1
|
Biological Calorimetry: Old Friend, New Insights. BIOPHYSICA 2023. [DOI: 10.3390/biophysica3010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Calorimetry is an old experimental technique (first instrument developed in S. XVIII), but it is broadly used and still provides key information for understanding biological processes at the molecular level, particularly, cooperative phenomena in protein interactions. Here, we review and highlight some key aspects of biological calorimetry. Several biological systems will be described in which calorimetry was instrumental for modeling the behavior of the protein and obtaining further biological insight.
Collapse
|
2
|
Chaplain C, Fritschi CJ, Anang S, Gong Z, Richard J, Bourassa C, Liang S, Mohammadi M, Park J, Finzi A, Madani N, Sodroski JG, Abrams CF, Hendrickson WA, Smith AB. Structural and Functional Characterization of Indane-Core CD4-Mimetic Compounds Substituted with Heterocyclic Amines. ACS Med Chem Lett 2023; 14:51-58. [PMID: 36655122 PMCID: PMC9841591 DOI: 10.1021/acsmedchemlett.2c00376] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
The human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer on the virion surface interacts with the host receptors, CD4 and CCR5/CXCR4, to mediate virus entry into the target cell. CD4-mimetic compounds (CD4mcs) bind the gp120 Env, block CD4 binding, and inactivate Env. Previous studies suggested that a C(5)-methylamino methyl moiety on a lead CD4mc, BNM-III-170, contributed to its antiviral potency. By replacing the C(5) chain with differentially substituted pyrrolidine, piperidine, and piperazine ring systems, guided by structural and computational analyses, we found that the 5-position of BNM-III-170 is remarkably tolerant of a variety of ring sizes and substitutions, both in regard to antiviral activity and sensitization to humoral responses. Crystallographic analyses of representative analogues from the pyrrolidine series revealed the potential for 5-substituents to hydrogen bond with gp120 Env residue Thr 283. Further optimization of these interactions holds promise for the development of CD4mcs with greater potency.
Collapse
Affiliation(s)
- Cheyenne Chaplain
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Christopher J. Fritschi
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Saumya Anang
- Department of Cancer Immunology and Virology, Dana-Farber
Cancer
Institute and Department of Microbiology, Harvard Medical
School, Boston, Massachusetts 02215, United States
| | - Zhen Gong
- Department of Biochemistry
and Molecular Biophysics and Department of Physiology and Cellular
Biophysics, Columbia University, New York, New York 10032, United States
| | - Jonathan Richard
- Centre
de
Recherche du CHUM, Montreal H2X 0A9, Canada
- Département
de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec H3T 1J4, Canada
| | - Catherine Bourassa
- Centre
de
Recherche du CHUM, Montreal H2X 0A9, Canada
- Département
de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec H3T 1J4, Canada
| | - Shuaiyi Liang
- Department of Biochemistry
and Molecular Biophysics and Department of Physiology and Cellular
Biophysics, Columbia University, New York, New York 10032, United States
| | - Mohammadjavad Mohammadi
- Department
of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Jun Park
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Andrés Finzi
- Centre
de
Recherche du CHUM, Montreal H2X 0A9, Canada
- Département
de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec H3T 1J4, Canada
| | - Navid Madani
- Department of Cancer Immunology and Virology, Dana-Farber
Cancer
Institute and Department of Microbiology, Harvard Medical
School, Boston, Massachusetts 02215, United States
| | - Joseph G. Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber
Cancer
Institute and Department of Microbiology, Harvard Medical
School, Boston, Massachusetts 02215, United States
- Department
of Immunology and Infectious Diseases, Harvard
School of Public Health, Boston, Massachusetts 02115, United States
| | - Cameron F. Abrams
- Department
of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Wayne A. Hendrickson
- Department of Biochemistry
and Molecular Biophysics and Department of Physiology and Cellular
Biophysics, Columbia University, New York, New York 10032, United States
| | - Amos B. Smith
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
3
|
Fritschi C, Liang S, Mohammadi M, Anang S, Moraca F, Chen J, Madani N, Sodroski JG, Abrams CF, Hendrickson WA, Smith AB. Identification of gp120 Residue His105 as a Novel Target for HIV-1 Neutralization by Small-Molecule CD4-Mimics. ACS Med Chem Lett 2021; 12:1824-1831. [PMID: 34795873 PMCID: PMC8591726 DOI: 10.1021/acsmedchemlett.1c00437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/21/2021] [Indexed: 01/24/2023] Open
Abstract
The design and synthesis of butyl chain derivatives at the indane ring 3-position of our lead CD4-mimetic compound BNM-III-170 that inhibits human immunodeficiency virus (HIV-1) infection are reported. Optimization efforts were guided by crystallographic and computational analysis of the small-molecule ligands of the Phe43 cavity of the envelope glycoprotein gp120. Biological evaluation of 11-21 revealed that members of this series of CD4-mimetic compounds are able to inhibit HIV-1 viral entry into target cells more potently and with greater breadth compared to BNM-III-170. Crystallographic analysis of the binding pocket of 14, 16, and 17 revealed a novel hydrogen bonding interaction between His105 and a primary hydroxyl group on the butyl side chain. Further optimization of this interaction with the His105 residue holds the promise of more potent CD4-mimetic compounds.
