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Kancharla P, Ortiz D, Fargo CM, Zhang X, Li Y, Sanchez M, Kumar A, Yeluguri M, Dodean RA, Caridha D, Madejczyk MS, Martin M, Jin X, Blount C, Chetree R, Pannone K, Dinh HT, DeLuca J, Evans M, Nadeau R, Vuong C, Leed S, Dennis WE, Roncal N, Pybus BS, Lee PJ, Roth A, Reynolds KA, Kelly JX, Landfear SM. Discovery and Optimization of Tambjamines as a Novel Class of Antileishmanial Agents. J Med Chem 2024; 67:8323-8345. [PMID: 38722757 PMCID: PMC11163866 DOI: 10.1021/acs.jmedchem.4c00517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Leishmaniasis is a neglected tropical disease that is estimated to afflict over 12 million people. Current drugs for leishmaniasis suffer from serious deficiencies, including toxicity, high cost, modest efficacy, primarily parenteral delivery, and emergence of widespread resistance. We have discovered and developed a natural product-inspired tambjamine chemotype, known to be effective against Plasmodium spp, as a novel class of antileishmanial agents. Herein, we report in vitro and in vivo antileishmanial activities, detailed structure-activity relationships, and metabolic/pharmacokinetic profiles of a large library of tambjamines. A number of tambjamines exhibited excellent potency against both Leishmania mexicana and Leishmania donovani parasites with good safety and metabolic profiles. Notably, tambjamine 110 offered excellent potency and provided partial protection to leishmania-infected mice at 40 and/or 60 mg/kg/10 days of oral treatment. This study presents the first account of antileishmanial activity in the tambjamine family and paves the way for the generation of new oral antileishmanial drugs.
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Affiliation(s)
- Papireddy Kancharla
- Department of Chemistry, Portland State University, Portland, Oregon 97201, United States
| | - Diana Ortiz
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, 97239, United States
| | - Corinne M. Fargo
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, 97239, United States
| | - Xiaowei Zhang
- Department of Veterans Affairs Medical Center, Portland, Oregon 97239, United States
| | - Yuexin Li
- Department of Veterans Affairs Medical Center, Portland, Oregon 97239, United States
| | - Marco Sanchez
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, 97239, United States
| | - Amrendra Kumar
- Department of Chemistry, Portland State University, Portland, Oregon 97201, United States
| | - Monish Yeluguri
- Department of Chemistry, Portland State University, Portland, Oregon 97201, United States
| | - Rozalia A. Dodean
- Department of Chemistry, Portland State University, Portland, Oregon 97201, United States
| | - Diana Caridha
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Michael S. Madejczyk
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Monica Martin
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Xiannu Jin
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Cameron Blount
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Ravi Chetree
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Kristina Pannone
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Hieu T. Dinh
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Jesse DeLuca
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Martin Evans
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Robert Nadeau
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Chau Vuong
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Susan Leed
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - William E. Dennis
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Norma Roncal
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Brandon S. Pybus
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Patricia J. Lee
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Alison Roth
- Experimental Therapeutics Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Kevin A. Reynolds
- Department of Chemistry, Portland State University, Portland, Oregon 97201, United States
| | - Jane X. Kelly
- Department of Chemistry, Portland State University, Portland, Oregon 97201, United States
- Department of Veterans Affairs Medical Center, Portland, Oregon 97239, United States
| | - Scott M. Landfear
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, 97239, United States
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2
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Diaz AP, Canal CAM, Valdés AJ, Delgado JEG, Varela-M RE. GSK-3 kinase a putative therapeutic target in trypanosomatid parasites. Braz J Infect Dis 2024; 28:103736. [PMID: 38467387 PMCID: PMC10955101 DOI: 10.1016/j.bjid.2024.103736] [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: 10/30/2023] [Revised: 02/11/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Trypanosomatids are an important group of parasites that predominate in tropical and subtropical areas of the planet, which cause diseases that are classified as forgotten and neglected by the world health organization. In this group of parasites, we find Trypanosoma cruzi, Trypanosoma brucei, Trypanosoma brucei rhodesiense and Leishmania spp, for which there is no vaccine available, and its control has focused mainly on pharmacological treatment. Due to the poverty situation where these diseases are found and the biological complexity of these parasites, there are multiple variables to control, including the diversity of species, the complexity of their life cycles, drug resistance, cytotoxicity, the limited use in pregnant women, the high costs of treatment and the little-known pharmacological mechanisms of action, among others. It is therefore necessary to find new strategies and approaches for the treatment of these parasitic diseases. Among these new approaches is the rational search for new targets based on the allosteric inhibition of protein kinases, which have been little studied in trypanosomatids. Among these kinases, we find Glycogen Synthase Kinase-3 (GSK-3), a kinase of great pharmacological interest, which is under intense basic and clinical research by pharmaceutical companies for the treatment of cancer. This kinase, highly studied in the PI3K/AKT/mTOR pathway signaling in humans, has an orthologous gene in these parasites (GSK-3 s), which has proven to be essential for them in response to different challenges; Therefore, it is notable to increase research in this kinase in order to achieve a broad structural and functional characterization in the different species of trypanosomatids.
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Affiliation(s)
| | | | | | | | - R E Varela-M
- Laboratory of Parasitology and Tropical Diseases, Faculty of Basic Sciences, Universidad Santiago de Cali, Cali, Colombia.
