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Ong J, Zarnegar A, Selvam A, Driban M, Chhablani J. The Complement System as a Therapeutic Target in Retinal Disease. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:945. [PMID: 38929562 PMCID: PMC11205777 DOI: 10.3390/medicina60060945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024]
Abstract
The complement cascade is a vital system in the human body's defense against pathogens. During the natural aging process, it has been observed that this system is imperative for ensuring the integrity and homeostasis of the retina. While this system is critical for proper host defense and retinal integrity, it has also been found that dysregulation of this system may lead to certain retinal pathologies, including geographic atrophy and diabetic retinopathy. Targeting components of the complement system for retinal diseases has been an area of interest, and in vivo, ex vivo, and clinical trials have been conducted in this area. Following clinical trials, medications targeting the complement system for retinal disease have also become available. In this manuscript, we discuss the pathophysiology of complement dysfunction in the retina and specific pathologies. We then describe the results of cellular, animal, and clinical studies targeting the complement system for retinal diseases. We then provide an overview of complement inhibitors that have been approved by the Food and Drug Administration (FDA) for geographic atrophy. The complement system in retinal diseases continues to serve as an emerging therapeutic target, and further research in this field will provide additional insights into the mechanisms and considerations for treatment of retinal pathologies.
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Affiliation(s)
- Joshua Ong
- Department of Ophthalmology and Visual Sciences, University of Michigan Kellogg Eye Center, Ann Arbor, MI 48105, USA
| | - Arman Zarnegar
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Amrish Selvam
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Matthew Driban
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jay Chhablani
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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2
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Brito M, Sorbier C, Mignet N, Boudy V, Borchard G, Vacher G. Understanding the Impact of Polyunsaturated Fatty Acids on Age-Related Macular Degeneration: A Review. Int J Mol Sci 2024; 25:4099. [PMID: 38612907 PMCID: PMC11012607 DOI: 10.3390/ijms25074099] [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: 03/01/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Age-related Macular Degeneration (AMD) is a multifactorial ocular pathology that destroys the photoreceptors of the macula. Two forms are distinguished, dry and wet AMD, with different pathophysiological mechanisms. Although treatments were shown to be effective in wet AMD, they remain a heavy burden for patients and caregivers, resulting in a lack of patient compliance. For dry AMD, no real effective treatment is available in Europe. It is, therefore, essential to look for new approaches. Recently, the use of long-chain and very long-chain polyunsaturated fatty acids was identified as an interesting new therapeutic alternative. Indeed, the levels of these fatty acids, core components of photoreceptors, are significantly decreased in AMD patients. To better understand this pathology and to evaluate the efficacy of various molecules, in vitro and in vivo models reproducing the mechanisms of both types of AMD were developed. This article reviews the anatomy and the physiological aging of the retina and summarizes the clinical aspects, pathophysiological mechanisms of AMD and potential treatment strategies. In vitro and in vivo models of AMD are also presented. Finally, this manuscript focuses on the application of omega-3 fatty acids for the prevention and treatment of both types of AMD.
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Affiliation(s)
- Maëlis Brito
- Unither Développement Bordeaux, Avenue Toussaint Catros, 33185 Le Haillan, France
- Université Paris Cité, CNRS, INSERM, UTCBS, Unité de Technologies Chimiques et Biologiques pour la Santé, F-75006 Paris, France
- Département de Recherche et Développement (DRDP), Agence Générale des Equipements et Produits de Santé (AGEPS), Assistance Publique Hôpitaux de Paris (AP-HP), 7 Rue du Fer-à-Moulin, 75005 Paris, France
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, 1206 Geneva, Switzerland
| | - Capucine Sorbier
- Unither Développement Bordeaux, Avenue Toussaint Catros, 33185 Le Haillan, France
| | - Nathalie Mignet
- Université Paris Cité, CNRS, INSERM, UTCBS, Unité de Technologies Chimiques et Biologiques pour la Santé, F-75006 Paris, France
| | - Vincent Boudy
- Université Paris Cité, CNRS, INSERM, UTCBS, Unité de Technologies Chimiques et Biologiques pour la Santé, F-75006 Paris, France
- Département de Recherche et Développement (DRDP), Agence Générale des Equipements et Produits de Santé (AGEPS), Assistance Publique Hôpitaux de Paris (AP-HP), 7 Rue du Fer-à-Moulin, 75005 Paris, France
| | - Gerrit Borchard
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, 1206 Geneva, Switzerland
| | - Gaëlle Vacher
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, 1206 Geneva, Switzerland
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3
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Computational analysis of complement inhibitor compstatin using molecular dynamics. J Mol Model 2020; 26:231. [PMID: 32789582 PMCID: PMC8851517 DOI: 10.1007/s00894-020-04472-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/14/2020] [Indexed: 11/17/2022]
Abstract
The complement system plays a major role in human immunity, but its abnormal activation can have severe pathological impacts. By mimicking a natural mechanism of complement regulation, the small peptide compstatin has proven to be a very promising complement inhibitor. Over the years, several compstatin analogs have been created, with improved inhibitory potency. A recent analog is being developed as a candidate drug against several pathological conditions, including COVID-19. However, the reasons behind its higher potency and increased binding affinity to complement proteins are not fully clear. This computational study highlights the mechanistic properties of several compstatin analogs, thus complementing previous experimental studies. We perform molecular dynamics simulations involving six analogs alone in solution and two complexes with compstatin bound to complement component 3. These simulations reveal that all the analogs we consider, except the original compstatin, naturally adopt a pre-bound conformation in solution. Interestingly, this set of analogs adopting a pre-bound conformation includes analogs that were not known to benefit from this behavior. We also show that the most recent compstatin analog (among those we consider) forms a stronger hydrogen bond network with its complement receptor than an earlier analog.
