1
|
Chen C, Lei Q, Geng W, Wang D, Gan X. Discovery of Novel Pyridazine Herbicides Targeting Phytoene Desaturase with Scaffold Hopping. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12425-12433. [PMID: 38781442 DOI: 10.1021/acs.jafc.3c09350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Phytoene desaturase (PDS) is a critical functional enzyme in blocking ζ-carotene biosynthesis and is one of the bleaching herbicide targets. At present, norflurazon (NRF) is the only commercial pyridazine herbicide targeting PDS. Therefore, developing new and diverse pyridazine herbicides targeting PDS is urgently required. In this study, diflufenican (BF) was used as the lead compound, and a scaffold-hopping strategy was employed to design and synthesize some pyridazine derivatives based on the action mode of BF and PDS. The preemergence herbicidal activity tests revealed that compound 6-chloro-N-(2,4-difluorophenyl)-3-(3-(trifluoromethyl)phenoxy)pyridazine-4-carboxamide (B1) with 2,4-diF substitution in the benzeneamino ring showed 100% inhibition rates against the roots and stems of Echinochloa crus-galli and Portulaca oleracea at 100 μg/mL, superior to the inhibition rates of BF. Meanwhile, compound B1 demonstrated excellent postemergence herbicidal activity against broadleaf weeds, which was similar to that of BF (inhibition rate of 100%) but superior to that of NRF. This indicated that 6-Cl in the pyridazine ring is the key group for postemergence herbicidal activity. In addition, compound B1 could induce downregulation of PDS gene expression, 15-cis-phytoene accumulation, and Y(II) deficiency and prevent photosynthesis. Therefore, B1 can be considered as a promising candidate for developing high-efficiency PDS inhibitors.
Collapse
Affiliation(s)
- Chao Chen
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
- State Key Laboratory of Functions and Applications of Medicinal Plants, Natural Products Research Center of Guizhou Province, Guizhou Medical University, Guiyang 550014, PR China
| | - Qiong Lei
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Wang Geng
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Daoping Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Natural Products Research Center of Guizhou Province, Guizhou Medical University, Guiyang 550014, PR China
| | - Xiuhai Gan
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| |
Collapse
|
2
|
Hoving M, Haaksma JJ, Stoppel A, Chronc L, Hoffmann J, Beil SB. Triplet Energy Transfer Mechanism in Copper Photocatalytic N- and O-Methylation. Chemistry 2024; 30:e202400560. [PMID: 38363220 DOI: 10.1002/chem.202400560] [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: 02/12/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/17/2024]
Abstract
Methylation reactions are chemically simple but challenging to perform under mild and non-toxic conditions. A photochemical energy transfer strategy was merged with copper catalysis to enable fast reaction times of minutes and broad applicability to N-heterocycles, (hetero-)aromatic carboxylic acids, and drug-like molecules in high yields and good functional group tolerance. Detailed mechanistic investigations, using kinetic analysis, aprotic MS, UV/Vis, and luminescence quenching experiments revealed a triplet-triplet energy transfer mechanism between hypervalent iodine(III) reagents and readily available photosensitizers.
Collapse
Affiliation(s)
- Martijn Hoving
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Jacob-Jan Haaksma
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Anne Stoppel
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Lukas Chronc
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Jonas Hoffmann
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Sebastian B Beil
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
| |
Collapse
|
3
|
Hao M, Imamichi T, Chang W. Modeling and Analysis of HIV-1 Pol Polyprotein as a Case Study for Predicting Large Polyprotein Structures. Int J Mol Sci 2024; 25:1809. [PMID: 38339086 PMCID: PMC10855158 DOI: 10.3390/ijms25031809] [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: 12/29/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) is caused by human immunodeficiency virus (HIV). HIV protease, reverse transcriptase, and integrase are targets of current drugs to treat the disease. However, anti-viral drug-resistant strains have emerged quickly due to the high mutation rate of the virus, leading to the demand for the development of new drugs. One attractive target is Gag-Pol polyprotein, which plays a key role in the life cycle of HIV. Recently, we found that a combination of M50I and V151I mutations in HIV-1 integrase can suppress virus release and inhibit the initiation of Gag-Pol autoprocessing and maturation without interfering with the dimerization of Gag-Pol. Additional mutations in integrase or RNase H domain in reverse transcriptase can compensate for the defect. However, the molecular mechanism is unknown. There is no tertiary structure of the full-length HIV-1 Pol protein available for further study. Therefore, we developed a workflow to predict the tertiary structure of HIV-1 NL4.3 Pol polyprotein. The modeled structure has comparable quality compared with the recently published partial HIV-1 Pol structure (PDB ID: 7SJX). Our HIV-1 NL4.3 Pol dimer model is the first full-length Pol tertiary structure. It can provide a structural platform for studying the autoprocessing mechanism of HIV-1 Pol and for developing new potent drugs. Moreover, the workflow can be used to predict other large protein structures that cannot be resolved via conventional experimental methods.
Collapse
Affiliation(s)
| | | | - Weizhong Chang
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (M.H.); (T.I.)
| |
Collapse
|
4
|
Han S, Lu Y. Fluorine in anti-HIV drugs approved by FDA from 1981 to 2023. Eur J Med Chem 2023; 258:115586. [PMID: 37393791 DOI: 10.1016/j.ejmech.2023.115586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 07/04/2023]
Abstract
Human immunodeficiency virus (HIV) is the etiological agent of acquired immunodeficiency syndrome (AIDS). Nowadays, FDA has approved over thirty antiretroviral drugs grouped in six categories. Interestingly, one-third of these drugs contain different number of fluorine atoms. The introduction of fluorine to obtain drug-like compounds is a well-accepted strategy in medicinal chemistry. In this review, we summarized 11 fluorine-containing anti-HIV drugs, focusing on their efficacy, resistance, safety, and specific roles of fluorine in the development of each drug. These examples may be of help for the discovery of new drug candidates bearing fluorine in their structures.
