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Martins LS, Kruger HG, Naicker T, Alves CN, Lameira J, Araújo Silva JR. Computational insights for predicting the binding and selectivity of peptidomimetic plasmepsin IV inhibitors against cathepsin D. RSC Adv 2022; 13:602-614. [PMID: 36605626 PMCID: PMC9773328 DOI: 10.1039/d2ra06246a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Plasmepsins (Plms) are aspartic proteases involved in the degradation of human hemoglobin by P. falciparum and are essential for the survival and growth of the parasite. Therefore, Plm enzymes are reported as an important antimalarial drug target. Herein, we have applied molecular docking, molecular dynamics (MD) simulations, and binding free energy with the Linear Interaction Energy (LIE) approach to investigate the binding of peptidomimetic PlmIV inhibitors with a particular focus on understanding their selectivity against the human Asp protease cathepsin D (CatD). The residual decomposition analysis results suggest that amino acid differences in the subsite S3 of PlmIV and CatD are responsible for the higher selectivity of the 5a inhibitor. These findings yield excellent agreement with experimental binding data and provide new details regarding van der Waals and electrostatic interactions of subsite residues as well as structural properties of the PlmIV and CatD systems.
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Affiliation(s)
- Lucas Sousa Martins
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do ParáBelémPará 66075-110Brazil
| | | | - Tricia Naicker
- Catalysis and Peptide Research Unit, University of KwaZulu-NatalDurban 4000South Africa
| | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do ParáBelémPará 66075-110Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do ParáBelémPará 66075-110Brazil
| | - José Rogério Araújo Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do ParáBelémPará 66075-110Brazil
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Khan A, Sohaib M, Ullah R, Hussain I, Niaz S, Malak N, de la Fuente J, Khan A, Aguilar-Marcelino L, Alanazi AD, Ben Said M. Structure-based in silico design and in vitro acaricidal activity assessment of Acacia nilotica and Psidium guajava extracts against Sarcoptes scabiei var. cuniculi. Parasitol Res 2022; 121:2901-2915. [PMID: 35972548 DOI: 10.1007/s00436-022-07615-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/31/2022] [Indexed: 12/01/2022]
Abstract
Infestation by Sarcoptes scabiei var. cuniculi mite causes scabies in humans and mange in animals. Alternative methods for developing environmentally friendly and effective plant-based acaricides are now a priority. The purpose of this research was the in silico design and in vitro evaluation of the efficacy of ethanol extracts of Acacia nilotica and Psidium guajava plant leaves against S. scabiei. Chem-Draw ultra-software (v. 12.0.2.1076.2010) was used to draw 36 distinct compounds from these plants that were employed as ligands in docking tests against S. scabiei Aspartic protease (SsAP). With docking scores of - 6.50993 and - 6.16359, respectively, clionasterol (PubChem CID 457801) and mangiferin (PubChem CID 5281647) from A. nilotica inhibited the targeted protein SsAP, while only beta-sitosterol (PubChem CID 222284) from P. guajava interacted with the SsAP active site with a docking score of - 6.20532. Mortality in contact bioassay at concentrations of 0.25, 0.5, 1.0, and 2.0 g/ml was determined to calculate median lethal time (LT50) and median lethal concentration (LC50) values. Acacia nilotica extract had an LC50 value of 0.218 g/ml compared to P. guajava extract, which had an LC50 value of 0.829 g/ml at 6 h. These results suggest that A. nilotica extract is more effective in killing mites, and these plants may have novel acaricidal properties against S. scabiei. Further research should focus on A. nilotica as a potential substitute for clinically available acaricides against resistant mites.