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4
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Wu J, Sun X. Complement system and age-related macular degeneration: drugs and challenges. DRUG DESIGN DEVELOPMENT AND THERAPY 2019; 13:2413-2425. [PMID: 31409975 PMCID: PMC6650090 DOI: 10.2147/dddt.s206355] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/01/2019] [Indexed: 01/08/2023]
Abstract
Age-related macular degeneration (AMD) is directly attributable to vision loss, posing significant pressure on public health. AMD is recognized to be a multi-factorial disease and among them, complement system is under heated discussion in recent years. In this review, we start with an overview of complement pathways involved in AMD and their therapies correspondingly. Finally, we discuss the development of the therapeutics existed now. Also, we enclose a list of drugs undergoing clinical trials.
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Affiliation(s)
- Jiali Wu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Xiaodong Sun
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Fundus Disease, Shanghai, People's Republic of China.,Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, People's Republic of China
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5
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Bujko K, Rzeszotek S, Hoehlig K, Yan J, Vater A, Ratajczak MZ. Signaling of the Complement Cleavage Product Anaphylatoxin C5a Through C5aR (CD88) Contributes to Pharmacological Hematopoietic Stem Cell Mobilization. Stem Cell Rev Rep 2018; 13:793-800. [PMID: 28918528 PMCID: PMC5730632 DOI: 10.1007/s12015-017-9769-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Several mechanisms have been postulated for orchestrating the mobilization of hematopoietic stem/progenitor cells (HSPCs), and we previously proposed that activation of the complement cascade plays a crucial role in the initiation and execution of the egress of HSPCs from bone marrow (BM) into peripheral blood (PB). In support of this notion, we demonstrated that mice deficient in the mannan-binding lectin (MBL) pathway, which activates the proximal part of the complement cascade, as well as mice deficient in the fifth component of the complement cascade (C5), which is part of the distal part of the complement cascade, are poor mobilizers. To further narrow down on the exact mechanisms and the molecules involved, we performed studies in mice that do not express the receptor C5aR, which binds the C5 cleavage fragments, C5a and C5adesArg. We also employed the plasma stable nucleic acid aptamer AON-D21 that binds and neutralizes C5a and C5adesArg. We present evidence that mice deficient in C5aR or treated with AON-D21 are poor HSPC mobilizers, thereby establishing a critical role for the C5a/C5adesArg-C5aR axis in the mobilization process. While enhancing mobilization is of clinical importance for poor mobilizers, inhibition of the complement cascade could be of therapeutic importance in patients suffering from paroxysmal nocturnal hemoglobinuria (PNH) or acquired hemolytic syndrome (aHUS).
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Affiliation(s)
- Kamila Bujko
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, 500 S. Floyd Street, Rm. 107, Louisville, KY, 40202, USA
| | - Sylwia Rzeszotek
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, 500 S. Floyd Street, Rm. 107, Louisville, KY, 40202, USA
| | | | - Jun Yan
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, 500 S. Floyd Street, Rm. 107, Louisville, KY, 40202, USA
| | | | - Mariusz Z Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, 500 S. Floyd Street, Rm. 107, Louisville, KY, 40202, USA. .,Department of Regenerative Medicine, Warsaw Medical University, Warsaw, Poland.
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6
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Berger N, Alayi TD, Resuello RRG, Tuplano JV, Reis ES, Lambris JD. New Analogs of the Complement C3 Inhibitor Compstatin with Increased Solubility and Improved Pharmacokinetic Profile. J Med Chem 2018; 61:6153-6162. [PMID: 29920096 DOI: 10.1021/acs.jmedchem.8b00560] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Improper regulation of complement is associated with various pathologies, and the clinical demand for compounds that can regulate complement activation is therefore imperative. Cp40, an analog of the peptide compstatin, inhibits all complement pathways at the level of the central component C3. We have further developed Cp40, using either PEGylation at the N-terminus or insertion of charged amino acids at the C-terminus. The PEGylated analogs are highly soluble and retained their inhibitory activity, with C3b binding affinity dependent on the length of the PEG chain. The addition of two or three residues of lysine, in turn, not only improved the peptide's solubility but also increased the binding affinity for C3b while retaining its inhibitory potency. Three of the new derivatives showed improved pharmacokinetic profiles in vivo in non-human primates. Given their compelling solubility and pharmacokinetic profiles, these new Cp40 analogs should broaden the spectrum of administration routes, likely reducing dosing frequency during chronic treatment and potentially expanding their range of clinical application.
