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Clark JM, Salgado-Polo F, Macdonald SJF, Barrett TN, Perrakis A, Jamieson C. Structure-Based Design of a Novel Class of Autotaxin Inhibitors Based on Endogenous Allosteric Modulators. J Med Chem 2022; 65:6338-6351. [PMID: 35440138 PMCID: PMC9059126 DOI: 10.1021/acs.jmedchem.2c00368] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Autotaxin (ATX) facilitates the hydrolysis of lysophosphatidylcholine to lysophosphatidic acid (LPA), a bioactive phospholipid, which facilitates a diverse range of cellular effects in multiple tissue types. Abnormal LPA expression can lead to the progression of diseases such as cancer and fibrosis. Previously, we identified a potent ATX steroid-derived hybrid (partially orthosteric and allosteric) inhibitor which did not form interactions with the catalytic site. Herein, we describe the design, synthesis, and biological evaluation of a focused library of novel steroid-derived analogues targeting the bimetallic catalytic site, representing an entirely unique class of ATX inhibitors of type V designation, which demonstrate significant pathway-relevant biochemical and phenotypic biological effects. The current compounds modulated LPA-mediated ATX allostery and achieved indirect blockage of LPA1 internalization, in line with the observed reduction in downstream signaling cascades and chemotaxis induction. These novel type V ATX inhibitors represent a promising tool to inactivate the ATX-LPA signaling axis.
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Affiliation(s)
- Jennifer M Clark
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Fernando Salgado-Polo
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Simon J F Macdonald
- Medicines Design, GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Tim N Barrett
- Medicines Design, GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Anastassis Perrakis
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Craig Jamieson
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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Tan Y, Wu J, Song L, Zhang M, Hipolito CJ, Wu C, Wang S, Zhang Y, Yin Y. Merging the Versatile Functionalities of Boronic Acid with Peptides. Int J Mol Sci 2021; 22:ijms222312958. [PMID: 34884766 PMCID: PMC8657650 DOI: 10.3390/ijms222312958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
Peptides inherently feature the favorable properties of being easily synthesized, water-soluble, biocompatible, and typically non-toxic. Thus, boronic acid has been widely integrated with peptides with the goal of discovering peptide ligands with novel biological activities, and this effort has led to broad applications. Taking the integration between boronic acid and peptide as a starting point, we provide an overview of the latest research advances and highlight the versatile and robust functionalities of boronic acid. In this review, we summarize the diverse applications of peptide boronic acids in medicinal chemistry and chemical biology, including the identification of covalent reversible enzyme inhibitors, recognition, and detection of glycans on proteins or cancer cell surface, delivery of siRNAs, development of pH responsive devices, and recognition of RNA or bacterial surfaces. Additionally, we discuss boronic acid-mediated peptide cyclization and peptide modifications, as well as the facile chemical synthesis of peptide boronic acids, which paved the way for developing a growing number of peptide boronic acids.
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Affiliation(s)
- Yahong Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
| | - Junjie Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
| | - Lulu Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
| | - Mengmeng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
| | - Christopher John Hipolito
- Screening & Compound Profiling, Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ 07033, USA;
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
| | - Siyuan Wang
- Department of Medicinal Chemistry, College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
- Correspondence: (S.W.); (Y.Y.)
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (Y.T.); (J.W.); (L.S.); (M.Z.); (C.W.); (Y.Z.)
- Correspondence: (S.W.); (Y.Y.)
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Tevyashova AN, Chudinov MV. Progress in the medicinal chemistry of organoboron compounds. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4977] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The review aims to draw attention to the latest advances in the organoboron chemistry and therapeutic use of organoboron compounds. The synthetic strategies towards boron-containing compounds with proven in vitro and/or in vivo biological activities, including derivatives of boronic acids, benzoxaboroles, benzoxaborines and benzodiazaborines, are summarized. Approaches to the synthesis of hybrid structures containing an organoboron moiety as one of the pharmacophores are considered, and the effect of this modification on the pharmacological activity of the initial molecules is analyzed. On the basis of analysis of the published data, the most promising areas of research in the field of organoboron compounds are identified, including the latest methods of synthesis, modification and design of effective therapeutic agents.
