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Maity T, Balachandran AK, Krishnamurthy LP, Nagar KL, Upadhyayula RS, Sengupta S, Maiti PK. Data-Driven Approaches to Predict Dendrimer Cytotoxicity. ACS OMEGA 2024; 9:24899-24906. [PMID: 38882163 PMCID: PMC11173563 DOI: 10.1021/acsomega.4c01775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024]
Abstract
Dendrimers are employed as functional elements in contrast agents and are proposed as nontoxic vehicles for drug delivery. Toxicity is a property that is to be evaluated for this novel class of bionanomaterials for in vivo applications. The current research is hampered due to the lack of structured data sets for toxicity studies for dendrimers. In this work, we have built a data set by curating literature for toxicity data and augmented it with structural and physicochemical features. We present a comprehensive, feature-rich database of dendrimer toxicity measured across various cell lines for prediction, design, and optimization studies. We have also explored novel computational approaches for predicting dendrimer cytotoxicity. We demonstrate superior outcomes for toxicity prediction using essential regression in the space of small data sets.
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Affiliation(s)
- Tarun Maity
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru 560012, India
| | - Anandu K Balachandran
- Accenture Labs, Technology & Innovation, Ecospace, Bellandur, Bengaluru 560087, India
| | | | - Karthik L Nagar
- Accenture Labs, Technology & Innovation, Ecospace, Bellandur, Bengaluru 560087, India
| | | | - Shubhashis Sengupta
- Accenture Labs, Technology & Innovation, Ecospace, Bellandur, Bengaluru 560087, India
| | - Prabal K Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru 560012, India
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2
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Rajendra D, Maroli N, Dixit NM, Maiti PK. Molecular dynamics simulations show how antibodies may rescue HIV-1 mutants incapable of infecting host cells. J Biomol Struct Dyn 2023:1-11. [PMID: 38111161 DOI: 10.1080/07391102.2023.2294835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/01/2023] [Indexed: 12/20/2023]
Abstract
High mutation and replication rates of HIV-1 result in the continuous generation of variants, allowing it to adapt to changing host environments. Mutations often have deleterious effects, but variants carrying them are rapidly purged. Surprisingly, a particular variant incapable of entering host cells was found to be rescued by host antibodies targeting HIV-1. Understanding the molecular mechanism of this rescue is important to develop and improve antibody-based therapies. To unravel the underlying mechanisms, we performed fully atomistic molecular dynamics simulations of the HIV-1 gp41 trimer responsible for viral entry into host cells, its entry-deficient variant, and its complex with the rescuing antibody. We find that the Q563R mutation, which the entry-deficient variant carries, prevents the native conformation of the gp41 6-helix bundle required for entry and stabilizes an alternative conformation instead. This is the consequence of substantial changes in the secondary structure and interactions between the domains of gp41. Binding of the antibody F240 to gp41 reverses these changes and re-establishes the native conformation, resulting in rescue. To test the generality of this mechanism, we performed simulations with the entry-deficient L565A variant and antibody 3D6. We find that 3D6 binding was able to reverse structural and interaction changes introduced by the mutation and restore the native gp41 conformation. Viral variants may not only escape antibodies but be aided by them in their survival, potentially compromising antibody-based therapies, including vaccination and passive immunization. Our simulation framework could serve as a tool to assess the likelihood of such resistance against specific antibodies.Communicated by Ramaswamy H. SarmaCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dharanish Rajendra
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, India
| | - Nikhil Maroli
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, India
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
- Department of Bioengineering, Indian Institute of Science, Bengaluru, India
| | - Prabal K Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, India
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3
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Duan H, Hu K, Zheng D, Cheng Y, Zhang Z, Wang Y, Liang L, Hu J, Luo T. Recognition and release of uridine and hCNT3: From multivariate interactions to molecular design. Int J Biol Macromol 2022; 223:1562-1577. [PMID: 36402394 DOI: 10.1016/j.ijbiomac.2022.11.145] [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: 09/29/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
