1
|
Mtemeli FL, Ndlovu J, Mugumbate G, Makwikwi T, Shoko R. Advances in schistosomiasis drug discovery based on natural products. All Life 2022. [DOI: 10.1080/26895293.2022.2080281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- F. L. Mtemeli
- Department of Biology, School of Natural Sciences and Mathematics Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - J. Ndlovu
- Department of Biology, School of Natural Sciences and Mathematics Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - G. Mugumbate
- Department of Chemical Technology, Midlands State University, Gweru, Zimbabwe
| | - T. Makwikwi
- Department of Pharmaceutical Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - R. Shoko
- Department of Biology, School of Natural Sciences and Mathematics Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| |
Collapse
|
2
|
Mtemeli FL, Shoko R, Ndlovu J, Mugumbate G. In Silico Study of Cucurbita maxima Compounds as Potential Therapeutics Against Schistosomiasis. Bioinform Biol Insights 2022; 16:11779322221100741. [PMID: 35615403 PMCID: PMC9125113 DOI: 10.1177/11779322221100741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/21/2022] [Indexed: 11/15/2022] Open
Abstract
Schistosomiasis, a disease usually related to poverty and poor sanitation, affects more than 200 million people worldwide. Since the 1970s, the medical sector has depended on a single drug, praziquantel, for the treatment of the disease. The emerging evidence of resistance of the Schistosoma parasite to praziquantel and the drug’s inefficacy against juvenile stages of the parasite makes the need to find alternative drugs an urgent matter. In this study, we explored the inhibition potential of compounds from Cucurbita maxima using molecular docking studies on Schistosoma mansoni purine nucleoside phosphorylase ( SmPNP) and Schistosoma haematobium 28-kDa glutathione S-transferase ( Sh28kDaGST). Following molecular docking studies and analysis of the active sites, the primary amino acids that were observed and shown to be involved in the SmPNP-ligand interaction are CYS 33, ARG 86, HIS 88, TYR 90, ALA 118, ALA 119, PRO 200, TYR 202, GLU 203, VAL 219, MET 221, THR 244, ASN 245, PRO 257 and HIS 259. For the Sh28dKa-ligand interaction, the primary amino acids were PHE 11, ARG 16, TRP 41, LEU 53, GLU 70 and SER 71. Momordicoside I aglycone binds to SmPNP with the lowest binding affinity of -7.9 kcal/mol by pi sigma bond interactions with HIS 88. Balsaminoside B binds to Sh28kDaGST with a binding affinity of −7.6 kcal/mol by hydrogen bond interaction with TRP 41, LEU 53 and SER 71. Pharmacokinetic studies showed favourable drug-like properties for the 10 compounds that exhibited the lowest binding energies. Therefore, we propose that bioactive compounds from C. maxima be considered as potential novel drug hits in the treatment of schistosomiasis.
Collapse
Affiliation(s)
- Floryn Lynorah Mtemeli
- Department of Biology, School of Natural Sciences and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Ryman Shoko
- Department of Biology, School of Natural Sciences and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Joice Ndlovu
- Department of Biology, School of Natural Sciences and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Grace Mugumbate
- Department of Chemical Technology, Midlands State University, Gweru, Zimbabwe
| |
Collapse
|
3
|
Mugumbate G, Nyathi B, Zindoga A, Munyuki G. Application of Computational Methods in Understanding Mutations in Mycobacterium tuberculosis Drug Resistance. Front Mol Biosci 2021; 8:643849. [PMID: 34651013 PMCID: PMC8505691 DOI: 10.3389/fmolb.2021.643849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 08/16/2021] [Indexed: 11/23/2022] Open
Abstract
The emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb) impedes the End TB Strategy by the World Health Organization aiming for zero deaths, disease, and suffering at the hands of tuberculosis (TB). Mutations within anti-TB drug targets play a major role in conferring drug resistance within Mtb; hence, computational methods and tools are being used to understand the mechanisms by which they facilitate drug resistance. In this article, computational techniques such as molecular docking and molecular dynamics are applied to explore point mutations and their roles in affecting binding affinities for anti-TB drugs, often times lowering the protein’s affinity for the drug. Advances and adoption of computational techniques, chemoinformatics, and bioinformatics in molecular biosciences and resources supporting machine learning techniques are in abundance, and this has seen a spike in its use to predict mutations in Mtb. This article highlights the importance of molecular modeling in deducing how point mutations in proteins confer resistance through destabilizing binding sites of drugs and effectively inhibiting the drug action.
