Affinity Energy Values Research Articles

The Influence of Clustered DNA Damage Containing Iz/Oz and OXOdG on the Charge Transfer through the Double Helix: A Theoretical Study.

The genome-the source of life and platform of evolution-is continuously exposed to harmful factors, both extra- and intra-cellular. Their activity causes different types of DNA damage, with approximately 80 different types of lesions having been identified so far. In this paper, the influence of a clustered DNA damage site containing imidazolone (Iz) or oxazolone (Oz) and 7,8-dihydro-8-oxo-2'-deoxyguanosine (OXOdG) on the charge transfer through the double helix as well as their electronic properties were investigated. To this end, the structures of oligo-Iz, d[A1Iz2A3OXOG4A5]*d[T5C4T3C2T1], and oligo-Oz, d[A1Oz2A3OXOG4A5]*d[T5C4T3C2T1], were optimized at the M06-2X/6-D95**//M06-2X/sto-3G level of theory in the aqueous phase using the ONIOM methodology; all the discussed energies were obtained at the M06-2X/6-31++G** level of theory. The non-equilibrated and equilibrated solvent-solute interactions were taken into consideration. The following results were found: (A) In all the discussed cases, OXOdG showed a higher predisposition to radical cation formation, and B) the excess electron migration toward Iz and Oz was preferred. However, in the case of oligo-Oz, the electron transfer from Oz2 to complementary C4 was noted during vertical to adiabatic anion relaxation, while for oligo-Iz, it was settled exclusively on the Iz2 moiety. The above was reflected in the charge transfer rate constant, vertical/adiabatic ionization potential, and electron affinity energy values, as well as the charge and spin distribution. It can be postulated that imidazolone moiety formation within the CDL ds-oligo structure and its conversion to oxazolone can significantly influence the charge migration process, depending on the C2 carbon hybridization sp2 or sp3. The above can confuse the single DNA damage recognition and removal processes, cause an increase in mutagenesis, and harm the effectiveness of anticancer therapy.

Gum Arabic-Derived Hydroxyproline-Rich Peptides Stimulate Intestinal Nonheme Iron Absorption via HIF2α-Dependent Upregulation of Iron Transport Proteins.

The stimulation of host iron absorption is a promising antianemia strategy adjunctive/alternative to iron intervention. Here, gum arabic (GA) containing 3.14 ± 0.56% hydroxyproline-rich protein with repetitive X-(Pro/Hyp)n motifs was found to increase iron reduction, uptake, and transport to upregulate duodenal cytochrome b (Dcytb), divalent metal transporter 1 (DMT1), ferroportin, and hephaestin to inhibit hypoxia-inducible factor (HIF) prolyl hydroxylase (PHD) and to stabilize HIF2α in polarized Caco-2 cell monolayers in a dose-dependent manner, and this was dependent on its protein fraction, rather than the polysaccharide fraction. Three abundant GA-derived hydroxyproline-containing dipeptides of Hyp-Hyp, Pro-Hyp, and Ser-Hyp were detected by liquid chromatography-mass spectrometry in the lysates of polarized Caco-2 cell monolayers at the maximum levels of 0.167 ± 0.021, 0.134 ± 0.017, and 0.089 ± 0.015 μg/mg of protein, respectively, and showed desirable docking affinity energy values of -7.53, - 7.91, and -7.39 kcal/mol, respectively, against human PHD3. GA-derived peptides also acutely increased duodenal HIF2α stability and Dcytb, DMT1, ferroportin, and hephaestin transcription in rats (P < 0.05). Overall, GA-derived hydroxyproline-rich peptides stimulated intestinal iron absorption via PHD inhibition, HIF2α stabilization, and subsequent upregulation of iron transport proteins.

An activity of flavonoid derived compounds from Medinilla speciosa as anti-hyperpigmentation against tyrosinase proteins with in silico methods

