1
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Ritonavir and xk263 Binding-Unbinding with HIV-1 Protease: Pathways, Energy and Comparison. LIFE (BASEL, SWITZERLAND) 2022; 12:life12010116. [PMID: 35054509 PMCID: PMC8779838 DOI: 10.3390/life12010116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 01/22/2023]
Abstract
Understanding non-covalent biomolecular recognition, which includes drug-protein bound states and their binding/unbinding processes, is of fundamental importance in chemistry, biology, and medicine. Fully revealing the factors that govern the binding/unbinding processes can further assist in designing drugs with desired binding kinetics. HIV protease (HIVp) plays an integral role in the HIV life cycle, so it is a prime target for drug therapy. HIVp has flexible flaps, and the binding pocket can be accessible by a ligand via various pathways. Comparing ligand association and dissociation pathways can help elucidate the ligand-protein interactions such as key residues directly involved in the interaction or specific protein conformations that determine the binding of a ligand under certain pathway(s). Here, we investigated the ligand unbinding process for a slow binder, ritonavir, and a fast binder, xk263, by using unbiased all-atom accelerated molecular dynamics (aMD) simulation with a re-seeding approach and an explicit solvent model. Using ritonavir-HIVp and xk263-HIVp ligand-protein systems as cases, we sampled multiple unbinding pathways for each ligand and observed that the two ligands preferred the same unbinding route. However, ritonavir required a greater HIVp motion to dissociate as compared with xk263, which can leave the binding pocket with little conformational change of HIVp. We also observed that ritonavir unbinding pathways involved residues which are associated with drug resistance and are distal from catalytic site. Analyzing HIVp conformations sampled during both ligand-protein binding and unbinding processes revealed significantly more overlapping HIVp conformations for ritonavir-HIVp rather than xk263-HIVp. However, many HIVp conformations are unique in xk263-HIVp unbinding processes. The findings are consistent with previous findings that xk263 prefers an induced-fit model for binding and unbinding, whereas ritonavir favors a conformation selection model. This study deepens our understanding of the dynamic process of ligand unbinding and provides insights into ligand-protein recognition mechanisms and drug discovery.
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2
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D’Orsi R, Funicello M, Laurita T, Lupattelli P, Berti F, Chiummiento L. The Pseudo-Symmetric N-benzyl Hydroxyethylamine Core in a New Series of Heteroarylcarboxyamide HIV-1 Pr Inhibitors: Synthesis, Molecular Modeling and Biological Evaluation. Biomolecules 2021; 11:1584. [PMID: 34827582 PMCID: PMC8615997 DOI: 10.3390/biom11111584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 11/16/2022] Open
Abstract
Here, we report the synthesis, enzyme inhibition and structure-activity relationship studies of a new potent class of HIV-1 protease inhibitors, which contain a pseudo-symmetric hydroxyethylamine core and heteroarylcarboxyamide moieties. The simple synthetic pathway furnished nine compounds in a few steps with high yields. The compounds were designed taking into account our previous results on other series of inhibitors with different substituents at P' and P'' and different ways of linking them to the inhibitor core. Potent inhibitory activity was obtained with nanomolar IC50 values measured with a standard fluorimetric test in 100 mM MES buffer, pH 5.5, containing 400 mM NaCl, 1 mM EDTA, 1 mM DTT and 1 mg/ml BSA. Compounds 9a-c, containing the indole ring in P1, exhibited an HIV-1 protease inhibitory activity more powerful than darunavir in the same assay. To obtain molecular insight into the binding properties of these compounds, docking analysis was performed, and their binding properties were also compared.
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Affiliation(s)
- Rosarita D’Orsi
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Maria Funicello
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Teresa Laurita
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Paolo Lupattelli
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Federico Berti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Lucia Chiummiento
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
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3
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Rösner HI, Caldarini M, Potel G, Malmodin D, Vanoni MA, Aliverti A, Broglia RA, Kragelund BB, Tiana G. The denatured state of HIV-1 protease under native conditions. Proteins 2021; 90:96-109. [PMID: 34312913 PMCID: PMC9290662 DOI: 10.1002/prot.26189] [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: 06/10/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/01/2022]
Abstract
The denatured state of several proteins has been shown to display transient structures that are relevant for folding, stability, and aggregation. To detect them by nuclear magnetic resonance (NMR) spectroscopy, the denatured state must be stabilized by chemical agents or changes in temperature. This makes the environment different from that experienced in biologically relevant processes. Using high‐resolution heteronuclear NMR spectroscopy, we have characterized several denatured states of a monomeric variant of HIV‐1 protease, which is natively structured in water, induced by different concentrations of urea, guanidinium chloride, and acetic acid. We have extrapolated the chemical shifts and the relaxation parameters to the denaturant‐free denatured state at native conditions, showing that they converge to the same values. Subsequently, we characterized the conformational properties of this biologically relevant denatured state under native conditions by advanced molecular dynamics simulations and validated the results by comparison to experimental data. We show that the denatured state of HIV‐1 protease under native conditions displays rich patterns of transient native and non‐native structures, which could be of relevance to its guidance through a complex folding process.
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Affiliation(s)
- Heike I Rösner
- BRIC, University of Copenhagen, Copenhagen N, Denmark.,Structural Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Martina Caldarini
- Department of Physics, Università degli Studi di Milano and INFN, Milan, Italy
| | - Gregory Potel
- Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Daniel Malmodin
- Structural Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Maria A Vanoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | | | - Ricardo A Broglia
- Department of Physics, Università degli Studi di Milano and INFN, Milan, Italy.,Niels Bohr Institutet, University of Copenhagen, Copenhagen Ø, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Guido Tiana
- Department of Physics, Università degli Studi di Milano and INFN, Milan, Italy.,Center for Complexity and Biosystems, Università degli Studi di Milano, Milan, Italy
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4
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Cruz JS, da Silva CA, Hamerski L. Natural Products from Endophytic Fungi Associated with Rubiaceae Species. J Fungi (Basel) 2020; 6:E128. [PMID: 32784526 PMCID: PMC7558492 DOI: 10.3390/jof6030128] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 02/06/2023] Open
Abstract
This review presents the chemical diversity and pharmacological properties of secondary metabolites produced by endophytic fungi associated with various genera of Rubiaceae. Several classes of natural products are described for these endophytes, although, this study highlights the importance of some metabolites, which are involved in antifungal, antibacterial, anti-protozoal activities; neurodegenerative diseases; cytotoxic activity; anti-inflammatory and antioxidant activity; and hyperglycemic control.
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Affiliation(s)
- Jacqueline Santos Cruz
- Department of Chemistry, Military Institute of Engineering, Praça General Tibúrcio 80, Rio de Janeiro 22290-270, Brazil;
| | - Carla Amaral da Silva
- Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rua Carlos Chagas Filho 373, Rio de Janeiro 21941-902, Brazil;
| | - Lidilhone Hamerski
- Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rua Carlos Chagas Filho 373, Rio de Janeiro 21941-902, Brazil;
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5
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Wang F, Zheng LS, Lang QW, Yin C, Wu T, Phansavath P, Chen GQ, Ratovelomanana-Vidal V, Zhang X. Rh(iii)-Catalyzed diastereoselective transfer hydrogenation: an efficient entry to key intermediates of HIV protease inhibitors. Chem Commun (Camb) 2020; 56:3119-3122. [DOI: 10.1039/c9cc09793g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A highly efficient diastereoselective transfer hydrogenation of α-aminoalkyl α′-chloromethyl ketones catalyzed by a tethered rhodium complex was developed and successfully utilized in the synthesis of the key intermediates of HIV protease inhibitors.