The bibliography includes 246 references.
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Benzoxaboroles-Novel Autotaxin Inhibitors. Molecules 2019; 24:molecules24193419. [PMID: 31547058 PMCID: PMC6804080 DOI: 10.3390/molecules24193419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 12/14/2022] Open
Abstract
Autotaxin (ATX) is an extracellular enzyme that hydrolyses lysophosphatidylcholine (LPC) to lysophosphatidic acid (LPA), which has a role in the mediation of inflammation, fibrosis and cancer. ATX is a drug target that has been the focus of many research groups during the last ten years. To date, only one molecule, Ziritaxestat (GLPG1690) has entered the clinic; it is currently in Phase 3 clinical trials for idiopathic pulmonary fibrosis. Other small molecules, with different binding modes, have been investigated as ATX inhibitors for cancer including compounds possessing a boronic acid motif such as HA155. In this work, we targeted new, improved inhibitors of ATX that mimic the important interactions of boronic acid using a benzoxaborole motif as the acidic warhead. Furthermore, we aimed to improve the plasma stability of the new compounds by using a more stable core spacer than that embedded in HA155. Compounds were synthesized, evaluated for their ATX inhibitory activity and ADME properties in vitro, culminating in a new benzoxaborole compound, 37, which retains the ATX inhibition activity of HA155 but has improved ADME properties (plasma protein binding, good kinetic solubility and rat/human plasma stability).
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Examining barbiturate scaffold for the synthesis of new agents with biological interest. Future Med Chem 2019; 11:2063-2079. [DOI: 10.4155/fmc-2018-0541] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim: Barbiturates have a long history of being used as drugs presenting wide varieties of biological activities (antimicrobial, anti-urease and antioxidant). Reactive oxygen species are associated with inflammation implicated in cancer, atherosclerosis and autoimmune diseases. Multitarget agents represent a powerful approach to the therapy of complicated inflammatory diseases. Results: A novel series of barbiturates has been synthesized and evaluated in several in vitro assays. Compound 16b (lipoxygenases inhibitor, 55.0 μM) was found to be a cyclooxygenase-2 inhibitor (27.5 μM). Compound 8b was profiled as a drug-like candidate. Conclusion: The barbiturate core represents a new scaffold for lipoxygenases inhibition, and the undertaken derivatives show promise as multiple-target agents to combat inflammatory diseases.
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Demianenko E, Rayevsky A, Soriano-Ursúa MA, Trujillo-Ferrara JG. Theoretical Coupling and Stability of Boronic Acid Adducts with Catecholamines. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180710101604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background:
Catecholamines combined with boric/boronic acids are attractive chemical
agents in drug design because some of their adducts have shown interesting biological activity.
Scant information exists about their stability.
Objective:
The aim of the present theoretical study was to explore the role of boron in molecules
that combine catecholamines and boric/boronic acids, with a particular interest in examining
stability.
Method:
The methodology was based on the US GAMESS program using DFT with the B3LYP
exchange-correlation functional and the 6-31G (d,p) split-valence basis set.
Results:
According to the current findings, the boron-containing compounds (BCCs) exhibit weaker
bonding to the hydroxyls on the ethylamine moiety than to those in the aromatic ring. The strongest
binding site of a hydroxyl group was often found to be in meta-position (relative to ethylamine
moiety) for boron-free compounds and in para-position for BCCs. Nonetheless, the methyl substituent
in the amino group was able to induce changes in this pattern. We analyzed feasible boronsubstituted
structures and assessed the relative strength of the respective C-B bonds, which allowed
for the identification of the favorable points for reaction and stability.