Collapse
Affiliation(s)
- Sheng Han
- School of Medicine, Shanghai University, Shanghai, China.
| | - Yiming Lu
- School of Medicine, Shanghai University, Shanghai, China; Department of Critical Care Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.
| |
Collapse
|
5
|
Ding C, Xia M, Wang F, Lei W, Ni Y. The sensitive detection and mechanism of Fe-3,5-dimethyl pyrazole fluorescent sensor to diethylenetriamine pentamethylene phosphonic acid: Experimental study and quantum chemical calculation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 281:121623. [PMID: 35872426 DOI: 10.1016/j.saa.2022.121623] [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: 04/30/2022] [Revised: 06/26/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
Diethylenetriamine pentamethylene phosphonic acid (DTPMP) is one of the most commonly used amino organic phosphonates. The existing methods for DTPMP detection are complicated, time-consuming, and cannot detect trace DTPMP in the natural environment. In the present work, the Fe-based 3,5-dimethyl pyrazole fluorescent sensor (Fe-DP) was constructed. The addition of Fe3+ to DP solution can greatly decrease the fluorescent intensity of DP, while the addition of different concentrations of DTPMP will restore the fluorescence intensity of DP to different degrees, to achieve quantitative detection of DTPMP, and the detection limit (LOD) of DTPMP was lower as 0.105 μΜ. The Fe-DP fluorescent sensor exhibited excellent anti-interference ability and good stability. Moreover, the fluorescence quenching mechanism of DP by Fe3+ was revealed by UV absorption spectrum and Multiwfn wavefunction analysis based on density function theory (DFT). The results revealed that the excitation of DP belonged to local excitation, in which the electrons were donated primarily by the N atom with double bond and redistributed within the pyrazole ring.The fluorescence quenching of adding Fe3+ was not caused by resonance energy transfer or charge transfer, which did not belong to dynamic quenching, but due to the ground state complex formed by the coordination of Fe3+ and the double bond N atom on the DP pyrazole ring.
Collapse
Affiliation(s)
- Chao Ding
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Mingzhu Xia
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Fengyun Wang
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Wu Lei
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Yue Ni
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| |
Collapse
|
6
|
Karati D, Mahadik KR, Kumar D. Pyrazole Scaffolds: Centrality in Anti-Inflammatory and Antiviral Drug Design. Med Chem 2022; 18:1060-1072. [PMID: 35410619 DOI: 10.2174/1573406418666220410181827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/06/2021] [Accepted: 02/01/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pyrazole is a component of a diversity of bioactive heterocyclic congeners with a broad-spectrum range of biological and pharmacological uses. Designing novel pyrazole and its analogues, revealing new routes for synthesizing this nucleus, exploring various potencies of that heterocycles, and looking for possible applications of pyrazoles are all becoming more important due to their numerous potential applications. OBJECTIVES Pyrazole scaffolds have been proven to be successful as anti-viral and anti-inflammatory therapeutic against multiple targets like HSV-1, NNRTI, H1N1, CoX-1, and CoX-2. Due to this miscellany in the biotic area, this moiety has engrossed the consideration of many scientists to study chemistry and pharmacological profile. RESULTS The review encompasses pyrazole having various scaffolds with multiple biological activities and attempts have also been made to correlate their structure-activity relationship. Multiple pyrazole correspondents have been synthesized as lead molecules and performed valuation for their actions. CONCLUSION The incorporation of pyrazole with other pharmacophores in the molecule might lead to novel potent therapeutic agents that will further help in designing potent lead molecules.
Collapse
Affiliation(s)
- Dipanjan Karati
- Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Erandwane, Pune- 411038, Maharashtra, India
| | - Kakasaheb Ramoo Mahadik
- Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Erandwane, Pune- 411038, Maharashtra, India
| | - Dileep Kumar
- Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Erandwane, Pune- 411038, Maharashtra, India
| |
Collapse
|
7
|
Wang Z, Cherukupalli S, Xie M, Wang W, Jiang X, Jia R, Pannecouque C, De Clercq E, Kang D, Zhan P, Liu X. Contemporary Medicinal Chemistry Strategies for the Discovery and Development of Novel HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors. J Med Chem 2022; 65:3729-3757. [PMID: 35175760 DOI: 10.1021/acs.jmedchem.1c01758] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) are a major component of the highly active anti-retroviral therapy (HAART) regimen. However, the occurrence of drug-resistant strains and adverse reactions after long-term usage have inevitably compromised the clinical application of NNRTIs. Therefore, the development of novel inhibitors with distinct anti-resistance profiles and better pharmacological properties is still an enormous challenge. Herein, we summarize state-of-the-art medicinal chemistry strategies for the discovery of potent NNRTIs, such as structure-based design strategies, contemporary computer-aided drug design, covalent-binding strategies, and the application of multi-target-directed ligands. The strategies described here will facilitate the identification of promising HIV-1 NNRTIs.
Collapse
Affiliation(s)
- Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Minghui Xie
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Wenbo Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Ruifang Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| |
Collapse
|
8
|
Leveraging nonstructural data to predict structures and affinities of protein-ligand complexes. Proc Natl Acad Sci U S A 2021; 118:2112621118. [PMID: 34921117 PMCID: PMC8713799 DOI: 10.1073/pnas.2112621118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2021] [Indexed: 01/02/2023] Open
Abstract
Structure-based drug design depends on the ability to predict both the three-dimensional structures of candidate molecules bound to their targets and the associated binding affinities. We demonstrate that one can substantially improve the accuracy of these predictions using easily obtained data about completely different molecules that bind to the same target without requiring any target-bound structures of these molecules. The approach we developed to integrate physical and data-driven modeling may find a variety of applications in the rapidly growing field of artificial intelligence for drug discovery. Over the past five decades, tremendous effort has been devoted to computational methods for predicting properties of ligands—i.e., molecules that bind macromolecular targets. Such methods, which are critical to rational drug design, fall into two categories: physics-based methods, which directly model ligand interactions with the target given the target’s three-dimensional (3D) structure, and ligand-based methods, which predict ligand properties given experimental measurements for similar ligands. Here, we present a rigorous statistical framework to combine these two sources of information. We develop a method to predict a ligand’s pose—the 3D structure of the ligand bound to its target—that leverages a widely available source of information: a list of other ligands that are known to bind the same target but for which no 3D structure is available. This combination of physics-based and ligand-based modeling improves pose prediction accuracy across all major families of drug targets. Using the same framework, we develop a method for virtual screening of drug candidates, which outperforms standard physics-based and ligand-based virtual screening methods. Our results suggest broad opportunities to improve prediction of various ligand properties by combining diverse sources of information through customized machine-learning approaches.
Collapse
|
9
|
Oukhrib R, Abdellaoui Y, Berisha A, Abou Oualid H, Halili J, Jusufi K, Ait El Had M, Bourzi H, El Issami S, Asmary FA, Parmar VS, Len C. DFT, Monte Carlo and molecular dynamics simulations for the prediction of corrosion inhibition efficiency of novel pyrazolylnucleosides on Cu(111) surface in acidic media. Sci Rep 2021; 11:3771. [PMID: 33580143 PMCID: PMC7881149 DOI: 10.1038/s41598-021-82927-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
Five novel pyrazolylnucleosides have been evaluated theoretically for their corrosion inhibition efficiency on the Cu(111) surface in acidic media. DFT calculations were carried out to exhibit the intrinsic properties such as lowest unoccupied (ELUMO) and highest occupied (EHOMO) molecular orbital energies, as well as energy gap (∆E), chemical hardness (η), chemical softness (σ), electronegativity (χ), electrophilicity (ω) and nucleophilicity (ε). The theoretical FT-IR spectra were recorded to indicate the presence of the specific bonds in the studied molecules. The surface interactions between the inhibitor molecules and the metal surface were investigated using molecular dynamics simulations and Monte Carlo (MC) simulations. As a result, we have found that the inhibitor pyrazolylnucleosides 5a-e have strong interactions with Cu(111) surface, and therefore have excellent predictive inhibition power against copper corrosion.
