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Guo H, Zhou B, Chang J, Chang W, Feng J, Zhang Z. Multicomponent cyclization with azides to synthesize N-heterocycles. Org Biomol Chem 2023; 21:8054-8074. [PMID: 37801029 DOI: 10.1039/d3ob01115a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Heterocyclic compounds, both naturally derived and synthetically produced, constitute a wide variety of biologically active and industrially important compounds. The synthesis and application of heterocyclic compounds have garnered significant attention and experienced rapid growth in recent decades. Organic azides, due to their unique properties and distinctive reactivity, have become a convenient chemical tool for achieving a wide range of heterocycles such as triazoles and tetrazoles. Importantly, the field of multicomponent reaction (MCR) chemistry provides a convergent approach to access various N-heterocyclic scaffolds, offering novelty, diversity, and complexity. However, the exploration of MCR pathways to N-heterocyclic compounds remains incomplete. Here, we review the use of multicomponent reactions for the preparation of N-heterocycles. A wide range of reactions based on azides for the synthesis of various types of N-heterocyclic systems have been developed.
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Affiliation(s)
- Hong Guo
- College of Science, China Agricultural University, Beijing 100193, China.
| | - Bei Zhou
- College of Science, China Agricultural University, Beijing 100193, China.
| | - Jingjing Chang
- College of Science, China Agricultural University, Beijing 100193, China.
| | - Wenxu Chang
- College of Science, China Agricultural University, Beijing 100193, China.
| | - Jiyao Feng
- College of Science, China Agricultural University, Beijing 100193, China.
| | - Zhenhua Zhang
- College of Science, China Agricultural University, Beijing 100193, China.
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2
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Pan Y, Luo ZL, Yang J, Han J, Yang J, yao Z, Xu L, Wang P, Shi Q. Cobalt‐Catalyzed Selective Transformation of Levulinic Acid and Amines into Pyrrolidines and Pyrrolidinones under H2. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | | | | | - zhen yao
- Renmin University of China CHINA
| | - Lijin Xu
- Renmin University of China CHINA
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3
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Hu S, Ma L, Dong B, Shan Q, Zhou J, Zhang G, Wang M, Cen S, Zhu M, Wang J, Wang Y. A kind of HIV-1 protease inhibitors containing phenols with antiviral activity against DRV-resistant variants. Bioorg Med Chem 2022; 64:116760. [PMID: 35483138 DOI: 10.1016/j.bmc.2022.116760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022]
Abstract
Based upon the preliminary design of enhancing genetic barrier to drug-resistant viral mutants by maximizing hydrogen-bonding or other van der Waals contacts, we have designed, synthesized and biologically evaluated a new class of HIV-1 protease inhibitors with phenol derived P2 ligands and nitro or halogens in P2' ligands. Results indicate that a majority of inhibitors exhibit robust enzyme inhibitory with IC50 values in picomolar or single digit nanomolar ranges. Among which, compound 17d displays potency with IC50 value of 21 pM and high protease selectivity. Of note, 17d exhibits greater antiviral activity against the DRV-resistant variant than the efficacy against the wild type virus. Furthermore, the molecular modeling studies demonstrate important interactions between 17d and the active sites of both the wild-type and DRV-resistant HIV-1 protease, as well as furnish insights for further optimization of new inhibitors.
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Affiliation(s)
- Shangjiu Hu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Biao Dong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Qi Shan
- Tianjin Institute of Pharmaceutical Research, Tianjin 300462, China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua 321004, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Minghua Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Mei Zhu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
| | - Juxian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
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4
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Wang R, Zheng Q. Multiple Molecular Dynamics Simulations and Energy Analysis Unravel the Dynamic Properties and Binding Mechanism of Mutants HIV-1 Protease with DRV and CA-p2. Microbiol Spectr 2022; 10:e0074821. [PMID: 35319278 PMCID: PMC9045218 DOI: 10.1128/spectrum.00748-21] [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: 06/29/2021] [Accepted: 02/10/2022] [Indexed: 11/20/2022] Open
Abstract
PRS17, a variant of human immunodeficiency virus type I protease (HIV-1 PR), has 17 mutated residues showing high levels of multidrug resistance. To describe the effects of these mutated residues on the dynamic properties and the binding mechanism of PR with substrate and inhibitor, focused on six systems (two complexes of WT PR and PRS17 with inhibitor Darunavir (DRV), two complexes of WT PR and PRS17 with substrate analogue CA-p2, two unligand WT PR and PRS17), we performed multiple molecular dynamics (MD) simulations combined with MM-PBSA and solvated interaction energy (SIE) methods. For both the unligand PRs and ligand-PR complexes, the results from simulations revealed 17 mutated residues alter the flap-flap distance, the distance from flap regions to catalytic sites, and the curling degree of the flap tips. These mutated residues changed the flexibility of the flap region in PR, and thus affected its binding energy with DRV and CA-p2, resulting in differences in sensitivity. Hydrophobic cavity makes an important contribution to the binding of PR and ligands. And most noticeable of all, the binding of the guanidine group in CA-p2 and Arg8' of PRS17 is useful for increasing their binding ability. These results have important guidance for the further design of drugs against multidrug resistant PR. IMPORTANCE Developing effective anti-HIV inhibitors is the current requirement to cope with the emergence of the resistance of mutants. Compared with the experiments, MD simulations along with energy calculations help reduce the time and cost of designing new inhibitors. Based on our simulation results, we propose two factors that may help design effective inhibitors against HIV-1 PR: (i) importance of hydrophobic cavity, and (ii) introduction of polar groups similar to the guanidine group.
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Affiliation(s)
- Ruige Wang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People's Republic of China
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People's Republic of China
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5
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Han B, He XH, Liu YQ, He G, Peng C, Li JL. Asymmetric organocatalysis: an enabling technology for medicinal chemistry. Chem Soc Rev 2021; 50:1522-1586. [PMID: 33496291 DOI: 10.1039/d0cs00196a] [Citation(s) in RCA: 162] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The efficacy and synthetic versatility of asymmetric organocatalysis have contributed enormously to the field of organic synthesis since the early 2000s. As asymmetric organocatalytic methods mature, they have extended beyond the academia and undergone scale-up for the production of chiral drugs, natural products, and enantiomerically enriched bioactive molecules. This review provides a comprehensive overview of the applications of asymmetric organocatalysis in medicinal chemistry. A general picture of asymmetric organocatalytic strategies in medicinal chemistry is firstly presented, and the specific applications of these strategies in pharmaceutical synthesis are systematically described, with a focus on the preparation of antiviral, anticancer, neuroprotective, cardiovascular, antibacterial, and antiparasitic agents, as well as several miscellaneous bioactive agents. The review concludes with a discussion of the challenges, limitations and future prospects for organocatalytic asymmetric synthesis of medicinally valuable compounds.
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Affiliation(s)
- Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Xiang-Hong He
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Yan-Qing Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Gu He
- State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Jun-Long Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China. and Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610106, China.
