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Structure-based antivirals for emerging and neglected RNA viruses: an emerging field for medicinal chemistry in academia. Future Med Chem 2011; 2:1061-7. [PMID: 21426155 DOI: 10.4155/fmc.10.211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
"Many [neglected viruses] predominantly hit developing countries in tropical and subtropical regions of the world (40% of the world's population are now at risk of contracting dengue fever), but developed countries are by no means immune to their impact."
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152
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Yedidi RS, Proteasa G, Martinez JL, Vickrey JF, Martin PD, Wawrzak Z, Liu Z, Kovari IA, Kovari LC. Contribution of the 80s loop of HIV-1 protease to the multidrug-resistance mechanism: crystallographic study of MDR769 HIV-1 protease variants. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:524-32. [PMID: 21636892 PMCID: PMC3107050 DOI: 10.1107/s0907444911011541] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 03/28/2011] [Indexed: 11/10/2022]
Abstract
The flexible flaps and the 80s loops (Pro79-Ile84) of HIV-1 protease are crucial in inhibitor binding. Previously, it was reported that the crystal structure of multidrug-resistant 769 (MDR769) HIV-1 protease shows a wide-open conformation of the flaps owing to conformational rigidity acquired by the accumulation of mutations. In the current study, the effect of mutations on the conformation of the 80s loop of MDR769 HIV-1 protease variants is reported. Alternate conformations of Pro81 (proline switch) with a root-mean-square deviation of 3-4.8 Å in the C(α) atoms of the I10V mutant and a side chain with a `flipped-out' conformation in the A82F mutant cause distortion in the S1/S1' binding pockets that affects inhibitor binding. The A82S and A82T mutants show local changes in the electrostatics of inhibitor binding owing to the mutation from nonpolar to polar residues. In summary, the crystallographic studies of four variants of MDR769 HIV-1 protease presented in this article provide new insights towards understanding the drug-resistance mechanism as well as a basis for design of future protease inhibitors with enhanced potency.
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Affiliation(s)
- Ravikiran S. Yedidi
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, 540 East Canfield Avenue, Detroit, MI 48201, USA
| | - Georghe Proteasa
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, 540 East Canfield Avenue, Detroit, MI 48201, USA
| | - Jorge L. Martinez
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, 540 East Canfield Avenue, Detroit, MI 48201, USA
| | - John F. Vickrey
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, 540 East Canfield Avenue, Detroit, MI 48201, USA
| | - Philip D. Martin
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, 540 East Canfield Avenue, Detroit, MI 48201, USA
| | - Zdzislaw Wawrzak
- Department of Biochemistry, Molecular Biology and Cell Biology, Life Science Collaborative Access Team, Northwestern University Center for Synchrotron Research, Argonne, IL 60439, USA
| | - Zhigang Liu
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, 540 East Canfield Avenue, Detroit, MI 48201, USA
| | - Iulia A. Kovari
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, 540 East Canfield Avenue, Detroit, MI 48201, USA
| | - Ladislau C. Kovari
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, 540 East Canfield Avenue, Detroit, MI 48201, USA
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153
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Barman A, Schürer S, Prabhakar R. Computational modeling of substrate specificity and catalysis of the β-secretase (BACE1) enzyme. Biochemistry 2011; 50:4337-49. [PMID: 21500768 DOI: 10.1021/bi200081h] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In this combined MD simulation and DFT study, interactions of the wild-type (WT) amyloid precursor protein (APP) and its Swedish variant (SW), Lys670 → Asn and Met671 → Leu, with the beta-secretase (BACE1) enzyme and their cleavage mechanisms have been investigated. BACE1 catalyzes the rate-limiting step in the generation of 40-42 amino acid long Alzheimer amyloid beta (Aβ) peptides. All key structural parameters such as position of the flap, volume of the active site, electrostatic binding energy, structures, and positions of the inserts A, D, and F and 10s loop obtained from the MD simulations show that, in comparison to the WT-substrate, BACE1 exhibits greater affinity for the SW-substrate and orients it in a more reactive conformation. The enzyme-substrate models derived from the MD simulations were further utilized to investigate the general acid/base mechanism used by BACE1 to hydrolytically cleave these substrates. This mechanism proceeds through the following two steps: (1) formation of the gem-diol intermediate and (2) cleavage of the peptide bond. For the WT-substrate, the overall barrier of 22.4 kcal/mol for formation of the gem-diol intermediate is 3.3 kcal/mol higher than for the SW-substrate (19.1 kcal/mol). This process is found to be the rate-limiting in the entire mechanism. The computed barrier is in agreement with the measured barrier of ca. 18.00 kcal/mol for the WT-substrate and supports the experimental observation that the cleavage of the SW-substrate is 60 times more efficient than the WT-substrate.