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Saldivia M, Lima APCA, Mottram JC. A promising pipeline of preclinical drug candidates for leishmaniasis and chronic Chagas' disease. Trends Parasitol 2024; 40:211-213. [PMID: 38368155 DOI: 10.1016/j.pt.2024.02.002] [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: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/19/2024]
Abstract
The drug discovery pipeline for leishmaniasis and trypanosomiasis has been filling with novel chemical entities with known mechanisms of action. González et al. and Braillard et al. report a cytochrome bc1 complex inhibitor as another promising preclinical candidate for visceral leishmaniasis (VL) and, in combination with benznidazole, for chronic Chagas' disease (CCD).
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Affiliation(s)
| | - Ana Paula C A Lima
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jeremy C Mottram
- York Biomedical Research Institute and Department of Biology, University of York, York, UK.
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4
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He Z, Wu M, Tian H, Wang L, Hu Y, Han F, Zhou J, Wang Y, Zhou L. Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism. Nat Commun 2024; 15:1628. [PMID: 38388527 PMCID: PMC10884005 DOI: 10.1038/s41467-024-46018-z] [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: 10/06/2023] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron transport chain. While structures of the electron transport chain complexes and supercomplexes of most other eukaryotic clades have been reported, no similar structure is currently available for Discoba, limiting the understandings of its core metabolism and leaving a gap in the evolutionary tree of eukaryotic bioenergetics. Here, we report high-resolution cryo-EM structures of Euglena's respirasome I + III2 + IV and supercomplex III2 + IV2. A previously unreported fatty acid synthesis domain locates on the tip of complex I's peripheral arm, providing a clear picture of its atypical subunit composition identified previously. Individual complexes are re-arranged in the respirasome to adapt to the non-uniform membrane curvature of the discoidal cristae. Furthermore, Euglena's conformationally rigid complex I is deactivated by restricting ubiquinone's access to its substrate tunnel. Our findings provide structural insights for therapeutic developments against euglenozoan parasite infections.
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Affiliation(s)
- Zhaoxiang He
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Mengchen Wu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hongtao Tian
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Liangdong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yiqi Hu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Fangzhu Han
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jiancang Zhou
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, China.
| | - Long Zhou
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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5
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González S, Wall RJ, Thomas J, Braillard S, Brunori G, Díaz IC, Cantizani J, Carvalho S, Castañeda Casado P, Chatelain E, Cotillo I, Fiandor JM, Francisco AF, Grimsditch D, Keenan M, Kelly JM, Kessler A, Luise C, Lyon JJ, MacLean L, Marco M, Martin JJ, Martinez MS, Paterson C, Read KD, Santos-Villarejo A, Zuccotto F, Wyllie S, Miles TJ, De Rycker M. Short-course combination treatment for experimental chronic Chagas disease. Sci Transl Med 2023; 15:eadg8105. [PMID: 38091410 PMCID: PMC7615676 DOI: 10.1126/scitranslmed.adg8105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023]
Abstract
Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, affects millions of people in the Americas and across the world, leading to considerable morbidity and mortality. Current treatment options, benznidazole (BNZ) and nifurtimox, offer limited efficacy and often lead to adverse side effects because of long treatment durations. Better treatment options are therefore urgently required. Here, we describe a pyrrolopyrimidine series, identified through phenotypic screening, that offers an opportunity to improve on current treatments. In vitro cell-based washout assays demonstrate that compounds in the series are incapable of killing all parasites; however, combining these pyrrolopyrimidines with a subefficacious dose of BNZ can clear all parasites in vitro after 5 days. These findings were replicated in a clinically predictive in vivo model of chronic Chagas disease, where 5 days of treatment with the combination was sufficient to prevent parasite relapse. Comprehensive mechanism of action studies, supported by ligand-structure modeling, show that compounds from this pyrrolopyrimidine series inhibit the Qi active site of T. cruzi cytochrome b, part of the cytochrome bc1 complex of the electron transport chain. Knowledge of the molecular target enabled a cascade of assays to be assembled to evaluate selectivity over the human cytochrome b homolog. As a result, a highly selective and efficacious lead compound was identified. The combination of our lead compound with BNZ rapidly clears T. cruzi parasites, both in vitro and in vivo, and shows great potential to overcome key issues associated with currently available treatments.
