Toward Structurally Novel and Metabolically Stable HIV-1 Capsid-Targeting Small Molecules

HIV-1 capsid protein (CA) plays an important role in many steps of viral replication and represents an appealing antiviral target. Several CA-targeting small molecules of various chemotypes have been studied, but the peptidomimetic PF74 has drawn particular interest due to its potent antiviral activity, well-characterized binding mode, and unique mechanism of action. Importantly, PF74 competes against important host factors for binding, conferring highly desirable antiviral phenotypes. However, further development of PF74 is hindered by its prohibitively poor metabolic stability, which necessitates the search for structurally novel and metabolically stable chemotypes. We have conducted a pharmacophore-based shape similarity search for compounds mimicking PF74. We report herein the analog synthesis and structure-activity relationship (SAR) of two hits from the search, and a third hit designed via molecular hybridization. All analogs were characterized for their effect on CA hexamer stability, antiviral activity, and cytotoxicity. These assays identified three active compounds that moderately stabilize CA hexamer and inhibit HIV-1. The most potent analog (10) inhibited HIV-1 comparably to PF74 but demonstrated drastically improved metabolic stability in liver microsomes (31 min vs. 0.7 min t1/2). Collectively, the current studies identified a structurally novel and metabolically stable PF74-like chemotype for targeting HIV-1 CA.

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Design, Synthesis and Characterization of HIV-1 CA-Targeting Small Molecules: Conformational Restriction of PF74

Viruses ◽

10.3390/v13030479 ◽

2021 ◽

Vol 13 (3) ◽

pp. 479

Author(s):

Rajkumar Lalji Sahani ◽

Raquel Diana-Rivero ◽

Sanjeev Kumar V. Vernekar ◽

Lei Wang ◽

Haijuan Du ◽

...

Keyword(s):

Small Molecules ◽

Liver Microsomes ◽

Imidazole Ring ◽

Metabolic Stability ◽

Binding Modes ◽

Conformational Restriction ◽

Design Synthesis ◽

Antiviral Activities ◽

Hiv 1

Small molecules targeting the PF74 binding site of the HIV-1 capsid protein (CA) confer potent and mechanistically unique antiviral activities. Structural modifications of PF74 could further the understanding of ligand binding modes, diversify ligand chemical classes, and allow identification of new variants with balanced antiviral activity and metabolic stability. In the current work, we designed and synthesized three series of PF74-like analogs featuring conformational constraints at the aniline terminus or the phenylalanine carboxamide moiety, and characterized them using a biophysical thermal shift assay (TSA), cell-based antiviral and cytotoxicity assays, and in vitro metabolic stability assays in human and mouse liver microsomes. These studies showed that the two series with the phenylalanine carboxamide moiety replaced by a pyridine or imidazole ring can provide viable hits. Subsequent SAR identified an improved analog 15 which effectively inhibited HIV-1 (EC50 = 0.31 μM), strongly stabilized CA hexamer (ΔTm = 8.7 °C), and exhibited substantially enhanced metabolic stability (t1/2 = 27 min for 15 vs. 0.7 min for PF74). Metabolic profiles from the microsomal stability assay also indicate that blocking the C5 position of the indole ring could lead to increased resistance to oxidative metabolism.

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Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA

Journal of Medicinal Chemistry ◽

10.1021/acs.jmedchem.6b01450 ◽

2016 ◽

Vol 59 (24) ◽

pp. 11148-11160 ◽

Cited By ~ 39

Author(s):

Fardokht A. Abulwerdi ◽

Matthew D. Shortridge ◽

Joanna Sztuba-Solinska ◽

Robert Wilson ◽

Stuart F. J. Le Grice ◽

...

Keyword(s):

Small Molecules ◽

Binding Mode ◽

Activation Response ◽

Tar Rna ◽

Hiv 1

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Potency and metabolic stability: a molecular hybrid case in the design of novel PF74-like small molecules targeting HIV-1 capsid protein

RSC Medicinal Chemistry ◽

10.1039/d1md00292a ◽

2021 ◽

Author(s):

Rajkumar Lalji Sahani ◽

Thamina Akther ◽

Maria E. Cilento ◽

Andres Emanuelli Castaner ◽

Huanchun Zhang ◽

...