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Affiliation(s)
- Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
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154
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Schlick T, Collepardo-Guevara R, Halvorsen LA, Jung S, Xiao X. Biomolecularmodeling and simulation: a field coming of age. Q Rev Biophys 2011; 44:191-228. [PMID: 21226976 PMCID: PMC3700731 DOI: 10.1017/s0033583510000284] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We assess the progress in biomolecular modeling and simulation, focusing on structure prediction and dynamics, by presenting the field’s history, metrics for its rise in popularity, early expressed expectations, and current significant applications. The increases in computational power combined with improvements in algorithms and force fields have led to considerable success, especially in protein folding, specificity of ligand/biomolecule interactions, and interpretation of complex experimental phenomena (e.g. NMR relaxation, protein-folding kinetics and multiple conformational states) through the generation of structural hypotheses and pathway mechanisms. Although far from a general automated tool, structure prediction is notable for proteins and RNA that preceded the experiment, especially by knowledge-based approaches. Thus, despite early unrealistic expectations and the realization that computer technology alone will not quickly bridge the gap between experimental and theoretical time frames, ongoing improvements to enhance the accuracy and scope of modeling and simulation are propelling the field onto a productive trajectory to become full partner with experiment and a field on its own right.
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Affiliation(s)
- Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA.
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155
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Oehme DP, Wilson DJD, Brownlee RTC. Effect of structural stress on the flexibility and adaptability of HIV-1 protease. J Chem Inf Model 2011; 51:1064-73. [PMID: 21500830 DOI: 10.1021/ci2000677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Resistance remains a major issue with regards to HIV-1 protease, despite the availability of numerous HIV-1 protease inhibitors and copious amounts of structural and binding data. In an effort to improve our understanding of how HIV-1 protease is able to "outsmart" new drugs, we have investigated the flexibility of HIV-1 protease and in particular how it adapts to different structural stresses. Our analysis has highlighted the effects of space group on the variability between structures of HIV-1 protease and suggests that consideration of multiple structures and appropriate consideration of different conformations of the Ile50 residue is necessary in any structural analysis. Calculation of the root-mean-square deviation on a per-residue basis has been used to identify 'natural variation', while mutational and ligand analyses have been carried out to identify the effect on structure as a result of specific stresses. It was observed that mutations readily cause changes to occur at sites both close to and distant from a mutation site, with changes more likely to occur at residues that are sites of other major mutations. It is also revealed that HIV-1 protease adaption is dependent on the type and the structure of any bound ligand. Identification of the specific changes that occur due to these stresses will aid in the understanding of resistance and also aid in the design of new drugs.
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Affiliation(s)
- Daniel P Oehme
- Department of Chemistry and La Trobe Institute for Molecular Sciences (LIMS), La Trobe University , Bundoora, Victoria, 3086, Australia
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156
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157
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Szecsi PB. The aspartic proteases. Scandinavian Journal of Clinical and Laboratory Investigation 2011. [DOI: 10.1080/00365519209104650] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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158
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Tang J, Lin Y, Co E, Hartsuck JA, Lin X. Understanding HIV protease: Can it be translated into effective therapy against AIDS? Scandinavian Journal of Clinical and Laboratory Investigation 2011. [DOI: 10.1080/00365519209104661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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159
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Öhrngren P, Wu X, Persson M, Ekegren JK, Wallberg H, Vrang L, Rosenquist Å, Samuelsson B, Unge T, Larhed M. HIV-1 protease inhibitors with a tertiary alcohol containing transition-state mimic and various P2 and P1′ substituents. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00077b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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160
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Ali A, Bandaranayake RM, Cai Y, King NM, Kolli M, Mittal S, Murzycki JF, Nalam MN, Nalivaika EA, Özen A, Prabu-Jeyabalan MM, Thayer K, Schiffer CA. Molecular Basis for Drug Resistance in HIV-1 Protease. Viruses 2010; 2:2509-2535. [PMID: 21994628 PMCID: PMC3185577 DOI: 10.3390/v2112509] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 10/22/2010] [Accepted: 10/28/2010] [Indexed: 02/01/2023] Open
Abstract
HIV-1 protease is one of the major antiviral targets in the treatment of patients infected with HIV-1. The nine FDA approved HIV-1 protease inhibitors were developed with extensive use of structure-based drug design, thus the atomic details of how the inhibitors bind are well characterized. From this structural understanding the molecular basis for drug resistance in HIV-1 protease can be elucidated. Selected mutations in response to therapy and diversity between clades in HIV-1 protease have altered the shape of the active site, potentially altered the dynamics and even altered the sequence of the cleavage sites in the Gag polyprotein. All of these interdependent changes act in synergy to confer drug resistance while simultaneously maintaining the fitness of the virus. New strategies, such as incorporation of the substrate envelope constraint to design robust inhibitors that incorporate details of HIV-1 protease’s function and decrease the probability of drug resistance, are necessary to continue to effectively target this key protein in HIV-1 life cycle.
