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Umumararungu T, Nyandwi JB, Katandula J, Twizeyimana E, Claude Tomani J, Gahamanyi N, Ishimwe N, Olawode EO, Habarurema G, Mpenda M, Uyisenga JP, Saeed SI. Current status of the small molecule anti-HIV drugs in the pipeline or recently approved. Bioorg Med Chem 2024; 111:117860. [PMID: 39094527 DOI: 10.1016/j.bmc.2024.117860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Human Immunodeficiency Virus (HIV) is the causative agent of Acquired Immunodeficiency Syndrome (AIDS) with high morbidity and mortality rates. Treatment of AIDS/HIV is being complicated by increasing resistance to currently used antiretroviral (ARV) drugs, mainly in low- and middle-income countries (LMICs) due to drug misuse, poor drug supply and poor treatment monitoring. However, progress has been made in the development of new ARV drugs, targeting different HIV components (Fig. 1). This review aims at presenting and discussing the progress made towards the discovery of new ARVs that are at different stages of clinical trials as of July 2024. For each compound, the mechanism of action, target biomolecule, genes associated with resistance, efficacy and safety, class, and phase of clinical trial are discussed. These compounds include analogues of nucleoside reverse transcriptase inhibitors (NRTIs) - islatravir and censavudine; non-nucleoside reverse transcriptase inhibitors (NNRTIs) - Rilpivirine, elsulfavirine and doravirine; integrase inhibitors namely cabotegravir and dolutegravir and chemokine coreceptors 5 and 2 (CC5/CCR2) antagonists for example cenicriviroc. Also, fostemsavir is being developed as an attachment inhibitor while lenacapavir, VH4004280 and VH4011499 are capsid inhibitors. Others are maturation inhibitors such as GSK-254, GSK3532795, GSK3739937, GSK2838232, and other compounds labelled as miscellaneous (do not belong to the classical groups of anti-HIV drugs or to the newer classes) such as obefazimod and BIT225. There is a considerable progress in the development of new anti-HIV drugs and the effort will continue since HIV infections has no cure or vaccine till now. Efforts are needed to reduce the toxicity of available drugs or discover new drugs with new classes which can delay the development of resistance.
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Affiliation(s)
- Théoneste Umumararungu
- Department of Industrial Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda.
| | - Jean Baptiste Nyandwi
- Department of Pharmacology and Toxicology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda; East African Community Regional Centre of Excellence for Vaccines, Immunization and Health Supply Chain Management, Kigali, Rwanda
| | - Jonathan Katandula
- Department of Pharmacology and Toxicology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Eric Twizeyimana
- Department of Physiology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Jean Claude Tomani
- Department of Chemistry, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Noël Gahamanyi
- Department of Biology, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Nestor Ishimwe
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Emmanuel Oladayo Olawode
- Department of Pharmaceutical Sciences, College of Pharmacy, Larkin University, 18301 N Miami Ave #1, Miami, FL 33169, USA
| | - Gratien Habarurema
- Department of Chemistry, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Matabishi Mpenda
- Department of Pharmacology and Toxicology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Jeanne Primitive Uyisenga
- Department of Biology, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Shamsaldeen Ibrahim Saeed
- Faculty of Veterinary Science, University of Nyala, P.O. Box: 155, Nyala, Sudan; Nanotechnology in Veterinary Medicine (NanoVet) Research Group, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kelantan 16100, Pengkalan Chepa, Malaysia
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Bhargava S, Adhikari N, Amin SA, Das K, Gayen S, Jha T. Hydroxyethylamine derivatives as HIV-1 protease inhibitors: a predictive QSAR modelling study based on Monte Carlo optimization. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:973-990. [PMID: 29072112 DOI: 10.1080/1062936x.2017.1388281] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/29/2017] [Indexed: 06/07/2023]
Abstract
Application of HIV-1 protease inhibitors (as an anti-HIV regimen) may serve as an attractive strategy for anti-HIV drug development. Several investigations suggest that there is a crucial need to develop a novel protease inhibitor with higher potency and reduced toxicity. Monte Carlo optimized QSAR study was performed on 200 hydroxyethylamine derivatives with antiprotease activity. Twenty-one QSAR models with good statistical qualities were developed from three different splits with various combinations of SMILES and GRAPH based descriptors. The best models from different splits were selected on the basis of statistically validated characteristics of the test set and have the following statistical parameters: r2 = 0.806, Q2 = 0.788 (split 1); r2 = 0.842, Q2 = 0.826 (split 2); r2 = 0.774, Q2 = 0.755 (split 3). The structural attributes obtained from the best models were analysed to understand the structural requirements of the selected series for HIV-1 protease inhibitory activity. On the basis of obtained structural attributes, 11 new compounds were designed, out of which five compounds were found to have better activity than the best active compound in the series.
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Affiliation(s)
- S Bhargava
- a Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr Harisingh Gour University (A Central University) , Madhya Pradesh , India
| | - N Adhikari
- b Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata , West Bengal , India
| | - S A Amin
- b Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata , West Bengal , India
| | - K Das
- c Department of Chemistry , Dr. Harisingh Gour University (A Central University) , Madhya Pradesh , India
| | - S Gayen
- a Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr Harisingh Gour University (A Central University) , Madhya Pradesh , India
| | - T Jha
- b Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata , West Bengal , India
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Craig JC, Duncan IB, Whittaker L, Roberts NA. Antiviral Synergy between Inhibitors of HIV Proteinase and Reverse Transcriptase. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029300400305] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ro 31–8959, a potent and specific inhibitor of HIV proteinases, is shown to interact synergistically in combination with nucleoside analogue inhibitors of HIV reverse transcriptase (AZT, ddC, 2′-FddC). Ninety per cent inhibition endpoints (IC90), obtained from checkerboard titrations of compound mixtures on CEM-T4 cells infected with HIV-i strain GB8, have been further analysed. Compared with concentrations needed when inhibitors are used individually, reductions of between 2- and 30-fold were observed in combination, depending on the nucleoside analogue and the ratio of concentrations employed. The results suggest that combinations of AZT or ddC with Ro 31–8959 should be considered for development as candidate antiviral treatments of patients with HIV infection.
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Affiliation(s)
- J. C. Craig
- Department of Biology, Roche Products Limited, PO Box 8, Welwyn Garden City, Herts AL7 3AY, UK
| | - I. B. Duncan
- Department of Biology, Roche Products Limited, PO Box 8, Welwyn Garden City, Herts AL7 3AY, UK
| | - L. Whittaker
- Department of Biology, Roche Products Limited, PO Box 8, Welwyn Garden City, Herts AL7 3AY, UK
| | - N. A. Roberts
- Department of Biology, Roche Products Limited, PO Box 8, Welwyn Garden City, Herts AL7 3AY, UK
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Craig JC, Grief C, Mills JS, Hockley D, Duncan IB, Roberts NA. Effects of a Specific Inhibitor of HIV Proteinase (Ro 31-8959) on Virus Maturation in a Chronically Infected Promonocytic Cell Line (U1). ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029100200308] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The human immunodeficiency virus (HIV) proteinase inhibitor Ro 31-8959 prevents the maturation of virus in phorbol 12-myristate 13-acetate (PMA)-stimulated U1 cells, a chronically infected promonocytic cell line. Inhibition of both the morphological maturation of virions and the enzymic processing of gag polyprotein (p56) to produce capsid protein p24 was demonstrated at nanomolar concentrations of the compound. Furthermore, prolonged inhibition of the processing of p56 antigen was confirmed in pulse-chase experiments. The conclusion is that Ro 31-8959 can inhibit production of mature virions in a promonocyte cell line which is infected chronically/latently with HIV.
