1
|
Talevi A. Computer-Aided Drug Discovery and Design: Recent Advances and Future Prospects. Methods Mol Biol 2024; 2714:1-20. [PMID: 37676590 DOI: 10.1007/978-1-0716-3441-7_1] [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] [Indexed: 09/08/2023]
Abstract
Computer-aided drug discovery and design involve the use of information technologies to identify and develop, on a rational ground, chemical compounds that align a set of desired physicochemical and biological properties. In its most common form, it involves the identification and/or modification of an active scaffold (or the combination of known active scaffolds), although de novo drug design from scratch is also possible. Traditionally, the drug discovery and design processes have focused on the molecular determinants of the interactions between drug candidates and their known or intended pharmacological target(s). Nevertheless, in modern times, drug discovery and design are conceived as a particularly complex multiparameter optimization task, due to the complicated, often conflicting, property requirements.This chapter provides an updated overview of in silico approaches for identifying active scaffolds and guiding the subsequent optimization process. Recent groundbreaking advances in the field have also analyzed the integration of state-of-the-art machine learning approaches in every step of the drug discovery process (from prediction of target structure to customized molecular docking scoring functions), integration of multilevel omics data, and the use of a diversity of computational approaches to assist target validation and assess plausible binding pockets.
Collapse
Affiliation(s)
- Alan Talevi
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata (UNLP), La Plata, Argentina.
- Argentinean National Council of Scientific and Technical Research (CONICET), La Plata, Argentina.
| |
Collapse
|
2
|
Porta EOJ, Kalesh K, Steel PG. Navigating drug repurposing for Chagas disease: advances, challenges, and opportunities. Front Pharmacol 2023; 14:1233253. [PMID: 37576826 PMCID: PMC10416112 DOI: 10.3389/fphar.2023.1233253] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/18/2023] [Indexed: 08/15/2023] Open
Abstract
Chagas disease is a vector-borne illness caused by the protozoan parasite Trypanosoma cruzi (T. cruzi). It poses a significant public health burden, particularly in the poorest regions of Latin America. Currently, there is no available vaccine, and chemotherapy has been the traditional treatment for Chagas disease. However, the treatment options are limited to just two outdated medicines, nifurtimox and benznidazole, which have serious side effects and low efficacy, especially during the chronic phase of the disease. Collectively, this has led the World Health Organization to classify it as a neglected disease. To address this problem, new drug regimens are urgently needed. Drug repurposing, which involves the use of existing drugs already approved for the treatment of other diseases, represents an increasingly important option. This approach offers potential cost reduction in new drug discovery processes and can address pharmaceutical bottlenecks in the development of drugs for Chagas disease. In this review, we discuss the state-of-the-art of drug repurposing approaches, including combination therapy with existing drugs, to overcome the formidable challenges associated with treating Chagas disease. Organized by original therapeutic area, we describe significant recent advances, as well as the challenges in this field. In particular, we identify candidates that exhibit potential for heightened efficacy and reduced toxicity profiles with the ultimate objective of accelerating the development of new, safe, and effective treatments for Chagas disease.
Collapse
Affiliation(s)
| | - Karunakaran Kalesh
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Darlington, United Kingdom
| | - Patrick G. Steel
- Department of Chemistry, Durham University, Durham, United Kingdom
| |
Collapse
|
3
|
Zaman N, Azam SS. Quantum Dynamics and Bi Metal Force Field Parameterization Yielding Significant Antileishmanial Targets. J Chem Inf Model 2023; 63:1371-1385. [PMID: 36730993 DOI: 10.1021/acs.jcim.2c01100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Amid emerging drug resistance to metal inhibitors, high toxicity, and onerous drug delivery procedures, the computational design of alternate formulations encompassing functional metal-containing compounds greatly relies on large-scale atomistic simulations. Simulations particularly with Au(I), Ag, Bi(V), and Sb(V) pose a major challenge to elucidate their molecular mechanism due to the absence of force field parameters. This study thus quantum mechanically derives force field parameters of Bi(V) as an extension of the previous experimental study conducted on heteroleptic triorganobismuth(V) biscarboxylates of type [BiR3(O2CR')2]. We have modeled two organo-bismuth(V) carboxylates, which are optimized and parameterized along with the famous pentavalent antimonial drug: meglumine antimoniate using quantum mechanics original Seminarian methods with the SBKJC effective core potential (ECP) basis set. Furthermore, molecular dynamics (MD) simulations of bismuth- and antimony-containing compounds in complex with two enzymes, trypanothione synthetase-amidase (TSA) and trypanothione reductase, are performed to target the (T(SH)2) pathway at multiple points. MD simulations provide novel insights into the binding mechanism of TSA and highlight the role of a single residue Arg569 in modulating the ligand dynamics. Moreover, the presence of an ortho group in a ligand is emphasized to facilitate interactions between Arg569 and the active site residue Arg313 for higher inhibitory activity of TSA. This preliminary generation of parameters specific to bismuth validated by simulations in replica will become a preamble of future computational and experimental research work to open avenues for newer and suitable drug targets.
