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da Costa RA, da Costa ADSS, da Rocha JAP, Lima MRDC, da Rocha ECM, Nascimento FCDA, Gomes AJB, do Rego JDAR, Brasil DDSB. Exploring Natural Alkaloids from Brazilian Biodiversity as Potential Inhibitors of the Aedes aegypti Juvenile Hormone Enzyme: A Computational Approach for Vector Mosquito Control. Molecules 2023; 28:6871. [PMID: 37836714 PMCID: PMC10574778 DOI: 10.3390/molecules28196871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/26/2023] [Accepted: 09/02/2023] [Indexed: 10/15/2023] Open
Abstract
This study explores the potential inhibitory activity of alkaloids, a class of natural compounds isolated from Brazilian biodiversity, against the mJHBP enzyme of the Aedes aegypti mosquito. This mosquito is a significant vector of diseases such as dengue, zika, and chikungunya. The interactions between the ligands and the enzyme at the molecular level were evaluated using computational techniques such as molecular docking, molecular dynamics (MD), and molecular mechanics with generalized Born surface area (MMGBSA) free energy calculation. The findings suggest that these compounds exhibit a high binding affinity with the enzyme, as confirmed by the binding free energies obtained in the simulation. Furthermore, the specific enzyme residues that contribute the most to the stability of the complex with the compounds were identified: specifically, Tyr33, Trp53, Tyr64, and Tyr129. Notably, Tyr129 residues were previously identified as crucial in the enzyme inhibition process. This observation underscores the significance of the research findings and the potential of the evaluated compounds as natural insecticides against Aedes aegypti mosquitoes. These results could stimulate the development of new vector control agents that are more efficient and environmentally friendly.
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Affiliation(s)
- Renato Araújo da Costa
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education, Science and Technology of Pará (IFPA) Campus Abaetetuba, Abaetetuba 68440-000, PA, Brazil; (M.R.d.C.L.); (A.J.B.G.)
| | - Andréia do Socorro Silva da Costa
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
| | - João Augusto Pereira da Rocha
- Graduate Program in Chemistry, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (J.A.P.d.R.); (E.C.M.d.R.)
| | - Marlon Ramires da Costa Lima
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education, Science and Technology of Pará (IFPA) Campus Abaetetuba, Abaetetuba 68440-000, PA, Brazil; (M.R.d.C.L.); (A.J.B.G.)
| | | | - Fabiana Cristina de Araújo Nascimento
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
| | - Anderson José Baia Gomes
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education, Science and Technology of Pará (IFPA) Campus Abaetetuba, Abaetetuba 68440-000, PA, Brazil; (M.R.d.C.L.); (A.J.B.G.)
| | - José de Arimatéia Rodrigues do Rego
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
| | - Davi do Socorro Barros Brasil
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
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Upadhyaya A, Panthi B, Verma S, Kumar S, Rajouria SK, Srivastava HK, Chandra P. Analogue and structure based approaches for modelling HIV-1 integrase inhibitors. J Biomol Struct Dyn 2023; 41:11946-11956. [PMID: 36734646 DOI: 10.1080/07391102.2023.2171129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/25/2022] [Indexed: 02/04/2023]
Abstract
A set of 220 inhibitors belonging to different structure classes and having HIV-1 integrase activity were collected along with their experimental pIC50 values. Geometries of all the inhibitors were fully optimized using B3LYP/6-31 + G(d) level of theory. These ligands were docked against 4 different HIV-1 integrase receptors (PDB IDs: 4LH5, 5KRS, 3ZSQ and 3ZSV). 30 docked poses were generated for all 220 inhibitors and ligand interaction of the first docked pose and the docked pose with the highest score were analysed. Residue GLU170 of 4LH5 receptor shows the highest number of interactions followed by ALA169, GLN168, HIS171 and ASP167 residues. Hydrogen bonding and stacking are mainly responsible for the interactions of these inhibitors with the receptor. We performed Molecular Dynamics (MD) simulation to observe the root-mean-square deviation (RMSD), for measure the average change of displacement between the atoms for a particular frame with respect to a reference and The Root Mean Square Fluctuation (RMSF) for characterization of local changes along the protein chain of the docked complexes. Analogue based models were generated to predict the pIC50 values for integrase inhibitors using various types of descriptors such as constitutional, geometrical, topological, quantum chemical and docking based descriptors. The best models were selected on the basis of statistical parameters and were validated by training and test set division. A few new inhibitors were designed on the basis of structure activity relationship and their pIC50 values were predicted using the generated models. All the designed new inhibitors a very high potential and may be used as potent inhibitors of HIV integrase. These models may be useful for further design and development of new and potent HIV integrase inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anurag Upadhyaya
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Bhavana Panthi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kalyanpur Kanpur, Uttar Pradesh, India
| | - Shubham Verma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Changsari, Guwahati, Assam, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Suresh Kumar
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- Department of Physics, Dyal Singh College, University of Delhi, Delhi, India
| | - Satish Kumar Rajouria
- Department of Physics, Zakir Husain Delhi College, University of Delhi, Delhi, India
| | - Hemant Kumar Srivastava
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Changsari, Guwahati, Assam, India
| | - Pranjal Chandra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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Ononamadu CJ, Abdalla M, Ihegboro GO, Li J, Owolarafe TA, John TD, Tian Q. In silico identification and study of potential anti-mosquito juvenile hormone binding protein (MJHBP) compounds as candidates for dengue virus - Vector insecticides. Biochem Biophys Rep 2021; 28:101178. [PMID: 34901473 PMCID: PMC8640742 DOI: 10.1016/j.bbrep.2021.101178] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 11/22/2022] Open
Abstract
Dengue has become a huge global health burden. It is currently recognized as the most rapidly spreading mosquito-borne viral disease. Yet, there are currently no licensed vaccines or specific therapeutics to manage the virus, thus, scaling up vector control approaches is important in controlling this viral spread. This study aimed to identify and study in silico, potential anti-mosquito compounds targeting Juvenile hormone (JH) mediated pathways via the Mosquito Juvenile Hormone Binding Protein (MJHBP). The study was implemented using series of computational methods. The query compounds included pyrethroids and those derived from ZINC and ANPDB databases using a simple pharmacophore model in Molecular Operating Environment (MOE). Molecular docking of selected compounds' library was implemented in MOE. The resultant high-score compounds were further validated by molecular dynamics simulation via Maestro 12.3 module and the respective Prime/Molecular Mechanics Generalized Born Surface Area (Prime/MM-GBSA) binding energies computed. The study identified compounds-pyrethroids, natural and synthetic - with high docking energy scores (ranging from 10.91-12.34 kcal/mol). On further analysis of the high-ranking (in terms of docking scores) compounds using MD simulation, the compounds - Ekeberin D4, Maesanin, Silafluofen and ZINC16919139- revealed very low binding energies (-122.99, -72.91 -104.50 and,-74.94 kcal/mol respectively), fairly stable complex and interesting interaction with JH-binding site amino acid residues on MJHBP. Further studies can explore these compounds in vitro/in vivo in the search for more efficient mosquito vector control.
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Affiliation(s)
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province, 250012, PR China
| | | | - Jin Li
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province, 250012, PR China
| | | | - Timothy Datit John
- Federal University Dutse, Department of Microbiology and Biotechnology, Kano, Nigeria
| | - Qiang Tian
- Department of Senile Neurology, The Central Hospital of Taian, Taian, Shandong, 271000, PR China
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Himmel DM, Arnold E. Non-Nucleoside Reverse Transcriptase Inhibitors Join Forces with Integrase Inhibitors to Combat HIV. Pharmaceuticals (Basel) 2020; 13:ph13060122. [PMID: 32545407 PMCID: PMC7345359 DOI: 10.3390/ph13060122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/17/2022] Open
Abstract
In the treatment of acquired immune deficiency syndrome (AIDS), the diarylpyrimidine (DAPY) analogs etravirine (ETR) and rilpivirine (RPV) have been widely effective against human immunodeficiency virus (HIV) variants that are resistant to other non-nucleoside reverse transcriptase inhibitors (NNRTIs). With non-inferior or improved efficacy, better safety profiles, and lower doses or pill burdens than other NNRTIs in the clinic, combination therapies including either of these two drugs have led to higher adherence than other NNRTI-containing treatments. In a separate development, HIV integrase strand transfer inhibitors (INSTIs) have shown efficacy in treating AIDS, including raltegravir (RAL), elvitegravir (EVG), cabotegravir (CAB), bictegravir (BIC), and dolutegravir (DTG). Of these, DTG and BIC perform better against a wide range of resistance mutations than other INSTIs. Nevertheless, drug-resistant combinations of mutations have begun to emerge against all DAPYs and INSTIs, attributable in part to non-adherence. New dual therapies that may promote better adherence combine ETR or RPV with an INSTI and have been safer and non-inferior to more traditional triple-drug treatments. Long-acting dual- and triple-therapies combining ETR or RPV with INSTIs are under study and may further improve adherence. Here, highly resistant emergent mutations and efficacy data on these novel treatments are reviewed. Overall, ETR or RPV, in combination with INSTIs, may be treatments of choice as long-term maintenance therapies that optimize efficacy, adherence, and safety.
