1
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Wang Z, Zhang H, Gao Z, Sang Z, De Clercq E, Pannecouque C, Kang D, Zhan P, Liu X. Structure-based design and optimization lead to the identification of novel dihydrothiopyrano[3,2- d]pyrimidine derivatives as potent HIV-1 inhibitors against drug-resistant variants. Acta Pharm Sin B 2024; 14:1257-1282. [PMID: 38486991 PMCID: PMC10935503 DOI: 10.1016/j.apsb.2023.11.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/03/2023] [Accepted: 11/14/2023] [Indexed: 03/17/2024] Open
Abstract
With our continuous endeavors in seeking potent anti-HIV-1 agents, we reported here the discovery, biological characterization, and druggability evaluation of a class of nonnucleoside reverse transcriptase inhibitors. To fully explore the chemical space of the NNRTI-binding pocket, novel series of dihydrothiopyrano [3,2-d]pyrimidines were developed by employing the structure-based design strategy. Most of the derivatives were endowed with prominent antiviral activities against HIV-1 wild-type and resistant strains at nanomolar levels. Among them, compound 23h featuring the aminopiperidine moiety was identified as the most potent inhibitor, with EC50 values ranging from 3.43 to 21.4 nmol/L. Especially, for the challenging double-mutants F227L + V106A and K103N + Y181C, 23h exhibited 2.3- to 14.5-fold more potent activity than the first-line drugs efavirenz and etravirine. Besides, the resistance profiles of 23h achieved remarkable improvement compared to efavirenz and etravirine. The binding target of 23h was further confirmed to be HIV-1 reverse transcriptase. Molecular modeling studies were also performed to elucidate the biological evaluation results and give guidance for the optimization campaign. Furthermore, no apparent inhibition of the major CYP450 enzymes and hERG channel was observed for 23h. Most importantly, 23h was characterized by good pharmacokinetic properties and excellent safety in vivo. Collectively, 23h holds great promise as a potential candidate for its effective antiviral efficacy and favorable drug-like profiles.
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Affiliation(s)
- Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan 250012, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, China
| | - Heng Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Zhen Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Zihao Sang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Leuven B-3000, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Leuven B-3000, Belgium
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan 250012, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan 250012, China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan 250012, China
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2
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Vanangamudi M, Palaniappan S, Kathiravan MK, Namasivayam V. Strategies in the Design and Development of Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs). Viruses 2023; 15:1992. [PMID: 37896769 PMCID: PMC10610861 DOI: 10.3390/v15101992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
AIDS (acquired immunodeficiency syndrome) is a potentially life-threatening infectious disease caused by human immunodeficiency virus (HIV). To date, thousands of people have lost their lives annually due to HIV infection, and it continues to be a big public health issue globally. Since the discovery of the first drug, Zidovudine (AZT), a nucleoside reverse transcriptase inhibitor (NRTI), to date, 30 drugs have been approved by the FDA, primarily targeting reverse transcriptase, integrase, and/or protease enzymes. The majority of these drugs target the catalytic and allosteric sites of the HIV enzyme reverse transcriptase. Compared to the NRTI family of drugs, the diverse chemical class of non-nucleoside reverse transcriptase inhibitors (NNRTIs) has special anti-HIV activity with high specificity and low toxicity. However, current clinical usage of NRTI and NNRTI drugs has limited therapeutic value due to their adverse drug reactions and the emergence of multidrug-resistant (MDR) strains. To overcome drug resistance and efficacy issues, combination therapy is widely prescribed for HIV patients. Combination antiretroviral therapy (cART) includes more than one antiretroviral agent targeting two or more enzymes in the life cycle of the virus. Medicinal chemistry researchers apply different optimization strategies including structure- and fragment-based drug design, prodrug approach, scaffold hopping, molecular/fragment hybridization, bioisosterism, high-throughput screening, covalent-binding, targeting highly hydrophobic channel, targeting dual site, and multi-target-directed ligand to identify and develop novel NNRTIs with high antiviral activity against wild-type (WT) and mutant strains. The formulation experts design various delivery systems with single or combination therapies and long-acting regimens of NNRTIs to improve pharmacokinetic profiles and provide sustained therapeutic effects.
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Affiliation(s)
- Murugesan Vanangamudi
- Department of Pharmaceutical Chemistry, Amity Institute of Pharmacy, Amity University Madhya Pradesh, Gwalior 474005, Madhya Pradesh, India;
| | - Senthilkumar Palaniappan
- Faculty of Pharmacy, Karpagam Academy of Higher Education, Coimbatore 641021, Tamilnadu, India;
- Center for Active Pharmaceutical Ingredients, Karpagam Academy of Higher Education, Coimbatore 641021, Tamilnadu, India
| | - Muthu Kumaradoss Kathiravan
- Dr. APJ Abdul Kalam Research Lab, SRM College of Pharmacy, SRMIST, Kattankulathur 603203, Tamilnadu, India;
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRMIST, Kattankulathur 603203, Tamilnadu, India
| | - Vigneshwaran Namasivayam
- Pharmaceutical Chemistry, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
- LIED, University of Lübeck and University Medical Center Schleswig-Holstein, Ratzeburger Allee 160, 23538 Lübeck, Germany
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3
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Sun Y, Zhou Z, Feng D, Jing L, Zhao F, Wang Z, Zhang T, Lin H, Song H, De Clercq E, Pannecouque C, Zhan P, Liu X, Kang D. Lead Optimization and Avoidance of Metabolic-perturbing Motif Developing Novel Diarylpyrimidines as Potent HIV-1 NNRTIs. J Med Chem 2022; 65:15608-15626. [PMID: 36411036 DOI: 10.1021/acs.jmedchem.2c00576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) represent an indispensable part of anti-HIV-1 therapy. To discover novel HIV-1 NNRTIs with increased drug resistance profiles and improved pharmacokinetic (PK) properties, a series of novel diarylpyrimidine derivatives were generated via the cocrystal structure-based drug design strategy. Among them, 36a exhibited outstanding antiviral activity against HIV-1 IIIB and a panel of mutant strains (L100I, K103N, Y181C, Y188L, E138K, F227L + V106A, and RES056), with EC50 ranging from 2.22 to 53.3 nM. Besides, 36a was identified with higher binding affinity (KD = 2.50 μM) and inhibitory activity (IC50 = 0.03 μM) to HIV-1 RT. Molecular docking and molecular dynamics simulation were performed to rationalize the design and the improved drug resistance of these novel inhibitors. Additionally, 36a·HCl exhibited favorable PK (T1/2 = 5.12 h, F = 12.1%) and safety properties (LD50 > 2000 mg/kg). All these suggested that 36a·HCl may serve as a novel drug candidate anti-HIV-1 therapy.
