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Donkor IO, Xu J, Liu J, Cameron K. Synthesis and antiproliferative activity of sulfonamide-based peptidomimetic calpain inhibitors. Bioorg Med Chem 2020; 28:115433. [PMID: 32199690 DOI: 10.1016/j.bmc.2020.115433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/01/2020] [Accepted: 03/11/2020] [Indexed: 10/24/2022]
Abstract
The calpains are a conserved family of cysteine proteases that includes several isoforms of which µ-calpain and m-calpain are the most widely distributed in mammalian cells. Calpains have been implicated in normal physiological processes as well as cellular abnormalities such as neurodegenerative disorders, cataract, and cancer. Therefore, calpain inhibitors are of interest as potential therapeutic agents. We have synthesized four new sulfonamide-based peptidomimetic compounds 2-5 as inhibitors of μ-calpain that incorporate (E)-1-(phenyl)-2-phenyldiazene and (E)-1-(phenyl)-2-phenylethene functionalities as the N-terminal capping groups of the inhibitors. Compound 5 with Ki value of 9 nM versus μ-calpain was the most potent member of the group. The compounds were predicted to be more lipophilic compared to MDL28170 based on CLogP estimation. They displayed moderate to good antiproliferative activity versus melanoma cell lines (A-375 and B-16F1) and PC-3 prostate cancer cells in vitro. Additionally, one member of the group (compound 3) inhibited DU-145 cell invasion by 80% at 2 μM concentration in the Matrigel cell invasion assay.
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Affiliation(s)
- Isaac O Donkor
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, United States.
| | - Jin Xu
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, United States
| | - Jiuyu Liu
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, United States
| | - Keyuna Cameron
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, United States
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2
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Das D, Khan HPA, Shivahare R, Gupta S, Sarkar J, Siddiqui MI, Ampapathi RS, Chakraborty TK. Synthesis, SAR and biological studies of sugar amino acid-based almiramide analogues: N-methylation leads the way. Org Biomol Chem 2018; 15:3337-3352. [PMID: 28368065 DOI: 10.1039/c6ob02610a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Leishmaniasis, caused by the protozoan parasites of the genus Leishmania, is one of the most neglected diseases endemic in many continents posing enormous global health threats and therefore the discovery of new antileishmanial compounds is of utmost urgency. The antileishmanial activities of a library of sugar amino acid-based linear lipopeptide analogues were examined with the aim to identify potential drug candidates to treat visceral leishmaniasis. It was found that among the synthesized analogues, most of the permethylated compounds exhibited more activity in in vitro studies against intra-macrophagic amastigotes than the non-methylated analogues. SAR and NMR studies revealed that introduction of the N-methyl groups inhibited the formation of any turn structure in these molecules, which led to their improved activities.
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Affiliation(s)
- Dipendu Das
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
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3
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Ji F, Peng H, Zhang X, Lu W, Liu S, Jiang H, Liu B, Yin B. Base-Mediated Decomposition of Amide-Substituted Furfuryl Tosylhydrazones: Synthesis and Cytotoxic Activities of Enynyl-Ketoamides. J Org Chem 2015; 80:2092-102. [DOI: 10.1021/jo502328j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Fanghua Ji
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Hui Peng
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Xiaoting Zhang
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Wenhua Lu
- State
Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
| | - Shubin Liu
- Research
Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
| | - Huanfeng Jiang
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Bo Liu
- Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou 510006, P.R. China
| | - Biaolin Yin
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510006, P.R. China
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4
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Neuroprotection by μ-calpain and matrix metalloproteinases inhibition by Piroxicam in cerebral ischemia: an in silico study. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0514-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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5
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Donkor IO. Calpain inhibitors: a survey of compounds reported in the patent and scientific literature. Expert Opin Ther Pat 2011; 21:601-36. [DOI: 10.1517/13543776.2011.568480] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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6
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Ovat A, Li ZZ, Hampton CY, Asress SA, Fernández FM, Glass JD, Powers JC. Peptidyl alpha-ketoamides with nucleobases, methylpiperazine, and dimethylaminoalkyl substituents as calpain inhibitors. J Med Chem 2010; 53:6326-36. [PMID: 20690647 DOI: 10.1021/jm901221v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of peptidyl alpha-ketoamides with the general structure Cbz-L-Leu-D,L-AA-CONH-R were synthesized and evaluated as inhibitors for the cysteine proteases calpain I, calpain II, and cathepsin B. Nucleobases, methylpiperazine, and dimethylaminoalkyl groups were incorporated into the primed region of the inhibitors to generate compounds that potentially cross the blood-brain barrier. Two of these compounds (Cbz-Leu-D,L-Abu-CONH-(CH(2))(3)-adenin-9-yl and Cbz-Leu-D,L-Abu-CONH-(CH(2))(3)-(4-methylpiperazin-1-yl) have been shown to have useful concentrations in the brain in animals. The best inhibitor for calpain I was Cbz-Leu-D,L-Abu-CONH-(CH(2))(3)-2-methoxyadenin-9-yl (K(i) = 23 nM), and the best inhibitor for calpain II was Cbz-Leu-D,L-Phe-CONH-(CH(2))(3)-adenin-9-yl (K(i) = 68 nM). On the basis of the crystal structure obtained with heterocyclic peptidyl alpha-ketoamides, we have improved inhibitor potency by introducing a small hydrophobic group on the adenine ring. These inhibitors have good potential to be used in the treatment of neurodegenerative diseases.
