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Choudhury A, Ojha PK, Ray S. Hazards of antiviral contamination in water: Dissemination, fate, risk and their impact on fish. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135087. [PMID: 38964042 DOI: 10.1016/j.jhazmat.2024.135087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/14/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Antiviral drugs are a cornerstone in the first line of antiviral therapy and their demand rises consistently with increments in viral infections and successive outbreaks. The drugs enter the waters due to improper disposal methods or via human excreta following their consumption; consequently, many of them are now classified as emerging pollutants. Hereby, we review the global dissemination of these medications throughout different water bodies and thoroughly investigate the associated risk they pose to the aquatic fauna, particularly our vertebrate relative fish, which has great economic and dietary importance and subsequently serves as a major doorway to the human exposome. Our risk assessment identifies eleven such drugs that presently pose high to moderate levels of risk to the fish. The antiviral drugs are likely to induce oxidative stress, alter the behaviour, affect different physiological processes and provoke various toxicological mechanisms. Many of the compounds exhibit elevated bioaccumulation potential, while, some have an increased tendency to leach through soil and contaminate the groundwater. Eight antiviral medications show a highly recalcitrant nature and would impact the aquatic life consistently in the long run and continue to influence the human exposome. Thereby, we call for urgent ecopharmacovigilance measures and modification of current water treatment methods.
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Affiliation(s)
- Abhigyan Choudhury
- Aquatic Toxicology Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Probir Kumar Ojha
- Drug Discovery and Development (DDD) Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India.
| | - Sajal Ray
- Aquatic Toxicology Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India.
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Swar R, Dessai PG, MamleDesai S, Chandavarkar S, Phadte S, Biradar B. Design, Synthesis, Characterisation, and Evaluation of Substituted Quinolin-2-one Derivatives as Possible Anti-lung Cancer Agents. Curr Drug Discov Technol 2024; 21:e261223224851. [PMID: 38151847 DOI: 10.2174/0115701638258479231220051227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/10/2023] [Accepted: 10/27/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND According to 2022, the estimated number of cancer cases in India was found to be 1,461,427. Lung cancers are the leading cause of death among Indian males. Research on cancer has been conducted to develop better treatments that are safe and effective and could be used to diagnose cancer at an early stage. It was found that quinolin-2-one possesses anticancer activity, which led us to synthesize substituted quinolin-2-one derivatives that can provide a longer future to cancer patients and decrease the risk of dying from cancer. OBJECTIVE This study aimed to carry out the design, synthesis, characterisation, and evaluation of novel substituted quinolin-2-one analogues as possible anti-lung cancer agents. METHODS Compound III a/III b on reaction with acids, sodium acetate and ethylchloroacetate, substituted benzaldehyde, phthalic anhydride, and 2N sodium hydroxide yielded compounds IV a/ IV b, V a/ V b, VI a/ VI b, VI c/ VI d, VI e/ VI f, VII a/ VII b, and VIII a/ VIII b, respectively. RESULT Among all the synthesised derivatives, compound VII a was found to be most potent with a MolDock score of -132.78 as compared to standard drug imatinib (-114.37) and active ligand 4- anilinoquinazoline (-126.71). All the synthesized derivatives showed a good ADME profile, but compound VII a showed the best ADME data among all the synthesised derivatives. All the synthesised compounds were tested for their in vitro anticancer activity against the Hop-62 (human lung cancer) cell line, out of which compound VII a was found to be most potent, with a percent control growth of -51.7% at a concentration of 80 μg/ml, which was in comparable to the positive control, Adriamycin (-70.5%) and standard imatinib (-84.0%). CONCLUSION Compound VII a showed the highest MolDock score and was most potent against human lung cancer cell line Hop-62.
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Affiliation(s)
- Riya Swar
- Department of Pharmaceutical Chemistry, PES's Rajaram and Tarabai Bandekar College of Pharmacy, Ponda, Goa 403 401, India
| | - Prachita Gauns Dessai
- Department of Pharmaceutical Chemistry, PES's Rajaram and Tarabai Bandekar College of Pharmacy, Ponda, Goa 403 401, India
| | - Shivalingrao MamleDesai
- Department of Pharmaceutical Chemistry, PES's Rajaram and Tarabai Bandekar College of Pharmacy, Ponda, Goa 403 401, India
| | - Sachin Chandavarkar
- Department of Pharmacognosy, PES's Rajaram and Tarabai Bandekar College of Pharmacy, Ponda, Goa 403 401, India
| | - Soniya Phadte
- Department of Pharmaceutical Chemistry, PES's Rajaram and Tarabai Bandekar College of Pharmacy, Ponda, Goa 403 401, India
| | - Bheemanagouda Biradar
- Department of Pharmacology, PES's Rajaram and Tarabai Bandekar College of Pharmacy, Ponda, Goa 403 401, India
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Ghosh AK. Four decades of continuing innovations in the development of antiretroviral therapy for HIV/AIDS: Progress to date and future challenges. Glob Health Med 2023; 5:194-198. [PMID: 37655189 PMCID: PMC10461327 DOI: 10.35772/ghm.2023.01013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/10/2023] [Indexed: 09/02/2023]
Abstract
The treatment of HIV-1 infection and AIDS represents one of the greatest challenges in medicine. While there is no cure for HIV/AIDS, truly remarkable progress has been made for treatment of HIV/AIDS patients today. The advent of combination antiretroviral therapy (cART) in the mid-1990s dramatically improved HIV-1 related morbidity, greatly prolonged life expectancy, and delayed progression of AIDS. Due to current antiretroviral therapy, the mortality rate for HIV infected patients is closely approaching the mortality rate for the general population. The long-term success of HIV-AIDS treatment requires continued enhancement of cART with further development of novel drugs that would exhibit fewer side effects, higher genetic barrier to the development of resistance, and longer action with durable virologic suppression. This editorial article provides a quick review of four decades of intense drug development research efforts targeting various viral enzymes and cellular host factors leading to the evolution of today's treatment of patients with HIV-1 infection and AIDS. It also touches on challenges of future treatment options.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
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Dessai PG, Dessai SP, Dabholkar R, Pednekar P, Naik S, Mamledesai S, Gopal M, Pavadai P, Kumar BK, Murugesan S, Chandavarkar S, Theivendren P, Selvaraj K. Design, synthesis, graph theoretical analysis and molecular modelling studies of novel substituted quinoline analogues as promising anti-breast cancer agents. Mol Divers 2023; 27:1567-1586. [PMID: 35976550 DOI: 10.1007/s11030-022-10512-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/02/2022] [Indexed: 11/26/2022]
Abstract
The most promising class of heterocyclic compounds in medicinal chemistry are those with the quinolin-2-one nucleus. It is a versatile heterocyclic molecule that has been put together with numerous pharmaceutical substances and is crucial in the creation of anticancer medications. In this view, the present research work deals with design, synthesis, and characterization of various analogous of quinolin-2-one nucleus and evaluation of their anticancer activity against MCF-7 cells (adenoma breast cancer cell line). Fourteen new compounds have been synthesised using suitable synthetic route and are characterized by FTIR, 1H NMR, 13C NMR and Mass spectral data. Molecular docking studies of the title compounds were carried out using PyRx 0.8 tool in AutoDock Vina program. All the synthesised compounds were exhibited well conserved hydrogen bonding with one or more amino acid residues in the active pocket of EGFR tyrosine kinase (PDB ID: 1m17). The docking score of the derivatives ranged from - 6.7 to - 9.5 kcal mol-1, standard drug Imatinib with - 9.6 kcal mol-1 and standard active ligand 4-anilinoquinazoline with - 7.7 kcal mol-1. The designed compound IV-A1 showed least binding energy (- 9.5 kcal mol-1) against EGFR tyrosine kinase receptor. Further, top scored compound, IV-A1 found to be most significant against MCF-7 cells with IC50 value of 0.0870 µM mL-1, TGI of 0.0958 µM mL-1, GI50 of 0.00499 µM mL-1, LC50 of 1.670 µM mL-1.
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Affiliation(s)
- Prachita Gauns Dessai
- Department of Pharmaceutical Chemistry, PES's Rajaram & Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, 403401, India
| | - Shivani Prabhu Dessai
- Department of Pharmaceutical Chemistry, PES's Rajaram & Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, 403401, India
| | - Renuka Dabholkar
- Department of Pharmaceutical Chemistry, PES's Rajaram & Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, 403401, India
| | - Padmashree Pednekar
- Department of Pharmaceutical Chemistry, PES's Rajaram & Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, 403401, India
| | - Sahili Naik
- Department of Pharmaceutical Chemistry, PES's Rajaram & Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, 403401, India
| | - Shivlingrao Mamledesai
- Department of Pharmaceutical Chemistry, PES's Rajaram & Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, 403401, India
| | - Murugananthan Gopal
- Department of Pharmacognosy, Swamy Vivekananda College of Pharmacy, Elayampalayam, 637205, India
| | - Parasuraman Pavadai
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M S R Nagar, Bengaluru, 560054, India
| | - Banoth Karan Kumar
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Pilani, 333031, India
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Pilani, 333031, India
| | - Sachin Chandavarkar
- Department of Pharmacognosy, ASPM College of Pharmacy, Sangulwadi, 416 810, India.
| | - Panneerselvam Theivendren
- Department of Pharmaceutical Chemistry, Swamy Vivekanandha College of Pharmacy, Elayampalayam, 637205, India.
| | - Kunjiappan Selvaraj
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, 626126, India.