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Affiliation(s)
- Daniel M. Himmel
- Himmel Sci Med Com, L.L.C., Bala Cynwyd, PA 19004, USA
- Correspondence: ; Tel.: +1-848-391-5973
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA;
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Structural Insights on Retroviral DNA Integration: Learning from Foamy Viruses. Viruses 2019; 11:v11090770. [PMID: 31443391 PMCID: PMC6784120 DOI: 10.3390/v11090770] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/28/2022] Open
Abstract
Foamy viruses (FV) are retroviruses belonging to the Spumaretrovirinae subfamily. They are non-pathogenic viruses endemic in several mammalian hosts like non-human primates, felines, bovines, and equines. Retroviral DNA integration is a mandatory step and constitutes a prime target for antiretroviral therapy. This activity, conserved among retroviruses and long terminal repeat (LTR) retrotransposons, involves a viral nucleoprotein complex called intasome. In the last decade, a plethora of structural insights on retroviral DNA integration arose from the study of FV. Here, we review the biochemistry and the structural features of the FV integration apparatus and will also discuss the mechanism of action of strand transfer inhibitors.
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Du W, Zuo K, Sun X, Liu W, Yan X, Liang L, Wan H, Chen F, Hu J. An effective HIV-1 integrase inhibitor screening platform: Rationality validation of drug screening, conformational mobility and molecular recognition analysis for PFV integrase complex with viral DNA. J Mol Graph Model 2017; 78:96-109. [PMID: 29055187 DOI: 10.1016/j.jmgm.2017.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 01/26/2023]
Abstract
As an important target for the development of novel anti-AIDS drugs, HIV-1 integrase (IN) has been widely concerned. However, the lack of a complete accurate crystal structure of HIV-1 IN greatly blocks the discovery of novel inhibitors. In this work, an effective HIV-1 IN inhibitor screening platform, namely PFV IN, was filtered from all species of INs. Next, the 40.8% similarity with HIV-1 IN, as well as the high efficiency of virtual screening and the good agreement between calculated binding free energies and experimental ones all proved PFV IN is a promising screening platform for HIV-1 IN inhibitors. Then, the molecular recognition mechanism of PFV IN by its substrate viral DNA and six naphthyridine derivatives (NRDs) inhibitors was investigated through molecular docking, molecular dynamics simulations and water-mediated interactions analyses. The functional partition of NRDs IN inhibitors could be divided into hydrophobic and hydrophilic ones, and the Mg2+ ions, water molecules and conserved DDE motif residues all interacted with the hydrophilic partition, while the bases in viral DNA and residues like Tyr212, Pro214 interacted with the hydrophobic one. Finally, the free energy landscape (FEL) and cluster analyses were performed to explore the molecular motion of PFV IN-DNA system. It is found that the association with NRDs inhibitors would obviously decrease the motion amplitude of PFV IN-DNA, which may be one of the most potential mechanisms of IN inhibitors. This work will provide a theoretical basis for the inhibitor design based on the structure of HIV-1 IN.
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Affiliation(s)
- Wenyi Du
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China
| | - Ke Zuo
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China
| | - Xin Sun
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China
| | - Wei Liu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China
| | - Xiao Yan
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China
| | - Li Liang
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China
| | - Hua Wan
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, China
| | - Fengzheng Chen
- Department of Chemistry, Leshan Normal University, Leshan, China
| | - Jianping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, China.
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Mandal S, Khandalavala K, Pham R, Bruck P, Varghese M, Kochvar A, Monaco A, Prathipati PK, Destache C, Shibata A. Cellulose Acetate Phthalate and Antiretroviral Nanoparticle Fabrications for HIV Pre-Exposure Prophylaxis. Polymers (Basel) 2017; 9. [PMID: 30450244 PMCID: PMC6239201 DOI: 10.3390/polym9090423] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To adequately reduce new HIV infections, development of highly effective pre-exposure prophylaxis (PrEP) against HIV infection in women is necessary. Cellulose acetate phthalate (CAP) is a pH sensitive polymer with HIV-1 entry inhibitory properties. Dolutegravir (DTG) is an integrase strand transfer inhibitor with potent antiretroviral activity. DTG delivered in combination with CAP may significantly improve current PrEP against HIV. In the present study, the development of DTG-loaded CAP nanoparticles incorporated in thermosensitive (TMS) gel at vaginal pH 4.2 and seminal fluid pH 7.4 is presented as proof-of-concept for improved PrEP. Water–oil–in–water homogenization was used to fabricate DTG-loaded CAP nanoparticles (DTG–CAP–NPs). Size, polydispersity, and morphological analyses illustrate that DTG–CAP–NPs were smooth and spherical, ≤200 nm in size, and monodispersed with a polydispersity index PDI ≤ 0.2. The drug encapsulation (EE%) and release profile of DTG–CAP–NPs was determined by HPLC analysis. The EE% of DTG in DTG–CAP–NPs was evaluated to be ~70%. The thermal sensitivity of the TMS gel was optimized and the pH dependency was evaluated by rheological analysis. DTG release studies in TMS gel revealed that DTG–CAP–NPs were stable in TMS gel at pH 4.2 while DTG–CAP–NPs in TMS gel at pH 7.4 rapidly release DTG (≥80% release within 1 h). Cytotoxicity studies using vaginal cell lines revealed that DTG–CAP–NPs were relatively non-cytotoxic at concentration <1 µg/mL. Confocal microscopic studies illustrate that ≥98% cells retained DTG–CAP–NPs intracellularly over seven days. Antiretroviral drug loaded nanocellulose fabrications in TMS gel delivered intravaginally may enhance both microbicidal and antiretroviral drug efficacy and may present a novel option for female PrEP against HIV.
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Affiliation(s)
- Subhra Mandal
- School of Pharmacy and Health Professions, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; (S.M.); (P.K.P.); (C.D.)
| | - Karl Khandalavala
- Department of Biology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; (K.K.); (R.P.); (M.V.); (A.K.); (A.M.)
| | - Rachel Pham
- Department of Biology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; (K.K.); (R.P.); (M.V.); (A.K.); (A.M.)
| | - Patrick Bruck
- Dana-Farber Cancer Institute, Harvard University, Boston, MA 02215, USA;
| | - Marisa Varghese
- Department of Biology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; (K.K.); (R.P.); (M.V.); (A.K.); (A.M.)
| | - Andrew Kochvar
- Department of Biology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; (K.K.); (R.P.); (M.V.); (A.K.); (A.M.)
| | - Ashley Monaco
- Department of Biology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; (K.K.); (R.P.); (M.V.); (A.K.); (A.M.)
| | - Pavan Kumar Prathipati
- School of Pharmacy and Health Professions, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; (S.M.); (P.K.P.); (C.D.)
| | - Christopher Destache
- School of Pharmacy and Health Professions, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; (S.M.); (P.K.P.); (C.D.)
| | - Annemarie Shibata
- Department of Biology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; (K.K.); (R.P.); (M.V.); (A.K.); (A.M.)
- Correspondence: ; Tel.: +1-402-280-3588
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Ronsard L, Ganguli N, Singh VK, Mohankumar K, Rai T, Sridharan S, Pajaniradje S, Kumar B, Rai D, Chaudhuri S, Coumar MS, Ramachandran VG, Banerjea AC. Impact of Genetic Variations in HIV-1 Tat on LTR-Mediated Transcription via TAR RNA Interaction. Front Microbiol 2017; 8:706. [PMID: 28484443 PMCID: PMC5399533 DOI: 10.3389/fmicb.2017.00706] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/05/2017] [Indexed: 01/10/2023] Open
Abstract
HIV-1 evades host defense through mutations and recombination events, generating numerous variants in an infected patient. These variants with an undiminished virulence can multiply rapidly in order to progress to AIDS. One of the targets to intervene in HIV-1 replication is the trans-activator of transcription (Tat), a major regulatory protein that transactivates the long terminal repeat promoter through its interaction with trans-activation response (TAR) RNA. In this study, HIV-1 infected patients (n = 120) from North India revealed Ser46Phe (20%) and Ser61Arg (2%) mutations in the Tat variants with a strong interaction toward TAR leading to enhanced transactivation activities. Molecular dynamics simulation data verified that the variants with this mutation had a higher binding affinity for TAR than both the wild-type Tat and other variants that lacked Ser46Phe and Ser61Arg. Other mutations in Tat conferred varying affinities for TAR interaction leading to differential transactivation abilities. This is the first report from North India with a clinical validation of CD4 counts to demonstrate the influence of Tat genetic variations affecting the stability of Tat and its interaction with TAR. This study highlights the co-evolution pattern of Tat and predominant nucleotides for Tat activity, facilitating the identification of genetic determinants for the attenuation of viral gene expression.
