1
|
Wapling J, Srivastava S, Shehu-Xhilaga M, Tachedjian G. Targeting Human Immunodeficiency Virus Type 1 Assembly, Maturation and Budding. Drug Target Insights 2017. [DOI: 10.1177/117739280700200020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Johanna Wapling
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
- Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
| | - Seema Srivastava
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
| | - Miranda Shehu-Xhilaga
- Department of Medicine, Monash University, Prahran, Victoria 3181, Australia
- Infectious Diseases Unit, Alfred Hospital, Prahran, Victoria 3181, Australia
| | - Gilda Tachedjian
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
- Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
- Department of Medicine, Monash University, Prahran, Victoria 3181, Australia
| |
Collapse
|
2
|
Turočkin A, Raven W, Selig P. Synthesis of Bicyclic and Tricyclic Chiral Guanidinium Salts by an Intramolecular Alkylation Approach. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Aleksej Turočkin
- Institute of Organic Chemistry; RWTH Aachen University; Landoltweg 1 52074 Aachen Germany
| | - William Raven
- Institute of Inorganic Chemistry; RWTH Aachen University; Landoltweg 1 52074 Aachen Germany
| | - Philipp Selig
- Institute of Organic Chemistry; RWTH Aachen University; Landoltweg 1 52074 Aachen Germany
| |
Collapse
|
3
|
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]
|
4
|
Ung PMU, Dunbar JB, Gestwicki JE, Carlson HA. An allosteric modulator of HIV-1 protease shows equipotent inhibition of wild-type and drug-resistant proteases. J Med Chem 2014; 57:6468-78. [PMID: 25062388 PMCID: PMC4136727 DOI: 10.1021/jm5008352] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
NMR
and MD simulations have demonstrated that the flaps of HIV-1 protease
(HIV-1p) adopt a range of conformations that are coupled with its
enzymatic activity. Previously, a model was created for an allosteric
site located between the flap and the core of HIV-1p, called the Eye
site (2008, 89, 643−65218381626). Here, results from our first study were
combined with a ligand-based, lead-hopping method to identify a novel
compound (NIT). NIT inhibits HIV-1p, independent of the presence of
an active-site inhibitor such as pepstatin A. Assays showed that NIT
acts on an allosteric site other than the dimerization interface.
MD simulations of the ligand–protein complex show that NIT
stably binds in the Eye site and restricts the flaps. That bound state
of NIT is consistent with a crystal structure of similar fragments
bound in the Eye site (2010, 75, 257−26820659109). Most importantly,
NIT is equally potent against wild-type and a multidrug-resistant
mutant of HIV-1p, which highlights the promise of allosteric inhibitors
circumventing existing clinical resistance.
Collapse
Affiliation(s)
- Peter M-U Ung
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | | | | | | |
Collapse
|
5
|
Fanelli R, Ressurreição AS, Dufau L, Soulier JL, Vidu A, Tonali N, Bernadat G, Reboud-Ravaux M, Ongeri S. Introduction of polar groups on the naphthalene scaffold of molecular tongs inhibiting wild-type and mutated HIV-1 protease dimerization. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00032c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new series of naphthalene-based molecular tongs containing polar groups at the 3-position of the naphthalene scaffold was synthesized and its anti-dimerization activity was evaluated against HIV-1 protease.
