1
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Tran L, Tu VL, Dadam MN, Aziz JMA, Duy TLD, Ahmed HHH, Kwaah PA, Quoc HN, Van Dat T, Mizuta S, Hirayama K, Huy NT. Antimalarial activities of benzothiazole analogs: A systematic review. Fundam Clin Pharmacol 2024; 38:410-464. [PMID: 38146774 DOI: 10.1111/fcp.12974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/25/2023] [Accepted: 11/10/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Benzothiazole derivatives have been reported to possess a wide range of biological activities, including antimalarial activity. This systematic review aims to summarize and evaluate the antimalarial activities of benzothiazole analogs. METHODS We conducted an electronic search using nine databases in October 2017 and subsequently updated in September 2022. We included all original in vitro and in vivo studies that documented the antimalarial activities of compounds containing benzothiazole analogs with no restriction. The risk of bias of each included study was assessed by ToxRTool. RESULTS Twenty-eight articles were included in our study, which are in vitro, in vivo, or both. Of these, 232 substances were identified to have potent antiplasmodial activity against various strains of the malaria parasite. Benzothiazole analogs show different antimalarial mechanisms, including inhibition of Plasmodium falciparum enzymes in in vitro studies and inhibition of blood parasites in in vivo studies. CONCLUSIONS Benzothiazole derivatives are promising substances for treating malaria. The structure-activity relationship studies suggest that the substitution pattern of the benzothiazole scaffold plays a crucial role in determining the antimalarial activity of the analog.
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Affiliation(s)
- Linh Tran
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City, Vietnam
- Faculty of Natural Sciences, Duy Tan University, Da Nang, Vietnam
| | - Vo Linh Tu
- Online Research Club (https://www.onlineresearchclub.org/), Nagasaki, Japan
- Faculty of Traditional Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Mohammad Najm Dadam
- Online Research Club (https://www.onlineresearchclub.org/), Nagasaki, Japan
- Department of Geriatrics, Helios Klinikum Schwelm, Schwelm, Germany
| | - Jeza Muhamad Abdul Aziz
- Biomedical Science Department, Komar University of Science and Technology, Sulaimaniyah, Kurdistan Region, Iraq
- Baxshin Research Center, Baxshin Hospital, Sulaimaniyah, Kurdistan Region, Iraq
| | - Tran Le Dinh Duy
- Online Research Club (https://www.onlineresearchclub.org/), Nagasaki, Japan
- College of Health Sciences, VinUniversity, Hanoi, Vietnam
| | - Hajer Hatim Hassan Ahmed
- Online Research Club (https://www.onlineresearchclub.org/), Nagasaki, Japan
- Faculty of Medicine, Alzaiem Alazhari University, Khartoum, Sudan
| | - Patrick Amanning Kwaah
- Online Research Club (https://www.onlineresearchclub.org/), Nagasaki, Japan
- Department of Internal Medicine, Yale School of Medicine, Yale-Waterbury Internal Medicine Program, Waterbury, Connecticut, USA
| | - Hoang Nghia Quoc
- Online Research Club (https://www.onlineresearchclub.org/), Nagasaki, Japan
- Vietnam Military Medical University, Hanoi, Vietnam
| | - Truong Van Dat
- Ministry of Health Cabinet, Ministry of Health, Ha Noi, Vietnam
| | - Satoshi Mizuta
- Center for Bioinformatics and Molecular Medicine, Nagasaki University, Nagasaki, Japan
| | - Kenji Hirayama
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Nguyen Tien Huy
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City, Vietnam
- Faculty of Natural Sciences, Duy Tan University, Da Nang, Vietnam
- Online Research Club (https://www.onlineresearchclub.org/), Nagasaki, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
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2
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Mishra V, Deshmukh A, Rathore I, Chakraborty S, Patankar S, Gustchina A, Wlodawer A, Yada RY, Bhaumik P. Inhibition of Plasmodium falciparum plasmepsins by drugs targeting HIV-1 protease: A way forward for antimalarial drug discovery. Curr Res Struct Biol 2024; 7:100128. [PMID: 38304146 PMCID: PMC10830516 DOI: 10.1016/j.crstbi.2024.100128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 02/03/2024] Open
Abstract
