1
|
Evbuomwan IO, Alejolowo OO, Elebiyo TC, Nwonuma CO, Ojo OA, Edosomwan EU, Chikwendu JI, Elosiuba NV, Akulue JC, Dogunro FA, Rotimi DE, Osemwegie OO, Ojo AB, Ademowo OG, Adeyemi OS, Oluba OM. In silico modeling revealed phytomolecules derived from Cymbopogon citratus (DC.) leaf extract as promising candidates for malaria therapy. J Biomol Struct Dyn 2024; 42:101-118. [PMID: 36974933 DOI: 10.1080/07391102.2023.2192799] [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: 01/02/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023]
Abstract
The emergence of varying levels of resistance to currently available antimalarial drugs significantly threatens global health. This factor heightens the urgency to explore bioactive compounds from natural products with a view to discovering and developing newer antimalarial drugs with novel mode of actions. Therefore, we evaluated the inhibitory effects of sixteen phytocompounds from Cymbopogon citratus leaf extract against Plasmodium falciparum drug targets such as P. falciparum circumsporozoite protein (PfCSP), P. falciparum merozoite surface protein 1 (PfMSP1) and P. falciparum erythrocyte membrane protein 1 (PfEMP1). In silico approaches including molecular docking, pharmacophore modeling and 3D-QSAR were adopted to analyze the inhibitory activity of the compounds under consideration. The molecular docking results indicated that a compound swertiajaponin from C. citratus exhibited a higher binding affinity (-7.8 kcal/mol) to PfMSP1 as against the standard artesunate-amodiaquine (-6.6 kcal/mol). Swertiajaponin also formed strong hydrogen bond interactions with LYS29, CYS30, TYR34, ASN52, GLY55 and CYS28 amino acid residues. In addition, quercetin another compound from C. citratus exhibited significant binding energies -6.8 and -8.3 kcal/mol with PfCSP and PfEMP1, respectively but slightly lower than the standard artemether-lumefantrine with binding energies of -7.4 kcal/mol against PfCSP and -8.7 kcal/mol against PfEMP1. Overall, the present study provides evidence that swertiajaponin and other phytomolecules from C. citratus have modulatory properties toward P. falciparum drug targets and thus may warrant further exploration in early drug discovery efforts against malaria. Furthermore, these findings lend credence to the folkloric use of C. citratus for malaria treatment.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ikponmwosa Owen Evbuomwan
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
- Department of Food Science and Microbiology, Landmark University, Omu-Aran, Nigeria
| | - Omokolade Oluwaseyi Alejolowo
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
| | | | - Charles Obiora Nwonuma
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
| | - Oluwafemi Adeleke Ojo
- Phytomedicine, Molecular Toxicology and Computational Biochemistry Research Group, Department of Biochemistry, Bowen University, Iwo, Nigeria
| | - Evelyn Uwa Edosomwan
- Department of Animal and Environmental Biology, University of Benin, Benin City, Nigeria
| | | | | | | | | | - Damilare Emmanuel Rotimi
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
| | | | | | - Olusegun George Ademowo
- Department of Pharmacology and Therapeutics, Faculty of Basic Medical Sciences, University of Ibadan, Ibadan, Nigeria
- Drug Research Laboratory, Institute of Advanced Medical Research and Training (IMRAT), College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oluyomi Stephen Adeyemi
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
| | - Olarewaju Michael Oluba
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
| |
Collapse
|
2
|
Thabet RH, Alshar BOS, Alabdallah DHS, Alhmoud NAZA, Alslameen STA, Thabet YRH. Structure-activity relationships andz interindividual variability of drug responses: pharmacogenomics with antimicrobial drugs as a paradigm. J Int Med Res 2023; 51:3000605231214065. [PMID: 38019107 PMCID: PMC10687969 DOI: 10.1177/03000605231214065] [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: 06/23/2023] [Accepted: 10/11/2023] [Indexed: 11/30/2023] Open
Abstract
Adverse drug reactions represent a major health burden because they cause notable patient morbidity and mortality. From this viewpoint, several strategies have been developed to prevent or reduce adverse drug reactions. One such strategy is the use of pharmacogenomics. Interindividual variability in drug response and adverse effects is mainly attributable to genetic variation in enzymes such as sulfotransferases and cytochrome P450s. The current narrative review discusses the relationship between the structure and activity of drugs. Specifically, the activity of drugs can be increased and/or their adverse effects can be reduced by altering specific positions in their structures.