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Affiliation(s)
- Afshan Khan
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Sohaib
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Rooh Ullah
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Imdad Hussain
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Sadaf Niaz
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Nosheen Malak
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - José de la Fuente
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005, Ciudad Real, Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Adil Khan
- Department of Zoology, Bacha Khan University Charsadda, Charsadda, Khyber Pakhtunkhwa, Pakistan.
| | - Liliana Aguilar-Marcelino
- National Center for Disciplinary Research in Animal Health and Safety (INIFAP), Km 11 Federal Road Cuernavaca-Cuautla, 62550, Jiutepec, Morelos, México
| | - Abdullah D Alanazi
- Department of Biological Sciences, Faculty of Science and Humanities, Shaqra University, 1040 Ad-Dawadimi, 11911, Shaqra, Saudi Arabia
| | - Mourad Ben Said
- Department of Basic Sciences, Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, 2010, Manouba, Tunisia.,Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, 2010, Manouba, Tunisia
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3
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Abstract
Sarcoptes scabiei is a causative organism for scabies that affects an estimated global population of 300 million and remains a disease of significant concern. Recently, a number of potential drug targets were identified for scabies, including hydrolytic enzymes, inactivated paralogues of hydrolytic enzymes, inhibitors of host proteolytic enzymes and other proteins of interest. These discoveries remain confined to academic laboratories and institutions, failing to attract interest from researchers in commercial drug development. Here, we summarize the latest developments in the scabies mite biology and the drug targets that were subsequently identified, and we propose several peptide and nonpeptide ligands targeting the hot spots for protein-protein interactions. We also identify gaps in the development of ligands as inhibitors or modulators of these macromolecules.
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4
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Cheuka PM, Dziwornu G, Okombo J, Chibale K. Plasmepsin Inhibitors in Antimalarial Drug Discovery: Medicinal Chemistry and Target Validation (2000 to Present). J Med Chem 2020; 63:4445-4467. [PMID: 31913032 DOI: 10.1021/acs.jmedchem.9b01622] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plasmepsins represent novel antimalarial drug targets. However, plasmepsin-based antimalarial drug discovery efforts in the past 2 decades have generally suffered some drawbacks including lack of translatability of target inhibition to potent parasite inhibition in vitro and in vivo as well as poor selectivity over the related human aspartic proteases. Most studies reported in this period have over-relied on the use of hemoglobinase plasmepsins I-IV (particularly I and II) as targets for the new inhibitors even though these are known to be nonessential at the asexual stage of parasite development. Therefore, future antimalarial drug discovery efforts seeking to identify plasmepsin inhibitors should focus on incorporating non-hemoglobinase plasmepsins such as V, IX, and X in their screening in order to maximize chances of success. Additionally, there is need to go beyond just target enzymatic activity profiling to establishing cellular activity, physicochemical as well as drug metabolism and pharmacokinetics properties and finally in vivo proof-of-concept while ensuring selectivity over related human host proteases.
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Affiliation(s)
- Peter Mubanga Cheuka
- Department of Chemistry, University of Zambia, Great East Road Campus, P.O. Box 32379, Lusaka, Zambia
| | - Godwin Dziwornu
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University, 701 West 168th Street, New York, New York 10032, United States
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.,Drug Discovery and Development Centre (H3D), 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 Research Unit, University of Cape Town, Rondebosch 7701, South Africa
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5
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Abiri A. Plerixafor and related macrocyclic amines are potential drug candidates in treatment of malaria by "filling the flap" region of plasmepsin enzymes. Med Hypotheses 2018; 118:68-73. [PMID: 30037618 DOI: 10.1016/j.mehy.2018.06.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/24/2018] [Accepted: 06/19/2018] [Indexed: 11/30/2022]
Abstract
Death by Plasmodium falsiparum, the leading cause of malaria, is going to remain a major obstacle among the infectious diseases. Plasmepsin aspartic proteases are key proteins in the pathogenesis of plasmodium species which break down the hemoglobin and exploit it as a source of amino acids. These enzymes are one of the favorite targeting agents for medicinal chemists to design new drugs. Plasmepsin proteins show a "flap" region in their N-terminal domain, predisposing them to a good "filler" drug with an exceptional affinity to this enzyme. Plerixafor (Mozobil®, AMD3100), a CXCR4 antagonist with a bicyclam ring, historically discovered as an impurity in a mixture which had anti-HIV properties, is now a FDA approved drug for mobilizing haematopoietic stem cells in cancer patients. In this hypothesis, we focused on the similarity of the structure of plerixafor and its analogues with heme functional group of hemoglobin, the main substrate of plasmepsin, and also with some other recent azamacrocyclic compounds demonstrating antimalarial activity, to test whether these compounds are capable of exhibiting antimalarial activity by inhibiting plasmepsin or not. A preliminary in silico docking study was used to evaluate this hypothesis and docking results indicated that macrocyclic cyclams and cyclens can reliably act as potent lead drug or central pharmacophore in developing new plasmepsin inhibitors as compared with previously designed plasmepsin II inhibitors.
