1
|
Dabburu GR, Jain A, Subbarao N, Kumar M. Designing dual inhibitors against potential drug targets of Plasmodium falciparum -M17 Leucyl Aminopeptidase and Plasmepsins. J Biomol Struct Dyn 2023; 41:8026-8041. [PMID: 36214679 DOI: 10.1080/07391102.2022.2129452] [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: 04/26/2022] [Accepted: 09/17/2022] [Indexed: 10/17/2022]
Abstract
Malaria is one of the major diseases of concern worldwide, especially in the African regions. According to a recent WHO report, 95% of deaths that occur due to malaria are in the African regions. Resistance to present antimalarial drugs is increasing rapidly and becoming a problem of concern. M17 Leucyl Aminopeptidase (PfM17LAP) and vacuolar Plasmepsins (PfPM) are two important enzymes involved in the haemoglobin degradation pathway of Plasmodium falciparum. PfM17LAP regulates the release of amino acids and PfPM mediates the conversion of haemoglobin proteins to oligopeptides. These enzymes thus play an essential role in the survival of malaria parasites inside the human body. In the present study, we used in-silico molecular docking, simulation and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) studies to find potential dual inhibitors of PfPM and PfM17LAP using the ChEMBL antimalarial library. Absorption, distribution, metabolism, excretion and toxicity (ADMET) profiling of the top ten ranked molecules was done using the BIOVIA Discovery Studio. The present investigation revealed that the compound CHEMBL426945 is stable in the binding site of both PfPM and PfM17LAP. In this study, we have reported novel dual-inhibitors that may act better than the present antimalarial drugs.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Govinda Rao Dabburu
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Aakriti Jain
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Valdés-Tresanco MS, Valdés-Tresanco ME, Rubio-Carrasquilla M, Valiente PA, Moreno E. Tailored Parameterization of the LIE Method for Calculating the Binding Free Energy of Vps34-Inhibitor Complexes. ACS OMEGA 2021; 6:29525-29536. [PMID: 34778624 PMCID: PMC8582068 DOI: 10.1021/acsomega.1c03582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/16/2021] [Indexed: 05/04/2023]
Abstract
Vps34 is the only isoform of the PI3K family in fungi, making this protein an attractive target to develop new treatments against pathogenic fungi. The high structural similarity between the active sites of the human and fungal Vps34 makes repurposing of human Vps34 inhibitors an appealing strategy. Nonetheless, while some of the cross-reactive inhibitors might have the potential to treat fungal infections, a safer approach to prevent undesired side effects would be to identify molecules that specifically inhibit the fungal Vps34. This study presents the parameterization of four LIE models for estimating the binding free energy of Vps34-inhibitor complexes. Two models are parameterized using a multiparametric linear regression leaving one or more free parameters, while the other two are based on the LIE-D model. All of the models show good predictive capacity (R 2 > 0.7, r > 0.85) and a low mean absolute error (MAE < 0.71 kcal/mol). The current study highlights the advantages of LIE-D-derived models when predicting the weight of the different contributions to the binding free energy. It is expected that this study will provide researchers with a valuable tool to identify new Vps34 inhibitors for relevant applications such as cancer treatment and the development of new antimicrobial agents.
