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González-Delgado JM, Thompson PM, Andrałojć W, Gdaniec Z, Ghiladi RA, Franzen S. Comparison of the Backbone Dynamics of Dehaloperoxidase-Hemoglobin Isoenzymes. J Phys Chem B 2024; 128:3383-3397. [PMID: 38563384 DOI: 10.1021/acs.jpcb.3c07176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Dehaloperoxidase (DHP) is a multifunctional hemeprotein with a functional switch generally regulated by the chemical class of the substrate. Its two isoforms, DHP-A and DHP-B, differ by only five amino acids and have an almost identical protein fold. However, the catalytic efficiency of DHP-B for oxidation by a peroxidase mechanism ranges from 2- to 6-fold greater than that of DHP-A depending on the conditions. X-ray crystallography has shown that many substrates and ligands have nearly identical binding in the two isoenzymes, suggesting that the difference in catalytic efficiency could be due to differences in the conformational dynamics. We compared the backbone dynamics of the DHP isoenzymes at pH 7 through heteronuclear relaxation dynamics at 11.75, 16.45, and 19.97 T in combination with four 300 ns MD simulations. While the overall dynamics of the isoenzymes are similar, there are specific local differences in functional regions of each protein. In DHP-A, Phe35 undergoes a slow chemical exchange between two conformational states likely coupled to a swinging motion of Tyr34. Moreover, Asn37 undergoes fast chemical exchange in DHP-A. Given that Phe35 and Asn37 are adjacent to Tyr34 and Tyr38, it is possible that their dynamics modulate the formation and migration of the active tyrosyl radicals in DHP-A at pH 7. Another significant difference is that both distal and proximal histidines have a 15-18% smaller S2 value in DHP-B, thus their greater flexibility could account for the higher catalytic activity. The distal histidine grants substrate access to the distal pocket. The greater flexibility of the proximal histidine could also accelerate H2O2 activation at the heme Fe by increased coupling of an amino acid charge relay to stabilize the ferryl Fe(IV) oxidation state in a Poulos-Kraut "push-pull"-type peroxidase mechanism.
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Affiliation(s)
| | - Peter M Thompson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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2
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S.Al-Otaibi J, Mary Y, Mary Y, Armaković SJ, Armaković S, Van Alsenoy C, Yathirajan H. Insights into the reactivity properties, docking, DFT and MD simulations of orphenadrinium dihydrogen citrate in different solvents. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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3
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Experimental spectra, electronic properties (liquid and gaseous phases) and activity against SARS-CoV-2 main protease of Fluphenazine dihydrochloride: DFT and MD simulations. J Mol Struct 2022; 1267:133633. [PMID: 35791370 PMCID: PMC9244788 DOI: 10.1016/j.molstruc.2022.133633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/23/2022] [Accepted: 06/29/2022] [Indexed: 11/21/2022]
Abstract
The Gaussian 09 DFT tool is used to investigate the formational electronic behaviour, reactivity analysis and biological properties of fluphenazine dihydrochloride (FDD). The quantum computation is used to determine the spectroscopic and vibrational assignments of FDD. The NBO method explains charge transfer and molecular interactions. Energy gap values are determined using FMO analysis in different solvents and toluene is a better solvent due to higher value of solvation energy. The UV-visible spectra are investigated in various solvents using the TD-DFT method. Electrostatic potential, the wave function related properties such as LOL, NCI and RDG are determined in gaseous phase. Furthermore, the drug likeness is analyzed. At last, a docking study with MD simulation is used to investigate FDD's antiviral activity against SARS-CoV-2 main protease.
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4
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Shabanpour Y, Sajjadi S, Behmard E, Abdolmaleki P, Keihan AH. The structural, dynamic, and thermodynamic basis of darunavir resistance of a heavily mutated HIV-1 protease using molecular dynamics simulation. Front Mol Biosci 2022; 9:927373. [PMID: 36046605 PMCID: PMC9420863 DOI: 10.3389/fmolb.2022.927373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
The human immunodeficiency virus type 1 protease (HIV-1 PR) is an important enzyme in the life cycle of the HIV virus. It cleaves inactive pre-proteins of the virus and changes them into active proteins. Darunavir (DRV) suppresses the wild-type HIV-1 PR (WT-Pr) activity but cannot inhibit some mutant resistant forms (MUT-Pr). Increasing knowledge about the resistance mechanism can be helpful for designing more effective inhibitors. In this study, the mechanism of resistance of a highly MUT-Pr strain against DRV was investigated. For this purpose, complexes of DRV with WT-Pr (WT-Pr-D) and MUT-Pr (MUT-Pr-D) were studied by all-atom molecular dynamics simulation in order to extract the dynamic and energetic properties. Our data revealed that mutations increased the flap-tip flexibility due to the reduction of the flap-flap hydrophobic interactions. So, the protease’s conformation changed from a closed state to a semi-open state that can facilitate the disjunction of DRV from the active site. On the other hand, energy analysis limited to the final basins of the energy landscape indicated that the entropy of binding of DRV to MUT-Pr was more favorable than that of WT-Pr. However, the enthalpy penalty overcomes it and makes binding more unfavorable relative to the WT-Pr. The unfavorable interaction of DRV with R8, I50, I84, D25′, and A28′ residues in MUT-Pr-D relative to WT-Pr-D is the reason for this enthalpy penalty. Thus, mutations drive resistance to DRV. The hydrogen bond analysis showed that compared with WT-Pr, the hydrogen bonds between DRV and the active-site residues of MUT-Pr were disrupted.
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Affiliation(s)
- Yaser Shabanpour
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Sharareh Sajjadi
- Department of Biology, Roudehen Branch, Islamic Azad University, Roudehen, Iran
| | - Esmaeil Behmard
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parviz Abdolmaleki
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amir Homayoun Keihan
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
- *Correspondence: Amir Homayoun Keihan, ,
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5
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Bobrovs R, Basens EE, Drunka L, Kanepe I, Matisone S, Velins KK, Andrianov V, Leitis G, Zelencova-Gopejenko D, Rasina D, Jirgensons A, Jaudzems K. Exploring Aspartic Protease Inhibitor Binding to Design-Selective Antimalarials. J Chem Inf Model 2022; 62:3263-3273. [PMID: 35712895 DOI: 10.1021/acs.jcim.2c00422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selectivity is a major issue in the development of drugs targeting pathogen aspartic proteases. Here, we explore the selectivity-determining factors by studying specifically designed malaria aspartic protease (plasmepsin) open-flap inhibitors. Metadynamics simulations are used to uncover the complex binding/unbinding pathways of these inhibitors and describe the critical transition states in atomistic resolution. The simulation results are compared with experimentally determined enzymatic activities. Our findings demonstrate that plasmepsin inhibitor selectivity can be achieved by targeting the flap loop with hydrophobic substituents that enable ligand binding under the flap loop, as such a behavior is not observed for several other aspartic proteases. The ability to estimate the selectivity of compounds before they are synthesized is of considerable importance in drug design; therefore, we expect that our approach will be useful in selective inhibitor designs against not only aspartic proteases but also other enzyme classes.
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Affiliation(s)
- Raitis Bobrovs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | | | - Laura Drunka
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Iveta Kanepe
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Sofija Matisone
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | | | - Victor Andrianov
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Gundars Leitis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | | | - Dace Rasina
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
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6
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Abstract
Viral proteases are diverse in structure, oligomeric state, catalytic mechanism, and substrate specificity. This chapter focuses on proteases from viruses that are relevant to human health: human immunodeficiency virus subtype 1 (HIV-1), hepatitis C (HCV), human T-cell leukemia virus type 1 (HTLV-1), flaviviruses, enteroviruses, and coronaviruses. The proteases of HIV-1 and HCV have been successfully targeted for therapeutics, with picomolar FDA-approved drugs currently used in the clinic. The proteases of HTLV-1 and the other virus families remain emerging therapeutic targets at different stages of the drug development process. This chapter provides an overview of the current knowledge on viral protease structure, mechanism, substrate recognition, and inhibition. Particular focus is placed on recent advances in understanding the molecular basis of diverse substrate recognition and resistance, which is essential toward designing novel protease inhibitors as antivirals.
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Affiliation(s)
- Jacqueto Zephyr
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, United States.
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7
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Insights into solvent, spectroscopic and pharmacological properties of rhynchophylline and isorhynchophylline: Experimental, DFT, MD and docking. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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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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9
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Laville P, Petitjean M, Regad L. Structural Impacts of Drug-Resistance Mutations Appearing in HIV-2 Protease. Molecules 2021; 26:molecules26030611. [PMID: 33503916 PMCID: PMC7865771 DOI: 10.3390/molecules26030611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
The use of antiretroviral drugs is accompanied by the emergence of HIV-2 resistances. Thus, it is important to elucidate the mechanisms of resistance to antiretroviral drugs. Here, we propose a structural analysis of 31 drug-resistant mutants of HIV-2 protease (PR2) that is an important target against HIV-2 infection. First, we modeled the structures of each mutant. We then located structural shifts putatively induced by mutations. Finally, we compared wild-type and mutant inhibitor-binding pockets and interfaces to explore the impacts of these induced structural deformations on these two regions. Our results showed that one mutation could induce large structural rearrangements in side-chain and backbone atoms of mutated residue, in its vicinity or further. Structural deformations observed in side-chain atoms are frequent and of greater magnitude, that confirms that to fight drug resistance, interactions with backbone atoms should be favored. We showed that these observed structural deformations modify the conformation, volume, and hydrophobicity of the binding pocket and the composition and size of the PR2 interface. These results suggest that resistance mutations could alter ligand binding by modifying pocket properties and PR2 stability by impacting its interface. Our results reinforce the understanding of the effects of mutations that occurred in PR2 and the different mechanisms of PR2 resistance.
