features.
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14
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Zachariassen ZG, Karlshøj S, Haug BE, Rosenkilde MM, Våbenø J. Probing the Molecular Interactions between CXC Chemokine Receptor 4 (CXCR4) and an Arginine-Based Tripeptidomimetic Antagonist (KRH-1636). J Med Chem 2015; 58:8141-53. [PMID: 26397724 DOI: 10.1021/acs.jmedchem.5b00987] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We here report an experimentally verified binding mode for the known tripeptidomimetic CXCR4 antagonist KRH-1636 (1). A limited SAR study based on the three functionalities of 1 was first conducted, followed by site-directed mutagenesis studies. The receptor mapping showed that both the potency and affinity of 1 were dependent on the transmembrane residues His(113), Asp(171), Asp(262), and His(281) and also suggested the involvement of Tyr(45) and Gln(200) (potency) and Tyr(116) and Glu(288) (affinity). Molecular docking of 1 to an X-ray structure of CXCR4 showed that the l-Arg guanidino group of 1 forms polar interactions with His(113) and Asp(171) and the (pyridin-2-ylmethyl)amino moiety is anchored by Asp(262) and His(281), whereas the naphthalene ring is tightly packed in a hydrophobic subpocket formed by the aromatic side chains of Trp(94), Tyr(45), and Tyr(116). The detailed picture of ligand-receptor interactions provided here will assist in structure-based design and further development of small-molecule peptidomimetic CXCR4 antagonists.
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Affiliation(s)
- Zack G Zachariassen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway , Breivika, NO-9037 Tromsø, Norway
| | - Stefanie Karlshøj
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen , Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Bengt Erik Haug
- Department of Chemistry and Centre for Pharmacy, University of Bergen , Allégaten 41, NO-5007 Bergen, Norway
| | - Mette M Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen , Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Jon Våbenø
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway , Breivika, NO-9037 Tromsø, Norway
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15
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Hamal S, D'huys T, Rowley WF, Vermeire K, Aquaro S, Frost BJ, Schols D, Bell TW. Metal complexes of pyridine-fused macrocyclic polyamines targeting the chemokine receptor CXCR4. Org Biomol Chem 2015; 13:10517-26. [PMID: 26338723 DOI: 10.1039/c5ob01557j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The chemokine receptor CXCR4 acts as a key cell surface receptor in HIV infections, multiple forms of cancer, and various other pathologies, such as rheumatoid arthritis and asthma. Macrocyclic polyamines and their metal complexes are known to exert anti-HIV activity, many acting as HIV entry inhibitors by specifically binding to CXCR4. Three series of pyridopentaazacylopentadecanes, in which the pyridine ring is fused to zero, one, or two saturated six-membered rings, were synthesized by manganese(ii)-templated Schiff-base cyclization of triethylenetetramine with various dicarbonyl compounds. By evaluating these macrocyclic polyamines and their complexes with Mn(2+), Cu(2+), Fe(3+), and Zn(2+), we have discovered novel CXCR4-binding compounds. The MnCl2 complex of a new pentaazacyclopentadecane with one fused carbocyclic ring (11) was found to have the greatest potency as an antagonist of the chemokine receptor CXCR4 (IC50: 0.014 μM), as evidenced by inhibiting binding of CXCL12 to PBMCs (peripheral blood mononuclear cells). Consequently, this compound inhibits replication of the CXCR4-using (X4) HIV-1 strain NL4-3 in the TZM-bl cell line with an IC50 value of 0.52 μM and low cytotoxicity (CC50: >100 μM). In addition, 18 other compounds were evaluated for their interaction with CXCR4 via their ability to interfere with ligand chemokine binding and HIV entry and infection. Of these, the metal complexes of the two more hydrophobic series with one or two fused carbocyclic rings exhibited the greatest potency. The Zn(2+) complex 21 was among the most potent, showing that redox activity of the metal center is not associated with CXCR4 antagonist activity.
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Affiliation(s)
- Sunil Hamal
- Department of Chemistry, University of Nevada, Reno, NV, USA.
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16
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Bartolowits M, Davisson VJ. Considerations of Protein Subpockets in Fragment-Based Drug Design. Chem Biol Drug Des 2015; 87:5-20. [PMID: 26307335 DOI: 10.1111/cbdd.12631] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
While the fragment-based drug design approach continues to gain importance, gaps in the tools and methods available in the identification and accurate utilization of protein subpockets have limited the scope. The importance of these features of small molecule-protein recognition is highlighted with several examples. A generalized solution for the identification of subpockets and corresponding chemical fragments remains elusive, but there are numerous advancements in methods that can be used in combination to address subpockets. Finally, additional examples of approaches that consider the relative importance of small-molecule co-dependence of protein conformations are highlighted to emphasize an increased significance of subpockets, especially at protein interfaces.
