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Sawant AA, Jadav SS, Nayani K, Mainkar PS. Development of Synthetic Approaches Towards HIV Integrase Strand Transfer Inhibitors (INSTIs). ChemistrySelect 2022. [DOI: 10.1002/slct.202201915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ashwini Amol Sawant
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Surender Singh Jadav
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
- Department of Applied Biology CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
| | - Kiranmai Nayani
- Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Prathama S. Mainkar
- Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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El Darazi P, El Khoury L, El Hage K, Maroun RG, Hobaika Z, Piquemal JP, Gresh N. Quantum-Chemistry Based Design of Halobenzene Derivatives With Augmented Affinities for the HIV-1 Viral G 4/C 16 Base-Pair. Front Chem 2020; 8:440. [PMID: 32637391 PMCID: PMC7317088 DOI: 10.3389/fchem.2020.00440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/27/2020] [Indexed: 01/14/2023] Open
Abstract
The HIV-1 integrase (IN) is a major target for the design of novel anti-HIV inhibitors. Among these, three inhibitors which embody a halobenzene ring derivative (HR) in their structures are presently used in clinics. High-resolution X-ray crystallography of the complexes of the IN-viral DNA transient complex bound to each of the three inhibitors showed in all cases the HR ring to interact within a confined zone of the viral DNA, limited to the highly conserved 5′CpA 3′/5′TpG 3′ step. The extension of its extracyclic CX bond is electron-depleted, owing to the existence of the “sigma-hole.” It interacts favorably with the electron-rich rings of base G4. We have sought to increase the affinity of HR derivatives for the G4/C16 base pair. We thus designed thirteen novel derivatives and computed their Quantum Chemistry (QC) intermolecular interaction energies (ΔE) with this base-pair. Most compounds had ΔE values significantly more favorable than those of the HR of the most potent halobenzene drug presently used in clinics, Dolutegravir. This should enable the improvement in a modular piece-wise fashion, the affinities of halogenated inhibitors for viral DNA (vDNA). In view of large scale polarizable molecular dynamics simulations on the entirety of the IN-vDNA-inhibitor complexes, validations of the SIBFA polarizable method are also reported, in which the evolution of each ΔE(SIBFA) contribution is compared to its QC counterpart along this series of derivatives.
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Affiliation(s)
- Perla El Darazi
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR7616 CNRS, Paris, France.,UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Léa El Khoury
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR7616 CNRS, Paris, France.,UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Krystel El Hage
- SABNP, Univ. Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Richard G Maroun
- UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Zeina Hobaika
- UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR7616 CNRS, Paris, France.,Institut Universitaire de France, Paris, France.,Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Nohad Gresh
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR7616 CNRS, Paris, France
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El Khoury L, El Hage K, Piquemal JP, Fermandjian S, Maroun RG, Gresh N, Hobaika Z. Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities. PEERJ PHYSICAL CHEMISTRY 2019. [DOI: 10.7717/peerj-pchem.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Three integrase strand transfer inhibitors are in intensive clinical use, raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG). The onset of integrase resistance mutations limits their therapeutic efficiency. As put forth earlier, the drug affinity for the intasome could be improved by targeting preferentially the retroviral nucleobases, which are little, if at all, mutation-prone. We report experimental results of anisotropy fluorescence titrations of viral DNA by these three drugs. These show the DTG > EVG > RAL ranking of their inhibitory activities of the intasome to correspond to that of their free energies of binding, ∆Gs, to retroviral DNA, and that such a ranking is only governed by the binding enthalpies, ∆H, the entropy undergoing marginal variations. We sought whether this ranking might be reproduced through quantum chemistry (QC) Density Functional Theory calculations of intermolecular interaction energies between simplified models consisting of sole halobenzene ring and the highly conserved retroviral nucleobases G4 and C16. These calculations showed that binding of EVG has a small preference over DTG, while RAL ranked third. This indicates that additional interactions of the diketoacid parts of the drugs with DNA could be necessary to further enable preferential binding of DTG. The corresponding ∆Etotvalues computed with a polarizable molecular mechanics/dynamics procedure, Sum of Interactions Between Fragments Ab initio computed (SIBFA), showed good correlations with this ∆E(QC) ranking. These validations are an important step toward the use of polarizable molecular dynamics simulations on DTG or EVG derivatives in their complexes with the complete intasome, an application now motivated and enabled by the advent of currently developed and improved massively parallel software.
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Affiliation(s)
- Léa El Khoury
- Laboratoire de Chimie Théorique, UMR7616 CNRS, Sorbonne Université, Paris, France
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
- Present address: Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Krystel El Hage
- Chemistry and Biology Nucleo(s)tides and Immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomedicale, Paris, France
- Present address: Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U829, Université Evry-Val d’Essonne, Evry, France
| | - Jean-Philip Piquemal
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Institut Universitaire de France, Paris, France
| | - Serge Fermandjian
- Chemistry and Biology Nucleo(s)tides and Immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomedicale, Paris, France
| | - Richard G. Maroun
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, UMR7616 CNRS, Sorbonne Université, Paris, France
| | - Zeina Hobaika
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
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El Khoury L, Piquemal JP, Fermandjian S, Maroun RG, Gresh N, Hobaika Z. The inhibition process of HIV-1 integrase by diketoacids molecules: Understanding the factors governing the better efficiency of dolutegravir. Biochem Biophys Res Commun 2017; 488:433-438. [PMID: 28478035 DOI: 10.1016/j.bbrc.2017.05.001] [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: 04/13/2017] [Accepted: 05/01/2017] [Indexed: 01/03/2023]
Abstract
The Human Immunodeficiency Virus-1 integrase is responsible for the covalent insertion of a newly synthesized double-stranded viral DNA into the host cells, and is an emerging target for antivirus drug design. Raltegravir (RAL) and elvitegravir (EVG) are the first two integrase strand transfer inhibitors used in therapy. However, treated patients eventually develop detrimental resistance mutations. By contrast, a recently approved drug, dolutegravir (DTG), presents a high barrier to resistance. This study aims to understand the increased efficiency of DTG upon focusing on its interaction properties with viral DNA. The results showed DTG to be involved in more extended interactions with viral DNA than EVG. Such interactions involve the halobenzene and scaffold of DTG and EVG and bases 5'G-43', 3'A35'and 3'C45'.
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Affiliation(s)
- Léa El Khoury
- UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, B.P. 11-514 Riad El Solh, Beirut 1107 2050, Lebanon; Laboratoire de Chimie Théorique, UMR7616 CNRS, UPMC, Sorbonne Universités, Paris 75005, France.
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UMR7616 CNRS, UPMC, Sorbonne Universités, Paris 75005, France; Institut Universitaire de France, Paris Cedex 05, 75231, France; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, United States.
| | - Serge Fermandjian
- Chemistry and Biology Nucleo(S)Tides and Immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomédicale, Paris, France.
| | - Richard G Maroun
- UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, B.P. 11-514 Riad El Solh, Beirut 1107 2050, Lebanon.
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, UMR7616 CNRS, UPMC, Sorbonne Universités, Paris 75005, France.
| | - Zeina Hobaika
- UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, B.P. 11-514 Riad El Solh, Beirut 1107 2050, Lebanon.
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