Collapse
Affiliation(s)
- Naila Zaman
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad45320, Pakistan
| |
Collapse
|
4
|
Llanos MA, Alberca LN, Ruiz MD, Sbaraglini ML, Miranda C, Pino-Martinez A, Fraccaroli L, Carrillo C, Alba Soto CD, Gavernet L, Talevi A. A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity. J Comput Aided Mol Des 2023; 37:75-90. [PMID: 36494599 DOI: 10.1007/s10822-022-00491-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022]
Abstract
Chagas disease, also known as American trypanosomiasis, is a neglected tropical disease caused by the protozoa Trypanosoma cruzi, affecting nearly 7 million people only in the Americas. Polyamines are essential compounds for parasite growth, survival, and differentiation. However, because trypanosomatids are auxotrophic for polyamines, they must be obtained from the host by specific transporters. In this investigation, an ensemble of QSAR classifiers able to identify polyamine analogs with trypanocidal activity was developed. Then, a multi-template homology model of the dimeric polyamine transporter of T. cruzi, TcPAT12, was created with Rosetta, and then refined by enhanced sampling molecular dynamics simulations. Using representative snapshots extracted from the trajectory, a docking model able to discriminate between active and inactive compounds was developed and validated. Both models were applied in a parallel virtual screening campaign to repurpose known drugs as anti-trypanosomal compounds inhibiting polyamine transport in T. cruzi. Montelukast, Quinestrol, Danazol, and Dutasteride were selected for in vitro testing, and all of them inhibited putrescine uptake in biochemical assays, confirming the predictive ability of the computational models. Furthermore, all the confirmed hits proved to inhibit epimastigote proliferation, and Quinestrol and Danazol were able to inhibit, in the low micromolar range, the viability of trypomastigotes and the intracellular growth of amastigotes.
Collapse
Affiliation(s)
- Manuel A Llanos
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina
| | - Lucas N Alberca
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina
| | - María D Ruiz
- Laboratorio de Biología Molecular y Bioquímica en Trypanosoma cruzi y otros agentes infecciosos, Instituto de Ciencia y Tecnología (ICT) Milstein - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - María L Sbaraglini
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina
| | - Cristian Miranda
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires., Buenos Aires, Argentina
| | - Agustina Pino-Martinez
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires., Buenos Aires, Argentina
| | - Laura Fraccaroli
- Laboratorio de Biología Molecular y Bioquímica en Trypanosoma cruzi y otros agentes infecciosos, Instituto de Ciencia y Tecnología (ICT) Milstein - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Carolina Carrillo
- Laboratorio de Biología Molecular y Bioquímica en Trypanosoma cruzi y otros agentes infecciosos, Instituto de Ciencia y Tecnología (ICT) Milstein - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Catalina D Alba Soto
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires., Buenos Aires, Argentina
| | - Luciana Gavernet
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina.
