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Sha H, Zhu F. Hexagonal Lattices of HIV Capsid Proteins Explored by Simulations Based on a Thermodynamically Consistent Model. J Phys Chem B 2024; 128:960-972. [PMID: 38251836 DOI: 10.1021/acs.jpcb.3c06881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
HIV capsid proteins (CAs) may self-assemble into a variety of shapes under in vivo and in vitro conditions. Here, we employed simulations based on a residue-level coarse-grained (CG) model with full conformational flexibility to investigate hexagonal lattices, which are the underlying structural pattern for CA aggregations. Facilitated by enhanced sampling simulations to rigorously calculate CA dimerization and polymerization affinities, we calibrated our model to reproduce the experimentally measured affinities. Using the calibrated model, we performed unbiased simulations on several large systems consisting of 1512 CA subunits, allowing reversible binding and unbinding of the CAs in a thermodynamically consistent manner. In one simulation, a preassembled hexagonal CA sheet developed spontaneous curvatures reminiscent of those observed in experiments, and the edges of the sheet exhibited local curvatures larger than those of the interior. In other simulations starting with randomly distributed CAs at different concentrations, existing CA assemblies grew by binding free capsomeres to the edges and by merging with other assemblies. At high CA concentrations, rapid establishment of predominant aggregates was followed by much slower adjustments toward more regular hexagonal lattices, with increasing numbers of intact CA hexamers and pentamers being formed. Our approach of adapting a general CG model to specific systems by using experimental binding data represents a practical and effective strategy for simulating and elucidating intricate protein aggregations.
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Affiliation(s)
- Hao Sha
- Department of Physics, Indiana University─Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Fangqiang Zhu
- Department of Physics, Indiana University─Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
- Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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2
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Xu S, Sun L, Barnett M, Zhang X, Ding D, Gattu A, Shi D, Taka JRH, Shen W, Jiang X, Cocklin S, De Clercq E, Pannecouque C, Goldstone DC, Liu X, Dick A, Zhan P. Discovery, Crystallographic Studies, and Mechanistic Investigations of Novel Phenylalanine Derivatives Bearing a Quinazolin-4-one Scaffold as Potent HIV Capsid Modulators. J Med Chem 2023; 66:16303-16329. [PMID: 38054267 PMCID: PMC10790229 DOI: 10.1021/acs.jmedchem.3c01647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Optimization of compound 11L led to the identification of novel HIV capsid modulators, quinazolin-4-one-bearing phenylalanine derivatives, displaying potent antiviral activities against both HIV-1 and HIV-2. Notably, derivatives 12a2 and 21a2 showed significant improvements, with 2.5-fold over 11L and 7.3-fold over PF74 for HIV-1, and approximately 40-fold over PF74 for HIV-2. The X-ray co-crystal structures confirmed the multiple pocket occupation of 12a2 and 21a2 in the binding site. Mechanistic studies revealed a dual-stage inhibition profile, where the compounds disrupted capsid-host factor interactions at the early stage and promoted capsid misassembly at the late stage. Remarkably, 12a2 and 21a2 significantly promoted capsid misassembly, outperforming 11L, PF74, and LEN. The substitution of easily metabolized amide bond with quinolin-4-one marginally enhanced the stability of 12a2 in human liver microsomes compared to controls. Overall, 12a2 and 21a2 highlight their potential as potent HIV capsid modulators, paving the way for future advancements in anti-HIV drug design.
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Affiliation(s)
- Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Michael Barnett
- School of Biological Sciences, The University of Auckland, 3A Symonds St, Auckland 1010, New Zealand
| | - Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Dang Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Anushka Gattu
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Dazhou Shi
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Jamie R H Taka
- School of Biological Sciences, The University of Auckland, 3A Symonds St, Auckland 1010, New Zealand
| | - Wenli Shen
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Simon Cocklin
- Specifica Inc., The Santa Fe Railyard, 1607 Alcaldesa Street, Santa Fe, New Mexico 87501, United States
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - David C Goldstone
- School of Biological Sciences, The University of Auckland, 3A Symonds St, Auckland 1010, New Zealand
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
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Zhang X, Sun L, Xu S, Huang T, Zhao F, Ding D, Liu C, Jiang X, Tao Y, Kang D, De Clercq E, Pannecouque C, Cocklin S, Dick A, Liu X, Zhan P. Design, synthesis, and mechanistic study of 2-piperazineone-bearing peptidomimetics as novel HIV capsid modulators. RSC Med Chem 2023; 14:1272-1295. [PMID: 37484571 PMCID: PMC10357934 DOI: 10.1039/d3md00134b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/29/2023] [Indexed: 07/25/2023] Open
Abstract
HIV-1 capsid (CA) is an attractive target for its indispensable roles in the viral life cycle. We report the design, synthesis, and mechanistic study of a novel series of 2-piperazineone peptidomimetics as HIV capsid modulators by mimicking the structure of host factors binding to CA. F-Id-3o was the most potent compound from the synthesized series, with an anti-HIV-1 EC50 value of 6.0 μM. However, this series of compounds showed a preference for HIV-2 inhibitory activity, in which Id-3o revealed an EC50 value of 2.5 μM (anti-HIV-2 potency), an improvement over PF74. Interestingly, F-Id-3o did bind HIV-1 CA monomers and hexamers with comparable affinity, unlike PF74, consequently showing antiviral activity in the early and late stages of the HIV-1 lifecycle. Molecular dynamics simulations shed light on F-Id-3o and Id-3o binding modes within the HIV-1/2 CA protein and provide a possible explanation for the increased anti-HIV-2 potency. Metabolic stability assays in human plasma and human liver microsomes indicated that although F-Id-3o has enhanced metabolic stability over PF74, further optimization is necessary. Moreover, we utilized computational prediction of drug-like properties and metabolic stability of F-Id-3o and PF74, which correlated well with experimentally derived metabolic stability, providing an efficient computational pipeline for future preselection based on metabolic stability prediction. Overall, the 2-piperazineone-bearing peptidomimetics are a promising new chemotype in the CA modulators class with considerable optimization potential.