Plasmodium species are causative agents of malaria, a disease that is a serious global health concern. FDA-approved HIV-1 protease inhibitors (HIV-1 PIs) have been reported to be effective in reducing the infection by Plasmodium parasites in the population co-infected with both HIV-1 and malaria. However, the mechanism of HIV-1 PIs in mitigating Plasmodium pathogenesis during malaria/HIV-1 co-infection is not fully understood. In this study we demonstrate that HIV-1 drugs ritonavir (RTV) and lopinavir (LPV) exhibit the highest inhibition activity against plasmepsin II (PMII) and plasmepsin X (PMX) of P. falciparum. Crystal structures of the complexes of PMII with both drugs have been determined. The inhibitors interact with PMII via multiple hydrogen bonding and hydrophobic interactions. The P4 moiety of RTV forms additional interactions compared to LPV and exhibits conformational flexibility in a large S4 pocket of PMII. Our study is also the first to report inhibition of P. falciparum PMX by RTV and the mode of binding of the drug to the PMX active site. Analysis of the crystal structures implies that PMs can accommodate bulkier groups of these inhibitors in their S4 binding pockets. Structurally similar active sites of different vacuolar and non-vacuolar PMs suggest the potential of HIV-1 PIs in targeting these enzymes with differential affinities. Our structural investigations and biochemical data emphasize PMs as crucial targets for repurposing HIV-1 PIs as antimalarial drugs.
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Affiliation(s)
- Vandana Mishra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Anuradha Deshmukh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Ishan Rathore
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD, 21702, USA
| | - Satadru Chakraborty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Alla Gustchina
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD, 21702, USA
| | - Alexander Wlodawer
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD, 21702, USA
| | - Rickey Y. Yada
- Faculty of Land and Food Systems, University of British Columbia, 248-2357 Main Mall, Vancouver, BC V6T 1Z4, Vancouver, Canada
| | - Prasenjit Bhaumik
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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3
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Orozco MI, Moreno P, Guevara M, Abonia R, Quiroga J, Insuasty B, Barreto M, Burbano ME, Crespo-Ortiz MDP. In silico prediction and in vitro assessment of novel heterocyclics with antimalarial activity. Parasitol Res 2023; 123:75. [PMID: 38155300 PMCID: PMC10754745 DOI: 10.1007/s00436-023-08089-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023]
Abstract
The development of new antimalarials is paramount to keep the goals on reduction of malaria cases in endemic regions. The search for quality hits has been challenging as many inhibitory molecules may not progress to the next development stage. The aim of this work was to screen an in-house library of heterocyclic compounds (HCUV) for antimalarial activity combining computational predictions and phenotypic techniques to find quality hits. The physicochemical determinants, pharmacokinetic properties (ADME), and drug-likeness of HCUV were evaluated in silico, and compounds were selected for structure-based virtual screening and in vitro analysis. Seven Plasmodium target proteins were selected from the DrugBank Database, and ligands and receptors were processed using UCSF Chimera and Open Babel before being subjected to docking using Autodock Vina and Autodock 4. Growth inhibition of P. falciparum (3D7) cultures was tested by SYBR Green assays, and toxicity was assessed using hemolytic activity tests and the Galleria mellonella in vivo model. From a total of 792 compounds, 341 with good ADME properties, drug-likeness, and no interference structures were subjected to in vitro analysis. Eight compounds showed IC50 ranging from 0.175 to 0.990 µM, and active compounds included pyridyl-diaminopyrimido-diazepines, pyridyl-N-acetyl- and pyridyl-N-phenyl-pyrazoline derivatives. The most potent compound (UV802, IC50 0.178 µM) showed no toxicophoric and was predicted to interact with P. falciparum 1-cysperoxidredoxin (PfPrx1). For the remaining 7 hits (IC50 < 1 μM), 3 showed in silico binding to PfPrx1, one was predicted to bind the haloacid dehalogenase-like hydrolase and plasmepsin II, and one interacted with the plasmodial heat shock protein 90.