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10
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Ugbaja SC, Appiah-Kubi P, Lawal MM, Gumede NS, Kumalo HM. Unravelling the molecular basis of AM-6494 high potency at BACE1 in Alzheimer's disease: an integrated dynamic interaction investigation. J Biomol Struct Dyn 2021; 40:5253-5265. [PMID: 33410374 DOI: 10.1080/07391102.2020.1869099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
β-amyloid precursor protein cleaving enzyme1 (BACE1) has prominently been an important drug design target implicated in Alzheimer's disease pathway. The failure rate of most of the already tested drugs at different clinical phases remains a major concern. Recently, AM-6494 was reported as a novel potent, highly selective, and orally effective inhibitor against BACE1. AM-6494 displayed no alteration of skin/fur colour in animal studies, an adverse effect common to previous BACE1 inhibitors. However, the atomistic molecular mechanism of BACE1 inhibition by AM-6494 remains unclear. To elucidate the binding mechanism of AM-6494 relative to umibecestat (CNP-520) as well as the structural changes when bound to BACE1, advanced computational techniques such as accelerated MD simulation and principal component analysis have been utilised. The results demonstrated higher binding affinity of AM-6494 at BACE1 with van der Waals as dominant energy contributor compared to umibecestat. Conformational monitoring of the β-hairpin flap covering the active site revealed an effective flap closure when bound with AM-6494 compared to CNP-520, which predominantly alternates between semi-open and closed conformations. The observed effective flap closure of AM-6494 explains its higher inhibitory power towards BACE1. Besides the catalytic Asp32/228 dyad, Tyr14, Leu30, Tyr71 and Gly230 represent critical residues in the potency of these inhibitors at BACE1 binding interface. The findings highlighted in this research provide a basis to explain AM-6494 high inhibitory potency and might assist in the design of new inhibitors with improved selectivity and potency for BACE1.
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Affiliation(s)
- Samuel C Ugbaja
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Patrick Appiah-Kubi
- Discipline of Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Monsurat M Lawal
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Nelisiwe S Gumede
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
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11
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Zondagh J, Basson AE, Achilonu I, Morris L, Dirr HW, Sayed Y. Drug susceptibility and replication capacity of a rare HIV-1 subtype C protease hinge region variant. Antivir Ther 2020; 24:333-342. [PMID: 30958309 DOI: 10.3851/imp3308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Protease inhibitors form the main component of second-line antiretroviral treatment in South Africa. Despite their efficacy, mutations arising within the HIV-1 gag and protease coding regions contribute to the development of resistance against this class of drug. In this paper we investigate a South African HIV-1 subtype C Gag-protease that contains a hinge region mutation and insertion (N37T↑V). METHODS In vitro single-cycle drug susceptibility and viral replication capacity assays were performed on W1201i, a wild-type reference isolate (MJ4) and a chimeric construct (MJ4GagN37T↑VPR). Additionally, enzyme assays were performed on the N37T↑V protease and a wild-type reference protease. RESULTS W1201i showed a small (threefold), but significant (P<0.0001) reduction in drug susceptibility to darunavir compared with MJ4. Substitution of W1201i-Gag with MJ4-Gag resulted in an additional small (twofold), but significant (P<0.01) reduction in susceptibility to lopinavir and atazanavir. The W1201i pseudovirus had a significantly (P<0.01) reduced replication capacity (16.4%) compared with the MJ4. However, this was dramatically increased to 164% (P<0.05) when W1201i-Gag was substituted with MJ4-Gag. Furthermore, the N37T↑V protease displayed reduced catalytic processing compared with the SK154 protease. CONCLUSIONS Collectively, these data suggest that the N37T↑V mutation and insertion increases viral infectivity and decreases drug susceptibility. These variations are classified as secondary mutations, and indirectly impact inhibitor binding, enzyme fitness and enzyme stability. Additionally, polymorphisms arising in Gag can modify the impact of protease with regards to viral replication and susceptibility to protease inhibitors.
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Affiliation(s)
- Jake Zondagh
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, South Africa
| | - Adriaan E Basson
- HIV Pathogenesis Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.,Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Ikechukwu Achilonu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, South Africa
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Heini W Dirr
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, South Africa
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12
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Lawal MM, Sanusi ZK, Govender T, Maguire GE, Honarparvar B, Kruger HG. From Recognition to Reaction Mechanism: An Overview on the Interactions between HIV-1 Protease and its Natural Targets. Curr Med Chem 2020; 27:2514-2549. [DOI: 10.2174/0929867325666181113122900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 11/04/2018] [Accepted: 11/07/2018] [Indexed: 12/28/2022]
Abstract
Current investigations on the Human Immunodeficiency Virus Protease (HIV-1
PR) as a druggable target towards the treatment of AIDS require an update to facilitate further
development of promising inhibitors with improved inhibitory activities. For the past two
decades, up to 100 scholarly reports appeared annually on the inhibition and catalytic mechanism
of HIV-1 PR. A fundamental literature review on the prerequisite of HIV-1 PR action
leading to the release of the infectious virion is absent. Herein, recent advances (both computationally
and experimentally) on the recognition mode and reaction mechanism of HIV-1 PR
involving its natural targets are provided. This review features more than 80 articles from
reputable journals. Recognition of the natural Gag and Gag-Pol cleavage junctions by this
enzyme and its mutant analogs was first addressed. Thereafter, a comprehensive dissect of
the enzymatic mechanism of HIV-1 PR on its natural polypeptide sequences from literature
was put together. In addition, we highlighted ongoing research topics in which in silico
methods could be harnessed to provide deeper insights into the catalytic mechanism of the
HIV-1 protease in the presence of its natural substrates at the molecular level. Understanding
the recognition and catalytic mechanism of HIV-1 PR leading to the release of an infective
virion, which advertently affects the immune system, will assist in designing mechanismbased
inhibitors with improved bioactivity.
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Affiliation(s)
- Monsurat M. Lawal
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Zainab K. Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Glenn E.M. Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
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13
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Weikl TR, Hemmateenejad B. Accessory mutations balance the marginal stability of the HIV-1 protease in drug resistance. Proteins 2019; 88:476-484. [PMID: 31599014 DOI: 10.1002/prot.25826] [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: 03/18/2019] [Revised: 08/21/2019] [Accepted: 09/17/2019] [Indexed: 01/27/2023]
Abstract
The HIV-1 protease is a major target of inhibitor drugs in AIDS therapies. The therapies are impaired by mutations of the HIV-1 protease that can lead to resistance to protease inhibitors. These mutations are classified into major mutations, which usually occur first and clearly reduce the susceptibility to protease inhibitors, and minor, accessory mutations that occur later and individually do not substantially affect the susceptibility to inhibitors. Major mutations are predominantly located in the active site of the HIV-1 protease and can directly interfere with inhibitor binding. Minor mutations, in contrast, are typically located distal to the active site. A central question is how these distal mutations contribute to resistance development. In this article, we present a systematic computational investigation of stability changes caused by major and minor mutations of the HIV-1 protease. As most small single-domain proteins, the HIV-1 protease is only marginally stable. Mutations that destabilize the folded, active state of the protease therefore can shift the conformational equilibrium towards the unfolded, inactive state. We find that the most frequent major mutations destabilize the HIV-1 protease, whereas roughly half of the frequent minor mutations are stabilizing. An analysis of protease sequences from patients in treatment indicates that the stabilizing minor mutations are frequently correlated with destabilizing major mutations, and that highly resistant HIV-1 proteases exhibit significant fractions of stabilizing mutations. Our results thus indicate a central role of minor mutations in balancing the marginal stability of the protease against the destabilization induced by the most frequent major mutations.
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Affiliation(s)
- Thomas R Weikl
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Science Park Golm, Potsdam, Germany
| | - Bahram Hemmateenejad
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Science Park Golm, Potsdam, Germany.,Department of Chemistry, Shiraz University, Shiraz, Iran
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14
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Ishima R, Kurt Yilmaz N, Schiffer CA. NMR and MD studies combined to elucidate inhibitor and water interactions of HIV-1 protease and their modulations with resistance mutations. JOURNAL OF BIOMOLECULAR NMR 2019; 73:365-374. [PMID: 31243634 PMCID: PMC6941145 DOI: 10.1007/s10858-019-00260-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/19/2019] [Indexed: 06/09/2023]
Abstract
Over the last two decades, both the sensitivity of NMR and the time scale of molecular dynamics (MD) simulation have increased tremendously and have advanced the field of protein dynamics. HIV-1 protease has been extensively studied using these two methods, and has presented a framework for cross-evaluation of structural ensembles and internal dynamics by integrating the two methods. Here, we review studies from our laboratories over the last several years, to understand the mechanistic basis of protease drug-resistance mutations and inhibitor responses, using NMR and crystal structure-based parallel MD simulations. Our studies demonstrate that NMR relaxation experiments, together with crystal structures and MD simulations, significantly contributed to the current understanding of structural/dynamic changes due to HIV-1 protease drug resistance mutations.
