Water Plays a Cocatalytic Role in Epoxide Ring Opening Reaction in Aspartate Proteases: A QM/MM Study

Comprehending the Structure, Dynamics, and Mechanism of Action of Drug-Resistant HIV Protease

Since the emergence of the Human Immunodeficiency Virus (HIV) in the 1980s, strategies to combat HIV-AIDS are continuously evolving. Among the many tested targets to tackle this virus, its protease enzyme (PR) was proven to be an attractive option that brought about numerous research publications and ten FDA-approved drugs to inhibit the PR activity. However, the drug-induced mutations in the enzyme made these small molecule inhibitors ineffective with prolonged usage. The research on HIV PR, therefore, remains a thrust area even today. Through this review, we reiterate the importance of understanding the various structural and functional components of HIV PR in redesigning the structure-based small molecule inhibitors. We also discuss at length the currently available FDA-approved drugs and how these drug molecules induced mutations in the enzyme structure. We then recapitulate the reported mechanisms on how these drug-resistant variants remain sufficiently active to cleave the natural substrates. We end with the future scope covering the recently proposed strategies that show promise to deal with the mutations.

Cobalt complexes with α-amino acid ligands catalyze the incorporation of CO2 into cyclic carbonates

Arguably one of the largest research areas involving carbon dioxide (CO₂) fixation is the coupling of CO₂ to epoxides to form cyclic carbonates and polycarbonates. In this sense, there is an ever-increasing demand for the development of higher-performing catalytic systems that could counterbalance sustainability and energy efficiency in the production of cyclic carbonates. The use of abundant first-row transition metals combined with naturally occurring amino acids may be an ideal catalytic platform to fulfill this demand. Nevertheless, detailed information on the interactions between metal centers and natural products as catalysts in this transformation is lacking. Here a series of Co(III) amino acid catalysts operating in a binary system showed outstanding performance for the coupling reaction of epoxides and CO₂. Nine new complexes of the type trans(N)-[Co(aa)₂(bipy)]Cl (aa: ala, asp, lys, met, phe, pro, ser, tyr, and val) were used to explore the structure-activity relationship influenced by the complex outer coordination sphere, and its effect on the catalytic activity in the coupling reaction of CO₂ and epoxides.

Structural Insights into the Antiparallel G-Quadruplex in the Presence of K+ and Mg2+ Ions

G-Quadruplex (GQ) is a secondary structural unit of DNA, formed at the telomere region of the chromosome with a high guanine content. It is reported that the GQs can hinder many biological processes. Thus, research thrives to explore the structural stability of GQs. Studies based on circular dichroism (CD) and nuclear magnetic resonance (NMR) experiments established the vital role of cations such as K⁺ and Mg²⁺ in the stability of antiparallel G-quadruplexes (AGQs). However, there is a need to understand how stability in AGQ is attained in the presence of cations. Here, we employed molecular dynamics (MD) simulations, steered MD (SMD) simulations, and QM/MM calculations to understand the biophysical and electronic bases of the stability imparted to AGQs via cation binding. Our results showed that Mg²⁺ prefers to bind in the plane with the guanine tetrad, whereas K⁺ binds in between the AGQ tetrads. Thus, three Mg²⁺ cations or two K⁺ ions are needed to stabilize an AGQ molecule, where each and every tetrad binds to Mg²⁺ more robustly with a higher binding affinity. SMD revealed that the traversal of K⁺ through the AGQ central channel required less force than that of Mg²⁺, illustrating the presence of more strong interactions between Mg²⁺ and AGQ tetrads compared to K⁺. The stabilization in the AGQ tetrads due to cation binding is reassessed by employing ab initio simulations. Mixed QM/MM calculations confirmed that Mg²⁺ binds strongly to AGQ compared to K⁺, and it induces higher interactions between the guanine tetrads. However, K⁺ binding to AGQ induces a higher stabilization energy than Mg²⁺ binding to AGQ tetrads. Despite the higher binding energy, Mg²⁺ binding imparts lower stabilization to AGQ due to its unfavorable fermionic quantum energy.

