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Article ; Online: PyComp: A Versatile Tool for Efficient Data Extraction, Conversion, and Management in High-throughput Virtual Drug Screening.

Sisakht, Mohsen / Shahrestanaki, Mohammad Keyvanloo / Fallahi, Jafar / Razban, Vahid

Current computer-aided drug design

2024

Abstract: Background: Virtual screening (VS) is essential for analyzing potential drug candidates in drug discovery. Often, this involves the conversion of large volumes of compound data into specific formats suitable for computational analysis. Managing and ... ...

Abstract	Background: Virtual screening (VS) is essential for analyzing potential drug candidates in drug discovery. Often, this involves the conversion of large volumes of compound data into specific formats suitable for computational analysis. Managing and processing this wealth of information, especially when dealing with vast numbers of compounds in various forms, such as names, identifiers, or SMILES strings, can present significant logistical and technical challenges. Methods: To streamline this process, we developed PyComp, a software tool using Python's PyQt5 library, and compiled it into an executable with Pyinstaller. PyComp provides a systematic way for users to retrieve and convert a list of compound names, IDs (even in a range), or SMILES strings into the desired 3D format. Results: PyComp greatly enhances the efficiency of data extraction, conversion, and storage processes involved in VS. It searches for similar compounds coupled with its ability to handle misidentified compounds and offers users an easy-to-use, customizable tool for managing largescale compound data. By streamlining these operations, PyComp allows researchers to save significant time and effort, thus accelerating the pace of drug discovery research. Conclusion: PyComp effectively addresses some of the most pressing challenges in highthroughput VS: efficient management and conversion of large volumes of compound data. As a user-friendly, customizable software tool, PyComp is pivotal in improving the efficiency and success of large-scale drug screening efforts, paving the way for faster discovery of potential therapeutic compounds.
Language	English
Publishing date	2024-01-08
Publishing country	United Arab Emirates
Document type	Journal Article
ISSN	1875-6697
ISSN (online)	1875-6697
DOI	10.2174/0115734099274495231218150611
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Article ; Online: Partial Reprogramming as a Method for Regenerating Neural Tissues in Aged Organisms.

Sichani, Ali Saber / Khoddam, Somayeh / Shakeri, Shayan / Tavakkoli, Zahra / Jafroodi, Arad Ranji / Dabbaghipour, Reza / Sisakht, Mohsen / Fallahi, Jafar

Cellular reprogramming

2024 Volume 26, Issue 1, Page(s) 10–23

Abstract: Aging causes numerous age-related diseases, leading the human species to death. Nevertheless, rejuvenating strategies based on cell epigenetic modifications are a possible approach to counteract disease progression while getting old. Cell reprogramming ... ...

Abstract	Aging causes numerous age-related diseases, leading the human species to death. Nevertheless, rejuvenating strategies based on cell epigenetic modifications are a possible approach to counteract disease progression while getting old. Cell reprogramming of adult somatic cells toward pluripotency ought to be a promising tool for age-related diseases. However, researchers do not have control over this process as cells lose their fate, and cause potential cancerous cells or unexpected cell phenotypes. Direct and partial reprogramming were introduced in recent years with distinctive applications. Although direct reprogramming makes cells lose their identity, it has various applications in regeneration medicine. Temporary and regulated
MeSH term(s)	Adult ; Humans ; Animals ; Mice ; Aged ; Aging ; Alzheimer Disease ; Cell Transformation, Neoplastic ; Cellular Reprogramming ; Epigenesis, Genetic
Language	English
Publishing date	2024-02-21
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2542436-1
ISSN	2152-4998 ; 1557-7457 ; 2152-4971
ISSN (online)	2152-4998 ; 1557-7457
ISSN	2152-4971
DOI	10.1089/cell.2023.0123
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Article ; Online: Plant-derived chemicals as potential inhibitors of SARS-CoV-2 main protease (6LU7), a virtual screening study.

Sisakht, Mohsen / Mahmoodzadeh, Amir / Darabian, Maryam

Phytotherapy research : PTR

2021 Volume 35, Issue 6, Page(s) 3262–3274

Abstract: SARS-CoV-2 has caused millions of infections and more than 700,000 deaths. Taking the urgent need to find new therapeutics for coronavirus disease 2019 (COVID-19), a dataset of plant-based natural compounds was selected for the screening of antiviral ... ...

