Won Hee Ryu

Lenacapavir (LEN), the first‐in‐class HIV‐1 capsid inhibitor (CAI) with picomolar potency and long pharmacokinetics (PK), is approved for both treatment and pre‐exposure prophylaxis (PrEP). However, the frequently selected M66I mutation confers complete resistance to LEN. Potent antivirals against the M66I variant remain elusive. In this work, we have designed LEN analogs featuring a distinctive R ² moiety to directly address the molecular mechanism of resistance. Our analog synthesis also entailed developing a new synthetic procedure for R ² incorporation. Significantly, the newly designed analogs were highly potent against both WT HIV‐1 and the M66I mutant. Particularly, lead compound 3S conferred 2.6‐fold higher potency than LEN against WT HIV‐1 and remained highly potent (EC ₅₀ = 5.8 nM) against the M66I mutant, a drastically advanced activity profile over LEN (EC ₅₀ > 15 µM). The unprecedented potency of our lead 3S against M66I was corroborated by a thermal shift assay. In a head‑to‑head intravenous (IV) PK study in rats, lead 3S demonstrated superior systemic exposure, showing a 4.6‑fold greater plasma area‐under‐curve (AUC) than LEN and largely retaining the long PK characteristic of LEN. These results strongly validate our design and represent a breakthrough in LEN‐based HIV‐1 therapy and prophylaxis.

Lenacapavir (LEN), the first‐in‐class HIV‐1 capsid inhibitor (CAI) with picomolar potency and long pharmacokinetics (PK), is approved for both treatment and pre‐exposure prophylaxis (PrEP). However, the frequently selected M66I mutation confers complete resistance to LEN. Potent antivirals against the M66I variant remain elusive. In this work, we have designed LEN analogs featuring a distinctive R ² moiety to directly address the molecular mechanism of resistance. Our analog synthesis also entailed developing a new synthetic procedure for R ² incorporation. Significantly, the newly designed analogs were highly potent against both WT HIV‐1 and the M66I mutant. Particularly, lead compound 3S conferred 2.6‐fold higher potency than LEN against WT HIV‐1 and remained highly potent (EC ₅₀ = 5.8 nM) against the M66I mutant, a drastically advanced activity profile over LEN (EC ₅₀ > 15 µM). The unprecedented potency of our lead 3S against M66I was corroborated by a thermal shift assay. In a head‑to‑head intravenous (IV) PK study in rats, lead 3S demonstrated superior systemic exposure, showing a 4.6‑fold greater plasma area‐under‐curve (AUC) than LEN and largely retaining the long PK characteristic of LEN. These results strongly validate our design and represent a breakthrough in LEN‐based HIV‐1 therapy and prophylaxis.

Weighted ensemble (WE) is a path-sampling method that is conceptually simple, widely applicable, and statistically unbiased. In a WE simulation, an ensemble of trajectories is periodically pruned or replicated to enhance the sampling of rare transitions and improve the estimation of mean first-passage times (MFPTs). However, poor choices of the parameters governing pruning and replication can lead to high variance in MFPT estimates. Our previous work [Aristoff et al., J. Chem. Phys. 158, 014108 (2023)] presented an optimal WE parameterization strategy and applied it to low-dimensional example systems. The strategy harnesses estimated local MFPTs from different initial configurations to a single target state. In the present work, we apply the optimal parameterization strategy to more challenging high-dimensional molecular models, namely, synthetic molecular dynamics (MD) models of Trp-cage folding and unfolding, as well as atomistic MD models of NTL9 folding in high-friction and low-friction continuum solvents. In each system, we use WE to estimate the MFPT for folding or unfolding events. We show that the optimal parameterization reduces the variance of MFPT estimates in three of four systems, with a dramatic improvement in the most challenging atomistic system. Overall, the parameterization strategy improves the accuracy and reliability of WE estimates for the kinetics of biophysical processes.

Feynman's imaginary time path integral formalism of quantum statistical mechanics and the corresponding quantum-classical isomorphism provide a tangible way of incorporating nuclear quantum effect (NQE) in the simulation of condensed matter systems using well-developed classical simulation techniques. Our previous work has presented the many-body coarse-graining of path integral (CG-PI) theory that builds an isomorphism between the quantum partition function of N distinguishable particles and the classical partition function of 2N pseudoparticles. In this present work, we develop a generalized version of the many-body CG-PI theory that incorporates many-body interactions in the force field. Based on the new derivation, we provide a numerical CG-PI (n-CG-PI) modeling strategy parametrized from the underlying path integral molecular dynamics (PIMD) trajectories using force matching and Boltzmann inversion. The n-CG-PI models for two liquid systems are shown to capture well both the intramolecular and intermolecular structural correlations of the reference PIMD simulations. The generalized derivation of the many-body CG-PI theory and the n-CG-PI model presented in this work extend the scope of the CG-PI formalism by generalizing the previously limited theory to incorporate force fields of realistic molecular systems.

Feynman’s imaginary time path integral approach to quantum statistical mechanics provides a theoretical formalism for including nuclear quantum effects (NQEs) in simulation of condensed matter systems. Sinitskiy and Voth [J. Chem. Phys. 143, 094104 (2015)] have presented the coarse-grained path integral (CG-PI) theory, which provides a reductionist coarse-grained representation of the imaginary time path integral based on the quantum-classical isomorphism. In this paper, the many-body generalization of the CG-PI theory is presented. It is shown that the N interacting particles obeying quantum Boltzmann statistics can be represented as a system of N pairs of classical-like pseudoparticles coupled to each other analogous to the pseudoparticle pair of the one-body theory. Moreover, we present a numerical CG-PI (n-CG-PI) method applying a simple approximation to the coupling scheme between the pseudoparticles due to numerical challenges of directly implementing the full many-body CG-PI theory. Structural correlations of two liquid systems are investigated to demonstrate the performance of the n-CG-PI method. Both the many-body CG-PI theory and the n-CG-PI method not only present reductionist views of the many-body quantum Boltzmann statistics but also provide theoretical and numerical insight into how to explicitly incorporate NQEs in the representation of condensed matter systems with minimal additional degrees of freedom.