Mechanism of darunavir binding to monomeric HIV-1 protease: a step forward in the rational design of dimerization inhibitors

HIV protease (HIVPR) is a key target in AIDS therapeutics. All ten FDA-approved drugs that compete with substrates in binding to this dimeric enzyme's active site have become ineffective due to the emergence of drug resistant mutants. Blocking the dimerization interface of HIVPR is thus being explored as an alternate strategy. The latest drug, darunavir (DRV), which exhibited a high genetic barrier to viral resistance, is said to have a dual mode of action - (i) binding to the dimeric active site, and (ii) preventing the dimerization by binding to the HIVPR monomer. Despite several reports on DRV complexation with dimeric HIVPR, the mode and mechanism of the binding of DRV to the HIVPR monomer are poorly understood. In this study, we utilized all-atomic MD simulations and umbrella sampling techniques to identify the best possible binding mode of DRV to the monomeric HIVPR and its mechanism of association. The results suggest that DRV binds between the active site and the flap of the monomer, and the flap plays a crucial role in directing the drug to bind and driving the other protein domains to undergo induced fit changes for stronger complexation. The obtained binding mode of DRV was validated by comparing with various mutational data from clinical isolates to reported in vitro mutations. The identified binding pose was also able to successfully reproduce the experimental K_i value in the picomolar range. The residue-level information extracted from this study could accelerate the structure-based drug designing approaches targeting HIVPR dimerization.

Mechanistic and thermodynamic characterization of oxathiazolones as potent and selective covalent immunoproteasome inhibitors

The ubiquitin–proteasome system is responsible for the degradation of proteins and plays a critical role in key cellular processes. While the constitutive proteasome (cPS) is expressed in all eukaryotic cells, the immunoproteasome (iPS) is primarily induced during disease processes, and its inhibition is beneficial in the treatment of cancer, autoimmune disorders and neurodegenerative diseases. Oxathiazolones were reported to selectively inhibit iPS over cPS, and the inhibitory activity of several oxathiazolones against iPS was experimentally determined. However, the detailed mechanism of the chemical reaction leading to irreversible iPS inhibition and the key selectivity drivers are unknown, and separate characterization of the noncovalent and covalent inhibition steps is not available for several compounds. Here, we investigate the chemical reaction between oxathiazolones and the Thr1 residue of iPS by quantum mechanics/molecular mechanics (QM/MM) simulations to establish a plausible reaction mechanism and to determine the rate-determining step of covalent complex formation. The modelled binding mode and reaction mechanism are in line with the selective inhibition of iPS versus cPS by oxathiazolones. The k_inact value of several ligands was estimated by constructing the potential of mean force of the rate-determining step by QM/MM simulations coupled with umbrella sampling. The equilibrium constant K_i of the noncovalent complex formation was evaluated by classical force field-based thermodynamic integration. The calculated K_i and k_inact values made it possible to analyse the contribution of the noncovalent and covalent steps to the overall inhibitory activity. Compounds with similar intrinsic reactivities exhibit varying selectivities for iPS versus cPS owing to subtle differences in the binding modes that slightly affect K_i, the noncovalent affinity, and importantly alter k_inact, the covalent reactivity of the bound compounds. A detailed understanding of the inhibitory mechanism of oxathiazolones is useful in designing iPS selective inhibitors with improved drug-like properties.

Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies

Experimental evidence for enzymatic mechanisms is often scarce, and in many cases inadvertently biased by the employed methods. Thus, apparently contradictory model mechanisms can result in decade long discussions about the correct interpretation of data and the true theory behind it. However, often such opposing views turn out to be special cases of a more comprehensive and superior concept. Molecular dynamics (MD) and the more advanced molecular mechanical and quantum mechanical approach (QM/MM) provide a relatively consistent framework to treat enzymatic mechanisms, in particular, the activity of proteolytic enzymes. In line with this, computational chemistry based on experimental structures came up with studies on all major protease classes in recent years; examples of aspartic, metallo-, cysteine, serine, and threonine protease mechanisms are well founded on corresponding standards. In addition, experimental evidence from enzyme kinetics, structural research, and various other methods supports the described calculated mechanisms. One step beyond is the application of this information to the design of new and powerful inhibitors of disease-related enzymes, such as the HIV protease. In this overview, a few examples demonstrate the high potential of the QM/MM approach for sophisticated pharmaceutical compound design and supporting functions in the analysis of biomolecular structures.

Hydrogen bonding catalysis by water in epoxide ring opening reaction

Water can act as catalyst is perhaps the most intriguing property reported of this molecule in the last decade. However, despite being an integral part of many enzyme structures, the role of water in catalyzing enzymatic reactions remains sparsely studied. In a recent study, we have shown that the epoxide ring opening in aspartate proteases follows a two-step process involving water. In this work, we attempt to unravel the electronic basis of the co-catalytic role of water in the epoxide ring opening reaction by employing high-level quantum mechanical calculations at M06-2X/6-31+G(d,p) level of accuracy. Our computed electron density and its reduced gradient show that water anchor the reactant molecules through strong H-bond bridges. In addition, the strong ionizing power of water allows better charge delocalization to stabilize the transition states and oxyanion intermediate. Electrostatic analyses suggest greater charge transfer from the aspartates to the epoxide in the transition state, which is found to be exergonic in nature rendering a low-barrier reaction compared to a control system where water was omitted in the reaction field. This elucidated mechanism at electronic level could promote further research to search for the co-catalytic role of water in other enzymes.

Understanding the mechanism of HIV-1 protease inhibition by monoclonal antibodies

HIV-1 protease is an essential enzyme in the life cycle of human immunodeficiency virus (HIV) and hence is one of the most important targets for antiviral drug design. Although there are ten FDA approved drugs against HIV protease (PR), their long term usage elicits mutations leading to drug resistance. As a result, novel therapeutic approaches are being explored including synthetic antibodies. Recently, a murine monoclonal antibody, mAB1696 (mAB) was reported to inhibit PR by preventing dimerization. Crystallographic data could reveal only six protease residues that interact with mAB. The present study employs a range of computational techniques, starting from protein-protein docking to all-atomic molecular dynamics simulations to generate plausible 3D structures of PR-mAB complex. Results show that mAB interacts very strongly with several PR dimer interface residues, such as Gln7, Arg8 (N-terminal), Cys95, Leu97 (C-terminal), Thr26, Gly27 (active site), Gly49, Ile50 (flap), apart from its interactions with the PR epitope region, Pro1-Trp6 (N-terminal). These observations support the hypothesis that binding of mAB prevents the dimerization of PR. The interactions and binding conformations identified in this study could form the basis for designing allosteric inhibitors preventing the dimerization of HIV-1 Protease.

Application of Quantum Computing to Biochemical Systems: A Look to the Future

Chemistry is considered as one of the more promising applications to science of near-term quantum computing. Recent work in transitioning classical algorithms to a quantum computer has led to great strides in improving quantum algorithms and illustrating their quantum advantage. Because of the limitations of near-term quantum computers, the most effective strategies split the work over classical and quantum computers. There is a proven set of methods in computational chemistry and materials physics that has used this same idea of splitting a complex physical system into parts that are treated at different levels of theory to obtain solutions for the complete physical system for which a brute force solution with a single method is not feasible. These methods are variously known as embedding, multi-scale, and fragment techniques and methods. We review these methods and then propose the embedding approach as a method for describing complex biochemical systems, with the parts not only treated with different levels of theory, but computed with hybrid classical and quantum algorithms. Such strategies are critical if one wants to expand the focus to biochemical molecules that contain active regions that cannot be properly explained with traditional algorithms on classical computers. While we do not solve this problem here, we provide an overview of where the field is going to enable such problems to be tackled in the future.