Keyword(s):

Molecular Modeling ◽

Small Molecules ◽

Capsid Protein ◽

Metabolic Stability ◽

Molecular Hybridization ◽

Hiv 1

To achieve balanced potency and metabolic stability profiles, a molecular hybridization approach was used to design a novel PF74-like chemotype 4. Synthesis, SAR and molecular modeling of chemotype 4 are reported.

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(Thia)calixarenephosphonic Acids as Potent Inhibitors of the Nucleic Acid Chaperone Activity of the HIV-1 Nucleocapsid Protein with a New Binding Mode and Multitarget Antiviral Activity

ACS Infectious Diseases ◽

10.1021/acsinfecdis.9b00290 ◽

2020 ◽

Vol 6 (4) ◽

pp. 687-702 ◽

Cited By ~ 2

Author(s):

Nicolas Humbert ◽

Lesia Kovalenko ◽

Francesco Saladini ◽

Alessia Giannini ◽

Manuel Pires ◽

...

Keyword(s):

Nucleic Acid ◽

Antiviral Activity ◽

Nucleocapsid Protein ◽

Binding Mode ◽

Chaperone Activity ◽

Nucleic Acid Chaperone ◽

Hiv 1

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Novel PF74-like small molecules targeting the HIV-1 capsid protein: balance of potency and metabolic stability

Acta Pharmaceutica Sinica B ◽

10.1016/j.apsb.2020.07.016 ◽

2020 ◽

Author(s):

Lei Wang ◽

Mary C. Casey ◽

Sanjeev Kumar V. Vernekar ◽

Rajkumar Lalji Sahani ◽

Karen A. Kirby ◽

...

Keyword(s):

Small Molecules ◽

Capsid Protein ◽

Metabolic Stability ◽

Protein Balance ◽

Hiv 1

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3D-QSAR Studies of S-DABO Derivatives as Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors

Letters in Drug Design & Discovery ◽

10.2174/1570180815666180810112321 ◽

2019 ◽

Vol 16 (8) ◽

pp. 868-881

Author(s):

Yueping Wang ◽

Jie Chang ◽

Jiangyuan Wang ◽

Peng Zhong ◽

Yufang Zhang ◽

...

Keyword(s):

Reverse Transcriptase ◽

Three Dimensional ◽

Predictive Ability ◽

3D Qsar ◽

Binding Mode ◽

Quantitative Structure Activity Relationship ◽

Field Analysis ◽

Reverse Transcriptase Inhibitors ◽

Qsar Studies ◽

Hiv 1

Background: S-dihydro-alkyloxy-benzyl-oxopyrimidines (S-DABOs) as non-nucleoside reverse transcriptase inhibitors have received considerable attention during the last decade due to their high potency against HIV-1. Methods: In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR) of a series of 38 S-DABO analogues developed in our lab was studied using Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA). The Docking/MMFF94s computational protocol based on the co-crystallized complex (PDB ID: 1RT2) was used to determine the most probable binding mode and to obtain reliable conformations for molecular alignment. Statistically significant CoMFA (q2=0.766 and r2=0.949) and CoMSIA (q2=0.827 and r2=0.974) models were generated using the training set of 30 compounds on the basis of hybrid docking-based and ligand-based alignment. Results: The predictive ability of CoMFA and CoMSIA models was further validated using a test set of eight compounds with predictive r2 pred values of 0.843 and 0.723, respectively. Conclusion: The information obtained from the 3D contour maps can be used in designing new SDABO derivatives with improved HIV-1 inhibitory activity.

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DFT based computational methodology of IC50 prediction

Current Computer - Aided Drug Design ◽

10.2174/1573409916666200219115112 ◽

2020 ◽

Vol 16 ◽

Author(s):

Arijit Bag

Keyword(s):

Present Method ◽

Dipole Moments ◽

Research Work ◽

Organometallic Compounds ◽

Computational Method ◽

Unknown Compound ◽

Drug Designing ◽

Further Development ◽

Similar Kind ◽

Hiv 1

Background: IC50 is one of the most important parameters of a drug. But, it is very difficult to predict this value of a new compound without experiment. There are only a few QSAR based methods available for IC50 prediction which is also highly dependable on huge number of known data. Thus, there is an immense demand for a sophisticated computational method of IC50 prediction, in the field of in-silico drug designing. Objective: Recently developed quantum computation based method of IC50 prediction by Bag and Ghorai requires an affordable known data. In present research work further development of this method is carried out such that the requisite number of known data being minimal. Methods: To retrench the cardinal data span and shrink the effects of variant biological parameters on the computed value of IC50, a relative approach of IC50 computation is pursued in the present method. To predict an approximate value of IC50 of a small molecule, only the IC50 of a similar kind of molecule is required for this method. Results: The present method of IC50 computation is tested for both organic and organometallic compounds as HIV-1 capsid A inhibitor and cancer drugs. Computed results match very well with the experiment. Conclusion: This method is easily applicable to both organic and organometallic com- pounds with acceptable accuracy. Since this method requires only the dipole moments of an unknown compound and the reference compound, IC50 based drug search is possible with this method. An algorithm is proposed here for IC50 based drug search.

