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Article ; Online: PARP1pred

Tassanee Lerksuthirat / Sermsiri Chitphuk / Wasana Stitchantrakul / Donniphat Dejsuphong / Aijaz Ahmad Malik / Chanin Nantasenamat

EXCLI Journal : Experimental and Clinical Sciences, Vol 22, Pp 84-

a web server for screening the bioactivity of inhibitors against DNA repair enzyme PARP-1

2023 Volume 107

Abstract: Cancer is the leading cause of death worldwide, resulting in the mortality of more than 10 million people in 2020, according to Global Cancer Statistics 2020. A potential cancer therapy involves targeting the DNA repair process by inhibiting PARP-1. In ... ...

Abstract	Cancer is the leading cause of death worldwide, resulting in the mortality of more than 10 million people in 2020, according to Global Cancer Statistics 2020. A potential cancer therapy involves targeting the DNA repair process by inhibiting PARP-1. In this study, classification models were constructed using a non-redundant set of 2018 PARP-1 inhibitors. Briefly, compounds were described by 12 fingerprint types and built using the random forest algorithm concomitant with various sampling approaches. Results indicated that PubChem with an oversampling approach yielded the best performance, with a Matthews correlation coefficient > 0.7 while also affording interpretable molecular features. Moreover, feature importance, as determined from the Gini index, revealed that the aromatic/cyclic/heterocyclic moiety, nitrogen-containing fingerprints, and the ether/aldehyde/alcohol moiety were important for PARP-1 inhibition. Finally, our predictive model was deployed as a web application called PARP1pred and is publicly available at https://parp1pred.streamlitapp.com, allowing users to predict the biological activity of query compounds using their SMILES notation as the input. It is anticipated that the model described herein will aid in the discovery of effective PARP-1 inhibitors.
Keywords	parp-1 ; dna repair ; machine learning ; qsar ; webserver ; cheminformatics ; Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282 ; Biology (General) ; QH301-705.5
Subject code	540
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: ERpred

Nalini Schaduangrat / Aijaz Ahmad Malik / Chanin Nantasenamat

PeerJ, Vol 9, p e

a web server for the prediction of subtype-specific estrogen receptor antagonists

2021 Volume 11716

Abstract: Estrogen receptors alpha and beta (ERα and ERβ) are responsible for breast cancer metastasis through their involvement of clinical outcomes. Estradiol and hormone replacement therapy targets both ERs, but this often leads to an increased risk of breast ... ...

Abstract	Estrogen receptors alpha and beta (ERα and ERβ) are responsible for breast cancer metastasis through their involvement of clinical outcomes. Estradiol and hormone replacement therapy targets both ERs, but this often leads to an increased risk of breast and endometrial cancers as well as thromboembolism. A major challenge is posed for the development of compounds possessing ER subtype specificity. Herein, we present a large-scale classification structure-activity relationship (CSAR) study of inhibitors from the ChEMBL database which consisted of an initial set of 11,618 compounds for ERα and 7,810 compounds for ERβ. The IC50 was selected as the bioactivity unit for further investigation and after the data curation process, this led to a final data set of 1,593 and 1,281 compounds for ERα and ERβ, respectively. We employed the random forest (RF) algorithm for model building and of the 12 fingerprint types, models built using the PubChem fingerprint was the most robust (Ac of 94.65% and 92.25% and Matthews correlation coefficient (MCC) of 89% and 76% for ERα and ERβ, respectively) and therefore selected for feature interpretation. Results indicated the importance of features pertaining to aromatic rings, nitrogen-containing functional groups and aliphatic hydrocarbons. Finally, the model was deployed as the publicly available web server called ERpred at http://codes.bio/erpred where users can submit SMILES notation as the input query for prediction of the bioactivity against ERα and ERβ.
Keywords	Breast cancer ; Estrogen ; Estrogen receptor ; Data science ; Machine learning ; Quantitative structure-activity relationship ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	540
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Towards combating antibiotic resistance by exploring the quantitative structure-activity relationship of NDM-1 inhibitors

Tianshi Yu / Aijaz Ahmad Malik / Nuttapat Anuwongcharoen / Warawan Eiamphungporn / Chanin Nantasenamat / Theeraphon Piacham

EXCLI Journal : Experimental and Clinical Sciences, Vol 21, Pp 1331-

2022 Volume 1351

Abstract: The emergence of New Delhi metallo-beta-lactamase-1 (NDM-1) has conferred enteric bacteria resistance to almost all beta-lactam antibiotics. Its capability of horizontal transfer through plasmids, amongst humans, animal reservoirs and the environment, ... ...