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6
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Wang R, Zheng Q. Multiple Molecular Dynamics Simulations of the Inhibitor GRL-02031 Complex with Wild Type and Mutant HIV-1 Protease Reveal the Binding and Drug-Resistance Mechanism. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13817-13832. [PMID: 33175558 DOI: 10.1021/acs.langmuir.0c02151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) protease is regarded as a fascinating target for drug development against HIV infection. However, mutations causing drug resistance severely limit the efficiency of the recently marketed drugs in the treatment of HIV replication. To elucidate the binding mechanism of HIV-1 protease with promising inhibitor GRL-02031 and further to probe the resistance mechanism associated with mutations (I47V, L76V, V82A, and N88D) to the inhibitor, we applied multiple molecular dynamics (MMD) simulations along with energy analysis by the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and solvated interaction energy (SIE) methodology on specific HIV-1 protease with GRL-0231 complexes. On the basis of detail analysis of the simulations, we revealed key characteristics that constitute the drug resistance of four mutation HIV-1 proteases toward GRL-02031: substitution of the side chain in these four mutation residues leads to a change in the distances between the flaps and catalytic sites, thereby reducing the affinity for GRL-02031 with these four mutation proteases, even though the L76V and N88D residues cannot directly contact GRL-02031. The results of energy analysis according to the MM-PBSA and SIE methods further indicated that hydrophobic interaction was considered to be the prime driving force for inhibitor GRL-02031 binding to protease and the decrease in van der Waals interactions between inhibitor GRL-02031 and mutant proteases as the primary cause of the drug resistance. Analyses of the hydrogen bonds and atomic interactions further provided detailed explanations for the resistance of these four mutation proteases toward inhibitor GRL-02031. The present study provides potential guidance on the structure-based inhibitors' design targeting HIV-1 protease.
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Affiliation(s)
- Ruige Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Qingchuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, P. R. China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130023, People's Republic of China
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7
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Ahsan M, Pindi C, Senapati S. Electrostatics Plays a Crucial Role in HIV-1 Protease Substrate Binding, Drugs Fail to Take Advantage. Biochemistry 2020; 59:3316-3331. [PMID: 32822154 DOI: 10.1021/acs.biochem.0c00341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV-1 protease (HIVPR) is an important drug target for combating AIDS. This enzyme is an aspartyl protease that is functionally active in its dimeric form. Nuclear magnetic resonance reports have convincingly shown that a pseudosymmetry exists at the HIVPR active site, where only one of the two aspartates remains protonated over the pH range of 2.5-7.0. To date, all HIVPR-targeted drug design strategies focused on maximizing the size-shape complementarity and van der Waals interactions of the small molecule drugs with the deprotonated, symmetric active site envelope of crystallized HIVPR. However, these strategies were ineffective with the emergence of drug resistant protease variants, primarily due to the steric clashes at the active site. In this study, we traced a specificity in the substrate binding motif that emerges primarily from the asymmetrical electrostatic potential present in the protease active site due to the uneven protonation. Our detailed results from atomistic molecular dynamics simulations show that while such a specific mode of substrate binding involves significant electrostatic interactions, none of the existing drugs or inhibitors could utilize this electrostatic hot spot. As the electrostatic is long-range interaction, it can provide sufficient binding strength without the necessity of increasing the bulkiness of the inhibitors. We propose that introducing the electrostatic component along with optimal fitting at the binding pocket could pave the way for promising designs that might be more effective against both wild type and HIVPR resistant variants.
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Affiliation(s)
- Mohd Ahsan
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Chinmai Pindi
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sanjib Senapati
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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8
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Zhou H, Zhu M, Ma L, Zhou J, Dong B, Zhang G, Cen S, Wang Y, Wang J. Piperidine scaffold as the novel P2-ligands in cyclopropyl-containing HIV-1 protease inhibitors: Structure-based design, synthesis, biological evaluation and docking study. PLoS One 2020; 15:e0235483. [PMID: 32697773 PMCID: PMC7375528 DOI: 10.1371/journal.pone.0235483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/17/2020] [Indexed: 11/19/2022] Open
Abstract
A series of potent HIV-1 protease inhibitors, containing diverse piperidine analogues as the P2-ligands, 4-substituted phenylsulfonamides as the P2'-ligands and a hydrophobic cyclopropyl group as the P1'-ligand, were designed, synthesized and evaluated in this work. Among these twenty-four target compounds, many of them exhibited excellent activity against HIV-1 protease with half maximal inhibitory concentration (IC50) values below 20 nM. Particularly, compound 22a containing a (R)-piperidine-3-carboxamide as the P2-ligand and a 4-methoxylphenylsulfonamide as the P2'-ligand exhibited the most effective inhibitory activity with an IC50 value of 3.61 nM. More importantly, 22a exhibited activity with inhibition of 42% and 26% against wild-type and Darunavir (DRV)-resistant HIV-1 variants, respectively. Additionally, the molecular docking of 22a with HIV-1 protease provided insight into the ligand-binding properties, which was of great value for further study.
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Affiliation(s)
- Huiyu Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Mei Zhu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua, China
| | - Biao Dong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Juxian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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9
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Peng C, Wang J, Xu Z, Cai T, Zhu W. Accurate prediction of relative binding affinities of a series of HIV-1 protease inhibitors using semi-empirical quantum mechanical charge. J Comput Chem 2020; 41:1773-1780. [PMID: 32352193 DOI: 10.1002/jcc.26218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 04/03/2020] [Accepted: 04/18/2020] [Indexed: 11/05/2022]
Abstract
A major challenge in computer-aided drug design is the accurate estimation of ligand binding affinity. Here, a new approach that combines the adaptive steered molecular dynamics (ASMD) and partial atomic charges calculated by semi-empirical quantum mechanics (SQMPC), namely ASMD-SQMPC, is suggested to predict the ligand binding affinities, with 24 HIV-1 protease inhibitors as testing examples. In the ASMD-SQMPC, the relative binding free energy (ΔG) is reflected by the average maximum potential of mean force (<PMF>max ) between bound and unbound states. The correlation coefficient (R2 ) between the <PMF>max and experimentally determined ΔG is 0.86, showing a significant improvement compared with the conventional ASMD (R2 = 0.52). Therefore, this study provides an efficient approach to predict the relative ΔG and reveals the significance of precise partial atomic charges in the theoretical simulations.
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Affiliation(s)
- Cheng Peng
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, China
| | - Jinan Wang
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, China
| | - Tingting Cai
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, China.,Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao, China
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10
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Design and biological evaluation of novel HIV-1 protease inhibitors with isopropanol as P1' ligand to enhance binding with S1' subsite. Bioorg Med Chem 2020; 28:115623. [PMID: 32690263 DOI: 10.1016/j.bmc.2020.115623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/27/2020] [Accepted: 06/27/2020] [Indexed: 10/23/2022]
Abstract
Newly designed HIV-1 protease inhibitors that maximize interactions with the protein backbone, especially in the form of hydrogen bonds, may enhance the antiviral potency of these compounds and minimize acquisition of drug-resistant mutations. Herein, we described a series of new HIV-1 PIs containing phenols as the P2 ligands and chiral isopropanol as the P1' ligands, in combination with 4-trifluoromethylphenylsulfonamide or 4-nitrophenylsulfonamide as the P2' ligands. And most of these compounds exhibited nanomolar inhibitory potency. In particular, inhibitors 13c and 13e with 4-trifluoromethylphenylsulfonamide as the P2' ligand and (R) - isopropanol as the P1' ligand, exhibited antiviral IC50 values of 1.64 nM and 2.33 nM, respectively. Furthermore, they also showed remarkable activity against wild-type and DRV-resistant HIV-1 variants that raised the prospect of designing more effective PIs further.
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11
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Zhu M, Dou Y, Ma L, Dong B, Zhang F, Zhang G, Wang J, Zhou J, Cen S, Wang Y. Novel HIV-1 Protease Inhibitors with Morpholine as the P2 Ligand to Enhance Activity against DRV-Resistant Variants. ACS Med Chem Lett 2020; 11:1196-1204. [PMID: 32551001 DOI: 10.1021/acsmedchemlett.0c00043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/31/2020] [Indexed: 11/29/2022] Open
Abstract
Flexible heterocyclic moieties as the P2 ligands of HIV-1 protease inhibitors may be adapted to the minimally distorted active site of mutations easily and enhance activity against DRV-resistant HIV-1 variants. Herein, the design, synthesis, and biological evaluation of a new series of inhibitors containing morpholine derivatives as the P2 ligands were described, among which, carbamate inhibitor 23a and carbamido inhibitor 27a exhibited almost 4- and 2-fold superior activity with enzyme Ki of 0.092 nM and 0.21 nM, as well as antiviral IC50 values of 0.41 nM and 0.95 nM, respectively, compared to DRV. Besides, they exhibited excellent activity with inhibition of 94% and 91%, respectively. Furthermore, they also showed appreciable antiviral activity against DRV-resistant HIV-1 variants.