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Affiliation(s)
- Nadja Berger
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Tchilabalo Dilezitoko Alayi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Ranillo R G Resuello
- Simian Conservation Breeding and Research Center (SICONBREC) , Makati City 1231 , Philippines
| | - Joel V Tuplano
- Simian Conservation Breeding and Research Center (SICONBREC) , Makati City 1231 , Philippines
| | - Edimara S Reis
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - John D Lambris
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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7
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Mohan R, Wilson M, Gorham RD, Harrison RES, Morikis VA, Kieslich CA, Orr AA, Coley AV, Tamamis P, Morikis D. Virtual Screening of Chemical Compounds for Discovery of Complement C3 Ligands. ACS OMEGA 2018; 3:6427-6438. [PMID: 30221234 PMCID: PMC6130793 DOI: 10.1021/acsomega.8b00606] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
The complement system is our first line of defense against foreign pathogens, but when it is not properly regulated, complement is implicated in the pathology of several autoimmune and inflammatory disorders. Compstatin is a peptidic complement inhibitor that acts by blocking the cleavage of complement protein C3 to the proinflammatory fragment C3a and opsonin fragment C3b. In this study, we aim to identify druglike small-molecule complement inhibitors with physicochemical, geometric, and binding properties similar to those of compstatin. We employed two approaches using various high-throughput virtual screening methods, which incorporate molecular dynamics (MD) simulations, pharmacophore model design, energy calculations, and molecular docking and scoring. We have generated a library of 274 chemical compounds with computationally predicted binding affinities for the compstatin binding site of C3. We have tested subsets of these chemical compounds experimentally for complement inhibitory activity, using hemolytic assays, and for binding affinity, using microscale thermophoresis. As a result, although none of the compounds showed inhibitory activity, compound 29 was identified to exhibit weak competitive binding against a potent compstatin analogue, therefore validating our computational approaches. Additional docking and MD simulation studies suggest that compound 29 interacts with C3 residues, which have been shown to be important in binding of compstatin to the C3c fragment of C3. Compound 29 is amenable to physicochemical optimization to acquire inhibitory properties. Additionally, it is possible that some of the untested compounds will demonstrate binding and inhibition in future experimental studies.
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Affiliation(s)
- Rohith
R. Mohan
- Department
of Bioengineering, University of California,
Riverside, 900 University
Avenue, Riverside, California 92521, United States
| | - Mark Wilson
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, Texas 77843, United
States
| | - Ronald D. Gorham
- Department
of Bioengineering, University of California,
Riverside, 900 University
Avenue, Riverside, California 92521, United States
| | - Reed E. S. Harrison
- Department
of Bioengineering, University of California,
Riverside, 900 University
Avenue, Riverside, California 92521, United States
| | - Vasilios A. Morikis
- Department
of Bioengineering, University of California,
Riverside, 900 University
Avenue, Riverside, California 92521, United States
| | - Chris A. Kieslich
- Department
of Bioengineering, University of California,
Riverside, 900 University
Avenue, Riverside, California 92521, United States
| | - Asuka A. Orr
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, Texas 77843, United
States
| | - Alexis V. Coley
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, Texas 77843, United
States
| | - Phanourios Tamamis
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, Texas 77843, United
States
| | - Dimitrios Morikis
- Department
of Bioengineering, University of California,
Riverside, 900 University
Avenue, Riverside, California 92521, United States
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8
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Zewde N, Morikis D. A computational model for the evaluation of complement system regulation under homeostasis, disease, and drug intervention. PLoS One 2018; 13:e0198644. [PMID: 29874282 PMCID: PMC5991421 DOI: 10.1371/journal.pone.0198644] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/22/2018] [Indexed: 12/21/2022] Open
Abstract
The complement system is an intricate defense network that rapidly removes invading pathogens. Although many complement regulators are present to protect host cells under homeostasis, the impairment of Factor H (FH) regulatory mechanism has been associated with several autoimmune and inflammatory diseases. To understand the dynamics involved in the pivotal balance between activation and regulation, we have developed a comprehensive computational model of the alternative and classical pathways of the complement system. The model is composed of 290 ordinary differential equations with 142 kinetic parameters that describe the state of complement system under homeostasis and disorder through FH impairment. We have evaluated the state of the system by generating concentration-time profiles for the biomarkers C3, C3a-desArg, C5, C5a-desArg, Factor B (FB), Ba, Bb, and fC5b-9 that are influenced by complement dysregulation. We show that FH-mediated disorder induces substantial levels of complement activation compared to homeostasis, by generating reduced levels of C3 and FB, and to a lesser extent C5, and elevated levels of C3a-desArg, Ba, Bb, C5a-desArg, and fC5b-9. These trends are consistent with clinically observed biomarkers associated with complement-mediated diseases. Furthermore, we introduced therapy states by modeling known inhibitors of the complement system, a compstatin variant (C3 inhibitor) and eculizumab (C5 inhibitor). Compstatin demonstrates strong restorative effects for early-stage biomarkers, such as C3a-desArg, FB, Ba, and Bb, and milder restorative effects for late-stage biomarkers, such as C5a-desArg and fC5b-9, whereas eculizumab has strong restorative effects on late-stage biomarkers, and negligible effects on early-stage biomarkers. These results highlight the need for patient-tailored therapies that target early complement activation at the C3 level, or late-stage propagation of the terminal cascade at the C5 level, depending on the specific FH-mediated disease and the manifestations of a patient's genetic profile in complement regulatory function.