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Affiliation(s)
- J. C. Craig
- Roche Products Limited, PO Box 8, Welwyn Garden City, Herts AL7 3AY, UK
| | - C. Grief
- Department of Electron Microscopy and AIDS Collaborative Centre, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Herts, UK
| | - J. S. Mills
- Roche Products Limited, PO Box 8, Welwyn Garden City, Herts AL7 3AY, UK
| | - D. Hockley
- Department of Electron Microscopy and AIDS Collaborative Centre, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Herts, UK
| | - I. B. Duncan
- Roche Products Limited, PO Box 8, Welwyn Garden City, Herts AL7 3AY, UK
| | - N. A. Roberts
- Roche Products Limited, PO Box 8, Welwyn Garden City, Herts AL7 3AY, UK
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Potts KE, Smidt ML, Tucker SP, Stiebel TR, McDonald JJ, Stallings WC, Bryant ML. In vitro Sequential Selection and Characterization of Human Immunodeficiency Virus Type 1 Variants with Reduced Sensitivity to Hydroxyethylurea Protease Inhibitors. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029700800508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In vitro resistance to the human immunodeficiency virus (HIV) protease inhibitors SC-52151 and SC-55389A was evaluated in an in vitro sequential selection scheme. HIVRF variants were selected for reduced sensitivity to SC-52151 and subsequently passaged in both SC-52151 and a structurally different hydroxyethylurea protease inhibitor, SC-55389A, to select for dual-resistant virus. SC-52151 selection alone resulted in a 23-fold reduction in virus sensitivity whereas selection in both inhibitors resulted in 34- and eightfold reductions in virus sensitivity to SC-52151 and SC-55389A, respectively. Sequence analysis of the protease gene revealed that SC-52151 -resistant virus had a Gly to Val substitution at residue 48 (G48V) and, in 58% of subclones, an accompanying Val to Ala substitution at residue 82 (V82A). Dual-resistant virus had both G48V and V82A substitutions present and, in the majority of subclones, an lle to Thr and/or Leu to Pro substitution at residues 54 and 63, respectively. Drug susceptibility assays with limiting dilution-cloned HIVRFR (G48V/V82A) and HIVRFRR (G48V/154T/L63P/V82A) viruses demonstrated moderate to high-level cross-resistance to additional structurally non-related protease inhibitors. Recombinant HIVHXB2 proviral clones with G48V, L63P and V82A substitutions showed that one active site mutation was permissible, but the presence of both G48V and V82A substitutions together significantly reduced infectious virus production. Insight into the contributions of the observed substitutions to drug resistance is presented in molecular modelling studies.
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Affiliation(s)
- KE Potts
- Infectious Disease Research, Searle, St Louis, MO 63198, USA
| | - ML Smidt
- Infectious Disease Research, Searle, St Louis, MO 63198, USA
| | - SP Tucker
- Infectious Disease Research, Searle, St Louis, MO 63198, USA
| | - TR Stiebel
- Infectious Disease Research, Searle, St Louis, MO 63198, USA
| | - JJ McDonald
- Medicinal and Structural Chemistry, Searle, St Louis, MO 63198, USA
| | - WC Stallings
- Medicinal and Structural Chemistry, Searle, St Louis, MO 63198, USA
| | - ML Bryant
- Infectious Disease Research, Searle, St Louis, MO 63198, USA
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Chung S, Miller JT, Lapkouski M, Tian L, Yang W, Le Grice SFJ. Examining the role of the HIV-1 reverse transcriptase p51 subunit in positioning and hydrolysis of RNA/DNA hybrids. J Biol Chem 2013; 288:16177-84. [PMID: 23595992 DOI: 10.1074/jbc.m113.465641] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent crystallographic analysis of p66/p51 human immunodeficiency virus (HIV) type 1 reverse transcriptase (RT) complexed with a non-polypurine tract RNA/DNA hybrid has illuminated novel and important contacts between structural elements at the C terminus of the noncatalytic p51 subunit and the nucleic acid duplex in the vicinity of the ribonuclease H (RNase H) active site. In particular, a short peptide spanning residues Phe-416-Pro-421 was shown to interact with the DNA strand, cross the minor groove of the helix, and then form Van der Waals contacts with the RNA strand adjacent to the scissile phosphate. At the base of the adjoining α-helix M', Tyr-427 forms a hydrogen bond with Asn-348, the latter of which, when mutated to Ile, is implicated in resistance to both nucleoside and non-nucleoside RT inhibitors. Based on our structural data, we analyzed the role of the p51 C terminus by evaluating selectively mutated p66/p51 heterodimers carrying (i) p51 truncations that encroach on α-M', (ii) alterations that interrupt the Asn-348-Tyr-427 interaction, and (iii) alanine substitutions throughout the region Phe-416-Pro-421. Collectively, our data support the notion that the p51 C terminus makes an important contribution toward hybrid binding and orienting the RNA strand for catalysis at the RNase H active site.
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Affiliation(s)
- Suhman Chung
- RT Biochemistry Section, HIV Drug Resistance Program, Center for Cancer Research, NCI, National Institutes of Health, Frederick Maryland 21702, USA
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Schader SM, Wainberg MA. Insights into HIV-1 pathogenesis through drug discovery: 30 years of basic research and concerns for the future. HIV & AIDS REVIEW 2011. [DOI: 10.1016/j.hivar.2011.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Abram ME, Sarafianos SG, Parniak MA. The mutation T477A in HIV-1 reverse transcriptase (RT) restores normal proteolytic processing of RT in virus with Gag-Pol mutated in the p51-RNH cleavage site. Retrovirology 2010; 7:6. [PMID: 20122159 PMCID: PMC2831009 DOI: 10.1186/1742-4690-7-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 02/01/2010] [Indexed: 12/04/2022] Open
Abstract
Background The p51 subunit of the HIV-1 reverse transcriptase (RT) p66/p51 heterodimer arises from proteolytic cleavage of the RT p66 subunit C-terminal ribonuclease H (RNH) domain during virus maturation. Our previous work showed that mutations in the RT p51↓RNH cleavage site resulted in virus with defects in proteolytic processing of RT and significantly attenuated infectivity. In some cases, virus fitness was restored after repeated passage of mutant viruses, due to reversion of the mutated sequences to wild-type. However, in one case, the recovered virus retained the mutated p51↓RNH cleavage site but also developed an additional mutation, T477A, distal to the cleavage site. In this study we have characterized in detail the impact of the T477A mutation on intravirion processing of RT. Results While the T477A mutation arose during serial passage only with the F440V mutant background, introduction of this substitution into a variety of RT p51↓RNH cleavage site lethal mutant backgrounds was able to restore substantial infectivity and normal RT processing to these mutants. T477A had no phenotypic effect on wild-type HIV-1. We also evaluated the impact of T477A on the kinetics of intravirion Gag-Pol polyprotein processing of p51↓RNH cleavage site mutants using the protease inhibitor ritonavir. Early processing intermediates accumulated in p51↓RNH cleavage site mutant viruses, whereas introduction of T477A promoted the completion of processing and formation of the fully processed RT p66/p51 heterodimer. Conclusions This work highlights the extraordinary plasticity of HIV-1 in adapting to seemingly lethal mutations that prevent RT heterodimer formation during virion polyprotein maturation. The ability of T477A to restore RT heterodimer formation and thus intravirion stability of the enzyme may arise from increased conformation flexibility in the RT p51↓RNH cleavage site region, due to loss of a hydrogen bond associated with the normal threonine residue, thereby enabling proteolytic cleavage near the normal RT p51↓RNH cleavage site.