Conclusion:
It is feasible to form adducts by bonding on the amine and catechol sides of catecholamines.
The presence of boron stabilizes the adducts in para-position. Since some of these BCCs
are promising therapeutic agents, understanding the mechanisms of reaction is relevant for drug
design.
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Affiliation(s)
- Eugeniy Demianenko
- Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, 17 General Naumov Str., Kyiv, 03164, Ukraine
| | - Alexey Rayevsky
- Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, 17 General Naumov Str., Kyiv, 03164, Ukraine
| | - Marvin A. Soriano-Ursúa
- Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron s/n, Mexico City, 11340, Mexico
| | - José G. Trujillo-Ferrara
- Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron s/n, Mexico City, 11340, Mexico
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Garcia AA, Rayevski A, Andrade-Jorge E, Trujillo-Ferrara JG. Structural and biological overview of Boron-containing amino acids in the medicinal chemistry field. Curr Med Chem 2018; 26:5077-5089. [PMID: 30259808 DOI: 10.2174/0929867325666180926150403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 11/22/2022]
Abstract
Amino acids are the basic structural units of proteins as well as the precursors of many compounds with biological activity. The addition of boron reportedly induces changes in the chemical-biological profile of amino acids. METHODS We compiled information on the biological effect of some compounds and discuss the structure-activity relationship of the addition of boron. The specific focus presently is on borinic derivatives of α-amino acids, the specific changes in biological activity caused by the addition of a boron-containing moiety, and the identification of some attractive compounds for testing as potential new drugs. RESULTS Borinic derivatives of α-amino acids have been widely synthesized and tested as potential new therapeutic tools. The B-N (1.65 A°) or B-C (1.61 A°) or B-O (1.50 A°) bond is often key for the stability at different pHs and temperatures and activity of these compounds. The chemical features of synthesized derivatives, such as the specific moieties and the logP, polarizability and position of the boron atom are clearly linked to their pharmacodynamic and pharmacokinetic profiles. Some mechanisms of action have been suggested or demonstrated, while those responsible for other effects remain unknown. CONCLUSION The increasing number of synthetic borinic derivatives of α-amino acids as well as the recently reported crystal structures are providing new insights into the stability of these compounds at different pHs and temperatures, their interactions on drug targets, and the ring formation of five-membered heterocycles. Further research is required to clarify the ways to achieve specific synthesis, the mechanisms involved in the observed biological effect, and the toxicological profile of this type of boron-containing compounds (BCCs).
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Affiliation(s)
- Antonio Abad Garcia
- Departamento de Bioquimica y Seccion de Estudios de Posgrado e Investigación. Escuela Superior de Medicina. Plan de San Luis y Diaz Miron s/n, 11340, Mexico City. Mexico
| | - Alexey Rayevski
- Chuiko Institute of Surface Chemistry, National Academy of Science of Ukranie. 17 Generala Naumova St., 03164, Kyiv. Ukraine
| | - Erik Andrade-Jorge
- Departamento de Bioquimica y Seccion de Estudios de Posgrado e Investigacion. Escuela Superior de Medicina. Plan de San Luis y Diaz Miron s/n, 11340, Mexico City. Mexico
| | - Jose G Trujillo-Ferrara
- Departamento de Bioquímica y Sección de Estudios de Posgrado e Investigación. Escuela Superior de Medicina. Plan de San Luis y Diaz Mirón s/n, 11340, Mexico City. Mexico
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Zhou SF, Zhong WZ. Drug Design and Discovery: Principles and Applications. Molecules 2017; 22:molecules22020279. [PMID: 28208821 PMCID: PMC6155886 DOI: 10.3390/molecules22020279] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 12/23/2022] Open
Affiliation(s)
- Shu-Feng Zhou
- Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian, China.
| | - Wei-Zhu Zhong
- Gordon Life Science Institute, Belmont, MA 02478, USA.
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