Inhibition and catalytic mechanism of HIV-1 aspartic protease

B(C6F5)3/Chiral Phosphoric Acid Promoted Asymmetric C-3 gem-Difluoroalkylation of Quinoxalin-2-ones with Difluoroenoxysilanes

The asymmetric Mannich-type reaction of quinoxalin-2-ones with difluoroenoxysilanes has been developed for the synthesis of chiral gem-difluoroalkylated quinoxalin-2-ones. The reaction worked in the presence of chiral phosphoric acid CPA 1 and B(C6F5)3 in THF at room temperature. The reaction exhibited a good substrate scope furnishing the products in good yields (up to 97%) with up to 96% ee.

Radical Decarboxylation-Initiated SH2' Reaction of β,β-Difluoroenol Sulfonates: Access to α,α-Difluoroketones

Reported herein is a novel radical decarboxylation-initiated SH2' reaction of β,β-difluoroenol sulfonates. This transformation is characterized by mild reaction conditions, a broad substrate scope, and late-stage modification of drug molecules, providing general and mechanistically distinct access to bioactive and synthetically versatile α,α-difluoroketones. Preliminary mechanistic studies demonstrate that this reaction proceeds through a succession of silver-mediated decarboxylative radical generation and radical-addition-induced β-elimination of the sulfonyl radical.

FMO-guided design of darunavir analogs as HIV-1 protease inhibitors

The prevalence of HIV-1 infection continues to pose a significant global public health issue, highlighting the need for antiretroviral drugs that target viral proteins to reduce viral replication. One such target is HIV-1 protease (PR), responsible for cleaving viral polyproteins, leading to the maturation of viral proteins. While darunavir (DRV) is a potent HIV-1 PR inhibitor, drug resistance can arise due to mutations in HIV-1 PR. To address this issue, we developed a novel approach using the fragment molecular orbital (FMO) method and structure-based drug design to create DRV analogs. Using combinatorial programming, we generated novel analogs freely accessible via an on-the-cloud mode implemented in Google Colab, Combined Analog generator Tool (CAT). The designed analogs underwent cascade screening through molecular docking with HIV-1 PR wild-type and major mutations at the active site. Molecular dynamics (MD) simulations confirmed the assess ligand binding and susceptibility of screened designed analogs. Our findings indicate that the three designed analogs guided by FMO, 19-0-14-3, 19-8-10-0, and 19-8-14-3, are superior to DRV and have the potential to serve as efficient PR inhibitors. These findings demonstrate the effectiveness of our approach and its potential to be used in further studies for developing new antiretroviral drugs.

Catalytic Mechanism of Human T-Cell Leukemia Virus Type 1 Protease Investigated by Combined QM/MM Molecular Dynamics Simulations

Combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations were performed to investigate the catalytic mechanism of human T-cell leukemia virus type 1 (HTLV-1) protease, a retroviral aspartic protease that is a potential therapeutic target for curing HTLV-1-associated diseases. To elucidate the proteolytic cleavage mechanism, we determined the two-dimensional free energy surfaces of the HTLV-1 protease-catalyzed reactions through various possible pathways. The free energy simulations suggest that the catalytic reactions of the HTLV-1 protease occur in the following sequential steps: (1) a proton is transferred from the lytic water to Asp32', followed by the nucleophilic addition of the resulting hydroxyl to the carbonyl carbon of the scissile bond, forming a tetrahedral oxyanion intermediate, and (2) a proton is transferred from Asp32 to the peptide nitrogen of the scissile bond, leading to the spontaneous breakage of the scissile bond. The rate-limiting step of this catalytic process is the proton transfer from Asp32 to the peptide nitrogen of the scissile bond, with a free energy of activation of 21.1 kcal/mol. This free energy barrier is close to the experimentally determined free energy of activation (16.3 kcal/mol) calculated from the measured catalytic rate constant (k_cat). This mechanistic study provides detailed dynamic and structural information that will facilitate the design of mechanism-based inhibitors for the treatment of HTLV-1-associated diseases.