Parijoto (Medinilla speciosa), a typical plant from Indonesia, contains flavonoid compounds as antioxidants. It is able to depigment skin by inhibiting tyrosinase activity during melanogenesis, or melanin formation. Melanogenesis occurs through UV light exposure; it stimulates ROS production and triggers the formation of free radicals and melanogenesis. If not prevented, it will have negative impacts on health. Currently, there is no further research regarding the existence of flavonoid compound derivatives found in parijoto fruit. The aim of this research is to initially identify potential flavonoid derivative compounds as tyrosinase inhibitors using in silico methods. The results can be used as an initial reference for making products based on natural ingredients with minimal side effects. This research uses a bioinformatics approach with the molecular docking method of ligands towards proteins. The stages in this research include: downloading and preparing receptors and ligands; docking with Autodock Vina; visualization of results with Biovia Discovery Studio; data analysis; and discussion. The analysis is carried out by looking at the affinity energy values and complex conformation between the receptor-ligand. The results show flavonoid derivative compounds have the potential to act as tyrosinase inhibitors, as proven by compounds interactions with the active site of tyrosinase to produce the amino acid residues phenylalanine, proline, asparagine, arginine, and histamine. Produce respective affinity energy values, namely -8.9; -7.7; -7.6; -7.5; -7.5; and 7.4 kcal/mol for chalcone, catechin, flavonol, flavanol, flavone, and flavonone compounds. Meanwhile, the comparison compound used is kojic acid, with an affinity energy of -5.5 kcal/mol.

Structural analysis and inhibition capacity of dioscorin protein yam: Theoretical study by molecular docking and dynamic simulations.

Proteases such as trypsins in the gut of Spodoptera frugiperda are responsible for breaking down dietary proteins into amino acids necessary for insect growth and development. In this study, we characterized the insecticidal potential of dioscorin, the storage protein of yam (Dioscorea alata), using molecular docking and molecular dynamics simulations to determine the interactions between trypsin enzymes and the protein inhibitor dioscorin. To achieve this, we used the three-dimensional structures of the trypsin-like digestive enzymes of S. frugiperda, a pest of corn and cotton, as receptors or target molecules. We performed protein-protein docking using Cluspro software, estimation of the binding free energy, and information on the dynamic and time-dependent behavior of dioscorin-trypsin complexes using the NAMD package. Our computational analysis showed that dioscorin can bind to the digestive trypsins of S. frugiperda, as confirmed by the affinity energy values (-1022.4 to -1236.9), stability of the complexes during the simulation trajectory, and binding free energy values between -57.3 and -66.9 kcal/mol. Additionally, dioscorin uses two reactive sites to bind trypsin, but the largest contribution to the interaction energy is made by amino acid residues between amino acid backbone positions 8-14 by hydrogen bonds, hydrophobic, and Van der Waals (VdW) interactions. VdW is the energy that makes the greatest contribution to the binding energy. Collectively, our findings demonstrate, for the first time, the binding capacity of the yam protein dioscorin to the digestive trypsin of S. frugiperda. These promising results suggest a possible bioinsecticide action of dioscorin.

The Influence of 5',8-Cyclo-2'-Deoxyguanosine on ds-DNA Charge Transfer Depends on Its Diastereomeric Form: A Theoretical Study.

The genetic information stored in the nucleobase sequence is continuously exposed to harmful extra- and intra-cellular factors, which can lead to different types of DNA damage, with more than 70 lesion types identified so far. In this article, the influence of a multi-damage site containing (5'R/S) 5',8-cyclo-2'-deoxyguanosine (cdG) and 7,8-dihydro-8-oxo-2'-deoxyguanosine (OXOdG) on charge transfer through ds-DNA was taken into consideration. The spatial geometries of oligo-RcdG: d[A1(5'R)cG2A3OXOG4A5]*d[T5C4T3C2T1] and oligo-ScdG: d[A1(5'S)cG2A3OXOG4A5]*d[T5C4T3C2T1] were optimized at the M06-2X/6-D95**//M06-2X/sto-3G level of theory in the aqueous phase using ONIOM methodology. For all the electronic property energies under discussion, the M06-2X/6-31++G** level of theory was used. Additionally, the non-equilibrated and equilibrated solvent-solute interactions were into consideration. The obtained results confirm the predisposition of OXOdG to radical cation formation regardless of the presence of other lesions in a ds-DNA structure. In the case of electron transfer, however, the situation is different. An excess electron migration towards (5'S)cdG was found to be preferred in the case of oligo-ScdG, while in the case of oligo-RcdG, OXOdG was favored. The above observation was confirmed by the charge transfer rate constant, vertical/adiabatic ionization potential, and electron affinity energy values, as well as the charge and spin distribution analysis. The obtained results indicate that 5',8-cyclo-2'-deoxyguanosine, depending on the C5' atom chirality, can significantly influence the charge migration process through the double helix. The above can be manifested by the slowdown of DNA lesion recognition and removal processes, which can increase the probability of mutagenesis and subsequent pathological processes. With regard to anticancer therapy (radio/chemo), the presence of (5'S)cdG in the structure of formed clustered DNA damage can lead to improvements in cancer treatment.

