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Grandgenett DP, Engelman AN. Brief Histories of Retroviral Integration Research and Associated International Conferences. Viruses 2024; 16:604. [PMID: 38675945 PMCID: PMC11054761 DOI: 10.3390/v16040604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
The field of retroviral integration research has a long history that started with the provirus hypothesis and subsequent discoveries of the retroviral reverse transcriptase and integrase enzymes. Because both enzymes are essential for retroviral replication, they became valued targets in the effort to discover effective compounds to inhibit HIV-1 replication. In 2007, the first integrase strand transfer inhibitor was licensed for clinical use, and subsequently approved second-generation integrase inhibitors are now commonly co-formulated with reverse transcriptase inhibitors to treat people living with HIV. International meetings specifically focused on integrase and retroviral integration research first convened in 1995, and this paper is part of the Viruses Special Issue on the 7th International Conference on Retroviral Integration, which was held in Boulder Colorado in the summer of 2023. Herein, we overview key historical developments in the field, especially as they pertain to the development of the strand transfer inhibitor drug class. Starting from the mid-1990s, research advancements are presented through the lens of the international conferences. Our overview highlights the impact that regularly scheduled, subject-specific international meetings can have on community-building and, as a result, on field-specific collaborations and scientific advancements.
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Affiliation(s)
- Duane P. Grandgenett
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St. Louis, MO 63104, USA
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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2
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Rakshit S, More A, Gaikwad S, Seniya C, Gade A, Muley VY, Mukherjee A, Kamble K. Role of diosgenin extracted from Helicteres isora L in suppression of HIV-1 replication: An in vitro preclinical study. Heliyon 2024; 10:e24350. [PMID: 38288021 PMCID: PMC10823083 DOI: 10.1016/j.heliyon.2024.e24350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/23/2023] [Accepted: 01/08/2024] [Indexed: 01/31/2024] Open
Abstract
Background Diosgenin, an essential sapogenin steroid with significant biological implications, is composed of a hydrophilic sugar moiety intricately linked to a hydrophobic steroid aglycone. While the antiviral properties of diosgenin against numerous RNA viruses have been extensively documented, its potential in combating Human Immunodeficiency Virus infections remains unexplored. Experimental procedure This current investigation presents a comprehensive and systematic analysis of extracts derived from the leaves of Helicteres isora, which are notably enriched with diosgenin. Rigorous methodologies, including established chromatographic techniques and Fourier-transform infrared spectroscopy were employed for the characterization of the active diosgenin compound followed by molecular interaction analyses with the key HIV enzymes and mechanistic validation of HIV inhibition. Key results The inhibitory effects of extracted diosgenin on the replication of HIV-1 were demonstrated using a permissive cellular system, encompassing two distinct subtypes of HIV-1 strains. Computational analyses involving molecular interactions highlighted the substantial occupancy of critical active site pocket residues within the key HIV-1 proteins by diosgenin. Additionally, the mechanistic underpinnings of diosgenin activity in conjunction with standard controls were elucidated through specialized colorimetric assays, evaluating its impact on HIV-1 Reverse Transcriptase and Integrase enzymes. Conclusions To our current state of knowledge, this study represents the inaugural demonstration of the anti-HIV efficacy inherent to diosgenin found in the leaves of Helicteres isora, and can be taken further for drug design and development for the management of HIV infection.
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Affiliation(s)
- Smita Rakshit
- Department of Microbiology, Sant Gadge Baba Amravati University, Amravati, MH, India
| | - Ashwini More
- Division of Virology, ICMR-National AIDS Research Institute, Pune, MH, India
| | - Shraddha Gaikwad
- Division of Virology, ICMR-National AIDS Research Institute, Pune, MH, India
| | - Chandrabhan Seniya
- VIT Bhopal University, School of Biosciences, Engineering and Technology, Bhopal, MP, India
| | - Aniket Gade
- Department of Biotechnology, Sant Gadge Baba Amravati University, Amravati, MH, India
- Department of Biological Science and Biotechnology, Institute of Chemical Technology, Mumbai, MH, India
| | | | - Anupam Mukherjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune, MH, India
| | - Kapil Kamble
- Department of Microbiology, Sant Gadge Baba Amravati University, Amravati, MH, India
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3
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Renzi G, Carta F, Supuran CT. The Integrase: An Overview of a Key Player Enzyme in the Antiviral Scenario. Int J Mol Sci 2023; 24:12187. [PMID: 37569561 PMCID: PMC10419282 DOI: 10.3390/ijms241512187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Integration of a desossiribonucleic acid (DNA) copy of the viral ribonucleic acid (RNA) into host genomes is a fundamental step in the replication cycle of all retroviruses. The highly conserved virus-encoded Integrase enzyme (IN; EC 2.7.7.49) catalyzes such a process by means of two consecutive reactions named 3'-processing (3-P) and strand transfer (ST). The Authors report and discuss the major discoveries and advances which mainly contributed to the development of Human Immunodeficiency Virus (HIV) -IN targeted inhibitors for therapeutic applications. All the knowledge accumulated over the years continues to serve as a valuable resource for the design and development of effective antiretroviral drugs.
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Affiliation(s)
| | - Fabrizio Carta
- Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (G.R.); (C.T.S.)
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4
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Han S, Lu Y. Fluorine in anti-HIV drugs approved by FDA from 1981 to 2023. Eur J Med Chem 2023; 258:115586. [PMID: 37393791 DOI: 10.1016/j.ejmech.2023.115586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 07/04/2023]
Abstract
Human immunodeficiency virus (HIV) is the etiological agent of acquired immunodeficiency syndrome (AIDS). Nowadays, FDA has approved over thirty antiretroviral drugs grouped in six categories. Interestingly, one-third of these drugs contain different number of fluorine atoms. The introduction of fluorine to obtain drug-like compounds is a well-accepted strategy in medicinal chemistry. In this review, we summarized 11 fluorine-containing anti-HIV drugs, focusing on their efficacy, resistance, safety, and specific roles of fluorine in the development of each drug. These examples may be of help for the discovery of new drug candidates bearing fluorine in their structures.
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Affiliation(s)
- Sheng Han
- School of Medicine, Shanghai University, Shanghai, China.
| | - Yiming Lu
- School of Medicine, Shanghai University, Shanghai, China; Department of Critical Care Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.
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5
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Cardoza S, Yadav P, Ajmani A, Das P, Tandon V. Synthesis of C3,C6-Diaryl 7-Azaindoles via One-Pot Suzuki-Miyaura Cross-Coupling Reaction and Evaluation of Their HIV-1 Integrase Inhibitory Activity. ACS OMEGA 2023; 8:8415-8426. [PMID: 36910947 PMCID: PMC9996623 DOI: 10.1021/acsomega.2c07372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
There is a continuing demand of new inhibitors of HIV-1 Integrase (HIV-1 IN) due to mutations of HIV-1. This study aims to develop the synthesis of 3,6-diaryl 7-azaindoles and introspect the role of aryl groups on the strand transfer (ST) inhibition of HIV-1 IN. An efficient and chemo-selective one-pot method is established for the synthesis of the unexplored diverse C3 → C6 diaryl 7-azaindoles starting from 6-chloro-3-iodo-N-protected 7-azaindoles. Here we report Pd2dba3/SPhos catalyzed synthesis of eight selective C3 monoaryl 7-azaindoles (10a-h) and eight C3,C6-diaryl 7-azaindoles (11a-f, 12a,b) with yields in the ranges of 67-93% and 43-88% respectively. The synthesized derivatives inhibit the strand transfer (ST) activity of HIV-1 IN enzyme at 10 μM dose with 11d and 11f exhibiting %ST inhibitions of 72% and 71%, respectively. SAR studies indicate the para-substitution on the C3 aryl ring and C6 aryl is essential for enhanced %ST inhibition. 11b,c, 11e-f, and 12b showed lower cytotoxicity (IC50 > 200 μM) against TZM-bl cells. Molecular docking of the diaryl 7-azaindoles and Raltegravir (RAL), to the PFV-integrase revealed favorable binding interactions.
