1
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Liu M, Xie DD, Guo YX, Zhao RY, Liu FD, Zhang H, Gao F. TAR RNA selective targeting ruthenium(II) complexes as HIV-1 reverse transcriptase inhibitors: On exploring structure-activity relationships of multiple positions. J Inorg Biochem 2024; 259:112664. [PMID: 39018747 DOI: 10.1016/j.jinorgbio.2024.112664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/07/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
HIV-1 reverse transcriptase (RT) inhibitors play a crucial role in the treatment of HIV by preventing the activity of the enzyme responsible for the replication of the virus. The HIV-1 Tat protein binds to transactivation response (TAR) RNA and recruits host factors to stimulate HIV-1 transcription. We have created a small library consisting of 4 × 6 polypyridyl Ru(II) complexes that selectively bind to TAR RNA, with targeting groups specific to HIV-1 TAR RNA. The molecule design was conducted by introducing hydroxyl or methoxy groups into an established potent TAR binder. The potential TAR binding ability was analysis from nature charge population and electrostatic potential by quantum chemistry calculations. Key modifications were found to be R1 and R3 groups. The most potent and selective TAR RNA binder was a3 with R1 = OH, R2 = H and R3 = Me. Through molecular recognition of hydrogen bonds and electrostatic attraction, they were able to firmly and selectively bind HIV-1 TAR RNA. Furthermore, they efficiently obstructed the contact between TAR RNA and Tat protein, and inhibited the reverse transcription activity of HIV-1 RT. The polypyridyl Ru(II) complexes were chemical and photo-stable, and sensitive and selective spectroscopic responses to TAR RNA. They exhibited little toxicity towards normal cells. Hence, this study might offer significant drug design approaches for researching AIDS and other illnesses associated with RT, including HCV, EBOV, and SARS-CoV-2. Moreover, it could contribute to fundamental research on the interactions of inorganic transition metal complexes with biomolecules.
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Affiliation(s)
- Meng Liu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China
| | - Dan-Dan Xie
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China
| | - Yuan-Xiao Guo
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China
| | - Run-Yu Zhao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China
| | - Fu-Dan Liu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China
| | - Hongbin Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China
| | - Feng Gao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China.
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2
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Angelo M, Zhang W, Vilseck JZ, Aoki ST. In silico λ-dynamics predicts protein binding specificities to modified RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577511. [PMID: 38328125 PMCID: PMC10849657 DOI: 10.1101/2024.01.26.577511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
RNA modifications shape gene expression through a smorgasbord of chemical changes to canonical RNA bases. Although numbering in the hundreds, only a few RNA modifications are well characterized, in part due to the absence of methods to identify modification sites. Antibodies remain a common tool to identify modified RNA and infer modification sites through straightforward applications. However, specificity issues can result in off-target binding and confound conclusions. This work utilizes in silico λ-dynamics to efficiently estimate binding free energy differences of modification-targeting antibodies between a variety of naturally occurring RNA modifications. Crystal structures of inosine and N6-methyladenosine (m6A) targeting antibodies bound to their modified ribonucleosides were determined and served as structural starting points. λ-Dynamics was utilized to predict RNA modifications that permit or inhibit binding to these antibodies. In vitro RNA-antibody binding assays supported the accuracy of these in silico results. High agreement between experimental and computed binding propensities demonstrated that λ-dynamics can serve as a predictive screen for antibody specificity against libraries of RNA modifications. More importantly, this strategy is an innovative way to elucidate how hundreds of known RNA modifications interact with biological molecules without the limitations imposed by in vitro or in vivo methodologies.
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Affiliation(s)
- Murphy Angelo
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Jonah Z. Vilseck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Scott T. Aoki
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, IN 46202, USA
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3
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Prucha GR, Henry S, Hollander K, Carter ZJ, Spasov KA, Jorgensen WL, Anderson KS. Covalent and noncovalent strategies for targeting Lys102 in HIV-1 reverse transcriptase. Eur J Med Chem 2023; 262:115894. [PMID: 37883896 PMCID: PMC10872499 DOI: 10.1016/j.ejmech.2023.115894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023]
Abstract
Reverse transcriptase (RT) is one of three key proteins responsible for the replication cycle of HIV-1 in the host. Several classes of inhibitors have been developed to target the enzyme, with non-nucleoside reverse transcriptase inhibitors forming first-line treatment. Previously, covalent RT inhibitors have been identified and found to bind irreversibly to commonly mutated residues such as Y181C. In this work we aim to circumvent the issue of NNRTI resistance through targeting K102, which has not yet been identified to confer drug resistance. As reported here, 34 compounds were synthesized and characterized biochemically and structurally with wild-type (WT) HIV-1 RT. Two of these inhibitors demonstrate covalent inhibition as evidenced by protein crystallography, enzyme kinetics, mass spectrometry, and antiviral potency in HIV-1 infected human T-cell assays.
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Affiliation(s)
- Giavana R Prucha
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520-8066, USA
| | - Sean Henry
- Department of Chemistry, Yale University, New Haven, CT, 06520-8107, USA
| | - Klarissa Hollander
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06520-8066, USA
| | - Zachary J Carter
- Department of Chemistry, Yale University, New Haven, CT, 06520-8107, USA
| | - Krasimir A Spasov
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520-8066, 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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4
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Hollander K, Chan AH, Frey KM, Hunker O, Ippolito JA, Spasov KA, Yeh YJ, Jorgensen WL, Ho Y, Anderson KS. Exploring novel HIV-1 reverse transcriptase inhibitors with drug-resistant mutants: A double mutant surprise. Protein Sci 2023; 32:e4814. [PMID: 37861472 PMCID: PMC10659932 DOI: 10.1002/pro.4814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 10/21/2023]
Abstract
HIV-1 reverse transcriptase (RT) remains a key target for HIV drug development. As successful management of the disease requires lifelong treatment, the emergence of resistance mutations is inevitable, making development of new RT inhibitors, which remain effective against resistant variants crucial. To this end, previous computationally guided drug design efforts have resulted in catechol diether compounds, which inhibit wildtype RT with picomolar affinities and appear to be promising preclinical candidates. To confirm that these compounds remain potent against Y181C, a widespread mutation conferring resistance to first generation inhibitors, they were screened against the HIV-1 N119 clinical isolate, reported as a Y181C single mutant. In comparison to a molecular clone with the same mutation, N119 appears less susceptible to inhibition by our preclinical candidate compounds. A more detailed sequencing effort determined that N119 was misidentified and carries V106A in combination with Y181C. While both indolizine and naphthalene substituted catechol diethers are potent against the classical Y181C single mutant, the addition of V106A confers more resistance against the indolizine derivatives than the naphthalene derivatives. Crystal structures presented in this study highlight key features of the naphthyl group, which allow these compounds to remain potent in the double mutant, including stronger interactions with F227 and less reliance on V106 for stabilization of the ethoxy-uracil ring, which makes critical hydrogen bonds with other residues in the binding pocket.