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Affiliation(s)
| | - Pedro Moreno
- Faculty of Engineering, Universidad del Valle, Cali, Colombia
| | - Miguel Guevara
- Faculty of Engineering, Universidad del Valle, Cali, Colombia
| | - Rodrigo Abonia
- Department of Chemistry, Universidad del Valle, Cali, Colombia
| | - Jairo Quiroga
- Department of Chemistry, Universidad del Valle, Cali, Colombia
| | | | - Mauricio Barreto
- Department of Microbiology, Group of Microbiology and Infectious Diseases, Universidad del Valle, San Fernando Campus, Calle 4 B #36-00, 760043, Cali, Colombia
| | - Maria Elena Burbano
- Department of Microbiology, Group of Microbiology and Infectious Diseases, Universidad del Valle, San Fernando Campus, Calle 4 B #36-00, 760043, Cali, Colombia
| | - Maria Del Pilar Crespo-Ortiz
- Department of Microbiology, Group of Microbiology and Infectious Diseases, Universidad del Valle, San Fernando Campus, Calle 4 B #36-00, 760043, Cali, Colombia.
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4
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Meller A, Bhakat S, Solieva S, Bowman GR. Accelerating Cryptic Pocket Discovery Using AlphaFold. J Chem Theory Comput 2023. [PMID: 36948209 PMCID: PMC10373493 DOI: 10.1021/acs.jctc.2c01189] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Cryptic pockets, or pockets absent in ligand-free, experimentally determined structures, hold great potential as drug targets. However, cryptic pocket openings are often beyond the reach of conventional biomolecular simulations because certain cryptic pocket openings involve slow motions. Here, we investigate whether AlphaFold can be used to accelerate cryptic pocket discovery either by generating structures with open pockets directly or generating structures with partially open pockets that can be used as starting points for simulations. We use AlphaFold to generate ensembles for 10 known cryptic pocket examples, including five that were deposited after AlphaFold's training data were extracted from the PDB. We find that in 6 out of 10 cases AlphaFold samples the open state. For plasmepsin II, an aspartic protease from the causative agent of malaria, AlphaFold only captures a partial pocket opening. As a result, we ran simulations from an ensemble of AlphaFold-generated structures and show that this strategy samples cryptic pocket opening, even though an equivalent amount of simulations launched from a ligand-free experimental structure fails to do so. Markov state models (MSMs) constructed from the AlphaFold-seeded simulations quickly yield a free energy landscape of cryptic pocket opening that is in good agreement with the same landscape generated with well-tempered metadynamics. Taken together, our results demonstrate that AlphaFold has a useful role to play in cryptic pocket discovery but that many cryptic pockets may remain difficult to sample using AlphaFold alone.
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Affiliation(s)
- Artur Meller
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, 660 S. Euclid Ave., St. Louis, Missouri 63110, United States
- Medical Scientist Training Program, Washington University in St. Louis, 660 S. Euclid Ave., St. Louis, Missouri 63110, United States
| | - Soumendranath Bhakat
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, 660 S. Euclid Ave., St. Louis, Missouri 63110, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Shahlo Solieva
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, 660 S. Euclid Ave., St. Louis, Missouri 63110, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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5
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Nwonuma CO, Balogun EA, Gyebi GA. Evaluation of Antimalarial Activity of Ethanolic Extract of Annona muricata L.: An in vivo and an in silico Approach. J Evid Based Integr Med 2023; 28:2515690X231165104. [PMID: 37019435 PMCID: PMC10084581 DOI: 10.1177/2515690x231165104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
In Nigeria, Annona muricata L. has been used to treat a variety of ailments. The mechanism of the antimalarial activity of ethanolic leaf extract of Annona muricata (EEAML) was investigated using both an in vivo and an in silico approach. The experimental mice were divided into five groups: A-F. The mice in groups B-F were inoculated with Plasmodium berghei NK-65 and treated accordingly. Groups A and B are the negative and positive controls (infected and untreated), respectively. Group C received 10 mg/kg chloroquine (standard drug), whereas groups D-F received 100, 200, and 300 mg/kg body weight of the extract orally respectively. The mice were euthanized eight days after infection, and their liver and blood were collected and used in biochemical tests. Molecular docking was performed using the extract's HPLC compounds and Plasmodium falciparum proteins. In the suppressive, prophylactic, and curative tests, there was a significant decrease (p < 0.05) in parasitemia levels in groups treated with the extract compared to the positive control and standard drug. When compared to the positive control, there was a significant (p < 0.05) reduction in liver MDA, total cholesterol, and total triglyceride levels. The binding energies of luteolin and apigenin-pfprotein complexes were significantly (p < 0.05) higher compared to their respective references. The anti-plasmodial activity of the extract may result from its hypolipidemic effect, which deprives the parasite of essential lipid molecules needed for parasite growth, as well as from the inhibitory effects of apigenin and luteolin on specific proteins required for the Plasmodium metabolic pathway.
