Structure-Based Identification of HIV-1 Nucleocapsid Protein Inhibitors Active against Wild-Type and Drug-Resistant HIV-1 Strains

Abstract

HIV/AIDS is still one of the leading causes of death worldwide. Current drugs that target the canonical steps of the HIV-1 life cycle are efficient in blocking viral replication but are unable to eradicate HIV-1 from infected patients. Moreover, drug resistance (DR) is often associated with the clinical use of these molecules, thus raising the need for novel drug candidates as well as novel putative drug targets. In this respect, pharmacological inhibition of the highly conserved and multifunctional nucleocapsid protein (NC) of HIV-1 is considered a promising alternative to current drugs, particularly to overcome DR. Here, using a multidisciplinary approach combining in silico screening, fluorescence-based molecular assays, and cellular antiviral assays, we identified nordihydroguaiaretic acid (6), as a novel natural product inhibitor of NC. By using NMR, mass spectrometry, fluorescence spectroscopy, and molecular modeling, 6 was found to act through a dual mechanism of action never highlighted before for NC inhibitors (NCIs). First, the molecule recognizes and binds NC noncovalently, which results in the inhibition of the nucleic acid chaperone properties of NC. In a second step, chemical oxidation of 6 induces a potent chemical inactivation of the protein. Overall, 6 inhibits NC and the replication of wild-type and drug-resistant HIV-1 strains in the low micromolar range with moderate cytotoxicity that makes it a profitable tool compound as well as a good starting point for the development of pharmacologically relevant NCIs.

Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1

“… 37 To this end, a computational protocol was established and refined in the group of Botta. 14 , 33 , 38 Several NC binding small molecules have already been discovered through this protocol, supporting its validity. 14 , 15 , 33 , 38

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“…3 Docking-based predicted binding conformation of 1–4 and guanine within the hydrophobic pocket of the NC. 14 , 33 , 38 A) distal fleximer guanine base ( 1 ), B) proximal fleximer guanine base ( 2 ), C) distal guanine bipyrimidine ( 3 ), D) proximal guanine bipyrimidine ( 4 ) and E) guanine bound to NC. The protein is shown as green cartoon and lines (residues within 4 Å from each ligand are shown and labelled).…”

“…In an effort to explore the fleximer approach to other viruses such as HIV-1, a virus with the ability to readily mutate and develop antiviral resistance, a series of fleximers were designed and studied in silico for their ability to inhibit the virus’ nucleocapsid protein, NC. 14 , 15 , 16 , 17 …”

“… 26 , 32 Thus, inhibitors of the interaction between NC and the viral nucleic acids could provide a new approach to antiretroviral therapy. 14 , 33 For this purpose, a series of fleximers were computationally designed with that goal in mind. Herein we report the synthesis and biological results for a series of compounds that were predicted to interact with NC.…”

Quinolone derivatives: Potential anti‐HIV agent—development and application

“…Acquired immune deficiency syndrome (AIDS), caused by human immunodeficiency virus (HIV), is one of the largest and most devastating public health pandemics . HIV interferes with the immune system and increases the risk of opportunistic infections such as tuberculosis, and tumors that rarely affect people who have working immune systems.…”