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Liu J, Ge C, Zha L, Lin L, Li R. Simple Nano-Luciferase-Based Assay for the Rapid and High-Throughput Detection of SARS-CoV-2 3C-Like Protease. Anal Chem 2023; 95:714-719. [PMID: 36576396 PMCID: PMC9843625 DOI: 10.1021/acs.analchem.2c02590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/09/2022] [Indexed: 12/29/2022]
Abstract
In this study, we described an easy-to-perform nano-luciferase (nLuc) sensor for the rapid detection of 3-chymotrypsin-like protease (3CLpro) encoded by SARS-CoV-2. The technology is based on the cleavage reaction of recombinant-nLuc via 3CLpro. The nLuc-based assay is a general, one-step method and is naturally specific in detection. The stability, sensitivity, detection range, and response time are fully characterized. The application of 3CLpro detection in artificial and human saliva as well as antiviral drug screening demonstrates that the method can quantify 3CLpro with high sensitivity in one step. With its unique features, the nLuc-based assay may find broad applications in the auxiliary diagnosis of SARS-CoV-2, as well as other types of coronavirus infection.
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Affiliation(s)
- Jingxin Liu
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
| | - Chenchen Ge
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
| | - Ling Zha
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
| | - Ligen Lin
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University
of Macau, Macao 999078, P. R. China
| | - Rongsong Li
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
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Ershov PV, Mezentsev YV, Ivanov AS. Interfacial Peptides as Affinity Modulating Agents of Protein-Protein Interactions. Biomolecules 2022; 12:106. [PMID: 35053254 PMCID: PMC8773757 DOI: 10.3390/biom12010106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 12/25/2022] Open
Abstract
The identification of disease-related protein-protein interactions (PPIs) creates objective conditions for their pharmacological modulation. The contact area (interfaces) of the vast majority of PPIs has some features, such as geometrical and biochemical complementarities, "hot spots", as well as an extremely low mutation rate that give us key knowledge to influence these PPIs. Exogenous regulation of PPIs is aimed at both inhibiting the assembly and/or destabilization of protein complexes. Often, the design of such modulators is associated with some specific problems in targeted delivery, cell penetration and proteolytic stability, as well as selective binding to cellular targets. Recent progress in interfacial peptide design has been achieved in solving all these difficulties and has provided a good efficiency in preclinical models (in vitro and in vivo). The most promising peptide-containing therapeutic formulations are under investigation in clinical trials. In this review, we update the current state-of-the-art in the field of interfacial peptides as potent modulators of a number of disease-related PPIs. Over the past years, the scientific interest has been focused on following clinically significant heterodimeric PPIs MDM2/p53, PD-1/PD-L1, HIF/HIF, NRF2/KEAP1, RbAp48/MTA1, HSP90/CDC37, BIRC5/CRM1, BIRC5/XIAP, YAP/TAZ-TEAD, TWEAK/FN14, Bcl-2/Bax, YY1/AKT, CD40/CD40L and MINT2/APP.
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Affiliation(s)
- Pavel V. Ershov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (Y.V.M.); (A.S.I.)
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Patel PK, Bhatt HG. Improved 3D-QSAR Prediction by Multiple Conformational Alignments and Molecular Docking Studies to Design and Discover HIV-I Protease Inhibitors. Curr HIV Res 2021; 19:154-171. [PMID: 33213349 DOI: 10.2174/1570162x18666201119143457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/18/2020] [Accepted: 10/02/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Inhibition of HIV-I protease enzyme is a strategic step for providing better treatment in retrovirus infections, which avoids resistance and possesses less toxicity. OBJECTIVES In the course of our research to discover new and potent protease inhibitors, 3D-QSAR (CoMFA and CoMSIA) models were generated using 3 different alignment techniques, including multifit alignment, docking based and Distill based alignment for 63 compounds. Novel molecules were designed from the output of this study. METHODS A total of 3 alignment methods were used to generate CoMFA and CoMSIA models. A Distill based alignment method was considered a better method according to different validation parameters. A 3D-QSAR model was generated and contour maps were discussed. The biological activity of designed molecules was predicted using the generated QSAR model to validate QSAR. The newly designed molecules were docked to predict binding affinity. RESULTS In CoMFA, leave one out cross-validated coefficient (q2), conventional coefficient (r2) and predicted correlation coefficient (r2Predicted) values were found to be 0.721, 0.991 and 0.780, respectively. The best obtained CoMSIA model also showed significant cross-validated coefficient (q2), conventional coefficient (r2) and predicted correlation coefficient (r2Predicted) values of 0.714, 0.987 and 0.721, respectively. Steric and electrostatic contour maps generated from CoMFA and hydrophobic and hydrogen bond donor and hydrogen bond acceptor contour maps from CoMSIA models were used to design new and bioactive protease inhibitors by incorporating bioisosterism and knowledge-based structure-activity relationship. CONCLUSION The results from both these approaches, ligand-based drug design and structure-based drug design, are adequate and promising to discover protease inhibitors.