Collapse
Affiliation(s)
- R. Fanelli
- Molécules Fluorées et Chimie Médicinale
- BioCIS UMR-CNRS 8076
- LabEx LERMIT
- Université Paris-Sud
- Faculté de Pharmacie
| | - A. S. Ressurreição
- Molécules Fluorées et Chimie Médicinale
- BioCIS UMR-CNRS 8076
- LabEx LERMIT
- Université Paris-Sud
- Faculté de Pharmacie
| | - L. Dufau
- Sorbonne Universités
- UPMC Univ Paris 06
- UMR 8256
- B2A
- Biological Adaptation and Ageing, Integrated Cellular Ageing and Inflammation, Molecular & Functional Enzymology
| | - J.-L. Soulier
- Molécules Fluorées et Chimie Médicinale
- BioCIS UMR-CNRS 8076
- LabEx LERMIT
- Université Paris-Sud
- Faculté de Pharmacie
| | - A. Vidu
- Molécules Fluorées et Chimie Médicinale
- BioCIS UMR-CNRS 8076
- LabEx LERMIT
- Université Paris-Sud
- Faculté de Pharmacie
| | - N. Tonali
- Molécules Fluorées et Chimie Médicinale
- BioCIS UMR-CNRS 8076
- LabEx LERMIT
- Université Paris-Sud
- Faculté de Pharmacie
| | - G. Bernadat
- Molécules Fluorées et Chimie Médicinale
- BioCIS UMR-CNRS 8076
- LabEx LERMIT
- Université Paris-Sud
- Faculté de Pharmacie
| | - M. Reboud-Ravaux
- Sorbonne Universités
- UPMC Univ Paris 06
- UMR 8256
- B2A
- Biological Adaptation and Ageing, Integrated Cellular Ageing and Inflammation, Molecular & Functional Enzymology
| | - S. Ongeri
- Molécules Fluorées et Chimie Médicinale
- BioCIS UMR-CNRS 8076
- LabEx LERMIT
- Université Paris-Sud
- Faculté de Pharmacie
| |
Collapse
|
6
|
Wen MF, Lin BT, He CS, Wu JZ. Hydrogen-bonding network of N,N'-bis[2-(tert-butyldimethylsiloxy)ethyl]ethylenediammonium dichloride. Acta Crystallogr C 2013; 69:787-9. [PMID: 23832044 DOI: 10.1107/s0108270113015084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 05/31/2013] [Indexed: 11/10/2022] Open
Abstract
The title salt, C18H46N2O2Si2(2+)·2Cl(-), has been synthesized by reaction of N,N'-bis(2-hydroxyethyl)ethylenediamine with tert-butyldimethylsilyl chloride. The zigzag backbone dication is located across an inversion centre and the two chloride anions are related by inversion symmetry. The ionic components form a supramolecular two-dimensional network via N-H···Cl hydrogen bonding, which is responsible for the high melting point compared with the oily compound N,N'-bis[2-(tert-butyldimethylsiloxy)ethyl]ethylenediamine.
Collapse
Affiliation(s)
- Mei-Feng Wen
- School of Chemistry and Environment, South China Normal University, Guangzhou 510006, People's Republic of China
| | | | | | | |
Collapse
|
7
|
Peptide inhibitors disrupt the serotonin 5-HT2C receptor interaction with phosphatase and tensin homolog to allosterically modulate cellular signaling and behavior. J Neurosci 2013; 33:1615-30. [PMID: 23345234 DOI: 10.1523/jneurosci.2656-12.2013] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Serotonin (5-hydroxytryptamine; 5-HT) signaling through the 5-HT(2C) receptor (5-HT(2C)R) is essential in normal physiology, whereas aberrant 5-HT(2C)R function is thought to contribute to the pathogenesis of multiple neural disorders. The 5-HT(2C)R interacts with specific protein partners, but the impact of such interactions on 5-HT(2C)R function is poorly understood. Here, we report convergent cellular and behavioral data that the interaction between the 5-HT(2C)R and protein phosphatase and tensin homolog (PTEN) serves as a regulatory mechanism to control 5-HT(2C)R-mediated biology but not that of the closely homologous 5-HT(2A)R. A peptide derived from the third intracellular loop of the human 5-HT(2C)R [3L4F (third loop, fourth fragment)] disrupted the association, allosterically augmented 5-HT(2C)R-mediated signaling in live cells, and acted as a positive allosteric modulator in rats in vivo. We identified the critical residues within an 8 aa fragment of the 3L4F peptide that maintained efficacy (within the picomolar range) in live cells similar to that of the 3L4F peptide. Last, molecular modeling identified key structural features and potential interaction sites of the active 3L4F peptides against PTEN. These compelling data demonstrate the specificity and importance of this protein assembly in cellular events and behaviors mediated by 5-HT(2C)R signaling and provide a chemical guidepost to the future development of drug-like peptide or small-molecule inhibitors as neuroprobes to study 5-HT(2C)R allostery and therapeutics for 5-HT(2C)R-mediated disorders.