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Affiliation(s)
- Ardavan Abiri
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran; Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
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6
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Kumar P, Kaalia R, Srinivasan A, Ghosh I. Multiple target-based pharmacophore design from active site structures. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:1-19. [PMID: 29243947 DOI: 10.1080/1062936x.2017.1401555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 11/02/2017] [Indexed: 06/07/2023]
Abstract
Health care systems have benefitted from rational drug discovery processes like vHTS, virtual high throughput screening pharmacophores and quantitative structure-activity relationships, and many challenges have been explored using such techniques: decisions on specificity and selectivity are made after screening millions of molecules for multiple targets. Recent challenges in drug research emphasize the design of drugs that bind with more than one target of interest (multi-target) and do not bind with undesirable targets. This work attempts to use a three-dimensional interaction profile of the active site of a class of proteins, identify selective positions for the binding of functional groups, called features, and develop ensembles of multi-targeted pharmacophores that retain specificity and selectivity. The goal of this study is to develop multi-target pharmacophores by computational methods using protein structures alone to guide the discovery of novel inhibitors of plasmepsins, displaying selectivity over their human homologs, cathepsin D and pepsin. The development of such novel tools is attempted using a combination of different approaches such as the molecular interaction field, clique graph and inductive logic programming to identify and compare specific and selective complementary features. The identification of selective combinations of features has resulted in the design of multi-featured specific and selective pharmacophores that are validated using antimalarial compounds in ChEMBL that are known for their anti-plasmepsin II activity. This novel method is computationally less intensive and is applicable to any known class of target structures for finding specific and selective binders simultaneously.
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Affiliation(s)
- P Kumar
- a School of Computational and Integrative Sciences , Jawaharlal Nehru University , New Delhi , India
| | - R Kaalia
- b Biomedical Informatics Lab , Nanyang Technological University , Singapore
| | - A Srinivasan
- c Department of Computer Science and Information Systems , BITS , Goa , India
| | - I Ghosh
- a School of Computational and Integrative Sciences , Jawaharlal Nehru University , New Delhi , India
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7
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Roy KK. Targeting the active sites of malarial proteases for antimalarial drug discovery: approaches, progress and challenges. Int J Antimicrob Agents 2017; 50:287-302. [PMID: 28668681 DOI: 10.1016/j.ijantimicag.2017.04.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 04/12/2017] [Accepted: 04/27/2017] [Indexed: 02/08/2023]
Abstract
Malaria is an infectious disease causing vast mortality and morbidity worldwide. Although antimalarial drugs are effective in several parts of the world, there is a serious threat to malaria control as malaria parasites are continuously developing widespread resistance against currently available antimalarial drugs, including artemisinin. Such widespread antimalarial drug resistance confirms the need to improve the efficacy of existing or new drugs as well as to develop alternative treatments through the identification of novel drug targets and the development of candidate drugs. Similar to proteases in other parasitic diseases such as leishmaniasis, schistosomiasis, Chagas disease and African sleeping sickness, malarial proteases constitute the major virulence factors in malaria. Malarial proteases belong to several classes and many of them have been targeted for the design and discovery of antimalarial agents. This review summarises the approaches, progress and challenges in the design of small-molecule inhibitors as antimalarial drugs targeting the inhibition of various malarial proteases.
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Affiliation(s)
- Kuldeep K Roy
- National Institute of Pharmaceutical Education and Research (NIPER), 4 Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India.