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Affiliation(s)
- Fangyuan Wang
- School of Chemistry and Chemical Engineering
- Harbin Institute of Technology
- Harbin 150001
- People's Republic of China
- Shenzhen Grubbs Institute and Department of Chemistry
| | - Long-Sheng Zheng
- Shenzhen Grubbs Institute and Department of Chemistry
- Southern University of Science and Technology
- Shenzhen 518000
- People's Republic of China
| | - Qi-Wei Lang
- Shenzhen Grubbs Institute and Department of Chemistry
- Southern University of Science and Technology
- Shenzhen 518000
- People's Republic of China
| | - Congcong Yin
- Shenzhen Grubbs Institute and Department of Chemistry
- Southern University of Science and Technology
- Shenzhen 518000
- People's Republic of China
| | - Ting Wu
- Shenzhen Grubbs Institute and Department of Chemistry
- Southern University of Science and Technology
- Shenzhen 518000
- People's Republic of China
| | - Phannarath Phansavath
- PSL University
- Chimie ParisTech
- CNRS
- Institute of Chemistry for Life and Health Sciences
- CSB2D team
| | - Gen-Qiang Chen
- Shenzhen Grubbs Institute and Department of Chemistry
- Southern University of Science and Technology
- Shenzhen 518000
- People's Republic of China
| | | | - Xumu Zhang
- Shenzhen Grubbs Institute and Department of Chemistry
- Southern University of Science and Technology
- Shenzhen 518000
- People's Republic of China
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6
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Voshavar C. Protease Inhibitors for the Treatment of HIV/AIDS: Recent Advances and Future Challenges. Curr Top Med Chem 2019; 19:1571-1598. [PMID: 31237209 DOI: 10.2174/1568026619666190619115243] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023]
Abstract
Acquired Immunodeficiency Syndrome (AIDS) is a chronic disease characterized by multiple life-threatening illnesses caused by a retro-virus, Human Immunodeficiency Virus (HIV). HIV infection slowly destroys the immune system and increases the risk of various other infections and diseases. Although, there is no immediate cure for HIV infection/AIDS, several drugs targeting various cruxes of HIV infection are used to slow down the progress of the disease and to boost the immune system. One of the key therapeutic strategies is Highly Active Antiretroviral Therapy (HAART) or ' AIDS cocktail' in a general sense, which is a customized combination of anti-retroviral drugs designed to combat the HIV infection. Since HAART's inception in 1995, this treatment was found to be effective in improving the life expectancy of HIV patients over two decades. Among various classes of HAART treatment regimen, Protease Inhibitors (PIs) are known to be widely used as a major component and found to be effective in treating HIV infection/AIDS. For the past several years, a variety of protease inhibitors have been reported. This review outlines the drug design strategies of PIs, chemical and pharmacological characteristics of some mechanism-based inhibitors, summarizes the recent developments in small molecule based drug discovery with HIV protease as a drug target. Further discussed are the pharmacology, PI drug resistance on HIV PR, adverse effects of HIV PIs and challenges/impediments in the successful application of HIV PIs as an important class of drugs in HAART regimen for the effective treatment of AIDS.
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Affiliation(s)
- Chandrashekhar Voshavar
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, United States
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7
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Agnello S, Brand M, Chellat MF, Gazzola S, Riedl R. A Structural View on Medicinal Chemistry Strategies against Drug Resistance. Angew Chem Int Ed Engl 2019; 58:3300-3345. [PMID: 29846032 DOI: 10.1002/anie.201802416] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/24/2018] [Indexed: 12/31/2022]
Abstract
The natural phenomenon of drug resistance is a widespread issue that hampers the performance of drugs in many major clinical indications. Antibacterial and antifungal drugs are affected, as well as compounds for the treatment of cancer, viral infections, or parasitic diseases. Despite the very diverse set of biological targets and organisms involved in the development of drug resistance, the underlying molecular mechanisms have been identified to understand the emergence of resistance and to overcome this detrimental process. Detailed structural information on the root causes for drug resistance is nowadays frequently available, so next-generation drugs can be designed that are anticipated to suffer less from resistance. This knowledge-based approach is essential for fighting the inevitable occurrence of drug resistance.
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Affiliation(s)
- Stefano Agnello
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Michael Brand
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Mathieu F Chellat
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Silvia Gazzola
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
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8
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Agnello S, Brand M, Chellat MF, Gazzola S, Riedl R. Eine strukturelle Evaluierung medizinalchemischer Strategien gegen Wirkstoffresistenzen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201802416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Stefano Agnello
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Michael Brand
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Mathieu F. Chellat
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Silvia Gazzola
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Rainer Riedl
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
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9
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Chen MH, Chang SS, Dong B, Yu LY, Wu YX, Wang RZ, Jiang W, Gao ZP, Si SY. Ahmpatinin iBu, a new HIV-1 protease inhibitor, from Streptomyces sp. CPCC 202950. RSC Adv 2018; 8:5138-5144. [PMID: 35542440 PMCID: PMC9078123 DOI: 10.1039/c7ra13241g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/04/2018] [Indexed: 12/16/2022] Open
Abstract
Ahmpatinin iBu (1) and statinin iBu (2), two new linear peptides, a novel pyrrolidine derivative, (−)-(S)-2-[3-(6-methylheptanamido)-2-oxopyrrolidin-1-yl] acetic acid (3), and three known pepstatin derivatives (4–6) along with their corresponding methanolysis artifacts (7–9) were isolated from Streptomyces sp. CPCC 202950. Their structures were elucidated on the basis of extensive spectroscopic data using Marfey's analysis, chiral-phase HPLC, and ECD and OR calculation to determine the absolute configurations. Compound 1 contains an unusual amino acid, 4-amino-3-hydroxy-5-(4-methoxyphenyl)pentanoic acid (Ahmppa), and 3 is the first natural product with a 2-(3-amino-2-oxopyrrolidin-1-yl)acetic acid system. Compounds 1, 2, and 4–9 are HIV-1 protease inhibitors. In particular, ahmpatinin iBu (1) exhibits significant inhibitory activity against HIV-1 protease with an IC50 value of 1.79 nM. A preliminary structure–activity relationship is discussed. Ahmpatinin iBu and statinin iBu, two new linear peptides, were isolated from Streptomyces sp. CPCC 202950. Ahmpatinin iBu exhibited significant inhibitory activity against HIV-1 protease with an IC50 value of 1.79 nM.![]()
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Affiliation(s)
- Ming-Hua Chen
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Shan-Shan Chang
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Biao Dong
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Ye-Xiang Wu
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Ren-Zhong Wang
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Wei Jiang
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Zeng-Ping Gao
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing 100102
- China
| | - Shu-Yi Si
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
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10
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Seif S, Planz V, Windbergs M. Delivery of Therapeutic Proteins Using Electrospun Fibers-Recent Developments and Current Challenges. Arch Pharm (Weinheim) 2017; 350. [PMID: 28845905 DOI: 10.1002/ardp.201700077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/26/2017] [Accepted: 07/29/2017] [Indexed: 12/22/2022]
Abstract
Proteins play a vital role within the human body by regulating various functions and even serving as structural constituent of many body parts. In this context, protein-based therapeutics have attracted a lot of attention in the last few decades as potential treatment of different diseases. Due to the steadily increasing interest in protein-based therapeutics, different dosage forms were investigated for delivering such complex macromolecules to the human body. Here, electrospun fibers hold a great potential for embedding proteins without structural damage and for controlled release of the protein for therapeutic applications. This review provides a comprehensive overview of the current state of protein-based carrier systems using electrospun fibers, with special emphasis on discussing their potential and key challenges in developing such therapeutic strategies, along with a prospective view of anticipated future directions.