Collapse
|
8
|
Ko E, Raghuraman A, Perez LM, Ioerger TR, Burgess K. Exploring key orientations at protein-protein interfaces with small molecule probes. J Am Chem Soc 2013; 135:167-73. [PMID: 23270593 PMCID: PMC3551583 DOI: 10.1021/ja3067258] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecule probes that selectively perturb protein-protein interactions (PPIs) are pivotal to biomedical science, but their discovery is challenging. We hypothesized that conformational resemblance of semirigid scaffolds expressing amino acid side-chains to PPI-interface regions could guide this process. Consequently, a data mining algorithm was developed to sample huge numbers of PPIs to find ones that match preferred conformers of a selected semirigid scaffold. Conformations of one such chemotype (1aaa; all methyl side-chains) matched several biomedically significant PPIs, including the dimerization interface of HIV-1 protease. On the basis of these observations, four molecules 1 with side-chains corresponding to the matching HIV-1 dimerization interface regions were prepared; all four inhibited HIV-1 protease via perturbation of dimerization. These data indicate this approach may inspire design of small molecule interface probes to perturb PPIs.
Collapse
Affiliation(s)
- Eunhwa Ko
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842
| | - Arjun Raghuraman
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842
| | - Lisa M. Perez
- Laboratory for Molecular Simulation, Texas A & M University, Box 30012, College Station, TX 77842
| | - Thomas R. Ioerger
- Department of Computer Science, Texas A & M University, College Station, TX 77843-3112
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842
| |
Collapse
|
9
|
Dufau L, Marques Ressurreição AS, Fanelli R, Kihal N, Vidu A, Milcent T, Soulier JL, Rodrigo J, Desvergne A, Leblanc K, Bernadat G, Crousse B, Reboud-Ravaux M, Ongeri S. Carbonylhydrazide-based molecular tongs inhibit wild-type and mutated HIV-1 protease dimerization. J Med Chem 2012; 55:6762-75. [PMID: 22800535 DOI: 10.1021/jm300181j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have designed and synthesized new molecular tongs based on a rigid naphthalene scaffold and evaluated their antidimer activity on HIV-1 protease (PR). We inserted carbonylhydrazide and oligohydrazide (azatide) fragments into their peptidomimetic arms to reduce hydrophobicity and increase metabolic stability. These fragments are designed to disrupt the protein-protein interactions by reproducing the hydrogen bond pattern found in the antiparallel β-sheet formed between the N- and C-ends of the two monomers in the native PR. Kinetic analyses and fluorescent probe binding studies showed that several molecular tongs can inhibit PR dimerization. The best nonpeptidic molecular tongs to date were obtained with an inhibition constant K(id) of 50 nM for PR and 80 nM for the multimutated protease ANAM-11. The PR inhibition was selective, the aspartic proteases renin and pepsin were not inhibited.
Collapse
Affiliation(s)
- Laure Dufau
- UMR-CNRS 8076, Molécules Fluorées et Chimie Médicinale, LabEx LERMIT, Faculté de Pharmacie, Université Paris-Sud 11, 5 rue J. B. Clément, 92296 Châtenay-Malabry Cedex, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Pinyol E, Frutos S, Grillo-Bosch D, Giralt E, Clotet B, Esté JA, Diez A. Applications of 3-aminolactams: design, synthesis, and biological evaluation of a library of potential dimerisation inhibitors of HIV1-protease. Org Biomol Chem 2012; 10:4348-54. [PMID: 22546925 DOI: 10.1039/c2ob25291k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the context of our studies on the applications of 3-aminolactams as conformationally restricted pseudodipeptides, we report here the synthesis of a library of potential dimerisation inhibitors of HIV1-protease. Two of the pseudopeptides were active on the wild type virus (HIV1) at micromolar levels (EC(50)). Although the peptides showed lower anti-viral activity than previously reported dimerisation inhibitors, our results demonstrate that the piperidone moiety does not prevent cell penetration, and hence that such derivatization is compatible with potential anti-HIV treatment.