| | - Alan Talevi
- Departamento de Ciencias Biológicas and Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata. La Plata (B1900ADU), Buenos Aires, Argentina
| |
Collapse
|
5
|
First Molecular Identification of Trypanosomes and Absence of Babesia sp. DNA in Faeces of Non-Human Primates in the Ecuadorian Amazon. Pathogens 2022; 11:pathogens11121490. [PMID: 36558823 PMCID: PMC9785249 DOI: 10.3390/pathogens11121490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/20/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Trypanosomes are a group of pathogens distributed in the continents of Africa, America, Asia and Europe, and they affect all vertebrates including the neotropical primate group. Information about the trypanosome's diversity, phylogeny, ecology and pathology in non-human primates (NHPs) from the neotropical region is scarce. The objective of the study was to identify Trypanosoma and Babesia molecularly in NHPs under the phylogenetic species concept. We extracted DNA from a total of 76 faecal samples collected between 2019 and 2021, from a total of 11 non-human primate species of which 46 are from captive NHPs and 30 are free-living NHPs in the Western Amazon region of Ecuador. We did not detect DNA of Babesia sp. by polymerase chain reaction test in any of the faecal samples. However, the nested-PCR-based method revealed Trypanosoma parasites by ITS gene amplification in two faecal samples; one for the species Leontocebus lagonotus (from the captive population) and a second one for Cebus albifrons (from the free-ranging population). Maximum parsimony and likelihood methods with the Kimura2+G+I model inferred the evolutionary history of the two records, which showed an evolutionary relationship with the genus Trypanosoma. Two sequences are monophyletic with Trypanosoma. However, the number of sequences available in GenBank for their species identification is limited. The two samples present different molecular identifications and evolutionary origins in the tree topology. We are most likely referring to two different species, and two different localities of infection. We suggest that health management protocols should be implemented to prevent the transmission of blood-borne pathogens such as Trypanosoma sp. among captive populations. In addition, these protocols also protect the personnel of wildlife rehabilitation centers working in close proximity to NHPs and vice versa.
Collapse
|
6
|
Jain S, Sahu U, Kumar A, Khare P. Metabolic Pathways of Leishmania Parasite: Source of Pertinent Drug Targets and Potent Drug Candidates. Pharmaceutics 2022; 14:pharmaceutics14081590. [PMID: 36015216 PMCID: PMC9416627 DOI: 10.3390/pharmaceutics14081590] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023] Open
Abstract
Leishmaniasis is a tropical disease caused by a protozoan parasite Leishmania that is transmitted via infected female sandflies. At present, leishmaniasis treatment mainly counts on chemotherapy. The currently available drugs against leishmaniasis are costly, toxic, with multiple side effects, and limitations in the administration route. The rapid emergence of drug resistance has severely reduced the potency of anti-leishmanial drugs. As a result, there is a pressing need for the development of novel anti-leishmanial drugs with high potency, low cost, acceptable toxicity, and good pharmacokinetics features. Due to the availability of preclinical data, drug repurposing is a valuable approach for speeding up the development of effective anti-leishmanial through pointing to new drug targets in less time, having low costs and risk. Metabolic pathways of this parasite play a crucial role in the growth and proliferation of Leishmania species during the various stages of their life cycle. Based on available genomics/proteomics information, known pathways-based (sterol biosynthetic pathway, purine salvage pathway, glycolysis, GPI biosynthesis, hypusine, polyamine biosynthesis) Leishmania-specific proteins could be targeted with known drugs that were used in other diseases, resulting in finding new promising anti-leishmanial therapeutics. The present review discusses various metabolic pathways of the Leishmania parasite and some drug candidates targeting these pathways effectively that could be potent drugs against leishmaniasis in the future.
Collapse
Affiliation(s)
- Surbhi Jain
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462026, Madhya Pradesh, India; (S.J.); (U.S.)
| | - Utkarsha Sahu
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462026, Madhya Pradesh, India; (S.J.); (U.S.)
- Division of Synthetic Biology, Absolute Foods, Plot 68, Sector 44, Gurugram 122003, Haryana, India
| | - Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur 492010, Chhattisgarh, India
- Correspondence: or (A.K.); (P.K.)
| | - Prashant Khare
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462026, Madhya Pradesh, India; (S.J.); (U.S.)