As a vital target for the development of novel anti-cancer drugs, human concentrative nucleoside transporter 3 (hCNT3) has been widely concerned. Nevertheless, the lack of a comprehensive understanding of molecular interactions and motion mechanism has greatly hindered the development of novel inhibitors against hCNT3. In this paper, molecular recognition of hCNT3 with uridine was investigated with molecular docking, conventional molecular dynamics (CMD) simulations and adaptive steered molecular dynamics (ASMD) simulations; and then, the uridine derivatives with possibly highly inhibitory activity were designed. The result of CMD showed that more water-mediated H-bonds and lower binding free energy both explained higher recognition ability and transported efficiency of hCNT3. While during the ASMD simulation, nucleoside transport process involved the significant side-chain flip of residues F321 and Q142, a typical substrate-induced conformational change. By considering electronegativity, atomic radius, functional group and key H-bonds factors, 25 novel uridine derivatives were constructed. Subsequently, the receptor-ligand binding free energy was predicted by solvated interaction energy (SIE) method to determine the inhibitor c8 with the best potential performance. This work not only revealed molecular recognition and release mechanism of uridine with hCNT3, but also designed a series of uridine derivatives to obtain lead compounds with potential high activity.
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Affiliation(s)
- Huaichuan Duan
- Department of Head, Neck and Mammary Gland Oncology, Cancer Center, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Kaixuan Hu
- School of Pharmaceutical Sciences, Jishou University, Jishou, China
| | - Dan Zheng
- Department of Head, Neck and Mammary Gland Oncology, Cancer Center, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Cheng
- Department of Head, Neck and Mammary Gland Oncology, Cancer Center, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Zelan Zhang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Yueteng Wang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Ting Luo
- Department of Head, Neck and Mammary Gland Oncology, Cancer Center, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China.
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4
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Rae JM, Jachimska B. Analysis of dendrimer-protein interactions and their implications on potential applications of dendrimers in nanomedicine. NANOSCALE 2021; 13:2703-2713. [PMID: 33496716 DOI: 10.1039/d0nr07607d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
This work addresses how G5.5 PAMAM dendrimers form complexes with bovine serum albumin (BSA). Analytical techniques, such as UV-vis spectrophotometry, dynamic light scattering, electrophoretic mobility, quartz crystal microbalance with dissipation monitoring (QCM-D), circular dichroism (CD), and contact angle were used to analyze the properties of the dendrimers systems. The binding of protein to dendrimers can alter the structure, mobility, conformation and functional activity of the dendrimer. The results show that BSA interactions with G5.5 dendrimer carriers are driven both by electrostatic and hydrophobic forces. Dendrimer surface charge is reduced upon contact with the protein. The protein shell formed on the surface of the carrier is very stable as evidenced by the QCM-D measurements. On the other hand, the CD spectra indicates a change in the secondary structure of the protein. The size of the changes is significantly dependent on the ratio of protein to dendrimer. Understanding the mechanism of interaction of potential carriers with proteins is important for their internalization into the cell.
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Affiliation(s)
- James Magnus Rae
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK
| | - Barbara Jachimska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
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5
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Desikan R, Antia R, Dixit NM. Physical 'strength' of the multi-protein chain connecting immune cells: Does the weakest link limit antibody affinity maturation?: The weakest link in the multi-protein chain facilitating antigen acquisition by B cells in germinal centres limits antibody affinity maturation. Bioessays 2021; 43:e2000159. [PMID: 33448042 DOI: 10.1002/bies.202000159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 12/19/2022]
Abstract
The affinities of antibodies (Abs) for their target antigens (Ags) gradually increase in vivo following an infection or vaccination, but reach saturation at values well below those realisable in vitro. This 'affinity ceiling' could in many cases restrict our ability to fight infections and compromise vaccines. What determines the affinity ceiling has been an unresolved question for decades. Here, we argue that it arises from the strength of the chain of protein complexes that is pulled by B cells during the process of Ag acquisition. The affinity ceiling is determined by the strength of the weakest link in the chain. We identify the weakest link and show that the resulting affinity ceiling can explain the Ab affinities realized in vivo, providing a conceptual understanding of Ab affinity maturation. We explore plausible evolutionary underpinnings of the affinity ceiling, examine supporting evidence and alternative hypotheses and discuss implications for vaccination strategies.
