Molecular Dynamics Simulation of Bioactive Compounds Against Six Protein Target of Sars-Cov-2 As Covid-19 Antivirus Candidates

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the virus that causes Coronavirus 2019 (COVID-19). To date, there has been no proven effective drug for the treatment or prevention of COVID-19. A study on developing inhibitors for this virus was performed using molecular dynamics simulation. 3CL-Pro, PL-Pro, Helicase, N, E, and M protein were used as protein targets. This study aimed to determine the stability of the selected protein-ligand complex through molecular dynamics simulation by Amber20 to propose bioactive compounds from natural products that have potential as a drug for COVID-19. Based on our previous study, the best value of free binding energy and protein-ligand interactions of the candidate compounds are obtained for each target protein through molecular docking. Corilagin (-14.42 kcal/mol), Scutellarein 7-rutinoside (-13.2 kcal/mol), Genistein 7-O-glucuronide (-10.52 kcal/mol), Biflavonoid-flavone base + 3O (-11.88 and -9.61 kcal/mol), and Enoxolone (-6.96 kcal/mol) has the best free energy value at each protein target. In molecular dynamics simulation, the 3CL-Pro-Corilagin complex was the most stable compared to other complexes, so that it was the most recommended compound. Further research is needed to test the selected ligand activity, which has the lowest free energy value of the six target proteins.

Selection for constrained peptides that bind to a single target protein

Peptide secondary metabolites are common in nature and have diverse pharmacologically-relevant functions, from antibiotics to cross-kingdom signaling. Here, we present a method to design large libraries of modified peptides in Escherichia coli and screen them in vivo to identify those that bind to a single target-of-interest. Constrained peptide scaffolds were produced using modified enzymes gleaned from microbial RiPP (ribosomally synthesized and post-translationally modified peptide) pathways and diversified to build large libraries. The binding of a RiPP to a protein target leads to the intein-catalyzed release of an RNA polymerase σ factor, which drives the expression of selectable markers. As a proof-of-concept, a selection was performed for binding to the SARS-CoV-2 Spike receptor binding domain. A 1625 Da constrained peptide (AMK-1057) was found that binds with similar affinity (990 ± 5 nM) as an ACE2-derived peptide. This demonstrates a generalizable method to identify constrained peptides that adhere to a single protein target, as a step towards “molecular glues” for therapeutics and diagnostics.

Quantitative Characterization of Partitioning in Selection of DNA Aptamers for Protein Targets by Capillary Electrophoresis

Partitioning of protein–DNA complexes from protein-unbound DNA is a key step in selection of DNA aptamers. Conceptually, the partitioning step is characterized by two parameters: transmittance for protein-bound DNA (binders) and transmittance for unbound DNA (nonbinders). Here we present the first study to reveal how these transmittances depend on experimental conditions; such studies are pivotal to the effective planning and control of selection. Our focus was capillary electrophoresis (CE) which is a partitioning approach of high efficiency. By combining a theoretical model and experimental data, we evaluated the dependence of transmittances of binders and nonbinders on the molecular weight of protein target in two modes of CE-based partitioning: nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) and ideal-filter capillary electrophoresis (IFCE). Our data suggest that as the molecular weight of the protein target decreases: (i) the transmittance for binders remains close to unity in NECEEM but decreases drastically in IFCE and (ii) the transmittance for nonbinders increases orders of magnitude in NECEEM but remains relatively stable at a very low level in IFCE. To determine the optimal CE conditions for a given size of protein target, a balance between transmittances of binders and nonbinder must be reached; such a balance would ensure the collection of binders of sufficient purity and quantity. We conclude that, as a rule of thumb, IFCE is preferable for large-size protein targets while NECEEM should be the method of choice for small-size protein targets

Unique N-Terminal Interactions Connect F-BOX STRESS INDUCED (FBS) Proteins to a WD40 Repeat-like Protein Pathway in Arabidopsis