MOLECULAR DOCKING ANALYSIS OF NATURAL PRODUCTS FROM Centella asiatica FOR INHIBITION OF RENIN

Renin inhibitors derived from natural ingredients often belong to the saponin or polyphenol chemical class. Pegagan (Centella asiatica) is a natural plant in Indonesia that contains saponins and polyphenols. The active compounds of Pegagan include asiaticoside, madasiatic acid, madecassoside, madecassic acid, and asiatic acid. This study investigates the possible renin-inhibitory properties of phytochemicals from Centella asiatica using in-silico molecular docking. Using AutoDock v4.2.6, up to five C. asiatica compounds were docked with 2V0Z Renin with Inhibitor 10 (Aliskiren) in human subjects (Homo sapiens 6LU7). These compounds included asiaticoside, madasiatic acid, madecassoside, madecassid acid, and asiatic acid. SwissADME was used to evaluate these drugs' pharmacokinetic characteristics. The molecular docking results of 5 test ligands obtained affinity energy values from -8.7 kcal/mol to -10.4 kcal/mol. In contrast, the affinity energy value for the comparison ligand (aliskiren) is -9.0 kcal/mol. Madecasosside has an affinity energy value of -10.4 kcal/mol, asiaticoside of -9.6 kcal/mol and asiatic acid of -9.2 kcal/mol. Based on this energy affinity value, the active compound C. asiatica has the potential as a renin inhibitor. Pharmacokinetic analysis revealed that asiatic acid, madecassic acid, madasiatic acid, and asiatic acid have good pharmacokinetic properties. It may be concluded based on in silico molecular docking and pharmacokinetics investigation that the molecule most strongly suggested for additional in vitro renin inhibitor research was asiatic acid.

Investigation renin inhibitor activity from flavonoids derivates by in silico study.

Flavonoids have various pharmacological activities, such as antihypertensive, anticancer, and and antidiabetic effects. Several studies have shown that luteolin, quercetin, kaempferol, myricetin, naringenin, hesperetin, and epicatechin have antihypertensive effects, but the mechanism of action has yet to be discovered with certainty. This study aims to identify flavonoids from luteolin, quercetin, kaempferol, myricetin, naringenin, hesperetin, and epicatechin as renin inhibitors through in silico study; seven flavonoid compounds were docked with 2V0Z with renin inhibitor (Aliskiren) in humans (Homo sapiens 6 LU7) using AutoDock v4.2.6. SwissADME was used to evaluate the pharmacokinetic characteristics of these substances. Results molecular binding of luteolin, quercetin, kaempferol, myricetin, naringenin, hesperetin, and epicatechin, has potential as renin inhibitors with affinity energy values lower than those of aliskiren of -9.3; -9.3; -10.0; -9.2; -9.9; -9.3; and -9.7 kcal/mol. The interactions of these seven compounds have the same catalytic activity as aliskiren on two aspartic acid residues, Asp32 and Asp215. The analysis of pharmacokinetic profiles and the search for physical and chemical properties showed that the seven compounds violated three of the five Lipinski rules, while aliskiren violated one. Hesperitin, kaempferol, and naringenin had similarities with aliskiren on the amino-acid residues in the renin-binding pocket. However, based on pharmacokinetic analysis, the three compounds had an oral pharmacokinetic profile that could have been better than aliskiren.

In-silico study for the identification of potential destabilizers between the spike protein of SARS-CoV-2 and human ACE-2

The emergence of the new SARS-CoV-2 virus, which causes the disease known as COVID-19, has generated a pandemic that has plunged the world into a health crisis. The infection process is triggered by the direct binding of the receptor-binding domain (RBD) of the spike (S) protein of SARS-CoV-2 to the angiotensin-converting enzyme 2 (ACE2) of the host cell. In the present study, virtual screening techniques such as molecular docking, molecular dynamics, calculation of free energy using the GBSA method, prediction of drug similarity, pharmacokinetic, and toxicological properties of various ligands interacting with the RBD-ACE2 complex were applied. The ligands radotinib, hinokiflavone, and ginkgetin were identified as potential destabilizers of the RBD-ACE2 interaction, which could produce their pharmacological effect by interacting at an allosteric site of ACE2, with affinity energy values of −10.2 ± 0.1, −9.8 ± 0.0, and −9.4 ± 0.0 kcal/mol, indicating strong receptor affinity. The complex with hinokiflavone showed the highest conformational stability and rigidity of the dynamic simulation and also obtained the best binding free energy of the three molecules, with an energy of −215.86 kcal/mol.

