1
|
Tu J, Adhikari B, Brennan MA, Bai W, Cheng P, Brennan CS. Shiitake polysaccharides acted as a non-competitive inhibitor to α-glucosidase and inhibited glucose transport of digested starch from Caco-2 cells monolayer. Food Res Int 2023; 173:113268. [PMID: 37803584 DOI: 10.1016/j.foodres.2023.113268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 10/08/2023]
Abstract
The inhibition mechanism of shitake mushroom polysaccharides (Lentinula edodes polysaccharides, LEP) against α-glucosidase was studied by enzyme kinetic assay, fluorescence quenching and molecular docking. The effect of LEP on glucose transport of digested starch was investigated via an in vitro digestion/Caco-2 transwell model. LEP exhibited a stronger inhibiting effect (IC50 = 0.66 mg/mL) than acarbose and presented a non-competitive inhibition mechanism. The interaction between LEP and α-glucosidase primarily involved electrostatic interaction and hydrogen bonding. Molecular docking modelling showed that the four structures of LEP were bound to the allosteric tunnel or adjacent pocket of α-glucosidase via electrostatic force and hydrogen bonds. The (1 → 6)-linkages in LEP structures favoured its binding affinity to the α-glucosidase. The α-glucosidase inhibiting activity of LEP was also found to emanate from the reduction in glucose transport of digested starch as deducted from the in vitro digestion/Caco-2 transwell data. The release of glucose from digested starch cooked with LEP was significantly reduced (33.7%) compared to the digested starch without LEP. The findings from the current study suggest that LEP could be a promising ingredient to inhibit α-glucosidase activity as well as control the level of postprandial blood glucose when incorporated into starchy foods.
Collapse
Affiliation(s)
- Juncai Tu
- School of Science, RMIT University, GPO Box 2474, Melbourne, VIC 3001, Australia
| | - Benu Adhikari
- School of Science, RMIT University, GPO Box 2474, Melbourne, VIC 3001, Australia.
| | - Margaret Anne Brennan
- School of Science, RMIT University, GPO Box 2474, Melbourne, VIC 3001, Australia; Department of Wine, Food and Molecular Biosciences, Lincoln University, PO Box 84, Lincoln 7647, Christchurch, New Zealand
| | - Weidong Bai
- College of Light Industry and Food Sciences, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Ping Cheng
- College of Light Industry and Food Sciences, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | | |
Collapse
|
2
|
Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation. Nat Commun 2022; 13:7607. [PMID: 36494361 PMCID: PMC9734150 DOI: 10.1038/s41467-022-34960-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
ATP phosphoribosyltransferase catalyses the first step of histidine biosynthesis and is controlled via a complex allosteric mechanism where the regulatory protein HisZ enhances catalysis by the catalytic protein HisGS while mediating allosteric inhibition by histidine. Activation by HisZ was proposed to position HisGS Arg56 to stabilise departure of the pyrophosphate leaving group. Here we report active-site mutants of HisGS with impaired reaction chemistry which can be allosterically restored by HisZ despite the HisZ:HisGS interface lying ~20 Å away from the active site. MD simulations indicate HisZ binding constrains the dynamics of HisGS to favour a preorganised active site where both Arg56 and Arg32 are poised to stabilise leaving-group departure in WT-HisGS. In the Arg56Ala-HisGS mutant, HisZ modulates Arg32 dynamics so that it can partially compensate for the absence of Arg56. These results illustrate how remote protein-protein interactions translate into catalytic resilience by restoring damaged electrostatic preorganisation at the active site.
