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Liu Y, Zou Y, Huang Y, Chen S, Zhang L. Identification of Balanol As a Potential Inhibitor of PAK1 That Induces Apoptosis and Cytoprotective Autophagy in Colorectal Cancer Cells. ChemMedChem 2023; 18:e202300114. [PMID: 37323074 DOI: 10.1002/cmdc.202300114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 06/17/2023]
Abstract
Colorectal cancer (CRC) is a common malignancy of the gastrointestinal tract, often accompanied by poor prognosis and high incidence and mortality. p21 activated kinases (PAKs) have been used as therapeutic targets because of their central role in many oncogenic signaling networks. By exploring tumor databases, we found that PAK1 overexpression is associated with poor prognosis in colorectal cancer, and therefore, PAK1-targeted inhibition is a new potential therapeutic strategy for colorectal cancer. We identified that Balanol (compound 6, DB04098) can effectively target PAK1 by high-throughput virtual screening. In vitro, compound 6 exhibited favorable PAK1 inhibition with potent anti-proliferative and anti-migration activity in SW480 cells. Additionally, we also found that compound 6 induced apoptosis and cytoprotective autophagy in SW480 cells. Together, these results indicate that compound 6 is a potential novel PAK1 inhibitor, which would be utilized as a candidate compound for future CRC treatment.
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Affiliation(s)
- Yi Liu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, 610031, Chengdu, China
| | - Yuling Zou
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, 610031, Chengdu, China
| | - Yunli Huang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, 610031, Chengdu, China
| | - Siwei Chen
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, 610031, Chengdu, China
| | - Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, 610031, Chengdu, China
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2
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Sinka V, Fernández I, Padrón JI. Synthesis of Tetrahydroazepines through Silyl Aza-Prins Cyclization Mediated by Iron(III) Salts. J Org Chem 2022; 87:11735-11742. [PMID: 35977416 PMCID: PMC9442639 DOI: 10.1021/acs.joc.2c01396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A new methodology for the synthesis of seven-membered
unsaturated
azacycles (tetrahydroazepines) was developed. It is based on the powerful
aza-Prins cyclization in combination with the Peterson-type elimination
reaction. In a single reaction step, a C–N, C–C bond
and an endocyclic double bond are formed. Under mild reaction conditions
and using iron(III) salts as sustainable catalysts, tetrahydroazepines
with different degrees of substitution are obtained directly and efficiently.
DFT calculations supported the proposed mechanism.
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Affiliation(s)
- Victoria Sinka
- Instituto de Productos Naturales y Agrobiología (IPNA), CSIC, 38206, Avda. Astrofísico Fco. Sánchez 3, 38206 La Laguna, Tenerife (Spain)
| | - Israel Fernández
- Departamento de Química Orgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Juan I Padrón
- Instituto de Productos Naturales y Agrobiología (IPNA), CSIC, 38206, Avda. Astrofísico Fco. Sánchez 3, 38206 La Laguna, Tenerife (Spain)
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Ahmad S, Akhtar R, Zahoor AF. Comprehensive Account on the Synthesis of (-)-Balanol and its Analogues. Curr Org Synth 2021; 19:56-85. [PMID: 34370642 DOI: 10.2174/1570179418666210809131917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/17/2021] [Accepted: 06/25/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND A variety of diseases have been associated with hyperactivation of protein kinase C (PKC) enzymes such as cancer, diabetes, asthma, cardiovascular and central nervous system disorders. There is a dire need to selectively inhibit these enzymes by synthesizing new potent inhibitors. Balanol, a fungal metabolite belonging to the PKC inhibitor family, is especially included in this aspect. Tremendous effort has been put towards the synthesis of balanol by different research groups. OBJECTIVE The aim of this review is to provide a detailed description of synthetic approaches adopted for the synthesis of key fragments of balanol (azepane and benzophenone). All the factors that resulted in excellent yield and high enantioselectivity have also been mentioned. CONCLUSION It has been shown throughout this review that the synthesis of hexahydroazepine and benzophenone cores of balanol was achieved by employing a variety of important key steps with commercially available starting precursors, which make this total synthesis more valuable. Moreover, this article provides ideas to the synthetic as well as pharmaceutical chemists for the synthesis of (-)-balanol and its analogues.
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Affiliation(s)
- Sajjad Ahmad
- Department of Chemistry, University of Engineering and Technology Lahore, Faisalabad Campus, 38000-Faisalabad, Pakistan
| | - Rabia Akhtar
- Department of Chemistry, Government College University Faisalabad, 38000-Faisalabad, Pakistan
| | - Ameer Fawad Zahoor
- Department of Chemistry, Government College University Faisalabad, 38000-Faisalabad, Pakistan
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Baier A, Szyszka R. Compounds from Natural Sources as Protein Kinase Inhibitors. Biomolecules 2020; 10:biom10111546. [PMID: 33198400 PMCID: PMC7698043 DOI: 10.3390/biom10111546] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022] Open
Abstract
The advantage of natural compounds is their lower number of side-effects when compared to most synthetic substances. Therefore, over the past several decades, the interest in naturally occurring compounds is increasing in the search for new potent drugs. Natural compounds are playing an important role as a starting point when developing new selective compounds against different diseases. Protein kinases play a huge role in several diseases, like cancers, neurodegenerative diseases, microbial infections, or inflammations. In this review, we give a comprehensive view of natural compounds, which are/were the parent compounds in the development of more potent substances using computational analysis and SAR studies.