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Affiliation(s)
- Klarissa Hollander
- Department of Molecular Biophysics and BiochemistryYale University School of MedicineNew HavenConnecticutUSA
- Department of PharmacologyYale University School of MedicineNew HavenConnecticutUSA
| | - Albert H. Chan
- Department of PharmacologyYale University School of MedicineNew HavenConnecticutUSA
| | - Kathleen M. Frey
- Department of PharmacologyYale University School of MedicineNew HavenConnecticutUSA
| | - Olivia Hunker
- Department of Molecular Biophysics and BiochemistryYale University School of MedicineNew HavenConnecticutUSA
| | - Joseph A. Ippolito
- Department of PharmacologyYale University School of MedicineNew HavenConnecticutUSA
- Department of ChemistryYale UniversityNew HavenConnecticutUSA
| | - Krasimir A. Spasov
- Department of PharmacologyYale University School of MedicineNew HavenConnecticutUSA
| | - Yang‐Hui J. Yeh
- Department of Microbial PathogenesisYale University School of MedicineNew HavenConnecticutUSA
| | | | - Ya‐Chi Ho
- Department of Microbial PathogenesisYale University School of MedicineNew HavenConnecticutUSA
| | - Karen S. Anderson
- Department of Molecular Biophysics and BiochemistryYale University School of MedicineNew HavenConnecticutUSA
- Department of PharmacologyYale University School of MedicineNew HavenConnecticutUSA
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5
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Tobajas-Curiel G, Sun Q, Sanders JKM, Ballester P, Hunter CA. Aromatic interactions with heterocycles in water. Chem Sci 2023; 14:11131-11140. [PMID: 37860651 PMCID: PMC10583712 DOI: 10.1039/d3sc03824f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/24/2023] [Indexed: 10/21/2023] Open
Abstract
Conformationally well-defined supramolecular complexes that can be studied in different solvents provide a platform for separating and quantifying free energy contributions due to functional group interactions and desolvation. Here 1:1 complexes formed between four different calix[4]pyrrole receptors and eleven different pyridine N-oxide guests have been used to dissect the factors that govern aromatic interactions with heterocycles in water and in chloroform solution. 1H NMR spectroscopy shows that the three-dimensional structures of the complexes are fixed by four H-bonding interactions between the pyrrole donors at the bottom of the receptor and the N-oxide acceptor on the guest, locking the geometrical arrangement of interacting functional groups in the binding pocket at the other end of the receptor. An aromatic heterocycle on the guest makes two stacking interactions and two edge-to-face interactions with the side walls of the receptor. Chemical double mutant cycles were used to measure the free energy contribution of these four aromatic interactions to the overall stability of the complex. In chloroform, the aromatic interactions measured with pyridine, pyrimidine, furan, thiophene and thiazole are similar to the interactions with a phenyl group, but the effect of introducing a heteroatom depends on where it sits with respect to the aromatic side-walls of the cavity. A nitrogen lone pair directed into a π-face of the side-walls of the binding site leads to repulsive interactions of up to 8 kJ mol-1. In water, the heterocycle aromatic interactions are all significantly more favourable (by up to 12 kJ mol-1). For the non-polar heterocycles, furan and thiophene, the increase in interaction energy correlates directly with hydrophobicity, as measured by the free energy of transfer of the heterocycle from n-hexadecane into water (ΔG°(water-hex)). For the heterocycles with polar nitrogen H-bond acceptors, water can access cracks in the walls of the receptor binding site to solvate the edges of the heterocycles without significantly affecting the geometry of the aromatic interactions, and these nitrogen-water H-bonds stabilise the complexes by about 15 kJ mol-1. The results highlight the complexity of the solvation processes that govern molecular recognition in water.
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Affiliation(s)
| | - Qingqing Sun
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST) Av. Països Catalans, 16 43007 Tarragona Spain
- Yangzhou University, School of Chemistry and Chemical Engineering Yangzhou 225002 Jiangsu China
| | - Jeremy K M Sanders
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Pablo Ballester
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST) Av. Països Catalans, 16 43007 Tarragona Spain
- ICREA Passeig Lluís Companys 23 08010 Barcelona Spain
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
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6
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Bieniek MK, Cree B, Pirie R, Horton JT, Tatum NJ, Cole DJ. An open-source molecular builder and free energy preparation workflow. Commun Chem 2022; 5:136. [PMID: 36320862 PMCID: PMC9607723 DOI: 10.1038/s42004-022-00754-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/11/2022] [Indexed: 01/27/2023] Open
Abstract
Automated free energy calculations for the prediction of binding free energies of congeneric series of ligands to a protein target are growing in popularity, but building reliable initial binding poses for the ligands is challenging. Here, we introduce the open-source FEgrow workflow for building user-defined congeneric series of ligands in protein binding pockets for input to free energy calculations. For a given ligand core and receptor structure, FEgrow enumerates and optimises the bioactive conformations of the grown functional group(s), making use of hybrid machine learning/molecular mechanics potential energy functions where possible. Low energy structures are optionally scored using the gnina convolutional neural network scoring function, and output for more rigorous protein-ligand binding free energy predictions. We illustrate use of the workflow by building and scoring binding poses for ten congeneric series of ligands bound to targets from a standard, high quality dataset of protein-ligand complexes. Furthermore, we build a set of 13 inhibitors of the SARS-CoV-2 main protease from the literature, and use free energy calculations to retrospectively compute their relative binding free energies. FEgrow is freely available at https://github.com/cole-group/FEgrow, along with a tutorial.
