Commenting on the link between Nazi Germany and the development thalidomide, Ray Stokes, Ph.D, Professor of Business History at the University of Glasgow, who has a special interest in the chemical and pharmaceutical industry, notes in his report about history of the drug that "We… can establish a background in the Nazi period of connections between Heinrich Mückter, one of the key scientists whose name is on the original patent of the thalidomide, and... other scientists who were involved in experiments on concentration camp inmates."
In an interview with the British newspaper Daily Mail, Martin W. Johnson BD PhD Msc FRSA, director of the Thalidomide Trust in the United Kingdom said that he has unearthed documents suggesting thalidomide was developped around 1944 by Otto Ambros, a Nazi scientist and one of the most powerful industrialists with direct access to Adolf Hitler, as a antidote to nerve toxins including Sarin* and Tabun** 
Ambros, who, during World War II, was the managing director of Anorgana GmbH, a company with nominal ties to IG Farben, the German chemical and pharmaceutical industry conglomerate notorious for its role in the holocaust, was Hitler's chief chemical weapons engineer and supplied scientists and engineers in the Third Reich with equipment and tools needed to built and operate production facilities for nerve gas. In 1948, he was convicted of war crimes and crimes against humanity at Nuremberg Trials, a series of military tribunals, held by the Allied forces of World War II for the prosecution of prominent members of the political, military, and economic leadership of Nazi Germany, and sentenced to eight years in prison.
After his release he became chairman of the advisory board of Chemie Grünenthal GmbH, the company in the center of the thalidomide saga. He served in this capacity until his death in 1990. Ambros was also an advisor for the British pharmaceutical company The Distillers Company (Biochemicals) Ltd, a subsidiary of Distillers Co. Ltd., which became part of Diageo plc in 1997. This company marketed thalidomide under the brand name Distavel® in the United Kingdom, Australia and New Zealand.
Coincidently, some historians claim that Ambros worked on the development of thalidomide before he joint Chemie Grünenthal in the 1950s.
Chemie Grunenthal was founded in 1946 by Hermann Wirtz to take advantage of the post-war demand for antibiotics and other pharmaceutical products. Wirtz came from a prosperous family that had run the successful Stolberg soap and perfume factory Mäurer & Wirtz since 1845. A capable businessman, Wirtz had used Hitler's Aryanisation program to take over two Jewish-owned firms in the 1930s. And despite Nazi Germany's defeat he emerged loaded with cash and valuable contacts necessary to establish his new company.
Interestingly, Chemie Grünenthal 1954 thalidomide patent mentions that the drug had already been tested on humans - before official tests began.  While representatives from Chemie Grünenthal suggest that thalidomide was originally developed in 1952 as a tranquilizer by Swiss pharmaceutical company Ciba AG (now part of Novartis), historical documents proof that the company had previously purchased the trade name Contergan®, and therefore presumably the drug, from Rhône-Poulenc (now Sanofi) a French pharmaceutical company which, during WWII, had been controlled by the Nazi's. From 1942 onwards, the company registered 14 new pharmaceutical agents, all ending with the the suffix ergan. The associated drugs had distinct similarities with thalidomide. 
The same chemical formula?
In his book Hitler's Laboratories the Argentinian writer Carlos De Nápoli states that he has discovered documents dated November 1944 from IG Farben AG, which refer to a chemical agent with the same chemical formula as thalidomide. According to De Nápoli, IG Farben's director Fritz ter Meer sent a memo to Karl Brandt, the SS general who ran Hitler's euthanasia program, explaining that a drug with number 4589 (with the same characteristics as thalidomide) had been tested and was ready for use.
After the war, in 1948, Ter Meer was sentenced to seven years in prison in the Nuremberg Trials for his role during World War II. Following his release in 1951 he became supervisory board chairman of Bayer AG, which, together with Agfa, BASF and Hoechst (now Sanofi), is one of the successor companies of IG Farben.
Based on growing evidence from a variety of resources, including patent documents, Martin Johnson believes that thalidomide was probably one of a number of products developed at Dyhernfurth, one of Nazi Germany's largest and most secret chemical laboratory located 40 kilometers from Breslau in Western Poland or the synthetic rubber and petrol processing plant in Auschwitz-Monowitz, near Krakow in southern Poland.
* SARIN is an acronym derived from letters in the names of the four key individuals in its development: Schrader and Ambros of IG Farben and Rüdiger and Linde of the Army Ordnance Office.
** Tabun is an extremely toxic chemical substance, is a clear, colorless, and tasteless liquid with a faint fruity odor. It is classified as a nerve agent because it fatally interferes with normal functioning of the mammalian nervous system. Its production is strictly controlled and stockpiling outlawed by the Chemical Weapons Convention of 1993. Tabun is the first of the so-called G-series nerve agents along with GB (sarin), GD (soman) and GF (cyclosarin). Based on a process developed by Gerhard Schrader, a German chemist who specialized in the discovery of new insecticides and best known for his accidental discovery of nerve agents, Nazi Germany manufactured at least 12,000 metric tons of Tabun were manufactured between 1942 and 1945 in the chemical agent factory in Dyhernfurth an der Oder.
For more information:
 Andrew Levy. Nazis developed Thalidomide and tested it on concentration camp prisoners, author claims. February 8, 2009 [Article]
 Robert Harris, Jeremy Paxman A Higher Form of Killing: The Secret History of Chemical and Biological Warfare. Random House Trade Paperbacks. ISBN-10: 0812966538.
 Josiah E. Dubois. The Devil's Chemists Hardcover. The Beacon Press; 1ST edition (1952) (Comment in: The Devil’s Chemists — 24 Conspirators of the International Farben Cartel Who Manufacture Wars [Article])
 Judy Stone. From the Holocaust to Thalidomide: A Nazi Legacy. Scientific American, November 8, 2012 [Article]
 Reversal of Fortune: How a Vilified Drug Became a Life-saving Agent in the "War" Against Cancer. Onco'Zine - The International Oncology Network. November 30, 2013. [Article]
 Controversy: The involvement of Ciba AG in the development of Thalidomide. Onco'Zine - The International Oncology Network. November 30, 2013 [Article]
 Thalidomide: In the Shadow of Death - Onco'Zine - The International Oncology Network [Video/Article]
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