Collapse
Affiliation(s)
- Romany H. Thabet
- Department of Basic Medical Sciences, Faculty of Medicine, Aqaba Medical Sciences University, Aqaba, Jordan
- Department of Pharmacology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | | | | | | | | | | |
Collapse
|
3
|
Gautam P, Bisht P, Gautam A, Gupta GD, Singh R, Verma SK. A comprehension on structure guided alignment dependent 3D-QSAR modelling, and molecular dynamics simulation on 2,4-thiazolidinediones as aldose reductase inhibitors for the management of diabetic complications. J Biomol Struct Dyn 2023:1-20. [PMID: 37904329 DOI: 10.1080/07391102.2023.2275190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023]
Abstract
Aldose reductase is an oxo-reductase enzyme belonging to the aldo-keto reductase class. Compounds having thiazolidine-2,4-dione scaffold are reported as potential aldose reductase inhibitors for diabetic complications. The present work uses structure-guided alignment-dependent Gaussian field- and atom-based 3D-QSAR on a dataset of 84 molecules. 3D-QSAR studies on two sets of dataset alignment have been carried out to understand the favourable and unfavourable structural features influencing the affinity of these inhibitors towards the enzyme. Using common pharmacophore hypotheses, the five-point pharmacophores for aldose reductase favourable features were generated. The molecular dynamics simulations (up to 100 ns) were performed for the potent molecule from each alignment set (compounds 24 and 65) compared to reference standard tolrestat and epalrestat to study target-ligand complexes' binding energy and stability. Compound 65 was most stable with better interactions in the aldose reductase binding pocket than tolrestat. The MM-PBSA study suggests compound 65 possessed better binding energy than reference standard tolrestat, i.e. -87.437 ± 19.728 and -73.424 ± 12.502 kJ/mol, respectively. The generated 3D-QSAR models provide information about structure-activity relationships and ligand-target binding energy. Target-specific stability data from MD simulation would be helpful for rational compound design with better aldose reductase activity.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Priyadarshi Gautam
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | - Priya Bisht
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | | | - Rajveer Singh
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, India
| | - Sant Kumar Verma
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| |
Collapse
|
4
|
Zothantluanga JH, Chetia D, Rajkhowa S, Umar AK. Unsupervised machine learning, QSAR modelling and web tool development for streamlining the lead identification process of antimalarial flavonoids. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023; 34:117-146. [PMID: 36744427 DOI: 10.1080/1062936x.2023.2169347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Identification of lead compounds with the traditional laboratory approach is expensive and time-consuming. Nowadays, in silico techniques have emerged as a promising approach for lead identification. In this study, we aim to develop robust and predictive 2D-QSAR models to identify lead flavonoids by predicting the IC50 against Plasmodium falciparum. We applied machine learning algorithms (Principal component analysis followed by K-means clustering) and Pearson correlation analysis to select 9 molecular descriptors (MDs) for model building. We selected and validated the three best QSAR models after execution of multiple linear regression (MLR) 100 times with different combinations of MDs. The developed models have fulfilled the five principles for QSAR models as specified by the Organization for Economic Co-operation and Development. The outcome of the study is a reliable and sustainable in silico method of IC50 (Mean ± SD) prediction that will positively impact the antimalarial drug development process by reducing the money and time required to identify potential antimalarial lead compounds from the class of flavonoids. We also developed a web tool (JazQSAR, https://etflin.com/news/4) to offer an easily accessible platform for the developed QSAR models.