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8
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Structural basis for plasmepsin V inhibition that blocks export of malaria proteins to human erythrocytes. Nat Struct Mol Biol 2015. [PMID: 26214367 DOI: 10.1038/nsmb.3061] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Plasmepsin V, an essential aspartyl protease of malaria parasites, has a key role in the export of effector proteins to parasite-infected erythrocytes. Consequently, it is an important drug target for the two most virulent malaria parasites of humans, Plasmodium falciparum and Plasmodium vivax. We developed a potent inhibitor of plasmepsin V, called WEHI-842, which directly mimics the Plasmodium export element (PEXEL). WEHI-842 inhibits recombinant plasmepsin V with a half-maximal inhibitory concentration of 0.2 nM, efficiently blocks protein export and inhibits parasite growth. We obtained the structure of P. vivax plasmepsin V in complex with WEHI-842 to 2.4-Å resolution, which provides an explanation for the strict requirements for substrate and inhibitor binding. The structure characterizes both a plant-like fold and a malaria-specific helix-turn-helix motif that are likely to be important in cleavage of effector substrates for export.
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9
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New paradigm of an old target: an update on structural biology and current progress in drug design towards plasmepsin II. Eur J Med Chem 2015; 95:324-48. [PMID: 25827401 DOI: 10.1016/j.ejmech.2015.03.049] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 03/09/2015] [Accepted: 03/20/2015] [Indexed: 11/20/2022]
Abstract
Malaria is one of the major parasitic disease whose rapid spreading and mortality rate affects all parts of the world especially several parts of Asia as well as Africa. The emergence of multi-drug resistant strains hamper the progress of current antimalarial therapy and displayed an urgent need for new antimalarials by targeting novel drug targets. Until now, several promising targets were explored in order to develop a promising Achilles hill to counter malaria. Plasmepsin, an aspartic protease, which is involved in the hemoglobin breakdown into smaller peptides emerged as a crucial target to develop new chemical entities to counter malaria. Due to early crystallographic evidence, plasmepsin II (Plm II) emerged as well explored target to develop novel antimalarials as well as a starting point to develop inhibitors targeting some other subtypes of plasmepsins i.e. Plm I, II, IV and V. With the advancements in drug discovery, several computational and synthetic approaches were employed in order to develop novel inhibitors targeting Plm II. Strategies such as fragment based drug design, molecular dynamics simulation, double drug approach etc. were employed in order to develop new chemical entities targeting Plm II. But majority of Plm II inhibitors suffered from poor selectivity over cathepsin D as well as other subtypes of plasmepsins. This review highlights an updated account of drug discovery efforts targeting plasmepsin II from a medicinal chemistry perspective.
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10
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Sleebs BE, Gazdik M, O'Neill MT, Rajasekaran P, Lopaticki S, Lackovic K, Lowes K, Smith BJ, Cowman AF, Boddey JA. Transition state mimetics of the Plasmodium export element are potent inhibitors of Plasmepsin V from P. falciparum and P. vivax. J Med Chem 2014; 57:7644-62. [PMID: 25167370 DOI: 10.1021/jm500797g] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Following erythrocyte invasion, malaria parasites export a catalogue of remodeling proteins into the infected cell that enable parasite development in the human host. Export is dependent on the activity of the aspartyl protease, plasmepsin V (PMV), which cleaves proteins within the Plasmodium export element (PEXEL; RxL↓xE/Q/D) in the parasite's endoplasmic reticulum. Here, we generated transition state mimetics of the native PEXEL substrate that potently inhibit PMV isolated from Plasmodium falciparum and Plasmodium vivax. Through optimization, we identified that the activity of the mimetics was completely dependent on the presence of P1 Leu and P3 Arg. Treatment of P. falciparum-infected erythrocytes with a set of optimized mimetics impaired PEXEL processing and killed the parasites. The striking effect of the compounds provides a clearer understanding of the accessibility of the PMV active site and reaffirms the enzyme as an attractive target for the design of future antimalarials.
