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Gaikwad SY, Tyagi S, Seniya C, More A, Chandane-Tak M, Kumar S, Mukherjee A. A nanoemulsified formulation of dolutegravir and epigallocatechin gallate inhibits HIV-1 replication in cellular models. FEBS Lett 2024. [PMID: 38789398 DOI: 10.1002/1873-3468.14936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024]
Abstract
Nanotechnology offers promising avenues for enhancing drug delivery systems, particularly in HIV-1 treatment. This study investigates a nanoemulsified formulation combining epigallocatechin gallate (EGCG) with dolutegravir (DTG) for managing HIV-1 infection. The combinatorial interaction between EGCG and DTG was explored through cellular, enzymatic, and molecular studies. In vitro assays demonstrated the potential of a dual drug-loaded nanoemulsion, NE-DTG-EGCG, in inhibiting HIV-1 replication, with EGCG serving as a supplementary treatment containing DTG. In silico molecular interaction studies highlighted EGCG's multifaceted inhibitory potential against HIV-1 integrase and reverse transcriptase enzymes. Further investigations are needed to validate the formulation's efficacy across diverse contexts. Overall, by integrating nanotechnology into drug delivery systems, this study represents a significant advancement in managing HIV-1 infection.
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Affiliation(s)
- Shraddha Y Gaikwad
- Division of Virology, ICMR-National AIDS Research Institute, Pune, India
| | - Shivani Tyagi
- Department of Pharmaceutical Technology, Meerut Institute of Engineering and Technology, India
| | - Chandrabhan Seniya
- School of Biosciences, Engineering and Technology, VIT Bhopal University, India
| | - Ashwini More
- Division of Virology, ICMR-National AIDS Research Institute, Pune, India
| | | | - Shobhit Kumar
- School of Biosciences, Engineering and Technology, VIT Bhopal University, India
| | - Anupam Mukherjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune, India
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2
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Pathak T, Bose A. 1,5-disubstituted 1,2,3-triazolylated carbohydrates and nucleosides. Carbohydr Res 2024; 541:109126. [PMID: 38823061 DOI: 10.1016/j.carres.2024.109126] [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: 01/07/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 06/03/2024]
Abstract
In general, 1,5-disubstituted 1,2,3-triazolyl moiety is much less common in the synthesis and applications in comparison to its regioisomeric counterpart. Moreover, the synthesis of 1,5-disubstituted 1,2,3-triazoles are not so straightforward as is the case for copper catalyzed strategy of 1,4-disubstituted 1,2,3-triazoles. The preparation of 1,5-triazolylated carbohydrates and nucleosides are even more complex because of the difficulties in accessing the appropriate starting materials as well as the compatibility of reaction conditions with the various protecting groups. 1,5-Disubstitution regioisomeric triazoles of carbohydrates and nucleosides were traditionally obtained as minor products through straightforward heating of the mixture of azides and terminal alkynes. However, the separation of isomers was tedious or in some cases futile. On the other hand, regioselective synthesis using ruthenium catalysis triggered serious concern of residual metal content in therapeutically important ingredients. Therefore, serious efforts are being made by several groups to develop non-toxic metal based or completely metal-free synthesis of 1,5-disubstituted 1,2,3-triazoles. This article strives to summarize the pre-Click era as well as the post-2001 reports on the synthesis and potential applications of 1,5-disubstituted 1,2,3-triazoles in biological systems.
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Affiliation(s)
- Tanmaya Pathak
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721 302, West Bengal, India.
| | - Amitabha Bose
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721 302, West Bengal, India
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3
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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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4
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Corona A, Meleddu R, Delelis O, Subra F, Cottiglia F, Esposito F, Distinto S, Maccioni E, Tramontano E. 5-Nitro-3-(2-(4-phenylthiazol-2-yl)hydrazineylidene)indolin-2-one derivatives inhibit HIV-1 replication by a multitarget mechanism of action. Front Cell Infect Microbiol 2023; 13:1193280. [PMID: 37424782 PMCID: PMC10328743 DOI: 10.3389/fcimb.2023.1193280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023] Open
Abstract
In the effort to identify and develop new HIV-1 inhibitors endowed with innovative mechanisms, we focused our attention on the possibility to target more than one viral encoded enzymatic function with a single molecule. In this respect, we have previously identified by virtual screening a new indolinone-based scaffold for dual allosteric inhibitors targeting both reverse transcriptase-associated functions: polymerase and RNase H. Pursuing with the structural optimization of these dual inhibitors, we synthesized a series of 35 new 3-[2-(4-aryl-1,3-thiazol-2-ylidene)hydrazin-1-ylidene]1-indol-2-one and 3-[3-methyl-4-arylthiazol-2-ylidene)hydrazine-1-ylidene)indolin-2-one derivatives, which maintain their dual inhibitory activity in the low micromolar range. Interestingly, compounds 1a, 3a, 10a, and 9b are able to block HIV-1 replication with EC50 < 20 µM. Mechanism of action studies showed that such compounds could block HIV-1 integrase. In particular, compound 10a is the most promising for further multitarget compound development.
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Affiliation(s)
- Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Olivier Delelis
- Laboratory of Biology and Applied Pharmacology (LBPA), Ecole Normale Supérieure (ENS) Cachan, Centre National de la Recherche Scientifique (CNRS), Cachan, France
| | - Frederic Subra
- Laboratory of Biology and Applied Pharmacology (LBPA), Ecole Normale Supérieure (ENS) Cachan, Centre National de la Recherche Scientifique (CNRS), Cachan, France
| | - Filippo Cottiglia
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
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5
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Sunitha V, Kumar AK, Saikrishna B. Synthesis of Novel Benzofuran Based 1,2,3-Triazoles, Their Antimicrobial and Cytotoxic Activities, and Molecular Docking Studies. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363222070258] [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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6
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N-propargylation reaction of substituted 4H-pyrano[2,3-d]pyrimidine derivatives under conventional, ultrasound- and microwave-assisted conditions. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02213-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Siddiqui MM, Nagargoje AA, Raza AK, Pisal PM, Shingate BB. [Et
3
NH][HSO
4
] catalyzed solvent‐free synthesis of new 1,2,3‐triazolidene‐indolinone derivatives. J Heterocycl Chem 2022. [DOI: 10.1002/jhet.4429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Madiha M. Siddiqui
- Department of Chemistry Dr. Babasaheb Ambedkar Marathwada University Aurangabad India
| | - Amol A. Nagargoje
- Department of Chemistry Dr. Babasaheb Ambedkar Marathwada University Aurangabad India
| | - Akram K. Raza
- Department of Chemistry Dr. Babasaheb Ambedkar Marathwada University Aurangabad India
| | - Parshuram M. Pisal
- School of Chemical Sciences Punyashlok Ahilyadevi Holkar Solapur University Solapur India
| | - Bapurao B. Shingate
- Department of Chemistry Dr. Babasaheb Ambedkar Marathwada University Aurangabad India
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8
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[HDBU][HSO4]-catalyzed facile synthesis of new 1,2,3-triazole-tethered 2,3-dihydroquinazolin-4[1H]-one derivatives and their DPPH radical scavenging activity. RESEARCH ON CHEMICAL INTERMEDIATES 2022. [DOI: 10.1007/s11164-021-04639-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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9
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A Recent Overview of 1,2,3-Triazole-Containing Hybrids as Novel Antifungal Agents: Focusing on Synthesis, Mechanism of Action, and Structure-Activity Relationship (SAR). J CHEM-NY 2022. [DOI: 10.1155/2022/7884316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A pharmacophore system has been found as 1,2,3-triazole, a five-membered heterocycle ring with nitrogen heteroatoms. These heterocyclic compounds can be produced using azide-alkyne cycloaddition processes catalyzed by ruthenium or copper. The bioactive compounds demonstrated antitubercular, antibacterial, anti-inflammatory, anticancer, antioxidant, antiviral, and antidiabetic properties. This heterocycle molecule, in particular, with one or more 1,2,3-triazole cores has been found to have the most powerful antifungal effects. The goal of this review is to highlight recent developments in the synthesis and structure-activity relationship (SAR) investigation of this prospective fungicidal chemical. Also there have been explained drugs and mechanism of action of a triazole compound with antifungal activity. This review will be useful in a variety of fields, including medicinal chemistry, organic chemistry, mycology, and pharmacology.