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Affiliation(s)
- Savio Cardoza
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
| | - Pooja Yadav
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
| | - Abhishek Ajmani
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
| | - Parthasarathi Das
- Department
of Chemistry and Chemical Biology, Indian
Institute of Technology (Indian School of Mines), Dhanbad 826004, India
| | - Vibha Tandon
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
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Ouzebla D, Ourhriss N, Fadare OA, Belghiti ME, El Abdallaoui HEA, Zeroual A. Efficient Synthesis of Acyclic Nucleosides by N-Alkylation Using K2CO3 Supported with Natural Phosphate (K2CO3@NP) as Catalyst and Docking Study Against VIH. CHEMISTRY AFRICA 2022. [DOI: 10.1007/s42250-022-00528-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Unveiling Natural and Semisynthetic Acylated Flavonoids: Chemistry and Biological Actions in the Context of Molecular Docking. Molecules 2022; 27:molecules27175501. [PMID: 36080269 PMCID: PMC9458193 DOI: 10.3390/molecules27175501] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Acylated flavonoids are widely distributed natural metabolites in medicinal plants and foods with several health attributes. A large diversity of chemical structures of acylated flavonoids with interesting biological effects was reported from several plant species. Of these, 123 compounds with potential antimicrobial, antiparasitic, anti-inflammatory, anti-nociceptive, analgesic, and anti-complementary effects were selected from several databases including SCI-Finder, Scopus, Google Scholar, Science Direct, PubMed, and others. Some selected reported biologically active flavonoids were docked in the active binding sites of some natural enzymes, namely acetylcholinesterase, butyrylcholinesterase, α-amylase, α-glucosidase, aldose reductase, and HIV integrase, in an attempt to underline the key interactions that might be responsible for their biological activities.
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8
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Urvashi, Senthil Kumar JB, Das P, Tandon V. Development of Azaindole-Based Frameworks as Potential Antiviral Agents and Their Future Perspectives. J Med Chem 2022; 65:6454-6495. [PMID: 35477274 PMCID: PMC9063994 DOI: 10.1021/acs.jmedchem.2c00444] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Indexed: 11/29/2022]
Abstract
The azaindole (AI) framework continues to play a significant role in the design of new antiviral agents. Modulating the position and isosteric replacement of the nitrogen atom of AI analogs notably influences the intrinsic physicochemical properties of lead compounds. The intra- and intermolecular interactions of AI derivatives with host receptors or viral proteins can also be fine tuned by carefully placing the nitrogen atom in the heterocyclic core. This wide-ranging perspective article focuses on AIs that have considerable utility in drug discovery programs against RNA viruses. The inhibition of influenza A, human immunodeficiency, respiratory syncytial, neurotropic alpha, dengue, ebola, and hepatitis C viruses by AI analogs is extensively reviewed to assess their plausible future potential in antiviral drug discovery. The binding interaction of AIs with the target protein is examined to derive a structural basis for designing new antiviral agents.
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Affiliation(s)
- Urvashi
- Drug Discovery Laboratory, Special Centre for
Molecular Medicine, Jawaharlal Nehru University, New Delhi 110
067, India
- Department of Chemistry, University of
Delhi, New Delhi 110007, India
| | - J. B. Senthil Kumar
- Drug Discovery Laboratory, Special Centre for
Molecular Medicine, Jawaharlal Nehru University, New Delhi 110
067, India
| | - Parthasarathi Das
- Department of Chemistry, Indian Institute
of Technology (ISM), Dhanbad 826004, India
| | - Vibha Tandon
- Drug Discovery Laboratory, Special Centre for
Molecular Medicine, Jawaharlal Nehru University, New Delhi 110
067, India
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9
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Parvez MK, Al-Dosari MS, Sinha GP. Machine learning-based predictive models for identifying high active compounds against HIV-1 integrase. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:387-402. [PMID: 35410555 DOI: 10.1080/1062936x.2022.2057588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
HIV-integrase is an important drug target because it catalyzes chromosomal integration of proviral DNA towards establishing latent infection. Computer-aided drug design has immensely contributed to identifying and developing novel antiviral drugs. We have developed various machine learning-based predictive models for identifying high activity compounds against HIV-integrase. Multiclass models were built using support vector machine with reasonable accuracy on the test and evaluation sets. The developed models were evaluated by rigorous validation approaches and the best features were selected by Boruta method. As compared to the model developed from all descriptors set, a slight improvement was observed among the selected descriptors. Validated models were further used for virtual screening of potential compounds from ChemBridge library. Of the six high active compounds predicted from selected models, compounds 9103124, 6642917 and 9082952 showed the most reasonable binding-affinity and stable-interaction with HIV-integrase active-site residues Asp64, Glu152 and Asn155. This was in agreement with previous reports on the essentiality of these residues against a wide range of inhibitors. We therefore highlight the rigorosity of validated classification models for accurate prediction and ranking of high active lead drugs against HIV-integrase.
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Affiliation(s)
- M K Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - M S Al-Dosari
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - G P Sinha
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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HIV-1 Integrase Inhibitory Effects of Major Compounds Present in CareVid™: An Anti-HIV Multi-Herbal Remedy. Life (Basel) 2022; 12:life12030417. [PMID: 35330168 PMCID: PMC8950597 DOI: 10.3390/life12030417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 11/21/2022] Open
Abstract
In our continued study on the anti-HIV activity of compounds present in CareVidTM, we report the HIV-1 integrase ((HIV-1 IN) inhibitory effects of pellitorine (1), oleuropein (2), magnoflorine (3), crotepoxide (4), ent-kaurane-16β,17-diol (5), crotocorylifuran (6), lupeol (7), betulin (8), and ellagic acid (9) in an in vitro enzyme assay, and in an in silico study. Ellagic acid, pellitorine, lupeol, and betulin showed an in vitro percentage inhibition against HIV-1 IN of 21.1%, 19.0%, 18.5%, and 16.8%, respectively, at a standard concentration of 25 μg/mL. However, from a pharmacokinetic perspective, ellagic acid has poor bioavailability, due to rapid elimination in metabolism in the gut microbiome. It was postulated that known gut catabolites of ellagic acid, urolithin A (10) and urolithin B (11) could be more promising candidates in exploring the anti-HIV activity of ellagic acid-rich medicinal species consumed orally. On the contrary, urolithin A and urolithin B demonstrated lower activity with comparison to ellagic acid. The binding affinity of compounds 1–9, urolithin A, and urolithin B against the catalytic domain of HIV-1 IN was also explored by in silico methods. Docking studies showed oleuropein as the best candidate, with a predicted energy of binding of ΔG −5.81 kcal/mol, while ellagic acid showed moderate predicted inhibition (ΔG −4.38 kcal/mol) caused by the interaction between the carbonyl and the key Mg2+ ion in the active site.
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11
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Tighadouini S, Roby O, Mortada S, Lakbaibi Z, Radi S, Al-Ali A, Faouzi MEA, Ferbinteanu M, Garcia Y, Al-Zaqri N, Zarrouk A, Warad I. Crystal structure, physicochemical, DFT, optical, keto-enol tautomerization, docking, and anti-diabetic studies of (Z)-pyrazol β-keto-enol derivative. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131308] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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12
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Advances in the development of HIV integrase strand transfer inhibitors. Eur J Med Chem 2021; 225:113787. [PMID: 34425310 DOI: 10.1016/j.ejmech.2021.113787] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/05/2021] [Accepted: 08/05/2021] [Indexed: 12/30/2022]
Abstract
HIV-1 integrase (IN) is a key enzyme in viral replication that catalyzes the covalent integration of viral cDNA into the host genome. Currently, five HIV-1 IN strand transfer inhibitors (INSTIs) are approved for clinical use. These drugs represent an important addition to the armamentarium for antiretroviral therapy. This review briefly illustrates the development history of INSTIs. The characteristics of the currently approved INSTIs, as well as their future perspectives, are critically discussed.
