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Komar AA. Molecular Peptide Grafting as a Tool to Create Novel Protein Therapeutics. Molecules 2023; 28:2383. [PMID: 36903628 PMCID: PMC10005171 DOI: 10.3390/molecules28052383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
The study of peptides (synthetic or corresponding to discrete regions of proteins) has facilitated the understanding of protein structure-activity relationships. Short peptides can also be used as powerful therapeutic agents. However, the functional activity of many short peptides is usually substantially lower than that of their parental proteins. This is (as a rule) due to their diminished structural organization, stability, and solubility often leading to an enhanced propensity for aggregation. Several approaches have emerged to overcome these limitations, which are aimed at imposing structural constraints into the backbone and/or sidechains of the therapeutic peptides (such as molecular stapling, peptide backbone circularization and molecular grafting), therefore enforcing their biologically active conformation and thus improving their solubility, stability, and functional activity. This review provides a short summary of approaches aimed at enhancing the biological activity of short functional peptides with a particular focus on the peptide grafting approach, whereby a functional peptide is inserted into a scaffold molecule. Intra-backbone insertions of short therapeutic peptides into scaffold proteins have been shown to enhance their activity and render them a more stable and biologically active conformation.
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Affiliation(s)
- Anton A. Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA; ; Tel.: +1-216-687-2516
- Department of Biochemistry and Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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Gomes B, Sanna G, Madeddu S, Hollmann A, Santos NC. Combining 25-Hydroxycholesterol with an HIV Fusion Inhibitor Peptide: Interaction with Biomembrane Model Systems and Human Blood Cells. ACS Infect Dis 2019; 5:582-591. [PMID: 30816690 DOI: 10.1021/acsinfecdis.8b00321] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The fusion between the viral and the target cell membrane is a crucial step in the life cycle of enveloped viruses. The blocking of this process is a well-known therapeutic approach that led to the development of the fusion inhibitor peptide enfuvirtide, clinically used against human immunodeficiency virus (HIV) type 1. Despite this significant advance on viral treatment, the appearance of resistance has limited its clinical use. Such a limitation has led to the development of other fusion inhibitor peptides, such as C34, that present the same structural domain as enfuvirtide (heptad repeat sequence) but have different functional domains (pocket-binding domain in the case of C34 and lipid-binding domain in the case of enfuvirtide). Recently, the antiviral properties of 25-hydroxycholesterol were demonstrated, which boosted the interest in this oxysterol. The combination of two distinct antiviral molecules, C34 and 25-hydroxycholesterol, may help to suppress the emergence of resistant viruses. In this work, we characterized the interaction of the C34-25-hydroxycholesterol conjugate with biomembrane model systems and human blood cells. Lipid vesicles and monolayers with defined lipid compositions were used as biomembrane model systems. The conjugate interacts preferentially with membranes rich in sphingomyelin (a lipid enriched in lipid rafts) and presents a poor partition to membranes composed solely of phosphatidylcholine and cholesterol. We hypothesize that cholesterol causes a repulsive effect that is overcome in the presence of sphingomyelin. Importantly, the peptide shows a preference for human peripheral blood mononuclear cells relative to erythrocytes, which shows its potential to target CD4+ cells. Antiviral activity results against different wild-type and drug-resistant HIV strains further demonstrated the potential of C34-HC as a good candidate for future studies.
