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Feder D, Mohd-Pahmi SH, Adibi H, Guddat LW, Schenk G, McGeary RP, Hussein WM. Optimization of an α-aminonaphthylmethylphosphonic acid inhibitor of purple acid phosphatase using rational structure-based design approaches. Eur J Med Chem 2023; 254:115383. [PMID: 37087894 DOI: 10.1016/j.ejmech.2023.115383] [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: 11/23/2022] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 04/25/2023]
Abstract
Purple acid phosphatases (PAPs) are ubiquitous binuclear metallohydrolases that have been isolated from various animals, plants and some types of fungi. In humans and mice, elevated PAP activity in osteoclasts is associated with osteoporosis, making human PAP an attractive target for the development of anti-osteoporotic drugs. Based on previous studies focusing on phosphonate scaffolds, as well as a new crystal structure of a PAP in complex with a derivative of a previously synthesized α-aminonaphthylmethylphosphonic acid, phosphonates 24-40 were designed as new PAP inhibitor candidates. Subsequent docking studies predicted that all of these compounds are likely to interact strongly with the active site of human PAP and most are likely to interact strongly with the active site of pig PAP. The seventeen candidates were synthesized with good yields and nine of them (26-28, 30, 33-36 and 38) inhibit in the sub-micromolar to nanomolar range against pig PAP, with 28 and 35 being the most potent mammalian PAP inhibitors reported with Ki values of 168 nM and 186 nM, respectively. This study thus paves the way for the next stage of drug development for phosphonate inhibitors of PAPs as anti-osteoporotic agents.
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Affiliation(s)
- Daniel Feder
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD, 4072, Australia
| | - Siti Hajar Mohd-Pahmi
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD, 4072, Australia
| | - Hadi Adibi
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD, 4072, Australia; Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Luke W Guddat
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD, 4072, Australia
| | - Gerhard Schenk
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD, 4072, Australia; The University of Queensland, Sustainable Minerals Institute, Brisbane, QLD, 4072, Australia; The University of Queensland, Australian Institute of Bioengineering and Nanotechnology, Brisbane, QLD, 4072, Australia
| | - Ross P McGeary
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD, 4072, Australia
| | - Waleed M Hussein
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD, 4072, Australia; Helwan University, Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Ein Helwan, Helwan, Egypt.
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Feder D, Mohd-Pahmi SH, Hussein WM, Guddat LW, McGeary RP, Schenk G. Rational Design of Potent Inhibitors of a Metallohydrolase Using a Fragment-Based Approach. ChemMedChem 2021; 16:3342-3359. [PMID: 34331400 DOI: 10.1002/cmdc.202100486] [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: 07/12/2021] [Indexed: 11/08/2022]
Abstract
Metallohydrolases form a large group of enzymes that have fundamental importance in a broad range of biological functions. Among them, the purple acid phosphatases (PAPs) have gained attention due to their crucial role in the acquisition and use of phosphate by plants and also as a promising target for novel treatments of bone-related disorders and cancer. To date, no crystal structure of a mammalian PAP with drug-like molecules bound near the active site is available. Herein, we used a fragment-based design approach using structures of a mammalian PAP in complex with the MaybridgeTM fragment CC063346, the amino acid L-glutamine and the buffer molecule HEPES, as well as various solvent molecules to guide the design of highly potent and efficient mammalian PAP inhibitors. These inhibitors have improved aqueous solubility when compared to the clinically most promising PAP inhibitors available to date. Furthermore, drug-like fragments bound in newly discovered binding sites mapped out additional scaffolds for further inhibitor discovery, as well as scaffolds for the design of inhibitors with novel modes of action.