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Chatzigoulas A, Cournia Z. Rational design of allosteric modulators: Challenges and successes. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1529] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alexios Chatzigoulas
- Biomedical Research Foundation Academy of Athens Athens Greece
- Department of Informatics and Telecommunications National and Kapodistrian University of Athens Athens Greece
| | - Zoe Cournia
- Biomedical Research Foundation Academy of Athens Athens Greece
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Wadhwa P, Jain P, Jadhav HR. Design, Synthesis and In Vitro Evaluation of 4-Oxo-6-Substituted Phenyl- 2-Thioxo1,2,3,4-Tetrahydropyrimidine-5-Carbonitrile Derivatives as HIV Integrase Strand Transfer Inhibitors. LETT DRUG DES DISCOV 2021. [DOI: 10.2174/1570180817999201022193325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aim::
To design, synthesis and in vitro evaluation of 4-oxo-6-substituted phenyl-2-
thioxo1,2,3,4-tetrahydropyrimidine-5-carbonitrile derivatives as HIV integrase strand transfer
inhibitors.
Background::
Human immunodeficiency virus-1 (HIV-1), a member of retroviridae family, is the
primary causative agent of acquired immunodeficiency syndrome (AIDS). Three enzymes viz: integrase
(IN), reverse transcriptase (RT) and protease play important role in its replication cycle. HIV-1
integrase is responsible for the incorporation of viral DNA into human chromosomal DNA by catalyzing
two independent reactions, 3′-processing (3′-P) and strand transfer (ST), which are observed
as the “point of no-return” in HIV infection.
Objective::
To develop inhibitors against HIV integrase strand transfer step.
Methods::
Our previous results indicated that tetrahydro pyrimidine-5-carboxamide derivatives are
potent HIV-1 IN inhibitors (unpublished results from our laboratory). Taking clue from above studies
and our own experience, we hypothesized 4-oxo-6-substituted phenyl-2-thioxo1,2,3,4-
tetrahydropyrimidine-5-carbonitrile analogues (14a to 14n) as inhibitors of HIV-1 Integrase strand
transfer. Prototype compound 14 can be viewed as hybrid structure having characteristics of dihydropyrimidine
derivatives 10-12 and tyrphostin 13.
Result::
A total of fourteen derivatives of 4-oxo-6-substituted phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-
5-carbonitrile (14a-14n) were synthesized and evaluated using HIV-1 Integrase Assay
Kit (Xpressbio Life Science Products, USA). The percentage inhibition of all compounds was investigated
at 10 μM concentration and IC50 value of few highly active compounds was studied. The
obtained results were validated by in silico molecular docking study using Glide (maestro version
9.3, Schrödinger suite) in extra precision (XP) mode.
Conclusion::
Fourteen 4-oxo-6-substituted phenyl-2-thioxo 1,2,3,4-tetrahydropyrimidine-5-carbonitrile
analogues were synthesized and evaluated for HIV-1 IN inhibitory activity. Three compounds 14a,
14e, and 14h exhibited significant percentage inhibition of HIV-1 IN. There was good in vitro - in
silico correlation. However, none of the derivative was active against HIV-1 and HIV-2 below their
cytotoxic concentration. It needs to be seen whether these compounds can be explored further for
their anti-HIV or cytotoxic potential.
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Affiliation(s)
- Pankaj Wadhwa
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani 333031, Rajasthan,India
| | - Priti Jain
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani 333031, Rajasthan,India
| | - Hemant R. Jadhav
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani 333031, Rajasthan,India
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Nilavar NM, Raghavan SC. HIV integrase inhibitors that inhibit strand transfer interact with RAG1 and hamper its activities. Int Immunopharmacol 2021; 95:107515. [PMID: 33735713 DOI: 10.1016/j.intimp.2021.107515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 12/16/2022]
Abstract
Multiple steps of the retroviral infection process have been targeted over the years to develop therapeutic approaches, starting from the entry of the virus into the cell till the viral DNA integration to host genome. Inhibitors against the Human Immunodeficiency Virus (HIV) integrase is the newest among the therapies employed against HIV. Recombination activating gene 1 (RAG1) is an integral protein involved in the generation of diversity of antibodies and T-cell receptors and is one of the partners of the RAG complex. Studies have shown structural and functional similarities between the HIV integrase and RAG1. Recently, we and others have shown that some of the integrase inhibitors can interfere with RAG binding and cleavage, hindering its physiological functions. This mini review focuses on the HIV integrase, integrase inhibitors and their effect on RAG activities.
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Affiliation(s)
- Namrata M Nilavar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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Esmaeili S, Mosaddeghi H, Ravari F. Molecular Docking Studies of HIV-1
Protease-, Integrase- and Reverse-Transcriptase with Delta-9-tetrahydrocannabinol
and Curcumin as Two Herbal Ligands. J EVOL BIOCHEM PHYS+ 2021. [DOI: 10.1134/s0022093021020101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Imani A, Soleymani S, Vahabpour R, Hajimahdi Z, Zarghi A. Design, Synthesis, Docking Study and Biological Evaluation of 4-Hydroxy-2 H-benzo[ e][1,2]thiazine-3-carboxamide 1,1-dioxide Derivatives as Anti-HIV Agents. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2021; 20:1-12. [PMID: 34903964 PMCID: PMC8653674 DOI: 10.22037/ijpr.2020.114153.14695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A novel series of benzothiazine-3-carboxamide 1,1-dioxide derivatives by modifying the piroxicam scaffold was designed, synthesized, and evaluated as anti-HIV agents. The 1,2-benzothiazine-3-carboxamide 1,1-dioxide scaffold consists of hydroxy and carboxamide groups as a chelating motif to form an interaction with Mg2+ ions within the integrase active site as a target. Most of the compounds displayed encouraging anti-HIV activity in a cell-based assay. Among them, compounds 13d, 13l and 13m were the most potent with EC50 values ranging from 20-25 µM and SI > 26. Docking study of compounds in integrase active site proposed that the mechanism of action of compounds might be through Mg2+ chelation within integrase active site. The lack of severe cytotoxicity and favorable anti-HIV activity of benzothiazine-3-carboxamide 1,1-dioxide derivatives support further modifications to improve the potency.
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Affiliation(s)
- Ali Imani
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Sepehr Soleymani
- Hepatitis and AIDS department, Pasteur Institute of Iran, Tehran, Iran.
| | - Rouhollah Vahabpour
- Medical Lab Technology Department, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Zahra Hajimahdi
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran. ,Corresponding authors:E-mail: ;
| | - Afshin Zarghi
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran. ,Corresponding authors:E-mail: ;
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18
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Pala N, Esposito F, Tramontano E, Singh PK, Sanna V, Carcelli M, Haigh LD, Satta S, Sechi M. Development of a Raltegravir-based Photoaffinity-Labeled Probe for Human Immunodeficiency Virus-1 Integrase Capture. ACS Med Chem Lett 2020; 11:1986-1992. [PMID: 33062183 DOI: 10.1021/acsmedchemlett.0c00009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/28/2020] [Indexed: 12/26/2022] Open
Abstract
Photoaffinity labeling (PAL) is one of the upcoming and powerful tools in the field of molecular recognition. It includes the determination of dynamic parameters, such as the identification and localization of the target protein and the site of drug binding. In this study, a photoaffinity-labeled probe for full-length human immunodeficiency virus-1 integrase (HIV-1 IN) capture was designed and synthesized, following the structure of the FDA-approved drug Raltegravir. This photoprobe was found to retain the HIV IN inhibitory potential in comparison with its parent molecule and demonstrates the ability to label the HIV-1 IN protein. Putative photoprobe/inhibitor binding sites near the catalytic site were then identified after protein digestion coupled to mass and molecular modeling analyses.
