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Small-Molecule HIV Entry Inhibitors Targeting gp120 and gp41. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1366:27-43. [DOI: 10.1007/978-981-16-8702-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Pu J, Zhou JT, Liu P, Yu F, He X, Lu L, Jiang S. Viral Entry Inhibitors Targeting Six-Helical Bundle Core Against Highly Pathogenic Enveloped Viruses with Class I Fusion Proteins. Curr Med Chem 2021; 29:700-718. [PMID: 33992055 DOI: 10.2174/0929867328666210511015808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 11/22/2022]
Abstract
TypeⅠ enveloped viruses bind to cell receptors through surface glycoproteins to initiate infection or undergo receptor-mediated endocytosis. They also initiate membrane fusion in the acidic environment of endocytic compartments, releasing genetic material into the cell. In the process of membrane fusion, envelope protein exposes fusion peptide, followed by insertion into the cell membrane or endosomal membrane. Further conformational changes ensue in which the type 1 envelope protein forms a typical six-helix bundle structure, shortening the distance between viral and cell membranes so that fusion can occur. Entry inhibitors targeting viral envelope proteins, or host factors, are effective antiviral agents and have been widely studied. Some have been used clinically, such as T20 and Maraviroc for human immunodeficiency virus 1 (HIV-1) or Myrcludex B for hepatitis D virus (HDV). This review focuses on entry inhibitors that target the six-helical bundle core against highly pathogenic enveloped viruses with class I fusion proteins, including retroviruses, coronaviruses, influenza A viruses, paramyxoviruses, and filoviruses.
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Affiliation(s)
- Jing Pu
- Key Laboratory of Medical Molecular Virology of MOE/MOH/CAMS, School of Basic Medical Sciences & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Joey Tianyi Zhou
- Institute of High Performance Computing, The Agency for Science, Technology and Research, Singapore
| | - Ping Liu
- Institute of High Performance Computing, The Agency for Science, Technology and Research, Singapore
| | - Fei Yu
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Xiaoyang He
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology of MOE/MOH/CAMS, School of Basic Medical Sciences & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of MOE/MOH/CAMS, School of Basic Medical Sciences & Shanghai Public Health Clinical Center, Fudan University, Shanghai 200032, China
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Pattnaik GP, Chakraborty H. Entry Inhibitors: Efficient Means to Block Viral Infection. J Membr Biol 2020; 253:425-444. [PMID: 32862236 PMCID: PMC7456447 DOI: 10.1007/s00232-020-00136-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
The emerging and re-emerging viral infections are constant threats to human health and wellbeing. Several strategies have been explored to develop vaccines against these viral diseases. The main effort in the journey of development of vaccines is to neutralize the fusion protein using antibodies. However, significant efforts have been made in discovering peptides and small molecules that inhibit the fusion between virus and host cell, thereby inhibiting the entry of viruses. This class of inhibitors is called entry inhibitors, and they are extremely efficient in reducing viral infection as the entry of the virus is considered as the first step of infection. Nevertheless, these inhibitors are highly selective for a particular virus as antibody-based vaccines. The recent COVID-19 pandemic lets us ponder to shift our attention towards broad-spectrum antiviral agents from the so-called ‘one bug-one drug’ approach. This review discusses peptide and small molecule-based entry inhibitors against class I, II, and III viruses and sheds light on broad-spectrum antiviral agents.
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Affiliation(s)
| | - Hirak Chakraborty
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha, 768 019, India. .,Centre of Excellence in Natural Products and Therapeutics, Sambalpur University, Jyoti Vihar, Burla, Odisha, 768 019, India.
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Jurado S, Cano-Muñoz M, Polo-Megías D, Conejero-Lara F, Morel B. Thermodynamic dissection of the interface between HIV-1 gp41 heptad repeats reveals cooperative interactions and allosteric effects. Arch Biochem Biophys 2020; 688:108401. [PMID: 32376316 DOI: 10.1016/j.abb.2020.108401] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/03/2020] [Accepted: 04/27/2020] [Indexed: 11/27/2022]
Abstract
HIV-1 glycoprotein 41 (gp41) mediates fusion between virus and target cells by folding into a fusion active state, in which the C-terminal heptad repeat (CHR) regions associate externally to the N-terminal heptad repeat (NHR) trimer and form a very stable six-helix bundle coiled-coil structure. Therefore, interfering with the NHR-CHR interaction of gp41 is a promising therapeutic approach against HIV-1. However, a full understanding of the molecular and mechanistic details of this interaction is still incomplete. Here, we use single-chain, chimeric proteins (named covNHR) that reproduce accurately the CHR-NHR interactions to analyze the binding thermodynamics of several peptides with different length from the CHR region. The results indicate that cooperative binding involving two or more pockets of the NHR groove is necessary to obtain relevant affinities and that the binding energy is broadly distributed along the interface, underlining a crucial role of a middle pocket to achieve tight binding. In contrast, targeting only the deep hydrophobic pocket is insufficient to achieve significant affinity. Moreover, calorimetry experiments in combination with limited proteolysis performed using a mutant with occluded binding in the N-terminal pocket reveal the existence of an allosteric communication between the different regions. This study is the first detailed thermodynamic dissection of the NHR-CHR interaction in gp41 and contributes therefore to a better understanding of HIV fusion. These results are relevant for the development of potential fusion inhibitors.