Collapse
Affiliation(s)
| | - Mario E. Valdés-Tresanco
- Biological
Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Marcela Rubio-Carrasquilla
- Faculty
of Basic Sciences, University of Medellin, Medellin 050026, Colombia
- Grupo
de Micología Médica y Experimental, Corporación para Investigaciones Biológicas (CIB), Medellin 050034, Colombia
| | - Pedro A. Valiente
- Faculty
of Medicine, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E2, Canada
- Center
of Protein Studies, Faculty of Biology, University of Havana, La Habana 10400, Cuba
| | - Ernesto Moreno
- Faculty
of Basic Sciences, University of Medellin, Medellin 050026, Colombia
| |
Collapse
|
4
|
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
| |
Collapse
|
5
|
Kumar Singh A, Rajendran V, Singh S, Kumar P, Kumar Y, Singh A, Miller W, Potemkin V, Poonam, Grishina M, Gupta N, Kempaiah P, Durvasula R, Singh BK, Dunn BM, Rathi B. Antiplasmodial activity of hydroxyethylamine analogs: Synthesis, biological activity and structure activity relationship of plasmepsin inhibitors. Bioorg Med Chem 2018; 26:3837-3844. [PMID: 29983285 DOI: 10.1016/j.bmc.2018.06.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 01/08/2023]
Abstract
Malaria, particularly in endemic countries remains a threat to the human health and is the leading the cause of mortality in the tropical and sub-tropical areas. Herein, we explored new C2 symmetric hydroxyethylamine analogs as the potential inhibitors of Plasmodium falciparum (P. falciparum; 3D7) in in-vitro cultures. All the listed compounds were also evaluated against crucial drug targets, plasmepsin II (Plm II) and IV (Plm IV), enzymes found in the digestive vacuole of the P. falciparum. Analog 10f showed inhibitory activities against both the enzymes Plm II and Plm IV (Ki, 1.93 ± 0.29 µM for Plm II; Ki, 1.99 ± 0.05 µM for Plm IV). Among all these analogs, compounds 10g selectively inhibited the activity of Plm IV (Ki, 0.84 ± 0.08 µM). In the in vitro screening assay, the growth inhibition of P. falciparum by both the analogs (IC50, 2.27 ± 0.95 µM for 10f; IC50, 3.11 ± 0.65 µM for 10g) displayed marked killing effect. A significant growth inhibition of the P. falciparum was displayed by analog 12c with IC50 value of 1.35 ± 0.85 µM, however, it did not show inhibitory activity against either Plms. The hemolytic assay suggested that the active compounds selectively inhibit the growth of the parasite. Further, potent analogs (10f and 12c) were evaluated for their cytotoxicity towards mammalian HepG2 and vero cells. The selectivity index (SI) values were noticed greater than 10 for both the analogs that suggested their poor toxicity. The present study indicates these analogs as putative lead structures and could serve as crucial for the development of new drug molecules.
Collapse
Affiliation(s)
- Amit Kumar Singh
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Vinoth Rajendran
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Snigdha Singh
- Department of Chemistry, University of Delhi, Delhi 110007, India; Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Prashant Kumar
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Yogesh Kumar
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Archana Singh
- Department of Botany, Hansraj College University Enclave, University of Delhi, Delhi 110007, India
| | - Whelton Miller
- Department of Chemistry & Physics, Lincoln University, Lincoln University, PA 19352, USA; Department of Chemical & Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vladimir Potemkin
- South Ural State University, Laboratory of Computational Modeling of Drugs, 454080, Russia
| | - Poonam
- South Ural State University, Laboratory of Computational Modeling of Drugs, 454080, Russia; Department of Chemistry, Miranda House University Enclave, University of Delhi, Delhi 110007 India
| | - Maria Grishina
- South Ural State University, Laboratory of Computational Modeling of Drugs, 454080, Russia
| | - Nikesh Gupta
- Special Centre for Nanosciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Prakasha Kempaiah
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Ravi Durvasula
- Department of Medicine, Loyola University Stritch School of Medicine, Maywood, IL 60153, USA
| | | | - Ben M Dunn
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, P.O. Box 100245, Gainesville, FL, USA
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India; South Ural State University, Laboratory of Computational Modeling of Drugs, 454080, Russia.