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Affiliation(s)
- Michael E Abram
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, Pittsburgh, PA 15219, USA
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Popov EM. Current advances in the X-ray crystallography of proteins. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1995v064n12abeh000194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Song R, Kafaie J, Yang L, Laughrea M. HIV-1 viral RNA is selected in the form of monomers that dimerize in a three-step protease-dependent process; the DIS of stem-loop 1 initiates viral RNA dimerization. J Mol Biol 2007; 371:1084-98. [PMID: 17599354 DOI: 10.1016/j.jmb.2007.06.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 05/28/2007] [Accepted: 06/04/2007] [Indexed: 11/29/2022]
Abstract
We have characterized the viral RNA conformation in wild-type, protease-inactive (PR-) and SL1-defective (DeltaDIS) human immunodeficiency virus type 1 (HIV-1), as a function of the age of the viruses, from newly released to grown-up (>or=24 h old). We report evidence for packaging HIV-1 genomic RNA (gRNA) in the form of monomers in PR- virions, viral RNA rearrangement (not maturation) within PR- HIV-1, protease-dependent formation of thermolabile dimeric viral RNAs, a new form of immature gRNA dimer at about 5 h post virion release, and slow-acting dimerization signals in SL1-defective viruses. The rates of gRNA dimer formation were >or=3-fold and >or=10-fold slower in DeltaDIS and PR- viruses than in wild-type, respectively. Thus, the DIS, i.e. the palindrome in the apical loop of SL1, is a dimerization initiation signal, but its role can be masked by one or several slow-acting dimerization site(s) when grown-up SL1-inactive virions are investigated. Grown-up PR- virions are not flawless models for immature virions because gRNA dimerization increases with the age of PR- virions, indicating that the PR- mutation does not "freeze" gRNA conformation in a nascent primordial state. Our study is the first on gRNA conformation in newly released mutant or primate retroviruses. It shows for the first time that the packaged retroviral gRNA matures in more than one step, and that formation of immature dimeric viral RNA requires viral protein maturation. The monomeric viral RNAs isolated from budding HIV-1, as modeled by newly released PR- virions, may be seen as dimers that are much more fragile than thermolabile dimers.
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Affiliation(s)
- Rujun Song
- McGill AIDS Center, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada H3T 1E2
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Abram ME, Parniak MA. Virion instability of human immunodeficiency virus type 1 reverse transcriptase (RT) mutated in the protease cleavage site between RT p51 and the RT RNase H domain. J Virol 2005; 79:11952-61. [PMID: 16140771 PMCID: PMC1212597 DOI: 10.1128/jvi.79.18.11952-11961.2005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2005] [Accepted: 06/18/2005] [Indexed: 01/20/2023] Open
Abstract
Each of the human immunodeficiency virus type 1 (HIV-1) pol-encoded enzymes, protease (PR), reverse transcriptase (RT), and integrase (IN), is active only as a dimer (or higher-order oligomer in the case of IN), but only RT comprises subunits of different masses. RT is a heterodimer of 66-kDa and 51-kDa subunits. The latter is formed by HIV PR-catalyzed cleavage of p66 during virion maturation, resulting in the removal of the RNase H (RNH) domain of a p66 subunit. In order to study the apparent need for RT heterodimers in the context of the virion, we introduced a variety of mutations in the RT p51-RNH protease cleavage site of an infectious HIV-1 molecular clone. Surprisingly, rather than leading to virions with increased RT p66 content, most of the mutations resulted in significantly attenuated virus that contained greatly decreased levels of RT that in many cases was primarily p51 RT. IN levels were also reduced in several mutants. However, most mutants showed normal levels of the Pr160(gag-pol) precursor polyprotein, suggesting that reduced virion RT arose from proteolytic instability rather than decreased incorporation. Mutant virion p24 Gag levels were equivalent to wild type, indicating that Gag incorporation and processing were not affected. Repeated passage of MT-2 cells exposed to mutant viruses led to the appearance of virus with improved replication capacity; these virions contained normally processed RT at near-wild-type levels. These results imply that additional proteolytic processing of RT to the p66/p51 heterodimer is essential to provide proteolytic stability of RT during HIV-1 maturation.
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Affiliation(s)
- Michael E Abram
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, Scaife Hall, Suite S817, 3550 Terrace Street, Pittsburgh, PA 15261, USA
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Chatterjee A, Mridula P, Mishra RK, Mittal R, Hosur RV. Folding Regulates Autoprocessing of HIV-1 Protease Precursor. J Biol Chem 2005; 280:11369-78. [PMID: 15632156 DOI: 10.1074/jbc.m412603200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Autoprocessing of HIV-1 protease (PR) precursors is a crucial step in the generation of the mature protease. Very little is known regarding the molecular mechanism and regulation of this important process in the viral life cycle. In this context we report here the first and complete residue level investigations on the structural and folding characteristics of the 17-kDa precursor TFR-PR-C(nn) (161 residues) of HIV-1 protease. The precursor shows autoprocessing activity indicating that the solution has a certain population of the folded active dimer. Removal of the 5-residue extension, C(nn) at the C-terminal of PR enhanced the activity to some extent. However, NMR structural characterization of the precursor containing a mutation, D25N in the PR at pH 5.2 and 32 degrees C under different conditions of partial and complete denaturation by urea, indicate that the precursor has a high tendency to be unfolded. The major population in the ensemble displays some weak folding propensities in both the TFR and the PR regions, and many of these in the PR region are the non-native type. As both D25N mutant and wild-type PR are known to fold efficiently to the same native dimeric form, we infer that TFR cleavage enables removal of the non-native type of preferences in the PR domain to cause constructive folding of the protein. These results indicate that intrinsic structural and folding preferences in the precursor would have important regulatory roles in the autoprocessing reaction and generation of the mature enzyme.
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Affiliation(s)
- Amarnath Chatterjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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Onoda A, Yamamoto H, Yamada Y, Lee K, Adachi S, Okamura TA, Yoshizawa-Kumagaye K, Nakajima K, Kawakami T, Aimoto S, Ueyama N. Switching of turn conformation in an aspartate anion peptide fragment by NH · · · O−hydrogen bonds. Biopolymers 2005; 80:233-48. [PMID: 15633197 DOI: 10.1002/bip.20187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Aspartic acid protease model peptides Z-Phe-Asp(COOH)-Thr-Gly-Ser-Ala-NHCy (1) and AdCO-Asp(COOH)-Val-Gly-NHBzl (3), and their aspartate anions (NEt4)[Z-Phe-Asp(COO-)-Thr-Gly-Ser-Ala-NHCy] (2) and (NEt4)[AdCO-Asp(COO-)-Val-Gly-NHBzl] (4), having an invariant primary sequence of the Asp-X(Thr,Ser)-Gly fragment, were synthesized and characterized by 1H-NMR, CD, and infrared (IR) spectroscopies. NMR structure analyses indicate that the Asp O(delta) atoms of the aspartate peptide 2 are intramolecularly hydrogen-bonded with Gly, Ser, Ala NH, and Ser OH, supporting the rigid beta-turn-like conformation in acetonitrile solution. The tripeptide in the aspartic acid 3 forms an inverse gamma-turn structure, which is converted to a beta-turn-like conformation because of the formation of the intramolecular NH . . . O- hydrogen bonds with the Asp O(delta) in 4. Such a conformational change is not detected between dipeptides AdCO-Asp(COOH)-Va-NHAd (5) and (NEt4)[AdCO-Asp(COO-)-Val-NHAd] (6). The pK(a) value of side-chain carboxylic acid (5.0) for 3 exhibits a lower shift (0.3 unit) from that of 5 in aqueous polyethyleneglycol lauryl ether micellar solution. NMR structure analyses for 3 in an aqueous micellar solution indicate that the preorganized turn structure, which readily forms the NH . . . O- hydrogen bonds, lowers the pK(a) value and that resulting hydrogen bonds stabilize the rigid conformation in the aspartate anion state. We found that the formation of the NH . . . O- hydrogen bonds involved in the hairpin turn is correlated with the protonation and deprotonation state of the Asp side chain in the conserved amino acid fragments.
