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Article ; Online: Molecular dynamics simulation of bioactive compounds of

Begum, Sartaz / Shadrack, Daniel M / Joseph, Ferister M / Ndensendo, Valence M K

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 19, Page(s) 9279–9286

Abstract: Medicinal plants have served humans as medicine for centuries. ...

Abstract	Medicinal plants have served humans as medicine for centuries.
Language	English
Publishing date	2021-05-21
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1927191
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Article ; Online: Accommodating receptor flexibility and free energy calculation to reduce false positive binders in the discovery of natural products blockers of SARS-COV-2 spike RBD-ACE2 interface.

Ogedjo, Marcelina / Onoka, Isaac / Sahini, Mtabazi / Shadrack, Daniel M

Biochemistry and biophysics reports

2021 Volume 27, Page(s) 101024

Abstract: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), which causes coronavirus disease-19 (COVID-19) has caused more than 2 million deaths around the globe. The high transmissibility rate of the disease is related to the strong ... ...

Abstract	The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), which causes coronavirus disease-19 (COVID-19) has caused more than 2 million deaths around the globe. The high transmissibility rate of the disease is related to the strong interaction between the virus spike receptor-binding domain (RBD) and the human angiotensin-converting enzyme 2 (ACE2) as documented in several reports. In this study, using state-of-the-art computational methods, natural products were screened and their molecular mechanism to disrupt spike RBD-ACE2 recognition was evaluated. There is the sensitivity of results to receptor ensemble docking calculations. Binding free energy and MD simulation are important tools to evaluate the thermodynamics of binding stability and the capacity of top hits to disrupt RBD-ACE2 recognition. The free energy profiles provide a slight decrease in binding affinity of the virus-receptor interaction. Three flavonoids parvisoflavone B (
Language	English
Publishing date	2021-05-25
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2831046-9
ISSN	2405-5808 ; 2405-5808
ISSN (online)	2405-5808
ISSN	2405-5808
DOI	10.1016/j.bbrep.2021.101024
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Article ; Online: In silico

Shadrack, Daniel M / Vuai, Said A H / Sahini, Mtabazi G / Onoka, Isaac

RSC advances

2021 Volume 11, Issue 43, Page(s) 26524–26533

Abstract: The outbreak of COVID-19, caused by SARS-COV-2, is responsible for higher mortality and morbidity rates across the globe. Until now, there is no specific treatment of the disease and hospitalized patients are treated according to the symptoms they ... ...

Abstract	The outbreak of COVID-19, caused by SARS-COV-2, is responsible for higher mortality and morbidity rates across the globe. Until now, there is no specific treatment of the disease and hospitalized patients are treated according to the symptoms they develop. Efforts to identify drugs and/or vaccines are ongoing processes. Natural products have shown great promise in the treatment of many viral related diseases. In this work, using
Language	English
Publishing date	2021-08-03
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d1ra04197e
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Article ; Online: Finding alternatives to 5-fluorouracil: application of ensemble-based virtual screening for drug repositioning against human thymidylate synthase.

Mteremko, Denis / Shadrack, Daniel M / Ntie-Kang, Fidele / Chilongola, Jaffu / Chacha, Musa

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 11, Page(s) 4873–4889

Abstract: 5-fluorouracil and analogs are used in the treatment of many solid tumours. However, there are many cases of resistance and high toxicity associated with 5-fluorouracil chemotherapy. Repurposing FDA drugs against human thymidylate synthase revealed a ... ...