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Affiliation(s)
- Brad E Sleebs
- The Walter and Eliza Hall Institute of Medical Research , 1G Royal Parade, Parkville 3052, Victoria, Australia
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11
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Jin H, Xu Z, Cui K, Zhang T, Lu W, Huang J. Dietary flavonoids fisetin and myricetin: dual inhibitors of Plasmodium falciparum falcipain-2 and plasmepsin II. Fitoterapia 2014; 94:55-61. [PMID: 24468190 DOI: 10.1016/j.fitote.2014.01.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 01/14/2014] [Accepted: 01/17/2014] [Indexed: 12/27/2022]
Abstract
Malaria is one of the most devastating infectious diseases in the developing world. Until now, only one candidate malaria vaccine RTS,S/AS01 has shown modest protection in phase 3 trial in African infants. Hence the treatment of malaria still depends on the current chemotherapeutic drugs. Considering the resistance of malaria parasites to almost all used antimalarial drugs, aiming at multi-targets rather than a single target will be a more promising strategy. Previous studies have shown that myricetin and fisetin exhibited in vitro antimalarial activity against Plasmodium falciparum, but very little research focused on the molecular mechanism for their parasiticidal activity. The cysteine protease falcipain-2 and aspartic protease plasmepsin II have long been considered as important antimalarial drug targets, especially combined inhibition of these two proteases. In this study, we determined that myricetin and fisetin are dual inhibitors of falcipain-2 and plasmepsin II, which might account for their antimalarial properties. Overall, the dual inhibition of falcipain-2 and plasmepsin II by myricetin and fisetin has shed light on a possible mechanism for their antimalarial activity and provided a rationale for further development as antimalarial drugs.
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Affiliation(s)
- Huangtao Jin
- Shanghai Key Laboratory of New Drug Design, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhongyu Xu
- Shanghai Key Laboratory of New Drug Design, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Kunqiang Cui
- Shanghai Key Laboratory of New Drug Design, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Tianshu Zhang
- Shanghai Key Laboratory of New Drug Design, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weiqiang Lu
- The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Jin Huang
- Shanghai Key Laboratory of New Drug Design, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
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Song Y, Jin H, Liu X, Zhu L, Huang J, Li H. Discovery of non-peptide inhibitors of Plasmepsin II by structure-based virtual screening. Bioorg Med Chem Lett 2013; 23:2078-82. [DOI: 10.1016/j.bmcl.2013.01.128] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/26/2013] [Accepted: 01/30/2013] [Indexed: 10/27/2022]
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13
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Sandgren V, Bäck M, Kvarnström I, Dahlgren A. Design and Synthesis of Hydroxyethylene-Based BACE-1 Inhibitors Incorporating Extended P1 Substituents. THE OPEN MEDICINAL CHEMISTRY JOURNAL 2013; 7:1-15. [PMID: 23585822 PMCID: PMC3617544 DOI: 10.2174/1874104501307010001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 11/18/2012] [Accepted: 11/26/2012] [Indexed: 01/14/2023]
Abstract
Novel BACE-1 inhibitors with a hydroxyethylene central core have been developed. Modified P1´ and extended P1 substituents were incorporated with the aim to explore potential interactions with the S1´ and the S1-S3 pocket, respectively, of BACE-1. Inhibitors were identified displaying IC50 values in the nanomolar range, i.e. 69 nM for the most potent compound. Possible inhibitor interactions with the enzyme are also discussed.