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Affiliation(s)
- Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
- Department of Pharmacy, Qilu Hospital of Shandong University 107 West Culture Road Jinan 250012 Shandong PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Tianguang Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Fabao Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Dang Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Chuanfeng Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Yucen Tao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven Herestraat 49 Postbus 1043 (09.A097) 3000 Leuven Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven Herestraat 49 Postbus 1043 (09.A097) 3000 Leuven Belgium
| | - Simon Cocklin
- Specifica, Inc. 1607 Alcaldesa Street Santa Fe NM 87501 USA
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine Philadelphia Pennsylvania, PA 19102 USA
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
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Canlas KKV, Hong J, Chae J, Seo HW, Kang SH, Choi J, Park H. Trends in nano-platforms for the treatment of viral infectious diseases. KOREAN J CHEM ENG 2023; 40:706-713. [PMID: 37025620 PMCID: PMC10026216 DOI: 10.1007/s11814-023-1388-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/12/2022] [Accepted: 12/26/2022] [Indexed: 03/22/2023]
Abstract
Viral diseases have always been a major health issue, from the currently eradicated poliovirus to the still unresolved human immunodeficiency virus, and have since become a recent global threat brought about by the COVID-19 pandemic. Pathogenic viruses easily spread through various means such as contaminated food and water intake, exchange of bodily fluids, or even inhalation of airborne particles mainly due to their miniscule size. Furthermore, viral coats contain virulent proteins which trigger assimilation into target cells on contact through either direct penetration or induction of endocytosis. In some viruses their outer envelope contains masking ligands that create a means of escape from detection of immune cells. To deal with the nanometer size range and biomolecular-based invasion mechanism, nanoparticles are highly suitable for the treatment. The review highlights the progress in nanoparticle technology, particularly viral therapeutics, including therapeutic strategies and existing clinical applications.
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Jiang X, Sharma PP, Rathi B, Ji X, Hu L, Gao Z, Kang D, Wang Z, Xie M, Xu S, Zhang X, De Clercq E, Cocklin S, Pannecouque C, Dick A, Liu X, Zhan P. Discovery of novel 1,2,4-triazole phenylalanine derivatives targeting an unexplored region within the interprotomer pocket of the HIV capsid protein. J Med Virol 2022; 94:5975-5986. [PMID: 35949003 PMCID: PMC10790228 DOI: 10.1002/jmv.28064] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/20/2022] [Accepted: 08/08/2022] [Indexed: 01/06/2023]
Abstract
Human immunodeficiency virus (HIV) capsid (CA) protein is a promising target for developing novel anti-HIV drugs. Starting from highly anticipated CA inhibitors PF-74, we used scaffold hopping strategy to design a series of novel 1,2,4-triazole phenylalanine derivatives by targeting an unexplored region composed of residues 106-109 in HIV-1 CA hexamer. Compound d19 displayed excellent antiretroviral potency against HIV-1 and HIV-2 strains with EC50 values of 0.59 and 2.69 µM, respectively. Additionally, we show via surface plasmon resonance (SPR) spectrometry that d19 preferentially interacts with the hexameric form of CA, with a significantly improved hexamer/monomer specificity ratio (ratio = 59) than PF-74 (ratio = 21). Moreover, we show via SPR that d19 competes with CPSF-6 for binding to CA hexamers with IC50 value of 33.4 nM. Like PF-74, d19 inhibits the replication of HIV-1 NL4.3 pseudo typed virus in both early and late stages. In addition, molecular docking and molecular dynamics simulations provide binding mode information of d19 to HIV-1 CA and rationale for improved affinity and potency over PF-74. Overall, the lead compound d19 displays a distinct chemotype form PF-74, improved CA affinity, and anti-HIV potency.
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Affiliation(s)
- Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Prem Prakash Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Xiangkai Ji
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Lide Hu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Zhen Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Minghui Xie
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U.Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Simon Cocklin
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U.Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012, Jinan, Shandong, PR China
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Xu S, Sun L, Zalloum WA, Huang T, Zhang X, Ding D, Shao X, Jiang X, Zhao F, Cocklin S, De Clercq E, Pannecouque C, Dick A, Liu X, Zhan P. Discovery and Mechanistic Investigation of Piperazinone Phenylalanine Derivatives with Terminal Indole or Benzene Ring as Novel HIV-1 Capsid Modulators. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238415. [PMID: 36500508 PMCID: PMC9739877 DOI: 10.3390/molecules27238415] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022]
Abstract
HIV-1 capsid (CA) performs multiple roles in the viral life cycle and is a promising target for antiviral development. In this work, we describe the design, synthesis, assessment of antiviral activity, and mechanistic investigation of 20 piperazinone phenylalanine derivatives with a terminal indole or benzene ring. Among them, F2-7f exhibited moderate anti-HIV-1 activity with an EC50 value of 5.89 μM, which was slightly weaker than the lead compound PF74 (EC50 = 0.75 μM). Interestingly, several compounds showed a preference for HIV-2 inhibitory activity, represented by 7f with an HIV-2 EC50 value of 4.52 μM and nearly 5-fold increased potency over anti-HIV-1 (EC50 = 21.81 μM), equivalent to PF74 (EC50 = 4.16 μM). Furthermore, F2-7f preferred to bind to the CA hexamer rather than to the monomer, similar to PF74, according to surface plasmon resonance results. Molecular dynamics simulation indicated that F2-7f and PF74 bound at the same site. Additionally, we computationally analyzed the ADMET properties for 7f and F2-7f. Based on this analysis, 7f and F2-7f were predicted to have improved drug-like properties and metabolic stability over PF74, and no toxicities were predicted based on the chemotype of 7f and F2-7f. Finally, the experimental metabolic stability results of F2-7f in human liver microsomes and human plasma moderately correlated with our computational prediction. Our findings show that F2-7f is a promising small molecule targeting the HIV-1 CA protein with considerable development potential.
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Affiliation(s)
- Shujing Xu
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Lin Sun
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
- Department of Pharmacy, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Waleed A. Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O. Box 2882, Amman 11821, Jordan
| | - Tianguang Huang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Xujie Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Dang Ding
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Xiaoyu Shao
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Xiangyi Jiang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Fabao Zhao
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Simon Cocklin
- Specifica Inc., The Santa Fe Railyard, 1607 Alcaldesa Street, Santa Fe, NM 87501, USA
| | - Erik De Clercq
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
| | - Xinyong Liu
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
| | - Peng Zhan
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
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7
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Yang H, Talledge N, Arndt WG, Zhang W, Mansky LM. Human Immunodeficiency Virus Type 2 Capsid Protein Mutagenesis Reveals Amino Acid Residues Important for Virus Particle Assembly. J Mol Biol 2022; 434:167753. [PMID: 35868362 PMCID: PMC11057910 DOI: 10.1016/j.jmb.2022.167753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022]
Abstract
Human immunodeficiency virus (HIV) Gag drives virus particle assembly. The capsid (CA) domain is critical for Gag multimerization mediated by protein-protein interactions. The Gag protein interaction network defines critical aspects of the retroviral lifecycle at steps such as particle assembly and maturation. Previous studies have demonstrated that the immature particle morphology of HIV-2 is intriguingly distinct relative to that of HIV-1. Based upon this observation, we sought to determine the amino acid residues important for virus assembly that might help explain the differences between HIV-1 and HIV-2. To do this, we conducted site-directed mutagenesis of targeted locations in the HIV-2 CA domain of Gag and analyzed various aspects of virus particle assembly. A panel of 31 site-directed mutants of residues that reside at the HIV-2 CA inter-hexamer interface, intra-hexamer interface and CA inter-domain linker were created and analyzed for their effects on the efficiency of particle production, particle morphology, particle infectivity, Gag subcellular distribution and in vitro protein assembly. Seven conserved residues between HIV-1 and HIV-2 (L19, A41, I152, K153, K157, N194, D196) and two non-conserved residues (G38, N127) were found to significantly impact Gag multimerization and particle assembly. Taken together, these observations complement structural analyses of immature HIV-2 particle morphology and Gag lattice organization as well as provide important comparative insights into the key amino acid residues that can help explain the observed differences between HIV immature particle morphology and its association with virus replication and particle infectivity.