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Affiliation(s)
- Nicolino Pala
- Department of Chemistry and Pharmacy, Laboratory of Drug Design and Nanomedicine, University of Sassari, Sassari 07100, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09042, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09042, Italy
| | - Pankaj Kumar Singh
- Department of Chemistry and Pharmacy, Laboratory of Drug Design and Nanomedicine, University of Sassari, Sassari 07100, Italy
| | - Vanna Sanna
- Nanomater s.r.l., c/o Porto Conte Ricerche, Alghero 07041, Italy
| | - Mauro Carcelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Lisa D. Haigh
- Department of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Sandro Satta
- Centre for Pharmacology & Therapeutics, Department of Medicine, Imperial College London, London W12 0NN, United Kingdom
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California 90095, United States
| | - Mario Sechi
- Department of Chemistry and Pharmacy, Laboratory of Drug Design and Nanomedicine, University of Sassari, Sassari 07100, Italy
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19
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Tighadouini S, Radi S, Benabbes R, Youssoufi MH, Shityakov S, El Massaoudi M, Garcia Y. Synthesis, Biochemical Characterization, and Theoretical Studies of Novel β-Keto-enol Pyridine and Furan Derivatives as Potent Antifungal Agents. ACS OMEGA 2020; 5:17743-17752. [PMID: 32715261 PMCID: PMC7377641 DOI: 10.1021/acsomega.0c02365] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 06/24/2020] [Indexed: 05/03/2023]
Abstract
In the present study, we report the design and synthesis of new derivatives of the β-keto-enol grafted on pyridine and furan moieties (L 1 -L 11 ). Structures of compounds were fully confirmed by Fourier transform infrared spectroscopy (FT-IR), 1H NMR, 13C NMR, electrospray ionization/liquid chromatography-mass spectrometry (ESI/LC-MS), and elemental analysis. The compounds were screened for antifungal and antibacterial activities (Escherichia coli, Bacillus subtilis, and Micrococcus luteus). In vitro evaluation showed significant fungicidal activity for L 1 , L 4 , and L 5 against fungal strains (Fusarium oxysporum f.sp albedinis) compared to the reference standard. Especially, the exceptional activity has been demonstrated for L 1 with IC50 = 12.83 μg/mL. This compound and the reference benomyl molecule also showed a correlation between experimental antifungal activity and theoretical predictions by Petra/Osiris/Molinspiration (POM) calculations and molecular coupling against the Fgb1 protein. The highest inhibition of bacterial growth for L 1 is due to its strongest binding to the target protein. This report may stimulate the further synthesis of examples of this substance class for the development of new drugs.
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Affiliation(s)
- Said Tighadouini
- Laboratory
of Organic Synthesis, Extraction and Valorization, Faculty of Sciences
Ain Chock, Hassan II University, Route d’El Jadida Km 2, BP 5366 Casablanca, Morocco
| | - Smaail Radi
- Laboratory
of Applied Chemistry & Environment, Faculty of Sciences, Mohammed First University, 60000 Oujda, Morocco
- ,
| | - Redouane Benabbes
- Department
of Biology, Faculty of Sciences, Mohammed
First University, 60000 Oujda, Morocco
| | - Moulay Hfid Youssoufi
- Laboratory
of Applied Chemistry & Environment, Faculty of Sciences, Mohammed First University, 60000 Oujda, Morocco
| | - Sergey Shityakov
- Department
of Bioinformatics, Würzburg University, Am Hubland, 97074 Würzburg, Germany
| | - Mohamed El Massaoudi
- Laboratory
of Applied Chemistry & Environment, Faculty of Sciences, Mohammed First University, 60000 Oujda, Morocco
| | - Yann Garcia
- Institute
of Condensed Matter and Nanosciences, Molecular Chemistry, Materials
and Catalysis (IMCN/MOST), Universite′
catholique de Louvain, Place Louis Pasteur 1, 1348 Louvain-la-Neuve, Belgium
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20
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Nilavar NM, Paranjape AM, Raghavan SC. Biochemical activity of RAGs is impeded by Dolutegravir, an HIV integrase inhibitor. Cell Death Discov 2020; 6:50. [PMID: 32566255 PMCID: PMC7293277 DOI: 10.1038/s41420-020-0281-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/26/2020] [Accepted: 04/22/2020] [Indexed: 02/03/2023] Open
Abstract
HIV is a retrovirus that infects CD4+ T lymphocytes in human beings and causes immunodeficiency. In the recent years, various therapies have been developed against HIV, including targeting the HIV specific protein, integrase, responsible for integration of HIV cDNA into host DNA. Although, integrase is specific to HIV, it has functional and structural similarity with RAG1, one of the partner proteins associated with V(D)J recombination, a process by which immune diversity is generated in humans. Currently, there are three HIV integrase inhibitors: Elvitegravir, Dolutegravir, and Raltegravir, in the market which have been approved by the FDA (USA). All three drugs are used in anti-retroviral therapy (ART). Previously, we showed that amongst the HIV inhibitors, Elvitegravir could significantly decrease B cell maturation in vivo and inhibit the physiological activities of RAGs in vitro, unlike Raltegravir. In the present study, we address the effect of second-generation integrase inhibitor, Dolutegravir on RAG activities. Binding and nicking studies showed that, Dolutegravir could decrease the binding efficiency of RAG1 domains and cleavage on DNA substrates, but not as considerably as Elvitegravir. Thus, we show that although the integrase inhibitors such as Elvitegravir show an affinity towards RAG1, the newer molecules may have lesser side-effects.
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Affiliation(s)
- Namrata M. Nilavar
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
| | - Amita M. Paranjape
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
| | - Sathees C. Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
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21
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Melo R, Lemos A, Preto AJ, Bueschbell B, Matos-Filipe P, Barreto C, Almeida JG, Silva RDM, Correia JDG, Moreira IS. An Overview of Antiretroviral Agents for Treating HIV Infection in Paediatric Population. Curr Med Chem 2020; 27:760-794. [PMID: 30182840 DOI: 10.2174/0929867325666180904123549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/11/2018] [Accepted: 07/11/2018] [Indexed: 12/19/2022]
Abstract
Paediatric Acquired ImmunoDeficiency Syndrome (AIDS) is a life-threatening and infectious disease in which the Human Immunodeficiency Virus (HIV) is mainly transmitted through Mother-To- Child Transmission (MTCT) during pregnancy, labour and delivery, or breastfeeding. This review provides an overview of the distinct therapeutic alternatives to abolish the systemic viral replication in paediatric HIV-1 infection. Numerous classes of antiretroviral agents have emerged as therapeutic tools for downregulation of different steps in the HIV replication process. These classes encompass Non- Nucleoside Analogue Reverse Transcriptase Inhibitors (NNRTIs), Nucleoside/Nucleotide Analogue Reverse Transcriptase Inhibitors (NRTIs/NtRTIs), INtegrase Inhibitors (INIs), Protease Inhibitors (PIs), and Entry Inhibitors (EIs). Co-administration of certain antiretroviral drugs with Pharmacokinetic Enhancers (PEs) may boost the effectiveness of the primary therapeutic agent. The combination of multiple antiretroviral drug regimens (Highly Active AntiRetroviral Therapy - HAART) is currently the standard therapeutic approach for HIV infection. So far, the use of HAART offers the best opportunity for prolonged and maximal viral suppression, and preservation of the immune system upon HIV infection. Still, the frequent administration of high doses of multiple drugs, their inefficient ability to reach the viral reservoirs in adequate doses, the development of drug resistance, and the lack of patient compliance compromise the complete HIV elimination. The development of nanotechnology-based drug delivery systems may enable targeted delivery of antiretroviral agents to inaccessible viral reservoir sites at therapeutic concentrations. In addition, the application of Computer-Aided Drug Design (CADD) approaches has provided valuable tools for the development of anti-HIV drug candidates with favourable pharmacodynamics and pharmacokinetic properties.
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Affiliation(s)
- Rita Melo
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal.,CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Agostinho Lemos
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal.,GIGA Cyclotron Research Centre In Vivo Imaging, University of Liège, Liège 4000, Belgium
| | - António J Preto
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Beatriz Bueschbell
- Pharmaceutical Chemistry I, PharmaCenter, Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | - Pedro Matos-Filipe
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Carlos Barreto
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - José G Almeida
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Rúben D M Silva
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal
| | - João D G Correia
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal
| | - Irina S Moreira
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal.,Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht 3584CH, Netherland
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22
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Mușat MG, Nițulescu GM, Surleac M, Tsatsakis A, Spandidos DA, Margină D. HIV‑1 integrase inhibitors targeting various DDE transposases: Retroviral integration versus RAG‑mediated recombination (Review). Mol Med Rep 2019; 20:4749-4762. [PMID: 31702817 PMCID: PMC6854553 DOI: 10.3892/mmr.2019.10777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022] Open
Abstract
Transposases are ubiquitous mobile genetic elements responsible for genome development, driving rearrangements, such as insertions, deletions and translocations. Across species evolution, some transposases are tamed by their host and are made part of complex cellular systems. The proliferation of retroviruses is also dependent on transposase related enzymes termed integrases. Recombination‑activating gene protein (RAG)1 and metnase are just two examples of transposase domestication and together with retroviral integrases (INs), they belong to the DDE polynucleotidyl transferases superfamily. They share mechanistic and structural features linked to the RNase H‑like fold, harboring a DDE(D) metal dependent catalytic motif. Recent antiretroviral compounds target the catalytic domain of integrase, but they also have the potential of inhibiting other related enzymes. In this review, we report the activity of different classes of integrase inhibitors on various DDE transposases. Computational simulations are useful to predict the extent of off‑target activity and have been employed to study the interactions between RAG1 recombinase and compounds from three different pharmacologic classes. We demonstrate that strand‑transfer inhibitors display a higher affinity towards the RAG1 RNase H domain, as suggested by experimental data compared to allosteric inhibitors. While interference with RAG1 and 2 recombination is associated with a negative impact on immune function, the inhibition of metnase or HTLV‑1 integrase opens the way for the development of novel therapies for refractory cancers.