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Xi Z, Ilina TV, Guerrero M, Fan L, Sluis‐Cremer N, Wang Y, Ishima R. Relative domain orientation of the L289K HIV-1 reverse transcriptase monomer. Protein Sci 2022; 31:e4307. [PMID: 35481647 PMCID: PMC8996465 DOI: 10.1002/pro.4307] [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: 12/17/2021] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 11/08/2022]
Abstract
HIV-1 reverse transcriptase (RT) is a heterodimer comprised p66 and p51 subunits (p66/p51). Several single amino acid substitutions in RT, including L289K, decrease p66/p51 dimer affinity, and reduce enzymatic functioning. Here, small-angle X-ray scattering (SAXS) with proton paramagnetic relaxation enhancement (PRE), 19 F site-specific NMR, and size exclusion chromatography (SEC) were performed for the p66 monomer with the L289K mutation, p66L289K . NMR and SAXS experiments clearly elucidated that the thumb and RNH domains in the monomer do not rigidly interact with each other but are spatially close to the RNH domain. Based on this structural model of the monomer, p66L289K and p51 were predicted to form a heterodimer while p66 and p51L289K not. We tested this hypothesis by SEC analysis of p66 and p51 containing L289K in different combinations and clearly demonstrated that L289K substitution in the p51 subunit, but not in the p66 subunit, reduces p66/p51 formation. Based on the derived monomer model and the importance of the inter-subunit RNH-thumb domain interaction in p66/p51, validated by SEC, the mechanism of p66 homodimer formation was discussed.
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Affiliation(s)
- Zhaoyong Xi
- Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Tatiana V. Ilina
- Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Michel Guerrero
- Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer ResearchSAXS Core Facility of the National Cancer InstituteFrederickMarylandUSA
| | - Nicolas Sluis‐Cremer
- Department of Medicine, Division of Infectious DiseasesUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Yun‐Xing Wang
- Protein‐Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer InstituteNational Institutes of HealthFrederickMarylandUSA
| | - Rieko Ishima
- Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
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In silico evaluation of atazanavir as a potential HIV main protease inhibitor and its comparison with new designed analogs. Comput Biol Med 2022; 145:105523. [DOI: 10.1016/j.compbiomed.2022.105523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/09/2022] [Accepted: 04/09/2022] [Indexed: 11/21/2022]
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Retinal Microvasculature And Immune Restoration Among South Eastern Asian HIV/AIDS Patients Over A 9-Month Antiretroviral Therapy. J Acquir Immune Defic Syndr 2022; 90:170-174. [PMID: 35135974 DOI: 10.1097/qai.0000000000002925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/18/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Longitudinal evidence on retinal microvasculature and subsequent systemic inflammatory alteration is lacking. We investigated the association between retinal microvasculature and immune response among HIV/AIDS patients over a 9-month antiretroviral therapy (ART). METHODS We conducted a prospective cohort on HIV/AIDS patients at Singapore Communicable Disease Centre (CDC) since June 2011. We recruited all eligible patients and then reviewed them every three months over a 9-month follow-up, including performing blood tests (CD4+/CD8+ T-cell counts, HIV viral load), blood pressure, anthropometry measurements, and retinal photography at each visit. We assessed retinal vascular indexes via a semi-automated computer-based program. Lastly, we applied a linear mixed model to analyze associations between baseline retinal vascular indexes and 9-month changes of CD4+/CD8+ T-cell cell counts and HIV viral load throughout study observation, after adjusting for major confounders. RESULTS We found that narrower arteriolar caliber (per 10 μm decrease), wider venular caliber (per 10 μm increase), and larger arteriolar branching angle (per 10 degrees increase) in the retina assessed at baseline were significantly associated with 9-month reductions in CD4+ T-cell count by 52.97 cells/µl (p=0.006), 33.55 cells/µl (p=0.01), and 39.09 cells/ µl (p=0.008), accordingly. CONCLUSION HIV/AIDS Patients with a suboptimal retinal microvascular morphology tended to fail immune restoration undertaking a 9-month ART.
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Eguida M, Rognan D. Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision. J Cheminform 2021; 13:90. [PMID: 34814950 PMCID: PMC8609734 DOI: 10.1186/s13321-021-00567-3] [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: 08/17/2021] [Accepted: 11/06/2021] [Indexed: 11/10/2022] Open
Abstract
Rationalizing the identification of hidden similarities across the repertoire of druggable protein cavities remains a major hurdle to a true proteome-wide structure-based discovery of novel drug candidates. We recently described a new computational approach (ProCare), inspired by numerical image processing, to identify local similarities in fragment-based subpockets. During the validation of the method, we unexpectedly identified a possible similarity in the binding pockets of two unrelated targets, human tumor necrosis factor alpha (TNF-α) and HIV-1 reverse transcriptase (HIV-1 RT). Microscale thermophoresis experiments confirmed the ProCare prediction as two of the three tested and FDA-approved HIV-1 RT inhibitors indeed bind to soluble human TNF-α trimer. Interestingly, the herein disclosed similarity could be revealed neither by state-of-the-art binding sites comparison methods nor by ligand-based pairwise similarity searches, suggesting that the point cloud registration approach implemented in ProCare, is uniquely suited to identify local and unobvious similarities among totally unrelated targets.
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Affiliation(s)
- Merveille Eguida
- Laboratoire d'Innovation Thérapeutique, UMR 7200 CNRS, Université de Strasbourg, 67400, Illkirch, France
| | - Didier Rognan
- Laboratoire d'Innovation Thérapeutique, UMR 7200 CNRS, Université de Strasbourg, 67400, Illkirch, France.
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Mathpal D, Almeleebia TM, Alshahrani KM, Alshahrani MY, Ahmad I, Asiri M, Kamal M, Jawaid T, Srivastava SP, Saeed M, Balaramnavar VM. Identification of 3-((1-(Benzyl(2-hydroxy-2-phenylethyl)amino)-1-oxo-3-phenylpropan-2-yl)carbamoyl)pyrazine-2-carboxylic Acid as a Potential Inhibitor of Non-Nucleosidase Reverse Transcriptase Inhibitors through InSilico Ligand- and Structure-Based Approaches. Molecules 2021; 26:molecules26175262. [PMID: 34500699 PMCID: PMC8433663 DOI: 10.3390/molecules26175262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/21/2021] [Accepted: 08/22/2021] [Indexed: 12/03/2022] Open
Abstract
Non-nucleosidase reverse transcriptase inhibitors (NNRTIs) are highly promising agents for use in highly effective antiretroviral therapy. We implemented a rational approach for the identification of promising NNRTIs based on the validated ligand- and structure-based approaches. In view of our state-of-the-art techniques in drug design and discovery utilizing multiple modeling approaches, we report here, for the first time, quantitative pharmacophore modeling (HypoGen), docking, and in-house database screening approaches in the identification of potential NNRTIs. The validated pharmacophore model with three hydrophobic groups, one aromatic ring group, and a hydrogen-bond acceptor explains the interactions at the active site by the inhibitors. The model was implemented in pharmacophore-based virtual screening (in-house and commercially available databases) and molecular docking for prioritizing the potential compounds as NNRTI. The identified leads are in good corroboration with binding affinities and interactions as compared to standard ligands. The model can be utilized for designing and identifying the potential leads in the area of NNRTIs.
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Affiliation(s)
- Deepti Mathpal
- School of Pharmacy and Research, Sanskriti University, 28 K. M. Stone, Mathura Delhi Highway, Chhata, Mathura 281401, Uttar Pradesh, India;
| | - Tahani M. Almeleebia
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, P.O. Box 61413, Abha 62529, Saudi Arabia;
| | - Kholoud M. Alshahrani
- College of Medicine, King Khalid University, P.O. Box 61413, Abha 62529, Saudi Arabia;
| | - Mohammad Y. Alshahrani
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha 62529, Saudi Arabia; (M.Y.A.); (I.A.); (M.A.)
| | - Irfan Ahmad
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha 62529, Saudi Arabia; (M.Y.A.); (I.A.); (M.A.)
| | - Mohammed Asiri
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha 62529, Saudi Arabia; (M.Y.A.); (I.A.); (M.A.)
| | - Mehnaz Kamal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam bin Abdulaziz University, P.O. Box 173, Al Kharj 11942, Saudi Arabia;
| | - Talha Jawaid
- Department of Pharmacology, College of Medicine, Al Imam Mohammad ibn Saud Islamic University (IMSIU), Othman ibn Affan Street, Riyadh 13317, Saudi Arabia;
| | - Swayam Prakash Srivastava
- Department of Pediatrics, Yale University School of Medicine CT, New Haven, CT 06520, USA;
- Vascular Biology and Therapeutic Program, Yale University School of Medicine CT, New Haven, CT 06511, USA
| | - Mohd Saeed
- Department of Biology College of Sciences, University of Hail, P.O. Box 2440, Hail 55425, Saudi Arabia
- Correspondence: (M.S.); (V.M.B.)
| | - Vishal M. Balaramnavar
- School of Pharmacy and Research, Sanskriti University, 28 K. M. Stone, Mathura Delhi Highway, Chhata, Mathura 281401, Uttar Pradesh, India;
- Correspondence: (M.S.); (V.M.B.)