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Affiliation(s)
- Veronica Sandgren
- Department of Chemistry, Linköping University, S-581 83 Linköping, Sweden
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14
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Dali B, Keita M, Megnassan E, Frecer V, Miertus S. Insight into Selectivity of Peptidomimetic Inhibitors with Modified Statine Core for Plasmepsin II of Plasmodium falciparum over Human Cathepsin D. Chem Biol Drug Des 2012; 79:411-30. [DOI: 10.1111/j.1747-0285.2011.01276.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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15
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Bhaumik P, Gustchina A, Wlodawer A. Structural studies of vacuolar plasmepsins. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1824:207-23. [PMID: 21540129 PMCID: PMC3154504 DOI: 10.1016/j.bbapap.2011.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Revised: 04/11/2011] [Accepted: 04/12/2011] [Indexed: 10/18/2022]
Abstract
Plasmepsins (PMs) are pepsin-like aspartic proteases present in different species of parasite Plasmodium. Four Plasmodium spp. (P. vivax, P. ovale, P. malariae, and the most lethal P. falciparum) are mainly responsible for causing human malaria that affects millions worldwide. Due to the complexity and rate of parasite mutation coupled with regional variations, and the emergence of P. falciparum strains which are resistant to antimalarial agents such as chloroquine and sulfadoxine/pyrimethamine, there is constant pressure to find new and lasting chemotherapeutic drug therapies. Since many proteases represent therapeutic targets and PMs have been shown to play an important role in the survival of parasite, these enzymes have recently been identified as promising targets for the development of novel antimalarial drugs. The genome of P. falciparum encodes 10 PMs (PMI, PMII, PMIV-X and histo-aspartic protease (HAP)), 4 of which (PMI, PMII, PMIV and HAP) reside within the food vacuole, are directly involved in degradation of human hemoglobin, and share 50-79% amino acid sequence identity. This review focuses on structural studies of only these four enzymes, including their orthologs in other Plasmodium spp.. Almost all original crystallographic studies were performed with PMII, but more recent work on PMIV, PMI, and HAP resulted in a more complete picture of the structure-function relationship of vacuolar PMs. Many structures of inhibitor complexes of vacuolar plasmepsins, as well as their zymogens, have been reported in the last 15 years. Information gained by such studies will be helpful for the development of better inhibitors that could become a new class of potent antimalarial drugs. This article is part of a Special Issue entitled: Proteolysis 50 years after the discovery of lysosome.
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Affiliation(s)
- Prasenjit Bhaumik
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Alla Gustchina
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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16
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Ojha PK, Roy K. Exploring molecular docking and QSAR studies of plasmepsin-II inhibitor di-tertiary amines as potential antimalarial compounds. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.548384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Probir Kumar Ojha
- a Drug Theoretics and Cheminformatics Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata, India
| | - Kunal Roy
- a Drug Theoretics and Cheminformatics Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata, India
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17
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Liu P, Marzahn MR, Robbins AH, Gutiérrez-de-Terán H, Rodríguez D, McClung SH, Stevens SM, Yowell CA, Dame JB, McKenna R, Dunn BM. Recombinant plasmepsin 1 from the human malaria parasite plasmodium falciparum: enzymatic characterization, active site inhibitor design, and structural analysis. Biochemistry 2009; 48:4086-99. [PMID: 19271776 DOI: 10.1021/bi802059r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A mutated form of truncated proplasmepsin 1 (proPfPM1) from the human malaria parasite Plasmodium falciparum, proPfPM1 K110pN, was generated and overexpressed in Escherichia coli. The automaturation process was carried out at pH 4.0 and 4.5, and the optimal catalytic pH of the resulting mature PfPM1 was determined to be pH 5.5. This mature PfPM1 showed comparable binding affinity to peptide substrates and inhibitors with the naturally occurring form isolated from parasites. The S3-S3' subsite preferences of the recombinant mature PfPM1 were explored using combinatorial chemistry based peptide libraries. On the basis of the results, a peptidomimetic inhibitor (compound 1) was designed and yielded 5-fold selectivity for binding to PfPM1 versus the homologous human cathepsin D (hcatD). The 2.8 A structure of the PfPM2-compound 1 complex is reported. Modeling studies were conducted using a series of peptidomimetic inhibitors (compounds 1-6, Table 3) and three plasmepsins: the crystal structure of PfPM2, and homology derived models of PfPM1 and PfPM4.