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Affiliation(s)
- Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
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15
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Bobrovs R, Jaudzems K, Jirgensons A. Exploiting Structural Dynamics To Design Open-Flap Inhibitors of Malarial Aspartic Proteases. J Med Chem 2019; 62:8931-8950. [DOI: 10.1021/acs.jmedchem.9b00184] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Raitis Bobrovs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
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16
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Conformational and dynamical basis for cross-reactivity observed between anti HIV-1 protease antibody with protease and an epitope peptide from it. Int J Biol Macromol 2018; 118:1696-1707. [PMID: 29990556 DOI: 10.1016/j.ijbiomac.2018.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 11/23/2022]
Abstract
F11.2.32 is a monoclonal antibody raised against HIV-1 protease and it inhibits protease activity. While the structure of the epitope peptide in complex with the antibody is known, how protease interacts with the antibody is not known. In this study, we model the conformational features of the free and bound epitope peptide and protease-antibody interactions. We find through our simulations, that the free epitope peptide P36-46 samples conformations akin to the bound conformation of the peptide in complex with the Ab, with a β-turn conformation sampled by the 38LPGR41 sequence highlighting the role of inherent conformational preferences of the peptide. Further, to determine the interactions present between the protease and antibody, we docked the protease in its conformation observed in the crystal structure, onto the antibody and simulated the dynamics of the complex in explicit water. We have identified the key residues involved in hydrogen-bond interactions and salt-bridges in Ag-Ab complex and examined the role of CDR flexibility in binding different conformations of the same epitope sequence in peptide and protein antigens. Thus, our results provide the basis for understanding the cross-reactivity observed between the antibody with protease and the epitope peptide from it.
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17
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Leidner F, Kurt Yilmaz N, Paulsen J, Muller YA, Schiffer CA. Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease. J Chem Theory Comput 2018; 14:2784-2796. [PMID: 29570286 DOI: 10.1021/acs.jctc.8b00097] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Water is essential in many biological processes, and the hydration structure plays a critical role in facilitating protein folding, dynamics, and ligand binding. A variety of biophysical spectroscopic techniques have been used to probe the water solvating proteins, often complemented with molecular dynamics (MD) simulations to resolve the spatial and dynamic features of the hydration shell, but comparing relative water structure is challenging. In this study 1 μs MD simulations were performed to identify and characterize hydration sites around HIV-1 protease bound to an inhibitor, darunavir (DRV). The water density, hydration site occupancy, extent and anisotropy of fluctuations, coordinated water molecules, and hydrogen bonds were characterized and compared to the properties of bulk water. The water density of the principal hydration shell was found to be higher than bulk, dependent on the topology and physiochemical identity of the biomolecular surface. The dynamics of water molecules occupying principal hydration sites was highly dependent on the number of water-water interactions and inversely correlated with hydrogen bonds to the protein-inhibitor complex. While many waters were conserved following the symmetry of homodimeric HIV protease, the asymmetry induced by DRV resulted in asymmetric lower-occupancy hydration sites at the concave surface of the active site. Key interactions between water molecules and the protease, that stabilize the protein in the inhibited form, were altered in a drug resistant variant of the protease indicating that modulation of solvent-solute interactions might play a key role in conveying drug resistance. Our analysis provides insights into the interplay between an enzyme inhibitor complex and the hydration shell and has implications in elucidating water structure in a variety of biological processes and applications including ligand binding, inhibitor design, and resistance.
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Affiliation(s)
- Florian Leidner
- 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
| | - Janet Paulsen
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Yves A Muller
- Division of Biotechnology , Friedrich-Alexander-Universität Erlangen-Nürnberg , Erlangen 91052 , Germany
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
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18
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Persons JD, Khan SN, Ishima R. An NMR strategy to detect conformational differences in a protein complexed with highly analogous inhibitors in solution. Methods 2018; 148:9-18. [PMID: 29656080 DOI: 10.1016/j.ymeth.2018.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/06/2018] [Accepted: 04/08/2018] [Indexed: 11/17/2022] Open
Abstract
This manuscript presents an NMR strategy to investigate conformational differences in protein-inhibitor complexes, when the inhibitors tightly bind to a protein at sub-nanomolar dissociation constants and are highly analogous to each other. Using HIV-1 protease (PR), we previously evaluated amide chemical shift differences, ΔCSPs, of PR bound to darunavir (DRV) compared to PR bound to several DRV analogue inhibitors, to investigate subtle but significant long-distance conformation changes caused by the inhibitor's chemical moiety variation [Khan, S. N., Persons, J. D. Paulsen, J. L., Guerrero, M., Schiffer, C. A., Kurt-Yilmaz, N., and Ishima, R., Biochemistry, (2018), 57, 1652-1662]. However, ΔCSPs are not ideal for investigating subtle PR-inhibitor interface differences because intrinsic differences in the electron shielding of the inhibitors affect protein ΔCSPs. NMR relaxation is also not suitable as it is not sensitive enough to detect small conformational differences in rigid regions among similar PR-inhibitor complexes. Thus, to gain insight into conformational differences at the inhibitor-protein interface, we recorded 15N-half filtered NOESY spectra of PR bound to two highly analogous inhibitors and assessed NOEs between PR amide protons and inhibitor protons, between PR amide protons and hydroxyl side chains, and between PR amide protons and water protons. We also verified the PR amide-water NOEs using 2D water-NOE/ROE experiments. Differences in water-amide proton NOE peaks, possibly due to amide-protein hydrogen bonds, were observed between subunit A and subunit B, and between the DRV-bound form and an analogous inhibitor-bound form, which may contribute to remote conformational changes.
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Affiliation(s)
- John D Persons
- Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Shahid N Khan
- Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA.
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19
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Huang YMM, McCammon JA, Miao Y. Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation. J Chem Theory Comput 2018; 14:1853-1864. [PMID: 29489349 PMCID: PMC6747702 DOI: 10.1021/acs.jctc.7b01226] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Through adding a harmonic boost potential to smooth the system potential energy surface, Gaussian accelerated molecular dynamics (GaMD) provides enhanced sampling and free energy calculation of biomolecules without the need of predefined reaction coordinates. This work continues to improve the acceleration power and energy reweighting of the GaMD by combining the GaMD with replica exchange algorithms. Two versions of replica exchange GaMD (rex-GaMD) are presented: force constant rex-GaMD and threshold energy rex-GaMD. During simulations of force constant rex-GaMD, the boost potential can be exchanged between replicas of different harmonic force constants with fixed threshold energy. However, the algorithm of threshold energy rex-GaMD tends to switch the threshold energy between lower and upper bounds for generating different levels of boost potential. Testing simulations on three model systems, including the alanine dipeptide, chignolin, and HIV protease, demonstrate that through continuous exchanges of the boost potential, the rex-GaMD simulations not only enhance the conformational transitions of the systems but also narrow down the distribution width of the applied boost potential for accurate energetic reweighting to recover biomolecular free energy profiles.
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Affiliation(s)
- Yu-ming M. Huang
- Department of Pharmacology and University of California, San Diego, La Jolla, CA 92093
| | - J. Andrew McCammon
- Department of Pharmacology and University of California, San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093
| | - Yinglong Miao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093
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20
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Khan SN, Persons JD, Paulsen JL, Guerrero M, Schiffer CA, Kurt-Yilmaz N, Ishima R. Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance. Biochemistry 2018; 57:1652-1662. [PMID: 29457713 PMCID: PMC5850901 DOI: 10.1021/acs.biochem.7b01238] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the era of state-of-the-art inhibitor design and high-resolution structural studies, detection of significant but small protein structural differences in the inhibitor-bound forms is critical to further developing the inhibitor. Here, we probed differences in HIV-1 protease (PR) conformation among darunavir and four analogous inhibitor-bound forms and compared them with a drug-resistant mutant using nuclear magnetic resonance chemical shifts. Changes in amide chemical shifts of wild-type (WT) PR among these inhibitor-bound forms, ΔCSP, were subtle but detectable and extended >10 Å from the inhibitor-binding site, asymmetrically between the two subunits of PR. Molecular dynamics simulations revealed differential local hydrogen bonding as the molecular basis of this remote asymmetric change. Inhibitor-bound forms of the drug-resistant mutant also showed a similar long-range ΔCSP pattern. Differences in ΔCSP values of the WT and the mutant (ΔΔCSPs) were observed at the inhibitor-binding site and in the surrounding region. Comparing chemical shift changes among highly analogous inhibitors and ΔΔCSPs effectively eliminated local environmental effects stemming from different chemical groups and enabled exploitation of these sensitive parameters to detect subtle protein conformational changes and to elucidate asymmetric and remote conformational effects upon inhibitor interaction.
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Affiliation(s)
- Shahid N Khan
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John D Persons
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Janet L. Paulsen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Michel Guerrero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Nese Kurt-Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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21
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Miao Y, Huang YMM, Walker RC, McCammon JA, Chang CEA. Ligand Binding Pathways and Conformational Transitions of the HIV Protease. Biochemistry 2018; 57:1533-1541. [PMID: 29394043 PMCID: PMC5915299 DOI: 10.1021/acs.biochem.7b01248] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
It is important to determine the binding pathways and mechanisms of ligand molecules to target proteins to effectively design therapeutic drugs. Molecular dynamics (MD) is a promising computational tool that allows us to simulate protein-drug binding at an atomistic level. However, the gap between the time scales of current simulations and those of many drug binding processes has limited the usage of conventional MD, which has been reflected in studies of the HIV protease. Here, we have applied a robust enhanced simulation method, Gaussian accelerated molecular dynamics (GaMD), to sample binding pathways of the XK263 ligand and associated protein conformational changes in the HIV protease. During two of 10 independent GaMD simulations performed over 500-2500 ns, the ligand was observed to successfully bind to the protein active site. Although GaMD-derived free energy profiles were not fully converged because of insufficient sampling of the complex system, the simulations still allowed us to identify relatively low-energy intermediate conformational states during binding of the ligand to the HIV protease. Relative to the X-ray crystal structure, the XK263 ligand reached a minimum root-mean-square deviation (RMSD) of 2.26 Å during 2.5 μs of GaMD simulation. In comparison, the ligand RMSD reached a minimum of only ∼5.73 Å during an earlier 14 μs conventional MD simulation. This work highlights the enhanced sampling power of the GaMD approach and demonstrates its wide applicability to studies of drug-receptor interactions for the HIV protease and by extension many other target proteins.
