Low-energy Conformations Research Articles

Characterization and conformational analysis of a novel hydrazonoyltetrazole: Crystallographic and theoretical investigations of an unexpected reaction product

A new hydrazonoyltetrazole was isolated as a byproduct from a previously reported reaction, and characterized by 1H and 13C NMR spectroscopy, infrared spectroscopy, single-crystal X-ray diffraction, and high-resolution mass spectroscopy. Intermolecular interactions in the crystal state were examined by Hirshfeld surface analysis (HSA), 2D fingerprint plots, and noncovalent interaction analysis (NCI). Geometry optimization in the gaseous phase was executed at the ωB97X-D4/def2-TZVPP level of theory, and subsequent maps of molecular electrostatic potential (MEP) were generated and analyzed. The calculated MEP was in good agreement with the HSA and NCI results. Conformational analysis was performed using a CREST/CENSO protocol. Two low-energy solution conformers were obtained. To confirm the presence of the second conformer, 1H NMR spectra were calculated, the transition state connecting the two conformers was found, and their energies were obtained with the DLPNOCCSD(T) scheme. A barrier of only 4 kcal mol-1 was found between them, and their MEP maps were also created. The dispersion energies between fragments of the three structures were calculated using the local energy decomposition (LED) scheme.

Multiple Parameter Replica Exchange Gaussian Accelerated Molecular Dynamics for Enhanced Sampling and Free Energy Calculation of Biomolecular Systems.

This study introduces a novel method named multiple parameter replica exchange Gaussian accelerated molecular dynamics (MP-Rex-GaMD), building on the Gaussian accelerated molecular dynamics (GaMD) algorithm. GaMD enhances sampling and retrieves free energy information for biomolecular systems by adding a harmonic boost potential to smooth the potential energy surface without the need for predefined reaction coordinates. Our innovative approach advances the acceleration power and energetic reweighting accuracy of GaMD by incorporating a replica exchange algorithm that enables the exchange of multiple parameters, including the GaMD boost parameters of force constant and energy threshold, as well as temperature. Applying MP-Rex-GaMD to the three model systems of dialanine, chignolin, and HIV protease, we demonstrate its superior capability over conventional molecular dynamics and GaMD simulations in exploring protein conformations and effectively navigating various biomolecular states across energy barriers. MP-Rex-GaMD allows users to accurately map free energy landscapes through energetic reweighting, capturing the ensemble of biomolecular states from low-energy conformations to rare high-energy transitions within practical computational time scales.

Riemannian geometry for efficient analysis of protein dynamics data

An increasingly common viewpoint is that protein dynamics datasets reside in a nonlinear subspace of low conformational energy. Ideal data analysis tools should therefore account for such nonlinear geometry. The Riemannian geometry setting can be suitable for a variety of reasons. First, it comes with a rich mathematical structure to account for a wide range of geometries that can be modeled after an energy landscape. Second, many standard data analysis tools developed for data in Euclidean space can be generalized to Riemannian manifolds. In the context of protein dynamics, a conceptual challenge comes from the lack of guidelines for constructing a smooth Riemannian structure based on an energy landscape. In addition, computational feasibility in computing geodesics and related mappings poses a major challenge. This work considers these challenges. The first part of the paper develops a local approximation technique for computing geodesics and related mappings on Riemannian manifolds in a computationally feasible manner. The second part constructs a smooth manifold and a Riemannian structure that is based on an energy landscape for protein conformations. The resulting Riemannian geometry is tested on several data analysis tasks relevant for protein dynamics data. In particular, the geodesics with given start- and end-points approximately recover corresponding molecular dynamics trajectories for proteins that undergo relatively ordered transitions with medium-sized deformations. The Riemannian protein geometry also gives physically realistic summary statistics and retrieves the underlying dimension even for large-sized deformations within seconds on a laptop.