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Affiliation(s)
- Mei Zhu
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Yue Dou
- Department of Pharmacy, Jinzhou Medical University, Jinzhou 121001, China
| | - Ling Ma
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Biao Dong
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Fan Zhang
- Department of Pharmacy, Jinzhou Medical University, Jinzhou 121001, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Juxian Wang
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua 321004, China
| | - Shan Cen
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Yucheng Wang
- Institute of Medicinal Biotechnology,Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
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12
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Synthesis and evaluation of potent human immunodeficiency virus 1 protease inhibitors with epimeric isopropanol as novel P1' ligands. Future Med Chem 2020; 12:775-794. [PMID: 32125179 DOI: 10.4155/fmc-2019-0331] [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] [Indexed: 11/17/2022] Open
Abstract
Aim: HIV-1 protease inhibitors regimens suffered from a number of drawbacks, among which, the most egregious issue was the growing emergence of drug-resistant strains. Materials & methods: The design strategy of maximizing the protease active site interactions with the inhibitor, especially promoting extensive hydrogen bonding with the protein backbone atoms, might be in favor of combating drug resistance. A series of HIV-1 protease inhibitors that incorporated enantiomeric isopropanols as the P1' ligands in combination with phenols as the P2 ligands were reported herein. Results: A number of inhibitors displayed potent protease enzyme inhibition activity. In particular, inhibitor 14c showed comparable potency as darunavir with IC50 value of 1.91 nM and activity against darunavir-resistant HIV-1 variants. Conclusion: The new kind of HIV-1 protease inhibitors deserves further study.
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13
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Ngo ST, Hong ND, Quynh Anh LH, Hiep DM, Tung NT. Effective estimation of the inhibitor affinity of HIV-1 protease via a modified LIE approach. RSC Adv 2020; 10:7732-7739. [PMID: 35492181 PMCID: PMC9049864 DOI: 10.1039/c9ra09583g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 02/06/2020] [Indexed: 01/07/2023] Open
Abstract
The inhibition of the Human Immunodeficiency Virus Type 1 Protease (HIV-1 PR) can prevent the synthesis of new viruses. Computer-aided drug design (CADD) would enhance the discovery of new therapies, through which the estimation of ligand-binding affinity is critical to predict the most efficient inhibitor. A time-consuming binding free energy method would reduce the usefulness of CADD. The modified linear interaction energy (LIE) approach emerges as an appropriate protocol that performs this task. In particular, the polar interaction free energy, which is obtained via numerically resolving the linear Poisson–Boltzmann equation, plays as an important role in driving the binding mechanism of the HIV-1 PR + inhibitor complex. The electrostatic interaction energy contributes to the attraction between two molecules, but the vdW interaction acts as a repulsive factor between the ligand and the HIV-1 PR. Moreover, the ligands were found to adopt a very strong hydrophobic interaction with the HIV-1 PR. Furthermore, the results obtained corroborate the high accuracy and precision of computational studies with a large correlation coefficient value R = 0.83 and a small RMSE δRMSE = 1.25 kcal mol−1. This method is less time-consuming than the other end-point methods, such as the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and free energy perturbation (FEP) approaches. Overall, the modified LIE approach would provide ligand-binding affinity with HIV-1 PR accurately, precisely, and rapidly, resulting in a more efficient design of new inhibitors. The inhibition of the Human Immunodeficiency Virus Type 1 Protease (HIV-1 PR) can prevent the synthesis of new viruses.![]()
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | - Nam Dao Hong
- University of Medicine and Pharmacy at Ho Chi Minh City
- Ho Chi Minh City
- Vietnam
| | - Le Huu Quynh Anh
- Department of Climate Change and Renewable Energy
- Ho Chi Minh City University of Natural Resources and Environment
- Ho Chi Minh City
- Vietnam
| | | | - Nguyen Thanh Tung
- Institute of Materials Science & Graduate University of Science and Technology
- Vietnam Academy of Science and Technology
- Hanoi
- Vietnam
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14
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Triki D, Kermarrec M, Visseaux B, Descamps D, Flatters D, Camproux AC, Regad L. Exploration of the effects of sequence variations between HIV-1 and HIV-2 proteases on their three-dimensional structures. J Biomol Struct Dyn 2019; 38:5014-5026. [PMID: 31830870 DOI: 10.1080/07391102.2019.1704877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
HIV protease inhibitors (PIs) approved by the FDA (US Food and Drug Administration) are a major class of antiretroviral. HIV-2 protease (PR2) is naturally resistant to most of them as PIs were designed for HIV-1 protease (PR1). In this study, we explored the impact of amino-acid substitutions between PR1 and PR2 on the structure of protease (PR) by comparing the structural variability of 13 regions using 24 PR1 and PR2 structures complexed with diverse ligands. Our analyses confirmed structural rigidity of the catalytic region and highlighted the important role of three regions in the conservation of the catalytic region conformation. Surprisingly, we showed that the flap region, corresponding to a flexible region, exhibits similar conformations in PR1 and PR2. Furthermore, we identified regions exhibiting different conformations in PR1 and PR2, which could be explained by the intrinsic flexibility of these regions, by crystal packing, or by PR1 and PR2 substitutions. Some substitutions induce structural changes in the R2 and R4 regions that could have an impact on the properties of PI-binding site and could thus modify PI binding mode. Substitutions involved in structural changes in the elbow region could alter the flexibility of the PR2 flap regions relative to PR1, and thus play a role in the transition from the semi-open form to the closed form, and have an impact on ligand binding. These results improve the understanding of the impact of sequence variations between PR1 and PR2 on the natural resistance of HIV-2 to commercially available PIs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhoha Triki
- Department of Chemistry, Bioinformatics Research Center, College of Science, North Carolina State University, Raleigh, North Carolina, USA.,Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, Paris, France
| | - Maxime Kermarrec
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, Paris, France
| | - Benoît Visseaux
- Université de Paris, IAME, UMR 1137, INSERM, AP-HP, Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - Diane Descamps
- Université de Paris, IAME, UMR 1137, INSERM, AP-HP, Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - Delphine Flatters
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, Paris, France
| | | | - Leslie Regad
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, Paris, France
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15
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Zhu M, Ma L, Zhou H, Dong B, Wang Y, Wang Z, Zhou J, Zhang G, Wang J, Liang C, Cen S, Wang Y. Preliminary SAR and biological evaluation of potent HIV-1 protease inhibitors with pyrimidine bases as novel P2 ligands to enhance activity against DRV-resistant HIV-1 variants. Eur J Med Chem 2019; 185:111866. [PMID: 31734023 DOI: 10.1016/j.ejmech.2019.111866] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 12/21/2022]
Abstract
Introducing pyrimidine bases, the basic components of nucleic acid, to P2 ligands might enhance the potency of Human Immunodeficiency Virus-1 (HIV-1) protease inhibitors because of the carbonyl and amino groups promoting the formation of extensive hydrogen bonding interactions. In this work, we provide evidence that inhibitor 10e, with N-2-(2,4-Dioxo-3,4-dihydropyrimidin-1(2H)-yl) acetamide as the P2 ligand and a 4-methoxylphenylsulfonamide as the P2' ligand, displayed remarkable enzyme inhibitory and antiviral activity, with the IC50 2.53 nM in vitro and a promising inhibition ratio with 68% against wild-type HIV-1 in vivo, with low cytotoxicity. This inhibitor also exhibited appreciable antiviral activity against DRV-resistant HIV-1 variants, which was of great value for further study.