Collapse
Affiliation(s)
- Rachid Oukhrib
- Apply Chemistry-Physic Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Youness Abdellaoui
- Faculty of Engineering, Environmental Engineering Department, Autonomous University of Yucatan, Mérida, Mexico
| | - Avni Berisha
- Department of Chemistry, Faculty of Natural and Mathematics Science, University of Prishtina, 10000, Pristina, Kosovo
| | - Hicham Abou Oualid
- Laboratory of Biotechnology, Materials and Environment, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
- Green Enenrgy Park, IRESEN, Ben Guerir, Morocco
| | - Jeton Halili
- Department of Chemistry, Faculty of Natural and Mathematics Science, University of Prishtina, 10000, Pristina, Kosovo
| | - Kaltrina Jusufi
- Department of Chemistry, Faculty of Natural and Mathematics Science, University of Prishtina, 10000, Pristina, Kosovo
| | - Mustapha Ait El Had
- Laboratoire de Chimie Biomoléculaire, substances naturelles et Réactivité (URAC 16), Faculté des Sciences Semlalia, Université Cadi Ayyad, B.P. 2390, Marrakech, Morocco
- Laboratoire de Chimie Bioorganique et Macromoléculaire, Faculty of Sciences and Technics Marrakech (FSTMG), Université Cadi Ayyad, Marrakech, Morocco
| | - Hassan Bourzi
- Apply Chemistry-Physic Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Souad El Issami
- Apply Chemistry-Physic Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Fatmah Ali Asmary
- Chemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Virinder S Parmar
- Department of Chemistry and Environmental Science, Medgar Evers College, The City University of New York, 1638 Bedford Avenue, Brooklyn, NY, 11225, USA
| | - Christophe Len
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences, 11 rue Pierre et Marie Curie, 75005, Paris, France.
| |
Collapse
|
10
|
Synthesis, biological activity and POM/DFT/docking analyses of annulated pyrano[2,3-d]pyrimidine derivatives: Identification of antibacterial and antitumor pharmacophore sites. Bioorg Chem 2020; 106:104480. [PMID: 33279245 DOI: 10.1016/j.bioorg.2020.104480] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/27/2020] [Accepted: 11/15/2020] [Indexed: 12/17/2022]
Abstract
New annulated pyrano[2,3-d]pyrimidine derivatives were synthesized with hydroxyl, methoxy, bromine, nitrile and nitro substituents on its skeleton. The correlated electronic effect of substituents on the magnitude of antibacterial activity was noted. The electron donating substituents (namely; 4-OH, 4-OCH3, 4-Br) and electron withdrawing substituents (4-NO2) on phenyl ring in the pyrano[2,3-d]pyrimidine skeleton exerted different influence on its antimicrobial activity against some Gram-positive and Gram-negative bacteria such as Pseudomonas aureus, E. coli, Staphylococcus aureus, Klebsiella pneumonia and Bacillus cereus. All the pyrano[2,3-d]pyrimidines were characterized by spectroscopic analyses. Antibacterial screening revealed that the presence of heteroaryl, cyano and amino groups on pyrano[2,3-d]pyrimidine skeleton increases its penetrating power on the bacterial cell wall so that the product becomes more biologically active. So the the nature of electron withdrawing or electro-donnor Impact of substituents should be taken in consideration in drug design. Hydrolysis of -CRN to amide restored vital Intramolecular interaction like ortho-nitrophenyl and ONOδ-…NHδ+/amide link, offering a crucial template for antibacterial NH, HO-pharmacophore sites, which ultimately elevated innate antimicrobial profiles. POM combinatorial analysis of tangible electronic contributions due to armed annulated pyrano[2,3-d]pyrimidines concluded their broad antimicrobial activity and viable/prominent drug score index through perspective parameters particularly: inter atomic distance/linkers, steric, electronic, polar parameters, and with a different polarising effect of electron donating/withdrawing environments of substituents. Furthermore, an anti-Kinase pharmacophore site (OCNHCO) was evaluated in continuation of the POM investigations. All synthesized products verified fewer side effects than standard streptomycin, but facile implication in selective cancer media (viz. breast or leucemia still needs to be screened).
Collapse
|
11
|
Melo R, Lemos A, Preto AJ, Bueschbell B, Matos-Filipe P, Barreto C, Almeida JG, Silva RDM, Correia JDG, Moreira IS. An Overview of Antiretroviral Agents for Treating HIV Infection in Paediatric Population. Curr Med Chem 2020; 27:760-794. [PMID: 30182840 DOI: 10.2174/0929867325666180904123549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/11/2018] [Accepted: 07/11/2018] [Indexed: 12/19/2022]
Abstract
Paediatric Acquired ImmunoDeficiency Syndrome (AIDS) is a life-threatening and infectious disease in which the Human Immunodeficiency Virus (HIV) is mainly transmitted through Mother-To- Child Transmission (MTCT) during pregnancy, labour and delivery, or breastfeeding. This review provides an overview of the distinct therapeutic alternatives to abolish the systemic viral replication in paediatric HIV-1 infection. Numerous classes of antiretroviral agents have emerged as therapeutic tools for downregulation of different steps in the HIV replication process. These classes encompass Non- Nucleoside Analogue Reverse Transcriptase Inhibitors (NNRTIs), Nucleoside/Nucleotide Analogue Reverse Transcriptase Inhibitors (NRTIs/NtRTIs), INtegrase Inhibitors (INIs), Protease Inhibitors (PIs), and Entry Inhibitors (EIs). Co-administration of certain antiretroviral drugs with Pharmacokinetic Enhancers (PEs) may boost the effectiveness of the primary therapeutic agent. The combination of multiple antiretroviral drug regimens (Highly Active AntiRetroviral Therapy - HAART) is currently the standard therapeutic approach for HIV infection. So far, the use of HAART offers the best opportunity for prolonged and maximal viral suppression, and preservation of the immune system upon HIV infection. Still, the frequent administration of high doses of multiple drugs, their inefficient ability to reach the viral reservoirs in adequate doses, the development of drug resistance, and the lack of patient compliance compromise the complete HIV elimination. The development of nanotechnology-based drug delivery systems may enable targeted delivery of antiretroviral agents to inaccessible viral reservoir sites at therapeutic concentrations. In addition, the application of Computer-Aided Drug Design (CADD) approaches has provided valuable tools for the development of anti-HIV drug candidates with favourable pharmacodynamics and pharmacokinetic properties.