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Affiliation(s)
- Huixin Yang
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Comparative Molecular Biosciences Graduate Program, University of Minnesota - Twin Cities, St. Paul, MN 55108, USA
| | - Nathaniel Talledge
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Division of Basic Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - William G Arndt
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Division of Basic Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Biochemistry, Molecular Biology & Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Wei Zhang
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Division of Basic Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Characterization Facility, College of Sciences and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Division of Basic Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Comparative Molecular Biosciences Graduate Program, University of Minnesota - Twin Cities, St. Paul, MN 55108, USA; Biochemistry, Molecular Biology & Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
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8
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Identification of New L-Heptanoylphosphatidyl Inositol Pentakisphosphate Derivatives Targeting the Interaction with HIV-1 Gag by Molecular Modelling Studies. Pharmaceuticals (Basel) 2022; 15:ph15101255. [PMID: 36297367 PMCID: PMC9610595 DOI: 10.3390/ph15101255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/29/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
The HIV-1 Gag protein binds to the host cell membrane and assembles into immature particles. Then, in the course of immature virion budding, activated protease cleaves Gag into its main components: MA, CA, NC, and p6 proteins. The highly basic residues of MA predominantly interact with the acidic head of phosphatidyl-inositol-4,5-bisphosphate (PI(4,5)P2) inserted into the membrane. Our research group developed L-Heptanoylphosphatidyl Inositol Pentakisphosphate (L-HIPPO) and previously confirmed that this compound bound to the MA more strongly than PI(4,5)P2 and inositol hexakisphosphate (IP6) did. Therefore, herein we rationally designed eight new L-HIPPO derivatives based on the fact that the most changeable parts of L-HIPPO were two acyl chains. After that, we employed molecular docking for eight compounds via Maestro software using high-resolution crystal structures of MA in complex with IP6 (PDB IDs: 7E1I, 7E1J, and 7E1K), which were recently elucidated by our research group. The most promising docking scores were obtained with benzene-inserted compounds. Thus, we generated a library containing 213 new aromatic group-inserted L-HIPPO derivatives and performed the same molecular docking procedure. According to the results, we determined the nine new L-HIPPO derivatives most effectively binding to the MA with the most favorable scoring functions and pharmacokinetic properties for further exploration.
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9
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Regueiro-Ren A, Sit SY, Chen Y, Chen J, Swidorski JJ, Liu Z, Venables BL, Sin N, Hartz RA, Protack T, Lin Z, Zhang S, Li Z, Wu DR, Li P, Kempson J, Hou X, Gupta A, Rampulla R, Mathur A, Park H, Sarjeant A, Benitex Y, Rahematpura S, Parker D, Phillips T, Haskell R, Jenkins S, Santone KS, Cockett M, Hanumegowda U, Dicker I, Meanwell NA, Krystal M. The Discovery of GSK3640254, a Next-Generation Inhibitor of HIV-1 Maturation. J Med Chem 2022; 65:11927-11948. [PMID: 36044257 DOI: 10.1021/acs.jmedchem.2c00879] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
GSK3640254 is an HIV-1 maturation inhibitor (MI) that exhibits significantly improved antiviral activity toward a range of clinically relevant polymorphic variants with reduced sensitivity toward the second-generation MI GSK3532795 (BMS-955176). The key structural difference between GSK3640254 and its predecessor is the replacement of the para-substituted benzoic acid moiety attached at the C-3 position of the triterpenoid core with a cyclohex-3-ene-1-carboxylic acid substituted with a CH2F moiety at the carbon atom α- to the pharmacophoric carboxylic acid. This structural element provided a new vector with which to explore structure-activity relationships (SARs) and led to compounds with improved polymorphic coverage while preserving pharmacokinetic (PK) properties. The approach to the design of GSK3640254, the development of a synthetic route and its preclinical profile are discussed. GSK3640254 is currently in phase IIb clinical trials after demonstrating a dose-related reduction in HIV-1 viral load over 7-10 days of dosing to HIV-1-infected subjects.
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Affiliation(s)
- Alicia Regueiro-Ren
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey08543, United States
| | - Sing-Yuen Sit
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Yan Chen
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Jie Chen
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Jacob J Swidorski
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Zheng Liu
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Brian L Venables
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Ny Sin
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Richard A Hartz
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Tricia Protack
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Zeyu Lin
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Sharon Zhang
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Zhufang Li
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Dauh-Rurng Wu
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Peng Li
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - James Kempson
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Xiaoping Hou
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Anuradha Gupta
- Department of Discovery Synthesis; Bristol Myers Squibb Research and Early Development, Bangalore 560099, India
| | - Richard Rampulla
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Arvind Mathur
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Hyunsoo Park
- Bristol Myers Squibb Chemical and Synthetic Development, New Brunswick, New Jersey08901, United States
| | - Amy Sarjeant
- Bristol Myers Squibb Chemical and Synthetic Development, New Brunswick, New Jersey08901, United States
| | - Yulia Benitex
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Sandhya Rahematpura
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Dawn Parker
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Thomas Phillips
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Roy Haskell
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Susan Jenkins
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Kenneth S Santone
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Mark Cockett
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Umesh Hanumegowda
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Ira Dicker
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Nicholas A Meanwell
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey08543, United States
| | - Mark Krystal
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
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Ji X, Li J, Sharma PP, Jiang X, Rathi B, Gao Z, Hu L, Kang D, De Clercq E, Cocklin S, Liu C, Pannecouque C, Dick A, Liu X, Zhan P. Design, Synthesis and Structure-Activity Relationships of Phenylalanine-Containing Peptidomimetics as Novel HIV-1 Capsid Binders Based on Ugi Four-Component Reaction. Molecules 2022; 27:molecules27185995. [PMID: 36144727 PMCID: PMC9502897 DOI: 10.3390/molecules27185995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
As a key structural protein, HIV capsid (CA) protein plays multiple roles in the HIV life cycle, and is considered a promising target for anti-HIV treatment. Based on the structural information of CA modulator PF-74 bound to HIV-1 CA hexamer, 18 novel phenylalanine derivatives were synthesized via the Ugi four-component reaction. In vitro anti-HIV activity assays showed that most compounds exhibited low-micromolar-inhibitory potency against HIV. Among them, compound I-19 exhibited the best anti-HIV-1 activity (EC50 = 2.53 ± 0.84 μM, CC50 = 107.61 ± 27.43 μM). In addition, I-14 displayed excellent HIV-2 inhibitory activity (EC50 = 2.30 ± 0.11 μM, CC50 > 189.32 μM) with relatively low cytotoxicity, being more potent than that of the approved drug nevirapine (EC50 > 15.02 μM, CC50 > 15.2 μM). Additionally, surface plasmon resonance (SPR) binding assays demonstrated direct binding to the HIV CA protein. Moreover, molecular docking and molecular dynamics simulations provided additional information on the binding mode of I-19 to HIV-1 CA. In summary, we further explored the structure—activity relationships (SARs) and selectivity of anti-HIV-1/HIV-2 of PF-74 derivatives, which is conducive to discovering efficient anti-HIV drugs.
