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Acharya B, Saha D, Armstrong D, Jabali B, Hanafi M, Herrera-Rueda A, Lakkaniga NR, Frett B. Kinase inhibitor macrocycles: a perspective on limiting conformational flexibility when targeting the kinome with small molecules. RSC Med Chem 2024; 15:399-415. [PMID: 38389874 PMCID: PMC10880908 DOI: 10.1039/d3md00457k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/10/2023] [Indexed: 02/24/2024] Open
Abstract
Methods utilized for drug discovery and development within the kinome have rapidly evolved since the approval of imatinib, the first small molecule kinase inhibitor. Macrocycles have received increasing interest as a technique to improve kinase inhibitor drug properties evident by the FDA approvals of lorlatinib, pacritinib, and repotrectinib. Compared to their acyclic counterparts, macrocycles can possess improved pharmacodynamic and pharmacokinetic properties. This review highlights clinical success stories when implementing macrocycles in kinase-based drug discovery and showcases that macrocyclization is a clinically validated drug discovery strategy when targeting the kinome.
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Affiliation(s)
- Baku Acharya
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| | - Debasmita Saha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
- Conrad Prebys Centre for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute San Diego CA USA
| | - Daniel Armstrong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| | - Baha'a Jabali
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| | - Maha Hanafi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University Cairo 11526 Egypt
| | - Alan Herrera-Rueda
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| | - Naga Rajiv Lakkaniga
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
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2
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Jachak GR, Kashinath K, Vasudevan N, Athawale PR, Choudhury R, Dange SS, Agarwal H, Barthwal MK, Reddy DS. Comprehensive Study on Solomonamides: Total Synthesis, Stereochemical Revision, and SAR Studies toward Identification of Simplified Lead. J Org Chem 2023; 88:17088-17133. [PMID: 38051995 DOI: 10.1021/acs.joc.3c01987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Solomonamides, a pair of macrocyclic peptide natural products originating from marine sources, have garnered significant attention within the synthetic community owing to their marked anti-inflammatory efficacy and intricate molecular architectures. In this paper, we present a very detailed investigation into solomonamides, including the challenges associated with the total synthesis, the evolution of our synthetic strategies, structural reassignment, synthesis of all possible stereoisomeric macrocycles, biological assessment, structure-activity relationship (SAR) studies, etc. Within the ambit of this total synthesis, diverse strategies for macrocyclization were rigorously explored, encompassing the Friedel-Crafts acylation, cyclization involving the aniline NH2 moiety, macrolactamization utilizing Gly-NH2, and Heck macrocyclization methodologies. In addition, an array of intriguing chemical transformations were devised, including but not limited to photo-Fries rearrangement, Wacker oxidation, ligand-free Heck macrocyclization, oxidative cleavage of indole, synthesis of contiguous stereocenters via substrate/reagent-controlled protocols, and simultaneous making and breaking of olefinic moieties. The findings of this investigation revealed a structurally simplified lead compound. Remarkably, the lead compound, while possessing structural simplification in comparison to the intricate solomonamide counterparts, demonstrates equipotent in vivo anti-inflammatory efficacy.
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Affiliation(s)
- Gorakhnath R Jachak
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - K Kashinath
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - N Vasudevan
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Paresh R Athawale
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rahul Choudhury
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Santoshkumar S Dange
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Heena Agarwal
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Pharmacology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India
| | - Manoj Kumar Barthwal
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Pharmacology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India
| | - D Srinivasa Reddy
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
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3
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Davis F, Higson SPJ. Synthetic Receptors for Early Detection and Treatment of Cancer. BIOSENSORS 2023; 13:953. [PMID: 37998127 PMCID: PMC10669836 DOI: 10.3390/bios13110953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/10/2023] [Accepted: 10/22/2023] [Indexed: 11/25/2023]
Abstract
Over recent decades, synthetic macrocyclic compounds have attracted interest from the scientific community due to their ability to selectively and reversibly form complexes with a huge variety of guest moieties. These molecules have been studied within a wide range of sensing and other fields. Within this review, we will give an overview of the most common synthetic macrocyclic compounds including cyclodextrins, calixarenes, calixresorcinarenes, pillarenes and cucurbiturils. These species all display the ability to form a wide range of complexes. This makes these compounds suitable in the field of cancer detection since they can bind to either cancer cell surfaces or indeed to marker compounds for a wide variety of cancers. The formation of such complexes allows sensitive and selective detection and quantification of such guests. Many of these compounds also show potential for the detection and encapsulation of environmental carcinogens. Furthermore, many anti-cancer drugs, although effective in in vitro tests, are not suitable for use directly for cancer treatment due to low solubility, inherent instability in in vivo environments or an inability to be adsorbed by or transported to the required sites for treatment. The reversible encapsulation of these species in a macrocyclic compound can greatly improve their solubility, stability and transport to required sites where they can be released for maximum therapeutic effect. Within this review, we intend to present the use of these species both in cancer sensing and treatment. The various macrocyclic compound families will be described, along with brief descriptions of their synthesis and properties, with an outline of their use in cancer detection and usage as therapeutic agents. Their use in the sensing of environmental carcinogens as well as their potential utilisation in the clean-up of some of these species will also be discussed.
