Small-sized human immunodeficiency virus type-1 protease inhibitors containing allophenylnorstatine to explore the S2' pocket

Conformational Space Profiling Enhances Generic Molecular Representation for AI-Powered Ligand-Based Drug Discovery

The molecular representation model is a neural network that converts molecular representations (SMILES, Graph) into feature vectors, and is an essential module applied across a wide range of artificial intelligence-driven drug discovery scenarios. However, current molecular representation models rarely consider the three-dimensional conformational space of molecules, losing sight of the dynamic nature of small molecules as well as the essence of molecular conformational space that covers the heterogeneity of molecule properties, such as the multi-target mechanism of action, recognition of different biomolecules, dynamics in cytoplasm and membrane. In this study, a new model named GeminiMol is proposed to incorporate conformational space profiles into molecular representation learning, which extracts the feature of capturing the complicated interplay between the molecular structure and the conformational space. Although GeminiMol is pre-trained on a relatively small-scale molecular dataset (39290 molecules), it shows balanced and superior performance not only on 67 molecular properties predictions but also on 73 cellular activity predictions and 171 zero-shot tasks (including virtual screening and target identification). By capturing the molecular conformational space profile, the strategy paves the way for rapid exploration of chemical space and facilitates changing paradigms for drug design.

Multiple Target Drug Design Using LigBuilder 3

Designing drugs that directly interact with multiple targets is a promising approach for treating complicated diseases. In order to successfully bind to multiple targets of different families and achieve the desired ligand efficiency, multi-target-directed ligands (MTDLs) require a higher level of diversity and complexity. De novo design strategies for creating more diverse chemical entities with desired properties may present an improved approach for developing MTDLs. In this chapter, we describe a computational protocol for developing MTDLs using the first reported multi-target de novo program, LigBuilder 3, which combines a binding site prediction module with de novo drug design and optimization modules. As an illustration of each detailed procedure, we design dual-functional compounds of two well-characterized virus enzymes, HIV protease and reverse transcriptase (PR and RT, respectively), using fragments extracted from known inhibitors. LigBuilder 3 is accessible at http://www.pkumdl.cn/ligbuilder3/ .

LigBuilder V3: A Multi-Target de novo Drug Design Approach

With the rapid development of systems-based pharmacology and poly-pharmacology, method development for rational design of multi-target drugs has becoming urgent. In this paper, we present the first de novo multi-target drug design program LigBuilder V3, which can be used to design ligands to target multiple receptors, multiple binding sites of one receptor, or various conformations of one receptor. LigBuilder V3 is generally applicable in de novo multi-target drug design and optimization, especially for the design of concise ligands for protein targets with large difference in binding sites. To demonstrate the utility of LigBuilder V3, we have used it to design dual-functional inhibitors targeting HIV protease and HIV reverse transcriptase with three different strategy, including multi-target de novo design, multi-target growing, and multi-target linking. The designed compounds were computational validated by MM/GBSA binding free energy estimation as highly potential multi-target inhibitors for both HIV protease and HIV reverse transcriptase. The LigBuilder V3 program can be downloaded at “http://www.pkumdl.cn/ligbuilder3/”.

Acquired Removability of Aspartic Protease Inhibitors by Direct Biotinylation

Protease inhibitors are used as both research tools and therapeutics. Many of these inhibitors consist of substrate amino acid sequence-derived structure with a transition state mimic to interact with the active site of the protease, suppressing enzymatic activity. However, once they bind, macrodilution or protein denaturation is required to remove them, limiting their usage. In this study, we describe a removable protease inhibitor, which is a directly biotinylated analogue to control the activities of HIV-1 protease and human cathepsin D. In the substrate cleavage assay, we observed that the nanomolar inhibitory activities were lost upon the addition of streptavidin, while the enzymatic activities sufficiently recovered. HIV-1 protease mixed with the removable inhibitor, avoiding autolysis, was still active to be detected by adding streptavidin after one year at room temperature. We also observed that the inhibitor was an effective eluent for the simple detection of the activity of proteases purified from human serum and cells. These results demonstrate that direct biotinylation of protease inhibitors could be a novel method for controlling the enzymatic activity from OFF to ON. We proposed the phenomenon that binding equilibrium of inhibitor was shifted from protease to streptavidin with higher affinity, named "inhibitor stripping action by affinity competition", or ISAAC. We anticipate that ISAAC could be applicable for preservatives of proteases and activity-based diagnosis of protease related diseases. Furthermore, removable inhibitor to be designed for targeted proteases changing the inhibitor structure may elucidate enzymatic activity in intrinsic form with natural modifications from various biological samples.

Related Endogenous Retrovirus-K Elements Harbor Distinct Protease Active Site Motifs

Background: Endogenous retrovirus-K is a group of related genomic elements descending from retroviral infections in human ancestors. HML2 is the clade of these viruses which contains the most intact provirus copies. These elements can be transcribed and translated in healthy and diseased tissues, and some of them produce active retroviral enzymes, such as protease. Retroviral gene products, including protease, contribute to illness in exogenous retroviral infections. There are ongoing efforts to test anti-retroviral regimens against endogenous retroviruses. Herein, we examine the potential activity and diversity of human endogenous retrovirus-K proteases, and their potential for impact on immunity and human disease.