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10
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Camara TE, Koffi Teki DSE, Chagnault V. Metal-free hydroxy and aminocyanation of furanos-3-uloses. Carbohydr Res 2021; 511:108486. [PMID: 34915327 DOI: 10.1016/j.carres.2021.108486] [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: 09/15/2021] [Revised: 11/05/2021] [Accepted: 11/29/2021] [Indexed: 11/25/2022]
Abstract
TSAO-T and ATSAO-T analogues are molecules of interest that are able to inhibit the reverse transcriptase (RT) of HIV-1 and HCV. We also recently highlighted their antiproliferative properties. In all cases, the spiro cycle was a required group for biological activities, which led chemists to produce many derivatives, especially on this ring. These structures can be accessed through the formation of glycoaminonitriles and glycocyanhydrins using methodologies not always adapted to the synthesis of large quantities. Moreover, these latter are poorly versatile (substrate-dependent), need expensive cyanogenic agents and implies the use of a metal in non-catalytic amounts. For this reason, we report here a new metal-free methodology for the synthesis of glycoaminonitriles and glycocyanhydrins using molecular iodine (I2).
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Affiliation(s)
- Tchambaga Etienne Camara
- Laboratoire de Constitution et Réaction de la Matière, Université Félix Houphouët-Boigny (UFHB) de Cocody - Côte d'Ivoire, 22 BP 582, Abidjan, 22, Cote d'Ivoire
| | - Dindet Steve-Evanes Koffi Teki
- Laboratoire de Glycochimie, des Antimicrobiens et des Agroressources (LG2A), UMR 7378 CNRS, Université de Picardie Jules Verne, 33 rue Saint Leu, F-80039, Amiens Cedex, France
| | - Vincent Chagnault
- Laboratoire de Glycochimie, des Antimicrobiens et des Agroressources (LG2A), UMR 7378 CNRS, Université de Picardie Jules Verne, 33 rue Saint Leu, F-80039, Amiens Cedex, France.
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11
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Effect of Selected Silyl Groups on the Anticancer Activity of 3,4-Dibromo-5-Hydroxy-Furan-2(5 H)-One Derivatives. Pharmaceuticals (Basel) 2021; 14:ph14111079. [PMID: 34832861 PMCID: PMC8620685 DOI: 10.3390/ph14111079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 02/01/2023] Open
Abstract
The pharmacological effects of carbon to silicon bioisosteric replacements have been widely explored in drug design and medicinal chemistry. Here, we present a systematic investigation of the impact of different silyl groups on the anticancer activity of mucobromic acid (MBA) bearing furan-2(5H)-one core. We describe a comprehensive characterization of obtained compounds with respect to their anticancer potency and selectivity towards cancer cells. All four novel compounds exert stronger antiproliferative activity than MBA. Moreover, 3b induce apoptosis in colon cancer cell lines. A detailed investigation of the mechanism of action revealed that 3b activity stems from the down-regulation of survivin and the activation of caspase-3. Furthermore, compound 3b attenuates the clonogenic potential of HCT-116 cells. Interestingly, we also found that depending on the type of the silyl group, compound selectivity towards cancer cells could be precisely controlled. Collectively, we demonstrated the utility of silyl groups for adjusting both the potency and selectivity of silicon-containing compounds. These data reveal a link between the types of silyl group and compound potency, which could have bearings for the design of novel silicon-based anticancer drugs.
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12
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Slavova KI, Todorov LT, Belskaya NP, Palafox MA, Kostova IP. Developments in the Application of 1,2,3-Triazoles in Cancer Treatment. Recent Pat Anticancer Drug Discov 2021; 15:92-112. [PMID: 32679022 DOI: 10.2174/1574892815666200717164457] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND The impact of cancer on modern society cannot be emphasized enough in terms of both economic and human costs. Cancer treatments are known, unfortunately, for their side effects - frequently numerous and severe. Drug resistance is another issue medical professionals have to tackle when dealing with neoplastic illnesses. Cancer rates are rising worldwide due to various factors - low-quality nutrition, air and water pollution, tobacco use, etc. For those and many other reasons, drug discovery in the field of oncology is a top priority in modern medical science. OBJECTIVE To present the reader with the latest in cancer drug discovery with regard to 1,2,3-triazole- containing molecules in a clear, concise way so as to make the present review a useful tool for researchers. METHODS Available information present on the role of 1,2,3-triazoles in cancer treatment was collected. Data was collected from scientific literature, as well as from patents. RESULTS A vast number of triazole-containing molecules with antiproliferative properties have been proposed, synthesized and tested for anticancer activity both in vitro and in vivo. The substances vary greatly when considering molecular structure, proposed mechanisms of action and affected cancer cell types. CONCLUSION Triazole-containing molecules with anticancer activity are being widely synthesized and extensively tested. They vary significantly in terms of both structure and mechanism of action. The methods for their preparation and administration are well established and with proven reproducibility. These facts suggest that triazoles may play an important role in the discovery of novel antiproliferative medications with improved effectiveness and safety profile.
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Affiliation(s)
- Katerina I Slavova
- Department of Chemistry, Faculty of Pharmacy, Medical University Sofia, Sofia, Bulgaria
| | - Lozan T Todorov
- Department of Chemistry, Faculty of Pharmacy, Medical University Sofia, Sofia, Bulgaria
| | | | - Mauricio A Palafox
- Departamento de Quimica-Fisica I, Facultad de Ciencias Quimicas, Universidad Complutense, Madrid 28040, Spain
| | - Irena P Kostova
- Department of Chemistry, Faculty of Pharmacy, Medical University Sofia, Sofia, Bulgaria
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13
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Haroun M, Tratrat C, Kochkar H, Nair AB. CDATA[Recent Advances in the Development of 1,2,3-Triazole-containing Derivatives as Potential Antifungal Agents and Inhibitors of Lanoster ol 14α-Demethylase. Curr Top Med Chem 2021; 21:462-506. [PMID: 33319673 DOI: 10.2174/1568026621999201214232018] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/12/2020] [Accepted: 11/03/2020] [Indexed: 11/22/2022]
Abstract
1,2,3-Triazole, a five-membered heterocyclic nucleus, is widely recognized as a key chromophore of great value in medicinal chemistry for delivering compounds possessing innumerable biological activities, including antimicrobial, antitubercular, antidiabetic, antiviral, antitumor, antioxidants, and anti-inflammatory activities. Mainly, in the past years, diverse conjugates carrying this biologically valuable core have been reported due to their attractive fungicidal potential and potent effects on various infective targets. Hence, hybridization of 1,2,3-triazole with other antimicrobial pharmacophores appears to be a judicious strategy to develop new effective anti-fungal candidates to combat the emergence of drug-sensitive and drug-resistant infectious diseases. Thus, the current review highlights the recent advances of this promising category of 1,2,3-triazole-containing hybrids incorporating diverse varieties of bioactive heterocycles such as conozole, coumarin, imidazole, benzimidazole, pyrazole, indole, oxindole, chromene, pyrane, quinazoline, chalcone, isoflavone, carbohydrates, and amides. It underlies their inhibition behavior against a wide array of infectious fungal species during 2015-2020.
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Affiliation(s)
- Michelyne Haroun
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Christophe Tratrat
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Hafedh Kochkar
- Department of Chemistry, College of Science, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Anroop B Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
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14
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Meleddu R, Corona A, Distinto S, Cottiglia F, Deplano S, Sequeira L, Secci D, Onali A, Sanna E, Esposito F, Cirone I, Ortuso F, Alcaro S, Tramontano E, Mátyus P, Maccioni E. Exploring New Scaffolds for the Dual Inhibition of HIV-1 RT Polymerase and Ribonuclease Associated Functions. Molecules 2021; 26:molecules26133821. [PMID: 34201561 PMCID: PMC8270338 DOI: 10.3390/molecules26133821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/30/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
Current therapeutic protocols for the treatment of HIV infection consist of the combination of diverse anti-retroviral drugs in order to reduce the selection of resistant mutants and to allow for the use of lower doses of each single agent to reduce toxicity. However, avoiding drugs interactions and patient compliance are issues not fully accomplished so far. Pursuing on our investigation on potential anti HIV multi-target agents we have designed and synthesized a small library of biphenylhydrazo 4-arylthiazoles derivatives and evaluated to investigate the ability of the new derivatives to simultaneously inhibit both associated functions of HIV reverse transcriptase. All compounds were active towards the two functions, although at different concentrations. The substitution pattern on the biphenyl moiety appears relevant to determine the activity. In particular, compound 2-{3-[(2-{4-[4-(hydroxynitroso)phenyl]-1,3-thiazol-2-yl} hydrazin-1-ylidene) methyl]-4-methoxyphenyl} benzamide bromide (EMAC2063) was the most potent towards RNaseH (IC50 = 4.5 mM)- and RDDP (IC50 = 8.0 mM) HIV RT-associated functions.