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SUMOylation of SAMHD1 at Lysine 595 is required for HIV-1 restriction in non-cycling cells

Nature Communications ◽

10.1038/s41467-021-24802-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Charlotte Martinat ◽

Arthur Cormier ◽

Joëlle Tobaly-Tapiero ◽

Noé Palmic ◽

Nicoletta Casartelli ◽

...

Keyword(s):

Antiviral Activity ◽

Reverse Transcription ◽

Immune Cells ◽

Viral Restriction ◽

Antiviral Function ◽

Hiv 1 ◽

Constitutively Active

AbstractSAMHD1 is a cellular triphosphohydrolase (dNTPase) proposed to inhibit HIV-1 reverse transcription in non-cycling immune cells by limiting the supply of the dNTP substrates. Yet, phosphorylation of T592 downregulates SAMHD1 antiviral activity, but not its dNTPase function, implying that additional mechanisms contribute to viral restriction. Here, we show that SAMHD1 is SUMOylated on residue K595, a modification that relies on the presence of a proximal SUMO-interacting motif (SIM). Loss of K595 SUMOylation suppresses the restriction activity of SAMHD1, even in the context of the constitutively active phospho-ablative T592A mutant but has no impact on dNTP depletion. Conversely, the artificial fusion of SUMO2 to a non-SUMOylatable inactive SAMHD1 variant restores its antiviral function, a phenotype that is reversed by the phosphomimetic T592E mutation. Collectively, our observations clearly establish that lack of T592 phosphorylation cannot fully account for the restriction activity of SAMHD1. We find that SUMOylation of K595 is required to stimulate a dNTPase-independent antiviral activity in non-cycling immune cells, an effect that is antagonized by cyclin/CDK-dependent phosphorylation of T592 in cycling cells.

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Specificity of the HIV-1 Protease on Substrates Representing the Cleavage Site in the Proximal Zinc-Finger of HIV-1 Nucleocapsid Protein

Viruses ◽

10.3390/v13061092 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1092

Author(s):

János András Mótyán ◽

Márió Miczi ◽

Stephen Oroszlan ◽

József Tőzsér

Keyword(s):

Amino Acid ◽

Zinc Finger ◽

Cleavage Site ◽

Potential Role ◽

Binding Mode ◽

Interaction Energies ◽

Vitro Assay ◽

Hiv 1

To explore the sequence context-dependent nature of the human immunodeficiency virus type 1 (HIV-1) protease’s specificity and to provide a rationale for viral mutagenesis to study the potential role of the nucleocapsid (NC) processing in HIV-1 replication, synthetic oligopeptide substrates representing the wild-type and modified versions of the proximal cleavage site of HIV-1 NC were assayed as substrates of the HIV-1 protease (PR). The S1′ substrate binding site of HIV-1 PR was studied by an in vitro assay using KIVKCF↓NCGK decapeptides having amino acid substitutions of N17 residue of the cleavage site of the first zinc-finger domain, and in silico calculations were also performed to investigate amino acid preferences of S1′ site. Second site substitutions have also been designed to produce “revertant” substrates and convert a non-hydrolysable sequence (having glycine in place of N17) to a substrate. The specificity constants obtained for peptides containing non-charged P1′ substitutions correlated well with the residue volume, while the correlation with the calculated interaction energies showed the importance of hydrophobicity: interaction energies with polar residues were related to substantially lower specificity constants. Cleavable “revertants” showed one residue shift of cleavage position due to an alternative productive binding mode, and surprisingly, a double cleavage of a substrate was also observed. The results revealed the importance of alternative binding possibilities of substrates into the HIV-1 PR. The introduction of the “revertant” mutations into infectious virus clones may provide further insights into the potential role of NC processing in the early phase of the viral life-cycle.

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