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Priolkar RNS, Shingade S, Palkar M, Desai SM. Design, Synthesis, and Characterization of Novel Linomide Analogues and their Evaluation for Anticancer Activity. Curr Drug Discov Technol 2021; 17:203-212. [PMID: 30306874 DOI: 10.2174/1570163815666181008151037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/29/2018] [Accepted: 09/27/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND According to WHO, in 2017, about 90.5 million people suffered from cancer and about 8.8 million deaths occurred due to disease. Although the chemotherapeutic agents have decreased the mortality among the cancer patients but high toxicity and non-specific targets are still major drawbacks. Many researchers have identified linomide, a 4-hydroxy-2-quinolone derivative, as a lead molecule for the development of anticancer agents. With this background, we thought of the following objective. OBJECTIVE The objective of this research work involves the synthesis of a series of N-(2-(4- hydroxy-2-oxo-1-phenyl-1,2-dihydroquinolin-3-yl)-2-oxoethyl)-N-alkyl substituted benzene sulfonamides IVa-d (1-3) by replacing the anilide moiety at the third position of linomide with sulfamoylacyl and also N-methyl by N-phenyl functionality. To perform in silico anticancer activity by using Molegro Virtual Docker (MVD-2013, 6.0) software and in vitro anticancer activity by MTT assay. METHODS The starting material 4-hydroxy-1-phenylquinolin-2(1H)-one was treated with N-bromosuccinamide to yield compound II. Condensation of compound II with primary amines resulted in compounds IIIa-d, which, on coupling with substituted aromatic sulfonyl chlorides yield the title compounds IVa-d (1-3). RESULTS All the synthesized compounds were satisfactorily characterized by spectral data. The results of docking revealed that the synthesized compounds exhibited well-conserved hydrogen bonds with one or more amino acid residues in the active pocket of EGFRK tyrosine kinase domain (PDB ID: 1m17). The MolDock Score of compound IVd-1 (-115.503) was the highest amongst those tested. The in vitro anticancer activity results showed that compound IVc-1 (R= - (CH2) 2-CH3 ; R'= -H) and IV d-1 (R= -CH2-C6H5; R'= -H) were found to be most potent against K562 cell line with an IC50 of 0.451 μM/ml and 0.455 μM/ml respectively. Compound IVd-1 also showed better potency against A549 cell line with IC50 value of 0.704 μM/ml. CONCLUSION The results of in silico and in vitro anticancer activity are in agreement with each other. Compound IV d-1 was found to be most active of the series.
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Affiliation(s)
- Rudrax N S Priolkar
- Department of Pharmaceutical Chemistry, PES's Rajaram and Tarabai Bandekar College of Pharmacy, Farmagudi, Goa 403401, India
| | - Sunil Shingade
- Department of Pharmaceutical Chemistry, PES's Rajaram and Tarabai Bandekar College of Pharmacy, Farmagudi, Goa 403401, India
| | - Mahesh Palkar
- Department of Pharmaceutical Chemistry, KLEU's College of Pharmacy, Hubli, Karnataka 580031, India
| | - Shivalingrao M Desai
- Department of Pharmaceutical Chemistry, PES's Rajaram and Tarabai Bandekar College of Pharmacy, Farmagudi, Goa 403401, India
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Large Multidomain Protein NMR: HIV-1 Reverse Transcriptase Precursor in Solution. Int J Mol Sci 2020; 21:ijms21249545. [PMID: 33333923 PMCID: PMC7765405 DOI: 10.3390/ijms21249545] [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: 11/22/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 11/17/2022] Open
Abstract
NMR studies of large proteins, over 100 kDa, in solution are technically challenging and, therefore, of considerable interest in the biophysics field. The challenge arises because the molecular tumbling of a protein in solution considerably slows as molecular mass increases, reducing the ability to detect resonances. In fact, the typical 1H-13C or 1H-15N correlation spectrum of a large protein, using a 13C- or 15N-uniformly labeled protein, shows severe line-broadening and signal overlap. Selective isotope labeling of methyl groups is a useful strategy to reduce these issues, however, the reduction in the number of signals that goes hand-in-hand with such a strategy is, in turn, disadvantageous for characterizing the overall features of the protein. When domain motion exists in large proteins, the domain motion differently affects backbone amide signals and methyl groups. Thus, the use of multiple NMR probes, such as 1H, 19F, 13C, and 15N, is ideal to gain overall structural or dynamical information for large proteins. We discuss the utility of observing different NMR nuclei when characterizing a large protein, namely, the 66 kDa multi-domain HIV-1 reverse transcriptase that forms a homodimer in solution. Importantly, we present a biophysical approach, complemented by biochemical assays, to understand not only the homodimer, p66/p66, but also the conformational changes that contribute to its maturation to a heterodimer, p66/p51, upon HIV-1 protease cleavage.
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Panigrahi D, Mishra A, Sahu SK, Azam MA, Vyshaag CM. A Combined approach of Pharmacophore Modeling, QSAR Study, Molecular Docking and in silico ADME/Tox prediction of 4-Arylthio & 4- Aryloxy-3- Iodopyridine-2(1H)-one analogs to identify potential Reverse Transcriptase inhibitor: Anti-HIV agents. Med Chem 2020; 18:51-87. [PMID: 33319692 DOI: 10.2174/1573406417666201214100822] [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: 05/01/2020] [Revised: 08/31/2020] [Accepted: 10/12/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Reverse transcriptase is an important therapeutic target to treat AIDS caused by the Human Immunodeficiency Virus (HIV). Despite many effective anti-HIV drugs, reverse transcriptase (RT) inhibitors remain the cornerstone of the drug regimen to treat AIDS. In the present work, we have expedited the use of different computational modules and presented an easy, cost-effective and high throughput screening method to identify potential reverse transcriptase inhibitors. METHODS A congeneric series of 4-Arylthio & 4-Aryloxy-3- Iodopyridine-2(1H)-one analogs having anti-HIV activity were subjected to structure-based 2D, 3D QSAR, Pharmacophore Modeling, and Molecular Docking to elucidate the structural properties required for the design of potent HIV-RT inhibitors. Prediction of preliminary Pharmacokinetic and the Drug Likeliness profile was performed for these compounds by in silico ADME study. RESULTS The 2D and 3D- QSAR models were developed by correlating two and three-dimensional descriptors with activity (pIC50) by sphere exclusion method and k-nearest neighbor molecular field analysis approach, respectively. The significant 2D- QSAR model developed by Partial Least Square associated with the Sphere Exclusion method (PLS-SE) having r2 and q2 values 0.9509 and 0.8038 respectively. The 3D-QSAR model by Step Wise variable selection method (SW-kNN MFA) is more significant which has a cross-validated squared correlation coefficient q2= 0.8509 and a non-cross-validated correlation coefficient pred_r2= 0.8102. The pharmacophore hypothesis was developed which comprised 5 features includes 3 aliphatic regions (Ala), 1 H-bond donor (HDr) and 1 H-bond acceptor (HAc). Docking studies of the selected inhibitors with the active site of reverse transcriptase enzyme showed hydrogen bond and π - π interaction with LYS-101, LYS-103, TYR- 181, TYR-188 and TRP-229 residues present at the active site. All the candidates with good bioavailability and ADMET drug likeliness properties. CONCLUSION The results of the present work provide more useful information and important structural insights for the discovery, design of novel and potent reverse transcriptase inhibitors with high therapeutic windows in the future.