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Affiliation(s)
- Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Filippo Cottiglia
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Serenella Deplano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Lisa Sequeira
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Daniela Secci
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Alessia Onali
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Erica Sanna
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Italo Cirone
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università Magna Graecia di Catanzaro, Campus ‘S. Venuta’, Viale Europa, 88100 Catanzaro, Italy; (F.O.); (S.A.)
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università Magna Graecia di Catanzaro, Campus ‘S. Venuta’, Viale Europa, 88100 Catanzaro, Italy; (F.O.); (S.A.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Péter Mátyus
- Institute of Digital Health Sciences, Faculty of Health and Public Services, Semmelweis University, Ferenc tér 15, 1094 Budapest, Hungary;
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
- Correspondence: ; Tel.: +39-070-6758744
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Xu Y, Zhang Z, Shi J, Liu X, Tang W. Recent developments of synthesis and biological activity of sultone scaffolds in medicinal chemistry. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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16
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Kumar AK, Sunitha V, Ramesh G, Jalapathi P. Synthesis and Antimicrobial Activity of Quinoxaline Based
1,2,3-Triazoles. RUSS J GEN CHEM+ 2020. [DOI: 10.1134/s1070363220120257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kumar R, Kumar M, Kumar V, Kumar A, Haque N, Kumar R, Prasad AK. Recent progress in the synthesis of C-4′-spironucleosides and its future perspectives. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1803914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Rajesh Kumar
- Department of Chemistry, R.D.S. College, B. R. A. Bihar University, Muzaffarpur, India
| | - Manish Kumar
- Department of Chemistry, Motilal Nehru College, University of Delhi, Delhi, India
| | - Vijay Kumar
- Department of Chemistry, L. S. College, B. R. A. Bihar University, Muzaffarpur, India
| | - Arbind Kumar
- Department of Chemistry, L. S. College, B. R. A. Bihar University, Muzaffarpur, India
| | - Navedul Haque
- University Department of Chemistry, B. R. A. Bihar University, Muzaffarpur, India
| | - Ram Kumar
- Department of Chemistry, R.D.S. College, B. R. A. Bihar University, Muzaffarpur, India
| | - Ashok K. Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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18
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Sánchez-Murcia PA, de Castro S, García-Aparicio C, Jiménez MA, Corona A, Tramontano E, Sluis-Cremer N, Menéndez-Arias L, Velázquez S, Gago F, Camarasa MJ. Peptides Mimicking the β7/β8 Loop of HIV-1 Reverse Transcriptase p51 as "Hotspot-Targeted" Dimerization Inhibitors. ACS Med Chem Lett 2020; 11:811-817. [PMID: 32435389 DOI: 10.1021/acsmedchemlett.9b00623] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/24/2020] [Indexed: 02/04/2023] Open
Abstract
A conformationally constrained short peptide designed to target a protein-protein interaction hotspot in HIV-1 reverse transcriptase (RT) disrupts p66-p51 interactions and paves the way to the development of novel RT dimerization inhibitors.
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Affiliation(s)
| | - Sonia de Castro
- Instituto de Química Médica (IQM, CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
| | | | - M. Angeles Jiménez
- Instituto de Química-Física Rocasolano (IQFR, CSIC), Serrano 119, E-28006Madrid, Spain
| | - Angela Corona
- University of Cagliari, Department of Life and Environmental Sciences, Cittadella Universitaria di
Monserrato, 09042 Monserrato, Cagliari, Italy
| | - Enzo Tramontano
- University of Cagliari, Department of Life and Environmental Sciences, Cittadella Universitaria di
Monserrato, 09042 Monserrato, Cagliari, Italy
| | - Nicolas Sluis-Cremer
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, Pittsburgh, Pennsylvania 15261, United States
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (CBMSO, CSIC & Universidad Autónoma de Madrid), Nicolás Cabrera 1, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Sonsoles Velázquez
- Instituto de Química Médica (IQM, CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Federico Gago
- Departamento de Ciencias Biomédicas, Universidad de Alcalá, Unidad Asociada CSIC, E-28805 Alcalá de Henares, Madrid, Spain
| | - María-José Camarasa
- Instituto de Química Médica (IQM, CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
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Raghavender M, Kumar AK, Sunitha V, Vishnu T, Jalapathi P. Synthesis and Cytotoxicity of Chalcone Based 1,2,3-Triazole Derivatives. RUSS J GEN CHEM+ 2020. [DOI: 10.1134/s1070363220040210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Improving the positional adaptability: structure-based design of biphenyl-substituted diaryltriazines as novel non-nucleoside HIV-1 reverse transcriptase inhibitors. Acta Pharm Sin B 2020; 10:344-357. [PMID: 32082978 PMCID: PMC7016291 DOI: 10.1016/j.apsb.2019.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 07/08/2019] [Accepted: 09/20/2019] [Indexed: 02/05/2023] Open
Abstract
In order to improve the positional adaptability of our previously reported naphthyl diaryltriazines (NP-DATAs), synthesis of a series of novel biphenyl-substituted diaryltriazines (BP-DATAs) with a flexible side chain attached at the C-6 position is presented. These compounds exhibited excellent potency against wild-type (WT) HIV-1 with EC50 values ranging from 2.6 to 39 nmol/L and most of them showed low nanomolar anti-viral potency against a panel of HIV-1 mutant strains. Compounds 5j and 6k had the best activity against WT, single and double HIV-1 mutants and reverse transcriptase (RT) enzyme comparable to two reference drugs (EFV and ETR) and our lead compound NP-DATA (1). Molecular modeling disclosed that the side chain at the C-6 position of DATAs occupied the entrance channel of the HIV-1 reverse transcriptase non-nucleoside binding pocket (NNIBP) attributing to the improved activity. The preliminary structure–activity relationship and PK profiles were also discussed.
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Key Words
- AIDS, acquired immunodeficiency syndrome
- BP-DATA, biphenyl-substituted diaryltriazine
- BP-DATAs
- CC50, 50% cytotoxicity concentration
- DAPY, diarylpyrimidine
- DATA, diaryltriazine
- EC50, the concentration causing 50% inhibition of antiviral activity
- EFV, efavirenz
- ETR, etravirine
- HEPT, 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine
- HIV, human immunodeficiency virus
- HIV-1
- MD, molecular dynamic
- Molecular modeling
- NNIBP, non-nucleoside inhibitor binding pocket
- NNRTI, non-nucleoside reverse transcriptase inhibitor
- NNRTIs
- NP-DATA, naphthyl diaryltriazine
- NP-DATAs
- NVP, nevirapine
- PK, pharmacokinetics
- Positional adaptability
- RMSD, root-mean square deviation
- RPV, rilpivirine
- RT, reverse transcriptase
- SAR, structure–activity relationship
- SI, selectivity index
- TSAO, tert-butyldimethylsilyl-spiroaminooxathioledioxide
- WT, wild-type
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Nandikolla A, Srinivasarao S, Karan Kumar B, Murugesan S, Aggarwal H, Major LL, Smith TK, Chandra Sekhar KVG. Synthesis, study of antileishmanial and antitrypanosomal activity of imidazo pyridine fused triazole analogues. RSC Adv 2020; 10:38328-38343. [PMID: 35517538 PMCID: PMC9057266 DOI: 10.1039/d0ra07881f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/13/2020] [Indexed: 11/21/2022] Open
Abstract
Thirty-five novel 1,2,3-triazole analogues of imidazo-[1,2-a]-pyridine-3-carboxamides were designed, synthesized and evaluated for in vitro antileishmanial and antitrypanosomal activity against L. major and T. brucei parasites, respectively.