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Affiliation(s)
- Andrea Baier
- Department of Animal Physiology and Toxicology, Institute of Biological Sciences, The John Paul II Catholic University of Lublin, 20-950 Lublin, Poland
- Correspondence:
| | - Ryszard Szyszka
- Department of Molecular Biology, Institute of Biological Sciences, The John Paul II Catholic University of Lublin, 20-950 Lublin, Poland;
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Hardianto A, Khanna V, Liu F, Ranganathan S. Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε. BMC Bioinformatics 2019; 19:342. [PMID: 30717648 PMCID: PMC7394325 DOI: 10.1186/s12859-018-2373-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/12/2018] [Indexed: 12/16/2022] Open
Abstract
Background (−)-Balanol is an ATP-mimicking inhibitor that non-selectively targets protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA). While PKA constantly shows tumor promoting activities, PKC isozymes can ambiguously be tumor promoters or suppressors. In particular, PKCε is frequently implicated in tumorigenesis and a potential target for anticancer drugs. We recently reported that the C5(S)-fluorinated balanol analogue (balanoid 1c) had improved binding affinity and selectivity for PKCε but not to the other novel PKC isozymes, which share a highly similar ATP site. The underlying basis for this fluorine-based selectivity is not entirely comprehended and needs to be investigated further for the development of ATP mimic inhibitors specific for PKCε. Results Using molecular dynamics (MD) simulations assisted by homology modelling and sequence analysis, we have studied the fluorine-based selectivity in the highly similar ATP sites of novel PKC (nPKC) isozymes. The study suggests that every nPKC isozyme has different dynamics behaviour in both apo and 1c-bound forms. Interestingly, the apo form of PKCε, where 1c binds strongly, shows the highest degree of flexibility which dramatically decreases after binding 1c. Conclusions For the first time to the best of our knowledge, we found that the origin of 1c selectivity for PKCε comes from the unique dynamics feature of each PKC isozyme. Fluorine conformational control in 1c can synergize with and lock down the dynamics of PKCε, which optimize binding interactions with the ATP site residues of the enzyme, particularly the invariant Lys437. This finding has implications for further rational design of balanol-based PKCε inhibitors for cancer drug development. Electronic supplementary material The online version of this article (10.1186/s12859-018-2373-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ari Hardianto
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Department of Chemistry, Universitas Padjadjaran, Jatinangor, West Java, 45363, Indonesia
| | - Varun Khanna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, SA, 5042, Australia
| | - Fei Liu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
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Qin L, Sankaran B, Aminzai S, Casteel DE, Kim C. Structural basis for selective inhibition of human PKG Iα by the balanol-like compound N46. J Biol Chem 2018; 293:10985-10992. [PMID: 29769318 PMCID: PMC6052212 DOI: 10.1074/jbc.ra118.002427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/11/2018] [Indexed: 12/18/2022] Open
Abstract
Activation of protein kinase G (PKG) Iα in nociceptive neurons induces long-term hyperexcitability that causes chronic pain. Recently, a derivative of the fungal metabolite balanol, N46, has been reported to inhibit PKG Iα with high potency and selectivity and attenuate thermal hyperalgesia and osteoarthritic pain. Here we determined co-crystal structures of the PKG Iα C-domain and cAMP-dependent protein kinase (PKA) Cα, each bound with N46, at 1.98 Å and 2.65 Å, respectively. N46 binds the active site with its external phenyl ring, specifically interacting with the glycine-rich loop and the αC helix. Phe-371 at the PKG Iα glycine-rich loop is oriented parallel to the phenyl ring of N46, forming a strong π-stacking interaction, whereas the analogous Phe-54 in PKA Cα rotates 30° and forms a weaker interaction. Structural comparison revealed that steric hindrance between the preceding Ser-53 and the propoxy group of the phenyl ring may explain the weaker interaction with PKA Cα. The analogous Gly-370 in PKG Iα, however, causes little steric hindrance with Phe-371. Moreover, Ile-406 on the αC helix forms a hydrophobic interaction with N46 whereas its counterpart in PKA, Thr-88, does not. Substituting these residues in PKG Iα with those in PKA Cα increases the IC50 values for N46, whereas replacing these residues in PKA Cα with those in PKG Iα reduces the IC50, consistent with our structural findings. In conclusion, our results explain the structural basis for N46-mediated selective inhibition of human PKG Iα and provide a starting point for structure-guided design of selective PKG Iα inhibitors.
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Affiliation(s)
- Liying Qin
- From the Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Banumathi Sankaran
- the Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Sahar Aminzai
- the Department of Medicine, University of California, San Diego, La Jolla, California 92093, and
| | - Darren E Casteel
- the Department of Medicine, University of California, San Diego, La Jolla, California 92093, and
| | - Choel Kim
- From the Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030,
- the Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030
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7
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Manick AD, Aubert S, Yalcouye B, Prangé T, Berhal F, Prestat G. Access to Functionalized Imidazolidin-2-one Derivatives by Iron-Catalyzed Oxyamination of Alkenes. Chemistry 2018; 24:11485-11492. [DOI: 10.1002/chem.201802190] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Anne-Doriane Manick
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601; Université Paris Descartes; 45 rue des Saints Pères 75006 Paris France
| | - Sidonie Aubert
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601; Université Paris Descartes; 45 rue des Saints Pères 75006 Paris France
| | - Boubacar Yalcouye
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601; Université Paris Descartes; 45 rue des Saints Pères 75006 Paris France
| | - Thierry Prangé
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015; Université Paris Descartes; 4 avenue de l'Observatoire 75270 Paris France
| | - Farouk Berhal
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601; Université Paris Descartes; 45 rue des Saints Pères 75006 Paris France
| | - Guillaume Prestat
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601; Université Paris Descartes; 45 rue des Saints Pères 75006 Paris France
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Hardianto A, Liu F, Ranganathan S. Molecular Dynamics Pinpoint the Global Fluorine Effect in Balanoid Binding to PKCε and PKA. J Chem Inf Model 2018; 58:511-519. [PMID: 29341608 DOI: 10.1021/acs.jcim.7b00504] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(-)-Balanol is an adenosine triphosphate mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with limited selectivity. While PKA is known as a tumor promoter, PKC isozymes can be tumor promoters or suppressors. In particular, PKCε is frequently involved in tumorigenesis and a potential target for anticancer drugs. We recently reported that stereospecific fluorination of balanol yielded a balanoid with enhanced selectivity for PKCε over other PKC isozymes and PKA, although the global fluorine effect behind the selectivity enhancement is not fully understood. Interestingly, in contrast to PKA, PKCε is more sensitive to this fluorine effect. Here we investigate the global fluorine effect on the different binding responses of PKCε and PKA to balanoids using molecular dynamics (MD) simulations. For the first time to the best of our knowledge, we found that a structurally equivalent residue in each kinase, Thr184 in PKA and Ala549 in PKCε, is essential for the different binding responses. Furthermore, the study revealed that the invariant Lys, Lys73 in PKA and Lys437 in PKCε, already known to have a crucial role in the catalytic activity of kinases, serves as the main anchor for balanol binding. Overall, while Thr184 in PKA attenuates the effect of fluorination, Ala549 permits remote response of PKCε to fluorine substitution, with implications for rational design of future balanol-based PKCε inhibitors.
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Affiliation(s)
- Ari Hardianto
- Department of Molecular Sciences, Macquarie University , Sydney, NSW 2109, Australia
| | - Fei Liu
- Department of Molecular Sciences, Macquarie University , Sydney, NSW 2109, Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University , Sydney, NSW 2109, Australia
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9
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Hardianto A, Yusuf M, Liu F, Ranganathan S. Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases. BMC Bioinformatics 2017; 18:572. [PMID: 29297286 PMCID: PMC5751415 DOI: 10.1186/s12859-017-1955-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND (-)-Balanol is an ATP mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with limited selectivity. While PKA is a tumour promoter, PKC isozymes act as tumour promoters or suppressors, depending on the cancer type. In particular, PKCε is frequently implicated in cancer promotion, making it a potential target for anticancer drugs. To improve isozyme selectivity of balanol, exhaustive structural and activity relationship (SAR) studies have been performed in the last two decades, but with limited success. More recently, fluorination on balanol has shown improved selectivity for PKCε, although the fluorine effect is not yet clearly understood. Understanding the origin to this fluorine-based selectivity will be valuable for designing better balanol-based ATP mimicking inhibitors. Computational approaches such as molecular dynamics (MD) simulations can decipher the fluorine effect, provided that correct charges have been assigned to a ligand. Balanol analogues have multiple ionisable functional groups and the effect of fluorine substitutions on the exact charge state of each analogue bound to PKA and to PKCε needs to be thoroughly investigated in order to design highly selective inhibitors for therapeutic applications. RESULTS We explored the charge states of novel fluorinated balanol analogues using MD simulations. For different potential charge states of these analogues, Molecular Mechanics Generalized Born Surface Area (MMGBSA) binding energy values were computed. This study suggests that balanol and the most potent fluorinated analogue (5S fluorine substitution on the azepane ring), have charges on the azepane ring (N1), and the phenolic (C6''OH) and the carboxylate (C15''O2H) groups on the benzophenone moiety, when bound to PKCε as well as PKA. CONCLUSIONS To the best our knowledge, this is the first study showing that the phenolate group is charged in balanol and its analogues binding to the ATP site of PKCε. Correct charge assignments of ligands are important to obtain predicted binding energy values from MD simulations that reflect experimental values. Both fluorination and the local enzymatic environment of the ATP site can influence the exact charge states of balanol analogues. Overall, this study is highly valuable for further rational design of potent balanol analogues selective to PKCε.