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Affiliation(s)
- Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Yu-ming M. Huang
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093, United States
| | - Ross C. Walker
- San Diego Supercomputer Center, University of California at San Diego, La Jolla, California 92093, United States
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093, United States
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - Chia-en A. Chang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
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22
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Gueto-Tettay C, Martinez-Consuegra A, Zuchniarz J, Gueto-Tettay LR, Drosos-Ramírez JC. A PM7 dynamic residue-ligand interactions energy landscape of the BACE1 inhibitory pathway by hydroxyethylamine compounds. Part I: The flap closure process. J Mol Graph Model 2017; 76:274-288. [PMID: 28746905 DOI: 10.1016/j.jmgm.2017.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 01/08/2023]
Abstract
BACE1 is an enzyme of scientific interest because it participates in the progression of Alzheimer's disease. Hydroxyethylamines (HEAs) are a family of compounds which exhibit inhibitory activity toward BACE1 at a nanomolar level, favorable pharmacokinetic properties and oral bioavailability. The first step in the inhibition of BACE1 by HEAs consists of their entrance into the protease active site and the resultant conformational change in the protein, from Apo to closed form. These two conformations differ in the position of an antiparallel loop (called the flap) which covers the entrance to the catalytic site. For BACE1, closure of this flap is vital to its catalytic activity and to inhibition of the enzyme due to the new interactions thereby formed with the ligand. In the present study a dynamic energy landscape of residue-ligand interaction energies (ReLIE) measured for 112 amino acids in the BACE1 active site and its immediate vicinity during the closure of the flap induced by 8 HEAs of different inhibitory power is presented. A total of 6.272 million ReLIE calculations, based on the PM7 semiempirical method, provided a deep and quantitative view of the first step in the inhibition of the aspartyl protease. The information suggests that residues Asp93, Asp289, Thr292, Thr293, Asn294 and Arg296 are anchor points for the ligand, accounting for approximately 45% of the total protein-ligand interaction. Additionally, flap closure improved the BACE1-HEA interaction by around 25%. Furthermore, the inhibitory activity of HEAs could be related to the capacity of these ligands to form said anchor point interactions and maintain them over time: the lack of some of these anchor interactions delayed flap closure or impeded it completely, or even caused the flap to reopen. The methodology employed here could be used as a tool to evaluate future structural modifications which lead to improvements in the favorability and stability of BACE1-HEA ReLIEs, aiding in the design of better inhibitors.
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Affiliation(s)
- Carlos Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia.
| | - Alejandro Martinez-Consuegra
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia
| | - Joshua Zuchniarz
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia
| | - Luis Roberto Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia
| | - Juan Carlos Drosos-Ramírez
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia.
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23
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Paulsen JL, Leidner F, Ragland DA, Kurt Yilmaz N, Schiffer CA. Interdependence of Inhibitor Recognition in HIV-1 Protease. J Chem Theory Comput 2017; 13:2300-2309. [PMID: 28358514 PMCID: PMC5425943 DOI: 10.1021/acs.jctc.6b01262] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Molecular recognition
is a highly interdependent process. Subsite
couplings within the active site of proteases are most often revealed
through conditional amino acid preferences in substrate recognition.
However, the potential effect of these couplings on inhibition and
thus inhibitor design is largely unexplored. The present study examines
the interdependency of subsites in HIV-1 protease using a focused
library of protease inhibitors, to aid in future inhibitor design.
Previously a series of darunavir (DRV) analogs was designed to systematically
probe the S1′ and S2′ subsites. Co-crystal structures
of these analogs with HIV-1 protease provide the ideal opportunity
to probe subsite interdependency. All-atom molecular dynamics simulations
starting from these structures were performed and systematically analyzed
in terms of atomic fluctuations, intermolecular interactions, and
water structure. These analyses reveal that the S1′ subsite
highly influences other subsites: the extension of the hydrophobic
P1′ moiety results in 1) reduced van der Waals contacts in
the P2′ subsite, 2) more variability in the hydrogen bond frequencies
with catalytic residues and the flap water, and 3) changes in the
occupancy of conserved water sites both proximal and distal to the
active site. In addition, one of the monomers in this homodimeric
enzyme has atomic fluctuations more highly correlated with DRV than
the other monomer. These relationships intricately link the HIV-1
protease subsites and are critical to understanding molecular recognition
and inhibitor binding. More broadly, the interdependency of subsite
recognition within an active site requires consideration in the selection
of chemical moieties in drug design; this strategy is in contrast
to what is traditionally done with independent optimization of chemical
moieties of an inhibitor.
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Affiliation(s)
- Janet L Paulsen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Florian Leidner
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Debra A Ragland
- 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
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
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24
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Gerlits O, Keen DA, Blakeley MP, Louis JM, Weber IT, Kovalevsky A. Room Temperature Neutron Crystallography of Drug Resistant HIV-1 Protease Uncovers Limitations of X-ray Structural Analysis at 100 K. J Med Chem 2017; 60:2018-2025. [PMID: 28195728 DOI: 10.1021/acs.jmedchem.6b01767] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature joint X-ray/neutron (XN) crystallography to obtain an atomic-resolution structure of the protease triple mutant (V32I/I47V/V82I) in complex with amprenavir. The XN structure reveals a D+ ion located midway between the inner Oδ1 oxygen atoms of the catalytic aspartic acid residues. Comparison of the current XN structure with our previous XN structure of the wild-type HIV-1 protease-amprenavir complex suggests that the three mutations do not significantly alter the drug-enzyme interactions. This is in contrast to the observations in previous 100 K X-ray structures of these complexes that indicated loss of interactions by the drug with the triple mutant protease. These findings, thus, uncover limitations of structural analysis of drug binding using X-ray structures obtained at 100 K.
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Affiliation(s)
- Oksana Gerlits
- UT/ORNL Joint Institute of Biological Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory , Harwell Campus, Didcot, OX11 0QX, U.K
| | - Matthew P Blakeley
- Large-Scale Structures Group, Institut Laue Langevin , 71 avenue des Martyrs, 38000 Grenoble, France
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , DHHS, Bethesda, Maryland 20892-0520, United States
| | - Irene T Weber
- Departments of Chemistry and Biology, Georgia State University , Atlanta, Georgia 30302, United States
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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25
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Huang YMM, Raymundo MAV, Chen W, Chang CEA. Mechanism of the Association Pathways for a Pair of Fast and Slow Binding Ligands of HIV-1 Protease. Biochemistry 2017; 56:1311-1323. [PMID: 28060481 DOI: 10.1021/acs.biochem.6b01112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Equilibrium constants, together with kinetic rate constants of binding, are key factors in the efficacy and safety of drug compounds, informing drug design. However, the association pathways of protein-ligand binding, which contribute to their kinetic behaviors, are little understood. In this work, we used unbiased all-atom molecular dynamics (MD) simulations with an explicit solvent model to study the association processes of protein-ligand binding. Using the HIV protease (HIVp)-xk263 and HIVp-ritonavir protein-ligand systems as cases, we observed that ligand association is a multistep process involving diffusion, localization, and conformational rearrangements of the protein, ligand, and water molecules. Moreover, these two ligands preferred different routes of binding, which reflect two well-known binding mechanisms: induced-fit and conformation selection models. Our study shows that xk263 has a stronger capacity for desolvating surrounding water molecules, thereby inducing a semiopen conformation of the HIVp flaps (induced-fit model). In contrast, the slow dehydration characteristic of ritonavir allows for gradual association with the binding pocket of HIVp when the protein's flap conformation is fully open (conformation selection model). By studying the mechanism of ligand association and understanding the role of solvent molecules during the binding event, we can obtain a different perspective on the mechanism of macromolecule recognition, providing insights into drug discovery.
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Affiliation(s)
- Yu-Ming M Huang
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
| | - Mark Anthony V Raymundo
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
| | - Wei Chen
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States.,ChemConsulting LLC , Frederick, Maryland 21704, United States
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
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26
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Gueto-Tettay C, Zuchniarz J, Fortich-Seca Y, Gueto-Tettay LR, Drosos-Ramirez JC. A molecular dynamics study of the BACE1 conformational change from Apo to closed form induced by hydroxyethylamine derived compounds. J Mol Graph Model 2016; 70:181-195. [PMID: 27750187 DOI: 10.1016/j.jmgm.2016.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/05/2016] [Accepted: 10/06/2016] [Indexed: 12/11/2022]
Abstract
BACE1 is an aspartyl protease which is a therapeutic target for Alzheimer's disease (AD) because of its participation in the rate-limiting step in the production of Aβ-peptide, the accumulation of which produces senile plaques and, in turn, the neurodegenerative effects associated with AD. The active site of this protease is composed in part by two aspartic residues (Asp93 and Asp289). Additionally, the catalytic site has been found to be covered by an antiparallel hairpin loop called the flap. The dynamics of this flap are fundamental to the catalytic function of the enzyme. When BACE1 is inactive (Apo), the flap adopts an open conformation, allowing a substrate or inhibitor to access the active site. Subsequent interaction with the ligand induces flap closure and the stabilization of the macromolecular complex. Further, the protonation state of the aspartic dyad is affected by the chemical nature of the species entering the active site, so that appropriate selection of protonation states for the ligand and the catalytic residues will permit the elucidation of the inhibitory pathway for BACE1. In the present study, comparative analysis of different combinations of protonation states for the BACE1-hydroxyethylamine (HEA) system is reported. HEAs are potent inhibitors of BACE1 with favorable pharmacological and kinetic properties, as well as oral bioavailability. The results of Molecular Dynamics (MD) simulations and population density calculations using 8 different parameters demonstrate that the LnAsp289 configuration (HEA with a neutral amine and the Asp289 residue protonated) is the only one which permits the expected conformational change in BACE1, from apo to closed form, after flap closure. Additionally, differences in their capacities to establish and maintain interactions with residues such as Asp93, Gly95, Thr133, Asp289, Gly291, and Asn294 during this step allow differentiation among the inhibitory activities of the HEAs. The results and methodology here reported will serve to elucidate the inhibitory pathway of other families of compounds that act as BACE1 inhibitors, as well as the design of better leader compounds for the treatment of AD.