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Affiliation(s)
- Adinarayana Nandikolla
- Department of Chemistry
- Birla Institute of Technology and Science, Pilani
- Hyderabad Campus
- Hyderabad – 500078
- India
| | - Singireddi Srinivasarao
- Department of Chemistry
- Birla Institute of Technology and Science, Pilani
- Hyderabad Campus
- Hyderabad – 500078
- India
| | - Banoth Karan Kumar
- Medicinal Chemistry Research Laboratory
- Department of Pharmacy
- Birla Institute of Technology and Science Pilani
- Pilani Campus
- Pilani-333031
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory
- Department of Pharmacy
- Birla Institute of Technology and Science Pilani
- Pilani Campus
- Pilani-333031
| | - Himanshu Aggarwal
- Department of Chemistry
- Birla Institute of Technology and Science, Pilani
- Hyderabad Campus
- Hyderabad – 500078
- India
| | - Louise L. Major
- Schools of Biology & Chemistry
- BSRC
- The University, St. Andrews
- Fife
- UK
| | - Terry K. Smith
- Schools of Biology & Chemistry
- BSRC
- The University, St. Andrews
- Fife
- UK
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22
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Recent progress in HIV-1 inhibitors targeting the entrance channel of HIV-1 non-nucleoside reverse transcriptase inhibitor binding pocket. Eur J Med Chem 2019; 174:277-291. [DOI: 10.1016/j.ejmech.2019.04.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 02/07/2023]
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Abstract
RT is a key enzyme in the life cycle of HIV, and is targeted by multiple antiviral drugs. Although for most of its function RT binds a dsDNA or RNA–DNA template–primer substrate, initiation of reverse transcription involves binding of dsRNA. The current study presents a structure of an RT/dsRNA complex that has the basic components of a reverse transcription initiation complex (RTIC). The unique structural features help understand the significantly slower rate of nucleotide incorporation by an RTIC compared with a catalytically efficient reverse transcription elongation complex. This complex may help in designing new experiments for understanding the intricate and slow process of reverse transcription initiation. The initiation phase of HIV reverse transcription has features that are distinct from its elongation phase. The first structure of a reverse transcription initiation complex (RTIC) that trapped the complex after incorporation of one ddCMP nucleotide was published recently [Larsen KP, et al. (2018) Nature 557:118–122]. Here we report a crystal structure of a catalytically active HIV-1 RT/dsRNA complex that mimics the state of the RTIC before the first nucleotide incorporation. The structure reveals that the dsRNA-bound conformation of RT is closer to that of RT bound to a nonnucleoside RT inhibitor (NNRTI) and dsDNA; a hyperextended thumb conformation helps to accommodate the relatively wide dsRNA duplex. The RNA primer 3′ end is positioned 5 Å away from the polymerase site; however, unlike in an NNRTI-bound state in which structural elements of RT restrict the movement of the primer, the primer terminus of dsRNA is not blocked from reaching the active site of RT. The observed structural changes and energetic cost of bringing the primer 3′ end to the priming site are hypothesized to explain the slower nucleotide incorporation rate of the RTIC. An unusual crystal lattice interaction of dsRNA with its symmetry mate is reminiscent of the RNA architecture within the extended vRNA–tRNALys3 in the RTIC. This RT/dsRNA complex captures the key structural characteristics and components of the RTIC, including the RT conformational changes and interactions with the dsRNA primer-binding site region, and these features have implications for better understanding of RT initiation.
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Victor MM, Farias RR, da Silva DL, do Carmo PHF, de Resende-Stoianoff MA, Viegas C, Espuri PF, Marques MJ. Synthesis and Evaluation of Antifungal and Antitrypanosomastid Activities of Symmetrical 1,4-Disubstituted-1,2,3-Bistriazoles Obtained by CuAAC Conditions. Med Chem 2018; 15:400-408. [PMID: 30360747 DOI: 10.2174/1573406414666181024111522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/23/2018] [Accepted: 10/10/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND The trypanosomatids, such as the protozoan Leishmania spp., have a demand by ergosterol, which is not present in the membrane from mammal cells. The suppression of the synthesis of ergosterol would be a new target of compounds with leishmanicidal activity, and bistriazole has shown trypanocidal activity by this mechanism. The incidence of fungal infections has increased at an alarming rate over the last decades. This is related both to the growing population of immune-compromised individuals and to the emergence of strains that are resistant to available antifungals. Therefore, there is a challenge for the search of potential new antifungal agents. OBJECTIVE The study aimed to synthesize 1,4-disubstituted-1,2,3-bistriazoles by optimized copper( I)-catalyzed alkyne-azide cycloaddition (CuAAC) and evaluate their antifungal and antitrypanosomastid activities. METHOD The synthesis of symmetrical bistriazoles with diazides as spacers was planned to be performed following the CuAAC reaction strategy. For evaluation of best conditions for the synthesis of symmetrical bistriazoles hex-1-yne 2 was chosen as leading compound, and a variety of catalysts were employed, choosing (3:1) alkyne:diazide stoichiometric relationship employing CuSO4.5H2O as the best condition. For the preparation of diversity in the synthesis of symmetrical bistriazoles, a 1,3-diazide-propan-2-ol 1a and 1,3-diazidepropane 1b were reacted with seven different alkynes, furnishing eleven symmetrical bistriazoles 9-13a,b and 14a. All compounds were essayed to cultures of promastigotes of L. amazonensis (1 x 106 cells mL-1) in the range of 0.10 - 40.00 µg mL-1 and incubated at 25ºC. After 72 h of incubation, the surviving parasites were counted. For antifungal assay, the minimum inhibitory concentrations (MIC) for yeasts and filamentous fungi were determined. Each compound was tested in 10 serial final concentrations (64 to 0.125 µg mL-1). RESULTS Eleven 1,4-disubstituted-1,2,3-bistriazoles were synthesized and their structures were confirmed by IR, 1H and 13C-NMR and Mass spectral analysis. The antifungal and antitrypanosomastid activities were evaluated. The best result to antifungal activity was reached by bistriazole 11a that showed the same MIC of fluconazole (32 µg mL-1) against Candida krusei ATCC 6258, an emerging and potentially multidrug-resistant fungal pathogen. Due to their intrinsically biological activity versatility, five derivatives compounds showed leishmanicidal inhibitory activity between 15.0 and 20.0% at concentrations of 20 and 40.0 µg mL-1. Among these compounds the derivative 13a showed best IC50 value of 63.34 µg mL-1 (182.86 µM). CONCLUSION The preliminary and promising results suggest that bistriazole derivatives, especially compound 13a, could represent an innovative scaffold for further studies and development of new antifungal and anti-parasitic drug candidates.
