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Sheikh SY, Hassan F, Shukla D, Bala S, Faruqui T, Akhter Y, Khan AR, Nasibullah M. A review on potential therapeutic targets for the treatment of leishmaniasis. Parasitol Int 2024; 100:102863. [PMID: 38272301 DOI: 10.1016/j.parint.2024.102863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 12/22/2023] [Accepted: 01/21/2024] [Indexed: 01/27/2024]
Abstract
Leishmania, a protozoan parasite, is responsible for the occurrence of leishmaniasis, a disease that is prevalent in tropical regions. Visceral Leishmaniasis (VL), also known as kala-azar in Asian countries, is one of the most significant forms of VL, along with Cutaneous Leishmaniasis (CL) and Mucocutaneous Leishmaniasis (ML). Management of this condition typically entails the use of chemotherapy as the sole therapeutic option. The current treatments for leishmaniasis present several drawbacks, including a multitude of side effects, prolonged treatment duration, disparate efficacy across different regions, and the emergence of resistance. To address this urgent need, it is imperative to identify alternative treatments that are both safer and more effective. The identification of appropriate pharmacological targets in conjunction with biological pathways constitutes the initial stage of drug discovery. In this review, we have addressed the key metabolic pathways that represent potential pharmacological targets as well as prominent treatment options for leishmaniasis.
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Affiliation(s)
- Sabahat Yasmeen Sheikh
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India
| | - Firoj Hassan
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India
| | - Deepanjali Shukla
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India
| | - Shashi Bala
- Department of Chemistry, Lucknow University, Lucknow 226026, India
| | - Tabrez Faruqui
- Department of Biosciences, Integral University, Lucknow 226026, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, India
| | - Abdul Rahman Khan
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India
| | - Malik Nasibullah
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India.
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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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Marín M, López M, Gallego-Yerga L, Álvarez R, Peláez R. Experimental structure based drug design (SBDD) applications for anti-leishmanial drugs: A paradigm shift? Med Res Rev 2024; 44:1055-1120. [PMID: 38142308 DOI: 10.1002/med.22005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Leishmaniasis is a group of neglected tropical diseases caused by at least 20 species of Leishmania protozoa, which are spread by the bite of infected sandflies. There are three main forms of the disease: cutaneous leishmaniasis (CL, the most common), visceral leishmaniasis (VL, also known as kala-azar, the most serious), and mucocutaneous leishmaniasis. One billion people live in areas endemic to leishmaniasis, with an annual estimation of 30,000 new cases of VL and more than 1 million of CL. New treatments for leishmaniasis are an urgent need, as the existing ones are inefficient, toxic, and/or expensive. We have revised the experimental structure-based drug design (SBDD) efforts applied to the discovery of new drugs against leishmaniasis. We have grouped the explored targets according to the metabolic pathways they belong to, and the key achieved advances are highlighted and evaluated. In most cases, SBDD studies follow high-throughput screening campaigns and are secondary to pharmacokinetic optimization, due to the majoritarian belief that there are few validated targets for SBDD in leishmaniasis. However, some SBDD strategies have significantly contributed to new drug candidates against leishmaniasis and a bigger number holds promise for future development.