Collapse
Affiliation(s)
- Eulàlia Pinyol
- Institute for Research in Biomedicine, Barcelona Science Park, 08028-Barcelona, Spain
| | | | | | | | | | | | | |
Collapse
|
11
|
Vidu A, Dufau L, Bannwarth L, Soulier JL, Sicsic S, Piarulli U, Reboud-Ravaux M, Ongeri S. Toward the First Nonpeptidic Molecular Tong Inhibitor of Wild-Type and Mutated HIV-1 Protease Dimerization. ChemMedChem 2010; 5:1899-906. [DOI: 10.1002/cmdc.201000308] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
12
|
Martos V, Castreño P, Royo M, Albericio F, Mendoza JD. Solid-Phase Synthesis of Chiral Bicyclic Guanidinium Oligomers. ACTA ACUST UNITED AC 2009; 11:410-21. [DOI: 10.1021/cc800207v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vera Martos
- Institute of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans 16, 43007 Tarragona, Spain, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain, Combinatorial Chemistry Unit, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain, and Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028
| | - Pilar Castreño
- Institute of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans 16, 43007 Tarragona, Spain, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain, Combinatorial Chemistry Unit, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain, and Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028
| | - Miriam Royo
- Institute of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans 16, 43007 Tarragona, Spain, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain, Combinatorial Chemistry Unit, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain, and Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028
| | - Fernando Albericio
- Institute of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans 16, 43007 Tarragona, Spain, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain, Combinatorial Chemistry Unit, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain, and Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028
| | - Javier de Mendoza
- Institute of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans 16, 43007 Tarragona, Spain, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain, Combinatorial Chemistry Unit, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain, and Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028
| |
Collapse
|
13
|
Bannwarth L, Rose T, Dufau L, Vanderesse R, Dumond J, Jamart-Grégoire B, Pannecouque C, De Clercq E, Reboud-Ravaux M. Dimer Disruption and Monomer Sequestration by Alkyl Tripeptides Are Successful Strategies for Inhibiting Wild-Type and Multidrug-Resistant Mutated HIV-1 Proteases. Biochemistry 2008; 48:379-87. [DOI: 10.1021/bi801422u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ludovic Bannwarth
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Thierry Rose
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Laure Dufau
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Régis Vanderesse
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Julien Dumond
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Brigitte Jamart-Grégoire
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Christophe Pannecouque
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Erik De Clercq
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Michèle Reboud-Ravaux
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS, Université Paris 6 UPMC, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 5, France, Institut Pasteur, PFBMI, Département de Biologie Structurale, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France, Laboratoire de Chimie Physique Macromoléculaire, UMR 7568 CNRS-INPL, ENSIC 1, rue Grandville, 54001 Nancy, France, and Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| |
Collapse
|
14
|
Obiol-Pardo C, Rubio-Martinez J. Homology modeling of human transketolase: description of critical sites useful for drug design and study of the cofactor binding mode. J Mol Graph Model 2008; 27:723-34. [PMID: 19111488 DOI: 10.1016/j.jmgm.2008.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 11/07/2008] [Accepted: 11/10/2008] [Indexed: 10/21/2022]
Abstract
Transketolase, the most critical enzyme of the non-oxidative branch of the pentose phosphate pathway, has been reported as a new target protein for cancer research. However, since the crystal structure of human Transketolase is unknown, no structure-based methods can be used to identify new inhibitors. We performed homology modeling of human Transketolase using the crystal structure of yeast as a template, and then refined the model through molecular dynamics simulations. Based on the resulting structure we propose five critical sites containing arginines (Arg 101, Arg 318, Arg 395, Arg 401 and Arg 474) that contribute to dimer stability or catalytic activity. In addition, an interaction analysis of its cofactor (thiamine pyrophosphate) and a binding site description were carried out, suggesting the substrate channel already identified in yeast Transketolase. A binding free energy calculation of its cofactor was performed to establish the main driving forces of binding. In summary, we describe a reliable model of human Transketolase that can be used in structure-based drug design and in the search for new Transketolase inhibitors that disrupt dimer stability and cover the critical sites found.
Collapse
Affiliation(s)
- Cristian Obiol-Pardo
- Dept. de Química Física, Universitat de Barcelona and The Institut de Recerca en Química Teòrica i Computacional (IQTCUB), Martí i Franqués 1, E-08028 Barcelona, Spain
| | | |
Collapse
|
15
|
Sidechain-linked inhibitors of HIV-1 protease dimerization. Bioorg Med Chem 2008; 17:967-76. [PMID: 18337105 DOI: 10.1016/j.bmc.2008.02.060] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Revised: 02/15/2008] [Accepted: 02/16/2008] [Indexed: 11/20/2022]
Abstract
There is a great need for alternative modes of inhibition for the design of anti-HIV therapies, due to the increased resistance of HIV to currently approved drugs. A novel strategy for generating potent dimerization inhibitors of HIV-1 protease is described based on sidechain-linked interfacial peptides. In a number of cases the activity of these agents against HIV-1 protease was found to be among the most potent reported, with inhibitory constants in the low nM range.