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Affiliation(s)
- Mauricio M Victor
- Department of Organic Chemistry, Chemistry Institute, Federal University of Bahia, Salvador 40170-115, BA, Brazil.,National Institute of Science and Technology for Energy and Environmental, Salvador 40170-115, BA, Brazil
| | - Ravir R Farias
- Department of Organic Chemistry, Chemistry Institute, Federal University of Bahia, Salvador 40170-115, BA, Brazil.,National Institute of Science and Technology for Energy and Environmental, Salvador 40170-115, BA, Brazil
| | - Danielle L da Silva
- Department of Microbiology, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte 31270- 901, MG, Brazil
| | - Paulo H F do Carmo
- Department of Microbiology, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte 31270- 901, MG, Brazil
| | - Maria A de Resende-Stoianoff
- Department of Microbiology, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte 31270- 901, MG, Brazil
| | - Cláudio Viegas
- PeQuim - Laboratory of Research in Medicinal Chemistry, Institute of Chemistry, Federal University of Alfenas, Alfenas 37130-000, MG, Brazil
| | - Patrícia F Espuri
- Biomedical Sciences Institute, Federal University of Alfenas, Alfenas 37130-000, MG, Brazil
| | - Marcos J Marques
- Biomedical Sciences Institute, Federal University of Alfenas, Alfenas 37130-000, MG, Brazil
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Sadiq SK, Mirambeau G, Meyerhans A. Equilibrium Model of Drug-Modulated GagPol-Embedded HIV-1 Reverse Transcriptase Dimerization to Enhance Premature Protease Activation. AIDS Res Hum Retroviruses 2018; 34:804-807. [PMID: 30056738 DOI: 10.1089/aid.2018.0111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Lack of effective strategies for killing cells latently infected with HIV-1 limits the eradication of AIDS. Unfortunately, current antiretroviral inhibitors are designed to target virus production but not latent infection. Interestingly, some non-nucleoside reverse transcriptase inhibitors (NNRTIs) have shown off-design effects, specifically, premature activation of HIV-1 protease (PR) within virus-infected cells that induces apoptosis. Here, we analyze an equilibrium model of HIV-1 reverse transcriptase (RT) binding to NNRTIs to understand the optimal binding characteristics that enhance RT dimerization within embedded GagPol dimers. This would allow NNRTIs to act as PR autoactivation enhancers (PAEs). We compute that ∼700-fold enhancement is theoretically possible by PAEs. Both a strong drug-dimer binding affinity (KD12 < 100 nM) and relatively weaker drug-monomer affinity (KD2/KD12 > 10) are required for significant enhancement (∼50-fold or more) relative to the drug-free dimer concentration within a drug concentration limit of 10 μM. Our approach rationalizes the observed effects of efavirenz on premature activation of PR and may be useful to guide the design of suitable drug candidates and their optimal dosage regimens for this therapy class.
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Affiliation(s)
- S. Kashif Sadiq
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Infection Biology Laboratory, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain
| | - Gilles Mirambeau
- Faculté des Sciences et Ingénierie, UFR de Biologie, Sorbonne Universités, Paris, France
| | - Andreas Meyerhans
- Infection Biology Laboratory, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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27
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Kishore Kumar A, Sunitha V, Shankaraiah P, Siddhartha M, Jalapathi P. Synthesis and Antibacterial Activity of Some {6-[(1H-1,2,3-Triazol-4-yl)methoxy]-3-methylbenzofuran-2-yl}(4-bromophenyl)methanone Derivatives. RUSS J GEN CHEM+ 2018. [DOI: 10.1134/s1070363218040254] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rungta P, Mangla P, Khatri V, Maity J, Prasad AK. Biocatalytic route to C-4′-spiro-oxetano-xylofuranosyl pyrimidine nucleosides. BIOCATAL BIOTRANSFOR 2018. [DOI: 10.1080/10242422.2018.1438416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Pallavi Rungta
- Department of Chemistry, Bioorganic Laboratory, University of Delhi, Delhi, India
| | - Priyanka Mangla
- Department of Chemistry, Bioorganic Laboratory, University of Delhi, Delhi, India
| | - Vinod Khatri
- Department of Chemistry, Bioorganic Laboratory, University of Delhi, Delhi, India
| | - Jyotirmoy Maity
- Department of Chemistry, Bioorganic Laboratory, University of Delhi, Delhi, India
| | - Ashok K. Prasad
- Department of Chemistry, Bioorganic Laboratory, University of Delhi, Delhi, India
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Kumar R, Kumar M, Singh A, Singh N, Maity J, Prasad AK. Synthesis of novel C -4ʹ-spiro-oxetano- α -L- ribo nucleosides. Carbohydr Res 2017; 445:88-92. [DOI: 10.1016/j.carres.2017.04.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/22/2017] [Accepted: 04/19/2017] [Indexed: 10/19/2022]
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Pagano N, Teriete P, Mattmann ME, Yang L, Snyder BA, Cai Z, Heil ML, Cosford NDP. An integrated chemical biology approach reveals the mechanism of action of HIV replication inhibitors. Bioorg Med Chem 2017; 25:6248-6265. [PMID: 28442262 DOI: 10.1016/j.bmc.2017.03.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/25/2017] [Accepted: 03/29/2017] [Indexed: 10/19/2022]
Abstract
Continuous flow (microfluidic) chemistry was employed to prepare a small focused library of dihydropyrimidinone (DHPM) derivatives. Compounds in this class have been reported to exhibit activity against the human immunodeficiency virus (HIV), but their molecular target had not been identified. We tested the initial set of DHPMs in phenotypic assays providing a hit (1i) that inhibited the replication of the human immunodeficiency virus HIV in cells. Flow chemistry-driven optimization of 1i led to the identification of HIV replication inhibitors such as 1l with cellular potency comparable with the clinical drug nevirapine (NVP). Mechanism of action (MOA) studies using cellular and biochemical assays coupled with 3D fingerprinting and in silico modeling demonstrated that these drug-like probe compounds exert their effects by inhibiting the viral reverse transcriptase polymerase (RT). This led to the design and synthesis of the novel DHPM 1at that inhibits the replication of drug resistant strains of HIV. Our work demonstrates that combining flow chemistry-driven analogue refinement with phenotypic assays, in silico modeling and MOA studies is a highly effective strategy for hit-to-lead optimization applicable to the discovery of future therapeutic agents.
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Affiliation(s)
- Nicholas Pagano
- Cancer Metabolism & Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Peter Teriete
- Cancer Metabolism & Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Margrith E Mattmann
- Cancer Metabolism & Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Li Yang
- Cancer Metabolism & Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Beth A Snyder
- Southern Research Institute, Drug Development Division, 431 Aviation Way, Frederick, MD 21701, United States
| | - Zhaohui Cai
- Southern Research Institute, Drug Development Division, 431 Aviation Way, Frederick, MD 21701, United States
| | - Marintha L Heil
- Southern Research Institute, Drug Development Division, 431 Aviation Way, Frederick, MD 21701, United States
| | - Nicholas D P Cosford
- Cancer Metabolism & Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, United States.
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Abstract
Application of silyl functionalities is one of the most promising strategies among various ‘elements chemistry’ approaches for the development of novel and distinctive drug candidates. Replacement of one or more carbon atoms of various biologically active compounds with silicon (so-called sila-substitution) has been intensively studied for decades, and is often effective for alteration of activity profile and improvement of metabolic profile. In addition to simple C/Si exchange, several novel approaches for utilizing silicon in medicinal chemistry have been suggested in recent years, focusing on the intrinsic differences between silicon and carbon. Sila-substitution offers great potential for enlarging the chemical space of medicinal chemistry, and provides many options for structural development of drug candidates.
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Meleddu R, Distinto S, Corona A, Tramontano E, Bianco G, Melis C, Cottiglia F, Maccioni E. Isatin thiazoline hybrids as dual inhibitors of HIV-1 reverse transcriptase. J Enzyme Inhib Med Chem 2016; 32:130-136. [PMID: 27766892 PMCID: PMC6010014 DOI: 10.1080/14756366.2016.1238366] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A series of 3-3-{2-[2-3-methyl-4-phenyl-2,3-dihydro-1,3-thiazol-2-ylidene]hydrazin-1-ylidene-2,3-dihydro-1H-indol-2-one derivatives has been designed and synthesized to study their activity on both HIV-1 (Human Immunodeficiency Virus type 1) RT (Reverse Transcriptase) associated functions. These derivatives are analogs of previously reported series whose biological activity and mode of action have been investigated. In this work we investigated the influence of the introduction of a methyl group in the position 3 of the dihydrothiazole ring and of a chlorine atom in the position 5 of the isatin nucleus. The new synthesized compounds are active towards both DNA polymerase and ribonuclease H in the µM range. The nature of the aromatic group in the position 4 of the thiazole was relevant in determining the biological activity.