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Affiliation(s)
- Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Rajintha M. Bandaranayake
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Yufeng Cai
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Nancy M. King
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Madhavi Kolli
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Seema Mittal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Jennifer F. Murzycki
- Department of Pediatrics, University of Rochester, Rochester, NY 14627, USA; E-Mail:
| | - Madhavi N.L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Ayşegül Özen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Moses M. Prabu-Jeyabalan
- Division of Basic Sciences, The Commonwealth Medical College, 150 N. Washington Avenue, Scranton, PA 18503, USA; E-Mail:
| | - Kelly Thayer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-508-856-8008; Fax: +1-508-856-6464
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161
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Adang AEP, Hermkens PHH, Linders JTM, Ottenheijm HCJ, van Staveren CJ. Case histories of peptidomimetics: Progression from peptides to drugs. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19941130202] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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162
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Bora RP, Barman A, Zhu X, Ozbil M, Prabhakar R. Which One Among Aspartyl Protease, Metallopeptidase, and Artificial Metallopeptidase is the Most Efficient Catalyst in Peptide Hydrolysis? J Phys Chem B 2010; 114:10860-75. [DOI: 10.1021/jp104294x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Ram Prasad Bora
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Mehmet Ozbil
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
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163
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164
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Perez MAS, Fernandes PA, Ramos MJ. Substrate recognition in HIV-1 protease: a computational study. J Phys Chem B 2010; 114:2525-32. [PMID: 20121080 DOI: 10.1021/jp910958u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HIV-1 protease is a crucial enzyme for the life cycle of the human immunodeficiency virus, the retrovirus that triggers AIDS. It is well documented that HIV-1 protease mediates the cleavage of Gag, Gag-Pol, and Nef precursor polyproteins and is highly selective concerning the set of 12 different amino acid sequences that cleaves. However, the governing principles and physical parameters, which determine substrate recognition and specificity, remain poorly understood despite the many speculative proposals that abound in the literature. In fact, it has been difficult so far to circumvent the fact that protease's substrates share little sequence identity and lack an obvious consensus binding motif. We have used microsecond time scale MD simulations to quantitatively show that some sequences of the polyprotein Gag-Pol that are not cleaved (nonsubstrates) have in fact a higher affinity to the active site of HIV-1 protease than a substrate; i.e., recognition is not governed by affinity to the active site. On the basis of a detailed analysis of the results and experimental data, we propose that the recognition is based on the geometric specificity of PR:Gag and PR:Gag-Pol multiprotein complex, that selects which residues lie in the specific position that makes them accessible to the active site for cleavage.
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Affiliation(s)
- M A S Perez
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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165
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Mehellou Y, Balzarini J, McGuigan C. Aryloxy phosphoramidate triesters: a technology for delivering monophosphorylated nucleosides and sugars into cells. ChemMedChem 2010; 4:1779-91. [PMID: 19760699 DOI: 10.1002/cmdc.200900289] [Citation(s) in RCA: 173] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Prodrug technologies aimed at delivering nucleoside monophosphates into cells (protides) have proved to be effective in improving the therapeutic potential of antiviral and anticancer nucleosides. In these cases, the nucleoside monophosphates are delivered into the cell, where they may then be further converted (phosphorylated) to their active species. Herein, we describe one of these technologies developed in our laboratories, known as the phosphoramidate protide method. In this approach, the charges of the phosphate group are fully masked to provide efficient passive cell-membrane penetration. Upon entering the cell, the masking groups are enzymatically cleaved to release the phosphorylated biomolecule. The application of this technology to various therapeutic nucleosides has resulted in improved antiviral and anticancer activities, and in some cases it has transformed inactive nucleosides to active ones. Additionally, the phosphoramidate technology has also been applied to numerous antiviral nucleoside phosphonates, and has resulted in at least three phosphoramidate-based nucleotides progressing to clinical investigations. Furthermore, the phosphoramidate technology has been recently applied to sugars (mainly glucosamine) in order to improve their therapeutic potential. The development of the phosphoramidate technology, mechanism of action and the application of the technology to various monophosphorylated nucleosides and sugars will be reviewed.