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Affiliation(s)
- Larance Ronsard
- Laboratory of Virology, National Institute of ImmunologyDelhi, India.,Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalDelhi, India
| | - Nilanjana Ganguli
- Laboratory of Virology, National Institute of ImmunologyDelhi, India
| | - Vivek K Singh
- Centre for Bioinformatics, School of Life Sciences, Pondicherry UniversityPondicherry, India
| | - Kumaravel Mohankumar
- Department of Biochemistry and Molecular Biology, Pondicherry UniversityPondicherry, India.,Department of Veterinary Physiology and Pharmacology, Texas A&M University, College StationTX, USA
| | - Tripti Rai
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical SciencesDelhi, India
| | - Subhashree Sridharan
- Department of Biochemistry and Molecular Biology, Pondicherry UniversityPondicherry, India.,Department of Symptom Research, The University of Texas MD Anderson Cancer Center, HoustonTX, USA
| | - Sankar Pajaniradje
- Department of Biochemistry and Molecular Biology, Pondicherry UniversityPondicherry, India
| | - Binod Kumar
- Department of Microbiology and Immunology, Rosalind Franklin University of Medicine and Science, ChicagoIL, USA
| | - Devesh Rai
- Department of Microbiology, All India Institute of Medical SciencesDelhi, India
| | - Suhnrita Chaudhuri
- Department of Neurological Surgery, Northwestern University, ChicagoIL, USA
| | - Mohane S Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry UniversityPondicherry, India
| | | | - Akhil C Banerjea
- Laboratory of Virology, National Institute of ImmunologyDelhi, India
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Martin TD, Hill EH, Whitten DG, Chi EY, Evans DG. Oligomeric Conjugated Polyelectrolytes Display Site-Preferential Binding to an MS2 Viral Capsid. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:12542-12551. [PMID: 27464311 DOI: 10.1021/acs.langmuir.6b01667] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Opportunistic bacteria and viruses are a worldwide health threat prompting the need to develop new targeting modalities. A class of novel synthetic poly(phenylene ethynylene) (PPE)-based oligomeric conjugated polyelectrolytes (OPEs) have demonstrated potent wide-spectrum biocidal activity. A subset of cationic OPEs display high antiviral activity against the MS2 bacteriophage. The oligomers have been found to inactivate the bacteriophage and perturb the morphology of the MS2 viral capsid. However, details of the initial binding and interactions between the OPEs and the viruses are not well understood. In this study, we use a multiscale computational approach, including random sampling, molecular dynamics, and electronic structure calculations, to gain an understanding of the molecular-level interactions of a series of OPEs that vary in length, charge, and functional groups with the MS2 capsid. Our results show that OPEs strongly bind to the MS2 capsid protein assembly with binding energies of up to -30 kcal/mol. Free-energy analysis shows that the binding is dominated by strong van der Waals interactions between the hydrophobic OPE backbone and the capsid surface and strong electrostatic free energy contributions between the OPE charged moieties and charged residues on the capsid surface. This knowledge provides molecular-level insight into how to tailor the OPEs to optimize viral capsid disruption and increase OPE efficacy to target amphiphilic protein coats of icosahedral-based viruses.
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Affiliation(s)
- Tye D Martin
- Department of Chemical and Biological Engineering and the Center for Biomedical Engineering, ‡The Nanoscience and Microsystems Engineering Program, and §Department of Chemistry and Chemical Biology, University of New Mexico , Albuquerque, New Mexico 87131, United States
| | - Eric H Hill
- Department of Chemical and Biological Engineering and the Center for Biomedical Engineering, ‡The Nanoscience and Microsystems Engineering Program, and §Department of Chemistry and Chemical Biology, University of New Mexico , Albuquerque, New Mexico 87131, United States
| | - David G Whitten
- Department of Chemical and Biological Engineering and the Center for Biomedical Engineering, ‡The Nanoscience and Microsystems Engineering Program, and §Department of Chemistry and Chemical Biology, University of New Mexico , Albuquerque, New Mexico 87131, United States
| | - Eva Y Chi
- Department of Chemical and Biological Engineering and the Center for Biomedical Engineering, ‡The Nanoscience and Microsystems Engineering Program, and §Department of Chemistry and Chemical Biology, University of New Mexico , Albuquerque, New Mexico 87131, United States
| | - Deborah G Evans
- Department of Chemical and Biological Engineering and the Center for Biomedical Engineering, ‡The Nanoscience and Microsystems Engineering Program, and §Department of Chemistry and Chemical Biology, University of New Mexico , Albuquerque, New Mexico 87131, United States
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10
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Zhao XZ, Metifiot M, Smith SJ, Maddali K, Marchand C, Hughes SH, Pommier Y, Burke TR. 6,7-Dihydroxyisoindolin-1-one and 7,8-Dihydroxy-3,4-Dihydroisoquinolin- 1(2H)-one Based HIV-1 Integrase Inhibitors. Curr Top Med Chem 2016; 16:435-40. [PMID: 26268341 DOI: 10.2174/1568026615666150813150058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/03/2015] [Accepted: 04/05/2015] [Indexed: 11/22/2022]
Abstract
Integrase (IN) is an essential viral enzyme required for HIV-1 replication, which has been targeted by anti-AIDS therapeutics. Integrase strand transfer inhibitors (INSTIs) represent a new class of antiretroviral agents developed for the treatment of HIV-1 infections. Important structural features that are shared by many INSTIs include a coplanar arrangement of three heteroatoms that chelate two catalytic Mg(2+) ions in the IN active site and a linked halophenyl ring that binds in the hydrophobic pocket formed by the complex of IN with viral DNA. We recently reported bicyclic 6,7-dihydroxyoxoisoindolin-1-one-based IN inhibitors. In the current study, we modified these inhibitors in three ways. First, we increased the spacer length between the metalchelating triad and the halophenyl group. Second, we replaced the indoline [5,6] bicycle with a fused dihydroxyisoquinolinones [6,6] ring system. Finally, we prepared bis-6,7-dihydroxyisoindolin-1-one-4-sulfonamides as dimeric HIV-1 IN inhibitors. These new analogues showed low micromolar inhibitory potency in in vitro HIV-1 integrase assays.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702, USA.
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Métifiot M, Johnson BC, Kiselev E, Marler L, Zhao XZ, Burke TR, Marchand C, Hughes SH, Pommier Y. Selectivity for strand-transfer over 3'-processing and susceptibility to clinical resistance of HIV-1 integrase inhibitors are driven by key enzyme-DNA interactions in the active site. Nucleic Acids Res 2016; 44:6896-906. [PMID: 27369381 PMCID: PMC5001616 DOI: 10.1093/nar/gkw592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 06/21/2016] [Indexed: 12/23/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) are highly effective against HIV infections. Co-crystal structures of the prototype foamy virus intasome have shown that all three FDA-approved drugs, raltegravir (RAL), elvitegravir and dolutegravir (DTG), act as interfacial inhibitors during the strand transfer (ST) integration step. However, these structures give only a partial sense for the limited inhibition of the 3′-processing reaction by INSTIs and how INSTIs can be modified to overcome drug resistance, notably against the G140S-Q148H double mutation. Based on biochemical experiments with modified oligonucleotides, we demonstrate that both the viral DNA +1 and −1 bases, which flank the 3′-processing site, play a critical role for 3′-processing efficiency and inhibition by RAL and DTG. In addition, the G140S-Q148H (SH) mutant integrase, which has a reduced 3′-processing activity, becomes more active and more resistant to inhibition of 3′-processing by RAL and DTG in the absence of the −1 and +1 bases. Molecular modeling of HIV-1 integrase, together with biochemical data, indicate that the conserved residue Q146 in the flexible loop of HIV-1 integrase is critical for productive viral DNA binding through specific contacts with the virus DNA ends in the 3′-processing and ST reactions. The potency of integrase inhibitors against 3′-processing and their ability to overcome resistance is discussed.