Collapse
Affiliation(s)
- Rita Melo
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal.,CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Agostinho Lemos
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal.,GIGA Cyclotron Research Centre In Vivo Imaging, University of Liège, Liège 4000, Belgium
| | - António J Preto
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Beatriz Bueschbell
- Pharmaceutical Chemistry I, PharmaCenter, Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | - Pedro Matos-Filipe
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Carlos Barreto
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - José G Almeida
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Rúben D M Silva
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal
| | - João D G Correia
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal
| | - Irina S Moreira
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal.,Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht 3584CH, Netherland
| |
Collapse
|
12
|
Zhao X, Chen H, Xing S, Yuan W, Wu L, Chen X, Zhan CG. Regioselective synthesis of 2- and 4-diarylpyridine ethers and their inhibitory activities against phosphodiesterase 4B. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.06.086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
13
|
Namasivayam V, Vanangamudi M, Kramer VG, Kurup S, Zhan P, Liu X, Kongsted J, Byrareddy SN. The Journey of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) from Lab to Clinic. J Med Chem 2018; 62:4851-4883. [PMID: 30516990 DOI: 10.1021/acs.jmedchem.8b00843] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human immunodeficiency virus (HIV) infection is now pandemic. Targeting HIV-1 reverse transcriptase (HIV-1 RT) has been considered as one of the most successful targets for the development of anti-HIV treatment. Among the HIV-1 RT inhibitors, 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. Until now, >50 structurally diverse classes of compounds have been reported as NNRTIs. Among them, six NNRTIs were approved for HIV-1 treatment, namely, nevirapine (NVP), delavirdine (DLV), efavirenz (EFV), etravirine (ETR), rilpivirine (RPV), and doravirine (DOR). In this perspective, we focus on the six NNRTIs and lessons learned from their journey through development to clinical studies. It demonstrates the obligatory need of understanding the physicochemical and biological principles (lead optimization), resistance mutations, synthesis, and clinical requirements for drugs.
Collapse
Affiliation(s)
- Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , 53121 Bonn , Germany
| | - Murugesan Vanangamudi
- Department of Medicinal and Pharmaceutical Chemistry , Sree Vidyanikethan College of Pharmacy , Tirupathi , Andhra Pradesh 517102 , India
| | | | - Sonali Kurup
- College of Pharmacy , Roosevelt University , Schaumburg , Illinois 60173 , United States
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , Jinan 250012 , P.R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , Jinan 250012 , P.R. China
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 , Odense M , Denmark
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience , University of Nebraska Medical Center , Omaha 68198-5880 , United States
| |
Collapse
|
14
|
Wang Y, Wang J, Zhong P, Li Y, Lai CC, He Y. Molecular insight into the interaction mechanisms of an annulated pyrazole (DB08446) with HIV-1 RT: a QM and QM/QM′ study. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-018-2239-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
15
|
Savant MM, Ladva KD, Pandit AB. Facile synthesis of highly functionalized novel pyrazolopyridones using oxoketene dithioacetal and their anti-HIV activity. SYNTHETIC COMMUN 2018. [DOI: 10.1080/00397911.2018.1458239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Mahesh M. Savant
- Department of Industrial Chemistry, Shree M. & N. Virani Science College, Rajkot, Gujarat, India
| | - Kartik D. Ladva
- Department of Chemistry, Shree M. & N. Virani Science College, Rajkot, Gujarat, India
| | - Archna B. Pandit
- Department of Chemistry, Shree M. & N. Virani Science College, Rajkot, Gujarat, India
| |
Collapse
|
16
|
Bhat AR, Shalla AH, Dongre RS. Dibutylamine (DBA): A highly efficient catalyst for the synthesis of pyrano[2,3-d]pyrimidine derivatives in aqueous media. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2018. [DOI: 10.1016/j.jtusci.2015.03.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Ajmal R. Bhat
- Department of Chemistry, R.T.M. Nagpur UniversityNagpur 440033India
| | - Aabid H. Shalla
- Islamic University of Science and TechnologyJammu Kashmir 192122India
| | | |
Collapse
|
17
|
Bhat AR, Dongre RS, Shalla AH, Naikoo GA, Ul Hassan I. Computational analysis for antimicrobial active pyrano[2,3-d]pyrimidine derivatives on the basis of theoretical and experimental ground. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.jaubas.2015.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ajmal R. Bhat
- Department of Chemistry, Islamic University of Science and Technology, Jammu and Kashmir 192122, India
| | | | - Aabid H. Shalla
- Department of Chemistry, Islamic University of Science and Technology, Jammu and Kashmir 192122, India
| | - Gowhar A. Naikoo
- Maths and Sciences Unit, College of Arts and Applied Sciences, Dhofar University, Oman
| | - Israr Ul Hassan
- Maths and Sciences Unit, College of Arts and Applied Sciences, Dhofar University, Oman
| |
Collapse
|
18
|
Dongre RS, Meshram JS, Selokar RS, Almalki FA, Hadda TB. Antibacterial activity of synthetic pyrido[2,3- d]pyrimidines armed with nitrile groups: POM analysis and identification of pharmacophore sites of nitriles as important pro-drugs. NEW J CHEM 2018. [DOI: 10.1039/c8nj02081g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A pyrido[2,3-d]pyrimidine series has exhibited inhibitory effects on the growth of bacterial strains.
Collapse
Affiliation(s)
| | | | | | - Faisal A. Almalki
- Department of Pharmaceutical Chemistry
- Faculty of Pharmacy
- Umm Al-Qura University
- Makkah
- Saudi Arabia
| | - Taibi Ben Hadda
- Materials Chemistry Laboratory
- Faculty of Sciences
- University Mohammed Premier
- 60000 Oujda
- Morocco
| |
Collapse
|
19
|
Bhat AR, Naikoo GA, Hassan IU, Dongra RS, Ara T. Ultrasound assisted one pot expeditious synthesis of new pyrido[2,3- d ]pyrimidine analogues using mild and inexpensive 4-dimethylaminopyridine (DMAP) catalyst. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2017. [DOI: 10.1016/j.bjbas.2017.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
|
20
|
Gaman MS, Matyugina ES, Novikov MS, Babkov DA, Solyev PN, Kochetkov SN, Khandazhinskaya AL. New benzophenone phosphonate derivatives. MENDELEEV COMMUNICATIONS 2017. [DOI: 10.1016/j.mencom.2017.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
21
|
Chander S, Wang P, Ashok P, Yang LM, Zheng YT, Sankaranarayanan M. Design, synthesis and anti-HIV-1 RT evaluation of 2-(benzyl(4-chlorophenyl)amino)-1-(piperazin-1-yl)ethanone derivatives. Bioorg Med Chem Lett 2016; 27:61-65. [PMID: 27894873 DOI: 10.1016/j.bmcl.2016.11.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/13/2016] [Accepted: 11/12/2016] [Indexed: 01/25/2023]
Abstract
In this study, using molecular hybridization approach, fourteen novel 2-(benzyl(4-chlorophenyl)amino)-1-(piperazin-1-yl)ethanone derivatives (7a-n) were designed as inhibitor of HIV-1 RT. The binding affinity of the designed compounds with HIV-1 RT as well as their drug-likeness behavior was predicted using in-silico studies. All the designed compounds were synthesized, characterized and in-vitro evaluated for HIV-1 RT inhibitory activity, in which tested compounds displayed significant to weak potency against the selected target. Moreover, best active compounds of the series, 7k and 7m inhibited the activity of RT with IC50 values 14.18 and 12.26μM respectively. Structure Activity Relationship (SAR) studies were also performed in order to predict the influence of substitution pattern on the RT inhibitory potency. Anti-HIV-1 and cytotoxicity studies of best five RT inhibitor (7a, 7d, 7k, 7L and 7m) revealed that, except compound 7d other compounds retained significant anti-HIV-1 potency with good safety index. Best scoring pose of compound 7m was analysed in order to predict its putative binding mode with wild HIV-1 RT.