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166
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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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167
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Hu GD, Zhu T, Zhang SL, Wang D, Zhang QG. Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations. Eur J Med Chem 2010; 45:227-35. [DOI: 10.1016/j.ejmech.2009.09.048] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 09/30/2009] [Accepted: 09/30/2009] [Indexed: 11/30/2022]
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168
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The story of Bulgarian nurses in Libya accused on no grounds of purposeful infection of children with HIV. HIV & AIDS REVIEW 2010. [DOI: 10.1016/s1730-1270(11)60004-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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169
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Abstract
Soon after its discovery, the attempts to develop anti-AIDS therapeutics focused on the retroviral protease (PR)-an enzyme used by lentiviruses to process the precursor polypeptide into mature viral proteins. An urgent need for the three-dimensional structure of PR to guide rational drug design prompted efforts to produce milligram quantities of this enzyme. However, only minute amounts of PR were present in the HIV-1 and HIV-2 viruses, and initial attempts to express this protein in bacteria were not successful. This review describes X-ray crystallographic studies of the retroviral proteases carried out at NCI-Frederick in the late 1980s and early 1990s and puts into perspective the crucial role that the total protein chemical synthesis played in unraveling the structure, mechanism of action, and inhibition of HIV-1 PR. Notably, the first fully correct structure of HIV-1 PR and the first cocrystal structure of its complex with an inhibitor (a substrate-derived, reduced isostere hexapeptide MVT-101) were determined using chemically synthesized protein. Most importantly, these sets of coordinates were made freely available to the research community and were used worldwide to solve X-ray structures of HIV-1 PR complexes with an array of inhibitors and set in motion a variety of theoretical studies. Publication of the structure of chemically synthesized HIV-1 PR complexed with MVT-101 preceded only by six years the approval of the first PR inhibitor as an anti-AIDS drug.
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Affiliation(s)
- Maria Miller
- Protein Structure Section, Macromolecular Crystallography Laboratory, NCI-Frederick, Frederick, MD 21702-1201, USA.
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170
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Fifteen years of HIV Protease Inhibitors: raising the barrier to resistance. Antiviral Res 2010; 85:59-74. [DOI: 10.1016/j.antiviral.2009.10.003] [Citation(s) in RCA: 241] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 10/02/2009] [Accepted: 10/10/2009] [Indexed: 11/20/2022]
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171
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Purohit R, Sethumadhavan R. Structural basis for the resilience of Darunavir (TMC114) resistance major flap mutations of HIV-1 protease. Interdiscip Sci 2009; 1:320-8. [DOI: 10.1007/s12539-009-0043-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Revised: 06/16/2009] [Accepted: 06/18/2009] [Indexed: 11/24/2022]
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172
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Shi SH, Chen JZ, Hu GD, Yi CH, Zhang SL, Zhang QG. Molecular insight into the interaction mechanisms of inhibitors BEC and BEG with HIV-1 protease by using MM-PBSA method and molecular dynamics simulation. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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173
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174
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Chen J, Zhang S, Liu X, Zhang Q. Insights into drug resistance of mutations D30N and I50V to HIV-1 protease inhibitor TMC-114: free energy calculation and molecular dynamic simulation. J Mol Model 2009; 16:459-68. [PMID: 19629548 DOI: 10.1007/s00894-009-0553-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 06/11/2009] [Indexed: 12/01/2022]
Abstract
The single mutations D30N and I50V are considered as the key residue mutations of the HIV-1 protease drug resistance to inhibitors in clinical use. In this work, molecular dynamics (MD) simulations combined with the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method have been performed to investigate the drug-resistant mechanisms of D30N and I50V to an inhibitor TMC-114. The analyses of absolute binding free energies using the separate trajectory approach suggests that the decrease in the van der Waals energy and electrostatic energy in the gas phase results in the drug resistance of D30N to TMC-114, while for I50V, the decrease in the electrostatic energy mainly drive its drug resistance to TMC-114. Detailed binding free energies between TMC-114 and individual protein residues are computed by using a per-residue basis decomposition method, which provides insights into the inhibitor-protein binding mechanism and also explains the drug-resistant mechanisms of mutations D30N and I50V to TMC-114. The study shows that the loss of the hydrogen bond between TMC-114 and the side chain of Asn30' is the main driving force of the resistance of D30N to TMC-114, and in the case of I50V, the increase in the polar solvation energies between TMC-114 and two residues Val50' and Asp30' definitively drives the resistance of I50V to TMC-114. We expect that this work can provide some helpful insights into the nature of mutational effect and aid the future design of better inhibitors.