Abstract	SARS-CoV-2 has caused millions of infections and more than 700,000 deaths. Taking the urgent need to find new therapeutics for coronavirus disease 2019 (COVID-19), a dataset of plant-based natural compounds was selected for the screening of antiviral activity. The viral 3-chymotrypsin-like cysteine protease (Mpro, 3CLpro) was selected as the target. Molecular docking was performed on 2,845 phytochemicals to estimate the spatial affinity for the active sites of the enzyme. The ADMET screening was used for the pharmacological and physicochemical properties of the hit compounds. Nelfinavir and Lopinavir were used as control for binding energy comparison. The top 10 hits, based on the binding energy (Kcal/mol), were Ginkgolide M (-11.2), Mezerein (-11), Tubocurarine (-10.9), Gnidicin (-10.4), Glycobismine A (-10.4), Sciadopitysin Z-10.2), Gnididin (-9.2), Glycobismine A (-10.4), Sciadopitysin (-10.2), Gnididin (-9.20, Emetine (-8.7), Vitexin (-8.3), Calophyllolide (-8.3), and 6-(3,3-Dimethylallyl)galangin (-7.9). The binding energy for nelfinavir and lopinavir were - 9.1 and - 8.4, respectively. Interestingly, some of these natural products were previously shown to possess antiviral properties against various viruses, such as HIV, Zika, and Ebola viruses. Herein, we suggest several phytochemicals as the inhibitors of the main protease of SARS-CoV-2 that could be used in the fight against COVID-19.
MeSH term(s)	Antiviral Agents/pharmacology ; Humans ; Molecular Docking Simulation ; Peptide Hydrolases/drug effects ; Phytochemicals/chemistry ; Phytochemicals/pharmacology ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; SARS-CoV-2/drug effects ; COVID-19 Drug Treatment
Chemical Substances	Antiviral Agents ; Phytochemicals ; Protease Inhibitors ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2021-03-23
Publishing country	England
Document type	Comparative Study ; Journal Article
ZDB-ID	639136-9
ISSN	1099-1573 ; 0951-418X
ISSN (online)	1099-1573
ISSN	0951-418X
DOI	10.1002/ptr.7041
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Article: Plant‐derived chemicals as potential inhibitors of SARS‐CoV‐2 main protease (6LU7), a virtual screening study

Sisakht, Mohsen / Mahmoodzadeh, Amir / Darabian, Maryam

Phytotherapy research. 2021 June, v. 35, no. 6

2021

Abstract: SARS‐CoV‐2 has caused millions of infections and more than 700,000 deaths. Taking the urgent need to find new therapeutics for coronavirus disease 2019 (COVID‐19), a dataset of plant‐based natural compounds was selected for the screening of antiviral ... ...

Abstract	SARS‐CoV‐2 has caused millions of infections and more than 700,000 deaths. Taking the urgent need to find new therapeutics for coronavirus disease 2019 (COVID‐19), a dataset of plant‐based natural compounds was selected for the screening of antiviral activity. The viral 3‐chymotrypsin‐like cysteine protease (Mpro, 3CLpro) was selected as the target. Molecular docking was performed on 2,845 phytochemicals to estimate the spatial affinity for the active sites of the enzyme. The ADMET screening was used for the pharmacological and physicochemical properties of the hit compounds. Nelfinavir and Lopinavir were used as control for binding energy comparison. The top 10 hits, based on the binding energy (Kcal/mol), were Ginkgolide M (−11.2), Mezerein (−11), Tubocurarine (−10.9), Gnidicin (−10.4), Glycobismine A (−10.4), Sciadopitysin Z‐10.2), Gnididin (−9.2), Glycobismine A (−10.4), Sciadopitysin (−10.2), Gnididin (−9.20, Emetine (−8.7), Vitexin (−8.3), Calophyllolide (−8.3), and 6‐(3,3‐Dimethylallyl)galangin (−7.9). The binding energy for nelfinavir and lopinavir were − 9.1 and − 8.4, respectively. Interestingly, some of these natural products were previously shown to possess antiviral properties against various viruses, such as HIV, Zika, and Ebola viruses. Herein, we suggest several phytochemicals as the inhibitors of the main protease of SARS‐CoV‐2 that could be used in the fight against COVID‐19.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; antiviral properties ; cysteine proteinases ; data collection ; emetine ; energy ; phytochemicals ; phytotherapy ; research
Language	English
Dates of publication	2021-06
Size	p. 3262-3274.
Publishing place	John Wiley & Sons, Ltd.
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	639136-9
ISSN	1099-1573 ; 0951-418X
ISSN (online)	1099-1573
ISSN	0951-418X
DOI	10.1002/ptr.7041
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: PyProtModel: An easy to use GUI for comparative protein modeling.