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Affiliation(s)
- Paresh K Patel
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad 382 481, India
| | - Hardik G Bhatt
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad 382 481, India
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Alves NG, Mata AI, Luís JP, Brito RMM, Simões CJV. An Innovative Sequence-to-Structure-Based Approach to Drug Resistance Interpretation and Prediction: The Use of Molecular Interaction Fields to Detect HIV-1 Protease Binding-Site Dissimilarities. Front Chem 2020; 8:243. [PMID: 32411655 PMCID: PMC7202381 DOI: 10.3389/fchem.2020.00243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/13/2020] [Indexed: 12/15/2022] Open
Abstract
In silico methodologies have opened new avenues of research to understanding and predicting drug resistance, a pressing health issue that keeps rising at alarming pace. Sequence-based interpretation systems are routinely applied in clinical context in an attempt to predict mutation-based drug resistance and thus aid the choice of the most adequate antibiotic and antiviral therapy. An important limitation of approaches based on genotypic data exclusively is that mutations are not considered in the context of the three-dimensional (3D) structure of the target. Structure-based in silico methodologies are inherently more suitable to interpreting and predicting the impact of mutations on target-drug interactions, at the cost of higher computational and time demands when compared with sequence-based approaches. Herein, we present a fast, computationally inexpensive, sequence-to-structure-based approach to drug resistance prediction, which makes use of 3D protein structures encoded by input target sequences to draw binding-site comparisons with susceptible templates. Rather than performing atom-by-atom comparisons between input target and template structures, our workflow generates and compares Molecular Interaction Fields (MIFs) that map the areas of energetically favorable interactions between several chemical probe types and the target binding site. Quantitative, pairwise dissimilarity measurements between the target and the template binding sites are thus produced. The method is particularly suited to understanding changes to the 3D structure and the physicochemical environment introduced by mutations into the target binding site. Furthermore, the workflow relies exclusively on freeware, making it accessible to anyone. Using four datasets of known HIV-1 protease sequences as a case-study, we show that our approach is capable of correctly classifying resistant and susceptible sequences given as input. Guided by ROC curve analyses, we fined-tuned a dissimilarity threshold of classification that results in remarkable discriminatory performance (accuracy ≈ ROC AUC ≈ 0.99), illustrating the high potential of sequence-to-structure-, MIF-based approaches in the context of drug resistance prediction. We discuss the complementarity of the proposed methodology to existing prediction algorithms based on genotypic data. The present work represents a new step toward a more comprehensive and structurally-informed interpretation of the impact of genetic variability on the response to HIV-1 therapies.