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Affiliation(s)
- Mateusz K. Bieniek
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Ben Cree
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Rachael Pirie
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Joshua T. Horton
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Natalie J. Tatum
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
| | - Daniel J. Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
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7
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Guo YX, Liu M, Zhou YQ, Bi XD, Gao F. Terpyridyl ruthenium complexes as visible spectral probe for poly(A) RNA and bifunctional TAR RNA binders and HIV-1 reverse transcriptase inhibitors. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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8
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Wang MF, Li Y, Bi XD, Guo YX, Liu M, Zhang H, Gao F. Polypyridyl ruthenium complexes as bifunctional TAR RNA binders and HIV-1 reverse transcriptase inhibitors. J Inorg Biochem 2022; 234:111880. [DOI: 10.1016/j.jinorgbio.2022.111880] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/28/2022] [Accepted: 05/28/2022] [Indexed: 12/18/2022]
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9
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Yang R, Bi XD, Li Y, Liu M, Hu MQ, Zhao LM, Zhang H, Gao F. Scorpion-Shaped Zinc Porphyrins as Tetrafunctional TAR RNA Predators and HIV-1 Reverse Transcriptase Inhibitors. Inorg Chem 2022; 61:10774-10780. [PMID: 35796528 DOI: 10.1021/acs.inorgchem.2c00975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HIV-1 reverse transcriptase (RT) inhibitors are fundamental to the discovery and development of anti-HIV drugs. Their main target is RT, and only a tiny number of them can bind to viral RNA. In this paper, five new Zn(II) porphyrin compounds were developed with different characters. ZnTPP4 has both the appearance and the functions of a scorpion with a rigid tail and stinger to selectively hunt HIV-1 TAR RNA based on the molecular recognition of hydrogen bonds, a fierce chelicera to bite RNA by metal coordination, mighty pedipalps to grasp the bound RNA by supramolecular inclusion, and a broad body maintaining the configuration of each functional area so that they can cooperate with each other and providing accommodation space for the bound RNA. This tetrafunctional Zn(II) porphyrin is relatively nontoxic to normal cells and can produce sensitive responses for RNA. Moreover, this work offers practical construction methodologies for medication of AIDS and other diseases closely related to RT like EBOV and SARS-CoV-2.
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Affiliation(s)
- Rong Yang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Xu-Dan Bi
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Yan Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Meng Liu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Man-Qi Hu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Li-Min Zhao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Hongbin Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Feng Gao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
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10
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Tedder ML, Dzeagu FO, Mason MM, Dixon DA, Carrick JD. Microwave-assisted C–H oxidation of methylpyridylheteroarenes via a Kornblum-Type reaction. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Hayes RL, Vilseck JZ, Brooks CL. Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods. J Chem Theory Comput 2022; 18:2114-2123. [PMID: 35255214 PMCID: PMC9700482 DOI: 10.1021/acs.jctc.1c00948] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alchemical free energy methods are playing a growing role in molecular design, both for computer-aided drug design of small molecules and for computational protein design. Multisite λ dynamics (MSλD) is a uniquely scalable alchemical free energy method that enables more efficient exploration of combinatorial alchemical spaces encountered in molecular design, but simulations have typically been limited to a few hundred ligands or sequences. Here, we focus on coupling between sites to enable scaling to larger alchemical spaces. We first discuss updates to the biasing potentials that facilitate MSλD sampling to include coupling terms and show that this can provide more thorough sampling of alchemical states. We then harness coupling between sites by developing a new free energy estimator based on the Potts models underlying direct coupling analysis, a method for predicting contacts from sequence coevolution, and find it yields more accurate free energies than previous estimators. The sampling requirements of the Potts model estimator scale with the square of the number of sites, a substantial improvement over the exponential scaling of the standard estimator. This opens up exploration of much larger alchemical spaces with MSλD for molecular design.
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Affiliation(s)
- Ryan L Hayes
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jonah Z Vilseck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, 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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12
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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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13
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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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14
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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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15
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Chen Y, Li H, Liu J, Zhong R, Li H, Fang S, Liu S, Lin S. Synthesis and biological evaluation of indole-based peptidomimetics as antibacterial agents against Gram-positive bacteria. Eur J Med Chem 2021; 226:113813. [PMID: 34520955 DOI: 10.1016/j.ejmech.2021.113813] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/15/2021] [Accepted: 08/28/2021] [Indexed: 01/06/2023]
Abstract
The emergence of bacterial multidrug resistance and the lack of new antimicrobial agents urgently demand the discovery and development of novel antibacterials that avoid bacterial resistance. Antimicrobial peptidomimetics represent a promising approach for overcoming antibiotic resistance. Herein we report the synthesis and evaluation of indole-based amphiphilic antimicrobial peptidomimetics, bearing hydrophobic side chains and hydrophilic cationic moieties. Among these derivatives, compound 28 demonstrated potent antimicrobial activity against Gram-positive bacteria, low hemolytic activity and low toxicity towards mammalian cells, as well as good stability in salt conditions. Moreover, compound 28 showed the rapid killing of bacteria via membrane-targeting action without developing bacterial resistance. More importantly, compound 28 displayed high antimicrobial potency against Gram-positive bacteria in a murine model of bacterial keratitis, and was found to be more efficient than vancomycin. Thus, compound 28 had great potential as a promising lead compound for the treatment of Gram-positive bacterial infection.
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Affiliation(s)
- Yongzhi Chen
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, PR China
| | - Hongxia Li
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, PR China
| | - Jiayong Liu
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, PR China
| | - Rongcui Zhong
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, PR China
| | - Haizhou Li
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, PR China
| | - Shanfang Fang
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, PR China
| | - Shouping Liu
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, PR China.
| | - Shuimu Lin
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, PR China.
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16
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Zhang T, Zhou Z, Zalloum WA, Wang Z, Fu Z, Cherukupalli S, Feng D, Sun Y, Gao S, De Clercq E, Pannecouque C, Kang D, Zhan P, Liu X. Design, synthesis, and antiviral evaluation of novel piperidine-substituted arylpyrimidines as HIV-1 NNRTIs by exploring the hydrophobic channel of NNIBP. Bioorg Chem 2021; 116:105353. [PMID: 34536931 DOI: 10.1016/j.bioorg.2021.105353] [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: 07/04/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 11/15/2022]
Abstract
Herein, alkenylpiperidine and alkynylpiperidine moieties were introduced into the left wing of DAPYs (diarylpyrimidines) to explore the new site of the NNIBP (non-nucleoside inhibitor binding pocket) protein-solvent interface region via the structure-based drug design strategy. All the synthesized compounds displayed nanomolar to submicromolar activity against WT (wild-type) HIV-1. Among all, compound FT1 (EC50 = 19 nM) was found to be the most active molecule, which is better than NVP (EC50 = 0.10 μM). In addition, most of the compounds displayed micromolar activity against K103N and E138K mutant strains, while FT1 (EC50(K103N) = 50 nM, EC50(E138K) = 0.19 µM) still has the most effective activity. The molecular dynamics simulation studies revealed that the presence of pyridine moiety of FT1 was essential and played a significant role in its binding with RT (reverse transcriptase).