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Affiliation(s)
- Samuel Jurado
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Mario Cano-Muñoz
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Daniel Polo-Megías
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Bertrand Morel
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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Sepehri S, Soleymani S, Zabihollahi R, Aghasadeghi MR, Sadat M, Saghaie L, Memarian HR, Fassihi A. Design, Synthesis, and Anti-HIV-1 Evaluation of a Novel Series of 1,2,3,4-Tetrahydropyrimidine-5-Carboxylic Acid Derivatives. Chem Biodivers 2018; 15:e1700502. [PMID: 29411517 DOI: 10.1002/cbdv.201700502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/02/2018] [Indexed: 01/04/2023]
Abstract
A series of tetrahydropyrimidine derivatives (2a - 2l) were designed, synthesized, and screened for anti-HIV-1 properties based on the structures of HIV-1 gp41 binding site inhibitors, NB-2 and NB-64. A computational study was performed to predict the pharmacodynamics, pharmacokinetics, and drug-likeness features of the studied molecules. Docking studies revealed that the carboxylic acid group in the molecules forms salt bridges with either Lys574 or Arg579. Physiochemical properties (e.g., molecular weight, number of hydrogen bond donors, number of hydrogen bond acceptors, and number of rotatable bonds) of the synthesized compounds confirmed and exhibited that these compounds were within the range set by Lipinski's rule of five. Compounds 2e and 2k with 4-chlorophenyl substituent and 4-methylphenyl group at C(4) position of the tetrahydropyrimidine ring was the most potent one among the tested compounds. This suggests that these compounds may serve as leads for development of novel small-molecule HIV-1 inhibitors.
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Affiliation(s)
- Saghi Sepehri
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran.,Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, 5618953141, Iran
| | - Sepehr Soleymani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, No. 69, Pasteur Ave, Tehran, 13169-43551, Iran
| | - Rezvan Zabihollahi
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, No. 69, Pasteur Ave, Tehran, 13169-43551, Iran
| | - Mohammad R Aghasadeghi
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, No. 69, Pasteur Ave, Tehran, 13169-43551, Iran
| | - Mehdi Sadat
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, No. 69, Pasteur Ave, Tehran, 13169-43551, Iran
| | - Lotfollah Saghaie
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
| | - Hamid R Memarian
- Department of Chemistry, Faculty of Sciences, University of Isfahan, Isfahan, 81746-73441, Iran
| | - Afshin Fassihi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
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Sepehri S, Soleymani S, Zabihollahi R, Aghasadeghi MR, Sadat M, Saghaie L, Fassihi A. Synthesis, Biological Evaluation, and Molecular Docking Studies of Novel 4-[4-Arylpyridin-1(4H)-yl]benzoic Acid Derivatives as Anti-HIV-1 Agents. Chem Biodivers 2017; 14. [DOI: 10.1002/cbdv.201700295] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/17/2017] [Indexed: 01/16/2023]
Affiliation(s)
- Saghi Sepehri
- Department of Medicinal Chemistry; School of Pharmacy and Pharmaceutical Sciences; Isfahan University of Medical Sciences; 81746-73461 Isfahan Iran
- Department of Medicinal Chemistry; School of Pharmacy; Ardabil University of Medical Sciences; 56189-53141 Ardabil Iran
| | - Sepehr Soleymani
- Department of Hepatitis and AIDS; Pasteur Institute of Iran; 13169-43551 Tehran Iran
| | - Rezvan Zabihollahi
- Department of Hepatitis and AIDS; Pasteur Institute of Iran; 13169-43551 Tehran Iran
| | | | - Mehdi Sadat
- Department of Hepatitis and AIDS; Pasteur Institute of Iran; 13169-43551 Tehran Iran
| | - Lotfollah Saghaie
- Department of Medicinal Chemistry; School of Pharmacy and Pharmaceutical Sciences; Isfahan University of Medical Sciences; 81746-73461 Isfahan Iran
| | - Afshin Fassihi
- Department of Medicinal Chemistry; School of Pharmacy and Pharmaceutical Sciences; Isfahan University of Medical Sciences; 81746-73461 Isfahan Iran