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Affiliation(s)
- Matthew Bartolowits
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
| | - V Jo Davisson
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
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17
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Cox BD, Mehta AK, DiRaddo JO, Liotta DC, Wilson LJ, Snyder JP. Structural analysis of CXCR4 - Antagonist interactions using saturation-transfer double-difference NMR. Biochem Biophys Res Commun 2015; 466:28-32. [PMID: 26301631 DOI: 10.1016/j.bbrc.2015.08.084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 08/19/2015] [Indexed: 11/15/2022]
Abstract
CXCR4 is a GPCR involved in leukocyte trafficking. Small molecule antagonists of the receptor may treat inflammatory disease, cancer and HIV. Here we probe the binding of a tetrahydroisoquinoline-based antagonist (TIQ-10) to CXCR4 using saturation transfer double-difference (STDD) NMR. STDD spectra were acquired using extracts from Chinese Hamster Ovary cells expressing membrane-embedded CXCR4. The experiments demonstrate competitive binding between TIQ-10 and established antagonists and provide the TIQ-10 - CXCR4 binding epitope. Molecular modeling of TIQ-10 into the binding pocket provides a pose consistent with STDD-derived interactions. This study paves the way for future investigations of GPCR-ligand interactions in a biological milieu for use in chemical biology, biochemistry, structural biology, and rational drug design.
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Affiliation(s)
- Bryan D Cox
- Emory University, Department of Chemistry, 1515 Dickey Dr., Atlanta, GA 30322, USA
| | - Anil K Mehta
- Emory University, Department of Chemistry, 1515 Dickey Dr., Atlanta, GA 30322, USA
| | - John O DiRaddo
- Emory University, Department of Chemistry, 1515 Dickey Dr., Atlanta, GA 30322, USA
| | - Dennis C Liotta
- Emory University, Department of Chemistry, 1515 Dickey Dr., Atlanta, GA 30322, USA
| | - Lawrence J Wilson
- Emory University, Department of Chemistry, 1515 Dickey Dr., Atlanta, GA 30322, USA
| | - James P Snyder
- Emory University, Department of Chemistry, 1515 Dickey Dr., Atlanta, GA 30322, USA.
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18
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Grimmer CD, Slabber CA. Conformational analysis: ³JHCOC and ³JHCCC Karplus relationships for methylene ¹H nuclei. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:590-595. [PMID: 26017915 DOI: 10.1002/mrc.4264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 04/26/2015] [Accepted: 04/28/2015] [Indexed: 06/04/2023]
Abstract
NAMFIS (NMR Analysis of Molecular Flexibility In Solution) was applied to 1-[2-(benzyloxy)phenyl]ethanone using quantitative (1)H-(1)H NOE distances and (3)J proton-carbon coupling constant (CC) restraints for averaged methylene proton (3)J(HCOC) and (3)J(HCCC) pathways H2-(3)J-X imposed by density functional theory-generated Karplus relationships. Comparison of the NOE-only versus the NOE + CC conformational selections illustrates that the experimentally measured average (3)J coupling constants of methylene protons can be used for solution conformational analysis, potentially valuable in the study of small-molecule drugs and natural products which lack the typically studied H1-(3)J-X Karplus relationships.
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Affiliation(s)
- Craig D Grimmer
- School of Chemistry and Physics, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Cathryn A Slabber
- School of Chemistry and Physics, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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19
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Cox BD, Prosser AR, Sun Y, Li Z, Lee S, Huang MB, Bond VC, Snyder JP, Krystal M, Wilson LJ, Liotta DC. Pyrazolo-Piperidines Exhibit Dual Inhibition of CCR5/CXCR4 HIV Entry and Reverse Transcriptase. ACS Med Chem Lett 2015; 6:753-7. [PMID: 26191361 DOI: 10.1021/acsmedchemlett.5b00036] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/06/2015] [Indexed: 01/19/2023] Open
Abstract
We report novel anti-HIV-1 agents with combined dual host-pathogen pharmacology. Lead compound 3, composed of a pyrazole-piperidine core, exhibits three concurrent mechanisms of action: (1) non-nucleoside reverse transcriptase inhibition, (2) CCR5-mediated M-tropic viral entry inhibition, and (3) CXCR4-based T-tropic viral entry inhibition that maintains native chemokine ligand binding. This discovery identifies important tool compounds for studying viral infectivity and prototype agents that block HIV-1 entry through dual chemokine receptor ligation.