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Affiliation(s)
- Akira Onoda
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
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Lather V, Madan AK. Topological models for the prediction of HIV-protease inhibitory activity of tetrahydropyrimidin-2-ones. J Mol Graph Model 2005; 23:339-45. [PMID: 15670954 DOI: 10.1016/j.jmgm.2004.11.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Revised: 10/21/2004] [Accepted: 11/02/2004] [Indexed: 11/28/2022]
Abstract
Relationship between the topological indices and HIV-protease inhibitory activity of tetrahydropyrimidine-2-ones has been investigated. Three topological indices, Wiener's index--a distance based topological descriptor, Zagreb group parameter--an adjacency based topological descriptor and eccentric connectivity index--an adjacency-cum-distance based topological descriptor were used for the present investigations. A dataset comprising of 80 substituted tetrahydropyrimidine-2-one analogues was selected for the present studies. The values of the Wiener's index, Zagreb group parameter and eccentric connectivity index for each of the 80 compounds comprising the dataset were computed using an in-house computer program. The dataset was divided randomly into training and test sets. Resultant data was analyzed and suitable models were developed after identifying the active ranges in the training set. Subsequently, a biological activity was assigned to each of the compound involved in the test set using these models, which was then compared with the reported HIV-protease inhibitory activity. Accuracy of prediction using these models was found to vary from a minimum of approximately 86% to a maximum of approximately 88%.
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Affiliation(s)
- Viney Lather
- Faculty of Pharmaceutical Sciences, M. D. University, Rohtak-124001, India
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Melón S, Gil-Roda C, de Oña M, Erice A. Altered replicative capacity of recombinant HIV type 1 containing mutations at codons 26 and 29 of the viral protease. AIDS Res Hum Retroviruses 2004; 20:1183-8. [PMID: 15588340 DOI: 10.1089/aid.2004.20.1183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 protease activity is essential for viral replication. In spite of the high rates of HIV mutation, the active site of protease (residues 24-29) is a conserved site, where mutations have not been previously described. To determine the effect of mutations at positions T26 and A29 of the viral protease and its viability in recombinant HIV-1 strains, Sup-t1 cells were transfected by electroporation with PCR products from a protease containing the 26X or 29X mutation. These mutations were constructed by mutagenesis site directed with degenerative primers. Both changes modified the replicative capacity of the virus: viruses containing the 26X mutation have delayed replication as compared to the control virus HTLVIII B; the presence of the 29X mutation in the viral protease results in the absence of HIV-1 replication. These findings confirm that this region of the viral protease appears to be necessary for the viability of HIV-1, and it could be a good target for antiviral therapy.
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18
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Laughrea M, Shen N, Jetté L, Darlix JL, Kleiman L, Wainberg MA. Role of distal zinc finger of nucleocapsid protein in genomic RNA dimerization of human immunodeficiency virus type 1; no role for the palindrome crowning the R-U5 hairpin. Virology 2001; 281:109-16. [PMID: 11222101 DOI: 10.1006/viro.2000.0778] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genomic RNA isolated from HIV-1 variously mutated in nucleocapsid protein (NC) was characterized by nondenaturing gel electrophoresis. Mutations in the C-terminal, the N-terminal, and the linker regions had no effect on genomic RNA dimerization [they are R7R10K11S, P31L, R32G, S3(32-34), and K59L], while a C36S/C39S mutation in the distal zinc knuckle (Cys-His box or zinc finger) inhibited genome dimerization as much as disrupting the kissing-loop domain. The four mutations which inhibited tRNA(Lys3) genomic placement (i.e., the in vivo placement of tRNA(Lys3) on the primer binding site) had no effect on genome dimerization. Among five mutations which inhibited genome packaging, four had no effect on genome dimerization. Thus the N-terminal and linker regions of NC control genome packaging/tRNA(Lys3) placement (two processes which do not require mature NC) but have little influence on genome dimerization and 2-base extension of tRNA(Lys3) (two processes which are likely to require mature NC). It has been suggested, based on electron microscopy, that the AAGCUU82 palindrome crowning the R-U5 hairpin stimulates genomic RNA dimerization. To test this hypothesis, we deleted AGCU81 from wild-type viruses and from viruses bearing a disrupted kissing-loop hairpin or kissing-loop domain; in another mutant, we duplicated AGCU81. The loss of AGCU81 reduced dimerization by 2.5 +/- 4%; its duplication increased it by 3 +/- 6%. Dissociation temperature was left unchanged. We reach two conclusions. First, the palindrome crowning the R-U5 hairpin has no impact on HIV-1 genome dimerization. Second, genomic RNA dimerization is differentially influenced by NC sequence: it is Zn finger dependent but independent of the basic nature of the N-terminal and linker subdomains. We propose that the NC regions implicated in 2-base extension of tRNA(Lys3) are required for a second (maturation) step of tRNA placement. Genome dimerization and mature tRNA placement would then become two RNA-RNA interactions sharing similar NC sequence requirements.
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Affiliation(s)
- M Laughrea
- McGill AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada.
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Affiliation(s)
- W Lewis
- Department of Pathology, Emory University School of Medicine, 7117 Woodruff Memorial Building, 1639 Pierce Drive, Atlanta, GA 30322, USA.
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Ikuta K, Suzuki S, Horikoshi H, Mukai T, Luftig RB. Positive and negative aspects of the human immunodeficiency virus protease: development of inhibitors versus its role in AIDS pathogenesis. Microbiol Mol Biol Rev 2000; 64:725-45. [PMID: 11104817 PMCID: PMC99012 DOI: 10.1128/mmbr.64.4.725-745.2000] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this review we summarize multiple aspects of the human immunodeficiency virus (HIV) protease from both structural and functional viewpoints. After an introductory overview, we provide an up-to-date status report on protease inhibitors (PI). This proceeds from a discussion of PI structural design, to how PI are optimally utilized in highly active antiretroviral triple therapy (one PI along with two reverse transcriptase inhibitors), the emergence of PI resistance, and the natural role of secretory leukocyte PI. Then we switch to another focus: the interaction of HIV protease with other genes in acute and persistent infection, which in turn may have an effect on AIDS pathogenesis. We conclude with a discussion on future directions in HIV treatment, involving multiple-target anti-HIV therapy, vaccine development, and novel reactivation-inhibitory reagents.
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Affiliation(s)
- K Ikuta
- Department of Virology, Research Institute for Microbial Diseases (Biken), Osaka University, Suita, Osaka 565-0871, Japan.
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21
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Dorsey BD, McDonough C, McDaniel SL, Levin RB, Newton CL, Hoffman JM, Darke PL, Zugay-Murphy JA, Emini EA, Schleif WA, Olsen DB, Stahlhut MW, Rutkowski CA, Kuo LC, Lin JH, Chen IW, Michelson SR, Holloway MK, Huff JR, Vacca JP. Identification of MK-944a: a second clinical candidate from the hydroxylaminepentanamide isostere series of HIV protease inhibitors. J Med Chem 2000; 43:3386-99. [PMID: 10978186 DOI: 10.1021/jm9903848] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Recent results from human clinical trials have established the critical role of HIV protease inhibitors in the treatment of acquired immune-deficiency syndrome (AIDS). However, the emergence of viral resistance, demanding treatment protocols, and adverse side effects have exposed the urgent need for a second generation of HIV protease inhibitors. The continued exploration of our hydroxylaminepentanamide (HAPA) transition-state isostere series of HIV protease inhibitors, which initially resulted in the identification of Crixivan (indinavir sulfate, MK-639, L-735,524), has now yielded MK-944a (L-756,423). This compound is potent, is selective, and competitively inhibits HIV-1 PR with a K(i) value of 0.049 nM. It stops the spread of the HIV(IIIb)-infected MT4 lymphoid cells at 25.0-50.0 nM, even in the presence of alpha(1) acid glycoprotein, human serum albumin, normal human serum, or fetal bovine serum. MK-944a has a longer half-life in several animal models (rats, dogs, and monkeys) than indinavir sulfate and is currently in advanced human clinical trials.
