A primer for the data scientist.
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.
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. …
A fraught debate on repurposed drugs
Update Sep 6th: The fluvoxamine Together Trial preprint came out Aug 23rd.
First, the good news in COVID-19 trialing. On Aug 11th, the repurposed drug fluvoxamine’s Phase III trial results for COVID-19 came out in the Together Trial. Through a 1,480 patient, randomized double-blind clinical trial it has been found to reduce risk of hospitalization with greater than 95% confidence (relevant slides start at 32:40), which is the clinical standard for reporting statistical significance. Caveating that the news is still so fresh that there is yet to be a preprint posted, we do already know:
- This was a double-blinded study…
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.
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?
(Prev article #3 of 5) Note: this is the 4th of 5 articles in the series. (Next article #5 of 5)
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?
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)
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)
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