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Affiliation(s)
- Mihaela Georgiana Mușat
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - George Mihai Nițulescu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Marius Surleac
- National Institute for Infectious Diseases ‘Matei Bals’, 021105 Bucharest, Romania
| | - Aristidis Tsatsakis
- Department of Forensic Sciences and Toxicology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Denisa Margină
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania
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23
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Maeda K, Das D, Kobayakawa T, Tamamura H, Takeuchi H. Discovery and Development of Anti-HIV Therapeutic Agents: Progress Towards Improved HIV Medication. Curr Top Med Chem 2019; 19:1621-1649. [PMID: 31424371 PMCID: PMC7132033 DOI: 10.2174/1568026619666190712204603] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/14/2019] [Accepted: 06/21/2019] [Indexed: 01/09/2023]
Abstract
The history of the human immunodeficiency virus (HIV)/AIDS therapy, which spans over 30 years, is one of the most dramatic stories of science and medicine leading to the treatment of a disease. Since the advent of the first AIDS drug, AZT or zidovudine, a number of agents acting on different drug targets, such as HIV enzymes (e.g. reverse transcriptase, protease, and integrase) and host cell factors critical for HIV infection (e.g. CD4 and CCR5), have been added to our armamentarium to combat HIV/AIDS. In this review article, we first discuss the history of the development of anti-HIV drugs, during which several problems such as drug-induced side effects and the emergence of drug-resistant viruses became apparent and had to be overcome. Nowadays, the success of Combination Antiretroviral Therapy (cART), combined with recently-developed powerful but nonetheless less toxic drugs has transformed HIV/AIDS from an inevitably fatal disease into a manageable chronic infection. However, even with such potent cART, it is impossible to eradicate HIV because none of the currently available HIV drugs are effective in eliminating occult “dormant” HIV cell reservoirs. A number of novel unique treatment approaches that should drastically improve the quality of life (QOL) of patients or might actually be able to eliminate HIV altogether have also been discussed later in the review.
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Affiliation(s)
- Kenji Maeda
- National Center for Global Health and Medicine (NCGM) Research Institute, Tokyo 162-8655, Japan
| | - Debananda Das
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health (NCI/NIH), Bethesda, MD, United States
| | - Takuya Kobayakawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Tokyo 101-0062, Japan
| | - Hirokazu Tamamura
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
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24
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Eurtivong C, Choowongkomon K, Ploypradith P, Ruchirawat S. Molecular docking study of lamellarin analogues and identification of potential inhibitors of HIV-1 integrase strand transfer complex by virtual screening. Heliyon 2019; 5:e02811. [PMID: 31763475 PMCID: PMC6861579 DOI: 10.1016/j.heliyon.2019.e02811] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/24/2019] [Accepted: 11/07/2019] [Indexed: 11/25/2022] Open
Abstract
Molecular docking has been applied to elucidate the binding of lamellarin analogues with HIV-1 integrase strand transfer complex (PDB ID: 5U1C). The results suggest hydrogen bond interaction with residue Glu92 is key, and stabilisation by π-π stacking interactions with DNA base is chiefly influential to strand transfer activity. Other residues involved in hydrogen bonding are Cys65, His67, Asp64, Asp116 and chelation with Mg2+ ion was seen for certain analogues. Furthermore, hydrophobic interactions can be accounted for several amino acids including Asp64, Cys65, Asp116, His67, Glu92, Tyr143, Phe121, Gly118, Pro142 and Val72, as well as the DNA base. The molecular docking results are in line with the reported literatures of other inhibitors and strand transfer activity observed previously by Faulkner. We further employed molecular docking simulation to virtually screen and identified 4 novel potential inhibitors of HIV-1 integrase strand transfer complex from a Chembridge diversity collection of 25,132 small molecule compounds; Chembridge ID compound codes: 22850303, 27553460, 24578440 and 27591056. The candidates clearly formed hydrogen bonding interactions with important residues: His67 and Glu92. In addition, hydrophobic interactions were seen with residues similar to interactions with lamellarin analogues. The calculated drug-like scores are suggestive of these compounds to have clinical potential and ADMET predictions implied of their acceptable pharmacokinetic and toxicity profiles.
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Affiliation(s)
- Chatchakorn Eurtivong
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Poonsakdi Ploypradith
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
- Laboratory of Medicinal Chemistry, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Somsak Ruchirawat
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
- Laboratory of Medicinal Chemistry, Chulabhorn Research Institute, Bangkok, 10210, Thailand
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25
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Park JH, Yun JH, Shi Y, Han J, Li X, Jin Z, Kim T, Park J, Park S, Liu H, Lee W. Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers. Int J Mol Sci 2019; 20:E1943. [PMID: 31010024 PMCID: PMC6514806 DOI: 10.3390/ijms20081943] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 12/22/2022] Open
Abstract
HIV-1 integrase (HIV-1 IN) is an enzyme produced by the HIV-1 virus that integrates genetic material of the virus into the DNA of infected human cells. HIV-1 IN acts as a key component of the Retroviral Pre-Integration Complex (PIC). Protein dynamics could play an important role during the catalysis of HIV-1 IN; however, this process has not yet been fully elucidated. X-ray free electron laser (XFEL) together with nuclear magnetic resonance (NMR) could provide information regarding the dynamics during this catalysis reaction. Here, we report the non-cryogenic crystal structure of HIV-1 IN catalytic core domain at 2.5 Å using microcrystals in XFELs. Compared to the cryogenic structure at 2.1 Å using conventional synchrotron crystallography, there was a good agreement between the two structures, except for a catalytic triad formed by Asp64, Asp116, and Glu152 (DDE) and the lens epithelium-derived growth factor binding sites. The helix III region of the 140-153 residues near the active site and the DDE triad show a higher dynamic profile in the non-cryogenic structure, which is comparable to dynamics data obtained from NMR spectroscopy in solution state.
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Affiliation(s)
- Jae-Hyun Park
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea.
| | - Ji-Hye Yun
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea.
| | - Yingchen Shi
- Complex Systems Division, Beijing Computational Science Research Center, Beijing 100193, China.
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China.
| | - Jeongmin Han
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea.
| | - Xuanxuan Li
- Complex Systems Division, Beijing Computational Science Research Center, Beijing 100193, China.
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China.
| | - Zeyu Jin
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea.
| | - Taehee Kim
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea.
| | - Jaehyun Park
- Pohang Accelerator Laboratory, Pohang 37673, Korea.
| | - Sehan Park
- Pohang Accelerator Laboratory, Pohang 37673, Korea.
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, Beijing 100193, China.
| | - Weontae Lee
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea.