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Affiliation(s)
- Bárbara Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon 1649-028, Portugal
| | - Giusepinna Sanna
- Department of Biomedical Sciences, Section of Microbiology and Virology, University of Cagliary, Cagliari 09123, Italy
| | - Silvia Madeddu
- Department of Biomedical Sciences, Section of Microbiology and Virology, University of Cagliary, Cagliari 09123, Italy
| | - Axel Hollmann
- Laboratory of Bioactive Compounds, CIBAAL−University of Santiago del Estero and CONICET, Santiago del Estero, Argentina
- Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, University of Quilmes, Bernal B1876BXD, Argentina
| | - Nuno C. Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon 1649-028, Portugal
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Bolarinwa O, Zhang M, Mulry E, Lu M, Cai J. Sulfono-γ-AA modified peptides that inhibit HIV-1 fusion. Org Biomol Chem 2018; 16:7878-7882. [PMID: 30306175 PMCID: PMC6209519 DOI: 10.1039/c8ob02159g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The utilization of bioactive peptides in the development of highly selective and potent pharmacological agents for the disruption of protein-protein interactions is appealing for drug discovery. It is known that HIV-1 entry into a host cell is through a fusion process that is mediated by the trimeric viral glycoprotein gp120/41, which is derived from gp160 through proteolytic processing. Peptides derived from the HIV gp41 C-terminus have proven to be potent in inhibiting the fusion process. These peptides bind tightly to the hydrophobic pocket on the gp-41 N-terminus, which was previously identified as a potential inhibitor binding site. In this study, we introduce modified 23-residue C-peptides, 3 and 4, bearing a sulfono-γ-AA residue substitution and hydrocarbon stapling, respectively, which were developed for HIV-1 gp-41 N-terminus binding. Intriguingly, both 3 and 4 were capable of inhibiting envelope-mediated membrane fusion in cell-cell fusion assays at nanomolar potency. Our study reveals that sulfono-γ-AA modified peptides could be used for the development of more potent anti-HIV agents.
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Affiliation(s)
- Olapeju Bolarinwa
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, USA.
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Guo Y, Fu L, Fan X, Shi X. Stapled SC34EK fusion inhibitors with high potency against HIV-1 and improved protease resistance. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.03.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Biophysical Properties and Antiviral Activities of Measles Fusion Protein Derived Peptide Conjugated with 25-Hydroxycholesterol. Molecules 2017; 22:molecules22111869. [PMID: 29088094 PMCID: PMC5775476 DOI: 10.3390/molecules22111869] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/26/2017] [Indexed: 12/12/2022] Open
Abstract
Measles virus (MV) infection is re-emerging, despite the availability of an effective vaccine. The mechanism of MV entry into a target cell relies on coordinated action between the MV hemagglutinin (H) receptor binding protein and the fusion envelope glycoprotein (F) which mediates fusion between the viral and cell membranes. Peptides derived from the C-terminal heptad repeat (HRC) of F can interfere with this process, blocking MV infection. As previously described, biophysical properties of HRC-derived peptides modulate their antiviral potency. In this work, we characterized a MV peptide fusion inhibitor conjugated to 25-hydroxycholesterol (25HC), a cholesterol derivative with intrinsic antiviral activity, and evaluated its interaction with membrane model systems and human blood cells. The peptide (MV.
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Mavioso ICVC, de Andrade VCR, Palace Carvalho AJ, Martins do Canto AMT. Molecular dynamics simulations of T-2410 and T-2429 HIV fusion inhibitors interacting with model membranes: Insight into peptide behavior, structure and dynamics. Biophys Chem 2017; 228:69-80. [PMID: 28711675 DOI: 10.1016/j.bpc.2017.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/24/2017] [Accepted: 06/26/2017] [Indexed: 11/17/2022]
Abstract
T-2410 and T-2429 are HIV fusion inhibitor peptides (FI) designed to present a higher efficiency even against HIV strains that developed resistance against other FIs. Similar peptides were shown to interact with model membranes both in the liquid disordered phase and in the liquid ordered state. Those results indicated that such interaction is important to function and could be correlated with their effectiveness. Extensive molecular dynamics simulations were carried out to investigate the interactions between both T-2410 and T-2429 with bilayers of pure 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and a mixture of POPC/cholesterol (Chol) (1:1). It was observed that both peptides interact strongly with both membrane systems, especially with the POPC/Chol systems, where these peptides show the highest number of H-bonds observed so far. T-2410 and T-2429 showed higher extent of interaction with bilayers when compared to T-20 or T-1249 in previous studies. This is most notable in POPC/Chol membranes where, although able to form H-bonds with Chol, they do so to a lesser extent than T-1249 does, the latter being the only FI peptide so far that was observed to form H-bonds with Chol. This behavior suggests that interaction of FI peptides with rigid Chol rich membranes may not be as dependent from peptide/Chol H-bond formation as previous results of T-1249 behavior led to believe. As in other similar peptides, the higher ability to interact with membranes shown by T-2410 and T2429 is probably correlated with its higher inhibitory efficiency.