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Affiliation(s)
- B D Dorsey
- Departments of Medicinal Chemistry, Antiviral Research, Drug Metabolism, and Molecular Systems, Merck Research Laboratories, West Point, Pennsylvania 19486, USA.
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22
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Bürgisser P, Vernazza P, Flepp M, Böni J, Tomasik Z, Hummel U, Pantaleo G, Schüpbach J. Performance of five different assays for the quantification of viral load in persons infected with various subtypes of HIV-1. Swiss HIV Cohort Study. J Acquir Immune Defic Syndr 2000; 23:138-44. [PMID: 10737428 DOI: 10.1097/00126334-200002010-00005] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Five methods for the assessment of plasma viral load (VL) were evaluated in 103 seropositive patients infected with various subtypes of HIV-1. The methods included three RNA-based assays (Amplicor Monitor 1.5, Quantiplex version 2.0, NucliSens), one ultrasensitive reverse transcriptase (PERT) assay and one "boosted" p24 antigen (Ag) enzyme immunoassay (EIA). Subtyping was based on sequencing in env. The sensitivities were, in decreasing order, Amplicor > PERT > p24 Ag > NucliSens > Quantiplex. The low sensitivity of NucliSens was related to the missing of several non-B (A, E, F, G) or recombinant strains, whereas that of Quantiplex did not depend on subtype. In the 1 group O sample and 4 group M samples, only PERT assay or p24Ag EIA produced a positive result. In the quantitative range, correlation was best between Amplicor and Quantiplex (r = 0.8848), fair between Amplicor and NucliSens (r = 0.7064) or PERT assay (r = 0.7266), lowest between Amplicor and p24Ag EIA (r = 0.3989). Amplicor underestimated VL in 1 subtype E sample. Thus, Amplicor performed best in terms of sensitivity (compared with all other assays) and accuracy (compared with NucliSens, PERT assay, and p24Ag) for non-B subtypes in group M samples. PERT assay appears useful for VL assessment in infections by group O or other highly divergent viruses.
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Affiliation(s)
- P Bürgisser
- Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
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23
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Bürgisser P, Vernazza P, Flepp M, Böni J, Tomasik Z, Hummel U, Pantaleo G, Schüpbach J. Performance of Five Different Assays for the Quantification of Viral Load in Persons Infected With Various Subtypes of HIV-1. J Acquir Immune Defic Syndr 2000. [DOI: 10.1097/00042560-200002010-00005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Wang CT, Lai HY, Li JJ. Analysis of minimal human immunodeficiency virus type 1 gag coding sequences capable of virus-like particle assembly and release. J Virol 1998; 72:7950-9. [PMID: 9733833 PMCID: PMC110128 DOI: 10.1128/jvi.72.10.7950-7959.1998] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We have constructed a series of human immunodeficiency virus (HIV) gag mutants by progressive truncation of the gag coding sequence from the C terminus and have combined these mutants with an assembly-competent matrix domain deletion mutation (DeltaMA). By using several methods, the particle-producing capabilities of each mutant were examined. Our analysis indicated that truncated Gag precursors lacking most of C-terminal gag gene products assembled and were released from 293T cells. Additionally, a mutant with a combined deletion of the MA (DeltaMA) and p6 domains even produced particles at levels comparable to that of the wild-type (wt) virus. However, most mutants derived from combination of the DeltaMA and the C-terminal truncation mutations did not release particles as well as the wt. Our smallest HIV gag gene product capable of virus-like particle formation was a 28-kDa protein which consists of a few MA amino acids and the CA-p2 domain. Sucrose density gradient fractionation analysis indicated that most mutants exhibited a wt retrovirus particle density. Exceptions to this rule were mutants with an intact MA domain but deleted downstream of the p2 domains. These C-terminal truncation mutants possessed particle densities of 1.13 to 1.15 g/ml, lower than that of the wt. The N-terminal portions of the CA domain, which have been shown to be dispensable for core assembly, became critical when most of the MA domain was deleted, suggesting a requirement for an intact CA domain to assemble and release particles.
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Affiliation(s)
- C T Wang
- Institute of Clinical Medicine, National Yang-Ming University, and Department of Medical Research, Veterans General Hospital-Taipei, Taipei, Taiwan 11217, Republic of China.
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25
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Affiliation(s)
- C Flexner
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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26
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Kempf DJ, Sham HL, Marsh KC, Flentge CA, Betebenner D, Green BE, McDonald E, Vasavanonda S, Saldivar A, Wideburg NE, Kati WM, Ruiz L, Zhao C, Fino L, Patterson J, Molla A, Plattner JJ, Norbeck DW. Discovery of ritonavir, a potent inhibitor of HIV protease with high oral bioavailability and clinical efficacy. J Med Chem 1998; 41:602-17. [PMID: 9484509 DOI: 10.1021/jm970636+] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The structure-activity studies leading to the potent and clinically efficacious HIV protease inhibitor ritonavir are described. Beginning with the moderately potent and orally bioavailable inhibitor A-80987, systematic investigation of peripheral (P3 and P2') heterocyclic groups designed to decrease the rate of hepatic metabolism provided analogues with improved pharmacokinetic properties after oral dosing in rats. Replacement of pyridyl groups with thiazoles provided increased chemical stability toward oxidation while maintaining sufficient aqueous solubility for oral absorption. Optimization of hydrophobic interactions with the HIV protease active site produced ritonavir, with excellent in vitro potency (EC50 = 0.02 microM) and high and sustained plasma concentrations after oral administration in four species. Details of the discovery and preclinical development of ritonavir are described.
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Affiliation(s)
- D J Kempf
- Pharmaceutical Products Division, Abbott Laboratory, Abbott Park, Illinois 60064, USA
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27
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Laco GS, Schalk-Hihi C, Lubkowski J, Morris G, Zdanov A, Olson A, Elder JH, Wlodawer A, Gustchina A. Crystal structures of the inactive D30N mutant of feline immunodeficiency virus protease complexed with a substrate and an inhibitor. Biochemistry 1997; 36:10696-708. [PMID: 9271500 DOI: 10.1021/bi9707436] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Crystal structures of complexes of a D30N mutant of feline immunodeficiency virus protease (FIV PR) complexed with a statine-based inhibitor (LP-149), as well as with a substrate based on a modification of this inhibitor (LP-149S), have been solved and refined at resolutions of 2.0 and 1.85 A, respectively. Both the inhibitor and the substrate are bound in the active site of the mutant protease in a similar mode, which also resembles the mode of binding of LP-149 to the native protease. The carbonyl oxygen of the scissile bond in the substrate is not hydrated and is located within the distance of a hydrogen bond to an amido nitrogen atom from one of the two asparagines in the active site of the enzyme. The nitrogen atom of the scissile bond is 3.25 A from the conserved water molecule (Wat301). A model of a tetrahedral intermediate bound to the active site of the native enzyme was built by considering the interactions observed in all three crystal structures of FIV PR. Molecular dynamics simulations of this model bound to native wild-type FIV PR were carried out, to investigate the final stages of the catalytic mechanism of aspartic proteases.