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Affiliation(s)
- Jianzhong Chen
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
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175
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Nimmanpipug P, Lee VS, Wolschann P, Hannongbua S. Litchi chinensis-derived terpenoid as anti-HIV-1 protease agent: structural design from molecular dynamics simulations. MOLECULAR SIMULATION 2009. [DOI: 10.1080/08927020802714841] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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176
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Bayden AS, Fornabaio M, Scarsdale JN, Kellogg GE. Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT. J Comput Aided Mol Des 2009; 23:621-32. [PMID: 19554265 DOI: 10.1007/s10822-009-9270-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Accepted: 01/22/2009] [Indexed: 10/20/2022]
Abstract
A public web server performing computational titration at the active site in a protein-ligand complex has been implemented. This calculation is based on the Hydropathic interaction noncovalent force field. From 3D coordinate data for the protein, ligand and bridging waters (if available), the server predicts the best combination of protonation states for each ionizable residue and/or ligand functional group as well as the Gibbs free energy of binding for the ionization-optimized protein-ligand complex. The 3D structure for the modified molecules is available as output. In addition, a graph depicting how this energy changes with acidity, i.e., as a function of added protons, can be obtained. This data may prove to be of use in preparing models for virtual screening and molecular docking. A few illustrative examples are presented. In beta secretase (2va7) computational titration flipped the amide groups of Gln12 and Asn37 and protonated a ligand amine yielding an improvement of 6.37 kcal mol(-1) in the protein-ligand binding score. Protonation of Glu139 in mutant HIV-1 reverse transcriptase (2opq) allows a water bridge between the protein and inhibitor that increases the protein-ligand interaction score by 0.16 kcal mol(-1). In human sialidase NEU2 complexed with an isobutyl ether mimetic inhibitor (2f11) computational titration suggested that protonating Glu218, deprotonating Arg237, flipping the amide bond on Tyr334, and optimizing the positions of several other polar protons would increase the protein-ligand interaction score by 0.71 kcal mol(-1).
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Affiliation(s)
- Alexander S Bayden
- Department of Medicinal Chemistry & Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298-0540, USA
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177
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Sureshbabu VV, Naik SA, Hemantha HP, Narendra N, Das U, Guru Row TN. N-Urethane-Protected Amino Alkyl Isothiocyanates: Synthesis, Isolation, Characterization, and Application to the Synthesis of Thioureidopeptides. J Org Chem 2009; 74:5260-6. [DOI: 10.1021/jo900675s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vommina V. Sureshbabu
- Peptide Research Laboratory, Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore 560 001, India
| | - Shankar A. Naik
- Peptide Research Laboratory, Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore 560 001, India
| | - H. P. Hemantha
- Peptide Research Laboratory, Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore 560 001, India
| | - N. Narendra
- Peptide Research Laboratory, Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore 560 001, India
| | - Ushati Das
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Tayur N. Guru Row
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
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178
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Affiliation(s)
- Peter M. Colman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia 3050;
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179
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Chen JZ, Yang MY, Yi CH, Shi SH, Zhang QG. Molecular dynamics simulation and free energy calculations of symmetric fluoro-substituted diol-based HIV-1 protease inhibitors. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.11.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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180
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Lim MD, Craik CS. Using specificity to strategically target proteases. Bioorg Med Chem 2009; 17:1094-100. [PMID: 18434168 PMCID: PMC2663002 DOI: 10.1016/j.bmc.2008.03.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Revised: 03/18/2008] [Accepted: 03/24/2008] [Indexed: 01/05/2023]
Abstract
Proteases are a family of naturally occurring enzymes in the body whose dysregulation has been implicated in numerous diseases and cancers. Their ability to selectively and catalytically turnover substrate adds both signal amplification and functionality as parameters for the detection of disease. This review will focus on the development of activity-based methodologies to characterize proteases, and in particular, the use of positional scanning, synthetic combinatorial libraries (PS-SCL's), and substrate activity screening (SAS) assays. The use of these approaches to better understand a protease's natural substrate will be discussed as well as the technologies that emerged.