Collapse
|
3
|
Kodchakorn K, Kongtawelert P. Molecular dynamics study on the strengthening behavior of Delta and Omicron SARS-CoV-2 spike RBD improved receptor-binding affinity. PLoS One 2022; 17:e0277745. [PMID: 36395151 PMCID: PMC9671323 DOI: 10.1371/journal.pone.0277745] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
The COVID-19 pandemic caused by a virus that can be transmitted from human to human via air droplets has changed the quality of life and economic systems all over the world. The viral DNA has mutated naturally over time leading to the diversity of coronavirus victims which has posed a serious threat to human security on a massive scale. The current variants have developed in a dominant way and are considered "Variants of Concern" by the World Health Organization (WHO). In this work, Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529) variants were obtained to evaluate whether naturally occurring mutations have strengthened viral infectivity. We apply reliable in silico structural dynamics and energetic frameworks of the mutated S-RBD protein for ACE2-binding to analyze and compare the structural information related to the wild-type. In particular, the hotspot residues at Q493, Q498, and N501 on the S-RBD protein were determined as contributing factors to the employment stability of the relevant binding interface. The L452R mutation induces an increment of the hydrogen bonds formed by changing the Q493 environment for ACE2 binding. Moreover, the Q493K exchange in Omicron enables the formation of two additional salt bridges, leading to a strong binding affinity by increased electrostatic interaction energy. These results could be used in proposing concrete informative data for a structure-based design engaged in finding better therapeutics against novel variants.
Collapse
Affiliation(s)
- Kanchanok Kodchakorn
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Prachya Kongtawelert
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- * E-mail:
| |
Collapse
|
4
|
Peters XQ, Agoni C, Soliman MES. Unravelling the Structural Mechanism of Action of 5-methyl-5-[4-(4-oxo-3H-quinazolin-2-yl)phenyl]imidazolidine-2,4-dione in Dual-Targeting Tankyrase 1 and 2: A Novel Avenue in Cancer Therapy. Cell Biochem Biophys 2022; 80:505-518. [PMID: 35637423 DOI: 10.1007/s12013-022-01076-2] [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: 03/16/2022] [Accepted: 05/21/2022] [Indexed: 11/03/2022]
Abstract
Tankyrase (TNKS) belonging to the poly(ADPribose) polymerase family, are known for their multi-functioning capabilities, and play an essential role in the Wnt β-catenin pathway and various other cellular processes. Although showing inhibitory potential at a nanomolar level, the structural dual-inhibitory mechanism of the novel TNKS inhibitor, 5-methyl-5-[4-(4-oxo-3H-quinazolin-2-yl)phenyl]imidazolidine-2,4-dione, remains unexplored. By employing advanced molecular modeling, this study provides these insights. Results of sequence alignments of binding site residues identified conserved residues; GLY1185 and ILE1224 in TNKS-1 and PHE1035 and PRO1034 in TNKS-2 as crucial mediators of the dual binding mechanism of 5-methyl-5-[4-(4-oxo-3H-quinazolin-2-yl)phenyl]imidazolidine-2,4-dione, corroborated by high per-residue energy contributions and consistent high-affinity interactions of these residues. Estimation of the binding free energy of 5-methyl-5-[4-(4-oxo-3H-quinazolin-2-yl)phenyl]imidazolidine-2,4-dione showed estimated total energy of -43.88 kcal/mol and -30.79 kcal/mol towards TNKS-1 and 2, respectively, indicating favorable analogous dual binding as previously reported. Assessment of the conformational dynamics of TNKS-1 and 2 upon the binding of 5-methyl-5-[4-(4-oxo-3H-quinazolin-2-yl)phenyl]imidazolidine-2,4-dione revealed similar structural changes characterized by increased flexibility and solvent assessible surface area of the residues inferring an analogous structural binding mechanism. Insights from this study show that peculiar, conserved residues are the driving force behind the dual inhibitory mechanism of 5-methyl-5-[4-(4-oxo-3H-quinazolin-2-yl)phenyl]imidazolidine-2,4-dione and could aid in the design of novel dual inhibitors of TNKS-1 and 2 with improved therapeutic properties.
Collapse
Affiliation(s)
- Xylia Q Peters
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.,West African Centre for Computational Analysis, Accra, Ghana
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
| |
Collapse
|
5
|
Velasco-Bolom JL, Domínguez L. Mechanistic regulation of γ-secretase by their substrates. Phys Chem Chem Phys 2022; 24:19223-19232. [DOI: 10.1039/d2cp01714h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
γ-Secretase (GS) is a transmembrane (TM) enzyme that plays important roles in the processing of approximately 90 substrates.