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Affiliation(s)
- Charles Obiora Nwonuma
- Department of Biochemistry, College of Pure and Applied Science, Landmark University, Omu-Aran, Kwara State, Nigeria
| | | | - Gideon Ampoma Gyebi
- Department of Biochemistry, Faculty of Science and Technology, Bingham University, Karu, Nigeria
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6
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Gupta Y, Sharma N, Singh S, Romero JG, Rajendran V, Mogire RM, Kashif M, Beach J, Jeske W, Poonam, Ogutu BR, Kanzok SM, Akala HM, Legac J, Rosenthal PJ, Rademacher DJ, Durvasula R, Singh AP, Rathi B, Kempaiah P. The Multistage Antimalarial Compound Calxinin Perturbates P. falciparum Ca 2+ Homeostasis by Targeting a Unique Ion Channel. Pharmaceutics 2022; 14:1371. [PMID: 35890267 PMCID: PMC9319510 DOI: 10.3390/pharmaceutics14071371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/30/2022] [Accepted: 06/07/2022] [Indexed: 12/22/2022] Open
Abstract
Malaria elimination urgently needs novel antimalarial therapies that transcend resistance, toxicity, and high costs. Our multicentric international collaborative team focuses on developing multistage antimalarials that exhibit novel mechanisms of action. Here, we describe the design, synthesis, and evaluation of a novel multistage antimalarial compound, 'Calxinin'. A compound that consists of hydroxyethylamine (HEA) and trifluoromethyl-benzyl-piperazine. Calxinin exhibits potent inhibitory activity in the nanomolar range against the asexual blood stages of drug-sensitive (3D7), multidrug-resistant (Dd2), artemisinin-resistant (IPC4912), and fresh Kenyan field isolated Plasmodium falciparum strains. Calxinin treatment resulted in diminished maturation of parasite sexual precursor cells (gametocytes) accompanied by distorted parasite morphology. Further, in vitro liver-stage testing with a mouse model showed reduced parasite load at an IC50 of 79 nM. A single dose (10 mg/kg) of Calxinin resulted in a 30% reduction in parasitemia in mice infected with a chloroquine-resistant strain of the rodent parasite P. berghei. The ex vivo ookinete inhibitory concentration within mosquito gut IC50 was 150 nM. Cellular in vitro toxicity assays in the primary and immortalized human cell lines did not show cytotoxicity. A computational protein target identification pipeline identified a putative P. falciparum membrane protein (Pf3D7_1313500) involved in parasite calcium (Ca2+) homeostasis as a potential Calxinin target. This highly conserved protein is related to the family of transient receptor potential cation channels (TRP-ML). Target validation experiments showed that exposure of parasitized RBCs (pRBCs) to Calxinin induces a rapid release of intracellular Ca2+ from pRBCs; leaving de-calcinated parasites trapped in RBCs. Overall, we demonstrated that Calxinin is a promising antimalarial lead compound with a novel mechanism of action and with potential therapeutic, prophylactic, and transmission-blocking properties against parasites resistant to current antimalarials.
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Affiliation(s)
- Yash Gupta
- Infectious Diseases, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.G.); (R.D.)
| | - Neha Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, New Delhi 110021, India; (N.S.); (S.S.)
| | - Snigdha Singh
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, New Delhi 110021, India; (N.S.); (S.S.)
| | - Jesus G. Romero
- Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60660, USA; (J.G.R.); (J.B.); (W.J.); (D.J.R.)