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Affiliation(s)
- Yanying Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Zhenzhen Zhou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Da Feng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Lanlan Jing
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Fabao Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Tao Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Hao Lin
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Hao Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 250012 Jinan, P.R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 250012 Jinan, P.R. China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 250012 Jinan, P.R. China
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4
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Wang Z, Cherukupalli S, Xie M, Wang W, Jiang X, Jia R, Pannecouque C, De Clercq E, Kang D, Zhan P, Liu X. Contemporary Medicinal Chemistry Strategies for the Discovery and Development of Novel HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors. J Med Chem 2022; 65:3729-3757. [PMID: 35175760 DOI: 10.1021/acs.jmedchem.1c01758] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) are a major component of the highly active anti-retroviral therapy (HAART) regimen. However, the occurrence of drug-resistant strains and adverse reactions after long-term usage have inevitably compromised the clinical application of NNRTIs. Therefore, the development of novel inhibitors with distinct anti-resistance profiles and better pharmacological properties is still an enormous challenge. Herein, we summarize state-of-the-art medicinal chemistry strategies for the discovery of potent NNRTIs, such as structure-based design strategies, contemporary computer-aided drug design, covalent-binding strategies, and the application of multi-target-directed ligands. The strategies described here will facilitate the identification of promising HIV-1 NNRTIs.
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Affiliation(s)
- Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Minghui Xie
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Wenbo Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Ruifang Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
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5
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Frey KM, Bertoletti N, Chan AH, Ippolito JA, Bollini M, Spasov KA, Jorgensen WL, Anderson KS. Structural Studies and Structure Activity Relationships for Novel Computationally Designed Non-nucleoside Inhibitors and Their Interactions With HIV-1 Reverse Transcriptase. Front Mol Biosci 2022; 9:805187. [PMID: 35237658 PMCID: PMC8882919 DOI: 10.3389/fmolb.2022.805187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Reverse transcriptase (RT) from the human immunodeficiency virus continues to be an attractive drug target for antiretroviral therapy. June 2022 will commemorate the 30th anniversary of the first Human Immunodeficiency Virus (HIV) RT crystal structure complex that was solved with non-nucleoside reverse transcriptase inhibitor nevirapine. The release of this structure opened opportunities for designing many families of non-nucleoside reverse transcriptase inhibitors (NNRTIs). In paying tribute to the first RT-nevirapine structure, we have developed several compound classes targeting the non-nucleoside inhibitor binding pocket of HIV RT. Extensive analysis of crystal structures of RT in complex with the compounds informed iterations of structure-based drug design. Structures of seven additional complexes were determined and analyzed to summarize key interactions with residues in the non-nucleoside inhibitor binding pocket (NNIBP) of RT. Additional insights comparing structures with antiviral data and results from molecular dynamics simulations elucidate key interactions and dynamics between the nucleotide and non-nucleoside binding sites.
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Affiliation(s)
- Kathleen M. Frey
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
| | - Nicole Bertoletti
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
| | - Albert H. Chan
- Department of Chemistry, Yale University, New Haven, CT, United States
| | | | - Mariela Bollini
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Krasimir A. Spasov
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
| | | | - Karen S. Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, United States
- *Correspondence: Karen S. Anderson,
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6
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Beloor J, Kudalkar SN, Buzzelli G, Yang F, Mandl HK, Rajashekar JK, Spasov KA, Jorgensen WL, Saltzman WM, Anderson KS, Kumar P. Long-acting and extended-release implant and nanoformulations with a synergistic antiretroviral two-drug combination controls HIV-1 infection in a humanized mouse model. Bioeng Transl Med 2022; 7:e10237. [PMID: 35079625 PMCID: PMC8780078 DOI: 10.1002/btm2.10237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/23/2021] [Accepted: 06/04/2021] [Indexed: 11/21/2022] Open
Abstract
The HIV pandemic has affected over 38 million people worldwide with close to 26 million currently accessing antiretroviral therapy (ART). A major challenge in the long-term treatment of HIV-1 infection is nonadherence to ART. Long-acting antiretroviral (LA-ARV) formulations, that reduce dosing frequency to less than once a day, are an urgent need that could tackle the adherence issue. Here, we have developed two LA-ART interventions, one an injectable nanoformulation, and the other, a removable implant, for the delivery of a synergistic two-drug ARV combination comprising a pre-clinical nonnucleoside reverse transcriptase inhibitor (NNRTI), Compound I, and the nucleoside reverse transcriptase inhibitor (NRTI), 4'-ethynyl-2-fluoro-2'-deoxyadenosine. The nanoformulation is poly(lactide-co-glycolide)-based and the implant is a copolymer of ω-pentadecalactone and p-dioxanone, poly(PDL-co-DO), a novel class of biocompatible, biodegradable materials. Both the interventions, packaged independently with each ARV, released sustained levels of the drugs, maintaining plasma therapeutic indices for over a month, and suppressed viremia in HIV-1-infected humanized mice for up to 42 days with maintenance of CD4+ T cells. These data suggest promise in the use of these new drugs as LA-ART formulations in subdermal implant and injectable mode.