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Affiliation(s)
- Salem Seif
- Department of Drug Delivery (DDEL), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Saarbruecken, Germany
| | - Viktoria Planz
- Department of Drug Delivery (DDEL), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Saarbruecken, Germany
- Institute of Pharmaceutical Technology and Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Maike Windbergs
- Department of Drug Delivery (DDEL), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Saarbruecken, Germany
- Institute of Pharmaceutical Technology and Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
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11
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Rösner HI, Caldarini M, Prestel A, Vanoni MA, Broglia RA, Aliverti A, Tiana G, Kragelund BB. Cold Denaturation of the HIV-1 Protease Monomer. Biochemistry 2017; 56:1029-1032. [DOI: 10.1021/acs.biochem.6b01141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Heike I. Rösner
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
- Biotech
Research and Innovation Centre (BRIC), Faculty of Health and Medical
Sciences, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
| | - Martina Caldarini
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
| | - Andreas Prestel
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
| | - Maria A. Vanoni
- Department
of Biosciences, University of Milano, via Celoria 26, 20133 Milano, Italy
| | - Ricardo A. Broglia
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
- Niels Bohr Institute, Blegdamsvej
17, 2100 Copenhagen Ø, Denmark
| | - Alessandro Aliverti
- Department
of Biosciences, University of Milano, via Celoria 26, 20133 Milano, Italy
| | - Guido Tiana
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
| | - Birthe B. Kragelund
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
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12
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Yellapu NK. Molecular Modelling, Dynamics, and Docking of Membrane Proteins. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Computational tools and techniques are now most popular and promising to progress the research at rapid rate. Molecular modelling studies contribute their maximum role in wide variety of disciplines especially in proteomics and drug discovery strategies. Molecular dynamics and molecular docking algorithms are now became an essential part in daily research activities of every laboratory throughout the world. These strategies are now well established and standardised to study any specific protein of interest and drug molecule. But still there exist considerable drawbacks in a special concern with membrane proteins as the presently available tools and methods cannot be applied directly to them. Modelling, dynamics and docking studies of membrane proteins need a special care and attention as several challenges are to be crossed with an intensive care to produce a reliable result. This chapter is aimed to discuss such challenges and solutions to handle membrane proteins.
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13
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Islam MA, Pillay TS. Structural requirements for potential HIV-integrase inhibitors identified using pharmacophore-based virtual screening and molecular dynamics studies. MOLECULAR BIOSYSTEMS 2016; 12:982-93. [PMID: 26809073 DOI: 10.1039/c5mb00767d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Acquired immunodeficiency syndrome (AIDS) is a life-threatening disease which is a collection of symptoms and infections caused by a retrovirus, human immunodeficiency virus (HIV). There is currently no curative treatment and therapy is reliant on the use of existing anti-retroviral drugs. Pharmacoinformatics approaches have already proven their pivotal role in the pharmaceutical industry for lead identification and optimization. In the current study, we analysed the binding preferences and inhibitory activity of HIV-integrase inhibitors using pharmacoinformatics. A set of 30 compounds were selected as the training set of a total 540 molecules for pharmacophore model generation. The final model was validated by statistical parameters and further used for virtual screening. The best mapped model (R = 0.940, RMSD = 2.847, Q(2) = 0.912, se = 0.498, Rpred(2) = 0.847 and rm(test)(2) = 0.636) explained that two hydrogen bond acceptor and one aromatic ring features were crucial for the inhibition of HIV-integrase. From virtual screening, initial hits were sorted using a number of parameters and finally two compounds were proposed as promising HIV-integrase inhibitors. Drug-likeness properties of the final screened compounds were compared to FDA approved HIV-integrase inhibitors. HIV-integrase structure in complex with the most active and final screened compounds were subjected to 50 ns molecular dynamics (MD) simulation studies to check comparative stability of the complexes. The study suggested that the screened compounds might be promising HIV-integrase inhibitors. The new chemical entities obtained from the NCI database will be subjected to experimental studies to confirm potential inhibition of HIV integrase.
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Affiliation(s)
- Md Ataul Islam
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.
| | - Tahir S Pillay
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Private Bag X323, Arcadia, Pretoria, 0007, South Africa. and Division of Chemical Pathology, University of Cape Town, South Africa
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14
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Islam MA, Pillay TS. Exploration of the structural requirements of HIV-protease inhibitors using pharmacophore, virtual screening and molecular docking approaches for lead identification. J Mol Graph Model 2015; 56:20-30. [DOI: 10.1016/j.jmgm.2014.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/24/2014] [Accepted: 11/30/2014] [Indexed: 12/19/2022]
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15
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Caldarini M, Sonar P, Valpapuram I, Tavella D, Volonté C, Pandini V, Vanoni M, Aliverti A, Broglia R, Tiana G, Cecconi C. The complex folding behavior of HIV-1-protease monomer revealed by optical-tweezer single-molecule experiments and molecular dynamics simulations. Biophys Chem 2014; 195:32-42. [DOI: 10.1016/j.bpc.2014.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/04/2014] [Accepted: 08/04/2014] [Indexed: 12/11/2022]
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16
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Ibraheem D, Elaissari A, Fessi H. Administration strategies for proteins and peptides. Int J Pharm 2014; 477:578-89. [PMID: 25445533 DOI: 10.1016/j.ijpharm.2014.10.059] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 10/24/2014] [Accepted: 10/28/2014] [Indexed: 02/01/2023]
Abstract
Proteins are a vital constituent of the body as they perform many of its major physiological and biological processes. Recently, proteins and peptides have attracted much attention as potential treatments for various dangerous and traditionally incurable diseases such as cancer, AIDS, dwarfism and autoimmune disorders. Furthermore, proteins could be used for diagnostics. At present, most therapeutic proteins are administered via parenteral routes that have many drawbacks, for example, they are painful, expensive and may cause toxicity. Finding more effective, easier and safer alternative routes for administering proteins and peptides is the key to therapeutic and commercial success. In this context, much research has been focused on non-invasive routes such as nasal, pulmonary, oral, ocular, and rectal for administering proteins and peptides. Unfortunately, the widespread use of proteins and peptides as drugs is still faced by many obstacles such as low bioavailability, short half-life in the blood stream, in vivo instability and numerous other problems. In order to overcome these hurdled and improve protein/peptide drug efficacy, various strategies have been developed such as permeability enhancement, enzyme inhibition, protein structure modification and protection by encapsulation. This review provides a detailed description of all the previous points in order to highlight the importance and potential of proteins and peptides as drugs.