- School of Biology, Institute of Experimental Biology, Central University of Venezuela, Caracas 1040, Venezuela
| | - Vinoth Rajendran
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India;
| | - Reagan M. Mogire
- Centre Clinical Research, Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya; (R.M.M.); (B.R.O.); (H.M.A.)
| | - Mohammad Kashif
- Infectious Diseases Laboratory, National Institute of Immunology, New Delhi 110067, India; (M.K.); (A.P.S.)
| | - Jordan Beach
- Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60660, USA; (J.G.R.); (J.B.); (W.J.); (D.J.R.)
| | - Walter Jeske
- Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60660, USA; (J.G.R.); (J.B.); (W.J.); (D.J.R.)
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi, New Delhi 110021, India;
- Delhi School of Public Health, Institute of Eminence, University of Delhi, New Delhi 110007, India
| | - Bernhards R. Ogutu
- Centre Clinical Research, Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya; (R.M.M.); (B.R.O.); (H.M.A.)
| | - Stefan M. Kanzok
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA;
| | - Hoseah M. Akala
- Centre Clinical Research, Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya; (R.M.M.); (B.R.O.); (H.M.A.)
| | - Jennifer Legac
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA; (J.L.); (P.J.R.)
| | - Philip J. Rosenthal
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA; (J.L.); (P.J.R.)
| | - David J. Rademacher
- Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60660, USA; (J.G.R.); (J.B.); (W.J.); (D.J.R.)
- Core Imaging Facility and Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Ravi Durvasula
- Infectious Diseases, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.G.); (R.D.)
| | - Agam P. Singh
- Infectious Diseases Laboratory, National Institute of Immunology, New Delhi 110067, India; (M.K.); (A.P.S.)
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, New Delhi 110021, India; (N.S.); (S.S.)
- Delhi School of Public Health, Institute of Eminence, University of Delhi, New Delhi 110007, India
| | - Prakasha Kempaiah
- Infectious Diseases, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.G.); (R.D.)
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Bhakat S, Söderhjelm P. Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems. J Chem Inf Model 2022; 62:914-926. [PMID: 35138093 PMCID: PMC8889585 DOI: 10.1021/acs.jcim.1c00840] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 11/28/2022]
Abstract
The flexibility of β hairpin structure known as the flap plays a key role in catalytic activity and substrate intake in pepsin-like aspartic proteases. Most of these enzymes share structural and sequential similarity. In this study, we have used apo Plm-II and BACE-1 as model systems. In the apo form of the proteases, a conserved tyrosine residue in the flap region remains in a dynamic equilibrium between the normal and flipped states through rotation of the χ1 and χ2 angles. Independent MD simulations of Plm-II and BACE-1 remained stuck either in the normal or flipped state. Metadynamics simulations using side-chain torsion angles (χ1 and χ2 of tyrosine) as collective variables sampled the transition between the normal and flipped states. Qualitatively, the two states were predicted to be equally populated. The normal and flipped states were stabilized by H-bond interactions to a tryptophan residue and to the catalytic aspartate, respectively. Further, mutation of tyrosine to an amino-acid with smaller side-chain, such as alanine, reduced the flexibility of the flap and resulted in a flap collapse (flap loses flexibility and remains stuck in a particular state). This is in accordance with previous experimental studies, which showed that mutation to alanine resulted in loss of activity in pepsin-like aspartic proteases. Our results suggest that the ring flipping associated with the tyrosine side-chain is the key order parameter that governs flap dynamics and opening of the binding pocket in most pepsin-like aspartic proteases.