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Affiliation(s)
- Silvia González
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | - Richard J. Wall
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - John Thomas
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | | | | | | | - Juan Cantizani
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | - Sandra Carvalho
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | | | | | - Ignacio Cotillo
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | - Jose M. Fiandor
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | | | | | | | - John M. Kelly
- London School for Hygiene and Tropical Medicine, London, UK
| | - Albane Kessler
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | - Chiara Luise
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | | | - Lorna MacLean
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Maria Marco
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | - J. Julio Martin
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | | | - Christy Paterson
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Kevin D. Read
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | | | - Fabio Zuccotto
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Susan Wyllie
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Tim J. Miles
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | - Manu De Rycker
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
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Braillard S, Keenan M, Breese KJ, Heppell J, Abbott M, Islam R, Shackleford DM, Katneni K, Crighton E, Chen G, Patil R, Lee G, White KL, Carvalho S, Wall RJ, Chemi G, Zuccotto F, González S, Marco M, Deakyne J, Standing D, Brunori G, Lyon JJ, Castañeda Casado P, Camino I, Martinez MSM, Zulfiqar B, Avery VM, Feijens PB, Van Pelt N, Matheeussen A, Hendrickx S, Maes L, Caljon G, Yardley V, Wyllie S, Charman SA, Chatelain E. DNDI-6174 is a preclinical candidate for visceral leishmaniasis that targets the cytochrome bc 1. Sci Transl Med 2023; 15:eadh9902. [PMID: 38091406 PMCID: PMC7615677 DOI: 10.1126/scitranslmed.adh9902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/12/2023] [Indexed: 12/18/2023]
Abstract
New drugs for visceral leishmaniasis that are safe, low cost, and adapted to the field are urgently required. Despite concerted efforts over the last several years, the number of new chemical entities that are suitable for clinical development for the treatment of Leishmania remains low. Here, we describe the discovery and preclinical development of DNDI-6174, an inhibitor of Leishmania cytochrome bc1 complex activity that originated from a phenotypically identified pyrrolopyrimidine series. This compound fulfills all target candidate profile criteria required for progression into preclinical development. In addition to good metabolic stability and pharmacokinetic properties, DNDI-6174 demonstrates potent in vitro activity against a variety of Leishmania species and can reduce parasite burden in animal models of infection, with the potential to approach sterile cure. No major flags were identified in preliminary safety studies, including an exploratory 14-day toxicology study in the rat. DNDI-6174 is a cytochrome bc1 complex inhibitor with acceptable development properties to enter preclinical development for visceral leishmaniasis.
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Affiliation(s)
- Stéphanie Braillard
- Drugs for Neglected Diseases initiative (DNDi), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | | | | | - Jacob Heppell
- Epichem Pty Ltd, Perth, Western Australia, Australia
| | | | - Rafiqul Islam
- Epichem Pty Ltd, Perth, Western Australia, Australia
| | - David M. Shackleford
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Elly Crighton
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Rahul Patil
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Given Lee
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Karen L. White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Sandra Carvalho
- Wellcome Centre for Anti-infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Richard J. Wall
- Wellcome Centre for Anti-infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Giulia Chemi
- Drug Discovery Unit, Wellcome Centre for Anti-infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Fabio Zuccotto
- Drug Discovery Unit, Wellcome Centre for Anti-infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Silvia González
- Global Health Medicines R&D, GlaxoSmithKline, Tres Cantos, Madrid 28760, Spain
| | - Maria Marco
- Global Health Medicines R&D, GlaxoSmithKline, Tres Cantos, Madrid 28760, Spain
| | | | | | - Gino Brunori
- Global Investigative Safety, GSK, Ware, United Kingdom
| | | | | | | | | | - Bilal Zulfiqar
- Discovery Biology, Griffith University, Nathan, Queensland, Australia 4111
| | - Vicky M. Avery
- Discovery Biology, Griffith University, Nathan, Queensland, Australia 4111
| | - Pim-Bart Feijens
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Natascha Van Pelt
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - An Matheeussen
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Sarah Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Vanessa Yardley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Susan Wyllie
- Wellcome Centre for Anti-infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Susan A. Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Eric Chatelain
- Drugs for Neglected Diseases initiative (DNDi), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
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Tulloch LB, Carvalho S, Lima M, Wall RJ, Tinti M, Pinto EG, MacLean L, Wyllie S. RES-Seq-a barcoded library of drug-resistant Leishmania donovani allowing rapid assessment of cross-resistance and relative fitness. mBio 2023; 14:e0180323. [PMID: 37929970 PMCID: PMC10746238 DOI: 10.1128/mbio.01803-23] [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: 07/16/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
Visceral leishmaniasis (VL) is a parasitic disease endemic across multiple regions of the world and is fatal if untreated. New therapeutic options with diverse mechanisms of actions (MoAs) are required to consolidate progress toward control of this disease and combat drug resistance. Here, we describe the development of a scalable resistance library screen (RES-Seq) as a tool to facilitate the identification and prioritization of anti-leishmanial compounds acting via novel MoA. We have amassed a large collection of Leishmania donovani cell lines resistant to frontline drugs and compounds in the VL pipeline, with resistance-conferring mutations fully characterized. New phenotypic hits screened against this highly curated panel of resistant lines can determine cross-resistance and potentially shared MoA. The ability to efficiently identify compounds acting via previously established MoA is vital to maintain diversity within drug development portfolios. To expedite screening, short identifier DNA barcodes were introduced into resistant clones enabling pooling and simultaneous screening of multiple cell lines. Illumina sequencing of barcodes enables the growth kinetics and relative fitness of multiple cell lines under compound selection to be tracked. Optimal conditions allowing discrimination of resistant and sensitive clones were established (3× and 10× EC50 for 3 days) and applied to screening of a complex library with VL preclinical and clinical drug candidates. RES-Seq is set to play an important role in ensuring that anti-leishmanial compounds exploiting diverse mechanisms of action are developed, ultimately providing options for future drug combination strategies.IMPORTANCEVisceral leishmaniasis (VL) remains the third largest parasitic killer worldwide, responsible for 20,000-30,000 deaths each year. Control and ultimate elimination of VL will require a range of therapeutic options with diverse mechanisms of action to combat drug resistance. One approach to ensure that compounds in development exploit diverse mechanisms of action is to screen them against highly curated cell lines resistant to drugs already in the VL pipeline. The identification of cross-resistant cell lines indicates that test compounds are likely acting via previously established mechanisms. Current cross-resistance screens are limited by the requirement to profile individual resistant cell lines one at a time. Here, we introduce unique DNA barcodes into multiple resistant cell lines to facilitate parallel profiling. Utilizing the power of Illumina sequencing, growth kinetics and relative fitness under compound selection can be monitored revolutionizing our ability to identify and prioritize compounds acting via novel mechanisms.