Collapse
|
16
|
Bannwarth L, Reboud-Ravaux M. An alternative strategy for inhibiting multidrug-resistant mutants of the dimeric HIV-1 protease by targeting the subunit interface. Biochem Soc Trans 2007; 35:551-4. [PMID: 17511649 DOI: 10.1042/bst0350551] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mutations that occur in response to the HIV-1 protease inhibitors are responsible for the development of multidrug cross-resistance to these antiproteases in AIDS treatment. One alternative to inhibiting the active site of HIV-1 protease is to target the dimer interface of the homodimeric enzyme at the antiparallel beta-sheet formed by the interdigitation of the C- and N-ends of each monomer. This region is highly conserved and is responsible for approx. 75% of the dimer-stabilization energy. The strategies that have been used to design small molecules to target the interface antiparallel beta-sheet have produced lipopeptides, guanidinium derivatives and peptides (or peptidomimetics) cross-linked with spacers. The mechanism of inhibition was determined using a combination of kinetic and biophysical methods. These dimerization inhibitors proved equally active in vitro against both wild-type and mutated proteases. They are therefore promising alternatives to active-site-directed inhibitors in AIDS therapy. Disruption of protein-protein interactions by small molecules is a new way to obtain potentially therapeutic molecules.
Collapse
Affiliation(s)
- L Bannwarth
- Enzymologie Moléculaire et Fonctionnelle, FRE 2852, CNRS-Université Paris 6, Institut Jacques Monod, 2 place Jussieu, 75251 Cedex 05, France
| | | |
Collapse
|
17
|
Frutos S, Rodriguez-Mias RA, Madurga S, Collinet B, Reboud-Ravaux M, Ludevid D, Giralt E. Disruption of the HIV-1 protease dimer with interface peptides: Structural studies using NMR spectroscopy combined with [2-13C]-Trp selective labeling. Biopolymers 2007; 88:164-73. [PMID: 17236209 DOI: 10.1002/bip.20685] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
HIV-1 protease (HIV-1 PR), which is encoded by retroviruses, is required for the processing of gag and pol polyprotein precursors, hence it is essential for the production of infectious viral particles. In vitro inhibition of the enzyme results in the production of progeny virions that are immature and noninfectious, suggesting its potential as a therapeutic target for AIDS. Although a number of potent protease inhibitor drugs are now available, the onset of resistance to these agents due to mutations in HIV-1 PR has created an urgent need for new means of HIV-1 PR inhibition. Whereas enzymes are usually inactivated by blocking of the active site, the structure of dimeric HIV-1 PR allows an alternative inhibitory mechanism. Since the active site is formed by two half-enzymes, which are connected by a four-stranded antiparallel beta-sheet involving the N- and C- termini of both monomers, enzyme activity can be abolished by reagents targeting the dimer interface in a region relatively free of mutations would interfere with formation or stability of the functional HIV-1 PR dimer. This strategy has been explored by several groups who targeted the four-stranded antiparallel beta-sheet that contributes close to 75% of the dimerization energy. Interface peptides corresponding to native monomer N- or C-termini of several of their mimetics demonstrated, mainly on the basis of kinetic analyses, to act as dimerization inhibitors. However, to the best of our knowledge, neither X-ray crystallography nor NMR structural studies of the enzyme-inhibitor complex have been performed to date. In this article we report a structural study of the dimerization inhibition of HIV-1 PR by NMR using selective Trp side chain labeling.
