65 research outputs found
What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling
We introduce the self-Relative Binding Free Energy (self-RBFE) approach to
evaluate the intrinsic statistical variance of dual-topology alchemical binding
free energy estimators. The self-RBFE is the relative binding free energy
between a ligand and a copy of the same ligand, and its true value is zero.
Nevertheless, because the two copies of the ligand move independently, the
self-RBFE value produced by a finite-length simulation fluctuates and can be
used to measure the variance of the model. The results of this validation
provide evidence that a significant fraction of the errors observed in
benchmark studies reflect the statistical fluctuations of unconverged estimates
rather than the models' accuracy. Furthermore, we find that ligand
reorganization is a significant contributing factor to the statistical variance
of binding free energy estimates and that metadynamics-accelerated
conformational sampling of torsional degrees of freedom of the ligand can
drastically reduce the time to convergence
Inclusion of Enclosed Hydration Effects in the Binding Free Energy Estimation of Dopamine D3 Receptor Complexes
Confined hydration and conformational flexibility are some of the challenges
encountered for the rational design of selective antagonists of G-protein
coupled receptors. We present a set of C3-substituted (-)-stepholidine
derivatives as potent binders of the dopamine D3 receptor. The compounds are
characterized biochemically, as well as by computer modeling using a novel
molecular dynamics-based alchemical binding free energy approach which
incorporates the effect of the displacement of enclosed water molecules from
the binding site. The free energy of displacement of specific hydration sites
is obtained using the Hydration Site Analysis method with explicit solvation.
This work underscores the critical role of confined hydration and
conformational reorganization in the molecular recognition mechanism of
dopamine receptors and illustrates the potential of binding free energy models
to represent these key phenomena.Comment: This is the first report of using enclosed hydration in estimating
binding free energies of protein-ligand complexes using implicit solvatio
Performance and Analysis of the Alchemical Transfer Method for Binding Free Energy Predictions of Diverse Ligands
The Alchemical Transfer Method (ATM) is herein validated against the relative
binding free energies of a diverse set of protein-ligand complexes. We employed
a streamlined setup workflow, a bespoke force field, and the AToM-OpenMM
software to compute the relative binding free energies (RBFE) of the benchmark
set prepared by Schindler and collaborators at Merck KGaA. This benchmark set
includes examples of standard small R-group ligand modifications as well as
more challenging scenarios, such as large R-group changes, scaffold hopping,
formal charge changes, and charge-shifting transformations. The novel
coordinate perturbation scheme and a dual-topology approach of ATM address some
of the challenges of single-topology alchemical relative binding free energy
methods. Specifically, ATM eliminates the need for splitting electrostatic and
Lennard-Jones interactions, atom mapping, defining ligand regions, and
post-corrections for charge-changing perturbations. Thus, ATM is simpler and
more broadly applicable than conventional alchemical methods, especially for
scaffold-hopping and charge-changing transformations. Here, we performed well
over 500 relative binding free energy calculations for eight protein targets
and found that ATM achieves accuracy comparable to existing state-of-the-art
methods, albeit with larger statistical fluctuations. We discuss insights into
specific strengths and weaknesses of the ATM method that will inform future
deployments. This study confirms that ATM is applicable as a production tool
for relative binding free energy (RBFE) predictions across a wide range of
perturbation types within a unified, open-source framework
3,7-Dihydroxytropolones Inhibit Initiation of Hepatitis B Virus Minus-Strand DNA Synthesis
Initiation of protein-primed (-) strand DNA synthesis in hepatitis B virus (HBV) requires interaction of the viral reverse transcriptase with epsilon (ε), a cis-acting regulatory signal located at the 5’ terminus of pre-genomic RNA (pgRNA), and several host-encoded chaperone proteins. Binding of the viral polymerase (P protein) to ε is necessary for pgRNA encapsidation and synthesis of a short primer covalently attached to its terminal domain. Although we identified small molecules that recognize HBV ε RNA, these failed to inhibit protein-primed DNA synthesis. However, since initiation of HBV (-) strand DNA synthesis occurs within a complex of viral and host components (e.g., Hsp90, DDX3 and APOBEC3G), we considered an alternative therapeutic strategy of allosteric inhibition by disrupting the initiation complex or modifying its topology. To this end, we show here that 3,7-dihydroxytropolones (3,7-dHTs) can inhibit HBV protein-primed DNA synthesis. Since DNA polymerase activity of a ribonuclease (RNase H)-deficient HBV reverse transcriptase that otherwise retains DNA polymerase function is also abrogated, this eliminates direct involvement of RNase (ribonuclease) H activity of HBV reverse transcriptase and supports the notion that the HBV initiation complex might be therapeutically targeted. Modeling studies also provide a rationale for preferential activity of 3,7-dHTs over structurally related α-hydroxytropolones (α-HTs)
Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease
Molecular docking is a powerful tool used in drug discovery and structural biology for predicting the structures of ligand–receptor complexes. However, the accuracy of docking calculations can be limited by factors such as the neglect of protein reorganization in the scoring function; as a result, ligand screening can produce a high rate of false positive hits. Although absolute binding free energy methods still have difficulty in accurately rank-ordering binders, we believe that they can be fruitfully employed to distinguish binders from nonbinders and reduce the false positive rate. Here we study a set of ligands that dock favorably to a newly discovered, potentially allosteric site on the flap of HIV-1 protease. Fragment binding to this site stabilizes a closed form of protease, which could be exploited for the design of allosteric inhibitors. Twenty-three top-ranked protein–ligand complexes from AutoDock were subject to the free energy screening using two methods, the recently developed binding energy analysis method (BEDAM) and the standard double decoupling method (DDM). Free energy calculations correctly identified most of the false positives (≥83%) and recovered all the confirmed binders. The results show a gap averaging ≥3.7 kcal/mol, separating the binders and the false positives. We present a formula that decomposes the binding free energy into contributions from the receptor conformational macrostates, which provides insights into the roles of different binding modes. Our binding free energy component analysis further suggests that improving the treatment for the desolvation penalty associated with the unfulfilled polar groups could reduce the rate of false positive hits in docking. The current study demonstrates that the combination of docking with free energy methods can be very useful for more accurate ligand screening against valuable drug targets
Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses
Background: The development of an effective AIDS vaccine has been a formidable task, but remains a critical necessity. The well conserved membrane-proximal external region (MPER) of the HIV-1 gp41 glycoprotein is one of the crucial targets for AIDS vaccine development, as it has the necessary attribute of being able to elicit antibodies capable of neutralizing diverse isolates of HIV.
Methodology/Principle Findings: Guided by X-ray crystallography, molecular modeling, combinatorial chemistry, and powerful selection techniques, we designed and produced six combinatorial libraries of chimeric human rhinoviruses (HRV) displaying the MPER epitopes corresponding to mAbs 2F5, 4E10, and/or Z13e1, connected to an immunogenic surface loop of HRV via linkers of varying lengths and sequences. Not all libraries led to viable chimeric viruses with the desired sequences, but the combinatorial approach allowed us to examine large numbers of MPERdisplaying chimeras. Among the chimeras were five that elicited antibodies capable of significantly neutralizing HIV-1 pseudoviruses from at least three subtypes, in one case leading to neutralization of 10 pseudoviruses from all six subtypes tested.
Conclusions: Optimization of these chimeras or closely related chimeras could conceivably lead to useful components of an effective AIDS vaccine. While the MPER of HIV may not be immunodominant in natural infection by HIV-1, its presence in a vaccine cocktail could provide critical breadth of protection
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