Anti-HIV Screening Libraries

It is evident that combination antiretroviral therapy is the critical approach to reducing the viral load in HIV-infected people [1-4]. Generally, it incorporates several medications with different activity types into an HIV treatment regimen, which curbs the infection and prevents its progression to AIDS. As typically the case with any medication therapy, however, the problem of HIV resistance to known and accepted drugs has eventually emerged [5]. This makes the discovery and development of new and effective small-molecule drugs for antiretroviral treatment even more urgent than ever.

In response to this acute need, Life Chemicals has contributed to antiretroviral research with its proprietary set of Anti-HIV Screening Libraries:

• Anti-HIV Focused Library (19,600 compounds)
• Anti-HIV Targeted Library (3,900 compounds)

The PAINS filters were not applied to the compound selection since this would have cut out many relevant analogs of known antiretroviral inhibitors from the reference sets, as those were originally not PAINS-compliant. Nevertheless, such filtering can be done at the customer’s request.

The compound selection can be customized based on your requirements, cherry picking is available.

Please, contact us at orders@lifechemicals.com for any additional information and price quotations.

Figure 1. Examples of approved anti-HIV infection drugs and similar compounds from the Life Chemicals Library.

Background

The multidrug strategy has become highly effective and usable over the years, having successfully enhanced the quality of life for HIV-positive individuals. Around 50 approved HIV medicines [6] may serve as components of a personalized treatment regimen. They form seven main drug classes depending on a viral target and active substance [7]. Various medications operate at different stages of the HIV life cycle [8]: some prevent the virus from entering the immune system cells; others can block enzymes that HIV needs to replicate – reverse transcriptase, protease, and integrase.

This variability of options stems from over 30 years of intense research efforts. However, the ability to control HIV as a chronic disease is just a step toward complete recovery. The cure remains one of the most significant medical challenges, which motivates a continuous search for innovative anti-HIV drugs and treatment strategies.

Anti-HIV Focused Library

Figure 2. Compound distribution targeting organism- and single protein targets within the HIV Focused Library

Anti-HIV Targeted Library

This Screening Set contains about 3,900 structurally diverse screening molecules with potential activity against the following HIV-focused drug targets:

• Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1)
• Proto-oncogene tyrosine-protein kinase Src (SRC)
• HIV-1 Protease
• HIV-1 Reverse Transcriptase
• HIV-1 Integrase

The drug-like compounds were picked out by high-throughput virtual screening based on the pharmacophore hypothesis. A more detailed description of each compound subset for specific antiretroviral protein targets can be found below.

It is known that the virus can remain in the central nervous system and reproduce, thus leading to neurological disorders. This may be due to the inability of anti-HIV drugs to cross the blood-brain barrier and inhibit HIV in the brain, which is critical to reversing or ameliorating HIV-related neurocognitive impairment [9]. Therefore, the Anti-HIV Targeted Library compounds were filtered according to their ability to adsorb and penetrate the blood-brain barrier, also taking into account the metabolism parameter, i.e., their ability to be excreted from the body.

Figure 3. Groups of anti-HIV drugs and mechanisms of their action [10]

Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1)

Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a protease that enhances BCL10-induced activation, resulting in the activation of NF-kappa-B and p38 MAP kinases [11], which stimulate the expression of genes encoding proinflammatory cytokines and chemokines. The protease is also involved in the induction of T helper 17 differentiation [12] and mediates the cleavage of N4BP1 in T cells after TCR-mediated activation, which leads to the inactivation of N4BP1. Since N4BP1 inhibits the replication of human immunodeficiency virus 1 (HIV1), MALT1-mediated inactivation of N4BP1 facilitates the reactivation of latent HIV1 proviruses [13]. Thus, MALT1 is a relevant target for targeted HIV therapy.

Key features:

• Method: high-throughput virtual screening
• X-Ray data used: 4MXO
• Filters applied: metabolism, QPPCaco, QPlogBB, QPPMDCK, PercentHuman-OralAbsorption
• Number of compounds selected: 821

Figure 4. Pharmacophore hypothesis based on the complex of MALT1 with inhibitor

Proto-oncogene tyrosine-protein kinase Src (SRC)

Proto-oncogene tyrosine-protein kinase Src is a non-receptor tyrosine kinase. It presents a component of many signaling pathways that control various processes within the cell [14], in particular, gene transcription, immune response, cell adhesion, cell cycle progression, apoptosis, migration, and transformation [15-16]. A potential role of the proto-oncogene tyrosine-protein kinase Src in the development of HIV infection has also been identified. It is known that after contact with human CD4 cells, HIV induces autophosphorylation of the protein tyrosine kinase 2 beta (PTK2B) inside the cell. Autophosphorylation of PTK2B at Tyr402 occurs with the participation of c-SRCs, which leads to focal adhesion and remodeling of the CD4 cell cytoskeleton. Thus, inhibiting the activity or expression of the proto-oncogene tyrosine-protein kinase Src can reduce HIV infection, making this protein a promising target for HIV treatment [9, 17].

