Non-covalent interactions involving halogenated derivatives of capecitabine and thymidylate synthase: a computational approach

Exploring Monomer-Amino Acid Interactions in Mimicking Mips for PSA Detection-Using the Novel MBASM Approach

Given the rising incidence of prostate cancer (PCa), there is an increasing demand for cost-effective and reliable methods for early detection using the prostate-specific antigen (PSA) biomarker. PCa remains a leading cause of mortality among individuals with prostates aged 55-80 years. Molecularly Imprinted Polymers (MIPs) represent a promising solution due to their selectivity, sensitivity, and stability for PSA detection. However, the synthesis of MIPs for protein targets presents significant challenges, particularly in the rational selection of functional monomers and cross-linkers. This study introduces a theoretical framework to aid the development of MIPs by assisting in the selection of optimal reagents for PSA targeting. A novel algorithm, the Molecular Binding Algorithm for Surface Mapping (MBASM), was developed to efficiently generate amino acid-monomer complexes. The integrated MBASM + DFT approach was validated through comparison with the GFN2-xTB method and the Quantum Cluster Growth approach implemented in the CREST program. The results demonstrated strong agreement between the methods, establishing MBASM + DFT as a viable and innovative alternative tool for predicting interaction structures and energies. Through this strategy, promising monomers for PSA-targeted MIP synthesis were identified, including itaconic acid, 4-imidazole acrylic acid, and methacrylic acid, with 1,4-divinylbenzene emerging as the most effective cross-linker. This computational methodology provides a powerful and systematic approach for optimizing MIP synthesis aimed at selective PSA detection.

Phytoconstituents from Urtica dioica (stinging nettle) of Sikkim Himalaya and their molecular docking interactions revealed their nutraceutical potential as α-amylase and α-glucosidase inhibitors

In this study, antioxidative methanolic leaf extract (MeOH-SIS) of Urtica dioica was characterized for anti-diabetic activity. The extract was purified on a column to yield seven homogenous fractions (F1-F7) which were further determined for DPPH radical scavenging activity. MeOH-SIS and the fraction F1 (selected based on % yield and activity) were evaluated for their in vitro α-amylase and α-glucosidase inhibitory activity. The results showed inhibition of both enzymes in a dose dependent manner and F1 exhibited relatively higher inhibition than its mother extract MeOH-SIS. GC-MS analyses of both the extracts identified 24 major compounds among which 10 were previously described as bioactive compounds. Among all, 5 compounds demonstrated to have quality pharmacokinetics profiles and were examined for possible binding affinity against the active sites of α-amylase and α-glucosidase using molecular docking. The binding interaction of 2R-acetoxymethyl-1,3,3-trimethyl-4 T-(3-methyl-2-buten-1-yl)-1 T-cyclohexanol within the active sites of the target receptors was found to be significant among others, and can be developed as a potential inhibitor of α-amylase and α-glucosidase. The leaf extract can be utilized to develop food additive for the control and management of oxidative stress induced diabetes.

Purification and Characterization of Novel Antihypertensive and Antioxidative Peptides From Whey Protein Fermentate: In Vitro, In Silico, and Molecular Interactions Studies

OBJECTIVE

The goal of this research was to purify and characterize the novel angiotensin-converting enzyme (ACE)-inhibitory and antioxidant peptides from fermented whey protein concentrate produced by Lactobacillus paracasei and Saccharomyces cerevisiae in a co-fermentation system.

METHOD

Whey protein fermented with lactic acid bacteria and yeast culture was analyzed for antioxidative, ACE inhibition, as well as anti-inflammatory activity followed by SDS-PAGE, isoelectric focusing, and 2-dimensional (2D) analysis. Anti-inflammatory activity of whey protein fermentate was also studied on the RAW 264.7 cell line. The bioactive peptides were separated from the whey protein fermentate using reverse-phase high-performance liquid chromatography (RP-HPLC) and reverse-phase liquid chromatography mass spectrometry (RPLC/MS), and thus identification and characterization of purified bioactive peptide was performed.