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Affiliation(s)
- Ari Hardianto
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109 Australia
| | - Muhammad Yusuf
- Department of Chemistry, Universitas Padjadjaran, Jatinangor, West Java 45363 Indonesia
| | - Fei Liu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109 Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109 Australia
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10
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Abstract
Supplemental Digital Content is Available in the Text. A novel and potent protein kinase G-1α (PKG-1α) inhibitor is used to demonstrate the important roles of PKG in capsaicin-induced acute pain and in persistent inflammatory pain. Activating PKG-1α induces a long-term hyperexcitability (LTH) in nociceptive neurons. Since the LTH correlates directly with chronic pain in many animal models, we tested the hypothesis that inhibiting PKG-1α would attenuate LTH-mediated pain. We first synthesized and characterized compound N46 (N-((3R,4R)-4-(4-(2-fluoro-3-methoxy-6-propoxybenzoyl)benzamido)pyrrolidin-3-yl)-1H-indazole-5-carboxamide). N46 inhibits PKG-1α with an IC50 of 7.5 nmol, was highly selective when tested against a panel of 274 kinases, and tissue distribution studies indicate that it does not enter the CNS. To evaluate its antinociceptive potential, we used 2 animal models in which the pain involves both activated PKG-1α and LTH. Injecting complete Freund's adjuvant (CFA) into the rat hind paw causes a thermal hyperalgesia that was significantly attenuated 24 hours after a single intravenous injection of N46. Next, we used a rat model of osteoarthritic knee joint pain and found that a single intra-articular injection of N46 alleviated the pain 14 days after the pain was established and the relief lasted for 7 days. Thermal hyperalgesia and osteoarthritic pain are also associated with the activation of the capsaicin-activated transient receptor protein vanilloid-1 (TRPV1) channel. We show that capsaicin activates PKG-1α in nerves and that a subcutaneous delivery of N46 attenuated the mechanical and thermal hypersensitivity elicited by exposure to capsaicin. Thus, PKG-1α appears to be downstream of the transient receptor protein vanilloid-1. Our studies provide proof of concept in animal models that a PKG-1α antagonist has a powerful antinociceptive effect on persistent, already existing inflammatory pain. They further suggest that N46 is a valid chemotype for the further development of such antagonists.
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Patel AR, Hardianto A, Ranganathan S, Liu F. Divergent response of homologous ATP sites to stereospecific ligand fluorination for selectivity enhancement. Org Biomol Chem 2017; 15:1570-1574. [PMID: 28119986 DOI: 10.1039/c7ob00129k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Acquiring a divergent response from homologous protein domains is essential for selective ligand-protein interactions. Stereospecific fluorination of (-)-balanol, an ATP mimic, uncovers a new source of selectivity from integrated chemical and conformational perturbation that differentiates homologous sites by the level of congruency in their response to local and remote fluorine effects.
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Affiliation(s)
- Alpesh Ramanlal Patel
- Department of Chemistry & Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility-mass spectrometry. Biochem J 2016; 473:3159-75. [PMID: 27444646 PMCID: PMC5095912 DOI: 10.1042/bcj20160648] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 07/21/2016] [Indexed: 12/21/2022]
Abstract
cAMP-dependent protein kinase (PKA) is an archetypal biological signaling module and a model for understanding the regulation of protein kinases. In the present study, we combine biochemistry with differential scanning fluorimetry (DSF) and ion mobility–mass spectrometry (IM–MS) to evaluate effects of phosphorylation and structure on the ligand binding, dynamics and stability of components of heteromeric PKA protein complexes in vitro. We uncover dynamic, conformationally distinct populations of the PKA catalytic subunit with distinct structural stability and susceptibility to the physiological protein inhibitor PKI. Native MS of reconstituted PKA R2C2 holoenzymes reveals variable subunit stoichiometry and holoenzyme ablation by PKI binding. Finally, we find that although a ‘kinase-dead’ PKA catalytic domain cannot bind to ATP in solution, it interacts with several prominent chemical kinase inhibitors. These data demonstrate the combined power of IM–MS and DSF to probe PKA dynamics and regulation, techniques that can be employed to evaluate other protein-ligand complexes, with broad implications for cellular signaling.
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Rohokale R, Dhavale D. Chiron approach towards the synthesis of (2S,3R)-3-hydroxyornithine, (2S,3R)-3-hydroxylysine and tetrahydroazepine core of (−)-balanol. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Kim J, Li G, Walters MA, Taylor SS, Veglia G. Uncoupling Catalytic and Binding Functions in the Cyclic AMP-Dependent Protein Kinase A. Structure 2016; 24:353-63. [PMID: 26833386 DOI: 10.1016/j.str.2015.11.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 01/07/2023]
Abstract
The canonical function of kinases is to transfer a phosphoryl group to substrates, initiating a signaling cascade; while their non-canonical role is to bind other kinases or substrates, acting as scaffolds, competitors, and signal integrators. Here, we show how to uncouple kinases' dual function by tuning the binding cooperativity between nucleotide (or inhibitors) and substrate allosterically. We demonstrate this new concept for the C subunit of protein kinase A (PKA-C). Using thermocalorimetry and nuclear magnetic resonance, we found a linear correlation between the degree of cooperativity and the population of the closed state of PKA-C. The non-hydrolyzable ATP analog (ATPγC) does not follow this correlation, suggesting that changing the chemical groups around the phosphoester bond can uncouple kinases' dual function. Remarkably, this uncoupling was also found for two ATP-competitive inhibitors, H89 and balanol. Since the mechanism for allosteric cooperativity is not conserved in different kinases, these results may suggest new approaches for designing selective kinase inhibitors.
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Affiliation(s)
- Jonggul Kim
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Geoffrey Li
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael A Walters
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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Homan KT, Waldschmidt HV, Glukhova A, Cannavo A, Song J, Cheung JY, Koch WJ, Larsen SD, Tesmer JJG. Crystal Structure of G Protein-coupled Receptor Kinase 5 in Complex with a Rationally Designed Inhibitor. J Biol Chem 2015; 290:20649-20659. [PMID: 26032411 DOI: 10.1074/jbc.m115.647370] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Indexed: 11/06/2022] Open
Abstract
G protein-coupled receptor kinases (GRKs) regulate cell signaling by initiating the desensitization of active G protein-coupled receptors. The two most widely expressed GRKs (GRK2 and GRK5) play a role in cardiovascular disease and thus represent important targets for the development of novel therapeutic drugs. In the course of a GRK2 structure-based drug design campaign, one inhibitor (CCG215022) exhibited nanomolar IC50 values against both GRK2 and GRK5 and good selectivity against other closely related kinases such as GRK1 and PKA. Treatment of murine cardiomyocytes with CCG215022 resulted in significantly increased contractility at 20-fold lower concentrations than paroxetine, an inhibitor with more modest selectivity for GRK2. A 2.4 Å crystal structure of the GRK5·CCG215022 complex was determined and revealed that the inhibitor binds in the active site similarly to its parent compound GSK180736A. As designed, its 2-pyridylmethyl amide side chain occupies the hydrophobic subsite of the active site where it forms three additional hydrogen bonds, including one with the catalytic lysine. The overall conformation of the GRK5 kinase domain is similar to that of a previously determined structure of GRK6 in what is proposed to be its active state, but the C-terminal region of the enzyme adopts a distinct conformation. The kinetic properties of site-directed mutants in this region are consistent with the hypothesis that this novel C-terminal structure is representative of the membrane-bound conformation of the enzyme.