| |
Collapse
|
6
|
Valdés-Tresanco ME, Valdés-Tresanco MS, Valiente PA, Cocho G, Mansilla R, Nieto-Villar JM. Protein surface roughness accounts for binding free energy of Plasmepsin II-ligand complexes. J Mol Recognit 2017; 31. [PMID: 28895236 DOI: 10.1002/jmr.2661] [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: 02/01/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 11/10/2022]
Abstract
The calculation of absolute binding affinities for protein-inhibitor complexes remains as one of the main challenges in computational structure-based ligand design. The present work explored the calculations of surface fractal dimension (as a measure of surface roughness) and the relationship with experimental binding free energies of Plasmepsin II complexes. Plasmepsin II is an attractive target for novel therapeutic compounds to treat malaria. However, the structural flexibility of this enzyme is a drawback when searching for specific inhibitors. Concerning that, we performed separate explicitly solvated molecular dynamics simulations using the available high-resolution crystal structures of different Plasmepsin II complexes. Molecular dynamics simulations allowed a better approximation to systems dynamics and, therefore, a more reliable estimation of surface roughness. This constitutes a novel approximation in order to obtain more realistic values of fractal dimension, because previous works considered only x-ray structures. Binding site fractal dimension was calculated considering the ensemble of structures generated at different simulation times. A linear relationship between binding site fractal dimension and experimental binding free energies of the complexes was observed within 20 ns. Previous studies of the subject did not uncover this relationship. Regression model, coined FD model, was built to estimate binding free energies from binding site fractal dimension values. Leave-one-out cross-validation showed that our model reproduced accurately the absolute binding free energies for our training set (R2 = 0.76; <|error|> =0.55 kcal/mol; SDerror = 0.19 kcal/mol). The fact that such a simple model may be applied raises some questions that are addressed in the article.
Collapse
Affiliation(s)
- Mario E Valdés-Tresanco
- Computational Biology and Biomolecular Dynamics Laboratory, Center for Proteins Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | | | - Pedro A Valiente
- Computational Biology and Biomolecular Dynamics Laboratory, Center for Proteins Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | - Germinal Cocho
- C3 Complex Systems Institute and UNAM Physics Institute, Mexico
| | - Ricardo Mansilla
- Center for Interdisciplinary Investigations of Humanities and Sciences, UNAM, Mexico
| | - J M Nieto-Villar
- Department of Chemical-Physics, Faculty of Chemistry and H. Poincare Group of Complex Systems, Faculty of Physics, University of Havana, Havana, Cuba
| |
Collapse
|
7
|
Singh AK, Rathore S, Tang Y, Goldfarb NE, Dunn BM, Rajendran V, Ghosh PC, Singh N, Latha N, Singh BK, Rawat M, Rathi B. Hydroxyethylamine Based Phthalimides as New Class of Plasmepsin Hits: Design, Synthesis and Antimalarial Evaluation. PLoS One 2015; 10:e0139347. [PMID: 26502278 PMCID: PMC4621027 DOI: 10.1371/journal.pone.0139347] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 09/12/2015] [Indexed: 11/18/2022] Open
Abstract
A novel class of phthalimides functionalized with privileged scaffolds was designed, synthesized and evaluated as potential inhibitors of plasmepsin 2 (Ki: 0.99 ± 0.1 μM for 6u) and plasmepsin 4 (Ki: 3.3 ± 0.3 μM for 6t), enzymes found in the digestive vacuole of the plasmodium parasite and considered as crucial drug targets. Three compounds were identified as potential candidates for further development. The listed compounds were also assayed for their antimalarial efficacy against chloroquine (CQ) sensitive strain (3D7) of Plasmodium falciparum. Assay of twenty seven hydroxyethylamine derivatives revealed four (5e, 6j, 6o and 6s) as strongly active, which were further evaluated against CQ resistant strain (7GB) of P. falciparum. Compound 5e possessing the piperidinopiperidine moiety exhibited promising antimalarial activity with an IC50 of 1.16 ± 0.04 μM. Further, compounds 5e, 6j, 6o and 6s exhibited low cytotoxic effect on MCF-7 cell line. Compound 6s possessing C2 symmetry was identified as the least cytotoxic with significant antimalarial activity (IC50: 1.30 ± 0.03 μM). The combined presence of hydroxyethylamine and cyclic amines (piperazines and piperidines) was observed as crucial for the activity. The current studies suggest that hydroxyethylamine based molecules act as potent antimalarial agent and may be helpful in drug development.