Collapse
Affiliation(s)
- Christopher
J. Fritschi
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Shuaiyi Liang
- Department of Biochemistry and Molecular Biophysics and Department of Physiology
and Cellular
Biophysics, Columbia University, New York, New York 10032, United States
| | - Mohammadjavad Mohammadi
- Department
of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Saumya Anang
- Department of Cancer
Immunology and Virology, Dana-Farber Cancer
Institute and Department of Microbiology, Harvard Medical
School, Boston, Massachusetts 02115, United States
| | - Francesca Moraca
- Department
of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Junhua Chen
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Navid Madani
- Department of Cancer
Immunology and Virology, Dana-Farber Cancer
Institute and Department of Microbiology, Harvard Medical
School, Boston, Massachusetts 02115, United States
| | - Joseph G. Sodroski
- Department of Cancer
Immunology and Virology, Dana-Farber Cancer
Institute and Department of Microbiology, Harvard Medical
School, Boston, Massachusetts 02115, United States
- Department
of Immunology and Infectious Diseases, Harvard
School of Public Health, Boston, Massachusetts 02115, United States
| | - Cameron F. Abrams
- Department
of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics and Department of Physiology
and Cellular
Biophysics, Columbia University, New York, New York 10032, United States
| | - Amos B. Smith
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
4
|
Binding Thermodynamics to Intrinsically Disordered Protein Domains. Methods Mol Biol 2020. [PMID: 32696371 DOI: 10.1007/978-1-0716-0524-0_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2023]
Abstract
Many proteins are intrinsically disordered or contain one or more disordered domains. These domains can participate in binding interactions with other proteins or small ligands. Binding to intrinsically disordered protein domains requires the folding or structuring of those regions such that they can establish well-defined stoichiometric interactions. Since, in such a situation binding is coupled to folding, the energetics of those two events is reflected in the measured binding thermodynamics. In this protocol, we illustrate the thermodynamic differences between binding coupled to folding and binding independent of folding for the same protein. As an example, we use the HIV-1 envelope glycoprotein gp120 that contains structured as well as disordered domains. In the experiments presented, the binding of gp120 to molecules that bind to disordered regions and trigger structuring (CD4 or MAb 17b) and to molecules that bind to structured regions and do not induce conformational structuring (MAb b12) is discussed.