Leishmanicidal and cytotoxic activity of essential oil from the fruit peel of Myrciaria floribunda (H. West ex Willd.) O. Berg: Molecular docking and molecular dynamics simulations of its major constituent onto Leishmania enzyme targets

Cutaneous Leishmaniasis (CL) is a neglected disease characterized by highest morbidity rates worldwide. The available treatment for CL has several limitations including serious side effects and resistance to the treatment. Herein we aimed to evaluate the activity of essential oil from the peel of Myrciaria floribunda fruits (MfEO) on Leishmania amazonensis. The cytotoxic potential of MfEO on host mammalian cells was evaluated by MTT. The in vitro leishmanicidal effects of MfEO were investigated on the promastigote and intracellular amastigote forms. The ultrastructural changes induced by MfEO were evaluated by Scanning Electron Microscopy (SEM). The molecular docking of the major compounds δ-Cadinene, γ-Cadinene, γ-Muurolene, α-Selinene, α-Muurolene and (E)–Caryophyllene onto the enzymes trypanothione reductase (TreR) and sterol 14-alpha demethylase (C14DM) were performed. Our results showed that MfEO presented moderate cytotoxicity for Vero cells and macrophages. The MfEO inhibited the growth of promastigote and the survival of intracellular amastigotes, in a dose- and time- dependent way. The MfEO presented high selectivity towards amastigote forms, being 44.1 times more toxic for this form than to macrophages. Molecular docking analysis showed that the major compounds of MfEO interact with Leishmania enzymes and that δ-Cadinene (δ-CAD) presented favorable affinity energy values over TreR and C14DM enzymes, when compared with the other major constituents. Molecular dynamics (MD) simulation studies revealed a stable binding of δ-CAD with lowest binding free energy values in MMGBSA assay. Our results suggested that δ-CAD may be a potent inhibitor of TreR and C14DM enzymes. Communicated by Ramaswamy H. Sarma

Detailed Quantum Mechanical Studies on Three Bioactive Benzimidazole Derivatives and Their Raman Enhancement on Adsorption over Graphene Sheets

Benzimidazole derivatives flubendazole (FD1) and similar derivatives, mebendazole (MD2) and ricobendazole (RD3) have been studied by using various computational tools to analyze their geometry and spectral characteristics. The various reactive descriptors obtained from the FMO analysis predict the reactive nature of the compound. The various lone pair/sigma to pi conjugation was analyzed using NBO formalism, which provides valuable information about intra-molecular electron transfer which is vital in predicting the inherent stability of the molecule. Nucleophilic and electrophilic regions of the molecules are identified using MESP, which adds to the reactivity information. The compounds were found to interact with graphene monolayer results show that there is enhancement in various physicochemical descriptors and surface-enhanced Raman spectra (SERS). Prediction of Activity Spectra provide activities, glutathione peroxidase inhibitor, general pump inhibitor, membrane permeability inhibitor for FD1, glutathione peroxidase inhibitor, antihelmintic, antiparasitic for MD2 and antihelmintic, antiparasitic, catalase inhibitor for RD3. Compounds form a stable complex on docking with the receptors. Results also indicate that the ligands adsorbed over graphene also form stable complexes with the receptors as indicated by the high binding affinity energy values.

Identification of New Rofecoxib-Based Cyclooxygenase-2 Inhibitors: A Bioinformatics Approach.