Collapse
Affiliation(s)
- Silvia Frutos
- Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, E-08028 Barcelona, Spain
| | | | | | | | | | | | | |
Collapse
|
18
|
Abstract
HIV infection is the leading cause of death worldwide and despite major advances in treatment, more new cases were diagnosed in 2004 than any previous year. Current treatment regimens are based on the use of two or more drugs from two or more classes of inhibitors termed highly active antiretroviral therapy (HAART). Although HAART is capable of suppressing viral loads to undetectable levels, problems of toxicity, patient adherence, and particularly the emergence of drug-resistant viruses continues to spur the development of new chemotherapeutics to combat HIV. Clinical candidates from the four existing classes of inhibitors are presented in this review along with lead compounds against new viral targets, with special emphasis on HIV integrase.
Collapse
Affiliation(s)
- D Christopher Meadows
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | | |
Collapse
|
19
|
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.
Collapse
Affiliation(s)
- María-José Camarasa
- Instituto de Química Médica (C.S.I.C.), Juan de la Cierva 3, 28006 Madrid, Spain.
| | | | | | | | | |
Collapse
|
20
|
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.
Collapse
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
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Dixon MJ, Maurer RI, Biggi C, Oyarzabal J, Essex JW, Bradley M. Mechanism and structure-activity relationships of norspermidine-based peptidic inhibitors of trypanothione reductase. Bioorg Med Chem 2005; 13:4513-26. [PMID: 15922604 DOI: 10.1016/j.bmc.2005.04.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 04/11/2005] [Accepted: 04/15/2005] [Indexed: 10/25/2022]
Abstract
A library of polyamine-peptide conjugates based around some previously identified inhibitors of trypanothione reductase was synthesised by parallel solid-phase chemistry and screened. Kinetic analysis of library members established that subtle structural changes altered their mechanism of action, switching between competitive and non-competitive inhibition. The mode of action of the non-competitive inhibitors was investigated in detail by a variety of techniques including enzyme kinetic analysis (looking at both NADPH and trypanothione disulfide substrates), gel filtration chromatography and analytical ultracentrifugation, leading to the identification of an allosteric mode of inhibition.
Collapse
Affiliation(s)
- Mark J Dixon
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | | | | | | | | | | |
Collapse
|
22
|
Merabet N, Dumond J, Collinet B, Van Baelinghem L, Boggetto N, Ongeri S, Ressad F, Reboud-Ravaux M, Sicsic S. New Constrained “Molecular Tongs” Designed To Dissociate HIV-1 Protease Dimer. J Med Chem 2004; 47:6392-400. [PMID: 15566308 DOI: 10.1021/jm040833q] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New "molecular tongs" based on naphthalene and quinoline scaffolds linked to two peptidic strands were synthesized. They were designed to prevent dimerization of HIV-1 protease by targeting the antiparallel beta-sheet involving N- and C-termini of each monomer. Compared to "molecular tongs" previously described (Bouras, A.; Boggetto, N.; Benatalah, Z.; de Rosny, E.; Sicsic, S.; Reboux-Ravaud, M. J. Med. Chem. 1999, 42, 957-962), two main different structural features were introduced: positively charged quinoline as a new scaffold and two peptidic strands displaying different sequences. Seventeen new "molecular tongs" with dipeptidic or tripeptidic strands were synthesized. These molecules were assayed on HIV-1 protease using the Zhang kinetic technique. Eleven molecules behaved as pure dimerization inhibitors, mostly at the submicromolar range. Compared to a naphthalene scaffold, the quinoline one was shown in several cases to favor dimerization inhibition. The simplified hydrophobic Val-Leu-Val-OMe strand was confirmed as particularly favorable. The C-terminal analogue strand Thr-Leu-Asn-OMe was shown to be the best one for inducing dimerization inhibition (K(id) of 80 nM for compound 30). The mechanism of inhibition was ascertained using ANS binding and gel filtration. Experimental results are in agreement with the dissociation of the HIV-1 protease dimeric form in the presence of the synthesized molecular tongs.
Collapse
Affiliation(s)
- Naïma Merabet
- Biocis, UMR-CNRS 8076, Faculté de Pharmacie, Université de Paris-Sud, 5 rue J. B. Clément, F-92296 Châtenay-Malabry Cedex, France
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Abstract
Combinatorial chemistry can be efficiently used for the synthesis and evaluation of binding properties of libraries of synthetic receptors. This approach has been applied particularly to 'tweezer' and other 'multi-armed' receptors, and has been used for the identification of receptors for peptides in aqueous media, and for the development of new sensors and sensor arrays.
Collapse
|