Staff Profile: Alexey V. Zakharov

Alexey V. Zakharov, Ph.D.


Division of Preclinical Innovation

National Center for Advancing Translational Sciences

National Institutes of Health

Email Alexey V. Zakharov


Alexey Zakharov is the informatics leader of an early therapeutic discovery project team in the informatics group within NCATS’ Division of Preclinical Innovation, where he manages and coordinates the team’s efforts to achieve project deliverables and milestones. Zakharov also manages the data science needs of early drug discovery projects, analyzing screening data, identifying chemical series for lead optimization and follow-up studies, and developing and applying artificial intelligence (AI) and modern machine learning approaches for therapeutic programs. He oversees the proper application of cheminformatics techniques and targeted molecular design to deliver compounds with improved properties, having better selectivity and safety margins. Zakharov also works on a variety of projects focused on cancer and cardiovascular, neurological, viral and inflammatory diseases.

Before joining NCATS in 2015, Zakharov worked in the Chemical Biology Laboratory at the National Cancer Institute (NCI), where he strengthened his expertise in the cheminformatics field, applying and developing in silico methods to aid in the drug discovery and design projects of the Computer-Aided Drug Design Group. His work focused on developing computer-based techniques for predicting the toxicity, metabolism and anti-cancer activities of chemical compounds. Prior to his tenure at NCI, Zakharov was a scientist in the Structure-Function Based Drug Design Laboratory at the Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, where he worked on developing computer methods for quantitative structure-activity relationships (QSAR) modeling to predict the biological activity of new chemical compounds. He also conducted independent computational drug discovery research, including target identification, hit finding and optimization.

Zakharov graduated with a master’s degree in biochemistry from Russian State Medical University, Moscow, Russia, in 2005. He received his doctorate in bioinformatics from the Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences in 2008.

Research Topics

Zakharov’s research is based on the strong overlap between different scientific fields, including bioinformatics, cheminformatics, biochemistry, computational chemistry and toxicology, statistics, and AI/machine learning. His main research interests are concentrated on computer-aided drug design (anti-cancer and anti-viral activity, selectivity to certain kinase and/or G-protein coupled receptors, etc.) and the development of innovative methodologies and applications in computational modeling. Problems of particular interest include novel approaches to modeling imbalanced datasets; implementation and usage of biological descriptors, as well as descriptor-free techniques; modeling of nanoparticles; new applications of deep learning and AI approaches; risk assessment of potential compound toxicity; system biology problems (modeling protein-protein interactions, pathway analysis); and computational chemistry modeling (predicting chemical reactions, reaction routes and yields).

Selected Publications

  1. Machine Learning Approaches as Tools to Accelerate Drug Discovery
  2. QSAR Modeling of Imbalanced High-Throughput Screening Data in PubChem
  3. Alarms About Structural Alerts
  4. Cell Lysate-Based AlphaLISA Deubiquitinase Assay Platform for Identification of Small Molecule Inhibitors
  5. Programmable Nucleic Acid Based Polygons with Controlled Neuroimmunomodulatory Properties for Predictive QSAR Modeling