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Affiliation(s)
- Jagadish Beloor
- Department of Internal Medicine, Section of Infectious DiseasesYale University School of MedicineNew HavenConnecticutUSA
| | - Shalley N. Kudalkar
- Department of PharmacologyYale University School of MedicineNew HavenConnecticutUSA
- Department of Molecular Biophysics and BiochemistryYale University School of MedicineNew HavenConnecticutUSA
| | - Gina Buzzelli
- Department of Biomedical EngineeringYale UniversityNew HavenConnecticutUSA
| | - Fan Yang
- Department of Biomedical EngineeringYale UniversityNew HavenConnecticutUSA
| | - Hanna K. Mandl
- Department of Biomedical EngineeringYale UniversityNew HavenConnecticutUSA
| | - Jyothi K. Rajashekar
- Department of Internal Medicine, Section of Infectious DiseasesYale University School of MedicineNew HavenConnecticutUSA
| | - Krasimir A. Spasov
- Department of PharmacologyYale University School of MedicineNew HavenConnecticutUSA
- Department of Molecular Biophysics and BiochemistryYale University School of MedicineNew HavenConnecticutUSA
| | | | - W. Mark Saltzman
- Department of Biomedical EngineeringYale UniversityNew HavenConnecticutUSA
| | - Karen S. Anderson
- Department of PharmacologyYale University School of MedicineNew HavenConnecticutUSA
- Department of Molecular Biophysics and BiochemistryYale University School of MedicineNew HavenConnecticutUSA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious DiseasesYale University School of MedicineNew HavenConnecticutUSA
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7
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Zavitsanou S, Tsengenes A, Papadourakis M, Amendola G, Chatzigoulas A, Dellis D, Cosconati S, Cournia Z. FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations. J Chem Inf Model 2021; 61:4131-4138. [PMID: 34519200 DOI: 10.1021/acs.jcim.1c00215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Relative binding free energy calculations in drug design are becoming a useful tool in facilitating lead binding affinity optimization in a cost- and time-efficient manner. However, they have been limited by technical challenges such as the manual creation of large numbers of input files to set up, run, and analyze free energy simulations. In this Application Note, we describe FEPrepare, a novel web-based tool, which automates the setup procedure for relative binding FEP calculations for the dual-topology scheme of NAMD, one of the major MD engines, using OPLS-AA force field topology and parameter files. FEPrepare provides the user with all necessary files needed to run a FEP/MD simulation with NAMD. FEPrepare can be accessed and used at https://feprepare.vi-seem.eu/.
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Affiliation(s)
- Stamatia Zavitsanou
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece.,Information Technologies in Medicine and Biology, Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Alexandros Tsengenes
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Michail Papadourakis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Giorgio Amendola
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Alexios Chatzigoulas
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece.,Information Technologies in Medicine and Biology, Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Dimitris Dellis
- Greek Research and Technology Network, S.A., 7 Kifissias Avenue, 11523 Athens, Greece
| | - Sandro Cosconati
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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8
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Chatzigoulas A, Cournia Z. Rational design of allosteric modulators: Challenges and successes. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1529] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alexios Chatzigoulas
- Biomedical Research Foundation Academy of Athens Athens Greece
- Department of Informatics and Telecommunications National and Kapodistrian University of Athens Athens Greece
| | - Zoe Cournia
- Biomedical Research Foundation Academy of Athens Athens Greece
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9
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Rajashekar JK, Richard J, Beloor J, Prévost J, Anand SP, Beaudoin-Bussières G, Shan L, Herndler-Brandstetter D, Gendron-Lepage G, Medjahed H, Bourassa C, Gaudette F, Ullah I, Symmes K, Peric A, Lindemuth E, Bibollet-Ruche F, Park J, Chen HC, Kaufmann DE, Hahn BH, Sodroski J, Pazgier M, Flavell RA, Smith AB, Finzi A, Kumar P. Modulating HIV-1 envelope glycoprotein conformation to decrease the HIV-1 reservoir. Cell Host Microbe 2021; 29:904-916.e6. [PMID: 34019804 PMCID: PMC8214472 DOI: 10.1016/j.chom.2021.04.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 02/01/2021] [Accepted: 04/20/2021] [Indexed: 11/21/2022]
Abstract
Small CD4-mimetic compounds (CD4mc) sensitize HIV-1-infected cells to antibody-dependent cellular cytotoxicity (ADCC) by facilitating antibody recognition of epitopes that are otherwise occluded on the unliganded viral envelope (Env). Combining CD4mc with two families of CD4-induced (CD4i) antibodies, which are frequently found in plasma of HIV-1-infected individuals, stabilizes Env in a conformation that is vulnerable to ADCC. We employed new-generation SRG-15 humanized mice, supporting natural killer (NK) cell and Fc-effector functions to demonstrate that brief treatment with CD4mc and CD4i-Abs significantly decreases HIV-1 replication, the virus reservoir and viral rebound after ART interruption. These effects required Fc-effector functions and NK cells, highlighting the importance of ADCC. Viral rebound was also suppressed in HIV-1+-donor cell-derived humanized mice supplemented with autologous HIV-1+-donor-derived plasma and CD4mc. These results indicate that CD4mc could have therapeutic utility in infected individuals for decreasing the size of the HIV-1 reservoir and/or achieving a functional cure.
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Affiliation(s)
- Jyothi K Rajashekar
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Canada
| | - Jagadish Beloor
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University Montreal, Montreal, QC, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Canada
| | - Liang Shan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | | | | | | | | | - Irfan Ullah
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Kelly Symmes
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew Peric
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Emily Lindemuth
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederic Bibollet-Ruche
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jun Park
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Hung-Ching Chen
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, and Department of Microbiology and Immunobiology, Division of AIDS, Harvard Medical School, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Marzena Pazgier
- Infectious Diseases Division, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| | - Amos B Smith
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA.
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Canada; Department of Microbiology and Immunology, McGill University Montreal, Montreal, QC, Canada.
| | - Priti Kumar
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA.
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10
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Zhang CH, Stone EA, Deshmukh M, Ippolito JA, Ghahremanpour MM, Tirado-Rives J, Spasov KA, Zhang S, Takeo Y, Kudalkar SN, Liang Z, Isaacs F, Lindenbach B, Miller SJ, Anderson KS, Jorgensen WL. Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations. ACS CENTRAL SCIENCE 2021; 7:467-475. [PMID: 33786375 PMCID: PMC7931627 DOI: 10.1021/acscentsci.1c00039] [Citation(s) in RCA: 170] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Indexed: 05/07/2023]
Abstract
Starting from our previous finding of 14 known drugs as inhibitors of the main protease (Mpro) of SARS-CoV-2, the virus responsible for COVID-19, we have redesigned the weak hit perampanel to yield multiple noncovalent, nonpeptidic inhibitors with ca. 20 nM IC50 values in a kinetic assay. Free-energy perturbation (FEP) calculations for Mpro-ligand complexes provided valuable guidance on beneficial modifications that rapidly delivered the potent analogues. The design efforts were confirmed and augmented by determination of high-resolution X-ray crystal structures for five analogues bound to Mpro. Results of cell-based antiviral assays further demonstrated the potential of the compounds for treatment of COVID-19. In addition to the possible therapeutic significance, the work clearly demonstrates the power of computational chemistry for drug discovery, especially FEP-guided lead optimization.