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Affiliation(s)
- Nuno G Alves
- Department of Chemistry, Coimbra Chemistry Centre, University of Coimbra, Coimbra, Portugal
| | - Ana I Mata
- Department of Chemistry, Coimbra Chemistry Centre, University of Coimbra, Coimbra, Portugal
| | - João P Luís
- Department of Chemistry, Coimbra Chemistry Centre, University of Coimbra, Coimbra, Portugal
| | - Rui M M Brito
- Department of Chemistry, Coimbra Chemistry Centre, University of Coimbra, Coimbra, Portugal.,BSIM Therapeutics, Instituto Pedro Nunes, Coimbra, Portugal
| | - Carlos J V Simões
- Department of Chemistry, Coimbra Chemistry Centre, University of Coimbra, Coimbra, Portugal.,BSIM Therapeutics, Instituto Pedro Nunes, Coimbra, Portugal
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Itoh R, Soejima T, Hiromatsu K. Anti-chlamydial activities of cell-permeable hydrophobic dipeptide-containing derivatives. J Infect Chemother 2019; 25:987-994. [PMID: 31230920 DOI: 10.1016/j.jiac.2019.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 01/09/2023]
Abstract
The obligate intracellular bacteria chlamydia is major human pathogen that causes millions of trachoma, sexually transmitted infections and pneumonia worldwide. We serendipitously found that both calpain inhibitors z-Val-Phe-CHO and z-Leu-Nle-CHO showed marked inhibitory activity against chlamydial growth in human epithelial HeLa cells, whereas other calpain inhibitors not. These peptidomimetic inhibitors consist of N-benzyloxycarbonyl group and hydrophobic dipeptide derivatives. Both compounds strongly restrict the chlamydial growth even addition at the 12 h post infection. Notably, inhibitors-mediated growth inhibition of chlamydia was independent on host calpain activity. Electron microscopic analysis revealed that z-Val-Phe-CHO inhibited chlamydial growth by arresting bacterial cell division and RB-EB re-transition, but not by changing into persistent state. We searched and found that z-Leu-Leu-CHO and z-Phe-Ala-FMK also inhibited chlamydial growth. Neither biotin-hydrophobic dipeptide nor morpholinoureidyl-hydrophobic dipeptide shows inhibitory effects on chlamydial intracellular growth. Our results suggested the possibility of some chemical derivatives based on z-hydrophobic dipeptide group for future therapeutic usage to the chlamydial infectious disease.
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Affiliation(s)
- Ryota Itoh
- Department of Microbiology & Immunology, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180, Japan.
| | - Toshinori Soejima
- Department of Microbiology & Immunology, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Kenji Hiromatsu
- Department of Microbiology & Immunology, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180, Japan
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Santos ALS, Matteoli FP, Sangenito LS, Branquinha MH, Cotrim BA, Resende GO. Asymmetric peptidomimetics containing L-tartaric acid core inhibit the aspartyl peptidase activity and growth of Leishmania amazonensis promastigotes. Acta Parasitol 2018; 63:114-124. [PMID: 29351078 DOI: 10.1515/ap-2018-0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 11/10/2017] [Indexed: 01/07/2023]
Abstract
Aspartyl-type peptidases are promising chemotherapeutic targets in protozoan parasites. In the present work, we identified an aspartyl peptidase activity from the soluble extract of Leishmania amazonensis promastigotes, which cleaved the fluorogenic peptide 7-methoxycoumarin-4-acetyl-Gly-Lys-Pro-Ile-Leu-Phe-Phe-Arg-Leu-Lys(DNP)-D-Arg-amide (cathepsin D substrate) under acidic pH conditions at 37°C, showing a KM of 0.58 μM and Vmax of 129.87 fluorescence arbitrary units/s mg protein. The leishmanial aspartyl peptidase activity was blocked by pepstatin A (IC50 = 6.8 μM) and diazo-acetyl-norleucinemetilester (IC50 = 10.2 μM), two classical aspartyl peptidase inhibitors. Subsequently, the effects of 6 asymmetric peptidomimetics, containing L-tartaric acid core, were tested on both aspartyl peptidase and growth of L. amazonensis promastigotes. The peptidomimetics named 88, 154 and 158 promoted a reduction of 50% on the leishmanial aspartyl peptidase activity at concentrations ranging from 40 to 85 μM, whereas the peptidomimetic 157 was by far the most effective, presenting IC50 of 0.04 μM. Furthermore, the peptidomimetics 157 and 154 reduced the parasite proliferation in a dose-dependent manner, displaying IC50 values of 33.7 and 44.5 μM, respectively. Collectively, the peptidomimetic 157 was the most efficient compound able to arrest both aspartyl peptidase activity and leishmanial proliferation, which raises excellent perspectives regarding its use against this human pathogenic protozoan.