Elucidation of the solution structure of macrocyclic paritaprevir and exploration of its antitumor potential through molecular docking

Macrocyclic molecules have emerged as significant contenders in drug development and supramolecular chemistry. Paritaprevir is a 15-membered macrocycle approved for the treatment of chronic Hepatitis C virus infection. The structural flexibility inherent in paritaprevir enables the presentation of diverse conformational features in solutions, thereby influencing its binding pattern with proteins. In this paper, we investigated the structural characteristics of paritaprevir in protic solvents (methanol and trifluoroethanol) as well as an aprotic solvent (acetonitrile) by using experimental electronic circular dichroism spectra combined with density functional theory calculations. Our study reveals that paritaprevir can adopt different molecular conformations due to its flexible carbon chain and the solvent environment. Conformer B is particularly stable in polar solvents because of the planar hydrophobic interactions between the phenanthridine and methylpyrazine groups. Density functional theory calculations-assisted structural analyses further disclosed the weak noncovalent interactions within the stable conformations of paritaprevir. Molecular docking of paritaprevir on different cancer proteins showed that the macrocycle was highly selective against lymphoma, endometrial carcinoma, colorectal cancer, and breast cancer. This suggests that paritaprevir could potentially serve as a promising lead compound for drug design targeting these specific types of cancers. The comparison between the low energy conformation and pharmacophore conformation (docking conformation) indicates that conformer B is the primary pharmacophore conformation of paritaprevir, providing important macrocyclic structural characteristics for future macrocyclic drug development.

Solvent effect, spectral (SERS and UV-Vis) and adsorption analysis of Gliadel (GL) anticancer drug with Ag/Au loaded silica nanocomposites

Drug delivery devices reduce drug molecule toxicity and nanostructure can be used to targeted drug delivery. A quantitative analysis of the interaction behavior of Gliadel (GL) with Ag/Au…SiO2 presented in this study in order to minimize drug molecule toxicity. The stabilized structure with the lowest energy conformer of GL in both the gas/water phases has been examined using potential energy surface (PES) analysis, after which the structure was optimized. In the reactivity study, silver/gold loaded silica nanocomposites formed by GL exhibit an increasing electrophilicity index, giving a characteristic to the systems. UV–Vis. analysis was studied to assess the excited state of the investigated complexes using time-dependent density function theory (TD-DFT) in both gas and water phases. The electron transfer within a molecule is determined by Frontier Molecular Orbitals, or FMOs. The charge distribution within the molecule was examined using a color-coded graphic representation of the molecular electrostatic potential (MEP) map. To the extent that to sort out whether a molecule was desirable for use as a medicine, the drug delivery procedure took into account its absorption, distribution, metabolism, and excretion (ADME) qualities. Finally, molecular docking with the selected proteins was examined using the complexes and pure.

Mechanistic Insights into UV Spectral Changes of Pyruvic Acid and Pyruvate Part 1: Interaction with Water Molecules

We investigate how the UV spectra of pyruvic acid (PA) and pyruvate are impacted by interactions with water molecules. In particular, we would like to understand the mechanistic origin of the blue shift in the n →− π∗ transition. Pyruvic acid is the simplest α-keto organic acid and is common in the environment. We use density functional theory to optimize geometries to determine excitation energies and find that the excitation energies of the two main pyruvic acid conformers and pyruvate blue shift when interacting with 1 to 4 water molecules, both in vacuo and in a solvent. The excitation wavelength is blue-shifted by 0.9-9.2 nm when adding water molecules to the lowest energy conformer of PA. Calculations of the UV spectra of pyruvic acid (PA) and pyruvate are crucial for understanding the impact of the interactions with water molecules.