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Affiliation(s)
- Debadash Panigrahi
- Drug Research Laboratory, Nodal Research Centre, College of Pharmaceutical Sciences, Puri, Baliguali, Puri- Konark Marine Drive road, Puri, Odisha. India
| | - Amiyakanta Mishra
- Drug Research Laboratory, Nodal Research Centre, College of Pharmaceutical Sciences, Puri, Baliguali, Puri- Konark Marine Drive road, Puri, Odisha. India
| | - Susanta Kumar Sahu
- Dept. of Pharmacy, Utkal University, VaniVihar, Bhubaneswar, Odisha. India
| | - Mohd Afzal Azam
- Dept. of Pharmaceutical Chemistry, J.S.S. College of Pharmacy, Ooty, Udhagamandalam, Tamil Nadu. India
| | - C M Vyshaag
- Dept. of Pharmaceutical Chemistry, J.S.S. College of Pharmacy, Ooty, Udhagamandalam, Tamil Nadu. India
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13
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Freedman H, Kundu J, Tchesnokov EP, Law JLM, Nieman JA, Schinazi RF, Tyrrell DL, Gotte M, Houghton M. Application of Molecular Dynamics Simulations to the Design of Nucleotide Inhibitors Binding to Norovirus Polymerase. J Chem Inf Model 2020; 60:6566-6578. [PMID: 33259199 DOI: 10.1021/acs.jcim.0c00742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The RNA-dependent RNA polymerase (RdRp) of norovirus is an attractive target of antiviral agents aimed at providing protection against norovirus-associated gastroenteritis. Here, we perform molecular dynamics simulations of the crystal structure of norovirus RdRp in complex with several known binders, as well as free-energy simulations by free-energy perturbation (FEP) to determine binding free energies of these molecules relative to the natural nucleotide substrates. We determine experimental EC50 values and nucleotide incorporation efficiencies for several of these compounds. Moreover, we investigate the mechanism of inhibition of some of these ligands. Using FEP, we screened a virtual nucleotide library with 121 elements for binding to the polymerase and successfully identified two novel chain terminators.
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Affiliation(s)
- Holly Freedman
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Juthika Kundu
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Egor Petrovitch Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John Lok Man Law
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - James A Nieman
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Raymond F Schinazi
- Center for AIDS Research, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - D Lorne Tyrrell
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Matthias Gotte
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Michael Houghton
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
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14
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Huang YM, Alharbi NS, Sun B, Shantharam CS, Rakesh KP, Qin HL. Synthetic routes and structure-activity relationships (SAR) of anti-HIV agents: A key review. Eur J Med Chem 2019; 181:111566. [PMID: 31401538 DOI: 10.1016/j.ejmech.2019.111566] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 01/05/2023]
Abstract
The worldwide increase of AIDS, an epidemic infection in constant development has an essential and still requires potent antiretroviral chemotherapeutic agents for reducing the integer of deaths caused by HIV. Thus, there is an urgent need for new anti-HIV drug candidates with increased strength, new targets, superior pharmacokinetic properties, and compact side effects. From this viewpoint, we first review present strategies of anti-HIV drug innovation and the synthesis of heterocyclic or natural compound as anti-HIV agents for facilitating the development of more influential and successful anti-HIV agents.
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Affiliation(s)
- Yu-Mei Huang
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR China
| | - Njud S Alharbi
- Biotechnology Research Group, Deportment of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bing Sun
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR China.
| | - C S Shantharam
- Department of Chemistry, Pooja Bhagavath Memorial Mahajana Education Centre, Mysuru, 570016, Karnataka, India
| | - K P Rakesh
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR China.
| | - Hua-Li Qin
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR China.
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15
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Agnello S, Brand M, Chellat MF, Gazzola S, Riedl R. A Structural View on Medicinal Chemistry Strategies against Drug Resistance. Angew Chem Int Ed Engl 2019; 58:3300-3345. [PMID: 29846032 DOI: 10.1002/anie.201802416] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/24/2018] [Indexed: 12/31/2022]
Abstract
The natural phenomenon of drug resistance is a widespread issue that hampers the performance of drugs in many major clinical indications. Antibacterial and antifungal drugs are affected, as well as compounds for the treatment of cancer, viral infections, or parasitic diseases. Despite the very diverse set of biological targets and organisms involved in the development of drug resistance, the underlying molecular mechanisms have been identified to understand the emergence of resistance and to overcome this detrimental process. Detailed structural information on the root causes for drug resistance is nowadays frequently available, so next-generation drugs can be designed that are anticipated to suffer less from resistance. This knowledge-based approach is essential for fighting the inevitable occurrence of drug resistance.
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Affiliation(s)
- Stefano Agnello
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Michael Brand
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Mathieu F Chellat
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Silvia Gazzola
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
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16
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Agnello S, Brand M, Chellat MF, Gazzola S, Riedl R. Eine strukturelle Evaluierung medizinalchemischer Strategien gegen Wirkstoffresistenzen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201802416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Stefano Agnello
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Michael Brand
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Mathieu F. Chellat
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Silvia Gazzola
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Rainer Riedl
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
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17
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Lu X, Yang J, Kang D, Gao P, Daelemans D, De Clercq E, Pannecouque C, Zhan P, Liu X. The discovery of novel diarylpyri(mi)dine derivatives with high level activity against a wide variety of HIV-1 strains as well as against HIV-2. Bioorg Med Chem 2018; 26:2051-2060. [DOI: 10.1016/j.bmc.2018.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 02/27/2018] [Accepted: 03/02/2018] [Indexed: 11/29/2022]
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18
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Loksha YM, Pedersen EB. Asymmetric Synthesis of Potential Precursors of the HIV Drug MC1220 and Its Analogues by Hydrogenation of (1-Arylvinyl)pyrimidines. J Heterocycl Chem 2018. [DOI: 10.1002/jhet.3168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yasser M. Loksha
- Nucleic Acid Centre, Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 DK-5230 Odense M Denmark
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy; Sinai University; Al-Arish North Sinai Egypt
| | - Erik B. Pedersen
- Nucleic Acid Centre, Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 DK-5230 Odense M Denmark
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19
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Peddi SR, Mohammed NA, Hussein AA, Sivan SK, Manga V. Multiple-receptor conformation docking, dock pose clustering, and 3D QSAR-driven approaches exploring new HIV-1 RT inhibitors. Struct Chem 2018. [DOI: 10.1007/s11224-018-1082-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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20
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Cai Y, Liu H, Chen H. Allosteric mechanism of quinoline inhibitors for HIV RT-associated RNase with MD simulation and dynamics fluctuation network. Chem Biol Drug Des 2017; 91:805-816. [DOI: 10.1111/cbdd.13146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/23/2017] [Accepted: 11/01/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Yi Cai
- Shanghai High School; Shanghai China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; College of Life Sciences and Biotechnology; Shanghai Jiaotong University; Shanghai China
| | - Haifeng Chen
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; College of Life Sciences and Biotechnology; Shanghai Jiaotong University; Shanghai China
- Shanghai Center for Bioinformation Technology; Shanghai China
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21
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Xu HR, Fu L, Zhan P, Liu XY. 3D-QSAR analysis of a series of S-DABO derivatives as anti-HIV agents by CoMFA and CoMSIA. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2016; 27:999-1014. [PMID: 27667445 DOI: 10.1080/1062936x.2016.1233580] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/04/2016] [Indexed: 06/06/2023]
Abstract
In this study, we retrieved a series of 59 dihydroalkylthio-benzyloxopyrimidine (S-DABO) derivatives, which is a class of highly potent HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) reported from published articles, and analysed them with comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Statistically significant three-dimensional quantitative structure-activity relationship (3D-QSAR) models by CoMFA and CoMSIA were derived from a training set of 46 compounds on the basis of the rigid body alignment. Further, the predictive ability of the QSAR models was validated by a test set of 13 compounds. Based on the information derived from CoMFA and CoMSIA contour maps, we have identified some steric and electrostatic features for improving the activities of these inhibitors, and we validated the 3D-QSAR results by a molecular docking method. On the basis of the obtained results, we designed a new series of S-DABO derivatives with high activities. Therefore, this study could be utilized to design more potent S-DABO analogues as anti-HIV agents.
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Affiliation(s)
- H R Xu
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education) , School of Pharmaceutical Sciences, Shandong University , Ji'nan , Shandong , PR China
| | - L Fu
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education) , School of Pharmaceutical Sciences, Shandong University , Ji'nan , Shandong , PR China
| | - P Zhan
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education) , School of Pharmaceutical Sciences, Shandong University , Ji'nan , Shandong , PR China
| | - X Y Liu
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education) , School of Pharmaceutical Sciences, Shandong University , Ji'nan , Shandong , PR China
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22
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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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23
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Gu SX, Xue P, Ju XL, Zhu YY. Advances in rationally designed dual inhibitors of HIV-1 reverse transcriptase and integrase. Bioorg Med Chem 2016; 24:5007-5016. [PMID: 27658796 DOI: 10.1016/j.bmc.2016.09.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/09/2016] [Accepted: 09/10/2016] [Indexed: 01/07/2023]
Abstract
Reverse transcriptase (RT) and integrase (IN) are two indispensable enzymes in human immunodeficiency virus type 1 (HIV-1) replication. RT is responsible for the transformation of the single-stranded RNA viral genome into double-stranded DNA, and IN catalyzes the integration of viral DNA into the host DNA. Although highly active antiretroviral therapy (HAART) combining nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs/NtRTIs) with nonnucleoside reverse transcriptase inhibitors (NNRTIs) or protease inhibitors (PIs) could suppress successfully HIV viral load and reduce evidently the mortality of HIV infected people, it involves the difficulty of perfect adherence, and other drawbacks such as viral rebound, toxicities and multi-drug resistances. Recently, rational drug design has become a dominant technique for the development of multi-target drugs. And the rationally designed dual inhibitors of HIV-1 RT and IN have become a hot topic of anti-HIV research. In this review, the advances in rationally designed dual inhibitors of HIV-1 RT and IN were summarized, including structurally diverse inhibitors, their structure-activity relationship (SAR) studies as well as binding mode analysis.