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Affiliation(s)
- Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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6
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Gorai B, Sahoo AK, Srivastava A, Dixit NM, Maiti PK. Concerted Interactions between Multiple gp41 Trimers and the Target Cell Lipidome May Be Required for HIV-1 Entry. J Chem Inf Model 2020; 61:444-454. [PMID: 33373521 DOI: 10.1021/acs.jcim.0c01291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The HIV-1 envelope glycoprotein gp41 mediates the fusion between viral and host cell membranes leading to virus entry and target cell infection. Despite years of research, important aspects of this process such as the number of gp41 trimers involved and how they orchestrate the rearrangement of the lipids in the apposed membranes along the fusion pathway remain obscure. To elucidate these molecular underpinnings, we performed coarse-grained molecular dynamics simulations of HIV-1 virions pinned to the CD4 T cell membrane by different numbers of gp41 trimers. We built realistic cell and viral membranes by mimicking their respective lipid compositions. We found that a single gp41 was inadequate for mediating fusion. Lipid mixing between membranes, indicating the onset of fusion, was efficient when three or more gp41 trimers pinned the membranes. The gp41 trimers interacted strongly with many different lipids in the host cell membrane, triggering lipid configurational rearrangements, exchange, and mixing. Simpler membranes, comprising fewer lipid types, displayed strong resistance to fusion, revealing the crucial role of the lipidomes in HIV-1 entry. Performing simulations at different temperatures, we estimated the free energy barrier to lipid mixing, and hence membrane stalk formation, with three and four tethering gp41 trimers to be ∼6.2 kcal/mol, a >4-fold reduction over estimates without gp41. Together, these findings present molecular-level, quantitative insights into the early stages of gp41-mediated HIV-1 entry. Preventing the requisite gp41 molecules from tethering the membranes or altering membrane lipid compositions may be potential intervention strategies.
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Affiliation(s)
- Biswajit Gorai
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore-560012, India
| | - Anil Kumar Sahoo
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore-560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Biological Sciences Division, Indian Institute of Science, Bangalore-560012, India
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore-560012, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore-560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore-560012, India
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7
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Relaño-Rodríguez I, Muñoz-Fernández MÁ. Emergence of Nanotechnology to Fight HIV Sexual Transmission: The Trip of G2-S16 Polyanionic Carbosilane Dendrimer to Possible Pre-Clinical Trials. Int J Mol Sci 2020; 21:ijms21249403. [PMID: 33321835 PMCID: PMC7764023 DOI: 10.3390/ijms21249403] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
Development of new, safe, and effective microbicides to prevent human immunodeficiency virus HIV sexual transmission is needed. Unfortunately, most microbicides proved ineffective to prevent the risk of HIV-infection in clinical trials. We are working with G2-S16 polyanionic carbosilane dendrimer (PCD) as a new possible vaginal topical microbicide, based on its short reaction times, wide availability, high reproducibility, and quantitative yields of reaction. G2-S16 PCD exerts anti-HIV activity at an early stage of viral replication, by blocking gp120/CD4/CCR5 interaction, and providing a barrier against infection for long periods of time. G2-S16 PCD was stable at different pH values, as well as in the presence of seminal fluids. It maintained the anti-HIV activity against R5/X4 HIV over time, did not generate any type of drug resistance, and retained the anti-HIV effect when exposed to semen-enhanced viral infection. Importantly, G2-S16 PCD did not modify vaginal microbiota neither in vitro or in vivo. Histopathological examination did not show vaginal irritation, inflammation, lesions, or damage in the vaginal mucosa, after administration of G2-S16 PCD at different concentrations and times in female mice and rabbit animal models. Based on these promising data, G2-S16 PCD could become a good, safe, and readily available candidate to use as a topical vaginal microbicide against HIV.