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Affiliation(s)
- Mathieu Métifiot
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Barry C Johnson
- HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Center for Cancer Research, National Institutes of Health, Frederick, MD 21702, USA
| | - Evgeny Kiselev
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Laura Marler
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, National Cancer Institute at Frederick, Center for Cancer Research, National Institutes of Health, Frederick, MD 21702, USA
| | - Terrence R Burke
- Chemical Biology Laboratory, National Cancer Institute at Frederick, Center for Cancer Research, National Institutes of Health, Frederick, MD 21702, USA
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Center for Cancer Research, National Institutes of Health, Frederick, MD 21702, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
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Sachithanandham J, Konda Reddy K, Solomon K, David S, Kumar Singh S, Vadhini Ramalingam V, Alexander Pulimood S, Cherian Abraham O, Rupali P, Sridharan G, Kannangai R. Effect of HIV-1 Subtype C integrase mutations implied using molecular modeling and docking data. Bioinformation 2016; 12:221-230. [PMID: 28149058 PMCID: PMC5267967 DOI: 10.6026/97320630012221] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 02/29/2016] [Accepted: 03/02/2016] [Indexed: 01/12/2023] Open
Abstract
The degree of sequence variation in HIV-1 integrase genes among infected patients and their impact on clinical response to Anti retroviral therapy (ART) is of interest. Therefore, we collected plasma samples from 161 HIV-1 infected individuals for subsequent integrase gene amplification (1087 bp). Thus, 102 complete integrase gene sequences identified as HIV-1 subtype-C was assembled. This sequence data was further used for sequence analysis and multiple sequence alignment (MSA) to assess position specific frequency of mutations within pol gene among infected individuals. We also used biophysical geometric optimization technique based molecular modeling and docking (Schrodinger suite) methods to infer differential function caused by position specific sequence mutations towards improved inhibitor selection. We thus identified accessory mutations (usually reduce susceptibility) leading to the resistance of some known integrase inhibitors in 14% of sequences in this data set. The Stanford HIV-1 drug resistance database provided complementary information on integrase resistance mutations to deduce molecular basis for such observation. Modeling and docking analysis show reduced binding by mutants for known compounds. The predicted binding values further reduced for models with combination of mutations among subtype C clinical strains. Thus, the molecular basis implied for the consequence of mutations in different variants of integrase genes of HIV-1 subtype C clinical strains from South India is reported. This data finds utility in the design, modification and development of a representative yet an improved inhibitor for HIV-1 integrase.
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Affiliation(s)
| | - Karnati Konda Reddy
- SNHRC Vellore and Computer-Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics Alagappa University, Karaikudi, Tamil Nadu, India
| | - King Solomon
- Departments of Clinical Virology Alagappa University, Karaikudi, Tamil Nadu, India
| | - Shoba David
- Departments of Clinical Virology Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- SNHRC Vellore and Computer-Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics Alagappa University, Karaikudi, Tamil Nadu, India
| | | | | | | | - Pricilla Rupali
- Departments of Internal Medicine, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Gopalan Sridharan
- Christian Medical College, Vellore, Sri Sakthi Amma Institute of Biomedical Research Institute
| | - Rajesh Kannangai
- Departments of Clinical Virology Alagappa University, Karaikudi, Tamil Nadu, India
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13
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Dayer MR. Comparison of Newly Assembled Full Length HIV-1 Integrase With Prototype Foamy Virus Integrase: Structure-Function Prospective. Jundishapur J Microbiol 2016; 9:e29773. [PMID: 27540450 PMCID: PMC4976072 DOI: 10.5812/jjm.29773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 11/17/2015] [Accepted: 11/30/2015] [Indexed: 01/24/2023] Open
Abstract
Background Drug design against human immunodeficiency virus type 1 (HIV-1) integrase through its mechanistic study is of great interest in the area in biological research. The main obstacle in this area is the absence of the full-length crystal structure for HIV-1 integrase to be used as a model. A complete structure, similar to HIV-1 of a prototype foamy virus integrase in complex with DNA, including all conservative residues, is available and has been extensively used in recent investigations. Objectives The aim of this study was to determine whether the above model is precisely representative of HIV-1 integrase. This would critically determine the success of any designed drug using the model in deactivation of integrase and AIDS treatment. Materials and Methods Primarily, a new structure for HIV-1 was constructed, using a crystal structure of prototype foamy virus as the starting structure. The constructed structure of HIV-1 integrase was simultaneously simulated with a prototype foamy virus integrase on a separate occasion. Results Our results indicate that the HIV-1 system behaves differently from the prototype foamy virus in terms of folding, hydration, hydrophobicity of binding site and stability. Conclusions Based on our findings, we can conclude that HIV-1 integrase is vastly different from the prototype foamy virus integrase and does not resemble it, and the modeling output of the prototype foamy virus simulations could not be simply generalized to HIV-1 integrase. Therefore, our HIV-1 model seems to be more representative and more useful for future research.
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Affiliation(s)
- Mohammad Reza Dayer
- Department of Biology, Faculty of Science, Shahid Chamran University, Ahvaz, IR Iran
- Corresponding author: Mohammad Reza Dayer, Department of Biology, Faculty of Sciences, Shahid Chamran University, Ahvaz, IR Iran. Tel: +98-6113331045, Fax: +98-6113331045, E-mail:
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14
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Su M, Tan J, Lin CY. Development of HIV-1 integrase inhibitors: recent molecular modeling perspectives. Drug Discov Today 2015. [PMID: 26220090 DOI: 10.1016/j.drudis.2015.07.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Of the three viral enzymes essential to HIV replication, HIV-1 integrase (IN) is gaining popularity as a target for the antiviral therapy of AIDS. Substantial work focusing on IN has been done over the past three decades, which has facilitated and led to the approval of three drugs. Here, we discuss in detail the development of IN inhibitors between January 2012 and May 2014, with a particular focus on molecular simulation. We highlight controversial aspects of computational drug design and refer to alternative practices where appropriate. The analysis of these computational approaches provides some useful clues to the possible future discovery of novel IN inhibitors.
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Affiliation(s)
- Min Su
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Jianjun Tan
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Chun-Yuan Lin
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan 33302, Taiwan.
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15
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Tambunan USF, Rachmania RA, Parikesit AA. In silico modification of oseltamivir as neuraminidase inhibitor of influenza A virus subtype H1N1. J Biomed Res 2014; 29:150-9. [PMID: 25859271 PMCID: PMC4389116 DOI: 10.7555/jbr.29.20130024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 06/26/2013] [Accepted: 08/18/2014] [Indexed: 11/28/2022] Open
Abstract
This research focused on the modification of the functional groups of oseltamivir as neuraminidase inhibitor against influenza A virus subtype H1N1. Interactions of three of the best ligands were evaluated in the hydrated state using molecular dynamics simulation at two different temperatures. The docking result showed that AD3BF2D ligand (N-[(1S,6R)-5-amino-5-{[(2R,3S,4S)-3,4-dihydroxy-4-(hydroxymethyl) tetrahydrofuran-2-yl]oxy}-4-formylcyclohex-3-en-1-yl]acetamide-3-(1-ethylpropoxy)-1-cyclohexene-1-carboxylate) had better binding energy values than standard oseltamivir. AD3BF2D had several interactions, including hydrogen bonds, with the residues in the catalytic site of neuraminidase as identified by molecular dynamics simulation. The results showed that AD3BF2D ligand can be used as a good candidate for neuraminidase inhibitor to cope with influenza A virus subtype H1N1.