Collapse
|
5
|
Choi Y, Furlon JM, Amos RB, Griswold KE, Bailey-Kellogg C. DisruPPI: structure-based computational redesign algorithm for protein binding disruption. Bioinformatics 2019; 34:i245-i253. [PMID: 29949961 PMCID: PMC6022686 DOI: 10.1093/bioinformatics/bty274] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Motivation Disruption of protein–protein interactions can mitigate antibody recognition of therapeutic proteins, yield monomeric forms of oligomeric proteins, and elucidate signaling mechanisms, among other applications. While designing affinity-enhancing mutations remains generally quite challenging, both statistically and physically based computational methods can precisely identify affinity-reducing mutations. In order to leverage this ability to design variants of a target protein with disrupted interactions, we developed the DisruPPI protein design method (DISRUpting Protein–Protein Interactions) to optimize combinations of mutations simultaneously for both disruption and stability, so that incorporated disruptive mutations do not inadvertently affect the target protein adversely. Results Two existing methods for predicting mutational effects on binding, FoldX and INT5, were demonstrated to be quite precise in selecting disruptive mutations from the SKEMPI and AB-Bind databases of experimentally determined changes in binding free energy. DisruPPI was implemented to use an INT5-based disruption score integrated with an AMBER-based stability assessment and was applied to disrupt protein interactions in a set of different targets representing diverse applications. In retrospective evaluation with three different case studies, comparison of DisruPPI-designed variants to published experimental data showed that DisruPPI was able to identify more diverse interaction-disrupting and stability-preserving variants more efficiently and effectively than previous approaches. In prospective application to an interaction between enhanced green fluorescent protein (EGFP) and a nanobody, DisruPPI was used to design five EGFP variants, all of which were shown to have significantly reduced nanobody binding while maintaining function and thermostability. This demonstrates that DisruPPI may be readily utilized for effective removal of known epitopes of therapeutically relevant proteins. Availability and implementation DisruPPI is implemented in the EpiSweep package, freely available under an academic use license. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Yoonjoo Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jacob M Furlon
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA
| | - Ryan B Amos
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA.,Norris Cotton Cancer Center at Dartmouth, Lebanon, NH, USA.,Department of Biological Sciences, Dartmouth, Hanover, NH, USA
| | | |
Collapse
|
6
|
Andrianov AM, Nikolaev GI, Kornoushenko YV, Xu W, Jiang S, Tuzikov AV. In Silico Identification of Novel Aromatic Compounds as Potential HIV-1 Entry Inhibitors Mimicking Cellular Receptor CD4. Viruses 2019; 11:v11080746. [PMID: 31412617 PMCID: PMC6723994 DOI: 10.3390/v11080746] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/13/2022] Open
Abstract
Despite recent progress in the development of novel potent HIV-1 entry/fusion inhibitors, there are currently no licensed antiviral drugs based on inhibiting the critical interactions of the HIV-1 envelope gp120 protein with cellular receptor CD4. In this connection, studies on the design of new small-molecule compounds able to block the gp120-CD4 binding are still of great value. In this work, in silico design of drug-like compounds containing the moieties that make the ligand active towards gp120 was performed within the concept of click chemistry. Complexes of the designed molecules bound to gp120 were then generated by molecular docking and optimized using semiempirical quantum chemical method PM7. Finally, the binding affinity analysis of these ligand/gp120 complexes was performed by molecular dynamic simulations and binding free energy calculations. As a result, five top-ranking compounds that mimic the key interactions of CD4 with gp120 and show the high binding affinity were identified as the most promising CD4-mimemic candidates. Taken together, the data obtained suggest that these compounds may serve as promising scaffolds for the development of novel, highly potent and broad anti-HIV-1 therapeutics.
Collapse
Affiliation(s)
- Alexander M Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus.
| | - Grigory I Nikolaev
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Belarus
| | - Yuri V Kornoushenko
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, 131 Dong An Road, Fuxing Building, Shanghai 200032, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, 131 Dong An Road, Fuxing Building, Shanghai 200032, China.
| | - Alexander V Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Belarus.
| |
Collapse
|
7
|
Moraca F, Rinaldo D, Smith AB, Abrams CF. Specific Noncovalent Interactions Determine Optimal Structure of a Buried Ligand Moiety: QM/MM and Pure QM Modeling of Complexes of the Small-Molecule CD4 Mimetics and HIV-1 gp120. ChemMedChem 2018; 13:627-633. [PMID: 29337418 DOI: 10.1002/cmdc.201700728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/06/2018] [Indexed: 01/25/2023]
Abstract
The small-molecule CD4 mimetics (smCD4mcs) are a class of highly potent HIV-1 entry inhibitors characterized by a unique structure-activity relationship (SAR). They share a halogenated phenyl ring (region 1) that deeply inserts into an otherwise water-filled cavity at the CD4 binding site on the gp120 surface, the so-called F43 cavity. Conservative modifications to region 1 away from this halogenated phenyl motif have all led to loss of activity, despite the fact that they are predicted by standard empirical computational approaches to bind equally well, making it difficult to further optimize this region of the compounds to increase binding to gp120. In this study we used quantum mechanical methods to understand the roots of the interactions between region 1 and the F43 cavity. We clearly demonstrate the presence of halogen bond/σ-hole and dispersion interactions between region 1 and the F43 cavity residues F376-N377, which are not captured by standard molecular mechanics approaches and the role played by the smCD4mc in the F43 cavity desolvation. These findings rationalize why the halogenated region 1 has proven so difficult to move beyond in smCD4mc optimization, in agreement with experimental evidence.
