Interacting Amino Acid Residues Research Articles

Screening, characterization of trace α-glucosidase inhibitors from the root of Pueraria lobata and evaluation of their hypoglycemic activity

Pueraria lobata (Willd.) Ohwi (Gegen) is a nutritious medicine food homology plant that has been recorded in many ancient remedies for diabetes. However, its hypoglycemic active components and related mechanisms have not been fully elucidated. In this study, potential α-glucosidase inhibitors in Pueraria lobata were investigated by liquid-liquid refined extraction, high-resolution profiling and their hypoglycemic activity were evaluated. Ten compounds showing α-glucosidase inhibitory bioactivity were separated and identified, including two new compounds, 8-geranyl-7, 3′, 4′-trihydroxy-isoflavone (4) and 8-geranyl-7, 2′, 4′-trihydroxy-isoflavone (6), and eight known compounds. All screened compounds showed potential hypoglycemic activity, in which compounds 4, 6, 7, 8, 9 and 10 showed strong inhibitory activity (IC50 < 8 μM). Furthermore, molecular docking simulation revealed binding energy and interacting amino acid residues of the screened compounds with α-glucosidase, strongly supporting their potential as α-glucosidase inhibitors.

Structural Basis of Dual Specificity of Sinorhizobium meliloti Clr, a cAMP and cGMP Receptor Protein.

In bacteria, the most prevalent receptor proteins of 3',5'-cyclic AMP (cAMP) and 3',5'-cyclic GMP (cGMP) are found among transcription factors of the Crp-Fnr superfamily. The prototypic Escherichia coli catabolite activator protein (CAP) represents the main Crp cluster of this superfamily and is known to bind cAMP and cGMP but to mediate transcription activation only in its cAMP-bound state. In contrast, both cyclic nucleotides mediate transcription activation by Sinorhizobium meliloti Clr, mapping to cluster G of Crp-like proteins. We present crystal structures of Clr-cAMP and Clr-cGMP bound to the core motif of the palindromic Clr DNA binding site (CBS). We show that both cyclic nucleotides shift ternary Clr-cNMP-CBS-DNA complexes (where cNMP is cyclic nucleotide monophosphate) to almost identical active conformations, unlike the situation known for the E. coli CAP-cNMP complex. Isothermal titration calorimetry measured similar affinities of cAMP and cGMP binding to Clr in the presence of CBS core motif DNA (equilibrium dissociation constant for cNMP (KDcNMP], ~7 to 11 μM). However, different affinities were determined in the absence of this DNA (KDcGMP, ~24 μM; KDcAMP, ~6 μM). Sequencing of Clr-coimmunoprecipitated DNA as well as electrophoretic mobility shift and promoter-probe assays expanded the list of experimentally proven Clr-regulated promoters and CBS. This comprehensive set of CBS features conserved nucleobases that are consistent with the sequence readout through interactions of Clr amino acid residues with these nucleobases, as revealed by the Clr-cNMP-CBS-DNA crystal structures. IMPORTANCE Cyclic 3',5'-AMP (cAMP) and cyclic 3',5'-GMP (cGMP) are both long known as important nucleotide secondary messengers in eukaryotes. This is also the case for cAMP in prokaryotes, whereas a signaling role for cGMP in this domain of life has been recognized only recently. Catabolite repressor proteins (CRPs) are the most ubiquitous bacterial cAMP receptor proteins. Escherichia coli CAP, the prototypic transcription regulator of the main Crp cluster, binds both cyclic mononucleotides, but only the CAP-cAMP complex promotes transcription activation. In contrast, Crp cluster G proteins studied so far are activated by cGMP or by both cAMP and cGMP. Here, we report a structural analysis of the cAMP- and cGMP-activatable cluster G member Clr from Sinorhizobium meliloti, how binding of cAMP and cGMP shifts Clr to its active conformation, and the structural basis of its DNA binding site specificity.

In vivo and in silico comparison analyses of Cry toxin activities toward the sugarcane giant borer

The sugarcane giant borer, Telchin licus licus, is an insect pest that causes significant losses in sugarcane crops and in the sugar-alcohol sector. Chemical and manual control methods are not effective. As an alternative, in the current study, we have screened Bacillus thuringiensis (Bt) Cry toxins with high toxicity against this insect. Bioassays were conducted to determine the activity of four Cry toxins (Cry1A (a, b, and c) and Cry2Aa) against neonate T. licus licus larvae. Notably, the Cry1A family toxins had the lowest LC50 values, in which Cry1Ac presented 2.1-fold higher activity than Cry1Aa, 1.7-fold larger than Cry1Ab, and 9.7-fold larger than Cry2Aa toxins. In silico analyses were performed as a perspective to understand putative interactions between T. licus licus receptors and Cry1A toxins. The molecular dynamics and docking analyses for three putative aminopeptidase N (APN) receptors (TlAPN1, TlAPN3, and TlAPN4) revealed evidence for the amino acids that may be involved in the toxin-receptor interactions. Notably, the properties of Cry1Ac point to an interaction site that increases the toxin's affinity for the receptor and likely potentiate toxicity. The interacting amino acid residues predicted for Cry1Ac in this work are probably those shared by the other Cry1A toxins for the same region of APNs. Thus, the presented data extend the existing knowledge of the effects of Cry toxins on T. licus licus and should be considered in further development of transgenic sugarcane plants resistant to this major occurring insect pest in sugarcane fields.

Spectrochemical, biological, and toxicological studies of DDT, DDD, and DDE: An in-silico approach

Pesticides are used to control the various pests and disease carriers. Degradation and/or biotransformation alter their chemical and toxicological nature. An attempt has been taken to investigate the physicochemical, spectral, and toxicological nature of DDT [1, 1'-(2, 2, 2-trichloroethylidene) bis(4-chlorobenzene)] and its major derivatives. DDT is transformed into DDD [l, l-dichloro-2, 2-bis(p,p-chlorophenylethane)], and DDE [l, l-dichloro-2, 2-bis(p,p-chlorophenylethylene)] under reductive dechlorination conditions. They last longer in the fatty tissue due to fat-soluble features, and exhibit some harmful effects on the environment and biological systems. Herein, density functional theory along with the CAM-B3LYP/6-311g ++ (d, p) basis set has been employed to investigate their physicochemical, and spectral properties. In-silico methods were incorporated to evaluate their biological, and toxicological properties. Molecular docking and nonbonding interaction calculations were performed to investigate their binding properties and mode(s) of action against the human estrogen receptor (PDB ID: 6PYF), and serine/threonine-protein kinase PIM-2 (PDB ID: 2IWI). Further, molecular dynamics simulation was performed to check the deformability and interactions of protein and amino acid residues, respectively. ADMET (absorption, distribution, metabolism, excretion, and toxicity) and PASS (prediction of activity spectra for substances) predictions were performed to compare their biological and toxicological properties. DDT has the highest free energy, dipole moment, and chemical reactivity; meanwhile, DDE and DDD have the highest binding affinity against both proteins. All the compounds exhibit hepato-toxicological, neuro-toxicological, and carcinogenic properties which depict their toxicological level. Based on their studied parameters, this study can help to increase awareness and provide a deeper understanding of the biochemical, and toxicological impacts on the environment and biological system.

Structural Optimization of an α-Hairpinin Blocking Potassium Channels K&lt;sub&gt;V&lt;/sub&gt;1.3

Obtaining compounds with specificity for certain isoforms of ion channels is a significant problem of curent physiology and pharmacology. In a series of papers, we have shown that the α-hairpinin fold can serve as a template for the rational design of peptide ligands of potassium channels. Here, we used molecular modeling to optimize the structure of the previously obtained Tk-hefu-10 peptide, a selective KV1.3 channel blocker, with a half-maximal inhibitory concentration (IC50) of ≈150 nM. Molecular dynamics simulation of the Tk-hefu-10–KV1.3 complex provided information on the interaction of individual amino acid residues of the peptide and channel, and the analysis of these interactions made it possible to propose amino acid substitutions in the structure of Tk-hefu-10 to increase its affinity. Novel Tk-hefu-12 peptide is a truncated analog of Tk-hefu-10 by one residue with five substitutions; it is characterized by an IC50 value of ≈70 nM against KV1.3. In addition, there are no methionine residues in the structure of Tk-hefu-12, which makes it possible to obtain Tk-hefu peptides using cyanogen bromide.

Physicochemical and toxicological studies of some commonly used triazine-based herbicides; In-silico approach

Pesticides play a significant role in modern agriculture and public health by protecting crops, preventing the spread of diseases, and ensuring food safety. However, the use of pesticides also raises concerns due to their potential negative consequences on human health and the ecosystem. This study has concentrated on commonly used triazine-based herbicides (atraton, atrazine, prometon, secbumeton, terbuthylazine, and trietazine) due to their unfavorable side effects, which include endocrine disruption, teratogenicity, embryogenicity, carcinogenicity, and hypoplasia of the adrenal cortex. Our investigation encompasses a thorough examination of the physicochemical, spectral, biological, and toxicological properties of these triazine-based herbicides. Density functional theory (DFT) and time-dependent DFT along with the B3LYP/6-311+G (d, p) basis set were used to enumerate the geometry, chemical, and spectral properties. To evaluate the chemical reactivity of triazine compounds, the HOMO-LUMO gap is calculated. FT-IR and UV spectroscopy have been performed to identify functional groups, determine bond lengths, and investigate molecular conformations of triazine derivatives. In addition, binding affinities and modes against human estrogen-related and cancer-causing receptor proteins (PDB IDs: 4MNF and 2E2R, respectively) have been observed utilizing molecular docking and non-bonding interactions. We selected both proteins that are associated with abnormal cell growth and malignancy, particularly breast cancer and melanoma. Normal mode analysis (NMA) was performed to get the deformability and interactions of protein and amino acid residues, respectively. Pharmacokinetics and biological parameters were accomplished to anticipate their toxicological properties. Terbuthylazine and trietazine have the highest Gibbs free energies, and atrazine has the highest binding affinity for both receptor proteins. All triazine derivatives exhibit nephrotoxicity, carcinogenicity, hematotoxicity, hepatotoxicity, and CYP2C9 inhibitory properties. Therefore, the goal of our inquiry was to gain a deeper comprehension of the risks associated with exposure to triazine-based herbicides, which would be useful for the subsequent investigation. In addition, our research will raise public awareness of the negative impacts of triazine-based herbicides.

Docking and Molecular Dynamic Investigations of Phenylspirodrimanes as Cannabinoid Receptor-2 Agonists.

Cannabinoid receptor ligands are renowned as being therapeutically crucial for treating diverse health disorders. Phenylspirodrimanes are meroterpenoids with unique and varied structural scaffolds, which are mainly reported from the Stachybotrys genus and display an array of bioactivities. In this work, 114 phenylspirodrimanes reported from Stachybotrys chartarum were screened for their CB2 agonistic potential using docking and molecular dynamic simulation studies. Compound 56 revealed the highest docking score (-11.222 kcal/mol) compared to E3R_6KPF (native agonist, gscore value -12.12 kcal/mol). The molecular docking and molecular simulation results suggest that compound 56 binds to the putative binding site in the CB2 receptor with good affinity involving key interacting amino acid residues similar to that of the native ligands, E3R. The molecular interactions displayed π-π stacking with Phe183 and hydrogen bond interactions with Thr114, Leu182, and Ser285. These findings identified the structural features of these metabolites that might lead to the design of selective novel ligands for CB2 receptors. Additionally, phenylspirodrimanes should be further investigated for their potential as a CB2 ligand.

Assessing chemical hazard and unraveling binding affinity of priority pollutants to lignin modifying enzymes for environmental remediation

Lignin-modifying enzymes (LMEs) are impactful biocatalysts in environmental remediation applications. However, LMEs-assisted experimental degradation neglects the molecular basis of pollutant degradation. Furthermore, throughout the remediation process, the inherent hazards of environmental pollutants remain untapped for in-depth toxicological endpoints. In this investigation, a predictive toxicological framework and a computational framework adopting LMEs were employed to assess the hazards of Priority Pollutants (PP) and its possible LMEs-assisted catalytic screening. The potential hazardous outcomes of PP were assessed using Quantitative structure-activity relationship (QSARs)-based techniques including Toxtree, ECOSAR, and T.E.S.T. tools. Toxicological findings revealed positive outcomes in a multitude of endpoints for all PP. The PP compound 2,3,7,8-TCDD (dioxin) was found to exhibit the lowest concentration of aquatic toxicity implementing aquatic model systems; LC50 as 0.01, 0.01, 0.04 (mg L−1) for Fish (96 H), Daphnid (48 H), Green algae (96 H) respectively. T.E.S.T. results revealed that chloroform, and 2-chlorophenol both seem to be developmental toxicants. Subsequently, LMEs-assisted docking procedure was employed in predictive mitigation of PP. The docking approach as predicted degradation revealed the far lowest docking energy score for Versatile peroxidase (VP)- 2,3,7,8-TCDD docked complex with a binding energy of −9.2 (kcal mol−1), involved PHE-46, PRO-139, PRO-141, ILE-148, LEU-165, HIS-169, LEU-228, MET-262, and MET-265 as key interacting amino acid residues. Second most ranked but lesser than VP, Lignin peroxidase (LiP)- 2,3,7,8-TCDD docked complex exhibited a rather lower binding affinity score (−8.8 kcal mol−1). Predictive degradation screening employing comparative docking revealed varying binding affinities, portraying that each LMEs member has independent feasibility to bind PP as substrate. Predictive findings endorsed the hazardous nature of associated PP in a multitude of endpoints, which could be attenuated by undertaking LMEs as a predictive approach to protect the environment and implement it in regulatory considerations.

IN SILICO STUDY OF 12 PHYTOSTEROL COMPOUNDS IN MORINGA (MORINGA OLEIFERA LAMK.) SEED OIL ON 5Α-REDUCTASE ENZYME INHIBITION ACTIVITY AS ANTI-ALOPECIA

Objective: This study aimed to determine the interaction of 12 phytosterol compounds in moringa seed oil to the 5α-reductase enzyme (PDB code: 7BW1) as anti-alopecia by in silico.&#x0D; Methods: The research was conducted using a molecular docking approach using autodock Tools 1.5.6. Data analysis was carried out by looked at the binding affinity values ​​and inhibition constants (Ki) of 12 phytosterol compounds, as well as visualization of amino acid interactions using Biovia Discovery Studio 2021.&#x0D; Results: 12 Phytosterol compounds had the potential to be a candidate for anti-alopecia medicines based on in silico test simulations using auto dock with high binding affinity values ​​in the range of-11.47 to-12.76 kcal/mol and stable inhibition constants in the range of 1.87. nM–4.30 nM involving hydrogen bonds with Arg179, Tyr178, Arg105, Arg114, Ser177, Tyr98, Glu57, and Tyr91 amino acids.&#x0D; Conclusion: Ergostadienol compound in moringa seed oil was predicted to be a better anti-alopecia on the inhibition of 5α-reductase enzyme with binding energy value was-11.60 kcal/mol, inhibition constant was 3.17 nM and interaction of amino acid residues on the inhibition of 5α-reductase enzyme was similar with native finasteride ligands namely Glu57 and Tyr91.

Interaction estimation of pathogenicity determinant protein βC1 encoded by Cotton leaf curl Multan Betasatellite with Nicotiana benthamiana Nuclear Transport Factor 2.

Begomovirus is one of the most devastating pathogens that can cause more than 90% yield loss in various crop plants. The pathogenicity determinant βC1, located on the betasatellite associated with monopartite begomoviruses, alters the host signaling mechanism to enhance the viral disease phenotype by undermining the host immunity. The understanding of its interacting proteins in host plants to develop disease symptoms such as curly leaves, enations, vein swelling, and chlorosis is crucial to enhance the disease resistance in crop plants. The current study was designed to reveal the contribution of βC1 in disease pathogenicity and to unveil potential interacting partners of βC1 protein in the model plant Nicotiana benthamiana. The βC1 gene was cloned in pGKBT7 and used as bait against the cDNA library of N. benthamiana and its pathogenesis was tested against the healthy plant and the plants infiltrated with empty vectors. The yeast two-hybrid-based screening was performed to find the interacting factors. Successful interacting proteins were screened and evaluated in various steps and confirmed by sequence analysis. The three-dimensional structure of the Nuclear Transport Factor 2 (NTF2) protein was predicted, and in-silico protein-protein interaction was evaluated. Furthermore, protein sequence alignment and molecular phylogenetic analysis were carried out to identify its homologues in other related families. In-silico analyses were performed to validate the binding affinity of βC1 protein with NTF2. The 3D model was predicted by using I-TASSER and then analyzed by SWISS MODEL-Workspace, RAMPAGE, and Verify 3D. The interacting amino acid residues of βC1 protein with NTF2 were identified by using PyMOL and Chimera. The agroinfiltrated leaf samples developed severe phenotypic symptoms of virus infection. The yeast-two-hybrid study identified the NTF2 as a strong interacting partner of the βC1. The NTF2 in Solanaceae and Nicotiana was found to be evolved from the Brassica and Gossypium species. The in-silico interaction studies showed a strong binding affinity with releasing energy value of -730.6 KJ/mol, and the involvement of 10 amino acids from the middle portion towards the C-terminus and five amino acid residues from the middle portion of βC1 to interact with six amino acids of NTF2. The study not only provided an insight into the molecular mechanism of pathogenicity but also put the foundation stone to develop the resistance genotypes for commercial purposes and food security.

Optimized tight binding between the S1 segment and KCNE3 is required for the constitutively open nature of the KCNQ1-KCNE3 channel complex.

Tetrameric voltage-gated K⁺ channels have four identical voltage sensor domains, and they regulate channel gating. KCNQ1 (Kv7.1) is a voltage-gated K⁺ channel, and its auxiliary subunit KCNE proteins dramatically regulate its gating. For example, KCNE3 makes KCNQ1 a constitutively open channel at physiological voltages by affecting the voltage sensor movement. However, how KCNE proteins regulate the voltage sensor domain is largely unknown. In this study, by utilizing the KCNQ1-KCNE3-calmodulin complex structure, we thoroughly surveyed amino acid residues on KCNE3 and the S1 segment of the KCNQ1 voltage sensor facing each other. By changing the side-chain bulkiness of these interacting amino acid residues (volume scanning), we found that the distance between the S1 segment and KCNE3 is elaborately optimized to achieve the constitutive activity. In addition, we identified two pairs of KCNQ1 and KCNE3 mutants that partially restored constitutive activity by co-expression. Our work suggests that tight binding of the S1 segment and KCNE3 is crucial for controlling the voltage sensor domains.

Dipeptidyl peptidase-4 inhibitory potentials of Glycyrrhiza uralensis and its bioactive compounds licochalcone A and licochalcone B: An in silico and in vitro study.

Type 2 diabetes mellitus (T2DM) is a growing global public health issue, and dipeptidyl peptidase-4 (DPP-4) is a potential therapeutic target in T2DM. Several synthetic anti-DPP-4 medications can be used to treat T2DM. However, because of adverse effects, there is an unmet demand for the development of safe and effective medications. Natural medicines are receiving greater interest due to the inherent safety of natural compounds. Glycyrrhiza uralensis (licorice) is widely consumed and used as medicine. In this study, we investigated the abilities of a crude water extract (CWE) of G. uralensis and two of its constituents (licochalcone A (LicA) and licochalcone B (LicB)) to inhibit the enzymatic activity of DPP-4 in silico and in vitro. In silico studies showed that LicA and LicB bind tightly to the catalytic site of DPP-4 and have 11 amino acid residue interactions in common with the control inhibitor sitagliptin. Protein-protein interactions studies of LicA-DPP4 and LicB-DPP4 complexes with GLP1 and GIP reduced the DPP-4 to GLP1 and GIP interactions, indicated that these constituents might reduce the degradations of GLP1 and GIP. In addition, molecular dynamics simulations revealed that LicA and LicB stably bound to DPP-4 enzyme. Furthermore, DPP-4 enzyme assay showed the CWE of G. uralensis, LicA, and LicB concentration-dependently inhibited DPP-4; LicA and LicB had an estimated IC50 values of 347.93 and 797.84 μM, respectively. LicA and LicB inhibited DPP-4 at high concentrations, suggesting that these compounds could be used as functional food ingredients to manage T2DM.