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Affiliation(s)
- Usman Sumo Friend Tambunan
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok Campus, Depok 16424, Indonesia
| | - Rizky Archintya Rachmania
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok Campus, Depok 16424, Indonesia
| | - Arli Aditya Parikesit
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok Campus, Depok 16424, Indonesia
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16
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Zhang D, Debnath B, Yu S, Sanchez TW, Christ F, Liu Y, Debyser Z, Neamati N, Zhao G. Design and discovery of 5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxamide inhibitors of HIV-1 integrase. Bioorg Med Chem 2014; 22:5446-53. [DOI: 10.1016/j.bmc.2014.07.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 07/20/2014] [Accepted: 07/22/2014] [Indexed: 02/04/2023]
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17
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Quevedo MA, Ribone SR, Briñón MC, Dehaen W. Development of a receptor model for efficient in silico screening of HIV-1 integrase inhibitors. J Mol Graph Model 2014; 52:82-90. [PMID: 25023663 DOI: 10.1016/j.jmgm.2014.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 12/01/2022]
Abstract
Integrase (IN) is a key viral enzyme for the replication of the type-1 human immunodeficiency virus (HIV-1), and as such constitutes a relevant therapeutic target for the development of anti-HIV agents. However, the lack of crystallographic data of HIV IN complexed with the corresponding viral DNA has historically hindered the application of modern structure-based drug design techniques to the discovery of new potent IN inhibitors (INIs). Consequently, the development and validation of reliable HIV IN structural models that may be useful for the screening of large databases of chemical compounds is of particular interest. In this study, four HIV-1 IN homology models were evaluated respect to their capability to predict the inhibition potency of a training set comprising 36 previously reported INIs with IC50 values in the low nanomolar to the high micromolar range. Also, 9 inactive structurally related compounds were included in this training set. In addition, a crystallographic structure of the IN-DNA complex corresponding to the prototype foamy virus (PFV) was also evaluated as structural model for the screening of inhibitors. The applicability of high throughput screening techniques, such as blind and ligand-guided exhaustive rigid docking was assessed. The receptor models were also refined by molecular dynamics and clustering techniques to assess protein sidechain flexibility and solvent effect on inhibitor binding. Among the studied models, we conclude that the one derived from the X-ray structure of the PFV integrase exhibited the best performance to rank the potencies of the compounds in the training set, with the predictive power being further improved by explicitly modeling five water molecules within the catalytic side of IN. Also, accounting for protein sidechain flexibility enhanced the prediction of inhibition potencies among the studied compounds. Finally, an interaction fingerprint pattern was established for the fast identification of potent IN inhibitors. In conclusion, we report an exhaustively validated receptor model if IN that is useful for the efficient screening of large chemical compounds databases in the search of potent HIV-1 IN inhibitors.
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Affiliation(s)
- Mario A Quevedo
- Departamento de Farmacia, Facultad de Ciencias Químicas, Ciudad Universitaria, Universidad Nacional de Córdoba, 5000 Córdoba, Argentina.
| | - Sergio R Ribone
- Departamento de Farmacia, Facultad de Ciencias Químicas, Ciudad Universitaria, Universidad Nacional de Córdoba, 5000 Córdoba, Argentina
| | - Margarita C Briñón
- Departamento de Farmacia, Facultad de Ciencias Químicas, Ciudad Universitaria, Universidad Nacional de Córdoba, 5000 Córdoba, Argentina
| | - Wim Dehaen
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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18
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Masso M, Chuang G, Hao K, Jain S, Vaisman II. Structure-based predictors of resistance to the HIV-1 integrase inhibitor Elvitegravir. Antiviral Res 2014; 106:5-12. [DOI: 10.1016/j.antiviral.2014.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 12/15/2022]
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19
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Chen Q, Buolamwini JK, Smith JC, Li A, Xu Q, Cheng X, Wei D. Impact of resistance mutations on inhibitor binding to HIV-1 integrase. J Chem Inf Model 2013; 53:3297-307. [PMID: 24205814 DOI: 10.1021/ci400537n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
HIV-1 integrase (IN) is essential for HIV-1 replication, catalyzing two key reaction steps termed 3' processing and strand transfer. Therefore, IN has become an important target for antiviral drug discovery. However, mutants have emerged, such as E92Q/N155H and G140S/Q148H, which confer resistance to raltegravir (RAL), the first IN strand transfer inhibitor (INSTI) approved by the FDA, and to the recently approved elvitegravir (EVG). To gain insights into the molecular mechanisms of ligand binding and drug resistance, we performed molecular dynamics (MD) simulations of homology models of the HIV-1 IN and four relevant mutants complexed with viral DNA and RAL. The results show that the structure and dynamics of the 140s' loop, comprising residues 140 to 149, are strongly influenced by the IN mutations. In the simulation of the G140S/Q148H double mutant, we observe spontaneous dissociation of RAL from the active site, followed by an intrahelical swing-back of the 3'-OH group of nucleotide A17, consistent with the experimental observation that the G140S/Q148H mutant exhibits the highest resistance to RAL compared to other IN mutants. An important hydrogen bond between residues 145 and 148 is present in the wild-type IN but not in the G140S/Q148H mutant, accounting for the structural and dynamical differences of the 140s' loop and ultimately impairing RAL binding in the double mutant. End-point free energy calculations that broadly capture the experimentally known RAL binding profiles elucidate the contributions of the 140s' loop to RAL binding free energies and suggest possible approaches to overcoming drug resistance.
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Affiliation(s)
- Qi Chen
- State Key Laboratory of Microbial Metabolism and College of Life Science and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
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20
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Miri L, Bouvier G, Kettani A, Mikou A, Wakrim L, Nilges M, Malliavin TE. Stabilization of the integrase-DNA complex by Mg2+ions and prediction of key residues for binding HIV-1 integrase inhibitors. Proteins 2013; 82:466-78. [DOI: 10.1002/prot.24412] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 07/18/2013] [Accepted: 08/14/2013] [Indexed: 01/02/2023]
Affiliation(s)
- Lamia Miri
- Laboratoire de Virologie; Institut Pasteur du Maroc; Casablanca 20360 Morocco
- Unité de modélisation moléculaire et d'ingénierie des biomolécules, Laboratoire de recherche sur les lipoprotéines et l'athérosclérose; Unité Associée au CNRST-URAC34, Faculté des Sciences Ben M'Sik; Casablanca Morocco
| | - Guillaume Bouvier
- Unité de Bioinformatique Structurale; UMR 3528 CNRS, Institut Pasteur; Paris 75724 France
| | - Anass Kettani
- Unité de modélisation moléculaire et d'ingénierie des biomolécules, Laboratoire de recherche sur les lipoprotéines et l'athérosclérose; Unité Associée au CNRST-URAC34, Faculté des Sciences Ben M'Sik; Casablanca Morocco
| | - Afaf Mikou
- Laboratoire de Catalyse et environnement; Faculté des Sciences Ain Chock; Casablanca Morocco
| | - Lahcen Wakrim
- Laboratoire de Virologie; Institut Pasteur du Maroc; Casablanca 20360 Morocco
| | - Michael Nilges
- Unité de Bioinformatique Structurale; UMR 3528 CNRS, Institut Pasteur; Paris 75724 France
| | - Thérèse E. Malliavin
- Unité de Bioinformatique Structurale; UMR 3528 CNRS, Institut Pasteur; Paris 75724 France
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DeAnda F, Hightower KE, Nolte RT, Hattori K, Yoshinaga T, Kawasuji T, Underwood MR. Dolutegravir interactions with HIV-1 integrase-DNA: structural rationale for drug resistance and dissociation kinetics. PLoS One 2013; 8:e77448. [PMID: 24146996 PMCID: PMC3797783 DOI: 10.1371/journal.pone.0077448] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/10/2013] [Indexed: 01/12/2023] Open
Abstract
Signature HIV-1 integrase mutations associated with clinical raltegravir resistance involve 1 of 3 primary genetic pathways, Y143C/R, Q148H/K/R and N155H, the latter 2 of which confer cross-resistance to elvitegravir. In accord with clinical findings, in vitro drug resistance profiling studies with wild-type and site-directed integrase mutant viruses have shown significant fold increases in raltegravir and elvitegravir resistance for the specified viral mutants relative to wild-type HIV-1. Dolutegravir, in contrast, has demonstrated clinical efficacy in subjects failing raltegravir therapy due to integrase mutations at Y143, Q148 or N155, which is consistent with its distinct in vitro resistance profile as dolutegravir's antiviral activity against these viral mutants is equivalent to its activity against wild-type HIV-1. Kinetic studies of inhibitor dissociation from wild-type and mutant integrase-viral DNA complexes have shown that dolutegravir also has a distinct off-rate profile with dissociative half-lives substantially longer than those of raltegravir and elvitegravir, suggesting that dolutegravir's prolonged binding may be an important contributing factor to its distinct resistance profile. To provide a structural rationale for these observations, we constructed several molecular models of wild-type and clinically relevant mutant HIV-1 integrase enzymes in complex with viral DNA and dolutegravir, raltegravir or elvitegravir. Here, we discuss our structural models and the posited effects that the integrase mutations and the structural and electronic properties of the integrase inhibitors may have on the catalytic pocket and inhibitor binding and, consequently, on antiviral potency in vitro and in the clinic.
