Influence of Disulfide Connectivity, Electrostatics, and Hydrophobicity on the Conformational Variations of α-Conotoxin GI Single-Disulfide Analogues: Simulations with Polarizable Force Field

Synthesis of the Most Potent Isomer of μ-Conotoxin KIIIA Using Different Strategies

In the chemical synthesis of conotoxins with multiple disulfide bonds, the oxidative folding process can result in diverse disulfide bond connectivities, which presents a challenge for determining the natural disulfide bond connectivities and leads to significant structural differences in the synthesized toxins. Here, we focus on KIIIA, a μ-conotoxin that has high potency in inhibiting Nav1.2 and Nav1.4. The non-natural connectivity pattern (C1-C9, C2-C15, C4-C16) of KIIIA exhibits the highest activity. In this study, we report an optimized Fmoc solid-phase synthesis of KIIIA using various strategies. Our results indicate that free random oxidation is the simplest method for peptides containing triple disulfide bonds, resulting in high yields and a simplified process. Alternatively, the semi-selective strategy utilizing Trt/Acm groups can also produce the ideal isomer, albeit with a lower yield. Furthermore, we performed distributed oxidation using three different protecting groups, optimizing their positions and cleavage order. Our results showed that prioritizing the cleavage of the Mob group over Acm may result in disulfide bond scrambling and the formation of new isomers. We also tested the activity of synthesized isomers on Nav1.4. These findings provide valuable guidance for the synthesis of multi-disulfide-bonded peptides in future studies.

Treating Polarization Effects in Charged and Polar Bio-Molecules Through Variable Electrostatic Parameters

Polarization plays important roles in charged and hydrogen bonding containing systems. Much effort ranging from the construction of physics-based models to quantum mechanism (QM)-based and machine learning (ML)-assisted models have been devoted to incorporating the polarization effect into the conventional force fields at different levels, such as atomic and coarse grained (CG). The application of polarizable force fields or polarization models was limited by two aspects, namely, computational cost and transferability. Different from physics-based models, no predetermining parameters were required in the QM-based approaches. Taking advantage of both the accuracy of QM calculations and efficiency of molecular mechanism (MM) and ML, polarization effects could be treated more efficiently while maintaining the QM accuracy. The computational cost could be reduced with variable electrostatic parameters, such as the charge, dipole, and electronic dielectric constant with the help of linear scaling fragmentation-based QM calculations and ML models. Polarization and entropy effects on the prediction of partition coefficient of druglike molecules are demonstrated by using both explicit or implicit all-atom molecular dynamics simulations and machine learning-assisted models. Directions and challenges for future development are also envisioned.

Influences of disulfide connectivity on structure and antimicrobial activity of tachyplesin I

Tachyplesin I is a potent antimicrobial peptide with broad spectrum of antimicrobial activity. It has 2 disulfide bonds and can form 3 disulfide bond isomers. In this study, the structure and antimicrobial activity of 3 tachyplesin I isomers (tachyplesin I, 3C12C, 3C7C) were investigated using molecular dynamic simulations, circular dichroism structural study, as well as antimicrobial activity and hemolysis assay. Our results suggest that in comparison to the native peptide, the 2 isomers (3C12C, 3C7C) have substantial structural and activity variations. The native peptide is in the ribbon conformation, while 3C12C and 3C7C possess remarkably different secondary structures, which are referred as "globular" and "beads" isomers, respectively. The substantially decreased hemolysis effects for these 2 isomers is accompanied by significantly decreased anti-gram-positive bacterial activity.

Efficient minimization of multipole electrostatic potentials in torsion space

The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. Most molecular force field development takes place in the context of models with full Cartesian coordinate degrees of freedom. Nevertheless, a number of macromolecular modeling programs use a reduced set of conformational variables limited to rotatable bonds. Efficient algorithms for minimizing the energies of macromolecular systems with torsional degrees of freedom have been developed with the assumption that all atom-atom interaction potentials are isotropic. We describe novel modifications to address the anisotropy of higher order multipole terms while retaining the efficiency of these approaches. In addition, we present a treatment for obtaining derivatives of atom-centered tensors with respect to torsional degrees of freedom. We apply these results to enable minimization of the Amoeba multipole electrostatics potential in a system with torsional degrees of freedom, and validate the correctness of the gradients by comparison to finite difference approximations. In the interest of enabling a complete model of electrostatics with implicit treatment of solvent-mediated effects, we also derive expressions for the derivative of solvent accessible surface area with respect to torsional degrees of freedom.