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Affiliation(s)
- Peng Liu
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida 32610-0245, USA
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18
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Bäck M, Nyhlén J, Kvarnström I, Appelgren S, Borkakoti N, Jansson K, Lindberg J, Nyström S, Hallberg A, Rosenquist Å, Samuelsson B. Design, synthesis and SAR of potent statine-based BACE-1 inhibitors: Exploration of P1 phenoxy and benzyloxy residues. Bioorg Med Chem 2008; 16:9471-86. [DOI: 10.1016/j.bmc.2008.09.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 09/10/2008] [Accepted: 09/16/2008] [Indexed: 10/21/2022]
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19
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Gayathri P, Balaram H, Murthy MRN. Structural biology of plasmodial proteins. Curr Opin Struct Biol 2007; 17:744-54. [PMID: 17875391 DOI: 10.1016/j.sbi.2007.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 08/01/2007] [Accepted: 08/02/2007] [Indexed: 11/29/2022]
Abstract
Malaria is a global disease infecting several million individuals annually. Malarial infection is particularly severe in the poorest parts of the world and is a major drain on their limited resources. Development of drug resistance and absence of a preventive vaccine have led to an immediate necessity for identifying new drug targets to combat malaria. Understanding the intricacies of parasite biology is essential to design novel intervention strategies that can prevent the growth of the parasite. The structural biology approach towards this goal involves the identification of key differences in the structures of the human and parasite enzymes and the determination of unique protein structures essential for parasite survival. This review covers the work on structural biology of plasmodial proteins carried out during the period of January 2006 to June 2007.
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Affiliation(s)
- P Gayathri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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20
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Ersmark K, Samuelsson B, Hallberg A. Plasmepsins as potential targets for new antimalarial therapy. Med Res Rev 2007; 26:626-66. [PMID: 16838300 DOI: 10.1002/med.20082] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Malaria is one of the major diseases in the world. Due to the rapid spread of parasite resistance to available antimalarial drugs there is an urgent need for new antimalarials with novel mechanisms of action. Several promising targets for drug intervention have been revealed in recent years. This review addresses the parasitic aspartic proteases termed plasmepsins (Plms) that are involved in the hemoglobin catabolism that occurs during the erythrocytic stage of the malarial parasite life cycle. Four Plasmodium species are responsible for human malaria; P. vivax, P. ovale, P. malariae, and P. falciparum. This review focuses on inhibitors of the haemoglobin-degrading plasmepsins of the most lethal species, P. falciparum; Plm I, Plm II, Plm IV, and histo-aspartic protease (HAP). Previously, Plm II has attracted the most attention. With the identification and characterization of new plasmepsins and the results from recent plasmepsin knockout studies, it now seems clear that in order to achieve high-antiparasitic activities in P. falciparum-infected erythrocytes it is necessary to inhibit several of the haemoglobin-degrading plasmepsins. Herein we summarize the structure-activity relationships of the Plm I, II, IV, and HAP inhibitors. These inhibitors represent all classes which, to the best of our knowledge, have been disclosed in journal articles to date. The 3D structures of inhibitor/plasmepsin II complexes available in the protein data bank are briefly discussed and compared.
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Affiliation(s)
- Karolina Ersmark
- Department of Medicinal Chemistry, Uppsala University, BMC, SE-751 23 Uppsala, Sweden
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21
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Kesavulu MM, Prakasha Gowda AS, Ramya TNC, Surolia N, Suguna K. Plasmepsin inhibitors: design, synthesis, inhibitory studies and crystal structure analysis. ACTA ACUST UNITED AC 2007; 66:211-9. [PMID: 16138859 DOI: 10.1111/j.1399-3011.2005.00288.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmepsin group of enzymes are key enzymes in the life cycle of malarial parasites. As inhibition of plasmepsins leads to the parasite's death, these enzymes can be utilized as potential drug targets. Although many drugs are available, it has been observed that Plasmodium falciparum, the species that causes most of the malarial infections and subsequent death, has developed resistance against most of the drugs. Based on the cleavage sites of hemglobin, the substrate for plasmepsins, we have designed two compounds (p-nitrobenzoyl-leucine-beta-alanine and p-nitrobenzoyl-leucine-isonipecotic acid), synthesized them, solved their crystal structures and studied their inhibitory effect using experimental and theoretical (docking) methods. In this paper, we discuss the synthesis, crystal structures and inhibitory nature of these two compounds which have a potential to inhibit plasmepsins.
