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Veselovsky AV, Zharkova MS, Poroikov VV, Nicklaus MC. Computer-aided design and discovery of protein-protein interaction inhibitors as agents for anti-HIV therapy. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:457-471. [PMID: 24716798 DOI: 10.1080/1062936x.2014.898689] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Protein-protein interactions (PPI) are involved in most of the essential processes that occur in organisms. In recent years, PPI have become the object of increasing attention in drug discovery, particularly for anti-HIV drugs. Although the use of combinations of existing drugs, termed highly active antiretroviral therapy (HAART), has revolutionized the treatment of HIV/AIDS, problems with these agents, such as the rapid emergence of drug-resistant HIV-1 mutants and serious adverse effects, have highlighted the need for further discovery of new drugs and new targets. Numerous investigations have shown that PPI play a key role in the virus's life cycle and that blocking or modulating them has a significant therapeutic potential. Here we summarize the recent progress in computer-aided design of PPI inhibitors, mainly focusing on the selection of the drug targets (HIV enzymes and virus entry machinery) and the utilization of peptides and small molecules to prevent a variety of protein-protein interactions (viral-viral or viral-host) that play a vital role in the progression of HIV infection.
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Affiliation(s)
- A V Veselovsky
- a Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences , Moscow , Russia
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2
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Lian W, Upadhyaya P, Rhodes CA, Liu Y, Pei D. Screening bicyclic peptide libraries for protein-protein interaction inhibitors: discovery of a tumor necrosis factor-α antagonist. J Am Chem Soc 2013; 135:11990-5. [PMID: 23865589 PMCID: PMC3856571 DOI: 10.1021/ja405106u] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein-protein interactions represent a new class of exciting but challenging drug targets, because their large, flat binding sites lack well-defined pockets for small molecules to bind. We report here a methodology for chemical synthesis and screening of large combinatorial libraries of bicyclic peptides displayed on rigid small-molecule scaffolds. With planar trimesic acid as the scaffold, the resulting bicyclic peptides are effective for binding to protein surfaces such as the interfaces of protein-protein interactions. Screening of a bicyclic peptide library against tumor necrosis factor-α (TNFα) identified a potent antagonist that inhibits the TNFα-TNFα receptor interaction and protects cells from TNFα-induced cell death. Bicyclic peptides of this type may provide a general solution for inhibition of protein-protein interactions.
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Affiliation(s)
- Wenlong Lian
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, OH 43210, USA
| | - Punit Upadhyaya
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, OH 43210, USA
| | - Curran A. Rhodes
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, OH 43210, USA
| | - Yusen Liu
- Center for Perinatal Research, The Research Institute at Nationwide Children’s Hospital, Department of Pediatrics, The Ohio State University College of Medicine, 700 Children’s Drive, Columbus, OH 43205, USA
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, OH 43210, USA
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Ivanov AS, Gnedenko OV, Molnar AA, Mezentsev YV, Lisitsa AV, Archakov AI. PROTEIN–PROTEIN INTERACTIONS AS NEW TARGETS FOR DRUG DESIGN: VIRTUAL AND EXPERIMENTAL APPROACHES. J Bioinform Comput Biol 2011; 5:579-92. [PMID: 17636863 DOI: 10.1142/s0219720007002825] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 02/08/2007] [Accepted: 02/08/2007] [Indexed: 11/18/2022]
Abstract
Protein–protein and protein–ligand interactions play a central role in biochemical reactions, and understanding these processes is an important task in different fields of biomedical science and drug discovery. Proteins often work in complex assemblies of several macromolecules and small ligands. The structural and functional description of protein–protein interactions (PPI) is very important for basic-, as well as applied research. The interface areas of protein complexes have unique structure and properties, so PPI represent prospective targets for a new generation of drugs. One of the key targets of PPI inhibitors are oligomeric enzymes. This report shows interactive links between virtual and experimental approaches in a total pipeline "from gene to drug" and using Surface Plasmon Resonance technology for experimentally assessing PPI. Our research is conducted on two oligomeric enzymes — HIV-1 protease (HIVp) (homo-dimer) and bacterial L-asparaginase (homo-tetramer). Using methods of molecular modeling and computational alanine scanning we obtained structural and functional description of PPI in these two enzymes. We also presented a real example of application of integral approach in searching inhibitors of HIVp dimerization — from virtual database mining up to experimental testing of lead compounds.
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Affiliation(s)
- Alexis S Ivanov
- V.N.Orechovich Institute of Biomedical Chemistry RAMS, Pogodinskaya str. 10, Moscow, 119121, Russia.