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Affiliation(s)
- Kristoff T Homan
- Life Sciences Institute and the Departments of Pharmacology and Biological Sciences, University of Michigan, Ann Arbor, Michigan 48109
| | - Helen V Waldschmidt
- Vahlteich Medicinal Chemistry Core and the Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Alisa Glukhova
- Life Sciences Institute and the Departments of Pharmacology and Biological Sciences, University of Michigan, Ann Arbor, Michigan 48109
| | - Alessandro Cannavo
- Center for Translational Medicine, Temple University School of Medicine, Philadelphia, Pennsylvania 19140
| | - Jianliang Song
- Center for Translational Medicine, Temple University School of Medicine, Philadelphia, Pennsylvania 19140
| | - Joseph Y Cheung
- Center for Translational Medicine, Temple University School of Medicine, Philadelphia, Pennsylvania 19140
| | - Walter J Koch
- Center for Translational Medicine, Temple University School of Medicine, Philadelphia, Pennsylvania 19140
| | - Scott D Larsen
- Vahlteich Medicinal Chemistry Core and the Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - John J G Tesmer
- Life Sciences Institute and the Departments of Pharmacology and Biological Sciences, University of Michigan, Ann Arbor, Michigan 48109.
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Saha T, Maitra R, Chattopadhyay SK. A unified approach to the important protein kinase inhibitor balanol and a proposed analogue. Beilstein J Org Chem 2013; 9:2910-5. [PMID: 24454570 PMCID: PMC3896276 DOI: 10.3762/bjoc.9.327] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 11/07/2013] [Indexed: 11/26/2022] Open
Abstract
A common approach to the important protein kinase inhibitor (−)-balanol and an azepine-ring-modified balanol derivative has been developed using an efficient fragment coupling protocol which proceeded in good overall yield.
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Affiliation(s)
- Tapan Saha
- Department of Chemistry, University of Kalyani, Kalyani - 741235, West Bengal, India
| | - Ratnava Maitra
- Department of Chemistry, University of Kalyani, Kalyani - 741235, West Bengal, India
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17
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Cheng F, Zhou Y, Li J, Li W, Liu G, Tang Y. Prediction of chemical-protein interactions: multitarget-QSAR versus computational chemogenomic methods. MOLECULAR BIOSYSTEMS 2012; 8:2373-84. [PMID: 22751809 DOI: 10.1039/c2mb25110h] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Elucidation of chemical-protein interactions (CPI) is the basis of target identification and drug discovery. It is time-consuming and costly to determine CPI experimentally, and computational methods will facilitate the determination of CPI. In this study, two methods, multitarget quantitative structure-activity relationship (mt-QSAR) and computational chemogenomics, were developed for CPI prediction. Two comprehensive data sets were collected from the ChEMBL database for method assessment. One data set consisted of 81 689 CPI pairs among 50 924 compounds and 136 G-protein coupled receptors (GPCRs), while the other one contained 43 965 CPI pairs among 23 376 compounds and 176 kinases. The range of the area under the receiver operating characteristic curve (AUC) for the test sets was 0.95 to 1.0 and 0.82 to 1.0 for 100 GPCR mt-QSAR models and 100 kinase mt-QSAR models, respectively. The AUC of 5-fold cross validation were about 0.92 for both 176 kinases and 136 GPCRs using the chemogenomic method. However, the performance of the chemogenomic method was worse than that of mt-QSAR for the external validation set. Further analysis revealed that there was a high false positive rate for the external validation set when using the chemogenomic method. In addition, we developed a web server named CPI-Predictor, , which is available for free. The methods and tool have potential applications in network pharmacology and drug repositioning.
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Affiliation(s)
- Feixiong Cheng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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18
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Fonteles CSR, Dos Santos CF, da Silva Alves KS, de Miranda Mota AC, Damasceno JX, Fonteles MC. Comparative proteomic analysis of human whole saliva of children with protein-energy undernutrition. Nutrition 2012; 28:744-8. [PMID: 22541058 DOI: 10.1016/j.nut.2011.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 09/05/2011] [Accepted: 10/06/2011] [Indexed: 11/16/2022]
Abstract
OBJECTIVE The aim of the present study was to investigate the protein profile of children with different levels of protein-energy undernutrition (PEU) through a proteomic approach of human whole saliva. METHODS Initially, saliva samples of children with mild, moderate, and severe PEU were collected and lyophilized. Saliva samples of healthy children were used as controls. Samples were analyzed for total protein using the Bradford method. Saliva samples were analyzed by two-dimensional electrophoresis according to their isoelectric point (pI) and their molecular weights (MWs). RESULTS Comparisons of protein bands among the healthy and mildly, moderately, and severely undernourished children showed significant differences in the MWs (P = 0.001) and pI values (P = 0.03). In total 159 spots were identified in the healthy children; 156, 168, and 221 spots were observed in mildly, moderately, and severely undernourished children, respectively. Mildly undernourished children presented with the spot with the highest MW of 293 kDa (pI = 7.77) and the lowest MW of 5 kDa (pI = 4.83). Moderately undernourished children were the only ones who did not present with a protein band with an MW of 30 kDa. The presence of a protein band with an MW of 123 kDa (pI = 516), possibly a cyclin-dependent protein kinase, was also observed only in this group. CONCLUSION The protein profile in saliva varies according to the presence or absence of PEU, and these variations are specifically expressed in different grades of undernutrition. Thus, saliva may be an important diagnostic tool for the assessment of PEU.
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Affiliation(s)
- Cristiane Sá Roriz Fonteles
- Laboratory of Metabolic Pharmacology and Cell Physiology, Federal University of Ceará, Fortaleza, Ceará, Brazil.