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Affiliation(s)
- D Ibraheem
- University of Lyon, F-69622, Lyon, France, University Lyon-1, Villeurbanne, CNRS, UMR-5007, LAGEP- CPE, 43 bd 11 Novembre 1918, F-69622 Villeurbanne, France
| | - A Elaissari
- University of Lyon, F-69622, Lyon, France, University Lyon-1, Villeurbanne, CNRS, UMR-5007, LAGEP- CPE, 43 bd 11 Novembre 1918, F-69622 Villeurbanne, France
| | - H Fessi
- University of Lyon, F-69622, Lyon, France, University Lyon-1, Villeurbanne, CNRS, UMR-5007, LAGEP- CPE, 43 bd 11 Novembre 1918, F-69622 Villeurbanne, France.
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18
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Towards tricking a pathogen's protease into fighting infection: the 3D structure of a stable circularly permuted onconase variant cleavedby HIV-1 protease. PLoS One 2013; 8:e54568. [PMID: 23349931 PMCID: PMC3548804 DOI: 10.1371/journal.pone.0054568] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 12/12/2012] [Indexed: 11/19/2022] Open
Abstract
Onconase® is a highly cytotoxic amphibian homolog of Ribonuclease A. Here, we describe the construction of circularly permuted Onconase® variants by connecting the N- and C-termini of this enzyme with amino acid residues that are recognized and cleaved by the human immunodeficiency virus protease. Uncleaved circularly permuted Onconase® variants are unusually stable, non-cytotoxic and can internalize in human T-lymphocyte Jurkat cells. The structure, stability and dynamics of an intact and a cleaved circularly permuted Onconase® variant were determined by Nuclear Magnetic Resonance spectroscopy and provide valuable insight into the changes in catalytic efficiency caused by the cleavage. The understanding of the structural environment and the dynamics of the activation process represents a first step toward the development of more effective drugs for the treatment of diseases related to pathogens expressing a specific protease. By taking advantage of the protease’s activity to initiate a cytotoxic cascade, this approach is thought to be less susceptible to known resistance mechanisms.
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Yadav D, Paliwal S, Yadav R, Pal M, Pandey A. Identification of novel HIV 1--protease inhibitors: application of ligand and structure based pharmacophore mapping and virtual screening. PLoS One 2012; 7:e48942. [PMID: 23145032 PMCID: PMC3493599 DOI: 10.1371/journal.pone.0048942] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 10/01/2012] [Indexed: 01/27/2023] Open
Abstract
A combined ligand and structure-based drug design approach provides a synergistic advantage over either methods performed individually. Present work bestows a good assembly of ligand and structure-based pharmacophore generation concept. Ligand-oriented study was accomplished by employing the HypoGen module of Catalyst in which we have translated the experimental findings into 3-D pharmacophore models by identifying key features (four point pharmacophore) necessary for interaction of the inhibitors with the active site of HIV-1 protease enzyme using a training set of 33 compounds belonging to the cyclic cyanoguanidines and cyclic urea derivatives. The most predictive pharmacophore model (hypothesis 1), consisting of four features, namely, two hydrogen bond acceptors and two hydrophobic, showed a correlation (r) of 0.90 and a root mean square of 0.71 and cost difference of 56.59 bits between null cost and fixed cost. The model was validated using CatScramble technique, internal and external test set prediction. In the second phase of our study, a structure-based five feature pharmacophore hypothesis was generated which signifies the importance of hydrogen bond donor, hydrogen bond acceptors and hydrophobic interaction between the HIV-1 protease enzyme and its inhibitors. This work has taken a significant step towards the full integration of ligand and structure-based drug design methodologies as pharmacophoric features retrieved from structure-based strategy complemented the features from ligand-based study hence proving the accuracy of the developed models. The ligand-based pharmacophore model was used in virtual screening of Maybridge and NCI compound database resulting in the identification of four structurally diverse druggable compounds with nM activities.
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Affiliation(s)
- Divya Yadav
- Department of Pharmacy, Banasthali University, Banasthali, Rajasthan, India
| | - Sarvesh Paliwal
- Department of Pharmacy, Banasthali University, Banasthali, Rajasthan, India
| | - Rakesh Yadav
- Department of Pharmacy, Banasthali University, Banasthali, Rajasthan, India
| | - Mahima Pal
- Department of Pharmacy, Banasthali University, Banasthali, Rajasthan, India
| | - Anubhuti Pandey
- Department of Pharmacy, Banasthali University, Banasthali, Rajasthan, India
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20
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Nimmanpipug P, Khampa C, Lee VS, Nangola S, Tayapiwatana C. Identification of amino acid residues of a designed ankyrin repeat protein potentially involved in intermolecular interactions with CD4: Analysis by molecular dynamics simulations. J Mol Graph Model 2011; 31:65-75. [DOI: 10.1016/j.jmgm.2011.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 08/30/2011] [Accepted: 09/01/2011] [Indexed: 11/16/2022]
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21
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Purohit R, Rajendran V, Sethumadhavan R. Studies on Adaptability of Binding Residues Flap Region of TMC-114 Resistance HIV-1 Protease Mutants. J Biomol Struct Dyn 2011; 29:137-52. [DOI: 10.1080/07391102.2011.10507379] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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22
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Liu Q, Zhou H, Liu L, Chen X, Zhu R, Cao Z. Multi-target QSAR modelling in the analysis and design of HIV-HCV co-inhibitors: an in-silico study. BMC Bioinformatics 2011; 12:294. [PMID: 21774796 PMCID: PMC3167801 DOI: 10.1186/1471-2105-12-294] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 07/20/2011] [Indexed: 12/13/2022] Open
Abstract
Background HIV and HCV infections have become the leading global public-health threats. Even more remarkable, HIV-HCV co-infection is rapidly emerging as a major cause of morbidity and mortality throughout the world, due to the common rapid mutation characteristics of the two viruses as well as their similar complex influence to immunology system. Although considerable progresses have been made on the study of the infection of HIV and HCV respectively, few researches have been conducted on the investigation of the molecular mechanism of their co-infection and designing of the multi-target co-inhibitors for the two viruses simultaneously. Results In our study, a multi-target Quantitative Structure-Activity Relationship (QSAR) study of the inhibitors for HIV-HCV co-infection were addressed with an in-silico machine learning technique, i.e. multi-task learning, to help to guide the co-inhibitor design. Firstly, an integrated dataset with 3 HIV inhibitor subsets targeted on protease, integrase and reverse transcriptase respectively, together with another 6 subsets of 2 HCV inhibitors targeted on NS3 serine protease and NS5B polymerase respectively were compiled. Secondly, an efficient multi-target QSAR modelling of HIV-HCV co-inhibitors was performed by applying an accelerated gradient method based multi-task learning on the whole 9 datasets. Furthermore, by solving the L-1-infinity regularized optimization, the Drug-like index features for compound description were ranked according to their joint importance in multi-target QSAR modelling of HIV and HCV. Finally, a drug structure-activity simulation for investigating the relationships between compound structures and binding affinities was presented based on our multiple target analysis, which is then providing several novel clues for the design of multi-target HIV-HCV co-inhibitors with increasing likelihood of successful therapies on HIV, HCV and HIV-HCV co-infection. Conclusions The framework presented in our study provided an efficient way to identify and design inhibitors that simultaneously and selectively bind to multiple targets from multiple viruses with high affinity, and will definitely shed new lights on the future work of inhibitor synthesis for multi-target HIV, HCV, and HIV-HCV co-infection treatments.