Collapse
Affiliation(s)
| | - David Rinaldo
- Schrödinger GmbH, Dynamostrasse 13, Mannheim, 68165, Germany
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA, 19104-6323, USA
| | - Cameron F Abrams
- Department of Chemical and Biological Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104-2875, USA
| |
Collapse
|
8
|
Claveria-Gimeno R, Vega S, Abian O, Velazquez-Campoy A. A look at ligand binding thermodynamics in drug discovery. Expert Opin Drug Discov 2017; 12:363-377. [DOI: 10.1080/17460441.2017.1297418] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Rafael Claveria-Gimeno
- Institute of Biocomputation and Physics of Complex Systems (BIFI), IQFR-CSIC-BIFI and GBsC-CSIC-BIFI Joint Units, Universidad de Zaragoza, Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), IQFR-CSIC-BIFI and GBsC-CSIC-BIFI Joint Units, Universidad de Zaragoza, Zaragoza, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), IQFR-CSIC-BIFI and GBsC-CSIC-BIFI Joint Units, Universidad de Zaragoza, Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), IQFR-CSIC-BIFI and GBsC-CSIC-BIFI Joint Units, Universidad de Zaragoza, Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Fundación ARAID, Government of Aragon, Zaragoza, Spain
| |
Collapse
|
9
|
Andrianov AM, Kashyn IA, Tuzikov AV. Computational identification of novel entry inhibitor scaffolds mimicking primary receptor CD4 of HIV-1 gp120. J Mol Model 2017; 23:18. [DOI: 10.1007/s00894-016-3189-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/15/2016] [Indexed: 11/24/2022]
|
10
|
Moraca F, Acharya K, Melillo B, Smith AB, Chaiken I, Abrams CF. Computational Evaluation of HIV-1 gp120 Conformations of Soluble Trimeric gp140 Structures as Targets for de Novo Docking of First- and Second-Generation Small-Molecule CD4 Mimics. J Chem Inf Model 2016; 56:2069-2079. [PMID: 27602436 DOI: 10.1021/acs.jcim.6b00393] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small-molecule CD4 mimics (SMCM's) bind to the gp120 subunit of the HIV-1 envelope glycoprotein (Env) and have been optimized to block cell infection in vitro. The lack of the V1/2 and V3 loops and the presence of the β2/3 and β20/21 strands (bridging sheet) in the available structures of the monomeric gp120 core may limit its applicability as a target for further synthetic optimization of SMCM potency and/or breadth. Here, we employ a combination of binding-site search, docking, estimation of protein-ligand interaction energy, all-atom molecular dynamics, and ELISA-based CD4-binding competition assays to create, characterize, and rationalize models of first- and second-generation of SMCM's bound to the distinct, trimeric BG505 SOSIP.664 structures 4NCO and 4TVP containing V1/2 and V3 loops with no bridging sheet. We demonstrate that the in silico neutralization of the highly conserved D368 is necessary to obtain the correct orientation of SMCM in their binding site when docking against the monomeric gp120 core. The computational results correlate with IC50's measured in CD4 binding competition ELISA and with KD's measured on gp120 core monomer. This supports the hypothesis that the 4NCO trimeric structure represents a viable target for further SMCM's optimization with advantages over both the 4TVP trimer and gp120 core monomer. Finally, the docking protocol has been optimized to screen compounds that can clearly interact with the highly conserved residue D368, increasing the likelihood of future optimizations to arrive at SMCM's with a broader spectrum of activity.