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Affiliation(s)
- Rita Meleddu
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Simona Distinto
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Angela Corona
- b Department of Life and Environmental Sciences , University of Cagliari, Cittadella Universitaria di Monserrato , Cagliari , Italy
| | - Enzo Tramontano
- b Department of Life and Environmental Sciences , University of Cagliari, Cittadella Universitaria di Monserrato , Cagliari , Italy
| | - Giulia Bianco
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Claudia Melis
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Filippo Cottiglia
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Elias Maccioni
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
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Structural Maturation of HIV-1 Reverse Transcriptase-A Metamorphic Solution to Genomic Instability. Viruses 2016; 8:v8100260. [PMID: 27690082 PMCID: PMC5086598 DOI: 10.3390/v8100260] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT)—a critical enzyme of the viral life cycle—undergoes a complex maturation process, required so that a pair of p66 precursor proteins can develop conformationally along different pathways, one evolving to form active polymerase and ribonuclease H (RH) domains, while the second forms a non-functional polymerase and a proteolyzed RH domain. These parallel maturation pathways rely on the structural ambiguity of a metamorphic polymerase domain, for which the sequence–structure relationship is not unique. Recent nuclear magnetic resonance (NMR) studies utilizing selective labeling techniques, and structural characterization of the p66 monomer precursor have provided important insights into the details of this maturation pathway, revealing many aspects of the three major steps involved: (1) domain rearrangement; (2) dimerization; and (3) subunit-selective RH domain proteolysis. This review summarizes the major structural changes that occur during the maturation process. We also highlight how mutations, often viewed within the context of the mature RT heterodimer, can exert a major influence on maturation and dimerization. It is further suggested that several steps in the RT maturation pathway may provide attractive targets for drug development.
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Santos LH, Ferreira RS, Caffarena ER. Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors. Mem Inst Oswaldo Cruz 2016; 110:847-64. [PMID: 26560977 PMCID: PMC4660614 DOI: 10.1590/0074-02760150239] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/08/2015] [Indexed: 01/05/2023] Open
Abstract
Reverse transcriptase (RT) is a multifunctional enzyme in the human immunodeficiency
virus (HIV)-1 life cycle and represents a primary target for drug discovery efforts
against HIV-1 infection. Two classes of RT inhibitors, the nucleoside RT inhibitors
(NRTIs) and the nonnucleoside transcriptase inhibitors are prominently used in the
highly active antiretroviral therapy in combination with other anti-HIV drugs.
However, the rapid emergence of drug-resistant viral strains has limited the
successful rate of the anti-HIV agents. Computational methods are a significant part
of the drug design process and indispensable to study drug resistance. In this
review, recent advances in computer-aided drug design for the rational design of new
compounds against HIV-1 RT using methods such as molecular docking, molecular
dynamics, free energy calculations, quantitative structure-activity relationships,
pharmacophore modelling and absorption, distribution, metabolism, excretion and
toxicity prediction are discussed. Successful applications of these methodologies are
also highlighted.
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Affiliation(s)
| | - Rafaela Salgado Ferreira
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
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Panayides JL, Mathieu V, Banuls LMY, Apostolellis H, Dahan-Farkas N, Davids H, Harmse L, Rey MEC, Green IR, Pelly SC, Kiss R, Kornienko A, van Otterlo WAL. Synthesis and in vitro growth inhibitory activity of novel silyl- and trityl-modified nucleosides. Bioorg Med Chem 2016; 24:2716-24. [PMID: 27157005 DOI: 10.1016/j.bmc.2016.04.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/14/2016] [Accepted: 04/19/2016] [Indexed: 12/17/2022]
Abstract
Seventeen silyl- and trityl-modified (5'-O- and 3',5'-di-O-) nucleosides were synthesized with the aim of investigating the in vitro antiproliferative activities of these nucleoside derivatives. A subset of the compounds was evaluated at a fixed concentration of 100μM against a small panel of tumor cell lines (HL-60, K-562, Jurkat, Caco-2 and HT-29). The entire set was also tested at varying concentrations against two human glioma lines (U373 and Hs683) to obtain GI50 values, with the best results being values of ∼25μM.
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Affiliation(s)
- Jenny-Lee Panayides
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO Wits, Johannesburg 2050, South Africa; Pioneering Health Sciences, CSIR Biosciences, PO Box 395, Pretoria 0001, South Africa
| | - Véronique Mathieu
- Laboratoire de Cancérologie et de Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
| | - Laetitia Moreno Y Banuls
- Laboratoire de Cancérologie et de Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
| | - Helen Apostolellis
- Department of Pharmacy and Pharmacology, Faculty of Health Sciences, University of the Witwatersrand, PO Wits, Johannesburg 2050, South Africa
| | - Nurit Dahan-Farkas
- Department of Pharmacy and Pharmacology, Faculty of Health Sciences, University of the Witwatersrand, PO Wits, Johannesburg 2050, South Africa
| | - Hajierah Davids
- Department of Pharmacy and Pharmacology, Faculty of Health Sciences, University of the Witwatersrand, PO Wits, Johannesburg 2050, South Africa; Department of Biochemistry and Microbiology, Nelson Mandela Metropolitan University, PO Box 77000, Port Elizabeth 6031, South Africa
| | - Leonie Harmse
- Department of Pharmacy and Pharmacology, Faculty of Health Sciences, University of the Witwatersrand, PO Wits, Johannesburg 2050, South Africa
| | - M E Christine Rey
- School of Molecular and Cellular Biology, University of the Witwatersrand, PO Wits, Johannesburg 2050, South Africa
| | - Ivan R Green
- Department of Chemistry and Polymer Science, Stellenbosch University, Stellenbosch, Matieland 7602, South Africa
| | - Stephen C Pelly
- Department of Chemistry and Polymer Science, Stellenbosch University, Stellenbosch, Matieland 7602, South Africa
| | - Robert Kiss
- Laboratoire de Cancérologie et de Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
| | - Alexander Kornienko
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Willem A L van Otterlo
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO Wits, Johannesburg 2050, South Africa; Department of Chemistry and Polymer Science, Stellenbosch University, Stellenbosch, Matieland 7602, South Africa.
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Smith SJ, Pauly GT, Akram A, Melody K, Rai G, Maloney DJ, Ambrose Z, Thomas CJ, Schneider JT, Hughes SH. Rilpivirine analogs potently inhibit drug-resistant HIV-1 mutants. Retrovirology 2016; 13:11. [PMID: 26880034 PMCID: PMC4754833 DOI: 10.1186/s12977-016-0244-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/05/2016] [Indexed: 11/10/2022] Open
Abstract
Background Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are a class of antiretroviral compounds that bind in an allosteric binding pocket in HIV-1 RT, located about 10 Å from the polymerase active site. Binding of an NNRTI causes structural changes that perturb the alignment of the primer terminus and polymerase active site, preventing viral DNA synthesis. Rilpivirine (RPV) is the most recent NNRTI approved by the FDA, but like all other HIV-1 drugs, suboptimal treatment can lead to the development of resistance. To generate better compounds that could be added to the current HIV-1 drug armamentarium, we have developed several RPV analogs to combat viral variants that are resistant to the available NNRTIs. Results Using a single-round infection assay, we identified several RPV analogs that potently inhibited a broad panel of NNRTI resistant mutants. Additionally, we determined that several resistant mutants selected by either RPV or Doravirine (DOR) caused only a small increase in susceptibility to the most promising RPV analogs. Conclusions The antiviral data suggested that there are RPV analogs that could be candidates for further development as NNRTIs, and one of the most promising compounds was modeled in the NNRTI binding pocket. This model can be used to explain why this compound is broadly effective against the panel of NNRTI resistance mutants. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0244-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steven J Smith
- HIV Drug Resistance Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA.
| | - Gary T Pauly
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA.
| | - Aamir Akram
- HIV Drug Resistance Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA.
| | - Kevin Melody
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Ganesha Rai
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, 9800 Medical Center Drive, Bethesda, MD, 3370, USA.
| | - David J Maloney
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, 9800 Medical Center Drive, Bethesda, MD, 3370, USA.
| | - Zandrea Ambrose
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA. .,Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Craig J Thomas
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, 9800 Medical Center Drive, Bethesda, MD, 3370, USA.
| | - Joel T Schneider
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA.
| | - Stephen H Hughes
- HIV Drug Resistance Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA.