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Affiliation(s)
- Qi Liu
- College of Life Science and Biotechnology, Tongji University, 200092, China
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23
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de Oliveira CM, Silva GH, Regasini LO, Flausino O, López SN, Abissi BM, Berlinck RGDS, Sette LD, Bonugli-Santos RC, Rodrigues A, Bolzani VDS, Araujo AR. Xylarenones C-E from an endophytic fungus isolated from Alibertia macrophylla. JOURNAL OF NATURAL PRODUCTS 2011; 74:1353-1357. [PMID: 21510613 DOI: 10.1021/np1005983] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Xylarenones C-E (2-4), three new eremophilane sesquiterpenes, have been isolated from solid substrate cultures of a Camarops-like endophytic fungus isolated from Alibertia macrophylla. The structures were elucidated by analysis of spectroscopic data. Compounds were evaluated in subtilisin and pepsin protease assays, and compound 2 showed potent inhibitory activity against both proteases.
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Affiliation(s)
- Camila Martins de Oliveira
- NuBBE, Núcleo de Bioensaios, Biossíntese e Ecofisiologia de Produtos Naturais, Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista, Rua Professor Francisco Degni s/n, Araraquara, São Paulo, Brazil
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Bonomi M, Barducci A, Gervasio FL, Parrinello M. Multiple routes and milestones in the folding of HIV-1 protease monomer. PLoS One 2010; 5:e13208. [PMID: 20967249 PMCID: PMC2954147 DOI: 10.1371/journal.pone.0013208] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 09/11/2010] [Indexed: 11/25/2022] Open
Abstract
Proteins fold on a time scale incompatible with a mechanism of random search in conformational space thus indicating that somehow they are guided to the native state through a funneled energetic landscape. At the same time the heterogeneous kinetics suggests the existence of several different folding routes. Here we propose a scenario for the folding mechanism of the monomer of HIV–1 protease in which multiple pathways and milestone events coexist. A variety of computational approaches supports this picture. These include very long all-atom molecular dynamics simulations in explicit solvent, an analysis of the network of clusters found in multiple high-temperature unfolding simulations and a complete characterization of free-energy surfaces carried out using a structure-based potential at atomistic resolution and a combination of metadynamics and parallel tempering. Our results confirm that the monomer in solution is stable toward unfolding and show that at least two unfolding pathways exist. In our scenario, the formation of a hydrophobic core is a milestone in the folding process which must occur along all the routes that lead this protein towards its native state. Furthermore, the ensemble of folding pathways proposed here substantiates a rational drug design strategy based on inhibiting the folding of HIV–1 protease.
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Affiliation(s)
- Massimiliano Bonomi
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, Lugano, Switzerland.
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26
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Welser K, Adsley R, Moore BM, Chan WC, Aylott JW. Protease sensing with nanoparticle based platforms. Analyst 2010; 136:29-41. [PMID: 20877821 DOI: 10.1039/c0an00429d] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanoparticulate systems in various unique configurations are highly effective at detecting protease activity both in vivo and in vitro. In this article, we have summarised the conventional modern methods for monitoring protease activity, and critically appraised recent advances in protease-responsive nanosensors.
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Affiliation(s)
- Katharina Welser
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, UK NG7 2RD
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27
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Genoni A, Morra G, Merz KM, Colombo G. Computational study of the resistance shown by the subtype B/HIV-1 protease to currently known inhibitors. Biochemistry 2010; 49:4283-95. [PMID: 20415450 DOI: 10.1021/bi100569u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human immunodeficiency virus type 1 protease (HIV-1 PR) is an essential enzyme in the HIV-1 life cycle. As such, this protein represents a major drug target in AIDS therapy, but emerging resistance to antiretroviral inhibitor cocktails, caused by high viral mutation rates, represents a significant challenge in AIDS treatment. Many mutations are not located within the active site or binding pocket, nor they do significantly modify the three-dimensional structural organization of the enzyme; hence, the mechanism(s) by which they alter inhibitor affinity for the protease remains uncertain. In this article, we present an all-atom computational analysis of the dynamic residue-residue coordination between the active site residues and the rest of the protein and of the energetic properties of different HIV-1 PR complexes. We analyze both the wild-type form and mutated forms that induce drug resistance. In particular, the results show differences between the wild type and the mutants in their mechanism of dynamic coordination, in the signal propagation between the active site residues and the rest of the protein, and in the energy networks responsible for the stabilization of the bound inhibitor conformation. Finally, we propose a dynamic and energetic explanation for HIV-1 protease drug resistance, and, through this model, we identify a possible new site that could be helpful in the design of a new family of HIV-1 PR allosteric inhibitors.
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Affiliation(s)
- Alessandro Genoni
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
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28
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Bonini C, Chiummiento L, De Bonis M, Di Blasio N, Funicello M, Lupattelli P, Pandolfo R, Tramutola F, Berti F. Synthesis of new thienyl ring containing HIV-1 protease inhibitors: promising preliminary pharmacological evaluation against recombinant HIV-1 proteases. J Med Chem 2010; 53:1451-7. [PMID: 20108932 DOI: 10.1021/jm900846f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A series of new thienyl ring containing analogues of nelfinavir and saquinavir with different substitution patterns were synthesized from suitable enantiopure diols. Their inhibitory activity against wild type recombinant HIV-1 protease was evaluated. In general thienyl groups spaced from the core by a methylene group gave products showing IC(50) in the nanomolar range, irrespective of the type and the substitution pattern of the heterocycle. The range of activity of the two most active compounds is substantially maintained or even increased against two commonly selected mutants, under drug pressure, such as V32I and V82A.
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Affiliation(s)
- Carlo Bonini
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via Nazario Sauro 85, 85100 Potenza, Italy.
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29
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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.
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Affiliation(s)
- Donald L Gardiner
- Malaria Biology Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Herston, QLD 4006, Australia.