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Affiliation(s)
- Xiangkai Ji
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Jing Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Prem Prakash Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Zhen Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Lide Hu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
| | - Erik De Clercq
- Laboratory of Virology and Chemotherapym, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Simon Cocklin
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19104, USA
| | - Chuanfeng Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapym, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19104, USA
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
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11
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Troyano-Hernáez P, Reinosa R, Holguín Á. HIV Capsid Protein Genetic Diversity Across HIV-1 Variants and Impact on New Capsid-Inhibitor Lenacapavir. Front Microbiol 2022; 13:854974. [PMID: 35495642 PMCID: PMC9039614 DOI: 10.3389/fmicb.2022.854974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/09/2022] [Indexed: 12/17/2022] Open
Abstract
The HIV p24 capsid protein has an essential, structural, and functional role in the viral replication cycle, being an interesting target for vaccine design, diagnostic tests, and new antiretroviral drugs (ARVs). The HIV-1 variability poses a challenge for the accuracy and efficiency of diagnostic and treatment tools. This study analyzes p24 diversity among HIV-1 variants and within its secondary structure in HIV-1 M, O, P, and N groups. All available HIV-1 p24 nucleotide sequences were downloaded from the Los Alamos HIV Sequence Database, selecting 23,671 sequences belonging to groups O, N, P, and M (9 subtypes, 7 sub-sub types, and 109 circulating recombinant forms or CRFs). Using a bioinformatics tool developed in our laboratory (EpiMolBio program), we analyzed the amino acid conservation compared to the HXB2 subtype B reference sequence and the V-markers, or amino acid changes that were specific for each variant with at least 10 available sequences. We inferred the p24 consensus sequence for HIV-1 and for each group to analyze the overall conservation in p24 main structural regions, reporting the percentage of substitutions per variant affecting the capsid assembly and molecule-binding, including those associated with resistance to the new capsid-inhibitor lenacapavir, and the key residues involved in lenacapavir-p24 interaction, according to the bibliography. Although the overall structure of p24 was highly conserved, the conservation in the secondary structure varied between HIV-1 variants and the type of secondary structure. All HIV-1 variants presented >80% amino acid conservation vs. HXB2 reference sequence, except for group M sub-subtype F1 (69.27%). Mutants affecting the capsid assembly or lenacapavir capsid-binding were found in <1% of the p24 consensus sequence. Our study reports the HIV-1 variants carrying 14 unique single V-markers in 9/38 group M variants and the level of p24 conservation in each secondary structure region among the 4 HIV-1 groups and group M variants, revealing no natural resistance to lenacapavir in any HIV-1 variant. We present a thorough analysis of p24 variability among all HIV-1 variants circulating to date. Since p24 genetic variability can impact the viral replication cycle and the efficacy of new p24-based diagnostic, therapeutic, and vaccine strategies, conservation studies must consider all HIV-1 variants circulating worldwide.
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Affiliation(s)
- Paloma Troyano-Hernáez
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), Madrid, Spain
| | - Roberto Reinosa
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), Madrid, Spain
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), Madrid, Spain
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12
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Harmon TS, Jülicher F. Molecular Assembly Lines in Active Droplets. PHYSICAL REVIEW LETTERS 2022; 128:108102. [PMID: 35333067 DOI: 10.1103/physrevlett.128.108102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/30/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific sequence of assembly steps. Using droplet interfaces to position compartment boundaries, we show that an assembly line can be self-organized by active droplets. As a consequence, assembly steps can be arranged spatially so that a specific order of assembly is achieved and incorrect assembly is strongly suppressed.
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Affiliation(s)
- Tyler S Harmon
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstraße 38, 01187 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohestraße 6, 01069 Dresden, Germany
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstraße 38, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, 01062 Dresden, Germany
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13
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Lerner G, Weaver N, Anokhin B, Spearman P. Advances in HIV-1 Assembly. Viruses 2022; 14:v14030478. [PMID: 35336885 PMCID: PMC8952333 DOI: 10.3390/v14030478] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/10/2022] Open
Abstract
The assembly of HIV-1 particles is a concerted and dynamic process that takes place on the plasma membrane of infected cells. An abundance of recent discoveries has advanced our understanding of the complex sequence of events leading to HIV-1 particle assembly, budding, and release. Structural studies have illuminated key features of assembly and maturation, including the dramatic structural transition that occurs between the immature Gag lattice and the formation of the mature viral capsid core. The critical role of inositol hexakisphosphate (IP6) in the assembly of both the immature and mature Gag lattice has been elucidated. The structural basis for selective packaging of genomic RNA into virions has been revealed. This review will provide an overview of the HIV-1 assembly process, with a focus on recent advances in the field, and will point out areas where questions remain that can benefit from future investigation.
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14
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Zhang X, Sun L, Meuser ME, Zalloum WA, Xu S, Huang T, Cherukupalli S, Jiang X, Ding X, Tao Y, Kang D, De Clercq E, Pannecouque C, Dick A, Cocklin S, Liu X, Zhan P. Design, synthesis, and mechanism study of dimerized phenylalanine derivatives as novel HIV-1 capsid inhibitors. Eur J Med Chem 2021; 226:113848. [PMID: 34592608 DOI: 10.1016/j.ejmech.2021.113848] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022]
Abstract
HIV-1 capsid (CA) plays indispensable and multiple roles in the life cycle of HIV-1, become an attractive target in antiviral therapy. Herein, we report the design, synthesis, and mechanism study of a novel series of dimerized phenylalanine derivatives as HIV-1 capsid inhibitors using 2-piperazineone or 2,5-piperazinedione as a linker. The structure-activity relationship (SAR) indicated that dimerized phenylalanines were more potent than monomers of the same chemotype. Further, the inclusion of fluorine substituted phenylalanine and methoxyl substituted aniline was found to be beneficial for antiviral activity. From the synthesized series, Q-c4 was found to be the most potent compound with an EC50 value of 0.57 μM, comparable to PF74. Interestingly, Q-c4 demonstrated a slightly higher affinity to the CA monomer than the CA hexamer, commensurate with its more significant effect in the late-stage of the HIV-1 lifecycle. Competitive SPR experiments with peptides from CPSF6 and NUP153 revealed that Q-c4 binds to the interprotomer pocket of hexameric CA as designed. Single-round infection assays showed that Q-c4 interferes with the HIV-1 life cycle in a dual-stage manner, affecting both pre-and post-integration. Stability assays in human plasma and human liver microsomes indicated that although Q-c4 has improved stability over PF74, this kind of inhibitor still requires further optimization. And the results of the online molinspiration software predicted that Q-c4 has desirable physicochemical properties but some properties still have some violation from the Lipinski rule of five. Overall, the dimerized phenylalanines are promising novel platforms for developing future HIV-1 CA inhibitors with considerable potential for optimization.