Abstract	The emergence of New Delhi metallo-beta-lactamase-1 (NDM-1) has conferred enteric bacteria resistance to almost all beta-lactam antibiotics. Its capability of horizontal transfer through plasmids, amongst humans, animal reservoirs and the environment, has added up to the totality of antimicrobial resistance control, animal husbandry and food safety. Thus far, there have been no effective drugs for neutralizing NDM-1. This study explores the structure-activity relationship of NDM-1 inhibitors. IC50 values of NDM-1 inhibitors were compiled from both the ChEMBL database and literature. After curation, a final set of 686 inhibitors were used for machine learning model building using the random forest algorithm against 12 sets of molecular fingerprints. Benchmark results indicated that the KlekotaRothCount fingerprint provided the best overall performance with an accuracy of 0.978 and 0.778 for the training and testing set, respectively. Model interpretation revealed that nitrogen-containing features (KRFPC 4080, KRFPC 3882, KRFPC 677, KRFPC 3608, KRFPC 3750, KRFPC 4287 and KRFPC 3943), sulfur-containing substructures (KRFPC 2855 and KRFPC 4843), aromatic features (KRFPC 1566, KRFPC 1564, KRFPC 1642, KRFPC 3608, KRFPC 4287 and KRFPC 3943), carbonyl features (KRFPC 1193 and KRFPC 3025), aliphatic features (KRFPC 2975, KRFPC 297, KRFPC 3224 and KRFPC 669) are features contributing to NDM-1 inhibitory activity. It is anticipated that findings from this study would help facilitate the drug discovery of NDM-1 inhibitors by providing guidelines for further lead optimization.
Keywords	antibiotic resistance ; beta-lactamase ; ndm-1 ; qsar ; drug discovery ; data science ; Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-11-01T00:00:00Z
Publisher	IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Tackling the Antibiotic Resistance Caused by Class A β-Lactamases through the Use of β-Lactamase Inhibitory Protein

Warawan Eiamphungporn / Nalini Schaduangrat / Aijaz Ahmad Malik / Chanin Nantasenamat

International Journal of Molecular Sciences, Vol 19, Iss 8, p

2018 Volume 2222

Abstract: β-Lactams are the most widely used and effective antibiotics for the treatment of infectious diseases. Unfortunately, bacteria have developed several mechanisms to combat these therapeutic agents. One of the major resistance mechanisms involves the ... ...

Abstract	β-Lactams are the most widely used and effective antibiotics for the treatment of infectious diseases. Unfortunately, bacteria have developed several mechanisms to combat these therapeutic agents. One of the major resistance mechanisms involves the production of β-lactamase that hydrolyzes the β-lactam ring thereby inactivating the drug. To overcome this threat, the small molecule β-lactamase inhibitors (e.g., clavulanic acid, sulbactam and tazobactam) have been used in combination with β-lactams for treatment. However, the bacterial resistance to this kind of combination therapy has evolved recently. Therefore, multiple attempts have been made to discover and develop novel broad-spectrum β-lactamase inhibitors that sufficiently work against β-lactamase producing bacteria. β-lactamase inhibitory proteins (BLIPs) (e.g., BLIP, BLIP-I and BLIP-II) are potential inhibitors that have been found from soil bacterium Streptomyces spp. BLIPs bind and inhibit a wide range of class A β-lactamases from a diverse set of Gram-positive and Gram-negative bacteria, including TEM-1, PC1, SME-1, SHV-1 and KPC-2. To the best of our knowledge, this article represents the first systematic review on β-lactamase inhibitors with a particular focus on BLIPs and their inherent properties that favorably position them as a source of biologically-inspired drugs to combat antimicrobial resistance. Furthermore, an extensive compilation of binding data from β-lactamase–BLIP interaction studies is presented herein. Such information help to provide key insights into the origin of interaction that may be useful for rationally guiding future drug design efforts.
Keywords	β-lactamase ; β-lactamase inhibitor protein ; antibiotic resistance ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	572
Language	English
Publishing date	2018-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Production and characterization of antibody against Opisthorchis viverrini via phage display and molecular simulation.