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Affiliation(s)
- Tao Zhang
- 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, PR China
| | - Zhongxia Zhou
- 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, PR China
| | - Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O Box 2882, Amman 11821, Jordan
| | - 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, PR China
| | - Zhipeng Fu
- 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, PR 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, PR China
| | - Da Feng
- 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, PR China
| | - Yanying Sun
- 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, PR China
| | - Shenghua Gao
- 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, PR China
| | - 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
| | - 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.
| | - 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, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR 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, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR 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, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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17
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Vilseck JZ, Ding X, Hayes RL, Brooks CL. Generalizing the Discrete Gibbs Sampler-Based λ-Dynamics Approach for Multisite Sampling of Many Ligands. J Chem Theory Comput 2021; 17:3895-3907. [PMID: 34101448 DOI: 10.1021/acs.jctc.1c00176] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this work, the discrete λ variant of the Gibbs sampler-based λ-dynamics (d-GSλD) method is developed to enable multiple functional group perturbations to be investigated at one or more sites of substitution off a common ligand core. The theoretical framework and special considerations for constructing discrete λ states for multisite d-GSλD are presented. The precision and accuracy of the d-GSλD method is evaluated with three test cases of increasing complexity. Specifically, methyl → methyl symmetric perturbations in water, 1,4-benzene hydration free energies and protein-ligand binding affinities for an example HIV-1 reverse transcriptase inhibitor series are computed with d-GSλD. Complementary MSλD calculations were also performed to compare with d-GSλD's performance. Excellent agreement between d-GSλD and MSλD is observed, with mean unsigned errors of 0.12 and 0.22 kcal/mol for computed hydration and binding free energy test cases, respectively. Good agreement with experiment is also observed, with errors of 0.5-0.7 kcal/mol. These findings support the applicability of the d-GSλD free energy method for a variety of molecular design problems, including structure-based drug design. Finally, a discussion of d-GSλD versus MSλD approaches is presented to compare and contrast features of both methods.
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Affiliation(s)
- Jonah Z Vilseck
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Xinqiang Ding
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ryan L Hayes
- 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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18
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Fu Z, Zhang T, Zhou Z, Kang D, Sun L, Gao S, Cherukupalli S, De Clercq E, Pannecouque C, Liu X, Zhan P. Exploiting the hydrophobic channel of the NNIBP: Discovery of novel diarylpyrimidines as HIV-1 NNRTIs against wild-type and K103N mutant viruses. Bioorg Med Chem 2021; 42:116239. [PMID: 34090079 DOI: 10.1016/j.bmc.2021.116239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 01/19/2023]
Abstract
To further explore the chemical space surrounding the "hydrophobic channel" of the NNRTI binding pocket (NNIBP), a new series of diarylpyrimidines (DAPYs) were designed and synthesized as potent HIV-1 non-nucleoside RT inhibitors (NNRTIs). The target compounds were evaluated for anti-HIV potency in MT-4 cells. Most of the synthesized DAPYs exhibited moderate to excellent activity against the HIV-1 wild-type (WT) strain with EC50 values ranging from 16 nM to 0.722 µM. Interestingly, few compounds displayed remarkable activity in inhibiting K103N mutant virus with EC50 values ranging from 39 nM to 1.708 µM. Notably, FS2 (EC50(IIIB) = 16 nM, EC50(K103N) = 39 nM, SI = 294) was identified as the most significant compound, which was considerably more potent than nevirapine, lamivudine, and comparable to zidovudine. Additionally, the HIV-1 RT inhibition assay confirmed their binding target. Preliminary structure-activity relationships (SARs) and molecular modeling studies were also performed, providing significant suggestions for further optimization.
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Affiliation(s)
- Zhipeng Fu
- 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, PR China
| | - Tao Zhang
- 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, PR China
| | - Zhongxia Zhou
- 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, PR China
| | - 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, PR China
| | - Lin Sun
- 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, PR China
| | - Shenghua Gao
- 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, PR 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, PR China
| | - 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
| | - 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.
| | - 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, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR 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, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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19
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Nelson L, Bariami S, Ringrose C, Horton JT, Kurdekar V, Mey ASJS, Michel J, Cole DJ. Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free-Energy Calculations. J Chem Inf Model 2021; 61:2124-2130. [PMID: 33886305 DOI: 10.1021/acs.jcim.1c00328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The quantum mechanical bespoke (QUBE) force-field approach has been developed to facilitate the automated derivation of potential energy function parameters for modeling protein-ligand binding. To date, the approach has been validated in the context of Monte Carlo simulations of protein-ligand complexes. We describe here the implementation of the QUBE force field in the alchemical free-energy calculation molecular dynamics simulation package SOMD. The implementation is validated by demonstrating the reproducibility of absolute hydration free energies computed with the QUBE force field across the SOMD and GROMACS software packages. We further demonstrate, by way of a case study involving two series of non-nucleoside inhibitors of HIV-1 reverse transcriptase, that the availability of QUBE in a modern simulation package that makes efficient use of graphics processing unit acceleration will facilitate high-throughput alchemical free-energy calculations.
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Affiliation(s)
- Lauren Nelson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Sofia Bariami
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Chris Ringrose
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Joshua T Horton
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Vadiraj Kurdekar
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Antonia S J S Mey
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Julien Michel
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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20
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Matthew AN, Leidner F, Lockbaum GJ, Henes M, Zephyr J, Hou S, Desaboini NR, Timm J, Rusere LN, Ragland DA, Paulsen JL, Prachanronarong K, Soumana DI, Nalivaika EA, Yilmaz NK, Ali A, Schiffer CA. Drug Design Strategies to Avoid Resistance in Direct-Acting Antivirals and Beyond. Chem Rev 2021; 121:3238-3270. [PMID: 33410674 PMCID: PMC8126998 DOI: 10.1021/acs.chemrev.0c00648] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Drug resistance is prevalent across many diseases, rendering therapies ineffective with severe financial and health consequences. Rather than accepting resistance after the fact, proactive strategies need to be incorporated into the drug design and development process to minimize the impact of drug resistance. These strategies can be derived from our experience with viral disease targets where multiple generations of drugs had to be developed to combat resistance and avoid antiviral failure. Significant efforts including experimental and computational structural biology, medicinal chemistry, and machine learning have focused on understanding the mechanisms and structural basis of resistance against direct-acting antiviral (DAA) drugs. Integrated methods show promise for being predictive of resistance and potency. In this review, we give an overview of this research for human immunodeficiency virus type 1, hepatitis C virus, and influenza virus and the lessons learned from resistance mechanisms of DAAs. These lessons translate into rational strategies to avoid resistance in drug design, which can be generalized and applied beyond viral targets. While resistance may not be completely avoidable, rational drug design can and should incorporate strategies at the outset of drug development to decrease the prevalence of drug resistance.