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Affiliation(s)
- Asli Ovat
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, USA
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7
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Qian J, Cuerrier D, Davies PL, Li Z, Powers JC, Campbell RL. Cocrystal structures of primed side-extending alpha-ketoamide inhibitors reveal novel calpain-inhibitor aromatic interactions. J Med Chem 2008; 51:5264-70. [PMID: 18702462 DOI: 10.1021/jm800045t] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calpains are intracellular cysteine proteases that catalyze the cleavage of target proteins in response to Ca(2+) signaling. When Ca(2+) homeostasis is disrupted, calpain overactivation causes unregulated proteolysis, which can contribute to diseases such as postischemic injury and cataract formation. Potent calpain inhibitors exist, but of these many cross-react with other cysteine proteases and will need modification to specifically target calpain. Here, we present crystal structures of rat calpain 1 protease core (muI-II) bound to two alpha-ketoamide-based calpain inhibitors containing adenyl and piperazyl primed-side extensions. An unexpected aromatic-stacking interaction is observed between the primed-side adenine moiety and the Trp298 side chain. This interaction increased the potency of the inhibitor toward muI-II and heterodimeric m-calpain. Moreover, stacking orients the adenine such that it can be used as a scaffold for designing novel primed-side address regions, which could be incorporated into future inhibitors to enhance their calpain specificity.
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Affiliation(s)
- Jin Qian
- Department of Biochemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
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8
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Gonçalves BT, Esteves PM, Pinto AC, Kaiser CR, da Silva FL, Miguez E, da Silva JFM. Anisotropic and hydrogen bonding effects in phenylglyoxamides and mandelamides: theoretical and NMR conformational evaluation. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:418-426. [PMID: 18327891 DOI: 10.1002/mrc.2192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Interesting anisotropic effects were observed for phenylglyoxamides and their respective mandelamides. Such effects were observed in experimental (1)H and (13)C NMR (in CDCl(3), CD(3)OD, and DMSO-d(6) solvents) and in some cases with good correlation to theoretical (1)H and (13)C NMR DFT-GIAO (B3LYP/6-311++G**//B3LYP/6-31G*) calculations. A systematic conformational analysis of these compounds was performed in a two-step methodology, using PM3 and DFT (B3LYP/6-31G*) calculations; with good accomplishment and computational time economy. It was observed that intramolecular hydrogen bonding plays a significant role in the conformation of such compounds. Finally, a geminal nonequivalence of an N-CH(2) moiety, in one of the alkyl side chain (R1 = R2), was found for the tertiary mandelamides studied.
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Affiliation(s)
- Biank T Gonçalves
- Departamento de Química Orgânica, Instituto de Química, Bloco A, 6 a Andar do CT, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, RJ, Brazil, 21949900
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9
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Yan S, Larson G, Wu JZ, Appleby T, Ding Y, Hamatake R, Hong Z, Yao N. Novel thiazolones as HCV NS5B polymerase allosteric inhibitors: Further designs, SAR, and X-ray complex structure. Bioorg Med Chem Lett 2007; 17:63-7. [PMID: 17049849 DOI: 10.1016/j.bmcl.2006.09.095] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Revised: 09/29/2006] [Accepted: 09/29/2006] [Indexed: 10/24/2022]
Abstract
Structure-activity relationships (SAR) of 1 against HCV NS5B polymerase were described. SAR explorations and further structure-based design led to the identifications of 2 and 3 as novel HCV NS5B inhibitors. X-ray structure of 3 in complex with NS5B polymerase was obtained at a resolution of 2.2A, and confirmed the design.