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Affiliation(s)
- Carlos Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia
| | - Joshua Zuchniarz
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia
| | - Yeyson Fortich-Seca
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia
| | - Luis Roberto Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia
| | - Juan Carlos Drosos-Ramirez
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Colombia.
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Louis JM, Roche J. Evolution under Drug Pressure Remodels the Folding Free-Energy Landscape of Mature HIV-1 Protease. J Mol Biol 2016; 428:2780-92. [PMID: 27170547 PMCID: PMC4905781 DOI: 10.1016/j.jmb.2016.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/27/2016] [Accepted: 05/02/2016] [Indexed: 01/08/2023]
Abstract
Using high-pressure NMR spectroscopy and differential scanning calorimetry, we investigate the folding landscape of the mature HIV-1 protease homodimer. The cooperativity of unfolding was measured in the absence or presence of a symmetric active site inhibitor for the optimized wild type protease (PR), its inactive variant PRD25N, and an extremely multidrug-resistant mutant, PR20. The individual fit of the pressure denaturation profiles gives rise to first order, ∆GNMR, and second order, ∆VNMR (the derivative of ∆GNMR with pressure); apparent thermodynamic parameters for each amide proton considered. Heterogeneity in the apparent ∆VNMR values reflects departure from an ideal cooperative unfolding transition. The narrow to broad distribution of ∆VNMR spanning the extremes from inhibitor-free PR20D25N to PR-DMP323 complex, and distinctively for PRD25N-DMP323 complex, indicated large variations in folding cooperativity. Consistent with this data, the shape of thermal unfolding transitions varies from asymmetric for PR to nearly symmetric for PR20, as dimer-inhibitor ternary complexes. Lack of structural cooperativity was observed between regions located close to the active site, including the hinge and tip of the glycine-rich flaps, and the rest of the protein. These results strongly suggest that inhibitor binding drastically decreases the cooperativity of unfolding by trapping the closed flap conformation in a deep energy minimum. To evade this conformational trap, PR20 evolves exhibiting a smoother folding landscape with nearly an ideal two-state (cooperative) unfolding transition. This study highlights the malleability of retroviral protease folding pathways by illustrating how the selection of mutations under drug pressure remodels the free-energy landscape as a primary mechanism.
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Affiliation(s)
- John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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28
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Soares RO, Torres PHM, da Silva ML, Pascutti PG. Unraveling HIV protease flaps dynamics by Constant pH Molecular Dynamics simulations. J Struct Biol 2016; 195:216-226. [PMID: 27291071 DOI: 10.1016/j.jsb.2016.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 11/15/2022]
Abstract
The active site of HIV protease (HIV-PR) is covered by two flaps. These flaps are known to be essential for the catalytic activity of the HIV-PR, but their exact conformations at the different stages of the enzymatic pathway remain subject to debate. Understanding the correct functional dynamics of the flaps might aid the development of new HIV-PR inhibitors. It is known that, the HIV-PR catalytic efficiency is pH-dependent, likely due to the influence of processes such as charge transfer and protonation/deprotonation of ionizable residues. Several Molecular Dynamics (MD) simulations have reported information about the HIV-PR flaps. However, in MD simulations the protonation of a residue is fixed and thus it is not possible to study the correlation between conformation and protonation state. To address this shortcoming, this work attempts to capture, through Constant pH Molecular Dynamics (CpHMD), the conformations of the apo, substrate-bound and inhibitor-bound HIV-PR, which differ drastically in their flap arrangements. The results show that the HIV-PR flaps conformations are defined by the protonation of the catalytic residues Asp25/Asp25' and that these residues are sensitive to pH changes. This study suggests that the catalytic aspartates can modulate the opening of the active site and substrate binding.
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Affiliation(s)
- Rosemberg O Soares
- Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Diretoria de Metrologia Aplicada às Ciências da Vida (DIMAV), Instituto Nacional de Metrologia Qualidade e Tecnologia (INMETRO), Xerém, Brazil.
| | - Pedro H M Torres
- Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Manuela L da Silva
- Diretoria de Metrologia Aplicada às Ciências da Vida (DIMAV), Instituto Nacional de Metrologia Qualidade e Tecnologia (INMETRO), Xerém, Brazil
| | - Pedro G Pascutti
- Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Diretoria de Metrologia Aplicada às Ciências da Vida (DIMAV), Instituto Nacional de Metrologia Qualidade e Tecnologia (INMETRO), Xerém, Brazil
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29
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Kurt Yilmaz N, Swanstrom R, Schiffer CA. Improving Viral Protease Inhibitors to Counter Drug Resistance. Trends Microbiol 2016; 24:547-557. [PMID: 27090931 DOI: 10.1016/j.tim.2016.03.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/18/2016] [Accepted: 03/30/2016] [Indexed: 12/13/2022]
Abstract
Drug resistance is a major problem in health care, undermining therapy outcomes and necessitating novel approaches to drug design. Extensive studies on resistance to viral protease inhibitors, particularly those of HIV-1 and hepatitis C virus (HCV) protease, revealed a plethora of information on the structural and molecular mechanisms underlying resistance. These insights led to several strategies to improve viral protease inhibitors to counter resistance, such as exploiting the essential biological function and leveraging evolutionary constraints. Incorporation of these strategies into structure-based drug design can minimize vulnerability to resistance, not only for viral proteases but for other quickly evolving drug targets as well, toward designing inhibitors one step ahead of evolution to counter resistance with more intelligent and rational design.
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Affiliation(s)
- Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics, and the UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
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30
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Mahanti M, Bhakat S, Nilsson UJ, Söderhjelm P. Flap Dynamics in Aspartic Proteases: A Computational Perspective. Chem Biol Drug Des 2016; 88:159-77. [PMID: 26872937 DOI: 10.1111/cbdd.12745] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in biochemistry and drug design have placed proteases as one of the critical target groups for developing novel small-molecule inhibitors. Among all proteases, aspartic proteases have gained significant attention due to their role in HIV/AIDS, malaria, Alzheimer's disease, etc. The binding cleft is covered by one or two β-hairpins (flaps) which need to be opened before a ligand can bind. After binding, the flaps close to retain the ligand in the active site. Development of computational tools has improved our understanding of flap dynamics and its role in ligand recognition. In the past decade, several computational approaches, for example molecular dynamics (MD) simulations, coarse-grained simulations, replica-exchange molecular dynamics (REMD) and metadynamics, have been used to understand flap dynamics and conformational motions associated with flap movements. This review is intended to summarize the computational progress towards understanding the flap dynamics of proteases and to be a reference for future studies in this field.
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Affiliation(s)
- Mukul Mahanti
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Soumendranath Bhakat
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden
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Nakashima M, Ode H, Suzuki K, Fujino M, Maejima M, Kimura Y, Masaoka T, Hattori J, Matsuda M, Hachiya A, Yokomaku Y, Suzuki A, Watanabe N, Sugiura W, Iwatani Y. Unique Flap Conformation in an HIV-1 Protease with High-Level Darunavir Resistance. Front Microbiol 2016; 7:61. [PMID: 26870021 PMCID: PMC4737996 DOI: 10.3389/fmicb.2016.00061] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/14/2016] [Indexed: 11/13/2022] Open
Abstract
Darunavir (DRV) is one of the most powerful protease inhibitors (PIs) for treating human immunodeficiency virus type-1 (HIV-1) infection and presents a high genetic barrier to the generation of resistant viruses. However, DRV-resistant HIV-1 infrequently emerges from viruses exhibiting resistance to other protease inhibitors. To address this resistance, researchers have gathered genetic information on DRV resistance. In contrast, few structural insights into the mechanism underlying DRV resistance are available. To elucidate this mechanism, we determined the crystal structure of the ligand-free state of a protease with high-level DRV resistance and six DRV resistance-associated mutations (including I47V and I50V), which we generated by in vitro selection. This crystal structure showed a unique curling conformation at the flap regions that was not found in the previously reported ligand-free protease structures. Molecular dynamics simulations indicated that the curled flap conformation altered the flap dynamics. These results suggest that the preference for a unique flap conformation influences DRV binding. These results provide new structural insights into elucidating the molecular mechanism of DRV resistance and aid to develop PIs effective against DRV-resistant viruses.