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Affiliation(s)
- Mei Zhu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Huiyu Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Biao Dong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Yujia Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Zhen Wang
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Jinming Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Juxian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
| | - Chen Liang
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China.
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16
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Voshavar C. Protease Inhibitors for the Treatment of HIV/AIDS: Recent Advances and Future Challenges. Curr Top Med Chem 2019; 19:1571-1598. [PMID: 31237209 DOI: 10.2174/1568026619666190619115243] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023]
Abstract
Acquired Immunodeficiency Syndrome (AIDS) is a chronic disease characterized by multiple life-threatening illnesses caused by a retro-virus, Human Immunodeficiency Virus (HIV). HIV infection slowly destroys the immune system and increases the risk of various other infections and diseases. Although, there is no immediate cure for HIV infection/AIDS, several drugs targeting various cruxes of HIV infection are used to slow down the progress of the disease and to boost the immune system. One of the key therapeutic strategies is Highly Active Antiretroviral Therapy (HAART) or ' AIDS cocktail' in a general sense, which is a customized combination of anti-retroviral drugs designed to combat the HIV infection. Since HAART's inception in 1995, this treatment was found to be effective in improving the life expectancy of HIV patients over two decades. Among various classes of HAART treatment regimen, Protease Inhibitors (PIs) are known to be widely used as a major component and found to be effective in treating HIV infection/AIDS. For the past several years, a variety of protease inhibitors have been reported. This review outlines the drug design strategies of PIs, chemical and pharmacological characteristics of some mechanism-based inhibitors, summarizes the recent developments in small molecule based drug discovery with HIV protease as a drug target. Further discussed are the pharmacology, PI drug resistance on HIV PR, adverse effects of HIV PIs and challenges/impediments in the successful application of HIV PIs as an important class of drugs in HAART regimen for the effective treatment of AIDS.
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Affiliation(s)
- Chandrashekhar Voshavar
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, United States
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17
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18
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Dascalu AE, Ghinet A, Billamboz M, Lipka E. Performance comparison of chlorinated chiral stationary phases in supercritical fluid chromatography for separation of selected pyrrolidone derivatives. J Pharm Anal 2019; 9:248-253. [PMID: 31452962 PMCID: PMC6702407 DOI: 10.1016/j.jpha.2019.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/23/2019] [Accepted: 03/04/2019] [Indexed: 11/12/2022] Open
Abstract
The effects of two chlorinated chiral stationary phases, namely, Lux Cellulose-2 and Lux i-Cellulose-5, flow-rate, percentage of co-solvent and chemical structures of the compounds on retention and resolution were studied within this article. In this work a backpressure of 150 bar, a temperature of 40 °C and 10% of methanol as co-solvent were chosen as operating conditions. The optimum flow-rate was 2 mL/min. The percentage of co-solvent was studied between 7.5% and 15%. We have observed that 15% of methanol gave the best results for most of the compounds. For all the derivatives, the Lux Cellulose-2 provided better resolutions going from 1.50 to 3.59 compared with Lux i-Cellulose-5.
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Affiliation(s)
- Anca-Elena Dascalu
- Univ. Lille, Inserm, U995 - LIRIC - Lille Inflammation Research International Center, F-59000 Lille, France.,Ecole des Hautes Etudes d'Ingénieur (HEI), Laboratoire de Pharmacochimie, 13 rue de Toul, F-59046 Lille, France.,UFR Pharmacie, Laboratoire de Chimie Analytique, BP 83, F-59006 Lille, France.,'Alexandru Ioan Cuza' University of Iasi, Faculty of Chemistry, Bd. Carol I nr. 11, 700506 Iasi, Romania
| | - Alina Ghinet
- Univ. Lille, Inserm, U995 - LIRIC - Lille Inflammation Research International Center, F-59000 Lille, France.,Ecole des Hautes Etudes d'Ingénieur (HEI), Laboratoire de Pharmacochimie, 13 rue de Toul, F-59046 Lille, France.,'Alexandru Ioan Cuza' University of Iasi, Faculty of Chemistry, Bd. Carol I nr. 11, 700506 Iasi, Romania
| | - Muriel Billamboz
- Univ. Lille, Inserm, U995 - LIRIC - Lille Inflammation Research International Center, F-59000 Lille, France.,Ecole des Hautes Etudes d'Ingénieur (HEI), Laboratoire de Pharmacochimie, 13 rue de Toul, F-59046 Lille, France
| | - Emmanuelle Lipka
- Univ. Lille, Inserm, U995 - LIRIC - Lille Inflammation Research International Center, F-59000 Lille, France.,UFR Pharmacie, Laboratoire de Chimie Analytique, BP 83, F-59006 Lille, France
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19
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Abstract
Tetrazole derivatives are a prime class of heterocycles, very important to medicinal chemistry and drug design due to not only their bioisosterism to carboxylic acid and amide moieties but also to their metabolic stability and other beneficial physicochemical properties. Although more than 20 FDA-approved drugs contain 1 H- or 2 H-tetrazole substituents, their exact binding mode, structural biology, 3D conformations, and in general their chemical behavior is not fully understood. Importantly, multicomponent reaction (MCR) chemistry offers convergent access to multiple tetrazole scaffolds providing the three important elements of novelty, diversity, and complexity, yet MCR pathways to tetrazoles are far from completely explored. Here, we review the use of multicomponent reactions for the preparation of substituted tetrazole derivatives. We highlight specific applications and general trends holding therein and discuss synthetic approaches and their value by analyzing scope and limitations, and also enlighten their receptor binding mode. Finally, we estimated the prospects of further research in this field.