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Affiliation(s)
- André L S Santos
- Laboratório de Investigação de Peptidases, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Filipe P Matteoli
- Laboratório de Investigação de Peptidases, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leandro S Sangenito
- Laboratório de Investigação de Peptidases, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marta H Branquinha
- Laboratório de Investigação de Peptidases, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno A Cotrim
- Instituto Federal de Educação Ciência e Tecnologia do Rio de Janeiro, Campus Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriel O Resende
- Instituto Federal de Educação Ciência e Tecnologia do Rio de Janeiro, Campus Rio de Janeiro, Rio de Janeiro, Brazil
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Trypanosoma brucei TbIF1 inhibits the essential F1-ATPase in the infectious form of the parasite. PLoS Negl Trop Dis 2017; 11:e0005552. [PMID: 28414727 PMCID: PMC5407850 DOI: 10.1371/journal.pntd.0005552] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 04/27/2017] [Accepted: 04/04/2017] [Indexed: 12/01/2022] Open
Abstract
The mitochondrial (mt) FoF1-ATP synthase of the digenetic parasite, Trypanosoma brucei, generates ATP during the insect procyclic form (PF), but becomes a perpetual consumer of ATP in the mammalian bloodstream form (BF), which lacks a canonical respiratory chain. This unconventional dependence on FoF1-ATPase is required to maintain the essential mt membrane potential (Δψm). Normally, ATP hydrolysis by this rotary molecular motor is restricted to when eukaryotic cells experience sporadic hypoxic conditions, during which this compulsory function quickly depletes the cellular ATP pool. To protect against this cellular treason, the highly conserved inhibitory factor 1 (IF1) binds the enzyme in a manner that solely inhibits the hydrolytic activity. Intriguingly, we were able to identify the IF1 homolog in T. brucei (TbIF1), but determined that its expression in the mitochondrion is tightly regulated throughout the life cycle as it is only detected in PF cells. TbIF1 appears to primarily function as an emergency brake in PF cells, where it prevented the restoration of the Δψm by FoF1-ATPase when respiration was chemically inhibited. In vitro, TbIF1 overexpression specifically inhibits the hydrolytic activity but not the synthetic capability of the FoF1-ATP synthase in PF mitochondria. Furthermore, low μM amounts of recombinant TbIF1 achieve the same inhibition of total mt ATPase activity as the FoF1-ATPase specific inhibitors, azide and oligomycin. Therefore, even minimal ectopic expression of TbIF1 in BF cells proved lethal as the indispensable Δψm collapsed due to inhibited FoF1-ATPase. In summary, we provide evidence that T. brucei harbors a natural and potent unidirectional inhibitor of the vital FoF1-ATPase activity that can be exploited for future structure-based drug design. Enzymes are catalysts that drive both a forward and reverse chemical reaction depending on the thermodynamic properties. FoF1-ATP synthase is a multiprotein enzyme that under normal physiological conditions generates ATP. However, when respiration is impeded, this rotary molecular machine reverses and hydrolyzes ATP to pump protons and maintain the essential mitochondrial membrane potential. While this activity is exceptional in most eukaryotic cells, the unique composition of the Trypanosoma brucei mitochondrion dictates that the infectious stage of this human parasite is utterly dependent on the hydrolytic activity of FoF1-ATPase. While searching for better chemotherapeutics against Human African Trypanosomiasis, several trypanocidal compounds were determined to interact with this enzyme, but they indiscriminately inhibit both the ATP hydrolytic and synthetic activities. A more promising approach involves the conserved eukaryotic protein IF1, a unidirectional inhibitor that prevents just ATP hydrolysis. Auspiciously, we identified this protein homolog in T. brucei (TbIF1) and its expression is tightly regulated between life stages of the parasite. Importantly, the introduction of exogenous TbIF1 protein specifically inhibits FoF1-ATPase and is lethal for the infectious stage of T. brucei. Therefore, we have identified a natural inhibitor of an essential and druggable enzyme that can be exploited for future structure-based drug design.
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Developing HIV-1 Protease Inhibitors through Stereospecific Reactions in Protein Crystals. Molecules 2016; 21:molecules21111458. [PMID: 27809253 PMCID: PMC6273989 DOI: 10.3390/molecules21111458] [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: 09/26/2016] [Revised: 10/26/2016] [Accepted: 10/26/2016] [Indexed: 11/30/2022] Open
Abstract
Protease inhibitors are key components in the chemotherapy of HIV infection. However, the appearance of viral mutants routinely compromises their clinical efficacy, creating a constant need for new and more potent inhibitors. Recently, a new class of epoxide-based inhibitors of HIV-1 protease was investigated and the configuration of the epoxide carbons was demonstrated to play a crucial role in determining the binding affinity. Here we report the comparison between three crystal structures at near-atomic resolution of HIV-1 protease in complex with the epoxide-based inhibitor, revealing an in-situ epoxide ring opening triggered by a pH change in the mother solution of the crystal. Increased pH in the crystal allows a stereospecific nucleophile attack of an ammonia molecule onto an epoxide carbon, with formation of a new inhibitor containing amino-alcohol functions. The described experiments open a pathway for the development of new stereospecific protease inhibitors from a reactive lead compound.