SCF-type E3 ubiquitin ligases provide specificity to numerous selective protein degradation events in plants, including those that enable survival under environmental stress. SCF complexes use F-box (FBX) proteins as interchangeable substrate adaptors to recruit protein targets for ubiquitylation. FBX proteins almost universally have structure with two domains: A conserved N-terminal F-box domain interacts with a SKP protein and connects the FBX protein to the core SCF complex, while a C-terminal domain interacts with the protein target and facilitates recruitment. The F-BOX STRESS INDUCED (FBS) subfamily of plant FBX proteins has an atypical structure, however, with a centrally located F-box domain and additional conserved regions at both the N- and C-termini. FBS proteins have been linked to environmental stress networks, but no ubiquitylation target(s) or biological function has been established for this subfamily. We have identified two WD40 repeat-like proteins in Arabidopsis that are highly conserved in plants and interact with FBS proteins, which we have named FBS INTERACTING PROTEINs (FBIPs). FBIPs interact exclusively with the N-terminus of FBS proteins, and this interaction occurs in the nucleus. FBS1 destabilizes FBIP1, consistent with FBIPs being ubiquitylation targets SCFFBS1 complexes. This work indicates that FBS proteins may function in stress-responsive nuclear events, and it identifies two WD40 repeat-like proteins as new tools with which to probe how an atypical SCF complex, SCFFBS, functions via FBX protein N-terminal interaction events.

Gene-teratogen interactions influence the penetrance of birth defects by altering Hedgehog signaling strength

ABSTRACT Birth defects result from interactions between genetic and environmental factors, but the mechanisms remain poorly understood. We find that mutations and teratogens interact in predictable ways to cause birth defects by changing target cell sensitivity to Hedgehog (Hh) ligands. These interactions converge on a membrane protein complex, the MMM complex, that promotes degradation of the Hh transducer Smoothened (SMO). Deficiency of the MMM component MOSMO results in elevated SMO and increased Hh signaling, causing multiple birth defects. In utero exposure to a teratogen that directly inhibits SMO reduces the penetrance and expressivity of birth defects in Mosmo−/− embryos. Additionally, tissues that develop normally in Mosmo−/− embryos are refractory to the teratogen. Thus, changes in the abundance of the protein target of a teratogen can change birth defect outcomes by quantitative shifts in Hh signaling. Consequently, small molecules that re-calibrate signaling strength could be harnessed to rescue structural birth defects.

Potensi Sinamaldehid sebagai Anti Hiperpigmentasi secara In Silico

Permasalahan kulit yang sering ditemui yaitu hiperpigmentasi yang terjadi akibat adanya sintesis melanin berlebihan yang menyebabkan penggelapan warna kulit. Hiperpigmentasi dapat diatasi dengan agen anti hiperpigmentasi yang beraktivitas dalam menghambat proses sintesis melanin. Sintesis melanin dapat dihambat dengan berbagai cara salah satunya dengan menghambat aktivitas tyrosinase. Tyrosinase merupakan enzim yang berperan dalam mengkatalisis proses biosintesis melanin. Sinamaldehid merupakan senyawa bahan alam banyak ditemukan pada tanaman Cinnamomum burmanni mempunyai aktivitas sebagai antioksidan. Penelitian ini bertujuan untuk mengetahui potensi sinamaldehid dalam menghambat tyrosinase yang akan dibandingkan dengan native liganya secara in silico. Uji in silico dilakukan secara docking molecular dengan tahapan yaitu preparasi dan optimasi sinamaldehid, preparasi tyrosinase serta validasi dan docking. Metode docking molecular telah dinyatakan valid karena RMSD (root mean square distance) yang diperoleh tidak lebih dari 3 Å. Analisis data dilakukan dengan melihat energi ikatan yang dihasilkan dan ikatan yang terbentuk antara senyawa dengan residu asam amino pada protein. Nilai energi ikatan yang diperoleh antara ikatan sinamaldehid dengan tyrosinase adalah-6,21 kkal/mol. Sedangkan energi ikatan antara tyrosinase dengan native ligandnya -4,79 kkal/mol. Hal tersebut menunjukkan afinitas dari sinamaldehid pada protein tyrosinase lebih besar dibandingkan native ligandnya, sehingga sinamaldehid dikatakan memiliki potensi sebagai anti hiperpigmentasi dengan mekanisme molecular berupa inhibitor protein target tyrosinase sehingga dapat menghambat aktivitas enzim tyrosinase.

