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Dong W, Zhang P. Predicting anti-trypanosome effect of carbazole-derived compounds by powerful SVM with novel kernel function and comprehensive learning PSO. Antimicrob Agents Chemother 2024; 68:e0026524. [PMID: 38808999 PMCID: PMC11232408 DOI: 10.1128/aac.00265-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/25/2024] [Indexed: 05/30/2024] Open
Abstract
In order to predict the anti-trypanosome effect of carbazole-derived compounds by quantitative structure-activity relationship, five models were established by the linear method, random forest, radial basis kernel function support vector machine, linear combination mix-kernel function support vector machine, and nonlinear combination mix-kernel function support vector machine (NLMIX-SVM). The heuristic method and optimized CatBoost were used to select two different key descriptor sets for building linear and nonlinear models, respectively. Hyperparameters in all nonlinear models were optimized by comprehensive learning particle swarm optimization with low complexity and fast convergence. Furthermore, the models' robustness and reliability underwent rigorous assessment using fivefold and leave-one-out cross-validation, y-randomization, and statistics including concordance correlation coefficient (CCC), [Formula: see text] , [Formula: see text] , and [Formula: see text] . Among all the models, the NLMIX-SVM model, which was established by support vector regression using a nonlinear combination of radial basis kernel function, sigmoid kernel function, and linear kernel function as a new kernel function, demonstrated excellent learning and generalization abilities as well as robustness: [Formula: see text] = 0.9581, mean square error (MSE) = 0.0199 for the training set and [Formula: see text] = 0.9528, MSE = 0.0174 for the test set. [Formula: see text] , [Formula: see text] , CCC, [Formula: see text] , [Formula: see text], and [Formula: see text] are 0.9539, 0.8908, 0.9752, 0.9529, 0.9528, and 0.9633, respectively. The NLMIX-SVM method proved to be a promising way in quantitative structure-activity relationship research. In addition, molecular docking experiments were conducted to analyze the properties of new derivatives, and a new potential candidate drug molecule was ultimately found. In summary, this study will provide help for the design and screening of novel anti-trypanosome drugs.
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Affiliation(s)
- Wenzhe Dong
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong Province, China
| | - Peijian Zhang
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong Province, China
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Singh B, Sharma A, Gunaganti N, Rivers M, Gadekar PK, Greene B, Chichioco M, Sanz-Rodriguez CE, Fu C, LeBlanc C, Burchfield E, Sharif N, Hoffman B, Kumar G, Purmal A, Mensa-Wilmot K, Pollastri MP. Chemical Optimization of CBL0137 for Human African Trypanosomiasis Lead Drug Discovery. J Med Chem 2023; 66:1972-1989. [PMID: 36695630 PMCID: PMC9923759 DOI: 10.1021/acs.jmedchem.2c01767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The carbazole CBL0137 (1) is a lead for drug development against human African trypanosomiasis (HAT), a disease caused by Trypanosoma brucei. To advance 1 as a candidate drug, we synthesized new analogs that were evaluated for the physicochemical properties, antitrypanosome potency, selectivity against human cells, metabolism in microsomes or hepatocytes, and efflux ratios. Structure-activity/property analyses of analogs revealed eight new compounds with higher or equivalent selectivity indices (5j, 5t, 5v, 5w, 5y, 8d, 13i, and 22e). Based on the overall compound profiles, compounds 5v and 5w were selected for assessment in a mouse model of HAT; while 5v demonstrated a lead-like profile for HAT drug development, 5w showed a lack of efficacy. Lessons from these studies will inform further optimization of carbazoles for HAT and other indications.
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Affiliation(s)
- Baljinder Singh
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Amrita Sharma
- Department
of Molecular and Cellular Biology, Kennesaw
State University, Kennesaw, Georgia 30144, United States
| | - Naresh Gunaganti
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Mitch Rivers
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Pradip K. Gadekar
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Brady Greene
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Michael Chichioco
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Carlos E. Sanz-Rodriguez
- Center
for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, United States
| | - Courtney Fu
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Catherine LeBlanc
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Erin Burchfield
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Nyle Sharif
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Benjamin Hoffman
- Center
for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, United States
| | - Gaurav Kumar
- Department
of Molecular and Cellular Biology, Kennesaw
State University, Kennesaw, Georgia 30144, United States
| | - Andrei Purmal
- Incuron
Inc., Buffalo, New York 14203, United States
| | - Kojo Mensa-Wilmot
- Department
of Molecular and Cellular Biology, Kennesaw
State University, Kennesaw, Georgia 30144, United States,Center
for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, United States,
| | - Michael P. Pollastri
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States,
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Sharma A, Cipriano M, Ferrins L, Hajduk SL, Mensa-Wilmot K. Hypothesis-generating proteome perturbation to identify NEU-4438 and acoziborole modes of action in the African Trypanosome. iScience 2022; 25:105302. [PMID: 36304107 PMCID: PMC9593816 DOI: 10.1016/j.isci.2022.105302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/24/2022] [Accepted: 09/29/2022] [Indexed: 11/29/2022] Open
Abstract
NEU-4438 is a lead for the development of drugs against Trypanosoma brucei, which causes human African trypanosomiasis. Optimized with phenotypic screening, targets of NEU-4438 are unknown. Herein, we present a cell perturbome workflow that compares NEU-4438's molecular modes of action to those of SCYX-7158 (acoziborole). Following a 6 h perturbation of trypanosomes, NEU-4438 and acoziborole reduced steady-state amounts of 68 and 92 unique proteins, respectively. After analysis of proteomes, hypotheses formulated for modes of action were tested: Acoziborole and NEU-4438 have different modes of action. Whereas NEU-4438 prevented DNA biosynthesis and basal body maturation, acoziborole destabilized CPSF3 and other proteins, inhibited polypeptide translation, and reduced endocytosis of haptoglobin-hemoglobin. These data point to CPSF3-independent modes of action for acoziborole. In case of polypharmacology, the cell-perturbome workflow elucidates modes of action because it is target-agnostic. Finally, the workflow can be used in any cell that is amenable to proteomic and molecular biology experiments.
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Affiliation(s)
- Amrita Sharma
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144, USA
| | - Michael Cipriano
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Lori Ferrins
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Stephen L. Hajduk
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Kojo Mensa-Wilmot
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144, USA,Corresponding author
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