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Affiliation(s)
- Miguel Marín
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Marta López
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Laura Gallego-Yerga
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Raquel Álvarez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
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Ma Y, Lai X, Wen Z, Zhou Z, Yang M, Chen Q, Wang X, Mei F, Yang L, Yin T, Sun S, Lu G, Qi J, Lin H, Han H, Yang Y. Design, synthesis and biological evaluation of novel modified dual-target shikonin derivatives for colorectal cancer treatment. Bioorg Chem 2023; 139:106703. [PMID: 37399615 DOI: 10.1016/j.bioorg.2023.106703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/15/2023] [Accepted: 06/25/2023] [Indexed: 07/05/2023]
Abstract
Warburg effect provides energy and material essential for tumor proliferation, the reverse of Warburg effect provides insights into the development of a novel anti-cancer strategy. Pyruvate kinase 2 (PKM2) and pyruvate dehydrogenase kinase 1 (PDK1) are two key enzymes in tumor glucose metabolism pathway that not only contribute to the Warburg effect through accelerating aerobic glycolysis, but also serve as druggable target for colorectal cancer (CRC). Considering that targeting PKM2 or PDK1 alone does not seem to be sufficient to remodel abnormal glucose metabolism and achieve significant antitumor activity, a series of novel benzenesulfonyl shikonin derivatives were designed to regulate PKM2 and PDK1 simultaneously. By means of molecular docking and antiproliferative screen, we found that compound Z10 could act as the combination of PKM2 activator and PDK1 inhibitor, thereby significantly inhibited glycolysis that reshaping tumor metabolism. Moreover, Z10 could inhibit proliferation, migration and induce apoptosis in CRC cell HCT-8. Finally, the in vivo anti-tumor activity of Z10 was evaluated in a colorectal cancer cell xenograft model in nude mice and the results demonstrated that Z10 induced tumor cell apoptosis and inhibited tumor cell proliferation with lower toxicity than shikonin. Our findings indicated that it is feasible to alter tumor energy metabolism through multi-target synergies, and the dual-target benzenesulfonyl shikonin derivative Z10 could be a potential anti-CRC agent.
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Affiliation(s)
- Yudi Ma
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaohui Lai
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; School of Biology and Geography Science, Yili Normal University, Yining 835000, China
| | - Zhongling Wen
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Ziling Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Minkai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qingqing Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xuan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Feng Mei
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Liu Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Shucun Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Guihua Lu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jinliang Qi
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyan Lin
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; School of Pharmacy, Changzhou University, Changzhou 213164, China.
| | - Hongwei Han
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Yonghua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
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Ayon NJ. High-Throughput Screening of Natural Product and Synthetic Molecule Libraries for Antibacterial Drug Discovery. Metabolites 2023; 13:625. [PMID: 37233666 PMCID: PMC10220967 DOI: 10.3390/metabo13050625] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Due to the continued emergence of resistance and a lack of new and promising antibiotics, bacterial infection has become a major public threat. High-throughput screening (HTS) allows rapid screening of a large collection of molecules for bioactivity testing and holds promise in antibacterial drug discovery. More than 50% of the antibiotics that are currently available on the market are derived from natural products. However, with the easily discoverable antibiotics being found, finding new antibiotics from natural sources has seen limited success. Finding new natural sources for antibacterial activity testing has also proven to be challenging. In addition to exploring new sources of natural products and synthetic biology, omics technology helped to study the biosynthetic machinery of existing natural sources enabling the construction of unnatural synthesizers of bioactive molecules and the identification of molecular targets of antibacterial agents. On the other hand, newer and smarter strategies have been continuously pursued to screen synthetic molecule libraries for new antibiotics and new druggable targets. Biomimetic conditions are explored to mimic the real infection model to better study the ligand-target interaction to enable the designing of more effective antibacterial drugs. This narrative review describes various traditional and contemporaneous approaches of high-throughput screening of natural products and synthetic molecule libraries for antibacterial drug discovery. It further discusses critical factors for HTS assay design, makes a general recommendation, and discusses possible alternatives to traditional HTS of natural products and synthetic molecule libraries for antibacterial drug discovery.
