Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

https://pubs.rsc.org/en/content/articlepdf/2019/NP/C8NP00092A

Marine natural products.

A new coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the aetiological agent responsible for the 2019–2020 viral pneumonia outbreak of coronavirus disease 2019 (COVID-19)1–4. Currently, there are no targeted therapeutic agents for the treatment of this disease, and effective treatment options remain very limited. Here we describe the results of a programme that aimed to rapidly discover lead compounds for clinical use, by combining structure-assisted drug design, virtual drug screening and high-throughput screening. This programme focused on identifying drug leads that target main protease (Mpro) of SARS-CoV-2: Mpro is a key enzyme of coronaviruses and has a pivotal role in mediating viral replication and transcription, making it an attractive drug target for SARS-CoV-25,6. We identified a mechanism-based inhibitor (N3) by computer-aided drug design, and then determined the crystal structure of Mpro of SARS-CoV-2 in complex with this compound. Through a combination of structure-based virtual and high-throughput screening, we assayed more than 10,000 compounds—including approved drugs, drug candidates in clinical trials and other pharmacologically active compounds—as inhibitors of Mpro. Six of these compounds inhibited Mpro, showing half-maximal inhibitory concentration values that ranged from 0.67 to 21.4 μM. One of these compounds (ebselen) also exhibited promising antiviral activity in cell-based assays. Our results demonstrate the efficacy of our screening strategy, which can lead to the rapid discovery of drug leads with clinical potential in response to new infectious diseases for which no specific drugs or vaccines are available. A programme of structure-assisted drug design and high-throughput screening identifies six compounds that inhibit the main protease of SARS-CoV-2, demonstrating the ability of this strategy to isolate drug leads with clinical potential.

/pdf/structure-of-mpro-from-sars-cov-2-and-discovery-of-its-2hyiph66s6.pdf

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

This report describes a number of substructural features which can help to identify compounds that appear as frequent hitters (promiscuous compounds) in many biochemical high throughput screens. The compounds identified by such substructural features are not recognized by filters commonly used to identify reactive compounds. Even though these substructural features were identified using only one assay detection technology, such compounds have been reported to be active from many different assays. In fact, these compounds are increasingly prevalent in the literature as potential starting points for further exploration, whereas they may not be.

/pdf/new-substructure-filters-for-removal-of-pan-assay-3e3dudtvn0.pdf

New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays

A variety of N-substituted 3-arylisoquinolone derivatives are synthesized via [2,3] or [3,3] rearrangement reactions of corresponding O-substituted 3-arylisoquinolines.

Discovery of N-Substituted 3-Arylisoquinolone Derivatives as Antitumor Agents Originating from O-Substituted 3-Arylisoquinolines via [2,3] or [3,3] Rearrangement.

Provided are 1-(3-aminopropyl) substituted cyclic amine compounds as represented by formula (I), pharmaceutically acceptable salts, enantiomers, diastereoisomers, racemates and mixtures thereof, and a method of synthesizing said 1-(3-aminopropyl) substituted cyclic amine compounds by using aromatic heterocyclic formaldehyde as raw material. Said compounds can be used as CCR 5 antagonist for the treatment of HIV infection.

1-(3-aminopropyl) substituted cyclic amine compounds, preparation method therefor, and pharmaceutical compositions and uses thereof

Synthesis and Antibacterial Activity of Oxazolidinone Containing Sulfonyl Group.

The present invention discloses 3D-structure of SARS-CoV Viral 3CL Protease obtained through molecular simulation. The 3D-structure is used as a drug target for screening the existing medical database CMC (Comprehensive Medicinal Chemistry, MDL Information System, Inc.), and a group of compounds which have the activity of inhibiting SARS-CoV virus 3CL Protease are found. Cinanserin was tested at molecular and viral levels, and it was found to be able to inhibit the SARS-CoV viral 3CL protease and SARS-CoV viruses. Cinanserin analogs were synthesized and tested at molecular and viral levels, they were found to be able to inhibit the SARS-CoV virus 3CL Protease and SARS-CoV viruses, and may be used for treating and/or preventing SARS-CoV virus infection.

Kaixian Chen

Papers

Discovery of N-Substituted 3-Arylisoquinolone Derivatives as Antitumor Agents Originating from O-Substituted 3-Arylisoquinolines via [2,3] or [3,3] Rearrangement.

1-(3-aminopropyl) substituted cyclic amine compounds, preparation method therefor, and pharmaceutical compositions and uses thereof

Synthesis and Antibacterial Activity of Oxazolidinone Containing Sulfonyl Group.

3D-structure model of SARS coronavirus 3CL protease and anti-SARS drugs

Microwave-Assisted Rapid Synthesis of 2,6,9-Substituted Purines.