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Affiliation(s)
- Shuang-Xi Gu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China.
| | - Ping Xue
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China
| | - Xiu-Lian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430073, China.
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24
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Maghrabi IA, Alghamdi S, Alrobaian M, Eldeab HA. Green Technique-Solvent Free Microwave Synthesis and Antimicrobial Evaluation of New Thiopyridine Arabinosides. Molecules 2016; 21:477. [PMID: 27104506 PMCID: PMC6273357 DOI: 10.3390/molecules21040477] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 01/23/2023] Open
Abstract
A green protocol has been applied to synthesize a novel series of 3-cyano-2-(tri-O-acetyl-β-D-arabinopyranosylthio)pyridines in a short reaction time, in higher yields and with simpler operations, when compared with the conventional heating method. Deacetylation of the obtained acetylated arabinosides produced 2-(β-D-arabinopyranosylthio)-3-cyanopyridines. The structures of the obtained products were confirmed on the basis of spectroscopic data (FT-IR, 1D, 2D-NMR). The synthesized compounds were screened for the antimicrobial activity against a selection of Gram positive and Gram negative bacteria.
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Affiliation(s)
- Ibrahim A Maghrabi
- Department of Clinical Pharmacy, College of Pharmacy, Taif University, Taif 5700, Saudi Arabia.
| | - Saleh Alghamdi
- Department of Microbiology, College of Pharmacy, Taif University, Taif 5700, Saudi Arabia.
| | - Majed Alrobaian
- Department of Microbiology, College of Pharmacy, Taif University, Taif 5700, Saudi Arabia.
| | - Hany A Eldeab
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif 5700, Saudi Arabia.
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25
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Zheng X, Pedersen LC, Gabel SA, Mueller GA, DeRose EF, London RE. Unfolding the HIV-1 reverse transcriptase RNase H domain--how to lose a molecular tug-of-war. Nucleic Acids Res 2016; 44:1776-88. [PMID: 26773054 PMCID: PMC4770237 DOI: 10.1093/nar/gkv1538] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/24/2015] [Indexed: 11/14/2022] Open
Abstract
Formation of the mature HIV-1 reverse transcriptase (RT) p66/p51 heterodimer requires subunit-specific processing of the p66/p66' homodimer precursor. Since the ribonuclease H (RH) domain contains an occult cleavage site located near its center, cleavage must occur either prior to folding or subsequent to unfolding. Recent NMR studies have identified a slow, subunit-specific RH domain unfolding process proposed to result from a residue tug-of-war between the polymerase and RH domains on the functionally inactive, p66' subunit. Here, we describe a structural comparison of the isolated RH domain with a domain swapped RH dimer that reveals several intrinsically destabilizing characteristics of the isolated domain that facilitate excursions of Tyr427 from its binding pocket and separation of helices B and D. These studies provide independent support for the subunit-selective RH domain unfolding pathway in which instability of the Tyr427 binding pocket facilitates its release followed by domain transfer, acting as a trigger for further RH domain destabilization and subsequent unfolding. As further support for this pathway, NMR studies demonstrate that addition of an RH active site-directed isoquinolone ligand retards the subunit-selective RH' domain unfolding behavior of the p66/p66' homodimer. This study demonstrates the feasibility of directly targeting RT maturation with therapeutics.
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Affiliation(s)
- Xunhai Zheng
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Scott A Gabel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Geoffrey A Mueller
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Eugene F DeRose
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental health Sciences, NIH, Research Triangle Park, NC 27709, USA
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26
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Loksha YM, Pedersen EB, La Colla P, Loddo R. Facile synthesis of the NNRTI microbicide MC-1220 and synthesis of its phosphoramidate prodrugs. Org Biomol Chem 2015; 14:940-6. [PMID: 26608715 DOI: 10.1039/c5ob02055g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A facile and novel synthetic route to MC-1220 was achieved by condensation of 4,6-dichloro-N,N-5-trimethylpyrimidin-2-amine (1) with the sodium salt of 2,6-difluorophenylacetonitrile, followed by methylation and strong acidic hydrolysis. The prodrugs of MC-1220 were synthesized by reaction of chlorophosphoramidate derivatives (7a-e) or α-acetobromoglucose with the sodium salt of MC-1220. The stability and anti-HIV-1 activity of phosphoramidate prodrugs turned out to be comparable to those of the parent drug MC-1220.
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Affiliation(s)
- Yasser M Loksha
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
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27
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John J, Kim Y, Bennett N, Das K, Liekens S, Naesens L, Arnold E, Maguire AR, Götte M, Dehaen W, Balzarini J. Pronounced Inhibition Shift from HIV Reverse Transcriptase to Herpetic DNA Polymerases by Increasing the Flexibility of α-Carboxy Nucleoside Phosphonates. J Med Chem 2015; 58:8110-27. [PMID: 26450273 DOI: 10.1021/acs.jmedchem.5b01180] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alpha-carboxynucleoside phosphonates (α-CNPs) are novel viral DNA polymerase inhibitors that do not need metabolic conversion for enzyme inhibition. The prototype contains a cyclopentyl linker between nucleobase and α-carboxyphosphonate and preferentially (50- to 100-fold) inhibits HIV-1 RT compared with herpetic DNA polymerases. A synthesis methodology involving three steps has been developed for the synthesis of a series of novel α-CNPs, including a Rh(II)-catalyzed O-H insertion that connects the carboxyphosphonate group to a linker moiety and an attachment of a nucleobase to the other end of the linker by a Mitsunobu reaction followed by final deprotection. Replacing the cyclopentyl moiety in the prototype α-CNPs by a more flexible entity results in a selectivity shift of ∼ 100-fold in favor of the herpetic DNA polymerases when compared to selectivity for HIV-1 RT. The nature of the kinetic interaction of the acyclic α-CNPs against the herpetic DNA polymerases differs from the nature of the nucleobase-specific kinetic interaction of the cyclopentyl α-CNPs against HIV RT.
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Affiliation(s)
| | | | - Nicholas Bennett
- Department of Medical Microbiology and Immunology, University of Alberta , 6-020 Katz Group Centre, Edmonton, Alberta T6G 2E1, Canada
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08901, United States
| | | | | | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08901, United States
| | - Anita R Maguire
- Department of Chemistry and School of Pharmacy, Analytical and Biological Chemistry Research Facility, University College Cork , Cork, Ireland
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta , 6-020 Katz Group Centre, Edmonton, Alberta T6G 2E1, Canada
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Khalid Z, Aslam S, Ahmad M, Munawar MA, Montero C, Detorio M, Parvez M, Schinazi RF. Anti-HIV activity of new pyrazolobenzothiazine 5,5-dioxide-based acetohydrazides. Med Chem Res 2015; 24:3671-3680. [PMID: 34316244 PMCID: PMC8312988 DOI: 10.1007/s00044-015-1411-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A series of fifteen new 2-[3-(3-chlorophenyl)-5,5-dioxidobenzo[e]pyrazolo[4,3-c][1,2]thiazin-4(2H)-yl]-N'-arylmethyleneacetohydrazides (5a-o) were synthesized and screened for their anti-HIV-1 and cytotoxicity activity. Out of fifteen pyrazolobenzothiazine-based hydrazones, thirteen were found to be active inhibitors of HIV with EC50 values <20 μM. Moreover, the cytotoxicity results showed that most of the compounds were toxic to PBM, CEM and Vero cell lines. This information could be used for structural modifications to acquire good candidates of HIV drugs.