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Affiliation(s)
- Ignacio Relaño-Rodríguez
- Head Section of Immunology, Molecular Immunology Laboratory, General Universitary Hospital Gregorio Marañón, C/Dr. Esquerdo 46, 28007 Madrid, Spain;
| | - Maria Ángeles Muñoz-Fernández
- Head Section of Immunology, Molecular Immunology Laboratory, General Universitary Hospital Gregorio Marañón, C/Dr. Esquerdo 46, 28007 Madrid, Spain;
- Health Research Institute Gregorio Marañon (IiSGM), C/Dr. Esquerdo 46, 28007 Madrid, Spain
- Spanish HIV HGM BioBank, C/Dr. Esquerdo 46, 28007 Madrid, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), C/Dr. Esquerdo 46, 28007 Madrid, Spain
- Correspondence: or ; Tel.: +34-91-586-8565
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8
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Akilesh M S, Wadhwani A. Novel Applications of Nanotechnology in Controlling HIV and HSV Infections. Curr Drug Res Rev 2020; 13:120-129. [PMID: 33238862 DOI: 10.2174/2589977512999201124121931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 11/22/2022]
Abstract
Infectious diseases have been prevalent since many decades and viral pathogens have caused global health crisis and economic meltdown on a devastating scale. High occurrence of newer viral infections in the recent years, in spite of the progress achieved in the field of pharmaceutical sciences defines the critical need for newer and more effective antiviral therapies and diagnostics. The incidence of multi-drug resistance and adverse effects due to the prolonged use of anti-viral therapy is also a major concern. Nanotechnology offers a cutting edge platform for the development of novel compounds and formulations for biomedical applications. The unique properties of nano-based materials can be attributed to the multi-fold increase in the surface to volume ratio at the nano-scale, tunable surface properties of charge and chemical moieties. Idealistic pharmaceutical properties such as increased bioavailability and retention times, lower toxicity profiles, sustained release formulations, lower dosage forms and most importantly, targeted drug delivery can be achieved through the approach of nanotechnology. The extensively researched nano-based materials are metal and polymeric nanoparticles, dendrimers and micelles, nano-drug delivery vesicles, liposomes and lipid based nanoparticles. In this review article, the impact of nanotechnology on the treatment of Human Immunodeficiency Virus (HIV) and Herpes Simplex Virus (HSV) viral infections during the last decade are outlined.
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Affiliation(s)
- Sai Akilesh M
- Department of Pharmaceutical Biotechnology, JSS Academy of Higher Education & Research - JSS College of Pharmacy, Ooty - 643001, The Nilgiris, Tamil Nadu. India
| | - Ashish Wadhwani
- Department of Pharmaceutical Biotechnology, JSS Academy of Higher Education & Research - JSS College of Pharmacy, Ooty - 643001, The Nilgiris, Tamil Nadu. India
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9
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Saurabh S, Sivakumar PM, Perumal V, Khosravi A, Sugumaran A, Prabhawathi V. Molecular Dynamics Simulations in Drug Discovery and Drug Delivery. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/978-3-030-36260-7_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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10