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Li W, Lu L, Li W, Jiang S. Small-molecule HIV-1 entry inhibitors targeting gp120 and gp41: a patent review (2010-2015). Expert Opin Ther Pat 2017; 27:707-719. [PMID: 28076686 DOI: 10.1080/13543776.2017.1281249] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION It is essential to discover and develop small-molecule HIV-1 entry inhibitors with suitable pharmaceutical properties. Areas covered: We review the development of small-molecule HIV-1 entry inhibitors as evidenced in patents, patent applications, and related research articles published between 2010 and 2015. Expert opinion: HIV-1 Env gp120 and gp41 are important targets for development of HIV-1 entry inhibitors. The Phe43 pocket in gp120 and the highly conserved hydrophobic pocket on gp41 NHR-trimer are important targets for identification of HIV-1 attachment and fusion inhibitors, respectively. Compounds that bind to Phe43 pocket can block viral gp120 binding to CD4 on T cells, thus inhibiting HIV-1 attachment. However, most compounds targeting Phe43 pocket identified so far are HIV-1 entry agonists with the ability to enhance infectivity of HIV-1 in CD4-negative cells. Therefore, it is essential to identify HIV-1 entry antagonist-based HIV-1 attachment/entry inhibitors. Compounds binding to the gp41 hydrophobic pocket may inhibit CHR binding to the gp41 NHR trimer, thus blocking six-helix bundle formation and gp41-mediated virus-cell fusion. However, most lead compounds targeting this pocket have low potency, possibly because the pocket is too big or too deep. Therefore, it is necessary to identify other pockets in gp41 for developing HIV-1 fusion/entry inhibitors.
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Affiliation(s)
- Wen Li
- a Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science , Fudan University , Shanghai , China
| | - Lu Lu
- a Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science , Fudan University , Shanghai , China
| | - Weihua Li
- b Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD , Fudan University , Shanghai , China
| | - Shibo Jiang
- a Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science , Fudan University , Shanghai , China.,b Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD , Fudan University , Shanghai , China.,c Lindsley F. Kimball Research Institute , New York Blood Center , New York , NY , USA
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Sofiyev V, Kaur H, Snyder BA, Hogan PA, Ptak RG, Hwang P, Gochin M. Enhanced potency of bivalent small molecule gp41 inhibitors. Bioorg Med Chem 2017; 25:408-420. [PMID: 27908751 PMCID: PMC5260928 DOI: 10.1016/j.bmc.2016.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/31/2016] [Accepted: 11/03/2016] [Indexed: 11/28/2022]
Abstract
Low molecular weight peptidomimetic inhibitors with hydrophobic pocket binding properties and moderate fusion inhibitory activity against HIV-1 gp41-mediated cell fusion were elaborated by increasing the available surface area for interacting with the heptad repeat-1 (HR1) coiled coil on gp41. Two types of modifications were tested: 1) increasing the overall hydrophobicity of the molecules with an extension that could interact in the HR1 groove, and 2) forming symmetrical dimers with two peptidomimetic motifs that could potentially interact simultaneously in two hydrophobic pockets on the HR1 trimer. The latter approach was more successful, yielding 40-60times improved potency against HIV fusion over the monomers. Biophysical characterization, including equilibrium binding studies by fluorescence and kinetic analysis by Surface Plasmon Resonance, revealed that inhibitor potency was better correlated to off-rates than to binding affinity. Binding and kinetic data could be fit to a model of bidentate interaction of dimers with the HR1 trimer as an explanation for the slow off-rate, albeit with minimal cooperativity due to the highly flexible ligand structures. The strong cooperativity observed in fusion inhibitory activity of the dimers implied accentuated potency due to the transient nature of the targeted intermediate. Optimization of monomer, dimer or higher order structures has the potential to lead to highly potent non-peptide fusion inhibitors by targeting multiple hydrophobic pockets.
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Affiliation(s)
- Vladimir Sofiyev
- Department of Basic Sciences, Touro University-California, Vallejo, CA 94592, United States
| | - Hardeep Kaur
- Department of Basic Sciences, Touro University-California, Vallejo, CA 94592, United States
| | - Beth A Snyder
- Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, United States
| | - Priscilla A Hogan
- Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, United States
| | - Roger G Ptak
- Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, United States
| | - Peter Hwang
- Department of Biophysics and Biochemistry, University of California San Francisco, CA 94143, United States
| | - Miriam Gochin
- Department of Basic Sciences, Touro University-California, Vallejo, CA 94592, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, CA 94143, United States.