- Division of Synthetic Biology, Absolute Foods, Plot 68, Sector 44, Gurugram 122003, Haryana, India
- Correspondence: or (A.K.); (P.K.)
| |
Collapse
|
7
|
Ros-Lucas A, Martinez-Peinado N, Bastida J, Gascón J, Alonso-Padilla J. The Use of AlphaFold for In Silico Exploration of Drug Targets in the Parasite Trypanosoma cruzi. Front Cell Infect Microbiol 2022; 12:944748. [PMID: 35909956 PMCID: PMC9329570 DOI: 10.3389/fcimb.2022.944748] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/23/2022] [Indexed: 11/23/2022] Open
Abstract
Chagas disease is a devastating neglected disease caused by the parasite Trypanosoma cruzi, which affects millions of people worldwide. The two anti-parasitic drugs available, nifurtimox and benznidazole, have a good efficacy against the acute stage of the infection. But this is short, usually asymptomatic and often goes undiagnosed. Access to treatment is mostly achieved during the chronic stage, when the cardiac and/or digestive life-threatening symptoms manifest. Then, the efficacy of both drugs is diminished, and their long administration regimens involve frequently associated adverse effects that compromise treatment compliance. Therefore, the discovery of safer and more effective drugs is an urgent need. Despite its advantages over lately used phenotypic screening, target-based identification of new anti-parasitic molecules has been hampered by incomplete annotation and lack of structures of the parasite protein space. Presently, the AlphaFold Protein Structure Database is home to 19,036 protein models from T. cruzi, which could hold the key to not only describe new therapeutic approaches, but also shed light on molecular mechanisms of action for known compounds. In this proof-of-concept study, we screened the AlphaFold T. cruzi set of predicted protein models to find prospective targets for a pre-selected list of compounds with known anti-trypanosomal activity using docking-based inverse virtual screening. The best receptors (targets) for the most promising ligands were analyzed in detail to address molecular interactions and potential drugs’ mode of action. The results provide insight into the mechanisms of action of the compounds and their targets, and pave the way for new strategies to finding novel compounds or optimize already existing ones.
Collapse
Affiliation(s)
- Albert Ros-Lucas
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic - University of Barcelona, Barcelona, Spain
- *Correspondence: Albert Ros-Lucas, ; Nieves Martinez-Peinado, ; Julio Alonso-Padilla,
| | - Nieves Martinez-Peinado
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic - University of Barcelona, Barcelona, Spain
- *Correspondence: Albert Ros-Lucas, ; Nieves Martinez-Peinado, ; Julio Alonso-Padilla,
| | - Jaume Bastida
- Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l´Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Joaquim Gascón
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic - University of Barcelona, Barcelona, Spain
- CIBERINFEC, ISCIII—CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Julio Alonso-Padilla
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic - University of Barcelona, Barcelona, Spain
- CIBERINFEC, ISCIII—CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Albert Ros-Lucas, ; Nieves Martinez-Peinado, ; Julio Alonso-Padilla,
| |
Collapse
|
8
|
Benítez D, Franco J, Sardi F, Leyva A, Durán R, Choi G, Yang G, Kim T, Kim N, Heo J, Kim K, Lee H, Choi I, Radu C, Shum D, No JH, Comini MA. Drug-like molecules with anti-trypanothione synthetase activity identified by high throughput screening. J Enzyme Inhib Med Chem 2022; 37:912-929. [PMID: 35306933 PMCID: PMC8942522 DOI: 10.1080/14756366.2022.2045590] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Trypanothione synthetase (TryS) catalyses the synthesis of N1,N8-bis(glutathionyl)spermidine (trypanothione), which is the main low molecular mass thiol supporting several redox functions in trypanosomatids. TryS attracts attention as molecular target for drug development against pathogens causing severe and fatal diseases in mammals. A drug discovery campaign aimed to identify and characterise new inhibitors of TryS with promising biological activity was conducted. A large compound library (n = 51,624), most of them bearing drug-like properties, was primarily screened against TryS from Trypanosoma brucei (TbTryS). With a true-hit rate of 0.056%, several of the TbTryS hits (IC50 from 1.2 to 36 µM) also targeted the homologue enzyme from Leishmania infantum and Trypanosoma cruzi (IC50 values from 2.6 to 40 µM). Calmidazolium chloride and Ebselen stand out for their multi-species anti-TryS activity at low µM concentrations (IC50 from 2.6 to 13.8 µM). The moieties carboxy piperidine amide and amide methyl thiazole phenyl were identified as novel TbTryS inhibitor scaffolds. Several