Collapse
Affiliation(s)
- Anil K. Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Sumit Rathore
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Yan Tang
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, P.O. Box 100245, Gainesville, FL, United States of America
| | - Nathan E. Goldfarb
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, P.O. Box 100245, Gainesville, FL, United States of America
| | - Ben M. Dunn
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, P.O. Box 100245, Gainesville, FL, United States of America
| | - Vinoth Rajendran
- Department of Biochemistry, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - Prahlad C. Ghosh
- Department of Biochemistry, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - Neelu Singh
- Bioinformatics Center, Sri Venkateswara College, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - N. Latha
- Bioinformatics Center, Sri Venkateswara College, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - Brajendra K. Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Manmeet Rawat
- Department of Internal Medicine, 1 University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Brijesh Rathi
- Bioorganic Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
- * E-mail:
| |
Collapse
|
8
|
McGillewie L, Soliman ME. Flap flexibility amongst plasmepsins I, II, III, IV, and V: Sequence, structural, and molecular dynamics analyses. Proteins 2015; 83:1693-705. [PMID: 26146842 DOI: 10.1002/prot.24855] [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: 04/11/2015] [Revised: 06/09/2015] [Accepted: 06/22/2015] [Indexed: 11/05/2022]
Abstract
Herein, for the first time, we comparatively report the opening and closing of apo plasmepsin I - V. Plasmepsins belong the aspartic protease family of enzymes, and are expressed during the various stages of the P. falciparum lifecycle, the species responsible for the most lethal and virulent malaria to infect humans. Plasmepsin I, II, IV and HAP degrade hemoglobin from infected red blood cells, whereas plasmepsin V transport proteins crucial to the survival of the malaria parasite across the endoplasmic reticulum. Flap-structures covering the active site of aspartic proteases (such as HIV protease) are crucial to the conformational flexibility and dynamics of the protein, and ultimately control the binding landscape. The flap-structure in plasmepsins is made up of a flip tip in the N-terminal lying perpendicular to the active site, adjacent to the flexible loop region in the C-terminal. Using molecular dynamics, we propose three parameters to better describe the opening and closing of the flap-structure in apo plasmepsins. Namely, the distance, d1, between the flap tip and the flexible region; the dihedral angle, ϕ, to account for the twisting motion; and the TriCα angle, θ1. Simulations have shown that as the flap-structure twists, the flap and flexible region move apart opening the active site, or move toward each other closing the active site. The data from our study indicate that of all the plasmepsins investigated in the present study, Plm IV and V display the highest conformational flexibility and are more dynamic structures versus Plm I, II, and HAP.
Collapse
Affiliation(s)
- Lara McGillewie
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Mahmoud E Soliman
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| |
Collapse
|
9
|
Huizing AP, Mondal M, Hirsch AKH. Fighting malaria: structure-guided discovery of nonpeptidomimetic plasmepsin inhibitors. J Med Chem 2015; 58:5151-63. [PMID: 25719272 DOI: 10.1021/jm5014133] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmepsins (Plms) are aspartic proteases involved in the degradation of human hemoglobin by Plasmodium falciparum. Given that the parasite needs the resulting amino acid building blocks for its growth and development, plasmepsins are an important antimalarial drug target. Over the past decade, tremendous progress has been achieved in the development of inhibitors of plasmepsin using two strategies: structure-based drug design (SBDD) and structure-based virtual screening (SBVS). Herein, we review the inhibitors of Plms I-IV developed by SBDD or SBVS with a particular focus on obtaining selectivity versus the human Asp proteases cathepsins and renin and activity in cell-based assays. By use of SBDD, the flap pocket of Plm II has been discovered and constitutes a convenient handle to obtain selectivity. In SBVS, activity against Plms I-IV and selectivity versus cathepsins are not always taken into account. A combination of SBVS, SBDD, and molecular dynamics simulations opens up opportunities for future design cycles.