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Liang G, Wang H, Chong H, Cheng S, Jiang X, He Y, Wang C, Liu K. An effective conjugation strategy for designing short peptide-based HIV-1 fusion inhibitors. Org Biomol Chem 2016; 14:7875-82. [PMID: 27454320 DOI: 10.1039/c6ob01334a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lengthy peptides corresponding to the C-terminal heptad repeat (C-peptides) of human immunodeficiency virus type 1 (HIV-1) gp41 are potent inhibitors against virus-cell fusion. Designing short C-peptide-based HIV-1 fusion inhibitors could potentially redress the physicochemical and technical liabilities of a long-peptide therapeutic. However, designing such inhibitors with high potency has been challenging. We generated a conjugated architecture by incorporating small-molecule inhibitors of gp41 into the N-terminus of a panel of truncated C-peptides. Among these small molecule-capped short peptides, the 26-residue peptide Indole-T26 inhibited HIV-1 Env-mediated cell-cell fusion and viral replication at low nanomolar levels, reaching the potency of the only clinically used 36-residue peptide T20 (enfuvirtide). Collectively, our work opens up a new avenue for developing short peptide-based HIV-1 fusion inhibitors, and may have broad applicability to the development of modulators of other class I fusion proteins.
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Affiliation(s)
- Guodong Liang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, 27 Tai-Ping Road, Beijing, 100850, China.
| | - Huixin Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Huihui Chong
- MOH Key Laboratory of Systems Biology of Pathogens and AIDS Research Center, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 9, Dong Dan San Tiao, Beijing 100730, China
| | - Siqi Cheng
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Xifeng Jiang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, 27 Tai-Ping Road, Beijing, 100850, China.
| | - Yuxian He
- MOH Key Laboratory of Systems Biology of Pathogens and AIDS Research Center, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 9, Dong Dan San Tiao, Beijing 100730, China
| | - Chao Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, 27 Tai-Ping Road, Beijing, 100850, China.
| | - Keliang Liu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, 27 Tai-Ping Road, Beijing, 100850, China.
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Abstract
Computational medicinal chemistry offers viable strategies for finding, characterizing, and optimizing innovative pharmacologically active compounds. Technological advances in both computer hardware and software as well as biological chemistry have enabled a renaissance of computer-assisted "de novo" design of molecules with desired pharmacological properties. Here, we present our current perspective on the concept of automated molecule generation by highlighting chemocentric methods that may capture druglike chemical space, consider ligand promiscuity for hit and lead finding, and provide fresh ideas for the rational design of customized screening of compound libraries.
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Affiliation(s)
- Petra Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.,inSili.com LLC , Segantinisteig 3, 8049 Zürich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
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Lu L, Yu F, Cai L, Debnath AK, Jiang S. Development of Small-molecule HIV Entry Inhibitors Specifically Targeting gp120 or gp41. Curr Top Med Chem 2016; 16:1074-90. [PMID: 26324044 PMCID: PMC4775441 DOI: 10.2174/1568026615666150901114527] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 05/17/2015] [Accepted: 05/27/2015] [Indexed: 12/31/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) envelope (Env) glycoprotein surface subunit gp120 and transmembrane subunit gp41 play important roles in HIV-1 entry, thus serving as key targets for the development of HIV-1 entry inhibitors. T20 peptide (enfuvirtide) is the first U.S. FDA-approved HIV entry inhibitor; however, its clinical application is limited by the lack of oral availability. Here, we have described the structure and function of the HIV-1 gp120 and gp41 subunits and reviewed advancements in the development of small-molecule HIV entry inhibitors specifically targeting these two Env glycoproteins. We then compared the advantages and disadvantages of different categories of HIV entry inhibitor candidates and further predicted the future trend of HIV entry inhibitor development.
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Affiliation(s)
| | | | | | | | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of MOE/MOH, Shanghai Medical College, Fudan University, 130 Dong An Road, Building #13, Shanghai 200032, China.
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Konstantinidou M, Gkermani A, Hadjipavlou-Litina D. Synthesis and Pharmacochemistry of New Pleiotropic Pyrrolyl Derivatives. Molecules 2015; 20:16354-74. [PMID: 26378503 PMCID: PMC6332026 DOI: 10.3390/molecules200916354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 01/04/2023] Open
Abstract
Within the framework of our attempts to synthesize pleiotropic anti-inflammatory agents, we have synthesized some chalcones and their corresponding 3,4-pyrrolyl derivatives. Chalcones constitute a class of compounds with high biological impact. They are known for a number of biological activities, including anti-inflammatory and free radical scavenging activities. They inhibit several enzymes implicated in the inflammatory process, such as lipoxygenase, cyclooxygenase (COX) and lysozymes. The synthesized pyrroles have been studied for: (1) their in vitro inhibition of lipoxygenase; (2) their in vitro inhibition of COX; (3) their in vitro inhibition of lipid peroxidation; (4) their interaction with the stable, N-centered, free radical, 2,2-diphenyl-1-picrylhydrazyl (DPPH); (5) their inhibition on interleukin-6 (IL-6); (6) their anti-proteolytic activity; and (7) their in vivo anti-inflammatory activity using carrageenan-induced rat paw edema. Their physicochemical properties were determined to explain the biological results. Lipophilicity was experimentally determined. 2i and 2v were found to be promising multifunctional molecules with high antiproteolytic and anti-inflammatory activities in combination with anti-interleukin-6 activity.