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Ledger S, Howe A, Turville S, Aggarwal A, Savkovic B, Ong A, Wolstein O, Boyd M, Millington M, Gorry PR, Murray JM, Symonds G. Analysis and dissociation of anti-HIV effects of shRNA to CCR5 and the fusion inhibitor C46. J Gene Med 2019; 20:e3006. [PMID: 29552747 DOI: 10.1002/jgm.3006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 12/31/2017] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The gene therapeutic Cal-1 comprises the anti-HIV agents: (i) sh5, a short hairpin RNA to CCR5 that down-regulates CCR5 expression and (ii) maC46 (C46), a peptide that inhibits viral fusion with the cell membrane. These constructs were assessed for inhibition of viral replication and selective cell expansion in a number of settings. METHODS HIV replication, selective outgrowth and cell surface viral binding were analysed with a single cycle infection assay of six pseudotyped HIV strains and a static and longitudinal passaging of MOLT4/CCR5 cells with HIV. Pronase digestion of surface virus and fluorescence microscopy assessed interactions between HIV virions and transduced cells. RESULTS Cal-1 reduced CCR5 expression in peripheral blood mononuclear cells to CCR5Δ32 heterozygote levels. Even low level transduction resulted in significant preferential expansion in MOLT4/CCR5 gene-containing cells over a 3-week HIV challenge regardless of viral suppression [12.5% to 47.0% (C46), 46.7% (sh5), 62.2% (Dual), respectively]. The sh5 and Dual constructs at > 95% transduction also significantly suppressed virus to day 12 in the passage assay and all constructs, at varying percentage transduction inhibited virus in static culture. No escape mutations were present through 9 weeks of challenge. The Dual construct significantly suppressed infection by a panel of CCR5-using viruses, with its efficacy being independently determined from the single constructs. Dual and sh5 inhibited virion internalisation, as determined via pronase digestion of surface bound virus, by 70% compared to 13% for C46. CONCLUSIONS The use of two anti-HIV genes allows optimal preferential survival and inhibition of HIV replication, with the impact on viral load being dependent on the percentage of gene marked cells.
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Affiliation(s)
- Scott Ledger
- Faculty of Medicine, UNSW Australia, Sydney, NSW, Australia.,St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - Annett Howe
- School of Mathematics and Statistics, UNSW Australia, Sydney, NSW, Australia
| | | | | | - Borislav Savkovic
- School of Mathematics and Statistics, UNSW Australia, Sydney, NSW, Australia
| | - Andrew Ong
- School of Mathematics and Statistics, UNSW Australia, Sydney, NSW, Australia
| | | | - Maureen Boyd
- St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW, Australia.,Calimmune Australia, Sydney, NSW, Australia
| | - Michelle Millington
- St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW, Australia.,Calimmune Australia, Sydney, NSW, Australia
| | - Paul R Gorry
- School of Applied Sciences and Program in Metabolism, Exercise and Disease, Health Initiatives Research Institute, RMIT University, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, University of Melbourne, Parkville, VIC, Australia
| | - John M Murray
- School of Mathematics and Statistics, UNSW Australia, Sydney, NSW, Australia
| | - Geoff Symonds
- Faculty of Medicine, UNSW Australia, Sydney, NSW, Australia.,St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW, Australia.,Calimmune Australia, Sydney, NSW, Australia
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11
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Abstract
Using fully atomistic molecular dynamics simulation that are several hundred nanoseconds long, we demonstrate the pH-controlled sponge action of PAMAM dendrimer. We show how at varying pH levels, the PAMAM dendrimer acts as a wet sponge; at neutral or low pH levels, the dendrimer expands noticeably and the interior of the dendrimer opens up to host several hundreds to thousands of water molecules depending on the generation number. Increasing the pH (i.e., going from low pH to high pH) leads to the collapse of the dendrimer size, thereby expelling the inner water, which mimics the ‘sponge’ action. As the dendrimer size swells up at a neutral pH or low pH due to the electrostatic repulsion between the primary and tertiary amines that are protonated at this pH, there is dramatic increase in the available solvent accessible surface area (SASA), as well as solvent accessible volume (SAV).