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Affiliation(s)
- Bryan D. Cox
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Anthony R. Prosser
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Yongnian Sun
- Bristol-Myers Squibb, Wallingford, Connecticut 06492, United States
| | - Zhufang Li
- Bristol-Myers Squibb, Wallingford, Connecticut 06492, United States
| | - Sangil Lee
- Bristol-Myers Squibb, Wallingford, Connecticut 06492, United States
| | - Ming B. Huang
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, Georgia 30310, United States
| | - Vincent C. Bond
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, Georgia 30310, United States
| | - James P. Snyder
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Mark Krystal
- Bristol-Myers Squibb, Wallingford, Connecticut 06492, United States
| | - Lawrence J. Wilson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Dennis C. Liotta
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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20
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Progress toward rationally designed small-molecule peptide and peptidomimetic CXCR4 antagonists. Future Med Chem 2015; 7:1261-83. [DOI: 10.4155/fmc.15.64] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Over the last 5 years, X-ray structures of CXCR4 in complex with three different ligands (the small-molecule antagonist IT1t, the polypeptide antagonist CVX15 and the viral chemokine antagonist vMIP-II) have been released. In addition to the inherent scientific value of these specific X-ray structures, they provide a reliable structural foundation for studies of the molecular interactions between CXCR4 and its key peptide ligands (CXCL12 and HIV-1 gp120), and serve as valuable templates for further development of small-molecule CXCR4 antagonists with therapeutic potential. We here review recent computational studies of the molecular interactions between CXCR4 and its peptide ligands – based on the X-ray structures of CXCR4 – and the current status of small-molecule peptide and peptidomimetic CXCR4 antagonists.
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21
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Planesas JM, Pérez-Nueno VI, Borrell JI, Teixidó J. Studying the binding interactions of allosteric agonists and antagonists of the CXCR4 receptor. J Mol Graph Model 2015; 60:1-14. [PMID: 26080355 DOI: 10.1016/j.jmgm.2015.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 05/06/2015] [Accepted: 05/07/2015] [Indexed: 12/01/2022]
Abstract
Several examples of allosteric modulators of GPCRs have been reported recently in the literature, but understanding their molecular mechanism presents a new challenge for medicinal chemistry. For the specific case of the cellular receptor CXCR4, it is known that pepducins (lipidated fragments of intracellular GPCR loops) such as ATI-2341 modulate CXCR4 activity agonistically via an allosteric mechanism. Moreover, there are also examples of small organic molecules such as AMD11070 and GSK812397 which may also act as allosteric antagonists. However, incomplete knowledge of the ligand-binding sites has hampered a detailed molecular understanding of how these inhibitors work. Here, we attempt to answer this question by analysing the binding interactions between the CXCR4 receptor and the above-mentioned allosteric modulators. We propose two different allosteric binding sites, one located in the intracellular loops 1, 2 and 3 (ICL1, ICL2 and ICL3) which binds the pepducin agonist ATI-2341, and the other at a subsite of the main extracellular orthosteric binding pocket between extracellular loops 1 and 2 and the N-terminus, which binds the antagonists AMD11070 and GSK812397. Allosteric interactions between the CXCR4 and ATI-2341 were predicted by combining different modeling approaches. First, a rotational blind docking search was applied and the best poses were subsequently refined using flexible docking methods and molecular dynamic simulations. For the AMD11070 and GSK812397 antagonists, the entire CXCR4 protein surface was explored by blind docking in order to define the binding region. A second docking analysis by subsites was then performed to refine the allosteric interactions. Finally, we identified the binding residues that appear to be essential for CXCR4 allosteric modulators.
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Affiliation(s)
- Jesús M Planesas
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain
| | - Violeta I Pérez-Nueno
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain; Harmonic Pharma, Espace Transfert, 615 rue du Jardin Botanique, 54600 Villers lès Nancy, France.
| | - José I Borrell
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain
| | - Jordi Teixidó
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain.
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22
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Zhao H, Prosser AR, Liotta DC, Wilson LJ. Discovery of novel N-aryl piperazine CXCR4 antagonists. Bioorg Med Chem Lett 2015; 25:4950-4955. [PMID: 25935642 DOI: 10.1016/j.bmcl.2015.04.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/06/2015] [Accepted: 04/10/2015] [Indexed: 10/24/2022]
Abstract
A novel series of CXCR4 antagonists with substituted piperazines as benzimidazole replacements is described. These compounds showed micromolar to nanomolar potency in CXCR4-mediated functional and HIV assays, namely inhibition of X4 HIV-1(IIIB) virus in MAGI-CCR5/CXCR4 cells and inhibition of SDF-1 induced calcium release in Chem-1 cells. Preliminary SAR investigations led to the identification of a series of N-aryl piperazines as the most potent compounds. Results show SAR that indicates type and position of the aromatic ring, as well as type of linker and stereochemistry are significant for activity. Profiling of several lead compounds showed that one (49b) reduced susceptibility towards CYP450 and hERG, and the best overall profile when considering both SDF-1 and HIV potencies (6-20 nM).