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26
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Tighadouini S, Radi S, Abrigach F, Benabbes R, Eddike D, Tillard M. Novel β-keto–enol Pyrazolic Compounds as Potent Antifungal Agents. Design, Synthesis, Crystal Structure, DFT, Homology Modeling, and Docking Studies. J Chem Inf Model 2019; 59:1398-1409. [DOI: 10.1021/acs.jcim.8b00828] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Said Tighadouini
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed First University, 60 000 Oujda, Morocco
| | - Smaail Radi
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed First University, 60 000 Oujda, Morocco
| | - Farid Abrigach
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed First University, 60 000 Oujda, Morocco
| | - Redouane Benabbes
- Laboratory of Biochemistry, Faculty of Sciences, Mohammed First University, 60 000 Oujda, Morocco
| | - Driss Eddike
- Laboratory of Mineral Solid and Analytical Chemistry, Faculty of Sciences, Mohammed First University, 60 000 Oujda, Morocco
| | - Monique Tillard
- ICGM, UMR 5253, CNRS, Université de Montpellier, ENSCM, Montpellier, 34095 France
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27
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Siwe-Noundou X, Musyoka TM, Moses V, Ndinteh DT, Mnkandhla D, Hoppe H, Tastan Bishop Ö, Krause RWM. Anti-HIV-1 integrase potency of methylgallate from Alchornea cordifolia using in vitro and in silico approaches. Sci Rep 2019; 9:4718. [PMID: 30886338 PMCID: PMC6423119 DOI: 10.1038/s41598-019-41403-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/05/2019] [Indexed: 01/18/2023] Open
Abstract
According to the 2018 report of the United Nations Programme on HIV/AIDS (UNAIDS), acquired immune deficiency syndrome (AIDS), a disease caused by the human immunodeficiency virus (HIV), remains a significant public health problem. The non-existence of a cure or effective vaccine for the disease and the associated emergence of resistant viral strains imply an urgent need for the discovery of novel anti-HIV drug candidates. The current study aimed to identify potential anti-retroviral compounds from Alchornea cordifolia. Bioactive compounds were identified using several chromatographic and spectroscopic techniques and subsequently evaluated for cytotoxicity and anti-HIV properties. Molecular modelling studies against HIV-1 integrase (HIV-1 IN) were performed to decipher the mode of action of methylgallate, the most potent compound (IC50 = 3.7 nM) and its analogues from ZINC database. Cytotoxicity assays showed that neither the isolated compounds nor the crude methanolic extract displayed cytotoxicity effects on the HeLa cell line. A strong correlation between the in vitro and in silico results was observed and important HIV-1 IN residues interacting with the different compounds were identified. These current results indicate that methylgallate is the main anti-HIV-1 compound in A. cordifolia stem bark, and could be a potential platform for the development of new HIV-1 IN inhibitors.
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Affiliation(s)
- Xavier Siwe-Noundou
- Department of Chemistry, Rhodes University, Grahamstown, 6140, South Africa.
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
| | - Thommas M Musyoka
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Vuyani Moses
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Derek T Ndinteh
- Department of Applied Chemistry, University of Johannesburg, Doornfontein, Johannesburg, 2028, South Africa
| | - Dumisani Mnkandhla
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Heinrich Hoppe
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
| | - Rui W M Krause
- Department of Chemistry, Rhodes University, Grahamstown, 6140, South Africa.
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28
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Idahosa KC, Davies-Coleman MT, Kaye PT. Exploratory applications of 2-nitrobenzaldehyde-derived Morita-Baylis-Hillman adducts as synthons in the construction of drug-like scaffolds. SYNTHETIC COMMUN 2019. [DOI: 10.1080/00397911.2018.1559333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Kenudi C. Idahosa
- Department of Chemistry and Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, South Africa
| | - Michael T. Davies-Coleman
- Department of Chemistry and Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, South Africa
| | - Perry T. Kaye
- Department of Chemistry and Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, South Africa
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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Hu X, Yu H, Wang W, Jiang S, Liu Q, He J. Synthesis of 3-Ethanoyl/Aroylacetylindoles in Water. CHINESE J ORG CHEM 2019. [DOI: 10.6023/cjoc201904002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Tighadouini S, Benabbes R, Tillard M, Eddike D, Haboubi K, Karrouchi K, Radi S. Synthesis, crystal structure, DFT studies and biological activity of (Z)-3-(3-bromophenyl)-1-(1,5-dimethyl-1H-pyrazol-3-yl)-3-hydroxyprop-2-en-1-one. Chem Cent J 2018; 12:122. [PMID: 30474759 PMCID: PMC6768133 DOI: 10.1186/s13065-018-0492-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/15/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Nowadays, is emerging a new generation of highly promising inhibitors bearing the β-ketoenol functionality. The present work relates to the first synthesis, the structure determination, the DFT studies and the use of a new biomolecule designed with a β-ketoenol group bounded to a pyrazolic moiety. RESULT A novel β-ketoenol-pyrazole has been synthesized, well characterized and its structure was confirmed by single crystal X-ray diffraction. The electron densities and the HOMO-LUMO gap have been calculated using the DFT method with BLYP, PW91, PWC functionals and 6-31G* basis set. An evaluation of the molecule stability is provided by a NBO analysis and the calculated Fukui and Parr functions have been used to locate the reactive electrophile and nucleophile centers in the molecule. The synthesized compound, screened for its in vitro antifungal behavior against the Fusarium oxysporum f.sp. albedinis FAO fungal strains, shows a moderate activity with an inhibition percentage of 46%. The product was also tested against three bacterial strains (Escherichia coli, Bacillus subtilis and Micrococcus luteus), but no significant effect was observed against these organisms. CONCLUSIONS Density functional calculations are used to evaluate the HOMO-LUMO energy gap, the molecular electrostatic potential and to provide a natural bond orbital analysis. The measured antimicrobial activities encourage us to continue searching for other structures, likely to be good antifungal candidates.
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Affiliation(s)
- Said Tighadouini
- Laboratoire de Chimie Appliquée et Environnement (LCAE), Faculté des Sciences, Université Mohamed I, 60000, Oujda, Morocco
| | - Redouane Benabbes
- Département de Biologie, Faculté des Sciences, Université Mohamed I, 60000, Oujda, Morocco
| | - Monique Tillard
- ICGM, CNRS, Université de Montpellier, ENSCM, Montpellier, France.
| | - Driss Eddike
- Laboratoire de Chimie du Solide Minéral et Analytique, Faculté des Sciences, Université Mohamed I, 60000, Oujda, Morocco
| | - Khadija Haboubi
- ENSA-AL Hociema, Université Mohamed I, 60000, Oujda, Morocco
| | - Khalid Karrouchi
- Laboratoire de Chimie Thérapeutique, Faculté de médecine et de Pharmacie, Université Mohamed V, Rabat, Morocco.
| | - Smaail Radi
- Laboratoire de Chimie Appliquée et Environnement (LCAE), Faculté des Sciences, Université Mohamed I, 60000, Oujda, Morocco
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Musyoka T, Tastan Bishop Ö, Lobb K, Moses V. The determination of CHARMM force field parameters for the Mg2+ containing HIV-1 integrase. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.09.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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33
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Recent advances in the discovery of small-molecule inhibitors of HIV-1 integrase. Future Sci OA 2018; 4:FSO338. [PMID: 30416746 PMCID: PMC6222271 DOI: 10.4155/fsoa-2018-0060] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022] Open
Abstract
AIDS caused by the infection of HIV is a prevalent problem today. Rapid development of drug resistance to existing drug classes has called for the discovery of new targets. Within the three major enzymes (i.e., HIV-1 protease, HIV-1 reverse transcriptase and HIV-1 integrase [IN]) of the viral replication cycle, HIV-1 IN has been of particular interest due to the absence of human cellular homolog. HIV-1 IN catalyzes the integration of viral genetic material with the host genome, a key step in the viral replication process. Several novel classes of HIV IN inhibitors have been explored by targeting different sites on the enzyme. This review strives to provide readers with updates on the recent developments of HIV-1 IN inhibitors. AIDS is an epidemic disease that endangers the lives of millions of people across the world. The AIDS virus, also known as HIV, has developed resistance to the majority of available drugs on the market, thus requiring the need for new drugs. HIV integrase is one of the key viral enzymes required for viral cell proliferation. Since there is no similar enzyme in the human body, major emphasis is being made to develop therapeutics for this novel target. The drugs that are at various stages of development for this target are reviewed here.