Collapse
Affiliation(s)
- Subhash Chander
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science, Pilani 333031, Rajasthan, India
| | - Ping Wang
- Laboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, PR China
| | - Penta Ashok
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science, Pilani 333031, Rajasthan, India
| | - Liu-Meng Yang
- Laboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, PR China
| | - Yong-Tang Zheng
- Laboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, PR China.
| | - Murugesan Sankaranarayanan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science, Pilani 333031, Rajasthan, India.
| |
Collapse
|
22
|
Best D, Jean M, van de Weghe P. Modular Synthesis of Arylacetic Acid Esters, Thioesters, and Amides from Aryl Ethers via Rh(II)-Catalyzed Diazo Arylation. J Org Chem 2016; 81:7760-70. [DOI: 10.1021/acs.joc.6b01426] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Daniel Best
- Université de
Rennes 1, UMR CNRS
6226, Institut des Sciences Chimiques de Rennes, Equipe PNSCM, UFR
des Sciences, Biologiques et Pharmaceutiques, 2 Avenue du Prof Leon Bernard, Rennes F-35043 Cedex, France
| | - Mickaël Jean
- Université de
Rennes 1, UMR CNRS
6226, Institut des Sciences Chimiques de Rennes, Equipe PNSCM, UFR
des Sciences, Biologiques et Pharmaceutiques, 2 Avenue du Prof Leon Bernard, Rennes F-35043 Cedex, France
| | - Pierre van de Weghe
- Université de
Rennes 1, UMR CNRS
6226, Institut des Sciences Chimiques de Rennes, Equipe PNSCM, UFR
des Sciences, Biologiques et Pharmaceutiques, 2 Avenue du Prof Leon Bernard, Rennes F-35043 Cedex, France
| |
Collapse
|
23
|
Synthesis, characterization and biological activity of platinum(II) complexes with a tetrapyrazole ligand. Polyhedron 2015. [DOI: 10.1016/j.poly.2015.09.065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
24
|
Meng Q, Liu N, Huang B, Zhan P, Liu X. Novel fluorine-containing DAPY derivatives as potent HIV-1 NNRTIs: a patent evaluation of WO2014072419. Expert Opin Ther Pat 2015; 25:1477-86. [PMID: 26415039 DOI: 10.1517/13543776.2016.1088832] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Diarylpyrimidine (DAPY) derivatives, one family of HIV non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) with superior activities against wild-type (WT) HIV-1 and NNRTI-resistant strains, have attracted much attention in the past decade. A series of DAPY derivatives featuring a fluorine atom on the central ring were reported as novel NNRTIs in the patent WO2014072419. Some compounds exhibited robust potency against both WT and mutant strains, which were approximately equal to or higher than those of the reference drug TMC120. Moreover, it has become evident that fluorinated molecules have a remarkable record in many other potent NNRTIs. Thus, this survey provides a sampling of renowned fluorinated NNRTIs and their mode of action, with an analysis clarifying the functional roles and impact of fluorine substitution on antiviral potency. We envision that fluorinated NNRTIs will play a continuing role in affording anti-HIV drug candidates for therapeutic applications.
Collapse
Affiliation(s)
- Qing Meng
- a Shandong University, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China ,
| | - Na Liu
- a Shandong University, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China ,
| | - Boshi Huang
- a Shandong University, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China ,
| | | | - Xinyong Liu
- a Shandong University, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China ,
| |
Collapse
|
25
|
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]
|
26
|
Wang HX, Wu LL, Wang YM, Zhou ZH. Organocatalyzed asymmetric tandem Michael-cyclization reaction of 4-benzylidene-3-methylpyrazol-5-ones and malononitrile: stereocontrolled construction of pyrano[2,3-c]pyrazole scaffold. RSC Adv 2015. [DOI: 10.1039/c5ra04356e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Stereocontrolled construction of pyrano[2,3-c]pyrazole scaffold has been realized via chiral squaramide catalyzed asymmetric tandem Michael addition/cyclization reaction of 4-benzylidenepyrazol-5(4H)-ones and malononitrile.
Collapse
Affiliation(s)
- H.-X. Wang
- State Key Laboratory of Elemento-Organic Chemistry
- Institute of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
| | - L.-L. Wu
- State Key Laboratory of Elemento-Organic Chemistry
- Institute of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
| | - Y.-M. Wang
- State Key Laboratory of Elemento-Organic Chemistry
- Institute of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
| | - Z.-H. Zhou
- State Key Laboratory of Elemento-Organic Chemistry
- Institute of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
| |
Collapse
|
27
|
Grover J, Kumar V, Sobhia ME, Jachak SM. Synthesis, biological evaluation and docking analysis of 3-methyl-1-phenylchromeno[4,3-c]pyrazol-4(1H)-ones as potential cyclooxygenase-2 (COX-2) inhibitors. Bioorg Med Chem Lett 2014; 24:4638-4642. [PMID: 25219899 DOI: 10.1016/j.bmcl.2014.08.050] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 07/17/2014] [Accepted: 08/21/2014] [Indexed: 10/24/2022]
Abstract
As a part of our continued efforts to discover new COX inhibitors, a series of 3-methyl-1-phenylchromeno[4,3-c]pyrazol-4(1H)-ones were synthesized and evaluated for in vitro COX inhibitory potential. Within this series, seven compounds (3a-d, 3h, 3k and 3q) were identified as potential and selective COX-2 inhibitors (COX-2 IC50's in 1.79-4.35μM range; COX-2 selectivity index (SI)=6.8-16.7 range). Compound 3b emerged as most potent (COX-2 IC50=1.79μM; COX-1 IC50 >30μM) and selective COX-2 inhibitor (SI >16.7). Further, compound 3b displayed superior anti-inflammatory activity (59.86% inhibition of edema at 5h) in comparison to celecoxib (51.44% inhibition of edema at 5h) in carrageenan-induced rat paw edema assay. Structure-activity relationship studies suggested that N-phenyl ring substituted with p-CF3 substituent (3b, 3k and 3q) leads to more selective inhibition of COX-2. To corroborate obtained experimental biological data, molecular docking study was carried out which revealed that compound 3b showed stronger binding interaction with COX-2 as compared to COX-1.
