Cheminformatics for Biomedical Drug Discovery

This program is designed for beginners and students who are eager to learn about this fascinating field of computational structural biology and cheminformatics. This collaborative training is prepared and delivered by leaders in various biotechnology and Pharma industries to address the need to introduce students and researchers to utilize public repositories, and open-source tools and to develop quality research projects using structural biology analysis and applying cheminformatics tools. The interested students/researchers will also have the opportunity to learn about the application of R & python for cheminformatics & drug discovery.

It has been well established that discovering and developing drugs is an extensive and expensive process. However, since 2020, there has been a phenomenal demand to increase the use of bioinformatics, cheminformatics, and the use of ML, and artificial intelligence for vaccine and drug development. With the rapidly growing amount of complex healthcare and biological data and the increasing complexities of analysis, every day cutting-edge innovations are bringing new things to learn, hence it is quite challenging for beginners to start their research journey in this fascinating field. To overcome these challenges and bring high-quality summer research training in the field of cheminformatics & drug discovery,  we developed & designed an innovative and industry-driven project-based training opportunity for everyone. 

Pre-Register for the Cheminformatics for Biomedical Drug Discovery Program

Topics & Computational Tools (Sessions)

  • Introduction to computational structural biology:  (RCSB Protein Data Bank, PDBSUM, PDBe, PDBj, BMRB, SCOP, and CATH)
  • Introduction to cheminformatics: Structures, Chemical interactions, and Databases  (PubChem, ZINC, ChEMBL)
  • Molecular Visualization, Molecular Modelling, AI for protein folding & prediction (PyMol, UCSF Chimera, Modeller & Alpha Fold)
  • Overview of modern data-driven drug discovery (DataWarrior)
  • Chemical & Protein Databases (Exploration and download data)
  • Structure-based drug discovery (Auto Dock & Argus lab)
  • Advanced Cheminformatics: (Machine learning, Chemical modifications & optimizations)
  • Cheminformatics Research Projects (Industry Projects, Skill Sets, Opportunities & Limitations)

Industry Panel Discussion  Cheminformatics, Bioinformatics & Drug Discovery

The training will be led by the recognized industry leaders and mentors from the elite group of Omics Logic Industry expert panel (FABA, Pine Biotech & Science gurus) to help students, researchers, and scientists utilize structure biology and apply cheminformatics for drug discovery.  This research training is designed to enable students to learn basic concepts of structural biology and to start applying by working and utilizing specialized algorithms and tools that have been utilized by industry and research labs to innovate, discover and answer some of the important biological questions. 

Cheminformatics for Biomedical Drug Discovery

PROGRAM SESSIONS


SESSION TOPICS, MENTORS & RESOURCES

Slide1

Mentor: Dr. Mohit Mazumder, Pine Biotech    

Hands-on session: Biomolecular Visualization

Computational Structural Biology

  • Molecular structure of biological macromolecules, History and techniques, Amino acids structure and function, 
  • Protein structures: Primary, Secondary, Tertiary, Quaternary structure, Structural domain, Structural motif, Protein subunit.
  • Protein-Protein Interactions, Conformational analysis, Protein folding, Sequence to structure to function relationship

Tutorial/ Course work:

Basics of structural Biology, History & Biological Repositories and Structure File formats. 

Tools & database: Pymol, Rasmol, RCSB Protein Data Bank, PDBSUM, PDBe, PDBj, BMRB, SCOP, and CATH

Slide2

Cheminformatics overview, cheminformatics in drug discovery pipeline, Key-business in cheminformatics

Introduction to Cheminformatics
  • Introduction to structure, chemical interaction
  •  Chemical Data: small molecule formulas, structures, properties, spectra, and activities (biological or industrial)
  • Cheminformatics overview, cheminformatics in drug discovery pipeline, Key-business in cheminformatics, 
Hands-on session: Chemical Space exploration 

Course work:

Tools & database: Data Warrier, Pubchem & Open-molecules

Tutorials:  Chemical Repositories, Small molecule structure File formats 

Slide3

Course work: Chemical & proteins DBs in Drug Discovery process, Tools for data exploration 
Tools & database:  PubChem, ZINC, ChEMBL, Drug Bank, Weka, CDK GitHub, Scikit learn, Datawarrior

Chemical & Protein Databases (Exploration and download data)

  • PubChem: The world's largest collection of freely available chemical information,
  • ZINC: It is a very similar database to Pubchem but with fewer chemicals.
  • ChEMBL: It is a manually curated dataset for bioactive molecules with drug-like properties.
  • RCSB, CAS SciFinder

Hands-on: Data warrior and UCSF chimera.