A bifunctional exolytic alginate lyase from Microbulbifer sp. ALW1 with salt activation and calcium-dependent catalysis

Alginate lyases can depolymerize alginate to oligomers with potential applications in many fields. Here a new alginate lyase, namely AlgL6, was characterized from Microbulbifer sp. ALW1, phylogenetically classified into the polysaccharide lyase family 6 (PL6). The recombinant alginate lyase AlgL6 exerted enzymatic activities towards polymannuronate, polyguluronate, and sodium alginate in an exolytic manner. AlgL6 had an optimum temperature of 35 °C and good stability at 30 °C or below. Its optimum pH was 8.0, and it had good stability over the pH range of 5.0–9.0. AlgL6 exhibited excellent halo-stability against Na+, and its activity can be increased up to about 1.8 times by 0.5 M NaCl. AlgL6 also showed strong stability in the presence of some nonionic detergents such as Tween 20 and Tween 80. The degradation products of sodium alginate by AlgL6 exhibited more effective antioxidant activities than the undigested polysaccharides. Structure analysis illustrated the catalytic mechanism defined by the coordination of the acid/base residues Arg269 and Lys248 of AlgL6. The replacement of Ca2+-interacting amino acid residues in AlgL6 and depletion of Ca2+ suggested the involvement of Ca2+ in the enzyme’s catalytic activity. These properties of AlgL6 supply support to its industrial application for development of alginate bioresource.

Probing interactions of aminoacyl-adenylate with Mycobacterium tuberculosis methionyl-tRNA synthetase through in silico site-directed mutagenesis and free energy calculation

Methionyl-tRNA synthetase (MetRS) is an attractive molecular target for antibiotic discovery. Recently, we have developed several classes of small-molecular inhibitors of Mycobacterium tuberculosis MetRS possessing antibacterial activity. In this article, we performed in silico site-directed mutagenesis of aminoacyl-adenylate binding site of M. tuberculosis MetRS in order to identify crucial amino acid residues for substrate interaction. The umbrella sampling algorithm was used to calculate the binding free energy (ΔG) of these mutated forms with methionyl-adenylate analogue. According to the obtained results, the replacement of Glu24 and Leu293 by alanine leads to the most significant decrease in the binding free energy (ΔG) for adenylate analogue with methionyl-tRNA synthetase indicating increasing of the affinity, which in turn causes the loss of compounds inhibitory activity. Therefore, these amino acid residues can be proposed for further experimental site-directed mutagenesis to confirm binding mode of inhibitors and should be taken into account during chemical optimization to overcome resistance due to mutations. Communicated by Ramaswamy H. Sarma

Synthesis, characterization, and biological evaluation of some novel ϒ-aminobutyric acid aminotransferase (GABA-AT) inhibitors

In our present work, some novel substituted 4-phenyl-5-vinylpyrrolidin-2-one derivatives were designed, synthesized, and evaluated for their γ-aminobutyric acid-aminotransferase (GABA-AT) inhibition and in-vivo anticonvulsant activity. Among all the synthesized derivatives, compound 7f was observed as the most potent and competitive inhibitor of GABA-AT (IC50 = 46.29 ± 3.19 µM, Ki = 0.106 ± 0.004 μM). The in-vivo anticonvulsant activity against maximum electroshock (MES) and PTZ, induced seizures test of compound 7f, was observed very significantly (P < 0.05) in comparison with standard Vigabatrin and have shown an increase in the level of GABA in the cortex region of the brain. The ex-vivo studies have also suggested reduced tissue necrosis. Finally, In-silico molecular docking and dynamics studies of compound 7f have shown that it forms desired amino acid residue interactions with the GABA-AT and was stable for 50 ns in the active site pocket of the enzyme.

Virtual Screening of Repurposed Drugs as Potential Spike Protein Inhibitors of Different SARS-CoV-2 Variants: Molecular Docking Study.