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Anderson L, Zhou M, Sharma V, McLaughlin JM, Santiago DN, Fronczek FR, Guida WC, McLaughlin ML. Facile iterative synthesis of 2,5-terpyrimidinylenes as nonpeptidic alpha-helical mimics. J Org Chem 2010; 75:4288-91. [PMID: 20469918 DOI: 10.1021/jo100272d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A facile iterative synthesis of 2,5-terpyrimidinylenes that are structurally analogous to alpha-helix mimics is presented. Condensation of amidines with readily prepared alpha,beta-unsaturated alpha-cyanoketones gives 5-cyano-substituted pyrimidines. Iterative transformation of the 5-cyano group into an amidine allows synthesis of 2,5-terpyrimidinylenes with variable groups at the 4-, 4'-, and 4''-positions. These compounds are designed to mimic the i, i + 4, and i + 7 sites of an alpha-helix.
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Affiliation(s)
- Laura Anderson
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE 205, Tampa, Florida 33620, USA
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Camarasa MJ, Velázquez S, San-Félix A, Pérez-Pérez MJ, Gago F. Dimerization inhibitors of HIV-1 reverse transcriptase, protease and integrase: A single mode of inhibition for the three HIV enzymes? Antiviral Res 2006; 71:260-7. [PMID: 16872687 DOI: 10.1016/j.antiviral.2006.05.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Revised: 05/25/2006] [Accepted: 05/30/2006] [Indexed: 10/24/2022]
Abstract
The genome of human immunodeficiency virus type 1 (HIV-1) encodes 15 distinct proteins, three of which provide essential enzymatic functions: a reverse transcriptase (RT), an integrase (IN), and a protease (PR). Since these enzymes are all homodimers, pseudohomodimers or multimers, disruption of protein-protein interactions in these retroviral enzymes may constitute an alternative way to achieve HIV-1 inhibition. A growing number of dimerization inhibitors for these enzymes is being reported. This mini review summarizes some approaches that have been followed for the development of compounds that inhibit those three enzymes by interfering with the dimerization interfaces between the enzyme subunits.
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Affiliation(s)
- María-José Camarasa
- Instituto de Química Médica (C.S.I.C.), Juan de la Cierva 3, 28006 Madrid, Spain.
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Trosset JY, Dalvit C, Knapp S, Fasolini M, Veronesi M, Mantegani S, Gianellini LM, Catana C, Sundström M, Stouten PFW, Moll JK. Inhibition of protein–protein interactions: The discovery of druglike β‐catenin inhibitors by combining virtual and biophysical screening. Proteins 2006; 64:60-7. [PMID: 16568448 DOI: 10.1002/prot.20955] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The interaction between beta-catenin and Tcf family members is crucial for the Wnt signal transduction pathway, which is commonly mutated in cancer. This interaction extends over a very large surface area (4800 A(2)), and inhibiting such interactions using low molecular weight inhibitors is a challenge. However, protein surfaces frequently contain "hot spots," small patches that are the main mediators of binding affinity. By making tight interactions with a hot spot, a small molecule can compete with a protein. The Tcf3/Tcf4-binding surface on beta-catenin contains a well-defined hot spot around residues K435 and R469. A 17,700 compounds subset of the Pharmacia corporate collection was docked to this hot spot with the QXP program; 22 of the best scoring compounds were put into a biophysical (NMR and ITC) screening funnel, where specific binding to beta-catenin, competition with Tcf4 and finally binding constants were determined. This process led to the discovery of three druglike, low molecular weight Tcf4-competitive compounds with the tightest binder having a K(D) of 450 nM. Our approach can be used in several situations (e.g., when selecting compounds from external collections, when no biochemical functional assay is available, or when no HTS is envisioned), and it may be generally applicable to the identification of inhibitors of protein-protein interactions.
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Affiliation(s)
- Jean-Yves Trosset
- Department of Chemistry, Nerviano Medical Sciences, Nerviano, MI, Italy.
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Loregian A, Palù G. Disruption of protein-protein interactions: towards new targets for chemotherapy. J Cell Physiol 2005; 204:750-62. [PMID: 15880642 DOI: 10.1002/jcp.20356] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Protein-protein interactions play a key role in various mechanisms of cellular growth and differentiation, and in the replication of pathogen organisms in host cells. Thus, inhibition of these interactions is a promising novel approach for rational drug design against a wide number of cellular and microbial targets. In the past few years, attempts to inhibit protein-protein interactions using antibodies, peptides, and synthetic or natural small molecules have met with varying degrees of success, and these will be the focus of this review.
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Affiliation(s)
- Arianna Loregian
- Department of Histology, Microbiology, and Medical Biotechnologies, University of Padova, Italy.