Abstract	5-fluorouracil and analogs are used in the treatment of many solid tumours. However, there are many cases of resistance and high toxicity associated with 5-fluorouracil chemotherapy. Repurposing FDA drugs against human thymidylate synthase revealed a number of FDA drugs that have a potential to be further developed for the treatment of various cancers for which 5-fluorouracil and analogs have been used for chemotherapy. Four FDA drugs prioritized for further validation included Erismodegib, Irinotecan, Conivaptan and Ergotamine. The role of water in mediating drug interactions and its contribution to the total binding energy was also shown. MM-PBSA calculations revealed that the binding affinity was the lowest for the hTS-Ergotamine complex (-66.702 ± 1.807 kJ/mol) suggesting moderate inhibition despite a large energetic contribution from van der Waal interactions (-190.889 ± 1.027 kJ/mol).Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; Fluorouracil/pharmacology ; Drug Repositioning ; Thymidylate Synthase ; Neoplasms/drug therapy ; Ergotamines
Chemical Substances	Fluorouracil (U3P01618RT) ; Thymidylate Synthase (EC 2.1.1.45) ; Ergotamines
Language	English
Publishing date	2022-05-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2074140
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Zs.A 2093: Show issues

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Article ; Online: Solvent effects on host-guest residence time and kinetics: further insights from metadynamics simulation of Toussaintine-A unbiding from chitosan nanoparticle.

Shadrack, Daniel M / Kiruri, Lucy W / Swai, Hulda / Nyandoro, Stephen S

Journal of molecular modeling

2021 Volume 27, Issue 5, Page(s) 127

Abstract: Solvents play an important role in host-guest intermolecular interactions. The kinetics and residence time of Toussaintine-A (TouA) unbinding from chitosan was investigated by means of well-tempered metadynamics and thermodynamic integration using two ... ...

Abstract	Solvents play an important role in host-guest intermolecular interactions. The kinetics and residence time of Toussaintine-A (TouA) unbinding from chitosan was investigated by means of well-tempered metadynamics and thermodynamic integration using two solvents, polar aprotic (DMSO), and polar protic (water). The kinetic rates were found to be strongly dependent on the solvent polarity; hence, the unbinding rate proceeded much faster in DMSO compared to water. DMSO tends to participate less in a chemical reaction by weakening the intermolecular interaction between chitosan and TouA due to lack of acidic hydrogen resulting in a reduction of the transition state. On the other hand, water, which ought to donate hydrogen atoms, sustains a strong interaction and hence large barrier heights. Consequently, this reduces the unbinding rate and increases the residence time. Binding free energy from thermodynamic integration suggests a thermodynamic stable chitosan-TouA complex in water than in DMSO. Graphical abstract.
MeSH term(s)	Chitosan/chemistry ; Cinnamates/chemistry ; Dimethyl Sulfoxide/chemistry ; Indoles/chemistry ; Kinetics ; Molecular Dynamics Simulation ; Nanoparticles/chemistry ; Solvents/chemistry ; Thermodynamics ; Water/analysis ; Water/chemistry
Chemical Substances	Cinnamates ; Indoles ; N-cinnamoyl-5,6-dehydro-4-hydroxyindolidin-2,7-dione ; Solvents ; Water (059QF0KO0R) ; Chitosan (9012-76-4) ; Dimethyl Sulfoxide (YOW8V9698H)
Language	English
Publishing date	2021-04-14
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-021-04735-y
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Article ; Online: A nanoscale study of the structure and electrical response of Sepia eumelanin.

Niyonkuru, Dieudonné / Camus, Anthony / Reali, Manuel / Gao, Zhaojing / Shadrack, Daniel M / Butyaev, Oleg / Surtchev, Marko / Santato, Clara

Nanoscale advances

2023 Volume 5, Issue 19, Page(s) 5295–5300

Abstract: Eumelanin, the brown-black member of the melanin biopigment family, is a prototype material for sustainable (green) organic electronics. Sepia eumelanin (Sepia) is a type of biosourced eumelanin extracted from the ink sac of cuttlefish. Electron ... ...

