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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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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.
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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

»Measuring the far side of the Galaxy
»3D gene expression blueprint of the fly
»Mechanical systems at the quantum level
»3D texture morphing for camouflage
»A signature event for organoids
»Forests out of balance
»Fevers, TRPV channels, and birth defects
»Newborn brain imaging made easier
»Light- and dark-zone death dynamics
»A radical route from methane to methanol


Date published: not known
Details

»Correction to "A Scale of Agonism and Allosteric Modulation for Assessment of Selectivity, Bias, and Receptor Mutation" [ERRATUM]
»E6130, a Novel CX3C Chemokine Receptor 1 (CX3CR1) Modulator, Attenuates Mucosal Inflammation and Reduces CX3CR1+ Leukocyte Trafficking in Mice with Colitis [Articles]
The chemokine fractalkine (CX3C chemokine ligand 1; CX3CL1) and its receptor CX3CR1 are involved in ...
»Selective HIF-1 Regulation under Nonhypoxic Conditions by the p42/p44 MAP Kinase Inhibitor PD184161 [Articles]
Hypoxia-inducible factor-1 (HIF-1) is a key gene regulator for cellular adaptation to low oxygen. I ...
»Transforming Growth Factor-{beta}1/Activin Receptor-like Kinase 5-Mediated Cell Migration is Dependent on the Protein Proteinase-Activated Receptor 2 but not on Proteinase-Activated Receptor 2-Stimulated Gq-Calcium Signaling [Articles]
Transforming growth factor-β (TGF-β), serine proteinases such as trypsin, and proteinase- ...
»Prostaglandin E2 Inhibits Histamine-Evoked Ca2+ Release in Human Aortic Smooth Muscle Cells through Hyperactive cAMP Signaling Junctions and Protein Kinase A [Articles]
In human aortic smooth muscle cells, prostaglandin E2 (PGE2) stimulates adenylyl cyclase (AC) and a ...
»A Single Amino Acid Substitution in the Third Transmembrane Region Has Opposite Impacts on the Selectivity of the Parasiticides Fluralaner and Ivermectin for Ligand-Gated Chloride Channels [Articles]
Fluralaner (Bravecto) is a recently marketed isoxazoline ectoparasiticide. This compound potently i ...
»The Actions of Drug Combinations on the GABAA Receptor Manifest as Curvilinear Isoboles of Additivity [Accelerated Communication]
Drug interactions are often analyzed in terms of isobolograms. In the isobologram, the line connect ...
»N-Acetyl-L-Cysteine Protects Astrocytes against Proteotoxicity without Recourse to Glutathione [Articles]
N-acetyl-l-cysteine (NAC) exhibits protective properties in brain injury models and has undergone a ...
»The Anthracycline Metabolite Doxorubicinol Abolishes RyR2 Sensitivity to Physiological Changes in Luminal Ca2+ through an Interaction with Calsequestrin [Articles]
The chemotherapeutic anthracycline metabolite doxorubicinol (doxOL) has been shown to interact with ...
»Agonist-Dependent and -Independent {kappa} Opioid Receptor Phosphorylation: Distinct Phosphorylation Patterns and Different Cellular Outcomes [Articles]
We reported previously that the selective agonist U50,488H promoted phosphorylation of the mouse o ...


Date published: not known
Details

»A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action
»Clusternomics: Integrative context-dependent clustering for heterogeneous datasets
»The role of glutamate in neuronal ion homeostasis: A case study of spreading depolarization
»Network approaches and applications in biology
»Ten simple rules for writing a response to reviewers
»BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions
»Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets
»Vicus: Exploiting local structures to improve network-based analysis of biological data
»Systematic, network-based characterization of therapeutic target inhibitors
»Network propagation in the cytoscape cyberinfrastructure
»Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases
»Structural host-microbiota interaction networks


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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