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Affiliation(s)
- G S Laco
- Macromolecular Structure Laboratory, NCI-Frederick Cancer Research and Development Center, Frederick, Maryland 21702, USA
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28
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Kozal MJ, Shah N, Shen N, Yang R, Fucini R, Merigan TC, Richman DD, Morris D, Hubbell E, Chee M, Gingeras TR. Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat Med 1996; 2:753-9. [PMID: 8673920 DOI: 10.1038/nm0796-753] [Citation(s) in RCA: 417] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Naturally occurring mutations in HIV-1-infected patients have important implications for therapy and the outcome of clinical studies. However, little is known about the prevalence of mutations that confer resistance to HIV-1 protease inhibitors in isolates derived from patients naive for such inhibitors. In the first clinical application of high-density oligonucleotide array sequencing, the sequences of 167 viral isolates from 102 patients have been determined. The DNA sequence of USA HIV-1 clade B proteases was found to be extremely variable and 47.5% of the 99 amino acid positions varied. This level of amino acid diversity is greater than that previously known for all worldwide HIV-1 clades combined (40%). Many of the amino acid changes that are known to contribute to drug resistance occurred as natural polymorphisms in isolates from patients who had never received protease inhibitors.
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Affiliation(s)
- M J Kozal
- Department of Molecular Biology, Affymetrix, Santa Clara, California 95051, USA
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29
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Dukes CS, Matthews TJ, Lambert DM, Dreyer GB, Petteway SR, Weinberg JB. Potent inhibition of HIV type 1 infection of mononuclear phagocytes by synthetic peptide analogs of HIV type 1 protease substrates. AIDS Res Hum Retroviruses 1996; 12:777-82. [PMID: 8738429 DOI: 10.1089/aid.1996.12.777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The HIV-1 genome encodes a protease that is required for viral processing of the precursor polyproteins Pr55gag and Pr160gag-pol. Interference with this process in human lymphocytes inhibits production of infectious virus. We tested the ability of several protease inhibitors to decrease replication of HIV-1BaL in human monocytes and peritoneal macrophages. The compounds tested are oligopeptide analogs of HIV-1 protease substrates in which the scissile dipeptide has been replaced by a hydroxyethylene isostere. The protease inhibitors were added only once, 1 hr prior to inoculation with virus. Every 3-5 days, half the medium was replaced with fresh medium. Inhibition of virus production was assessed by measuring reverse transcriptase (RT) activity in supernatant medium 14 days after infection. The concentration of drug required to inhibit infection by 50% (IC50) in monocytes ranged from 0.17 to 2.99 microM; IC50 values for peritoneal macrophages ranged from 0.21 to 1.9 microM. The IC50 values for these compounds were 1.1- to 10-fold higher when tested in monocytes compared to their inhibitory effect in lymphocytes, although still potently effective in the dosage range that appeared nontoxic to cells. Cell toxicity was seen only at concentrations greater than 10 microM, and varied among the drugs tested. Immunoblot analysis of two of the drugs (SB205700 and SB108922) confirmed inhibition of polyprotein processing. In control cells, 22% of viral protein pr55 was processed to p24 by 24 hr, and 51% was processed by 48 hr. In cells treated with the protease inhibitors (2 microM), Pr55 processing was inhibited 77% at 24 hr and 89% at 48 hr. Thus, these synthetic peptide analogs potently inhibit productive infection of mononuclear phagocytes by HIV-1. Drugs of this class may be useful for the treatment of HIV-1 infection in humans.
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Affiliation(s)
- C S Dukes
- Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
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30
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Chen P, Cheng PT, Alam M, Beyer BD, Bisacchi GS, Dejneka T, Evans AJ, Greytok JA, Hermsmeier MA, Humphreys WG, Jacobs GA, Kocy O, Lin PF, Lis KA, Marella MA, Ryono DE, Sheaffer AK, Spergel SH, Sun CQ, Tino JA, Vite G, Colonno RJ, Zahler R, Barrish JC. Aminodiol HIV protease inhibitors. Synthesis and structure-activity relationships of P1/P1' compounds: correlation between lipophilicity and cytotoxicity. J Med Chem 1996; 39:1991-2007. [PMID: 8642558 DOI: 10.1021/jm950717a] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A series of novel aminodiol inhibitors of HIV protease based on the lead compound 1 with structural modifications at P1' were synthesized in order to reduce the cytotoxicity of 1. We have observed a high degree of correlation between the lipophilicity and cytotoxicity of this series of inhibitors. It was found that appropriate substitution at the para position of the P1' phenyl group of 1 resulted in the identification of equipotent (both against the enzyme and in cell culture) compounds (10l, 10m, 10n, and 15c) which possess significantly decreased cytotoxicity.
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Affiliation(s)
- P Chen
- Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, New Jersey 08543-4000, USA
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31
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Arts EJ, Wainberg MA. Human immunodeficiency virus type 1 reverse transcriptase and early events in reverse transcription. Adv Virus Res 1996; 46:97-163. [PMID: 8824699 DOI: 10.1016/s0065-3527(08)60071-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- E J Arts
- McGill University AIDS Centre, Sir Mortimer B. Davis-Jewish General Hospital, Montréal, Québec, Canada
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32
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Leonard JM. Perspectives in HIV protease inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1996; 394:319-25. [PMID: 8815696 DOI: 10.1007/978-1-4757-9209-6_29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- J M Leonard
- Antiviral Venture, Pharmaceutical Products, Research & Development, Abbott Laboratories, Abbott Park, Illinois, USA
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33
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Beveridge A, Dealwis C, Cooper J. A theoretical study of the active site complexes formed between endothiapepsin and three potent inhibitors: pepstatin A, and peptide analogues containing difluorostatone and phosphostatine. Implications for inhibitor design. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/0166-1280(94)03937-g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Jacobsen H, Yasargil K, Winslow DL, Craig JC, Kröhn A, Duncan IB, Mous J. Characterization of human immunodeficiency virus type 1 mutants with decreased sensitivity to proteinase inhibitor Ro 31-8959. Virology 1995; 206:527-34. [PMID: 7831807 DOI: 10.1016/s0042-6822(95)80069-7] [Citation(s) in RCA: 168] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A human immunodeficiency virus type 1 (HIV-1) variant with highly reduced susceptibility to Ro 31-8959, an inhibitor of the viral proteinase, has been selected by repeated passage of wild-type virus in CEM cells in the presence of increasing concentrations of the inhibitor. Peptide sequences of the proteinase of selected virus were obtained from proviral DNA. Sequence comparison to wild-type (wt) proteinase demonstrated two amino acid substitutions in the resistant virus, a Gly to Val exchange at position 48 and a Leu to Met exchange at position 90. Furthermore, sequences of intermediate passage virus suggest contributions from positions 12, 36, 57, and 63 in early steps of resistance development. The selected virus showed a ca. 40-fold increase in 50% inhibitory concentration of Ro 31-8959. Growth kinetics of resistant virus were comparable to wild-type virus and the resistant genotype proved to be stable in the absence of inhibitor. Directed mutagenesis of the HIV-1 HXB2 proteinase at positions 48 and 90 suggested that each mutation alone led to a moderate decrease in sensitivity of the recombinant virus to proteinase inhibitor. However, a recombinant virus carrying both mutations in the proteinase gene showed a significant reduction in its sensitivity to Ro 31-8959 thus proving the importance of these exchanges for the resistance phenotype.