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Affiliation(s)
- I C V C Mavioso
- Departamento de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - V C R de Andrade
- Departamento de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - A J Palace Carvalho
- Departamento de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal; Centro de Química de Évora, IIFA, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - A M T Martins do Canto
- Departamento de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal; Centro de Química de Évora, IIFA, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal.
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Shin Y, Yoon CH, Yang HJ, Lim H, Choi BS, Kim SS, Kang C. Functional characteristics of the natural polymorphisms of HIV-1 gp41 in HIV-1 isolates from enfuvirtide-naïve Korean patients. Arch Virol 2016; 161:1547-57. [PMID: 26997611 DOI: 10.1007/s00705-016-2807-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/24/2016] [Indexed: 11/30/2022]
Abstract
HIV-1 gp41 plays a key role in viral entry. The insertion of Thr at position 4 and Met/Val/Phe substitutions at position 7 are frequently observed in the fusion peptide (FP) motif of gp41 without major enfuvirtide resistance associated with mutation in heptad repeats 1/2 (HR1/2) of HIV-1 isolates from Korean patients. Here, the influence of these mutations on their biological function was evaluated by employing HIV-1 variants with mutant FPs as shown previously and with recombinant HIV-1 using the env genes of 20 HIV-1 isolates from Korean patients. In an infectivity assay, all FP mutants showed lower infectivity than the wild-type NL4-3. In particular, the substitutions at position 7 led to much greater reductions in infectivity than the insertions at position 4. Nevertheless, the replication kinetics of most mutants were similar to those of the wild type, except that the FP mutants with an Ile insertion at position 4 and a Phe substitution at position 7 showed reduced replication. Moreover, most point mutants showed lower IC50 values for enfuvirtide than the wild type, whereas the L7M substitution resulted in a slightly increased IC50 value. The infectivity using the HIV-1 env recombinant viruses decreased in 14 cases but increased slightly in six cases compared with the wild type. Most recombinants were more susceptible to enfuvirtide than the wild type, except for three recombinants that showed slight resistance. Our findings may help to explain the potential mechanisms corresponding to the natural polymorphism of gp41 and to predict the efficiency of enfuvirtide in treatment of HIV-1-infected patients in Korea.
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Affiliation(s)
- YoungHyun Shin
- Division of AIDS, Center for Immunology and Pathology, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Osong-yeup, Cheongju, Chungbuk, 363-951, Republic of Korea
| | - Cheol-Hee Yoon
- Division of AIDS, Center for Immunology and Pathology, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Osong-yeup, Cheongju, Chungbuk, 363-951, Republic of Korea
| | - Hyo-Jin Yang
- Division of AIDS, Center for Immunology and Pathology, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Osong-yeup, Cheongju, Chungbuk, 363-951, Republic of Korea
| | - Hoyong Lim
- Division of AIDS, Center for Immunology and Pathology, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Osong-yeup, Cheongju, Chungbuk, 363-951, Republic of Korea
| | - Byeong-Sun Choi
- Division of AIDS, Center for Immunology and Pathology, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Osong-yeup, Cheongju, Chungbuk, 363-951, Republic of Korea
| | - Sung Soon Kim
- Division of Respiratory Viruses, Korea National Institute of Health, Chungbuk, Republic of Korea
| | - Chun Kang
- Division of AIDS, Center for Immunology and Pathology, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Osong-yeup, Cheongju, Chungbuk, 363-951, Republic of Korea.
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Komar AA, Hatzoglou M. Exploring Internal Ribosome Entry Sites as Therapeutic Targets. Front Oncol 2015; 5:233. [PMID: 26539410 PMCID: PMC4611151 DOI: 10.3389/fonc.2015.00233] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 10/05/2015] [Indexed: 12/12/2022] Open
Abstract
Initiation of eukaryotic mRNA translation may proceed via several different routes, each requiring a different subset of factors and relying on different and specific interactions between the mRNA and the ribosome. Two modes predominate: (i) so-called cap-dependent initiation, which requires all canonical initiation factors and is responsible for about 95–97% of all initiation events in eukaryotic cells; and (ii) cap-independent internal initiation, which requires a reduced subset of initiation factors and accounts for up to 5% of the remaining initiation events. Internal initiation relies on the presence of so-called internal ribosome entry site (IRES) elements in the 5′ UTRs of some viral and cellular mRNAs. These elements (often possessing complex secondary and tertiary structures) promote efficient interaction of the mRNA with the 40S ribosome and allow for internal ribosome entry. Internal initiation of translation of specific mRNAs may contribute to development of severe disease and pathological states, such as hepatitis C and cancer. Therefore, this cellular mechanism represents an attractive target for pharmacological modulation. The purpose of this review is to provide insight into current strategies used to target viral and cellular IRESs and discuss the physiological consequences (and potential therapeutic implications) of abrogation/modulation of IRES-mediated translation.