Abstract	Eumelanin, the brown-black member of the melanin biopigment family, is a prototype material for sustainable (green) organic electronics. Sepia eumelanin (Sepia) is a type of biosourced eumelanin extracted from the ink sac of cuttlefish. Electron microscopy and scanning probe microscopy images of Sepia show distinguishable near spherical granules with diameters of about 150-200 nm. We have recently reported on predominant electronic transport in printed films of Sepia formulated inks including the (insulating) binder Polyvinyl-butyral (PVB). In that work, we proposed that inter-granular percolative transport, observed for micrometric interelectrode distances, is promoted by the confining action of the PVB binder on the Sepia granules. Considering that inter-granular transport implies intra-granular transport, in this work we proceeded to a nanoscale study of Sepia granules by High Resolution Atomic Force Microscopy (HR-AFM) and Conductive-AFM (c-AFM). We have observed protrusions on the surface of the Sepia granules, suggesting sub-granular structures compatible with the hierarchical development of Sepia, as proposed elsewhere. For films of Sepia formulated inks deposited on gold-coated substrates, c-AFM revealed, for the very first time, a nanoscale electrical response. Nanoscale studies provide the key to structure-property relationships in biosourced materials strategic for sustainable organic electronics.
Language	English
Publishing date	2023-09-01
Publishing country	England
Document type	Journal Article
ISSN	2516-0230
ISSN (online)	2516-0230
DOI	10.1039/d3na00355h
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Article ; Online: Neuroprotective potential of cinnamoyl derivatives against Parkinson's disease indicators in Drosophila melanogaster and in silico models.

Tibashailwa, Nelson / Stephano, Flora / Shadrack, Daniel M / Munissi, Joan J E / Nyandoro, Stephen S

Neurotoxicology

2022 Volume 94, Page(s) 147–157

Abstract: Parkinson's disease (PD) is a movement disorder resulting from the loss of dopaminergic neurons over time. While there is no cure for PD, available conventional therapies aid to manage the motor symptoms. Natural products (NPs) derived from plants are ... ...

Abstract	Parkinson's disease (PD) is a movement disorder resulting from the loss of dopaminergic neurons over time. While there is no cure for PD, available conventional therapies aid to manage the motor symptoms. Natural products (NPs) derived from plants are among the most potent alternative therapies for PD. This study explored the neuroprotective potential of selected cinnamoyl derivatives namely toussaintine A (1), E-toussaintine E (2), asperphenamate (3) and julocrotine (4) against PD indicators using rotenone-challenged Drosophila melanogaster and in silico models. The compounds were first assessed for their toxicity preceding treatment experiments. Adult flies (aged 1-4 days) were exposed to varying concentrations of the compounds for 7 days. During the experiment, the mortality of flies was observed, and the lethal concentration (LC
MeSH term(s)	Animals ; Drosophila melanogaster ; Parkinson Disease/drug therapy ; Parkinson Disease/prevention & control ; Rotenone/toxicity ; Oxidative Stress ; Neuroprotective Agents/pharmacology ; Neuroprotective Agents/therapeutic use ; Computer Simulation ; Disease Models, Animal
Chemical Substances	Rotenone (03L9OT429T) ; N-cinnamoyl-5,6-dehydro-4-hydroxyindolidin-2,7-dione ; Neuroprotective Agents
Language	English
Publishing date	2022-11-21
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	800820-6
ISSN	1872-9711 ; 0161-813X
ISSN (online)	1872-9711
ISSN	0161-813X
DOI	10.1016/j.neuro.2022.11.010
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Zs.A 1547: Show issues

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Article ; Online: A computational study on the role of water and conformational fluctuations in Hsp90 in response to inhibitors.

Shadrack, Daniel M / Swai, Hulda S / Hassanali, Ali

Journal of molecular graphics & modelling

2019 Volume 96, Page(s) 107510

Abstract: Molecular chaperone Heat Shock Protein 90 (Hsp90) represents an interesting chemotherapeutic target for cancer treatments as it plays a role in cancer proliferation. Thus, continued effort to identify novel inhibitors of this target is an important task. ...