Collapse
Affiliation(s)
- Grace Mugumbate
- Department of Chemical Sciences, Midlands State University, Gweru, Zimbabwe
| | - Brilliant Nyathi
- Department of Chemistry, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Albert Zindoga
- Department of Chemistry, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Gadzikano Munyuki
- Department of Chemistry, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| |
Collapse
|
4
|
Moyo P, Mugumbate G, Eloff JN, Louw AI, Maharaj VJ, Birkholtz LM. Natural Products: A Potential Source of Malaria Transmission Blocking Drugs? Pharmaceuticals (Basel) 2020; 13:E251. [PMID: 32957668 PMCID: PMC7558993 DOI: 10.3390/ph13090251] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/17/2022] Open
Abstract
The ability to block human-to-mosquito and mosquito-to-human transmission of Plasmodium parasites is fundamental to accomplish the ambitious goal of malaria elimination. The WHO currently recommends only primaquine as a transmission-blocking drug but its use is severely restricted by toxicity in some populations. New, safe and clinically effective transmission-blocking drugs therefore need to be discovered. While natural products have been extensively investigated for the development of chemotherapeutic antimalarial agents, their potential use as transmission-blocking drugs is comparatively poorly explored. Here, we provide a comprehensive summary of the activities of natural products (and their derivatives) of plant and microbial origins against sexual stages of Plasmodium parasites and the Anopheles mosquito vector. We identify the prevailing challenges and opportunities and suggest how these can be mitigated and/or exploited in an endeavor to expedite transmission-blocking drug discovery efforts from natural products.
Collapse
Affiliation(s)
- Phanankosi Moyo
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag x20, Hatfield, 0028 Pretoria, South Africa;
| | - Grace Mugumbate
- Department of Chemistry, School of Natural Sciences and Mathematics, Chinhoyi University of Technology, Private Bag, 7724 Chinhoyi, Zimbabwe;
| | - Jacobus N. Eloff
- Phytomedicine Programme, Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Private Bag x04, Onderstepoort 0110 Pretoria, South Africa;
| | - Abraham I. Louw
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag x20, Hatfield, 0028 Pretoria, South Africa;
| | - Vinesh J. Maharaj
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag x20, Hatfield, 0028 Pretoria, South Africa;
| | - Lyn-Marié Birkholtz
- Malaria Parasite Molecular Laboratory, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag x20, Hatfield, 0028 Pretoria, South Africa;
| |
Collapse
|
5
|
Mendez D, Gaulton A, Bento AP, Chambers J, De Veij M, Félix E, Magariños MP, Mosquera JF, Mutowo P, Nowotka M, Gordillo-Marañón M, Hunter F, Junco L, Mugumbate G, Rodriguez-Lopez M, Atkinson F, Bosc N, Radoux CJ, Segura-Cabrera A, Hersey A, Leach AR. ChEMBL: towards direct deposition of bioassay data. Nucleic Acids Res 2020; 47:D930-D940. [PMID: 30398643 PMCID: PMC6323927 DOI: 10.1093/nar/gky1075] [Citation(s) in RCA: 962] [Impact Index Per Article: 240.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 10/18/2018] [Indexed: 12/31/2022] Open
Abstract
ChEMBL is a large, open-access bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012, 2014 and 2017 Nucleic Acids Research Database Issues. In the last two years, several important improvements have been made to the database and are described here. These include more robust capture and representation of assay details; a new data deposition system, allowing updating of data sets and deposition of supplementary data; and a completely redesigned web interface, with enhanced search and filtering capabilities.