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Ribonuclease H/DNA Polymerase HIV-1 Reverse Transcriptase Dual Inhibitor: Mechanistic Studies on the Allosteric Mode of Action of Isatin-Based Compound RMNC6. PLoS One 2016; 11:e0147225. [PMID: 26800261 PMCID: PMC4723341 DOI: 10.1371/journal.pone.0147225] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/30/2015] [Indexed: 12/11/2022] Open
Abstract
The DNA polymerase and ribonuclease H (RNase H) activities of human immunodeficiency virus type 1 (HIV-1) are needed for the replication of the viral genome and are validated drug targets. However, there are no approved drugs inhibiting RNase H and the efficiency of DNA polymerase inhibitors can be diminished by the presence of drug resistance mutations. In this context, drugs inhibiting both activities could represent a significant advance towards better anti-HIV therapies. We report on the mechanisms of allosteric inhibition of a newly synthesized isatin-based compound designated as RMNC6 that showed IC50 values of 1.4 and 9.8 μM on HIV-1 RT-associated RNase H and polymerase activities, respectively. Blind docking studies predict that RMNC6 could bind two different pockets in the RT: one in the DNA polymerase domain (partially overlapping the non-nucleoside RT inhibitor [NNRTI] binding pocket), and a second one close to the RNase H active site. Enzymatic studies showed that RMNC6 interferes with efavirenz (an approved NNRTI) in its binding to the RT polymerase domain, although NNRTI resistance-associated mutations such as K103N, Y181C and Y188L had a minor impact on RT susceptibility to RMNC6. In addition, despite being naturally resistant to NNRTIs, the polymerase activity of HIV-1 group O RT was efficiently inhibited by RMNC6. The compound was also an inhibitor of the RNase H activity of wild-type HIV-1 group O RT, although we observed a 6.5-fold increase in the IC50 in comparison with the prototypic HIV-1 group M subtype B enzyme. Mutagenesis studies showed that RT RNase H domain residues Asn474 and Tyr501, and in a lesser extent Ala502 and Ala508, are critical for RMNC6 inhibition of the endonuclease activity of the RT, without affecting its DNA polymerization activity. Our results show that RMNC6 acts as a dual inhibitor with allosteric sites in the DNA polymerase and the RNase H domains of HIV-1 RT.
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Kumar M, Sharma VK, Kumar R, Prasad AK. Biocatalytic route to C-3'-azido/-hydroxy-C-4'-spiro-oxetanoribonucleosides. Carbohydr Res 2015; 417:19-26. [PMID: 26386197 DOI: 10.1016/j.carres.2015.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 08/25/2015] [Accepted: 08/26/2015] [Indexed: 11/28/2022]
Abstract
The lipase, Novozyme(®)-435, exclusively deacetylates the 5-O-acetyl over 4-C-acetyloxymethyl group of almost identical reactivity in 5-O-acetyl-4-C-acetyloxymethyl-3-azido-3-deoxy-1,2-O-isopropylidene-α-D-ribofuranose that led to the development of first and efficient synthesis of 3'-azido-/3'-amino-C-4'-spiro-oxetanoribonucleosides T, U, C and A in 20-24% overall yields. The X-ray study on the compound obtained by tosylation of lipase-mediated monodeacetylated product unambiguously confirmed the point of diastereoselective monodeacetylation on diacetoxy-azido-ribofuranose derivative. The capability of Novozyme(®)-435 for selective deacylation of 5-O-acetyl group in 5-O-acetyl-4-C-acetyloxymethyl-3-O-benzyl-1,2-O-isopropylidene-α-D-ribofuranose recently discovered by us has been successfully used for the synthesis of C-4'-spiro-oxetanoribonucleosides A and C in good yields. These results clearly indicate that the broader substrate specificity and highly selective capability of Novozyme(®)-435 for carrying out acetylation/deacetylation reactions can be utilized for the development of environment friendly selective methodologies in organic synthesis.
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Affiliation(s)
- Manish Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Vivek K Sharma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India; Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Rajesh Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Ashok K Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India.
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Stanton RA, Nettles JH, Schinazi RF. Ligand similarity guided receptor selection enhances docking accuracy and recall for non-nucleoside HIV reverse transcriptase inhibitors. J Mol Model 2015; 21:282. [PMID: 26450349 DOI: 10.1007/s00894-015-2826-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/22/2015] [Indexed: 11/27/2022]
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTI) are allosteric inhibitors of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), a viral polymerase essential to infection. Despite the availability of >150 NNRTI-bound RT crystal structures, rational design of new NNRTI remains challenging because of the variability of their induced fit, hydrophobic binding patterns. Docking NNRTI yields inconsistent results that vary markedly depending on the receptor structure used, as only 27% of the >20k cross-docking calculations we performed using known NNRTI were accurate. In order to determine if a hospitable receptor for docking could be selected a priori, we evaluated more than 40 chemical descriptors for their ability to pre-select a best receptor for NNRTI cross-docking. The receptor selection was based on similarity scores between the bound- and target-ligands generated by each descriptor. The top descriptors were able to double the probability of cross-docking accuracy over random receptor selection. Additionally, recall of known NNRTI from a large library of similar decoys was increased using the same approach. The results demonstrate the utility of pre-selecting receptors when docking into difficult targets. Graphical Abstract Cross-docking accuracy increases when using chemical descriptors to determine the NNRTI with maximum similarity to the new compound and then docking into its respective receptor.
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Affiliation(s)
- Richard A Stanton
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - James H Nettles
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Veterans Affairs Medical Center, Atlanta, GA, 30033, USA.
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40
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Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase γ. Proc Natl Acad Sci U S A 2015; 112:8596-601. [PMID: 26124101 DOI: 10.1073/pnas.1421733112] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Nucleoside analog reverse transcriptase inhibitors (NRTIs) are the essential components of highly active antiretroviral (HAART) therapy targeting HIV reverse transcriptase (RT). NRTI triphosphates (NRTI-TP), the biologically active forms, act as chain terminators of viral DNA synthesis. Unfortunately, NRTIs also inhibit human mitochondrial DNA polymerase (Pol γ), causing unwanted mitochondrial toxicity. Understanding the structural and mechanistic differences between Pol γ and RT in response to NRTIs will provide invaluable insight to aid in designing more effective drugs with lower toxicity. The NRTIs emtricitabine [(-)-2,3'-dideoxy-5-fluoro-3'-thiacytidine, (-)-FTC] and lamivudine, [(-)-2,3'-dideoxy-3'-thiacytidine, (-)-3TC] are both potent RT inhibitors, but Pol γ discriminates against (-)-FTC-TP by two orders of magnitude better than (-)-3TC-TP. Furthermore, although (-)-FTC-TP is only slightly more potent against HIV RT than its enantiomer (+)-FTC-TP, it is discriminated by human Pol γ four orders of magnitude more efficiently than (+)-FTC-TP. As a result, (-)-FTC is a much less toxic NRTI. Here, we present the structural and kinetic basis for this striking difference by identifying the discriminator residues of drug selectivity in both viral and human enzymes responsible for substrate selection and inhibitor specificity. For the first time, to our knowledge, this work illuminates the mechanism of (-)-FTC-TP differential selectivity and provides a structural scaffold for development of novel NRTIs with lower toxicity.
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Sharma VK, Kumar M, Sharma D, Olsen CE, Prasad AK. Chemoenzymatic Synthesis of C-4′-Spiro-oxetanoribonucleosides. J Org Chem 2014; 79:8516-21. [DOI: 10.1021/jo501655j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Vivek K. Sharma
- Bioorganic
Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Manish Kumar
- Bioorganic
Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Deepti Sharma
- Bioorganic
Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Carl E. Olsen
- Faculty
of Life Sciences, Department of Plant and Environmental Sciences, University of Copenhagen, DK- 1871 Frederiksberg C, Denmark
| | - Ashok K. Prasad
- Bioorganic
Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
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Meleddu R, Cannas V, Distinto S, Sarais G, Del Vecchio C, Esposito F, Bianco G, Corona A, Cottiglia F, Alcaro S, Parolin C, Artese A, Scalise D, Fresta M, Arridu A, Ortuso F, Maccioni E, Tramontano E. Design, synthesis, and biological evaluation of 1,3-diarylpropenones as dual inhibitors of HIV-1 reverse transcriptase. ChemMedChem 2014; 9:1869-79. [PMID: 24850787 DOI: 10.1002/cmdc.201402015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/12/2022]
Abstract
A small library of 1,3-diarylpropenones was designed and synthesized as dual inhibitors of both HIV-1 reverse transcriptase (RT) DNA polymerase (DP) and ribonuclease H (RNase H) associated functions. Compounds were assayed on these enzyme activities, which highlighted dual inhibition properties in the low-micromolar range. Interestingly, mutations in the non-nucleoside RT inhibitor binding pocket strongly affected RNase H inhibition by the propenone derivatives without decreasing their capacity to inhibit DP activity, which suggests long-range RT structural effects. Biochemical and computational studies indicated that the propenone derivatives bind two different interdependent allosteric pockets.