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Tsutsumi H, Nakano K, Mihara H. Dihydrofolate reductase inhibitory peptides screened from a structured designed β-loop peptide library displayed on phage. MOLECULAR BIOSYSTEMS 2016; 11:2713-6. [PMID: 26118677 DOI: 10.1039/c5mb00316d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzyme inhibitory peptides with a loop structure stabilized using an antiparallel β-sheet scaffold (β-loop peptide) were obtained from a designed peptide phage library. Human dihydrofolate reductase (hDHFR) was used as the target enzyme. The obtained β-loop peptides were competitive inhibitors of hDHFR with micromolar inhibition constants and dissociation constants.
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Affiliation(s)
- Hiroshi Tsutsumi
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-40, Midori-ku, Yokohama 226-8501, Japan.
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Sroczyński D, Malinowski Z, Szcześniak AK, Pakulska W. New 1(2H)-phthalazinone derivatives as potent nonpeptidic HIV-1 protease inhibitors: molecular docking studies, molecular dynamics simulation, oral bioavailability and ADME prediction. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1067808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Ng TB, Cheung RCF, Wong JH, Chan WY. Proteins, peptides, polysaccharides, and nucleotides with inhibitory activity on human immunodeficiency virus and its enzymes. Appl Microbiol Biotechnol 2015; 99:10399-414. [PMID: 26411457 DOI: 10.1007/s00253-015-6997-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/04/2015] [Accepted: 09/08/2015] [Indexed: 12/15/2022]
Abstract
Human immunodeficiency virus (HIV), the causative agent of acquired immune deficiency syndrome, has claimed innumerable lives in the past. Many biomolecules which suppress HIV replication and also other biomolecules that inhibit enzymes essential to HIV replication have been reported. Proteins including a variety of milk proteins, ribosome-inactivating proteins, ribonucleases, antifungal proteins, and trypsin inhibitors; peptides comprising cathelicidins, defensins, synthetic peptides, and others; polysaccharides and polysaccharopeptides; nucleosides, nucleotides, and ribozymes, demonstrated anti-HIV activity. In many cases, the mechanism of anti-HIV action has been elucidated. Strategies have been devised to augment the anti-HIV potency of these compounds.
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Affiliation(s)
- Tzi Bun Ng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, New Territories, China.
| | - Randy Chi Fai Cheung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, New Territories, China
| | - Jack Ho Wong
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, New Territories, China
| | - Wai Yee Chan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, New Territories, China.
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Cunha JD, Maselli LMF, Stern ACB, Spada C, Bydlowski SP. Impact of antiretroviral therapy on lipid metabolism of human immunodeficiency virus-infected patients: Old and new drugs. World J Virol 2015; 4:56-77. [PMID: 25964872 PMCID: PMC4419122 DOI: 10.5501/wjv.v4.i2.56] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/15/2015] [Accepted: 03/09/2015] [Indexed: 02/05/2023] Open
Abstract
For human immunodeficiency virus (HIV)-infected patients, the 1990s were marked by the introduction of highly active antiretroviral therapy (HAART) representing a new perspective of life for these patients. The use of HAART was shown to effectively suppress the replication of HIV-1 and dramatically reduce mortality and morbidity, which led to a better and longer quality of life for HIV-1-infected patients. Apart from the substantial benefits that result from the use of various HAART regimens, laboratory and clinical experience has shown that HAART can induce severe and considerable adverse effects related to metabolic complications of lipid metabolism, characterized by signs of lipodystrophy, insulin resistance, central adiposity, dyslipidemia, increased risk of cardiovascular disease and even an increased risk of atherosclerosis. New drugs are being studied, new therapeutic strategies are being implemented, and the use of statins, fibrates, and inhibitors of intestinal cholesterol absorption have been effective alternatives. Changes in diet and lifestyle have also shown satisfactory results.
