A primer for the data scientist.

A compound (‘ligand’) docking into an enzyme protein (left: ‘cartoon’ view, right: ‘surface’ view). Source: EMSKE Phytochem, Software: PyMol

When it comes to drug trials, it’s necessary to shortlist high-potential candidates before incurring the extraordinary expenses of in-laboratory (in vitro) and clinical (in vivo) trials. Most pharmaceutical companies do “in silico” screenings in advance of real-world trials: They want the best possible chance of filtering through a ‘hit’ with as few ‘miss’ costs as possible.

In background research for our most recent pieces on antivirals efficacy that fundamentally rely on data science and drug-docking, I realized that there aren’t a lot of drug docking “how-to’s” for the data scientist audience. This apparent gap in the data science arsenal made…

How a novel approach to discovering and trialing plant-based antivirals is being attempted in Kenya to fight the pandemic

(Prev article #4 of 5) Note: this is the 5th of 5 articles in our series on flavonoids.

vImportant sources of key flavonoids — Citrus × sinensis (sweet orange), mangifera indica (common mango), menthe piperita (common peppermint)

As we’re preparing for engaging here in Kenya to champion a distributed clinical trial of key flavonoids against covid, I think it’s an appropriate time to discuss the Big Picture in what we are doing.

What is a flavonoid?

When I first learned the word ‘flavonoid’, I thought it must have to do with flavoring. …

What you’ll need to get your feet wet in biotech

Today I thought we would diverge from our usual data-science heavy stories and focus more on how our agroceutical venture, EMSKE Phytochem began. Along the way, we’ll highlight what we feel the table-stakes are for participating in the biotech startup scene today, and how to think about entering this risk-fraught sector.

EMSKE’s identity and motivations are inextricably linked to the fact that we are based in Africa. This geographical reality applies to about half of our volunteer contributors. …

A (limited) in silico perspective.

image: ChiralJon licensed under CC BY 2.0

The story of hydroxychloroquine during this pandemic is a sad and winding one. I think this article from Tablet does a great job articulating the tensions and misadventures that took place in the quest to either support or refute the case for its efficacy as a coronavirus therapeutic. In any case, while the FDA withdrew its emergency use authorization (EUA) for hydroxychloroquine (hcq for short) use, there are some other jurisdictions that still administer it for coronavirus indication.

When people ask what is our ability at EMSKE to support or refute a given small molecule drug’s therapeutic efficacy for patients…

COVID likely derived from the bat caves of Southern China’s Yunnan province originally. Ethnic groups in the region have been living in close proximity to these caves for millenia. Could the traditional plant-based medicines they developed be the key to managing the pandemic?

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In the midst of all our plant medicinals studying, one very stressful pressure always comes up: It’s tough to get clinical trials of any promising candidate compound initiated anywhere in the world. But the class of compounds we study aren’t typical pharma drugs formulated straight from a laboratory drawing board; these are plant medicinals. So why not try to look for opportunities in the wild where people (or animals) are unwittingly already consuming candidate plant medicinals?

(image credit: Stefan Rodriguez | Unsplash)

Doing so would…

A machine-learning approach to in silico drug docking sheds light

So over here in eastern Africa, a lot of news has been made of Madagascar’s COVID-Organics extract made from a local plant, introduced by that country’s Institut Malgache de Recherches Appliquées (Malagasy Institute of Applied Research) IMRA, and promulgated especially by the president of Madagascar himself, Andry Rajoelina.

(Prev article #2 of 5) Note: this is the 3rd of 5 articles in our series on flavonoids. Here is an easier reading version of it. (Next article #4 of 5)

COVID-Organics as extracted from Artemisia Annua (Credit: LHS: EMSKE Phytochem; RHS: Photo by Mathias Katz on Unsplash)

My experience is that articles on the topic particularly written for audiences outside Africa, like this one from the WSJ, tend…

(Prev article #1 of 5) Note: this is the 2nd of 5 articles in our series on flavonoids. (Next article #3 of 5)

Leschenault’s Rousette bat, of Chiroptera Pteropodidae

Update Jan 2021: This article documents what to date remains an inconclusive result based on the limited data available in the literature.

So it’s been an intense week of studying and research on hesperidin and COVID-19. But in the process of trying to find longitudinal datasets for demonstrating a de-facto in vivo efficacy test in order to support *actual* in vivo testing, we offer a new, hitherto unexplored hypothesis for why bats are a reservoir for coronaviruses.

With the coronavirus epidemic still reaching its zenith in the US, I observe friends and family in San Francisco who work in ER wards and nearby county clinics post their scary treatment stories and PPE fundraisers on Facebook. It’s evident that something is very wrong.

Note: this is the 1st of 5 articles in the series. (Article #2 is here)

Meanwhile, I’m stuck at home in Kenya with a lot of time outside my social venture work to occupy. And as former astronaut Chris Hadfield says, “Become an expert on the thing that threatens you”. So in spite of my layman’s credentials (I’m an engineer, not a biochemist or molecular biologist) I’ve been reviewing the literature on this disease. …

Rick Sheridan

Coming from a multidisciplinary MIT technical background and startups in San Francisco & SE Asia, Rick leads @EMSKEPhyto . linkedin.com/in/rick-phyto

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