Results: Sequences similar to the endogenous retrovirus-K HML2 protease and reverse transcriptase were identified in the human genome, classified by phylogenetic inference and compared to Repbase reference sequences. The topologies of trees inferred from protease and reverse transcriptase sequences were similar and agreed with the classification using reference sequences. Surprisingly, only 62/480 protease sequences identified by BLAST were classified as HML2; the remainder were classified as other HML groups, with the majority (216) classified as HML3. Variation in functionally significant protease motifs was explored, and two major active site variants were identified – the DTGAD variant is common in all groups, but the DTGVD motif appears limited to HML3, HML5, and HML6. Furthermore, distinct RNA expression patterns of protease variants are seen in disease states, such as amyotrophic lateral sclerosis, breast cancer, and prostate cancer.

Conclusion: Transcribed ERVK proteases exhibit a diversity which could impact immunity and inhibitor-based treatments, and these facets should be considered when designing therapeutic regimens.

Identification of Highly Potent Human Immunodeficiency Virus Type-1 Protease Inhibitors against Lopinavir and Darunavir Resistant Viruses from Allophenylnorstatine-Based Peptidomimetics with P2 Tetrahydrofuranylglycine

The emergence of drug-resistant HIV from a widespread antiviral chemotherapy targeting HIV protease in the past decades is unavoidable and provides a challenge to develop alternative inhibitors. We synthesized a series of allophenylnorstatine-based peptidomimetics with various P₃, P₂, and P₂́ moieties. The derivatives with P₂ tetrahydrofuranylglycine (Thfg) were found to be potent against wild type HIV-1 protease and the virus, leading to a highly potent compound 21f (KNI-1657) against lopinavir/ritonavir- or darunavir-resistant strains. Co-crystal structures of 21f and the wild-type protease revealed numerous key hydrogen bonding interactions with Thfg. These results suggest that the strategy to design allophenylnorstatine-based peptidomimetics combined with Thfg residue would be promising for generating candidates to overcome multidrug resistance.

Evaluation of novel protease inhibitors against darunavir-resistant variants of HIV type 1

HIV disease became a manageable chronic disease since combination antiretroviral therapy (cART) was introduced as the standard treatment regimen. However, the emergence of drug‐resistant viruses is a major problem associated with cART. A phenotypic drug susceptibility test using a lentiviral vector was established and applied to evaluate new protease inhibitors (PIs). Lentiviral vectors representing a wild‐type (WT‐lentivector) and darunavir (DRV)‐resistant HIV type 1 (HIV‐1) (DRV^r‐lentivector) were generated. Nine clinically approved protease inhibitors (PIs) inhibited the transduction ability of WT‐lentivector similar to their inhibitory effects on the replication of WT HIV‐1. Three new PIs reduced the transduction ability of WT‐ and DRV^r‐lentivector, suggesting that these PIs may be the candidates as novel antiretroviral drugs against drug‐resistant variants of HIV‐1.

Recent Progress in the Development of HIV-1 Protease Inhibitors for the Treatment of HIV/AIDS

HIV-1 protease inhibitors continue to play an important role in the treatment of HIV/AIDS, transforming this deadly ailment into a more manageable chronic infection. Over the years, intensive research has led to a variety of approved protease inhibitors for the treatment of HIV/AIDS. In this review, we outline current drug design and medicinal chemistry efforts toward the development of next-generation protease inhibitors beyond the currently approved drugs.

Structural insights into the activation and inhibition of histo-aspartic protease from Plasmodium falciparum

Histo-aspartic protease (HAP) from Plasmodium falciparum is a promising target for the development of novel antimalarial drugs. The sequence of HAP is highly similar to those of pepsin-like aspartic proteases, but one of the two catalytic aspartates, Asp32, is replaced with histidine. Crystal structures of the truncated zymogen of HAP and of the complex of the mature enzyme with inhibitor KNI-10395 have been determined at 2.1 and 2.5 Å resolution, respectively. As in other proplasmepsins, the propeptide of the zymogen interacts with the C-terminal domain of the enzyme, forcing the N- and C-terminal domains apart, thereby separating His32 and Asp215 and preventing formation of the mature active site. In the inhibitor complex, the enzyme forms a tight domain-swapped dimer, not previously seen in any aspartic proteases. The inhibitor is found in an unprecedented conformation resembling the letter U, stabilized by two intramolecular hydrogen bonds. Surprisingly, the location and conformation of the inhibitor are similar to those of the fragment of helix 2 comprising residues 34p-38p in the prosegments of the zymogens of gastric aspartic proteases; a corresponding helix assumes a vastly different orientation in proplasmepsins. Each inhibitor molecule is in contact with two molecules of HAP, interacting with the carboxylate group of the catalytic Asp215 of one HAP protomer through a water molecule, while also making a direct hydrogen bond to Glu278A' of the other protomer. A comparison of the shifts in the positions of the catalytic residues in the inhibitor complex presented here with those published previously gives further hints regarding the enzymatic mechanism of HAP.

Tetrahydrofuran, tetrahydropyran, triazoles and related heterocyclic derivatives as HIV protease inhibitors

HIV/AIDS remains a formidable disease with millions of individuals inflicted worldwide. Although treatment regimens have improved considerably, drug resistance brought on by viral mutation continues to erode their effectiveness. Intense research efforts are currently underway in search of new and improved therapies. This review is concerned with the design of novel HIV-1 protease inhibitors that incorporate heterocyclic scaffolds and which have been reported within the recent literature (2005-2010). Various examples in this review showcase the essential role heterocycles play as scaffolds and bioisosteres in HIV-1 protease inhibitor drug development. This review will hopefully stimulate the widespread application of these heterocycles in the design of other therapeutic agents.