Collapse
Affiliation(s)
| | | | - Bruno Melillo
- Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | | | | |
Collapse
|
11
|
Berinyuy E, Soliman MES. Identification of Novel Potential gp120 of HIV-1 Antagonist Using Per-Residue Energy Contribution-Based Pharmacophore modelling. Interdiscip Sci 2016; 9:406-418. [PMID: 27165479 DOI: 10.1007/s12539-016-0174-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 04/11/2016] [Accepted: 04/15/2016] [Indexed: 01/01/2023]
Abstract
Inhibition of HIV-1 target cell entry, by targeting gp120, has been identified as a promising approach for the identification and development of prophylactic and salvage HIV infection inhibitors. A small molecule compound 18A is an important chemotype in the development of novel and diverse viral cell entry inhibitors, as it inhibits a wide variety of HIV strains by disrupting allosteric structuring on gp120. This study combines residue energy contribution (REC) pharmacophore mapping of 18A and in silico molecular docking in a virtual screening campaign to identify novel and diverse antagonists of gp120. The binding free energy of a validated docked complex of gp120-18A and the quantitative contribution of interacting residues were obtained with a more accurate molecular mechanics/generalised born surface area (MM/GBSA) method followed by mapping the energetically favourable residue contributions onto atom centres in 18A to obtain a pharmacophore model. The generated pharmacophore hypothesis was used to search the ZINC database for 3D structures that match the pharmacophore. Further, molecular docking, molecular dynamics simulations and binding free energy analysis were performed on retrieved hits in order to rank hits based on their affinity and interactions in the CD4 binding cavity of a gp120. Interestingly, the top scoring compound designated with ZINC database ID as ZINC64700951 (docking score = -8.8 kcal/mol, ∆G = -43.77 kcal/mol) showed higher affinity compared to compound 18A docking score = -7.3 kcal/mol, ∆G = -31.97 kcal/mol) and interaction of ZN64700951 with validated allosteric hot spot residues, Asp368 and Met426, and binding hot spot residues, Asn425, Glu370, Gly473, Trp427 and Met475 in gp120, suggest that ZN64700951 is a promising antagonist of gp120. Thus, ZN64700951 could serve as an additional prototype for further optimisation as an HIV target cell viral entry inhibitor.
Collapse
Affiliation(s)
- Emiliene Berinyuy
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4000, South Africa
| | - Mahmoud E S Soliman
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4000, South Africa.
| |
Collapse
|
12
|
Melillo B, Liang S, Park J, Schön A, Courter JR, LaLonde JM, Wendler DJ, Princiotto AM, Seaman MS, Freire E, Sodroski J, Madani N, Hendrickson WA, Smith AB. Small-Molecule CD4-Mimics: Structure-Based Optimization of HIV-1 Entry Inhibition. ACS Med Chem Lett 2016; 7:330-4. [PMID: 26985324 DOI: 10.1021/acsmedchemlett.5b00471] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/13/2016] [Indexed: 11/29/2022] Open
Abstract
The optimization, based on computational, thermodynamic, and crystallographic data, of a series of small-molecule ligands of the Phe43 cavity of the envelope glycoprotein gp120 of human immunodeficiency virus (HIV) has been achieved. Importantly, biological evaluation revealed that the small-molecule CD4 mimics (4-7) inhibit HIV-1 entry into target cells with both significantly higher potency and neutralization breadth than previous congeners, while maintaining high selectivity for the target virus. Their binding mode was characterized via thermodynamic and crystallographic studies.