Collapse
Affiliation(s)
- David Mendez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Anna Gaulton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - A Patrícia Bento
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jon Chambers
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Marleen De Veij
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eloy Félix
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - María Paula Magariños
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Juan F Mosquera
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Prudence Mutowo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Michal Nowotka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - María Gordillo-Marañón
- Institute of Cardiovascular Science, University College London, Gower Street, London WC1E 6BT, UK
| | - Fiona Hunter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Laura Junco
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Grace Mugumbate
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Milagros Rodriguez-Lopez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Francis Atkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Nicolas Bosc
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Chris J Radoux
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Aldo Segura-Cabrera
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Anne Hersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| |
Collapse
|
6
|
Shoko R, Manasa J, Maphosa M, Mbanga J, Mudziwapasi R, Nembaware V, Sanyika WT, Tinago T, Chikwambi Z, Mawere C, Matimba A, Mugumbate G, Mufandaedza J, Mulder N, Patterton H. Strategies and opportunities for promoting bioinformatics in Zimbabwe. PLoS Comput Biol 2018; 14:e1006480. [PMID: 30496170 PMCID: PMC6264469 DOI: 10.1371/journal.pcbi.1006480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Ryman Shoko
- Department of Biology, School of Natural Science and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
- * E-mail:
| | - Justen Manasa
- African Institute of Biomedical Science & Technology, Harare, Zimbabwe
| | - Mcebisi Maphosa
- Department of Crop and Soil Science, School of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | - Joshua Mbanga
- Department of Applied Biology and Biochemistry, Faculty of Applied Sciences, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Reagan Mudziwapasi
- Department of Crop and Soil Science, School of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | - Victoria Nembaware
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Walter T. Sanyika
- Department of Biotechnology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Tawanda Tinago
- Department of Biology, School of Natural Science and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Zedias Chikwambi
- Department of Biotechnology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Cephas Mawere
- Department of Biotechnology, School of Industrial Science and Technology, Harare Institute of Technology, Harare, Zimbabwe
| | - Alice Matimba
- Department of Clinical Pharmacology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Grace Mugumbate
- Department of Chemistry, School of Natural Science and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | | | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Hugh Patterton
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| |
Collapse
|
7
|
Malhotra S, Mugumbate G, Blundell TL, Higueruelo AP. TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species. Database (Oxford) 2018; 2017:3866794. [PMID: 29220433 PMCID: PMC5502366 DOI: 10.1093/database/bax041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/25/2017] [Indexed: 02/03/2023]
Abstract
Database URL http://www-cryst.bioc.cam.ac.uk/tible/.
Collapse
Affiliation(s)
- Sony Malhotra
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Grace Mugumbate
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Alicia P Higueruelo
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| |
Collapse
|
8
|
Mugumbate G, Mendes V, Blaszczyk M, Sabbah M, Papadatos G, Lelievre J, Ballell L, Barros D, Abell C, Blundell TL, Overington JP. Target Identification of Mycobacterium tuberculosis Phenotypic Hits Using a Concerted Chemogenomic, Biophysical, and Structural Approach. Front Pharmacol 2017; 8:681. [PMID: 29018348 PMCID: PMC5623190 DOI: 10.3389/fphar.2017.00681] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 09/12/2017] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium phenotypic hits are a good reservoir for new chemotypes for the treatment of tuberculosis. However, the absence of defined molecular targets and modes of action could lead to failure in drug development. Therefore, a combination of ligand-based and structure-based chemogenomic approaches followed by biophysical and biochemical validation have been used to identify targets for Mycobacterium tuberculosis phenotypic hits. Our approach identified EthR and InhA as targets for several hits, with some showing dual activity against these proteins. From the 35 predicted EthR inhibitors, eight exhibited an IC50 below 50 μM against M. tuberculosis EthR and three were confirmed to be also simultaneously active against InhA. Further hit validation was performed using X-ray crystallography yielding eight new crystal structures of EthR inhibitors. Although the EthR inhibitors attain their activity against M. tuberculosis by hitting yet undefined targets, these results provide new lead compounds that could be further developed to be used to potentiate the effect of EthA activated pro-drugs, such as ethionamide, thus enhancing their bactericidal effect.
