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Rahman ASMZ, Liu C, Sturm H, Hogan AM, Davis R, Hu P, Cardona ST. A machine learning model trained on a high-throughput antibacterial screen increases the hit rate of drug discovery. PLoS Comput Biol 2022; 18:e1010613. [PMID: 36228001 PMCID: PMC9624395 DOI: 10.1371/journal.pcbi.1010613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 11/01/2022] [Accepted: 09/26/2022] [Indexed: 01/24/2023] Open
Abstract
Screening for novel antibacterial compounds in small molecule libraries has a low success rate. We applied machine learning (ML)-based virtual screening for antibacterial activity and evaluated its predictive power by experimental validation. We first binarized 29,537 compounds according to their growth inhibitory activity (hit rate 0.87%) against the antibiotic-resistant bacterium Burkholderia cenocepacia and described their molecular features with a directed-message passing neural network (D-MPNN). Then, we used the data to train an ML model that achieved a receiver operating characteristic (ROC) score of 0.823 on the test set. Finally, we predicted antibacterial activity in virtual libraries corresponding to 1,614 compounds from the Food and Drug Administration (FDA)-approved list and 224,205 natural products. Hit rates of 26% and 12%, respectively, were obtained when we tested the top-ranked predicted compounds for growth inhibitory activity against B. cenocepacia, which represents at least a 14-fold increase from the previous hit rate. In addition, more than 51% of the predicted antibacterial natural compounds inhibited ESKAPE pathogens showing that predictions expand beyond the organism-specific dataset to a broad range of bacteria. Overall, the developed ML approach can be used for compound prioritization before screening, increasing the typical hit rate of drug discovery.
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Affiliation(s)
| | - Chengyou Liu
- Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Hunter Sturm
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew M. Hogan
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Rebecca Davis
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Pingzhao Hu
- Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Silvia T. Cardona
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, Canada
- * E-mail:
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Singh S, Numan A, Somaily HH, Gorain B, Ranjan S, Rilla K, Siddique HR, Kesharwani P. Nano-enabled strategies to combat methicillin-resistant Staphylococcus aureus. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 129:112384. [PMID: 34579903 DOI: 10.1016/j.msec.2021.112384] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 12/24/2022]
Abstract
The emergence of methicillin-resistant Staphylococcus aureus (MRSA) has become a threat to global health because of limited treatments. MRSA infections are difficult to treat due to increasingly developing resistance in combination with protective biofilms of Staphylococcus aureus (S. aureus). Nanotechnology-based research revealed that effective MRSA treatments could be achieved through targeted nanoparticles (NPs) that withstand biological films and drug resistance. Thus, the principal aim towards improving MRSA treatment is to advance drug delivery tools, which successfully address the delivery-related problems. These potential delivery tools would also carry drugs to the desired sites of therapeutic action to overcome the adverse effects. This review focused on different types of nano-engineered carriers system for antimicrobial agents with improved therapeutic efficacy of entrapped drugs. The structural characteristics that play an essential role in the effectiveness of delivery systems have also been addressed with a description of recent scientific advances in antimicrobial treatment, emphasizing challenges in MRSA treatments. Consequently, existing gaps in the literature are highlighted, and reported contradictions are identified, allowing for the development of roadmaps for future research.
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Affiliation(s)
- Sima Singh
- IES Institute of Pharmacy, IES University, Kalkheda, Ratibad Main Road, Bhopal 462044, Madhya Pradesh, India
| | - Arshid Numan
- Graphene & Advanced 2D Materials Research Group (GAMRG), School of Engineering and Technology, Sunway University, No. 5, Jalan University, Bandar Sunway, 47500 Petaling Jaya, Selangor, Malaysia.
| | - Hamoud H Somaily
- Department of Physics, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, P. O. Box 9004, Saudi Arabia
| | - Bapi Gorain
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor 47500, Malaysia
| | - Sanjeev Ranjan
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Kirsi Rilla
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Hifzur R Siddique
- Molecular Cancer Genetics & Translational Research Lab, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh 202002, India
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India.
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