Host-guest interaction of β-cyclodextrin with isomeric ursolic acid and oleanolic acid: physicochemical characterization and molecular modeling study

Ursolic acid (UA) and oleanolic acid (OA) are insoluble drugs. The objective of this study was to encapsulate them into β-cyclodextrin (β-CD) and compare the solubility and intermolecular force of β-CD with the two isomeric triterpenic acids. The host-guest interaction was explored in liquid and solid state by ultraviolet-visible absorption,1 H NMR, phase solubility analysis, and differential scanning calorimetry, X-ray powder diffractometry, and molecular modeling studies. Both experimental and theoretical studies revealed that β-CD formed 1: 1 water soluble inclusion complexes and the complexation process was naturally favorable. In addition, the overall results suggested that ring E with a carboxyl group of the drug was encapsulated into the hydrophobic CD nanocavity. Therefore, a clear different inclusion behavior was observed, and UA exhibited better affinity to β-CD compared with OA in various media due to little steric interference, which was beneficial to form stable inclusion complex with β-CD and increase its water solubility effectively.

Factor Analysis of Conformations and NMR Signals of Rotaxanes: AIMD and Polarizable MD Simulations

The interlocked ⟨rod | ring⟩ structures of pseudorotaxanes and [2]rotaxanes are usually maintained by the complex hydrogen-bonding (H-bonding) network between the rod and ring. Ab initio molecular dynamics (AIMD) using generalized energy-based fragmentation approach and polarizable force field (polar FF)-based molecular dynamics (MD) simulations were performed to investigate the conformational changes of mechanically interlocked systems and to obtain the ensemble-averaged NMR chemical shifts. Factor analysis (FA) demonstrates that the ring H-donor (2,6 pyridinedicarboxamide group) plays an important role in the ring-rod recognition. In comparison to the conventional fixed-charge force field, the polarization effect is crucial to account for the H-bonding interactions in supramolecular systems. In the hybrid scheme, the polar FF-based MD simulations are used to generate different initial states for the AIMD simulations, which are able to give better prediction of ensemble-averaged NMR signals for chemically equivalent amide protons. The magnitude of the deshielding shift of NMR signal is correlated with the length of hydrogen bond. The polar FF model with variable charges shows that the dipole-dipole interactions between the flexible diethylene glycol chain of ring and polar solvents induce the upfield shifts of NMR signals of rod H-donors and the directional distribution of the neighboring CH3CN solvents.

Assignment of absolute stereostructures through quantum mechanics electronic and vibrational circular dichroism calculations

Elucidation of absolute configuration of chiral molecules including structurally complex natural products remains a challenging problem in organic chemistry. A reliable method for assigning the absolute stereostructure is to combine the experimental circular dichroism (CD) techniques such as electronic and vibrational CD (ECD and VCD), with quantum mechanics (QM) ECD and VCD calculations. The traditional QM methods as well as their continuing developments make them more applicable with accuracy. Taking some chiral natural products with diverse conformations as examples, this review describes the basic concepts and new developments of QM approaches for ECD and VCD calculations in solution and solid states.

Drugs from slugs. Part II--conopeptide bioengineering

The biological transformation of toxins as research probes, or as pharmaceutical drug leads, is an onerous and drawn out process. Issues regarding changes to pharmacological specificity, desired potency, and bioavailability are compounded naturally by their inherent toxicity. These often scuttle their progress as they move up the narrowing drug development pipeline. Yet one class of peptide toxins, from the genus Conus, has in many ways spearheaded the expansion of new peptide bioengineering techniques to aid peptide toxin pharmaceutical development. What has now emerged is the sequential bioengineering of new research probes and drug leads that owe their lineage to these highly potent and isoform specific peptides. Here we discuss the progressive bioengineering steps that many conopeptides have transitioned through, and specifically illustrate some of the biochemical approaches that have been established to maximize their biological research potential and pharmaceutical worth.

Rational design of core-shell molecularly imprinted polymer based on computational simulation and Doehlert experimental optimization: application to the separation of tanshinone IIA from Salvia miltiorrhiza Bunge

Computational simulation and Doehlert experimental optimization were done for the rational design of a core-shell molecularly imprinted polymer (CS-MIP) for use in the highly selective separation of Tanshinone IIA (TSIIA) from the crude extracts of Salvia miltiorrhiza Bunge (SMB). The functional monomer layer of the polymer shells directed the selective occurrence of imprinting polymerization at the surface of silica through the copolymerization of vinyl end groups with functional monomers and also drove TSIIA templates into the formed polymer shells through the charge-transfer complex interactions between TSIIA and the functional monomer layer. As a result, the maximum rebinding capacity was achieved with the use of optimal grafting ratio by the Doehlert design. The CS-MIP exhibited high recognition selectivity and binding affinity to TSIIA. When the imprinted particles were used as dispersive solid phase extraction sorbents, the recovery yield of TSIIA reached 93% by a one-step extraction from the crude extracts of SMB, and the purity of TSIIA was larger than 98% by HPLC analysis. These results show the possibility of a highly selective separation and enrichment of TSIIA from the SMB using the TSIIA-imprinted core-shell molecularly imprinted polymers.