In silico evaluation of Philippine Natural Products against SARS-CoV-2 Main Protease.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is a novel strain of coronavirus first reported in December 2019 which rapidly spread throughout the world and was subsequently declared a pandemic by the World Health Organization (WHO) in March 2020. Although vaccines, as well as treatments, have been rapidly developed and deployed, these are still spread thin, especially in the developing world. There is also a continuing threat of the emergence of mutated variants which may not be as responsive to available vaccines and drugs. Accessible and affordable sources of antiviral drugs against SARS-CoV-2 offer wider options for the clinical treatment of populations at risk for severe COVID-19. Using in silico methods, this study identified potential inhibitors against the SARS-CoV-2 main protease (Mpro), the protease directly responsible for the activation of the viral replication enzyme, from a consolidated database of 1516 Philippine natural products. Molecular docking experiments, along with in silico ADME predictions, determined top ligands from this database with the highest potential inhibitory effects against Mpro. Molecular dynamic trajectories of the apo and diosmetin-7-O-b-D-glucopyranoside (DG) in complex with the protein predicted potential mechanisms of action for the ligand-by separating the Cys145-His41 catalytic dyad and by influencing the protein network through key intra-signaling residues within the Mpro binding site. These findings show the inhibitory potential of DG against the SARS-CoV-2 Mpro, and further validation is recommended through in vitro or in vivo experimentation.

In Silico Strategies in Tuberculosis Drug Discovery.

Tuberculosis (TB) remains a serious threat to global public health, responsible for an estimated 1.5 million mortalities in 2018. While there are available therapeutics for this infection, slow-acting drugs, poor patient compliance, drug toxicity, and drug resistance require the discovery of novel TB drugs. Discovering new and more potent antibiotics that target novel TB protein targets is an attractive strategy towards controlling the global TB epidemic. In silico strategies can be applied at multiple stages of the drug discovery paradigm to expedite the identification of novel anti-TB therapeutics. In this paper, we discuss the current TB treatment, emergence of drug resistance, and the effective application of computational tools to the different stages of TB drug discovery when combined with traditional biochemical methods. We will also highlight the strengths and points of improvement in in silico TB drug discovery research, as well as possible future perspectives in this field.

In silico discovery and in vitro activity of inhibitors against Mycobacterium tuberculosis 7,8-diaminopelargonic acid synthase (Mtb BioA).

Computer-aided drug discovery and development approaches such as virtual screening, molecular docking, and in silico drug property calculations have been utilized in this effort to discover new lead compounds against tuberculosis. The enzyme 7,8-diaminopelargonic acid aminotransferase (BioA) in Mycobacterium tuberculosis (Mtb), primarily involved in the lipid biosynthesis pathway, was chosen as the drug target due to the fact that humans are not capable of synthesizing biotin endogenously. The computational screening of 4.5 million compounds from the Enamine REAL database has ultimately yielded 45 high-scoring, high-affinity compounds with desirable in silico absorption, distribution, metabolism, excretion, and toxicity properties. Seventeen of the 45 compounds were subjected to bioactivity validation using the resazurin microtiter assay. Among the 4 actives, compound 7 ((Z)-N-(2-isopropoxyphenyl)-2-oxo-2-((3-(trifluoromethyl)cyclohexyl)amino)acetimidic acid) displayed inhibitory activity up to 83% at 10 µg/mL concentration against the growth of the Mtb H37Ra strain.

Synthesis and crystal structure of [2,7,12-trimethyl-3,7,11,17-tetra-aza-bicyclo-[11.3.1]hepta-deca-1(17),13,15-triene-κ(4) N]copper(II) bis-(perchlorate).

The title copper(II) complex of a pyridine-containing macrocycle (PyMAC), [Cu(C16H28N4)](ClO4)2, has been prepared. The crystal structure reveals the Cu(II) atom to be octahedrally coordinated by a tetradentate aminopyridine macrocyclic ligand surrounding the metal cation in a square-planar geometry. Two weakly bound perchlorate counter-ions occupy the axial sites above and below the macrocyclic plane. The crystal studied was refined as a two-component pseudo-merohedral twin; the refined fractional contribution of the minor component is 38.77 (8).

Toward antituberculosis drugs: in silico screening of synthetic compounds against Mycobacterium tuberculosisl,d-transpeptidase 2.

Mycobacterium tuberculosis (Mtb) the main causative agent of tuberculosis, is the main reason why this disease continues to be a global public health threat. It is therefore imperative to find a novel antitubercular drug target that is unique to the structural machinery or is essential to the growth and survival of the bacterium. One such target is the enzyme l,d-transpeptidase 2, also known as LdtMt2, a protein primarily responsible for the catalysis of 3→3 cross-linkages that make up the mycolyl-arabinogalactan-peptidoglycan complex of Mtb. In this study, structure-based pharmacophore screening, molecular docking, and in silico toxicity evaluations were employed in screening compounds from a database of synthetic compounds. Out of the 4.5 million database compounds, 18 structures were identified as high-scoring, high-binding hits with very satisfactory absorption, distribution, metabolism, excretion, and toxicity properties. Two out of the 18 compounds were further subjected to in vitro bioactivity assays, with one exhibiting a good inhibitory activity against the Mtb H37Ra strain.

Improved screening efficiency for phenylketonuria using a modified bacterial inhibition assay protocol- Autoclaving the bloodspot

The Guthrie bacterial inhibition assay (BIA) tests for elevated phenylalanine (PHE) by measuring B. subtilis growth zone density in an agar medium. Dried blood spots with elevated PHE on initial BIA screening undergo repeat BIA testing and thin-layer chromatography (TLC). Specimens with elevated PHE by TLC or BIA on second-tier testing require recall. To streamline PKU screening and reduce the recall rate, we tested a modified BIA protocol incorporating autoclaving of dried blood spots. Autoclaving improves growth zone appearance and has been previously reported to reduce the number of specimen requiring repeat testing. From June to October 2006, dried blood spot samples with initially elevated PHE were autoclaved at 110°C for 5 min, then retested by BIA. Samples with still-elevated PHE were analyzed by TLC. 1078 of 37,268 samples (2.89%) had initially elevated PHE. After autoclaving, 1036 no longer exhibited elevated PHE decreasing to 42 (0.11%) the number requiring TLC. By comparison, the unmodified algorithm resulted in 3.14% of samples received from July - December 2006 requiring both repeat BIA and TLC testing. We have since modified our PKU screening algorithm to require repeat BIA testing from autoclaved samples prior to TLC analysis. This translates to a significant reduction in time and resources for second-tier testing and follow-up, and prevents stress for the parents of a newborn who would have been recalled unnecessarily.