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Affiliation(s)
- Navid J Ayon
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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Battisti UM, Gao C, Nilsson O, Akladios F, Lulla A, Bogucka A, Nain-Perez A, Håversen L, Kim W, Boren J, Hyvönen M, Uhlen M, Mardinoglu A, Grøtli M. Serendipitous Identification of a Covalent Activator of Liver Pyruvate Kinase. Chembiochem 2023; 24:e202200339. [PMID: 36250581 PMCID: PMC10099687 DOI: 10.1002/cbic.202200339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/14/2022] [Indexed: 01/05/2023]
Abstract
Enzymes are effective biological catalysts that accelerate almost all metabolic reactions in living organisms. Synthetic modulators of enzymes are useful tools for the study of enzymatic reactions and can provide starting points for the design of new drugs. Here, we report on the discovery of a class of biologically active compounds that covalently modifies lysine residues in human liver pyruvate kinase (PKL), leading to allosteric activation of the enzyme (EC50 =0.29 μM). Surprisingly, the allosteric activation control point resides on the lysine residue K282 present in the catalytic site of PKL. These findings were confirmed by structural data, MS/MS experiments, and molecular modelling studies. Altogether, our study provides a molecular basis for the activation mechanism and establishes a framework for further development of human liver pyruvate kinase covalent activators.
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Affiliation(s)
- Umberto Maria Battisti
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Chunxia Gao
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Oscar Nilsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Fady Akladios
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Agnieszka Bogucka
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Amalyn Nain-Perez
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Liliana Håversen
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Woonghee Kim
- Science for Life Laboratory, KTH-Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Mathias Uhlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
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Arora S, Joshi G, Chaturvedi A, Heuser M, Patil S, Kumar R. A Perspective on Medicinal Chemistry Approaches for Targeting Pyruvate Kinase M2. J Med Chem 2022; 65:1171-1205. [PMID: 34726055 DOI: 10.1021/acs.jmedchem.1c00981] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The allosteric regulation of pyruvate kinase M2 (PKM2) affects the switching of the PKM2 protein between the high-activity and low-activity states that allow ATP and lactate production, respectively. PKM2, in its low catalytic state (dimeric form), is chiefly active in metabolically energetic cells, including cancer cells. More recently, PKM2 has emerged as an attractive target due to its role in metabolic dysfunction and other interrelated conditions. PKM2 (dimer) activity can be inhibited by modulating PKM2 dimer-tetramer dynamics using either PKM2 inhibitors that bind at the ATP binding active site of PKM2 (dimer) or PKM2 activators that bind at the allosteric site of PKM2, thus activating PKM2 from the dimer formation to the tetrameric formation. The present perspective focuses on medicinal chemistry approaches to design and discover PKM2 inhibitors and activators and further provides a scope for the future design of compounds targeting PKM2 with better efficacy and selectivity.
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Affiliation(s)
- Sahil Arora
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
| | - Gaurav Joshi
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
- School of Pharmacy, Graphic Era Hill University, Dehradun, Uttarakhand 248171, India
| | - Anuhar Chaturvedi
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover 30625, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover 30625, Germany
| | - Santoshkumar Patil
- Discovery Services, Syngene International Ltd., Biocon Park, SEZ, Bommasandra Industrial Area-Phase-IV, Bommasandra-Jigani Link Road, Bengaluru, Karnataka 560099, India
| | - Raj Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
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Efstathiou A, Smirlis D. Leishmania Protein Kinases: Important Regulators of the Parasite Life Cycle and Molecular Targets for Treating Leishmaniasis. Microorganisms 2021; 9:microorganisms9040691. [PMID: 33801655 PMCID: PMC8066228 DOI: 10.3390/microorganisms9040691] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
Leishmania is a protozoan parasite of the trypanosomatid family, causing a wide range of diseases with different clinical manifestations including cutaneous, mucocutaneous and visceral leishmaniasis. According to WHO, one billion people are at risk of Leishmania infection as they live in endemic areas while there are 12 million infected people worldwide. Annually, 0.9-1.6 million new infections are reported and 20-50 thousand deaths occur due to Leishmania infection. As current chemotherapy for treating leishmaniasis exhibits numerous drawbacks and due to the lack of effective human vaccine, there is an urgent need to develop new antileishmanial therapy treatment. To this end, eukaryotic protein kinases can be ideal target candidates for rational drug design against leishmaniasis. Eukaryotic protein kinases mediate signal transduction through protein phosphorylation and their inhibition is anticipated to be disease modifying as they regulate all essential processes for Leishmania viability and completion of the parasitic life cycle including cell-cycle progression, differentiation and virulence. This review highlights existing knowledge concerning the exploitation of Leishmania protein kinases as molecular targets to treat leishmaniasis and the current knowledge of their role in the biology of Leishmania spp. and in the regulation of signalling events that promote parasite survival in the insect vector or the mammalian host.