The cyclooxygenase-2 receptor is a therapeutic target for planning potential drugs with anti-inflammatory activity. The selective cyclooxygenase-2 (COX-2) inhibitor rofecoxib was selected as a pivot molecule to perform virtual ligand-based screening from six commercial databases. We performed the search for similarly shaped Rapid Overlay of Chemical Structures (ROCS) and electrostatic (EON) compounds. After, we used pharmacokinetic and toxicological parameters to determine the best potential compounds, obtained through the softwares QikProp and Derek, respectively. Then, the compounds proceeded to the molecular anchorage study, which showed promising results of binding affinity with the hCOX-2 receptor: LMQC72 (∆G = −11.0 kcal/mol), LMQC36 (∆G = −10.6 kcal/mol), and LMQC50 (∆G = −10.2 kcal/mol). LMQC72 and LMQC36 showed higher binding affinity compared to rofecoxib (∆G = −10.4 kcal/mol). Finally, molecular dynamics (MD) simulations were used to evaluate the interaction of the compounds with the target hCOX-2 during 150 ns. In all MD simulation trajectories, the ligands remained interacting with the protein until the end of the simulation. The compounds were also complexing with hCOX-2 favorably. The compounds obtained the following affinity energy values: rofecoxib: ΔGbind = −45.31 kcal/mol; LMQC72: ΔGbind = −38.58 kcal/mol; LMQC36: ΔGbind = −36.10 kcal/mol; and LMQC50: ΔGbind = −39.40 kcal/mol. The selected LMQC72, LMQC50, and LMQC36 structures showed satisfactory pharmacokinetic results related to absorption and distribution. The toxicological predictions of these compounds did not display alerts for possible toxic groups and lower risk of cardiotoxicity compared to rofecoxib. Therefore, future in vitro and in vivo studies are needed to confirm the anti-inflammatory potential of the compounds selected here with bioinformatics approaches based on rofecoxib ligand.

Detailed quantum mechanical studies on bioactive benzodiazepine derivatives and their adsorption over graphene sheets.

Estazolam (Z1) and related derivatives, adinazolam (Z2), alprazolam (Z3), 4-hydroxyalprazolam (Z4) and triazolam (Z5) have been studied by using various computational tools to analyze their geometry and spectral characteristics. The compounds were found to interact with graphene monolayer results shows that there is enhancement in various physico-chemical descriptors and surface enhanced Raman spectra (SERS). The various reactive descriptors obtained from the FMO analysis predict the reactive nature of the compound. The various lone pair/sigma to pi conjugation was analyzed using NBO formalism, which provides valuable information about intra molecular electron transfer which is vital in predicting the inherent stability of the molecule. Simulated electronic spectra using TD-DFT and CAM-B3LYP functional are discussed in detail with respect to electronic transitions and light harvesting efficiency. Suitability of candidates as a photo sensitizer in dye sensitized solar cells was studied and 4-Hydroxyalprazolam is identified as a suitable candidate. Nucleophilic and electrophilic regions of the molecules are identified using MESP, which adds to the reactivity information. It can be seen that the highest interaction energy has been obtained in the case of the Z5-graphene system, while the lowest interaction energy has been obtained in the case of the Z1-graphene system. Docking indicates that the ligands adsorbed over graphene also form stable complexes with the receptors as indicated by the high binding affinity energy values.

In silico study of ginsenoside analogues as possible BACE1 inhibitors involved in Alzheimer's disease

Background: Neurodegenerative disorders such as Alzheimer's disease show an alarming prevalence in the population, with around 50 million affected individuals worldwide, and is associated with the development of dementia, mainly affecting the elderly population. Currently, the treatments used are based on slowing the progression of the clinical symptoms of Alzheimer’s; however, no specific treatment has been found that induces reversion of the disease. Natural products may induce a wide range of palliative effects, such as ginseng (Panax ginseng), which produces secondary metabolites called ginsenosides, which have multiple therapeutic applications, including for neurodegenerative diseases such as Alzheimer’s. Methods: A virtual screening was carried out, using the CHEMBL database to find analogs of ginsenosides based on the ginsenoside Rg1 (CHEMBL501637). Next, the molecules were optimized and their format modified. The structure of BACE1 was downloaded from the Protein Data Bank database (ID: 1FKN) and prepared for the development of molecular docking using the PyRx software. A database of the ligands was created and molecular docking experiments were carried out, obtaining affinity energy values ​​in Kcal/mol. Results: Of the 27 analogues studied, it was found that the molecules CHEMBL451292, CHEMBL510371 and CHEMBL503302 showed considerable affinity with BACE1 when compared with the reference molecules (verubecestat and donepezil). These affinity energy values for CHEMBL451292, CHEMBL510371 and CHEMBL503302 ​​were -9.6, -8.1 and -7.6 Kcal/mol, respectively. Likewise, the binding site of the ligands to BACE1 were identified, with the main interactions being van der Waals and hydrogen bonding. Conclusions: Three ginsenoside analogues showed a similar binding energy with BACE1 compared to the reference drugs. The residues involved in the inhibitory activity of BACE1 and the type of predominant interactions were identified, which agreed with previous reports.