Collapse
Affiliation(s)
- Grace Mugumbate
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom.,Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Michal Blaszczyk
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mohamad Sabbah
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - George Papadatos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Joel Lelievre
- Diseases of the Developing World, GlaxoSmithKline, Madrid, Spain
| | - Lluis Ballell
- Diseases of the Developing World, GlaxoSmithKline, Madrid, Spain
| | - David Barros
- Diseases of the Developing World, GlaxoSmithKline, Madrid, Spain
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - John P Overington
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom.,Medicines Discovery Catapult, Alderley Edge, United Kingdom
| |
Collapse
|
9
|
Cox JAG, Mugumbate G, Del Peral LVG, Jankute M, Abrahams KA, Jervis P, Jackenkroll S, Perez A, Alemparte C, Esquivias J, Lelièvre J, Ramon F, Barros D, Ballell L, Besra GS. Novel inhibitors of Mycobacterium tuberculosis GuaB2 identified by a target based high-throughput phenotypic screen. Sci Rep 2016; 6:38986. [PMID: 27982051 PMCID: PMC5159837 DOI: 10.1038/srep38986] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/16/2016] [Indexed: 12/16/2022] Open
Abstract
High-throughput phenotypic screens have re-emerged as screening tools in antibiotic discovery. The advent of such technologies has rapidly accelerated the identification of 'hit' compounds. A pre-requisite to medicinal chemistry optimisation programmes required to improve the drug-like properties of a 'hit' molecule is identification of its mode of action. Herein, we have combined phenotypic screening with a biased target-specific screen. The inosine monophosphate dehydrogenase (IMPDH) protein GuaB2 has been identified as a drugable target in Mycobacterium tuberculosis, however previously identified compounds lack the desired characteristics necessary for further development into lead-like molecules. This study has identified 7 new chemical series from a high-throughput resistance-based phenotypic screen using Mycobacterium bovis BCG over-expressing GuaB2. Hit compounds were identified in a single shot high-throughput screen, validated by dose response and subjected to further biochemical analysis. The compounds were also assessed using molecular docking experiments, providing a platform for their further optimisation using medicinal chemistry. This work demonstrates the versatility and potential of GuaB2 as an anti-tubercular drug target.
Collapse
Affiliation(s)
- Jonathan A. G. Cox
- Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Grace Mugumbate
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom, CB10 1SD
| | - Laura Vela-Glez Del Peral
- Molecular Discovery Research, GlaxoSmithKline, Santiago Grisolia 4, 28760 Tres Cantos, Madrid, Spain
| | - Monika Jankute
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Peter Jervis
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Stefan Jackenkroll
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Arancha Perez
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Carlos Alemparte
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Jorge Esquivias
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Joël Lelièvre
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Fernando Ramon
- Molecular Discovery Research, GlaxoSmithKline, Santiago Grisolia 4, 28760 Tres Cantos, Madrid, Spain
| | - David Barros
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Lluis Ballell
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| |
Collapse
|
10
|
Rebollo-Lopez MJ, Lelièvre J, Alvarez-Gomez D, Castro-Pichel J, Martínez-Jiménez F, Papadatos G, Kumar V, Colmenarejo G, Mugumbate G, Hurle M, Barroso V, Young RJ, Martinez-Hoyos M, González del Río R, Bates RH, Lopez-Roman EM, Mendoza-Losana A, Brown JR, Alvarez-Ruiz E, Marti-Renom MA, Overington JP, Cammack N, Ballell L, Barros-Aguire D. Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery. PLoS One 2015; 10:e0142293. [PMID: 26642067 PMCID: PMC4671658 DOI: 10.1371/journal.pone.0142293] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/19/2015] [Indexed: 12/12/2022] Open
Abstract
As a follow up to the antimycobacterial screening exercise and the release of GSK´s first Tres Cantos Antimycobacterial Set (TCAMS-TB), this paper presents the results of a second antitubercular screening effort of two hundred and fifty thousand compounds recently added to the GSK collection. The compounds were further prioritized based on not only antitubercular potency but also on physicochemical characteristics. The 50 most attractive compounds were then progressed for evaluation in three different predictive computational biology algorithms based on structural similarity or GSK historical biological assay data in order to determine their possible mechanisms of action. This effort has resulted in the identification of novel compounds and their hypothesized targets that will hopefully fuel future TB drug discovery and target validation programs alike.