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Affiliation(s)
- Ashley N. Matthew
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Virginia Commonwealth University
| | - Florian Leidner
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Gordon J. Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Jacqueto Zephyr
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Shurong Hou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Nages Rao Desaboini
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Jennifer Timm
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Rutgers University
| | - Linah N. Rusere
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Raybow Pharmaceutical
| | - Debra A. Ragland
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- University of North Carolina, Chapel Hill
| | - Janet L. Paulsen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Schrodinger, Inc
| | - Kristina Prachanronarong
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Icahn School of Medicine at Mount Sinai
| | - Djade I. Soumana
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
- Cytiva
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Nese Kurt Yilmaz
- 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
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
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21
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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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22
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Jin S, Wang L, Han H, Liu X, Bu Z, Wang Q. Assembly of functionalized π-extended indolizine polycycles through dearomative [3+2] cycloaddition/oxidative decarbonylation. Chem Commun (Camb) 2021; 57:359-362. [PMID: 33319883 DOI: 10.1039/d0cc07116a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Reported herein is an unexpected construction of functionalized π-extended indolizine polycycles through a one-pot two-step cascade process comprising the base-promoted dearomative [3+2] cycloaddition of quinilinium salts and 3-alkenyl oxindoles, followed by a DDQ-mediated oxidative decarbonylation. Moreover, we could achieve the substrate-controlled diverse synthesis of structurally strained cyclopropane spirooxindole by using pyridinium salts as starting materials.
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Affiliation(s)
- Shaojing Jin
- Institute of Functional Organic Molecular Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, China.
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23
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He XL, Wang C, Wen YW, Zhao YB, Yang H, Qian S, Yang L, Wang Z. Highly stereoselective dearomative [3 + 2] cycloadditon of cyclic pyridinium ylides to access spiro-indolizidine scaffolds. Org Chem Front 2021. [DOI: 10.1039/d1qo00886b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A novel type of pyridinium salt bearing a EWG on the pyridine was developed as an efficient pyridinium ylide precursor in the [3 + 2] cycloaddition with nitroolefins to construct various spiro-indolizidine scaffolds via a dearomative pathway.
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Affiliation(s)
- Xiao-Long He
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Cheng Wang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - You-Wu Wen
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Yi-Bing Zhao
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Huan Yang
- The management commission of Yibin campus, Xihua University, Yibin 644000, China
| | - Shan Qian
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Lingling Yang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Zhouyu Wang
- School of Science, Xihua University, Chengdu 610039, China
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24
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Roy SA, Zgheib J, Zhou C, Arndtsen BA. Palladium catalyzed synthesis of indolizines via the carbonylative coupling of bromopyridines, imines and alkynes. Chem Sci 2020; 12:2251-2256. [PMID: 34163991 PMCID: PMC8179343 DOI: 10.1039/d0sc03977b] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We report herein the development of a palladium-catalyzed, multicomponent synthesis of indolizines. The reaction proceeds via the carbonylative formation of a high energy, mesoionic pyridine-based 1,3-dipole, which can undergo spontaneous cycloaddition with alkynes. Overall, this provides a route to prepare indolizines in a modular fashion from combinations of commercially available or easily generated reagents: 2-bromopyridines, imines and alkynes. A palladium catalyzed, multicomponent synthesis of indolizines is described via the carbon monoxide driven generation of reactive, pyridine-based 1,3-dipoles.![]()
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Affiliation(s)
- Sébastien A Roy
- Department of Chemistry, McGill University 801 Sherbrooke Street W. Montreal QC H3A 0B8 Canada
| | - José Zgheib
- Department of Chemistry, McGill University 801 Sherbrooke Street W. Montreal QC H3A 0B8 Canada
| | - Cuihan Zhou
- Department of Chemistry, McGill University 801 Sherbrooke Street W. Montreal QC H3A 0B8 Canada
| | - Bruce A Arndtsen
- Department of Chemistry, McGill University 801 Sherbrooke Street W. Montreal QC H3A 0B8 Canada
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25
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Song LF, Merz KM. Evolution of Alchemical Free Energy Methods in Drug Discovery. J Chem Inf Model 2020; 60:5308-5318. [DOI: 10.1021/acs.jcim.0c00547] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lin Frank Song
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Kenneth M. Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
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26
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Cai Q, Zhou W. Ullmann‐Ma
Reaction: Development, Scope and Applications in Organic Synthesis
†. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000075] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Qian Cai
- College of Pharmacy, Jinan University No. 601 Huangpu Avenue West Guangzhou Guangdong 510632 China
| | - Wei Zhou
- College of Pharmacy, Jinan University No. 601 Huangpu Avenue West Guangzhou Guangdong 510632 China
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27
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Limongelli V. Ligand binding free energy and kinetics calculation in 2020. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1455] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Vittorio Limongelli
- Faculty of Biomedical Sciences, Institute of Computational Science – Center for Computational Medicine in Cardiology Università della Svizzera italiana (USI) Lugano Switzerland
- Department of Pharmacy University of Naples “Federico II” Naples Italy
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28
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Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors. Eur J Med Chem 2019; 183:111673. [PMID: 31536894 DOI: 10.1016/j.ejmech.2019.111673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/31/2019] [Accepted: 09/01/2019] [Indexed: 02/08/2023]
Abstract
Cryptosporidiosis is a human gastrointestinal disease caused by protozoans of the genus Cryptosporidium, which can be fatal in immunocompromised individuals. The essential enzyme, thymidylate synthase (TS), is responsible for de novo synthesis of deoxythymidine monophosphate. The TS active site is relatively conserved between Cryptosporidium and human enzymes. In previous work, we identified compound 1, (2-amino-4-oxo-4,7-dihydro-pyrrolo[2,3-d]pyrimidin-methyl-phenyl-l-glutamic acid), as a promising selective Cryptosporidium hominis TS (ChTS) inhibitor. In the present study, we explore the structure-activity relationship around 1 glutamate moiety by synthesizing and biochemically evaluating the inhibitory activity of analogues against ChTS and human TS (hTS). X-Ray crystal structures were obtained for compounds bound to both ChTS and hTS. We establish the importance of the 2-phenylacetic acid moiety methylene linker in optimally positioning compounds 23, 24, and 25 within the active site. Moreover, through the comparison of structural data for 5, 14, 15, and 23 bound in both ChTS and hTS identified that active site rigidity is a driving force in determining inhibitor selectivity.
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29
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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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30
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Frey KM, Tabassum T. Current structure-based methods for designing non-nucleoside reverse transcriptase inhibitors. Future Virol 2019. [DOI: 10.2217/fvl-2019-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In 2019, structure-based methods continue to guide the design of novel antiretroviral therapies targeting HIV reverse transcriptase. This Review summarizes key findings from reverse transcriptase–non-nucleoside reverse transcriptase inhibitor analog crystal structure complexes reported from 2015 to 2019. Results from the literature and structure analysis have informed new ideas for structure-guided non-nucleoside reverse transcriptase inhibitor drug design.