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Affiliation(s)
- Lindsay B. Tulloch
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Sandra Carvalho
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Marta Lima
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Richard J. Wall
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michele Tinti
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Erika G. Pinto
- Drug Discovery Unit, Wellcome Centre for Anti-infectives Research, University of Dundee, Dundee, United Kingdom
| | - Lorna MacLean
- Drug Discovery Unit, Wellcome Centre for Anti-infectives Research, University of Dundee, Dundee, United Kingdom
| | - Susan Wyllie
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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8
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Laureano de Souza M, Lapierre TJWJD, Vitor de Lima Marques G, Ferraz WR, Penteado AB, Henrique Goulart Trossini G, Murta SMF, de Oliveira RB, de Oliveira Rezende C, Ferreira RS. Molecular targets for Chagas disease: validation, challenges and lead compounds for widely exploited targets. Expert Opin Ther Targets 2023; 27:911-925. [PMID: 37772733 DOI: 10.1080/14728222.2023.2264512] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/24/2023] [Indexed: 09/30/2023]
Abstract
INTRODUCTION Chagas disease (CD) imposes social and economic burdens, yet the available treatments have limited efficacy in the disease's chronic phase and cause serious adverse effects. To address this challenge, target-based approaches are a possible strategy to develop new, safe, and active treatments for both phases of the disease. AREAS COVERED This review delves into target-based approaches applied to CD drug discovery, emphasizing the studies from the last five years. We highlight the proteins cruzain (CZ), trypanothione reductase (TR), sterol 14 α-demethylase (CPY51), iron superoxide dismutase (Fe-SOD), proteasome, cytochrome b (Cytb), and cleavage and polyadenylation specificity factor 3 (CPSF3), chosen based on their biological and chemical validation as drug targets. For each, we discuss its biological relevance and validation as a target, currently related challenges, and the status of the most promising inhibitors. EXPERT OPINION Target-based approaches toward developing potential CD therapeutics have yielded promising leads in recent years. We expect a significant advance in this field in the next decade, fueled by the new options for Trypanosoma cruzi genetic manipulation that arose in the past decade, combined with recent advances in computational chemistry and chemical biology.
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Affiliation(s)
- Mariana Laureano de Souza
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Gabriel Vitor de Lima Marques
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Witor Ribeiro Ferraz
- Departamento de Farmacia, Faculdade de Ciencias Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - André Berndt Penteado
- Departamento de Farmacia, Faculdade de Ciencias Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Renata Barbosa de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
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9
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Kruth S, Nett M. Aurachins, Bacterial Antibiotics Interfering with Electron Transport Processes. Antibiotics (Basel) 2023; 12:1067. [PMID: 37370386 DOI: 10.3390/antibiotics12061067] [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: 05/31/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Aurachins are farnesylated quinolone alkaloids of bacterial origin and excellent inhibitors of the respiratory chain in pro- and eukaryotes. Therefore, they have become important tool compounds for the investigation of electron transport processes and they also serve as lead structures for the development of antibacterial and antiprotozoal drugs. Especially aurachin D proved to be a valuable starting point for structure-activity relationship studies. Aurachin D is a selective inhibitor of the cytochrome bd oxidase, which has received increasing attention as a target for the treatment of infectious diseases caused by mycobacteria. Moreover, aurachin D possesses remarkable activities against Leishmania donovani, the causative agent of leishmaniasis. Aurachins are naturally produced by myxobacteria of the genus Stigmatella as well as by some Streptomyces and Rhodococcus strains. The recombinant production of these antibiotics turned out to be challenging due to their complex biosynthesis and their inherent toxicity. Recently, the biotechnological production of aurachin D was established in E. coli with a titer which is higher than previously reported from natural producer organisms.
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Affiliation(s)
- Sebastian Kruth
- Laboratory of Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Markus Nett
- Laboratory of Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
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10
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Fairlamb AH, Wyllie S. The critical role of mode of action studies in kinetoplastid drug discovery. FRONTIERS IN DRUG DISCOVERY 2023; 3:fddsv.2023.1185679. [PMID: 37600222 PMCID: PMC7614965 DOI: 10.3389/fddsv.2023.1185679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Understanding the target and mode of action of compounds identified by phenotypic screening can greatly facilitate the process of drug discovery and development. Here, we outline the tools currently available for target identification against the neglected tropical diseases, human African trypanosomiasis, visceral leishmaniasis and Chagas' disease. We provide examples how these tools can be used to identify and triage undesirable mechanisms, to identify potential toxic liabilities in patients and to manage a balanced portfolio of target-based campaigns. We review the primary targets of drugs that are currently in clinical development that were initially identified via phenotypic screening, and whose modes of action affect protein turnover, RNA trans-splicing or signalling in these protozoan parasites.