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Affiliation(s)
- Soumendranath Bhakat
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
- Department
of Biochemistry and Molecular Biophysics, Washington University, School of Medicine, St. Louis, Missouri 63110, United States
| | - Pär Söderhjelm
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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8
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Bhakat S. Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments. RSC Adv 2021; 11:11026-11047. [PMID: 35423571 PMCID: PMC8695779 DOI: 10.1039/d0ra10359d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/21/2021] [Indexed: 01/26/2023] Open
Abstract
Pepsin-like aspartic proteases (PAPs) are a class of aspartic proteases which shares tremendous structural similarity with human pepsin. One of the key structural features of PAPs is the presence of a β-hairpin motif otherwise known as flap. The biological function of the PAPs is highly dependent on the conformational dynamics of the flap region. In apo PAPs, the conformational dynamics of the flap is dominated by the rotational degrees of freedom associated with χ1 and χ2 angles of conserved Tyr (or Phe in some cases). However it is plausible that dihedral order parameters associated with several other residues might play crucial roles in the conformational dynamics of apo PAPs. Due to their size, complexities associated with conformational dynamics and clinical significance (drug targets for malaria, Alzheimer's disease etc.), PAPs provide a challenging testing ground for computational and experimental methods focusing on understanding conformational dynamics and molecular recognition in biomolecules. The opening of the flap region is necessary to accommodate substrate/ligand in the active site of the PAPs. The BIG challenge is to gain atomistic details into how reversible ligand binding/unbinding (molecular recognition) affects the conformational dynamics. Recent reports of kinetics (K i, K d) and thermodynamic parameters (ΔH, TΔS, and ΔG) associated with macro-cyclic ligands bound to BACE1 (belongs to PAP family) provide a perfect challenge (how to deal with big ligands with multiple torsional angles and select optimum order parameters to study reversible ligand binding/unbinding) for computational methods to predict binding free energies and kinetics beyond typical test systems e.g. benzamide-trypsin. In this work, i reviewed several order parameters which were proposed to capture the conformational dynamics and molecular recognition in PAPs. I further highlighted how machine learning methods can be used as order parameters in the context of PAPs. I then proposed some open ideas and challenges in the context of molecular simulation and put forward my case on how biophysical experiments e.g. NMR, time-resolved FRET etc. can be used in conjunction with biomolecular simulation to gain complete atomistic insights into the conformational dynamics of PAPs.
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Affiliation(s)
- Soumendranath Bhakat
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University P. O. Box 124 SE-22100 Lund Sweden +46-769608418
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9
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Bobrovs R, Jaudzems K, Jirgensons A. Exploiting Structural Dynamics To Design Open-Flap Inhibitors of Malarial Aspartic Proteases. J Med Chem 2019; 62:8931-8950. [DOI: 10.1021/acs.jmedchem.9b00184] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Raitis Bobrovs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
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10
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Olanlokun JO, Olotu AF, David OM, Idowu TO, Soliman EM, Olorunsogo OO. A novel compound purified from Alstonia boonei inhibits Plasmodium falciparum lactate dehydrogenase and plasmepsin II. J Biomol Struct Dyn 2018; 37:2193-2200. [DOI: 10.1080/07391102.2018.1483840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- John Oludele Olanlokun
- Laboratories for Biomembrane Research and Biotechnology, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Andrew Fisayo Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Oluwole Moses David
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado-Ekiti, Nigeria
| | - Thomas Oyebode Idowu
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo, University, Ile-Ife, Nigeria
| | - ElSayed Mahmoud Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
- College of Pharmacy and Pharmaceutical Sciences, Florida Agricultural and Mechanical University, FAMU, Tallahassee, Florida, USA
| | - Olufunso Olabode Olorunsogo
- Laboratories for Biomembrane Research and Biotechnology, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Nigeria
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11
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Mishra V, Rathore I, Arekar A, Sthanam LK, Xiao H, Kiso Y, Sen S, Patankar S, Gustchina A, Hidaka K, Wlodawer A, Yada RY, Bhaumik P. Deciphering the mechanism of potent peptidomimetic inhibitors targeting plasmepsins - biochemical and structural insights. FEBS J 2018; 285:3077-3096. [PMID: 29943906 DOI: 10.1111/febs.14598] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/10/2018] [Accepted: 06/22/2018] [Indexed: 11/28/2022]
Abstract