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Abdeldayem A, Raouf YS, Constantinescu SN, Moriggl R, Gunning PT. Advances in covalent kinase inhibitors. Chem Soc Rev 2020; 49:2617-2687. [DOI: 10.1039/c9cs00720b] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This comprehensive review details recent advances, challenges and innovations in covalent kinase inhibition within a 10 year period (2007–2018).
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Affiliation(s)
- Ayah Abdeldayem
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | - Yasir S. Raouf
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | | | - Richard Moriggl
- Institute of Animal Breeding and Genetics
- University of Veterinary Medicine
- 1210 Vienna
- Austria
| | - Patrick T. Gunning
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
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10
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Site-selective covalent reactions on proteinogenic amino acids. Curr Opin Biotechnol 2017; 48:220-227. [DOI: 10.1016/j.copbio.2017.06.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/05/2017] [Indexed: 11/20/2022]
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Jiao GS, Kim S, Moayeri M, Thai A, Cregar-Hernandez L, McKasson L, O'Malley S, Leppla SH, Johnson AT. Small molecule inhibitors of anthrax edema factor. Bioorg Med Chem Lett 2017; 28:134-139. [PMID: 29198864 DOI: 10.1016/j.bmcl.2017.11.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 11/19/2022]
Abstract
Anthrax is a highly lethal disease caused by the Gram-(+) bacteria Bacillus anthracis. Edema toxin (ET) is a major contributor to the pathogenesis of disease in humans exposed to B. anthracis. ET is a bipartite toxin composed of two proteins secreted by the vegetative bacteria, edema factor (EF) and protective antigen (PA). Our work towards identifying a small molecule inhibitor of anthrax edema factor is the subject of this letter. First we demonstrate that the small molecule probe 5'-Fluorosulfonylbenzoyl 5'-adenosine (FSBA) reacts irreversibly with EF and blocks enzymatic activity. We then show that the adenosine portion of FSBA can be replaced to provide more drug-like molecules which are up to 1000-fold more potent against EF relative to FSBA, display low cross reactivity when tested against a panel of kinases, and are nanomolar inhibitors of EF in a cell-based assay of cAMP production.
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Affiliation(s)
- Guan-Sheng Jiao
- Hawaii Biotech, 650 Iwilei Road, Suite 204, Honolulu, HI 96817, USA
| | - Seongjin Kim
- Hawaii Biotech, 650 Iwilei Road, Suite 204, Honolulu, HI 96817, USA
| | - Mahtab Moayeri
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - April Thai
- Hawaii Biotech, 650 Iwilei Road, Suite 204, Honolulu, HI 96817, USA
| | | | - Linda McKasson
- Hawaii Biotech, 650 Iwilei Road, Suite 204, Honolulu, HI 96817, USA
| | - Sean O'Malley
- Hawaii Biotech, 650 Iwilei Road, Suite 204, Honolulu, HI 96817, USA
| | - Stephen H Leppla
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alan T Johnson
- Hawaii Biotech, 650 Iwilei Road, Suite 204, Honolulu, HI 96817, USA.