Sitthinon Siripanthong / Anchalee Techasen / Chanin Nantasenamat / Aijaz Ahmad Malik / Paiboon Sithithaworn / Chanvit Leelayuwat / Amonrat Jumnainsong

PLoS ONE, Vol 16, Iss 3, p e

2021 Volume 0248887

Abstract: In this study, a key issue to be addressed is the safe disposal of hybridoma instability. Hybridoma technology was used to produce anti-O. viverrini monoclonal antibody. Previous studies have shown that antibody production via antibody phage display can ... ...

Abstract	In this study, a key issue to be addressed is the safe disposal of hybridoma instability. Hybridoma technology was used to produce anti-O. viverrini monoclonal antibody. Previous studies have shown that antibody production via antibody phage display can sustain the hybridoma technique. This paper presents the utility of antibody phage display technology for producing the phage displayed KKU505 Fab fragment and using experiments in concomitant with molecular simulation for characterization. The phage displayed KKU505 Fab fragment and characterization were successfully carried out. The KKU505 hybridoma cell line producing anti-O. viverrini antibody predicted to bind to myosin was used to synthesize cDNA so as to amplify the heavy chain and the light chain sequences. The KKU505 displayed phage was constructed and characterized by a molecular modeling in which the KKU505 Fab fragment and -O. viverrini myosin head were docked computationally and it is assumed that the Fab fragment was specific to -O. viverrini on the basis of mass spectrometry and Western blot. This complex interaction was confirmed by molecular simulation. Furthermore, the KKU505 displayed phage was validated using indirect enzyme-linked immunosorbent assays (ELISA) and immunohistochemistry. It is worthy to note that ELISA and immunohistochemistry results confirmed that the Fab fragment was specific to the -O. viverrini antigen. Results indicated that the approach presented herein can generate anti-O. viverrini antibody via the phage display technology. This study integrates the use of phage display technology together with molecular simulation for further development of monoclonal antibody production. Furthermore, the presented work has profound implications for antibody production, particularly by solving the problem of hybridoma stability issues.
Keywords	Medicine ; R ; Science ; Q
Subject code	500
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: CryoProtect

Reny Pratiwi / Aijaz Ahmad Malik / Nalini Schaduangrat / Virapong Prachayasittikul / Jarl E. S. Wikberg / Chanin Nantasenamat / Watshara Shoombuatong

Journal of Chemistry, Vol

A Web Server for Classifying Antifreeze Proteins from Nonantifreeze Proteins

2017 Volume 2017

Abstract: Antifreeze protein (AFP) is an ice-binding protein that protects organisms from freezing in extremely cold environments. AFPs are found across a diverse range of species and, therefore, significantly differ in their structures. As there are no consensus ... ...

Abstract	Antifreeze protein (AFP) is an ice-binding protein that protects organisms from freezing in extremely cold environments. AFPs are found across a diverse range of species and, therefore, significantly differ in their structures. As there are no consensus sequences available for determining the ice-binding domain of AFPs, thus the prediction and characterization of AFPs from their sequence is a challenging task. This study addresses this issue by predicting AFPs directly from sequence on a large set of 478 AFPs and 9,139 non-AFPs using machine learning (e.g., random forest) as a function of interpretable features (e.g., amino acid composition, dipeptide composition, and physicochemical properties). Furthermore, AFPs were characterized using propensity scores and important physicochemical properties via statistical and principal component analysis. The predictive model afforded high performance with an accuracy of 88.28% and results revealed that AFPs are likely to be composed of hydrophobic amino acids as well as amino acids with hydroxyl and sulfhydryl side chains. The predictive model is provided as a free publicly available web server called CryoProtect for classifying query protein sequence as being either AFP or non-AFP. The data set and source code are for reproducing the results which are provided on GitHub.
Keywords	Chemistry ; QD1-999
Subject code	612
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Identification and production of mouse scFv to specific epitope of enterovirus-71 virion protein-2 (VP2)