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Affiliation(s)
- Zunera Khalid
- Institute of Chemistry, University of the Punjab, Lahore 54590, Pakistan
| | - Sana Aslam
- Institute of Chemistry, University of the Punjab, Lahore 54590, Pakistan
- Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | | | - Catherine Montero
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Emory University School of Medicine/Veterans Affairs Medical Center, 1760 Haygood Drive, Atlanta, GA 30322, USA
| | - Mervi Detorio
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Emory University School of Medicine/Veterans Affairs Medical Center, 1760 Haygood Drive, Atlanta, GA 30322, USA
| | - Masood Parvez
- Department of Chemistry, The University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Raymond F. Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Emory University School of Medicine/Veterans Affairs Medical Center, 1760 Haygood Drive, Atlanta, GA 30322, USA
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29
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Li W, Li X, De Clercq E, Zhan P, Liu X. Discovery of potent HIV-1 non-nucleoside reverse transcriptase inhibitors from arylthioacetanilide structural motif. Eur J Med Chem 2015; 102:167-79. [DOI: 10.1016/j.ejmech.2015.07.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 11/26/2022]
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30
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Interactions of HIV-1 proteins as targets for developing anti-HIV-1 peptides. Future Med Chem 2015; 7:1055-77. [DOI: 10.4155/fmc.15.46] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Protein–protein interactions (PPI) are essential in every step of the HIV replication cycle. Mapping the interactions between viral and host proteins is a fundamental target for the design and development of new therapeutics. In this review, we focus on rational development of anti-HIV-1 peptides based on mapping viral–host and viral–viral protein interactions all across the HIV-1 replication cycle. We also discuss the mechanism of action, specificity and stability of these peptides, which are designed to inhibit PPI. Some of these peptides are excellent tools to study the mechanisms of PPI in HIV-1 replication cycle and for the development of anti-HIV-1 drug leads that modulate PPI.
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31
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Matusevich O, Egorov V, Gluzdikov I, Titov M, Zarubaev V, Shtro A, Slita A, Dukov M, Shurygina AP, Smirnova T, Kudryavtsev I, Vasin A, Kiselev O. Synthesis and antiviral activity of PB1 component of the influenza A RNA polymerase peptide fragments. Antiviral Res 2015; 113:4-10. [DOI: 10.1016/j.antiviral.2014.10.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 11/30/2022]
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32
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Bernardo CEP, Silva PJ. Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ 2014; 2:e470. [PMID: 25071993 PMCID: PMC4103094 DOI: 10.7717/peerj.470] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/16/2014] [Indexed: 11/23/2022] Open
Abstract
The binding of several rubromycin-based ligands to HIV1-reverse transcriptase was analyzed using molecular docking and molecular dynamics simulations. MM-PBSA analysis and examination of the trajectories allowed the identification of several promising compounds with predicted high affinity towards reverse transcriptase mutants which have proven resistant to current drugs. Important insights on the complex interplay of factors determining the ability of ligands to selectively target each mutant have been obtained.
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Affiliation(s)
- Carlos E P Bernardo
- REQUIMTE/Faculdade de Ciências da Saúde, Universidade Fernando Pessoa , Rua Carlos da Maia, Porto , Portugal
| | - Pedro J Silva
- REQUIMTE/Faculdade de Ciências da Saúde, Universidade Fernando Pessoa , Rua Carlos da Maia, Porto , Portugal
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Rai D, Chen W, Zhan P, Liu H, Tian Y, Liang X, De Clercq E, Pannecouque C, Balzarini J, Liu X. Synthesis and Anti-HIV Activity of 4-(Naphthalen-1-yl)-1,2,5-thiadiazol-3-hydroxyl Derivatives. Chem Biol Drug Des 2014; 84:420-30. [DOI: 10.1111/cbdd.12328] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 02/10/2014] [Accepted: 03/13/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Diwakar Rai
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Educational Ministry of China); School of Pharmaceutical Sciences; Shandong University; No. 44 Wenhuaxi Road Jinan 250012 China
| | - Wenmin Chen
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Educational Ministry of China); School of Pharmaceutical Sciences; Shandong University; No. 44 Wenhuaxi Road Jinan 250012 China
| | - Peng Zhan
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Educational Ministry of China); School of Pharmaceutical Sciences; Shandong University; No. 44 Wenhuaxi Road Jinan 250012 China
| | - Hong Liu
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Educational Ministry of China); School of Pharmaceutical Sciences; Shandong University; No. 44 Wenhuaxi Road Jinan 250012 China
| | - Ye Tian
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Educational Ministry of China); School of Pharmaceutical Sciences; Shandong University; No. 44 Wenhuaxi Road Jinan 250012 China
| | - Xin Liang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Educational Ministry of China); School of Pharmaceutical Sciences; Shandong University; No. 44 Wenhuaxi Road Jinan 250012 China
| | - Erik De Clercq
- Rega Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 B-3000 Leuven Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 B-3000 Leuven Belgium
| | - Jan Balzarini
- Rega Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 B-3000 Leuven Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Educational Ministry of China); School of Pharmaceutical Sciences; Shandong University; No. 44 Wenhuaxi Road Jinan 250012 China
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Ilina T, LaBarge K, Sarafianos SG, Ishima R, Parniak MA. Inhibitors of HIV-1 Reverse Transcriptase-Associated Ribonuclease H Activity. BIOLOGY 2014; 1:521-41. [PMID: 23599900 PMCID: PMC3627382 DOI: 10.3390/biology1030521] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
HIV-1 enzyme reverse transcriptase (RT) is a major target for antiviral drug development, with over half of current FDA-approved therapeutics against HIV infection targeting the DNA polymerase activity of this enzyme. HIV-1 RT is a multifunctional enzyme that has RNA and DNA dependent polymerase activity, along with ribonuclease H (RNase H) activity. The latter is responsible for degradation of the viral genomic RNA template during first strand DNA synthesis to allow completion of reverse transcription and the viral dsDNA. While the RNase H activity of RT has been shown to be essential for virus infectivity, all currently used drugs directed at RT inhibit the polymerase activity of the enzyme; none target RNase H. In the last decade, the increasing prevalence of HIV variants resistant to clinically used antiretrovirals has stimulated the search for inhibitors directed at stages of HIV replication different than those targeted by current drugs. HIV RNase H is one such novel target and, over the past few years, significant progress has been made in identifying and characterizing new RNase H inhibitor pharmacophores. In this review we focus mainly on the most potent low micromolar potency compounds, as these provide logical bases for further development. We also discuss why HIV RNase H has been a difficult target for antiretroviral drug development.
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Affiliation(s)
- Tatiana Ilina
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, S.414, Pittsburgh, PA 15219, USA; (T.I.); (K.L.)
| | - Krystal LaBarge
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, S.414, Pittsburgh, PA 15219, USA; (T.I.); (K.L.)
- Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO, USA;
| | - Stefan G. Sarafianos
- Structural Biology, University of Pittsburgh School of Medicine, 450 Technology Drive, S.414, Pittsburgh, PA 15219, USA;
| | - Rieko Ishima
- Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO, USA;
| | - Michael A. Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, S.414, Pittsburgh, PA 15219, USA; (T.I.); (K.L.)
- Author to whom correspondence should be addressed; ; Tel.: +1-412-648-1927; Fax: +1-412-648-9653
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35
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36
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Zhang L, Zhan P, Chen X, Li Z, Xie Z, Zhao T, Liu H, De Clercq E, Pannecouque C, Balzarini J, Liu X. Design, synthesis and preliminary SAR studies of novel N-arylmethyl substituted piperidine-linked aniline derivatives as potent HIV-1 NNRTIs. Bioorg Med Chem 2014; 22:633-42. [DOI: 10.1016/j.bmc.2013.10.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 10/21/2013] [Accepted: 10/22/2013] [Indexed: 01/19/2023]
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37
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Duplessis M, Morency L, James C, Minville J, Deroy P, Morin S, Thavonekham B, Tremblay M, Halmos T, Simoneau B, Bousquet Y, Sturino C. Multi-gram synthesis of a nucleotide-competing reverse transcriptase inhibitor. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.01.129] [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]
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38
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Identification of potent and orally bioavailable nucleotide competing reverse transcriptase inhibitors: in vitro and in vivo optimization of a series of benzofurano[3,2-d]pyrimidin-2-one derived inhibitors. Bioorg Med Chem Lett 2013; 23:3967-75. [PMID: 23673016 DOI: 10.1016/j.bmcl.2013.04.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/10/2013] [Accepted: 04/16/2013] [Indexed: 02/05/2023]
Abstract
Recently, a new class of HIV reverse transcriptase (HIV-RT) inhibitors has been reported. The novel mechanism of inhibition by this class involves competitive binding to the active site of the RT enzyme and has been termed Nucleotide-Competing Reverse Transcriptase Inhibitors (NcRTIs). In this publication we describe the optimization of a novel benzofurano[3,2-d]pyrimidin-2-one series of NcRTIs. The starting point for the current study was inhibitor 2, which had high biochemical and antiviral potency but only moderate permeability in a Caco-2 assay and high B-to-A efflux, resulting in moderate rat bioavailability and low Cmax. We present herein the results and strategies we employed to optimize both the potency as well as the permeability, metabolic stability and pharmacokinetic profile of this series. One of the key observations of the present study was the importance of shielding polar functionality, at least in the context of the current chemotype, to enhance permeability. These studies led to the identification of inhibitors 39 and 45, which display sub-nanomolar antiviral potency in a p24 ELISA assay with significantly reduced efflux ratios (ratios <1.5). These inhibitors also display excellent rat pharmacokinetic profiles with high bioavailabilities and low clearance.