RESULTS

Whey protein fermentate samples' bioactivity was analyzed at specific time intervals at 12, 24, 36, and 48 hours at 37 °C for M11 and at 25 °C for WBS2A. The development settings (incubation time [12, 24, 36, and 48 hours) and inoculation rates [1.5%, 2.0%, and 2.5%]) were optimized for peptide synthesis via the o-phthaldialdehyde (OPA) method (proteolytic activity). Maximum proteolytic activity was observed at 37 °C for M11 (6.50 mg/mL) and at 25 °C for WBS2A (8.59 mg/mL) for 48 hours of incubation. Protein profiling was carried out using SDS-PAGE and 2D gel electrophoresis, in which Sodium dodecyl-sulfate (SDS) exhibited protein bands in the 10- to 55-kDa range, while 2D showed protein bands varying from 10 to 70 kDa. Every spot from 2D was digested by trypsin and identified by RPLC/MS. Protein fractionations (3- and 10-kDa permeates) were carried out employing RP-HPLC. Whey protein fermentate has anti-inflammatory action in RAW 264.7 macrophages that have been exposed to lipopolysaccharide. A molecular docking system was also used to investigate the interactions of peptides (AFLDSRTR, ILGAFIQIITFR) with human myeloperoxidase enzyme.

CONCLUSIONS

The antihypertensive and antioxidative peptides discovered from whey protein fermentate may be helpful in the design of pharmacologically active healthy ingredients in the upcoming years.

Production and characterization of bioactive peptides from rice beans using Bacillus subtilis

A bioprocess was developed for production of bioactive peptides on microbial fermentation of rice beans using proteolytic Bacillus subtilis strains. The peptides produced were identified by LC-MS/MS analysis, revealing the presence of many unique peptide sequences to individual hydrolysates. On functional properties prediction, antihypertensive peptides (3.90%) were found to be higher in comparison to other bioactive peptides. Among different strains, B. subtilis KN2B fermented hydrolysate exhibited highest angiotensin converting enzyme (ACE)-inhibitory activity (45.73%). Furthermore, 19 selected peptides, including the common and unique peptides were examined for their affinity towards the binding cavity of ACE using molecular docking. The results showed a common peptide PFPIPFPIPIPLP, and another IPFPPIPFLPPI unique to B. subtilis KN2B fermented hydrolysate exhibited promising binding at the ACE binding site with substantial free binding energy. The process developed can be used for the production of bioactive peptides from rice bean for application in nutraceutical industries.

Interactions of selected cardiovascular active natural compounds with CXCR4 and CXCR7 receptors: a molecular docking, molecular dynamics, and pharmacokinetic/toxicity prediction study

BACKGROUND

The chemokine CXCL12 and its two receptors (CXCR4 and CXCR7) are involved in inflammation and hematopoietic cell trafficking. This study was designed to investigate molecular docking interactions of four popular cardiovascular-active natural compounds; curcumin, resveratrol, quercetin, and eucalyptol; with these receptors and to predict their drug-like properties. We hypothesize that these compounds can modify CXCL12/CXCR4/CXCR7 pathway offering benefits for coronary artery disease patients.

METHODS

Docking analyses were carried and characterized by Molecular Environment (MOE) software. Protein Data Bank ( http://www.rcsb.org/ ) has been retrieved from protein structure generation and crystal structures of CXCR4 and CXCR7 receptors (PDB code = 3ODU and 6K3F). The active sites of these receptors were evaluated and extracted from full protein and molecular docking protocol was done for compounds against them. The presented parameters included docking scores, ligand binding efficiency, and hydrogen bonding. The pharmacokinetic/toxic properties (ADME/T) were calculated using SwissADME, ProTox-II, and Pred-hERG softwares to predict drug-like properties of the compounds. The thermochemical and molecular orbital analysis, and molecular dynamics simulations were also done.