Sisakht, Mohsen / Bemani, Peyman / Ghadim, Mir Behrad Aghazadeh / Rahimi, Amir / Sakhteman, Amirhossein

Journal of molecular graphics & modelling

2022 Volume 112, Page(s) 108134

Abstract: A deep insight into the 3D structures of the proteins is essential to understand their functions and will be helpful in drug design and making decisions for the treatment of diseases. The 3D structure for less than one-thousandth of the protein sequences ...

Abstract	A deep insight into the 3D structures of the proteins is essential to understand their functions and will be helpful in drug design and making decisions for the treatment of diseases. The 3D structure for less than one-thousandth of the protein sequences has been determined so far due to the slow structure elucidation procedures with experimental methods, such as X-ray. For this reason, different computational methods were used to determine the structure of the proteins, including template-based and de novo approaches. Much software has been developed to facilitate the computational approaches in protein modeling, some of which need user expertise and extensive knowledge in bioinformatics. The present study attempted to provide a user-friendly environment to motivate the researchers in computational biology, a Python-based interface based on MODELLER software. PyProtModel can be used as a toolbox in structural bioinformatics for protein modeling from sequence to the prediction of 3D structure. In addition, the users can take benefits of PyProtModel in order to prepare and evaluate protein PDB files prior to other in silico experiments. PyProtModel allows the user to apply different MODELLER options, automates, and speeds up time-consuming homology modeling steps. Different aspects of PyProtModel and a comprehensive view of the application will be discussed in this paper. The application is available for download and use at: https://github.com/msisakht/pyprotmodel.git.
MeSH term(s)	Amino Acid Sequence ; Computational Biology/methods ; Molecular Dynamics Simulation ; Proteins/chemistry ; Software
Chemical Substances	Proteins
Language	English
Publishing date	2022-01-17
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.2022.108134
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Article: Extremely Low Frequency-Electromagnetic Fields (ELF-EMF) Can Decrease Spermatocyte Count and Motility and Change Testicular Tissue.

Karbalay-Doust, Saeid / Darabyan, Maryam / Sisakht, Mohsen / Haddadi, Gholamhassan / Sotoudeh, Narges / Haghani, Masoud / Mortazavi, Seyed Mohammad Javad

Journal of biomedical physics & engineering

2023 Volume 13, Issue 2, Page(s) 135–146

Abstract: Background: Substantial evidence indicates that exposure to extremely low frequency-electromagnetic fields (ELF-EMFs) affects male reproductive system.: Objective: The goal of this study was to evaluate the effects of long-term irradiation with ELF- ... ...

Abstract	Background: Substantial evidence indicates that exposure to extremely low frequency-electromagnetic fields (ELF-EMFs) affects male reproductive system. Objective: The goal of this study was to evaluate the effects of long-term irradiation with ELF-EMF on sperm quality and quantity and testicular structure. Material and methods: In this case-control study, sixty male Sprague-Dawley rats were randomly divided into six groups. Experimental groups were exposed to ELF-EMF (50 Hz EMF, 100 µT) for either 1 h/day for 52 days (Group 1), 4 h/day for 52 days (Group 3), 1 h/day for 5 days (Group 5), 4 h/day for 52 days (Group 7). Groups 2, 4, 6 and 8 were only sham exposed at durations equal to Groups 1, 3, 5 and 7, respectively. Results: Both count and motility of sperms were significantly decreased in animals exposed to ELF-EMF (1 h/day for 52 days, 4 h/day for 52 day, and 4 h/day for 5 days) compared to the sham-exposed groups ( Conclusion: Our results show that ELF-EMF can reduce spermatocyte count and motility and is able to induce structural changes in testicular tissue.
Language	English
Publishing date	2023-04-01
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2673599-4
ISSN	2251-7200
ISSN	2251-7200
DOI	10.31661/jbpe.v0i0.2011-1234
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Article: Adrenomedullin increases cAMP accumulation and BDNF expression in rat DRG and spinal motor neurons.

Sisakht, Mohsen / Khoshdel, Zahra / Mahmoodazdeh, Amir / Shafiee, Sayed Mohammad / Takhshid, Mohammad Ali

Iranian journal of basic medical sciences

2021 Volume 24, Issue 7, Page(s) 978–985

Abstract: Objectives: Adrenomedullin (AM) has high expression in the spinal cord. In this study, we investigated the expression of AM and its receptor components, including calcitonin receptor-like receptor (CLR) and receptor activity modifying proteins (RAMPs) ... ...

