The chief executive of the world's second biggest pharmaceutical company will today announce that he is putting into the public domain thousands of potential drugs that might cure malaria.

Andrew Witty, the British boss of Glaxo-SmithKline, will say in a major speech that multinational drug companies have to balance social responsibility alongside the need to make profits for their shareholders. There is, he will say, an "imperative to earn the trust of society, not just by meeting expectations but by exceeding them".

GSK will publish details of 13,500 chemical compounds from its own library that have potential to act against the parasite that causes malaria in sub-Saharan Africa, killing at least one million children every year.

It took a team of five investigators a year to screen the two million compounds in GSK's library – its entire collection of potential drugs and possibly the biggest such library in the world.

The move was given a cautious welcome by charities such as Médecins Sans Frontières, although Oxfam questioned whether other big drug companies would want to develop treatments from GSK patents.

Witty, though, believes scientists would and should seize the opportunity.

Speaking to the Guardian in advance of the announcement in New York, he said: "To my knowledge nobody's ever put confirmed-hit structures into the public domain. Universities have done stuff like this but on a much smaller scale.

"I think it's a significant contribution to give scientists around the world 13,500 new opportunities to start research."

Witty will also announce an $8m fund to pay for scientists to explore these chemicals or others in an "open lab" within its research centre at Tres Cantos, Spain, which is dedicated to work on malaria and other diseases of the developing world.

"It's trying to create a permissiveness around scientific research in an area where we know the marketplace isn't going to stimulate massive research," he said.

"Given that there is only a handful of big companies who focus on malaria, this is a chance to get thousands of researchers involved – just like software companies encourage thousands of people to contribute their new ideas for software – and we'll see what comes of it."

Witty's speech takes forward the agenda he set out nearly a year ago at Harvard University, when he pledged to put all the potential drugs for neglected diseases GSK holds in a "patent pool", waiving the company's intellectual property rights so that any scientists could investigate them. He also promised to cut the price of all GSK drugs in the world's poorest countries and to reinvest 20% of all profits it made there in projects to help local people.

He admitted he was disappointed other drug companies had not taken up the invitation he had held out to put their patents into the neglected diseases pool as well.

"I think they're just nervous. I don't think they have crossed … I crossed the bridge a year ago ... that you can have a [different] approach to the way you think about intellectual property and openness in an area like neglected tropical diseases. There is no financial market stimulating discovery so we need to find ways to stimulate discovery. This is a way to do it."

While it was pleased at GSK's new initiatives and praised the leadership the company had shown, Oxfam in effect accused Witty of naivety in thinking that other drug giants would come on board.

"Last year he announced some new, interesting ideas. But they stayed for a whole year as ideas. GSK should know how the industry works. As long as this is run by one company, others are not going to join in," said the charity's senior health adviser, Dr Mohga Kamal-Yanni. "I'm glad they realise now they need to do more than just put ideas on the table.

"It is quite exciting what they have decided to do, but we have to watch whether it becomes something interesting at the end of the day."

Tido von Schoen-Angerer, director of Médecins sans Frontières' campaign for essential medicines, said: "The fact that they are opening up their compounds for malaria is a good step. It is something like we have been calling for for some years. It would be good if other companies would do the same thing, and for other diseases." But Oxfam, Médecins sans Frontières and other NGOs are still very critical of GSK's reluctance to wholeheartedly embrace a patent pool for HIV drugs that is being set up by Unitaid.

Witty's view is that Aids is not a neglected disease. There is a lot of research and development going on because of a lucrative market for HIV drugs in Europe and the USA. But he told the Guardian that he might join in if he believed the pool would succeed in improving access for the poorest to HIV drugs.

"I'm not saying no but I need to see the detail," he said. GSK was now meeting and working with Unitaid. "We'd really like to be in the position of helping them work out detail that works."

His company has licensed its HIV drugs to generic companies to make cheap copies and allowed them to combine the drugs with those of other companies, which is what the Unitaid pool aims to do. But he said: "If Unitaid has a better mousetrap, we're happy to be part of a better mousetrap."