Collapse
Affiliation(s)
- J H Zothantluanga
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, India
| | - D Chetia
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, India
| | - S Rajkhowa
- Centre for Biotechnology and Bioinformatics, Faculty of Biological Sciences, Dibrugarh University, Dibrugarh, India
| | - A K Umar
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| |
Collapse
|
5
|
Chen Y, Yan D, Xu J, Xiong H, Luan S, Xiao C, Huang Q. The importance of selecting crystal form for triazole fungicide tebuconazole to enhance its botryticidal activity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158778. [PMID: 36122714 DOI: 10.1016/j.scitotenv.2022.158778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
The growing evidences of resistant fungi stimulate fully understanding tebuconazole regarding its crystal structure on fungicidal activity. In this study, the crystal structures of six technical tebuconazoles (BX, HH, JP, QZ, SJ, and YT) were characterized by using high-resolution X-ray powder diffraction and three-dimensional crystal structure modeling. A structure-activity relationship of the tebuconazoles on the susceptible (HLS and YJS) or resistant (XHR) Botrytis cinerea isolates was analyzed, the differential tricarboxylic acid (TCA) cycle metabolism was determined, and molecular docking with sterol 14α-demethylase (CYP51) was performed. The results showed that tebuconazole existed in three types of crystal forms: an overlapping-pair conformation, a side-by-side-pair conformation, and a parallel-pair conformation. QZ with the parallel-pair conformation and the minimum crystal cell volume exhibited a higher activity and a lower resistant level. XHR possessed a higher content of TCA cycle metabolites and phosphate than YJS, but the exposure to QZ significantly reduced the contents of citrate, isocitrate, α-ketoglutarate and oxaloacetate in XHR, as did the exposure to other technical tebuconazoles. Moreover, the point mutations F487L, G464S, and G443S altered the binding properties of chiral stereoscopic R-QZ with CYP51 protein. Especially the G443S mutation promoted a weak linking of R-QZ with LEU380 and TYR126, and greatly slashed the binding action at lower docking score. In conclusion, our results evidenced an efficient crystal conformation of tebuconazole to improve botryticidal activity and a potential adaptability of B. cinerea to tebuconazole inhibition in TCA cycle metabolism and CYP51 protein mutation.
Collapse
Affiliation(s)
- Yongjun Chen
- Shanghai Key Lab of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, PR China
| | - Dongmei Yan
- Shanghai Key Lab of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, PR China
| | - Jialin Xu
- Shanghai Key Lab of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, PR China
| | - Hui Xiong
- Shanghai Key Lab of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, PR China
| | - Shaorong Luan
- School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China.
| | - Ciying Xiao
- School of Biological Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Qingchun Huang
- Shanghai Key Lab of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, PR China.
| |
Collapse
|
6
|
Seetin S, Saparpakorn P, Vanichtanankul J, Vitsupakorn D, Yuthavong Y, Kamchonwongpaisan S, Hannongbua S. Key interactions of pyrimethamine derivatives specific to wild-type and mutant P. falciparum dihydrofolate reductase based on 3D-QSAR, MD simulations and quantum chemical calculations. J Biomol Struct Dyn 2022:1-16. [DOI: 10.1080/07391102.2022.2096114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Sasipha Seetin
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Patchreenart Saparpakorn
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, PathumThani, Thailand
| | - Danoo Vitsupakorn
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, PathumThani, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, PathumThani, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, PathumThani, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, Kasetsart University, Chatuchak, Bangkok, Thailand
| |
Collapse
|
7
|
Oguike OE, Ugwuishiwu CH, Asogwa CN, Nnadi CO, Obonga WO, Attama AA. Systematic review on the application of machine learning to quantitative structure-activity relationship modeling against Plasmodium falciparum. Mol Divers 2022; 26:3447-3462. [PMID: 35064444 PMCID: PMC8782692 DOI: 10.1007/s11030-022-10380-1] [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: 10/05/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022]
Abstract
Malaria accounts for over two million deaths globally. To flatten this curve, there is a need to develop new and high potent drugs against Plasmodium falciparum. Some major challenges include the dearth of suitable animal models for anti-P. falciparum assays, resistance to first-line drugs, lack of vaccines and the complex life cycle of Plasmodium. Gladly, newer approaches to antimalarial drug discovery have emerged due to the release of large datasets by pharmaceutical companies. This review provides insights into these new approaches to drug discovery covering different machine learning tools, which enhance the development of new compounds. It provides a systematic review on the use and prospects of machine learning in predicting, classifying and clustering IC50 values of bioactive compounds against P. falciparum. The authors identified many machine learning tools yet to be applied for this purpose. However, Random Forest and Support Vector Machines have been extensively applied though on a limited dataset of compounds.