Like most of the RNA viruses, SARS-CoV-2 continuously mutates. Although many mutations have an insignificant impact on the virus properties, mutations in the surface protein, especially those in the receptor-binding domain, may lead to immune or vaccine escape variants, or altered binding activities to both the cell receptor and the drugs targeting such a protein. The current study intended to assess the ability of different variants of interest (VOIs) and variants of concern (VOCs) of SARS-CoV-2 for their affinities of binding to different repurposed drugs. Seven FDA approved drugs, namely, camostat, nafamostat mesylate, fenofibrate, umifenovir, nelfinavir, cefoperazone and ceftazidime, were selected based on their reported in vitro and clinical activities against SARA-CoV-2. The S1 protein subunit from eleven different variants, including the latest highly contiguous omicron variant, were used as targets for the docking study. The docking results revealed that all tested drugs possess moderate to high binding energies to the receptor-binding domain (RBD) of the S1 protein for all different variants. Cefoperazone was found to possess the highest binding energy to the RBD of the S1 protein of all the eleven variants. Ceftazidime was the second-best drug in terms of binding affinity towards the S1 RBD of the investigated variants. On the other hand, fenofibrate showed the least binding affinity towards the RBD of the S1 protein of all eleven variants. The binding affinities of anti-spike drugs varied among different variants. Most of the interacting amino acid residues of the receptor fall within the RBD (438–506).

Interactions of Fibrillar Insulin with Proteins: A Molecular Docking Study

During the last decades growing attention has been paid to ascertaining the factors responsible for the toxic potential of particular protein aggregates, amyloid fibrils, whose formation is associated with a range of human pathologies, including the neurodegenerative diseases, systemic amyloidosis, type II diabetes, etc. Despite significant progress in elucidating the mechanisms of cytotoxic action of amyloid fibrils, the role of fibril-protein interactions in determining the amyloid toxicity remains poorly understood. In view of this, in the present study the molecular docking techniques has been employed to investigate the interactions between the insulin amyloid fibrils (InsF) and three biologically important multifunctional proteins, viz. serum albumin, lysozyme and insulin in their native globular state. Using the ClusPro, HDOCK, PatchDock and COCOMAPS web servers, along with BIOVIA Discovery Studio software, the structural characteristics of fibril-protein complexes such as the number of interacting amino acid residues, the amount of residues at fibril and protein interfaces, the contributions of various kinds of interactions, buried area upon the complex formation, etc. It was found that i) hydrophilic-hydrophilic and hydrophilic-hydrophobic interactions play dominating role in the formation of fibril-protein complexes; ii) there is no significant differences between the investigated proteins in the number of fibrillar interacting residues; iii) the dominating hydrogen bond forming residues are represented by glutamine and asparagine in fibrillar insulin, lysine in serum albumin and arginine in lysozyme; iv) polar buried area exceeds the nonpolar one upon the protein complexation with the insulin fibrils. The molecular docking evidence for the localization of phosphonium fluorescent dye TDV at the fibril-protein interface was obtained.

Identification of novel HDAC8 selective inhibitors through ligand and structure based studies: Exploiting the acetate release channel differences among class I isoforms

Histone deacetylases (HDACs) are key regulators of gene expression and have emerged as crucial therapeutic targets for cancer. Among the HDACs, inhibition of HDAC8 enzyme has been reported to be a novel strategy in the treatment of female-specific cancers. Most of the HDAC inhibitors discovered so far inhibit multiple HDAC isoforms causing toxicities in the clinic thus limiting their potential. Therefore, the discovery of isoform-selective HDAC8 inhibitors is highly desirable. In the present study, a combination of ligand and structure based drug design tools were utilized to build a statistically significant pharmacophore based 3D QSAR model with statistical parameters R 2 : 0.9964, and Q 2 : 0.7154, from a series of 31 known HDAC8 inhibitors. Top 1000 hits obtained from Virtual screening of Phase database were subjected to docking studies against HDAC8. Top 100 hits obtained were redocked into HDAC Class I (HDAC 1,2,3) and Class II isoforms (HDAC 4, 6) and rescored with XP Glide Score. Based on fitness score, XP glide score and interacting amino acid residues, five HDAC8 inhibitors ( 1 – 5 ) were selected for in vitro studies. The HDAC8 activity assay followed by enzyme kinetics clearly indicated Compounds 1 , 2 and 3 to be potent HDAC8 selective inhibitors with IC 50 of 126 pM, 112 nM, and 442 nM respectively. These compounds were cytotoxic to HeLa cells where HDAC8 is overexpressed but not to normal cells, HEK293. Also, they were able to induce apoptosis by modulating Bax/Bcl2, cleavage of PARP and release of Cytochrome C . Molecular Dynamics simulations observed most favorable interaction patterns and presented a rationale for the activities of the identified compounds. Selectivity against HDAC8 was due to exploitation of the architectural difference in the acetate release channel among class I HDAC isoforms.