Key features:

• Method: high-throughput virtual screening
• X-Ray data used: 4I1R
• Filters applied: metabolism, QPPCaco, QPlogBB, QPPMDCK, PercentHuman-OralAbsorption
• Number of compounds selected: 780

Figure 5. Pharmacophore hypothesis based on the complex of SRC with inhibitor

HIV-1 Protease

HIV protease is an enzyme involved in the hydrolysis of peptide bonds in retroviruses. It plays an essential part in the HIV life cycle, as it splits proteins into smaller units and uses them to create the mature protein components of an infectious HIV virion [18]. Inhibition of HIV protease disrupts the ability of the retrovirus to replicate and infect other cells.

The mature HIV protease is a 22 kDa homodimer, with each subunit consisting of 99 amino acids. The active site is located between the identical subunits and contains the sequence of the catalytic triad (Asp25, Thr26, and Gly27) [19]. HIV protease performs two main essential functions: the HIV pre-protease is responsible for auto-processing, and the mature protease can hydrolyze peptide bonds on Gag-Pol polyproteins at nine specific sites, converting the resulting subunits into mature, fully functional proteins [20]. The HIV protease can mutate in two major ways: in the active site and the periphery of the protein, thus impairing binding to the inhibitor [21]. Considering this fact, the search for new and effective drugs targeting HIV protease is of great importance in the pharmaceutical industry.

Key features:

• Method: high-throughput virtual screening
• X-Ray data used: 7DOZ
• Filters applied: metabolism, QPPCaco, QPlogBB, QPPMDCK, PercentHuman-OralAbsorption
• Number of compounds selected: 517

Figure 6. Pharmacophore hypothesis based on the complex of HIV-1 protease with inhibitor

HIV-1 Reverse Transcriptase

HIV reverse transcriptase (HIV RT) is one of the enzymes used by the retrovirus for self-copying. This enzyme catalyzes the conversion of single-stranded viral RNA into proviral DNA, which further infects the host cell DNA [22, 23]. Its inhibition allows hindering virus replication. Corresponding targeted drugs (nucleoside and non-nucleoside reverse transcriptase inhibitors) exclude reverse transcriptase from the infectious process by either blocking it or altering its structure.

HIV reverse transcriptase consists of two subunits of 51 and 66 kDa [24]. This reverse transcriptase has three consecutive biochemical activities: RNA-dependent DNA polymerase activity, ribonuclease H (RNase H), and DNA-dependent DNA polymerase activity. Functioning together, these activities allow the enzyme to convert single-stranded RNA into double-stranded complementary DNA [25]. HIV reverse transcriptase is currently one of the most important targets in the treatment of AIDS. However, mutations in the structure of HIV-1 RT can lead to appearing drug-resistant strains of the virus [26], making the development and clinical trials of new drugs even more imperative.

Key features:

• Method: high-throughput virtual screening
• X-Ray data used: 4I7F
• Filters applied: metabolism, QPPCaco, QPlogBB, QPPMDCK, PercentHuman-OralAbsorption
• Number of compounds selected: 538

Figure 7. Pharmacophore hypothesis based on the complex of HIV-1 reverses transcriptase with inhibitor

HIV integrase

HIV integrase is a crucial enzyme in the life cycle of the Human Immunodeficiency Virus (HIV). This enzyme facilitates the integration of viral DNA into the host cell's genome, a vital step for viral replication and persistence. Structurally, HIV integrase belongs to the family of integrase enzymes, characterized by their ability to bind and process DNA. The enzyme operates in three main steps: 1) 3'-processing, where it cleaves the viral DNA ends, 2) strand transfer, where it joins the viral DNA to the host DNA, and 3) gap repair, finalizing the integration. HIV integrase consists of three domains: the N-terminal zinc finger domain, the catalytic core domain, and the C-terminal DNA-binding domain [27]. Each domain plays a specific role in the integration process, making integrase a prime target for antiretroviral therapy.

Targeting HIV integrase is vital due to its indispensable role in HIV replication as inhibitors of HIV integrase can effectively block the virus from integrating into the host genome, thus preventing the establishment of a productive infection.

In order to design such selection we used data on the crystallographic structure of HIV Integrase I (PDB ID: 8buv) as well as the binding site described by Al-Mawsawi et al. [28]. The protein was prepared and optimized with the Schrödinger software. The Glide Docking (Schrödinger) protocol was applied for docking and screening procedures against the HTS Compound Collection and _ compounds were selected as potential therapeutic agents.

Key features:

• Method: high-throughput virtual screening
• X-Ray data used: 8BUV
• Number of compounds selected: 1310

Figure 8. Structure of the binding site with F2471-1884 compound.

References

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