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Affiliation(s)
| | - Séamus P. J. Higson
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK;
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4
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Bhujbal SP, Hah JM. An Intriguing Purview on the Design of Macrocyclic Inhibitors for Unexplored Protein Kinases through Their Binding Site Comparison. Pharmaceuticals (Basel) 2023; 16:1009. [PMID: 37513921 PMCID: PMC10386424 DOI: 10.3390/ph16071009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/02/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Kinases play an important role in regulating various intracellular signaling pathways that control cell proliferation, differentiation, survival, and other cellular processes, and their deregulation causes more than 400 diseases. Consequently, macrocyclization can be considered a noteworthy approach to developing new therapeutic agents for human diseases. Macrocyclization has emerged as an effective drug discovery strategy over the past decade to improve target selectivity and potency of small molecules. Small compounds with linear structures upon macrocyclization can lead to changes in their physicochemical and biological properties by firmly reducing conformational flexibility. A number of distinct protein kinases exhibit similar binding sites. Comparison of protein binding sites provides crucial insights for drug discovery and development. Binding site similarities are helpful in understanding polypharmacology, identifying potential off-targets, and repurposing known drugs. In this review, we focused on comparing the binding sites of those kinases for which macrocyclic inhibitors are available/studied so far. Furthermore, we calculated the volume of the binding site pocket for each targeted kinase and then compared it with the binding site pocket of the kinase for which only acyclic inhibitors were designed to date. Our review and analysis of several explored kinases might be useful in targeting new protein kinases for macrocyclic drug discovery.
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Affiliation(s)
- Swapnil P Bhujbal
- College of Pharmacy, Hanyang University, Ansan 426-791, Republic of Korea
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Republic of Korea
| | - Jung-Mi Hah
- College of Pharmacy, Hanyang University, Ansan 426-791, Republic of Korea
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Republic of Korea
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Amrhein J, Wang G, Berger BT, Berger LM, Kalampaliki AD, Krämer A, Knapp S, Hanke T. Design and Synthesis of Pyrazole-Based Macrocyclic Kinase Inhibitors Targeting BMPR2. ACS Med Chem Lett 2023; 14:833-840. [PMID: 37312836 PMCID: PMC10258821 DOI: 10.1021/acsmedchemlett.3c00127] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/22/2023] [Indexed: 06/15/2023] Open
Abstract
Bone morphogenetic protein (BMP) signaling is mediated by transmembrane protein kinases that form heterotetramers consisting of type-I and type-II receptors. Upon BMP binding, the constitutively active type-II receptors activate specific type-I receptors by transphosphorylation, resulting in the phosphorylation of SMAD effector proteins. Drug discovery in the receptor tyrosine kinase-like (TKL) family has largely focused on type-I receptors, with few inhibitors that have been published targeting type-II receptors. BMPR2 is involved in several diseases, most notably pulmonary arterial hypertension, but also contributes to Alzheimer's disease and cancer. Here, we report that macrocyclization of the promiscuous inhibitor 1, based on a 3-amino-1H-pyrazole hinge binding moiety, led to a selective and potent BMPR2 inhibitor 8a.
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Affiliation(s)
- Jennifer
A. Amrhein
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Guiqun Wang
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
- German
Cancer Consortium (DKTK), German Cancer
Research Center (DKFZ), DKTK Site Frankfurt-Mainz, 69120 Heidelberg, Germany
| | - Benedict-Tilman Berger
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Lena M. Berger
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Amalia D. Kalampaliki
- Department
of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Andreas Krämer
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
- German
Cancer Consortium (DKTK), German Cancer
Research Center (DKFZ), DKTK Site Frankfurt-Mainz, 69120 Heidelberg, Germany
| | - Stefan Knapp
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
- German
Cancer Consortium (DKTK), German Cancer
Research Center (DKFZ), DKTK Site Frankfurt-Mainz, 69120 Heidelberg, Germany
| | - Thomas Hanke
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
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Cai J, Sun B, Yu S, Zhang H, Zhang W. Heck Macrocyclization in Forging Non-Natural Large Rings including Macrocyclic Drugs. Int J Mol Sci 2023; 24:ijms24098252. [PMID: 37175956 PMCID: PMC10179193 DOI: 10.3390/ijms24098252] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
The intramolecular Heck reaction is a well-established strategy for natural product total synthesis. When constructing large rings, this reaction is also referred to as Heck macrocyclization, which has proved a viable avenue to access diverse naturally occurring macrocycles. Less noticed but likewise valuable, it has created novel macrocycles of non-natural origin that neither serve as nor derive from natural products. This review presents a systematic account of the title reaction in forging this non-natural subset of large rings, thereby addressing a topic rarely covered in the literature. Walking through two complementary sections, namely (1) drug discovery research and (2) synthetic methodology development, it demonstrates that beyond the well-known domain of natural product synthesis, Heck macrocyclization also plays a remarkable role in forming synthetic macrocycles, in particular macrocyclic drugs.
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Affiliation(s)
- Jiayou Cai
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China
| | - Bin Sun
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China
| | - Siqi Yu
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China
| | - Han Zhang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China
| | - Weicheng Zhang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China
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