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Affiliation(s)
- Kathleen M Frey
- Fairleigh Dickinson University, Division of Pharmaceutical Sciences, School of Pharmacy & Health Sciences, 230 Park Avenue, M-SP1-01, Florham Park, NJ 07932, USA
| | - Tasnim Tabassum
- Long Island University, Division of Pharmaceutical Sciences, Arnold & Marie Schwartz College of Pharmacy & Health Sciences, 75 Dekalb Avenue, Brooklyn, NY 11201, USA
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31
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Abstract
Predicting the strength of stacking interactions involving heterocycles is vital for several fields, including structure-based drug design. While quantum chemical computations can provide accurate stacking interaction energies, these come at a steep computational cost. To address this challenge, we recently developed quantitative predictive models of stacking interactions between druglike heterocycles and the aromatic amino acids Phe, Tyr, and Trp (DOI: 10.1021/jacs.9b00936 ). These models depend on heterocycle descriptors derived from electrostatic potentials (ESPs) computed using density functional theory and provide accurate stacking interactions without the need for expensive computations on stacked dimers. Herein, we show that these ESP-based descriptors can be reliably evaluated directly from the atom connectivity of the heterocycle, providing a means of predicting both the descriptors and the potential for a given heterocycle to engage in stacking interactions without resorting to any quantum chemical computations. This enables the rapid conversion of simple molecular representations (e.g., SMILES) directly into accurate stacking interaction energies using a freely available online tool, thereby providing a way to rank the stacking abilities of large sets of heterocycles.
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Affiliation(s)
- Andrea N Bootsma
- Center for Computational Quantum Chemistry, Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
| | - Steven E Wheeler
- Center for Computational Quantum Chemistry, Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
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32
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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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33
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Cole DJ, Cabeza de Vaca I, Jorgensen WL. Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields. MEDCHEMCOMM 2019; 10:1116-1120. [PMID: 31391883 PMCID: PMC6644397 DOI: 10.1039/c9md00017h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/26/2019] [Indexed: 12/17/2022]
Abstract
A quantum mechanical bespoke molecular mechanics force field is derived for the L99A mutant of T4 lysozyme and used to compute absolute binding free energies of six benzene analogs to the protein. Promising agreement between theory and experiment highlights the potential for future use of system-specific force fields in computer-aided drug design.
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Affiliation(s)
- Daniel J Cole
- School of Natural and Environmental Sciences , Newcastle University , Newcastle upon Tyne NE1 7RU , UK .
| | - Israel Cabeza de Vaca
- Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , USA
| | - William L Jorgensen
- Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , USA
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34
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Discovery of piperidine-substituted thiazolo[5,4-d]pyrimidine derivatives as potent and orally bioavailable HIV-1 non-nucleoside reverse transcriptase inhibitors. Commun Chem 2019. [DOI: 10.1038/s42004-019-0174-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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35
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Bootsma AN, Doney AC, Wheeler SE. Predicting the Strength of Stacking Interactions between Heterocycles and Aromatic Amino Acid Side Chains. J Am Chem Soc 2019; 141:11027-11035. [DOI: 10.1021/jacs.9b00936] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Andrea N. Bootsma
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Analise C. Doney
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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36
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Kang D, Zhang H, Wang Z, Zhao T, Ginex T, Luque FJ, Yang Y, Wu G, Feng D, Wei F, Zhang J, De Clercq E, Pannecouque C, Chen CH, Lee KH, Murugan NA, Steitz TA, Zhan P, Liu X. Identification of Dihydrofuro[3,4- d]pyrimidine Derivatives as Novel HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors with Promising Antiviral Activities and Desirable Physicochemical Properties. J Med Chem 2019; 62:1484-1501. [PMID: 30624934 DOI: 10.1021/acs.jmedchem.8b01656] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To address drug resistance to HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs), a series of novel diarylpyrimidine (DAPY) derivatives targeting "tolerant region I" and "tolerant region II" of the NNRTIs binding pocket (NNIBP) were designed utilizing a structure-guided scaffold-hopping strategy. The dihydrofuro[3,4- d]pyrimidine derivatives 13c2 and 13c4 proved to be exceptionally potent against a wide range of HIV-1 strains carrying single NNRTI-resistant mutations (EC50 = 0.9-8.4 nM), which were remarkably superior to that of etravirine (ETV). Meanwhile, both compounds exhibited comparable activities with ETV toward the virus with double mutations F227L+V106A and K103N+Y181C. Furthermore, the most active compound 13c2 showed favorable pharmacokinetic properties with an oral bioavailability of 30.96% and a half-life of 11.1 h, which suggested that 13c2 is worth further investigation as a novel NNRTI to circumvent drug resistance.
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Affiliation(s)
- 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
| | - Heng 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
| | - 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
| | - Tong 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
| | - Tiziana Ginex
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy, Campus Torribera, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB) , University of Barcelona , 08921 Santa Coloma de Gramenet , Spain
| | - Francisco Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy, Campus Torribera, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB) , University of Barcelona , 08921 Santa Coloma de Gramenet , Spain
| | - Yang Yang
- Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06520-8114 , United States
| | - Gaochan Wu
- 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
| | - Fenju Wei
- 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
| | - Jian 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
| | - Erik De Clercq
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research , KU Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research , KU Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Chin Ho Chen
- Surgical Oncology Research Facility , Duke University Medical Center , Box 2926, Durham , North Carolina 27710 , United States
| | - Kuo-Hsiung Lee
- Natural Products Research Laboratories, Eshelman School of Pharmacy , University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Chinese Medicine Research and Development Center , China Medical University and Hospital , Taichung 40402 , Taiwan
| | - N Arul Murugan
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH) , AlbaNova University Center , S-106 91 Stockholm , Sweden
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06520-8114 , 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 , 250012 Jinan , Shandong , 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
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37
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De Simone A, Georgiou C, Ioannidis H, Gupta AA, Juárez-Jiménez J, Doughty-Shenton D, Blackburn EA, Wear MA, Richards JP, Barlow PN, Carragher N, Walkinshaw MD, Hulme AN, Michel J. A computationally designed binding mode flip leads to a novel class of potent tri-vector cyclophilin inhibitors. Chem Sci 2019; 10:542-547. [PMID: 30746096 PMCID: PMC6335623 DOI: 10.1039/c8sc03831g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/14/2018] [Indexed: 12/27/2022] Open
Abstract
Cyclophilins (Cyps) are a major family of drug targets that are challenging to prosecute with small molecules because the shallow nature and high degree of conservation of the active site across human isoforms offers limited opportunities for potent and selective inhibition. Herein a computational approach based on molecular dynamics simulations and free energy calculations was combined with biophysical assays and X-ray crystallography to explore a flip in the binding mode of a reported urea-based Cyp inhibitor. This approach enabled access to a distal pocket that is poorly conserved among key Cyp isoforms, and led to the discovery of a new family of sub-micromolar cell-active inhibitors that offer unprecedented opportunities for the development of next-generation drug therapies based on Cyp inhibition. The computational approach is applicable to a broad range of organic functional groups and could prove widely enabling in molecular design.