Collapse
Affiliation(s)
- José-Luis Velasco-Bolom
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Laura Domínguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| |
Collapse
|
6
|
Akawa OB, Soremekun OS, Olotu FA, Soliman MES. Atomistic insights into the selective therapeutic activity of 6-(2,4-difluorophenoxy)-5-((ethylmethyl)pyridine-3-yl)-8-methylpyrrolo[1,2-a]pyrazin-1(2H)-one towards bromodomain-containing proteins. Comput Biol Chem 2021; 95:107592. [PMID: 34710811 DOI: 10.1016/j.compbiolchem.2021.107592] [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: 09/24/2020] [Revised: 09/29/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
Cross-target effect has been one of the major mechanisms of drug toxicity, this has necessitated the design of inhibitors that are specifically tailored to target particular biomolecules. 6-(2,4-difluorophenoxy)-5-((ethylmethyl)pyridine-3-yl)-8-methylpyrrolo[1,2-a] pyrazin-1(2H)-one (Cpd38) is an inhibitor possessing high inhibition rate and tailored specificity towards bromodomain-containing protein 4 (BRD4). In this research, we used an array of computational techniques to provide insight at the atomistic level the specific targeting of BRD4 by Cpd38 relative to the binding of Cpd38 with E1A binding protein P300 (EP300); another bromodomain-containing protein (BCP). Comparatively, binding of Cpd38 improved the conformational stability and compactness of BRD4 protein when compared to the Cpd38 bound EP300. Also, Cpd38 induced a conformational change in the active site of BRD4 that facilitated a complementary pose between Cpd38 and BRD4 suitable for effective atomistic interactions. Expectedly, thermodynamic calculations revealed that the Cpd38-BRD4 system had higher binding energy (-36.11 Kcal/mol) than the Cpd38-EP300 system with a free binding energy of -15.86 Kcal/mol. Noteworthy is the opposing role Trp81 (acting as hydrogen bond acceptor) and Pro1074 (acting as hydrogen bond donor) found on the WPF and LPF loops respectively play in maintaining Cpd38 stability. Furthermore, the hydrogen bond acceptor/donator ratio was approximately 4:1 in Cpd38-BRD4 system compared with 2:1 in Cpd38-EP300 system. Taken together, atomistic insights and structural perspectives detailed in this report supplements the experimental report supporting the improved selectivity of Cpd38 for BRD4 ahead of other BCPs while providing leeway for the future design of BET selective agents with better pharmacological profile.
Collapse
Affiliation(s)
- Oluwole B Akawa
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Opeyemi S Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa.
| |
Collapse
|
7
|
Abstract
Amongst the several types of brain cancers known to humankind, glioma is one of the most severe and life-threatening types of cancer, comprising 40% of all primary brain tumors. Recent reports have shown the incident rate of gliomas to be 6 per 100,000 individuals per year globally. Despite the various therapeutics used in the treatment of glioma, patient survival rate remains at a median of 15 months after undergoing first-line treatment including surgery, radiation, and chemotherapy with Temozolomide. As such, the discovery of newer and more effective therapeutic agents is imperative for patient survival rate. The advent of computer-aided drug design in the development of drug discovery has emerged as a powerful means to ascertain potential hit compounds with distinctively high therapeutic effectiveness against glioma. This review encompasses the recent advances of bio-computational in-silico modeling that have elicited the discovery of small molecule inhibitors and/or drugs against various therapeutic targets in glioma. The relevant information provided in this report will assist researchers, especially in the drug design domains, to develop more effective therapeutics against this global disease.