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Affiliation(s)
- Masaaki Nakashima
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan
| | - Hirotaka Ode
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Koji Suzuki
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan
| | - Masayuki Fujino
- AIDS Research Center, National Institute of Infectious Diseases Tokyo, Japan
| | - Masami Maejima
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yuki Kimura
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan
| | - Takashi Masaoka
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Junko Hattori
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Masakazu Matsuda
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Atsuko Hachiya
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yoshiyuki Yokomaku
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Atsuo Suzuki
- Department of Biotechnology, Nagoya University Graduate School of Engineering Nagoya, Japan
| | - Nobuhisa Watanabe
- Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan; Synchrotron Radiation Research Center, Nagoya UniversityNagoya, Japan
| | - Wataru Sugiura
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yasumasa Iwatani
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of AIDS Research, Nagoya University Graduate School of MedicineNagoya, Japan
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Kumalo HM, Soliman ME. A comparative molecular dynamics study on BACE1 and BACE2 flap flexibility. J Recept Signal Transduct Res 2016; 36:505-14. [PMID: 26804314 DOI: 10.3109/10799893.2015.1130058] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Beta-amyloid precursor protein cleavage enzyme1 (BACE1) and beta-amyloid precursor protein cleavage enzyme2 (BACE2), members of aspartyl protease family, are close homologs and have high similarity in their protein crystal structures. However, their enzymatic properties are different, which leads to different clinical outcomes. In this study, we performed sequence analysis and all-atom molecular dynamic (MD) simulations for both enzymes in their ligand-free states in order to compare their dynamical flap behaviors. This is to enhance our understanding of the relationship between sequence, structure and the dynamics of this protein family. Sequence analysis shows that in BACE1 and BACE2, most of the ligand-binding sites are conserved, indicative of their enzymatic property as aspartyl protease members. The other conserved residues are more or less unsystematically localized throughout the structure. Herein, we proposed and applied different combined parameters to define the asymmetric flap motion; the distance, d1, between the flap tip and the flexible region; the dihedral angle, φ, to account for the twisting motion and the TriCα angle, θ2 and θ1. All four combined parameters were found to appropriately define the observed "twisting" motion during the flaps different conformational states. Additional analysis of the parameters indicated that the flaps can exist in an ensemble of conformations, i.e. closed, semi-open and open conformations for both systems. However, the behavior of the flap tips during simulations is different between BACE1 and BACE2. The BACE1 active site cavity is more spacious as compared to that of BACE2. The analysis of 10S loop and 113S loop showed a similar trend to that of flaps, with the BACE1 loops being more flexible and less stable than those of BACE2. We believe that the results, methods and perspectives highlighted in this report would assist researchers in the discovery of BACE inhibitors as potential Alzheimer's disease therapies.
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Affiliation(s)
- H M Kumalo
- a Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal , Westville , Durban , South Africa
| | - Mahmoud E Soliman
- a Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal , Westville , Durban , South Africa
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33
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C-5-Modified Tetrahydropyrano-Tetrahydofuran-Derived Protease Inhibitors (PIs) Exert Potent Inhibition of the Replication of HIV-1 Variants Highly Resistant to Various PIs, including Darunavir. J Virol 2015; 90:2180-94. [PMID: 26581995 DOI: 10.1128/jvi.01829-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/06/2015] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED We identified three nonpeptidic HIV-1 protease inhibitors (PIs), GRL-015, -085, and -097, containing tetrahydropyrano-tetrahydrofuran (Tp-THF) with a C-5 hydroxyl. The three compounds were potent against a wild-type laboratory HIV-1 strain (HIV-1(WT)), with 50% effective concentrations (EC50s) of 3.0 to 49 nM, and exhibited minimal cytotoxicity, with 50% cytotoxic concentrations (CC50) for GRL-015, -085, and -097 of 80, >100, and >100 μM, respectively. All the three compounds potently inhibited the replication of highly PI-resistant HIV-1 variants selected with each of the currently available PIs and recombinant clinical HIV-1 isolates obtained from patients harboring multidrug-resistant HIV-1 variants (HIVMDR). Importantly, darunavir (DRV) was >1,000 times less active against a highly DRV-resistant HIV-1 variant (HIV-1DRV(R) P51); the three compounds remained active against HIV-1DRV(R) P51 with only a 6.8- to 68-fold reduction. Moreover, the emergence of HIV-1 variants resistant to the three compounds was considerably delayed compared to the case of DRV. In particular, HIV-1 variants resistant to GRL-085 and -097 did not emerge even when two different highly DRV-resistant HIV-1 variants were used as a starting population. In the structural analyses, Tp-THF of GRL-015, -085, and -097 showed strong hydrogen bond interactions with the backbone atoms of active-site amino acid residues (Asp29 and Asp30) of HIV-1 protease. A strong hydrogen bonding formation between the hydroxyl moiety of Tp-THF and a carbonyl oxygen atom of Gly48 was newly identified. The present findings indicate that the three compounds warrant further study as possible therapeutic agents for treating individuals harboring wild-type HIV and/or HIVMDR. IMPORTANCE Darunavir (DRV) inhibits the replication of most existing multidrug-resistant HIV-1 strains and has a high genetic barrier. However, the emergence of highly DRV-resistant HIV-1 strains (HIVDRV(R) ) has recently been observed in vivo and in vitro. Here, we identified three novel HIV-1 protease inhibitors (PIs) containing a tetrahydropyrano-tetrahydrofuran (Tp-THF) moiety with a C-5 hydroxyl (GRL-015, -085, and -097) which potently suppress the replication of HIVDRV(R) . Moreover, the emergence of HIV-1 strains resistant to the three compounds was considerably delayed compared to the case of DRV. The C-5 hydroxyl formed a strong hydrogen bonding interaction with the carbonyl oxygen atom of Gly48 of protease as examined in the structural analyses. Interestingly, a compound with Tp-THF lacking the hydroxyl moiety substantially decreased activity against HIVDRV(R) . The three novel compounds should be further developed as potential drugs for treating individuals harboring wild-type and multi-PI-resistant HIV variants as well as HIVDRV(R) .
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34
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Kumalo HM, Bhakat S, Soliman ME. Investigation of flap flexibility of β-secretase using molecular dynamic simulations. J Biomol Struct Dyn 2015. [DOI: 10.1080/07391102.2015.1064831] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hezekiel M. Kumalo
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Soumendranath Bhakat
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
- Division of Biophysical Chemistry, Lund University, P.O. Box 124, SE, 22100 Lund, Sweden
| | - Mahmoud E. Soliman
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
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35
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Effects of drug-resistant mutations on the dynamic properties of HIV-1 protease and inhibition by Amprenavir and Darunavir. Sci Rep 2015; 5:10517. [PMID: 26012849 PMCID: PMC4444956 DOI: 10.1038/srep10517] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/16/2015] [Indexed: 12/20/2022] Open
Abstract
Molecular dynamics simulations are performed to investigate the dynamic properties of wild-type HIV-1 protease and its two multi-drug-resistant variants (Flap + (L10I/G48V/I54V/V82A) and Act (V82T/I84V)) as well as their binding with APV and DRV inhibitors. The hydrophobic interactions between flap and 80 s (80’s) loop residues (mainly I50-I84’ and I50’-I84) play an important role in maintaining the closed conformation of HIV-1 protease. The double mutation in Act variant weakens the hydrophobic interactions, leading to the transition from closed to semi-open conformation of apo Act. APV or DRV binds with HIV-1 protease via both hydrophobic and hydrogen bonding interactions. The hydrophobic interactions from the inhibitor is aimed to the residues of I50 (I50’), I84 (I84’), and V82 (V82’) which create hydrophobic core clusters to further stabilize the closed conformation of flaps, and the hydrogen bonding interactions are mainly focused with the active site of HIV-1 protease. The combined change in the two kinds of protease-inhibitor interactions is correlated with the observed resistance mutations. The present study sheds light on the microscopic mechanism underlying the mutation effects on the dynamics of HIV-1 protease and the inhibition by APV and DRV, providing useful information to the design of more potent and effective HIV-1 protease inhibitors.
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36
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De Conto V, Braz ASK, Perahia D, Scott LPB. Recovery of the wild type atomic flexibility in the HIV-1 protease double mutants. J Mol Graph Model 2015; 59:107-16. [PMID: 25948548 DOI: 10.1016/j.jmgm.2015.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 04/09/2015] [Accepted: 04/17/2015] [Indexed: 02/04/2023]
Abstract
The emergence of drug resistant mutations due to the selective pressure exerted by antiretrovirals, including protease inhibitors (PIs), remains a major problem in the treatment of AIDS. During PIs therapy, the occurrence of primary mutations in the wild type HIV-1 protease reduces both the affinity for the inhibitors and the viral replicative capacity compared to the wild type (WT) protein, but additional mutations compensate for this reduced viral fitness. To investigate this phenomenon from the structural point of view, we combined Molecular Dynamics and Normal Mode Analysis to analyze and compare the variations of the flexibility of C-alpha atoms and the differences in hydrogen bond (h-bond) network between the WT and double mutants. In most cases, the flexibility profile of the double mutants was more often similar to that of the WT than to that of the related single base mutants. All single mutants showed a significant alteration in h-bond formation compared to WT. Most of the significant changes occur in the border between the flap and cantilever regions. We found that all the considered double mutants have their h-bond pattern significantly altered in comparison to the respective single base mutants affecting their flexibility profile that becomes more similar to that of WT. This WT flexibility restoration in the double mutants appears as an important factor for the HIV-1 fitness recovery observed in patients.
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Affiliation(s)
- Valderes De Conto
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Antônio S K Braz
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), Ecole Normale Supérieure de Cachan, Cachan, France
| | - Luis P B Scott
- Laboratório de Biologia Computacional e Bioinformática, Universidade Federal do ABC, Santo André, SP, Brazil; Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), Ecole Normale Supérieure de Cachan, Cachan, France.