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Affiliation(s)
- Alan H. Fairlamb
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Susan Wyllie
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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11
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Screening the Pathogen Box to Discover and Characterize New Cruzain and TbrCatL Inhibitors. Pathogens 2023; 12:pathogens12020251. [PMID: 36839523 PMCID: PMC9967275 DOI: 10.3390/pathogens12020251] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Chagas disease and Human African Trypanosomiasis, caused by Trypanosoma cruzi and T. brucei, respectively, pose relevant health challenges throughout the world, placing 65 to 70 million people at risk each. Given the limited efficacy and severe side effects associated with current chemotherapy, new drugs are urgently needed for both diseases. Here, we report the screening of the Pathogen Box collection against cruzain and TbrCatL, validated targets for Chagas disease and Human African Trypanosomiasis, respectively. Enzymatic assays were applied to screen 400 compounds, validate hits, determine IC50 values and, when possible, mechanisms of inhibition. In this case, 12 initial hits were obtained and ten were prioritized for follow-up. IC50 values were obtained for six of them (hit rate = 1.5%) and ranged from 0.46 ± 0.03 to 27 ± 3 µM. MMV687246 was found to be a mixed inhibitor of cruzain (Ki = 57 ± 6 µM) while MMV688179 was found to be a competitive inhibitor of cruzain with a nanomolar potency (Ki = 165 ± 63 nM). A putative binding mode for MMV688179 was obtained by docking. The six hits discovered against cruzain and TbrCatL are of great interest for further optimization by the medicinal chemistry community.
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12
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In silico investigation of cytochrome bc1 molecular inhibition mechanism against Trypanosoma cruzi. PLoS Negl Trop Dis 2023; 17:e0010545. [PMID: 36689459 PMCID: PMC9894551 DOI: 10.1371/journal.pntd.0010545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 02/02/2023] [Accepted: 01/05/2023] [Indexed: 01/24/2023] Open
Abstract
Chagas' disease is a neglected tropical disease caused by the kinetoplastid protozoan Trypanosoma cruzi. The only therapies are the nitroheterocyclic chemicals nifurtimox and benznidazole that cause various adverse effects. The need to create safe and effective medications to improve medical care remains critical. The lack of verified T. cruzi therapeutic targets hinders medication research for Chagas' disease. In this respect, cytochrome bc1 has been identified as a promising therapeutic target candidate for antibacterial medicines of medical and agricultural interest. Cytochrome bc1 belongs to the mitochondrial electron transport chain and transfers electrons from ubiquinol to cytochrome c1 by the action of two catalytic sites named Qi and Qo. The two binding sites are highly selective, and specific inhibitors exist for each site. Recent studies identified the Qi site of the cytochrome bc1 as a promising drug target against T. cruzi. However, a lack of knowledge of the drug mechanism of action unfortunately hinders the development of new therapies. In this context, knowing the cause of binding site selectivity and the mechanism of action of inhibitors and substrates is crucial for drug discovery and optimization processes. In this paper, we provide a detailed computational investigation of the Qi site of T. cruzi cytochrome b to shed light on the molecular mechanism of action of known inhibitors and substrates. Our study emphasizes the action of inhibitors at the Qi site on a highly unstructured portion of cytochrome b that could be related to the biological function of the electron transport chain complex.
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13
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Abstract
Leishmaniasis (visceral and cutaneous), Chagas disease and human African trypanosomiasis cause substantial death and morbidity, particularly in low- and middle-income countries. Although the situation has improved for human African trypanosomiasis, there remains an urgent need for new medicines to treat leishmaniasis and Chagas disease; the clinical development pipeline is particularly sparse for Chagas disease. In this Review, we describe recent advances in our understanding of the biology of the causative pathogens, particularly from the drug discovery perspective, and we explore the progress that has been made in the development of new drug candidates and the identification of promising molecular targets. We also explore the challenges in developing new clinical candidates and discuss potential solutions to overcome such hurdles.
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14
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Amporndanai K, Pinthong N, O’Neill PM, Hong WD, Amewu RK, Pidathala C, Berry NG, Leung SC, Ward SA, Biagini GA, Hasnain SS, Antonyuk SV. Targeting the Ubiquinol-Reduction (Q i) Site of the Mitochondrial Cytochrome bc1 Complex for the Development of Next Generation Quinolone Antimalarials. BIOLOGY 2022; 11:biology11081109. [PMID: 35892964 PMCID: PMC9330653 DOI: 10.3390/biology11081109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022]
Abstract
Antimalarials targeting the ubiquinol-oxidation (Qo) site of the Plasmodium falciparum bc1 complex, such as atovaquone, have become less effective due to the rapid emergence of resistance linked to point mutations in the Qo site. Recent findings showed a series of 2-aryl quinolones mediate inhibitions of this complex by binding to the ubiquinone-reduction (Qi) site, which offers a potential advantage in circumventing drug resistance. Since it is essential to understand how 2-aryl quinolone lead compounds bind within the Qi site, here we describe the co-crystallization and structure elucidation of the bovine cytochrome bc1 complex with three different antimalarial 4(1H)-quinolone sub-types, including two 2-aryl quinolone derivatives and a 3-aryl quinolone analogue for comparison. Currently, no structural information is available for Plasmodial cytochrome bc1. Our crystallographic studies have enabled comparison of an in-silico homology docking model of P. falciparum with the mammalian's equivalent, enabling an examination of how binding compares for the 2- versus 3-aryl analogues. Based on crystallographic and computational modeling, key differences in human and P. falciparum Qi sites have been mapped that provide new insights that can be exploited for the development of next-generation antimalarials with greater selective inhibitory activity against the parasite bc1 with improved antimalarial properties.
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Affiliation(s)
- Kangsa Amporndanai
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Nattapon Pinthong
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Paul M. O’Neill
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Correspondence: (P.M.O.); (S.V.A.); Tel.: +44-(0)-1517955145 (S.V.A.); +44-(0)-1517943552 (P.M.O.)
| | - W. David Hong
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Richard K. Amewu
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Department of Chemistry, School of Physical and Mathematical Sciences, University of Ghana, Accra P.O. Box LG 586, Ghana
| | - Chandrakala Pidathala
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Composite Interceptive Med-Science Laboratories Pvt. Ltd., Bengaluru 60099, Karnataka, India
| | - Neil G. Berry
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Suet C. Leung
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Stephen A. Ward
- Centre for Drugs and Diagnostics, Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (S.A.W.); (G.A.B.)
| | - Giancarlo A. Biagini
- Centre for Drugs and Diagnostics, Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (S.A.W.); (G.A.B.)
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Correspondence: (P.M.O.); (S.V.A.); Tel.: +44-(0)-1517955145 (S.V.A.); +44-(0)-1517943552 (P.M.O.)
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15
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Kratz JM, Gonçalves KR, Romera LM, Moraes CB, Bittencourt-Cunha P, Schenkman S, Chatelain E, Sosa-Estani S. The translational challenge in Chagas disease drug development. Mem Inst Oswaldo Cruz 2022; 117:e200501. [PMID: 35613156 PMCID: PMC9128742 DOI: 10.1590/0074-02760200501] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/13/2021] [Indexed: 12/20/2022] Open
Abstract
Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. There is an urgent need for safe, effective, and accessible new treatments since the currently approved drugs have serious limitations. Drug development for Chagas disease has historically been hampered by the complexity of the disease, critical knowledge gaps, and lack of coordinated R&D efforts. This review covers some of the translational challenges associated with the progression of new chemical entities from preclinical to clinical phases of development, and discusses how recent technological advances might allow the research community to answer key questions relevant to the disease and to overcome hurdles in R&D for Chagas disease.
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Affiliation(s)
- Jadel M Kratz
- Drugs for Neglected Diseases initiative, Geneva, Switzerland
| | - Karolina R Gonçalves
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | - Lavínia Md Romera
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | - Carolina Borsoi Moraes
- Universidade Federal de São Paulo, Departamento de Ciências Farmacêuticas, Diadema, SP, Brasil
| | - Paula Bittencourt-Cunha
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil.,Universidade Federal de São Paulo, Departamento de Microbiologia, Imunologia e Parasitologia, São Paulo, SP, Brasil
| | - Sergio Schenkman
- Universidade Federal de São Paulo, Departamento de Microbiologia, Imunologia e Parasitologia, São Paulo, SP, Brasil
| | - Eric Chatelain
- Drugs for Neglected Diseases initiative, Geneva, Switzerland
| | - Sergio Sosa-Estani
- Drugs for Neglected Diseases initiative, Geneva, Switzerland.,Epidemiology and Public Health Research Centre, CIESP-CONICET, Buenos Aires, Argentina
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16
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Approaches to advance drug discovery for neglected tropical diseases. Drug Discov Today 2022; 27:2278-2287. [DOI: 10.1016/j.drudis.2022.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/21/2022] [Accepted: 04/02/2022] [Indexed: 12/19/2022]
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17
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de Oliveira RG, Cruz LR, Mollo MC, Dias LC, Kratz JM. Chagas Disease Drug Discovery in Latin America-A Mini Review of Antiparasitic Agents Explored Between 2010 and 2021. Front Chem 2021; 9:771143. [PMID: 34778217 PMCID: PMC8581468 DOI: 10.3389/fchem.2021.771143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/15/2021] [Indexed: 11/13/2022] Open
Abstract
Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi that endangers almost 70 million people worldwide. The only two drugs that are currently approved for its treatment, benznidazole and nifurtimox, have controversial efficacy in adults and restricting safety issues, leaving thousands of patients without a suitable treatment. The neglect of Chagas disease is further illustrated by the lack of a robust and diverse drug discovery and development portfolio of new chemical entities, and it is of paramount importance to build a strong research and development network for antichagasic drugs. Focusing on drug discovery programs led by scientists based in Latin America, the main endemic region for this disease, we discuss herein what has been published in the last decade in terms of identification of new antiparasitic drugs to treat Chagas disease, shining a spotlight on the origin, chemical diversity, level of characterization of hits, and strategies used for optimization of lead compounds. Finally, we identify strengths and weaknesses in these drug discovery campaigns and highlight the importance of multidisciplinary collaboration and knowledge sharing.