Collapse
|
8
|
Exploration of alternate therapeutic remedies in Ebola virus disease: the case of reported antiviral phytochemical derived from the leaves Spondias Mombin Linn. ADVANCES IN TRADITIONAL MEDICINE 2021. [DOI: 10.1007/s13596-021-00603-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
9
|
Rowaiye AB, Mendes YJT, Olofinsae SA, Oche JB, Oladipo OH, Okpalefe OA, Ogidigo JO. Camptothecin shows better promise than Curcumin in the inhibition of the Human Telomerase: A computational study. Heliyon 2021; 7:e07742. [PMID: 34485722 PMCID: PMC8405929 DOI: 10.1016/j.heliyon.2021.e07742] [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: 03/04/2021] [Revised: 05/17/2021] [Accepted: 08/05/2021] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES The Human Telomerase enzyme has become a drug target in the treatment of cancers and age-related disorders. This study aims to identify potential natural inhibitors of the Human Telomerase from compounds derived from edible African plants. MATERIALS AND METHODS A library of 1,126 natural compounds was molecularly docked against the Telomerase Reverse Transcriptase (PDB ID: 5ugw), the catalytic subunit of the target protein. Curcumin, a known Telomerase inhibitor was used as the standard. The front-runner compounds were screened for bioavailability, pharmacokinetic properties, and bioactivity using the SWISSADME, PKCSM, and Molinspiration webservers respectively. The molecular dynamic simulation and analyses of the apo and holo proteins were performed by the Galaxy supercomputing webserver. RESULTS The results of the molecular docking and virtual screening reveal Augustamine and Camptothecin as lead compounds. Augustamine has better drug-likeness and pharmacokinetic properties while Camptothecin showed better bioactivity and stronger binding affinity (-8.2 kcal/mol) with the target. The holo structure formed by Camptothecin showed greater inhibitory activity against the target with a total RMSF of 169.853, B-Factor of 20.164, and 108 anti-correlating residues. CONCLUSION Though they both act at the same binding site, Camptothecin induces greater Telomerase inhibition and better molecular stability than the standard, Curcumin. Further tests are required to investigate the inhibitory activities of the lead compounds.
Collapse
Affiliation(s)
| | | | - Samson Ayodeji Olofinsae
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | | | | | | | - Joyce Oloaigbe Ogidigo
- Bioresources Development Centre, National Biotechnology Development Agency, Abuja, Nigeria
| |
Collapse
|
10
|
Kodchakorn K, Viriyakhasem N, Wongwichai T, Kongtawelert P. Structural Determination, Biological Function, and Molecular Modelling Studies of Sulfoaildenafil Adulterated in Herbal Dietary Supplement. Molecules 2021; 26:949. [PMID: 33670094 PMCID: PMC7916901 DOI: 10.3390/molecules26040949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 11/17/2022] Open
Abstract
Unapproved ingredients included in herbal medicines and dietary supplements have been detected as adulterated synthetic drugs used for erectile dysfunction. Extraction from a dietary supplement was performed to isolate the compounds by HPLC analysis. The structural characterization was confirmed using mass spectrometry (ESI-TOF/MS and LC-MS/MS), 1H NMR, and 13C NMR spectroscopy techniques. Results identified the thus-obtained compound to be sulfoaildenafil, a thioketone analogue of sildenafil. The biological activities of this active compound have been focused for the first time by the experimental point of view performance in vitro. The results revealed that sulfoaildenafil can affect the therapeutic level of nitric oxide through the upregulation of nitric oxide synthase and phosphodiesterase type 5 (PDE5) gene expressions. This bulk material, which displays structural similarity to sildenafil, was analyzed for the presence of a PDE5 inhibitor using a theoretical calculation. These unique features of the potential activity of PDE5 protein and its inhibitors, sildenafil and sulfoaildenafil, may play a key consideration for understanding the mode of actions and predicting the biological activities of PDE5 inhibitors.
Collapse
Affiliation(s)
- Kanchanok Kodchakorn
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (K.K.); (T.W.)
| | - Nawarat Viriyakhasem
- School of Traditional and Alternative Medicine, Chiang Rai Rajabhat University, Chiang Rai 57100, Thailand;
| | - Tunchanok Wongwichai
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (K.K.); (T.W.)
| | - Prachya Kongtawelert
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (K.K.); (T.W.)
| |
Collapse
|
11
|
Kodchakorn K, Poovorawan Y, Suwannakarn K, Kongtawelert P. Molecular modelling investigation for drugs and nutraceuticals against protease of SARS-CoV-2. J Mol Graph Model 2020; 101:107717. [PMID: 32861974 PMCID: PMC7434411 DOI: 10.1016/j.jmgm.2020.107717] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
The widespread problem of a 2019-novel coronavirus (SARS-CoV-2) strain outbreak in Wuhan, China has prompted a search for new drugs to protect against and treat this disease. It is necessary to immediately investigate this due to the mutation of the viral genome and there being no current protective vaccines or therapeutic drugs. Molecular modelling and molecular docking based on in silico screening strategies were employed to determine the potential activities of seven HIV protease (HIV-PR) inhibitors, two flu drugs, and eight natural compounds. The computational approach was carried out to discover the structural modes with a high binding affinity for these drugs on the homology structure of the Wuhan coronavirus protease (SARS-CoV-2 PR). From the theoretical calculations, all the drugs and natural compounds demonstrated various favorable binding affinities. An interesting finding was that the natural compounds tested had a higher potential binding activity with the pocket sites of SARS-CoV-2 PR compared to the groups of HIV-PR inhibitors. The binding modes of each complex illustrated between the drugs and compounds interacted with the functional group of amino acids in the binding pocket via hydrophilic, hydrophobic, and hydrogen bond interactions using the molecular dynamics simulation technique. This result supports the idea that existing protease inhibitors and natural compounds could be used to treat the new coronavirus. This report sought to provide fundamental knowledge as preliminary experimental data to propose an existing nutraceutical material against viral infection. Collectively, it is suggested that molecular modelling and molecular docking are suitable tools to search and screen for new drugs and natural compounds that can be used as future treatments for viral diseases.