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Affiliation(s)
- Prabal K. Maiti
- Center for Condensed Matter Theory, Department of Physics, Bangalore, India, 560012
- Center for Condensed Matter Theory, Department of Physics, Bangalore, India, 560012
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12
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Malik T, Chauhan G, Rath G, Murthy RSR, Goyal AK. "Fusion and binding inhibition" key target for HIV-1 treatment and pre-exposure prophylaxis: targets, drug delivery and nanotechnology approaches. Drug Deliv 2017; 24:608-621. [PMID: 28240046 PMCID: PMC8241151 DOI: 10.1080/10717544.2016.1228717] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
More than 35 million people are living with HIV worldwide with approximately 2.3 million new infections per year. Cascade of events (cell entry, virus replication, assembly and release of newly formed virions) is involved in the HIV-1 transmission process. Every single step offers a potential therapeutic strategy to halt this progression and HIV fusion into the human host cell is one such stage. Controlling the initial event of HIV-1 transmission is the best way to control its dissemination especially when prophylaxis is concerned. Action is required either on the HIV’s or host’s cell surface which is logically more rational when compared with other intracellular acting moieties. Aim of this manuscript is to detail the significance and current strategies to halt this initial step, thus blocking the entry of HIV-1 for further infection. Both HIV-1 and the possible host cell’s receptors/co-receptors are under focus while specifying the targets available for inhibiting this fusion. Current and under investigation moieties are categorized based on their versatile mechanisms. Advanced drug delivery and nanotechnology approaches present a key tool to exploit the therapeutic potential in a boosted way. Current drug delivery and the impact of nanotechnology in potentiating this strategy are detailed.
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Affiliation(s)
- Tanushree Malik
- a DBT Lab, Indo Soviet Friendship College of Pharmacy , Moga , India and
| | - Gaurav Chauhan
- a DBT Lab, Indo Soviet Friendship College of Pharmacy , Moga , India and.,b Centre for Nanosciences, Department of Chemical Engineering, Indian Institute of Technology Kanpur , Kanpur , India
| | - Goutam Rath
- a DBT Lab, Indo Soviet Friendship College of Pharmacy , Moga , India and
| | - R S R Murthy
- a DBT Lab, Indo Soviet Friendship College of Pharmacy , Moga , India and
| | - Amit K Goyal
- a DBT Lab, Indo Soviet Friendship College of Pharmacy , Moga , India and
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13
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Sepúlveda-Crespo D, Ceña-Díez R, Jiménez JL, Ángeles Muñoz-Fernández M. Mechanistic Studies of Viral Entry: An Overview of Dendrimer-Based Microbicides As Entry Inhibitors Against Both HIV and HSV-2 Overlapped Infections. Med Res Rev 2016; 37:149-179. [PMID: 27518199 DOI: 10.1002/med.21405] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 06/16/2016] [Accepted: 07/06/2016] [Indexed: 12/12/2022]
Abstract
This review provides an overview of the development of different dendrimers, mainly polyanionic, against human immunodeficiency virus (HIV) and genital herpes (HSV-2) as topical microbicides targeting the viral entry process. Vaginal topical microbicides to prevent sexually transmitted infections such as HIV and HSV-2 are urgently needed. To inhibit HIV/HSV-2 entry processes, new preventive targets have been established to maximize the current therapies against wild-type and drug-resistant viruses. The entry of HIV/HSV-2 into target cells is a multistep process that triggers a cascade of molecular interactions between viral envelope proteins and cell surface receptors. Polyanionic dendrimers are highly branched nanocompounds with potent activity against HIV/HSV-2. Inhibitors of each entry step have been identified with regard to generations and surface groups, and possible roles for these agents in anti-HIV/HSV-2 therapies have also been discussed. Four potential binding sites for impeding HIV infection (HSPG, DC-SIGN, GSL, and CD4/gp120 inhibitors) and HSV-2 infection (HS, gB, gD, and gH/gL inhibitors) exist according to their mechanisms of action and structures. This review clarifies that inhibition of HIV/HSV-2 entry continues to be a promising target for drug development because nanotechnology can transform the field of HIV/HSV-2 prevention by improving the efficacy of the currently available antiviral treatments.