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Kalathiya U, Padariya M, Baginski M. Extracting functional groups of ALLINI to design derivatives of FDA-approved drugs: Inhibition of HIV-1 integrase. Biotechnol Appl Biochem 2018; 65:594-607. [DOI: 10.1002/bab.1646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/23/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Umesh Kalathiya
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
| | - Monikaben Padariya
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
| | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
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35
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Parveen N, Borrenberghs D, Rocha S, Hendrix J. Single Viruses on the Fluorescence Microscope: Imaging Molecular Mobility, Interactions and Structure Sheds New Light on Viral Replication. Viruses 2018; 10:E250. [PMID: 29748498 PMCID: PMC5977243 DOI: 10.3390/v10050250] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/24/2018] [Accepted: 05/04/2018] [Indexed: 12/13/2022] Open
Abstract
Viruses are simple agents exhibiting complex reproductive mechanisms. Decades of research have provided crucial basic insights, antiviral medication and moderately successful gene therapy trials. The most infectious viral particle is, however, not always the most abundant one in a population, questioning the utility of classic ensemble-averaging virology. Indeed, viral replication is often not particularly efficient, prone to errors or containing parallel routes. Here, we review different single-molecule sensitive fluorescence methods that we employ routinely to investigate viruses. We provide a brief overview of the microscopy hardware needed and discuss the different methods and their application. In particular, we review how we applied (i) single-molecule Förster resonance energy transfer (smFRET) to probe the subviral human immunodeficiency virus (HIV-1) integrase (IN) quaternary structure; (ii) single particle tracking to study interactions of the simian virus 40 with membranes; (iii) 3D confocal microscopy and smFRET to quantify the HIV-1 pre-integration complex content and quaternary structure; (iv) image correlation spectroscopy to quantify the cytosolic HIV-1 Gag assembly, and finally; (v) super-resolution microscopy to characterize the interaction of HIV-1 with tetherin during assembly. We hope this review is an incentive for setting up and applying similar single-virus imaging studies in daily virology practice.
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Affiliation(s)
- Nagma Parveen
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, Chemistry Department, KU Leuven, B-3001 Leuven, Belgium.
| | - Doortje Borrenberghs
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, Chemistry Department, KU Leuven, B-3001 Leuven, Belgium.
| | - Susana Rocha
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, Chemistry Department, KU Leuven, B-3001 Leuven, Belgium.
| | - Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, Chemistry Department, KU Leuven, B-3001 Leuven, Belgium.
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt University, B-3590 Diepenbeek, Belgium.
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36
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A structure-based design approach to advance the allyltyrosine-based series of HIV integrase inhibitors. Tetrahedron 2018. [DOI: 10.1016/j.tet.2017.11.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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37
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Sureshkumar K, Maheshwaran V, Dharma Rao T, Themmila K, Ponnuswamy M, Kadhirvel S, Dhandayutham S. Synthesis, characterization, crystal structure, in-vitro anti-inflammatory and molecular docking studies of 5-mercapto-1-substituted tetrazole incorporated quinoline derivative. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.05.085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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38
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Weber IT, Harrison RW. Decoding HIV resistance: from genotype to therapy. Future Med Chem 2017; 9:1529-1538. [PMID: 28791894 PMCID: PMC5694023 DOI: 10.4155/fmc-2017-0048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/03/2017] [Indexed: 01/14/2023] Open
Abstract
Genetic variation in HIV poses a major challenge for prevention and treatment of the AIDS pandemic. Resistance occurs by mutations in the target proteins that lower affinity for the drug or alter the protein dynamics, thereby enabling viral replication in the presence of the drug. Due to the prevalence of drug-resistant strains, monitoring the genotype of the infecting virus is recommended. Computational approaches for predicting resistance from genotype data and guiding therapy are discussed. Many prediction methods rely on rules derived from known resistance-associated mutations, however, statistical or machine learning can improve the classification accuracy and assess unknown mutations. Adding classifiers such as information on the atomic structure of the protein can further enhance the predictions.
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Affiliation(s)
- Irene T Weber
- Department of Biology, Georgia State University, PO Box 4010, Atlanta, GA 30302-4010, USA
| | - Robert W Harrison
- Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA
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39
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de Campos LJ, de Melo EB. A QSAR study of integrase strand transfer inhibitors based on a large set of pyrimidine, pyrimidone, and pyridopyrazine carboxamide derivatives. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.03.103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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Nishana M, Nilavar NM, Kumari R, Pandey M, Raghavan SC. HIV integrase inhibitor, Elvitegravir, impairs RAG functions and inhibits V(D)J recombination. Cell Death Dis 2017; 8:e2852. [PMID: 28569776 PMCID: PMC5520896 DOI: 10.1038/cddis.2017.237] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/24/2017] [Accepted: 04/05/2017] [Indexed: 12/13/2022]
Abstract
Integrase inhibitors are a class of antiretroviral drugs used for the treatment of AIDS that target HIV integrase, an enzyme responsible for integration of viral cDNA into host genome. RAG1, a critical enzyme involved in V(D)J recombination exhibits structural similarity to HIV integrase. We find that two integrase inhibitors, Raltegravir and Elvitegravir, interfered with the physiological functions of RAGs such as binding, cleavage and hairpin formation at the recombination signal sequence (RSS), though the effect of Raltegravir was limited. Circular dichroism studies demonstrated a distinct change in the secondary structure of RAG1 central domain (RAG1 shares DDE motif amino acids with integrases), and when incubated with Elvitegravir, an equilibrium dissociation constant (Kd) of 32.53±2.9 μM was determined by Biolayer interferometry, leading to inhibition of its binding to DNA. Besides, using extrachromosomal assays, we show that Elvitegravir inhibited both coding and signal joint formation in pre-B cells. Importantly, treatment with Elvitegravir resulted in significant reduction of mature B lymphocytes in 70% of mice studied. Thus, our study suggests a potential risk associated with the use of Elvitegravir as an antiretroviral drug, considering the evolutionary and structural similarities between HIV integrase and RAGs.
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Affiliation(s)
| | - Namrata M Nilavar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Rupa Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Monica Pandey
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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41
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Debnath U, Kumar P, Agarwal A, Kesharwani A, Gupta SK, Katti SB. N-hydroxy-substituted 2-aryl acetamide analogs: A novel class of HIV-1 integrase inhibitors. Chem Biol Drug Des 2017; 90:527-534. [PMID: 28294572 DOI: 10.1111/cbdd.12974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 02/16/2017] [Accepted: 02/19/2017] [Indexed: 12/17/2022]
Abstract
An in silico method has been used to discover N-hydroxy-substituted 2-aryl acetamide analogs as a new class of HIV-1 integrase inhibitors. Based on the molecular requirements of the binding pocket of catalytic active site, two molecules (compounds 2 and 4b) were designed as fragments. These were further synthesized and biologically evaluated. In vitro potency along with docking studies highlighted compound 4b as an active fragment which was further used to synthesize new leads as HIV-1 integrase inhibitors. Finally, six promising compounds (compounds 5b, 5c, 5e, 6-2c, 6-3b, and 6-5b) were identified by integrase inhibition assay (>50% inhibition). Based on in vitro anti-HIV-1 activity in a reporter gene-based cell assay system, compounds 5d, 6s, and 6k were found as novel HIV-1 integrase inhibitors due to its better selectivity index. Additionally, docking study revealed the importance of H-bond as well as hydrophobic interactions with Asn155, Lys156, and Lys159 which were required for their anti-HIV-1 activity.
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Affiliation(s)
- Utsab Debnath
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Prachi Kumar
- Reproductive Cell Biology Laboratory, National Institute of Immunology, New Delhi, India
| | - Aakanksha Agarwal
- Reproductive Cell Biology Laboratory, National Institute of Immunology, New Delhi, India
| | - Ajay Kesharwani
- Reproductive Cell Biology Laboratory, National Institute of Immunology, New Delhi, India
| | - Satish K Gupta
- Reproductive Cell Biology Laboratory, National Institute of Immunology, New Delhi, India
| | - Seturam B Katti
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
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42
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Matthews BW. David Davies: Structural biologist and mentor. Protein Sci 2017; 26:636-637. [DOI: 10.1002/pro.3130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 02/01/2017] [Indexed: 11/08/2022]
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43
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Crystal structure of ( Z)-1-(1,5-dimethyl-1 H-pyrazol-3-yl)-3-hydroxy-3-phenylprop-2-en-1-one, C 14H 14N 2O 2. Z KRIST-NEW CRYST ST 2017. [DOI: 10.1515/ncrs-2016-0194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C14H14N2O2, orthorhombic, P212121 (no. 19), a = 5.6736(2) Å, b = 7.7803(4) Å, c = 28.7821(13) Å, V = 1270.5(1) Å3, Z = 4, R
gt(F) = 0.0454, wR
ref(F
2) = 0.0879, T = 298 K.