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de Miranda AS, Simon RC, Grischek B, de Paula GC, Horta BAC, de Miranda LSM, Kroutil W, Kappe CO, de Souza ROMA. Chiral Chlorohydrins from the Biocatalyzed Reduction of Chloroketones: Chiral Building Blocks for Antiretroviral Drugs. ChemCatChem 2015. [DOI: 10.1002/cctc.201403023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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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.
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BoseDasgupta S, Pieters J. Coronin 1 trimerization is essential to protect pathogenic mycobacteria within macrophages from lysosomal delivery. FEBS Lett 2014; 588:3898-905. [PMID: 25217836 DOI: 10.1016/j.febslet.2014.08.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 08/23/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
Abstract
Coronin 1 is a member of the evolutionarily conserved coronin protein family. Coronin proteins are characterized by the presence of a central WD repeat and a C-terminal coiled coil that in coronin 1 is responsible for trimerization. Coronin 1 was identified as a host protein protecting intracellularly residing mycobacteria from degradation by activating the Ca(2+)/calcineurin pathway but whether or not trimerization is essential for this function remains unknown. We here show that trimerization is essential to promote mycobacterial survival within macrophages and activate calcineurin. Furthermore, macrophage activation that induces serine-phosphorylation on coronin 1 resulted in coronin 1 monomerization. These results suggest that modulation of coronin 1 oligomerization is an effective way to determine the outcome of a mycobacterial infection in macrophages.
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Kang D, Song Y, Chen W, Zhan P, Liu X. “Old Dogs with New Tricks”: exploiting alternative mechanisms of action and new drug design strategies for clinically validated HIV targets. MOLECULAR BIOSYSTEMS 2014; 10:1998-2022. [DOI: 10.1039/c4mb00147h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Qiu X, Zhao GD, Tang LQ, Liu ZP. Design and synthesis of highly potent HIV-1 protease inhibitors with novel isosorbide-derived P2 ligands. Bioorg Med Chem Lett 2014; 24:2465-8. [PMID: 24767846 DOI: 10.1016/j.bmcl.2014.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/03/2014] [Accepted: 04/05/2014] [Indexed: 11/19/2022]
Abstract
The design, synthesis, and biological evaluation of a series of six HIV-1 protease inhibitors incorporating isosorbide moiety as novel P2 ligands are described. All the compounds are very potent HIV-1 protease inhibitors with IC50 values in the nanomolar or picomolar ranges (0.05-0.43 nM). Molecular docking studies revealed the formation of an extensive hydrogen-bonding network between the inhibitor and the active site. Particularly, the isosorbide-derived P2 ligand is involved in strong hydrogen bonding interactions with the backbone atoms.
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Affiliation(s)
- Xin Qiu
- Institute of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong Province, PR China
| | - Guo-Dong Zhao
- Institute of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong Province, PR China
| | - Long-Qiang Tang
- Institute of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong Province, PR China
| | - Zhao-Peng Liu
- Institute of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong Province, PR China.
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Vadlapatla RK, Patel M, Paturi DK, Pal D, Mitra AK. Clinically relevant drug-drug interactions between antiretrovirals and antifungals. Expert Opin Drug Metab Toxicol 2014; 10:561-80. [PMID: 24521092 PMCID: PMC4516223 DOI: 10.1517/17425255.2014.883379] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
INTRODUCTION Complete delineation of the HIV-1 life cycle has resulted in the development of several antiretroviral drugs. Twenty-five therapeutic agents belonging to five different classes are currently available for the treatment of HIV-1 infections. Advent of triple combination antiretroviral therapy has significantly lowered the mortality rate in HIV patients. However, fungal infections still represent major opportunistic diseases in immunocompromised patients worldwide. AREAS COVERED Antiretroviral drugs that target enzymes and/or proteins indispensable for viral replication are discussed in this article. Fungal infections, causative organisms, epidemiology and preferred treatment modalities are also outlined. Finally, observed/predicted drug-drug interactions between antiretrovirals and antifungals are summarized along with clinical recommendations. EXPERT OPINION Concomitant use of amphotericin B and tenofovir must be closely monitored for renal functioning. Due to relatively weak interactive potential with the CYP450 system, fluconazole is the preferred antifungal drug. High itraconazole doses (> 200 mg/day) are not advised in patients receiving booster protease inhibitor (PI) regimen. Posaconazole is contraindicated in combination with either efavirenz or fosamprenavir. Moreover, voriconazole is contraindicated with high-dose ritonavir-boosted PI. Echinocandins may aid in overcoming the limitations of existing antifungal therapy. An increasing number of documented or predicted drug-drug interactions and therapeutic drug monitoring may aid in the management of HIV-associated opportunistic fungal infections.