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Affiliation(s)
- H Jacobsen
- Hoffmann-LaRoche AG, Pharmaceutical Research New Technologies/Biology, Basel, Switzerland
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36
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Camplo M, Niddam V, Barthélémy P, Faury P, Mourier N, Simon V, Charvet AS, Trabaud C, Graciet JC, Chermann JC, Kraus JL. Synthesis and anti-human immunodeficiency virus type 1 activities of new peptido-nucleoside analogues. Eur J Med Chem 1995. [DOI: 10.1016/0223-5234(96)88298-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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37
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Affiliation(s)
- C Carter
- Stonybrook Health Sciences Center, Department of Microbiology, State University of New York at Stonybrook 11794
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38
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Lang M, Roesel J. HIV-1 protease inhibitors: development, status, and potential role in the treatment of AIDS. Arch Pharm (Weinheim) 1993; 326:921-4. [PMID: 8122962 DOI: 10.1002/ardp.19933261202] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- M Lang
- Pharmaceuticals Division, CIBA-GEIGY Limited, Basel, Switzerland
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39
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Wang CT, Barklis E. Assembly, processing, and infectivity of human immunodeficiency virus type 1 gag mutants. J Virol 1993; 67:4264-73. [PMID: 7685414 PMCID: PMC237796 DOI: 10.1128/jvi.67.7.4264-4273.1993] [Citation(s) in RCA: 168] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We studied the effects of gag mutations on human immunodeficiency virus type 1 (HIV-1) assembly, processing, and infectivity by using a replication-defective HIV expression system. HIV mutants were screened for infectivity by transduction of a selectable marker and were examined for assembly by monitoring particle release from transfected cells. Gag protein processing and reverse transcriptase activities of mutant particles were also assayed. Surprisingly, most Gag protein mutants were assembled and processed. The two exceptions to this rule were a myristylation-minus mutant, and one gag matrix domain mutant which expressed proteins that were trapped intracellularly. Interestingly, a mutant with a 56-amino-acid deletion within the HIV gag capsid domain still could assemble and process virus particles, exhibited a wild-type retrovirus particle density, and had wild-type reverse transcriptase activity. Indeed, although most HIV-1 gag mutants were noninfectious or poorly infectious, they produced apparently normal particles which possessed significant reverse transcriptase activities. These results strongly support the notion that the HIV-1 Gag proteins are functionally involved in post-assembly, postprocessing stages of virus infectivity.
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Affiliation(s)
- C T Wang
- Vollum Institute for Advanced Biomedical Research, Oregon Health Sciences University, Portland 97201
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40
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Luban J, Lee C, Goff SP. Effect of linker insertion mutations in the human immunodeficiency virus type 1 gag gene on activation of viral protease expressed in bacteria. J Virol 1993; 67:3630-4. [PMID: 8497070 PMCID: PMC237714 DOI: 10.1128/jvi.67.6.3630-3634.1993] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have expressed the human immunodeficiency virus type 1 (HIV-1) protease (PR) in bacteria as a Gag-PR polyprotein (J. Luban and S.P. Goff, J. Virol. 65:3203-3212, 1991). The protein displays enzymatic activity, cleaving the Gag polyprotein precursor Pr55gag to the expected products. The PR enzyme is only active as a dimer, and we hypothesized that PR activation might be used as an indicator of polyprotein multimerization. We constructed 25 linker insertion mutations throughout gag and assessed the PR activity of mutant Gag-PR polyproteins by the appearance of Gag cleavage products in bacterial lysates. All mutant constructs produced stable protein in bacteria. PR activity of the majority of the Gag-PR mutants was indistinguishable from that of the wild type. Six mutants, one with an insertion in the matrix (MA), four with insertions in the capsid (CA), and one with insertions in the nucleocapsid (NC), globally disrupted polyprotein processing. When PR was provided in trans on a separate plasmid, the Gag proteins were cleaved with wild-type efficiency. These results suggest that the gag mutations identified as disruptive of polyprotein processing did not conceal the scissile bonds of the polyprotein. Rather, the mutations prevented PR activation in the context of a Gag-PR polyprotein, perhaps by preventing polyprotein dimerization.
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Affiliation(s)
- J Luban
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York 10032
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41
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Shoeman RL, Sachse C, Höner B, Mothes E, Kaufmann M, Traub P. Cleavage of human and mouse cytoskeletal and sarcomeric proteins by human immunodeficiency virus type 1 protease. Actin, desmin, myosin, and tropomyosin. THE AMERICAN JOURNAL OF PATHOLOGY 1993; 142:221-30. [PMID: 8424456 PMCID: PMC1886840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
HeLa cell actin was cleaved by human immunodeficiency virus type 1 protease when in its soluble, globular form (G-actin). No cleavage of the polymerized, filamentous form of actin (F-actin) was observed when examined by denaturing gel electrophoresis; however, electron microscopy revealed a low level of cleavage of F-actin. Immunoblotting of mouse skeletal and human pectoral muscle myofibrils treated in vitro with human immunodeficiency virus type 1 protease showed that myosin heavy chain, desmin, tropomyosin, and a fraction of the actin were all cleaved. Electron microscopy of these myofibrils demonstrated changes consistent with cleavage of these proteins: Z-lines were rapidly lost, the length of the A bands was shortened, and the thick filaments (myosin filaments) were often laterally frayed such that the structures disintegrated. Nonmuscle myosin heavy chains were also cleaved by this enzyme in vitro. These data demonstrate that this protease can cause alterations in muscle cell ultrastructure in vitro that may be of clinical relevance in infected individuals.
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Affiliation(s)
- R L Shoeman
- Max-Planck-Institut für Zellbiologie, Ladenburg, Federal Republic of Germany
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42
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Phylip LH, Mills JS, Parten BF, Dunn BM, Kay J. Intrinsic activity of precursor forms of HIV-1 proteinase. FEBS Lett 1992; 314:449-54. [PMID: 1468583 DOI: 10.1016/0014-5793(92)81524-p] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The wild-type -Phe*Pro- bond located at the N-terminus of the mature aspartic proteinase of HIV-1 was replaced by -Ile-Pro- or -Val-Pro-. By this means, processing at this cleavage junction was prevented and so, extended or precursor forms of HIV-proteinase were generated. These constructs were expressed in Escherichia coli, purified therefrom, and their specificity, activity at different pH values and susceptibility to the potent inhibitor, Ro31-8959, was assessed. A hitherto unobserved cleavage junction (at approximately Ala-Phe*Leu-Gln approximately) in the frame-shift region of the gag-pol viral genome was identified and confirmed by demonstrating cleavage of a synthetic peptide corresponding to this region. The implications for viral replication of self-processing at neural pH by proteinase whilst still present (in a precursor form) as a component of the polyprotein are considered; such reactions, however, are still blocked even at pH values as high as 8.0 by Ro31-8959.
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Affiliation(s)
- L H Phylip
- Department of Biochemistry, University of Wales College of Cardiff, UK
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43
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Takatsuji H, Yamauchi H, Watanabe S, Kato H, Ikeda J. Cauliflower mosaic virus reverse transcriptase. Activation by proteolytic processing and functional alteration by terminal deletion. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)49950-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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44
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Abstract
HIV produces a small , dimeric aspartyl protease which specifically cleaves the polyprotein precursors encoding the structural proteins and enzymes of the virus. This proteolytic activity is absolutely required for the production of mature, infectious virions and is therefore an attractive target for therapeutic intervention. This review summarizes the strategies and multidisciplinary efforts that have been applied to date to the identification of specific inhibitors of this critical viral enzyme. These inhibitors include rationally designed peptide substrate analogs, compounds conceived from tertiary structure information on the enzyme and natural products. Future directions in the discovery and development of HIV-1 protease inhibitors are also discussed.