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Affiliation(s)
- Nehemiah Zewde
- Department of Bioengineering, University of California, Riverside, California, United States of America
| | - Dimitrios Morikis
- Department of Bioengineering, University of California, Riverside, California, United States of America
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9
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Abstract
Age-related macular degeneration (AMD) and related macular dystrophies (MDs) are a major cause of vision loss. However, the mechanisms underlying their progression remain ill-defined. This is partly due to the lack of disease models recapitulating the human pathology. Furthermore, in vivo studies have yielded limited understanding of the role of specific cell types in the eye vs. systemic influences (e.g., serum) on the disease pathology. Here, we use human induced pluripotent stem cell-retinal pigment epithelium (hiPSC-RPE) derived from patients with three dominant MDs, Sorsby's fundus dystrophy (SFD), Doyne honeycomb retinal dystrophy/malattia Leventinese (DHRD), and autosomal dominant radial drusen (ADRD), and demonstrate that dysfunction of RPE cells alone is sufficient for the initiation of sub-RPE lipoproteinaceous deposit (drusen) formation and extracellular matrix (ECM) alteration in these diseases. Consistent with clinical studies, sub-RPE basal deposits were present beneath both control (unaffected) and patient hiPSC-RPE cells. Importantly basal deposits in patient hiPSC-RPE cultures were more abundant and displayed a lipid- and protein-rich "drusen-like" composition. Furthermore, increased accumulation of COL4 was observed in ECM isolated from control vs. patient hiPSC-RPE cultures. Interestingly, RPE-specific up-regulation in the expression of several complement genes was also seen in patient hiPSC-RPE cultures of all three MDs (SFD, DHRD, and ADRD). Finally, although serum exposure was not necessary for drusen formation, COL4 accumulation in ECM, and complement pathway gene alteration, it impacted the composition of drusen-like deposits in patient hiPSC-RPE cultures. Together, the drusen model(s) of MDs described here provide fundamental insights into the unique biology of maculopathies affecting the RPE-ECM interface.
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10
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Yang P, Skiba NP, Tewkesbury GM, Treboschi VM, Baciu P, Jaffe GJ. Complement-Mediated Regulation of Apolipoprotein E in Cultured Human RPE Cells. Invest Ophthalmol Vis Sci 2017. [PMID: 28632844 PMCID: PMC5482245 DOI: 10.1167/iovs.16-20083] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Purpose. Complement activation is implicated in the pathogenesis of age-related macular degeneration (AMD). Apolipoprotein E (ApoE) and complement activation products such as membrane attack complex (MAC) are present in eyes of individuals with AMD. Herein, we investigated the effect of complement activation on induction of ApoE accumulation in human retinal pigment epithelial (RPE) cells. Methods. Cultured human RPE cells were primed with a complement-fixing antibody followed by treatment with C1q-depleted (C1q-Dep) human serum to elicit alternative pathway complement activation. Controls included anti-C5 antibody-treated serum and heat-inactivated C1q-Dep. Total protein was determined on RPE cell extracts, conditioned media, and extracellular matrix (ECM) by Western blot. ApoE and MAC colocalization was assessed on cultured RPE cells and human eyes by immunofluorescent stain. ApoE mRNA expression was evaluated by quantitative PCR (qPCR). Results. Complement challenge upregulated cell-associated ApoE, but not apolipoprotein A1. ApoE accumulation was blocked by anti-C5 antibody and enhanced by repetitive complement challenge. ApoE mRNA levels were not affected by complement challenge. ApoE was frequently colocalized with MAC in complement-treated cells and drusen from human eyes. ApoE was released into complement-treated conditioned media after a single complement challenge and accumulated on ECM after repetitive complement challenge. Conclusions. Complement challenge induces time-dependent ApoE accumulation in RPE cells. An understanding of the mechanisms by which complement affects RPE ApoE accumulation may help to better explain drusen composition, and provide insights into potential therapeutic targets.