SPATIAL STRUCTURE OF THE HEPTAPEPTIDE ANALOGUE OF NOCICEPTIN MOLECULE

<p>It is known that nociceptins are a new type of regulatory peptide. Knowledge of these peptide molecules' structural and functional properties is of great practical importance for medicine and pharmacology. Their mechanisms of action are considered anti-opioid. This scientific work is devoted to studying the spatial structure of the heptapeptide H-Phe1-Gly2-Gly3-Phe4-Val5-Gly6-Pro7-OH. It examines the conformational capabilities of this heptapeptide molecule. This neuropeptide molecule is a stable analog of the nociceptin. The biologically active conformation of the peptide molecule, which is realized upon interaction with the receptor, is included in the set of low-energy structures. Therefore, studying the spatial structure of peptide molecules is of great interest. Theoretical conformational analysis about nonvalent, electrostatic, and torsional interactions, the energy of the hydrogen bonds, and a special computer program carried out the calculations. The 10 low-energy conformations of this molecule and the values of the dihedral angles of the main chain and side chains are found, and the energy of the intra- and inter-residue interactions is estimated. It is revealed that low energy conformations of this molecule have the half-folded and folded type of backbone. The side chains of the Phe1 and Phe4 amino acids in low-energy conformations carry out effective interactions and are conformationally labile amino acids; they bring together the regions of the main chain and the side chains of the amino acids included in the heptapeptide. These folded forms bring parts of the backbone and the amino acids' side chains together, resulting in important interactions.</p>

Unveiling the molecular insights of 2-(carboxymethyl) benzoic acid: A density functional theory approach towards structural and biological attributes

Nowadays density functional theory (DFT) is one of the best methods to explore the vibrational modes and structure of the biological system. Quantum mechanical calculations are performed using gas phase and different solvents (DMSO, methanol and water). The derived global reactive parameters, structural and topological study provides the clear insight of the 2-(Carboxymethyl) benzoic acid. Depth studies of DFT proves the existence of hydrogen bonds between donor and acceptor in the compound, which is supportive for the biological applications. In this paper, different experimental and computational simulated FT-IR, FT-Raman, UV–Vis spectral studies are used to explicate vibration assignments of the 2-(Carboxymethyl) benzoic acid. Experimentally observed vibrational frequency is compared with theoretically simulated spectrum. B3LYP method with 6–311++G (d, p) basis set is used in DFT to optimize the 2-(Carboxymethyl)benzoic acid structure. The most stable lower energy conformer is identified using potential energy surface (PES) analysis using Gaussian 16 W software. ESP, HOMO-LUMO, NBO, and QTAIM calculations have evinced an adequate electronic characterization of 2-(Carboxymethyl) benzoic acid. Further, van der Waals and steric interactions among 2-(Carboxymethyl) benzoic acid have been discussed with the help of RDG study. Hirshfeld surface studies establish the existing various interaction among molecules and total packing arrangement of the crystal structure. Due to the high biological activity score, 2-(Carboxymethyl) benzoic acid is a good therapeutic candidate. Lipophilicity analysis of 2-(Carboxymethyl)benzoic acid clearly explicates the bioactivity properties and its effective drug applications. Further, molecular docking investigates that the compound can be used as anticancer medication. The detailed DFT study of the 2-(Carboxymethyl) benzoic acid justified its biological applications of the present communication. The calculated NLO parameters of 2-(Carboxymethyl)benzoic acid evidenced for good efficacy in diverse filed application has been discussed.

Multitargeted molecular docking and dynamics simulation of thymol-based chalcones against cancer protein markers: Synthesis, characterization, and computational study

Cancer prevention has become a significant public health concern in the 21st century, ranking as the second leading cause of global mortality following cardiovascular diseases. Despite prominent advancements in treatment, addressing cancer remains a substantial public health challenge, necessitating precise interventions tailored to diverse cancer types. The targeting of Epidermal Growth Factor Receptor (EGFR) has emerged as a fundamental strategy in modern cancer therapy due to its critical role in oncogenesis. Chalcones, a subclass of flavonoids, are promising anticancer agents due to their ability to target multiple cellular pathways implicated in cancer progression. The presence of α, β-unsaturated carbonyl moiety is a key structural feature attributed to their biological activity. This study presents an efficient synthesis approach for chalcone derivatives 4a-f designed from natural thymol. The synthesized compounds were further characterized by HRMS, 1H and 13C NMR spectral data, and further evaluated for in silico studies through molecular docking, molecular dynamic simulation, and ADMET screening. All the designed compounds 4a-f displayed favourable physicochemical properties and ADMET profiles. Molecular docking revealed favourable interactions between compounds 4a-f and the EGFR target protein. Compound 4d (p-nitro) and 4b (p-methyl) showed the more favourable docking score with low energy conformation (-8.02 kcal/mol), (-7.42 kcal/mol) respectively compared to the standard drug Gefitinib. Molecular dynamic simulations confirmed the stability of compounds 4d and 4b, exhibiting consistent structural stability in ligand-protein complexes throughout the 100 ns simulation. Acceptable RMSF values for amino acid residues indicated structural integrity and a stable protein-ligand interaction. The study identified 4d and 4b as promising leads for targeting EGFR.