Collapse
Affiliation(s)
- Anja P Huizing
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747 AG Groningen, The Netherlands
| | - Milon Mondal
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747 AG Groningen, The Netherlands
| | - Anna K H Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747 AG Groningen, The Netherlands
| |
Collapse
|
10
|
Costa MGS, Benetti-Barbosa TG, Desdouits N, Blondel A, Bisch PM, Pascutti PG, Batista PR. Impact of M36I polymorphism on the interaction of HIV-1 protease with its substrates: insights from molecular dynamics. BMC Genomics 2014; 15 Suppl 7:S5. [PMID: 25573486 PMCID: PMC4243740 DOI: 10.1186/1471-2164-15-s7-s5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background Over the last decades, a vast structural knowledge has been gathered on the HIV-1 protease (PR). Noticeably, most of the studies focused the B-subtype, which has the highest prevalence in developed countries. Accordingly, currently available anti-HIV drugs target this subtype, with considerable benefits for the corresponding patients. However, in developing countries, there is a wide variety of HIV-1 subtypes carrying PR polymorphisms related to reduced drug susceptibility. The non-active site mutation, M36I, is the most frequent polymorphism, and is considered as a non-B subtype marker. Yet, the structural impact of this substitution on the PR structure and on the interaction with natural substrates remains poorly documented. Results Herein, we used molecular dynamics simulations to investigate the role of this polymorphism on the interaction of PR with six of its natural cleavage-sites substrates. Free energy analyses by MMPB/SA calculations showed an affinity decrease of M36I-PR for the majority of its substrates. The only exceptions were the RT-RH, with equivalent affinity, and the RH-IN, for which an increased affinity was found. Furthermore, molecular simulations suggest that, unlike other peptides, RH-IN induced larger structural fluctuations in the wild-type enzyme than in the M36I variant. Conclusions With multiple approaches and analyses we identified structural and dynamical determinants associated with the changes found in the binding affinity of the M36I variant. This mutation influences the flexibility of both PR and its complexed substrate. The observed impact of M36I, suggest that combination with other non-B subtype polymorphisms, could lead to major effects on the interaction with the 12 known cleavage sites, which should impact the virion maturation.
Collapse
|
11
|
Da Rocha Pita SS, Batista PR, Albuquerque MG, Pascutti PG. Molecular Dynamics Simulations of Peptide Inhibitors Complexed WithTrypanosoma cruziTrypanothione Reductase. Chem Biol Drug Des 2012; 80:561-71. [DOI: 10.1111/j.1747-0285.2012.01429.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
12
|
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]
|
13
|
Predicting functional residues of the Solanum lycopersicum aspartic protease inhibitor (SLAPI) by combining sequence and structural analysis with molecular docking. J Mol Model 2011; 18:2673-87. [DOI: 10.1007/s00894-011-1290-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 10/25/2011] [Indexed: 02/02/2023]
|
14
|
Computational perspectives into plasmepsins structure-function relationship: implications to inhibitors design. J Trop Med 2011; 2011:657483. [PMID: 21760810 PMCID: PMC3134243 DOI: 10.1155/2011/657483] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 05/01/2011] [Accepted: 05/03/2011] [Indexed: 11/20/2022] Open
Abstract
The development of efficient and selective antimalariais remains a challenge for the pharmaceutical industry. The aspartic proteases plasmepsins, whose inhibition leads to parasite death, are classified as targets for the design of potent drugs. Combinatorial synthesis is currently being used to generate inhibitor libraries for these enzymes, and together with computational methodologies have been demonstrated capable for the selection of lead compounds. The high structural flexibility of plasmepsins, revealed by their X-ray structures and molecular dynamics simulations, made even more complicated the prediction of putative binding modes, and therefore, the use of common computational tools, like docking and free-energy calculations. In this review, we revised the computational strategies utilized so far, for the structure-function relationship studies concerning the plasmepsin family, with special focus on the recent advances in the improvement of the linear interaction estimation (LIE) method, which is one of the most successful methodologies in the evaluation of plasmepsin-inhibitor binding affinity.