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Affiliation(s)
- Constantinos G. Neochoritis
- Drug Design Group, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Ting Zhao
- Drug Design Group, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Alexander Dömling
- Drug Design Group, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
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20
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Ghosh AK, Sean Fyvie W, Brindisi M, Steffey M, Agniswamy J, Wang YF, Aoki M, Amano M, Weber IT, Mitsuya H. Design, synthesis, X-ray studies, and biological evaluation of novel macrocyclic HIV-1 protease inhibitors involving the P1'-P2' ligands. Bioorg Med Chem Lett 2017; 27:4925-4931. [PMID: 28958624 DOI: 10.1016/j.bmcl.2017.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/03/2017] [Indexed: 11/30/2022]
Abstract
Design, synthesis, and evaluation of a new class of HIV-1 protease inhibitors containing diverse flexible macrocyclic P1'-P2' tethers are reported. Inhibitor 5a with a pyrrolidinone-derived macrocycle exhibited favorable enzyme inhibitory and antiviral activity (Ki=13.2nM, IC50=22nM). Further incorporation of heteroatoms in the macrocyclic skeleton provided macrocyclic inhibitors 5m and 5o. These compounds showed excellent HIV-1 protease inhibitory (Ki=62pM and 14pM, respectively) and antiviral activity (IC50=5.3nM and 2.0nM, respectively). Inhibitor 5o also remained highly potent against a DRV-resistant HIV-1 variant.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - W Sean Fyvie
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Melinda Steffey
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Johnson Agniswamy
- Departments of Biology and Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Yuan-Fang Wang
- Departments of Biology and Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Manabu Aoki
- Departments of Hematology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan
| | - Masayuki Amano
- Departments of Hematology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan
| | - Irene T Weber
- Departments of Biology and Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Hiroaki Mitsuya
- Departments of Hematology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD 20892, USA; Center for Clinical Sciences, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655, Japan
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21
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Asymmetric cross-benzoin condensation promoted by a chiral triazolium precatalyst bearing a pyridine moiety. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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22
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Lutete LM, Ikemoto T. Novel Diarylprolinol-derived Amino Perfluoroalkanesulfonamide Catalysts: Highly Enantio- and Diastereoselective Aldol Reaction. CHEM LETT 2017. [DOI: 10.1246/cl.170034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Léopold M. Lutete
- Health and Crop Sciences Research Laboratory, Sumitomo Chemical Co., Ltd., 3-1-98 Kasugadenaka, Konohana-ku, Osaka 554-8558
| | - Tetsuya Ikemoto
- Health and Crop Sciences Research Laboratory, Sumitomo Chemical Co., Ltd., 3-1-98 Kasugadenaka, Konohana-ku, Osaka 554-8558
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23
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Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work. J Comput Chem 2016; 37:2734-2742. [DOI: 10.1002/jcc.24502] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/29/2016] [Accepted: 09/06/2016] [Indexed: 02/06/2023]
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24
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Ghosh AK, Osswald HL, Prato G. Recent Progress in the Development of HIV-1 Protease Inhibitors for the Treatment of HIV/AIDS. J Med Chem 2016; 59:5172-208. [PMID: 26799988 PMCID: PMC5598487 DOI: 10.1021/acs.jmedchem.5b01697] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
HIV-1 protease inhibitors continue to play an important role in the treatment of HIV/AIDS, transforming this deadly ailment into a more manageable chronic infection. Over the years, intensive research has led to a variety of approved protease inhibitors for the treatment of HIV/AIDS. In this review, we outline current drug design and medicinal chemistry efforts toward the development of next-generation protease inhibitors beyond the currently approved drugs.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Heather L. Osswald
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Gary Prato
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
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25
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Kanemitsu T, Inoue M, Yoshimura N, Yoneyama K, Watarai R, Miyazaki M, Odanaka Y, Nagata K, Itoh T. A Concise One-Pot Organo- and Biocatalyzed Preparation of Enantiopure Hexahydrofuro[2,3-b]furan-3-ol: An Approach to the Synthesis of HIV Protease Inhibitors. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Synthesis of a series of ω-dimethylaminoalkyl substituted ethylenediamine ligands for use in enantioselective catalysis. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.tetasy.2015.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Mass spectrometry study of N-alkylbenzenesulfonamides with potential antagonist activity to potassium channels. Amino Acids 2015; 48:445-59. [PMID: 26395182 DOI: 10.1007/s00726-015-2099-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 09/09/2015] [Indexed: 10/23/2022]
Abstract
Herein, we report the synthesis and mass spectrometry studies of several N-alkylbenzenesulfonamides structurally related to sulfanilic acid. The compounds were synthesized using a modified Schotten-Baumann reaction coupled with Meisenheimer arylation. Sequential mass spectrometry by negative mode electrospray ionization (ESI(-)-MS/MS) showed the formation of sulfoxylate anion (m/z 65) observed in the mass spectrum of p-chloro-N-alkylbenzenesulfonamides. Investigation of the unexpected loss of two water molecules, as observed by electron ionization mass spectrometry (EI-MS) analysis of p-(N-alkyl)lactam sulfonamides, led to the proposal of corresponding fragmentation pathways. These compounds showed loss of neutral iminosulfane dioxide molecule (M-79) with formation of ions observed at m/z 344 and 377. These ions were formed by rearrangement on ESI(+)-MS/MS analysis. Some of the molecules showed antagonistic activity against Kv3.1 voltage-gated potassium channels.
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28
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Wei Y, Li J, Chen Z, Wang F, Huang W, Hong Z, Lin J. Multistage virtual screening and identification of novel HIV-1 protease inhibitors by integrating SVM, shape, pharmacophore and docking methods. Eur J Med Chem 2015; 101:409-18. [PMID: 26185005 DOI: 10.1016/j.ejmech.2015.06.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 06/28/2015] [Accepted: 06/29/2015] [Indexed: 11/30/2022]
Abstract
The HIV-1 protease has proven to be a crucial component of the HIV replication machinery and a reliable target for anti-HIV drug discovery. In this study, we applied an optimized hierarchical multistage virtual screening method targeting HIV-1 protease. The method sequentially applied SVM (Support Vector Machine), shape similarity, pharmacophore modeling and molecular docking. Using a validation set (270 positives, 155,996 negatives), the multistage virtual screening method showed a high hit rate and high enrichment factor of 80.47% and 465.75, respectively. Furthermore, this approach was applied to screen the National Cancer Institute database (NCI), which contains 260,000 molecules. From the final hit list, 6 molecules were selected for further testing in an in vitro HIV-1 protease inhibitory assay, and 2 molecules (NSC111887 and NSC121217) showed inhibitory potency against HIV-1 protease, with IC50 values of 62 μM and 162 μM, respectively. With further chemical development, these 2 molecules could potentially serve as HIV-1 protease inhibitors.
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Affiliation(s)
- Yu Wei
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; College of Pharmacy, Nankai University, Tianjin 300071, PR China
| | - Jinlong Li
- College of Pharmacy, Nankai University, Tianjin 300071, PR China
| | - Zeming Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Fengwei Wang
- Department of Oncology, Tianjin Union Medical Center, Tianjin 300180, PR China
| | | | - Zhangyong Hong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; College of Life Sciences, Nankai University, Tianjin 300071, PR China.
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; College of Pharmacy, Nankai University, Tianjin 300071, PR China.
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29
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Agniswamy J, Louis JM, Shen CH, Yashchuk S, Ghosh AK, Weber IT. Substituted Bis-THF Protease Inhibitors with Improved Potency against Highly Resistant Mature HIV-1 Protease PR20. J Med Chem 2015; 58:5088-95. [PMID: 26010498 DOI: 10.1021/acs.jmedchem.5b00474] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An extremely drug resistant mutant of HIV-1 protease (PR) bearing 20 mutations (PR20) has been studied with two potent antiviral investigational inhibitors. GRL-5010A and GRL-4410A were designed to introduce hydrogen bond interactions with the flexible flaps of the PR by incorporating gem-difluorines and alkoxy, respectively, at the C4 position of the bis-THF of darunavir. PR20 provides an excellent model for high level resistance, since clinical inhibitors are >1000-fold less active on PR20 than on wild-type enzyme. GRL-5010A and GRL-4410A show inhibition constants of 4.3 ± 7.0 and 1.7 ± 1.8 nM, respectively, for PR20, compared to the binding affinity of 41 ± 1 nM measured for darunavir. Crystal structures of PR20 in complexes with the two inhibitors confirmed the new hydrogen bond interactions with Gly 48 in the flap of the enzyme. The two new compounds are more effective than darunavir in inhibiting mature PR20 and show promise for further development of antiviral agents targeting highly resistant PR mutants.
