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Welcome to Parham Academy | Brief discription about the founder


Parham Jabbarzadeh Kaboli, PhD (in progress) in brief:

- A research leader in cancer discovery and cell signaling
- An experienced lecturer in cell and molecular biology
- An young investigator member of the European Association of Cancer Research (EACR)
- An associate member of the American Association of Cancer Research (AACR)
- A member of the American Society for Pharmacology and Experimental Therapeutics (ASPET)
- A member of the American Association for Advancement of Science (AAAS)

►Cellular & molecular pharmacologist
►Research scientist
►Expert in: Cell therapy/drug discovery/Data science
►Problem solver

Parham Jabbarzadeh Kaboli in detailed:

► CAREER PROFILE

• University Lecturer with management experience and exceptional people skills.
• Versed in laboratory tests and bioinformatics with focus on cell biology and cell-based assays.
• Desires a challenging role as a research scientist involving in drug discovery.
• Sale manager in pharmaceutical industry with background as reseller and consultant looking to join a growing entrepreneurial organization as part of the R&D team.

► PHD PROFILE

• Establishment of a virtual high-throughput screening platform to find out more suitable compounds compared with berberine which led to ONE innovation, SIX journal papers, ONE silver medal, and ONE governmental grant ($25000).
• Leading a team to develop virtual high-throughput screening platform (algorithm) by which thousands compounds can be automatically modeled against a specific target, and eventually binding efficiency index and ADMET parameters are predicted.

► COMMUNICATION

• Presenting research results at international scientific meetings in the UK and Italy held by British, European, and American associations for cancer research - BACR, EACR, and AACR respectively.
• Preparing PhD thesis (45,000 words) and annual progress report for grant awarding bodies.
• Teaching and demonstrating at undergraduate practical and tutorial sessions (2000-2013) and online training workshops (2011- present).
• NINE journal papers, FOUR conference papers, and TWO books have been authored which will be available upon request.

► INTERPERSONAL SKILLS

• Collaborating with colleagues to schedule and manage their needs in laboratories, and keeping in touch with suppliers.
• Supporting the development of new colleagues/lecturers through assisting with their professional training to ensure competence and personal safety.
• Recruiting and interviewing with new lecturers (2006-2013).

► CONTACT

parham@gromacs.net



Each weekend, you are linked to the best article that , during each week, I have read and found it great in the field of Cancer and Pharmacology. I try to encourage the fellow researchers and post-graduate students to read so much as they can about new therapeutics.
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Weekend Recipe for February 2016 - the fourth week

The birth of modern chemotherapy

This paper published in the Pharmacologist is very interesting showing you how chemotherapy has been evolved as a tool to treat cancer.


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Each weekend, you are linked to the best article that , during each week, I have read and found it great in the field of Cancer and Pharmacology. I try to encourage the fellow researchers and post-graduate students to read so much as they can about new therapeutics.
-------------------------------------------

Weekend Recipe for February 2016 - the second week

The impact of molecular dynamics on drug design: applications for the characterization of ligand– macromolecule complexes

This week I would like to suggest this paper. This paper is very great review paper which is useful for those are interested in drug discovery and are got a little bit confused.

Abstract——Among all tools available to design new drugs, molecular dynamics (MD) simulations have become an essential technique. Initially developed to investigate molecular models with a limited number of atoms, computers now enable investigations of large macromolecular systems with a simulation time reaching the microsecond range.

The reviewed articles cover four years of research to give an overview on the actual impact of MD on the current medicinal chemistry landscape with a particular emphasis on studies of ligand–protein interactions. With a special focus on studies combining computational approaches with data gained from other techniques, this review shows how deeply embedded MD simulations are in drug design strategies and articulates what the future of this technique could be.


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If interested in the field of drug discovery I would also like to suggest these articles. These are well-written too.

To download other weekend recipes click here.

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Each weekend, you are linked to the best article that , during each week, I have read and found it great in the field of Cancer and Pharmacology. I try to encourage the fellow researchers and post-graduate students to read so much as they can about new therapeutics.
-------------------------------------------

Weekend Recipe for February 2016 - the first week

Ligand efficiency indices for effective drug discovery

This week I would like to suggest this paper. This paper written by Prof. Cele Abad-Zapatero help me a lot to make new insights in drug discovery in my projects. The paper is incredibly insightful and provide new indices to better understanding of drug/target interaction.

Abstract——Successful drug discovery requires the optimization of a large number of variables ranging from strictly physicochemical parameters such as molecular weight to more complex parameters related to toxicity and bioavailability. Presently, structure-based methodologies influence many aspects of the drug discovery process from lead discovery to the final preclinical characterization. However, critical biological issues along the path to the market have diminished the impact and power of this methodology. The physicochemical properties of the novel chemical entities designed and guided by structural methods have become the subject of intense scrutiny from lead discovery to drug candidate. The idea of ligand efficiency (binding energy/non-hydrogen atoms) has recently emerged as a useful guide to optimize fragment and lead selection in the discovery process.

More generalized concepts of ligand efficiency, related to efficiency per dalton and per unit of polar surface area, have also been introduced and will be discussed in the broader context. Preliminary results and trends obtained using ligand efficiencies as guides are reviewed and their future application to guide drug discovery will be discussed, as well as their integration into the structure-based drug design methods to make them more effective and numerically robust.


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One of the objectives of this manuscript is studying of BRAF-MEK interaction.

Water systems were generated so that each docked protein was placed in the center of a triclinic box with the minimum distance between the solutes and the edge of the box of 1.0 nm. The size of the system is 286000 atoms. This system is a huge system and took one month for simulation.