Collapse
|
15
|
Valiente PA, Gil A, Batista PR, Caffarena ER, Pons T, Pascutti PG. New parameterization approaches of the LIE method to improve free energy calculations of PlmII-Inhibitors complexes. J Comput Chem 2010; 31:2723-34. [PMID: 20839299 DOI: 10.1002/jcc.21566] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Pedro A Valiente
- Laboratorio de Biología Computacional y Diseño de Proteínas, Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana, Cuba.
| | | | | | | | | | | |
Collapse
|
16
|
Understanding the HIV-1 protease nelfinavir resistance mutation D30N in subtypes B and C through molecular dynamics simulations. J Mol Graph Model 2010; 29:137-47. [PMID: 20541446 DOI: 10.1016/j.jmgm.2010.05.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 05/12/2010] [Accepted: 05/14/2010] [Indexed: 11/24/2022]
Abstract
A major concern in the antiretroviral (ARV) treatment of HIV infections with protease inhibitors (PI) is the emergence of resistance, which results from the selection of distinct mutations within the viral protease (PR) gene. Among patients who do not respond to treatment with the PI nelfinavir (NFV), the D30N mutation is often observed. However, several reports have shown that D30N emerges with different frequencies in distinct HIV-1 genetic forms or subtypes. In the present work, we analyzed the binding of NFV and the Gag substrate CA/p2 to PR from HIV-1 subtypes B and C through molecular dynamics (MD) simulations. The wild-type and drug-resistant D30N mutants were investigated in both subtypes. The compensatory mutations N83T and N88D, observed in vitro and in vivo when subtype C acquires D30N, were also studied. D30N appears to facilitate conformational changes in subtype B PR, but not in that from subtype C, and this could be associated with disestablishment of an alpha-helical region of the PR. Furthermore, the total contact areas of NFV or the CA/p2 substrate with the mutant PR correlated with changes in the resistance patterns and replicative capacity. Finally, we observed in our MD simulations that mutant PR proteins show different patterns for hydrophobic/van der Waals contact. These findings suggest that different molecular mechanisms contribute to resistance, and we propose that a single mutation has distinct impacts on different HIV-1 subtypes.
Collapse
|
17
|
Gardiner DL, Skinner-Adams TS, Brown CL, Andrews KT, Stack CM, McCarthy JS, Dalton JP, Trenholme KR. Plasmodium falciparum: new molecular targets with potential for antimalarial drug development. Expert Rev Anti Infect Ther 2010; 7:1087-98. [PMID: 19883329 DOI: 10.1586/eri.09.93] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Malaria remains one of the world's most devastating infectious diseases. Drug resistance to all classes of antimalarial agents has now been observed, highlighting the need for new agents that act against novel parasite targets. The complete sequencing of the Plasmodium falciparum genome has allowed the identification of new molecular targets within the parasite that may be amenable to chemotherapeutic intervention. In this review, we investigate four possible targets for the future development of new classes of antimalarial agents. These targets include histone deacetylase, the aspartic proteases or plasmepsins, aminopeptidases and the purine salvage enzyme hypoxanthine-xanthine-guanine phosphoribosyltransferase.
Collapse
Affiliation(s)
- Donald L Gardiner
- Malaria Biology Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Herston, QLD 4006, Australia.
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Luksch T, Blum A, Klee N, Diederich W, Sotriffer C, Klebe G. Pyrrolidine Derivatives as Plasmepsin Inhibitors: Binding Mode Analysis Assisted by Molecular Dynamics Simulations of a Highly Flexible Protein. ChemMedChem 2010; 5:443-54. [DOI: 10.1002/cmdc.200900452] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|