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30
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Batista PR, Robert CH, Maréchal JD, Hamida-Rebaï MB, Pascutti PG, Bisch PM, Perahia D. Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 protease. Phys Chem Chem Phys 2010; 12:2850-9. [DOI: 10.1039/b919148h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Abstract
Progress in understanding protein folding allows to simulate, with atomic detail, the evolution of amino-acid sequences folding to a given native conformation. A particularly attractive example is the HIV-1 protease, main target of therapies to fight AIDS, which under drug pressure is able to develop resistance within few months from the starting of therapy. By comparing the results of simulations of the evolution of the protease with the corresponding proteomic data, one can approximately determine the value of the associated evolution pressure under which the enzyme has become and, as a consequence, map out the energy landscape in sequence space of the HIV-1 protease. It is found that there are several families of sequences folding to the native conformations of the enzyme. Each of these families are characterized by different sets of highly conserved ("hot") amino acids which play a critical role in the folding and stability of the protease. There are two main possibilities for the virus to move from one family to a different one: (a) in a single generation, through the concerted mutations of the hot amino acids, a highly unlikely event, (b) through a folding path (if it exists), again a very improbable event. In fact, the number of generations needed by the virus to change stepwise its sequence from one family to another is astronomically large. These results point to the "hot" segments of the protease as promising targets for a nonconventional inhibition strategy, likely not to create resistance.
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Affiliation(s)
- G Tiana
- Department of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy.
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32
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Lascar RM, Benn P. Role of darunavir in the management of HIV infection. HIV AIDS-RESEARCH AND PALLIATIVE CARE 2009; 1:31-9. [PMID: 22096377 PMCID: PMC3218677 DOI: 10.2147/hiv.s5397] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
There is an ongoing need for potent antiretroviral therapies to deal with the increasing pool of treatment-experienced patients with multiple drug resistance. The last few years have seen the arrival of 2 new and very potent protease inhibitors – darunavir and tipranavir – alongside 2 whole new classes of anti-HIV agents – the integrase inhibitors and chemokine receptor CCR5 antagonists. This review focuses on the role of darunavir in managing HIV infection, with an emphasis on darunavir’s exceptional resistance profile and related clinical effectiveness, pharmacokinetics, tolerability and toxicity data. Darunavir in combination with the pharmacokinetic booster ritonavir has proved to be very effective in the treatment of highly treatment-experienced HIV patients with multiple drug resistance. The favorable tolerability and toxicity profile alongside the drug’s high genetic barrier to the development of resistance prompted approval of darunavir for HIV-treatment naïve patients. Furthermore, the paradigm of treating HIV with a combination of anti-HIV agents is currently being challenged by ongoing darunavir monotherapy trials and these preliminary data will be discussed.
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Chiummiento L, Funicello M, Lupattelli P, Tramutola F, Campaner P. New indolic non-peptidic HIV protease inhibitors from (S)-glycidol: synthesis and preliminary biological activity. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.05.089] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Structure-based design and synthesis of macrocyclic peptidomimetic β-secretase (BACE-1) inhibitors. Bioorg Med Chem Lett 2009; 19:1361-5. [DOI: 10.1016/j.bmcl.2009.01.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 01/09/2009] [Accepted: 01/14/2009] [Indexed: 11/22/2022]
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35
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Assessing ligand efficiencies using template-based molecular docking and Tabu-clustering on tetrahydroimidazo-[4,5,1-jk][1,4]-benzodiazepin-2(1H)-one and-thione (TIBO) derivatives as HIV-1RT inhibitors. J CHEM SCI 2008. [DOI: 10.1007/s12039-008-0063-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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36
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Sherman W, Tidor B. Novel method for probing the specificity binding profile of ligands: applications to HIV protease. Chem Biol Drug Des 2008; 71:387-407. [PMID: 18384529 DOI: 10.1111/j.1747-0285.2008.00659.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A detailed understanding of factors influencing the binding specificity of a ligand to a set of desirable targets and undesirable decoys is a key step in the design of potent and selective therapeutics. We have developed a general method for optimizing binding specificity in ligand-receptor complexes based on the theory of electrostatic charge optimization. This methodology can be used to tune the binding of a ligand to a panel of potential targets and decoys, along the continuum from narrow binding to only one partner to broad binding to the entire panel. Using HIV-1 protease as a model system, we probe specificity in three distinct ways. First, we probe interactions that could make the promiscuous protease inhibitor pepstatin more selective toward HIV-1 protease. Next, we study clinically approved HIV-1 protease inhibitors and probe ways to broaden the binding profiles toward both wild-type HIV-1 protease and drug-resistant mutants. Finally, we study a conformational ensemble of wild-type HIV-1 protease to 'design in' broad specificity to known drugs before resistance mutations arise. The results from this conformational ensemble were similar to those from the drug-resistant ensemble, suggesting the use of a conformational wild-type ensemble as a tool to develop escape-mutant-resistant inhibitors.
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Affiliation(s)
- Woody Sherman
- Schrodinger, Inc., 120 West 45th Street, New York, NY 10036, USADepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USAComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USADepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USADepartment of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Bruce Tidor
- Schrodinger, Inc., 120 West 45th Street, New York, NY 10036, USADepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USAComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USADepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USADepartment of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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Cullen MD, Cheung YF, Houslay M, Hartman TL, Watson KM, Buckheit RW, Pannecouque C, De Clercq E, Cushman M. Investigation of the alkenyldiarylmethane non-nucleoside reverse transcriptase inhibitors as potential cAMP phosphodiesterase-4B2 inhibitors. Bioorg Med Chem Lett 2008; 18:1530-3. [PMID: 18222088 PMCID: PMC2268889 DOI: 10.1016/j.bmcl.2007.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 12/02/2007] [Accepted: 12/06/2007] [Indexed: 11/25/2022]
Abstract
The alkenyldiarylmethanes (ADAMs) are currently being investigated as non-nucleoside HIV-1 reverse transcriptase inhibitors (NNRTIs) of potential value in the treatment of HIV infection and AIDS. During the course of these studies, a number of ADAM analogues have been identified that protect HIV-infected cells from the cytopathic effects of the virus by an unknown, HIV-1 RT-independent mechanism. Since the phosphodiesterase 4 family is required for HIV infection, the effect of various ADAMs on the activity of PDE4B2 was investigated in an effort to determine if the ADAMs could possibly be targeting phosphodiesterases. Six compounds representative of the ADAM class were tested for inhibition of cAMP hydrolysis by PDE4B2 enzymatic activity. Four ADAMs were found to be weak inhibitors of PDE4B2 and two of them were inactive. The experimental results are consistent with an antiviral mechanism that does not include inhibition of PDE4 isoforms.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Mark Cushman
- To whom correspondence should be addressed. . Phone: 765-494-1465. Fax: 765-494-6790
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Broglia RA, Levy Y, Tiana G. HIV-1 protease folding and the design of drugs which do not create resistance. Curr Opin Struct Biol 2008; 18:60-6. [DOI: 10.1016/j.sbi.2007.10.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 10/29/2007] [Indexed: 10/22/2022]
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39
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Ravna AW, Sager G, Dahl SG, Sylte I. Membrane Transporters: Structure, Function and Targets for Drug Design. TOPICS IN MEDICINAL CHEMISTRY 2008. [DOI: 10.1007/7355_2008_023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Bonomi M, Gervasio FL, Tiana G, Provasi D, Broglia RA, Parrinello M. Insight into the folding inhibition of the HIV-1 protease by a small peptide. Biophys J 2007; 93:2813-21. [PMID: 17573430 PMCID: PMC1989711 DOI: 10.1529/biophysj.107.106369] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has recently been shown that the highly protected segments 24-34 (S2) and 83-93 (S8) of each of the two 99-mers of human immunodeficiency virus type 1 protease play an essential role in the folding of the monomers, giving rise to the so-called (postcritical) folding nucleus ((FN) minimum condensation unit ensuring folding) when they dock. This scenario received further support from model calculations that demonstrated that the peptide p-S8, displaying an amino acid sequence identical to the corresponding (83-93) segment of the monomer, can be used to interfere with the formation of the FN and eventually to inhibit folding by docking the fragment 24-34. Experiments in vitro and in cells infected with ex vivo wild-type and multiresistant HIV isolates confirm that the inhibition power of p-S8 is robust. On the other hand, there is no direct evidence demonstrating the validity of the proposed mechanism of inhibition associated with p-S8. To shed light on this question and to provide the basis for the design of a molecule mimetic to p-S8, to be used as lead of an eventual drug against AIDS, we study, in this paper, with the help of all-atom simulations in explicit solvent and the novel method of metadynamics combined with parallel tempering: a), the free energy and the equilibrium structure of each of the peptides p-S2 and p-S8; b), the details of the docking mechanism of the two peptides and the free energy associated with this process. Whereas p-S8 is found to be well structured, p-S2 is rather flexible, wrapping itself around p-S8 to give rise to the FN, which is stabilized by three particular hydrogen bonds.