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Affiliation(s)
- Chun-Hui Zhang
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Elizabeth A. Stone
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Maya Deshmukh
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
- M.
D. – Ph. D. Program, Yale University
School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Joseph A. Ippolito
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
| | | | - Julian Tirado-Rives
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Krasimir A. Spasov
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Shuo Zhang
- Department
of Microbial Pathogenesis, Yale University
School of Medicine, New Haven, Connecticut 06536-0812, United States
| | - Yuka Takeo
- Department
of Microbial Pathogenesis, Yale University
School of Medicine, New Haven, Connecticut 06536-0812, United States
| | - Shalley N. Kudalkar
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Zhuobin Liang
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, United States
| | - Farren Isaacs
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, United States
| | - Brett Lindenbach
- Department
of Microbial Pathogenesis, Yale University
School of Medicine, New Haven, Connecticut 06536-0812, United States
| | - Scott J. Miller
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Karen S. Anderson
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - William L. Jorgensen
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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11
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Ippolito JA, Niu H, Bertoletti N, Carter ZJ, Jin S, Spasov KA, Cisneros JA, Valhondo M, Cutrona KJ, Anderson KS, Jorgensen WL. Covalent Inhibition of Wild-Type HIV-1 Reverse Transcriptase Using a Fluorosulfate Warhead. ACS Med Chem Lett 2021; 12:249-255. [PMID: 33603971 DOI: 10.1021/acsmedchemlett.0c00612] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/04/2021] [Indexed: 11/28/2022] Open
Abstract
Covalent inhibitors of wild-type HIV-1 reverse transcriptase (CRTIs) are reported. Three compounds derived from catechol diether non-nucleoside inhibitors (NNRTIs) with addition of a fluorosulfate warhead are demonstrated to covalently modify Tyr181 of HIV-RT. X-ray crystal structures for complexes of the CRTIs with the enzyme are provided, which fully demonstrate the covalent attachment, and confirmation is provided by appropriate mass shifts in ESI-TOF mass spectra. The three CRTIs and six noncovalent analogues are found to be potent inhibitors with both IC50 values for in vitro inhibition of WT RT and EC50 values for cytopathic protection of HIV-1-infected human T-cells in the 5-320 nM range.
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Affiliation(s)
- Joseph A. Ippolito
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Haichan Niu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
| | - Nicole Bertoletti
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Zachary J. Carter
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
| | - Shengyan Jin
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Krasimir A. Spasov
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - José A. Cisneros
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
| | - Margarita Valhondo
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
| | - Kara J. Cutrona
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
| | - Karen S. Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - William L. Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
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12
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Panwar U, Chandra I, Selvaraj C, Singh SK. Current Computational Approaches for the Development of Anti-HIV Inhibitors: An Overview. Curr Pharm Des 2020; 25:3390-3405. [PMID: 31538884 DOI: 10.2174/1381612825666190911160244] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/05/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Today, HIV-1 infection has become an extensive problem to public health and a greater challenge to all working researchers throughout the world. Since the beginning of HIV-1 virus, several antiviral therapeutic agents have been developed at various stages to combat HIV-1 infection. But, many of antiviral drugs are on the platform of drug resistance and toxicology issues, needs an urgent constructive investigation for the development of productive and protective therapeutics to make an improvement of individual life suffering with viral infection. As developing a novel agent is very costly, challenging and time taking route in the recent times. METHODS The review summarized about the modern approaches of computational aided drug discovery to developing a novel inhibitor within a short period of time and less cost. RESULTS The outcome suggests on the premise of reported information that the computational drug discovery is a powerful technology to design a defensive and fruitful therapeutic agents to combat HIV-1 infection and recover the lifespan of suffering one. CONCLUSION Based on survey of the reported information, we concluded that the current computational approaches is highly supportive in the progress of drug discovery and controlling the viral infection.
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Affiliation(s)
- Umesh Panwar
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 004, Tamil Nadu, India
| | - Ishwar Chandra
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 004, Tamil Nadu, India
| | - Chandrabose Selvaraj
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice, Czech Republic
| | - Sanjeev K Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 004, Tamil Nadu, India
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13
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Vattathara JJ, Prakash O, Subhramanian S, Satheeshkumar MK, Xavier T, Anil M, Pillai GS, Anandakuttan A, Radhakrishnan S, Sivanarayanan TB, Akk U, Mohan CG, Menon KN. Substrate Specific Inhibitor Designed against the Immunomodulator GMF-beta Reversed the Experimental Autoimmune Encephalomyelitis. Sci Rep 2020; 10:3790. [PMID: 32123210 PMCID: PMC7051966 DOI: 10.1038/s41598-020-60710-2] [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: 08/19/2019] [Accepted: 02/14/2020] [Indexed: 01/16/2023] Open
Abstract
The concept of substrate inhibition to prevent its phosphorylation has potential in drug discovery and is envisioned to treat the autoimmune disorder multiple sclerosis (MS). Glia maturation factor-β (GMF-β) Ser83 phosphorylation by protein kinase A (PKA) is pivotal in the activation of GMF-β-p38MAPK-NFκB biochemical pathway towards proinflammatory response induction in experimental autoimmune encephalomyelitis (EAE). Using structure-based drug design, we identified the small molecule inhibitor 1-H-indazole-4yl methanol (GMFBI.1) that specifically blocked Ser83 phosphorylation site on GMF-β substrate. Using in vitro and in vivo techniques, molecular mechanism of action of GMFBI.1’s direct interaction with GMF-β substrate and prevention of its Ser83 phosphorylation was established. GMFBI.1 down regulated p38MAPK phosphorylation and NFκB expression essential for proinflammatory response. Further, GMFBI.1 administration at peak of EAE reversed clinical symptoms, immunopathology, proinflammatory cytokine response and up regulated the anti-inflammatory cytokines. Present strategy of substrate inhibition against the key immunomodulatory target has immense therapeutic potential in MS.