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39
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Ehteshami M, Nijhuis M, Bernatchez JA, Ablenas CJ, McCormick S, de Jong D, Jochmans D, Götte M. Formation of a quaternary complex of HIV-1 reverse transcriptase with a nucleotide-competing inhibitor and its ATP enhancer. J Biol Chem 2013; 288:17336-46. [PMID: 23598281 DOI: 10.1074/jbc.m112.433441] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleotide-competing reverse transcriptase inhibitors were shown to bind reversibly to the nucleotide-binding site of the reverse transcriptase (RT) enzyme of human immunodeficiency virus type 1 (HIV-1). Here, we show that the presence of ATP can enhance the inhibitory effects of the prototype compound INDOPY-1. We employed a combination of cell-free and cell-based assays to shed light on the underlying molecular mechanism. Binding studies and site-specific footprinting experiments demonstrate the existence of a stable quaternary complex with HIV-1 RT, its nucleic acid substrate, INDOPY-1, and ATP. The complex is frozen in the post-translocational state that usually accommodates the incoming nucleotide substrate. Structure-activity relationship studies show that both the base and the phosphate moieties of ATP are elements that play important roles in enhancing the inhibitory effects of INDOPY-1. In vitro susceptibility measurements with mutant viruses containing amino acid substitutions K70G, V75T, L228R, and K219R in the putative ATP binding pocket revealed unexpectedly a hypersusceptible phenotype with respect to INDOPY-1. The same mutational cluster was previously shown to reduce susceptibility to the pyrophosphate analog phosphonoformic acid. However, in the absence of INDOPY-1, ATP can bind and act as a pyrophosphate donor under conditions that favor formation of the pre-translocated RT complex. We therefore conclude that the mutant enzyme facilitates simultaneous binding of INDOPY-1 and ATP to the post-translocated complex. Based on these data, we propose a model in which the bound ATP traps the inhibitor, which, in turn, compromises its dissociation.
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Affiliation(s)
- Maryam Ehteshami
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
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40
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Identification and characterization of a novel HIV-1 nucleotide-competing reverse transcriptase inhibitor series. Antimicrob Agents Chemother 2013; 57:2712-8. [PMID: 23545531 DOI: 10.1128/aac.00113-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Several groups have recently reported on the identification of nucleotide-competing reverse transcriptase inhibitors (NcRTIs), a new class of RT inhibitors. NcRTIs reversibly inhibit binding of the incoming nucleotide to the RT active site but do not act as chain terminators, unlike the nucleos(t)ide reverse transcriptase inhibitor (NRTI) class. We identified a novel benzo[4,5]furo[3,2,d]pyrimidin-2-one NcRTI chemical series. Structure-activity relationship evaluation of this series with both RT and viral replication assays led to the identification of compound A, a new NcRTI. Compound A inhibited HIV-1 RT in a primer extension assay (50% inhibitory concentration, 2.6 nM) but had no measurable activity against human DNA polymerase γ at 10 μM. It potently inhibited HIV-1 replication in vitro (50% effective concentration, 1.5 nM). The antiviral potency of compound A was unaffected by the presence of nonnucleotide RT inhibitor (NNRTI) mutations tested (L100I, K103N/Y181C, V106A, or Y188L). Notably, viruses encoding K65R were hypersusceptible to inhibition by compound A. Compound A also retained full activity against viruses encoding M184V. In vitro selection for resistant virus to compound A led to the selection of a single substitution within RT: W153L. A recombinant virus encoding the RT W153L was highly resistant to compound A (fold change, 160). W153 is a highly conserved residue in HIV RT and has not been previously associated with drug resistance. In summary, a novel NcRTI series with optimized antiviral activity, minimal cross-resistance to existing RT inhibitor classes, and a distinct resistance profile has been discovered. These results further establish NcRTIs as an emerging class of antiretroviral agents.
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41
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James CA, DeRoy P, Duplessis M, Edwards PJ, Halmos T, Minville J, Morency L, Morin S, Simoneau B, Tremblay M, Bethell R, Cordingley M, Duan J, Lamorte L, Pelletier A, Rajotte D, Salois P, Tremblay S, Sturino CF. Nucleotide competing reverse transcriptase inhibitors: discovery of a series of non-basic benzofurano[3,2-d]pyrimidin-2-one derived inhibitors. Bioorg Med Chem Lett 2013; 23:2781-6. [PMID: 23545107 DOI: 10.1016/j.bmcl.2013.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/24/2013] [Accepted: 02/01/2013] [Indexed: 10/27/2022]
Abstract
A HTS screen led to the identification of a benzofurano[3,2-d]pyrimidin-2-one core structure which upon further optimization resulted in 1 as a potent HIV-1 nucleotide competing reverse transcriptase inhibitor (NcRTI). Investigation of the SAR at N-1 allowed significant improvements in potency and when combined with the incorporation of heterocycles at C-8 resulted in potent analogues not requiring a basic amine to achieve antiviral activity. Additional modifications at N-1 resulted in 33 which demonstrated excellent antiviral potency and improved physicochemical properties.
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Affiliation(s)
- Clint A James
- Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5.
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42
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Pirhadi S, Ghasemi JB. Pharmacophore Identification, Molecular Docking, Virtual Screening, and In Silico ADME Studies of Non-Nucleoside Reverse Transcriptase Inhibitors. Mol Inform 2012; 31:856-66. [PMID: 27476739 DOI: 10.1002/minf.201200018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 11/19/2012] [Indexed: 01/26/2023]
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) have gained a definitive place due to their unique antiviral potency, high specificity and low toxicity in antiretroviral combination therapies used to treat HIV. In this study, chemical feature based pharmacophore models of different classes of NNRT inhibitors of HIV-1 have been developed. The best HypoRefine pharmacophore model, Hypo 1, which has the best correlation coefficient (0.95) and the lowest RMS (0.97), contains two hydrogen bond acceptors, one hydrophobic and one ring aromatic feature, as well as four excluded volumes. Hypo 1 was further validated by test set and Fischer validation method. The best pharmacophore model was then utilized as a 3D search query to perform a virtual screening to retrieve potential inhibitors. The hit compounds were subsequently subjected to filtering by Lipinski's rule of five and docking studies by Libdock and Gold methods to refine the retrieved hits. Finally, 7 top ranked compounds based on Gold score fitness function were subjected to in silico ADME studies to investigate for compliance with the standard ranges.
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Affiliation(s)
- Somayeh Pirhadi
- Chemistry Department, Faculty of Sciences, K. N. Toosi University of Technology, Tehran, Iran fax: +98-21-22853650; tel: +98-21-22850266
| | - Jahan B Ghasemi
- Chemistry Department, Faculty of Sciences, K. N. Toosi University of Technology, Tehran, Iran fax: +98-21-22853650; tel: +98-21-22850266.
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43
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Christen MT, Menon L, Myshakina NA, Ahn J, Parniak MA, Ishima R. Structural basis of the allosteric inhibitor interaction on the HIV-1 reverse transcriptase RNase H domain. Chem Biol Drug Des 2012; 80:706-16. [PMID: 22846652 PMCID: PMC3465473 DOI: 10.1111/cbdd.12010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
HIV-1 reverse transcriptase (RT) has been an attractive target for the development of antiretroviral agents. Although this enzyme is bi-functional, having both DNA polymerase and ribonuclease H (RNH) activities, there is no clinically approved inhibitor of the RNH activity. Here, we characterize the structural basis and molecular interaction of an allosteric site inhibitor, BHMP07, with the wild-type (WT) RNH fragment. Solution NMR experiments for inhibitor titration on WT RNH showed relatively wide chemical shift perturbations, suggesting a long-range conformational effect on the inhibitor interaction. Comparisons of the inhibitor-induced NMR chemical shift changes of RNH with those of RNH dimer, in the presence and absence of Mg(2+) , were performed to determine and verify the interaction site. The NMR results, with assistance of molecular docking, indicate that BHMP07 preferentially binds to a site that is located between the RNH active site and the region encompassing helices B and D (the 'substrate-handle region'). The interaction site is consistent with the previous proposed site, identified using a chimeric RNH (p15-EC) [Gong et al. (2011) Chem Biol Drug Des 77, 39-47], but with slight differences that reflect the characteristics of the amino acid sequences in p15-EC compared to the WT RNH.