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37
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Abstract
![]()
Biological activities of enzymes, including
regulation or coordination of mechanistic stages preceding or following
the chemical step, may depend upon kinetic or equilibrium changes
in protein conformations. Exchange of more open or flexible conformational
states with more closed or constrained states can influence inhibition,
allosteric regulation, substrate recognition, formation of the Michaelis
complex, side reactions, and product release. NMR spectroscopy has
long been applied to the study of conformational dynamic processes
in enzymes because these phenomena can be characterized over multiple
time scales with atomic site resolution. Laboratory-frame spin-relaxation
measurements, sensitive to reorientational motions on picosecond–nanosecond
time scales, and rotating-frame relaxation-dispersion measurements,
sensitive to chemical exchange processes on microsecond–millisecond
time scales, provide information on both conformational distributions
and kinetics. This Account reviews NMR spin relaxation studies of
the enzymes ribonuclease HI from mesophilic (Escherichia coli) and thermophilic (Thermus thermophilus) bacteria, E. coli AlkB, and Saccharomyces cerevisiae triosephosphate isomerase to illustrate the contributions of conformational
flexibility and dynamics to diverse steps in enzyme mechanism. Spin relaxation measurements and molecular dynamics (MD) simulations
of the bacterial ribonuclease H enzymes show that the handle region,
one of three loop regions that interact with substrates, interconverts
between two conformations. Comparison of these conformations with
the structure of the complex between Homo sapiens ribonuclease H and a DNA:RNA substrate suggests that the more closed
state is inhibitory to binding. The large population of the closed
conformation in T. thermophilus ribonuclease H contributes
to the increased Michaelis constant compared with the E. coli enzyme. NMR spin relaxation and fluorescence spectroscopy have characterized
a conformational transition in AlkB between an open state, in which
the side chains of methionine residues in the active site are disordered,
and a closed state, in which these residues are ordered. The open
state is highly populated in the AlkB/Zn(II) complex, and the closed
state is highly populated in the AlkB/Zn(II)/2OG/substrate complex,
in which 2OG is the 2-oxoglutarate cosubstrate and the substrate is
a methylated DNA oligonucleotide. The equilibrium is shifted to approximately
equal populations of the two conformations in the AlkB/Zn(II)/2OG
complex. The conformational shift induced by 2OG ensures that 2OG
binds to AlkB/Zn(II) prior to the substrate. In addition, the opening
rate of the closed conformation limits premature release of substrate,
preventing generation of toxic side products by reaction with water.
Closure of active site loop 6 in triosephosphate isomerase is critical
for forming the Michaelis complex, but reopening of the loop after
the reaction is (partially) rate limiting. NMR spin relaxation and
MD simulations of triosephosphate isomerase in complex with glycerol
3-phosphate demonstrate that closure of loop 6 is a highly correlated
rigid-body motion. The MD simulations also indicate that motions of
Gly173 in the most flexible region of loop 6 contribute to opening
of the active site loop for product release. Considered together,
these three enzyme systems illustrate the power of NMR spin relaxation
investigations in providing global insights into the role of conformational
dynamic processes in the mechanisms of enzymes from initial activation
to final product release.
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Affiliation(s)
- Arthur G. Palmer
- Department of Biochemistry and
Molecular Biophysics, Columbia University, 701 West 168th Street, New York, New York 10032, United States
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38
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Karubiu W, Bhakat S, McGillewie L, Soliman MES. Flap dynamics of plasmepsin proteases: insight into proposed parameters and molecular dynamics. MOLECULAR BIOSYSTEMS 2015; 11:1061-6. [DOI: 10.1039/c4mb00631c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, for the first time, we report the flap opening and closing in Plasmepsin proteases – plasmepsin II (PlmII) was used as a prototype model.
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Affiliation(s)
- Wilson Karubiu
- School of Health Sciences
- University of KwaZulu-Natal
- Durban-4000
- South Africa
| | | | - Lara McGillewie
- School of Health Sciences
- University of KwaZulu-Natal
- Durban-4000
- South Africa
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Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease. Proc Natl Acad Sci U S A 2014; 111:15993-8. [PMID: 25355911 DOI: 10.1073/pnas.1414063111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Drug resistance mutations in response to HIV-1 protease inhibitors are selected not only in the drug target but elsewhere in the viral genome, especially at the protease cleavage sites in the precursor protein Gag. To understand the molecular basis of this protease-substrate coevolution, we solved the crystal structures of drug resistant I50V/A71V HIV-1 protease with p1-p6 substrates bearing coevolved mutations. Analyses of the protease-substrate interactions reveal that compensatory coevolved mutations in the substrate do not restore interactions lost due to protease mutations, but instead establish other interactions that are not restricted to the site of mutation. Mutation of a substrate residue has distal effects on other residues' interactions as well, including through the induction of a conformational change in the protease. Additionally, molecular dynamics simulations suggest that restoration of active site dynamics is an additional constraint in the selection of coevolved mutations. Hence, protease-substrate coevolution permits mutational, structural, and dynamic changes via molecular mechanisms that involve distal effects contributing to drug resistance.
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40
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Ragland DA, Nalivaika EA, Nalam MNL, Prachanronarong KL, Cao H, Bandaranayake RM, Cai Y, Kurt-Yilmaz N, Schiffer CA. Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease. J Am Chem Soc 2014; 136:11956-63. [PMID: 25091085 PMCID: PMC4151706 DOI: 10.1021/ja504096m] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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HIV-1 protease inhibitors are part
of the highly active antiretroviral
therapy effectively used in the treatment of HIV infection and AIDS.
Darunavir (DRV) is the most potent of these inhibitors, soliciting
drug resistance only when a complex combination of mutations occur
both inside and outside the protease active site. With few exceptions,
the role of mutations outside the active site in conferring resistance
remains largely elusive. Through a series of DRV–protease complex
crystal structures, inhibition assays, and molecular dynamics simulations,
we find that single and double site mutations outside the active site
often associated with DRV resistance alter the structure and dynamic
ensemble of HIV-1 protease active site. These alterations correlate
with the observed inhibitor binding affinities for the mutants, and
suggest a network hypothesis on how the effect of
distal mutations are propagated to pivotal residues at the active
site and may contribute to conferring drug resistance.
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Affiliation(s)
- Debra A Ragland
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
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41
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Carter JD, Gonzales EG, Huang X, Smith AN, de Vera IMS, D'Amore PW, Rocca JR, Goodenow MM, Dunn BM, Fanucci GE. Effects of PRE and POST therapy drug-pressure selected mutations on HIV-1 protease conformational sampling. FEBS Lett 2014; 588:3123-8. [PMID: 24983495 DOI: 10.1016/j.febslet.2014.06.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 06/16/2014] [Accepted: 06/16/2014] [Indexed: 01/11/2023]
Abstract
Conformational sampling of pre- and post-therapy subtype B HIV-1 protease sequences derived from a pediatric subject infected via maternal transmission with HIV-1 were characterized by double electron-electron resonance spectroscopy. The conformational ensemble of the PRE construct resembles native-like inhibitor bound states. In contrast, the POST construct, which contains accumulated drug-pressure selected mutations, has a predominantly semi-open conformational ensemble, with increased populations of open-like states. The single point mutant L63P, which is contained in PRE and POST, has decreased dynamics, particularly in the flap region, and also displays a closed-like conformation of inhibitor-bound states. These findings support our hypothesis that secondary mutations accumulate in HIV-1 protease to shift conformational sampling to stabilize open-like conformations, while maintaining the predominant semi-open conformation for activity.
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Affiliation(s)
- Jeffrey D Carter
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Estrella G Gonzales
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Xi Huang
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Adam N Smith
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | | | - Peter W D'Amore
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - James R Rocca
- Advanced Magnetic Resonance Imaging and Spectroscopy Facility, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Maureen M Goodenow
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL 32610-3633, USA
| | - Ben M Dunn
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610-0245, USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA.
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42
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Zhang Y, Chang YCE, Louis JM, Wang YF, Harrison RW, Weber IT. Structures of darunavir-resistant HIV-1 protease mutant reveal atypical binding of darunavir to wide open flaps. ACS Chem Biol 2014; 9:1351-8. [PMID: 24738918 PMCID: PMC4076034 DOI: 10.1021/cb4008875] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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The molecular basis for high resistance
to clinical inhibitors
of HIV-1 protease (PR) was examined for the variant designated PRP51 that was selected for resistance to darunavir (DRV). High
resolution crystal structures of PRP51 with the active
site D25N mutation revealed a ligand-free form and an inhibitor-bound
form showing a unique binding site and orientation for DRV. This inactivating
mutation is known to increase the dimer dissociation constant and
decrease DRV affinity of PR. The PRP51-D25N dimers
were in the open conformation with widely separated flaps, as reported
for other highly resistant variants. PRP51-D25N dimer
bound two DRV molecules and showed larger separation of 8.7 Å
between the closest atoms of the two flaps compared with 4.4 Å
for the ligand-free structure of this mutant. The ligand-free structure,
however, lacked van der Waals contacts between Ile50 and Pro81′
from the other subunit in the dimer, unlike the majority of PR structures.
DRV is bound inside the active site cavity; however, the inhibitor
is oriented almost perpendicular to its typical position and exhibits
only 2 direct hydrogen bond and two water-mediated interactions with
atoms of PRP51-D25N compared with 11 hydrogen bond
interactions seen for DRV bound in the typical position in wild-type
enzyme. The atypical location of DRV may provide opportunities for
design of novel inhibitors targeting the open conformation of PR drug-resistant
mutants.
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Affiliation(s)
| | | | - John M. Louis
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
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43
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Cai Y, Myint W, Paulsen JL, Schiffer CA, Ishima R, Kurt Yilmaz N. Drug Resistance Mutations Alter Dynamics of Inhibitor-Bound HIV-1 Protease. J Chem Theory Comput 2014; 10:3438-3448. [PMID: 25136270 PMCID: PMC4132871 DOI: 10.1021/ct4010454] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Indexed: 12/22/2022]
Abstract
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Under the selective pressure of therapy,
HIV-1 protease mutants
resistant to inhibitors evolve to confer drug resistance. Such mutations
can impact both the dynamics and structures of the bound and unbound
forms of the enzyme. Flap+ is a multidrug-resistant variant of HIV-1
protease with a combination of primary and secondary resistance mutations
(L10I, G48V, I54V, V82A) and a strikingly altered thermodynamic profile
for darunavir (DRV) binding relative to the wild-type protease. We
elucidated the impact of these mutations on protein dynamics in the
DRV-bound state using molecular dynamics simulations and NMR relaxation
experiments. Both methods concur in that the conformational ensemble
and dynamics of protease are impacted by the drug resistance mutations
in Flap+ variant. Surprisingly this change in ensemble dynamics is
different from that observed in the unliganded form of the same variant
(Cai, Y. et al. J. Chem. Theory Comput.2012, 8, 3452–3462). Our comparative
analysis of both inhibitor-free and bound states presents a comprehensive
picture of the altered dynamics in drug-resistant mutant HIV-1 protease
and underlies the importance of incorporating dynamic analysis of
the whole system, including the unliganded state, into revealing drug
resistance mechanisms.