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Affiliation(s)
- Alessio De Simone
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Charis Georgiou
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Harris Ioannidis
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Arun A Gupta
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Jordi Juárez-Jiménez
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Dahlia Doughty-Shenton
- Edinburgh Phenotypic Assay Centre , University of Edinburgh , Queen's Medical Research Institute , Little France Cres , Edinburgh , Scotland EH16 4TJ , UK
| | - Elizabeth A Blackburn
- The Edinburgh Protein Production Facility (EPPF) , University of Edinburgh , Level 3 Michael Swann Building, King's Buildings, Max Born Crescent , Edinburgh , Scotland EH9 3BF , UK
| | - Martin A Wear
- The Edinburgh Protein Production Facility (EPPF) , University of Edinburgh , Level 3 Michael Swann Building, King's Buildings, Max Born Crescent , Edinburgh , Scotland EH9 3BF , UK
| | - Jonathan P Richards
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Paul N Barlow
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Neil Carragher
- Cancer Research UK Edinburgh Centre , University of Edinburgh , MRC Institute of Genetics and Molecular Medicine , Crewe Road South , Edinburgh , Scotland EH4 2XR , UK
| | - Malcolm D Walkinshaw
- University of Edinburgh , Michael Swann Building, Max Born Crescent , Edinburgh , Scotland EH9 3BF , UK
| | - Alison N Hulme
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Julien Michel
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
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38
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Kaye PT. Applications of the Morita–Baylis–Hillman Reaction in the Synthesis of Heterocyclic Systems. ADVANCES IN HETEROCYCLIC CHEMISTRY 2019. [DOI: 10.1016/bs.aihch.2018.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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39
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Zhou Z, Liu T, Wu G, Kang D, Fu Z, Wang Z, De Clercq E, Pannecouque C, Zhan P, Liu X. Targeting the hydrophobic channel of NNIBP: discovery of novel 1,2,3-triazole-derived diarylpyrimidines as novel HIV-1 NNRTIs with high potency against wild-type and K103N mutant virus. Org Biomol Chem 2019; 17:3202-3217. [DOI: 10.1039/c9ob00032a] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Novel 1,2,3-triazole-derived diarylpyrimidines were discovered as potent HIV-1 NNRTIs.
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Affiliation(s)
- Zhongxia Zhou
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Tao Liu
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Gaochan Wu
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Dongwei Kang
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Zhipeng Fu
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Zhao Wang
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Erik De Clercq
- Rega Institute for Medical Research
- K.U. Leuven
- B-3000 Leuven
- Belgium
| | | | - Peng Zhan
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Xinyong Liu
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
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40
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Gilabert JF, Lecina D, Estrada J, Guallar V. Monte Carlo Techniques for Drug Design: The Success Case of PELE. BIOMOLECULAR SIMULATIONS IN STRUCTURE-BASED DRUG DISCOVERY 2018. [DOI: 10.1002/9783527806836.ch5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Joan F. Gilabert
- Barcelona Supercomputing Center (BSC); Life Science Department; Jordi Girona 29 08034 Barcelona Spain
| | - Daniel Lecina
- Barcelona Supercomputing Center (BSC); Life Science Department; Jordi Girona 29 08034 Barcelona Spain
| | - Jorge Estrada
- Barcelona Supercomputing Center (BSC); Life Science Department; Jordi Girona 29 08034 Barcelona Spain
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC); Life Science Department; Jordi Girona 29 08034 Barcelona Spain
- ICREA; Passeig Lluís Companys 23 08010 Barcelona Spain
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41
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Torsional flexibility of undecorated catechol diether compound as potent NNRTI targeting HIV-1 reverse transcriptase. J Mol Graph Model 2018; 86:286-297. [PMID: 30445408 DOI: 10.1016/j.jmgm.2018.10.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 10/28/2018] [Accepted: 10/29/2018] [Indexed: 11/22/2022]
Abstract
Conformational adaptation of non-nucleoside reverse transcriptase inhibitor (NNRTI) via torsional flexibility is found to be very significant for targeting human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) mutants. Catechol diether derivative including flexible torsions is new potent NNRTI with picomolar activity. Moreover, this derivative also reveals the good solubility, low toxicity and potent inhibition for HIV-1 mutants. In this study, torsional flexibility of an undecorated catechol diether compound in the binding pocket of wild type and mutants (Y181C and K103N/Y181C) HIV-1 RT is investigated by using QM/MM calculations. From the results, the uracil ring is found to exhibit more flexibility in the NNIBP. On the contrary, potential energy surfaces show that high energy is encountered by changing of the corresponding torsion of the cyanovinyl aryl ring indicating the limitation for torsional flexibility. For pointing out the key interaction for the binding, the residual interaction energies are performed by means of QM calculations. Important attractive interactions through hydrogen bonds between the inhibitor and K102, K/N103, V106, and Y188 are observed. The catechol ring is proposed to be modified in order to strengthen interactions with surrounding amino acids. The results may help for the designing of new potent NNRTIs.
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42
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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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43
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Sadiq SK, Mirambeau G, Meyerhans A. Equilibrium Model of Drug-Modulated GagPol-Embedded HIV-1 Reverse Transcriptase Dimerization to Enhance Premature Protease Activation. AIDS Res Hum Retroviruses 2018; 34:804-807. [PMID: 30056738 DOI: 10.1089/aid.2018.0111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Lack of effective strategies for killing cells latently infected with HIV-1 limits the eradication of AIDS. Unfortunately, current antiretroviral inhibitors are designed to target virus production but not latent infection. Interestingly, some non-nucleoside reverse transcriptase inhibitors (NNRTIs) have shown off-design effects, specifically, premature activation of HIV-1 protease (PR) within virus-infected cells that induces apoptosis. Here, we analyze an equilibrium model of HIV-1 reverse transcriptase (RT) binding to NNRTIs to understand the optimal binding characteristics that enhance RT dimerization within embedded GagPol dimers. This would allow NNRTIs to act as PR autoactivation enhancers (PAEs). We compute that ∼700-fold enhancement is theoretically possible by PAEs. Both a strong drug-dimer binding affinity (KD12 < 100 nM) and relatively weaker drug-monomer affinity (KD2/KD12 > 10) are required for significant enhancement (∼50-fold or more) relative to the drug-free dimer concentration within a drug concentration limit of 10 μM. Our approach rationalizes the observed effects of efavirenz on premature activation of PR and may be useful to guide the design of suitable drug candidates and their optimal dosage regimens for this therapy class.