Does Aromaticity Play a Role in Electronic and Structural Properties of YBn (n=2-14) Clusters?

Nanoclusters exhibit electronic, optical, and magnetic properties that differ significantly from those of extended and molecular systems with comparable stoichiometries. In this work, we examined the structural, energetic, and electronic characteristics of yttrium-doped boron clusters (YBn, where n ranges from 2 to 14) with the aid of robust wavefunction analysis tools. Special emphasis is placed on the elucidation of the potential aromatic character exhibited by the resultant molecules and how it can affect their chemical bonding and stability. Our results revealed that the YBn stability is governed by the maximization of the ionic Y-B interactions. This circumstance is evidenced from the lowest-energy conformations, which manifest as half-sandwich structures wherein the majority of boron atoms are bonded to yttrium. The stabilization of such chemical contacts comes at the expense of a notorious depletion of the Y local electron density, crystallizing in a considerable ionic character, close to Y2++ . Such a prominent charge transfer is coupled to the enhancement of the electron delocalization within the Bn lattice, resulting in quite remarkable local and global aromatic characters. Altogether, this study shows how the toolkit of real space chemical bonding descriptors can offer valuable insights into the structural and electronic properties, along with the chemical bonding, of YBn clusters, contributing to a more comprehensive understanding of their behavior.

N···C═O n → π* Interaction: Gas-Phase Electronic and Vibrational Spectroscopy Combined with Quantum Chemistry Calculations.

Herein, we have used gas-phase electronic and vibrational spectroscopic techniques for the first time to study the N···C═O n → π* interaction in ethyl 2-(2-(dimethylamino) phenyl) acetate (NMe2-Ph-EA). We have measured the electronic spectra of NMe2-Ph-EA in the mass channels of its two distinct fragments of m/z = 15 and 192 using a resonant two-photon ionization technique as there was extensive photofragmentation of NMe2-Ph-EA. Identical electronic spectra obtained in the mass channels of both fragments confirm the dissociation of NMe2-Ph-EA in the ionic state, and hence, the electronic spectrum of the fragment represents that of NMe2-Ph-EA only. UV-UV hole-burning spectroscopy proved the presence of a single conformer of NMe2-Ph-EA in the experiment. Detailed quantum chemistry calculations reveal the existence of a N···C═O n → π* interaction in all six low-energy conformers of NMe2-Ph-EA. A comparison of the IR spectrum of NMe2-Ph-EA acquired from the gas-phase experiment with those obtained from theoretical calculations indicates that the experimentally observed conformer has a N···C═O n → π* interaction. The present finding might be further valuable in drug design and their recognition based on the N···C═O n → π* interaction.

Competitive Intramolecular Hydrogen Bonding: Offering Molecules a Choice.

The conformational preferences of N-((6-methylpyridin-2-yl)carbamothioyl)benzamide were studied in solution, the gas phase and the solid state via a combination of NMR, density functional theory (DFT) and single crystal X-ray techniques. This acyl thiourea derivative can adopt two classes of low energy conformation, each stabilized by a different 6-membered intramolecular hydrogen bond (IHB) pseudoring. Analysis in different solvents revealed that the conformational preference of this molecule is polarity dependent, with increasingly polar environments yielding a higher proportion of the minor conformer containing an NH⋅⋅⋅N IHB. The calculated barrier to interconversion is consistent with dynamic behaviour at room temperature, despite the propensity of 6-membered IHB pseudorings to be static. This work demonstrates that introducing competitive IHB pathways can render static IHBs more dynamic and that such systems could have potential as chameleons in drug design.