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Affiliation(s)
- Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Megan E Meuser
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O Box 2882, Amman, 11821, Jordan
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Tianguang Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Xiao Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Yucen Tao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000, Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000, Leuven, Belgium.
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
| | - Simon Cocklin
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
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15
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Xu S, Sun L, Dick A, Zalloum WA, Huang T, Meuser ME, Zhang X, Tao Y, Cherukupalli S, Ding D, Ding X, Gao S, Jiang X, Kang D, De Clercq E, Pannecouque C, Cocklin S, Liu X, Zhan P. Design, synthesis, and mechanistic investigations of phenylalanine derivatives containing a benzothiazole moiety as HIV-1 capsid inhibitors with improved metabolic stability. Eur J Med Chem 2021; 227:113903. [PMID: 34653770 DOI: 10.1016/j.ejmech.2021.113903] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/03/2021] [Accepted: 10/03/2021] [Indexed: 12/17/2022]
Abstract
Further clinical development of PF74, a lead compound targeting HIV-1 capsid, is impeded by low antiviral activity and inferior metabolic stability. By modifying the benzene (region I) and indole of PF74, we identified two potent compounds (7m and 7u) with significantly improved metabolic stability. Compared to PF74, 7u displayed greater metabolic stability in human liver microsomes (HLMs) with half-life (t1/2) 109-fold that of PF74. Moreover, mechanism of action (MOA) studies demonstrated that 7m and 7u effectively mirrored the MOA of compounds that interact within the PF74 interprotomer pocket, showing direct and robust interactions with recombinant CA, and 7u displaying antiviral effects in both the early and late stages of HIV-1 replication. Furthermore, MD simulation corroborated that 7u was bound to the PF74 binding site, and the results of the online molinspiration software predicted that 7m and 7u had desirable physicochemical properties. Unexpectedly, this series of compounds exhibited better antiviral activity than PF74 against HIV-2, represented by compound 7m whose anti-HIV-2 activity was almost 5 times increased potency over PF74. Therefore, we have rationally redesigned the PF74 chemotype to inhibitors with novel structures and enhanced metabolic stability in this study. We hope that these new compounds can serve as a blueprint for developing a new generation of HIV treatment regimens.
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Affiliation(s)
- Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, PA, 19102, USA
| | - Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O Box 2882, Amman, 11821, Jordan
| | - Tianguang Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Megan E Meuser
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, PA, 19102, USA
| | - Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Yucen Tao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Dang Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Xiao Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000, Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000, Leuven, Belgium.
| | - Simon Cocklin
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, PA, 19102, USA.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
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16
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Fiorino S, Tateo F, Biase DD, Gallo CG, Orlandi PE, Corazza I, Budriesi R, Micucci M, Visani M, Loggi E, Hong W, Pica R, Lari F, Zippi M. SARS-CoV-2: lessons from both the history of medicine and from the biological behavior of other well-known viruses. Future Microbiol 2021; 16:1105-1133. [PMID: 34468163 PMCID: PMC8412036 DOI: 10.2217/fmb-2021-0064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 is the etiological agent of the current pandemic worldwide and its associated disease COVID-19. In this review, we have analyzed SARS-CoV-2 characteristics and those ones of other well-known RNA viruses viz. HIV, HCV and Influenza viruses, collecting their historical data, clinical manifestations and pathogenetic mechanisms. The aim of the work is obtaining useful insights and lessons for a better understanding of SARS-CoV-2. These pathogens present a distinct mode of transmission, as SARS-CoV-2 and Influenza viruses are airborne, whereas HIV and HCV are bloodborne. However, these viruses exhibit some potential similar clinical manifestations and pathogenetic mechanisms and their understanding may contribute to establishing preventive measures and new therapies against SARS-CoV-2.
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Affiliation(s)
- Sirio Fiorino
- Internal Medicine Unit, Budrio Hospital, Budrio (Bologna), Azienda USL, Bologna, 40054, Italy
| | - Fabio Tateo
- Institute of Geosciences & Earth Resources, CNR, c/o Department of Geosciences, Padova University, 35127, Italy
| | - Dario De Biase
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Claudio G Gallo
- Fisiolaserterapico Emiliano, Castel San Pietro Terme, Bologna, 40024, Italy
| | | | - Ivan Corazza
- Department of Experimental, Diagnostic & Specialty Medicine, University of Bologna, Bologna, 40126, Italy
| | - Roberta Budriesi
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, 40126, Italy
| | - Matteo Micucci
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, 40126, Italy
| | - Michela Visani
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Elisabetta Loggi
- Hepatology Unit, Department of Medical & Surgical Sciences, University of Bologna, Bologna, 40126, Italy
| | - Wandong Hong
- Department of Gastroenterology & Hepatology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang, 325035, PR China
| | - Roberta Pica
- Unit of Gastroenterology & Digestive Endoscopy, Sandro Pertini Hospital, Rome, 00157, Italy
| | - Federico Lari
- Internal Medicine Unit, Budrio Hospital, Budrio (Bologna), Azienda USL, Bologna, 40054, Italy
| | - Maddalena Zippi
- Unit of Gastroenterology & Digestive Endoscopy, Sandro Pertini Hospital, Rome, 00157, Italy
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17
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Sikdar A, Gupta R, Boura E. Reviewing Antiviral Research Against Viruses Causing Human Diseases - A Structure Guided Approach. Curr Mol Pharmacol 2021; 15:306-337. [PMID: 34348638 DOI: 10.2174/1874467214666210804152836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 11/22/2022]
Abstract
The littlest of all the pathogens, viruses have continuously been the foremost strange microorganisms to consider. Viral Infections can cause extreme sicknesses as archived by the HIV/AIDS widespread or the later Ebola or Zika episodes. Apprehensive framework distortions are too regularly watched results of numerous viral contaminations. Besides, numerous infections are oncoviruses, which can trigger different sorts of cancer. Nearly every year a modern infection species rises debilitating the world populace with an annihilating episode. Subsequently, the need of creating antivirals to combat such rising infections. In any case, from the innovation of to begin with antiviral medicate Idoxuridine in 1962 to the revelation of Baloxavir marboxil (Xofluza) that was FDA-approved in 2018, the hone of creating antivirals has changed significantly. In this article, different auxiliary science strategies have been described that can be referral for therapeutics innovation.