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Affiliation(s)
- Felix DeAnda
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | - Kendra E. Hightower
- Biological Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | - Robert T. Nolte
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | | | | | - Takashi Kawasuji
- Chemistry Infectious Diseases, Shionogi & Co., Ltd., Osaka, Japan
| | - Mark R. Underwood
- Medicines Development Infectious Diseases, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
- * E-mail:
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Biochemical analysis of the role of G118R-linked dolutegravir drug resistance substitutions in HIV-1 integrase. Antimicrob Agents Chemother 2013; 57:6223-35. [PMID: 24080645 DOI: 10.1128/aac.01835-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Drug resistance mutations (DRMs) have been reported for all currently approved anti-HIV drugs, including the latest integrase strand transfer inhibitors (INSTIs). We previously used the new INSTI dolutegravir (DTG) to select a G118R integrase resistance substitution in tissue culture and also showed that secondary substitutions emerged at positions H51Y and E138K. Now, we have characterized the impact of the G118R substitution, alone or in combination with either H51Y or E138K, on 3' processing and integrase strand transfer activity. The results show that G118R primarily impacted the strand transfer step of integration by diminishing the ability of integrase-long terminal repeat (LTR) complexes to bind target DNA. The addition of H51Y and E138K to G118R partially restored strand transfer activity by modulating the formation of integrase-LTR complexes through increasing LTR DNA affinity and total DNA binding, respectively. This unique mechanism, in which one function of HIV integrase partially compensates for the defect in another function, has not been previously reported. The G118R substitution resulted in low-level resistance to DTG, raltegravir (RAL), and elvitegravir (EVG). The addition of either of H51Y or E138K to G118R did not enhance resistance to DTG, RAL, or EVG. Homology modeling provided insight into the mechanism of resistance conferred by G118R as well as the effects of H51Y or E138K on enzyme activity. The G118R substitution therefore represents a potential avenue for resistance to DTG, similar to that previously described for the R263K substitution. For both pathways, secondary substitutions can lead to either diminished integrase activity and/or increased INSTI susceptibility.
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Computational design of a full-length model of HIV-1 integrase: modeling of new inhibitors and comparison of their calculated binding energies with those previously studied. J Mol Model 2013; 19:4349-68. [PMID: 23907552 DOI: 10.1007/s00894-013-1943-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 07/11/2013] [Indexed: 12/28/2022]
Abstract
A full-length model of integrase (IN) of the human immunodeficiency virus type 1 (HIV-1) was constructed based on the distinctly resolved X-ray crystal structures of its three domains, named N-terminal, catalytic core and C-terminal. Thirty-one already known inhibitors with varieties of structural differences as well as nine newly tested ones were docked into the catalytic core. The molecular dynamic (MD) and binding properties of these complexes were obtained by MD calculations. The binding energies calculated by molecular mechanic/Poisson Boltzmann solvation area were significantly correlationed with available IC50. Four inhibitors including two newly designed were also docked into the full-length model and their MD behaviors and binding properties were calculated. It was found that one of the newly designed compounds forms a better complex with HIV-1 IN compared to the rest including raltegravir. MD calculations were performed with AMBER suite of programs using ff99SB force field for the proteins and the general Amber force field for the ligands. In conclusion, the results have produced a promising standpoint not only in the construction of the full-length model but also in development of new drugs against it. However, the role of multimer formation and the involvement of DNAs, and their subsequent effect on the complexation and inhibition, are required to arrive at a conclusive decision.
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Tambunan USF, Bakri R, Prasetia T, Parikesit AA, Kerami D. Molecular dynamics simulation of complex Histones Deacetylase (HDAC) Class II Homo Sapiens with suberoylanilide hydroxamic acid (SAHA) and its derivatives as inhibitors of cervical cancer. Bioinformation 2013; 9:696-700. [PMID: 23930022 PMCID: PMC3732443 DOI: 10.6026/97320630009696] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 06/01/2013] [Indexed: 11/23/2022] Open
Abstract
Cervical cancer is second most common cancer in woman worldwide. Cervical cancer caused by human papillomavirus (HPV)
oncogene. Inhibition of histone deacetylase (HDAC) activity has been known as a potential strategy for cancer therapy. SAHA is an
HDAC inhibitor that has been used in cancer therapy but still has side effects. SAHA modification proposed to minimize side
effects. Triazole attachment on the chain of SAHA has been known to enhance the inhibition ability of SAHA and less toxic. In this
study, it will be carried out with molecular dynamic simulations of SAHA modifications consisting ligand 1a, 2a and, 2c to interact
with six HDAC in hydrated conditions. To all six HDAC Class II, performed docking with SAHA and a modified inhibitor. The
docking results were then carried out molecular dynamics simulations to determine the inhibitor affinities in hydrated conditions.
The molecular dynamic simulations results show better affinities of ligand 2c with HDAC 4, 6, and 7 than SAHA itself, and good
affinity was also shown by ligand 2a and 1c on HDAC 5 and 9. The results of this study can be a reference to obtain better
inhibitors.
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Affiliation(s)
- Usman Sumo Friend Tambunan
- Department of Chemistry, Faculty of Mathematics and Science, University of Indonesia, Depok 16424 Indonesia
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Arora R, de Beauchene IC, Polanski J, Laine E, Tchertanov L. Raltegravir flexibility and its impact on recognition by the HIV-1 IN targets. J Mol Recognit 2013; 26:383-401. [PMID: 23836466 DOI: 10.1002/jmr.2277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 04/04/2013] [Accepted: 04/07/2013] [Indexed: 01/10/2023]
Abstract
HIV-1 IN is a pertinent target for the development of AIDS chemotherapy. The first IN-specific inhibitor approved for the treatment of HIV/AIDS, RAL, was designed to block the ST reaction. We characterized the structural and conformational features of RAL and its recognition by putative HIV-1 targets - the unbound IN, the vDNA, and the IN•vDNA complex - mimicking the IN states over the integration process. RAL binding to the targets was studied by performing an extensive sampling of the inhibitor conformational landscape and by using four different docking algorithms: Glide, Autodock, VINA, and SurFlex. The obtained data evidenced that: (i) a large binding pocket delineated by the active site and an extended loop in the unbound IN accommodates RAL in distinct conformational states all lacking specific interactions with the target; (ii) a well-defined cavity formed by the active site, the vDNA, and the shortened loop in the IN•vDNA complex provide a more optimized inhibitor binding site in which RAL chelates Mg(2+) cations; (iii) a specific recognition between RAL and the unpaired cytosine of the processed DNA is governed by a pair of strong H-bonds similar to those observed in DNA base pair G-C. The identified RAL pose at the cleaved vDNA shed light on a putative step of RAL inhibition mechanism. This modeling study indicates that the inhibition process may include as a first step RAL recognition by the processed vDNA bound to a transient intermediate IN state, and thus provides a potentially promising route to the design of IN inhibitors with improved affinity and selectivity.
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Affiliation(s)
- Rohit Arora
- Bioinformatics, Molecular Dynamics & Modeling (BiMoDyM), Laboratoire de Biologie et Pharmacologie Appliquée (LBPA-CNRS), Ecole Normale Supérieure de Cachan, 61 avenue du Président Wilson, 94235, Cachan, France
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26
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Johnson BC, Métifiot M, Ferris A, Pommier Y, Hughes SH. A homology model of HIV-1 integrase and analysis of mutations designed to test the model. J Mol Biol 2013; 425:2133-46. [PMID: 23542006 DOI: 10.1016/j.jmb.2013.03.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 01/26/2023]
Abstract
Although there are structures of the different domains of human immunodeficiency virus type 1 (HIV-1) integrase (IN), there is no structure of the entire protein. The recently determined crystal structures of the prototype foamy virus (PFV) IN tetramer, in complexes with viral DNA, led to the generation of models of full-length HIV-1 IN. These models were generated, in part, by superimposing the structures of the domains of HIV-1 IN onto the structure of full-length PFV IN. We developed a model for HIV-1 IN-based solely on its sequence alignment with PFV IN-that differs in several ways from the previous models. Specifically, in our model, the junction between the catalytic core domain and C-terminal domain adopts a helix-loop-helix motif that is similar to the corresponding segment of PFV IN and differs from the crystal structures of these two HIV-1 IN domains. The alignment of residues in the C-terminal domain also differs from the previous models. Our model can be used to explain the phenotype of previously published HIV-1 IN mutants. We made additional mutants, and the behavior of these new mutants provides additional support for the model.
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Affiliation(s)
- Barry C Johnson
- HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, P.O. Box B, Frederick, MD 21702, USA.