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19
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Liu J, Hu Y, Waller DL, Wang J, Liu Q. Natural products as kinase inhibitors. Nat Prod Rep 2012; 29:392-403. [DOI: 10.1039/c2np00097k] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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20
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Louvel J, Chemla F, Demont E, Ferreira F, Pérez-Luna A, Voituriez A. Stereoselective Synthesis of syn-β-Amino Propargylic Ethers: Application to the Asymmetric Syntheses of (+)-β-Conhydrine and (−)-Balanol. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100333] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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21
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Thal DM, Yeow RY, Schoenau C, Huber J, Tesmer JJG. Molecular mechanism of selectivity among G protein-coupled receptor kinase 2 inhibitors. Mol Pharmacol 2011; 80:294-303. [PMID: 21596927 DOI: 10.1124/mol.111.071522] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are key regulators of cell physiology and control processes ranging from glucose homeostasis to contractility of the heart. A major mechanism for the desensitization of activated GPCRs is their phosphorylation by GPCR kinases (GRKs). Overexpression of GRK2 is strongly linked to heart failure, and GRK2 has long been considered a pharmaceutical target for the treatment of cardiovascular disease. Several lead compounds developed by Takeda Pharmaceuticals show high selectivity for GRK2 and therapeutic potential for the treatment of heart failure. To understand how these drugs achieve their selectivity, we determined crystal structures of the bovine GRK2-Gβγ complex in the presence of two of these inhibitors. Comparison with the apoGRK2-Gβγ structure demonstrates that the compounds bind in the kinase active site in a manner similar to that of the AGC kinase inhibitor balanol. Both balanol and the Takeda compounds induce a slight closure of the kinase domain, the degree of which correlates with the potencies of the inhibitors. Based on our crystal structures and homology modeling, we identified five amino acids surrounding the inhibitor binding site that we hypothesized could contribute to inhibitor selectivity. However, our results indicate that these residues are not major determinants of selectivity among GRK subfamilies. Rather, selectivity is achieved by the stabilization of a unique inactive conformation of the GRK2 kinase domain.
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Affiliation(s)
- David M Thal
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Room 3425, Ann Arbor, MI 48109, USA.
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22
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Meanwell NA. Synopsis of Some Recent Tactical Application of Bioisosteres in Drug Design. J Med Chem 2011; 54:2529-91. [DOI: 10.1021/jm1013693] [Citation(s) in RCA: 1876] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Medicinal Chemistry, Bristol-Myers Squibb Pharmaceutical Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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Srivastava AK, Panda G. Total synthesis of (-)-balanol, all stereoisomers, their N-tosyl analogues, and fully protected ophiocordin: an easy route to hexahydroazepine cores from garner aldehydes. Chemistry 2008; 14:4675-88. [PMID: 18399526 DOI: 10.1002/chem.200701991] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Total syntheses of (-)-balanol and all of its stereoisomers starting from easily available Garner aldehydes are described. Diastereoselective Grignard reactions on Garner aldehydes and ring-closing metatheses are the key steps for the construction of hexahydroazepine subunits. The benzophenone subunits were constructed through coupling of suitably functionalized aromatic aldehyde and bromo components. The synthetic route constitutes a convenient and scalable reaction sequence to generate all of the stereoisomers of balanol. The methodology is explored further for the synthesis of N-tosyl analogues of balanol and of fully protected ophiocordin.
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Affiliation(s)
- Ajay Kumar Srivastava
- Medicinal and Process Chemistry Division, Central Drug Research Institute, Lucknow, UP, India
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25
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Page CS, Bates PA. Can MM-PBSA calculations predict the specificities of protein kinase inhibitors? J Comput Chem 2007; 27:1990-2007. [PMID: 17036304 DOI: 10.1002/jcc.20534] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
An application of the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) protocol to the prediction of protein kinase inhibitor selectivity is presented. Six different inhibitors are placed in equivalent orientations in each of six different receptors. Fully solvated molecular dynamics is then run for 1 ns on each of the 36 complexes, and the resulting trajectories scored, using the implicit solvent model. The results show some correlation with experimentally-determined specificities; anomalies may be attributed to a variety of causes, including difficulties in quantifying induced fit penalties and variabilities in normal modes calculations. Decomposing interaction energies on a per-residue basis yields more useful insights into the natures of the binding modes and suggests that the real value of such calculations lies in understanding interactions rather than outright prediction.
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Affiliation(s)
- Christopher S Page
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London, GB-WC2A 3PX, United Kingdom
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26
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Sheinerman FB, Giraud E, Laoui A. High Affinity Targets of Protein Kinase Inhibitors Have Similar Residues at the Positions Energetically Important for Binding. J Mol Biol 2005; 352:1134-56. [PMID: 16139843 DOI: 10.1016/j.jmb.2005.07.074] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2005] [Revised: 07/07/2005] [Accepted: 07/29/2005] [Indexed: 10/25/2022]
Abstract
Inhibition of protein kinase activity is a focus of intense drug discovery efforts in several therapeutic areas. Major challenges facing the field include understanding of the factors determining the selectivity of kinase inhibitors and the development of compounds with the desired selectivity profile. Here, we report the analysis of sequence variability among high and low affinity targets of eight different small molecule kinase inhibitors (BIRB796, Tarceva, NU6102, Gleevec, SB203580, balanol, H89, PP1). It is observed that all high affinity targets of each inhibitor are found among a relatively small number of kinases, which have similar residues at the specific positions important for binding. The findings are highly statistically significant, and allow one to exclude the majority of kinases in a genome from a list of likely targets for an inhibitor. The findings have implications for the design of novel inhibitors with a desired selectivity profile (e.g. targeted at multiple kinases), the discovery of new targets for kinase inhibitor drugs, comparative analysis of different in vivo models, and the design of "a-la-carte" chemical libraries tailored for individual kinases.
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Affiliation(s)
- Felix B Sheinerman
- Informatics, Aventis, Sanofi Aventis Group 1041 Route 202-206, Bridgewater, NJ 08807, USA.
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27
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Nicolaou KC. Joys of Molecules. 2. Endeavors in Chemical Biology and Medicinal Chemistry. J Med Chem 2005; 48:5613-38. [PMID: 16134928 DOI: 10.1021/jm050524f] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K C Nicolaou
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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Breitenlechner CB, Wegge T, Berillon L, Graul K, Marzenell K, Friebe WG, Thomas U, Schumacher R, Huber R, Engh RA, Masjost B. Structure-Based Optimization of Novel Azepane Derivatives as PKB Inhibitors. J Med Chem 2004; 47:1375-90. [PMID: 14998327 DOI: 10.1021/jm0310479] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novel azepane derivatives were prepared and evaluated for protein kinase B (PKB-alpha) and protein kinase A (PKA) inhibition. The original (-)-balanol-derived lead structure (4R)-4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzoic acid (3R)-3-[(pyridine-4-carbonyl)amino]-azepan-4-yl ester (1) (IC(50) (PKB-alpha) = 5 nM) which contains an ester moiety was found to be plasma unstable and therefore unsuitable as a drug. Based upon molecular modeling studies using the crystal structure of the complex between PKA and 1, the five compounds N-[(3R,4R)-4-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzoylamino]-azepan-3-yl]-isonicotinamide (4), (3R,4R)-N-[4-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzyloxy]-azepan-3-yl]-isonicotinamide (5), N-[(3R,4S)-4-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-phenylamino]-methyl]-azepan-3-yl)-isonicotinamide (6), N-[(3R,4R)-4-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzylamino]-azepan-3-yl]-isonicotinamide (7), and N-[(3R,4S)-4-(4-[trans-2-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-phenyl]-vinyl]-azepan-3-yl)-isonicotinamide (8) with linkers isosteric to the ester were designed, synthesized, and tested for in vitro inhibitory activity against PKA and PKB-alpha and for plasma stability in mouse plasma.(1) Compound 4 was found to be plasma stable and highly active (IC(50) (PKB-alpha) = 4 nM). Cocrystals with PKA were obtained for 4, 5, and 8 and analyzed for binding interactions and conformational changes in the ligands and protein in order to rationalize the different activities of the molecules.