Collapse
Affiliation(s)
- Jagdeep Grover
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar (Mohali) 160062, Punjab, India
| | - Vivek Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar 160062, Punjab, India
| | - M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar 160062, Punjab, India
| | - Sanjay M Jachak
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar (Mohali) 160062, Punjab, India.
| |
Collapse
|
28
|
Grover J, Roy SK, Jachak SM. Potassium Carbonate–Mediated Efficient and Convenient Synthesis of 3-Methyl-1-phenylchromeno[4,3-c]pyrazol-4(1H)-ones. SYNTHETIC COMMUN 2014. [DOI: 10.1080/00397911.2013.879184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Jagdeep Grover
- a Department of Natural Products , National Institute of Pharmaceutical Education and Research , Mohali , Punjab , India
| | - Somendu Kumar Roy
- a Department of Natural Products , National Institute of Pharmaceutical Education and Research , Mohali , Punjab , India
| | - Sanjay Madhukar Jachak
- a Department of Natural Products , National Institute of Pharmaceutical Education and Research , Mohali , Punjab , India
| |
Collapse
|
29
|
Rocha IM, Galvão TLP, Ribeiro da Silva MDMC, Ribeiro da Silva MAV. Thermodynamic Study of Chlorobenzonitrile Isomers: A Survey on the Polymorphism, Pseudosymmetry, and the Chloro···Cyano Interaction. J Phys Chem A 2014; 118:1502-10. [DOI: 10.1021/jp410187q] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Inês M. Rocha
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal
| | - Tiago L. P. Galvão
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal
| | - Maria D. M. C. Ribeiro da Silva
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal
| | - Manuel A. V. Ribeiro da Silva
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal
| |
Collapse
|
30
|
Usach I, Melis V, Peris JE. Non-nucleoside reverse transcriptase inhibitors: a review on pharmacokinetics, pharmacodynamics, safety and tolerability. J Int AIDS Soc 2013; 16:1-14. [PMID: 24008177 PMCID: PMC3764307 DOI: 10.7448/ias.16.1.18567] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 06/21/2013] [Accepted: 07/29/2013] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION Human immunodeficiency virus (HIV) type-1 non-nucleoside and nucleoside reverse transcriptase inhibitors (NNRTIs) are key drugs of highly active antiretroviral therapy (HAART) in the clinical management of acquired immune deficiency syndrome (AIDS)/HIV infection. DISCUSSION First-generation NNRTIs, nevirapine (NVP), delavirdine (DLV) and efavirenz (EFV) are drugs with a low genetic barrier and poor resistance profile, which has led to the development of new generations of NNRTIs. Second-generation NNRTIs, etravirine (ETR) and rilpivirine (RPV) have been approved by the Food and Drug Administration and European Union, and the next generation of drugs is currently being clinically developed. This review describes recent clinical data, pharmacokinetics, metabolism, pharmacodynamics, safety and tolerability of commercialized NNRTIs, including the effects of sex, race and age differences on pharmacokinetics and safety. Moreover, it summarizes the characteristics of next-generation NNRTIs: lersivirine, GSK 2248761, RDEA806, BILR 355 BS, calanolide A, MK-4965, MK-1439 and MK-6186. CONCLUSIONS This review presents a wide description of NNRTIs, providing useful information for researchers interested in this field, both in clinical use and in research.
Collapse
Affiliation(s)
| | | | - José-Esteban Peris
- Department of Pharmacy and Pharmaceutical Technology, Burjassot, Valencia, Spain
| |
Collapse
|
31
|
Hao L, Hong JJ, Zhu J, Zhan ZP. One-Pot Synthesis of Pyrazoles through a Four-Step Cascade Sequence. Chemistry 2013; 19:5715-20. [DOI: 10.1002/chem.201204322] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/18/2013] [Indexed: 11/09/2022]
|
32
|
Novikov MS, Valuev-Elliston VT, Babkov DA, Paramonova MP, Ivanov AV, Gavryushov SA, Khandazhinskaya AL, Kochetkov SN, Pannecouque C, Andrei G, Snoeck R, Balzarini J, Seley-Radtke KL. N1,N3-disubstituted uracils as nonnucleoside inhibitors of HIV-1 reverse transcriptase. Bioorg Med Chem 2013; 21:1150-8. [PMID: 23357038 PMCID: PMC7125863 DOI: 10.1016/j.bmc.2012.12.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/18/2012] [Accepted: 12/25/2012] [Indexed: 11/17/2022]
Abstract
A series of phenyloxyethyl and cinnamyl derivatives of substituted uracils were synthesized and found to exhibit potent activity against HIV-RT and HIV replication in cell culture. In general, the cinnamyl derivatives proved superior to the phenyloxyethyl derivatives, however 1-[2-(4-methylphenoxy)ethyl]-3-(3,5-dimethylbenzyl)uracil (19) exhibited the highest activity (EC(50)=0.27 μM) thus confirming that the 3-benzyluracil fragment in the NNRTI structure can be regarded as a functional analogue of the benzophenone pharmacophore typically found in NNRTIs.