Hesperidin Interaction with HMG-CoA-Reductase Enzyme in Hypercholesterolemia: A Study in Silico

Dyslipidemia is a degenerative disease occurred with increased levels of fat and cholesterol levels in blood. One of the proteins used as anti-cholesterol is an HMG-CoA-Reductase. Hesperidin in orange peel can reduce cholesterol levels by interacting with HMG-CoA-Reductase. To prove this, an in silico method was used by using swissdock.ch (http://swissdock.ch/docking#). The receptor protein in dyslipidemia was obtained from the RCSB Protein Data Bank (https://www.rcsb.org) namely HMG-CoA-reductase receptor with code PDB: 1HW9. The natural ligand, hesperidin, was obtained from PubChem with code: 10621 (https://pubchem.ncbi.nlm.nih.gov/). Protein was prepared by omitting the natural ligand residues present in the protein. Ligand and protein preparations were used by the chimera 1.15. The result of this study indicated that the interaction of hesperidin with several amino acid recidues was predicted to provide inhibitory activity on HMG-CoA reductase as the protein target. Inhibition of HMG-CoA reductase will reduce mevalonate synthesis so that cholesterol levels will decrease. Keywords: hesperidin, HMG-CoA-Reductase, cholesterol, dyslhahipidemia

Selective Covalent Targeting of SARS-CoV-2 Main Protease by Enantiopure Chlorofluoroacetamide

The pandemic of COVID-2019 has urged the development of antiviral agents against its causative pathogen SARS-CoV-2. The main protease (Mpro), a cysteine protease essential for viral replication, is a promising protein target. Here we report an irreversible SARS-CoV-2 Mpro inhibitor possessing chlorofluoroacetamide (CFA) as the warhead for covalent modification of Mpro. Ugi multi-component reaction employing chlorofluoroacetic acid allowed rapid generation of CFA derivatives, of which diastereomers displayed significantly different inhibitory activity against Mpro. We established a practical protocol for the optical resolution of chlorofluoroacetic acid, which enable the isolation of the stereoisomers of the best CFA compound. Kinetic analysis revealed that (R)-CFA is crucial for both binding affinity and the rate of irreversible inactivation of Mpro. Our findings highlight the prominent influence of the CFA chirality on the covalent modification of cysteine, and provide the basis for improving the potency and selectivity in the development of novel CFA-based covalent inhibitors.

Searching Anti-Zika Virus Activity in 1H-1,2,3-Triazole Based Compounds

Zika virus (ZIKV) is a mosquito-borne virus belonging to the Flaviviridae family and is responsible for an exanthematous disease and severe neurological manifestations, such as microcephaly and Guillain-Barré syndrome. ZIKV has a single strand positive-sense RNA genome that is translated into structural and non-structural (NS) proteins. Although it has become endemic in most parts of the tropical world, Zika still does not have a specific treatment. Thus, in this work we evaluate the cytotoxicity and antiviral activities of 14 hybrid compounds formed by 1H-1,2,3-triazole, naphthoquinone and phthalimide groups. Most compounds showed low cytotoxicity to epithelial cells, specially the 3b compound. After screening with all compounds, 4b was the most active against ZIKV in the post-infection test, obtaining a 50% inhibition concentration (IC50) of 146.0 µM and SI of 2.3. There were no significant results for the pre-treatment test. According to the molecular docking compound, 4b was suggested with significant binding affinity for the NS5 RdRp protein target, which was further corroborated by molecular dynamic simulation studies.

Triple Targeting of Human IMPDH and Both RdRps of SARS-CoV-2 and Rhizopus Oryzae: An in Silico Perspective

Mucormycosis has been reported in many regions associated with SARS-CoV-2 infections during the past few months. The viral RNA-dependent RNA polymerase (RdRp) is a crucial protein target in viral and fungal pathogens. Molecular docking combined with molecular dynamics simulation (MDS) is utilized to test nucleotide-based inhibitors against the RdRps of SARS-CoV-2 solved structure and Rhizopus oryzae RdRp model built in silico. Additionally, the human Inosine monophosphate dehydrogenase (IMPDH) was targeted by the same inhibitors. The results reveal a comparable binding affinity of four nucleotide derivatives compared to remdesivir and sofosbuvir against both IMPDH and the RdRps of SARS-CoV-2 and Rhizopus oryzae, the main causing agent of mucormycosis. The binding affinities are calculated using different conformations of the RdRps after 100 ns MDS and trajectories clustering. The present study suggests the triple inhibition potential of four nucleotide inhibitors against SARS-CoV-2 & R. oryzae RdRps and the human IMPDH, while experimental validation is yet to be performed.