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Affiliation(s)
- Jane Jose Vattathara
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682 041, Kerala, India
| | - Ohm Prakash
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682 041, Kerala, India
| | - Sunitha Subhramanian
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682 041, Kerala, India
| | - Madathiparambil Kumaran Satheeshkumar
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682 041, Kerala, India
| | - Tessy Xavier
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682 041, Kerala, India
| | - Meenakshi Anil
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682 041, Kerala, India
| | - Gopal S Pillai
- Department of Ophthalmology, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682 041, Kerala, India
| | - Anandkumar Anandakuttan
- Department of Neurology, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682 041, Kerala, India
| | - Sureshkumar Radhakrishnan
- Department of Neurology, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682 041, Kerala, India
| | - T B Sivanarayanan
- Central Animal Laboratory, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682 041, Kerala, India
| | - Unni Akk
- Central Animal Laboratory, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682 041, Kerala, India
| | - Chethampadi Gopi Mohan
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682 041, Kerala, India.
| | - Krishnakumar N Menon
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi-682 041, Kerala, India.
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14
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Wang Y, De Clercq E, Li G. Current and emerging non-nucleoside reverse transcriptase inhibitors (NNRTIs) for HIV-1 treatment. Expert Opin Drug Metab Toxicol 2019; 15:813-829. [PMID: 31556749 DOI: 10.1080/17425255.2019.1673367] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Introduction: Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are essential components of highly active antiretroviral therapy against HIV-1 infections. Here, we provide a comprehensive overview of approved and emerging NNRTIs. Areas covered: This review covers the latest trend of NNRTIs regarding their pharmacodynamics, pharmacokinetics, mechanisms of drug action, drug resistance as well as new applications such as two-drug regimens and long-acting formulations. Expert opinion: Since the first NNRTI, nevirapine, was approved in 1996, antiviral drug discovery led to the approval of seven NNRTIs, including nevirapine, delavirdine (discontinued), etravirine, elsulfavirine, efavirenz, rilpivirine, and doravirine. The latter three compounds with favorable pharmacodynamic profiles and minimal adverse effects are often combined with one integrase inhibitor or two NRTIs in once-daily fixed-dose tablets. NNRTI-anchored regimens have been approved as initial therapies in treatment-naïve patients (efficacy: 72% to 86%) or maintaining therapies in virologically-suppressed patients (efficacy: 91% to 95%). Future development of NNRTIs includes: (i) better resistance and cross-resistance profiles; (ii) reduction of drug burden by optimizing two-drug or three-drug combinations; and (iii) improvement of patient adherence by novel long-acting formulations with weekly or monthly administration. Overall, NNRTIs play an important role in the management of HIV-1 infections, especially in resource-limited countries.
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Affiliation(s)
- Yali Wang
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University , Changsha , Hunan , China
| | - Erik De Clercq
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research , Leuven , Belgium
| | - Guangdi Li
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University , Changsha , Hunan , China
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15
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Soni D, Bade AN, Gautam N, Herskovitz J, Ibrahim IM, Smith N, Wojtkiewicz MS, Dyavar Shetty BL, Alnouti Y, McMillan J, Gendelman HE, Edagwa BJ. Synthesis of a long acting nanoformulated emtricitabine ProTide. Biomaterials 2019; 222:119441. [PMID: 31472458 DOI: 10.1016/j.biomaterials.2019.119441] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 08/04/2019] [Accepted: 08/19/2019] [Indexed: 01/20/2023]
Abstract
While antiretroviral therapy (ART) has revolutionized treatment and prevention of human immunodeficiency virus type one (HIV-1) infection, regimen adherence, viral mutations, drug toxicities and access stigma and fatigue are treatment limitations. These have led to new opportunities for the development of long acting (LA) ART including implantable devices and chemical drug modifications. Herein, medicinal and formulation chemistry were used to develop LA prodrug nanoformulations of emtricitabine (FTC). A potent lipophilic FTC phosphoramidate prodrug (M2FTC) was synthesized then encapsulated into a poloxamer surfactant (NM2FTC). These modifications extended the biology, apparent drug half-life and antiretroviral activities of the formulations. NM2FTC demonstrated a >30-fold increase in macrophage and CD4+ T cell drug uptake with efficient conversion to triphosphates (FTC-TP). Intracellular FTC-TP protected macrophages against an HIV-1 challenge for 30 days. A single intramuscular injection of NM2FTC, at 45 mg/kg native drug equivalents, into Sprague Dawley rats resulted in sustained prodrug levels in blood, liver, spleen and lymph nodes and FTC-TP in lymph node and spleen cells at one month. In contrast, native FTC-TPs was present for one day. These results are an advance in the transformation of FTC into a LA agent.
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Affiliation(s)
- Dhruvkumar Soni
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Aditya N Bade
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nagsen Gautam
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jonathan Herskovitz
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ibrahim M Ibrahim
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nathan Smith
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Melinda S Wojtkiewicz
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Bhagya Laxmi Dyavar Shetty
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Yazen Alnouti
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - JoEllyn McMillan
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Howard E Gendelman
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Benson J Edagwa
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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16
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Sasaki T, Gannam ZTK, Kudalkar SN, Frey KM, Lee WG, Spasov KA, Jorgensen WL, Anderson KS. Molecular and cellular studies evaluating a potent 2-cyanoindolizine catechol diether NNRTI targeting wildtype and Y181C mutant HIV-1 reverse transcriptase. Bioorg Med Chem Lett 2019; 29:2182-2188. [PMID: 31281023 PMCID: PMC6690785 DOI: 10.1016/j.bmcl.2019.06.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 10/26/2022]
Abstract
The development of efficacious NNRTIs for HIV/AIDS therapy is commonly met with the emergence of drug resistant strains, including the Y181C variant. Using a computationally-guided approach, we synthesized the catechol diether series of NNRTIs, which display sub-nanomolar potency in cellular assays. Among the most potent were a series of 2-cyanoindolizine substituted catechol diethers, including Compound 1. We present here a thorough evaluation of this compound, including biochemical, cellular, and structural studies. The compound demonstrates low nanomolar potency against both WT and Y181C HIV-1 RT in in vitro and cellular assays. Our crystal structures of both the wildtype and mutant forms of RT in complex with Compound 1 allow the interrogation of this compound's features that allow it to maintain strong efficacy against the drug resistant mutant. Among these are compensatory shifts in the NNRTI binding pocket, persistence of multiple hydrogen bonds, and van der Waals contacts throughout the binding site. Further, the fluorine at the C6 position of the indolizine moiety makes multiple favorable interactions with both RT forms. The present study highlights the indolizine-substituted catechol diether class of NNRTIs as promising therapeutic candidates possessing optimal pharmacological properties and significant potency against multiple RT variants.