Invariant point message passing for protein side chain packing.

Protein side chain packing (PSCP) is a fundamental problem in the field of protein engineering, as high-confidence and low-energy conformations of amino acid side chains are crucial for understanding (and designing) protein folding, protein-protein interactions, and protein-ligand interactions. Traditional PSCP methods (such as the Rosetta Packer) often rely on a library of discrete side chain conformations, or rotamers, and a forcefield to guide the structure to low-energy conformations. Recently, deep learning (DL) based methods (such as DLPacker, AttnPacker, and DiffPack) have demonstrated state-of-the-art predictions and speed in the PSCP task. Building off the success of geometric graph neural networks for protein modeling, we present the Protein Invariant Point Packer (PIPPack) which effectively processes local structural and sequence information to produce realistic, idealized side chain coordinates using -angle distribution predictions and geometry-aware invariant point message passing (IPMP). On a test set of ∼1400 high-quality protein chains, PIPPack is highly competitive with other state-of-the-art PSCP methods in rotamer recovery and per-residue RMSD but is significantly faster.

Effect of chalcogen atoms on the electronic band gaps of the quinoxaline containing donor-acceptor-donor type semiconducting polymers: a systematic DFT investigation.

Due to the widely known positive contributions of the quinoxaline group in organic semiconductors, we conducted a fully computational study using quantum mechanical methods to investigate the effect of quinoxaline in the electron acceptor unit with the combination of different chalcogen atoms on the band gap of a series of donor-acceptor-donor type conjugated polymers. Using density functional theory, we mainly calculated the electronic band gap values of the structures containing four different chalcogen atoms (O, S, Se, and Te) in the electron donor and acceptor units. While chalcogendiazoloquinoxaline groups were used as the electron acceptor units, furan, thiophene, selenophene, and tellurophene were used as the donor units. Our theoretical results showed that the use of heavy chalcogen atoms in both donor and acceptor units resulted in a low band gap. Besides this, the effect of heavy chalcogen atoms used in the electron donor units is much more pronounced compared to the ones used in the acceptor units. More importantly, our findings proved that the inclusion of the chalcogendiazoloquinoxaline group instead of benzochalcogenadiazole as the acceptor unit significantly decreases the electronic band gap of the conjugated polymer. The lowest band gap was found to be 0.10eV for the 4,9-di(tellurophen-2-yl)-[1,2,5]telluradiazolo[3,4-g]quinoxaline polymer. Conformational analysis of the monomers and their corresponding oligomers was performed at the B3LYP/LANL2DZ level of theory. Then, long-range corrected hybrid functional LC-BLYP in a combination with the LANL2DZ basis set was utilized for the calculation of electronic properties and HOMO and LUMO energy gaps of monomers and oligomers through the reoptimization of the lowest energy conformers obtained from the B3LYP/LANL2DZ calculations in the previous step. All energy minimum structures were confirmed through vibrational frequency analysis at both calculation levels. The Gaussian 09 rev. D.01 software was used for all calculations, and GaussView 5.0.9 for visualizations.

ТЕОРЕТИЧЕСКОЕ ИССЛЕДОВАНИЕ N1H ТАУТОМЕРА КАРНОЗИНА В ЦВИТТЕРИОННОЙ ФОРМЕ

. In the present work, the spatial and electronic structures of the lowest energy conformation of the carnosine N1H tautomer in the zwitterionic form, which has a wide range of applications, have been studied. The calculations were performed by the DFT quantum-chemical method based on the B3LYP hybrid functional and the 6-31+G(d,p) basis set in gas, water, and DMSO using the Gaussian 09 and GaussView 6.0.16 programs. The geometry parameters, values of electronic energy, dipole moments, values of partial charges on atoms, HOMO and LUMO energies, descriptors of reactivity of a molecule were calculated and NBO analysis is carried out. The molecular electrostatic potential (MEP) maps and frontier orbitals were visualized. The structural and electronic rearrangements in the molecule and changes in various parameters depending on the dielectric constant of the medium were analyzed. It was found that the influence of the solvent does not play a significant role for this structure, very similar results were obtained for the aqueous medium and DMSO. However, the optimization of the geometry of this carnosine zwitterion tautomer in the gas phase, led to the elimination of the hydrogen atom from the terminal NH3+ group and its addition to the COO- group, actually converting the zwitterionic form into a neutral one.