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Affiliation(s)
- Martin T. Christen
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA-15260
| | - Lakshmi Menon
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA-15260
| | - Nataliya A. Myshakina
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA-15260
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA-15260
| | - Michael A. Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA-15260
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA-15260
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44
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Abstract
Antibody-based therapeutics have been successfully used for the treatment of various diseases and as research tools. Several well characterized, broadly neutralizing monoclonal antibodies (bnmAbs) targeting HIV-1 envelope glycoproteins or related host cell surface proteins show sterilizing protection of animals, but they are not effective when used for therapy of an established infection in humans. Recently, a number of novel bnmAbs, engineered antibody domains (eAds), and multifunctional fusion proteins have been reported which exhibit exceptionally potent and broad neutralizing activity against a wide range of HIV-1 isolates from diverse genetic subtypes. eAds could be more effective in vivo than conventional full-size antibodies generated by the human immune system. Because of their small size (12∼15 kD), they can better access sterically restricted epitopes and penetrate densely packed tissue where HIV-1 replicates than the larger full-size antibodies. HIV-1 possesses a number of mechanisms to escape neutralization by full-size antibodies but could be less likely to develop resistance to eAds. Here, we review the in vitro and in vivo antiviral efficacies of existing HIV-1 bnmAbs, summarize the development of eAds and multispecific fusion proteins as novel types of HIV-1 inhibitors, and discuss possible strategies to generate more potent antibody-based candidate therapeutics against HIV-1, including some that could be used to eradicate the virus.
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Affiliation(s)
- Rui Gong
- Protein Interactions Group, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, MD 21702-1201, USA.
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45
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Virological and molecular characterization of a simian human immunodeficiency virus (SHIV) encoding the envelope and reverse transcriptase genes from HIV-1. Virology 2012; 432:173-83. [PMID: 22769870 DOI: 10.1016/j.virol.2012.05.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/04/2012] [Accepted: 05/31/2012] [Indexed: 11/24/2022]
Abstract
Simian-human immunodeficiency virus encoding both reverse transcriptase (RT) and envelope genes of HIV-1 (RT Env SHIV) is important for evaluating biomedical prevention modalities for HIV/AIDS. We describe virological characterization of a clade B RT Env SHIV following infection of macaques via multiple routes. In vivo passage of the RT Env SHIV through Indian rhesus macaque enhanced infectivity. Expanded virus had minimal envelope heterogeneity and was inhibited by NNRTIs and CCR5 antagonists. Infection of macaques with RT Env SHIV via mucosal or intravenous routes resulted in stable infection accompanied by peak plasma viremia of approximately 5×10(6) copies/ml that was controlled beyond set point. Molecular homogeneity of the virus was maintained following in vivo passage. Inhibition of RT Env SHIV by RT and entry inhibitors and ease of in vivo transmission make it a useful model for testing the efficacy of combinations of entry and RT inhibitors in nonhuman primates.
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Reynolds C, de Koning CB, Pelly SC, van Otterlo WAL, Bode ML. In search of a treatment for HIV--current therapies and the role of non-nucleoside reverse transcriptase inhibitors (NNRTIs). Chem Soc Rev 2012; 41:4657-70. [PMID: 22618809 DOI: 10.1039/c2cs35058k] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The human immunodeficiency virus (HIV) causes AIDS (acquired immune deficiency syndrome), a disease in which the immune system progressively deteriorates, making sufferers vulnerable to all manner of opportunistic infections. Currently, world-wide there are estimated to be 34 million people living with HIV, with the vast majority of these living in sub-Saharan Africa. Therefore, an important research focus is development of new drugs that can be used in the treatment of HIV/AIDS. This review gives an overview of the disease and addresses the drugs currently used for treatment, with specific emphasis on new developments within the class of allosteric non-nucleoside reverse transcriptase inhibitors (NNRTIs).
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Affiliation(s)
- Chevonne Reynolds
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Private Bag 3, PO WITS, 2050, South Africa
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Distinto S, Esposito F, Kirchmair J, Cardia MC, Gaspari M, Maccioni E, Alcaro S, Markt P, Wolber G, Zinzula L, Tramontano E. Identification of HIV-1 reverse transcriptase dual inhibitors by a combined shape-, 2D-fingerprint- and pharmacophore-based virtual screening approach. Eur J Med Chem 2012; 50:216-29. [PMID: 22361685 DOI: 10.1016/j.ejmech.2012.01.056] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 12/26/2011] [Accepted: 01/27/2012] [Indexed: 01/23/2023]
Abstract
We report the first application of ligand-based virtual screening (VS) methods for discovering new compounds able to inhibit both human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT)-associated functions, DNA polymerase and ribonuclease H (RNase H) activities. The overall VS campaign consisted of two consecutive screening processes. In the first, the VS platform Rapid Overlay of Chemical Structures (ROCS) was used to perform in silico shape-based similarity screening on the NCI compounds database in which a hydrazone derivative, previously shown to inhibit the HIV-1 RT, was chosen. As a result, 34 hit molecules were selected and assayed on both RT-associated functions. In the second, the 4 most potent RT inhibitors identified were selected as queries for parallel VS performed by combining shape-based, 2D-fingerprint and 3D-pharmacophore VS methods. Overall, a set of molecules characterized by new different scaffolds were identified as novel inhibitors of both HIV-1 RT-associated activities in the low micromolar range.
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Affiliation(s)
- Simona Distinto
- Dipartimento di Scienze della Salute, Università degli Studi Magna Grecia di Catanzaro, Campus Salvatore Venuta, 88100, Catanzaro, Italy
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Bollini M, Domaoal RA, Thakur VV, Gallardo-Macias R, Spasov KA, Anderson KS, Jorgensen WL. Computationally-guided optimization of a docking hit to yield catechol diethers as potent anti-HIV agents. J Med Chem 2011; 54:8582-91. [PMID: 22081993 DOI: 10.1021/jm201134m] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A 5-μM docking hit has been optimized to an extraordinarily potent (55 pM) non-nucleoside inhibitor of HIV reverse transcriptase. Use of free energy perturbation (FEP) calculations to predict relative free energies of binding aided the optimizations by identifying optimal substitution patterns for phenyl rings and a linker. The most potent resultant catechol diethers feature terminal uracil and cyanovinylphenyl groups. A halogen bond with Pro95 likely contributes to the extreme potency of compound 42. In addition, several examples are provided illustrating failures of attempted grafting of a substructure from a very active compound onto a seemingly related scaffold to improve its activity.
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Affiliation(s)
- Mariela Bollini
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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Cheng Y, Redinbo MR. Activation of the human nuclear xenobiotic receptor PXR by the reverse transcriptase-targeted anti-HIV drug PNU-142721. Protein Sci 2011; 20:1713-9. [PMID: 21805522 PMCID: PMC3218365 DOI: 10.1002/pro.706] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 06/06/2011] [Accepted: 07/09/2011] [Indexed: 01/07/2023]
Abstract
The human pregnane X receptor (PXR) is a member of the nuclear receptor superfamily of ligand-regulated transcription factors. PXR responds to a structurally diverse variety of endogenous and xenobiotic compounds, and coordinates the expression of genes central to the metabolism and excretion of potentially harmful chemicals, including human therapeutics. The reverse transcriptase inhibitor PNU-142721 has been designed to treat human immunodeficiency virus (HIV) infection. Although this compound has anti-HIV activity, it was established using cell-based assays that PNU-142721 is an efficacious PXR agonist. We present here the 2.8 Å resolution crystal structure of the human PXR ligand-binding domain in complex with PNU-142721. PXR employs one hydrogen bond and fourteen van der Waals contacts to interact with the ligand, but allows two loops adjacent to the ligand-binding pocket to remain disordered in the structure. These observations highlight the role structural flexibility plays in PXR's promiscuous responses to xenobiotics. The crystal structure also explains why PNU-173575, a thiomethyl metabolite of PNU-142721, exhibits enhanced PXR activation relative to the unmodified compound and why PNU-142721 can also activate rat PXR. Taken together, the results presented here elucidate the structural basis for PXR activation by PNU-142721 and related chemicals.
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Affiliation(s)
- Yuan Cheng
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel HillChapel Hill, North Carolina 27599,Program in Molecular & Cellular Biophysics, University of North Carolina at Chapel HillChapel Hill, North Carolina 27599
| | - Matthew R Redinbo
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel HillChapel Hill, North Carolina 27599,Program in Molecular & Cellular Biophysics, University of North Carolina at Chapel HillChapel Hill, North Carolina 27599,Department of Chemistry, University of North Carolina at Chapel HillChapel Hill, North Carolina 27599,Department of Microbiology & Immunology, University of North Carolina at Chapel HillChapel Hill, North Carolina 27599,*Correspondence to: Matthew R. Redinbo, Department of Chemistry, Campus Box # 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290. E-mail:
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Abstract
In recent decades, nucleosides analogs have been the cornerstone in the treatment of various diseases, such as AIDS, herpes and hepatitis. More than 40 modified nucleosides are officially approved by the US FDA and represent the major compound class for inhibition of viral replication. By comparison with traditional conditions, microwave irradiation offers a powerful tool that can increase yields and decrease reaction time, with simple manipulation and an environmentally friendly way. Here, we report the latest progress in nucleoside synthesis using microwave irradiation.
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