Malaria is a deadly disease killing worldwide hundreds of thousands people each year and the responsible parasite has acquired resistance to the available drug combinations. The four vacuolar plasmepsins (PMs) in Plasmodium falciparum involved in hemoglobin (Hb) catabolism represent promising targets to combat drug resistance. High antimalarial activities can be achieved by developing a single drug that would simultaneously target all the vacuolar PMs. We have demonstrated for the first time the use of soluble recombinant plasmepsin II (PMII) for structure-guided drug discovery with KNI inhibitors. Compounds used in this study (KNI-10742, 10743, 10395, 10333, and 10343) exhibit nanomolar inhibition against PMII and are also effective in blocking the activities of PMI and PMIV with the low nanomolar Ki values. The high-resolution crystal structures of PMII-KNI inhibitor complexes reveal interesting features modulating their differential potency. Important individual characteristics of the inhibitors and their importance for potency have been established. The alkylamino analog, KNI-10743, shows intrinsic flexibility at the P2 position that potentiates its interactions with Asp132, Leu133, and Ser134. The phenylacetyl tripeptides, KNI-10333 and KNI-10343, accommodate different ρ-substituents at the P3 phenylacetyl ring that determine the orientation of the ring, thus creating novel hydrogen-bonding contacts. KNI-10743 and KNI-10333 possess significant antimalarial activity, block Hb degradation inside the food vacuole, and show no cytotoxicity on human cells; thus, they can be considered as promising candidates for further optimization. Based on our structural data, novel KNI derivatives with improved antimalarial activity could be designed for potential clinical use. DATABASE: Structural data are available in the PDB under the accession numbers 5YIE, 5YIB, 5YID, 5YIC, and 5YIA.
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Affiliation(s)
- Vandana Mishra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ishan Rathore
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Anagha Arekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Lakshmi Kavitha Sthanam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Huogen Xiao
- Department of Molecular and Cellular Biology, University of Guelph, ON, Canada
| | - Yoshiaki Kiso
- Laboratory of Peptide Sciences, Nagahama Institute of Bio-Science and Technology, Japan
| | - Shamik Sen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Alla Gustchina
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Koushi Hidaka
- Division of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Japan
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Rickey Y Yada
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada
| | - Prasenjit Bhaumik
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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12
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Pino P, Caldelari R, Mukherjee B, Vahokoski J, Klages N, Maco B, Collins CR, Blackman MJ, Kursula I, Heussler V, Brochet M, Soldati-Favre D. A multistage antimalarial targets the plasmepsins IX and X essential for invasion and egress. Science 2018; 358:522-528. [PMID: 29074775 DOI: 10.1126/science.aaf8675] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 09/18/2017] [Indexed: 12/20/2022]
Abstract
Regulated exocytosis by secretory organelles is important for malaria parasite invasion and egress. Many parasite effector proteins, including perforins, adhesins, and proteases, are extensively proteolytically processed both pre- and postexocytosis. Here we report the multistage antiplasmodial activity of the aspartic protease inhibitor hydroxyl-ethyl-amine-based scaffold compound 49c. This scaffold inhibits the preexocytosis processing of several secreted rhoptry and microneme proteins by targeting the corresponding maturases plasmepsins IX (PMIX) and X (PMX), respectively. Conditional excision of PMIX revealed its crucial role in invasion, and recombinantly active PMIX and PMX cleave egress and invasion factors in a 49c-sensitive manner.
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Affiliation(s)
- Paco Pino
- Department of Microbiology and Molecular Medicine, Faculty of Medicine-University of Geneva, Centre Médical Universitaire (CMU), 1211 Geneva, Switzerland.
| | - Reto Caldelari
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Budhaditya Mukherjee
- Department of Microbiology and Molecular Medicine, Faculty of Medicine-University of Geneva, Centre Médical Universitaire (CMU), 1211 Geneva, Switzerland
| | - Juha Vahokoski
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Natacha Klages
- Department of Microbiology and Molecular Medicine, Faculty of Medicine-University of Geneva, Centre Médical Universitaire (CMU), 1211 Geneva, Switzerland
| | - Bohumil Maco
- Department of Microbiology and Molecular Medicine, Faculty of Medicine-University of Geneva, Centre Médical Universitaire (CMU), 1211 Geneva, Switzerland
| | - Christine R Collins
- Malaria Biochemistry Laboratory, The Francis Crick Institute, Mill Hill, London NW1 1AT, UK
| | - Michael J Blackman
- Malaria Biochemistry Laboratory, The Francis Crick Institute, Mill Hill, London NW1 1AT, UK.,Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Inari Kursula
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway.,Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Volker Heussler
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Mathieu Brochet
- Department of Microbiology and Molecular Medicine, Faculty of Medicine-University of Geneva, Centre Médical Universitaire (CMU), 1211 Geneva, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine-University of Geneva, Centre Médical Universitaire (CMU), 1211 Geneva, Switzerland.