Collapse
Affiliation(s)
- Osondu Everestus Oguike
- Machine Learning Research Group, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.,Department of Computer Science, Faculty of Physical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| | - Chikodili Helen Ugwuishiwu
- Machine Learning Research Group, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.,Department of Computer Science, Faculty of Physical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| | - Caroline Ngozi Asogwa
- Machine Learning Research Group, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.,Department of Computer Science, Faculty of Physical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| | - Charles Okeke Nnadi
- Machine Learning Research Group, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria. .,Deprtment of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.
| | - Wilfred Ofem Obonga
- Machine Learning Research Group, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.,Deprtment of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| | - Anthony Amaechi Attama
- Machine Learning Research Group, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.,Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| |
Collapse
|
8
|
Zhou H, Rui Z, Yang Y, Xu S, Shao Y, Liu L. First total synthesis of hoshinoamide A. Beilstein J Org Chem 2021; 17:2924-2931. [PMID: 34956412 PMCID: PMC8685559 DOI: 10.3762/bjoc.17.201] [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: 09/14/2021] [Accepted: 11/26/2021] [Indexed: 11/23/2022] Open
Abstract
Hoshinoamides A, B and C, linear lipopeptides, were isolated from the marine cyanobacterium Caldora penicillata, with potent antiplasmodial activity against chloroquine-sensitive Plasmodium falciparum. Herein, we describe the first total synthesis of hoshinoamide A by the combination of liquid-phase and solid-phase peptide synthesis. Liquid-phase synthesis is to improve the coupling yield of ʟ-Val3 and N-Me-ᴅ-Phe2. Connecting other amino acids efficiency and convergence is achieved by solid-state synthesis. Our synthetic strategy could synthesize the target peptide in high yield with good purity.
Collapse
Affiliation(s)
- Haipin Zhou
- College of Materials & Chemical Engineering, Chuzhou University, Chuzhou 239000, China
| | - Zihan Rui
- College of Materials & Chemical Engineering, Chuzhou University, Chuzhou 239000, China
| | - Yiming Yang
- College of Materials & Chemical Engineering, Chuzhou University, Chuzhou 239000, China
| | - Shengtao Xu
- College of Materials & Chemical Engineering, Chuzhou University, Chuzhou 239000, China.,State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University,24 Tong Jia Xiang, Nanjing 210009, China
| | - Yutian Shao
- College of Materials & Chemical Engineering, Chuzhou University, Chuzhou 239000, China
| | - Long Liu
- Taizhou Medical Hi-Tech Development Public Services Platform, Taizhou 225300, China
| |
Collapse
|
9
|
Coumarins as Potential Antiprotozoal Agents: Biological Activities and Mechanism of Action. REVISTA BRASILEIRA DE FARMACOGNOSIA 2021. [DOI: 10.1007/s43450-021-00169-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
10
|
Nguyen PTV, Van Dat T, Mizukami S, Nguyen DLH, Mosaddeque F, Kim SN, Nguyen DHB, Đinh OT, Vo TL, Nguyen GLT, Quoc Duong C, Mizuta S, Tam DNH, Truong MP, Huy NT, Hirayama K. 2D-quantitative structure-activity relationships model using PLS method for anti-malarial activities of anti-haemozoin compounds. Malar J 2021; 20:264. [PMID: 34116665 PMCID: PMC8196453 DOI: 10.1186/s12936-021-03775-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/16/2021] [Indexed: 11/18/2022] Open
Abstract