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Affiliation(s)
- Huanyu Zhao
- Emory Institute for Drug Development, 954 Gatewood Road NE, Atlanta, GA 30329, United States
| | - Anthony R Prosser
- Department of Chemistry, Emory University, 1521 Dickey Drive, Atlanta, GA 30322, United States
| | - Dennis C Liotta
- Emory Institute for Drug Development, 954 Gatewood Road NE, Atlanta, GA 30329, United States; Department of Chemistry, Emory University, 1521 Dickey Drive, Atlanta, GA 30322, United States
| | - Lawrence J Wilson
- Department of Chemistry, Emory University, 1521 Dickey Drive, Atlanta, GA 30322, United States.
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23
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Shetty D, Kim YJ, Shim H, Snyder JP. Eliminating the heart from the curcumin molecule: monocarbonyl curcumin mimics (MACs). Molecules 2014; 20:249-92. [PMID: 25547726 PMCID: PMC4312668 DOI: 10.3390/molecules20010249] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/10/2014] [Indexed: 12/17/2022] Open
Abstract
Curcumin is a natural product with several thousand years of heritage. Its traditional Asian application to human ailments has been subjected in recent decades to worldwide pharmacological, biochemical and clinical investigations. Curcumin’s Achilles heel lies in its poor aqueous solubility and rapid degradation at pH ~ 7.4. Researchers have sought to unlock curcumin’s assets by chemical manipulation. One class of molecules under scrutiny are the monocarbonyl analogs of curcumin (MACs). A thousand plus such agents have been created and tested primarily against cancer and inflammation. The outcome is clear. In vitro, MACs furnish a 10–20 fold potency gain vs. curcumin for numerous cancer cell lines and cellular proteins. Similarly, MACs have successfully demonstrated better pharmacokinetic (PK) profiles in mice and greater tumor regression in cancer xenografts in vivo than curcumin. The compounds reveal limited toxicity as measured by murine weight gain and histopathological assessment. To our knowledge, MAC members have not yet been monitored in larger animals or humans. However, Phase 1 clinical trials are certainly on the horizon. The present review focuses on the large and evolving body of work in cancer and inflammation, but also covers MAC structural diversity and early discovery for treatment of bacteria, tuberculosis, Alzheimer’s disease and malaria.
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Affiliation(s)
- Dinesh Shetty
- Center for Self-assembly and Complexity, Institute for Basic Science, Pohang 790-784, Korea.
| | - Yong Joon Kim
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA.
| | - Hyunsuk Shim
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA 30322, USA.
| | - James P Snyder
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA.
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24
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Grimmer C, Moore TW, Padwa A, Prussia A, Wells G, Wu S, Sun A, Snyder JP. Antiviral atropisomers: conformational energy surfaces by NMR for host-directed myxovirus blockers. J Chem Inf Model 2014; 54:2214-23. [PMID: 25058809 DOI: 10.1021/ci500204j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biologically active organic molecules characterized by a high single bond torsional barrier generate isolable isomers (atropisomers) and offer a unique stereochemical component to the design of selective therapeutic agents. The present work presents a nanomolar active inhibitor of myxoviruses, which most likely acts by blocking one or more cellular host proteins but also, serendipitously, exhibits axial chirality with an energy barrier of ΔG((++)) ≥30 kcal/mol. The latter has been probed by variable temperature NMR and microwave irradiation and by high level DFT transition state analysis and force field calculations. Full conformational profiles of the corresponding (aR,S) and (aS,S) atropisomers at ambient temperature were derived by conformer deconvolution with NAMFIS (NMR Analysis by Molecular Flexibility In Solution) methodology to generate seven and eight individual conformations, each assigned a % population. An accurate evaluation of a key torsion angle at the center of the molecules associated with a (3)JC-S-C-H coupling constant was obtained by mapping the S-C bond rotation with the MPW1PW91/6-31G-d,p DFT method followed by fitting the resulting dihedral angles and J-values to a Karplus expression. Accordingly, we have developed a complete conformational profile of diastereomeric atropisomers consistent with both high and low rotational barriers. We expect this assessment to assist the rationalization of the selectivity of the two (aR,S) and (aS,S) forms against host proteins, while offering insights into their divergent toxicity behavior.
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Affiliation(s)
- Craig Grimmer
- School of Chemistry and Physics, University of KwaZulu-Natal , Pietermaritzburg, South Africa
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