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Affiliation(s)
- Arunima Sikdar
- Department of Hematology and Oncology, School of Medicine, The University of Tennessee Health Science Center, 920 Madison Ave, P.O.Box-38103, Memphis, Tennessee. United States
| | - Rupali Gupta
- Department of Neurology, Duke University Medical Center, Durham, North Carolina. United States
| | - Evzen Boura
- Department of Molecular Biology and Biochemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, P.O. Box:16000, Prague. Czech Republic
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18
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Synthesis, Enantiomeric Resolution and Biological Evaluation of HIV Capsid Inhibition Activity for Racemic, ( S)- and ( R)-PF74. Molecules 2021; 26:molecules26133919. [PMID: 34206893 PMCID: PMC8272108 DOI: 10.3390/molecules26133919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
PF74 is a capsid-targeting inhibitor of HIV replication that effectively perturbs the highly sensitive viral uncoating process. A lack of information regarding the optical purity (enantiomeric excess) of the single stereogenic centre of PF74 has resulted in ambiguity as to the potency of different samples of this compound. Herein is described the synthesis of enantiomerically enriched (S)- and (R)-PF74 and further enrichment of the samples (≥98%) using chiral HPLC resolution. The biological activities of each enantiomer were then evaluated, which determined (S)-PF74 (IC50 1.5 µM) to be significantly more active than (R)-PF74 (IC50 19 µM). Computational docking studies were then conducted to rationalise this large discrepancy in activity, which indicated different binding conformations for each enantiomer. The binding energy of the conformation adopted by the more active (S)-PF74 (ΔG = -73.8 kcal/mol) was calculated to be more favourable than the conformation adopted by the less active (R)-enantiomer (ΔG = -55.8 kcal/mol) in agreement with experimental observations.
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19
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Briolay T, Petithomme T, Fouet M, Nguyen-Pham N, Blanquart C, Boisgerault N. Delivery of cancer therapies by synthetic and bio-inspired nanovectors. Mol Cancer 2021; 20:55. [PMID: 33761944 PMCID: PMC7987750 DOI: 10.1186/s12943-021-01346-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND As a complement to the clinical development of new anticancer molecules, innovations in therapeutic vectorization aim at solving issues related to tumor specificity and associated toxicities. Nanomedicine is a rapidly evolving field that offers various solutions to increase clinical efficacy and safety. MAIN: Here are presented the recent advances for different types of nanovectors of chemical and biological nature, to identify the best suited for translational research projects. These nanovectors include different types of chemically engineered nanoparticles that now come in many different flavors of 'smart' drug delivery systems. Alternatives with enhanced biocompatibility and a better adaptability to new types of therapeutic molecules are the cell-derived extracellular vesicles and micro-organism-derived oncolytic viruses, virus-like particles and bacterial minicells. In the first part of the review, we describe their main physical, chemical and biological properties and their potential for personalized modifications. The second part focuses on presenting the recent literature on the use of the different families of nanovectors to deliver anticancer molecules for chemotherapy, radiotherapy, nucleic acid-based therapy, modulation of the tumor microenvironment and immunotherapy. CONCLUSION This review will help the readers to better appreciate the complexity of available nanovectors and to identify the most fitting "type" for efficient and specific delivery of diverse anticancer therapies.
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Affiliation(s)
- Tina Briolay
- Université de Nantes, Inserm, CRCINA, F-44000, Nantes, France
| | | | - Morgane Fouet
- Université de Nantes, Inserm, CRCINA, F-44000, Nantes, France
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20
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Zhou XR, Liu Y, Huang Z, Yao Q, He F, Gao Y. Gag Protein Oriented Supramolecular Nets as Potential HIV Traps. Bioconjug Chem 2021; 32:106-110. [PMID: 33405891 DOI: 10.1021/acs.bioconjchem.0c00706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For HIV/AIDS treatment, the cocktail therapy which uses a combination of anti-retroviral drugs remains the most widely accepted practice. However, the potential drug toxicity, patient tolerability, and emerging drug resistance have limited its long-term efficiency. Here, we design a HIV Gag protein-targeting redox supramolecular assembly (ROSA) system for potential HIV inhibition. An assembling precursor was constructed through conjugation of an oxidation-activatable fluorogenic compound BQA with a selected tetrapeptide GGFF. Since BQA shares a similar structure with the known Gag inhibitor, the precursor could bind to HIV Gag protein with moderate affinity. Moreover, after oxidation, the corresponding nanofibers could bind to Gag protein and trap HIV to realize virus control, thus providing a potential anti-HIV strategy.
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Affiliation(s)
- Xi-Rui Zhou
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China
| | - Ye Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming 650031, China
| | - Zhentao Huang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Qingxin Yao
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Fangfei He
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yuan Gao
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
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21
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Bruinsma RF, Wuite GJL, Roos WH. Physics of viral dynamics. NATURE REVIEWS. PHYSICS 2021; 3:76-91. [PMID: 33728406 PMCID: PMC7802615 DOI: 10.1038/s42254-020-00267-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 05/12/2023]
Abstract
Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.
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Affiliation(s)
- Robijn F. Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, USA
| | - Gijs J. L. Wuite
- Fysica van levende systemen, Vrije Universiteit, Amsterdam, the Netherlands
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
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22
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Valbuena A, Maity S, Mateu MG, Roos WH. Visualization of Single Molecules Building a Viral Capsid Protein Lattice through Stochastic Pathways. ACS NANO 2020; 14:8724-8734. [PMID: 32633498 PMCID: PMC7392527 DOI: 10.1021/acsnano.0c03207] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/26/2020] [Indexed: 05/20/2023]
Abstract
Direct visualization of pathways followed by single molecules while they spontaneously self-assemble into supramolecular biological machines may provide fundamental knowledge to guide molecular therapeutics and the bottom-up design of nanomaterials and nanodevices. Here, high-speed atomic force microscopy is used to visualize self-assembly of the bidimensional lattice of protein molecules that constitutes the framework of the mature human immunodeficiency virus capsid. By real-time imaging of the assembly reaction, individual transient intermediates and reaction pathways followed by single molecules could be revealed. As when assembling a jigsaw puzzle, the capsid protein lattice is randomly built. Lattice patches grow independently from separate nucleation events whereby individual molecules follow different paths. Protein subunits can be added individually, while others form oligomers before joining a lattice or are occasionally removed from the latter. Direct real-time imaging of supramolecular self-assembly has revealed a complex, chaotic process involving multiple routes followed by individual molecules that are inaccessible to bulk (averaging) techniques.