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Affiliation(s)
- Johnson Agniswamy
- †Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
| | - John M Louis
- ‡Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
| | - Chen-Hsiang Shen
- †Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
| | - Sofiya Yashchuk
- §Department of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Arun K Ghosh
- §Department of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Irene T Weber
- †Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
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30
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Mbita Z, Hull R, Dlamini Z. Human immunodeficiency virus-1 (HIV-1)-mediated apoptosis: new therapeutic targets. Viruses 2014; 6:3181-227. [PMID: 25196285 PMCID: PMC4147692 DOI: 10.3390/v6083181] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 06/12/2014] [Accepted: 07/08/2014] [Indexed: 12/18/2022] Open
Abstract
HIV has posed a significant challenge due to the ability of the virus to both impair and evade the host’s immune system. One of the most important mechanisms it has employed to do so is the modulation of the host’s native apoptotic pathways and mechanisms. Viral proteins alter normal apoptotic signaling resulting in increased viral load and the formation of viral reservoirs which ultimately increase infectivity. Both the host’s pro- and anti-apoptotic responses are regulated by the interactions of viral proteins with cell surface receptors or apoptotic pathway components. This dynamic has led to the development of therapies aimed at altering the ability of the virus to modulate apoptotic pathways. These therapies are aimed at preventing or inhibiting viral infection, or treating viral associated pathologies. These drugs target both the viral proteins and the apoptotic pathways of the host. This review will examine the cell types targeted by HIV, the surface receptors exploited by the virus and the mechanisms whereby HIV encoded proteins influence the apoptotic pathways. The viral manipulation of the hosts’ cell type to evade the immune system, establish viral reservoirs and enhance viral proliferation will be reviewed. The pathologies associated with the ability of HIV to alter apoptotic signaling and the drugs and therapies currently under development that target the ability of apoptotic signaling within HIV infection will also be discussed.
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Affiliation(s)
- Zukile Mbita
- College of Agriculture and Environmental Sciences, University of South Africa, Florida Science Campus, C/o Christiaan de Wet and Pioneer Avenue P/Bag X6, Johannesburg 1710, South Africa.
| | - Rodney Hull
- College of Agriculture and Environmental Sciences, University of South Africa, Florida Science Campus, C/o Christiaan de Wet and Pioneer Avenue P/Bag X6, Johannesburg 1710, South Africa.
| | - Zodwa Dlamini
- College of Agriculture and Environmental Sciences, University of South Africa, Florida Science Campus, C/o Christiaan de Wet and Pioneer Avenue P/Bag X6, Johannesburg 1710, South Africa.
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31
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Boltjes A, Liao GP, Zhao T, Herdtweck E, Dömling A. Ugi 4-CR Synthesis of γ- and δ-Lactams providing new access to diverse enzyme interactions, a PDB analysis. MEDCHEMCOMM 2014; 5:949-952. [PMID: 25013719 DOI: 10.1039/c4md00162a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A three step synthesis of N-unsubstituted tetrazolo γ- and δ-lactams involving a key Ugi-4CR is presented. The compounds, otherwise difficult to access, are conveniently synthesized in overall good yields by our route. PDB analysis of the N-unsubstituted γ- and δ-lactam fragment reveals a strongly tri-directional hydrogen bond donor acceptor interaction with the amino acids of the binding sites.
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Affiliation(s)
- André Boltjes
- Department of Pharmacy University of Groningen A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - George P Liao
- Department of Pharmacy University of Groningen A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ting Zhao
- Department of Pharmacy University of Groningen A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Eberhardt Herdtweck
- Department Chemie Technische Universität München Lichtenbergstrasse 4, D-85747 Garching bei München, Germany
| | - Alexander Dömling
- Department of Pharmacy University of Groningen A. Deusinglaan 1, 9713 AV Groningen, The Netherlands ; Department of Chemistry University of Pittsburgh 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
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32
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Recent patents and emerging therapeutics for HIV infections: a focus on protease inhibitors. Pharm Pat Anal 2014; 2:513-38. [PMID: 24237127 DOI: 10.4155/ppa.13.33] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The inclusion of protease inhibitors (PIs) in highly active antiretroviral therapy has significantly improved clinical outcomes in HIV-1-infected patients. To date, PIs are considered to be the most important therapeutic agents for the treatment of HIV infections. Despite high anti-HIV-1 potency, poor oral bioavailability of PIs has been a major concern. For achieving therapeutic concentrations, large doses of PIs are administered, which results in unacceptable systemic toxicities. Such severe and long-term toxicities necessitate the development of safer and potentially promising PIs. Recently, considerable attention has been paid to the development of newer compounds capable of inhibiting wild-type and resistant HIV-1 protease. Some of these PIs have displayed potent HIV-1 protease inhibitory activity. In this review, we have made an attempt to provide an overview on clinically approved and newly developing PIs, and related recent patents in the development of novel PIs.
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Nalam MN, Ali A, Reddy GKK, Cao H, Anjum SG, Altman MD, Yilmaz NK, Tidor B, Rana TM, Schiffer CA. Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance. CHEMISTRY & BIOLOGY 2013; 20:1116-24. [PMID: 24012370 PMCID: PMC3934494 DOI: 10.1016/j.chembiol.2013.07.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 07/12/2013] [Accepted: 07/23/2013] [Indexed: 01/07/2023]
Abstract
The rapid evolution of HIV under selective drug pressure has led to multidrug resistant (MDR) strains that evade standard therapies. We designed highly potent HIV-1 protease inhibitors (PIs) using the substrate envelope model, which confines inhibitors within the consensus volume of natural substrates, providing inhibitors less susceptible to resistance because a mutation affecting such inhibitors will simultaneously affect viral substrate processing. The designed PIs share a common chemical scaffold but utilize various moieties that optimally fill the substrate envelope, as confirmed by crystal structures. The designed PIs retain robust binding to MDR protease variants and display exceptional antiviral potencies against different clades of HIV as well as a panel of 12 drug-resistant viral strains. The substrate envelope model proves to be a powerful strategy to develop potent and robust inhibitors that avoid drug resistance.
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Affiliation(s)
- Madhavi N.L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
| | - G.S. Kiran Kumar Reddy
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
| | - Hong Cao
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
| | - Saima G. Anjum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
| | - Michael D. Altman
- Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
| | - Bruce Tidor
- Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Corresponding Authors: Bruce Tidor: Phone: +1 (617) 253-7258, , Tariq M. Rana: Phone: +1 (858)795-5325, , Celia A. Schiffer: Phone: +1 (508) 856-8008,
| | - Tariq M. Rana
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
- Corresponding Authors: Bruce Tidor: Phone: +1 (617) 253-7258, , Tariq M. Rana: Phone: +1 (858)795-5325, , Celia A. Schiffer: Phone: +1 (508) 856-8008,
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
- Corresponding Authors: Bruce Tidor: Phone: +1 (617) 253-7258, , Tariq M. Rana: Phone: +1 (858)795-5325, , Celia A. Schiffer: Phone: +1 (508) 856-8008,
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Agniswamy J, Shen CH, Wang YF, Ghosh AK, Rao KV, Xu CX, Sayer JM, Louis JM, Weber IT. Extreme multidrug resistant HIV-1 protease with 20 mutations is resistant to novel protease inhibitors with P1'-pyrrolidinone or P2-tris-tetrahydrofuran. J Med Chem 2013; 56:4017-27. [PMID: 23590295 DOI: 10.1021/jm400231v] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Extreme drug resistant mutant of HIV-1 protease (PR) bearing 20 mutations (PR20) has been studied with the clinical inhibitor amprenavir (1) and two potent antiviral investigational inhibitors GRL-02031 (2) and GRL-0519 (3). Clinical inhibitors are >1000-fold less active on PR20 than on wild-type enzyme, which is consistent with dissociation constants (KL) from isothermal titration calorimetry of 40 nM for 3, 178 nM for amprenavir, and 960 nM for 2. High resolution crystal structures of PR20-inhibitor complexes revealed altered interactions compared with the corresponding wild-type PR complexes in agreement with relative inhibition. Amprenavir lacks interactions due to PR20 mutations in the S2/S2' subsites relative to PR. Inhibitors 2 and 3 lose interactions with Arg8' in PR20 relative to the wild-type enzyme because Arg8' shifts to interact with mutated L10F side chain. Overall, inhibitor 3 compares favorably with darunavir in affinity for PR20 and shows promise for further development.