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Affiliation(s)
- Markella Konstantinidou
- Department of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
| | - Alice Gkermani
- Department of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
| | - Dimitra Hadjipavlou-Litina
- Department of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
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One-pot synthesis of 3-hydroxyanthranilate derivatives using furans, bromoalkyne, and secondary amines. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.03.098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Walsh JD, Chu S, Zhang SQ, Gochin M. Design and characterization of swapped-domain constructs of HIV-1 glycoprotein-41 as receptors for drug discovery. Protein Eng Des Sel 2015; 28:107-16. [PMID: 25792539 PMCID: PMC4366113 DOI: 10.1093/protein/gzv006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/08/2015] [Accepted: 01/28/2015] [Indexed: 11/14/2022] Open
Abstract
Four new swapped-domain constructs of the ectodomain of human immunodeficiency virus type 1 glycoprotein-41 (gp41) were prepared. The gp41 ectodomain consists of 50-residue N-heptad repeat (NHR), 36-residue disulfide-bonded loop and 39-residue C-heptad repeat (CHR). It folds into a hairpin structure that forms a trimer along the NHR axis. The swapped-domain proteins feature CHR domains of length 39, 28 or 21 residues preceding a 4-residue loop and a 49- or 50-residue NHR domain. The effect of CHR truncation was to expose increasing lengths of the NHR groove, including the conserved hydrophobic pocket, an important drug target. A novel method for preparing proteins with extended exposed hydrophobic surfaces was demonstrated. Biophysical measurements, including analytical ultracentrifugation and ligand-detected Water-Ligand Observed via Gradient Spectroscopy and (1)H-(15)N-HSQC NMR experiments, were used to confirm that the proteins formed stable trimers in solution with exposed binding surfaces. These proteins could play an important role as receptors in structure-based drug discovery.
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Affiliation(s)
- Joseph D Walsh
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Shidong Chu
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Shao-Qing Zhang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19014, USA
| | - Miriam Gochin
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
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Sepehri S, Gharagani S, Saghaie L, Aghasadeghi MR, Fassihi A. QSAR and docking studies of some 1,2,3,4-tetrahydropyrimidines: evaluation of gp41 as possible target for anti-HIV-1 activity. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1246-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Munnaluri R, Sivan SK, Manga V. Molecular docking and MM/GBSA integrated protocol for designing small molecule inhibitors against HIV-1 gp41. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1185-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wang C, Shi W, Cai L, Lu L, Yu F, Wang Q, Jiang X, Xu X, Wang K, Xu L, Jiang S, Liu K. Artificial peptides conjugated with cholesterol and pocket-specific small molecules potently inhibit infection by laboratory-adapted and primary HIV-1 isolates and enfuvirtide-resistant HIV-1 strains. J Antimicrob Chemother 2014; 69:1537-45. [DOI: 10.1093/jac/dku010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Chu S, Gochin M. Identification of fragments targeting an alternative pocket on HIV-1 gp41 by NMR screening and similarity searching. Bioorg Med Chem Lett 2013; 23:5114-8. [PMID: 23932360 DOI: 10.1016/j.bmcl.2013.07.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/02/2013] [Accepted: 07/16/2013] [Indexed: 01/12/2023]
Abstract
The HIV-1 envelope glycoprotein gp41 fusion intermediate is a promising drug target for inhibiting viral entry. However, drug development has been impeded by challenges inherent in mediating the underlying protein-protein interaction. Here we report on the identification of fragments that bind to a C-terminal sub-pocket adjacent to the well-known hydrophobic pocket on the NHR coiled coil. Using a specifically designed assay and ligand-based NMR screening of a fragment library, we identified a thioenylaminopyrazole compound with a dissociation constant of ~500 μM. Interaction with the C-terminal sub-pocket was confirmed by paramagnetic relaxation enhancement NMR experiments, which also yielded the binding mode. Shape-based similarity searching detected additional phenylpyrazole and phenyltriazole fragments within the library, enriching the hit rate over random screening, and revealing molecular features required for activity. Discovery of the novel scaffolds and binding mechanism suggests avenues for extending the interaction surface and improving the potency of a hydrophobic pocket binding inhibitor.