Abstract	Objectives: Adrenomedullin (AM) has high expression in the spinal cord. In this study, we investigated the expression of AM and its receptor components, including calcitonin receptor-like receptor (CLR) and receptor activity modifying proteins (RAMPs) in dorsal root ganglion (DRG) and spinal motor (SM) neurons. Furthermore, the effects of AM on cAMP/cAMP response element-binding protein (CREB), AKT/glycogen synthase kinase-3 beta (GSK-3β) signaling pathways, and expressions of brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3) were evaluated. Materials and methods: Rat embryonic DRG and SM neurons were isolated, purified, and cultured. Real-time PCR was used to assess expressions of AM, CLR, and RAMPs. cAMP levels, p-CREB, BDNF, and NT-3 were determined using an enzyme-linked immunosorbent assay. p-AKT and p-GSK-3β levels were determined by western blotting. Real-time PCR showed expressions of AM, CLR, RAMP2, and RAMP3 in both DRG and SM neurons. Results: AM increased cAMP accumulation and p-CREB levels in DRG and SM neurons. AM increased p-AKT and p-GSK-3β in DRG, but not SM neurons. AM significantly increased BDNF expression in both DRG and SM neurons. There was also an increase in NT-3 level in both DRG and SM neurons, which is statistically significant in SM neurons. Conclusion: These results showed both DRG and SM neurons are targets of AM actions in the spinal cord. An increase in BDNF expression by AM in both DRG and SM neurons suggests the possible beneficial role of AM in protecting, survival, and regeneration of sensory and motor neurons.
Language	English
Publishing date	2021-10-19
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2500485-2
ISSN	2008-3874 ; 2008-3866
ISSN (online)	2008-3874
ISSN	2008-3866
DOI	10.22038/ijbms.2021.54796.12289
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Article ; Online: Extremely Low Frequency-Electromagnetic Fields (ELF-EMF) Can Decrease Spermatocyte Count and Motility and Change Testicular Tissue

Saeid Karbalay-Doust / Maryam Darabyan / Mohsen Sisakht / Gholamhassan Haddadi / Narges Sotoudeh / Masoud Haghani / Seyed Mohammad Javad Mortazavi‌

Journal of Biomedical Physics and Engineering, Vol 13, Iss 2, Pp 135-

2023 Volume 146

Abstract: Background: Substantial evidence indicates that exposure to extremely low frequency-electromagnetic fields (ELF-EMFs) affects male reproductive system. Objective: The goal of this study was to evaluate the effects of long-term irradiation with ELF-EMF on ...

Abstract	Background: Substantial evidence indicates that exposure to extremely low frequency-electromagnetic fields (ELF-EMFs) affects male reproductive system. Objective: The goal of this study was to evaluate the effects of long-term irradiation with ELF-EMF on sperm quality and quantity and testicular structure.Material and Methods: In this case-control study, sixty male Sprague-Dawley rats were randomly divided into six groups. Experimental groups were exposed to ELF-EMF (50 Hz EMF, 100 µT) for either 1 h/day for 52 days (Group 1), 4 h/day for 52 days (Group 3), 1 h/day for 5 days (Group 5), 4 h/day for 52 days (Group 7). Groups 2, 4, 6 and 8 were only sham exposed at durations equal to Groups 1, 3, 5 and 7, respectively. Results: Both count and motility of sperms were significantly decreased in animals exposed to ELF-EMF (1 h/day for 52 days, 4 h/day for 52 day, and 4 h/day for 5 days) compared to the sham-exposed groups (P<0.05). Serum testosterone levels showed a significant decrease in the animals exposed to ELF-EMF (4 h/day for 5 days) compared to the control groups (P<0.05). A significant decrease was observed in the volume of the seminiferous tubules, seminiferous tubules epithelium and interstitial tissue in the animals exposed to ELF-EMF for 4 h/day for 5 days. Tubules length was also reduced by 18% in animals exposed to ELF-EMF (4 h/day for 5 days). Conclusion: Our results show that ELF-EMF can reduce spermatocyte count and motility and is able to induce structural changes in testicular tissue.
Keywords	low frequency electromagnetic field ; stereology ; testis ; Medical physics. Medical radiology. Nuclear medicine ; R895-920
Subject code	630
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Shiraz University of Medical Sciences
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Potential inhibitors of the main protease of SARS-CoV-2 and modulators of arachidonic acid pathway: Non-steroidal anti-inflammatory drugs against COVID-19.