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Affiliation(s)
- Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, USA
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Kawasoko CY, Foletto P, Rodrigues OED, Dornelles L, Schwab RS, Braga AL. Straightforward synthesis of non-natural l-chalcogen and l-diselenide N-Boc-protected-γ-amino acid derivatives. Org Biomol Chem 2013; 11:5173-83. [DOI: 10.1039/c3ob40879e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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36
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Cao D, Chai Z, Zhang J, Ye Z, Xiao H, Wang H, Chen J, Wu X, Zhao G. Thiourea-phosphonium salts from amino acids: cooperative phase-transfer catalysts in the enantioselective aza-Henry reaction. Chem Commun (Camb) 2013; 49:5972-4. [DOI: 10.1039/c3cc42864h] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Asahchop EL, Oliveira M, Quashie PK, Moisi D, Martinez-Cajas JL, Brenner BG, Tremblay CL, Wainberg MA. In vitro and structural evaluation of PL-100 as a potential second-generation HIV-1 protease inhibitor. J Antimicrob Chemother 2012; 68:105-12. [DOI: 10.1093/jac/dks342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Wang Y, Lin Y, Liu Y. Reactions of Propargyl Compounds Containing a Cyclobutyl Group Induced by a Ruthenium Complex. Chem Asian J 2012; 7:2703-10. [DOI: 10.1002/asia.201200589] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Yung‐Ching Wang
- Department of Chemistry, National Taiwan University, Taipei, 106 (Taiwan), Fax: (+886) 223636359
| | - Ying‐Chih Lin
- Department of Chemistry, National Taiwan University, Taipei, 106 (Taiwan), Fax: (+886) 223636359
| | - Yi‐Hung Liu
- Department of Chemistry, National Taiwan University, Taipei, 106 (Taiwan), Fax: (+886) 223636359
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Chang YCE, Yu X, Zhang Y, Tie Y, Wang YF, Yashchuk S, Ghosh AK, Harrison RW, Weber IT. Potent antiviral HIV-1 protease inhibitor GRL-02031 adapts to the structures of drug resistant mutants with its P1'-pyrrolidinone ring. J Med Chem 2012; 55:3387-97. [PMID: 22401672 PMCID: PMC3355519 DOI: 10.1021/jm300072d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
GRL-02031 (1) is an HIV-1 protease (PR) inhibitor containing a novel P1' (R)-aminomethyl-2-pyrrolidinone group. Crystal structures at resolutions of 1.25-1.55 Å were analyzed for complexes of 1 with the PR containing major drug resistant mutations, PR(I47V), PR(L76V), PR(V82A), and PR(N88D). Mutations of I47V and V82A alter residues in the inhibitor-binding site, while L76V and N88D are distal mutations having no direct contact with the inhibitor. Substitution of a smaller amino acid in PR(I47V) and PR(L76V) and the altered charge of PR(N88D) are associated with significant local structural changes compared to the wild-type PR(WT), while substitution of alanine in PR(V82A) increases the size of the S1' subsite. The P1' pyrrolidinone group of 1 accommodates to these local changes by assuming two different conformations. Overall, the conformation and interactions of 1 with PR mutants resemble those of PR(WT) with similar inhibition constants in good agreement with the antiviral potency on multidrug resistant HIV-1.
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Affiliation(s)
- Yu Chung E. Chang
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
| | - XiaXia Yu
- Department of Computer Science, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
| | - Ying Zhang
- Department of Chemistry, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
| | - Yunfeng Tie
- Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
| | - Yuan Fang Wang
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
| | - Sofiya Yashchuk
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Robert W. Harrison
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
,Department of Computer Science, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
| | - Irene T. Weber
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
,Department of Chemistry, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
,To whom correspondence should be addressed. I.T. Weber, Department of Biology, Georgia State University, P.O. Box 4010, Atlanta, GA 30302, USA; Tel: (404) 413-5411; Fax: (404) 413-5301;
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Ghosh AK, Anderson DD, Weber IT, Mitsuya H. Enhancing protein backbone binding--a fruitful concept for combating drug-resistant HIV. Angew Chem Int Ed Engl 2012; 51:1778-802. [PMID: 22290878 PMCID: PMC7159617 DOI: 10.1002/anie.201102762] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Indexed: 12/02/2022]
Abstract
The evolution of drug resistance is one of the most fundamental problems in medicine. In HIV/AIDS, the rapid emergence of drug-resistant HIV-1 variants is a major obstacle to current treatments. HIV-1 protease inhibitors are essential components of present antiretroviral therapies. However, with these protease inhibitors, resistance occurs through viral mutations that alter inhibitor binding, resulting in a loss of efficacy. This loss of potency has raised serious questions with regard to effective long-term antiretroviral therapy for HIV/AIDS. In this context, our research has focused on designing inhibitors that form extensive hydrogen-bonding interactions with the enzyme's backbone in the active site. In doing so, we limit the protease's ability to acquire drug resistance as the geometry of the catalytic site must be conserved to maintain functionality. In this Review, we examine the underlying principles of enzyme structure that support our backbone-binding concept as an effective means to combat drug resistance and highlight their application in our recent work on antiviral HIV-1 protease inhibitors.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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41
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Substituent effects on P2-cyclopentyltetrahydrofuranyl urethanes: design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors. Bioorg Med Chem Lett 2012; 22:2308-11. [PMID: 22364812 DOI: 10.1016/j.bmcl.2012.01.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 01/17/2012] [Indexed: 11/21/2022]
Abstract
The design, synthesis, and biological evaluation of novel C3-substituted cyclopentyltetrahydrofuranyl (Cp-THF)-derived HIV-1 protease inhibitors are described. Various C3-functional groups on the Cp-THF ligand were investigated in order to maximize the ligand-binding site interactions in the flap region of the protease. Inhibitors 3c and 3d have displayed the most potent enzyme inhibitory and antiviral activity. Both inhibitors have maintained impressive activity against a panel of multidrug resistant HIV-1 variants. A high-resolution X-ray crystal structure of 3c-bound HIV-1 protease revealed a number of important molecular insights into the ligand-binding site interactions.
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42
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Ghosh AK, Anderson DD, Weber IT, Mitsuya H. Verstärkung der Bindung an das Proteinrückgrat - ein fruchtbares Konzept gegen die Arzneimittelresistenz von HIV. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201102762] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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43
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Degoey DA, Grampovnik DJ, Chen HJ, Flosi WJ, Klein LL, Dekhtyar T, Stoll V, Mamo M, Molla A, Kempf DJ. P1-substituted symmetry-based human immunodeficiency virus protease inhibitors with potent antiviral activity against drug-resistant viruses. J Med Chem 2011; 54:7094-104. [PMID: 21899332 DOI: 10.1021/jm201109t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Because there is currently no cure for HIV infection, patients must remain on long-term drug therapy, leading to concerns over potential drug side effects and the emergence of drug resistance. For this reason, new and safe antiretroviral agents with improved potency against drug-resistant strains of HIV are needed. A series of HIV protease inhibitors (PIs) with potent activity against both wild-type (WT) virus and drug-resistant strains of HIV was designed and synthesized. The incorporation of substituents with hydrogen bond donor and acceptor groups at the P1 position of our symmetry-based inhibitor series resulted in significant potency improvements against the resistant mutants. By this approach, several compounds, such as 13, 24, and 29, were identified that demonstrated similar or improved potencies compared to 1 against highly mutated strains of HIV derived from patients who previously failed HIV PI therapy. Overall, compound 13 demonstrated the best balance of potency against drug resistant strains of HIV and oral bioavailability in pharmacokinetic studies. X-ray analysis of an HIV PI with an improved resistance profile bound to WT HIV protease is also reported.