Collapse
Affiliation(s)
- Bruno Melillo
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | - Jongwoo Park
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Arne Schön
- Department
of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joel R. Courter
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Judith M. LaLonde
- Department
of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
| | - Daniel J. Wendler
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | | | - Ernesto Freire
- Department
of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joseph Sodroski
- Department
of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, United States
| | | | | | - Amos B. Smith
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
13
|
Sangphukieo A, Nawae W, Laomettachit T, Supasitthimethee U, Ruengjitchatchawalya M. Computational Design of Hypothetical New Peptides Based on a Cyclotide Scaffold as HIV gp120 Inhibitor. PLoS One 2015; 10:e0139562. [PMID: 26517259 PMCID: PMC4627658 DOI: 10.1371/journal.pone.0139562] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/15/2015] [Indexed: 11/19/2022] Open
Abstract
Cyclotides are a family of triple disulfide cyclic peptides with exceptional resistance to thermal/chemical denaturation and enzymatic degradation. Several cyclotides have been shown to possess anti-HIV activity, including kalata B1 (KB1). However, the use of cyclotides as anti-HIV therapies remains limited due to the high toxicity in normal cells. Therefore, grafting anti-HIV epitopes onto a cyclotide might be a promising approach for reducing toxicity and simultaneously improving anti-HIV activity. Viral envelope glycoprotein gp120 is required for entry of HIV into CD4+ T cells. However, due to a high degree of variability and physical shielding, the design of drugs targeting gp120 remains challenging. We created a computational protocol in which molecular modeling techniques were combined with a genetic algorithm (GA) to automate the design of new cyclotides with improved binding to HIV gp120. We found that the group of modified cyclotides has better binding scores (23.1%) compared to the KB1. By using molecular dynamic (MD) simulation as a post filter for the final candidates, we identified two novel cyclotides, GA763 and GA190, which exhibited better interaction energies (36.6% and 22.8%, respectively) when binding to gp120 compared to KB1. This computational design represents an alternative tool for modifying peptides, including cyclotides and other stable peptides, as therapeutic agents before the synthesis process.
Collapse
Affiliation(s)
- Apiwat Sangphukieo
- Bioinformatics and Systems Biology program, King Mongkut’s University of Technology Thonburi (KMUTT), Bang Khun Thian, Bangkok, 10150, Thailand
| | - Wanapinun Nawae
- Pilot Plant Development and Training Institute, KMUTT (Bang Khun Thian), Bangkok, 10150, Thailand
| | - Teeraphan Laomettachit
- Bioinformatics and Systems Biology program, King Mongkut’s University of Technology Thonburi (KMUTT), Bang Khun Thian, Bangkok, 10150, Thailand
| | | | - Marasri Ruengjitchatchawalya
- Bioinformatics and Systems Biology program, King Mongkut’s University of Technology Thonburi (KMUTT), Bang Khun Thian, Bangkok, 10150, Thailand
- Biotechnology program, School of Bioresources and Technology, KMUTT (Bang Khun Thian), Bangkok, 10150, Thailand
- * E-mail:
| |
Collapse
|
14
|
Double Variational Binding--(SMILES) Conformational Analysis by Docking Mechanisms for Anti-HIV Pyrimidine Ligands. Int J Mol Sci 2015; 16:19553-601. [PMID: 26295229 PMCID: PMC4581313 DOI: 10.3390/ijms160819553] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/30/2015] [Accepted: 08/11/2015] [Indexed: 12/11/2022] Open
Abstract
Variational quantitative binding–conformational analysis for a series of anti-HIV pyrimidine-based ligands is advanced at the individual molecular level. This was achieved by employing ligand-receptor docking algorithms for each molecule in the 1,3-disubstituted uracil derivative series that was studied. Such computational algorithms were employed for analyzing both genuine molecular cases and their simplified molecular input line entry system (SMILES) transformations, which were created via the controlled breaking of chemical bonds, so as to generate the longest SMILES molecular chain (LoSMoC) and Branching SMILES (BraS) conformations. The study identified the most active anti-HIV molecules, and analyzed their special and relevant bonding fragments (chemical alerts), and the recorded energetic and geometric docking results (i.e., binding and affinity energies, and the surface area and volume of bonding, respectively). Clear computational evidence was also produced concerning the ligand-receptor pocket binding efficacies of the LoSMoc and BraS conformation types, thus confirming their earlier presence (as suggested by variational quantitative structure-activity relationship, variational-QSAR) as active intermediates for the molecule-to-cell transduction process.