Analysis of Affinity Energy Between Biphenyl Dioxygenase and Polychlorinated Biphenyls Using Molecular Docking

Molecular docking was used to calculate the affinity energy between biphenyl dioxygenases(BphA), i ncluding 1ULJ, 1WQL, 2YFJ, 2YFL, 2GBX, 2XSH, 2E4P, 3GZX, and 3GZY(selected from the Protein Data Bank) and 209 polychlorinated biphenyl(PCB) congeners. The relationships between the calculated affinity energy and the persistent organic pollutant characteristics(migration, octanol-air partition coefficients, lgKOA; persistence, half-life, lgt1/2; toxicity, half-maximal inhibitory concentration, lgIC50; bioaccumulation, bioconcentration factor, lgBCF) of the PCBs were studied to understand the BphA mediated degradation of PCBs. The effect of substituent characteristics on the affinity energy was explored through full factorial experimental design. The affinities of nine kinds of BphA pr oteins on PCBs ranked as follows: 2GBX>2YFJ>2YFL>3GZX>2XSH>3GZY>2E4P>1WQL>1ULJ. The relationships between the calculated affinity energy and the molecular weight, lgKOA, lgBCF, and lgt1/2 of the PCBs were statistically significant(p 0.05). PCBs were more difficult to degrade following an increase in the free energy of binding. Correlation analysis showed that the average affinity energy values of PCBs gradually increased as the number of chlorine atoms increased, r egardless of the substituent position. The substituents at the ortho-positions interacted mainly through a second-order interaction, whereas those at the para-positions did not participate via a second-order interaction.

Discerning the Potential of Chitosan Extracted from Bio Resources as a Competent Brain Drug Carrier to Cross the Blood Brain Barrier

Biopolymer such as chitosan is more favoured as a drug carrier in particular to the brain due to its potential to cross the blood brain barrier. This study is a comparative assessment of the extraction of chitosan from natural sources such as mushroom, crab and shrimp using alkali method pursued by physicochemical assays that surmise the excellence of the biopolymer in permeating a central nervous system drug. Commercially, chitosan extracted from crustaceans have been widely used but this study revealed that mushrooms are also a good source for chitosan. An in silico assay enumerates the structural affiliation of the polymer and its binding efficiency. Molecular docking study facilitates to attest the brain targeting efficiency of chitosan on disparity with sodium alginate against the efflux permeability glycoprotein furnishing a minimum binding affinity energy values of -37.2 kcal/mol. The pharmacologically significant descriptors propose a low solubility that avoids the untargeted discharge of drug. Chitosan extracted from a rich protein source such as mushroom in a mild alkaline condition with a high degree of deacetylation has freer amine groups can act as a drug by itself and can readily bind with a drug as a carrier. The synchronised work of biopolymer extraction with that of in silico analysis can further take chitosan as a lead compound for brain drug development and targeting studies.

Molecular docking between the RNA polymerase of the Moniliophthora perniciosa mitochondrial plasmid and Rifampicin produces a highly stable complex

BackgroundMoniliophthora perniciosa (Stahel) Aime & Phillips-Mora is the causal agent of witches’ broom disease (WBD) in cacao (Theobroma cacao). When the mitochondrial genome of this fungus had been completely sequenced, an integrated linear-type plasmid that encodes viral-like RNA polymerases was found. The structure of this polymerase was previously constructed using a homology modeling approach.MethodsUsing a virtual screening process, accessing the Kegg, PubChem and ZINC databases, we selected the eight most probable macrocyclic polymerase inhibitors to test against M. perniciosa RNA polymerase (RPO). AutoDock Vina was used to perform docking calculations for each molecule. This software returned affinity energy values for several ligand conformations. Subsequently, we used PyMOL 1.4 and Ligand Scout 3.1 to check the stereochemistry of chiral carbons, substructure, superstructure, number of rotatable bonds, number of rings, number of donor groups, and hydrogen bond receptors.ResultsOn the basis of this evidence we selected Rifampicin, a bacterial RNA polymerase inhibitor, and then AMBER 12 was used to simulate the behavior of the RPO-Rifampicin complex after a set of 5000 ps and up to 300 K in water. This calculation returned a graph of potential energy against simulation time and showed that the ligand remained inside the active site after the simulation was complete, with an average energy of -15 x 102 Kcal/Mol.ConclusionsThe results indicate that Rifampicin could be a good inhibitor for testing in vitro and in vivo against M. perniciosa.