A novel Imidazo[1,2-a]pyridine derivative modulates active KRASG12D through off-like conformational shifts in switch-I and switch-II regions, mimicking inactive KRASG12D

KRASG12D are the most prevalent oncogenic mutations and a promising target for solid tumor therapies. However, its inhibition exhibits tremendous challenge due to the necessity of high binding affinity to obviate the need for covalent binders. Here we report the evidence of a novel class of Imidazo[1,2-a]pyridine derivative as potentially significant novel inhibitors of KRASG12D, discovered through extensive ligand-based screening against 2-[(2R)-piperidin-2-yl]-1H-indole, an important scaffold for KRASG12D inhibition via switch-I/II (S-I/II) pocket. The proposed compounds exhibited similar binding affinities and overlapped pose configurations to 2-[(2R)-piperidin-2-yl]-1H-indole, serving as a reliable starting point for drug discovery. Comparative free energy profiles demonstrated that C4 [2-methyl-3-((5-phenyl-1H-1,2,4-triazol-3-yl)methyl)imidazo[1,2-a]pyridine] effectively shifted the protein to a stable low-energy conformation via a prominent transition state. The conformational changes across the transition revealed the conformational shift of switch-I and II to a previously known off-like conformation of inactive KRASG12D with rmsd of 0.91 Å. These conformations were even more prominent than the privileged scaffold 2-[(2R)-piperidin-2-yl]-1H-indole. The representative structure overlay of C4 and another X-ray crystallography solved BI-2852 bound inactive KRASG12D revealed that Switch-I and II exhibited off-like conformations. The cumulative variance across the first eigenvalue that accounted for 57 % of the collective variance validated this on-to-off transition. In addition, the relative interaction of C4 binding showed consistent patterns with BI-2852. Taken together, our results support the inhibitory activity of [2-methyl-3-((5-phenyl-1H-1,2,4-triazol-3-yl)methyl)imidazo[1,2-a]pyridine] by shifting active KRASG12D to an inactive conformation.

Molecular modeling and simulation approaches to characterize potential molecular targets for burdock inulin to instigate protection against autoimmune diseases.

In the current study, we utilized molecular modeling and simulation approaches to define putative potential molecular targets for Burdock Inulin, including inflammatory proteins such as iNOS, COX-2, TNF-alpha, IL-6, and IL-1β. Molecular docking results revealed potential interactions and good binding affinity for these targets; however, IL-1β, COX-2, and iNOS were identified as the best targets for Inulin. Molecular simulation-based stability assessment demonstrated that inulin could primarily target iNOS and may also supplementarily target COX-2 and IL-1β during DSS-induced colitis to reduce the role of these inflammatory mechanisms. Furthermore, residual flexibility, hydrogen bonding, and structural packing were reported with uniform trajectories, showing no significant perturbation throughout the simulation. The protein motions within the simulation trajectories were clustered using principal component analysis (PCA). The IL-1β-Inulin complex, approximately 70% of the total motion was attributed to the first three eigenvectors, while the remaining motion was contributed by the remaining eigenvectors. In contrast, for the COX2-Inulin complex, 75% of the total motion was attributed to the eigenvectors. Furthermore, in the iNOS-Inulin complex, the first three eigenvectors contributed to 60% of the total motion. Furthermore, the iNOS-Inulin complex contributed 60% to the total motion through the first three eigenvectors. To explore thermodynamically favorable changes upon mutation, motion mode analysis was carried out. The Free Energy Landscape (FEL) results demonstrated that the IL-1β-Inulin achieved a single conformation with the lowest energy, while COX2-Inulin and iNOS-Inulin exhibited two lowest-energy conformations each. IL-1β-Inulin and COX2-Inulin displayed total binding free energies of - 27.76kcal/mol and - 37.78kcal/mol, respectively, while iNOS-Inulin demonstrated the best binding free energy results at - 45.89kcal/mol. This indicates a stronger pharmacological potential of iNOS than the other two complexes. Thus, further experiments are needed to use inulin to target iNOS and reduce DSS-induced colitis and other autoimmune diseases.