Collapse
Affiliation(s)
- Mikhail S Novikov
- Department of Pharmaceutical & Toxicological Chemistry, Volgograd State Medical University, Pavshikh Bortsov Sq., 1, Volgograd 400131, Russia
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Matyugina ES, Valuev-Elliston VT, Babkov DA, Novikov MS, Ivanov AV, Kochetkov SN, Balzarini J, Seley-Radtke KL, Khandazhinskaya AL. 5′-Nor carbocyclic nucleosides: unusual nonnucleoside inhibitors of HIV-1 reverse transcriptase. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00036b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
34
|
Das O, Malakar T, Mandal A, Paul A, Paine TK. Copper(II) Complexes of 3,4,5-Trisubstituted Pyrazolates: In Situ Formation of Pyrazole Rings from Different Carbon Centers. Chem Asian J 2012; 8:623-9. [DOI: 10.1002/asia.201200858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 10/29/2012] [Indexed: 11/09/2022]
|
35
|
Johnson BC, Pauly GT, Rai G, Patel D, Bauman JD, Baker HL, Das K, Schneider JP, Maloney DJ, Arnold E, Thomas CJ, Hughes SH. A comparison of the ability of rilpivirine (TMC278) and selected analogues to inhibit clinically relevant HIV-1 reverse transcriptase mutants. Retrovirology 2012; 9:99. [PMID: 23217210 PMCID: PMC3549755 DOI: 10.1186/1742-4690-9-99] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 11/12/2012] [Indexed: 11/16/2022] Open
Abstract
Background The recently approved anti-AIDS drug rilpivirine (TMC278, Edurant) is a nonnucleoside inhibitor (NNRTI) that binds to reverse transcriptase (RT) and allosterically blocks the chemical step of DNA synthesis. In contrast to earlier NNRTIs, rilpivirine retains potency against well-characterized, clinically relevant RT mutants. Many structural analogues of rilpivirine are described in the patent literature, but detailed analyses of their antiviral activities have not been published. This work addresses the ability of several of these analogues to inhibit the replication of wild-type (WT) and drug-resistant HIV-1. Results We used a combination of structure activity relationships and X-ray crystallography to examine NNRTIs that are structurally related to rilpivirine to determine their ability to inhibit WT RT and several clinically relevant RT mutants. Several analogues showed broad activity with only modest losses of potency when challenged with drug-resistant viruses. Structural analyses (crystallography or modeling) of several analogues whose potencies were reduced by RT mutations provide insight into why these compounds were less effective. Conclusions Subtle variations between compounds can lead to profound differences in their activities and resistance profiles. Compounds with larger substitutions replacing the pyrimidine and benzonitrile groups of rilpivirine, which reorient pocket residues, tend to lose more activity against the mutants we tested. These results provide a deeper understanding of how rilpivirine and related compounds interact with the NNRTI binding pocket and should facilitate development of novel inhibitors.
Collapse
Affiliation(s)
- Barry C Johnson
- HIV Drug Resistance Program, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Chong P, Sebahar P, Youngman M, Garrido D, Zhang H, Stewart EL, Nolte RT, Wang L, Ferris RG, Edelstein M, Weaver K, Mathis A, Peat A. Rational Design of Potent Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase. J Med Chem 2012; 55:10601-9. [DOI: 10.1021/jm301294g] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pek Chong
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Paul Sebahar
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Michael Youngman
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Dulce Garrido
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Huichang Zhang
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Eugene L. Stewart
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Robert T. Nolte
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Liping Wang
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Robert G. Ferris
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Mark Edelstein
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Kurt Weaver
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Amanda Mathis
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| | - Andrew Peat
- GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States
| |
Collapse
|
37
|
Abstract
Structure-based drug design has become an essential tool for rapid lead discovery and optimization. As available structural information has increased, researchers have become increasingly aware of the importance of protein flexibility for accurate description of the native state. Typical protein-ligand docking efforts still rely on a single rigid receptor, which is an incomplete representation of potential binding conformations of the protein. These rigid docking efforts typically show the best performance rates between 50 and 75%, while fully flexible docking methods can enhance pose prediction up to 80-95%. This review examines the current toolbox for flexible protein-ligand docking and receptor surface mapping. Present limitations and possibilities for future development are discussed.
Collapse
Affiliation(s)
- Katrina W. Lexa
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, MI 48109-1065, USA
| | - Heather A. Carlson
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, MI 48109-1065, USA
| |
Collapse
|
38
|
Gomez R, Jolly S, Williams T, Tucker T, Tynebor R, Vacca J, McGaughey G, Lai MT, Felock P, Munshi V, DeStefano D, Touch S, Miller M, Yan Y, Sanchez R, Liang Y, Paton B, Wan BL, Anthony N. Design and synthesis of pyridone inhibitors of non-nucleoside reverse transcriptase. Bioorg Med Chem Lett 2011; 21:7344-50. [DOI: 10.1016/j.bmcl.2011.10.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/05/2011] [Accepted: 10/07/2011] [Indexed: 11/28/2022]
|
39
|
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.
Collapse
Affiliation(s)
- Mariela Bollini
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | | | | | | | | | | | | |
Collapse
|
40
|
Gomez R, Jolly SJ, Williams T, Vacca JP, Torrent M, McGaughey G, Lai MT, Felock P, Munshi V, DiStefano D, Flynn J, Miller M, Yan Y, Reid J, Sanchez R, Liang Y, Paton B, Wan BL, Anthony N. Design and Synthesis of Conformationally Constrained Inhibitors of Non-Nucleoside Reverse Transcriptase. J Med Chem 2011; 54:7920-33. [PMID: 21985673 DOI: 10.1021/jm2010173] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robert Gomez
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Samson J. Jolly
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Theresa Williams
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Joseph P. Vacca
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Maricel Torrent
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Georgia McGaughey
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Ming-Tain Lai
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Peter Felock
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Vandna Munshi
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Daniel DiStefano
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Jessica Flynn
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Mike Miller
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Youwei Yan
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - John Reid
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Rosa Sanchez
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Yuexia Liang
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Brenda Paton
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Bang-Lin Wan
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| | - Neville Anthony
- Departments of †West Point Discovery Chemistry, ‡Chemistry Modeling and Informatics, §In Vitro Pharmacology, ∥Vaccine Research, ⊥ID Antiviral HIV
Discovery, #Structural
Chemistry, and ∞DMPK Preclinical WP, Merck Research Labs., 770 Sumneytown Pike, P.O. Box 4, West Point,
Pennsylvania 19486-0004, United States
| |
Collapse
|
41
|
Perspective: the potential of pyrazole-based compounds in medicine. Biometals 2011; 25:9-21. [DOI: 10.1007/s10534-011-9496-4] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 09/14/2011] [Indexed: 12/20/2022]
|
42
|
Khodairy A, Abass M. Substituted quinolinones 15*. Preparation and enzymatic activity of some pyrazoloazines linked to the 4-hydroxy-1-methyl- quinolin-2(1H)-one moiety. Chem Heterocycl Compd (N Y) 2011. [DOI: 10.1007/s10593-011-0806-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
43
|
Gu SX, Zhang X, He QQ, Yang LM, Ma XD, Zheng YT, Yang SQ, Chen FE. Synthesis and biological evaluation of naphthyl phenyl ethers (NPEs) as novel nonnucleoside HIV-1 reverse transcriptase inhibitors. Bioorg Med Chem 2011; 19:4220-6. [DOI: 10.1016/j.bmc.2011.05.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 05/26/2011] [Accepted: 05/27/2011] [Indexed: 10/18/2022]
|
44
|
Babinski DJ, Aguilar HR, Still R, Frantz DE. Synthesis of substituted pyrazoles via tandem cross-coupling/electrocyclization of enol triflates and diazoacetates. J Org Chem 2011; 76:5915-23. [PMID: 21682322 DOI: 10.1021/jo201042c] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of 3,4,5-trisubstituted pyrazoles via a tandem catalytic cross-coupling/electrocyclization of enol triflates and diazoacetates is presented. The initial scope of this methodology is demonstrated on a range of differentially substituted acyclic and cyclic enol triflates as well as an elaborated set of diazoacetates to provide the corresponding pyrazoles with a high degree of structural complexity.