of the TryS hits presented one-digit µM EC50 against T. cruzi and L. donovani amastigotes but proved cytotoxic against the human osteosarcoma and macrophage host cells (selectivity index ≤ 3). In contrast, seven hits showed a significantly higher selectivity against T. b. brucei (selectivity index from 11 to 182). Non-invasive redox assays confirmed that Ebselen, a multi-TryS inhibitor, induces an intracellular oxidative milieu in bloodstream T. b. brucei. Kinetic and mass spectrometry analysis revealed that Ebselen is a slow-binding inhibitor that modifies irreversible a highly conserved cysteine residue from the TryS’s synthetase domain. The most potent TbTryS inhibitor (a singleton containing an adamantine moiety) exerted a non-covalent, non-competitive (with any of the substrates) inhibition of the enzyme. These data feed the drug discovery pipeline for trypanosomatids with novel and valuable information on chemical entities with drug potential.
Collapse
Affiliation(s)
- Diego Benítez
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Jaime Franco
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Florencia Sardi
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alejandro Leyva
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Rosario Durán
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Gahee Choi
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Gyongseon Yang
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Taehee Kim
- Assay Development and Screening, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Namyoul Kim
- Assay Development and Screening, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Jinyeong Heo
- Assay Development and Screening, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Kideok Kim
- Automation and Logistics Management, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Honggun Lee
- Automation and Logistics Management, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Inhee Choi
- Medicinal Chemistry, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Constantin Radu
- Automation and Logistics Management, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - David Shum
- Assay Development and Screening, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Joo Hwan No
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Marcelo A Comini
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| |
Collapse
|
9
|
Alice JI, Bellera CL, Benítez D, Comini MA, Duchowicz PR, Talevi A. Ensemble learning application to discover new trypanothione synthetase inhibitors. Mol Divers 2021; 25:1361-1373. [PMID: 34264440 DOI: 10.1007/s11030-021-10265-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/24/2021] [Indexed: 11/28/2022]
Abstract
Trypanosomatid-caused diseases are among the neglected infectious diseases with the highest disease burden, affecting about 27 million people worldwide and, in particular, socio-economically vulnerable populations. Trypanothione synthetase (TryS) is considered one of the most attractive drug targets within the thiol-polyamine metabolism of typanosomatids, being unique, essential and druggable. Here, we have compiled a dataset of 401 T. brucei TryS inhibitors that includes compounds with inhibitory data reported in the literature, but also in-house acquired data. QSAR classifiers were derived and validated from such dataset, using publicly available and open-source software, thus assuring the portability of the obtained models. The performance and robustness of the resulting models were substantially improved through ensemble learning. The performance of the individual models and the model ensembles was further assessed through retrospective virtual screening campaigns. At last, as an application example, the chosen model-ensemble has been applied in a prospective virtual screening campaign on DrugBank 5.1.6 compound library. All the in-house scripts used in this study are available on request, whereas the dataset has been included as supplementary material.
Collapse
Affiliation(s)
- Juan I Alice
- Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), La Plata, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CCT La Plata, La Plata, Argentina
| | - Carolina L Bellera
- Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), La Plata, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CCT La Plata, La Plata, Argentina
| | - Diego Benítez
- Group Redox Biology of Trypanosomes, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Marcelo A Comini
- Group Redox Biology of Trypanosomes, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Pablo R Duchowicz
- Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), La Plata, Argentina
| | - Alan Talevi
- Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), La Plata, Buenos Aires, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CCT La Plata, La Plata, Argentina.