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Affiliation(s)
- Ping Yang
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Nikolai P Skiba
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Grace M Tewkesbury
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Victoria M Treboschi
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Peter Baciu
- Department of Biology, Allergan, Inc., Irvine, California, United States
| | - Glenn J Jaffe
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
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11
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Orr AA, Wördehoff MM, Hoyer W, Tamamis P. Uncovering the Binding and Specificity of β-Wrapins for Amyloid-β and α-Synuclein. J Phys Chem B 2016; 120:12781-12794. [DOI: 10.1021/acs.jpcb.6b08485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Michael M. Wördehoff
- Institut
für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institut
für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
- Institute
of Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
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12
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Mohan RR, Cabrera AP, Harrison RES, Gorham RD, Johnson LV, Ghosh K, Morikis D. Peptide redesign for inhibition of the complement system: Targeting age-related macular degeneration. Mol Vis 2016; 22:1280-1290. [PMID: 27829783 PMCID: PMC5082644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 10/24/2016] [Indexed: 11/30/2022] Open
Abstract
PURPOSE To redesign a complement-inhibiting peptide with the potential to become a therapeutic for dry and wet age-related macular degeneration (AMD). METHODS We present a new potent peptide (Peptide 2) of the compstatin family. The peptide is developed by rational design, based on a mechanistic binding hypothesis, and structural and physicochemical properties derived from molecular dynamics (MD) simulation. The inhibitory activity, efficacy, and solubility of Peptide 2 are evaluated using a hemolytic assay, a human RPE cell-based assay, and ultraviolet (UV) absorption properties, respectively, and compared to the respective properties of its parent peptide (Peptide 1). RESULTS The sequence of Peptide 2 contains an arginine-serine N-terminal extension (a characteristic of parent Peptide 1) and a novel 8-polyethylene glycol (PEG) block C-terminal extension. Peptide 2 has significantly improved aqueous solubility compared to Peptide 1 and comparable complement inhibitory activity. In addition, Peptide 2 is more efficacious in inhibiting complement activation in a cell-based model that mimics the pathobiology of dry AMD. CONCLUSIONS We have designed a new peptide analog of compstatin that combines N-terminal polar amino acid extensions and C-terminal PEGylation extensions. This peptide demonstrates significantly improved aqueous solubility and complement inhibitory efficacy, compared to the parent peptide. The new peptide overcomes the aggregation limitation for clinical translation of previous compstatin analogs and is a candidate to become a therapeutic for the treatment of AMD.
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Affiliation(s)
- Rohith R. Mohan
- Department of Bioengineering, University of California, Riverside, CA
| | - Andrea P. Cabrera
- Department of Bioengineering, University of California, Riverside, CA
| | | | - Ronald D. Gorham
- Department of Bioengineering, University of California, Riverside, CA
| | - Lincoln V. Johnson
- Center for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, CA
| | - Kaustabh Ghosh
- Department of Bioengineering, University of California, Riverside, CA
| | - Dimitrios Morikis
- Department of Bioengineering, University of California, Riverside, CA
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13
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Xu H, Chen M. Targeting the complement system for the management of retinal inflammatory and degenerative diseases. Eur J Pharmacol 2016; 787:94-104. [PMID: 26948311 PMCID: PMC5026403 DOI: 10.1016/j.ejphar.2016.03.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/12/2016] [Accepted: 03/01/2016] [Indexed: 12/20/2022]
Abstract
The retina, an immune privileged tissue, has specialized immune defense mechanisms against noxious insults that may exist in diseases such as age-related macular degeneration (AMD), diabetic retinopathy (DR), uveoretinitis and glaucoma. The defense system consists of retinal innate immune cells (including microglia, perivascular macrophages, and a small population of dendritic cells) and the complement system. Under normal aging conditions, retinal innate immune cells and the complement system undergo a low-grade activation (parainflammation) which is important for retinal homeostasis. In disease states such as AMD and DR, the parainflammatory response is dysregulated and develops into detrimental chronic inflammation. Complement activation in the retina is an important part of chronic inflammation and may contribute to retinal pathology in these disease states. Here, we review the evidence that supports the role of uncontrolled or dysregulated complement activation in various retinal degenerative and angiogenic conditions. We also discuss current strategies that are used to develop complement-based therapies for retinal diseases such as AMD. The potential benefits of complement inhibition in DR, uveoretinitis and glaucoma are also discussed, as well as the need for further research to better understand the mechanisms of complement-mediated retinal damage in these disease states.
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Affiliation(s)
- Heping Xu
- Centre for Experimental Medicine, School of Medicine, Dentistry & Biomedical Sciences, Queen's University Belfast, UK.
| | - Mei Chen
- Centre for Experimental Medicine, School of Medicine, Dentistry & Biomedical Sciences, Queen's University Belfast, UK.