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Affiliation(s)
- Ramon G. de Oliveira
- Laboratory of Synthetic Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - Luiza R. Cruz
- Laboratory of Synthetic Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - María C. Mollo
- Laboratory of Synthetic Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - Luiz C. Dias
- Laboratory of Synthetic Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - Jadel M. Kratz
- Drugs for Neglected Diseases Initiative (DNDi) Latin America, Rio de Janeiro, Brazil
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18
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Sindhu T, Debnath P. Cytochrome bc1-aa3 oxidase supercomplex as emerging and potential drug target against tuberculosis. Curr Mol Pharmacol 2021; 15:380-392. [PMID: 34602044 DOI: 10.2174/1874467214666210928152512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/26/2021] [Accepted: 06/06/2021] [Indexed: 11/22/2022]
Abstract
The cytochrome bc1-aa3 supercomplex plays an essential role in the cellular respiratory system of Mycobacterium Tuberculosis. It transfers electrons from menaquinol to cytochrome aa3 (Complex IV) via cytochrome bc1 (Complex III), which reduces the oxygen. The electron transfer from a variety of donors into oxygen through the respiratory electron transport chain is essential to pump protons across the membrane creating an electrochemical transmembrane gradient (proton motive force, PMF) that regulates the synthesis of ATP via the oxidative phosphorylation process. Cytochrome bc1-aa3 supercomplex in M. tuberculosis is, therefore, a major drug target for antibiotic action. In recent years, several respiratory chain components have been targeted for developing new candidate drugs, illustrating the therapeutic potential of obstructing energy conversion of M. tuberculosis. The recently available cryo-EM structure of mycobacterial cytochrome bc1-aa3 supercomplex with open and closed conformations has opened new avenues for understanding its structure and function for developing more effective, new therapeutics against pulmonary tuberculosis. In this review, we discuss the role and function of several components, subunits, and drug targeting elements of the supercomplex cytochrome bc1-aa3, and its potential inhibitors in detail.
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Affiliation(s)
- Thangaraj Sindhu
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka. India
| | - Pal Debnath
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka. India
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19
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Cantizani J, Gamallo P, Cotillo I, Alvarez-Velilla R, Martin J. Rate-of-Kill (RoK) assays to triage large compound sets for Chagas disease drug discovery: Application to GSK Chagas Box. PLoS Negl Trop Dis 2021; 15:e0009602. [PMID: 34270544 PMCID: PMC8318231 DOI: 10.1371/journal.pntd.0009602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/28/2021] [Accepted: 06/28/2021] [Indexed: 11/18/2022] Open
Abstract
Chagas disease (CD) is a human disease caused by Trypanosoma cruzi. Whilst endemic in Latin America, the disease is spread around the world due to migration flows, being estimated that 8 million people are infected worldwide and over 10,000 people die yearly of complications linked to CD. Current chemotherapeutics is restricted to only two drugs, i.e. benznidazole (BNZ) and nifurtimox (NIF), both being nitroaromatic compounds sharing mechanism of action and exerting suboptimal efficacy and serious adverse effects. Recent clinical trials conducted to reposition antifungal azoles have turned out disappointing due to poor efficacy outcomes despite their promising preclinical profile. This apparent lack of translation from bench models to the clinic raises the question of whether we are using the right in vitro tools for compound selection. We propose that speed of action and cidality, rather than potency, are properties that can differentiate those compounds with better prospect of success to show efficacy in animal models of CD. Here we investigate the use of in vitro assays looking at the kinetics of parasite kill as a valuable surrogate to tell apart slow- (i.e. azoles targeting CYP51) and fast-acting (i.e. nitroaromatic) compounds. Data analysis and experimental design have been optimised to make it amenable for high-throughput compound profiling. Automated data reduction of experimental kinetic points to tabulated curve descriptors in conjunction with PCA, k-means and hierarchical clustering provide drug discoverers with a roadmap to guide navigation from hit qualification of a screening campaign to compound optimisation programs and assessment of combo therapy potential. As an example, we have studied compounds belonging to the GSK Chagas Box stemmed from the HTS campaign run against the full GSK 1.8 million compounds collection [1]. One of the challenges in early drug discovery of small molecules is the improvement of the poor success rate in the translation from in vitro biological profile into efficacy in disease models, and ultimately in the clinic. Reductionist in vitro models on the bench may not properly recapitulate disease biology, thus overlooking critical properties of candidate compounds. Chagas Disease is a neglected tropical disease caused by Trypanosoma cruzi, a protozoan parasite with a complex life cycle. Despite the promising prospect based on in vitro and in vivo preclinical studies, efforts to reposition antifungal azoles turned out to be disappointing in clinical trials, with treatment failure in Chagas patients. This raises the question of whether we are using the right preclinical tools for decision-making about moving compounds forward for the treatment of this disease. We hypothesise that in vitro potency and efficacy values alone might be distorting the translational power of preclinical compounds, and we propose the use of rate-of-kill (RoK) assays in high-throughput mode. Herewith we disclose a simple, systematic, and automated methodology of analysis of the otherwise complex kinetic patterns, which provides drug discoverers with a navigation guide along a compound optimisation program or prioritisation of best exemplars across different chemical series.