RESULTS

All compounds showed efficient interactions with the CXCR4 and CXCR7 receptors. The docking scores toward proteins 3ODU of CXCR4 and 6K3F of CXCR7 were - 7.71 and - 7.17 for curcumin, - 5.97 and - 6.03 for quercetin, - 5.68 and - 5.49 for trans-resveratrol, and - 4.88 and - 4.70 for (1 s,4 s)-eucalyptol respectively indicating that all compounds, except quercetin, have more interactions with CXCR4 than with CXCR7. The structurally and functionally important residues in the interactive sites of docked CXCR4-complex and CXCR7-complex were identified. The ADME analysis showed that the compounds have drug-like properties. Only (1 s,4 s)-Eucalyptol has potential weak cardiotoxicity. The results of thermochemical and molecular orbital analysis and molecular dynamics simulation validated outcomes of molecular docking study.

CONCLUSIONS

Curcumin showed the top binding interaction against active sites of CXCR4 and CXCR7 receptors, with the best safety profile, followed by quercetin, resveratrol, and eucalyptol. All compounds demonstrated drug-like properties. Eucalyptol has promising potential because it can be used by inhalation or skin massage. To our knowledge, this is the first attempt to find binding interactions of these natural agents with CXCR4 and CXCR7 receptors and to predict their druggability.

Isolation and Characterization of an Endophytic Fungus Colletotrichum coccodes Producing Tyrosol From Houttuynia cordata Thunb. Using ITS2 RNA Secondary Structure and Molecular Docking Study

An endophytic fungus isolated from healthy leaf tissues of Houttuynia cordata Thunb., an ethnomedicinal plant of North East India, showed a considerable amount of antimicrobial activity. The ethyl acetate extract of the fungal culture filtrates displayed promising antimicrobial activity against a panel of clinically significant pathogens including Candida albicans, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. Bioassay guided purification of the organic extract using column and thin layer chromatography yielded a pure homogenous compound which was identified using spectroscopic methods (essentially by ¹H NMR and MS) as tyrosol, a well-known phenylethanoid present in several natural sources. Besides, molecular docking studies against tyrosyl tRNA synthetases (TyrRS) of S. aureus (PDB ID: 1JIL) and E. coli (PDB ID: 1VBM), and CYP45014α-lanosterol demethylase (CYP51) of C. albicans (PDB ID: 5FSA) revealed tyrosol has a strong binding affinity with the enzyme active site residues. The fungus was identified as Colletotrichum sp. and characterized by its genomic ITS rDNA and ITS2 sequences. Phylogenetic analyses showed clustering of our isolate with Colletotrichum coccodes. Species of Colletotrichum are also reported to be plant pathogens. Therefore, to confirm the endophytic lifestyle of the isolate, ITS2 RNA secondary structure study was undertaken. The result indicated our isolate exhibited differences in the folding pattern as well as in motif structures when compared to those of pathogenic C. coccodes. The findings indicated that endophytic fungi harboring H. cordata could be explored as a potent source of antimicrobial agents.

A Multifunctional Peptide From Bacillus Fermented Soybean for Effective Inhibition of SARS-CoV-2 S1 Receptor Binding Domain and Modulation of Toll Like Receptor 4: A Molecular Docking Study