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Affiliation(s)
- Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Via Ospedale 72, 09124 Cagliari (Italy)
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Kang D, Song Y, Chen W, Zhan P, Liu X. “Old Dogs with New Tricks”: exploiting alternative mechanisms of action and new drug design strategies for clinically validated HIV targets. MOLECULAR BIOSYSTEMS 2014; 10:1998-2022. [DOI: 10.1039/c4mb00147h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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de Carvalho da Silva F, Cardoso MFDC, Ferreira PG, Ferreira VF. Biological Properties of 1H-1,2,3- and 2H-1,2,3-Triazoles. TOPICS IN HETEROCYCLIC CHEMISTRY 2014. [DOI: 10.1007/7081_2014_124] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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45
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Bellucci L, Angeli L, Tafi A, Radi M, Botta M. Unconventional plasticity of HIV-1 reverse transcriptase: how inhibitors could open a connection "gate" between allosteric and catalytic sites. J Chem Inf Model 2013; 53:3117-22. [PMID: 24256065 DOI: 10.1021/ci400414s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeted molecular dynamics (TMD) simulations allowed for identifying the chemical/structural features of the nucleotide-competitive HIV-1 inhibitor DAVP-1, which is responsible for the disruption of the T-shape motif between Try183 and Trp229 of the reverse transcriptase (RT). DAVP-1 promoted the opening of a connection "gate" between allosteric and catalytic sites of HIV-1 RT, thus explaining its peculiar mechanism of action and providing useful insights to develop novel nucleotide-competitive RT inhibitors.
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Affiliation(s)
- Luca Bellucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via Aldo Moro 2, 53100 Siena, Italy
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Moura M, Josse S, Postel D. Preparation of Spiro[4.4]oxaphospholene and -azaphospholene Systems from Carbohydrate Templates. J Org Chem 2013; 78:8994-9003. [DOI: 10.1021/jo400954p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marina Moura
- Laboratoire
des Glucides, CNRS-FRE 3517, 10 rue Baudelocque, 80039 Amiens, France
- Institut
de Chimie de Picardie (FRE 3085), UFR des Sciences-UPJV, 33, rue
Saint Leu, 80039 Amiens Cedex 1, France
| | - Solen Josse
- Laboratoire
des Glucides, CNRS-FRE 3517, 10 rue Baudelocque, 80039 Amiens, France
- Institut
de Chimie de Picardie (FRE 3085), UFR des Sciences-UPJV, 33, rue
Saint Leu, 80039 Amiens Cedex 1, France
| | - Denis Postel
- Laboratoire
des Glucides, CNRS-FRE 3517, 10 rue Baudelocque, 80039 Amiens, France
- Institut
de Chimie de Picardie (FRE 3085), UFR des Sciences-UPJV, 33, rue
Saint Leu, 80039 Amiens Cedex 1, France
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Das K, Arnold E. HIV-1 reverse transcriptase and antiviral drug resistance. Part 2. Curr Opin Virol 2013; 3:119-28. [PMID: 23602470 DOI: 10.1016/j.coviro.2013.03.014] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/12/2013] [Accepted: 03/20/2013] [Indexed: 11/29/2022]
Abstract
Structures of RT and its complexes combined with biochemical and clinical data help in illuminating the molecular mechanisms of different drug-resistance mutations. The NRTI drugs that are used in combinations have different primary mutation sites. RT mutations that confer resistance to one drug can be hypersensitive to another RT drug. Structure of an RT-DNA-nevirapine complex revealed how NNRTI binding forbids RT from forming a polymerase competent complex. Collective knowledge about various mechanisms of drug resistance by RT has broader implications for understanding and targeting drug resistance in general. In Part 1, we discussed the role of RT in developing HIV-1 drug resistance, structural and functional states of RT, and the nucleoside/nucleotide analog (NRTI) and non-nucleoside (NNRTI) drugs used in treating HIV-1 infections. In this part, we discuss structural understanding of various mechanisms by which RT confers antiviral drug resistance.
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Affiliation(s)
- Kalyan Das
- Center for Advanced Biotechnology and Medicine (CABM), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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Chung S, Miller JT, Lapkouski M, Tian L, Yang W, Le Grice SFJ. Examining the role of the HIV-1 reverse transcriptase p51 subunit in positioning and hydrolysis of RNA/DNA hybrids. J Biol Chem 2013; 288:16177-84. [PMID: 23595992 DOI: 10.1074/jbc.m113.465641] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent crystallographic analysis of p66/p51 human immunodeficiency virus (HIV) type 1 reverse transcriptase (RT) complexed with a non-polypurine tract RNA/DNA hybrid has illuminated novel and important contacts between structural elements at the C terminus of the noncatalytic p51 subunit and the nucleic acid duplex in the vicinity of the ribonuclease H (RNase H) active site. In particular, a short peptide spanning residues Phe-416-Pro-421 was shown to interact with the DNA strand, cross the minor groove of the helix, and then form Van der Waals contacts with the RNA strand adjacent to the scissile phosphate. At the base of the adjoining α-helix M', Tyr-427 forms a hydrogen bond with Asn-348, the latter of which, when mutated to Ile, is implicated in resistance to both nucleoside and non-nucleoside RT inhibitors. Based on our structural data, we analyzed the role of the p51 C terminus by evaluating selectively mutated p66/p51 heterodimers carrying (i) p51 truncations that encroach on α-M', (ii) alterations that interrupt the Asn-348-Tyr-427 interaction, and (iii) alanine substitutions throughout the region Phe-416-Pro-421. Collectively, our data support the notion that the p51 C terminus makes an important contribution toward hybrid binding and orienting the RNA strand for catalysis at the RNase H active site.
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Affiliation(s)
- Suhman Chung
- RT Biochemistry Section, HIV Drug Resistance Program, Center for Cancer Research, NCI, National Institutes of Health, Frederick Maryland 21702, USA
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Motea EA, Lee I, Berdis AJ. Insights into the roles of desolvation and π-electron interactions during DNA polymerization. Chembiochem 2013; 14:489-98. [PMID: 23404822 DOI: 10.1002/cbic.201200649] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Indexed: 01/22/2023]
Abstract
This report describes the use of several isosteric non-natural nucleotides as probes to evaluate the roles of nucleobase shape, size, solvation energies, and π-electron interactions as forces influencing key kinetic steps of the DNA polymerization cycle. Results are provided using representative high- and low-fidelity DNA polymerases. Results generated with the E. coli Klenow fragment reveal that this high-fidelity polymerase utilizes hydrophobic nucleotide analogues with higher catalytic efficiencies compared to hydrophilic analogues. These data support a major role for nucleobase desolvation during nucleotide selection and insertion. In contrast, the low-fidelity HIV-1 reverse transcriptase discriminates against hydrophobic analogues and only tolerates non-natural nucleotides that are capable of hydrogen-bonding or π-stacking interactions. Surprisingly, hydrophobic analogues that function as efficient substrates for the E. coli Klenow fragment behave as noncompetitive or uncompetitive inhibitors against HIV-1 reverse transcriptase. In these cases, the mode of inhibition depends upon the absence or presence of a templating nucleobase. Molecular modeling studies suggest that these analogues bind to the active site of reverse transcriptase as well as to a nearby hydrophobic binding pocket. Collectively, the studies using these non-natural nucleotides reveal important mechanistic differences between representative high- and low-fidelity DNA polymerases during nucleotide selection and incorporation.
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Affiliation(s)
- Edward A Motea
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106 (USA)
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Ferreira VF, da Rocha DR, da Silva FC, Ferreira PG, Boechat NA, Magalhães JL. Novel 1H-1,2,3-, 2H-1,2,3-, 1H-1,2,4- and 4H-1,2,4-triazole derivatives: a patent review (2008 – 2011). Expert Opin Ther Pat 2013; 23:319-31. [DOI: 10.1517/13543776.2013.749862] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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