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14
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Forest DL, Johnson LV, Clegg DO. Cellular models and therapies for age-related macular degeneration. Dis Model Mech 2016; 8:421-7. [PMID: 26035859 PMCID: PMC4415892 DOI: 10.1242/dmm.017236] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Age-related macular degeneration (AMD) is a complex neurodegenerative visual disorder that causes profound physical and psychosocial effects. Visual impairment in AMD is caused by the loss of retinal pigmented epithelium (RPE) cells and the light-sensitive photoreceptor cells that they support. There is currently no effective treatment for the most common form of this disease (dry AMD). A new approach to treating AMD involves the transplantation of RPE cells derived from either human embryonic or induced pluripotent stem cells. Multiple clinical trials are being initiated using a variety of cell therapies. Although many animal models are available for AMD research, most do not recapitulate all aspects of the disease, hampering progress. However, the use of cultured RPE cells in AMD research is well established and, indeed, some of the more recently described RPE-based models show promise for investigating the molecular mechanisms of AMD and for screening drug candidates. Here, we discuss innovative cell-culture models of AMD and emerging stem-cell-based therapies for the treatment of this vision-robbing disease. Summary: Here, we discuss the emerging cell-culture models and potential stem-cell-based therapies for AMD, a blinding disorder that affects millions of people worldwide.
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Affiliation(s)
- David L Forest
- Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Lincoln V Johnson
- Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Dennis O Clegg
- Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9625, USA
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15
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Polydorides S, Michael E, Mignon D, Druart K, Archontis G, Simonson T. Proteus and the Design of Ligand Binding Sites. Methods Mol Biol 2016; 1414:77-97. [PMID: 27094287 DOI: 10.1007/978-1-4939-3569-7_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This chapter describes the organization and use of Proteus, a multitool computational suite for the optimization of protein and ligand conformations and sequences, and the calculation of pK α shifts and relative binding affinities. The software offers the use of several molecular mechanics force fields and solvent models, including two generalized Born variants, and a large range of scoring functions, which can combine protein stability, ligand affinity, and ligand specificity terms, for positive and negative design. We present in detail the steps for structure preparation, system setup, construction of the interaction energy matrix, protein sequence and structure optimizations, pK α calculations, and ligand titration calculations. We discuss illustrative examples, including the chemical/structural optimization of a complex between the MHC class II protein HLA-DQ8 and the vinculin epitope, and the chemical optimization of the compstatin analog Ac-Val4Trp/His9Ala, which regulates the function of protein C3 of the complement system.
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Affiliation(s)
- Savvas Polydorides
- Theoretical and Computational Biophysics Group, Department of Physics, University of Cyprus, 1678, Nicosia, Cyprus
| | - Eleni Michael
- Theoretical and Computational Biophysics Group, Department of Physics, University of Cyprus, 1678, Nicosia, Cyprus
| | - David Mignon
- Department of Biology, Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, 91128, Palaiseau, France
| | - Karen Druart
- Department of Biology, Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, 91128, Palaiseau, France
| | - Georgios Archontis
- Theoretical and Computational Biophysics Group, Department of Physics, University of Cyprus, 1678, Nicosia, Cyprus.
| | - Thomas Simonson
- Department of Biology, Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, 91128, Palaiseau, France.
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16
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Gorham R, Forest DL, Khoury GA, Smadbeck J, Beecher CN, Healy ED, Tamamis P, Archontis G, Larive C, Floudas CA, Radeke MJ, Johnson LV, Morikis D. New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics. J Med Chem 2015; 58:814-26. [PMID: 25494040 PMCID: PMC4306506 DOI: 10.1021/jm501345y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Indexed: 01/21/2023]
Abstract
Compstatin peptides are complement inhibitors that bind and inhibit cleavage of complement C3. Peptide binding is enhanced by hydrophobic interactions; however, poor solubility promotes aggregation in aqueous environments. We have designed new compstatin peptides derived from the W4A9 sequence (Ac-ICVWQDWGAHRCT-NH2, cyclized between C2 and C12), based on structural, computational, and experimental studies. Furthermore, we developed and utilized a computational framework for the design of peptides containing non-natural amino acids. These new compstatin peptides contain polar N-terminal extensions and non-natural amino acid substitutions at positions 4 and 9. Peptides with α-modified non-natural alanine analogs at position 9, as well as peptides containing only N-terminal polar extensions, exhibited similar activity compared to W4A9, as quantified via ELISA, hemolytic, and cell-based assays, and showed improved solubility, as measured by UV absorbance and reverse-phase HPLC experiments. Because of their potency and solubility, these peptides are promising candidates for therapeutic development in numerous complement-mediated diseases.