Fermented soybean products are traditionally consumed and popular in many Asian countries and the northeastern part of India. To search for potential agents for the interruption of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike glycoprotein 1 (S1) and human angiotensin-converting enzyme 2 (ACE2) receptor interactions, the in silico antiviral prospective of peptides identified from the proteome of kinema was investigated. Soybean was fermented using Bacillus licheniformis KN1G, Bacillus amyloliquefaciens KN2G and two different strains of Bacillus subtilis (KN2B and KN2M). The peptides were screened in silico for possible antiviral activity using two different web servers (AVPpred and meta-iAVP), and binding interactions of selected 44 peptides were further explored against the receptor-binding domain (RBD) of the S1 protein (PDB ID: 6M0J) by molecular docking using ZDOCK. The results showed that a peptide ALPEEVIQHTFNLKSQ (P13) belonging to B. licheniformis KN1G fermented kinema was able to make contacts with the binding motif of RBD by blocking specific residues designated as critical (GLN493, ASN501) in the binding of human angiotensin-converting enzyme 2 (ACE2) cell receptor. The selected peptide was also observed to have a significant affinity towards human toll like receptor 4 (TLR4)/Myeloid Differentiation factor 2 (MD2) (PDB ID: 3FXI) complex known for its essential role in cytokine storm. The energy properties of the docked complexes were analyzed through the Generalized Born model and Solvent Accessibility method (MM/GBSA) using HawkDock server. The results showed peptidyl amino acids GLU5, GLN8, PHE11, and LEU13 contributed most to P13-RBD binding. Similarly, ARG90, PHE121, LEU61, PHE126, and ILE94 were appeared to be significant in P13-TLR4/MD2 complex. The findings of the study suggest that the peptides from fermented soy prepared using B. licheniformis KN1G have better potential to be used as antiviral agents. The specific peptide ALPEEVIQHTFNLKSQ could be synthesized and used in combination with experimental studies to validate its effect on SARS-CoV-2-hACE2 interaction and modulation of TLR4 activity. Subsequently, the protein hydrolysate comprising these peptides could be used as prophylaxis against viral diseases, including COVID-19.

Distinguishing the optimal binding mechanism through reversible and irreversible inhibition analysis of HSP72 protein in cancer therapy

Over the past two decades, covalent inhibitors have gained much interest and are living up to their reputation as a powerful tool in drug discovery. Covalent inhibitors possess several significant advantages, including increased biochemical efficiency, prolonged duration and the ability to target shallow, solvent-exposed substrate-binding domains. One of the enzymes that have been both covalently and non-covalently targeted is the heat shock protein 72 (HSP72). This elevated enzyme expression in cancer cells may be responsible for tumorigenesis and tumor progression by providing chemotherapy resistance. A critical gap remains in the molecular understanding of the structural mechanism's covalent and non-covalent binding to HSP72. In this study, we explore the most optimal binding mechanism in the inhibition of the HSP72. Based on the molecular dynamic analyses, it was evident that the non-covalent complex showed more stability than the covalent complex. The covalent ligand, however, was more able to induce and stabilize the sealed conformation of the HSP72-NBD ATP binding domain throughout the. Also, the non-covalent ligand does not induce any significant conformational change as it remained close to the shape of the unbound complex; and the affinity is only dependent on the multiple hydrogen bonds in contrast to the covalent ligand. This is supported by the secondary structure elements and principal component analysis that was more dominant in the covalently inhibited complex. Covalent bond induced the α-helices sealed conformation of the HSP72-NBD; based on our findings, this will prevent other small molecules from interacting at the ATP binding site domain. Moreover, inhibition of the ATP binding domain can directly affect the ATPs protein folding mechanism of the HSP72 enzyme. The essential dynamic analysis presented in this report compliments the binding mechanism of HSP72, establishing covalent inhibition as the preferred method of inhibiting the HSP72 protein. The findings from this study may assist in the design of more target-specific HSP72 covalent inhibitors exploring the surface-exposed lysine residues.