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Affiliation(s)
- Ramya Krishna Vadlapatla
- University of Missouri-Kansas City, School of Pharmacy, Division of Pharmaceutical Sciences, Kansas City, MO 64108, USA
| | - Mitesh Patel
- University of Missouri-Kansas City, School of Pharmacy, Division of Pharmaceutical Sciences, Kansas City, MO 64108, USA
| | - Durga K Paturi
- University of Missouri-Kansas City, School of Pharmacy, Division of Pharmaceutical Sciences, Kansas City, MO 64108, USA
| | - Dhananjay Pal
- University of Missouri-Kansas City, School of Pharmacy, Division of Pharmaceutical Sciences, Kansas City, MO 64108, USA
| | - Ashim K Mitra
- Professor of Pharmacy, Chairman-Division of Pharmaceutical Sciences, Vice-Provost for Interdisciplinary Research, University of Missouri Curators’, 2464 Charlotte Street HSB 5258, Kansas City, MO 64108-2718, USA, Tel: +1 816 235 1615; Fax: +1 816 235 5779;
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Proteomic analysis of Vibrio cholerae outer membrane vesicles. Proc Natl Acad Sci U S A 2014; 111:E1548-56. [PMID: 24706774 DOI: 10.1073/pnas.1403683111] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Outer membrane vesicles (OMVs) produced by Gram-negative bacteria provide an interesting research material for defining cell-envelope proteins without experimental cell disruption. OMVs are also promising immunogenic platforms and may play important roles in bacterial survival and pathogenesis. We used in-solution trypsin digestion coupled to mass spectrometry to identify 90 proteins present in OMVs of Vibrio cholerae when grown under conditions that activate the TCP pilus virulence regulatory protein (ToxT) virulence regulon. The ToxT expression profile and potential contribution to virulence of these proteins were assessed using ToxT and in vivo RNA-seq, Tn-seq, and cholera stool proteomic and other genome-wide data sets. Thirteen OMV-associated proteins appear to be essential for cell growth, and therefore may represent antibacterial drug targets. Another 12 nonessential OMV proteins, including DegP protease, were required for intestinal colonization in rabbits. Comparative proteomics of a degP mutant revealed the importance of DegP in the incorporation of nine proteins into OMVs, including ones involved in biofilm matrix formation and various substrates of the type II secretion system. Taken together, these results suggest that DegP plays an important role in determining the content of OMVs and also affects phenotypes such as intestinal colonization, proper function of the type II secretion system, and formation of biofilm matrix.
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Kunze J, Todoroff N, Schneider P, Rodrigues T, Geppert T, Reisen F, Schreuder H, Saas J, Hessler G, Baringhaus KH, Schneider G. Targeting Dynamic Pockets of HIV-1 Protease by Structure-Based Computational Screening for Allosteric Inhibitors. J Chem Inf Model 2014; 54:987-91. [DOI: 10.1021/ci400712h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jens Kunze
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Nickolay Todoroff
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Petra Schneider
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Tiago Rodrigues
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Tim Geppert
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Felix Reisen
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Herman Schreuder
- Sanofi-Aventis Deutschland GmbH R&D, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Joachim Saas
- Sanofi-Aventis Deutschland GmbH R&D, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Gerhard Hessler
- Sanofi-Aventis Deutschland GmbH R&D, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Karl-Heinz Baringhaus
- Sanofi-Aventis Deutschland GmbH R&D, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Gisbert Schneider
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
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Abad Martínez MJ, del Olmo LMB, Benito PB. Interactions Between Natural Health Products and Antiretroviral Drugs. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2014. [DOI: 10.1016/b978-0-444-63430-6.00006-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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