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Affiliation(s)
- Ronald
D. Gorham
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
| | - David L. Forest
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - George A. Khoury
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - James Smadbeck
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Consuelo N. Beecher
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Evangeline D. Healy
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - Phanourios Tamamis
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus
| | - Georgios Archontis
- Department
of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus
| | - Cynthia
K. Larive
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Christodoulos A. Floudas
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Monte J. Radeke
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - Lincoln V. Johnson
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - Dimitrios Morikis
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
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17
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Khoury GA, Smadbeck J, Tamamis P, Vandris AC, Kieslich CA, Floudas CA. Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family. ACS Synth Biol 2014; 3:855-69. [PMID: 24932669 PMCID: PMC4277759 DOI: 10.1021/sb400168u] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We describe the development and testing of ab initio derived, AMBER ff03 compatible charge parameters for a large library of 147 noncanonical amino acids including β- and N-methylated amino acids for use in applications such as protein structure prediction and de novo protein design. The charge parameter derivation was performed using the RESP fitting approach. Studies were performed assessing the suitability of the derived charge parameters in discriminating the activity/inactivity between 63 analogs of the complement inhibitor Compstatin on the basis of previously published experimental IC50 data and a screening procedure involving short simulations and binding free energy calculations. We found that both the approximate binding affinity (K*) and the binding free energy calculated through MM-GBSA are capable of discriminating between active and inactive Compstatin analogs, with MM-GBSA performing significantly better. Key interactions between the most potent Compstatin analog that contains a noncanonical amino acid are presented and compared to the most potent analog containing only natural amino acids and native Compstatin. We make the derived parameters and an associated web interface that is capable of performing modifications on proteins using Forcefield_NCAA and outputting AMBER-ready topology and parameter files freely available for academic use at http://selene.princeton.edu/FFNCAA . The forcefield allows one to incorporate these customized amino acids into design applications with control over size, van der Waals, and electrostatic interactions.
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Affiliation(s)
- George A. Khoury
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - James Smadbeck
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Phanourios Tamamis
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Andrew C. Vandris
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Chris A. Kieslich
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Christodoulos A. Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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18
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Exploring the potential benefits of vaccinia virus complement control protein in controlling complement activation in pathogenesis of the central nervous system diseases. Mol Immunol 2014; 61:204-9. [PMID: 25052409 DOI: 10.1016/j.molimm.2014.06.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/08/2014] [Accepted: 06/11/2014] [Indexed: 02/03/2023]
Abstract
Aging is a major risk factor for the development of diseases related to the central nervous system (CNS), such as Alzheimer's disease (AD) and age-related macular degeneration (AMD). In both cases, linkage studies and genome-wide association studies found strong links with complement regulatory genes and disease risk. In AD, both CLU and CR1 genes were implicated in the late-onset form of the disease. In AMD, polymorphisms in CFH, CFB and C2 were similarly implicated. The cost of caring for patients with AD or AMD is approaching billions of dollars, and with the baby boomers reaching their 60's, this amount is likely to increase further. Intervention using complement inhibitors for individuals in their early 50s who are at a higher risk of disease development, (testing positive for genetic risk factors), could slow the progression of AD or AMD and possibly prevent the severity of late stage symptoms. Although we have used the vaccinia virus complement control protein (VCP) to elucidate the role of complement in CNS diseases, it has merely been an investigational tool but not the only possible potential therapeutic agent.
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19
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Elucidating a key anti-HIV-1 and cancer-associated axis: the structure of CCL5 (Rantes) in complex with CCR5. Sci Rep 2014; 4:5447. [PMID: 24965094 PMCID: PMC4894430 DOI: 10.1038/srep05447] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/05/2014] [Indexed: 01/01/2023] Open
Abstract
CCL5 (RANTES) is an inflammatory chemokine which binds to chemokine receptor CCR5 and induces signaling. The CCL5:CCR5 associated chemotactic signaling is of critical biological importance and is a potential HIV-1 therapeutic axis. Several studies provided growing evidence for the expression of CCL5 and CCR5 in non-hematological malignancies. Therefore, the delineation of the CCL5:CCR5 complex structure can pave the way for novel CCR5-targeted drugs. We employed a computational protocol which is primarily based on free energy calculations and molecular dynamics simulations, and report, what is to our knowledge, the first computationally derived CCL5:CCR5 complex structure which is in excellent agreement with experimental findings and clarifies the functional role of CCL5 and CCR5 residues which are associated with binding and signaling. A wealth of polar and non-polar interactions contributes to the tight CCL5:CCR5 binding. The structure of an HIV-1 gp120 V3 loop in complex with CCR5 has recently been derived through a similar computational protocol. A comparison between the CCL5 : CCR5 and the HIV-1 gp120 V3 loop : CCR5 complex structures depicts that both the chemokine and the virus primarily interact with the same CCR5 residues. The present work provides insights into the blocking mechanism of HIV-1 by CCL5.