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Affiliation(s)
- Shunqi Yan
- Valeant Pharmaceuticals Research and Development, 3300 Hyland Ave., Costa Mesa, CA 92626, USA.
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10
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Cuerrier D, Moldoveanu T, Inoue J, Davies PL, Campbell RL. Calpain Inhibition by α-Ketoamide and Cyclic Hemiacetal Inhibitors Revealed by X-ray Crystallography,. Biochemistry 2006; 45:7446-52. [PMID: 16768440 DOI: 10.1021/bi060425j] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calpains are intracellular calcium-activated cysteine proteases whose unregulated proteolysis following the loss of calcium homeostasis can lead to acute degeneration during ischemic episodes and trauma, as well as Alzheimer's disease and cataract formation. The determination of the crystal structure of the proteolytic core of mu-calpain (muI-II) in a calcium-bound active conformation has made structure-guided design of active site inhibitors feasible. We present here high-resolution crystal structures of rat muI-II complexed with two reversible calpain-specific inhibitors employing cyclic hemiacetal (SNJ-1715) and alpha-ketoamide (SNJ-1945) chemistries that reveal new details about the interactions of inhibitors with this enzyme. The SNJ-1715 complex confirms that the free aldehyde is the reactive species of the cornea-permeable cyclic hemiacetal. The alpha-ketoamide warhead of SNJ-1945 binds with the hydroxyl group of the tetrahedral adduct pointing toward the catalytic histidine rather than the oxyanion hole. The muI-II-SNJ-1945 complex shows residue Glu261 displaced from the S1' site by the inhibitor, resulting in an extended "open" conformation of the domain II gating loop and an unobstructed S1' site. This conformation offers an additional template for structure-based drug design extending to the primed subsites. An important role for the highly conserved Glu261 is proposed.
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Affiliation(s)
- D Cuerrier
- Department of Biochemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
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11
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Shirasaki Y, Miyashita H, Yamaguchi M, Inoue J, Nakamura M. Exploration of orally available calpain inhibitors: peptidyl alpha-ketoamides containing an amphiphile at P3 site. Bioorg Med Chem 2005; 13:4473-84. [PMID: 15921914 DOI: 10.1016/j.bmc.2005.04.059] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2005] [Revised: 04/15/2005] [Accepted: 04/15/2005] [Indexed: 10/25/2022]
Abstract
A novel series of dipeptidyl alpha-ketoamide derivatives with amphiphile was designed and synthesized as water-soluble calpain inhibitors. The introduction of amphiphiles at the P3 site increased water solubility without loss of membrane permeability and provided the oral available inhibitors. Extension of the ethylene glycol chain at the P3 site led to an improvement in persistence of plasma levels. In particular, introduction of a combination of a diethylene glycol methyl ether moiety at the P3 site, a phenylalanine residue at the P1 site and a cyclopropyl moiety at the P' site was the most effective modification for an increase in plasma drug exposure.
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Affiliation(s)
- Yoshihisa Shirasaki
- Research Laboratory of Ocular Science, Senju Pharmaceutical Co., Ltd, 1-5-4 Murotani Nishi-ku Kobe, Hyogo 651-2241, Japan.
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12
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Payne RJ, Brown KM, Coxon JM, Morton JD, Lee HYY, Abell AD. Peptidic Aldehydes Based on α- and β-Amino Acids: Synthesis, Inhibition of m-Calpain, and Anti-Cataract Properties. Aust J Chem 2004. [DOI: 10.1071/ch04080] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We present a new synthesis of SJA6017 (a potent m-calpain inhibitor) and its adaptation in order to prepare analogues in which the constituent Leu and Val residues are systematically replaced with their corresponding β-amino acids and/or the N-terminal fluorophenylsulfonyl group is replaced by a water solubilizing N-pyridin-3-ylmethoxycarbonyl group. All compounds have been assayed against m-calpain, and the best inhibitor, SJA6017, has been shown to inhibit the development of opacity in a lens culture system design to mimic cataract.
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