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Affiliation(s)
- Daniel Feder
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Siti H Mohd-Pahmi
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
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Alimoradi N, Ashrafi-Kooshk MR, Shahlaei M, Maghsoudi S, Adibi H, McGeary RP, Khodarahmi R. Diethylalkylsulfonamido(4-methoxyphenyl)methyl)phosphonate/phosphonic acid derivatives act as acid phosphatase inhibitors: synthesis accompanied by experimental and molecular modeling assessments. J Enzyme Inhib Med Chem 2016; 32:20-28. [PMID: 27766897 PMCID: PMC6010023 DOI: 10.1080/14756366.2016.1230109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Purple acid phosphatases (PAPs) are binuclear metallo-hydrolases that have been isolated from various mammals, plants, fungi and bacteria. In mammals, PAP activity is associated with bone resorption and can lead to bone metabolic disorders such as osteoporosis; thus human PAP is an attractive target to develop anti-osteoporotic drugs. The aim of the present study was to investigate inhibitory effect of synthesized diethylalkylsulfonamido(4-methoxyphenyl)methyl)phosphonate/phosphonic acid derivatives as potential red kidney bean PAP (rkbPAP) inhibitors accompanied by experimental and molecular modeling assessments. Enzyme kinetic data showed that they are good rkbPAP inhibitors whose potencies improve with increasing alkyl chain length. Hexadecyl derivatives, as most potent compounds (Ki = 1.1 µM), inhibit rkbPAP in the mixed manner, while dodecyl derivatives act as efficient noncompetitive inhibitor. Also, analysis by molecular modeling of the structure of the rkbPAP-inhibitor complexes reveals factors, which may be important for the determination of inhibition specificity.
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Affiliation(s)
- Nahid Alimoradi
- a Student Research Committee , Kermanshah University of Medical Sciences , Kermanshah , Iran
| | | | - Mohsen Shahlaei
- c Nano Drug Delivery Research Center , Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Shabnam Maghsoudi
- b Medical Biology Research Center , Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Hadi Adibi
- d Pharmaceutical Sciences Research Center, Faculty of Pharmacy , Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Ross P McGeary
- e The University of Queensland, School of Chemistry and Molecular Biosciences , St. Lucia , QLD , Australia
| | - Reza Khodarahmi
- b Medical Biology Research Center , Kermanshah University of Medical Sciences , Kermanshah , Iran
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Mohd-Pahmi SH, Hussein WM, Schenk G, McGeary RP. Synthesis, modelling and kinetic assays of potent inhibitors of purple acid phosphatase. Bioorg Med Chem Lett 2011; 21:3092-4. [DOI: 10.1016/j.bmcl.2011.03.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2011] [Revised: 03/07/2011] [Accepted: 03/08/2011] [Indexed: 11/26/2022]
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Fang H, Chen W, Hong B, Zhao Y, Fang M. Synthesis, Characterizations, and Crystal Structures of α-Hydroxyphosphonic Acid Esters. PHOSPHORUS SULFUR 2010. [DOI: 10.1080/10426500903299935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Hua Fang
- a The Third Institute of Oceanography of the State Oceanic Administration , Xiamen , People's Republic of China
| | - Weizhu Chen
- a The Third Institute of Oceanography of the State Oceanic Administration , Xiamen , People's Republic of China
| | - Bihong Hong
- a The Third Institute of Oceanography of the State Oceanic Administration , Xiamen , People's Republic of China
| | - Yufen Zhao
- b Department of Pharmaceutical Science, Medical College , Xiamen University , Xiamen , People's Republic of China
- c Department of Chemistry, Key Laboratory for Chemical Biology of Fujian Province College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , People's Republic of China
- d The Key Laboratory for Bioorganic Phosphorus Chemistry and Chemical Biology, National Ministry of Education, Department of Chemistry , Tsinghua University , Beijing , People's Republic of China
| | - Meijuan Fang
- b Department of Pharmaceutical Science, Medical College , Xiamen University , Xiamen , People's Republic of China
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Ordóñez M, Rojas-Cabrera H, Cativiela C. An Overview of Stereoselective Synthesis of α-Aminophosphonic Acids and Derivatives. Tetrahedron 2009; 65:17-49. [PMID: 20871799 PMCID: PMC2943650 DOI: 10.1016/j.tet.2008.09.083] [Citation(s) in RCA: 222] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
An overview of all methodologies published during the last few years focused to the stereoselective (diastereoselective or enantioselective) synthesis of α-aminophosphonic acids and derivatives is reported. The procedures have been classified according a retrosynthetic strategy and taking into account the formation of each one of the bonds connected to the chiral centre.
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Affiliation(s)
- Mario Ordóñez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, 62209 Cuernavaca, Morelos (México)
| | - Haydée Rojas-Cabrera
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, 62209 Cuernavaca, Morelos (México)
| | - Carlos Cativiela
- Departamento de Química Orgánica, ICMA, Universidad de Zaragoza-CSIC, 50009 Zaragoza (Spain)
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