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Affiliation(s)
- David A Degoey
- Antiviral Research, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064, United States.
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44
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Munshi P, Padmanabhan S, Sullivan SZ, Mustafa TA, Brezden AM, Ghosh A. An Economically Viable Process for the Synthesis of a Chiral Oxazolidinone ((S)-4-Benzyl-2-oxazolidinone) from Amino Acid. PARTICULATE SCIENCE AND TECHNOLOGY 2011. [DOI: 10.1080/02726351.2010.510550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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45
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Ghosh AK, Chapsal BD, Parham GL, Steffey M, Agniswamy J, Wang YF, Amano M, Weber IT, Mitsuya H. Design of HIV-1 protease inhibitors with C3-substituted hexahydrocyclopentafuranyl urethanes as P2-ligands: synthesis, biological evaluation, and protein-ligand X-ray crystal structure. J Med Chem 2011; 54:5890-901. [PMID: 21800876 PMCID: PMC3164320 DOI: 10.1021/jm200649p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We report the design, synthesis, biological evaluation, and the X-ray crystal structure of a novel inhibitor bound to the HIV-1 protease. Various C3-functionalized cyclopentanyltetrahydrofurans (Cp-THF) were designed to interact with the flap Gly48 carbonyl or amide NH in the S2-subsite of the HIV-1 protease. We investigated the potential of those functionalized ligands in combination with hydroxyethylsulfonamide isosteres. Inhibitor 26 containing a 3-(R)-hydroxyl group on the Cp-THF core displayed the most potent enzyme inhibitory and antiviral activity. Our studies revealed a preference for the 3-(R)-configuration over the corresponding 3-(S)-derivative. Inhibitor 26 exhibited potent activity against a panel of multidrug-resistant HIV-1 variants. A high resolution X-ray structure of 26-bound HIV-1 protease revealed important molecular insight into the ligand-binding site interactions.
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Affiliation(s)
- Arun K. Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907,The corresponding author: Departments of Chemistry and Medicinal Chemistry Purdue University 560 Oval Drive West Lafayette, IN 47907 Phone: (765)-494-5323; Fax: (765)-496-1612
| | - Bruno D. Chapsal
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Garth L. Parham
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Melinda Steffey
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303
| | - Yuan-Fang Wang
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303
| | - Masayuki Amano
- Departments of Hematology and Infectious Diseases, Kumamoto University Graduate School of Medical and Pharmaceutical Sciences, Kumamoto 860-8556, Japan
| | - Irene T. Weber
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303
| | - Hiroaki Mitsuya
- Departments of Hematology and Infectious Diseases, Kumamoto University Graduate School of Medical and Pharmaceutical Sciences, Kumamoto 860-8556, Japan,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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46
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Ghosh AK, Anderson DD. Tetrahydrofuran, tetrahydropyran, triazoles and related heterocyclic derivatives as HIV protease inhibitors. Future Med Chem 2011; 3:1181-97. [PMID: 21806380 PMCID: PMC3164575 DOI: 10.4155/fmc.11.68] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
HIV/AIDS remains a formidable disease with millions of individuals inflicted worldwide. Although treatment regimens have improved considerably, drug resistance brought on by viral mutation continues to erode their effectiveness. Intense research efforts are currently underway in search of new and improved therapies. This review is concerned with the design of novel HIV-1 protease inhibitors that incorporate heterocyclic scaffolds and which have been reported within the recent literature (2005-2010). Various examples in this review showcase the essential role heterocycles play as scaffolds and bioisosteres in HIV-1 protease inhibitor drug development. This review will hopefully stimulate the widespread application of these heterocycles in the design of other therapeutic agents.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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47
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Loughlin WA, Tyndall JDA, Glenn MP, Hill TA, Fairlie DP. Update 1 of: Beta-Strand Mimetics. Chem Rev 2011; 110:PR32-69. [DOI: 10.1021/cr900395y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wendy A. Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Matthew P. Glenn
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Timothy A. Hill
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - David P. Fairlie
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
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Ali A, Bandaranayake RM, Cai Y, King NM, Kolli M, Mittal S, Murzycki JF, Nalam MN, Nalivaika EA, Özen A, Prabu-Jeyabalan MM, Thayer K, Schiffer CA. Molecular Basis for Drug Resistance in HIV-1 Protease. Viruses 2010; 2:2509-2535. [PMID: 21994628 PMCID: PMC3185577 DOI: 10.3390/v2112509] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 10/22/2010] [Accepted: 10/28/2010] [Indexed: 02/01/2023] Open
Abstract
HIV-1 protease is one of the major antiviral targets in the treatment of patients infected with HIV-1. The nine FDA approved HIV-1 protease inhibitors were developed with extensive use of structure-based drug design, thus the atomic details of how the inhibitors bind are well characterized. From this structural understanding the molecular basis for drug resistance in HIV-1 protease can be elucidated. Selected mutations in response to therapy and diversity between clades in HIV-1 protease have altered the shape of the active site, potentially altered the dynamics and even altered the sequence of the cleavage sites in the Gag polyprotein. All of these interdependent changes act in synergy to confer drug resistance while simultaneously maintaining the fitness of the virus. New strategies, such as incorporation of the substrate envelope constraint to design robust inhibitors that incorporate details of HIV-1 protease’s function and decrease the probability of drug resistance, are necessary to continue to effectively target this key protein in HIV-1 life cycle.
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Affiliation(s)
- Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Rajintha M. Bandaranayake
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Yufeng Cai
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Nancy M. King
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Madhavi Kolli
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Seema Mittal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Jennifer F. Murzycki
- Department of Pediatrics, University of Rochester, Rochester, NY 14627, USA; E-Mail:
| | - Madhavi N.L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Ayşegül Özen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Moses M. Prabu-Jeyabalan
- Division of Basic Sciences, The Commonwealth Medical College, 150 N. Washington Avenue, Scranton, PA 18503, USA; E-Mail:
| | - Kelly Thayer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; E-Mails: (A.A.); (R.M.B.); (Y.C.); (N.M.K.); (M.K.); (S.M.), (M.N.L.N.); (E.A.N.); (A.Ö.); (K.T.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-508-856-8008; Fax: +1-508-856-6464
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Ghosh AK, Xu CX, Rao KV, Baldridge A, Agniswamy J, Wang YF, Weber IT, Aoki M, Miguel SGP, Amano M, Mitsuya H. Probing multidrug-resistance and protein-ligand interactions with oxatricyclic designed ligands in HIV-1 protease inhibitors. ChemMedChem 2010; 5:1850-4. [PMID: 20827746 PMCID: PMC3523686 DOI: 10.1002/cmdc.201000318] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Indexed: 11/12/2022]
Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA.
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50
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Gonçalves RS, Abdelnur PV, Santos VG, Simas RC, Eberlin MN, Magalhães A, Pérez González ER. Synthesis of potentially bioactive PABA-related N-(aminoalkyl)lactamic amino acids and esters via selective S(N)Ar reactions. Amino Acids 2010; 40:197-204. [PMID: 20512597 DOI: 10.1007/s00726-010-0634-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Accepted: 05/15/2010] [Indexed: 11/26/2022]
Abstract
Potentially bioactive N-(aminoalkyl)lactamic amino acids and esters were synthesized in satisfactory to good yields by S(N)Ar reactions of aromatic acids with N-(3-aminopropyl)lactams followed by esterification with tertiary amino alcohols. The addition-elimination S(N)Ar mechanism was confirmed by NMR and MS measurements.
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Affiliation(s)
- Renato S Gonçalves
- Programa de Pós-Graduação em Ciência e Tecnologia de Materiais (POSMAT), Universidade Estadual Paulista, São Paulo, Brazil
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