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Affiliation(s)
- Shidong Chu
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Mare Island, Vallejo, CA 94592, USA
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19
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Wang C, Shi W, Cai L, Lu L, Wang Q, Zhang T, Li J, Zhang Z, Wang K, Xu L, Jiang X, Jiang S, Liu K. Design, synthesis, and biological evaluation of highly potent small molecule-peptide conjugates as new HIV-1 fusion inhibitors. J Med Chem 2013; 56:2527-39. [PMID: 23458727 DOI: 10.1021/jm3018964] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The small molecule fusion inhibitors N-(4-carboxy-3-hydroxyphenyl)-2,5-dimethylpyrrole (NB-2) and N-(3-carboxy-4-hydroxyphenyl)-2,5-dimethylpyrrole (A12) target a hydrophobic pocket of HIV-1 gp41 and have moderate anti-HIV-1 activity. In this paper, we report the design, synthesis, and structure-activity relationship of a group of hybrid molecules in which the pocket-binding domain segment of the C34 peptide was replaced with NB-2 and A12 derivatives. In addition, the synergistic effect between the small molecule and peptide moieties was analyzed, and lead compounds with a novel scaffold were discovered. We found that either the nonpeptide or peptide part alone showed weak activity against HIV-1-mediated cell-cell fusion, but the conjugates properly generated a strong synergistic effect. Among them, conjugates Aoc-βAla-P26 and Noc-βAla-P26 exhibited a low nanomolar IC50 in the cell-cell fusion assay and effectively inhibited T20-sensitive and -resistant HIV-1 strains. Furthermore, the new molecules exhibited better stability against proteinase K digestion than T20 and C34.
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Affiliation(s)
- Chao Wang
- Beijing Institute of Pharmacology & Toxicology, 27 Tai-Ping Road, Beijing 100850, China
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20
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Approaches for identification of HIV-1 entry inhibitors targeting gp41 pocket. Viruses 2013; 5:127-49. [PMID: 23344560 PMCID: PMC3564113 DOI: 10.3390/v5010127] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/03/2013] [Accepted: 01/03/2013] [Indexed: 01/08/2023] Open
Abstract
The hydrophobic pocket in the HIV-1 gp41 N-terminal heptad repeat (NHR) domain plays an important role in viral fusion and entry into the host cell, and serves as an attractive target for development of HIV-1 fusion/entry inhibitors. The peptide anti-HIV drug targeting gp41 NHR, T-20 (generic name: enfuvirtide; brand name: Fuzeon), was approved by the U.S. FDA in 2003 as the first HIV fusion/entry inhibitor for treatment of HIV/AIDS patients who fail to respond to the current antiretroviral drugs. However, because T20 lacks the pocket-binding domain (PBD), it exhibits low anti-HIV-1 activity and short half-life. Therefore, several next-generation HIV fusion inhibitory peptides with PBD have been developed. They possess longer half-life and more potent antiviral activity against a broad spectrum of HIV-1 strains, including the T-20-resistant variants. Nonetheless, the clinical application of these peptides is still limited by the lack of oral availability and the high cost of production. Thus, development of small molecule compounds targeting the gp41 pocket with oral availability has been promoted. This review describes the main approaches for identification of HIV fusion/entry inhibitors targeting the gp41 pocket and summarizes the latest progress in developing these inhibitors as a new class of anti-HIV drugs.
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Abstract
This chapter reviews studies that have used in silico techniques to design or identify potential HIV-1 entry inhibitors targeting cellular receptors CD4, CCR5, and CXCR4 and envelope glycoproteins, gp120 and gp41 of HIV-1. Both structure- and ligand-based design techniques have been used in those studies by applying diverse modeling techniques such as quantitative structure-activity relationship analysis, conformational analysis, molecular dynamics, pharmacophore generation, docking, virtual screening (using docking software and also shape-based ROCS techniques), and fragment-based design.
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Affiliation(s)
- Asim K Debnath
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, USA
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22
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Cai L, Gochin M, Liu K. Biochemistry and biophysics of HIV-1 gp41 - membrane interactions and implications for HIV-1 envelope protein mediated viral-cell fusion and fusion inhibitor design. Curr Top Med Chem 2012; 11:2959-84. [PMID: 22044229 DOI: 10.2174/156802611798808497] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 03/16/2011] [Accepted: 12/01/2011] [Indexed: 11/22/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1), the pathogen of acquired immunodeficiency syndrome (AIDS), causes ~2 millions death every year and still defies an effective vaccine. HIV-1 infects host cells through envelope protein - mediated virus-cell fusion. The transmembrane subunit of envelope protein, gp41, is the molecular machinery which facilitates fusion. Its ectodomain contains several distinguishing functional domains, fusion peptide (FP), Nterminal heptad repeat (NHR), C-terminal heptad repeat (CHR) and membrane proximal extracellular region (MPER). During the fusion process, FP inserts into the host cell membrane, and an extended gp41 prehairpin conformation bridges the viral and cell membranes through MPER and FP respectively. Subsequent conformational change of the unstable prehairpin results in a coiled-coil 6-helix bundle (6HB) structure formed between NHR and CHR. The energetics of 6HB formation drives membrane apposition and fusion. Drugs targeting gp41 functional domains to prevent 6HB formation inhibit HIV-1 infection. T20 (enfuvirtide, Fuzeon) was approved by the US FDA in 2003 as the first fusion inhibitor. It is a 36-residue peptide from the gp41 CHR, and it inhibits 6HB formation by targeting NHR and lipids. Development of new fusion inhibitors, especially small molecule drugs, is encouraged to overcome the shortcomings of T20 as a peptide drug. Hydrophobic characteristics and membrane association are critical for gp41 function and mechanism of action. Research in gp41-membrane interactions, using peptides corresponding to specific functional domains, or constructs including several interactive domains, are reviewed here to get a better understanding of gp41 mediated virus-cell fusion that can inform or guide the design of new HIV-1 fusion inhibitors.