Collapse
Affiliation(s)
- Kanchanok Kodchakorn
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Kamol Suwannakarn
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| | - Prachya Kongtawelert
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.
| |
Collapse
|
12
|
Wu F, Zhou Y, Li L, Shen X, Chen G, Wang X, Liang X, Tan M, Huang Z. Computational Approaches in Preclinical Studies on Drug Discovery and Development. Front Chem 2020; 8:726. [PMID: 33062633 PMCID: PMC7517894 DOI: 10.3389/fchem.2020.00726] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
Because undesirable pharmacokinetics and toxicity are significant reasons for the failure of drug development in the costly late stage, it has been widely recognized that drug ADMET properties should be considered as early as possible to reduce failure rates in the clinical phase of drug discovery. Concurrently, drug recalls have become increasingly common in recent years, prompting pharmaceutical companies to increase attention toward the safety evaluation of preclinical drugs. In vitro and in vivo drug evaluation techniques are currently more mature in preclinical applications, but these technologies are costly. In recent years, with the rapid development of computer science, in silico technology has been widely used to evaluate the relevant properties of drugs in the preclinical stage and has produced many software programs and in silico models, further promoting the study of ADMET in vitro. In this review, we first introduce the two ADMET prediction categories (molecular modeling and data modeling). Then, we perform a systematic classification and description of the databases and software commonly used for ADMET prediction. We focus on some widely studied ADMT properties as well as PBPK simulation, and we list some applications that are related to the prediction categories and web tools. Finally, we discuss challenges and limitations in the preclinical area and propose some suggestions and prospects for the future.
Collapse
Affiliation(s)
- Fengxu Wu
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, China
| | - Yuquan Zhou
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Langhui Li
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Xianhuan Shen
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Ganying Chen
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Xiaoqing Wang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Xianyang Liang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Mengyuan Tan
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Zunnan Huang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
- Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China
| |
Collapse
|
13
|
'Polymorphism-aided' Selective Targeting and Inhibition of Caspase-6 by a Novel Allosteric Inhibitor Towards Efficient Alzheimer's Disease Treatment. Cell Biochem Biophys 2020; 78:291-299. [PMID: 32592127 DOI: 10.1007/s12013-020-00927-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/17/2020] [Indexed: 10/23/2022]
Abstract
The predominance of Alzheimer's disease (AD) among the aged remains a global challenge. As such, the search for alternative and effective therapeutic options continuous unabated. Among the therapeutic targets explored over the years toward impeding the progression of AD is caspase-6 (Casp6), although selectively targeting Casp6 remains a challenge due to high homology with other members of the caspase family. Methyl 3-[(2,3-dihydro-1-benzofuran-2-yl formamido) methyl]-5-(furan-2-amido) benzoate (C13), a novel allosteric inhibitor, is reportedly shown to exhibit selective inhibition against mutant human Casp6 variants (E35K). However, structural and atomistic insights accounting for the reported inhibitory prowess of C13 remains unresolved. In this study, we seek to unravel the mechanistic selectivity of C13 coupled with the complementary effects of E35K single-nucleotide polymorphism (SNP) relative to Casp6 inhibition. Analyses of binding dynamics revealed that the variant Lysine-35 mediated consistent high-affinity interactions with C13 at the allosteric site, possibly forming the molecular basis of the selectivity of C13 as well as its high binding free energy as estimated. Analysis of residue interaction network around Glu35 and Lys35 revealed prominent residue network distortions in the mutant Casp6 conformation evidenced by a decrease in node degree, reduced number of edges and an increase short in path length relative to a more compact conformation in the wild system. The relatively higher binding free energy of C13 coupled with the stronger intermolecular interactions elicited in the mutant conformation further suggests that the mutation E35K probably favours the inhibitory activity of C13. Further analysis of atomistic changes showed increased C-α atom deviations consistent with structural disorientations in the mutant Casp6. Structural Insights provided could open up a novel paradigm of structure-based design of selective allosteric inhibition of Casp6 towards the treatment of neurodegenerative diseases.