| |
Collapse
|
10
|
Saccoliti F, Di Santo R, Costi R. Recent Advancement in the Search of Innovative Antiprotozoal Agents Targeting Trypanothione Metabolism. ChemMedChem 2020; 15:2420-2435. [PMID: 32805075 DOI: 10.1002/cmdc.202000325] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/13/2020] [Indexed: 01/28/2023]
Abstract
Leishmania and Trypanosoma parasites are responsible for the challenging neglected tropical diseases leishmaniases, Chagas disease, and human African trypanosomiasis, which account for up to 40,000 deaths annually mainly in developing countries. Current chemotherapy relies on drugs with significant limitations in efficacy and safety, prompting the urgent need to explore innovative approaches to improve the drug discovery pipeline. The unique trypanothione-based redox pathway, which is absent in human hosts, is vital for all trypanosomatids and offers valuable opportunities to guide the rational development of specific, broad-spectrum and innovative anti-trypanosomatid agents. Major efforts focused on the key metabolic enzymes trypanothione synthetase-amidase and trypanothione reductase, whose inhibition should affect the entire pathway and, finally, parasite survival. Herein, we will report and comment on the most recent studies in the search for enzyme inhibitors, underlining the promising opportunities that have emerged so far to drive the exploration of future successful therapeutic approaches.
Collapse
Affiliation(s)
- Francesco Saccoliti
- D3 PharmaChemistry, Italian Institute of Technology, Via Morego 30, 16163, Genova, Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P. le Aldo Moro 5, 00185, Roma, Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P. le Aldo Moro 5, 00185, Roma, Italy
| |
Collapse
|
11
|
Francisco AF, Jayawardhana S, Olmo F, Lewis MD, Wilkinson SR, Taylor MC, Kelly JM. Challenges in Chagas Disease Drug Development. Molecules 2020; 25:E2799. [PMID: 32560454 PMCID: PMC7355550 DOI: 10.3390/molecules25122799] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 02/08/2023] Open
Abstract
The protozoan parasite Trypanosoma cruzi causes Chagas disease, an important public health problem throughout Latin America. Current therapeutic options are characterised by limited efficacy, long treatment regimens and frequent toxic side-effects. Advances in this area have been compromised by gaps in our knowledge of disease pathogenesis, parasite biology and drug activity. Nevertheless, several factors have come together to create a more optimistic scenario. Drug-based research has become more systematic, with increased collaborations between the academic and commercial sectors, often within the framework of not-for-profit consortia. High-throughput screening of compound libraries is being widely applied, and new technical advances are helping to streamline the drug development pipeline. In addition, drug repurposing and optimisation of current treatment regimens, informed by laboratory research, are providing a basis for new clinical trials. Here, we will provide an overview of the current status of Chagas disease drug development, highlight those areas where progress can be expected, and describe how fundamental research is helping to underpin the process.
Collapse
Affiliation(s)
- Amanda F. Francisco
- Department of Infection Biology, London School of Hygiene and Tropical Medicine Keppel Street, London WC1E 7HT, UK; (A.F.F.); (S.J.); (F.O.); (M.D.L.); (M.C.T.)
| | - Shiromani Jayawardhana
- Department of Infection Biology, London School of Hygiene and Tropical Medicine Keppel Street, London WC1E 7HT, UK; (A.F.F.); (S.J.); (F.O.); (M.D.L.); (M.C.T.)
| | - Francisco Olmo
- Department of Infection Biology, London School of Hygiene and Tropical Medicine Keppel Street, London WC1E 7HT, UK; (A.F.F.); (S.J.); (F.O.); (M.D.L.); (M.C.T.)
| | - Michael D. Lewis
- Department of Infection Biology, London School of Hygiene and Tropical Medicine Keppel Street, London WC1E 7HT, UK; (A.F.F.); (S.J.); (F.O.); (M.D.L.); (M.C.T.)
| | - Shane R. Wilkinson
- School of Biological and Chemical Sciences, Queen Mary University of London Mile End Road, London E1 4NS, UK;
| | - Martin C. Taylor
- Department of Infection Biology, London School of Hygiene and Tropical Medicine Keppel Street, London WC1E 7HT, UK; (A.F.F.); (S.J.); (F.O.); (M.D.L.); (M.C.T.)
| | - John M. Kelly
- Department of Infection Biology, London School of Hygiene and Tropical Medicine Keppel Street, London WC1E 7HT, UK; (A.F.F.); (S.J.); (F.O.); (M.D.L.); (M.C.T.)