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Affiliation(s)
- Mark D Lim
- Department of Pharmaceutical Chemistry, University of California, School of Pharmacy, 513 Parnassus Avenue Room S-926, San Francisco, CA 94158, USA
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181
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Chow WA, Jiang C, Guan M. Anti-HIV drugs for cancer therapeutics: back to the future? Lancet Oncol 2009; 10:61-71. [PMID: 19111246 DOI: 10.1016/s1470-2045(08)70334-6] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The use of anti-HIV drugs as cancer treatments is not new. Azidothymidine was studied as an antineoplastic in the 1990s, but despite promising in vitro data, clinical trials showed little antitumour activity. HIV protease inhibitors were developed in the early 1990s, and their subsequent incorporation into highly active antiretroviral therapy (HAART) has profoundly changed the natural history of HIV infection. The potential antitumour properties of these drugs have been investigated because of their success in treating HIV-related Kaposi's sarcoma. HAART's effects on Kaposi's sarcoma did not always correlate with immune reconstitution, and activity against other solid and haematological malignancies has been established. Inhibition of tumour-cell invasion and angiogenesis were properties first ascribed to inhibition of HIV protease; however, they have pleiotropic antitumour effects, including inhibition of inflammatory cytokine production, proteasome activity, cell proliferation and survival, and induction of apoptosis. HIV protease inhibitors are thus a new class of anticancer drugs with multiple effects, and other anti-HIV drugs might hold similar promise.
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Affiliation(s)
- Warren A Chow
- Beckman Research Institute of the City of Hope, Division of Medical Oncology, Department of Clinical and Molecular Pharmacology, Duarte, CA USA
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182
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Kogo H, Takeuchi K, Inoue H, Kihara H, Kojima M, Takahashi K. Urea-dependent unfolding of HIV-1 protease studied by circular dichroism and small-angle X-ray scattering. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:70-4. [DOI: 10.1016/j.bbapap.2008.09.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2008] [Revised: 09/20/2008] [Accepted: 09/28/2008] [Indexed: 11/28/2022]
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183
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Arul Murugan N, Chandra Jha P, Ågren H. Solvation shell structure of cyclooctylpyranone in water solvent and its comparative structure, dynamics and dipole moment in HIV protease. Phys Chem Chem Phys 2009; 11:6482-9. [DOI: 10.1039/b902816a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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184
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Devenish SRA, Gerrard JA. The role of quaternary structure in (β/α)8-barrel proteins: evolutionary happenstance or a higher level of structure-function relationships? Org Biomol Chem 2009; 7:833-9. [DOI: 10.1039/b818251p] [Citation(s) in RCA: 28] [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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185
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Böttcher J, Blum A, Dörr S, Heine A, Diederich WE, Klebe G. Targeting the open-flap conformation of HIV-1 protease with pyrrolidine-based inhibitors. ChemMedChem 2008; 3:1337-44. [PMID: 18720485 DOI: 10.1002/cmdc.200800113] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
HIV protease is a well-established drug target in antiviral chemotherapy. Immense research efforts have been made to discover effective inhibitors, thus making the enzyme one of the most studied and best characterized proteins. Although the protease exhibits high flexibility, all approved drugs target virtually the same protein conformation. The development of viral cross-resistance demands the generation of inhibitors with novel scaffolds and deviating modes of binding. Herein we report the design and the short, high-yielding stereoselective synthesis of a series of chiral, symmetric pyrrolidine-based inhibitors targeting the open-flap conformation of the protease. The obtained co-crystal structure with one derivative provides a valuable starting point for further inhibitor design.
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Affiliation(s)
- Jark Böttcher
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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186
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187
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Tsantrizos YS. Peptidomimetic therapeutic agents targeting the protease enzyme of the human immunodeficiency virus and hepatitis C virus. Acc Chem Res 2008; 41:1252-63. [PMID: 18681464 DOI: 10.1021/ar8000519] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
During the past two decades, great strides have been made in the design of peptidomimetic drugs for the treatment of viral infections, despite the stigma of poor drug-like properties, low oral absorption, and high clearance associated with such compounds. This Account summarizes the progress made toward overcoming such liabilities and highlights the drug discovery efforts that have focused specifically on human immunodeficiency virus (HIV) and hepatitis C virus (HCV) protease inhibitors. The arsenal against the incurable disease AIDS, which is caused by HIV infection, includes peptidomimetic compounds that target the virally encoded aspartic protease enzyme. This enzyme is essential to the production of mature HIV particles and plays a key role in maintaining infectivity. However, because of the rapid genomic evolution of viruses, an inevitable consequence in the treatment of all viral infections is the emergence of resistance to the drugs. Therefore, the incomplete suppression of HIV in treatment-experienced AIDS patients will continue to drive the search for more effective therapeutic agents that exhibit efficacy against the mutants raised by the earlier generation of protease inhibitors. Currently, a number of substrate-based peptidomimetic agents that target the virally encoded HCV NS3/4A protease are in clinical development. Mechanistically, these inhibitors can be generally divided into activated carbonyls that are transition-state mimics or compounds that tap into the feedback mode of enzyme-product inhibition. In the HCV field, there is justified optimism that a number of these compounds will soon reach commercialization as therapeutic agents for the treatment of HCV infections. Structural research has guided the successful design of both HIV and HCV protease inhibitors. X-ray crystallography, NMR, and computational studies have provided valuable insight in to the free-state preorganization of peptidomimetic ligands and their enzyme-bound conformation. Researchers have designed a variety of novel bioisosteric replacements of amino acids and short peptides that contain all of the required pharmacophore moieties and play a key role in inducing conformational changes to the overall molecule. The knowledge gained from these studies will undoubtedly guide the future design of therapeutic agents and further contribute to the success of this field.