Thanongsaksrikul, Jeeraphong / Potjanee Srimanote / Pongsri Tongtawe / Kittirat Glab-ampai / Aijaz Ahmad Malik / Oratai Supasorn / Phatcharaporn Chiawwit / Yong Poovorawan / Wanpen Chaicumpa

Archives of virology. 2018 May, v. 163, no. 5

2018

Abstract: Enterovirus-71 (EV71) and coxsackievirus-A16 (CA16) frequently cause hand-foot-mouth disease (HFMD) epidemics among infants and young children. CA16 infections are usually mild, while EV71 disease may be fatal due to neurologic complications. As such, ... ...

Abstract	Enterovirus-71 (EV71) and coxsackievirus-A16 (CA16) frequently cause hand-foot-mouth disease (HFMD) epidemics among infants and young children. CA16 infections are usually mild, while EV71 disease may be fatal due to neurologic complications. As such, the ability to rapidly and specifically recognize EV71 is needed to facilitate proper case management and epidemic control. Accordingly, the aim of this study was to generate antibodies to EV71-virion protein-2 (VP2) by phage display technology for further use in specific detection of EV71. A recombinant peptide sequence of EV71-VP2, carrying a predicted conserved B cell epitope fused to glutathione-S-transferase (GST) (designated GST-EV71-VP2/131-160), was produced. The fusion protein was used as bait in in-solution biopanning to separate protein-bound phages from a murine scFv (MuscFv) phage display library constructed from an immunoglobulin gene repertoire from naïve ICR mice. Three phage-transformed E. coli clones (clones 63, 82, and 83) produced MuscFvs that bound to the GST-EV71-VP2/131-160 peptide. The MuscFv of clone 83 (MuscFv83), which produced the highest ELISA signal to the target antigen, was further tested. MuscFv83 also bound to full-length EV71-VP2 and EV71 particles, but did not bind to GST, full-length EV71-VP1, or the antigenically related CA16. MuscFv83 could be a suitable reagent for rapid antigen-based immunoassay, such as immunochromatography (ICT), for the specific detection and/or diagnosis of EV71 infection as well as epidemic surveillance.
Keywords	B-lymphocytes ; Escherichia coli ; antibodies ; bacteriophages ; baits ; children ; clones ; disease outbreaks ; enzyme-linked immunosorbent assay ; epitopes ; glutathione transferase ; hand, foot and mouth disease ; immunoaffinity chromatography ; immunoglobulin genes ; infants ; mice ; monitoring ; recombinant peptides ; virion
Language	English
Dates of publication	2018-05
Size	p. 1141-1152.
Publishing place	Springer Vienna
Document type	Article
ZDB-ID	7491-3
ISSN	1432-8798 ; 0304-8608
ISSN (online)	1432-8798
ISSN	0304-8608
DOI	10.1007/s00705-018-3731-z
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Roles of d-Amino Acids on the Bioactivity of Host Defense Peptides

Hao Li / Nuttapat Anuwongcharoen / Aijaz Ahmad Malik / Virapong Prachayasittikul / Jarl E. S. Wikberg / Chanin Nantasenamat

International Journal of Molecular Sciences, Vol 17, Iss 7, p

2016 Volume 1023

Abstract: Host defense peptides (HDPs) are positively-charged and amphipathic components of the innate immune system that have demonstrated great potential to become the next generation of broad spectrum therapeutic agents effective against a vast array of ... ...