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Affiliation(s)
- Tomoaki Sasaki
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States
| | - Zira T K Gannam
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States
| | - Shalley N Kudalkar
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States
| | - Kathleen M Frey
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States
| | - Won-Gil Lee
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06520, United States
| | - Krasimir A Spasov
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06520, United States
| | - Karen S Anderson
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States; Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, New Haven, CT 06520, United States.
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17
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Kudalkar SN, Ullah I, Bertoletti N, Mandl HK, Cisneros JA, Beloor J, Chan AH, Quijano E, Saltzman WM, Jorgensen WL, Kumar P, Anderson KS. Structural and pharmacological evaluation of a novel non-nucleoside reverse transcriptase inhibitor as a promising long acting nanoformulation for treating HIV. Antiviral Res 2019; 167:110-116. [PMID: 31034849 PMCID: PMC6554724 DOI: 10.1016/j.antiviral.2019.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/23/2019] [Indexed: 11/24/2022]
Abstract
Combination antiretroviral therapy (cART) has been proven effective in inhibiting human immunodeficiency virus type 1 (HIV-1) infection and has significantly improved the health outcomes in acquired immune deficiency syndrome (AIDS) patients. The therapeutic benefits of cART have been challenged because of the toxicity and emergence of drug-resistant HIV-1 strains along with lifelong patient compliance resulting in non-adherence. These issues also hinder the clinical benefits of non-nucleoside reverse transcriptase inhibitors (NNRTIs), which are one of the vital components of cART for the treatment of HIV-1 infection. In this study, using a computational and structural based drug design approach, we have discovered an effective HIV -1 NNRTI, compound I (Cmpd I) that is very potent in biochemical assays and which targets key residues in the allosteric binding pocket of wild-type (WT)-RT as revealed by structural studies. Furthermore, Cmpd I exhibited very potent antiviral activity in HIV-1 infected T cells, lacked cytotoxicity (therapeutic index >100,000), and no significant off-target effects were noted in pharmacological assays. To address the issue of non-adherence, we developed a long-acting nanoformulation of Cmpd I (Cmpd I-NP) using poly (lactide-coglycolide) (PLGA) particles. The pharmacokinetic studies of free and nanoformulated Cmpd I were carried out in BALB/c mice. Intraperitoneal administration of Cmpd I and Cmpd I-NP in BALB/c mice revealed prolonged serum residence time of 48 h and 30 days, respectively. The observed serum concentrations of Cmpd I in both cases were sufficient to provide >97% inhibition in HIV-1 infected T-cells. The significant antiviral activity along with favorable pharmacological and pharmacokinetic profile of Cmpd I, provide compelling and critical support for its further development as an anti-HIV therapeutic agent.
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Affiliation(s)
- Shalley N Kudalkar
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520-8066, USA
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nicole Bertoletti
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520-8066, USA
| | - Hanna K Mandl
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - José A Cisneros
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Jagadish Beloor
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Albert H Chan
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520-8066, USA
| | - Elias Quijano
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - W Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | | | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520-8066, USA.
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18
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Leporati A, Gupta S, Bolotin E, Castillo G, Alfaro J, Gottikh MB, Bogdanov AA. Antiretroviral Hydrophobic Core Graft-Copolymer Nanoparticles: The Effectiveness against Mutant HIV-1 Strains and in Vivo Distribution after Topical Application. Pharm Res 2019; 36:73. [PMID: 30919089 DOI: 10.1007/s11095-019-2604-9] [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] [Received: 12/07/2018] [Accepted: 03/05/2019] [Indexed: 11/25/2022]
Abstract
PURPOSE Developing and testing of microbicides for pre-exposure prophylaxis and post-exposure protection from HIV are on the list of major HIV/AIDS research priorities. To improve solubility and bioavailability of highly potent anti-retroviral drugs, we explored the use of a nanoparticle (NP) for formulating a combination of two water-insoluble HIV inhibitors. METHODS The combination of a non-nucleoside HIV reverse transcriptase inhibitor (NNRTI), Efavirenz (EFV), and an inhibitor of HIV integrase, Elvitegravir (ELV) was stabilized with a graft copolymer of methoxypolyethylene glycol-polylysine with a hydrophobic core (HC) composed of fatty acids (HC-PGC). Formulations were tested in TZM-bl cells infected either with wild-type HIV-1IIIB, or drug-resistant HIV-1 strains. In vivo testing of double-labeled NP formulations was performed in female rats after a topical intravaginal administration using SPECT/CT imaging and fluorescence microscopy. RESULTS We observed a formation of stable 23-30 nm NP with very low cytotoxicity when EFV and ELV were combined with HC-PGC at a 1:10 weight ratio. For NP containing ELV and EFV (at 1:1 by weight) we observed a remarkable improvement of EC50 of EFV by 20 times in the case of A17 strain. In vivo imaging and biodistribution showed in vivo presence of NP components at 24 and 48 h after administration, respectively. CONCLUSIONS insoluble orthogonal inhibitors of HIV-1 life cycle may be formulated into the non-aggregating ultrasmall NP which are highly efficient against NNRTI-resistant HIV-1 variant.