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Pettinger J, Jones K, Cheeseman MD. Lysine-Targeting Covalent Inhibitors. Angew Chem Int Ed Engl 2017; 56:15200-15209. [PMID: 28853194 DOI: 10.1002/anie.201707630] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/23/2017] [Indexed: 12/11/2022]
Abstract
Targeted covalent inhibitors have gained widespread attention in drug discovery as a validated method to circumvent acquired resistance in oncology. This strategy exploits small-molecule/protein crystal structures to design tightly binding ligands with appropriately positioned electrophilic warheads. Whilst most focus has been on targeting binding-site cysteine residues, targeting nucleophilic lysine residues can also represent a viable approach to irreversible inhibition. However, owing to the basicity of the ϵ-amino group in lysine, this strategy generates a number of specific challenges. Herein, we review the key principles for inhibitor design, give historical examples, and present recent developments that demonstrate the potential of lysine targeting for future drug discovery.
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Affiliation(s)
- Jonathan Pettinger
- Cancer Research, UK, Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Keith Jones
- Cancer Research, UK, Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Matthew D Cheeseman
- Cancer Research, UK, Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
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13
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Affiliation(s)
- Jonathan Pettinger
- Cancer Research, UK, Cancer Therapeutics Unit; The Institute of Cancer Research; London SW7 3RP Großbritannien
| | - Keith Jones
- Cancer Research, UK, Cancer Therapeutics Unit; The Institute of Cancer Research; London SW7 3RP Großbritannien
| | - Matthew D. Cheeseman
- Cancer Research, UK, Cancer Therapeutics Unit; The Institute of Cancer Research; London SW7 3RP Großbritannien
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14
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Pettinger J, Le Bihan Y, Widya M, van Montfort RLM, Jones K, Cheeseman MD. An Irreversible Inhibitor of HSP72 that Unexpectedly Targets Lysine-56. Angew Chem Int Ed Engl 2017; 56:3536-3540. [PMID: 28225177 PMCID: PMC5412842 DOI: 10.1002/anie.201611907] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/04/2015] [Indexed: 01/08/2023]
Abstract
The stress-inducible molecular chaperone, HSP72, is an important therapeutic target in oncology, but inhibiting this protein with small molecules has proven particularly challenging. Validating HSP72 inhibitors in cells is difficult owing to competition with the high affinity and abundance of its endogenous nucleotide substrates. We hypothesized this could be overcome using a cysteine-targeted irreversible inhibitor. Using rational design, we adapted a validated 8-N-benzyladenosine ligand for covalent bond formation and confirmed targeted irreversible inhibition. However, no cysteine in the protein was modified; instead, we demonstrate that lysine-56 is the key nucleophilic residue. Targeting this lysine could lead to a new design paradigm for HSP72 chemical probes and drugs.
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Affiliation(s)
- Jonathan Pettinger
- Cancer Research UK Cancer Therapeutics UnitThe Institute of Cancer ResearchLondonSW7 3RPUK
| | - Yann‐Vaï Le Bihan
- Cancer Research UK Cancer Therapeutics UnitThe Institute of Cancer ResearchLondonSW7 3RPUK
- Division of Structural BiologyThe Institute of Cancer ResearchLondonSW7 3RPUK
| | - Marcella Widya
- Proteomics Core FacilityThe Institute of Cancer ResearchLondonSW7 3RPUK
| | - Rob L. M. van Montfort
- Cancer Research UK Cancer Therapeutics UnitThe Institute of Cancer ResearchLondonSW7 3RPUK
- Division of Structural BiologyThe Institute of Cancer ResearchLondonSW7 3RPUK
| | - Keith Jones
- Cancer Research UK Cancer Therapeutics UnitThe Institute of Cancer ResearchLondonSW7 3RPUK
| | - Matthew D. Cheeseman
- Cancer Research UK Cancer Therapeutics UnitThe Institute of Cancer ResearchLondonSW7 3RPUK