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Affiliation(s)
- Youla S. Tsantrizos
- Boehringer Ingelheim (Canada) Ltd., Research and Development, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
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188
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Active-site mutations in the South african human immunodeficiency virus type 1 subtype C protease have a significant impact on clinical inhibitor binding: kinetic and thermodynamic study. J Virol 2008; 82:11476-9. [PMID: 18768960 DOI: 10.1128/jvi.00726-08] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Human immunodeficiency virus (HIV) infections in sub-Saharan Africa represent about 56% of global infections. Study of active-site mutations (the V82A single mutation and the V82F I84V double mutation) in the less-studied South African HIV type 1 subtype C (C-SA) protease indicated that neither mutation had a significant impact on the proteolytic functioning of the protease. However, the binding affinities of, and inhibition by, saquinavir, ritonavir, indinavir, and nelfinavir were weaker for each variant than for the wild-type protease, with the double mutant exhibiting the most dramatic change. Therefore, our results show that the C-SA V82F I84V double mutation decreased the binding affinities of protease inhibitors to levels significantly lower than that required for effective inhibition.
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189
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Mahmoud KA, Luong JHT. Impedance Method for Detecting HIV-1 Protease and Screening For Its Inhibitors Using Ferrocene−Peptide Conjugate/Au Nanoparticle/Single-Walled Carbon Nanotube Modified Electrode. Anal Chem 2008; 80:7056-62. [DOI: 10.1021/ac801174r] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Khaled A. Mahmoud
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada H4P 2R2, and Department of Chemistry, University College Cork, Cork, Ireland
| | - John H. T. Luong
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada H4P 2R2, and Department of Chemistry, University College Cork, Cork, Ireland
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190
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Braun K, Frank M, Pipkorn R, Reed J, Spring H, Debus J, Didinger B, von der Lieth CW, Wiessler M, Waldeck W. HIV-1 capsid assembly inhibitor (CAI) peptide: structural preferences and delivery into human embryonic lung cells and lymphocytes. Int J Med Sci 2008; 5:230-9. [PMID: 18695744 PMCID: PMC2500149 DOI: 10.7150/ijms.5.230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Accepted: 07/29/2008] [Indexed: 11/16/2022] Open
Abstract
The Human immunodeficiency virus 1 derived capsid assembly inhibitor peptide (HIV-1 CAI-peptide) is a promising lead candidate for anti-HIV drug development. Its drawback, however, is that it cannot permeate cells directly. Here we report the transport of the pharmacologically active CAI-peptide into human lymphocytes and Human Embryonic Lung cells (HEL) using the BioShuttle platform. Generally, the transfer of pharmacologically active substances across membranes, demonstrated by confocal laser scanning microscopy (CLSM), could lead to a loss of function by changing the molecule's structure. Molecular dynamics (MD) simulations and circular dichroism (CD) studies suggest that the CAI-peptide has an intrinsic capacity to form a helical structure, which seems to be critical for the pharmacological effect as revealed by intensive docking calculations and comparison with control peptides. This coupling of the CAI-peptide to a BioShuttle-molecule additionally improved its solubility. Under the conditions described, the HIV-1 CAI peptide was transported into living cells and could be localized in the vicinity of the mitochondria.
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Affiliation(s)
- Klaus Braun
- Division of Molecular Toxicology, German Cancer Research Center, Heidelberg, Germany
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191
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Schlick P, Skern T. Investigating human immunodeficiency virus-1 proteinase specificity at positions P4 to P2 using a bacterial screening system. Anal Biochem 2008; 377:162-9. [DOI: 10.1016/j.ab.2008.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 02/28/2008] [Accepted: 03/10/2008] [Indexed: 11/27/2022]
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192
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Abstract
This overview provides an illustrated, comprehensive survey of some commonly observed protein‐fold families and structural motifs, chosen for their functional significance. It opens with descriptions and definitions of the various elements of protein structure and associated terminology. Following is an introduction into web‐based structural bioinformatics that includes surveys of interactive web servers for protein fold or domain annotation, protein‐structure databases, protein‐structure‐classification databases, structural alignments of proteins, and molecular graphics programs available for personal computers. The rest of the overview describes selected families of protein folds in terms of their secondary, tertiary, and quaternary structural arrangements, including ribbon‐diagram examples, tables of representative structures with references, and brief explanations pointing out their respective biological and functional significance.