Collapse
Affiliation(s)
| | - Joël Lelièvre
- Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid, Spain
- * E-mail: (JL); (MAMR)
| | | | - Julia Castro-Pichel
- Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Francisco Martínez-Jiménez
- Genome Biology Group, Centre Nacional d’Anàlisi Genòmica (CNAG), Barcelona, Spain
- Gene Regulation Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - George Papadatos
- European Molecular Biology Laboratory–European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom
| | - Vinod Kumar
- Computational Biology, Quantitative Sciences, GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
| | - Gonzalo Colmenarejo
- Centro de Investigación Básica, CSci Computational Chemistry, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Grace Mugumbate
- European Molecular Biology Laboratory–European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom
| | - Mark Hurle
- Computational Biology, Quantitative Sciences, GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
| | - Vanessa Barroso
- Centro de Investigación Básica, Platform Technology & Science, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Rob J. Young
- CSC Medicinal Chemistry, Medicines Research Centre, GlaxoSmithKline, Stevenage, Hertfordshire, United Kingdom
| | | | | | - Robert H. Bates
- Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | | | | | - James R. Brown
- Computational Biology, Quantitative Sciences, GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
| | - Emilio Alvarez-Ruiz
- Centro de Investigación Básica, Platform Technology & Science, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Marc A. Marti-Renom
- Genome Biology Group, Centre Nacional d’Anàlisi Genòmica (CNAG), Barcelona, Spain
- Gene Regulation Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- * E-mail: (JL); (MAMR)
| | - John P. Overington
- European Molecular Biology Laboratory–European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom
| | - Nicholas Cammack
- Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Lluís Ballell
- Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - David Barros-Aguire
- Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| |
Collapse
|
11
|
Mugumbate G, Overington JP. The relationship between target-class and the physicochemical properties of antibacterial drugs. Bioorg Med Chem 2015; 23:5218-24. [PMID: 25975639 PMCID: PMC4537081 DOI: 10.1016/j.bmc.2015.04.063] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 11/04/2022]
Abstract
The discovery of novel mechanism of action (MOA) antibacterials has been associated with the concept that antibacterial drugs occupy a differentiated region of physicochemical space compared to human-targeted drugs. With, in broad terms, antibacterials having higher molecular weight, lower logP and higher polar surface area (PSA). By analysing the physicochemical properties of about 1700 approved drugs listed in the ChEMBL database, we show, that antibacterials for whose targets are riboproteins (i.e., composed of a complex of RNA and protein) fall outside the conventional human 'drug-like' chemical space; whereas antibacterials that modulate bacterial protein targets, generally comply with the 'rule-of-five' guidelines for classical oral human drugs. Our analysis suggests a strong target-class association for antibacterials-either protein-targeted or riboprotein-targeted. There is much discussion in the literature on the failure of screening approaches to deliver novel antibacterial lead series, and linkage of this poor success rate for antibacterials with the chemical space properties of screening collections. Our analysis suggests that consideration of target-class may be an underappreciated factor in antibacterial lead discovery, and that in fact bacterial protein-targets may well have similar binding site characteristics to human protein targets, and questions the assumption that larger, more polar compounds are a key part of successful future antibacterial discovery.
Collapse
Affiliation(s)
- Grace Mugumbate
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - John P Overington
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom.
| |
Collapse
|
12
|
Mugumbate G, Abrahams KA, Cox JAG, Papadatos G, van Westen G, Lelièvre J, Calus ST, Loman NJ, Ballell L, Barros D, Overington JP, Besra GS. Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation. PLoS One 2015; 10:e0121492. [PMID: 25799414 PMCID: PMC4370846 DOI: 10.1371/journal.pone.0121492] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/01/2015] [Indexed: 01/21/2023] Open
Abstract
The lack of success in target-based screening approaches to the discovery of antibacterial agents has led to reemergence of phenotypic screening as a successful approach of identifying bioactive, antibacterial compounds. A challenge though with this route is then to identify the molecular target(s) and mechanism of action of the hits. This target identification, or deorphanization step, is often essential in further optimization and validation studies. Direct experimental identification of the molecular target of a screening hit is often complex, precisely because the properties and specificity of the hit are not yet optimized against that target, and so many false positives are often obtained. An alternative is to use computational, predictive, approaches to hypothesize a mechanism of action, which can then be validated in a more directed and efficient manner. Specifically here we present experimental validation of an in silico prediction from a large-scale screen performed against Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. The two potent anti-tubercular compounds studied in this case, belonging to the tetrahydro-1,3,5-triazin-2-amine (THT) family, were predicted and confirmed to be an inhibitor of dihydrofolate reductase (DHFR), a known essential Mtb gene, and already clinically validated as a drug target. Given the large number of similar screening data sets shared amongst the community, this in vitro validation of these target predictions gives weight to computational approaches to establish the mechanism of action (MoA) of novel screening hit.