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Affiliation(s)
- Massimiliano Bonomi
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zürich, Lugano, Switzerland.
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41
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Righi G, Ciambrone S, Bonini C. Stereocontrolled Transformations oftransα,β‐Aziridine Aldehydes toward Different Amino Hydroxylated Structures. SYNTHETIC COMMUN 2007. [DOI: 10.1080/00397910500514048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Steindl TM, Schuster D, Laggner C, Langer T. Parallel screening: a novel concept in pharmacophore modeling and virtual screening. J Chem Inf Model 2006; 46:2146-57. [PMID: 16995745 DOI: 10.1021/ci6002043] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Parallel screening comprises a novel in silico method to predict the potential biological activities of a compound by screening it with a multitude of pharmacophore models. Our aim is to provide a fast, large-scale system that allows for virtual activity profiling. In this proof of principle study, carried out with the software tools LigandScout and Catalyst, we present a model work for the application of parallel pharmacophore-based virtual screening on a set of 50 structure-based pharmacophore models built for various viral targets and 100 antiviral compounds. The latter were screened against all pharmacophore models in order to determine if their biological targets could be correctly predicted via an enrichment of corresponding pharmacophores matching these ligands. The results demonstrate that the desired enrichment, that is, successful virtual activity profiling, was achieved for approximately 90% of all input molecules. We discuss descriptors for output validation, as well as various aspects influencing the analysis of the obtained activity profiles, and the effect of the utilized search modus for screening.
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Affiliation(s)
- Theodora M Steindl
- Institute of Pharmacy, Computer Aided Molecular Design Group, University of Innsbruck, Innrain 52c, Austria
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43
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Skinner-Adams TS, Andrews KT, Melville L, McCarthy J, Gardiner DL. Synergistic interactions of the antiretroviral protease inhibitors saquinavir and ritonavir with chloroquine and mefloquine against Plasmodium falciparum in vitro. Antimicrob Agents Chemother 2006; 51:759-62. [PMID: 17088482 PMCID: PMC1797772 DOI: 10.1128/aac.00840-06] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The antimalarial activity of several antiretroviral protease inhibitor combinations was investigated. Data demonstrate that ritonavir and saquinavir behave synergistically with chloroquine and mefloquine. These data, and interactions with pepstatin-A, E-64, and bestatin, suggest that human immunodeficiency virus protease inhibitors do not target digestive-vacuole plasmepsins.
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Affiliation(s)
- T S Skinner-Adams
- University of Queensland, Department of Medicine, Brisbane, Australia.
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44
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Sousa SF, Fernandes PA, Ramos MJ. Protein-ligand docking: current status and future challenges. Proteins 2006; 65:15-26. [PMID: 16862531 DOI: 10.1002/prot.21082] [Citation(s) in RCA: 600] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Understanding the ruling principles whereby protein receptors recognize, interact, and associate with molecular substrates and inhibitors is of paramount importance in drug discovery efforts. Protein-ligand docking aims to predict and rank the structure(s) arising from the association between a given ligand and a target protein of known 3D structure. Despite the breathtaking advances in the field over the last decades and the widespread application of docking methods, several downsides still exist. In particular, protein flexibility-a critical aspect for a thorough understanding of the principles that guide ligand binding in proteins-is a major hurdle in current protein-ligand docking efforts that needs to be more efficiently accounted for. In this review the key concepts of protein-ligand docking methods are outlined, with major emphasis being given to the general strengths and weaknesses that presently characterize this methodology. Despite the size of the field, the principal types of search algorithms and scoring functions are reviewed and the most popular docking tools are briefly depicted. Recent advances that aim to address some of the traditional limitations associated with molecular docking are also described. A selection of hand-picked examples is used to illustrate these features.
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Affiliation(s)
- Sérgio Filipe Sousa
- REQUIMTE, Departamento de Química, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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45
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Camarasa MJ, Velázquez S, San-Félix A, Pérez-Pérez MJ, Gago F. Dimerization inhibitors of HIV-1 reverse transcriptase, protease and integrase: A single mode of inhibition for the three HIV enzymes? Antiviral Res 2006; 71:260-7. [PMID: 16872687 DOI: 10.1016/j.antiviral.2006.05.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Revised: 05/25/2006] [Accepted: 05/30/2006] [Indexed: 10/24/2022]
Abstract
The genome of human immunodeficiency virus type 1 (HIV-1) encodes 15 distinct proteins, three of which provide essential enzymatic functions: a reverse transcriptase (RT), an integrase (IN), and a protease (PR). Since these enzymes are all homodimers, pseudohomodimers or multimers, disruption of protein-protein interactions in these retroviral enzymes may constitute an alternative way to achieve HIV-1 inhibition. A growing number of dimerization inhibitors for these enzymes is being reported. This mini review summarizes some approaches that have been followed for the development of compounds that inhibit those three enzymes by interfering with the dimerization interfaces between the enzyme subunits.
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Affiliation(s)
- María-José Camarasa
- Instituto de Química Médica (C.S.I.C.), Juan de la Cierva 3, 28006 Madrid, Spain.