Collapse
|
14
|
Human Rhinovirus Inhibition Through Capsid “Canyon” Perturbation: Structural Insights into The Role of a Novel Benzothiophene Derivative. Cell Biochem Biophys 2019; 78:3-13. [DOI: 10.1007/s12013-019-00896-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023]
|
15
|
Washah H, Agoni C, Olotu FA, Munsamy G, Soliman MES. Tweaking α -Galactoceramides: Probing the Dynamical Mechanisms of Improved Recognition for Invariant Natural Killer T-cell Receptor in Cancer Immunotherapeutics. Curr Pharm Biotechnol 2019; 21:1354-1367. [PMID: 31738132 DOI: 10.2174/1389201020666191118103342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/29/2019] [Accepted: 11/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The last few decades have witnessed groundbreaking research geared towards immune surveillance mechanisms and have yielded significant improvements in the field of cancer immunotherapy. This approach narrows down on the development of therapeutic agents that either activate or enhance the recognitive function of the immune system to facilitate the destruction of malignant cells. The α -galactosylceramide derivative, KRN7000, is an immunotherapeutic agent that has gained attention due to its pharmacological ability to activate CD1d-restricted invariant natural killer T(iNKT) cells with notable potency against cancer cells in mouse models; a therapeutic success was not well replicated in human models. Dual structural modification of KRN7000 entailing the incorporation of hydrocinnamoyl ester on C6" and C4-OH truncation of the sphingoid base led to the development of AH10-7 which, interestingly, exhibited high potency in human cells. OBJECTIVE/METHODS Therefore, to gain molecular insights into the structural dynamics and selective mechanisms of AH10-7 for human variants, we employed integrative molecular dynamics simulations and thermodynamic calculations to investigate the inhibitory activities of KRN7000 andAH10-7 on hTCR-CD1d towards activating iNKT. RESULTS Interestingly, our findings revealed that AH10-7 exhibited higher affinity binding and structural effects on hTCR-CD1d, as mediated by the incorporated hydrocinnamoyl ester moiety which accounted for stronger intermolecular interactions with 'non-common' binding site residues. CONCLUSION Findings extracted from this study further reveal important molecular and structural perspectives that could aid in the design of novel α-GalCer derivatives for cancer immunotherapeutics.
Collapse
Affiliation(s)
- Houda Washah
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Clement Agoni
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Fisayo A Olotu
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Geraldene Munsamy
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| |
Collapse
|
16
|
Agoni C, Salifu EY, Munsamy G, Olotu FA, Soliman M. CF3‐Pyridinyl Substitution on Antimalarial Therapeutics: Probing Differential Ligand Binding and Dynamical Inhibitory Effects of a Novel Triazolopyrimidine‐Based Inhibitor onPlasmodium falciparumDihydroorotate Dehydrogenase. Chem Biodivers 2019; 16:e1900365. [DOI: 10.1002/cbdv.201900365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/07/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Clement Agoni
- Molecular Bio-Computation & Drug Design Lab, School of Health SciencesUniversity of KwaZulu-Natal, Westville Durban 4000 South Africa
| | - Elliasu Y. Salifu
- Molecular Bio-Computation & Drug Design Lab, School of Health SciencesUniversity of KwaZulu-Natal, Westville Durban 4000 South Africa
| | - Geraldene Munsamy
- Molecular Bio-Computation & Drug Design Lab, School of Health SciencesUniversity of KwaZulu-Natal, Westville Durban 4000 South Africa
| | - Fisayo A. Olotu
- Molecular Bio-Computation & Drug Design Lab, School of Health SciencesUniversity of KwaZulu-Natal, Westville Durban 4000 South Africa
| | - Mahmoud Soliman
- Molecular Bio-Computation & Drug Design Lab, School of Health SciencesUniversity of KwaZulu-Natal, Westville Durban 4000 South Africa
| |
Collapse
|
17
|
Broadening the horizon: Integrative pharmacophore-based and cheminformatics screening of novel chemical modulators of mitochondria ATP synthase towards interventive Alzheimer's disease therapy. Med Hypotheses 2019; 130:109277. [PMID: 31383337 DOI: 10.1016/j.mehy.2019.109277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/03/2019] [Accepted: 06/10/2019] [Indexed: 01/14/2023]