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Affiliation(s)
- Anita Leporati
- Laboratory of Molecular Imaging Probes, Department of Radiology, University of Massachusetts Medical School, S6-434, 55 Lake Ave North, Worcester, MA, 01655, USA
| | - Suresh Gupta
- Laboratory of Molecular Imaging Probes, Department of Radiology, University of Massachusetts Medical School, S6-434, 55 Lake Ave North, Worcester, MA, 01655, USA
| | - Elijah Bolotin
- PharmaIn Corp, 11812 North Creek Parkway N. Suite 10, Bothell, Washington, USA
| | - Gerardo Castillo
- PharmaIn Corp, 11812 North Creek Parkway N. Suite 10, Bothell, Washington, USA
| | - Joshua Alfaro
- PharmaIn Corp, 11812 North Creek Parkway N. Suite 10, Bothell, Washington, USA
| | - Marina B Gottikh
- A.N. Belozersky Institute of Physico-Chemical Biology and Department of Chemistry, Moscow State University, Moscow, Russia
| | - Alexei A Bogdanov
- Laboratory of Molecular Imaging Probes, Department of Radiology, University of Massachusetts Medical School, S6-434, 55 Lake Ave North, Worcester, MA, 01655, USA. .,Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia. .,Laboratory of Molecular Imaging, A. N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Laboratory of Molecular Imaging, Moscow, Russia.
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19
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Yang F, Zheng G, Fu T, Li X, Tu G, Li YH, Yao X, Xue W, Zhu F. Prediction of the binding mode and resistance profile for a dual-target pyrrolyl diketo acid scaffold against HIV-1 integrase and reverse-transcriptase-associated ribonuclease H. Phys Chem Chem Phys 2019; 20:23873-23884. [PMID: 29947629 DOI: 10.1039/c8cp01843j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The rapid emergence of drug-resistant variants is one of the most common causes of highly active antiretroviral therapeutic (HAART) failure in patients infected with HIV-1. Compared with the existing HAART, the recently developed pyrrolyl diketo acid scaffold targeting both HIV-1 integrase (IN) and reverse transcriptase-associated ribonuclease H (RNase H) is an efficient approach to counteract the failure of anti-HIV treatment due to drug resistance. However, the binding mode and potential resistance profile of these inhibitors with important mechanistic principles remain poorly understood. To address this issue, an integrated computational method was employed to investigate the binding mode of inhibitor JMC6F with HIV-1 IN and RNase H. By using per-residue binding free energy decomposition analysis, the following residues: Asp64, Thr66, Leu68, Asp116, Tyr143, Gln148 and Glu152 in IN, Asp443, Glu478, Trp536, Lys541 and Asp549 in RNase H were identified as key residues for JMC6F binding. And then computational alanine scanning was carried to further verify the key residues. Moreover, the resistance profile of the currently known major mutations in HIV-1 IN and 2 mutations in RNase H against JMC6F was predicted by in silico mutagenesis studies. The results demonstrated that only three mutations in HIV-1 IN (Y143C, Q148R and N155H) and two mutations in HIV-1 RNase H (Y501R and Y501W) resulted in a reduction of JMC6F potency, thus indicating their potential role in providing resistance to JMC6F. These data provided important insights into the binding mode and resistance profile of the inhibitors with a pyrrolyl diketo acid scaffold in HIV-1 IN and RNase H, which would be helpful for the development of more effective dual HIV-1 IN and RNase H inhibitors.
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Affiliation(s)
- Fengyuan Yang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China.
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20
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Zorn KM, Lane TR, Russo DP, Clark AM, Makarov V, Ekins S. Multiple Machine Learning Comparisons of HIV Cell-based and Reverse Transcriptase Data Sets. Mol Pharm 2019; 16:1620-1632. [PMID: 30779585 DOI: 10.1021/acs.molpharmaceut.8b01297] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The human immunodeficiency virus (HIV) causes over a million deaths every year and has a huge economic impact in many countries. The first class of drugs approved were nucleoside reverse transcriptase inhibitors. A newer generation of reverse transcriptase inhibitors have become susceptible to drug resistant strains of HIV, and hence, alternatives are urgently needed. We have recently pioneered the use of Bayesian machine learning to generate models with public data to identify new compounds for testing against different disease targets. The current study has used the NIAID ChemDB HIV, Opportunistic Infection and Tuberculosis Therapeutics Database for machine learning studies. We curated and cleaned data from HIV-1 wild-type cell-based and reverse transcriptase (RT) DNA polymerase inhibition assays. Compounds from this database with ≤1 μM HIV-1 RT DNA polymerase activity inhibition and cell-based HIV-1 inhibition are correlated (Pearson r = 0.44, n = 1137, p < 0.0001). Models were trained using multiple machine learning approaches (Bernoulli Naive Bayes, AdaBoost Decision Tree, Random Forest, support vector classification, k-Nearest Neighbors, and deep neural networks as well as consensus approaches) and then their predictive abilities were compared. Our comparison of different machine learning methods demonstrated that support vector classification, deep learning, and a consensus were generally comparable and not significantly different from each other using 5-fold cross validation and using 24 training and test set combinations. This study demonstrates findings in line with our previous studies for various targets that training and testing with multiple data sets does not demonstrate a significant difference between support vector machine and deep neural networks.