Sisakht, Mohsen / Solhjoo, Aida / Mahmoodzadeh, Amir / Fathalipour, Mohammad / Kabiri, Maryam / Sakhteman, Amirhossein

Computers in biology and medicine

2021 Volume 136, Page(s) 104686

Abstract: The main protease of SARS-CoV-2 is one of the key targets to develop and design antiviral drugs. There is no general agreement on the use of non-steroidal anti-inflammatory drugs (NSAIDs) in COVID-19. In this study, we investigated NSAIDs as potential ... ...

Abstract	The main protease of SARS-CoV-2 is one of the key targets to develop and design antiviral drugs. There is no general agreement on the use of non-steroidal anti-inflammatory drugs (NSAIDs) in COVID-19. In this study, we investigated NSAIDs as potential inhibitors for chymotrypsin-like protease (3CLpro) and the main protease of the SARS-CoV-2 to find out the best candidates, which can act as potent inhibitors against the main protease. We also predicted the effect of NSAIDs on the arachidonic pathway and evaluated the hepatotoxicity of the compounds using systems biology techniques. Molecular docking was conducted via AutoDock Vina to estimate the interactions and binding affinities between selected NSAIDs and the main protease. Molecular docking results showed the presence of 10 NSAIDs based on lower binding energy (kcal/mol) toward the 3CLpro inhibition site compared to the co-crystal native ligand Inhibitor N3 (-6.6 kcal/mol). To validate the docking results, molecular dynamic (MD) simulations on the top inhibitor, Talniflumate, were performed. To obtain differentially-expressed genes under the 27 NSAIDs perturbations, we utilized the L1000 final Z-scores from the NCBI GEO repository (GSE92742). The obtained dataset included gene expression profiling signatures for 27 NSAIDs. The hepatotoxicity of NSAIDs was studied by systems biology modeling of Disturbed Metabolic Pathways. This study highlights the new application of NSAIDs as anti-viral drugs used against COVID-19. NSAIDs may also attenuate the cytokine storm through the downregulation of inflammatory mediators in the arachidonic acid pathway.
MeSH term(s)	Anti-Inflammatory Agents, Non-Steroidal/pharmacology ; Antiviral Agents/pharmacology ; Arachidonic Acid ; COVID-19 ; Coronavirus 3C Proteases/antagonists & inhibitors ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Peptide Hydrolases ; Protease Inhibitors/pharmacology ; SARS-CoV-2
Chemical Substances	Anti-Inflammatory Agents, Non-Steroidal ; Antiviral Agents ; Protease Inhibitors ; Arachidonic Acid (27YG812J1I) ; Peptide Hydrolases (EC 3.4.-) ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2021-07-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2021.104686
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Article: Adrenomedullin protects rat dorsal root ganglion neurons against doxorubicin-induced toxicity by ameliorating oxidative stress.

Mahmoodazdeh, Amir / Shafiee, Sayed Mohammad / Sisakht, Mohsen / Khoshdel, Zahra / Takhshid, Mohammad Ali

Iranian journal of basic medical sciences

2020 Volume 23, Issue 9, Page(s) 1197–1206

Abstract: Objectives: Despite effective anticancer effects, the use of doxorubicin (DOX) is hindered due to its cardio and neurotoxicity. The neuroprotective effect of adrenomedullin (AM) was shown in several studies. The present study aimed to evaluate the ... ...

Abstract	Objectives: Despite effective anticancer effects, the use of doxorubicin (DOX) is hindered due to its cardio and neurotoxicity. The neuroprotective effect of adrenomedullin (AM) was shown in several studies. The present study aimed to evaluate the possible protective effects of AM against DOX-induced toxicity in dorsal root ganglia (DRGs) neurons. Materials and methods: Rat embryonic DRG neurons were isolated and cultured. The effect of various concentrations of DOX (0.0 to 100 µM) in the absence or presence of AM (3.125 -100 nM) on cell death, apoptosis, oxidative stress, expression of tumor necrosis-α (TNF-α), interleukin1- β (IL-1β), inducible nitric oxide synthase (iNOS), matrix metalloproteinase (MMP) 3 and 13, and SRY-related protein 9 (SOX9) were examined. Results: Based on MTT assay data, DOX decreased the viability of DRG neurons in a dose and time-dependent manner (IC Conclusion: Our findings suggest that AM can be considered a novel ameliorating drug against DOX-induced neurotoxicity.
Language	English
Publishing date	2020-09-09
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2500485-2
ISSN	2008-3874 ; 2008-3866
ISSN (online)	2008-3874
ISSN	2008-3866
DOI	10.22038/ijbms.2020.45134.10514
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