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Affiliation(s)
- Peter D Sun
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
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193
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Nakatani S, Hidaka K, Ami E, Nakahara K, Sato A, Nguyen JT, Hamada Y, Hori Y, Ohnishi N, Nagai A, Kimura T, Hayashi Y, Kiso Y. Combination of non-natural D-amino acid derivatives and allophenylnorstatine-dimethylthioproline scaffold in HIV protease inhibitors have high efficacy in mutant HIV. J Med Chem 2008; 51:2992-3004. [PMID: 18426195 DOI: 10.1021/jm701555p] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several non-natural D-amino acid derivatives were introduced as P2/P3 residues in allophenylnorstatine-containing (Apns; (2S,3S)-3-amino-2-hydroxy-4-phenylbutyric acid) HIV protease inhibitors. The synthetic analogues exhibited potent inhibitory activity against HIV-1 protease enzyme and HIV-1 replication in MT-4 cells. Structure-activity relationships revealed that D-cysteine or serine derivatives contributed to highly potent anti-HIV activities. Interestingly, anti-HIV activity of all the D-amino acid-introduced inhibitors was remarkably enhanced in their anti-HIV activities against a Nelfinavir-resistant clone, which has a D30N mutation in the protease, over that of the wild-type strain. HIV inhibitory activity of several analogues was moderately affected by an inclusion of alpha1-acid glycoprotein in the test medium.
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Affiliation(s)
- Shingo Nakatani
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, 21st Century COE Program, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
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194
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Wollmann J, Baumert C, Erlenkamp G, Sippl W, Hilgeroth A. Novel Insight into Inhibitor Binding of Highly Symmetric HIV-1 Protease. Chembiochem 2008; 9:874-8. [DOI: 10.1002/cbic.200700646] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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195
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Hamilton R, Wharry S, Walker B, Walker BJ. The Synthesis of Phosphinic Acid Based Proteinase Inhibitors. PHOSPHORUS SULFUR 2008. [DOI: 10.1080/10426509908546356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Robert Hamilton
- a School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
- b School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
- c School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
- d School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
| | - Scott Wharry
- a School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
- b School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
- c School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
- d School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
| | - Brian Walker
- a School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
- b School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
- c School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
- d School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
| | - Brian J. Walker
- a School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
- b School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
- c School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
- d School of Chemistry and The Queen's University of Belfast , Belfast, BT9 5AG, N. Ireland., U.K
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198
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Dimerization of N-methyltransferases involved in caffeine biosynthesis. Biochimie 2008; 90:547-51. [DOI: 10.1016/j.biochi.2007.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Accepted: 10/04/2007] [Indexed: 11/18/2022]
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199
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Tripathi A, Fornabaio M, Spyrakis F, Mozzarelli A, Cozzini P, Kellogg GE. Complexity in modeling and understanding protonation states: computational titration of HIV-1-protease-inhibitor complexes. Chem Biodivers 2008; 4:2564-77. [PMID: 18027371 DOI: 10.1002/cbdv.200790210] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The computational-titration (CT) algorithm based on the 'natural' Hydropathic INTeractions (HINT) force field is described. The HINT software model is an empirical, non-Newtonian force field derived from experimentally measured partition coefficients for solvent transfer between octanol and H(2)O (log P(o/w)). The CT algorithm allows the identification, modeling, and optimization of multiple protonation states of residues and ligand functional groups at the protein-ligand active site. The importance of taking into account pH and ionization states of residues, which strongly affect the process of ligand binding, for correctly predicting binding free energies is discussed. The application of the CT protocol to a set of six cyclic inhibitors in their complexes with HIV-1 protease is presented, and the advance of HINT as a virtual-screening tool is outlined.
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Affiliation(s)
- Ashutosh Tripathi
- Department of Medicinal Chemistry & Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298-0540, USA
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200
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Sureshbabu VV, Chennakrishnareddy G, Narendra N. A facile and one-pot synthesis of Nα-Fmoc/Bsmoc/Boc/Z-protected ureidopeptides and peptidyl ureas employing diphenylphosphoryl azide [DPPA]. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2007.12.060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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