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Jiang S, Lu H, Liu S, Zhao Q, He Y, Debnath AK. N-substituted pyrrole derivatives as novel human immunodeficiency virus type 1 entry inhibitors that interfere with the gp41 six-helix bundle formation and block virus fusion. Antimicrob Agents Chemother 2004; 48:4349-59. [PMID: 15504864 PMCID: PMC525433 DOI: 10.1128/aac.48.11.4349-4359.2004] [Citation(s) in RCA: 218] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A recently approved peptidic human immunodeficiency virus type 1 (HIV-1) fusion inhibitor, T-20 (Fuzeon; Trimeris Inc.), has shown significant promise in clinical application for treating HIV-1-infected individuals who have failed to respond to the currently available antiretroviral drugs. However, T-20 must be injected twice daily and is too expensive. Therefore, it is essential to develop orally available small molecule HIV-1 fusion inhibitors. By screening a chemical library consisting of "drug-like" compounds, we identified two N-substituted pyrroles, designated NB-2 and NB-64, that inhibited HIV-1 replication at a low micromolar range. The absence of the COOH group in NB-2 and NB-64 resulted in a loss of anti-HIV-1 activity, suggesting that this acid group plays an important role in mediating the antiviral activity. NB-2 and NB-64 inhibited HIV-1 fusion and entry by interfering with the gp41 six-helix bundle formation and disrupting the alpha-helical conformation. They blocked a d-peptide binding to the hydrophobic pocket on surface of the gp41 internal trimeric coiled-coil domain. Computer-aided molecular docking analysis has shown that they fit inside the hydrophobic pocket and that their COOH group interacts with a positively charged residue (K574) around the pocket to form a salt bridge. These results suggest that NB-2 and NB-64 may bind to the gp41 hydrophobic pocket through hydrophobic and ionic interactions and block the formation of the fusion-active gp41 core, thereby inhibiting HIV-1-mediated membrane fusion and virus entry. Therefore, NB-2 and NB-64 can be used as lead compounds toward designing and developing more potent small molecule HIV-1 fusion inhibitors targeting gp41.
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Affiliation(s)
- Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th St., New York, NY 10021, USA.
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Arkin MR, Wells JA. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat Rev Drug Discov 2004; 3:301-17. [PMID: 15060526 DOI: 10.1038/nrd1343] [Citation(s) in RCA: 1212] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michelle R Arkin
- Sunesis Pharmaceuticals, 341 Oyster Point Boulevard, South San Francisco, California 94080, USA.
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Wilson J, Rossi CP, Carboni S, Fremaux C, Perrin D, Soto C, Kosco-Vilbois M, Scheer A. A homogeneous 384-well high-throughput binding assay for a TNF receptor using alphascreen technology. ACTA ACUST UNITED AC 2004; 8:522-32. [PMID: 14567779 DOI: 10.1177/1087057103257804] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To take advantage of the growing knowledge of cellular signaling pathways, modern-day drug discovery faces an increasing challenge to develop assays to screen for compounds that modulate protein-protein interactions. One bottleneck in achieving this goal is a lack of suitable and robust assay technologies amenable to a high-throughput format. In this report, we describe how we utilized Alphascreen trade mark technology to develop a high-throughput assay to monitor ligand binding to a member of the tumor necrosis factor receptor superfamily. We expressed a fusion protein consisting of the extracellular domain of the OX40 receptor with the constant domains of human IgG. In the presence of OX40 ligand, we determined a binding affinity constant consistent with reported values and optimized the protocol to develop a simple, homogeneous, and sensitive binding assay in a 384-well format. Finally, we assessed if this system could identify small peptides capable of inhibiting the OX40 receptor and ligand interaction. The results showed that the assay was able to detect such peptides and could be used to launch a high-throughput screening campaign for small molecules able to prevent OX40 receptor activation.
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Affiliation(s)
- Janet Wilson
- Serono Pharmaceutical Research Institute, 14 Ch. des Aulx, 1228 Plan-les-Ouates, Geneva, Switzerland
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Abstract
A case study of the discovery of small molecule antagonists to the integrins GPIIbIIIa (alphaII(B)beta3), alphavbeta3, LFA-1 (alphaLbeta2), alpha4beta1 and alpha4beta7 is presented from the perspective of a biotechnology research organization. A strategy incorporating protein mutagenesis and structural studies to develop a structure-activity relationship (SAR) that described the 'epitope' of the integrin ligand was crucial to the identification of peptide analogs of these proteins, and subsequently, through parallel trends in SAR, to the identification of small molecule mimetics of these peptides, which are active analogs of the protein ligands themselves.
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Affiliation(s)
- Thomas R Gadek
- Genentech, One DNA Way, South San Francisco, CA 94080, USA.
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12
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Abstract
The identification of small molecule antagonists of protein function is at the core of the pharmaceutical industry. Successful approaches to this problem, including screening and rational design, have been developed over the years to identify antagonists of enzymes and cellular receptors. These methods have been extended to the search for inhibitors of protein-protein interactions. While the very possibility of designing a small molecule inhibitor for such interactions was once doubted, there are examples of such inhibitors that are currently marketed products and many more inhibitors in various stages of research and development. Here we review the progress in identifying and designing small molecule protein inhibitors, with particular attention to those that block protein-protein interactions. We also discuss the physical character of protein-protein interfaces, and the resulting implications for small molecule lead discovery and design.
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Affiliation(s)
- Thomas R Gadek
- Department of Bioorganic Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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