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46
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Bannwarth L, Kessler A, Pèthe S, Collinet B, Merabet N, Boggetto N, Sicsic S, Reboud-Ravaux M, Ongeri S. Molecular tongs containing amino acid mimetic fragments: new inhibitors of wild-type and mutated HIV-1 protease dimerization. J Med Chem 2006; 49:4657-64. [PMID: 16854071 DOI: 10.1021/jm060576k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have designed, synthesized, and evaluated the inhibitory activity and metabolic stability of new peptidomimetic molecular tongs based on a naphthalene scaffold for inhibiting HIV-1 protease dimerization. Peptidomimetic motifs were inserted into one peptidic strand to make it resistant to proteolysis. The peptidic character of the molecular tongs can be decreased without changing the way they inhibit dimerization. Mutated HIV-1 proteases are also vulnerable to dimerization inhibitors, and the multimutated protease ANAM-11 is twice as sensitive to the inhibitor compared to wild-type protease. Thus, the metabolic stability of antidimeric molecular tongs can be increased without compromising their ability to inhibit wild-type and mutated HIV-1 proteases in vitro.
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Affiliation(s)
- Ludovic Bannwarth
- Université de Paris-Sud XI, IFR 141, Biocis, UMR-CNRS 8076, Faculté de Pharmacie, 5 Rue J. B. Clément, F-92296 Châtenay-Malabry Cedex, France
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Mastrolorenzo A, Rusconi S, Scozzafava A, Supuran CT. Inhibitors of HIV-1 protease: 10 years after. Expert Opin Ther Pat 2006. [DOI: 10.1517/13543776.16.8.1067] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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48
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Wegner GJ, Wark AW, Lee HJ, Codner E, Saeki T, Fang S, Corn RM. Real-time surface plasmon resonance imaging measurements for the multiplexed determination of protein adsorption/desorption kinetics and surface enzymatic reactions on peptide microarrays. Anal Chem 2006; 76:5677-84. [PMID: 15456285 DOI: 10.1021/ac0494275] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The kinetics of protein adsorption/desorption onto peptide microarrays was studied using real-time surface plasmon resonance (SPR) imaging. S protein binding interactions were examined using an array composed of five different peptides: N terminal and C terminal immobilized wild-type S peptide (S1 and S2), an alternate binding sequence derived by phage display (LB2), an NVOC-protected S peptide, and a FLAG peptide control sequence (F). Kinetic measurements of the S protein-S1 peptide interaction were analyzed to determine a desorption rate constant (k(d)) of 1.1 (+/-0.08) x 10(-2) s(-1), an adsorption rate constant (k(a)) of 1.9 (+/-0.05) x 10(5) M(-1) s(-1), and an equilibrium adsorption constant (K(Ads)) of 1.7 (+/-0.08) x 10(7) M(-1). SPR imaging equilibrium measurements of S protein to S1 peptide were performed to independently confirm the kinetically determined value of K(Ads). Rate constants for the S2 and LB2 peptides on the array were measured as follows: 1.6 (+/-0.04) x 10(5) M(-1) s(-1) (k(a)) and 1.1 (+/-0.07) x 10(-2) s(-1) (k(d)) for S2, 1.2 (+/-0.05) x 10(5) M(-1) s(-1) (k(a)) and 1.1 (+/-0.03) x 10(-2) s(-1) (k(d)) for LB2. In addition to S protein adsorption/desorption, real-time SPR imaging of peptide arrays was applied to study the surface enzymatic activities of the protease factor Xa. Enzymatic cleavage of the substrate peptide (P1) was shown to follow first-order kinetics and proceed at a rate 10 times faster than that of the mutant peptide (P2), with cleavage velocities of 5.6 (+/-0.3) x 10(-4) s(-1) for P1 and 5.7 (+/-0.3) x 10(-5) s(-1) for P2.
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Affiliation(s)
- Greta J Wegner
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706, USA
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49
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Broglia RA, Tiana G, Sutto L, Provasi D, Simona F. Design of HIV-1-PR inhibitors that do not create resistance: blocking the folding of single monomers. Protein Sci 2005; 14:2668-81. [PMID: 16195553 PMCID: PMC2253289 DOI: 10.1110/ps.051670905] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The main problems found in designing drugs are those of optimizing the drug-target interaction and of avoiding the insurgence of resistance. We suggest a scheme for the design of inhibitors that can be used as leads for the development of a drug and that do not face either of these problems, and then apply it to the case of HIV-1-PR. It is based on the knowledge that the folding of single-domain proteins, such as each of the monomers forming the HIV-1-PR homodimer, is controlled by local elementary structures (LES), stabilized by local contacts among hydrophobic, strongly interacting, and highly conserved amino acids that play a central role in the folding process. Because LES have evolved over many generations to recognize and strongly interact with each other so as to make the protein fold fast and avoid aggregation with other proteins, highly specific (and thus little toxic) as well as effective folding-inhibitor molecules suggest themselves: short peptides (or eventually their mimetic molecules) displaying the same amino acid sequence of that of LES (p-LES). Aside from being specific and efficient, these inhibitors are expected not to induce resistance; in fact, mutations in HIV-1-PR that successfully avoid the action of p-LES imply the destabilization of one or more LES and thus should lead to protein denaturation. Making use of Monte Carlo simulations, we first identify the LES of the HIV-1-PR and then show that the corresponding p-LES peptides act as effective inhibitors of the folding of the protease.
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Chen C, Lu XH, Yan S, Chai H, Yao Q. HIV protease inhibitor ritonavir increases endothelial monolayer permeability. Biochem Biophys Res Commun 2005; 335:874-82. [PMID: 16105660 DOI: 10.1016/j.bbrc.2005.07.155] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Accepted: 07/25/2005] [Indexed: 11/30/2022]
Abstract
HIV protease inhibitors (PIs) are often associated with metabolic and cardiovascular complications although they are effective anti-HIV drugs. In this study, we determined whether HIV PI ritonavir could increase endothelial permeability, one of the important mechanisms of vascular lesion formation. Human dermal microvascular endothelial cells (HMECs) treated with ritonavir showed a significant increase of endothelial permeability in a dose- and time-dependent manner assayed with a transwell system. Ritonavir significantly reduced the mRNA levels of tight junction proteins zonula occluden-1, occludin, and claudin-1 by 40-60% as compared to controls (P<0.05) by real-time PCR analysis. Protein levels of these tight junction molecules were also substantially reduced in the ritonavir-treated cells. In addition, HMECs treated with ritonavir (7.5, 15, and 30microM) showed a substantial increase of superoxide anion production by 10%, 32%, and 65%, respectively, as compared to controls. Antioxidants (EGCG and SeMet) effectively reduced ritonavir-induced endothelial permeability. Furthermore, ritonavir activated ERK1/2 (phosphorylation), but not P38 and JNK. Specific ERK1/2 inhibitor, PD89059, significantly abolished ritonavir-induced endothelial permeability by 92%. Thus, HIV PI ritonavir increases endothelial permeability, decreases levels of tight junction proteins, and increases superoxide anion production. ERK1/2 activation is involved in the signal transduction pathway of ritonavir-induced endothelial permeability.
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Affiliation(s)
- Changyi Chen
- Molecular Surgeon Research Center, Division of Vascular Surgery and Endovascular Therapy, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA.
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