Collapse
|
15
|
Courter JR, Madani N, Sodroski J, Schön A, Freire E, Kwong PD, Hendrickson WA, Chaiken IM, LaLonde JM, Smith AB. Structure-based design, synthesis and validation of CD4-mimetic small molecule inhibitors of HIV-1 entry: conversion of a viral entry agonist to an antagonist. Acc Chem Res 2014; 47:1228-37. [PMID: 24502450 PMCID: PMC3993944 DOI: 10.1021/ar4002735] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
This
Account provides an overview of a multidisciplinary consortium focused
on structure-based strategies to devise small molecule antagonists
of HIV-1 entry into human T-cells, which if successful would hold
considerable promise for the development of prophylactic modalities
to prevent HIV transmission and thereby alter the course of the AIDS
pandemic. Entry of the human immunodeficiency virus (HIV) into
target T-cells entails an interaction between CD4 on the host T-cell
and gp120, a component of the trimeric envelope glycoprotein spike
on the virion surface. The resultant interaction initiates a series
of conformational changes within the envelope spike that permits binding
to a chemokine receptor, formation of the gp41 fusion complex, and
cell entry. A hydrophobic cavity at the CD4–gp120 interface,
defined by X-ray crystallography, provided an initial site for small
molecule antagonist design. This site however has evolved to facilitate
viral entry. As such, the binding of prospective small molecule inhibitors
within this gp120 cavity can inadvertently trigger an allosteric entry
signal. Structural characterization of the CD4–gp120
interface, which provided the foundation for small molecule structure-based
inhibitor design, will be presented first. An integrated approach
combining biochemical, virological, structural, computational, and
synthetic studies, along with a detailed analysis of ligand binding
energetics, revealed that modestly active small molecule inhibitors
of HIV entry can also promote viral entry into cells lacking the CD4
receptor protein; these competitive inhibitors were termed small molecule
CD4 mimetics. Related congeners were subsequently identified with
both improved binding affinity and more potent viral entry inhibition.
Further assessment of the affinity-enhanced small molecule CD4 mimetics
demonstrated
that premature initiation of conformational change within the viral envelope spike, prior to cell encounter, can lead to irreversible
deactivation of viral entry machinery. Related congeners, which bind the same gp120 site, possess different propensities to elicit the
allosteric response that underlies the undesired enhancement of CD4-independent viral entry. Subsequently, key hotspots in the CD4–gp120 interface were categorized using mutagenesis and isothermal titration calorimetry according to the capacity to increase binding affinity without triggering the allosteric signal. This analysis, combined with cocrystal structures of small molecule viral entry agonists with gp120, led to the development of fully functional antagonists of HIV-1 entry. Additional structure-based design exploiting two hotspots followed by synthesis has now yielded low micromolar inhibitors of viral entry.
Collapse
Affiliation(s)
- Joel R. Courter
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Navid Madani
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, Massachusetts 02115, United States
| | - Joseph Sodroski
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Immunology, Harvard Medical School, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02115, United States
| | - Arne Schön
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ernesto Freire
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics and Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, United States
| | - Irwin M. Chaiken
- Department of Biochemistry and Molecular
Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
16
|
CD4-mimetic small molecules sensitize human immunodeficiency virus to vaccine-elicited antibodies. J Virol 2014; 88:6542-55. [PMID: 24696475 DOI: 10.1128/jvi.00540-14] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Approaches to prevent human immunodeficiency virus (HIV-1) transmission are urgently needed. Difficulties in eliciting antibodies that bind conserved epitopes exposed on the unliganded conformation of the HIV-1 envelope glycoprotein (Env) trimer represent barriers to vaccine development. During HIV-1 entry, binding of the gp120 Env to the initial receptor, CD4, triggers conformational changes in Env that result in the formation and exposure of the highly conserved gp120 site for interaction with the coreceptors, CCR5 and CXCR4. The DMJ compounds (+)-DMJ-I-228 and (+)-DMJ-II-121 bind gp120 within the conserved Phe 43 cavity near the CD4-binding site, block CD4 binding, and inhibit HIV-1 infection. Here we show that the DMJ compounds sensitize primary HIV-1, including transmitted/founder viruses, to neutralization by monoclonal antibodies directed against CD4-induced (CD4i) epitopes and the V3 region, two gp120 elements involved in coreceptor binding. Importantly, the DMJ compounds rendered primary HIV-1 sensitive to neutralization by antisera elicited by immunization of rabbits with HIV-1 gp120 cores engineered to assume the CD4-bound state. Thus, small molecules like the DMJ compounds may be useful as microbicides to inhibit HIV-1 infection directly and to sensitize primary HIV-1 to neutralization by readily elicited antibodies. IMPORTANCE Preventing HIV-1 transmission is a priority for global health. Eliciting antibodies that can neutralize many different strains of HIV-1 is difficult, creating problems for the development of a vaccine. We found that certain small-molecule compounds can sensitize HIV-1 to particular antibodies. These antibodies can be elicited in rabbits. These results suggest an approach to prevent HIV-1 sexual transmission in which a virus-sensitizing microbicide is combined with a vaccine.