IDENTIFICATION OF NEW CYCLOOXYGENASE-2 SELECTIVE INHIBITORS VIA VIRTUAL SCREENING AND COMPLEX-BASED PHARMACOPHORE MAPPING

Background: New and effective COX-2-targeted medications may cure cancer, inflammation, and other disorders.It’s difficult to produce druggable site inhibitors for target protein inhibition that are strong and selective. Such medications need a more informed structure-based or ligand-based drug discovery technique. MOE was used to create asix-point COX-2 selective inhibitor pharmacophore from 43 compounds. The structure includes three aromatic rings,one hydrophobic group (Hyd), one donor (Don), and three H-bond acceptors. A pharmacophore was used to digitallyfilter the Chembridge database to locate additional structural poses that fulfilled the model’s requirements. We found2090 structurally diverse hits after filtering. Molecular docking was performed on 767 hits after Lipinski’s rule of fivedetermined druggability. Twenty compounds with high active site amino acid residue interactions and diverse scaffoldswere chosen. The first COX-2 isoform-inhibiting medicines were discovered using structure-based pharmacophores.Objectives Using complex-based pharmacophore mapping and virtual screening, this research seeks novel selectiveCOX-2 inhibitors. This involves filtering through a chemical database, defining critical interactions, maximizing hits,and extending drug development for safer and more effective inflammation and pain managemStudy design : Employing Advanced Computational And Pharmacological Approaches StudyDuration and place of study :The study was conducted at Abdul Wali Khan University Mardan from jan2017 to jan 2018Methods: The investigation used a structure-based drug discovery methodology to find novel cyclooxygenase-2 (COX-2)selective inhibitors. The COX-2 crystal structure was used to create a pharmacophore model, which was then used tovirtually search a chemical database. In order to identify potential lead compounds based on interactions with importantCOX-2 residues, binding energies were computed, and molecular docking was used to refine hits.Results: The goal of the project was to use virtual screening and complex-based pharmacophore mapping to findnovel selective COX-2 inhibitors. After the COX-2 crystal structure was used to create a pharmacophore model,2090 hits were discovered in a database. Following the druggability assessment, 767 hits were chosen for moleculardocking. Ultimately, twenty compounds were found to be promising COX-2 inhibitors due to their strong interactionswith COX-2 and variety of scaffolds.Conclusion: This study found 20 possible lead drugs that selectively block cyclooxygenase-2 (COX-2) using complex-based pharmacophore mapping and virtual screening. These substances show a variety of scaffolds and robustinteractions with COX-2, making them attractive candidates for further research and development as anti-inflammatoryand anti-cancer medications with maybe fewer adverse effects.Keywords: Cyclooxygenase-2 (COX-2),Pharmacophore mapping,Virtual screening,Drug discovery

Kajian Molecular Docking Senyawa Karwinaphthol B dari Tanaman Bawang Dayak (Eleutherine palmifolia (L.) Merr) sebagai Inhibitor Enzim Glukokinase

Karwinaphthol B is a compound of the naphthoquinone group. Karwinaphthol B is a chemical compound found in Bawang Dayak. Karwinaphthol B is one of the compounds considered to have antidiabetic effects. Diabetes Mellitus is a chronic disease that occurs when the body cannot produce enough insulin or cannot use insulin (insulin resistance) which causes blood glucose levels to rise (hyperglycaemia) under normal conditions. This study aims to see the potential of karwinaphthol B as a glucokinase inhibitor with parameters such as ∆G value and interaction of amino acid residues with molecular docking and pharmacophore studies using filter Lipinski, pkCSM, and SwissADME. The results of molecular docking showed that karwinaphthol B compound had potential as antidiabetic based on the ∆G value of -8.39 kcal/mole. Karwinaphthol B compound has an LD50 value of 2.168 mole/kg which is included in the non-toxic category; does not have hepatotoxicity, skin sensitization, and has a good bioavailability value. The interaction of Karwinaphthol B compounds with glucokinase enzymes at amino acid residues VAL62, ARG63, SER64,THR65, PRO66, GLU67, GLY68, SER69, GLN98, MET210 , ILE211, TYR214, TYR215, CYS220, GLU221, MET235, CYS252, LEU451, VAL452, and VAL455.