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Affiliation(s)
- C Debouck
- Department of Molecular Genetics, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406
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45
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Mergener K, Fäcke M, Welker R, Brinkmann V, Gelderblom HR, Kräusslich HG. Analysis of HIV particle formation using transient expression of subviral constructs in mammalian cells. Virology 1992; 186:25-39. [PMID: 1727601 DOI: 10.1016/0042-6822(92)90058-w] [Citation(s) in RCA: 118] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Segments of the human immunodeficiency virus (HIV) type 1 gag and pol genes and mutants thereof were transiently expressed in mammalian cells. Expression was dependent on the presence of the rev responsive element in cis and the rev protein in trans and was readily detected by indirect immunofluorescence or Western blotting. Transfection of constructs encoding the entire gag and pol open reading frames yielded efficient release of particles banding at a density of 1.16 g of sucrose per milliliter and consisting mainly of processed gag proteins. In addition, these particles contained the p66/p51 heterodimer of reverse transcriptase (RT), had associated RT activity, and contained RNA. Electron micrographs revealed immature retrovirus-like particles budding primarily from the plasma membrane and extracellular particles with morphological characteristics of HIV. Particle production was independent of the pol open reading frame or an active HIV proteinase (PR) but without active PR, cell-associated and particle-associated proteins remained completely uncleaved and budding occurred primarily into intracellular vacuoles. A mutation preventing myristoylation of the viral polyproteins abolished particle release but did not interfere with polyprotein synthesis and did not prevent processing. Expression of gag and PR in the same reading frame yielded complete processing of polyproteins but no budding and led to increased cell toxicity. A mutation of the PR active site in this construct prevented cytotoxicity and restored particle release indicating that the observed phenotype was caused by the overexpression of PR. These particles were aberrant in size and morphology when analyzed on sucrose density gradients and by electron microscopy. Budding was arrested at an early stage and extracellular particles appeared to be released by a different mechanism. Only short C-terminal extensions were compatible with this release mechanism since expression of a similar mutant construct encoding the entire gag-pol open reading frame did not yield particles.
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Affiliation(s)
- K Mergener
- Angewandte Tumorvirologie, Deutsches Krebsforschungszentrum, Heidelberg, Germany
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Abstract
A successful AIDS vaccine must elicit an immune state that will prevent the establishment of an HIV-1 persistent infection. This is a unique and difficult goal for a vaccine. Most vaccines elicit or prime for immune responses that prevent or attenuate the expression of clinical disease following infection with the pathogen. However, current evidence suggest that, following persistent infection with HIV-1, antiviral immune responses do not prevent the long-term progression to disease. Hence, it seems that the development of the persistent infection must be prevented. The ability of the immune response to accomplish this goal depends upon the efficiency with which the virus establishes persistence in the host. This is unknown for HIV-1. As a result, early efforts at vaccine development have focused on humoral immune responses directed against the virus particle in the attempt to prevent any infection of the host's cells. Studies with chimpanzees, as a model for HIV-1 infection, suggest that virus-neutralizing antibodies directed against the third hypervariable (V3) domain of the viral gp120 envelope glycoprotein may be particularly effective in preventing this infection. Studies also are in progress, both in chimpanzees and humans, to define the immunogenicity and effectiveness of various immunogens derived from the viral envelope and core structural proteins. Efforts that have concentrated on the gp120 V3 domain (or PND) have defined the extent of this region's variability and have established elements of generally conserved structure and sequence. The construction of these elements into practical and effective immunogens is an important goal. Finally, it is essential that basic studies be performed to determine if humoral or cellular immune responses directed against virus-infected cells would aid in preventing the establishment of an HIV-1 persistent infection. Such immune responses, if effective and in conjunction with specific virus-neutralizing antibody responses, would enhance the probability that an effective HIV-1 vaccine could be developed.
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Hellen CU, Wimmer E. The role of proteolytic processing in the morphogenesis of virus particles. EXPERIENTIA 1992; 48:201-15. [PMID: 1740191 PMCID: PMC7087542 DOI: 10.1007/bf01923512] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Proteinases are encoded by many RNA viruses, all retroviruses and several DNA viruses. They play essential roles at various stages in viral replication, including the coordinated assembly and maturation of virions. Most of these enzymes belong to one of three (Ser, Cys or Asp) of the four major classes of proteinases, and have highly substrate-selective and cleavage specific activities. They can be thought of as playing one of two general roles in viral morphogenesis. Structural proteins are encoded by retroviruses and many RNA viruses as part of large polyproteins. Their proteolytic release is a prerequisite to particle assembly; consequent structural rearrangement of the capsid domains serves to regulate and direct association and assembly of capsid subunits. The second general role of proteolysis is in assembly-dependent maturation of virus particles, which is accompanied by the acquisition of infectivity.
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Affiliation(s)
- C U Hellen
- Department of Microbiology, State University of New York, Stony Brook 11794-8631
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48
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Grafstrom RH, Zachariasewycz K, Brigandi RA, Block TM. Genetically engineered bacteria to identify and produce anti-viral agents. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1992; 312:25-40. [PMID: 1514444 DOI: 10.1007/978-1-4615-3462-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have prepared a strain of Escherichia coli that expresses both the HIV protease and a Tet protein which has been modified to contain the HIV protease recognition sequence. When the protease is expressed, the bacteria will not grow in the presence of tetracycline. However, when the protease is inhibited the bacteria can grow in tetracycline containing media (Block and Grafstrom 1990). We have selected spontaneously arising Tet resistant mutants and have screened them for those that could be producing an inhibitor of HIV protease. The problems in the construction of this strain and the characterization of the various Tetr mutants are discussed.
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Affiliation(s)
- R H Grafstrom
- Department of Microbiology and Immunology, Jefferson Medical College, Philadelphia, PA 19107
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Hayakawa T, Misumi Y, Kobayashi M, Ohi Y, Fujisawa Y, Kakinuma A, Hatanaka M. Expression of human T-cell leukemia virus type I protease in Escherichia coli. Biochem Biophys Res Commun 1991; 181:1281-7. [PMID: 1764078 DOI: 10.1016/0006-291x(91)92077-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Human T-cell leukemia virus type I (HTLV-I) genome is believed to encode its own protease, although the protease has not yet been detected. To identify the HTLV-I protease, an in-frame gag (3' portion)-prt region was expressed in Escherichia coli. The 14-kDa product was detected using antisera against a synthetic peptide mimicking the fragment of HTLV-I protease, although the molecular weight of the primary translational product was 27,000. A cell extract had a proteolytic activity to cleave a synthetic peptide substrate containing the cleavage site of gag p19/p24 at the correct site in vitro. Replacement of the putative active site Asp-64 with Gly abolished both in vivo processing activity and in vitro proteolytic activity. These results suggest that the 14-kDa product is the mature enzymatically active HTLV-I protease generated through posttranslational autoprocessing in E. coli.
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Affiliation(s)
- T Hayakawa
- Biotechnology Research Laboratories, Takeda Chemical Industries, Ltd., Osaka, Japan
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50
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Le Grice SF, Panin M, Kalayjian RC, Richter NJ, Keith G, Darlix JL, Payne SL. Purification and characterization of recombinant equine infectious anemia virus reverse transcriptase. J Virol 1991; 65:7004-7. [PMID: 1719238 PMCID: PMC250816 DOI: 10.1128/jvi.65.12.7004-7007.1991] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A 1.67-kb segment of the equine infectious anemia virus pol gene, encoding a 66-kDa reverse transcriptase (RT), was cloned and expressed in Escherichia coli. Recombinant RT, purified by a combination of metal chelate affinity chromatography and ion-exchange chromatography, displays both RNA-dependent DNA polymerase and RNase H activity. The affinity of purified RT for its replication primer, tRNA(3Lys) was equivalent to that observed for human immunodeficiency virus RT. Our data suggest that an additional domain between RT-RNase H and integrase on the equine infectious anemia virus pol open reading frame is not an integral component of the RT polypeptide.
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Affiliation(s)
- S F Le Grice
- Division of Infectious Diseases, Case Western Reserve University School of Medicine, Cleveland, Ohio 44016
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