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Affiliation(s)
- Yufeng Cai
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Wazo Myint
- Department of Structural Biology, School of Medicine, University of Pittsburgh Biomedical Science Tower 3 , 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Janet L Paulsen
- 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
| | - Rieko Ishima
- Department of Structural Biology, School of Medicine, University of Pittsburgh Biomedical Science Tower 3 , 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
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44
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Affiliation(s)
- Alan C. Gibbs
- Janssen Pharmaceutical Research and Development, LLC, Welsh and McKean Road, Spring House, Pennsylvania 19477-0776, United States
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45
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Huang X, Britto MD, Kear-Scott JL, Boone CD, Rocca JR, Simmerling C, Mckenna R, Bieri M, Gooley PR, Dunn BM, Fanucci GE. The role of select subtype polymorphisms on HIV-1 protease conformational sampling and dynamics. J Biol Chem 2014; 289:17203-14. [PMID: 24742668 DOI: 10.1074/jbc.m114.571836] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
HIV-1 protease is an essential enzyme for viral particle maturation and is a target in the fight against HIV-1 infection worldwide. Several natural polymorphisms are also associated with drug resistance. Here, we utilized both pulsed electron double resonance, also called double electron-electron resonance, and NMR (15)N relaxation measurements to characterize equilibrium conformational sampling and backbone dynamics of an HIV-1 protease construct containing four specific natural polymorphisms commonly found in subtypes A, F, and CRF_01 A/E. Results show enhanced backbone dynamics, particularly in the flap region, and the persistence of a novel conformational ensemble that we hypothesize is an alternative flap orientation of a curled open state or an asymmetric configuration when interacting with inhibitors.
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Affiliation(s)
- Xi Huang
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Manuel D Britto
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Jamie L Kear-Scott
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Christopher D Boone
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - James R Rocca
- the Advanced Magnetic Resonance Imaging and Spectroscopy Facility, McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Carlos Simmerling
- the Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, and
| | - Robert Mckenna
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Michael Bieri
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul R Gooley
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ben M Dunn
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Gail E Fanucci
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611,
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46
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Kožíšek M, Lepšík M, Grantz Šašková K, Brynda J, Konvalinka J, Řezáčová P. Thermodynamic and structural analysis of HIV protease resistance to darunavir - analysis of heavily mutated patient-derived HIV-1 proteases. FEBS J 2014; 281:1834-47. [DOI: 10.1111/febs.12743] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Gilead Sciences and IOCB Research Center; Prague Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Gilead Sciences and IOCB Research Center; Prague Czech Republic
| | - Klára Grantz Šašková
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Gilead Sciences and IOCB Research Center; Prague Czech Republic
- Department of Biochemistry; Faculty of Science; Charles University; Prague Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Gilead Sciences and IOCB Research Center; Prague Czech Republic
- Institute of Molecular Genetics; Academy of Sciences of the Czech Republic; Prague Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Gilead Sciences and IOCB Research Center; Prague Czech Republic
- Department of Biochemistry; Faculty of Science; Charles University; Prague Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Gilead Sciences and IOCB Research Center; Prague Czech Republic
- Institute of Molecular Genetics; Academy of Sciences of the Czech Republic; Prague Czech Republic
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47
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Xia J, Deng NJ, Levy RM. NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations. J Phys Chem B 2013; 117:6625-34. [PMID: 23638941 DOI: 10.1021/jp400797y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Calculating NMR relaxation effects for proteins with dynamics on multiple time scales generally requires very long trajectories based on conventional molecular dynamics simulations. In this report, we have built Markov state models from multiple MD trajectories and used the resulting MSM to capture the very fast internal motions of the protein within a free energy basin on a time scale up to hundreds of picoseconds and the more than 3 orders of magnitude slower conformational exchange between macrostates. To interpret the relaxation data, we derive new equations using the model-free framework which includes two slowly exchanging macrostates, each of which also exhibits fast local motions. Using simulations of HIV-1 protease as an example, we show how the populations of slowly exchanging conformational states as well as order parameters for the different states can be determined from the NMR relaxation data.
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Affiliation(s)
- Junchao Xia
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, USA
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48
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de Vera IMS, Smith AN, Dancel MCA, Huang X, Dunn BM, Fanucci GE. Elucidating a relationship between conformational sampling and drug resistance in HIV-1 protease. Biochemistry 2013; 52:3278-88. [PMID: 23566104 DOI: 10.1021/bi400109d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Enzyme targets in rapidly replicating systems, such as retroviruses, commonly respond to drug-selective pressure with mutations arising in the active site pocket that limit inhibitor effectiveness by introducing steric hindrance or by eliminating essential molecular interactions. However, these primary mutations are disposed to compromising pathogenic fitness. Emerging secondary mutations, which are often found outside of the binding cavity, may or can restore fitness while maintaining drug resistance. The accumulated drug pressure selected mutations could have an indirect effect in the development of resistance, such as altering protein flexibility or the dynamics of protein-ligand interactions. Here, we show that accumulation of mutations in a drug-resistant HIV-1 protease (HIV-1 PR) variant, D30N/M36I/A71V, changes the fractional occupancy of the equilibrium conformational sampling ensemble. Correlations are made among populations of the conformational states, namely, closed-like, semiopen, and open-like, with inhibition constants, as well as kinetic parameters. Mutations that stabilize a closed-like conformation correlate with enzymes of lowered activity and with higher affinity for inhibitors, which is corroborated by a further increase in the fractional occupancy of the closed state upon addition of inhibitor or substrate-mimic. Cross-resistance is found to correlate with combinations of mutations that increase the population of the open-like conformations at the expense of the closed-like state while retaining native-like occupancy of the semiopen population. These correlations suggest that at least three states are required in the conformational sampling model to establish the emergence of drug resistance in HIV-1 PR. More importantly, these results shed light on a possible mechanism whereby mutations combine to impart drug resistance while maintaining catalytic activity.
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Affiliation(s)
- Ian Mitchelle S de Vera
- Department of Chemistry, P.O. Box 117200, University of Florida , Gainesville, Florida 32611-7200, United States
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49
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Foulkes-Murzycki JE, Rosi C, Kurt Yilmaz N, Shafer RW, Schiffer CA. Cooperative effects of drug-resistance mutations in the flap region of HIV-1 protease. ACS Chem Biol 2013; 8:513-8. [PMID: 23252515 DOI: 10.1021/cb3006193] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the interdependence of multiple mutations in conferring drug resistance is crucial to the development of novel and robust inhibitors. As HIV-1 protease continues to adapt and evade inhibitors while still maintaining the ability to specifically recognize and efficiently cleave its substrates, the problem of drug resistance has become more complicated. Under the selective pressure of therapy, correlated mutations accumulate throughout the enzyme to compromise inhibitor binding, but characterizing their energetic interdependency is not straightforward. A particular drug resistant variant (L10I/G48V/I54V/V82A) displays extreme entropy-enthalpy compensation relative to wild-type enzyme but a similar variant (L10I/G48V/I54A/V82A) does not. Individual mutations of sites in the flaps (residues 48 and 54) of the enzyme reveal that the thermodynamic effects are not additive. Rather, the thermodynamic profile of the variants is interdependent on the cooperative effects exerted by a particular combination of mutations simultaneously present.
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Affiliation(s)
- Jennifer E. Foulkes-Murzycki
- Department of Biochemistry and
Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts
01605, United States
| | - Christina Rosi
- Department of Biochemistry and
Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts
01605, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and
Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts
01605, United States
| | - Robert W. Shafer
- Division
of Infectious Diseases,
Department of Medicine, Stanford University, Stanford, California 94305, United States
| | - Celia A. Schiffer
- Department of Biochemistry and
Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts
01605, United States
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50
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Meher BR, Patel S. Structural and dynamical aspects of HIV-1 protease and its role in drug resistance. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 92:299-324. [PMID: 23954105 DOI: 10.1016/b978-0-12-411636-8.00008-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Acquired immunodeficiency syndrome (AIDS) caused by the retrovirus human immunodeficiency virus (HIV) has become a major epidemic afflicting mankind. The Joint United Nations Program on HIV/AIDS (UNAIDS) projection shows the existence of millions of AIDS patients at the end of 2012. All the Food and Drug Administration (FDA)-approved drugs are getting ineffective due to resistance offered by the mutation-prone HIV. Hence, there is an urgent need for developing new drugs with greater potential. HIV life cycle is controlled by the activities of its essential proteins like glycoproteins (gp41 and gp120), HIV reverse transcriptase (HIV-RT), HIV integrase (HIV-IN), and HIV-1 protease (HIV-pr). This chapter focuses on the protein HIV-pr, which is important for the cleavage of Gag and Gag-Pol polyproteins to form mature, structural, and functional virions. The conformation and dynamics of the protein HIV-pr play a pivotal role in ligand binding and the catalytic process, which is affected by the rapid point mutations and various physiological parameters. The effect of the mutations and the varied simulation protocols on conformational dynamics and drug resistance of HIV-pr is discussed.
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Affiliation(s)
- Biswa Ranjan Meher
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia, USA.
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