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Affiliation(s)
- Alejandro Valbuena
- Centro
de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Sourav Maity
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
| | - Mauricio G. Mateu
- Centro
de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Wouter H. Roos
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
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23
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Sun L, Dick A, Meuser ME, Huang T, Zalloum WA, Chen CH, Cherukupalli S, Xu S, Ding X, Gao P, Kang D, De Clercq E, Pannecouque C, Cocklin S, Lee KH, Liu X, Zhan P. Design, Synthesis, and Mechanism Study of Benzenesulfonamide-Containing Phenylalanine Derivatives as Novel HIV-1 Capsid Inhibitors with Improved Antiviral Activities. J Med Chem 2020; 63:4790-4810. [PMID: 32298111 DOI: 10.1021/acs.jmedchem.0c00015] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The HIV-1 CA protein has gained remarkable attention as a promising therapeutic target for the development of new antivirals, due to its pivotal roles in HIV-1 replication (structural and regulatory). Herein, we report the design and synthesis of three series of benzenesulfonamide-containing phenylalanine derivatives obtained by further structural modifications of PF-74 to aid in the discovery of more potent and drug-like HIV-1 CA inhibitors. Structure-activity relationship studies of these compounds led to the identification of new phenylalanine derivatives with a piperazinone moiety, represented by compound 11l, which exhibited anti-HIV-1NL4-3 activity 5.78-fold better than PF-74. Interestingly, 11l also showed anti-HIV-2ROD activity (EC50 = 31 nM), with almost 120 times increased potency over PF-74. However, due to the higher significance of HIV-1 as compared to HIV-2 for the human population, this manuscript focuses on the mechanism of action of our compounds in the context of HIV-1. SPR studies on representative compounds confirmed CA as the binding target. The action stage determination assay demonstrated that these inhibitors exhibited antiviral activities with a dual-stage inhibition profile. The early-stage inhibitory activity of compound 11l was 6.25 times more potent as compared to PF-74 but appeared to work via the accelerating capsid core assembly rather than stabilization. However, the mechanism by which they exert their antiviral activity in the late stage appears to be the same as PF-74 with less infectious HIV-1 virions produced in their presence, as judged p24 content studies. MD simulations provided the key rationale for the promising antiviral potency of 11l. Additionally, 11l exhibited a modest increase in HLM and human plasma metabolic stabilities as compared to PF-74, as well as a moderately improved pharmacokinetic profile, favorable oral bioavailability, and no acute toxicity. These studies provide insights and serve as a starting point for subsequent medicinal chemistry efforts in optimizing these promising HIV inhibitors.
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Affiliation(s)
- Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Megan E Meuser
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Tianguang Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O Box 2882, Amman 11821, Jordan
| | - Chin-Ho Chen
- Duke University Medical Center, Surgical Oncology Research Facility, Box 2926, Durham, North Carolina 27710, United States
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Xiao Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000, Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000, Leuven, Belgium
| | - Simon Cocklin
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Kuo-Hsiung Lee
- Natural Products Research Laboratories, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji'nan, Shandong 250012, People's Republic of China
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24
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Regueiro-Ren A, Dicker IB, Hanumegowda U, Meanwell NA. Second Generation Inhibitors of HIV-1 Maturation. ACS Med Chem Lett 2019; 10:287-294. [PMID: 30891128 DOI: 10.1021/acsmedchemlett.8b00656] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 01/28/2019] [Indexed: 12/19/2022] Open
Abstract
The strategy and tactics subtending the discovery and development of the second generation HIV-1 maturation inhibitor GSK-3532795/BMS-955176, a compound that exhibits a broader spectrum of antiviral effect in vitro and in clinical studies than the prototypical maturation inhibitor bevirimat, are described.
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Affiliation(s)
- Alicia Regueiro-Ren
- Department of Discovery Chemistry and Molecular Technologies Bristol-Myers Squibb Research and Development, 350 Carter Road, Room 126, Hopewell, New Jersey 08540, United States
| | - Ira B. Dicker
- ViiV Healthcare, 36 East Industrial Road, Branford, Connecticut 06405, United States
| | - Umesh Hanumegowda
- ViiV Healthcare, 36 East Industrial Road, Branford, Connecticut 06405, United States
| | - Nicholas A. Meanwell
- Department of Discovery Chemistry and Molecular Technologies Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, New Jersey 08543-4000, United States
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25
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Na H, Song G. All-atom normal mode dynamics of HIV-1 capsid. PLoS Comput Biol 2018; 14:e1006456. [PMID: 30226840 PMCID: PMC6161923 DOI: 10.1371/journal.pcbi.1006456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/28/2018] [Accepted: 08/22/2018] [Indexed: 01/25/2023] Open
Abstract
Dynamics of biomolecular assemblies offer invaluable insights into their functional mechanisms. For extremely large biomolecular systems, such as HIV-1 capsid that has nearly 5 millions atoms, obtaining its normal mode dynamics using even coarse-grained models can be a challenging task. In this work, we have successfully carried out a normal mode analysis of an entire HIV-1 capsid in full all-atom details. This is made possible through our newly developed BOSE (Block of Selected Elasticity) model that is founded on the principle of resonance discovered in our recent work. The resonance principle makes it possible to most efficiently compute the vibrations of a whole capsid at any given frequency by projecting the motions of component capsomeres into a narrow subspace. We have conducted also assessments of the quality of the BOSE modes by comparing them with benchmark modes obtained directly from the original Hessian matrix. Our all-atom normal mode dynamics study of the HIV-1 capsid reveals the dynamic role of the pentamers in stabilizing the capsid structure and is in agreement with experimental findings that suggest capsid disassembly and uncoating start when the pentamers become destabilized. Our results on the dynamics of hexamer pores suggest that nucleotide transport should take place mostly at hexamers near pentamers, especially at the larger hemispherical end. Supramolecular assemblies are large biomolecular complexes composed of hundreds or even thousands of protein chains. They function as molecular machines or as large containers that store or facilitate the chemical reactions of other molecules. Whatever they do, their functional mechanisms are tightly linked to their structures and intrinsic dynamics. Recently, due to breakthroughs in experimental techniques, many supramolecular assemblies have been determined, such as the capsid of human immunodeficiency virus (HIV) that is composed of nearly 5 millions of atoms. Computational studies of these systems are challenging due to their extremely large sizes. In this work, we have successfully carried out a dynamics study of an entire HIV capsid in full all-atom details. Our study reveals new insights into the dynamics of the N-terminal loops, the stabilizing role of the pentamers, and where the nucleotide transport may take place.