Asymmetric difluorocarbonylation reactions of non-active imines catalyzed by Bi(OAc)3/chiral phosphoric acid

Difluorinated carbonyl has been identified as the basic skeleton of multitudinous biologically active molecules.

Recent progress in the chemistry of β-aminoketones

The current study highlighted the significance of β-aminoketones as privileged biologically active molecules, recent synthetic strategies, and synthetic applications.

α-C–H difluoroalkylation of alkyl sulfoxides via intermolecular Pummerer reaction

A simple and practical intermolecular Pummerer reaction using difluoroenol silyl ethers as nucleophiles is described. The protocol allows for highly efficient α-difluoroalkylation of a wide spectrum of alkyl sulfoxides.

Exploring the concerted mechanistic pathway for HIV-1 PR-substrate revealed by umbrella sampling simulation

HIV-1 protease (HIV-1 PR) is an essential enzyme for the replication process of its virus, and therefore considered an important target for the development of drugs against the acquired immunodeficiency syndrome (AIDS). Our previous study shows that the catalytic mechanism of subtype B/C-SA HIV-1 PR follows a one-step concerted acyclic hydrolysis reaction process using a two-layered ONIOM B3LYP/6-31++G(d,p) method. This present work is aimed at exploring the proposed mechanism of the proteolysis catalyzed by HIV-1 PR and to ensure our proposed mechanism is not an artefact of a single theoretical technique. Hence, we present umbrella sampling method that is suitable for calculating potential mean force (PMF) for non-covalent ligand/substrate-enzyme association/dissociation interactions which provide thermodynamic details for molecular recognition. The free activation energy results were computed in terms of PMF analysis within the hybrid QM(DFTB)/MM approach. The theoretical findings suggest that the proposed mechanism corresponds in principle with experimental data. Given our observations, we suggest that the QM/MM MD method can be used as a reliable computational technique to rationalize lead compounds against specific targets such as the HIV-1 protease.

Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design

HIV-1 protease is indispensable for virus propagation and an important therapeutic target for antiviral inhibitors to treat AIDS. As such inhibitors are transition-state mimics, a detailed understanding of the enzyme mechanism is crucial for the development of better anti-HIV drugs. Here, we used room-temperature joint X-ray/neutron crystallography to directly visualize hydrogen atoms and map hydrogen bonding interactions in a protease complex with peptidomimetic inhibitor KVS-1 containing a reactive nonhydrolyzable ketomethylene isostere, which, upon reacting with the catalytic water molecule, is converted into a tetrahedral intermediate state, KVS-1_TI. We unambiguously determined that the resulting tetrahedral intermediate is an oxyanion, rather than the gem-diol, and both catalytic aspartic acid residues are protonated. The oxyanion tetrahedral intermediate appears to be unstable, even though the negative charge on the oxyanion is delocalized through a strong n → π* hyperconjugative interaction into the nearby peptidic carbonyl group of the inhibitor. To better understand the influence of the ketomethylene isostere as a protease inhibitor, we have also examined the protease structure and binding affinity with keto-darunavir (keto-DRV), which similar to KVS-1 includes the ketomethylene isostere. We show that keto-DRV is a significantly less potent protease inhibitor than DRV. These findings shed light on the reaction mechanism of peptide hydrolysis catalyzed by HIV-1 protease and provide valuable insights into further improvements in the design of protease inhibitors.

Elucidating the multiple roles of hydration for accurate protein-ligand binding prediction via deep learning

Accurate and efficient prediction of protein-ligand interactions has been a long-lasting dream of practitioners in drug discovery. The insufficient treatment of hydration is widely recognized to be a major limitation for accurate protein-ligand scoring. Using an integration of molecular dynamics simulations on thousands of protein structures with novel big-data analytics based on convolutional neural networks and deep Taylor decomposition, we consistently identify here three different patterns of hydration to be essential for protein-ligand interactions. In addition to desolvation and water-mediated interactions, the formation of enthalpically favorable networks of first-shell water molecules around solvent-exposed ligand moieties is identified to be essential for protein-ligand binding. Despite being currently neglected in drug discovery, this hydration phenomenon could lead to new avenues in optimizing the free energy of ligand binding. Application of deep neural networks incorporating hydration to docking provides 89% accuracy in binding pose ranking, an essential step for rational structure-based drug design.