Abstract	Molecular chaperone Heat Shock Protein 90 (Hsp90) represents an interesting chemotherapeutic target for cancer treatments as it plays a role in cancer proliferation. Thus, continued effort to identify novel inhibitors of this target is an important task. Drug design using computational approach has gained significant attention in recent years. This work aims to propose docking protocols to re-purpose FDA-approved drugs targeting Hsp90. Sensitivity of results to different docking protocols such apo, holo and receptor ensembles (relaxed complex) structures, the role of water and conformational changes of Hsp90, are described. We show that the protein conformation and water have effects on drug binding. Holo relaxed complex receptors ensembles improves the binding energy of ligands to the protein. We also compare and contrast structural stability of three drugs namely: ezetimibe, pitavastatin and vilazodon in the Hsp90 protein. The results obtained serves as a possible basis towards developing Hsp90 inhibitors.
MeSH term(s)	Drug Design ; HSP90 Heat-Shock Proteins/metabolism ; Ligands ; Protein Conformation ; Water
Chemical Substances	HSP90 Heat-Shock Proteins ; Ligands ; Water (059QF0KO0R)
Language	English
Publishing date	2019-12-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2019.107510
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Zs.A 3491: Show issues

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Article: In silico study of the inhibition of SARS-COV-2 viral cell entry by neem tree extracts

Shadrack, Daniel M. / Vuai, Said A. H. / Sahini, Mtabazi G. / Onoka, Isaac

RSC advances. 2021 Aug. 03, v. 11, no. 43

2021

Abstract	The outbreak of COVID-19, caused by SARS-COV-2, is responsible for higher mortality and morbidity rates across the globe. Until now, there is no specific treatment of the disease and hospitalized patients are treated according to the symptoms they develop. Efforts to identify drugs and/or vaccines are ongoing processes. Natural products have shown great promise in the treatment of many viral related diseases. In this work, using in silico methods, bioactive compounds from the neem tree were investigated for their ability to block viral cell entry as spike RBD-ACE2 inhibitors. Azadirachtin H, quentin and margocin were identified as potential compounds that demonstrated viral cell entry inhibition properties. The structural re-orientation of azadirachtin H was observed as the mechanism for viral cell entry inhibition. These compounds possessed good pharmacodynamic properties. The proposed molecules can serve as a starting point towards developing effective anti-SARS-COV-2 drugs targeting the inhibition of viral cell entry upon further in vitro and in vivo validation.
Keywords	Azadirachta indica ; COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; azadirachtin ; computer simulation ; morbidity ; mortality ; pharmacodynamics ; trees
Language	English
Dates of publication	2021-0803
Size	p. 26524-26533.
Publishing place	The Royal Society of Chemistry
Document type	Article
ISSN	2046-2069
DOI	10.1039/d1ra04197e
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Cation-π interactions drive hydrophobic self-assembly and aggregation of niclosamide in water.

Vuai, Said A H / Sahini, Mtabazi G / Onoka, Isaac / Kiruri, Lucy W / Shadrack, Daniel M

RSC advances

2021 Volume 11, Issue 52, Page(s) 33136–33147

Abstract: The beneficial medicinal effects of niclosamide have been reported to be hampered by poor aqueous solubility and so a higher concentration dosage is required. In this work, we have studied the aggregation properties of niclosamide in water by varying the ...

Abstract	The beneficial medicinal effects of niclosamide have been reported to be hampered by poor aqueous solubility and so a higher concentration dosage is required. In this work, we have studied the aggregation properties of niclosamide in water by varying the number of monomers. We have employed all-atom classical molecular dynamics simulation in order to explore such properties. The equilibrium structure exists in an aggregated state with structural rearrangements of the stacking units. Niclosamide monomers tend to form clusters in an orderly manner and tend to aggregate in parallel and antiparallel orientations of the phenyl rings as the monomers are increased in number from 4 to 9. Upon increasing the size from 9 to 14, and from 49 to 150, a considerable dominance of the metastable parallel arrangement is observed, resulting in the formation of a closely packed cluster with hydrophobic contacts. The metastable conformation self-arranges to a T-shape before forming a stable planar antiparallel displaced conformation. The aggregated π-π parallel and cation-π antiparallel clusters in water exist in a β-conformer. We further observed that formation of a stable cluster aggregate entails the formation of an intermediate metastable cluster that disperses in solution forming a large stable cluster. We also discovered that movement of the water is faster in less aggregated clusters and as the cluster size increases, the mobility rate becomes much slower.
Language	English
Publishing date	2021-10-07
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d1ra05358b
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