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29
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Yadav J, Srinivas C. Ring expansion approach for the synthesis of the (3S,4S)-hexahydroazepine core of balanol and ophiocordin. Tetrahedron 2003. [DOI: 10.1016/j.tet.2003.09.089] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Lampe JW, Biggers CK, Defauw JM, Foglesong RJ, Hall SE, Heerding JM, Hollinshead SP, Hu H, Hughes PF, Jagdmann GE, Johnson MG, Lai YS, Lowden CT, Lynch MP, Mendoza JS, Murphy MM, Wilson JW, Ballas LM, Carter K, Darges JW, Davis JE, Hubbard FR, Stamper ML. Synthesis and protein kinase inhibitory activity of balanol analogues with modified benzophenone subunits. J Med Chem 2002; 45:2624-43. [PMID: 12036372 DOI: 10.1021/jm020018f] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of analogues of the protein kinase C (PKC) inhibitory natural product balanol which bear modified benzophenone subunits are described. The analogues were designed with the goal of uncovering structure-activity features that could be used in the development of PKC inhibitors with a reduced polar character compared to balanol itself. The results of these studies suggest that most of the benzophenone features found in the natural product are important for obtaining potent PKC inhibitory compounds. However, several modifications were found to lead to selective inhibitors of the related enzyme protein kinase A (PKA), and several specific modifications to the polar structural elements of the benzophenone were found to provide potent PKC inhibitors. In particular, it was found that replacement of the benzophenone carboxylate with bioisosteric equivalents could lead to potent analogues. Further, a tolerance for lipophilic substituents on the terminal benzophenone ring was uncovered. These results are discussed in light of recently available structural information for PKA.
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Affiliation(s)
- John W Lampe
- Sphinx Laboratories, Lilly Research Laboratories, Eli Lilly and Company, 20 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA.
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Aznar S, Lacal JC. Searching new targets for anticancer drug design: the families of Ras and Rho GTPases and their effectors. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2001; 67:193-234. [PMID: 11525383 DOI: 10.1016/s0079-6603(01)67029-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The Ras superfamily of low-molecular-weight GTPases are proteins that, in response to diverse stimuli, control key cellular processes such as cell growth and development, apoptosis, lipid metabolism, cytoarchitecture, membrane trafficking, and transcriptional regulation. More than 100 genes of this superfamily grouped in six subfamilies have been described so far, pointing to the complexities and specificities of their cellular functions. Dysregulation of members of at least two of these families (the Ras and the Rho families) is involved in the events that lead to the uncontrolled proliferation and invasiveness of human tumors. In recent years, the cloning and characterization of downstream effectors for Ras and Rho proteins have given crucial clues to the specific pathways that lead to aberrant cellular growth and ultimately to tumorigenesis. A direct link between the functions of some of these effectors with the appearance of transformed cells and their ability to proliferate and invade surrounding tissues has been made. Accordingly, drugs that specifically alter their functions display antineoplasic properties, and some of these drugs are already under clinical trials. In this review, we survey the progress made in understanding the underlying molecular connections between carcinogenesis and the specific cellular functions elicited by some of these effectors. We also discuss new drugs with antineoplastic or antimetastatic activity that are targeted to specific effectors for Ras or Rho proteins.
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Affiliation(s)
- S Aznar
- Instituto de Investigaciones Biomédicas, CSIC, Madrid, Spain
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33
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Maroney AC, Finn JP, Connors TJ, Durkin JT, Angeles T, Gessner G, Xu Z, Meyer SL, Savage MJ, Greene LA, Scott RW, Vaught JL. Cep-1347 (KT7515), a semisynthetic inhibitor of the mixed lineage kinase family. J Biol Chem 2001; 276:25302-8. [PMID: 11325962 DOI: 10.1074/jbc.m011601200] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
CEP-1347 (KT7515) promotes neuronal survival at dosages that inhibit activation of the c-Jun amino-terminal kinases (JNKs) in primary embryonic cultures and differentiated PC12 cells after trophic withdrawal and in mice treated with 1-methyl-4-phenyl tetrahydropyridine. In an effort to identify molecular target(s) of CEP-1347 in the JNK cascade, JNK1 and known upstream regulators of JNK1 were co-expressed in Cos-7 cells to determine whether CEP-1347 could modulate JNK1 activation. CEP-1347 blocked JNK1 activation induced by members of the mixed lineage kinase (MLK) family (MLK3, MLK2, MLK1, dual leucine zipper kinase, and leucine zipper kinase). The response was selective because CEP-1347 did not inhibit JNK1 activation in cells induced by kinases independent of the MLK cascade. CEP-1347 inhibition of recombinant MLK members in vitro was competitive with ATP, resulting in IC(50) values ranging from 23 to 51 nm, comparable to inhibitory potencies observed in intact cells. In addition, overexpression of MLK3 led to death in Chinese hamster ovary cells, and CEP-1347 blocked this death at doses comparable to those that inhibited MLK3 kinase activity. These results identify MLKs as targets of CEP-1347 in the JNK signaling cascade and demonstrate that CEP-1347 can block MLK-induced cell death.
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Affiliation(s)
- A C Maroney
- Cephalon Inc., 145 Brandywine Pkwy., West Chester, Pennsylvania 19380, USA.
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Fürstner A, Thiel OR. Formal total synthesis of (-)-balanol: concise approach to the hexahydroazepine segment based on RCM. J Org Chem 2000; 65:1738-42. [PMID: 10750493 DOI: 10.1021/jo991611g] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A concise synthesis of the hexahydroazepine moiety 13 of (-)-balanol 1 is described that comprises only eight steps and is distinctly shorter than all previous reported approaches to this particular compound. Sharpless epoxidation of divinylcarbinol 4 and ring closing alkene metathesis (RCM) reaction for the formation of the heterocyclic scaffold 9 constitute the key transformations of this sequence. The latter reaction is best achieved with catalytic amounts of the ruthenium indenylidene complex 18 recently reported. Furthermore, it is demonstrated that RCM can be successfully carried out even in the presence of an azido function provided that Schrock's molybdenum alkylidene complex Mo(=NAr)(=CHCMe2Ph)[OC(Me)(CF3)2]2 (Ar = 2,6-diisopropylphenyl) is used as precatalyst.
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Affiliation(s)
- A Fürstner
- Max-Planck-Institut für Kohlenforschung, Germany
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35
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Abstract
Several tyrosine and serine/threonine protein kinases have emerged in the last few years as attractive targets in the search for new therapeutic agents being applicable in many different disease indications. Initially, inhibition of these protein kinases by ATP site-directed inhibitors was considered less prone to success, but medicinal chemists from both academia and industry have been able to impart potency and selectivity to a limited number of scaffolds by modulating and fine-tuning the interactions of the modified template with the ATP binding site of the selected kinase. The chemical templates that have been used in the synthesis of ATP site-directed protein kinase inhibitors are reviewed with emphasis on the kinase inhibitors that have entered or are about to enter clinical trials. Examples have been selected to illustrate how structure-based design approaches and new methods to increase compound diversity have had an impact on this area of research.