| |
Collapse
|
12
|
Mesías AC, Garg NJ, Zago MP. Redox Balance Keepers and Possible Cell Functions Managed by Redox Homeostasis in Trypanosoma cruzi. Front Cell Infect Microbiol 2019; 9:435. [PMID: 31921709 PMCID: PMC6932984 DOI: 10.3389/fcimb.2019.00435] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/05/2019] [Indexed: 12/11/2022] Open
Abstract
The toxicity of oxygen and nitrogen reactive species appears to be merely the tip of the iceberg in the world of redox homeostasis. Now, oxidative stress can be seen as a two-sided process; at high concentrations, it causes damage to biomolecules, and thus, trypanosomes have evolved a strong antioxidant defense system to cope with these stressors. At low concentrations, oxidants are essential for cell signaling, and in fact, the oxidants/antioxidants balance may be able to trigger different cell fates. In this comprehensive review, we discuss the current knowledge of the oxidant environment experienced by T. cruzi along the different phases of its life cycle, and the molecular tools exploited by this pathogen to deal with oxidative stress, for better or worse. Further, we discuss the possible redox-regulated processes that could be governed by this oxidative context. Most of the current research has addressed the importance of the trypanosomes' antioxidant network based on its detox activity of harmful species; however, new efforts are necessary to highlight other functions of this network and the mechanisms underlying the fine regulation of the defense machinery, as this represents a master key to hinder crucial pathogen functions. Understanding the relevance of this balance keeper program in parasite biology will give us new perspectives to delineate improved treatment strategies.
Collapse
Affiliation(s)
- Andrea C Mesías
- Instituto de Patología Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Salta, Salta, Argentina
| | - Nisha J Garg
- Department of Microbiology and Immunology, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, United States
| | - M Paola Zago
- Instituto de Patología Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Salta, Salta, Argentina
| |
Collapse
|
13
|
Kumar R, Harilal S, Gupta SV, Jose J, Thomas Parambi DG, Uddin MS, Shah MA, Mathew B. Exploring the new horizons of drug repurposing: A vital tool for turning hard work into smart work. Eur J Med Chem 2019; 182:111602. [PMID: 31421629 PMCID: PMC7127402 DOI: 10.1016/j.ejmech.2019.111602] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023]
Abstract
Drug discovery and development are long and financially taxing processes. On an average it takes 12-15 years and costs 1.2 billion USD for successful drug discovery and approval for clinical use. Many lead molecules are not developed further and their potential is not tapped to the fullest due to lack of resources or time constraints. In order for a drug to be approved by FDA for clinical use, it must have excellent therapeutic potential in the desired area of target with minimal toxicities as supported by both pre-clinical and clinical studies. The targeted clinical evaluations fail to explore other potential therapeutic applications of the candidate drug. Drug repurposing or repositioning is a fast and relatively cheap alternative to the lengthy and expensive de novo drug discovery and development. Drug repositioning utilizes the already available clinical trials data for toxicity and adverse effects, at the same time explores the drug's therapeutic potential for a different disease. This review addresses recent developments and future scope of drug repositioning strategy.
Collapse
Affiliation(s)
- Rajesh Kumar
- Department of Pharmacy, Kerala University of Health Sciences, Thrissur, Kerala, India
| | - Seetha Harilal
- Department of Pharmacy, Kerala University of Health Sciences, Thrissur, Kerala, India
| | - Sheeba Varghese Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, 33612, USA
| | - Jobin Jose
- Department of Pharmaceutics, NGSM Institute of Pharmaceutical Science, NITTE Deemed to be University, Manglore, 575018, India
| | - Della Grace Thomas Parambi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf, 2014, Saudi Arabia
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh; Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
| | - Muhammad Ajmal Shah
- Department of Pharmacogonosy, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad, Pakistan
| | - Bijo Mathew
- Division of Drug Design and Medicinal Chemistry Research Lab, Department of Pharmaceutical Chemistry, Ahalia School of Pharmacy, Palakkad, 678557, Kerala, India.
| |
Collapse
|