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Affiliation(s)
- Juan Cantizani
- Kinetoplastid DPU, Global Health R&D, GSK, Tres Cantos, Madrid, Spain
| | - Pablo Gamallo
- Kinetoplastid DPU, Global Health R&D, GSK, Tres Cantos, Madrid, Spain
| | - Ignacio Cotillo
- Kinetoplastid DPU, Global Health R&D, GSK, Tres Cantos, Madrid, Spain
| | | | - Julio Martin
- Kinetoplastid DPU, Global Health R&D, GSK, Tres Cantos, Madrid, Spain
- * E-mail:
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20
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Paradela LS, Wall RJ, Carvalho S, Chemi G, Corpas-Lopez V, Moynihan E, Bello D, Patterson S, Güther MLS, Fairlamb AH, Ferguson MAJ, Zuccotto F, Martin J, Gilbert IH, Wyllie S. Multiple unbiased approaches identify oxidosqualene cyclase as the molecular target of a promising anti-leishmanial. Cell Chem Biol 2021; 28:711-721.e8. [PMID: 33691122 PMCID: PMC8153249 DOI: 10.1016/j.chembiol.2021.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/25/2021] [Accepted: 02/11/2021] [Indexed: 12/31/2022]
Abstract
Phenotypic screening identified a benzothiophene compound with activity against Leishmania donovani, the causative agent of visceral leishmaniasis. Using multiple orthogonal approaches, oxidosqualene cyclase (OSC), a key enzyme of sterol biosynthesis, was identified as the target of this racemic compound and its enantiomers. Whole genome sequencing and screening of a genome-wide overexpression library confirmed that OSC gene amplification is associated with resistance to compound 1. Introduction of an ectopic copy of the OSC gene into wild-type cells reduced susceptibility to these compounds confirming the role of this enzyme in resistance. Biochemical analyses demonstrated the accumulation of the substrate of OSC and depletion of its product in compound (S)-1-treated-promastigotes and cell-free membrane preparations, respectively. Thermal proteome profiling confirmed that compound (S)-1 binds directly to OSC. Finally, modeling and docking studies identified key interactions between compound (S)-1 and the LdOSC active site. Strategies to improve the potency for this promising anti-leishmanial are proposed. Genetics and chemo-proteomics identify the target of a promising anti-leishmanial Biochemical assays confirm the direct inhibition of oxidosqualene cyclase in cells Docking and modeling studies identify key interactions between compound and target Strategies to improve the potency of this benzothiophene are proposed
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Affiliation(s)
- Luciana S Paradela
- Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Richard J Wall
- Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sandra Carvalho
- Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Giulia Chemi
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Victoriano Corpas-Lopez
- Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Eoin Moynihan
- Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Davide Bello
- Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Stephen Patterson
- Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Maria Lucia S Güther
- Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Alan H Fairlamb
- Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Michael A J Ferguson
- Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Fabio Zuccotto
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Julio Martin
- Global Health R&D, GlaxoSmithKline, Tres Cantos 28760, Spain
| | - Ian H Gilbert
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Susan Wyllie
- Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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Wilkinson IVL, Terstappen GC, Russell AJ. Combining experimental strategies for successful target deconvolution. Drug Discov Today 2020; 25:S1359-6446(20)30373-1. [PMID: 32971235 DOI: 10.1016/j.drudis.2020.09.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/10/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023]
Abstract
Investment in phenotypic drug discovery has led to increased demand for rapid and robust target deconvolution to aid successful drug development. Although methods for target identification and mechanism of action (MoA) discovery are flourishing, they typically lead to lists of putative targets. Validating which target(s) are involved in the therapeutic mechanism of a compound poses a significant challenge, requiring direct binding, target engagement, and functional studies in relevant physiological contexts. A combination of orthogonal approaches can allow target identification beyond the proteome as well as aid prioritisation for resource-intensive target validation studies.
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Affiliation(s)
- Isabel V L Wilkinson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Georg C Terstappen
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3PQ, UK
| | - Angela J Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK; Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3PQ, UK.
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Harrison JR, Sarkar S, Hampton S, Riley J, Stojanovski L, Sahlberg C, Appelqvist P, Erath J, Mathan V, Rodriguez A, Kaiser M, Pacanowska DG, Read KD, Johansson NG, Gilbert IH. Discovery and Optimization of a Compound Series Active against Trypanosoma cruzi, the Causative Agent of Chagas Disease. J Med Chem 2020; 63:3066-3089. [PMID: 32134269 DOI: 10.1021/acs.jmedchem.9b01852] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chagas disease is caused by the protozoan parasite Trypanosoma cruzi. It is endemic in South and Central America and recently has been found in other parts of the world, due to migration of chronically infected patients. The current treatment for Chagas disease is not satisfactory, and there is a need for new treatments. In this work, we describe the optimization of a hit compound resulting from the phenotypic screen of a library of compounds against T. cruzi. The compound series was optimized to the level where it had satisfactory pharmacokinetics to allow an efficacy study in a mouse model of Chagas disease. We were able to demonstrate efficacy in this model, although further work is required to improve the potency and selectivity of this series.
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Affiliation(s)
- Justin R Harrison
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Sandipan Sarkar
- Syngene International Ltd, Biocon Park, SEZ, Bommasandra Industrial Area, Phase-IV, Bommasandra-Jigani Link Road, Bangalore 560 099, India
| | - Shahienaz Hampton
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Jennifer Riley
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Laste Stojanovski
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | | | | | - Jessey Erath
- New York University School of Medicine, 430 East 29th Street, Alexandria Center West Tower, Room 511, Lab 524, New York, New York 10010, United States
| | - Vinodhini Mathan
- Syngene International Ltd, Biocon Park, SEZ, Bommasandra Industrial Area, Phase-IV, Bommasandra-Jigani Link Road, Bangalore 560 099, India
| | - Ana Rodriguez
- New York University School of Medicine, 430 East 29th Street, Alexandria Center West Tower, Room 511, Lab 524, New York, New York 10010, United States
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute (Swiss TPH), Socinstrasse 57, Basel CH-4051, Switzerland.,University of Basel, Petersplatz 1, Basel CH-4003, Switzerland
| | - Dolores Gonzalez Pacanowska
- Instituto de Parasitología y Biomedicina "López-Neyra", Avda. Conocimiento S/N, Parque Tecnológico Ciencias de la Salud18016 Armilla, Granada Spain
| | - Kevin D Read
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | | | - Ian H Gilbert
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
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