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36
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Storm JP, Andersson CM. An organoiron approach to the benzophenone appendage of the protein kinase C inhibitor balanol. Org Lett 1999; 1:1451-3. [PMID: 10825993 DOI: 10.1021/ol9910060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[formula: see text] A new synthetic route to the benzophenone appendage of balanol, based on sequential iron-assisted nucleophilic aromatic substitution and ring-opening as well as regioselective oxidative cyanation, is described.
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Affiliation(s)
- J P Storm
- Department of Chemistry, Lund University, Sweden
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37
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Majumdar S, Bhattacharjya A, Patra A. Regioselective synthesis of chiral six- and seven-membered N-heterocycles from N-allyl carbohydrate nitrones: Tuning of regioselectivity by N-substitution. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00694-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Gustafsson AB, Brunton LL. Differential and selective inhibition of protein kinase A and protein kinase C in intact cells by balanol congeners. Mol Pharmacol 1999; 56:377-82. [PMID: 10419557 DOI: 10.1124/mol.56.2.377] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The fungal metabolite balanol is a potent inhibitor of protein kinase A (PKA) and protein kinase C (PKC) in vitro that acts by competing with ATP for binding (K(i) approximately 4 nM); congeners of balanol show specificity for PKA over PKC. We have characterized the effects of balanol and 10"-deoxybalanol in intact cells to determine whether these compounds cross the cell membrane and whether the potency and specificity noted in vitro are preserved in vivo. In neonatal rat myocytes and cultured A431 cells transiently transfected with a cyclic AMP response element-luciferase reporter construct, balanol inhibits the induction of luciferase activity by isoproterenol, indicating inhibition of PKA. Western analysis shows that both balanol and 10"-deoxybalanol reduce phosphorylation of cAMP response element-binding protein in isoproterenol-stimulated A431 cells; inhibition is concentration dependent with an IC(50) value of approximately 3 microM. Balanol, but not 10"-deoxybalanol, inhibits phosphorylation of the myristoylated alanine-rich C kinase substrate protein, a PKC substrate, in phorbol ester-stimulated A431 cells (IC(50) approximately 7 microM). Our data demonstrate that balanol is a potent inhibitor of PKA and PKC in several whole-cell systems and causes no obvious toxicity. In addition, balanol congeners inhibit PKA and PKC with the specificity and potency predicted by in vitro experiments.
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Affiliation(s)
- A B Gustafsson
- Department of Pharmacology, Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA.
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Setyawan J, Koide K, Diller TC, Bunnage ME, Taylor SS, Nicolaou KC, Brunton LL. Inhibition of protein kinases by balanol: specificity within the serine/threonine protein kinase subfamily. Mol Pharmacol 1999; 56:370-6. [PMID: 10419556 DOI: 10.1124/mol.56.2.370] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Balanol is a potent inhibitor of cyclic AMP-dependent protein kinase and protein kinase C, acting competitively with ATP with an affinity 3000 times that of ATP. We tested the capacity of balanol to inhibit representative serine- and threonine-specific protein kinases from the protein kinase subfamily that shares a common conserved catalytic core with cyclic AMP-dependent protein kinase. Balanol's pattern of interactions indicates considerable diversity of the ATP/balanol-binding sites of protein kinases within familial groups and even among isoforms of the same kinase. We propose that balanol is a protean structure that may be modified to produce selective, high-affinity inhibitors and probes of the ATP-binding sites of serine/threonine protein kinases.
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Affiliation(s)
- J Setyawan
- Department of Pharmacology and Medicine, University of California at San Diego, La Jolla, California, USA
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40
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Denieul MP, Skrydstrup T. Application of an intramolecular Heck reaction for the construction of the balanol aryl core structure. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(99)00907-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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41
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Hünenberger PH, Helms V, Narayana N, Taylor SS, McCammon JA. Determinants of ligand binding to cAMP-dependent protein kinase. Biochemistry 1999; 38:2358-66. [PMID: 10029529 DOI: 10.1021/bi982064g] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein kinases are essential for the regulation of cellular growth and metabolism. Since their dysfunction leads to debilitating diseases, they represent key targets for pharmaceutical research. The rational design of kinase inhibitors requires an understanding of the determinants of ligand binding to these proteins. In the present study, a theoretical model based on continuum electrostatics and a surface-area-dependent nonpolar term is used to calculate binding affinities of balanol derivatives, H-series inhibitors, and ATP analogues toward the catalytic subunit of cAMP-dependent protein kinase (cAPK or protein kinase A). The calculations reproduce most of the experimental trends and provide insight into the driving forces responsible for binding. Nonpolar interactions are found to govern protein-ligand affinity. Hydrogen bonds represent a negligible contribution, because hydrogen bond formation in the complex requires the desolvation of the interacting partners. However, the binding affinity is decreased if hydrogen-bonding groups of the ligand remain unsatisfied in the complex. The disposition of hydrogen-bonding groups in the ligand is therefore crucial for binding specificity. These observations should be valuable guides in the design of potent and specific kinase inhibitors.
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Affiliation(s)
- P H Hünenberger
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093-0365, USA.
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42
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Narayana N, Diller TC, Koide K, Bunnage ME, Nicolaou KC, Brunton LL, Xuong NH, Ten Eyck LF, Taylor SS. Crystal structure of the potent natural product inhibitor balanol in complex with the catalytic subunit of cAMP-dependent protein kinase. Biochemistry 1999; 38:2367-76. [PMID: 10029530 DOI: 10.1021/bi9820659] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Endogenous protein kinase inhibitors are essential for a wide range of physiological functions. These endogenous inhibitors may mimic peptide substrates as in the case of the heat-stable protein kinase inhibitor (PKI), or they may mimic nucleotide triphosphates. Natural product inhibitors, endogenous to the unique organisms producing them, can be potent exogenous inhibitors against foreign protein kinases. Balanol is a natural product inhibitor exhibiting low nanomolar Ki values against serine and threonine specific kinases, while being ineffective against protein tyrosine kinases. To elucidate balanol's specific inhibitory effects and provide a basis for understanding inhibition-regulated biological processes, a 2.1 A resolution crystal structure of balanol in complex with cAMP-dependent protein kinase (cAPK) was determined. The structure reveals conserved binding regions and displays extensive complementary interactions between balanol and conserved cAPK residues. This report describes the structure of a protein kinase crystallized with a natural ATP mimetic in the absence of metal ions and peptide inhibitor.