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27
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Métifiot M, Maddali K, Johnson BC, Hare S, Smith SJ, Zhao X, Marchand C, Burke TR, Hughes SH, Cherepanov P, Pommier Y. Activities, crystal structures, and molecular dynamics of dihydro-1H-isoindole derivatives, inhibitors of HIV-1 integrase. ACS Chem Biol 2013; 8:209-17. [PMID: 23075516 PMCID: PMC3548936 DOI: 10.1021/cb300471n] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
On the basis of a series of lactam and phthalimide derivatives that inhibit HIV-1 integrase, we developed a new molecule, XZ-259, with biochemical and antiviral activities comparable to raltegravir. We determined the crystal structures of XZ-259 and four other derivatives in complex with the prototype foamy virus intasome. The compounds bind at the integrase-Mg(2+)-DNA interface of the integrase active site. In biochemical and antiviral assays, XZ-259 inhibits raltegravir-resistant HIV-1 integrases harboring the Y143R mutation. Molecular modeling is also presented suggesting that XZ-259 can bind in the HIV-1 intasome with its dimethyl sulfonamide group adopting two opposite orientations. Molecular dynamics analyses of the HIV-1 intasome highlight the importance of the viral DNA in drug potency.
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Affiliation(s)
| | | | - Barry C. Johnson
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Stephen Hare
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Steven J. Smith
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - XueZhi Zhao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Christophe Marchand
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Terrence R. Burke
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Stephen H. Hughes
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Peter Cherepanov
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
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Korolev SP, Kondrashina OV, Druzhilovsky DS, Starosotnikov AM, Dutov MD, Bastrakov MA, Dalinger IL, Filimonov DA, Shevelev SA, Poroikov VV, Agapkina YY, Gottikh MB. Structural-Functional Analysis of 2,1,3-Benzoxadiazoles and Their N-oxides As HIV-1 Integrase Inhibitors. Acta Naturae 2013; 5:63-72. [PMID: 23556131 PMCID: PMC3612826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Human immunodeficiency virus type 1 integrase is one of the most attractive targets for the development of anti-HIV-1 inhibitors. The capacity of a series of 2,1,3-benzoxadiazoles (benzofurazans) and their N-oxides (benzofuroxans) selected using the PASS software to inhibit the catalytic activity of HIV-1 integrase was studied in the present work. Only the nitro-derivatives of these compounds were found to display inhibitory activity. The study of the mechanism of inhibition by nitro-benzofurazans/benzofuroxans showed that they impede the substrate DNA binding at the integrase active site. These inhibitors were also active against integrase mutants resistant to raltegravir, which is the first HIV-1 integrase inhibitor approved for clinical use. The comparison of computer-aided estimations of the pharmacodynamic and pharmacokinetic properties of the compounds studied and raltegravir led us to conclude that these compounds show promise and need to be further studied as potential HIV-1 integrase inhibitors.
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Affiliation(s)
- S. P. Korolev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, 1/3, Moscow, Russia, 119991
- Belozersky Research Institute of Physicochemical Biology, Lomonosov Moscow State University, Leniskie gory, 1/40, Moscow, Russia, 119991
| | - O. V. Kondrashina
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, 1/3, Moscow, Russia, 119991
- Belozersky Research Institute of Physicochemical Biology, Lomonosov Moscow State University, Leniskie gory, 1/40, Moscow, Russia, 119991
| | - D. S. Druzhilovsky
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Pogodinskaya Str., 10/8, Moscow, Russia, 119121
| | - A. M. Starosotnikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninskiy prospekt, 47, Moscow, Russia, 119991
| | - M. D. Dutov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninskiy prospekt, 47, Moscow, Russia, 119991
| | - M. A. Bastrakov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninskiy prospekt, 47, Moscow, Russia, 119991
| | - I. L. Dalinger
- Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninskiy prospekt, 47, Moscow, Russia, 119991
| | - D. A. Filimonov
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Pogodinskaya Str., 10/8, Moscow, Russia, 119121
| | - S. A. Shevelev
- Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninskiy prospekt, 47, Moscow, Russia, 119991
| | - V. V. Poroikov
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Pogodinskaya Str., 10/8, Moscow, Russia, 119121
| | - Y. Y. Agapkina
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, 1/3, Moscow, Russia, 119991
- Belozersky Research Institute of Physicochemical Biology, Lomonosov Moscow State University, Leniskie gory, 1/40, Moscow, Russia, 119991
| | - M. B. Gottikh
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, 1/3, Moscow, Russia, 119991
- Belozersky Research Institute of Physicochemical Biology, Lomonosov Moscow State University, Leniskie gory, 1/40, Moscow, Russia, 119991
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Métifiot M, Marchand C, Pommier Y. HIV integrase inhibitors: 20-year landmark and challenges. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2013; 67:75-105. [PMID: 23885999 DOI: 10.1016/b978-0-12-405880-4.00003-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Since the discovery of HIV as the cause for AIDS 30 years ago, major progress has been made, including the discovery of drugs that now control the disease. Here, we review the integrase (IN) inhibitors from the discovery of the first compounds 20 years ago to the approval of two highly effective IN strand transfer inhibitors (INSTIs), raltegravir (Isentress) and elvitegravir (Stribild), and the promising clinical activity of dolutegravir. After summarizing the molecular mechanism of action of the INSTIs as interfacial inhibitors, we discuss the remaining challenges. Those include: overcoming resistance to clinical INSTIs, long-term safety of INSTIs, cost of therapy, place of the INSTIs in prophylactic treatments, and the development of new classes of inhibitors (the LEDGINs) targeting IN outside its catalytic site. We also discuss the role of chromatin and host DNA repair factor for the completion of integration.
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Affiliation(s)
- Mathieu Métifiot
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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30
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Xue W, Jin X, Ning L, Wang M, Liu H, Yao X. Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis. J Chem Inf Model 2012; 53:210-22. [DOI: 10.1021/ci300541c] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Weiwei Xue
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Xiaojie Jin
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Lulu Ning
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Meixia Wang
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Huanxiang Liu
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State
Key Laboratory of Applied Organic Chemistry, Department of Chemistry, ‡School of Pharmacy, and §Key Lab of Preclinical
Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
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31
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Bobadilla AD, Samuel ELG, Tour JM, Seminario JM. Calculating the Hydrodynamic Volume of Poly(ethylene oxylated) Single-Walled Carbon Nanotubes and Hydrophilic Carbon Clusters. J Phys Chem B 2012. [DOI: 10.1021/jp305302y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Alfredo D. Bobadilla
- Department of Chemical Engineering, ‡Department of Electrical and Computer Engineering, and §Materials Science and Engineering Graduate Program, Texas A&M University, College Station, Texas 77843, United States, and ¶Department of Chemistry, ∥Department of Mechanical Engineering and Materials Science, and ⊥Smalley Institute for Nanoscale Science and Technology, Rice University, 6100 Main Street, Houston Texas 77005, United States
| | - Errol. L. G. Samuel
- Department of Chemical Engineering, ‡Department of Electrical and Computer Engineering, and §Materials Science and Engineering Graduate Program, Texas A&M University, College Station, Texas 77843, United States, and ¶Department of Chemistry, ∥Department of Mechanical Engineering and Materials Science, and ⊥Smalley Institute for Nanoscale Science and Technology, Rice University, 6100 Main Street, Houston Texas 77005, United States
| | - James M. Tour
- Department of Chemical Engineering, ‡Department of Electrical and Computer Engineering, and §Materials Science and Engineering Graduate Program, Texas A&M University, College Station, Texas 77843, United States, and ¶Department of Chemistry, ∥Department of Mechanical Engineering and Materials Science, and ⊥Smalley Institute for Nanoscale Science and Technology, Rice University, 6100 Main Street, Houston Texas 77005, United States
| | - Jorge M. Seminario
- Department of Chemical Engineering, ‡Department of Electrical and Computer Engineering, and §Materials Science and Engineering Graduate Program, Texas A&M University, College Station, Texas 77843, United States, and ¶Department of Chemistry, ∥Department of Mechanical Engineering and Materials Science, and ⊥Smalley Institute for Nanoscale Science and Technology, Rice University, 6100 Main Street, Houston Texas 77005, United States
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Balaraju T, Kumar A, Bal C, Chattopadhyay D, Jena N, Bal NC, Sharon A. Aromatic interaction profile to understand the molecular basis of raltegravir resistance. Struct Chem 2012. [DOI: 10.1007/s11224-012-0181-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Wright DW, Wan S, Shublaq N, Zasada SJ, Coveney PV. From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:585-98. [PMID: 22899636 DOI: 10.1002/wsbm.1186] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Despite the promises made that genomic sequencing would transform therapy by introducing a new era of personalized medicine, relatively few tangible breakthroughs have been made. This has led to the recognition that complex interactions at multiple spatial, temporal, and organizational levels may often combine to produce disease. Understanding this complexity requires that existing and future models are used and interpreted within a framework that incorporates knowledge derived from investigations at multiple levels of biological function. It also requires a computational infrastructure capable of dealing with the vast quantities of data generated by genomic approaches. In this review, we discuss the use of molecular modeling to generate quantitative and qualitative insights at the smallest scales of the systems biology hierarchy, how it can play an important role in the development of a systems understanding of disease and in the application of such knowledge to help discover new therapies and target existing ones on a personal level.