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Affiliation(s)
- Daniel Sepúlveda-Crespo
- Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Spanish HIV-HGM BioBank, Madrid, Spain.,Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Rafael Ceña-Díez
- Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Spanish HIV-HGM BioBank, Madrid, Spain.,Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - José Luis Jiménez
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Spanish HIV-HGM BioBank, Madrid, Spain.,Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain.,Plataforma de Laboratorio, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Ma Ángeles Muñoz-Fernández
- Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Spanish HIV-HGM BioBank, Madrid, Spain.,Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
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Nandy B, Saurabh S, Sahoo AK, Dixit NM, Maiti PK. The SPL7013 dendrimer destabilizes the HIV-1 gp120-CD4 complex. NANOSCALE 2015; 7:18628-18641. [PMID: 26495445 DOI: 10.1039/c5nr04632g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The poly (l-lysine)-based SPL7013 dendrimer with naphthalene disulphonate surface groups blocks the entry of HIV-1 into target cells and is in clinical trials for development as a topical microbicide. Its mechanism of action against R5 HIV-1, the HIV-1 variant implicated in transmission across individuals, remains poorly understood. Using docking and fully atomistic MD simulations, we find that SPL7013 binds tightly to R5 gp120 in the gp120-CD4 complex but weakly to gp120 alone. Further, the binding, although to multiple regions of gp120, does not occlude the CD4 binding site on gp120, suggesting that SPL7013 does not prevent the binding of R5 gp120 to CD4. Using MD simulations to compute binding energies of several docked structures, we find that SPL7013 binding to gp120 significantly weakens the gp120-CD4 complex. Finally, we use steered molecular dynamics (SMD) to study the kinetics of the dissociation of the gp120-CD4 complex in the absence of the dendrimer and with the dendrimer bound in each of the several stable configurations to gp120. We find that SPL7013 significantly lowers the force required to rupture the gp120-CD4 complex and accelerates its dissociation. Taken together, our findings suggest that SPL7013 compromises the stability of the R5 gp120-CD4 complex, potentially preventing the accrual of the requisite number of gp120-CD4 complexes across the virus-cell interface, thereby blocking virus entry.
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Affiliation(s)
- Bidisha Nandy
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India.
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15
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Lakshminarayanan A, Reddy BU, Raghav N, Ravi VK, Kumar A, Maiti PK, Sood AK, Jayaraman N, Das S. A galactose-functionalized dendritic siRNA-nanovector to potentiate hepatitis C inhibition in liver cells. NANOSCALE 2015; 7:16921-16931. [PMID: 26411288 DOI: 10.1039/c5nr02898a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A RNAi based antiviral strategy holds the promise to impede hepatitis C viral (HCV) infection overcoming the problem of emergence of drug resistant variants, usually encountered in the interferon free direct-acting antiviral therapy. Targeted delivery of siRNA helps minimize adverse 'off-target' effects and maximize the efficacy of therapeutic response. Herein, we report the delivery of siRNA against the conserved 5'-untranslated region (UTR) of HCV RNA using a liver-targeted dendritic nano-vector functionalized with a galactopyranoside ligand (DG). Physico-chemical characterization revealed finer details of complexation of DG with siRNA, whereas molecular dynamic simulations demonstrated sugar moieties projecting "out" in the complex. Preferential delivery of siRNA to the liver was achieved through a highly specific ligand-receptor interaction between dendritic galactose and the asialoglycoprotein receptor. The siRNA-DG complex exhibited perinuclear localization in liver cells and co-localization with viral proteins. The histopathological studies showed the systemic tolerance and biocompatibility of DG. Further, whole body imaging and immunohistochemistry studies confirmed the preferential delivery of the nucleic acid to mice liver. Significant decrease in HCV RNA levels (up to 75%) was achieved in HCV subgenomic replicon and full length HCV-JFH1 infectious cell culture systems. The multidisciplinary approach provides the 'proof of concept' for restricted delivery of therapeutic siRNAs using a target oriented dendritic nano-vector.