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Affiliation(s)
- Kimberley M Zorn
- Collaborations Pharmaceuticals, Inc. , Main Campus Drive, Lab 3510 , Raleigh , North Carolina 27606 , United States
| | - Thomas R Lane
- Collaborations Pharmaceuticals, Inc. , Main Campus Drive, Lab 3510 , Raleigh , North Carolina 27606 , United States
| | - Daniel P Russo
- Collaborations Pharmaceuticals, Inc. , Main Campus Drive, Lab 3510 , Raleigh , North Carolina 27606 , United States.,The Rutgers Center for Computational and Integrative Biology , Camden , New Jersey 08102 , United States
| | - Alex M Clark
- Molecular Materials Informatics, Inc. , 2234 Duvernay Street , Montreal , Quebec H3J2Y3 , Canada
| | - Vadim Makarov
- Bach Institute of Biochemistry , Research Center of Biotechnology of the Russian Academy of Sciences , Leninsky Prospekt 33-2 , Moscow 119071 , Russia
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc. , Main Campus Drive, Lab 3510 , Raleigh , North Carolina 27606 , United States
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21
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Namasivayam V, Vanangamudi M, Kramer VG, Kurup S, Zhan P, Liu X, Kongsted J, Byrareddy SN. The Journey of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) from Lab to Clinic. J Med Chem 2018; 62:4851-4883. [PMID: 30516990 DOI: 10.1021/acs.jmedchem.8b00843] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human immunodeficiency virus (HIV) infection is now pandemic. Targeting HIV-1 reverse transcriptase (HIV-1 RT) has been considered as one of the most successful targets for the development of anti-HIV treatment. Among the HIV-1 RT inhibitors, non-nucleoside reverse transcriptase inhibitors (NNRTIs) have gained a definitive place due to their unique antiviral potency, high specificity, and low toxicity in antiretroviral combination therapies used to treat HIV. Until now, >50 structurally diverse classes of compounds have been reported as NNRTIs. Among them, six NNRTIs were approved for HIV-1 treatment, namely, nevirapine (NVP), delavirdine (DLV), efavirenz (EFV), etravirine (ETR), rilpivirine (RPV), and doravirine (DOR). In this perspective, we focus on the six NNRTIs and lessons learned from their journey through development to clinical studies. It demonstrates the obligatory need of understanding the physicochemical and biological principles (lead optimization), resistance mutations, synthesis, and clinical requirements for drugs.
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Affiliation(s)
- Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , 53121 Bonn , Germany
| | - Murugesan Vanangamudi
- Department of Medicinal and Pharmaceutical Chemistry , Sree Vidyanikethan College of Pharmacy , Tirupathi , Andhra Pradesh 517102 , India
| | | | - Sonali Kurup
- College of Pharmacy , Roosevelt University , Schaumburg , Illinois 60173 , United States
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , Jinan 250012 , P.R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , Jinan 250012 , P.R. China
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 , Odense M , Denmark
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience , University of Nebraska Medical Center , Omaha 68198-5880 , United States
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Battini L, Bollini M. Challenges and approaches in the discovery of human immunodeficiency virus type‐1 non‐nucleoside reverse transcriptase inhibitors. Med Res Rev 2018; 39:1235-1273. [DOI: 10.1002/med.21544] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/04/2018] [Accepted: 10/04/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Leandro Battini
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION), CONICETCiudad de Buenos Aires Argentina
| | - Mariela Bollini
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION), CONICETCiudad de Buenos Aires Argentina
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23
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Do the pharmacokinetic and pharmacodynamic graphs warrant additional explanation? Proc Natl Acad Sci U S A 2018; 115:E8113. [PMID: 30097541 DOI: 10.1073/pnas.1808640115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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24
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Reply to Pandey et al.: Understanding the efficacy of a potential antiretroviral drug candidate in humanized mouse model of HIV infection. Proc Natl Acad Sci U S A 2018; 115:E8114-E8115. [DOI: 10.1073/pnas.1810136115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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25
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Natural product-derived compounds in HIV suppression, remission, and eradication strategies. Antiviral Res 2018; 158:63-77. [PMID: 30063970 DOI: 10.1016/j.antiviral.2018.07.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/10/2018] [Accepted: 07/21/2018] [Indexed: 12/12/2022]
Abstract
While combination antiretroviral therapy (cART) has successfully converted HIV to a chronic but manageable infection in many parts of the world, HIV continues to persist within latent cellular reservoirs, which can become reactivated at any time to produce infectious virus. New therapies are therefore needed not only for HIV suppression but also for containing or eliminating HIV reservoirs. Compounds derived from plant, marine, and other natural products have been found to combat HIV infection and/or target HIV reservoirs, and these discoveries have substantially guided current HIV therapy-based studies. Here we summarize the role of natural product-derived compounds in current HIV suppression, remission, and cure strategies.
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Rachman MM, Barril X, Hubbard RE. Predicting how drug molecules bind to their protein targets. Curr Opin Pharmacol 2018; 42:34-39. [PMID: 30041063 DOI: 10.1016/j.coph.2018.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/01/2018] [Indexed: 01/27/2023]
Abstract
There have been substantial advances in the application of molecular modelling and simulation to drug discovery in recent years, as massive increases in computer power are coupled with continued development in the underlying methods and understanding of how to apply them. Here, we survey recent advances in one particular area-predicting how a known ligand binds to a particular protein. We focus on the four contributing classes of calculation: predicting where a binding site is on a protein; characterizing where chemical functional groups will bind to that site; molecular docking to generate a binding mode for a ligand and dynamics simulations to refine that pose and allow for protein conformation change. Examples of successful application are provided for each class.
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Affiliation(s)
- Moira M Rachman
- Facultat de Farmàcia and Institut de Biomedicina, Universitat de Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
| | - Xavier Barril
- Facultat de Farmàcia and Institut de Biomedicina, Universitat de Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Roderick E Hubbard
- YSBL, University of York, Heslington, York YO10 5DD, UK; Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB21 6GB, UK.
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27
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Vilseck JZ, Armacost KA, Hayes RL, Goh GB, Brooks CL. Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics. J Phys Chem Lett 2018; 9:3328-3332. [PMID: 29847134 PMCID: PMC6091208 DOI: 10.1021/acs.jpclett.8b01284] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this study, we demonstrate the extensive scalability of the biasing potential replica exchange multisite λ dynamics (BP-REX MSλD) free energy method by calculating binding affinities for 512 inhibitors to HIV Reverse Transcriptase (HIV-RT). This is the largest exploration of chemical space using free energy methods known to date, requires only a few simulations, and identifies 55 new inhibitor designs against HIV-RT predicted to be at least as potent as a tight binding reference compound (i.e., as potent as 56 nM). We highlight that BP-REX MSλD requires an order of magnitude less computational resources than conventional free energy methods while maintaining a similar level of precision, overcomes the inherent poor scalability of conventional free energy methods, and enables the exploration of combinatorially large chemical spaces in the context of in silico drug discovery.
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Affiliation(s)
- Jonah Z. Vilseck
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kira A. Armacost
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ryan L. Hayes
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Garrett B. Goh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles L. Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
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