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Affiliation(s)
- Hyuntae Na
- Department of Computer Science, Penn State Harrisburg, Middletown, Pennsylvania, United States of America
- * E-mail:
| | - Guang Song
- Department of Computer Science, Iowa State University, Ames, Iowa, United States of America
- Program of Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, United States of America
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26
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Zuo X, Huo Z, Kang D, Wu G, Zhou Z, Liu X, Zhan P. Current insights into anti-HIV drug discovery and development: a review of recent patent literature (2014-2017). Expert Opin Ther Pat 2018; 28:299-316. [PMID: 29411697 DOI: 10.1080/13543776.2018.1438410] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION To deal with the rapid emergence of drug resistance challenges, together with the difficulty to eradicate the virus, off-target effects and significant cumulative drug toxicities, it is still imperative to develop next-generation anti-HIV agents with novel chemical classes or new mechanisms of action. AREAS COVERED We primarily focused on current strategies to discover novel anti-HIV agents. Moreover, examples of anti-HIV lead compounds were mainly selected from recently patented publications (reported between 2014 and 2017). In particular, 'privileged structure'-focused substituents decorating approach, scaffold hopping, natural-product diversification and prodrug are focused on. Furthermore, exploitation of new compounds with unexplored mechanisms of action and medicinal chemistry strategies to deplete the HIV reservoir were also described. Perspectives that could inspire future anti-HIV drug discovery are delineated. EXPERT OPINION Even if a large number of patents have been disclosed recently, additional HIV inhibitors are still required, especially novel chemical skeletons displaying a unexploited mechanism of action. Current medicinal chemistry strategies are inadequate, and appropriate and new methodologies and technologies should be exploited to identify novel anti-HIV drug candidates in a time- and cost- effective manner.
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Affiliation(s)
- Xiaofang Zuo
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
| | - Zhipeng Huo
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
| | - Dongwei Kang
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
| | - Gaochan Wu
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
| | - Zhongxia Zhou
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
| | - Xinyong Liu
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
| | - Peng Zhan
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Ji'nan , PR China
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27
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Ashley J, Cordy B, Lucia D, Fradkin LG, Budnik V, Thomson T. Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons. Cell 2018; 172:262-274.e11. [PMID: 29328915 PMCID: PMC5793882 DOI: 10.1016/j.cell.2017.12.022] [Citation(s) in RCA: 272] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 08/15/2017] [Accepted: 12/18/2017] [Indexed: 12/31/2022]
Abstract
Arc/Arg3.1 is required for synaptic plasticity and cognition, and mutations in this gene are linked to autism and schizophrenia. Arc bears a domain resembling retroviral/retrotransposon Gag-like proteins, which multimerize into a capsid that packages viral RNA. The significance of such a domain in a plasticity molecule is uncertain. Here, we report that the Drosophila Arc1 protein forms capsid-like structures that bind darc1 mRNA in neurons and is loaded into extracellular vesicles that are transferred from motorneurons to muscles. This loading and transfer depends on the darc1-mRNA 3' untranslated region, which contains retrotransposon-like sequences. Disrupting transfer blocks synaptic plasticity, suggesting that transfer of dArc1 complexed with its mRNA is required for this function. Notably, cultured cells also release extracellular vesicles containing the Gag region of the Copia retrotransposon complexed with its own mRNA. Taken together, our results point to a trans-synaptic mRNA transport mechanism involving retrovirus-like capsids and extracellular vesicles.
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Affiliation(s)
- James Ashley
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Benjamin Cordy
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Diandra Lucia
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lee G Fradkin
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Vivian Budnik
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Travis Thomson
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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28
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Valbuena A, Mateu MG. Kinetics of Surface-Driven Self-Assembly and Fatigue-Induced Disassembly of a Virus-Based Nanocoating. Biophys J 2017; 112:663-673. [PMID: 28256226 DOI: 10.1016/j.bpj.2016.11.3209] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/19/2016] [Accepted: 11/21/2016] [Indexed: 02/02/2023] Open
Abstract
Self-assembling protein layers provide a "bottom-up" approach for precisely organizing functional elements at the nanoscale over a large solid surface area. The design of protein sheets with architecture and physical properties suitable for nanotechnological applications may be greatly facilitated by a thorough understanding of the principles that underlie their self-assembly and disassembly. In a previous study, the hexagonal lattice formed by the capsid protein (CA) of human immunodeficiency virus (HIV) was self-assembled as a monomolecular layer directly onto a solid substrate, and its mechanical properties and dynamics at equilibrium were analyzed by atomic force microscopy. Here, we use atomic force microscopy to analyze the kinetics of self-assembly of the planar CA lattice on a substrate and of its disassembly, either spontaneous or induced by materials fatigue. Both self-assembly and disassembly of the CA layer are cooperative reactions that proceed until a phase equilibrium is reached. Self-assembly requires a critical protein concentration and is initiated by formation of nucleation points on the substrate, followed by lattice growth and eventual merging of CA patches into a continuous monolayer. Disassembly of the CA layer showed hysteresis and appears to proceed only after large enough defects (nucleation points) are formed in the lattice, whose number is largely increased by inducing materials fatigue that depends on mechanical load and its frequency. Implications of the kinetic results obtained for a better understanding of self-assembly and disassembly of the HIV capsid and protein-based two-dimensional nanomaterials and the design of anti-HIV drugs targeting (dis)assembly and biocompatible nanocoatings are discussed.
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Affiliation(s)
- Alejandro Valbuena
- Centro de Biologia Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biologia Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Madrid, Spain.
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29
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Sha H, Zhu F. Parameter Optimization for Interaction between C-Terminal Domains of HIV-1 Capsid Protein. J Chem Inf Model 2017; 57:1134-1141. [PMID: 28426204 DOI: 10.1021/acs.jcim.7b00011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
HIV-1 capsid proteins (CAs) assemble into a capsid that encloses the viral RNA. The binding between a pair of C-terminal domains (CTDs) constitutes a major interface in both the CA dimers and the large CA assemblies. Here, we attempt to use a general residue-level coarse-grained model to describe the interaction between two isolated CTDs in Monte Carlo simulations. With the standard parameters that depend only on the residue types, the model predicts a much weaker binding in comparison to the experiments. Detailed analysis reveals that some Lennard-Jones parameters are not compatible with the experimental CTD dimer structure, thus resulting in an unfavorable interaction energy. To improve the model for the CTD binding, we introduce ad hoc modifications to a small number of Lennard-Jones parameters for some specific pairs of residues at the binding interface. Through a series of extensive Monte Carlo simulations, we identify the optimal parameters for the CTD-CTD interactions. With the refined model parameters, both the binding affinity (with a dissociation constant of 13 ± 2 μM) and the binding mode are in good agreement with the experimental data. This study demonstrates that the general interaction model based on the Lennard-Jones potential, with some modest adjustment of the parameters for key residues, could correctly reproduce the reversible protein binding, thus potentially applicable for simulating the thermodynamics of the CA assemblies.
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Affiliation(s)
- Hao Sha
- Department of Physics, Indiana University - Purdue University Indianapolis , 402 N. Blackford, LD 154, Indianapolis, Indiana 46202, United States
| | - Fangqiang Zhu
- Department of Physics, Indiana University - Purdue University Indianapolis , 402 N. Blackford, LD 154, Indianapolis, Indiana 46202, United States
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