Abstract	Host defense peptides (HDPs) are positively-charged and amphipathic components of the innate immune system that have demonstrated great potential to become the next generation of broad spectrum therapeutic agents effective against a vast array of pathogens and tumor. As such, many approaches have been taken to improve the therapeutic efficacy of HDPs. Amongst these methods, the incorporation of d-amino acids (d-AA) is an approach that has demonstrated consistent success in improving HDPs. Although, virtually all HDP review articles briefly mentioned about the role of d-AA, however it is rather surprising that no systematic review specifically dedicated to this topic exists. Given the impact that d-AA incorporation has on HDPs, this review aims to fill that void with a systematic discussion of the impact of d-AA on HDPs.
Keywords	">d-amino acid ; host defense peptide ; antimicrobial peptide ; anticancer peptide ; diastereomer ; HDP ; AMP ; bioactivity ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Language	English
Publishing date	2016-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking

Saw Simeon / Nuttapat Anuwongcharoen / Watshara Shoombuatong / Aijaz Ahmad Malik / Virapong Prachayasittikul / Jarl E.S. Wikberg / Chanin Nantasenamat

PeerJ, Vol 4, p e

2016 Volume 2322

Abstract: Alzheimer’s disease (AD) is a chronic neurodegenerative disease which leads to the gradual loss of neuronal cells. Several hypotheses for AD exists (e.g., cholinergic, amyloid, tau hypotheses, etc.). As per the cholinergic hypothesis, the deficiency of ... ...

Abstract	Alzheimer’s disease (AD) is a chronic neurodegenerative disease which leads to the gradual loss of neuronal cells. Several hypotheses for AD exists (e.g., cholinergic, amyloid, tau hypotheses, etc.). As per the cholinergic hypothesis, the deficiency of choline is responsible for AD; therefore, the inhibition of AChE is a lucrative therapeutic strategy for the treatment of AD. Acetylcholinesterase (AChE) is an enzyme that catalyzes the breakdown of the neurotransmitter acetylcholine that is essential for cognition and memory. A large non-redundant data set of 2,570 compounds with reported IC50 values against AChE was obtained from ChEMBL and employed in quantitative structure-activity relationship (QSAR) study so as to gain insights on their origin of bioactivity. AChE inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 different data splits using random forest. Generated models afforded R2, ${Q}_{\mathrm{CV }}^{2}$ Q CV 2 and ${Q}_{\mathrm{Ext}}^{2}$ Q Ext 2 values in ranges of 0.66–0.93, 0.55–0.79 and 0.56–0.81 for the training set, 10-fold cross-validated set and external set, respectively. The best model built using the substructure count was selected according to the OECD guidelines and it afforded R2, ${Q}_{\mathrm{CV }}^{2}$ Q CV 2 and ${Q}_{\mathrm{Ext}}^{2}$ Q Ext 2 values of 0.92 ± 0.01, 0.78 ± 0.06 and 0.78 ± 0.05, respectively. Furthermore, Y-scrambling was applied to evaluate the possibility of chance correlation of the predictive model. Subsequently, a thorough analysis of the substructure fingerprint count was conducted to provide informative insights on the inhibitory activity of AChE inhibitors. Moreover, Kennard–Stone sampling of the actives were applied to select 30 diverse compounds for further molecular docking studies in order to gain structural insights on the origin of AChE inhibition. Site-moiety mapping of compounds from the diversity set revealed three binding anchors encompassing both hydrogen bonding and van der Waals ...
Keywords	Acetylcholinesterase ; Acetylcholinesterase inhibitor ; Alzheimer’s disease ; Dementia ; Neurodegenerative disease ; Quantitative structure-activity relationship ; Medicine ; R
Subject code	540
Language	English
Publishing date	2016-08-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Publisher Correction

Kittirat Glab-ampai / Monrat Chulanetra / Aijaz Ahmad Malik / Thanate Juntadech / Jeeraphong Thanongsaksrikul / Potjanee Srimanote / Kanyarat Thueng-in / Nitat Sookrung / Pongsri Tongtawe / Wanpen Chaicumpa

Scientific Reports, Vol 8, Iss 1, Pp 1-

Human single chain-transbodies that bound to domain-I of non-structural protein 5A (NS5A) of hepatitis C virus

2018 Volume 3

Abstract: A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper. ...

Abstract	A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2018-04-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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