Production, characterization and molecular docking of antioxidant peptides from peptidome of kinema fermented with proteolytic Bacillus spp

Kinema is an alkaline traditionally fermented soybean product popularly consumed in Sikkim Himalayan region. Kinema was prepared by soybean fermented with different species of Bacillus and analyzed for peptide content, antioxidant activity and consequence of gastrointestinal enzymes (pepsin and pancreatin) on the antioxidant effect. Antioxidant effect was enhanced during soybean fermentation using different starters, which further increased during gastrointestinal digestion. The peptides formed during soybean fermentation were analyzed using LC-MS/MS. Soybean fermented using different starters resulted in the production of some common peptides and a large number of unique peptides, which may affect the functional property of kinema. Peptides having antioxidative amino acids (histidine, phenylalanine, methionine, tryptophan and tyrosine) and significant GRAVY value were selected for their molecular interaction with myeloperoxidase (MPO), a key enzyme responsible for elevated oxidative stress. A peptide SEDDVFVIPAAYPF produced in kinema fermented using Bacillus licheniformis 1G had interaction with four out of five catalytic residues identified in MPO. Kinema prepared using specific starter can produce unique peptides responsible for specific health benefits.

ADMET profile and virtual screening of plant and microbial natural metabolites as SARS-CoV-2 S1 glycoprotein receptor binding domain and main protease inhibitors

In an attempt to search for selective inhibitors against the SARS-CoV-2 which caused devastating of lives and livelihoods across the globe, 415 natural metabolites isolated from several plants, fungi and bacteria, belonging to different classes, were investigated. The drug metabolism and safety profiles were computed in silico and the results showed seven compounds namely fusaric acid, jasmonic acid, jasmonic acid methyl ester, putaminoxin, putaminoxin B and D, and stagonolide K were predicted to having considerable absorption, metabolism, distribution and excretion parameters (ADME) and safety indices. Molecular docking against the receptor binding domain (RBD) of spike glycoprotein (S1) and the main protease (Mpro) exposed the compounds having better binding affinity to main protease as compared to the S1 receptor binding domain. The docking results were compared to an antiviral drug penciclovir reportedly of clinical significance in treating the SARS-CoV-2 infected patients. The results demonstrated the test compounds jasmonic acid, putaminoxins B and D bound to the HIS-CYS catalytic dyad as well as to other residues within the MPro active site with much greater affinity than penciclovir. The findings of the study suggest that these compounds could be explored as potential SARS-CoV-2 inhibitors, and could further be combined with the experimental investigations to develop effective therapeutics to deal with the present pandemic.

Molecular Recognition of Azelaic Acid and Related Molecules with DNA Polymerase I Investigated by Molecular Modeling Calculations

Molecular recognition has central role on the development of rational drug design. Binding affinity and interactions are two key components which aid to understand the molecular recognition in drug-receptor complex and crucial for structure-based drug design in medicinal chemistry. Herein, we report the binding affinity and the nonbonding interactions of azelaic acid and related compounds with the receptor DNA polymerase I (2KFN). Quantum mechanical calculation was employed to optimize the modified drugs using B3LYP/6-31G(d,p) level of theory. Charge distribution, dipole moment and thermodynamic properties such as electronic energy, enthalpy and free energy of these optimized drugs are also explored to evaluate how modifications impact the drug properties. Molecular docking calculation was performed to evaluate the binding affinity and nonbonding interactions between designed molecules and the receptor protein. We notice that all modified drugs are thermodynamically more stable and some of them are more chemically reactive than the unmodified drug. Promise in enhancing hydrogen bonds is found in case of fluorine-directed modifications as well as in the addition of trifluoroacetyl group. Fluorine participates in forming fluorine bonds and also stimulates alkyl, pi-alkyl interactions in some drugs. Designed drugs revealed increased binding affinity toward 2KFN. A1, A2 and A3 showed binding affinities of -8.7, -8.6 and -7.9 kcal/mol, respectively against 2KFN compared to the binding affinity -6.7 kcal/mol of the parent drug. Significant interactions observed between the drugs and Thr358 and Asp355 residues of 2KFN. Moreover, designed drugs demonstrated improved pharmacokinetic properties. This study disclosed that 9-octadecenoic acid and drugs containing trifluoroacetyl and trifluoromethyl groups are the best 2KFN inhibitors. Overall, these results can be useful for the design of new potential candidates against DNA polymerase I.