Collapse
Affiliation(s)
- Grace Mugumbate
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Katherine A. Abrahams
- Institute of Microbiology and Infection (IMI), School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Jonathan A. G. Cox
- Institute of Microbiology and Infection (IMI), School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - George Papadatos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gerard van Westen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Joël Lelièvre
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Szymon T. Calus
- Institute of Microbiology and Infection (IMI), School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Nicholas J. Loman
- Institute of Microbiology and Infection (IMI), School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Lluis Ballell
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - David Barros
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - John P. Overington
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- * E-mail: (JPO); (GSB)
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection (IMI), School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- * E-mail: (JPO); (GSB)
| |
Collapse
|
13
|
Sharma RK, Younis Y, Mugumbate G, Njoroge M, Gut J, Rosenthal PJ, Chibale K. Synthesis and structure-activity-relationship studies of thiazolidinediones as antiplasmodial inhibitors of the Plasmodium falciparum cysteine protease falcipain-2. Eur J Med Chem 2014; 90:507-18. [PMID: 25486422 DOI: 10.1016/j.ejmech.2014.11.061] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 11/25/2014] [Accepted: 11/29/2014] [Indexed: 10/24/2022]
Abstract
Following a structure-based virtual screening, a series of 2,4 thiazolidinediones was synthesized in order to explore structure activity relationships for inhibition of the Plasmodium falciparum cysteine protease falcipain-2 (FP-2) and of whole cell antiparasitic activity. Most compounds exhibited low micromolar antiplasmodial activities against the P. falciparum drug resistant W2 strain. The most active compounds of the series were tested for in vitro microsomal metabolic stability and found to be susceptible to hepatic metabolism. Subsequent metabolite identification studies highlighted the metabolic hot spots. Molecular docking studies of a frontrunner inhibitor were carried out to determine the probable binding mode of this class of inhibitors in the active site of FP-2.
Collapse
Affiliation(s)
- Rajni Kant Sharma
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Yassir Younis
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Grace Mugumbate
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Mathew Njoroge
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Jiri Gut
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council, Drug Discovery and Development Unit, University of Cape Town, Rondebosch 7701, South Africa.
| |
Collapse
|
14
|
Mugumbate G, Papadatos G, Overington J. Deorphaning anti-tuberculosis compounds using chemogenomic approaches and data from the ChEMBL database. Int J Infect Dis 2014. [DOI: 10.1016/j.ijid.2014.03.834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
15
|
Jackson GE, Gamieldien R, Mugumbate G, Gäde G. Structural studies of adipokinetic hormones in water and DPC micelle solution using NMR distance restrained molecular dynamics. Peptides 2014; 53:270-7. [PMID: 24444447 DOI: 10.1016/j.peptides.2013.12.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 01/21/2023]
Abstract
Melme-CC (pGlu-Leu-Asn-Tyr-Ser-Pro-Asp-Trp amide) and Declu-CC (pGlu-Leu-Asn-Phe-Ser-Pro-Asn-Trp-Gly-Asn amide) are members of the insect adipokinetic hormone family with very different activities in the locust bioassay. The conformations of both peptides were determined in water and in a phospholipid (DPC) micelle solution using nuclear magnetic resonance (NMR) restrained molecular dynamics simulations. In water, Melme-CC has one dominant conformation while in DPC solution it has two preferred conformation. In water, Declu-CC has two conformations but in DPC solution it has one preferred conformation, which is similar to one of the water conformations. All the conformations have type IV β-turn between residues 4 and 7. The binding of the two peptides to the DPC micelle is different. Melme-CC does not bind strongly to the surface and is oriented with the β-turn facing the surface. Declu-CC interacts more strongly with the β-turn facing away from the surface. Both termini having hydrophobic interactions with the surface. In Declu-CC the side chain of Asn(7) projects away from the chain while in Melme-CC the Asp(7) side chain is folded inside the chain. The different orientation of these side chains may account for the much higher biological activity of Declu-CC in mobilizing lipids in the locust compared to the poor biological effect of Melme-CC in this bioassay. Receptor binding of Declu-CC was tested using a model AKH receptor from Anopheles gambiae. A free energy of binding of -38.5 kJ mol(-1) was found.