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15
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Pettinger J, Le Bihan Y, Widya M, van Montfort RLM, Jones K, Cheeseman MD. An Irreversible Inhibitor of HSP72 that Unexpectedly Targets Lysine‐56. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611907] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Jonathan Pettinger
- Cancer Research UK Cancer Therapeutics Unit The Institute of Cancer Research London SW7 3RP UK
| | - Yann‐Vaï Le Bihan
- Cancer Research UK Cancer Therapeutics Unit The Institute of Cancer Research London SW7 3RP UK
- Division of Structural Biology The Institute of Cancer Research London SW7 3RP UK
| | - Marcella Widya
- Proteomics Core Facility The Institute of Cancer Research London SW7 3RP UK
| | - Rob L. M. van Montfort
- Cancer Research UK Cancer Therapeutics Unit The Institute of Cancer Research London SW7 3RP UK
- Division of Structural Biology The Institute of Cancer Research London SW7 3RP UK
| | - Keith Jones
- Cancer Research UK Cancer Therapeutics Unit The Institute of Cancer Research London SW7 3RP UK
| | - Matthew D. Cheeseman
- Cancer Research UK Cancer Therapeutics Unit The Institute of Cancer Research London SW7 3RP UK
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16
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Merritt C, Silva L, Tanner AL, Stuart K, Pollastri MP. Kinases as druggable targets in trypanosomatid protozoan parasites. Chem Rev 2014; 114:11280-304. [PMID: 26443079 PMCID: PMC4254031 DOI: 10.1021/cr500197d] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Christopher Merritt
- Seattle
Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109-5219, United States
| | - Lisseth
E. Silva
- Department
of Chemistry & Chemical Biology, Northeastern
University, 417 Egan
Research Center, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Angela L. Tanner
- Department
of Chemistry & Chemical Biology, Northeastern
University, 417 Egan
Research Center, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Kenneth Stuart
- Seattle
Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109-5219, United States
| | - Michael P. Pollastri
- Department
of Chemistry & Chemical Biology, Northeastern
University, 417 Egan
Research Center, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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Morgan HP, Zhong W, McNae IW, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. Structures of pyruvate kinases display evolutionarily divergent allosteric strategies. ROYAL SOCIETY OPEN SCIENCE 2014; 1:140120. [PMID: 26064527 PMCID: PMC4448766 DOI: 10.1098/rsos.140120] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 08/11/2014] [Indexed: 05/13/2023]
Abstract
The transition between the inactive T-state (apoenzyme) and active R-state (effector bound enzyme) of Trypanosoma cruzi pyruvate kinase (PYK) is accompanied by a symmetrical 8° rigid body rocking motion of the A- and C-domain cores in each of the four subunits, coupled with the formation of additional salt bridges across two of the four subunit interfaces. These salt bridges provide increased tetramer stability correlated with an enhanced specificity constant (k cat/S 0.5). A detailed kinetic and structural comparison between the potential drug target PYKs from the pathogenic protists T. cruzi, T. brucei and Leishmania mexicana shows that their allosteric mechanism is conserved. By contrast, a structural comparison of trypanosomatid PYKs with the evolutionarily divergent PYKs of humans and of bacteria shows that they have adopted different allosteric strategies. The underlying principle in each case is to maximize (k cat/S 0.5) by stabilizing and rigidifying the tetramer in an active R-state conformation. However, bacterial and mammalian PYKs have evolved alternative ways of locking the tetramers together. In contrast to the divergent allosteric mechanisms, the PYK active sites are highly conserved across species. Selective disruption of the varied allosteric mechanisms may therefore provide a useful approach for the design of species-specific inhibitors.