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Affiliation(s)
- David W Wright
- Centre for Computational Science, University College London, London, UK
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34
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Maes M, Loyter A, Friedler A. Peptides that inhibit HIV-1 integrase by blocking its protein-protein interactions. FEBS J 2012; 279:2795-809. [PMID: 22742518 DOI: 10.1111/j.1742-4658.2012.08680.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HIV-1 integrase (IN) is one of the key enzymes in the viral replication cycle. It mediates the integration of viral cDNA into the host cell genome. IN activity requires interactions with several viral and cellular proteins, as well as IN oligomerization. Inhibition of IN is an important target for the development of anti-HIV therapies, but there is currently only one anti-HIV drug used in the clinic that targets IN. Several other small-molecule anti-IN drug leads are either undergoing clinical trials or in earlier stages of development. These molecules specifically inhibit one of the IN-mediated reactions necessary for successful integration. However, small-molecule inhibitors of protein-protein interactions are difficult to develop. In this review, we focus on peptides that inhibit IN. Peptides have advantages over small-molecule inhibitors of protein-protein interactions: they can mimic the structures of the binding domains within proteins, and are large enough to competitively inhibit protein-protein interactions. The development of peptides that bind IN and inhibit its protein-protein interactions will increase our understanding of the IN mode of action, and lead to the development of new drug leads, such as small molecules derived from these peptides, for better anti-HIV therapy.
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Affiliation(s)
- Michal Maes
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
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35
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Ammar FF, Abdel-Azeim S, Zargarian L, Hobaika Z, Maroun RG, Fermandjian S. Unprocessed viral DNA could be the primary target of the HIV-1 integrase inhibitor raltegravir. PLoS One 2012; 7:e40223. [PMID: 22768342 PMCID: PMC3388078 DOI: 10.1371/journal.pone.0040223] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 06/02/2012] [Indexed: 12/18/2022] Open
Abstract
Integration of HIV DNA into host chromosome requires a 3'-processing (3'-P) and a strand transfer (ST) reactions catalyzed by virus integrase (IN). Raltegravir (RAL), commonly used in AIDS therapy, belongs to the family of IN ST inhibitors (INSTIs) acting on IN-viral DNA complexes (intasomes). However, studies show that RAL fails to bind IN alone, but nothing has been reported on the behaviour of RAL toward free viral DNA. Here, we assessed whether free viral DNA could be a primary target for RAL, assuming that the DNA molecule is a receptor for a huge number of pharmacological agents. Optical spectroscopy, molecular dynamics and free energy calculations, showed that RAL is a tight binder of both processed and unprocessed LTR (long terminal repeat) ends. Complex formation involved mainly van der Waals forces and was enthalpy driven. Dissociation constants (Kds) revealed that RAL affinity for unbound LTRs was stronger than for bound LTRs. Moreover, Kd value for binding of RAL to LTRs and IC50 value (half concentration for inhibition) were in same range, suggesting that RAL binding to DNA and ST inhibition are correlated events. Accommodation of RAL into terminal base-pairs of unprocessed LTR is facilitated by an extensive end fraying that lowers the RAL binding energy barrier. The RAL binding entails a weak damping of fraying and correlatively of 3'-P inhibition. Noteworthy, present calculated RAL structures bound to free viral DNA resemble those found in RAL-intasome crystals, especially concerning the contacts between the fluorobenzyl group and the conserved 5'C(4)pA(3)3' step. We propose that RAL inhibits IN, in binding first unprocessed DNA. Similarly to anticancer drug poisons acting on topoisomerases, its interaction with DNA does not alter the cut, but blocks the subsequent joining reaction. We also speculate that INSTIs having viral DNA rather IN as main target could induce less resistance.
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Affiliation(s)
- Farah F. Ammar
- LBPA, UMR8113 du CNRS, Ecole Normale Supérieure de Cachan, Cedex, Cachan, France
- Unité de Biochimie, Département SVT, Faculté des Sciences, Université Saint-Joseph, CST-Mar Roukoz, Beyrouth, Liban
| | - Safwat Abdel-Azeim
- LBPA, UMR8113 du CNRS, Ecole Normale Supérieure de Cachan, Cedex, Cachan, France
| | - Loussinée Zargarian
- LBPA, UMR8113 du CNRS, Ecole Normale Supérieure de Cachan, Cedex, Cachan, France
| | - Zeina Hobaika
- Unité de Biochimie, Département SVT, Faculté des Sciences, Université Saint-Joseph, CST-Mar Roukoz, Beyrouth, Liban
| | - Richard G. Maroun
- Unité de Biochimie, Département SVT, Faculté des Sciences, Université Saint-Joseph, CST-Mar Roukoz, Beyrouth, Liban
| | - Serge Fermandjian
- LBPA, UMR8113 du CNRS, Ecole Normale Supérieure de Cachan, Cedex, Cachan, France
- * E-mail:
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36
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Marchand C. The elvitegravir Quad pill: the first once-daily dual-target anti-HIV tablet. Expert Opin Investig Drugs 2012; 21:901-4. [PMID: 22571404 DOI: 10.1517/13543784.2012.685653] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Anti-HIV combination therapies in a single formulation currently target only HIV-1 reverse transcriptase via two different mechanisms of action by associating a nucleoside and a non-nucleoside reverse transcriptase inhibitor. These combination therapies are therefore referred to as multi-class combination products. The elvitegravir Quad pill (Gilead Sciences), when approved by the Food and Drug Administration for the treatment of HIV/AIDS, will become the first once-daily dual-target anti-HIV tablet. This "4 in 1" tablet targets HIV-1 integrase by elvitegravir boosted by the pharmaco-enhancer cobicistat and HIV-1 reverse transcriptase by the two nucleoside reverse transcriptase inhibitors emtricitabine + tenofovir disoproxil fumarate. A second pill referred to as the 572-Trii pill (Shionogi-ViiV Healthcare, LLC), also based on the dual inhibition of integrase and reverse transcriptase, is currently in late-phase clinical trials. The availability of these novel once-daily anti-HIV tablets will improve treatment adherence and offer new perspective for patient failing existing antiviral regimens.
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Quashie PK, Sloan RD, Wainberg MA. Novel therapeutic strategies targeting HIV integrase. BMC Med 2012; 10:34. [PMID: 22498430 PMCID: PMC3348091 DOI: 10.1186/1741-7015-10-34] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 04/12/2012] [Indexed: 01/17/2023] Open
Abstract
Integration of the viral genome into host cell chromatin is a pivotal and unique step in the replication cycle of retroviruses, including HIV. Inhibiting HIV replication by specifically blocking the viral integrase enzyme that mediates this step is an obvious and attractive therapeutic strategy. After concerted efforts, the first viable integrase inhibitors were developed in the early 2000s, ultimately leading to the clinical licensure of the first integrase strand transfer inhibitor, raltegravir. Similarly structured compounds and derivative second generation integrase strand transfer inhibitors, such as elvitegravir and dolutegravir, are now in various stages of clinical development. Furthermore, other mechanisms aimed at the inhibition of viral integration are being explored in numerous preclinical studies, which include inhibition of 3' processing and chromatin targeting. The development of new clinically useful compounds will be aided by the characterization of the retroviral intasome crystal structure. This review considers the history of the clinical development of HIV integrase inhibitors, the development of antiviral drug resistance and the need for new antiviral compounds.
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Affiliation(s)
- Peter K Quashie
- McGill University AIDS Centre, Lady Davis Institute, Montreal, Canada
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Xue W, Qi J, Yang Y, Jin X, Liu H, Yao X. Understanding the effect of drug-resistant mutations of HIV-1 intasome on raltegravir action through molecular modeling study. MOLECULAR BIOSYSTEMS 2012; 8:2135-44. [DOI: 10.1039/c2mb25114k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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