Collapse
Affiliation(s)
- Graham E Jackson
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa.
| | - Riedaa Gamieldien
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Grace Mugumbate
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Gerd Gäde
- Biological Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| |
Collapse
|
16
|
Mugumbate G, Newton AS, Rosenthal PJ, Gut J, Moreira R, Chibale K, Guedes RC. Novel anti-plasmodial hits identified by virtual screening of the ZINC database. J Comput Aided Mol Des 2013; 27:859-71. [PMID: 24158745 DOI: 10.1007/s10822-013-9685-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/12/2013] [Indexed: 01/16/2023]
Abstract
Increased resistance of Plasmodium falciparum to most available drugs challenges the control of malaria. Studies with protease inhibitors have suggested important roles for the falcipain family of cysteine proteases. These enzymes act in concert with other proteases to hydrolyze host erythrocyte hemoglobin in the parasite food vacuole. In order to find potential new antimalarial drugs, we screened in silico the ZINC database using two different protocols involving structure- and ligand-based methodologies. Our search identified 19 novel low micromolar inhibitors of cultured chloroquine resistant P. falciparum. The most active compound presented an IC50 value of 0.5 μM against cultured parasites and it also inhibited the cysteine protease falcipain-2 (IC50 = 25.5 μM). These results identify novel classes of antimalarials that are structurally different from those currently in use and which can be further derivatized to deliver leads suitable for optimisation.
Collapse
Affiliation(s)
- Grace Mugumbate
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | | | | | | | | | | | | |
Collapse
|
17
|
Chigorimbo-Murefu NTL, Njoroge M, Louw S, Mugumbate G, Chibale K. Drug metabolite generation using a laboratory evolved NADPH independent cytochrome P450: application of in vitro and in silico approaches. Drug Metab Lett 2013; 7:68-77. [PMID: 23957950 DOI: 10.2174/18723128112069990014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 07/07/2013] [Accepted: 07/07/2013] [Indexed: 11/22/2022]
Abstract
Twelve disparate drugs were subjected to metabolite generation by a laboratory evolved bacterial cytochrome P450 to investigate feasibility of the bacterial CYP to generate drug metabolites. Seven drugs were metabolised by the bacterial cytochromes to give diverse metabolites, which were compared to human metabolites reported in literature. Several non human metabolites were also generated by the bacterial CYP in addition to the known human metabolites. From docking studies and in silico sites of metabolism results, it was shown that the binding mode of the drug molecule and its distance from the active site in the binding pocket of the CYP was important for metabolism. This contribution reports, for the first time, previously uncharacterised metabolites of this bacterial cytochrome and demonstrates the potential usefulness of human CYP-based prediction software when used in combination with bacterial CYPs for metabolite generation.
Collapse
Affiliation(s)
| | | | | | | | - Kelly Chibale
- Institute of Infectious Diseases and Molecular Medicine University of Cape Town, Rondebosch 7701, South Africa.