BRAF-MEK1 complex docked by four molecules of BBR-9 can be seen here. Here, we have four BRAFs, four MEK1s, and four ligands. We have done MD to see whether BBR-9 affect BRAF-MEK1 interactions or not.

BBR-9 is one of our newly generated ligands against BRAF. I will also show that BBR-9 is a dual RAF inhibitor because it could affect CRAF as well.

After publication, article and all related supplimentary files will be available here.

RAF-MEK1

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Archives

Selected journal articles watson @ (11:59:34) (Curriculum Vitae)
بسته آمادگی کارشناسی ارشد - صد ساعت watson @ (12:03:46) (کارگاه ها و دوره های حرفه ای)
مدرسه پیشرفته مقاله نویسی watson @ (12:01:41) (کارگاه ها و دوره های حرفه ای)
طراحی دارو و تکنولوژی دراگ دیسکاوری watson @ (12:01:08) (کارگاه ها و دوره های حرفه ای)
Data Science in Genomic Studies watson @ (12:00:31) (کارگاه ها و دوره های حرفه ای)


Our article: Therapeutic miRNAs


 Pharmacological Research




Headlines





Date published: not known
Details

»Two timelines for extinction
»Probing the dynamics of anyons
»Scaled-up sodium-free Birch reductions
»Concentrated news precedes legislation
»A key to potassium channel activation
»The key to keyhole formation
»Expanding the genetic code
»Sleep may protect the brain from AD
»Digging skin deep
»A topological paradigm shift


Date published: not known
Details

»Mexiletine Block of Voltage-Gated Sodium Channels: Isoform- and State-Dependent Drug-Pore Interactions [Articles]
Mexiletine is a class Ib antiarrhythmic drug and is also used clinically to reduce or prevent myoto ...
»Molecular Basis of Action of a Small-Molecule Positive Allosteric Modulator Agonist at the Type 1 Cholecystokinin Holoreceptor [Articles]
Allosteric modulation of receptors provides mechanistic safety while effectively achieving biologic ...
»Repeated Exposure to 4-Methyl-2,4-bis(4-hydroxyphenyl)pent-1-ene (MBP), an Active Metabolite of Bisphenol A, Aggressively Stimulates Breast Cancer Cell Growth in an Estrogen Receptor {beta} (ER{beta})-Dependent Manner [Articles]
Bisphenol A (BPA), recognized as an endocrine disruptor, is thought to exert its activity through a ...
»S29434, a Quinone Reductase 2 Inhibitor: Main Biochemical and Cellular Characterization [Articles]
Quinone reductase 2 (QR2, E.C. 1.10.5.1) is an enzyme with a feature that has attracted attention f ...
»Structural Basis of p97 Inhibition by the Site-Selective Anticancer Compound CB-5083 [Articles]
Inhibition of p97, a key player in the ubiquitin-proteasome degradation pathway, has been proposed ...
»Inhibition of Interleukin 10 Transcription through the SMAD2/3 Signaling Pathway by Ca2+-Activated K+ Channel KCa3.1 Activation in Human T-Cell Lymphoma HuT-78 Cells [Articles]
The hyperpolarization induced by intermediate-conductance Ca2+-activated K+ channel (KCa3.1) activa ...
»Functional Selectivity and Partial Efficacy at the Monoamine Transporters: A Unified Model of Allosteric Modulation and Amphetamine-Induced Substrate Release [Minireview]
All clinically approved drugs targeting the plasmalemmal transporters for dopamine, norepinephrine, ...
»Hyperforin-Induced Activation of the Pregnane X Receptor Is Influenced by the Organic Anion-Transporting Polypeptide 2B1 [Articles]
The herbal remedy St. John’s wort (SJW) is used in the treatment of mild depressive symptoms ...
»Belinostat, at Its Clinically Relevant Concentrations, Inhibits Rifampicin-Induced CYP3A4 and MDR1 Gene Expression [Articles]
Activation of human pregnane X receptor (hPXR) has been associated with induction of chemoresistanc ...


Date published: not known
Details

»Independent working memory resources for egocentric and allocentric spatial information
»Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas
»Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions
»Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis
»A saturated reaction in repressor synthesis creates a daytime dead zone in circadian clocks
»Multi-modality in gene regulatory networks with slow promoter kinetics
»A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications
»A numerical approach for a discrete Markov model for progressing drug resistance of cancer
»Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes
»Identifying individual risk rare variants using protein structure guided local tests (POINT)
»Efficient neural decoding of self-location with a deep recurrent network
»Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion


Date published: not known
Details


THE FOUNDER and CEO

Parham Jabbarzadeh Kaboli, PhD

Research scientist
in molecular medicine


Expert in:

Cell and molecular Biology
Modelling and drug discovery
Cancer signaling pathways

H-index= 3 (Google Scholar)
i10-index= 3
Overall ISI impact factor= 18.15
Overall citation= 110 (Google Scholar)

Memberships:

The American Society for Pharmacology and Experimental Therapeutics (ASPET)

American Association for Cancer Research (AACR)

European Association for Cancer Research (EACR)

American Association for Advancement of Science (AAAS)



CONTACT INFORMATION


Affiliation:
Department of Biomedical Science,
Faculty of Medicine and Health Sciences,
Universiti Putra Malaysia,
UPM Serdang 43400,
Selangor, Malaysia

E-Mail: parham@gromacs.net
Telegram: telegram.me/parhamacademy
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