Practical fluorothiolation and difluorothiolation of alkenes using pyridine-HF and N-thiosuccinimides

Fluorothiolation and difluorothiolation of alkenes using pyridine-HF and N-thiosuccinimides.

NMR and MD studies combined to elucidate inhibitor and water interactions of HIV-1 protease and their modulations with resistance mutations

Over the last two decades, both the sensitivity of NMR and the time scale of molecular dynamics (MD) simulation have increased tremendously and have advanced the field of protein dynamics. HIV-1 protease has been extensively studied using these two methods, and has presented a framework for cross-evaluation of structural ensembles and internal dynamics by integrating the two methods. Here, we review studies from our laboratories over the last several years, to understand the mechanistic basis of protease drug-resistance mutations and inhibitor responses, using NMR and crystal structure-based parallel MD simulations. Our studies demonstrate that NMR relaxation experiments, together with crystal structures and MD simulations, significantly contributed to the current understanding of structural/dynamic changes due to HIV-1 protease drug resistance mutations.

A Sc(OTf)3 catalyzed Mukaiyama–Mannich reaction of difluoroenoxysilanes with unactivated ketimines

The first example of a Mukaiyama–Mannich reaction of difluoroenoxysilanes with unactivated ketimines catalyzed by Sc(OTf)₃ is described.

Catalytic selective mono- and difluoroalkylation using fluorinated silyl enol ethers

This feature article highlights our recent achievements in catalytic selective mono- and difluoroalkylation using fluorinated silyl enol ethers (FSEEs).

Organocatalytic Decarboxylative Cyanomethylation of Difluoromethyl and Trifluoromethyl Ketones

An efficient organocatalytic method for the synthesis of difluoromethyl and trifluoromethyl substituted β-hydroxynitriles is introduced. The decarboxylative cyanomethylation of fluorinated ketones with readily available cyanoacetic acid gives a variety of tertiary alcohols in high yields and without concomitant water elimination. The reaction occurs in the presence of catalytic amounts of triethylamine, can be upscaled and applied to chlorofluoromethyl ketones and difluoromethyl ketimines.

Atom Efficient Synthesis of Selectively Difluorinated Carbocycles through a Gold(I)-Catalyzed Cyclization

The intramolecular carbocyclization of difluorinated enol acetals has been achieved for the first time using gold(I) catalysis. Difluorinated enol acetals bearing a pendant alkene group can be cyclized and reduced in one pot to form fluorinated diol motifs. Alternatively, the cyclization of terminal alkynes allows for the synthesis of fluorinated pyran scaffolds. Both cyclization processes can be performed under mild conditions allowing access to complex products rich in functionality. The cyclic systems are synthesized concisely (maximum four steps) from trifluoroethanol, an inexpensive fluorinated feedstock.

Magnesium-Promoted Additions of Difluoroenolates to Unactivated Imines

Although there are many synthetic methods to produce fluorinated and trifluoromethylated organic structures, the construction of difluoromethylated compounds remains a synthetic challenge. We have discovered that unactivated imines will react with difluoroenolates under exceedingly mild conditions when using magnesium salts and organic bases. We have applied this approach to the iminoaldol reaction to produce difluoromethylene groups as α,α-difluoro-β-amino-carbonyl groups. This method provides synthetically useful quantities of difficult to access α,α-difluoro-β-aminoketones without the need of protecting groups or the use of activated imines. Moreover, we have applied this strategy to create analogues of the dual orexin receptor antagonist, almorexant, in only two synthetic steps.

Copper-Catalyzed Coupling of Acyl Chlorides with gem-Difluorinated Organozinc Reagents via Acyl Dithiocarbamates

A cross-coupling of acyl chlorides with gem-difluorinated organozinc reagents affording difluorinated ketones is described. In the reaction, acyl chlorides are first treated with potassium dithiocarbamate to generate S-acyl dithiocarbamates, which couple with organozincs in the presence of a copper(I) catalyst.

Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease

HIV-1 Protease (HIV-1 PR) is one of the three enzymes essential for the replication process of HIV-1 virus, which explains why it has been the main target for design of drugs against acquired immunodeficiency syndrome (AIDS). This work is focused on exploring the proteolysis reaction catalyzed by HIV-1 PR, with special attention to the dynamic and electrostatic effects governing its catalytic power. Free energy surfaces for all possible mechanisms have been computed in terms of potentials of mean force (PMFs) within hybrid QM/MM potentials, with the QM subset of atoms described at semiempirical (AM1) and DFT (M06-2X) level. The results suggest that the most favorable reaction mechanism involves formation of a gem-diol intermediate, whose decomposition into the product complex would correspond to the rate-limiting step. The agreement between the activation free energy of this step with experimental data, as well as kinetic isotope effects (KIEs), supports this prediction. The role of the protein dynamic was studied by protein isotope labeling in the framework of the Variational Transition State Theory. The predicted enzyme KIEs, also very close to the values measured experimentally, reveal a measurable but small dynamic effect. Our calculations show how the contribution of dynamic effects to the effective activation free energy appears to be below 1 kcal·mol^-1. On the contrary, the electric field created by the protein in the active site of the enzyme emerges as being critical for the electronic reorganization required during the reaction. These electrostatic properties of the active site could be used as a mold for future drug design.

Drug resistance mechanisms of three mutations V32I, I47V and V82I in HIV-1 protease toward inhibitors probed by molecular dynamics simulations and binding free energy predictions

Molecular dynamics simulation and binding free energy calculations were used to probe drug resistance of HIV-1 protease mutations toward inhibitors.

Organocatalytic enantioselective Mukaiyama–Mannich reaction of fluorinated enol silyl ethers and cyclic N-sulfonyl ketimines

The first catalytic asymmetric Mukaiyama–Mannich reaction of fluorinated silyl enol ethers and ketimines is developed, allowing highly enantioselective synthesis of benzosultam based β-fluorinated C^α-tetrasubstituted α-amino acid derivatives.

Designing Fluorescent Peptide Sensors with Dual Specificity for the Detection of HIV-1 Protease

HIV-1 protease is a key enzyme in the life cycle of HIV/AIDS, as it is responsible for the formation of the mature virus particle. We demonstrate here that phage-display peptides raised against this enzyme can be used as peptide sensors for the detection of HIV-1 protease in a simple, one-pot assay. The presence of the enzyme is detected through an energy transfer between two peptide sensors when simultaneously complexed with the target protein. The multivalent nature of this assay increases the specificity of the detection by requiring all molecules to be interacting in order for there to be a FRET signal. We also perform molecular dynamics simulations to explore the interaction between the protease and the peptides in order to guide the design of these peptide sensors and to understand the mechanisms which cause these simultaneous binding events. This approach aims to facilitate the development of new assays for enzymes that are not dependent on the cleavage of a substrate and do not require multiple washing steps.

Halogenative difluorohomologation of ketones

A method for the difluorohomologation of ketones accompanied by halogenation of a C-H bond is described. The reaction involves silylation, difluorocarbene addition using Me3SiCF2Br activated by a bromide ion, and halogenation of intermediate cyclopropanes with N-bromo- or N-iodosuccinimide. The whole process is performed without isolation of intermediates. The resulting α,α-difluoro-β-halo-substituted ketones can be readily converted into fluorine containing pyrazole derivatives and oxetanes.

A highly efficient Mukaiyama–Mannich reaction of N-Boc isatin ketimines and other active cyclic ketimines using difluoroenol silyl ethers catalyzed by Ph3PAuOTf

A Ph₃PAuOTf catalyzed highly efficient reaction of difluoroenoxysilanes and active ketimines is reported, which represents the first Au(i)-catalyzed Mukaiyama–Mannich reaction.