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Affiliation(s)
- M M Kesavulu
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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22
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Weik S, Luksch T, Evers A, Böttcher J, Sotriffer CA, Hasilik A, Löffler HG, Klebe G, Rademann J. The potential of P1 site alterations in peptidomimetic protease inhibitors as suggested by virtual screening and explored by the use of C-C-coupling reagents. ChemMedChem 2006; 1:445-57. [PMID: 16892380 DOI: 10.1002/cmdc.200500027] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A synthetic concept is presented that allows the construction of peptide isostere libraries through polymer-supported C-acylation reactions. A phosphorane linker reagent is used as a carbanion equivalent; by employing MSNT as a coupling reagent, the C-acylation can be conducted without racemization. Diastereoselective reduction was effected with L-selectride. The reagent linker allows the preparation of a norstatine library with full variation of the isosteric positions including the P1 side chain that addresses the protease S1 pocket. Therefore, the concept was employed to investigate the P1 site specificity of peptide isostere inhibitors systematically. The S1 pocket of several aspartic proteases including plasmepsin II and cathepsin D was modeled and docked with approximately 500 amino acid side chains. Inspired by this virtual screen, a P1 site mutation library was designed, synthesized, and screened against three aspartic proteases (plasmepsin II, HIV protease, and cathepsin D). The potency of norstatine inhibitors was found to depend strongly on the P1 substituent. Large, hydrophobic residues such as biphenyl, 4-bromophenyl, and 4-nitrophenyl enhanced the inhibitory activity (IC50) by up to 70-fold against plasmepsin II. In addition, P1 variation introduced significant selectivity, as up to 9-fold greater activity was found against plasmepsin II relative to human cathepsin D. The active P1 site residues did not fit into the crystal structure; however, molecular dynamics simulation suggested a possible alternative binding mode.
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Affiliation(s)
- Steffen Weik
- Leibniz Institute for Molecular Pharmacology (FMP), and Free University Berlin, Takustrasse 3, 14195 Berlin, Germany
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Nyborg AC, Ladd TB, Jansen K, Kukar T, Golde TE. Intramembrane proteolytic cleavage by human signal peptide peptidase like 3 and malaria signal peptide peptidase. FASEB J 2006; 20:1671-9. [PMID: 16873890 DOI: 10.1096/fj.06-5762com] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Signal peptide peptidase (SPP) is an intramembrane cleaving protease (I-CLiP) identified by its cleavage of several type II membrane signal peptides. To date, only human SPP has been directly shown to have proteolytic activity. Here we demonstrate that the most closely related human homologue of SPP, signal peptide peptidase like 3 (SPPL3), cleaves a SPP substrate, but a more distantly related homologue, signal peptide peptidase like 2b (SPPL2b), does not. These data provide strong evidence that the SPP and SPPL3 have conserved active sites and suggest that the active sites SPPL2b is distinct. We have also synthesized a cDNA designed to express the single SPP gene present in Plasmodium falciparum and cloned this into a mammalian expression vector. When the malaria SPP protein is expressed in mammalian cells it cleaves a SPP substrate. Notably, several human SPP inhibitors block the proteolytic activity of malarial SPP (mSPP). Studies from several model organisms that express multiple SPP homologs demonstrate that the silencing of a single SPP homologue is lethal. Based on these data, we hypothesize that mSPP is a potential a novel therapeutic target for malaria.
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Affiliation(s)
- Andrew C Nyborg
- Department of Neuroscience, Mayo Clinic Jacksonville, Mayo Clinic College of Medicine, 4500 San Pablo Rd., Jacksonville, Florida 32224, USA
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Boss C, Corminboeuf O, Grisostomi C, Weller T. Inhibitors of aspartic proteases – potential antimalarial agents. Expert Opin Ther Pat 2006. [DOI: 10.1517/13543776.16.3.295] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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