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Affiliation(s)
- Anton A Komar
- Department of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University , Cleveland, OH , USA
| | - Maria Hatzoglou
- Department of Pharmacology, School of Medicine, Case Western Reserve University , Cleveland, OH , USA
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Meher BR, Patel S. Structural and dynamical aspects of HIV-1 protease and its role in drug resistance. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 92:299-324. [PMID: 23954105 DOI: 10.1016/b978-0-12-411636-8.00008-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Acquired immunodeficiency syndrome (AIDS) caused by the retrovirus human immunodeficiency virus (HIV) has become a major epidemic afflicting mankind. The Joint United Nations Program on HIV/AIDS (UNAIDS) projection shows the existence of millions of AIDS patients at the end of 2012. All the Food and Drug Administration (FDA)-approved drugs are getting ineffective due to resistance offered by the mutation-prone HIV. Hence, there is an urgent need for developing new drugs with greater potential. HIV life cycle is controlled by the activities of its essential proteins like glycoproteins (gp41 and gp120), HIV reverse transcriptase (HIV-RT), HIV integrase (HIV-IN), and HIV-1 protease (HIV-pr). This chapter focuses on the protein HIV-pr, which is important for the cleavage of Gag and Gag-Pol polyproteins to form mature, structural, and functional virions. The conformation and dynamics of the protein HIV-pr play a pivotal role in ligand binding and the catalytic process, which is affected by the rapid point mutations and various physiological parameters. The effect of the mutations and the varied simulation protocols on conformational dynamics and drug resistance of HIV-pr is discussed.
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Affiliation(s)
- Biswa Ranjan Meher
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia, USA.
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Bentley AA, Merkulov SM, Peng Y, Rozmarynowycz R, Qi X, Pusztai-Carey M, Merrick WC, Yee VC, McCrae KR, Komar AA. Chimeric glutathione S-transferases containing inserts of kininogen peptides: potential novel protein therapeutics. J Biol Chem 2012; 287:22142-50. [PMID: 22577144 DOI: 10.1074/jbc.m112.372854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The study of synthetic peptides corresponding to discrete regions of proteins has facilitated the understanding of protein structure-activity relationships. Short peptides can also be used as powerful therapeutic agents. However, in many instances, small peptides are prone to rapid degradation or aggregation and may lack the conformation required to mimic the functional motifs of the protein. For peptides to function as pharmacologically active agents, efficient production or expression, high solubility, and retention of biological activity through purification and storage steps are required. We report here the design, expression, and functional analysis of eight engineered GST proteins (denoted GSHKTs) in which peptides ranging in size from 8 to 16 amino acids and derived from human high molecular weight kininogen (HK) domain 5 were inserted into GST (between Gly-49 and Leu-50). Peptides derived from HK are known to inhibit cell proliferation, angiogenesis, and tumor metastasis, and the biological activity of the HK peptides was dramatically (>50-fold) enhanced following insertion into GST. GSHKTs are soluble and easily purified from Escherichia coli by affinity chromatography. Functionally, these hybrid proteins cause inhibition of endothelial cell proliferation. Crystallographic analysis of GSHKT10 and GSHKT13 (harboring 10- and 13-residue HK peptides, respectively) showed that the overall GST structure was not perturbed. These results suggest that the therapeutic efficacy of short peptides can be enhanced by insertion into larger proteins that are easily expressed and purified and that GST may potentially be used as such a carrier.
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Affiliation(s)
- Amber A Bentley
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, Ohio 44115, USA
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