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20
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Tamamis P, Floudas CA. Molecular recognition of CCR5 by an HIV-1 gp120 V3 loop. PLoS One 2014; 9:e95767. [PMID: 24763408 PMCID: PMC3999033 DOI: 10.1371/journal.pone.0095767] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/29/2014] [Indexed: 12/04/2022] Open
Abstract
The binding of protein HIV-1 gp120 to coreceptors CCR5 or CXCR4 is a key step of the HIV-1 entry to the host cell, and is predominantly mediated through the V3 loop fragment of HIV-1 gp120. In the present work, we delineate the molecular recognition of chemokine receptor CCR5 by a dual tropic HIV-1 gp120 V3 loop, using a comprehensive set of computational tools predominantly based on molecular dynamics simulations and free energy calculations. We report, what is to our knowledge, the first complete HIV-1 gp120 V3 loop : CCR5 complex structure, which includes the whole V3 loop and the N-terminus of CCR5, and exhibits exceptional agreement with previous experimental findings. The computationally derived structure sheds light into the functional role of HIV-1 gp120 V3 loop and CCR5 residues associated with the HIV-1 coreceptor activity, and provides insights into the HIV-1 coreceptor selectivity and the blocking mechanism of HIV-1 gp120 by maraviroc. By comparing the binding of the specific dual tropic HIV-1 gp120 V3 loop with CCR5 and CXCR4, we observe that the HIV-1 gp120 V3 loop residues 13-21, which include the tip, share nearly identical structural and energetic properties in complex with both coreceptors. This result paves the way for the design of dual CCR5/CXCR4 targeted peptides as novel potential anti-AIDS therapeutics.
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Affiliation(s)
- Phanourios Tamamis
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Christodoulos A. Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
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21
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Tamamis P, Floudas CA. Elucidating a key component of cancer metastasis: CXCL12 (SDF-1α) binding to CXCR4. J Chem Inf Model 2014; 54:1174-88. [PMID: 24660779 PMCID: PMC4004218 DOI: 10.1021/ci500069y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The chemotactic signaling induced
by the binding of chemokine CXCL12
(SDF-1α) to chemokine receptor CXCR4 is of significant biological
importance and is a potential therapeutic axis against HIV-1. However,
as CXCR4 is overexpressed in certain cancer cells, the CXCL12:CXCR4
signaling is involved in tumor metastasis, progression, angiogenesis,
and survival. Motivated by the pivotal role of the CXCL12:CXCR4 axis
in cancer, we employed a comprehensive set of computational tools,
predominantly based on free energy calculations and molecular dynamics
simulations, to obtain insights into the molecular recognition of
CXCR4 by CXCL12. We report, what is to our knowledge, the first computationally
derived CXCL12:CXCR4 complex structure which is in remarkable agreement
with experimental findings and sheds light into the functional role
of CXCL12 and CXCR4 residues which are associated with binding and
signaling. Our results reveal that the CXCL12 N-terminal domain is
firmly bound within the CXCR4 transmembrane domain, and the central
24–50 residue domain of CXCL12 interacts with the upper N-terminal
domain of CXCR4. The stability of the CXCL12:CXCR4 complex structure
is attributed to an abundance of nonpolar and polar intermolecular
interactions, including salt bridges formed between positively charged
CXCL12 residues and negatively charged CXCR4 residues. The success
of the computational protocol can mainly be attributed to the nearly
exhaustive docking conformational search, as well as the heterogeneous
dielectric implicit water-membrane-water model used to simulate and
select the optimum conformations. We also recently utilized this protocol
to elucidate the binding of an HIV-1 gp120 V3 loop in complex with
CXCR4, and a comparison between the molecular recognition of CXCR4
by CXCL12 and the HIV-1 gp120 V3 loop shows that both CXCL12 and the
HIV-1 gp120 V3 loop share the same CXCR4 binding pocket, as they mostly
interact with the same CXCR4 residues.
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Affiliation(s)
- Phanourios Tamamis
- Department of Chemical and Biological Engineering, Princeton University , New Jersey 08544, United States
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22
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Khoury GA, Smadbeck J, Kieslich CA, Floudas CA. Protein folding and de novo protein design for biotechnological applications. Trends Biotechnol 2013; 32:99-109. [PMID: 24268901 DOI: 10.1016/j.tibtech.2013.10.008] [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] [Received: 09/05/2013] [Revised: 10/10/2013] [Accepted: 10/18/2013] [Indexed: 11/19/2022]
Abstract
In the postgenomic era, the medical/biological fields are advancing faster than ever. However, before the power of full-genome sequencing can be fully realized, the connection between amino acid sequence and protein structure, known as the protein folding problem, needs to be elucidated. The protein folding problem remains elusive, with significant difficulties still arising when modeling amino acid sequences lacking an identifiable template. Understanding protein folding will allow for unforeseen advances in protein design; often referred to as the inverse protein folding problem. Despite challenges in protein folding, de novo protein design has recently demonstrated significant success via computational techniques. We review advances and challenges in protein structure prediction and de novo protein design, and highlight their interplay in successful biotechnological applications.
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Affiliation(s)
- George A Khoury
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - James Smadbeck
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Chris A Kieslich
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Christodoulos A Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
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