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44
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Grawenhoff J, Engelman AN. Retroviral integrase protein and intasome nucleoprotein complex structures. World J Biol Chem 2017; 8:32-44. [PMID: 28289517 PMCID: PMC5329712 DOI: 10.4331/wjbc.v8.i1.32] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/24/2016] [Accepted: 01/14/2017] [Indexed: 02/05/2023] Open
Abstract
Retroviral replication proceeds through the integration of a DNA copy of the viral RNA genome into the host cellular genome, a process that is mediated by the viral integrase (IN) protein. IN catalyzes two distinct chemical reactions: 3’-processing, whereby the viral DNA is recessed by a di- or trinucleotide at its 3’-ends, and strand transfer, in which the processed viral DNA ends are inserted into host chromosomal DNA. Although IN has been studied as a recombinant protein since the 1980s, detailed structural understanding of its catalytic functions awaited high resolution structures of functional IN-DNA complexes or intasomes, initially obtained in 2010 for the spumavirus prototype foamy virus (PFV). Since then, two additional retroviral intasome structures, from the α-retrovirus Rous sarcoma virus (RSV) and β-retrovirus mouse mammary tumor virus (MMTV), have emerged. Here, we briefly review the history of IN structural biology prior to the intasome era, and then compare the intasome structures of PFV, MMTV and RSV in detail. Whereas the PFV intasome is characterized by a tetrameric assembly of IN around the viral DNA ends, the newer structures harbor octameric IN assemblies. Although the higher order architectures of MMTV and RSV intasomes differ from that of the PFV intasome, they possess remarkably similar intasomal core structures. Thus, retroviral integration machineries have adapted evolutionarily to utilize disparate IN elements to construct convergent intasome core structures for catalytic function.
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Srivastav V, Tiwari M. QSAR and docking studies of coumarin derivatives as potent HIV-1 integrase inhibitors. ARAB J CHEM 2017. [DOI: 10.1016/j.arabjc.2013.01.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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46
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Vyas VK, Shah S, Ghate M. Generation of new leads as HIV-1 integrase inhibitors: 3D QSAR, docking and molecular dynamics simulation. Med Chem Res 2017. [DOI: 10.1007/s00044-016-1772-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Islam MA, Pillay TS. Structural requirements for potential HIV-integrase inhibitors identified using pharmacophore-based virtual screening and molecular dynamics studies. MOLECULAR BIOSYSTEMS 2016; 12:982-93. [PMID: 26809073 DOI: 10.1039/c5mb00767d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Acquired immunodeficiency syndrome (AIDS) is a life-threatening disease which is a collection of symptoms and infections caused by a retrovirus, human immunodeficiency virus (HIV). There is currently no curative treatment and therapy is reliant on the use of existing anti-retroviral drugs. Pharmacoinformatics approaches have already proven their pivotal role in the pharmaceutical industry for lead identification and optimization. In the current study, we analysed the binding preferences and inhibitory activity of HIV-integrase inhibitors using pharmacoinformatics. A set of 30 compounds were selected as the training set of a total 540 molecules for pharmacophore model generation. The final model was validated by statistical parameters and further used for virtual screening. The best mapped model (R = 0.940, RMSD = 2.847, Q(2) = 0.912, se = 0.498, Rpred(2) = 0.847 and rm(test)(2) = 0.636) explained that two hydrogen bond acceptor and one aromatic ring features were crucial for the inhibition of HIV-integrase. From virtual screening, initial hits were sorted using a number of parameters and finally two compounds were proposed as promising HIV-integrase inhibitors. Drug-likeness properties of the final screened compounds were compared to FDA approved HIV-integrase inhibitors. HIV-integrase structure in complex with the most active and final screened compounds were subjected to 50 ns molecular dynamics (MD) simulation studies to check comparative stability of the complexes. The study suggested that the screened compounds might be promising HIV-integrase inhibitors. The new chemical entities obtained from the NCI database will be subjected to experimental studies to confirm potential inhibition of HIV integrase.
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Affiliation(s)
- Md Ataul Islam
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.
| | - Tahir S Pillay
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Private Bag X323, Arcadia, Pretoria, 0007, South Africa. and Division of Chemical Pathology, University of Cape Town, South Africa
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48
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Balasubramanian S, Rajagopalan M, Bojja RS, Skalka AM, Andrake MD, Ramaswamy A. The conformational feasibility for the formation of reaching dimer in ASV and HIV integrase: a molecular dynamics study. J Biomol Struct Dyn 2016; 35:3469-3485. [PMID: 27835934 DOI: 10.1080/07391102.2016.1257955] [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] [Indexed: 02/08/2023]
Abstract
Retroviral integrases are reported to form alternate dimer assemblies like the core-core dimer and reaching dimer. The core-core dimer is stabilized predominantly by an extensive interface between two catalytic core domains. The reaching dimer is stabilized by N-terminal domains that reach to form intermolecular interfaces with the other subunit's core and C-terminal domains (CTD), as well as CTD-CTD interactions. In this study, molecular dynamics (MD), Brownian dynamics (BD) simulations, and free energy analyses, were performed to elucidate determinants for the stability of the reaching dimer forms of full-length Avian Sarcoma Virus (ASV) and Human Immunodeficiency Virus (HIV) IN, and to examine the role of the C-tails (the last ~16-18 residues at the C-termini) in their structural dynamics. The dynamics of an HIV reaching dimer derived from small angle X-ray scattering and protein crosslinking data, was compared with the dynamics of a core-core dimer model derived from combining the crystal structures of two-domain fragments. The results showed that the core domains in the ASV reaching dimer express free dynamics, whereas those in the HIV reaching dimer are highly stable. BD simulations suggest a higher rate of association for the HIV core-core dimer than the reaching dimer. The predicted stability of these dimers was therefore ranked in the following order: ASV reaching dimer < HIV reaching dimer < composite core-core dimer. Analyses of MD trajectories have suggested residues that are critical for intermolecular contacts in each reaching dimer. Tests of these predictions and insights gained from these analyses could reveal a potential pathway for the association and dissociation of full-length IN multimers.
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Affiliation(s)
- Sangeetha Balasubramanian
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , Puducherry 605014 , India
| | - Muthukumaran Rajagopalan
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , Puducherry 605014 , India
| | - Ravi Shankar Bojja
- b Institute for Cancer Research , Fox Chase Cancer Center , Philadelphia , PA 19111 , USA
| | - Anna Marie Skalka
- b Institute for Cancer Research , Fox Chase Cancer Center , Philadelphia , PA 19111 , USA
| | - Mark D Andrake
- b Institute for Cancer Research , Fox Chase Cancer Center , Philadelphia , PA 19111 , USA
| | - Amutha Ramaswamy
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , Puducherry 605014 , India
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Hotspots of MLV integration in the hematopoietic tumor genome. Oncogene 2016; 36:1169-1175. [PMID: 27721401 PMCID: PMC5340798 DOI: 10.1038/onc.2016.285] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 06/15/2016] [Accepted: 07/08/2016] [Indexed: 01/16/2023]
Abstract
Extensive research has been performed regarding the integration sites of murine leukemia retrovirus (MLV) for the identification of proto-oncogenes. To date, the overlap of mutations within specific oligonucleotides across different tumor genomes has been regarded as a rare event; however, a recent study of MLV integration into the oncogene Zfp521 suggested the existence of a hotspot oligonucleotide for MLV integration. In the current review, we discuss the hotspots of MLV integration into several genes: c-Myc, Stat5a and N-myc, as well as ZFP521, as examined in tumor genomes. From this, MLV integration convergence within specific oligonucleotides is not necessarily a rare event. This short review aims to promote re-consideration of MLV integration within the tumor genome, which involves both well-known and potentially newly identified and novel mechanisms and specifications.
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Ercan S. Docking and Molecular Dynamics Calculations of Some Previously Studied and newly Designed Ligands to Catalytic Core Domain of HIV-1 Integrase and an Investigation to Effects of Conformational Changes of Protein on Docking Results. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2016. [DOI: 10.18596/jotcsa.287327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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