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Affiliation(s)
- Lifeng Cai
- Beijing Institute of Pharmacology & Toxicology, Haidian District, Beijing 100850, China.
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23
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Green KD, Chen W, Garneau-Tsodikova S. Identification and characterization of inhibitors of the aminoglycoside resistance acetyltransferase Eis from Mycobacterium tuberculosis. ChemMedChem 2012; 7:73-7. [PMID: 21898832 PMCID: PMC3401626 DOI: 10.1002/cmdc.201100332] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/18/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Keith D. Green
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA) Fax: (+ 1)734-615-5521
| | - Wenjing Chen
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA) Fax: (+ 1)734-615-5521
- Chemical Biology Doctoral Program, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA)
| | - Sylvie Garneau-Tsodikova
- Chemical Biology Doctoral Program, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA)
- Department of Medicinal Chemistry in the College of Pharmacy, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109 (USA)
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24
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Synthesis and antiviral activities of novel gossypol derivatives. Bioorg Med Chem Lett 2011; 22:1415-20. [PMID: 22226654 DOI: 10.1016/j.bmcl.2011.12.076] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 11/25/2011] [Accepted: 12/07/2011] [Indexed: 11/22/2022]
Abstract
In this study, a series of novel gossypol derivatives were synthesized and screened in vitro for their anti-HIV-1 and anti-H(5)N(1) activities, respectively. Replacing the aldehyde groups of gossypol with some amino acids not only reduced the cytotoxicity but also enhanced the activities against HIV-1 and H(5)N(1). Compounds 13-17 showed more potent activities against HIV-1 and H(5)N(1) than the other gossypol derivatives. Meanwhile, these compounds also exhibited more potent activities against H(5)N(1) than 1-adamantylamine. The absence of the COONa group in gossypol derivatives resulted in a loss of anti-HIV-1 activity, suggesting that this group might play an important role in mediating the antiviral activity. Time-of-addition assays indicated that compounds 13-17 had the similar mechanism of anti-HIV-1 action with T20. Molecular modeling analysis demonstrated that compounds 13-17 could fit inside the gp41 hydrophobic pocket through hydrogen bonding network, hydrophobic contacts and strong electrostatic interactions.
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25
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Zhou G, Wu D, Snyder B, Ptak RG, Kaur H, Gochin M. Development of indole compounds as small molecule fusion inhibitors targeting HIV-1 glycoprotein-41. J Med Chem 2011; 54:7220-31. [PMID: 21928824 DOI: 10.1021/jm200791z] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nonpeptide inhibition of fusion remains an important goal in anti-HIV research, due to its potential for low cost prophylaxis or prevention of cell-cell transmission of the virus. We report here on a series of indole compounds that have been identified as fusion inhibitors of gp41 through a structure-based drug design approach. Experimental binding affinities of the compounds for the hydrophobic pocket were strongly correlated to fusion inhibitory data (R(2) = 0.91), and corresponding inhibition of viral replication confirmed the hydrophobic pocket as a valid target for low molecular weight fusion inhibitors. The most active compound bound to the hydrophobic pocket and inhibited cell-cell fusion and viral replication at submicromolar levels. A common binding mode for the inhibitors in this series was established by carrying out docking studies using structures of gp41 in the Protein Data Bank. The molecules were flexible enough to conform to the contours of the pocket, and the most active compound was able to adopt a structure mimicking the hydrophobic contacts of the D-peptide PIE7. The results enhance our understanding of indole compounds as inhibitors of gp41.
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Affiliation(s)
- Guangyan Zhou
- Department of Basic Sciences, Touro University-California, 1310 Club Drive, Mare Island, Vallejo, California 94592, United States.