Collapse
|
17
|
LaLonde JM, Le-Khac M, Jones DM, Courter JR, Park J, Schön A, Princiotto AM, Wu X, Mascola JR, Freire E, Sodroski J, Madani N, Hendrickson WA, Smith AB. Structure-Based Design and Synthesis of an HIV-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization. ACS Med Chem Lett 2013; 4:338-343. [PMID: 23667716 DOI: 10.1021/ml300407y] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The design, synthesis, thermodynamic and crystallographic characterization of a potent, broad spectrum, second-generation HIV-1 entry inhibitor that engages conserved carbonyl hydrogen bonds within gp120 has been achieved. The optimized antagonist exhibits a sub-micromolar binding affinity (110 nM) and inhibits viral entry of clade B and C viruses (IC50 geometric mean titer of 1.7 and 14.0 μM, respectively), without promoting CD4-independent viral entry. thermodynamic signatures indicate a binding preference for the (R,R)-over the (S,S)-enantiomer. The crystal structure of the small molecule-gp120 complex reveals the displacement of crystallographic water and the formation of a hydrogen bond with a backbone carbonyl of the bridging sheet. Thus, structure-based design and synthesis targeting the highly conserved and structurally characterized CD4:gp120 interface is an effective tactic to enhance the neutralization potency of small molecule HIV-1 entry inhibitors.
Collapse
Affiliation(s)
- Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United
States
| | | | - David M. Jones
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Joel R. Courter
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Jongwoo Park
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Arne Schön
- Department
of Biology, The Johns Hopkins University, Baltimore, Maryland 21218,
United States
| | - Amy M. Princiotto
- Department of Cancer
Immunology and
AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Xueling Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda,
Maryland 20892, United States
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda,
Maryland 20892, United States
| | - Ernesto Freire
- Department
of Biology, The Johns Hopkins University, Baltimore, Maryland 21218,
United States
| | - Joseph Sodroski
- Department of Cancer
Immunology and
AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Microbiology and
Immunobiology, Harvard Medical School; Department of Immunology and
Infectious Diseases, Harvard School of Public Health; Ragon Institute
of MGH, MIT, and Harvard, Boston, Massachusetts 02115, United States
| | - Navid Madani
- Department of Cancer
Immunology and
AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wayne A. Hendrickson
- Department of Physiology and
Cellular Biophysics, Columbia University, New York, New York 10032, United States
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| |
Collapse
|
18
|
Bastos M, Alves N, Maia S, Gomes P, Inaba A, Miyazaki Y, Zanotti JM. Hydration water and peptide dynamics – two sides of a coin. A neutron scattering and adiabatic calorimetry study at low hydration and cryogenic temperatures. Phys Chem Chem Phys 2013; 15:16693-703. [DOI: 10.1039/c3cp51937f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
19
|
Abstract
The advent of silicon chip based technologies for genome sequencing promises continuing exponential falls in the reagent costs of sequencing. When every patient has a full genome sequence as part of their medical records the science of drug discovery and drug design must adapt and improve to meet this challenge. This series covers computational, and experimental approaches for small molecules and biologics. From the virtual patient - a computational model of a complete human being, through in silico screening to RNA editing and antibody directed therapies.
Collapse
Affiliation(s)
- David L Selwood
- The Wolfson Institute for Biomedical Research, University College London, Gower Street, London, UK.
| |
Collapse
|