Abstract
The proven efficacy of J147 in the treatment of Alzheimer's disease (AD) has been emphatic, particularly since its selective modulatory roles towards mitochondrial ATP synthase (mATPase) were defined. This prospect, if methodically probed, could further pave way for the discovery of novel anti-AD drugs with improved pharmacokinetics and therapeutic potential. To this effect, for the first time, we employed a four-step paradigm that integrated our in-house per-residue energy decomposition (PRED) protocol coupled with molecular dynamics, cheminformatics and analytical binding free energy methods. This was geared towards the screening and identification of new leads that exhibit modulatory potentials towards mATPase in a J147-similar pattern. Interestingly, from a large-scale library of compounds, we funnelled down on three potential hits that demonstrated selective and high-affinity binding activities towards α-F1-ATP synthase (ATP5A) relative to J147. Moreover, these compounds exhibited higher binding propensity with a differential ΔGs greater than -1 kcal/mol comparative to J147, and also elicited distinct modulatory effects on ATP5A domain structures. More interestingly, per-residue pharmacophore modeling of these lead compounds revealed similar interactive patterns with crucial residues at the α-site region of ATP5A characterized by high energy contributions based on binding complementarity. Recurrent target residues involved in high-affinity interactions with the hit molecules relative to J147 include Arg1112 and Gln426. Furthermore, assessments of pharmacokinetics revealed that the lead compounds were highly drug-like with minimal violations of the Lipinski's rule of five. As developed in this study, the most extrapolative pharmacophore model of the selected hits encompassed three electron donors and one electron acceptor. We speculate that these findings will be fundamental to the reformation of anti-AD drug discovery procedures.
Collapse
|
18
|
Salifu EY, Agoni C, Olotu FA, Dokurugu YM, Soliman MES. Deciphering the canonical blockade of activated Hageman factor (FXIIa) by benzamidine in the coagulation cascade: A thorough dynamical perspective. Chem Biol Drug Des 2019; 94:1905-1918. [PMID: 31148409 DOI: 10.1111/cbdd.13573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/09/2019] [Accepted: 05/15/2019] [Indexed: 12/11/2022]
Abstract
The experimental inhibitory potency of benzamidine (BEN) paved way for further design and development of inhibitors that target β-FXIIa. Structural dynamics of the loops and catalytic residues that encompass the binding pocket of β-FXIIa and all serine proteases are crucial to their overall activity. Employing molecular dynamics and post-MD analysis, this study sorts to unravel the structural and molecular events that accompany the inhibitory activity of BEN on human β-FXIIa upon selective non-covalent binding. Analysis of conformational dynamics of crucial loops revealed prominent alterations of the original conformational posture of FXIIa, evidenced by increased flexibility, decreased compactness, and an increased exposure to solvent upon binding of BEN, which could have in turn interfered with the essential roles of these loops in enhancing their procoagulation interactions with biological substrates and cofactors, altogether resulting in the consequential inactivation of FXIIa. A sustained interaction of the catalytic triad residues and key residues of the autolysis loop impeded their roles in catalysis which equally enhanced the inhibitory potency of BEN toward β-FXIIa evidenced by a favorable binding. Findings provide essential structural and molecular insights that could facilitate the structure-based design of novel antithrombotic compounds with enhanced inhibitory activities and low therapeutic risk.
Collapse
Affiliation(s)
- Elliasu Y Salifu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Yussif M Dokurugu
- College of Pharmacy and Pharmaceutical Sciences, Florida Agricultural and Mechanical University, FAMU, Tallahassee, FL, USA
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| |
Collapse
|