| |
Collapse
|
18
|
Mugumbate G, Jackson GE, van der Spoel D, Kövér KE, Szilágyi L. Anopheles gambiae, Anoga-HrTH hormone, free and bound structure--a nuclear magnetic resonance experiment. Peptides 2013; 41:94-100. [PMID: 23439319 DOI: 10.1016/j.peptides.2013.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 01/31/2023]
Abstract
The spread of malaria by the female mosquito, Anopheles gambiae, is dependent, amongst other things, on its ability to fly. This in turn, is dependent on the adipokinetic hormone, Anoga-HrTH (pGlu-Leu-Thr-Phe-Thr-Pro-Ala-Trp-NH2). No crystal structure of this important neuropeptide is available and hence NMR restrained molecular dynamics was used to investigate its conformational space in aqueous solution and when bound to a membrane surface. The results showed that Anoga-HrTH has an almost cyclic conformation that is stabilized by a hydrogen bond between the C-terminus and Thr3. Upon docking of the agonist to its receptor, this H-bond is broken and the molecule adopts a more extended structure. Preliminary AKHR docking calculations give the free energy of binding to be -47.30 kJ/mol. There is a close correspondence between the structure of the docked ligand and literature structure-activity studies. Information about the 3D structure and binding mode of Anoga-HrTH to its receptor is vital for the design of suitable mimetics which can act as insecticides.
Collapse
Affiliation(s)
- Grace Mugumbate
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, South Africa
| | | | | | | | | |
Collapse
|
19
|
Espinoza-Moraga M, Njuguna NM, Mugumbate G, Caballero J, Chibale K. In silico comparison of antimycobacterial natural products with known antituberculosis drugs. J Chem Inf Model 2013; 53:649-60. [PMID: 23410241 DOI: 10.1021/ci300467b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The chemical space based on physicochemical properties and structural features of a diverse group of natural products with reported in vitro activity against different Mycobacterium tuberculosis strains is investigated using in silico tools. This is compared to the chemical space occupied by drugs currently recommended for the treatment of various forms of tuberculosis as well as compounds in preclinical and clinical development. Docking studies exploring possible binding affinities and modes of two main clusters of natural products on two different mycobacterial targets are also reported. Our docking results suggest that scytoscalarol, an antibacterial and antifungal guanidine-bearing sesterterpene, can inhibit arabinosyltransferase Mtb EmbC, and the β-carboline alkaloids 8-hydroxymanzamine A and manzamine A can bind to the oxidoreductase of Mtb INHA. On this basis, these products showing high binding affinities to the two targets in silico could be rationally selected for in vitro testing against these targets and/or semisynthetic modification.
Collapse
|
20
|
Mugumbate G, Jackson GE, van der Spoel D. Open conformation of adipokinetic hormone receptor from the malaria mosquito facilitates hormone binding. Peptides 2011; 32:553-9. [PMID: 20804800 DOI: 10.1016/j.peptides.2010.08.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 08/19/2010] [Accepted: 08/22/2010] [Indexed: 11/20/2022]
Abstract
Insect flight requires rapid mobilization of energy reserves during flight, which is mediated and regulated by hormonal control via adipokinetic hormones. The structure of the G-protein receptors to which these hormones bind, are crucial in understanding many of the physiological processes in which they play a central role. To date no 3D structure of an insect G-protein coupled receptor (GPCR) is available. Here, the first models of the 3D structures of a GPCR from the malaria mosquito are presented. Homology modeling of the receptor identified from the genome of Anopheles gambiae was used to construct two models of the receptor. The 7 transmembrane helical bundles of these two models are based on the crystal structures of beta2-adrenergic receptor and rhodopsin. The flexible loop regions were modeled using high temperature simulated annealing and constrained molecular dynamic simulations. The two receptor models differ in a number of critical features, the most important of which is that the rhodopsin-based model has a 'closed' structure while the beta2-based structure is 'open'. The 'open' conformation provides easy access of the hormone to the binding pocket. Docking calculations with the insect adipokinetic hormones, AKH-1 (pGlu-Leu-Thr-Phe-Thr-Pro-Ala-Trp-NH(2)) from the malaria mosquito and Del-CC (pGlu-Lys-Asn-Phe-Ser-Pro-Asn-Trp-Gly-Asn-NH(2)) from the blister beetle showed that while the binding motif of the two is similar, AKH-1 has more than 30 times higher affinity than Del-CC, which strongly suggests that the binding is specific, and that the correct binding site was identified. Using these models it is possible to design antagonists, which block the binding site and are thus species-specific insecticides.
Collapse
Affiliation(s)
- Grace Mugumbate
- Department of Chemistry, University of Cape Town, Private Bag x3, Rondebosch, 7701, Cape Town, South Africa
| | | | | |
Collapse
|