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13
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Mukherjee B, Tessaro F, Vahokoski J, Kursula I, Marq JB, Scapozza L, Soldati-Favre D. Modeling and resistant alleles explain the selectivity of antimalarial compound 49c towards apicomplexan aspartyl proteases. EMBO J 2018. [PMID: 29519896 DOI: 10.15252/embj.201798047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Toxoplasma gondii aspartyl protease 3 (TgASP3) phylogenetically clusters with Plasmodium falciparum Plasmepsins IX and X (PfPMIX, PfPMX). These proteases are essential for parasite survival, acting as key maturases for secreted proteins implicated in invasion and egress. A potent antimalarial peptidomimetic inhibitor (49c) originally developed against Plasmepsin II selectively targets TgASP3, PfPMIX, and PfPMX To unravel the molecular basis for the selectivity of 49c, we constructed homology models of PfPMIX, PfPMX, and TgASP3 that were first validated by identifying the determinants of microneme and rhoptry substrate recognition. The flap and flap-like structures of several reported Plasmepsins are highly flexible and critically modulate the access to the binding cavity. Molecular docking of 49c to TgASP3, PfPMIX, and PfPMX models predicted that the conserved phenylalanine residues in the flap, F344, F291, and F305, respectively, account for the sensitivity toward 49c. Concordantly, phenylalanine mutations in the flap of the three proteases increase twofold to 15-fold the IC50 values of 49c. Compellingly the selection of mutagenized T. gondii resistant strains to 49c reproducibly converted F344 to a cysteine residue.
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Affiliation(s)
- Budhaditya Mukherjee
- Department of Microbiology and Molecular Medicine, University of Geneva CMU, Geneva 4, Switzerland
| | - Francesca Tessaro
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Lausanne University of Geneva CMU, Geneva, Switzerland
| | - Juha Vahokoski
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Inari Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Jean-Baptiste Marq
- Department of Microbiology and Molecular Medicine, University of Geneva CMU, Geneva 4, Switzerland
| | - Leonardo Scapozza
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Lausanne University of Geneva CMU, Geneva, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, University of Geneva CMU, Geneva 4, Switzerland
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14
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Recacha R, Jaudzems K, Akopjana I, Jirgensons A, Tars K. Crystal structure of Plasmodium falciparum proplasmepsin IV: the plasticity of proplasmepsins. Acta Crystallogr F Struct Biol Commun 2016; 72:659-66. [PMID: 27599854 PMCID: PMC5012203 DOI: 10.1107/s2053230x16011663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/18/2016] [Indexed: 11/10/2022] Open
Abstract
Plasmepsin IV from Plasmodium falciparum (PM IV) is a promising target for the development of novel antimalarial drugs. Here, the crystal structure of the truncated zymogen of PM IV (pPM IV), consisting of the mature enzyme plus a prosegment of 47 residues, has been determined at 1.5 Å resolution. pPM IV presents the fold previously described for studied proplasmepsins, displaying closer similarities to proplasmepin IV from P. vivax (pPvPM) than to the other two proplasmepsins from P. falciparum. The study and comparison of the pPM IV structure with the proplasmepsin structures described previously provide information about the similarities and differences in the inactivation-activation mechanisms among the plasmepsin zymogens.
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Affiliation(s)
- Rosario Recacha
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Inara Akopjana
- Biomedical Research and Study Centre, Ratsupites 1, Riga, LV-1067, Latvia
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Kaspars Tars
- Biomedical Research and Study Centre, Ratsupites 1, Riga, LV-1067, Latvia
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