Collapse
Affiliation(s)
- David J Babinski
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, USA
| | | | | | | |
Collapse
|
45
|
Zhan P, Chen X, Li D, Fang Z, De Clercq E, Liu X. HIV-1 NNRTIs: structural diversity, pharmacophore similarity, and implications for drug design. Med Res Rev 2011; 33 Suppl 1:E1-72. [PMID: 21523792 DOI: 10.1002/med.20241] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) nowadays represent very potent and most promising anti-AIDS agents that specifically target the HIV-1 reverse transcriptase (RT). However, the effectiveness of NNRTI drugs can be hampered by rapid emergence of drug-resistant viruses and severe side effects upon long-term use. Therefore, there is an urgent need to develop novel, highly potent NNRTIs with broad spectrum antiviral activity and improved pharmacokinetic properties, and more efficient strategies that facilitate and shorten the drug discovery process would be extremely beneficial. Fortunately, the structural diversity of NNRTIs provided a wide space for novel lead discovery, and the pharmacophore similarity of NNRTIs gave valuable hints for lead discovery and optimization. More importantly, with the continued efforts in the development of computational tools and increased crystallographic information on RT/NNRTI complexes, structure-based approaches using a combination of traditional medicinal chemistry, structural biology, and computational chemistry are being used increasingly in the design of NNRTIs. First, this review covers two decades of research and development for various NNRTI families based on their chemical scaffolds, and then describes the structural similarity of NNRTIs. We have attempted to assemble a comprehensive overview of the general approaches in NNRTI lead discovery and optimization reported in the literature during the last decade. The successful applications of medicinal chemistry strategies, crystallography, and computational tools for designing novel NNRTIs are highlighted. Future directions for research are also outlined.
Collapse
Affiliation(s)
- Peng Zhan
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, PR China
| | | | | | | | | | | |
Collapse
|
46
|
Nayak M, Batra S. Copper-Catalyzed Cascade Reactions of Substituted 4-Iodopyrazolecarbaldehydes with 1,2-Phenylenediamines and 2-Aminophenols. Adv Synth Catal 2010. [DOI: 10.1002/adsc.201000662] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
47
|
van Westen GJP, Wegner JK, Bender A, Ijzerman AP, van Vlijmen HWT. Mining protein dynamics from sets of crystal structures using "consensus structures". Protein Sci 2010; 19:742-52. [PMID: 20120021 DOI: 10.1002/pro.350] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In this work, we describe two novel approaches to utilize the dynamic structure information implicitly contained in large crystal structure data sets. The first approach visualizes both consistent as well as variable ligand-induced changes in ligand-bound compared with apo protein crystal structures. For this purpose, information was mined from B-factors and ligand-induced residue displacements in multiple crystal structures, minimizing experimental error and noise. With this approach, the mechanism of action of non-nucleoside reverse transcriptase inhibitors (NNRTIs) as an inseparable combination of distortion of protein dynamics and conformational changes of HIV-1 reverse transcriptase was corroborated (a combination of the previously proposed "molecular arthritis" and "distorted site" mechanisms). The second approach presented here uses "consensus structures" to map common binding features that are present in a set of structures of NNRTI-bound HIV-1 reverse transcriptase. Consensus structures are based on different levels of structural overlap of multiple crystal structures and are used to analyze protein-ligand interactions. The structures are shown to yield information about conserved hydrogen bonding interactions as well as binding-pocket flexibility, shape, and volume. From the consensus structures, a common wild type NNRTI binding pocket emerges. Furthermore, we were able to identify a conserved backbone hydrogen bond acceptor at P236 and a novel hydrophobic subpocket, which are not yet utilized by current drugs. Our methods introduced here reinterpret the atom information and make use of the data variability by using multiple structures, complementing classical 3D structural information of single structures.
Collapse
Affiliation(s)
- Gerard J P van Westen
- Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | | | | | | | | |
Collapse
|
48
|
Biaryl ethers as potent allosteric inhibitors of reverse transcriptase and its key mutant viruses: Aryl substituted pyrazole as a surrogate for the pyrazolopyridine motif. Bioorg Med Chem Lett 2010; 20:4328-32. [DOI: 10.1016/j.bmcl.2010.06.083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 06/10/2010] [Accepted: 06/14/2010] [Indexed: 11/24/2022]
|
49
|
Villaseñor AG, Wong A, Shao A, Garg A, Kuglstatter A, Harris SF. Acoustic matrix microseeding: improving protein crystal growth with minimal chemical bias. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:568-76. [PMID: 20445232 DOI: 10.1107/s0907444910005512] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 02/10/2010] [Indexed: 11/10/2022]
Abstract
A crystal seeding technique is introduced that uses acoustic waves to deliver nanolitre volumes of seed suspension into protein drops. The reduction in delivery volume enables enhanced crystal growth in matrix-seeding experiments without concern for bias from chemical components in the seed-carrying buffer suspension. Using this technique, it was found that while buffer components alone without seed can marginally promote crystal growth in some cases, crystal seeding is far more effective in boosting the number of sparse-matrix conditions that yield protein crystals.
Collapse
Affiliation(s)
- Armando G Villaseñor
- Department of Discovery Technologies, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304, USA.
| | | | | | | | | | | |
Collapse
|
50
|
Stellbrink HJ. Novel compounds for the treatment of HIV type-1 infection. Antivir Chem Chemother 2010; 19:189-200. [PMID: 19483267 DOI: 10.1177/095632020901900502] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Despite the recent licensure of several new antiretroviral compounds, there is still a need to develop additional agents. Problems with antiviral activity, tolerability, ease of administration, extent of cross-resistance and pharmacokinetic as well as pharmacodynamic interactions still represent important obstacles to life-long control of HIV type-1 replication by highly active antiretroviral therapy. Several compounds stem from the same classes as currently available drugs: apricitabine and elvucitabine (nucleoside reverse transcriptase inhibitors), rilpivirine (non-nucleoside reverse transcriptase inhibitor), vicriviroc and INCB009471 (CCR5 inhibitors) and elvitegravir (integrase inhibitor). The potential of other compounds with new modes of action is less clear. Currently, maturation inhibitors appear promising but for other drugs, obstacles to continued development, such as the need of parenteral application (that is, monoclonal antibodies) or toxicity (for example, immune modulating agents and pegylated interferon), are already apparent. For even more compounds in the preclinical development phase, an assessment of their possible clinical role is still premature. This review provides an overview and a summary of the current status of drug development in the field.
Collapse
|