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Smirlis D, Soares MBP. Selection of molecular targets for drug development against trypanosomatids. Subcell Biochem 2014; 74:43-76. [PMID: 24264240 DOI: 10.1007/978-94-007-7305-9_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Trypanosomatid parasites are a group of flagellated protozoa that includes the genera Leishmania and Trypanosoma, which are the causative agents of diseases (leishmaniases, sleeping sickness and Chagas disease) that cause considerable morbidity and mortality, affecting more than 27 million people worldwide. Today no effective vaccines for the prevention of these diseases exist, whereas current chemotherapy is ineffective, mainly due to toxic side effects of current drugs and to the emergence of drug resistance and lack of cost effectiveness. For these reasons, rational drug design and the search of good candidate drug targets is of prime importance. The search for drug targets requires a multidisciplinary approach. To this end, the completion of the genome project of many trypanosomatid species gives a vast amount of new information that can be exploited for the identification of good drug candidates with a prediction of "druggability" and divergence from mammalian host proteins. In addition, an important aspect in the search for good drug targets is the "target identification" and evaluation in a biological pathway, as well as the essentiality of the gene in the mammalian stage of the parasite, which is provided by basic research and genetic and proteomic approaches. In this chapter we will discuss how these bioinformatic tools and experimental evaluations can be integrated for the selection of candidate drug targets, and give examples of metabolic and signaling pathways in the parasitic protozoa that can be exploited for rational drug design.
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Mah R, Thomas JR, Shafer CM. Drug discovery considerations in the development of covalent inhibitors. Bioorg Med Chem Lett 2013; 24:33-9. [PMID: 24314671 DOI: 10.1016/j.bmcl.2013.10.003] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/27/2013] [Accepted: 10/01/2013] [Indexed: 12/31/2022]
Abstract
In recent years, the number of drug candidates with a covalent mechanism of action progressing through clinical trials or being approved by the FDA has increased significantly. And as interest in covalent inhibitors has increased, the technical challenges for characterizing and optimizing these inhibitors have become evident. A number of new tools have been developed to aid this process, but these have not gained wide-spread use. This review will highlight a number of methods and tools useful for prosecuting covalent inhibitor drug discovery programs.
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Affiliation(s)
- Robert Mah
- Global Discovery Chemistry/Oncology & Exploratory Chemistry, Novartis Institutes for Biomedical Research, Klybeckstrasse 141, CH-4057 Basel, Switzerland
| | - Jason R Thomas
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Cynthia M Shafer
- Global Discovery Chemistry/Oncology & Exploratory Chemistry, Novartis Institutes for Biomedical Research, 4560 Horton Street, Emeryville, CA 94608, USA.
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In-silico Leishmania target selectivity of antiparasitic terpenoids. Molecules 2013; 18:7761-847. [PMID: 23823876 PMCID: PMC6270436 DOI: 10.3390/molecules18077761] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/23/2013] [Accepted: 06/26/2013] [Indexed: 01/21/2023] Open
Abstract
Neglected Tropical Diseases (NTDs), like leishmaniasis, are major causes of mortality in resource-limited countries. The mortality associated with these diseases is largely due to fragile healthcare systems, lack of access to medicines, and resistance by the parasites to the few available drugs. Many antiparasitic plant-derived isoprenoids have been reported, and many of them have good in vitro activity against various forms of Leishmania spp. In this work, potential Leishmania biochemical targets of antiparasitic isoprenoids were studied in silico. Antiparasitic monoterpenoids selectively docked to L. infantum nicotinamidase, L. major uridine diphosphate-glucose pyrophosphorylase and methionyl t-RNA synthetase. The two protein targets selectively targeted by germacranolide sesquiterpenoids were L. major methionyl t-RNA synthetase and dihydroorotate dehydrogenase. Diterpenoids generally favored docking to L. mexicana glycerol-3-phosphate dehydrogenase. Limonoids also showed some selectivity for L. mexicana glycerol-3-phosphate dehydrogenase and L. major dihydroorotate dehydrogenase while withanolides docked more selectively with L. major uridine diphosphate-glucose pyrophosphorylase. The selectivity of the different classes of antiparasitic compounds for the protein targets considered in this work can be explored in fragment- and/or structure-based drug design towards the development of leads for new antileishmanial drugs.
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Johns MA. ICBS2012 catalyzes robust response from global chemical biology community. ACS Chem Biol 2013; 8:12-8. [PMID: 23273421 DOI: 10.1021/cb3007049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Margaret A. Johns
- Emory Chemical Biology
Discovery Center, Emory University, Atlanta,
Georgia 30322 , United States
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