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16
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Hou W, Fang C, Liu J, Yu H, Qi J, Zhang Z, Yuan R, Xiong D, Gao S, Adam Yuan Y, Li S, Gu Y, Xia N. Molecular insights into the inhibition of HIV-1 infection using a CD4 domain-1-specific monoclonal antibody. Antiviral Res 2015; 122:101-11. [PMID: 26259811 DOI: 10.1016/j.antiviral.2015.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 08/01/2015] [Accepted: 08/07/2015] [Indexed: 12/19/2022]
Abstract
An HIV-1 infection in a host cell occurs through an ordered process that involves HIV-1 attachment to the host's cellular CD4 receptor, co-receptor binding to CCR5 or CXCR4, and the subsequent fusion with the cellular membrane. The natural viral entry pathway into a host cell provides an opportunity to develop agents for the treatment of HIV-1 infections. Several engineered monoclonal antibodies specifically targeting CD4 have shown antiviral activities in clinical trials. Here, we report on an anti-CD4 mAb (15A7) that displays a unique binding specificity for domain 1 of CD4, whose epitope partially overlaps with the gp120 binding region. Moreover, 15A7 displays a much stronger binding affinity to CD4(+) cell lines after HIV infection. 15A7 is able to block and neutralize a broad range of primary HIV-1 isolates and T cell-line passage strains. Notably, the bivalent F(ab')2 form of 15A7 is more effective than the Fab form in blocking HIV-1 infection, which is further supported by molecular docking analyses. Together, these results suggest that this novel antibody may exert its antiviral activity by blocking gp120 targeting to the CD4 receptor or competing with gp120 for CD4 receptor binding and might present post-attachment neutralization activity. This antibody could provide a new candidate to efficiently block HIV-1 infection or provide new starting materials for HIV treatment, especially when HIV-1-resistant strains against the current CD4 mAb treatments have already been identified.
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Affiliation(s)
- Wangheng Hou
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Chu Fang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Jiayan Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Hai Yu
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China
| | - Jialong Qi
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China
| | - Zhiqing Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Ruixue Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Dan Xiong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Shuangquan Gao
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China
| | - Y Adam Yuan
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China; National University of Singapore (Suzhou) Research Institute, Suzhou 215123, China
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China; National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China
| | - Ying Gu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China; National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China.
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China; National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China
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17
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Sepúlveda-Crespo D, Gómez R, De La Mata FJ, Jiménez JL, Muñoz-Fernández MÁ. Polyanionic carbosilane dendrimer-conjugated antiviral drugs as efficient microbicides: Recent trends and developments in HIV treatment/therapy. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2015; 11:1481-98. [DOI: 10.1016/j.nano.2015.03.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/20/2015] [Accepted: 03/19/2015] [Indexed: 12/22/2022]
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18
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Barraza LF, Jiménez VA, Alderete JB. Effect of PEGylation on the Structure and Drug Loading Capacity of PAMAM-G4 Dendrimers: A Molecular Modeling Approach on the Complexation of 5-Fluorouracil with Native and PEGylated PAMAM-G4. MACROMOL CHEM PHYS 2015. [DOI: 10.1002/macp.201500179] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Luis F. Barraza
- Departamento de Química Orgánica; Facultad de Ciencias Químicas; Universidad de Concepción; Casilla 160-C Concepción 4070371 Chile
| | - Verónica A. Jiménez
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas; Universidad Andres Bello; Sede Concepción; Talcahuano 4260000 Chile
| | - Joel B. Alderete
- Departamento de Química Orgánica; Facultad de Ciencias Químicas; Universidad de Concepción; Casilla 160-C Concepción 4070371 Chile
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19
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Ozer G, Keyes T, Quirk S, Hernandez R. Multiple branched adaptive steered molecular dynamics. J Chem Phys 2014; 141:064101. [DOI: 10.1063/1.4891807] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Gungor Ozer
- Department of Chemistry, Boston University, Boston, Massachusetts 02215-2521, USA
| | - Thomas Keyes
- Department of Chemistry, Boston University, Boston, Massachusetts 02215-2521, USA
| | - Stephen Quirk
- Kimberly-Clark Corporation, Atlanta, Georgia 30076-2199, USA
- Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Rigoberto Hernandez
- Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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