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Affiliation(s)
- S. Kashif Sadiq
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Infection Biology Laboratory, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain
| | - Gilles Mirambeau
- Faculté des Sciences et Ingénierie, UFR de Biologie, Sorbonne Universités, Paris, France
| | - Andreas Meyerhans
- Infection Biology Laboratory, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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44
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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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45
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Iglesias J, Saen‐oon S, Soliva R, Guallar V. Computational structure‐based drug design: Predicting target flexibility. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1367] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | | | | | - Victor Guallar
- Life Science DepartmentBarcelonaSpain
- ICREA, Passeig Lluís Companys 23BarcelonaSpain
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46
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Zhou Z, Liu T, Kang D, Huo Z, Wu G, Daelemans D, De Clercq E, Pannecouque C, Zhan P, Liu X. Discovery of novel diarylpyrimidines as potent HIV-1 NNRTIs by investigating the chemical space of a less explored “hydrophobic channel”. Org Biomol Chem 2018; 16:1014-1028. [DOI: 10.1039/c7ob02828h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We described the identification of novel HIV-1 NNRTIs via exploration of the chemical space of a seldom explored “hydrophobic channel”.
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Affiliation(s)
- Zhongxia Zhou
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Tao Liu
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Dongwei Kang
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Zhipeng Huo
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Gaochan Wu
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Dirk Daelemans
- Rega Institute for Medical Research
- K.U.Leuven
- B-3000 Leuven
- Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research
- K.U.Leuven
- B-3000 Leuven
- Belgium
| | | | - Peng Zhan
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
| | - Xinyong Liu
- Department of Medicinal Chemistry
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
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47
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From in silico hit to long-acting late-stage preclinical candidate to combat HIV-1 infection. Proc Natl Acad Sci U S A 2017; 115:E802-E811. [PMID: 29279368 DOI: 10.1073/pnas.1717932115] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The HIV-1 pandemic affecting over 37 million people worldwide continues, with nearly one-half of the infected population on highly active antiretroviral therapy (HAART). Major therapeutic challenges remain because of the emergence of drug-resistant HIV-1 strains, limitations because of safety and toxicity with current HIV-1 drugs, and patient compliance for lifelong, daily treatment regimens. Nonnucleoside reverse transcriptase inhibitors (NNRTIs) that target the viral polymerase have been a key component of the current HIV-1 combination drug regimens; however, these issues hamper them. Thus, the development of novel more effective NNRTIs as anti-HIV-1 agents with fewer long-term liabilities, efficacy on new drug-resistant HIV-1 strains, and less frequent dosing is crucial. Using a computational and structure-based design strategy to guide lead optimization, a 5 µM virtual screening hit was transformed to a series of very potent nanomolar to picomolar catechol diethers. One representative, compound I, was shown to have nanomolar activity in HIV-1-infected T cells, potency on clinically relevant HIV-1 drug-resistant strains, lack of cytotoxicity and off-target effects, and excellent in vivo pharmacokinetic behavior. In this report, we show the feasibility of compound I as a late-stage preclinical candidate by establishing synergistic antiviral activity with existing HIV-1 drugs and clinical candidates and efficacy in HIV-1-infected humanized [human peripheral blood lymphocyte (Hu-PBL)] mice by completely suppressing viral loads and preventing human CD4+ T-cell loss. Moreover, a long-acting nanoformulation of compound I [compound I nanoparticle (compound I-NP)] in poly(lactide-coglycolide) (PLGA) was developed that shows sustained maintenance of plasma drug concentrations and drug efficacy for almost 3 weeks after a single dose.
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48
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Cournia Z, Allen B, Sherman W. Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations. J Chem Inf Model 2017; 57:2911-2937. [PMID: 29243483 DOI: 10.1021/acs.jcim.7b00564] [Citation(s) in RCA: 391] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Accurate in silico prediction of protein-ligand binding affinities has been a primary objective of structure-based drug design for decades due to the putative value it would bring to the drug discovery process. However, computational methods have historically failed to deliver value in real-world drug discovery applications due to a variety of scientific, technical, and practical challenges. Recently, a family of approaches commonly referred to as relative binding free energy (RBFE) calculations, which rely on physics-based molecular simulations and statistical mechanics, have shown promise in reliably generating accurate predictions in the context of drug discovery projects. This advance arises from accumulating developments in the underlying scientific methods (decades of research on force fields and sampling algorithms) coupled with vast increases in computational resources (graphics processing units and cloud infrastructures). Mounting evidence from retrospective validation studies, blind challenge predictions, and prospective applications suggests that RBFE simulations can now predict the affinity differences for congeneric ligands with sufficient accuracy and throughput to deliver considerable value in hit-to-lead and lead optimization efforts. Here, we present an overview of current RBFE implementations, highlighting recent advances and remaining challenges, along with examples that emphasize practical considerations for obtaining reliable RBFE results. We focus specifically on relative binding free energies because the calculations are less computationally intensive than absolute binding free energy (ABFE) calculations and map directly onto the hit-to-lead and lead optimization processes, where the prediction of relative binding energies between a reference molecule and new ideas (virtual molecules) can be used to prioritize molecules for synthesis. We describe the critical aspects of running RBFE calculations, from both theoretical and applied perspectives, using a combination of retrospective literature examples and prospective studies from drug discovery projects. This work is intended to provide a contemporary overview of the scientific, technical, and practical issues associated with running relative binding free energy simulations, with a focus on real-world drug discovery applications. We offer guidelines for improving the accuracy of RBFE simulations, especially for challenging cases, and emphasize unresolved issues that could be improved by further research in the field.
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Affiliation(s)
- Zoe Cournia
- Biomedical Research Foundation, Academy of Athens , 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Bryce Allen
- Silicon Therapeutics , 300 A Street, Boston, Massachusetts 02210, United States
| | - Woody Sherman
- Silicon Therapeutics , 300 A Street, Boston, Massachusetts 02210, United States
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49
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Poongavanam V, Namasivayam V, Vanangamudi M, Al Shamaileh H, Veedu RN, Kihlberg J, Murugan NA. Integrative approaches in
HIV
‐1 non‐nucleoside reverse transcriptase inhibitor design. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1328] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - Murugesan Vanangamudi
- Department of Medicinal and Pharmaceutical ChemistrySree Vidyanikethan College of Pharmacy Tirupathi India
| | | | - Rakesh N Veedu
- Centre for Comparative GenomicsMurdoch University Perth Australia
- Perron Institute for Neurological and Translational Science Perth Australia
| | - Jan Kihlberg
- Department of Chemistry‐BMCUppsala University Uppsala Sweden
| | - N Arul Murugan
- Division of Theoretical Chemistry and Biology, School of BiotechnologyKTH‐Royal Institute of Technology Stockholm Sweden
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50
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Zhong W, Zhu H, Zou H. “One-pot” cascade approach to 5,6-dihydroindolizines and indolizines from pyrrole-2-carbaldehydes and nitroethylenes. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.03.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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