Background Emergence of cross-resistance to current anti-malarial drugs has led to an urgent need for identification of potential compounds with novel modes of action and anti-malarial activity against the resistant strains. One of the most promising therapeutic targets of anti-malarial agents related to food vacuole of malaria parasite is haemozoin, a product formed by the parasite through haemoglobin degradation. Methods With this in mind, this study developed two-dimensional-quantitative structure–activity relationships (QSAR) models of a series of 21 haemozoin inhibitors to explore the useful physicochemical parameters of the active compounds for estimation of anti-malarial activities. The 2D-QSAR model with good statistical quality using partial least square method was generated after removing the outliers. Results Five two-dimensional descriptors of the training set were selected: atom count (a_ICM); adjacency and distance matrix descriptor (GCUT_SLOGP_2: the third GCUT descriptor using atomic contribution to logP); average total charge sum (h_pavgQ) in pKa prediction (pH = 7); a very low negative partial charge, including aromatic carbons which have a heteroatom-substitution in “ortho” position (PEOE_VSA-0) and molecular descriptor (rsynth: estimating the synthesizability of molecules as the fraction of heavy atoms that can be traced back to starting material fragments resulting from retrosynthetic rules), respectively. The model suggests that the anti-malarial activity of haemozoin inhibitors increases with molecules that have higher average total charge sum in pKa prediction (pH = 7). QSAR model also highlights that the descriptor using atomic contribution to logP or the distance matrix descriptor (GCUT_SLOGP_2), and structural component of the molecules, including topological descriptors does make for better anti-malarial activity. Conclusions The model is capable of predicting the anti-malarial activities of anti-haemozoin compounds. In addition, the selected molecular descriptors in this QSAR model are helpful in designing more efficient compounds against the P. falciparum 3D7A strain.
Collapse
Affiliation(s)
- Phuong Thuy Viet Nguyen
- Faculty of Pharmacy, University of Medicine and Pharmacy At Ho Chi Minh City, Ho Chi Minh City, 700000, Viet Nam.
| | - Truong Van Dat
- Faculty of Pharmacy, University of Medicine and Pharmacy At Ho Chi Minh City, Ho Chi Minh City, 700000, Viet Nam
| | - Shusaku Mizukami
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Leading Programme, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Duy Le Hoang Nguyen
- Faculty of Pharmacy, University of Medicine and Pharmacy At Ho Chi Minh City, Ho Chi Minh City, 700000, Viet Nam
| | - Farhana Mosaddeque
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Son Ngoc Kim
- Faculty of Pharmacy, University of Medicine and Pharmacy At Ho Chi Minh City, Ho Chi Minh City, 700000, Viet Nam
| | - Duy Hoang Bao Nguyen
- Faculty of Pharmacy, University of Medicine and Pharmacy At Ho Chi Minh City, Ho Chi Minh City, 700000, Viet Nam
| | - Oanh Thi Đinh
- Faculty of Pharmacy, University of Medicine and Pharmacy At Ho Chi Minh City, Ho Chi Minh City, 700000, Viet Nam
| | - Tu Linh Vo
- Faculty of Pharmacy, University of Medicine and Pharmacy At Ho Chi Minh City, Ho Chi Minh City, 700000, Viet Nam
| | - Giang Le Tra Nguyen
- Faculty of Pharmacy, University of Medicine and Pharmacy At Ho Chi Minh City, Ho Chi Minh City, 700000, Viet Nam
| | - Cuong Quoc Duong
- Faculty of Pharmacy, University of Medicine and Pharmacy At Ho Chi Minh City, Ho Chi Minh City, 700000, Viet Nam
| | - Satoshi Mizuta
- Center for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo, Nagasaki, Japan
| | - Dao Ngoc Hien Tam
- Asia Shine Trading & Service Co. Ltd., Ho Chi Minh City, 70000, Vietnam
| | - M Phuong Truong
- American University of the Carribean School of Medicine, 1 University Drive at Jordan Road, Cupecoy, Sint Maarten
| | - Nguyen Tien Huy
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
| | - Kenji Hirayama
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
| |
Collapse
|