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26
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Baranova EO, Shastina NS, Shvets VI. Polyanionic inhibitors of HIV adsorption. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:592-608. [DOI: 10.1134/s1068162011050037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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27
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HIV microbicides: state-of-the-art and new perspectives on the development of entry inhibitors. Future Med Chem 2011; 2:1141-59. [PMID: 21426161 DOI: 10.4155/fmc.10.203] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Since the discovery of HIV at the beginning of the 1980s, numerous efforts have been devoted to the search of an efficient vaccine. There are at least 25 drugs available for HIV treatment, but no cure is available. The observation that therapy for HIV disease is life long and that these drugs are associated with a number of side effects underlines the need for approaches aimed at preventing rather than treating infection. Additionally, the economic burden of treatment for the HIV infection occupies an increasing share of healthcare expenditure, making current practices likely to become difficult to sustain in the long run. Unfortunately, no effective vaccine for this disease is foreseeable in the near future. Microbicides could be an alternate way to build preventative approaches to HIV infection. Strategies based on preventing the virus from reaching its target cells seem to have some room for development and application. In this review we explore the state-of-the-art of available microbicides, focusing on HIV entry inhibitors. In addition, we discuss new compounds that show anti-HIV activity, which could be effective candidates.
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28
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Gochin M, Zhou G, Phillips AH. Paramagnetic relaxation assisted docking of a small indole compound in the HIV-1 gp41 hydrophobic pocket. ACS Chem Biol 2011; 6:267-74. [PMID: 21155611 DOI: 10.1021/cb100368d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The hydrophobic pocket contained within the gp41 coiled coil is an important target for small molecules designed to inhibit HIV-1 fusion. While various screening experiments have identified molecules purported to bind in this pocket, few have confirmed details of the interaction, instead relying on computational docking to predict the binding mode. This is made more challenging by the fact that residues lining the hydrophobic pocket are highly flexible, as is typical for a protein-protein interaction site, limiting the predictive power of computational tools. In this study, we report on an NMR method to define the binding mode of 1-5i, a compound in a series of newly developed indole inhibitors. We show that paramagnetic relaxation enhancement of ligand protons due to an MTSL group positioned close to the binding pocket could be applied quantitatively to distinguish between more than 30 different computational poses, selecting a single pose that agreed with the NMR data. In this pose, important hydrophobic and polar contacts occur with pocket lysine, tryptophan, and glutamine residues, including putative hydrogen bonds between the ligand carboxylate and the lysine ε-amino group. A study of the ligand orientation suggests directions for optimization.
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Affiliation(s)
- Miriam Gochin
- Department of Basic Sciences, Touro University-California, Vallejo, California 94592, United States
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Guangyan Zhou
- Department of Basic Sciences, Touro University-California, Vallejo, California 94592, United States
| | - Aaron H. Phillips
- Department of Basic Sciences, Touro University-California, Vallejo, California 94592, United States
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29
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Cai L, Jiang S. Development of peptide and small-molecule HIV-1 fusion inhibitors that target gp41. ChemMedChem 2011; 5:1813-24. [PMID: 20845360 DOI: 10.1002/cmdc.201000289] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
It has been 25 years since the development of the first efficient HIV-1/AIDS treatment. Scientists now know more about the HIV-1 infection life cycle, and more than 30 antiretroviral drugs have been developed, including HIV-1 fusion inhibitors. Fundamental work was begun in the early 1990s and led to the development of a novel class of anti-HIV-1 drugs, culminating in a peptide known as T20, which is currently the only HIV-1 fusion inhibitor approved by the US Food and Drug Administration. However, more work needs to be done to perfect the development of peptide and small-molecule HIV fusion inhibitors, particularly those that target gp41. Herein we present a brief overview of the development of this class of anti-HIV-1 drug by focusing on the achievements, challenges, and lessons learned. We cite hallmark studies of the past and comment on future drug development.
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Affiliation(s)
- Lifeng Cai
- Department of Medicinal Chemistry, Beijing Institute of Pharmacology & Toxicology, 27 Taiping Road, Haidian District, Beijing 100850, China.
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30
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Kutchukian PS, Shakhnovich EI. De novo design: balancing novelty and confined chemical space. Expert Opin Drug Discov 2010; 5:789-812. [PMID: 22827800 DOI: 10.1517/17460441.2010.497534] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD De novo drug design serves as a tool for the discovery of new ligands for macromolecular targets as well as optimization of known ligands. Recently developed tools aim to address the multi-objective nature of drug design in an unprecedented manner. AREAS COVERED IN THIS REVIEW This article discusses recent advances in de novo drug design programs and accessory programs used to evaluate compounds post-generation. WHAT THE READER WILL GAIN The reader is introduced to the challenges inherent in de novo drug design and will become familiar with current trends in de novo design. Furthermore, the reader will be better prepared to assess the value of a tool, and be equipped to design more elegant tools in the future. TAKE HOME MESSAGE De novo drug design can assist in the efficient discovery of new compounds with a high affinity for a given target. The inclusion of existing chemoinformatic methods with current structure-based de novo design tools provides a means of enhancing the therapeutic value of these generated compounds.
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Affiliation(s)
- Peter S Kutchukian
- Harvard University, Chemistry and Chemical Biology Department, 12 Oxford Street, Cambridge, MA 02138, USA
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