ELECTRONIC PARAMETERS OF CONFORMATIONAL STATES OF ABETA-AMYLOID PEPTIDE (25-35)

ELECTRONIC PARAMETERS OF CONFORMATIONAL STATES OF ABETA-AMYLOID PEPTIDE (25-35)

КОНФОРМАЦИОННЫЕ СВОЙСТВА И ЭЛЕКТРОННАЯ СТРУКТУРА ПРОТИВООПУХОЛЕВОГО АГЕНТА TYR-SER-LEU

Molecular modeling methods were used to study the features of the spatial and electronic structure of the antitumor tripeptide YSL (Tyr-Ser-Leu), developed by Chinese scientists. The conformational analysis of the molecule revealed a limited set of its energetically preferable conformational states in a certain range of relative energy. The nature of the forces stabilizing the low-energy conformations of the tripeptide molecule was determined. As a result of the study, the energetically preferable ranges of dihedral angles, the energy contributions of interresidual interactions and hydrogen bonds, as well as the mutual arrangement of residues and their side chains in low-energy conformations of the tripeptide were also determined. Using the methods of molecular mechanics, the energy contributions of intramolecular interactions in low-energy conformational states of the molecule were obtained. Based on quantum-chemical calculations, the distribution of electron density and the values of dipole moments of the most optimal spatial structures of the YSL tripeptide molecule were determined. The reactivity of the tripeptide was also studied by quantum chemical calculations based on the obtained electronic characteristics of each low-energy conformation of the molecule. Using the calculated coordinates of the atoms of the energetically preferable structures of the molecule, their molecular models were built, the comparison of which makes it possible to identify the structural criteria necessary to create a drug suitable for clinical use.

СТРУКТУРНАЯ ОРГАНИЗАЦИЯ МОЛЕКУЛ СОЙМОРФИНОВ

The conformational capabilities of soymorphine-5 (Thr1-Pro2-Phe3-Val4-Val5-NH2), soymorphine-6 (Tyr1-Pro2-Phe3-Val4-Val5-Asn6-NH2) and soymorphine-7 (Tyr1- Pro2-Tyr3-Val4-Val5-Asn6-Ala7-NH2) molecules have been studied by the method of theoretical conformational analysis. The potential function of the system is chosen as the sum of non-valence, electrostatic and torsion interactions and the energy of hydrogen bonds. The low-energy conformations of soymorphine-5, soymorphine-6 and soymorphine-7 molecules were found, the dihedral angles of the main and side chains of amino acid residues that make up the molecule were found, and the energy of intra- and interresidual interactions was estimated. Thus, the spatial structure of soymorphine-5, soymorphine-6 and soymorphine-7 molecules can be represented by eight structural types. It can be assumed that the molecules perform their physiological functions in these structures. Comparison of the low-energy structures of soymorphins shows that in all molecules the first four low-energy conformations are representatives of the structural types efef, efee, efff, effe for soymorphine-5, effff, efeff, efffe, effee for soymorphine-6, efffff, efeffe, efffef, effeee for soymorphine-6. soymorphine-7. On the basis of these structures, it is possible to propose their artificial analogues for synthesis. It was shown that the spatial structure of soymorphine-5, soymorphine-6 and soymorphine-7 molecules is represented by the conformations of eight shapes of the peptide skeleton. The results obtained can be used to elucidate the structural and structural-functional organization of soymorphine molecules.