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Affiliation(s)
- N Narayana
- The Howard Hughes Medical Institute, Department of Biology, University of California, San Diego, La Jolla, USA
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43
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44
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Majumdar S, Bhattacharjya A, Patra A. Expeditious synthesis of chiral six and seven membered nitrogen heterocycles from carbohydrate amines by N-allyl carbohydrate nitrone cycloaddition: Tuning of regioselectivity by N-substitution. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)10287-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Hu H, Mendoza JS, Lowden CT, Ballas LM, Janzen WP. Synthesis and protein kinase C inhibitory activities of balanol analogues with modification of 4-hydroxybenzamido moiety. Bioorg Med Chem 1997; 5:1873-82. [PMID: 9354244 DOI: 10.1016/s0968-0896(97)00125-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A series of racemic balanol analogues with modification of the benzamido moiety of balanol have been synthesized and evaluated for their inhibitory activities against human protein kinase C isozymes (PKC-alpha, -beta I, -beta II, -gamma, -delta, -epsilon, and -eta). The structural modification includes replacement of the 4-hydroxyphenyl group with variously substituted phenyl rings, substitution of the amide linkage with a sulfonamide or an ester, and replacement of the 4-hydroxyphenyl substructure with a hydroxyl substituted indole or a hydroxybenzyl group. in general, these analogues were found to be less potent than balanol, but a number of analogues were identified with improved isozyme selectivity. The structure-activity relationship studies of these analogues also indicated that (1) the optimal general PKC inhibition requires a free 4-hydroxyl group in the benzamido portion of the molecule, (2) the amide linkage of the benzamido moiety is important for PKC inhibition, and (3) the conformation associated with the benzamido moiety seems to have a profound effect on PKC inhibition. The requirement of a free 4-hydroxyl group in conjunction with an appropriate conformation of the benzamido moiety for optimal PKC inhibition suggests that the 4-hydroxyphenyl group may be involved in a specific inhibitor-enzyme interaction important for PKC inhibition.
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Affiliation(s)
- H Hu
- Sphinx Pharmaceuticals, Division of Eli Lilly & Company, Durham, NC 27707, USA
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46
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Nilsson J, Andersson CM. A divergent route to substituted benzophenones based on cationic η6-(Arene)iron intermediates. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)00954-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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47
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Young PR, McLaughlin MM, Kumar S, Kassis S, Doyle ML, McNulty D, Gallagher TF, Fisher S, McDonnell PC, Carr SA, Huddleston MJ, Seibel G, Porter TG, Livi GP, Adams JL, Lee JC. Pyridinyl imidazole inhibitors of p38 mitogen-activated protein kinase bind in the ATP site. J Biol Chem 1997; 272:12116-21. [PMID: 9115281 DOI: 10.1074/jbc.272.18.12116] [Citation(s) in RCA: 459] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The site of action of a series of pyridinyl imidazole compounds that are selective inhibitors of p38 mitogen-activated protein kinase in vitro and block proinflammatory cytokine production in vivo has been determined. Using Edman sequencing, 125I-SB206718 was shown to cross-link to the nonphosphorylated Escherichia coli-expressed p38 kinase at Thr175, which is proximal to the ATP binding site. Titration calorimetric studies with E. coli-expressed p38 kinase showed that SB203580 bound with a stoichiometry of 1:1 and that binding was blocked by preincubation of p38 kinase with the ATP analogue, FSBA (5'-[p-(fluorosulfonyl)benzoyl]adenosine), which covalently modifies the ATP binding site. The intrinsic ATPase activity of the nonphosphorylated enzyme was inhibited by SB203580 with a Km of 9.6 mM. Kinetic studies of active, phosphorylated yeast-expressed p38 kinase using a peptide substrate showed that SB203580 was competitive with ATP with a Ki of 21 nM and that kinase inhibition correlated with binding and biological activity. Mutagenesis indicated that binding of 125I-SB206718 was dependent on the catalytic residues K53 and D168 in the ATP pocket. These findings indicate that the pyridinyl imidazoles act in vivo by inhibiting p38 kinase activity through competition with ATP and that their selectivity is probably determined by differences in nonconserved regions within or near the ATP binding pocket.
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Affiliation(s)
- P R Young
- Department of Comparative Genetics, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406-0939, USA.
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48
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Defauw JM, Murphy MM, Jagdmann GE, Hu H, Lampe JW, Hollinshead SP, Mitchell TJ, Crane HM, Heerding JM, Mendoza JS, Davis JE, Darges JW, Hubbard FR, Hall SE. Synthesis and protein kinase C inhibitory activities of acyclic balanol analogs that are highly selective for protein kinase C over protein kinase A. J Med Chem 1996; 39:5215-27. [PMID: 8978850 DOI: 10.1021/jm960581w] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A series of balanol analogs in which the perhydroazepine ring and the p-hydroxybenzamide moiety were combined into an acyclic linked unit have been prepared and evaluated for their inhibitory properties against the serine/threonine kinase PKC. Several low-micromolar to low-nanomolar inhibitors of the alpha, beta I, beta II, gamma, delta, epsilon and eta PKC isozymes were prepared. In general, these acyclic balanol analogs were found to be highly selective for PKC over the serine/threonine kinase PKA. The type and number of atoms linking the benzophenone ester to the p-hydroxyphenyl group necessary for optimal PKC inhibition were investigated. The most potent compounds contained a three-carbon linker in which the carboxamide moiety of balanol had been replaced by a methylene group. The effect of placing substituents on the three-carbon chain was also investigated. The preferred compounds contained either a 2-benzenesulfonamido (6b) or a 1-methyl (21b) substituent. The preferred compounds 6b and 21b were tested against a panel of serine/threonine kinases and found to be highly selective for PKC. The more active enantiomer of 6b, (S)-12b, was 3-10-fold more active than the R-enantiomer against the PKC isozymes. The effect of making the analogs more rigid by making the three-carbon chain part of a five-membered ring, but with retention of the methylene replacement for the carboxamide moiety, led to potent PKC inhibitors including anti-substituted pyrrolidine analog 35b and the most potent PKC inhibitor in the series, anti-substituted cyclopentane analog 29b. The anti cyclopentane analog 29b, was a low-micromolar inhibitor of the PMA-induced superoxide burst in neutrophils, and its carboxylic ester was a high-nanomolar inhibitor of neutrophils. Finally esterification of 21b, (S)-12b, and 35b turned these potent PKC inhibitors into low-micromolar inhibitors of neutrophils.
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Affiliation(s)
- J M Defauw
- Sphinx Pharmaceuticals, a Division of Eli Lilly and Company, Durham, North Carolina 27707, USA
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Tuch A, Sanière M, Le Merrer Y, Depezay JC. Synthesis of (2S,3R)-3-amino-2-hydroxydecanoic acid and (3R,4R)-3-amino-4-hydroxyazepane from D-isoascorbic acid. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/0957-4166(96)00381-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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50
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Lampe JW, Hughes PF, Biggers CK, Smith SH, Hu H. Total Synthesis of (-)- and (+)-Balanol(1). J Org Chem 1996; 61:4572-4581. [PMID: 11667382 DOI: 10.1021/jo952280k] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two total syntheses of the potent protein kinase C inhibitory fungal metabolite balanol are described. In the first approach, the core aminohydroxyazepane subunit was prepared in racemic form by stereospecific functionalization of N-benzyl-epsilon-caprolactam. Resolution prior to coupling to the benzophenone subunit provided access to both enantiomers of balanol. In the second approach, an efficient silicon-mediated cyclization of (2S,3R)-3-hydroxylysine followed by reduction provided the azepane subunit in enantiomerically pure form. The sterically congested benzophenone subunit was assembled from two highly substituted aromatic precursors by way of an anionic homo-Fries rearrangement.
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Affiliation(s)
- John W. Lampe
- Department of Chemical Research, Sphinx Pharmaceuticals, A Division of Eli Lilly and Company, 4615 University Drive, Durham, North Carolina 27707
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