Tutorial: Exploration and download data:  PubChem, ZINC, ChEMBL, Data warrior     

Slide4

Hands-on: 

  • Molecular Modelling using Swiss Model and Alpha Fold
  • Tools for 3D structure analysis (Binding Site analysis & predictions)

Target Structure Prediction

  • Overview of Drug Discovery Pipeline, Target prediction & assessment in Industry and Pharma: A case study  
  • Introduction to  3D-Structure prediction: 

Tutorial/ Course work:

Overview of Target structure prediction, Overview of Molecular Modelling: Tutorial: Modeller & Alpha Fold 

Online  Tools & database: Modeller, Swiss-Model, AlphaFold, Chimera, Swiss-Prot & EMBL Repositories  

Slide5

Session 5: Target Identification & Virtual screening

 

  • Molecular structure of biological macromolecules, History and techniques, Amino acids structure and function
  • Protein structures: Primary, Secondary, Tertiary, Quaternary structure, Structural domain, Structural motif, Protein subunit.
  • Protein-Protein Interactions, Conformational analysis, Protein folding, Sequence to structure to function relationship
  • Hands-on session: Biomolecular Visualization

Slide6

Tutorials: Autodock & ArgusLab

Tools & database:  Autodock & ArgusLab

Practical experience in Docking

  • Molecular Docking and stage of Drug Discovery Process 
  • Screening using Public repositories 
  • Ligand target binding, Virtual Screening, target fishing & Profiling, Adverse drug reaction, Pharmacology & Drug repurposing 
  • Hands-on: Autodock/ArgusLab
  • Practical aspects of ligand conformations, rigidity, and the number of degrees of freedom

Course work: Molecular Docking and stage of Drug Discovery Process 

Slide7

 

 Data Science & AI in Healthcare: Cheminformatics using R

  • SMILES Notation
  • SMARTS: Highlight substructural patterns/Pharmacophores bold text
  • Highlight atoms based on attributes
  • Operator precedence
  • Recursive SMARTS
  • Component level grouping
  • Substructure/pharmacophore search
  • Chemical databases
  • In-silico toxicity prediction

Slide8

Recent Advances in Drug Discovery

  • Introduction to Drug Discovery Process
  • High Throughput Process
  • Structural Biology & SBDD
  • Biology
  • Selectivity Screen
  • Discovery of Crizotinib,  a kinase inhibitor for lung cancer
  • Summary

Slide9

 AI in Molecular Drug Discovery

  • Molecular structure of biological macromolecules, History and techniques, Amino acids structure and function
  • Protein structures: Primary, Secondary, Tertiary, Quaternary structure, Structural domain, Structural motif, Protein subunit.
  • Protein-Protein Interactions, Conformational analysis, Protein folding, Sequence to structure to function relationship
  • Hands-on session: Biomolecular Visualization

 

Slide10

 

 Advanced Cheminformatics 

  • Calculation of key Chemical properties
  • Generation of new chemical compounds
  • Identification of chemical representatives
  • Hands-on Practical sessions on DataWarrior

 

Slide11

 

  Cheminformatics Research Projects: Expert discussions 

  • Designing a cheminformatics research project 
  • Stages of computational research projects
  • Challenges and limitations of computational research projects 
  • Full Drug Discovery Summer program and Omics Logic Research Fellowship 

Tutorial/ Course work: Designing a research project & Project Proposal 

Online  Tools & database: PubMed & Knowledge and Data-Mining logical workflows

Slide12

 

Case Study: Examples of Successful & Failed Drug Development

 

 

 

NOTE : For interested participants in different time zones, the sessions will be recorded and made available to the registered cohort.

Register for the Upcoming Webinar Session & Program details: